Multiple sequence alignment - TraesCS5A01G104600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G104600 chr5A 100.000 3170 0 0 1 3170 168865908 168862739 0.000000e+00 5854.0
1 TraesCS5A01G104600 chr5A 99.048 630 6 0 2541 3170 168850591 168849962 0.000000e+00 1131.0
2 TraesCS5A01G104600 chr5A 93.819 631 35 2 2540 3170 196498445 196499071 0.000000e+00 946.0
3 TraesCS5A01G104600 chr5A 89.593 221 19 4 1 220 516800183 516800400 8.660000e-71 278.0
4 TraesCS5A01G104600 chr5A 86.122 245 29 5 1 242 516808574 516808332 3.140000e-65 259.0
5 TraesCS5A01G104600 chr5D 87.739 1778 124 40 661 2393 136349467 136351195 0.000000e+00 1989.0
6 TraesCS5A01G104600 chr5D 89.807 569 35 13 1 556 136348779 136349337 0.000000e+00 708.0
7 TraesCS5A01G104600 chr5B 85.705 1490 101 33 950 2393 149331170 149329747 0.000000e+00 1469.0
8 TraesCS5A01G104600 chr5B 91.139 395 13 3 261 653 149331852 149331478 1.690000e-142 516.0
9 TraesCS5A01G104600 chr5B 84.502 271 23 12 670 927 149331494 149331230 1.890000e-62 250.0
10 TraesCS5A01G104600 chr4A 94.787 633 30 2 2538 3170 501665130 501665759 0.000000e+00 983.0
11 TraesCS5A01G104600 chr2A 94.453 631 30 4 2541 3170 535695220 535695846 0.000000e+00 966.0
12 TraesCS5A01G104600 chr2A 93.997 633 36 2 2539 3170 697876400 697875769 0.000000e+00 957.0
13 TraesCS5A01G104600 chr2A 93.810 630 38 1 2541 3170 479370116 479369488 0.000000e+00 946.0
14 TraesCS5A01G104600 chr2A 93.651 630 38 2 2541 3170 535682508 535683135 0.000000e+00 941.0
15 TraesCS5A01G104600 chr1A 93.839 633 36 3 2538 3169 382038584 382039214 0.000000e+00 950.0
16 TraesCS5A01G104600 chr3A 93.651 630 38 1 2541 3170 362938561 362937934 0.000000e+00 941.0
17 TraesCS5A01G104600 chr1D 89.362 235 20 5 1 234 341232884 341232654 1.110000e-74 291.0
18 TraesCS5A01G104600 chr1D 87.815 238 25 4 1 236 462095311 462095546 3.110000e-70 276.0
19 TraesCS5A01G104600 chr7D 87.342 237 27 3 1 236 189174696 189174930 5.210000e-68 268.0
20 TraesCS5A01G104600 chr7B 85.650 223 30 2 1 222 628985045 628985266 1.900000e-57 233.0
21 TraesCS5A01G104600 chr1B 90.476 63 5 1 1 62 629093582 629093644 7.290000e-12 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G104600 chr5A 168862739 168865908 3169 True 5854.0 5854 100.000000 1 3170 1 chr5A.!!$R2 3169
1 TraesCS5A01G104600 chr5A 168849962 168850591 629 True 1131.0 1131 99.048000 2541 3170 1 chr5A.!!$R1 629
2 TraesCS5A01G104600 chr5A 196498445 196499071 626 False 946.0 946 93.819000 2540 3170 1 chr5A.!!$F1 630
