Supplemental Data 1. Predicted miRNA target sites of Arabidopsis miRNAs in sequences of 63 extended 3' UTRs

>ath-miR395a MIMAT0000938	Score: 2.5	AT5G03200

Query:          1 CTGAAGTGTTTGGGGGAACTC 21
                  |||||||:||||::|:||*||
Sbjct:       1527 GACTTCATAAACTTCTTT-AG 1508


>ath-miR5021 MIMAT0020525	Score: 2.5	AT5G41900

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  |||:||:||:||:||:||||
Sbjct:         97 ACTTTTTTTTTTTTTTTTTT 78


>ath-miR5021 MIMAT0020525	Score: 2.0	AT5G63790

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  *|*|||:|||||||||||||
Sbjct:       2690 TCACTTTTTCTTCTTCTTTT 2671


>ath-miR5021 MIMAT0020525	Score: 1.8	AT2G31090

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  ::||||||||||||*|||||
Sbjct:         34 GTTCTTCTTCTTCTGCTTTT 15


>ath-miR5021 MIMAT0020525	Score: 0.5	AT4G04020

Query:          1 TGAGAAGAAGAAGAAGAA-AA 20
                  ||||||||||||||||||*||
Sbjct:        376 ACTCTTCTTCTTCTTCTTCTT 356


>ath-miR5021 MIMAT0020525	Score: 2.0	AT4G15550

Query:          1 TGAGAAGAAGAAGAAGAA-AA 20
                  *:||||||||||||||||**|
Sbjct:       1526 CTTCTTCTTCTTCTTCTTCCT 1506


>ath-miR5021 MIMAT0020525	Score: 1.2	AT5G23610

Query:          1 TGAGAAGAAGAAGAAGAA-AA 20
                  ::||||||||||||||||*||
Sbjct:        586 GTTCTTCTTCTTCTTCTTCTT 566


>ath-miR5021 MIMAT0020525	Score: 1.5	AT1G69260

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  ||*||||||:||||||||||
Sbjct:       1799 ACACTTCTTTTTCTTCTTTT 1780


>ath-miR5021 MIMAT0020525	Score: 2.5	AT2G03240

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  *:*||||||||||||||||*
Sbjct:         70 TTCCTTCTTCTTCTTCTTTG 51


>ath-miR5021 MIMAT0020525	Score: 1.5	AT4G19450

Query:          1 TGAGAAGAAGAAGAAGAA-AA 20
                  *:||||||||||||||||*||
Sbjct:         61 CTTCTTCTTCTTCTTCTTCTT 41


>ath-miR5021 MIMAT0020525	Score: 2.5	AT5G06220

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  *|||||:||||||||||***
Sbjct:       1351 TCTCTTTTTCTTCTTCTGAA 1332


>ath-miR5021 MIMAT0020525	Score: 1.5	AT2G01630

Query:          1 TGAGAAGAAGAAGAAGAA-AA 20
                  *:||||||||||||||||*||
Sbjct:       1053 CTTCTTCTTCTTCTTCTTCTT 1033


>ath-miR5021 MIMAT0020525	Score: 2.5	AT5G15650

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  |||*|||||||||||:|**|
Sbjct:        758 ACTATTCTTCTTCTTTTCGT 739


>ath-miR5021 MIMAT0020525	Score: 2.5	AT1G74470

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  |||||||*||||||*||*||
Sbjct:        170 ACTCTTCCTCTTCTCCTGTT 151


>ath-miR5021 MIMAT0020525	Score: 2.2	AT1G74470

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  ::|||*|||||||||||*||
Sbjct:         77 GTTCTCCTTCTTCTTCTCTT 58


>ath-miR5021 MIMAT0020525	Score: 2.5	AT4G02370

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  *:||||||||||*|||||*|
Sbjct:        604 CTTCTTCTTCTTGTTCTTAT 585


>ath-miR5021 MIMAT0020525	Score: 2.5	AT3G29010

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  |:|||||||||||||:*|*|
Sbjct:       1144 ATTCTTCTTCTTCTTTGTCT 1125


