Comparison of: (A) HS_intron gene CD4, 2nd intron: HS_11__2 - 13670 nt (B) MM_intron gene CD4, 2nd intron: MM_5__2 - 6175 nt using matrix file: DNA, gap open/ext: -12/-4 E(limit) 1e-06 61.3% identity in 550 nt overlap (9732-10265:3959-4464); score: 581 E: 5.3e-42 9740 9750 9760 9770 9780 9790 9800 9810 HS_11_ CTTTTAAGTCTTCATTCAATACCAGTTGTCC--CATGAATTTGTCCCAGACTCACTCATATGCTTAGACCTTTCATATTATCTTGCCATA :::::::: ::: : ::: :: : : ::: :: :::::::: :::: : : ::: :::::: ::: : : ::: :: MM_5__ CTTTTAAGACTTAGTCCAACACT-GCTCTCCTCCAGCAATTTGTCTCAGATTTGCCCATTCTCTTAGATACCCTATACTCTTTTGA-ATC 3960 3970 3980 3990 4000 4010 4020 4030 4040 9820 9830 9840 9850 9860 9870 9880 9890 9900 HS_11_ GCTTTTTCAAAGTATGGGACAGCATGGACAAGCAGGCCATGGTTTTCTTTTGAAGAGAAGCAAGGAGGCAGAGTTATTTTAGGAGGAGGG : :::::: : :: :: :: ::: ::::: : :::: ::::::: :: : ::::: ::: : :::::::::::: :: MM_5__ GAGTTTTCAGATTACAGGGCATCATAGACAATCGCATCATGATTTTCTTCATCAGGAAGGCAAGCAGGAGGGCTTATTTTAGGAGAGAGG 4050 4060 4070 4080 4090 4100 4110 4120 4130 9910 9920 9930 9940 9950 9960 9970 9980 9990 HS_11_ TTATACATTTCATTTTGAACCAATTGCGTTTGGGGTGATGGCAGGATATT--AACATA---AACTTATTTCTTGGACCATTGGAAATGTG :::: : : ::::::: :: : : ::: ::: ::: ::: : :: :::: : :::: ::: ::::: : : ::::: MM_5__ CGATACGCATTACTTTGAACAGGTTAC-TCTGGTGTGGTGG-AGGTTGTTGAAACACAGCTAACT-ATTCCTTGGGCTACAGGAAACACA 4140 4150 4160 4170 4180 4190 4200 4210 4220 10000 10010 10020 10030 10040 10050 10060 10070 10080 HS_11_ TGCCTAGAACTGAGGAGAGAGGTCAGGGCTGGCAGTAACAACTTGGCCACAATCTGCAGAGCTGACTGGGG--ATGAGGTGGAATTTAGA ::::::: ::: ::: ::: : ::::::: : : :: ::::::: : ::: : :: : :::: : ::: MM_5__ AGCCTAGAGGCGAGCAGA-AGG-CTGGGCTGGGAATCTCA------------TCTGCAGTGAATGATGGAGCTATTTAGGGGAAGTCAGA 4230 4240 4250 4260 4270 4280 4290 10090 10100 10110 10120 10130 10140 10150 10160 10170 HS_11_ ATGTCTGTAGAAACGGGGAAG-AGAACCAAAGACAGAGTCTGGGACAACACCTAAATGTAGATGTCAGAGCAAGAGTTCAAGACGAAGAA ::: ::::::::: :::::: ::: : :::: :: : :: ::::::: : ::: :: : :: ::::::: : : : MM_5__ ATGGATGTAGAAACAGGGAAGCAGAGCAGAAGATAGT---TAGGGCAACACCAGACAATAG---TCTG------AGGTCAAGACCA-GCA 4300 4310 4320 4330 4340 4350 4360 4370 10180 10190 10200 10210 10220 10230 10240 10250 HS_11_ AAACGAATCATACTTAGAAATGGAGGGGAGGAACAAAAGAGGCGGAGCAAAGTGGGGCAGAAC------CAGAGTAGGCCACGCTTTTAA :: ::: :: :: :: ::::::: :: ::: :: :::: ::: ::: : ::: ::: :::: : : MM_5__ AAGGGAA-----CTAAGGTGTGAAGGGGAGAAAGAAA------GGGTGAAAGGGGGTGAGACCGGTCAGCAGGTAAGGGCACG-TCCCAC 4380 4390 4400 4410 4420 4430 4440 4450 10260 HS_11_ GAAGTTTGGT :::: :::: MM_5__ CAAGTCTGGT 4460 ---------- 63.4% identity in 276 nt overlap (13365-13630:5885-6144); score: 363 E: 8e-24 13370 13380 13390 13400 13410 13420 13430 