3 TraesCS5A01G104600 chr5D 136348779 136351195 2416 False 1348.5 1989 88.773000 1 2393 2 chr5D.!!$F1 2392
4 TraesCS5A01G104600 chr5B 149329747 149331852 2105 True 745.0 1469 87.115333 261 2393 3 chr5B.!!$R1 2132
5 TraesCS5A01G104600 chr4A 501665130 501665759 629 False 983.0 983 94.787000 2538 3170 1 chr4A.!!$F1 632
6 TraesCS5A01G104600 chr2A 535695220 535695846 626 False 966.0 966 94.453000 2541 3170 1 chr2A.!!$F2 629
7 TraesCS5A01G104600 chr2A 697875769 697876400 631 True 957.0 957 93.997000 2539 3170 1 chr2A.!!$R2 631
8 TraesCS5A01G104600 chr2A 479369488 479370116 628 True 946.0 946 93.810000 2541 3170 1 chr2A.!!$R1 629
9 TraesCS5A01G104600 chr2A 535682508 535683135 627 False 941.0 941 93.651000 2541 3170 1 chr2A.!!$F1 629
10 TraesCS5A01G104600 chr1A 382038584 382039214 630 False 950.0 950 93.839000 2538 3169 1 chr1A.!!$F1 631
11 TraesCS5A01G104600 chr3A 362937934 362938561 627 True 941.0 941 93.651000 2541 3170 1 chr3A.!!$R1 629

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
812 890 0.106918 TTCTTTTGGTGACACGGCCT 60.107 50.0 0.0 0.0 42.67 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2421 2604 0.030638 CCCATGCGCCGGAATTTTAG 59.969 55.0 5.05 0.0 0.0 1.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.138859 TGGGTGACAGCATAATCTCCG 59.861 52.381 7.01 0.00 30.65 4.63
38 39 2.325583 TAATCTCCGGATTGGTGCAC 57.674 50.000 8.80 8.80 41.66 4.57
59 61 2.307768 CACCTCCTTCGACCTAGCATA 58.692 52.381 0.00 0.00 0.00 3.14
81 83 4.082845 AGTGTCGGTCCTATATGATCCTG 58.917 47.826 0.00 0.00 0.00 3.86
85 87 2.828520 CGGTCCTATATGATCCTGCTGT 59.171 50.000 0.00 0.00 0.00 4.40
88 90 4.040952 GGTCCTATATGATCCTGCTGTTGT 59.959 45.833 0.00 0.00 0.00 3.32
100 102 3.491619 CCTGCTGTTGTAGATATGTCGCT 60.492 47.826 0.00 0.00 0.00 4.93
144 146 9.980780 GTTTATTTTTGTTTAGTTGTGTGCATT 57.019 25.926 0.00 0.00 0.00 3.56
154 156 9.458374 GTTTAGTTGTGTGCATTTTAGTTATGT 57.542 29.630 0.00 0.00 0.00 2.29
164 166 5.607477 CATTTTAGTTATGTAGAGGCCGGA 58.393 41.667 5.05 0.00 0.00 5.14
165 167 5.881923 TTTTAGTTATGTAGAGGCCGGAT 57.118 39.130 5.05 0.00 0.00 4.18
174 176 2.088104 AGAGGCCGGATGATACTCAA 57.912 50.000 5.05 0.00 0.00 3.02
190 192 7.100409 TGATACTCAACATGTTTTGTATCCGA 58.900 34.615 31.88 22.53 37.68 4.55
196 198 7.825681 TCAACATGTTTTGTATCCGATTGATT 58.174 30.769 8.77 0.00 37.68 2.57
197 199 7.754475 TCAACATGTTTTGTATCCGATTGATTG 59.246 33.333 8.77 0.00 37.68 2.67
198 200 6.035843 ACATGTTTTGTATCCGATTGATTGC 58.964 36.000 0.00 0.00 36.57 3.56