>ath-miR5021 MIMAT0020525	Score: 2.5	AT1G49000

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  **|:||||||||||||||*|
Sbjct:        309 TGTTTTCTTCTTCTTCTTAT 290


>ath-miR5021 MIMAT0020525	Score: 1.8	AT1G49000

Query:          1 TGAGAAGAAGAAGAAGAA-AA 20
                  ::||||:|||||||||||*||
Sbjct:        262 GTTCTTTTTCTTCTTCTTATT 242


>ath-miR5021 MIMAT0020525	Score: 1.5	AT4G00100

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  *:||||||||||||||||*|
Sbjct:       1672 TTTCTTCTTCTTCTTCTTCT 1653


>ath-miR5021 MIMAT0020525	Score: 1.5	AT2G31890

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  *:||||||||||||||||*|
Sbjct:        745 CTTCTTCTTCTTCTTCTTCT 726


>ath-miR5021 MIMAT0020525	Score: 2.5	AT1G19570

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  |:||||||||||:||:*|||
Sbjct:       2137 ATTCTTCTTCTTTTTTGTTT 2118


>ath-miR5021 MIMAT0020525	Score: 2.2	AT1G71040

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  ::|||||||||*||||||*|
Sbjct:        254 GTTCTTCTTCTGCTTCTTCT 235


>ath-miR5021 MIMAT0020525	Score: 2.5	AT1G76630

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  *||:|||||||*|||||*||
Sbjct:        286 TCTTTTCTTCTCCTTCTATT 267


>ath-miR5021 MIMAT0020525	Score: 2.0	AT5G03030

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  *:||||||||||:||:||||
Sbjct:       1080 CTTCTTCTTCTTTTTTTTTT 1061


>ath-miR5021 MIMAT0020525	Score: 1.0	AT3G59970

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  *:||||||||||||||||||
Sbjct:       3593 CTTCTTCTTCTTCTTCTTTT 3574


>ath-miR5021 MIMAT0020525	Score: 2.5	AT4G38250

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  *|||||:||:||:||:||||
Sbjct:       1076 CCTCTTTTTTTTTTTTTTTT 1057


>ath-miR5021 MIMAT0020525	Score: 2.0	AT5G58060

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  *||:|||||:|||||||*||
Sbjct:        792 TCTTTTCTTTTTCTTCTCTT 773


>ath-miR5021 MIMAT0020525	Score: 1.0	AT4G16950

Query:          1 TGAGAAGAAGAAGAAGAA-AA 20
                  *|||||||||||||||||*||
Sbjct:       1158 CCTCTTCTTCTTCTTCTTCTT 1138


>ath-miR5021 MIMAT0020525	Score: 2.5	AT2G18700

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  |||:|||*|:|||||||||*
Sbjct:       2477 ACTTTTCCTTTTCTTCTTTA 2458


>ath-miR5021 MIMAT0020525	Score: 2.2	AT1G47128

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  ::||||:|||||:||:||||
Sbjct:        343 GTTCTTTTTCTTTTTTTTTT 324


>ath-miR5021 MIMAT0020525	Score: 2.5	AT1G06680

Query:          1 TGAGAAGAAGAAGAAGAAAA 20
                  |||:||:||:||:||:||||
Sbjct:       2917 ACTTTTTTTTTTTTTTTTTT 2898


>ath-miR5021 MIMAT0020525	Score: 2.5	AT3G01510

Query:          1 TGAGAAGAAGAAGAAGAAA-A 20
                  *|||||:|*||||||||||*|
Sbjct:         50 TCTCTTTTACTTCTTCTTTAT 30


>ath-miR5021 MIMAT0020525	Score: 2.5	AT1G05630

Query:          1 TGAGAAGAAGAAGAAGAA-AA 20
                  |||||*|||||||||||***|
Sbjct:       1769 ACTCTCCTTCTTCTTCTGACT 1749