13440 13450 HS_11_ ACAGTATCTATTTCTCGGAATTATTGTGGAGATTACTG-AGATGATGCCTGTAAAGTATTTGGCATGTAGGAGTTGGTGCTCTCCAAATA ::::: : :::: :::::::::::: :::: : : ::::: : :::: ::: :: : :::: :::: : ::::: :::::: MM_5__ ACAGTCTGTATTCTCAGGAATTATTGTGAAGATCATGGTAGATGGT--ATGTACAGTGTTCAGTTTGTAAGAGTGGTTGCTCCCCAAATC 5890 5900 5910 5920 5930 5940 5950 5960 5970 13460 13470 13480 13490 13500 13510 13520 13530 HS_11_ AGGATATGATTTTATTTGTATTTGTGAGCTA--------CTGTCCCAGCCAGGTAAATGGATATGATGAGACCTCCTTGCCAGACCGGGT :: : : :: :::: :::::: ::::::: :::: :: ::: :::::: :: :: : ::: :: ::: : : MM_5__ AGCAGAGTATCTTATG-GTATTTTTGAGCTAGTGGGATACTGTTCCCACCATGTAAATAGACATTGGTGGGCCTTCTCATCAGTTCAGAG 5980 5990 6000 6010 6020 6030 6040 6050 6060 13540 13550 13560 13570 13580 13590 13600 13610 13620 HS_11_ TTCTCTGATTAGAACGAGGAGCAGATGTTGCAGGAAATTAGCAACTGATATCAGAAGAGCCGTGGGCATTCTCTTGC-CAGAGGTGCCCT : :: : :: :: :: : : :: :: : : ::::: : : ::: :::: ::::::: ::: :: :::::::::: MM_5__ TCCT-TCATGAG-----GGTGAA----TTAAAG---ACTGCCAACTCAGACCAGCAGAGTTGTGGGCACTCTTTTCAGCAGAGGTGCCAG 6070 6080 6090 6100 6110 6120 6130 13630 HS_11_ GTCTCC : : :: MM_5__ GGCACC 6140 ---------- 59.9% identity in 347 nt overlap (9094-9434:2660-2977); score: 280 E: 6.6e-17 9100 9110 9120 9130 9140 9150 9160 9170 9180 HS_11_ GGCTCACATACCTCCCACCTGGATTACAGTGAGCTTCCAGGTAATTTGGTCTGCTACTAGTCTCGCCTACTTGGATTTCCCTTCCCCCTG ::: : : : :: : : : : ::::::::: :: :: ::: :: : :: :::: : : ::::: : :: :: : : ::: MM_5__ GGCACGCCTGTCTGTCTCAGGCACCACAGTGAGCAACCTGGCTATT----CT--TTCTTGTCTTTCTT-CTTGGGTCTCTCT-CTCTCTG 2660 2670 2680 2690 2700 2710 2720 2730 2740 9190 9200 9210 9220 9230 9240 9250 9260 9270 HS_11_ CTGCAGCATTGCCTTCCAAAGCCATGCTTTGCACATGCCACATCCTAGCCCATTAGACTAAGCCTAGAAGCCTCTGCAGGACGTTCACCC ::: : ::: :: : : ::::::: :: ::: : :: ::: :::::::: ::: : : :::: ::: : MM_5__ ATGCTGAGGTGC-------AGAC-----TGGCACATGTCATCCCCT-GTGAAT--GACCAAGCCTAGGAGCACCCACTGGACTTTCTGCT 2750 2760 2770 2780 2790 2800 2810 9280 9290 9300 9310 9320 9330 9340 9350 HS_11_ T-CTCAGCGCCAC-TGCTCA--GTTTCCCAG-TGGAAACCTCTGCACCCAGGAGGTTTCCCCACAGCTTGCCT-GTGCTGCCTCTCTGGA : :: :: :::: : :::: : ::::: :: ::: ::: : :: : : :: :: ::::::::::: : ::: : : ::: : MM_5__ TTCTTTGCACCACGTCCTCACAGCACCCCAGCTGAAAAGCTCCACGTCCTG-ATGTCTCTTGACAGCTTGCCTTGAGCTACTT-TCTTGT 2820 2830 2840 2850 2860 2870 2880 2890 2900 9360 9370 9380 9390 9400 9410 9420 9430 HS_11_ GCTTTTCTCCCTTCCTGTAATGTCCTTGCTGCTCCCCGTCTCTAGTCCATTGCCTATACCTCTTTTTTTTTTTTTTT : : ::::::::: :: ::::: : :: : :: : : : : : :: :::: :::: :: :: :: : MM_5__ GTCATCTCCCCTTCCTG-AACCTCCTTC---CCCCGCATCCATTTTTCTGTTCTTAAACCTTTTTTCTTCTTCTTGT 2910 2920 2930 2940 2950 2960 2970 ---------- 56.9% identity in 429 