243 246 8.757164 AATGGTCTTTATCGAAAATTGAAACC 57.243 30.769 0.00 0.00 0.00 3.27
244 247 6.375377 TGGTCTTTATCGAAAATTGAAACCG 58.625 36.000 0.00 0.00 0.00 4.44
257 260 1.133915 TGAAACCGGGCAGAGTTTTCT 60.134 47.619 6.32 0.00 36.36 2.52
264 278 2.437413 GGGCAGAGTTTTCTAAGGTGG 58.563 52.381 0.00 0.00 30.73 4.61
310 329 3.757493 ACTAGTAGTCAGAACAGAACCCG 59.243 47.826 0.00 0.00 0.00 5.28
420 439 2.554462 GGTTGAACAAGCTCCTTCCTTC 59.446 50.000 9.09 0.00 36.02 3.46
421 440 2.554462 GTTGAACAAGCTCCTTCCTTCC 59.446 50.000 0.00 0.00 0.00 3.46
422 441 2.057922 TGAACAAGCTCCTTCCTTCCT 58.942 47.619 0.00 0.00 0.00 3.36
423 442 2.443255 TGAACAAGCTCCTTCCTTCCTT 59.557 45.455 0.00 0.00 0.00 3.36
513 532 5.068723 CCATCAATTCATCTCCTTTCCTTGG 59.931 44.000 0.00 0.00 0.00 3.61
522 541 1.078426 CTTTCCTTGGCCCGATCGT 60.078 57.895 15.09 0.00 0.00 3.73
565 635 3.155501 AGACCTACATATACGCCTCACC 58.844 50.000 0.00 0.00 0.00 4.02
580 650 3.231736 ACCGGCGTGTTCTGACCT 61.232 61.111 6.01 0.00 0.00 3.85
636 706 4.377841 CGAGAAATCAACAAGAACAGCCTC 60.378 45.833 0.00 0.00 0.00 4.70
637 707 4.723309 AGAAATCAACAAGAACAGCCTCT 58.277 39.130 0.00 0.00 0.00 3.69
638 708 5.136105 AGAAATCAACAAGAACAGCCTCTT 58.864 37.500 0.00 0.00 36.02 2.85
639 709 5.240403 AGAAATCAACAAGAACAGCCTCTTC 59.760 40.000 0.00 0.00 33.25 2.87
640 710 3.845781 TCAACAAGAACAGCCTCTTCT 57.154 42.857 0.00 0.00 33.25 2.85
641 711 4.156455 TCAACAAGAACAGCCTCTTCTT 57.844 40.909 0.00 0.00 38.29 2.52
642 712 4.130118 TCAACAAGAACAGCCTCTTCTTC 58.870 43.478 0.00 0.00 36.09 2.87
643 713 4.133078 CAACAAGAACAGCCTCTTCTTCT 58.867 43.478 0.00 0.00 36.09 2.85
644 714 4.429854 ACAAGAACAGCCTCTTCTTCTT 57.570 40.909 0.00 0.00 36.09 2.52
645 715 4.384940 ACAAGAACAGCCTCTTCTTCTTC 58.615 43.478 0.00 0.00 36.09 2.87
646 716 4.102367 ACAAGAACAGCCTCTTCTTCTTCT 59.898 41.667 0.00 0.00 36.09 2.85
647 717 4.972751 AGAACAGCCTCTTCTTCTTCTT 57.027 40.909 0.00 0.00 0.00 2.52
648 718 4.893608 AGAACAGCCTCTTCTTCTTCTTC 58.106 43.478 0.00 0.00 0.00 2.87
649 719 4.592778 AGAACAGCCTCTTCTTCTTCTTCT 59.407 41.667 0.00 0.00 0.00 2.85
650 720 4.972751 ACAGCCTCTTCTTCTTCTTCTT 57.027 40.909 0.00 0.00 0.00 2.52
651 721 4.893608 ACAGCCTCTTCTTCTTCTTCTTC 58.106 43.478 0.00 0.00 0.00 2.87
652 722 4.592778 ACAGCCTCTTCTTCTTCTTCTTCT 59.407 41.667 0.00 0.00 0.00 2.85
653 723 5.071653 ACAGCCTCTTCTTCTTCTTCTTCTT 59.928 40.000 0.00 0.00 0.00 2.52
654 724 5.639082 CAGCCTCTTCTTCTTCTTCTTCTTC 59.361 44.000 0.00 0.00 0.00 2.87