>ath-miR5021 MIMAT0020525	Score: 1.5	AT5G05270

Query:          1 TGAGAAGAAGAAGAAGAA-AA 20
                  |:||||:|||||||||||*||
Sbjct:       1093 ATTCTTTTTCTTCTTCTTCTT 1073


>ath-miR5658 MIMAT0022431	Score: 2.5	AT1G17130

Query:          1 ATGATGATGATGATGATGAAA 21
                  *|||||||*|||||||||*|*
Sbjct:        127 GACTACTAATACTACTACCTG 107


>ath-miR5658 MIMAT0022431	Score: 2.0	AT3G28740

Query:          1 ATGATGATGATGATGATGAAA 21
                  ||:|||||||||||||||***
Sbjct:        871 TATTACTACTACTACTACGAC 851


>ath-miR5658 MIMAT0022431	Score: 2.5	AT1G06240

Query:          1 ATGATGATGATGATGATGA-AA 21
                  ||||||*|||||*||||||*||
Sbjct:        194 TACTACAACTACGACTACTGTT 173


>ath-miR5658 MIMAT0022431	Score: 0.5	AT2G39800

Query:          1 ATGATGATGATGATGATGAAA 21
                  ||||||||||||||||||||*
Sbjct:        492 TACTACTACTACTACTACTTC 472


>ath-miR5658 MIMAT0022431	Score: 2.5	AT2G22090

Query:          1 ATGATGATGATGATGATGA-AA 21
                  |:|||||:||*||||||||*||
Sbjct:        394 TGCTACTGCTCCTACTACTATT 373


>ath-miR5658 MIMAT0022431	Score: 2.5	AT4G39890

Query:          1 ATGATGATGATGATGATGAAA 21
                  *|:|||||||||||||*||*|
Sbjct:        211 CATTACTACTACTACT-CTCT 192


>ath-miR5658 MIMAT0022431	Score: 1.0	AT3G11820

Query:          1 ATGATGATGATGATGATGAAA 21
                  |||||||||||||||||||**
Sbjct:        397 TACTACTACTACTACTACTAG 377


>ath-miR5658 MIMAT0022431	Score: 2.0	AT4G01026

Query:          1 ATGATGATGATGATGATGAA-A 21
                  |||||||||||||*||:|||*|
Sbjct:       3065 TACTACTACTACTTCTGCTTCT 3044


>ath-miR5658 MIMAT0022431	Score: 2.2	AT1G52230

Query:          1 ATGATGATGATGATGATGAAA 21
                  |||||||||||:||||::**|
Sbjct:       1425 TACTACTACTATTACTGTACT 1405


>ath-miR5658 MIMAT0022431	Score: 2.5	AT1G50740

Query:          1 ATGATGATGATGATGATGAAA 21
                  ||:|||||||*||||||*||*
Sbjct:       1113 TATTACTACTTCTACTA-TTG 1094


>ath-miR5658 MIMAT0022431	Score: 2.5	AT3G48690

Query:          1 ATGATGATGATGATGATGAAA 21
                  ||||*||||||:|||*|||||
Sbjct:         83 TACTTCTACTATTACCACTTT 63


>ath-miR5658 MIMAT0022431	Score: 2.0	AT5G61020

Query:          1 ATGATGATGATGATGATGAAA 21
                  ||||||||||||||||:***|
Sbjct:        643 TACTACTACTACTACTGAACT 623


>ath-miR395d MIMAT0000941	Score: 2.5	AT5G03200

Query:          1 CTGAAGTGTTTGGGGGAACTC 21
                  |||||||:||||::|:||*||
Sbjct:       1527 GACTTCATAAACTTCTTT-AG 1508


>ath-miR847 MIMAT0004278	Score: 2.2	AT1G13940

Query:          1 TCACTCCTCTTCTTCTTGATG 21
                  :||*|||||||||||||:*|:
Sbjct:        208 GGTTAGGAGAAGAAGAATGAT 188


>ath-miR5017 MIMAT0020521	Score: 2.5	AT3G55830

Query:          1 TTATACCAAATTAATAGCAAA 21
                  ||||*|||||*||||||*|||
Sbjct:       1610 AATAAGGTTTTATTATC-TTT 1591