nt overlap (3293-3708:215-611); score: 252 E: 1.4e-14 3300 3310 3320 3330 3340 3350 3360 3370 HS_11_ GACAGAGTGAGACTCCATC-ACAAAAAATAA-AT---AAATAAATAAATAAAATATAAATAAGTAAATAAAGGTCAGGAGTGGTGGCTCA :::: :: : ::: :: : :::: ::: :: :: :: :::: : : :::: :: : : : :::: : : : : MM_5__ GACATTGTCAAACTTAATGTATAAAATATATGATCTCAAGAGTATTAATACTACAGTAATACTACAAGAGATGATAGGATACATTGTTTA 220 230 240 250 260 270 280 290 300 3380 3390 3400 3410 3420 3430 3440 3450 3460 HS_11_ CGCCTGT-AATCCCAGCACTTTGGGAGGCCGAGGTGGACAGATCATGAGGTCATGAGATCAAGACCAT--CCTGGCTAAC--ACAGTGAA : ::::: :: :: :: : : :: : ::: :: : : :: :::: : : : :: : :::: : : ::: :: MM_5__ CACCTGTGAAGAGCAACAGCTAGTGATGTAGAG-TGCT----TGACTAGAACATG---TAAGGGCCCTGGCCTGATTCCCCAACAACAAA 310 320 330 340 350 360 370 380 3470 3480 3490 3500 3510 3520 3530 3540 3550 HS_11_ ACCCTGCCTCTACTAAAAATACAAA-AAGTCATCCAGGTG-TGGTGGCACACACCTATAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAG : : :: : ::: : ::::: :: : ::: ::: :::: : :::: : :: ::::::: ::: ::::: ::::::: MM_5__ AAAATCAATCAATCAAACAAACAAACAACAAAGCCAAGTGGTGGTAGTGCACATTTTTAATCCCAGC-ACTCAAGAGGCAGAGGCAGACA 390 400 410 420 430 440 450 460 470 3560 3570 3580 3590 3600 3610 3620 3630 HS_11_ AATCACT-TGAACCCAGGAGGCAGAGGTTGCAGTGAGCTGAGATCGCGCCACTACACTCCAGCCTAGGCGACAGAGCAAGACTCTGTCTC ::: :: ::: : :: : :: : ::: :::: :: : :: :::: :: ::: :: : :: :::::: MM_5__ GATCTCTGTGAGTCTGAGACCAACTTATTCTATAGAG-TGAGTTCT-GTGAC--------AGCCAGAGCTACATAGAGAAACCCTGTCTT 480 490 500 510 520 530 540 550 3640 3650 3660 3670 3680 3690 3700 HS_11_ AAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAATAAAAAGCACACACACACACACAC ::: :: :: ::: :: ::: ::: :: ::: :: :: ::::::::::::::::: MM_5__ GAAA------AACAAGCAAA--AACAAACAAACAAGCAAAAAACCTA-----CACACACACACACACAC 560 570 580 590 600 610 ---------- 59.2% identity in 191 nt overlap (8553-8740:2462-2644); score: 193 E: 1.2e-09 8560 8570 8580 8590 8600 8610 8620 8630 8640 HS_11_ GTTTCTATGGAT-CTCATCTTCCTTCAGAACAGCTCCCCTTCCCAACTTCCTGATTTCTAACAATAACAGTATCACCCTCCTTGTTCTCC ::::: : : : ::: : :: : :: ::::: :: :::::::::: : ::::::: ::: ::::::: ::::: :: MM_5__ GTTTCGAAGCAGGCTCTTTATCTATTGAGCCACCTCCCTCCCCTCACTTCCTGATGTTTAACAATGGCAGAGGCACCCTC-TTGTTGTCT 2470 2480 2490 2500 2510 2520 2530 2540 2550 8650 8660 8670 8680 8690 8700 8710 8720 HS_11_ CAATTTCTGAAACACAGAGTCATGTTTTTTTCTCTGCTTCAA--TCCCTGGTTTCCTATCGTCATCAATTATGACCTTTCCTTGCTTTGA : :: :: : : :: : : ::: :::: :: :: :::: : :: : :: :: : : : :::: :::::: MM_5__ TGACTTGTGGACCTCAAACCC------TTTCCTCTCCTCCAGGCTCCCACCTCTCACCAC-TCCCCAGCTGCAATCGCCCCTTTCTTTGA 2560 2570 2580 2590 2600 2610 2620 2630 8730 8740 HS_11_ AAGTGTTTTGG : :::::: MM_5__ CTGATTTTTGG 2640 ----------