655 725 5.543790 AGCCTCTTCTTCTTCTTCTTCTTCT 59.456 40.000 0.00 0.00 0.00 2.85
656 726 6.043127 AGCCTCTTCTTCTTCTTCTTCTTCTT 59.957 38.462 0.00 0.00 0.00 2.52
657 727 6.368791 GCCTCTTCTTCTTCTTCTTCTTCTTC 59.631 42.308 0.00 0.00 0.00 2.87
658 728 7.670364 CCTCTTCTTCTTCTTCTTCTTCTTCT 58.330 38.462 0.00 0.00 0.00 2.85
659 729 8.150296 CCTCTTCTTCTTCTTCTTCTTCTTCTT 58.850 37.037 0.00 0.00 0.00 2.52
738 811 2.176273 CCAGAAGAATGGAGCGCGG 61.176 63.158 8.83 0.00 43.57 6.46
788 866 2.680339 GCTGTCCCTGCTTGATTTCTAC 59.320 50.000 0.00 0.00 0.00 2.59
789 867 3.620966 GCTGTCCCTGCTTGATTTCTACT 60.621 47.826 0.00 0.00 0.00 2.57
790 868 4.383118 GCTGTCCCTGCTTGATTTCTACTA 60.383 45.833 0.00 0.00 0.00 1.82
791 869 5.344743 TGTCCCTGCTTGATTTCTACTAG 57.655 43.478 0.00 0.00 0.00 2.57
792 870 4.123506 GTCCCTGCTTGATTTCTACTAGC 58.876 47.826 0.00 0.00 36.85 3.42
799 877 7.120432 CCTGCTTGATTTCTACTAGCTTCTTTT 59.880 37.037 0.00 0.00 37.13 2.27
803 881 7.672983 TGATTTCTACTAGCTTCTTTTGGTG 57.327 36.000 0.00 0.00 0.00 4.17
810 888 0.317854 GCTTCTTTTGGTGACACGGC 60.318 55.000 0.00 0.00 42.67 5.68
812 890 0.106918 TTCTTTTGGTGACACGGCCT 60.107 50.000 0.00 0.00 42.67 5.19
813 891 0.817634 TCTTTTGGTGACACGGCCTG 60.818 55.000 0.00 0.21 42.67 4.85
814 892 1.077357 TTTTGGTGACACGGCCTGT 60.077 52.632 0.00 4.09 42.67 4.00
815 893 0.681564 TTTTGGTGACACGGCCTGTT 60.682 50.000 0.00 0.00 42.67 3.16
830 912 2.554893 GCCTGTTGGTTCACGGAAATTA 59.445 45.455 0.00 0.00 35.27 1.40
945 1040 8.200792 CCTAATACTAGCACTCTGTTTCAGATT 58.799 37.037 0.00 0.00 39.92 2.40
946 1041 7.840342 AATACTAGCACTCTGTTTCAGATTG 57.160 36.000 11.09 11.09 41.84 2.67
947 1042 5.474578 ACTAGCACTCTGTTTCAGATTGA 57.525 39.130 17.09 1.63 41.59 2.57
948 1043 5.477510 ACTAGCACTCTGTTTCAGATTGAG 58.522 41.667 17.09 10.72 41.59 3.02
1016 1149 0.105593 CCGATGGAGGTCATGACTGG 59.894 60.000 24.50 11.43 35.97 4.00
1027 1160 2.040544 ATGACTGGAAAAGGCGGCG 61.041 57.895 0.51 0.51 36.26 6.46
1059 1192 1.502231 CCAACTATCTTCGGCCATCG 58.498 55.000 2.24 0.00 40.90 3.84
1118 1251 3.620286 CGCGTTCGTGGAGAAACA 58.380 55.556 0.00 0.00 41.10 2.83
1119 1252 1.487231 CGCGTTCGTGGAGAAACAG 59.513 57.895 0.00 0.00 41.10 3.16
1120 1253 1.860078 GCGTTCGTGGAGAAACAGG 59.140 57.895 0.00 0.00 41.10 4.00
1132 1265 2.039084 GAGAAACAGGAAGCTCCAAGGA 59.961 50.000 5.21 0.00 39.61 3.36
1185 1318 1.066858 TCAGCTTCGGATGACCAGAAC 60.067 52.381 0.00 0.00 35.27 3.01
1186 1319 0.250513 AGCTTCGGATGACCAGAACC 59.749 55.000 0.00 0.00 35.59 3.62