>ath-miR156i MIMAT0022421	Score: 2.0	AT4G22530

Query:          1 TGACAGAAGAGAGAGAGCAG 20
                  *:|||:|||||||||||||*
Sbjct:        428 TTTGTTTTCTCTCTCTCGTA 409


>ath-miR833b MIMAT0022419	Score: 2.5	AT1G69260

Query:          1 TGTTTGTTGACATCGGTCTAG 21
                  |||||||||||||*|||*|**
Sbjct:       1058 ACAAACAACTGTAACCATAAG 1038


>ath-miR854d MIMAT0004283	Score: 2.5	AT2G22090

Query:          1 GATGAGGATAGGGAGGAGGA-G 21
                  |||||:|||*:|||||||||*|
Sbjct:        359 CTACTTCTACTCCTCCTCCTAC 338


>ath-miR399b MIMAT0000952	Score: 2.5	AT1G79880

Query:          1 TGCCAAAGGAGAGTTGCCCTG 21
                  |*|||||:||:||||||*|||
Sbjct:         64 AAGGTTTTCTTTCAACGTGAC 44


>ath-miR859 MIMAT0004303	Score: 2.0	AT1G62600

Query:          1 TCTCTCTGTTGTGAAGTCAA-A 21
                  ||||||||||*||||:||||*|
Sbjct:        653 AGAGAGACAAGACTTTAGTTGT 632


>ath-miR2938 MIMAT0014142	Score: 2.5	AT3G01970

Query:          1 GATCTTTTGAGAGGGTTCCAG 21
                  *|||||||||||:|:||*|*|
Sbjct:        291 ATAGAAAACTCTTCTAA-GAC 272


>ath-miR5025 MIMAT0020531	Score: 2.5	AT4G30620

Query:          1 ACTGTATATATGTAAGTGACA 21
                  ||||:||||||:||*||*|||
Sbjct:        328 TGACGTATATATATACA-TGT 309


>ath-miR419 MIMAT0001327	Score: 2.0	AT2G40880

Query:          1 TTATGAATGCTGAGGATGTTG 21
                  |||||||:|||||:|*|||||
Sbjct:       1188 AATACTTGCGACTTCCACAAC 1168


>ath-miR2934-3p MIMAT0020364	Score: 2.5	AT1G06570

Query:          1 CATCCAAGGTGTTTGTAGAAA 21
                  *|||*||:||||||||||*||
Sbjct:        884 TTAGATTTCACAAACATCATT 864


>ath-miR156j MIMAT0022423	Score: 2.0	AT4G22530

Query:          1 TGACAGAAGAGAGAGAGCAC 20
                  *:|||:|||||||||||||*
Sbjct:        428 TTTGTTTTCTCTCTCTCGTA 409


>ath-miR395e MIMAT0000942	Score: 2.5	AT5G03200

Query:          1 CTGAAGTGTTTGGGGGAACTC 21
                  |||||||:||||::|:||*||
Sbjct:       1527 GACTTCATAAACTTCTTT-AG 1508


>ath-miR164c MIMAT0001017	Score: 2.2	AT5G16050

Query:          1 TGGAGAAGCAGGGCACGTGCG 21
                  ||||:|||||||||||*:*||
Sbjct:        362 ACCTTTTCGTCCCGTGAGAGC 342


>ath-miR854e MIMAT0018504	Score: 2.5	AT2G22090

Query:          1 GATGAGGATAGGGAGGAGGA-G 21
                  |||||:|||*:|||||||||*|
Sbjct:        359 CTACTTCTACTCCTCCTCCTAC 338


>ath-miR399c MIMAT0000953	Score: 2.5	AT1G79880

Query:          1 TGCCAAAGGAGAGTTGCCCTG 21
                  |*|||||:||:||||||*|||
Sbjct:         64 AAGGTTTTCTTTCAACGTGAC 44