1187 1320 0.036388 GCTTCGGATGACCAGAACCA 60.036 55.000 0.00 0.00 35.59 3.67
1188 1321 1.610624 GCTTCGGATGACCAGAACCAA 60.611 52.381 0.00 0.00 35.59 3.67
1189 1322 2.778299 CTTCGGATGACCAGAACCAAA 58.222 47.619 0.00 0.00 35.59 3.28
1190 1323 2.940994 TCGGATGACCAGAACCAAAA 57.059 45.000 0.00 0.00 35.59 2.44
1224 1357 2.639286 GTACGGTCGGTGTCACGT 59.361 61.111 0.00 0.00 42.71 4.49
1320 1453 3.290776 GGACATCGTGGCCTATGAC 57.709 57.895 16.92 11.83 44.12 3.06
1385 1530 2.921221 ACCTGATGGGAGGAAGAAGAA 58.079 47.619 0.00 0.00 36.51 2.52
1387 1532 3.110705 CCTGATGGGAGGAAGAAGAAGA 58.889 50.000 0.00 0.00 34.69 2.87
1388 1533 3.134442 CCTGATGGGAGGAAGAAGAAGAG 59.866 52.174 0.00 0.00 34.69 2.85
1389 1534 3.110705 TGATGGGAGGAAGAAGAAGAGG 58.889 50.000 0.00 0.00 0.00 3.69
1553 1713 2.048222 CGCCGCTGACAAGAAGGA 60.048 61.111 0.00 0.00 0.00 3.36
1564 1724 0.037303 CAAGAAGGAGGCTGGCAAGA 59.963 55.000 3.38 0.00 0.00 3.02
1565 1725 0.327591 AAGAAGGAGGCTGGCAAGAG 59.672 55.000 3.38 0.00 0.00 2.85
1566 1726 0.546267 AGAAGGAGGCTGGCAAGAGA 60.546 55.000 3.38 0.00 0.00 3.10
1567 1727 0.326264 GAAGGAGGCTGGCAAGAGAA 59.674 55.000 3.38 0.00 0.00 2.87
1568 1728 0.037447 AAGGAGGCTGGCAAGAGAAC 59.963 55.000 3.38 0.00 0.00 3.01
1569 1729 1.130054 AGGAGGCTGGCAAGAGAACA 61.130 55.000 3.38 0.00 0.00 3.18
1570 1730 0.676151 GGAGGCTGGCAAGAGAACAG 60.676 60.000 3.38 0.00 35.40 3.16
1571 1731 0.322975 GAGGCTGGCAAGAGAACAGA 59.677 55.000 3.38 0.00 34.21 3.41
1572 1732 0.324285 AGGCTGGCAAGAGAACAGAG 59.676 55.000 3.38 0.00 34.21 3.35
1573 1733 0.322975 GGCTGGCAAGAGAACAGAGA 59.677 55.000 0.00 0.00 34.21 3.10
1574 1734 1.675415 GGCTGGCAAGAGAACAGAGAG 60.675 57.143 0.00 0.00 34.21 3.20
1575 1735 1.001860 GCTGGCAAGAGAACAGAGAGT 59.998 52.381 0.00 0.00 34.21 3.24
1576 1736 2.686235 CTGGCAAGAGAACAGAGAGTG 58.314 52.381 0.00 0.00 34.21 3.51
1577 1737 2.036992 CTGGCAAGAGAACAGAGAGTGT 59.963 50.000 0.00 0.00 43.24 3.55
1578 1738 3.230976 TGGCAAGAGAACAGAGAGTGTA 58.769 45.455 0.00 0.00 39.03 2.90
1579 1739 3.641436 TGGCAAGAGAACAGAGAGTGTAA 59.359 43.478 0.00 0.00 39.03 2.41
1580 1740 4.100963 TGGCAAGAGAACAGAGAGTGTAAA 59.899 41.667 0.00 0.00 39.03 2.01
1581 1741 4.688413 GGCAAGAGAACAGAGAGTGTAAAG 59.312 45.833 0.00 0.00 39.03 1.85
1584 1744 3.898123 AGAGAACAGAGAGTGTAAAGCCA 59.102 43.478 0.00 0.00 39.03 4.75
1593 1753 0.110373 GTGTAAAGCCACCGAAAGCG 60.110 55.000 0.00 0.00 37.24 4.68
1600 1760 0.385598 GCCACCGAAAGCGAAGAAAC 60.386 55.000 0.00 0.00 40.82 2.78
1603 1763 0.179040 ACCGAAAGCGAAGAAACCCA 60.179 50.000 0.00 0.00 40.82 4.51
1604 1764 1.165270 CCGAAAGCGAAGAAACCCAT 58.835 50.000 0.00 0.00 40.82 4.00
1609 1769 1.523758 AGCGAAGAAACCCATGACAC 58.476 50.000 0.00 0.00 0.00 3.67
1645 1805 2.286365 GGAAATTGTCCAGGGTGACA 57.714 50.000 0.00 0.00 46.97 3.58
1651 1814 0.180171 TGTCCAGGGTGACACAACTG 59.820 55.000 17.80 17.80 40.22 3.16
1652 1815 4.481195 CCAGGGTGACACAACTGG 57.519 61.111 25.09 25.09 43.87 4.00
1686 1849 2.557901 GGGGAAGTCACTCTACACTCCT 60.558 54.545 0.00 0.00 0.00 3.69
1792 1970 0.949105 CTTCCCGTTCACCCGACAAG 60.949 60.000 0.00 0.00 0.00 3.16
1796 1974 2.654912 CGTTCACCCGACAAGCGAC 61.655 63.158 0.00 0.00 44.57 5.19
1800 1978 1.671054 CACCCGACAAGCGACCAAT 60.671 57.895 0.00 0.00 44.57 3.16
1866 2044 1.134670 GTCCTCCCATCCGAACAAGAG 60.135 57.143 0.00 0.00 0.00 2.85
2008 2186 4.681978 GCTTCGTGGTGCCGGAGT 62.682 66.667 5.05 0.00 35.81 3.85
2090 2268 4.116328 CGAGGAGACGGCGAGCAA 62.116 66.667 16.62 0.00 35.49 3.91
2108 2286 2.438075 GCTGGCCAAGAGCAGGAG 60.438 66.667 7.01 0.00 46.50 3.69
2143 2321 1.351076 CCTGGTTGGGGCTTTTGAAT 58.649 50.000 0.00 0.00 0.00 2.57
2149 2327 3.157087 GTTGGGGCTTTTGAATCTCTCA 58.843 45.455 0.00 0.00 0.00 3.27
2160 2338 7.067251 GCTTTTGAATCTCTCATCTCCAAGATT 59.933 37.037 0.00 0.00 40.29 2.40
2194 2372 3.367743 CAGCCGCACTGCACCAAT 61.368 61.111 1.11 0.00 40.19 3.16
2199 2377 0.664166 CCGCACTGCACCAATGTTTC 60.664 55.000 1.11 0.00 0.00 2.78
2213 2391 4.867608 CCAATGTTTCGTTTTGTTTGTCCT 59.132 37.500 0.00 0.00 0.00 3.85
2224 2402 4.664150 TTGTTTGTCCTTGGGTTGATTC 57.336 40.909 0.00 0.00 0.00 2.52
2225 2403 3.909732 TGTTTGTCCTTGGGTTGATTCT 58.090 40.909 0.00 0.00 0.00 2.40
2226 2404 5.055265 TGTTTGTCCTTGGGTTGATTCTA 57.945 39.130 0.00 0.00 0.00 2.10
2227 2405 5.070001 TGTTTGTCCTTGGGTTGATTCTAG 58.930 41.667 0.00 0.00 0.00 2.43
2228 2406 5.163141 TGTTTGTCCTTGGGTTGATTCTAGA 60.163 40.000 0.00 0.00 0.00 2.43
2229 2407 4.826274 TGTCCTTGGGTTGATTCTAGAG 57.174 45.455 0.00 0.00 0.00 2.43
2230 2408 4.168101 TGTCCTTGGGTTGATTCTAGAGT 58.832 43.478 0.00 0.00 0.00 3.24
2231 2409 4.020218 TGTCCTTGGGTTGATTCTAGAGTG 60.020 45.833 0.00 0.00 0.00 3.51
2232 2410 4.223032 GTCCTTGGGTTGATTCTAGAGTGA 59.777 45.833 0.00 0.00 0.00 3.41
2233 2411 5.032846 TCCTTGGGTTGATTCTAGAGTGAT 58.967 41.667 0.00 0.00 0.00 3.06
2234 2412 5.104776 TCCTTGGGTTGATTCTAGAGTGATG 60.105 44.000 0.00 0.00 0.00 3.07
2235 2413 5.104776 CCTTGGGTTGATTCTAGAGTGATGA 60.105 44.000 0.00 0.00 0.00 2.92