>ath-miR782 MIMAT0003941	Score: 2.5	AT2G19190

Query:          1 ACAAACACCTTGGATGTTCTT 21
                  |||||*|||||||||||*|**
Sbjct:        252 TGTTTATGGAACCTACATGTC 232


>ath-miR407 MIMAT0001010	Score: 2.5	AT1G64380

Query:          1 TTTAAATCATATACTTTTGGT 21
                  ||:||||||||*||*||||||
Sbjct:        310 AAGTTTAGTATTTGTAAACCA 290


>ath-miR838 MIMAT0004260	Score: 2.0	AT1G09760

Query:          1 TTTTCTTCTACTTCTTGCACA 21
                  *||||||||*|||||||*|||
Sbjct:       1555 TAAAGAAGAAGAAGAAC-TGT 1536


>ath-miR838 MIMAT0004260	Score: 2.5	AT4G38250

Query:          1 TTTTCTTCTACTTCTTGCACA 21
                  ||||||||||*||||::*|||
Sbjct:        948 AAAAGAAGATAAAGAGT-TGT 929


>ath-miR854b MIMAT0004281	Score: 2.5	AT2G22090

Query:          1 GATGAGGATAGGGAGGAGGA-G 21
                  |||||:|||*:|||||||||*|
Sbjct:        359 CTACTTCTACTCCTCCTCCTAC 338


>ath-miR414 MIMAT0001322	Score: 2.5	AT2G29420

Query:          1 TCATCTTCATCATCATCGTCA 21
                  :||||*|||:|||||||:|*|
Sbjct:        557 GGTAGTAGTGGTAGTAGTATT 537


>ath-miR414 MIMAT0001322	Score: 2.2	AT5G06220

Query:          1 TCATCTTCATCATCATCGTCA 21
                  *||||*|||||||||||:||*
Sbjct:       1082 CGTAGTAGTAGTAGTAGTAGG 1062


>ath-miR414 MIMAT0001322	Score: 1.5	AT2G30780

Query:          1 TCATCTTCATCATCATCGTCA 21
                  |||||||||||*||||||||*
Sbjct:       1142 AGTAGAAGTAGAAGTAGCAGC 1122


>ath-miR854a MIMAT0004280	Score: 2.5	AT2G22090

Query:          1 GATGAGGATAGGGAGGAGGA-G 21
                  |||||:|||*:|||||||||*|
Sbjct:        359 CTACTTCTACTCCTCCTCCTAC 338


>ath-miR855 MIMAT0004279	Score: 2.5	AT1G72600

Query:          1 AGCAAAAGCTAAGGAAAAGGAA 22
                  |:||||||*||||:||||::||
Sbjct:        302 TTGTTTTCTATTCTTTTTTTTT 281


>ath-miR858a MIMAT0004302	Score: 2.2	AT2G01630

Query:          1 TTTCGTTGTCTGTTCGACCTT 21
                  :|||:||*|||||||||*|||
Sbjct:        990 GAAGTAAGAGACAAGCTCGAA 970


>ath-miR773b-3p MIMAT0017736	Score: 2.5	AT5G20010

Query:          1 TTTGATTCCAGCTTTTGTCTC 21
                  ||*|||||||*||||||*|||
Sbjct:        549 AATCTAAGGTAGAAAACCGAG 529


>ath-miR854c MIMAT0004282	Score: 2.5	AT2G22090

Query:          1 GATGAGGATAGGGAGGAGGA-G 21
                  |||||:|||*:|||||||||*|
Sbjct:        359 CTACTTCTACTCCTCCTCCTAC 338


>ath-miR5996 MIMAT0023519	Score: 2.2	AT2G30780

Query:          1 TGACATCCAGATAGAAGCTTTG 22
                  :||||||||:|:|||||*||*|
Sbjct:       1338 GCTGTAGGTTTGTCTTCTAATC 1317


>ath-miR867 MIMAT0004318	Score: 2.2	AT5G43060

Query:          1 TTGAACATGGTTTATTAGGAA 21
                  *||||*|||||||||||*:||
Sbjct:       1194 TACTTATACCAAATAATATTT 1174