2236 2414 5.344743 TGGGTTGATTCTAGAGTGATGAC 57.655 43.478 0.00 0.00 0.00 3.06
2237 2415 4.777366 TGGGTTGATTCTAGAGTGATGACA 59.223 41.667 0.00 0.00 0.00 3.58
2238 2416 5.426509 TGGGTTGATTCTAGAGTGATGACAT 59.573 40.000 0.00 0.00 0.00 3.06
2239 2417 5.988561 GGGTTGATTCTAGAGTGATGACATC 59.011 44.000 8.59 8.59 0.00 3.06
2240 2418 5.988561 GGTTGATTCTAGAGTGATGACATCC 59.011 44.000 12.90 4.61 0.00 3.51
2241 2419 5.444663 TGATTCTAGAGTGATGACATCCG 57.555 43.478 12.90 0.00 0.00 4.18
2270 2448 2.568956 TGCTAGTTCAATCAGGCAGAGT 59.431 45.455 0.00 0.00 0.00 3.24
2281 2459 3.023119 TCAGGCAGAGTTGAAAGCAAAA 58.977 40.909 0.00 0.00 35.42 2.44
2282 2460 3.067180 TCAGGCAGAGTTGAAAGCAAAAG 59.933 43.478 0.00 0.00 35.42 2.27
2283 2461 3.026694 AGGCAGAGTTGAAAGCAAAAGT 58.973 40.909 0.00 0.00 35.42 2.66
2284 2462 3.448660 AGGCAGAGTTGAAAGCAAAAGTT 59.551 39.130 0.00 0.00 35.42 2.66
2297 2475 8.465999 TGAAAGCAAAAGTTGATGTTTTCTCTA 58.534 29.630 21.19 8.19 43.15 2.43
2301 2479 6.697019 GCAAAAGTTGATGTTTTCTCTAAGCA 59.303 34.615 0.00 0.00 0.00 3.91
2303 2481 9.252962 CAAAAGTTGATGTTTTCTCTAAGCATT 57.747 29.630 0.00 0.00 37.74 3.56
2349 2527 6.829229 ATATGTTCGATGATTGCATGGAAT 57.171 33.333 12.76 12.76 46.30 3.01
2352 2530 4.201940 TGTTCGATGATTGCATGGAATCAC 60.202 41.667 35.72 27.57 46.30 3.06
2364 2542 4.497674 GCATGGAATCACTTCATCTTCAGC 60.498 45.833 0.00 0.00 32.70 4.26
2368 2551 3.883830 ATCACTTCATCTTCAGCGTCT 57.116 42.857 0.00 0.00 0.00 4.18
2371 2554 3.062763 CACTTCATCTTCAGCGTCTTGT 58.937 45.455 0.00 0.00 0.00 3.16
2374 2557 5.349817 CACTTCATCTTCAGCGTCTTGTAAT 59.650 40.000 0.00 0.00 0.00 1.89
2388 2571 5.350640 CGTCTTGTAATCTTAACCCCTTGTC 59.649 44.000 0.00 0.00 0.00 3.18
2393 2576 6.007703 TGTAATCTTAACCCCTTGTCCAAAG 58.992 40.000 0.00 0.00 0.00 2.77
2394 2577 3.518992 TCTTAACCCCTTGTCCAAAGG 57.481 47.619 0.00 0.00 37.17 3.11
2395 2578 1.893137 CTTAACCCCTTGTCCAAAGGC 59.107 52.381 0.00 0.00 36.10 4.35
2396 2579 0.113580 TAACCCCTTGTCCAAAGGCC 59.886 55.000 0.00 0.00 36.10 5.19
2397 2580 1.955458 AACCCCTTGTCCAAAGGCCA 61.955 55.000 5.01 0.00 36.10 5.36
2398 2581 1.908299 CCCCTTGTCCAAAGGCCAC 60.908 63.158 5.01 0.00 36.10 5.01
2399 2582 1.152567 CCCTTGTCCAAAGGCCACA 60.153 57.895 5.01 0.00 36.10 4.17
2400 2583 1.181098 CCCTTGTCCAAAGGCCACAG 61.181 60.000 5.01 0.00 36.10 3.66
2401 2584 1.662044 CTTGTCCAAAGGCCACAGC 59.338 57.895 5.01 0.00 38.76 4.40
2402 2585 0.825010 CTTGTCCAAAGGCCACAGCT 60.825 55.000 5.01 0.00 39.73 4.24
2403 2586 0.476338 TTGTCCAAAGGCCACAGCTA 59.524 50.000 5.01 0.00 39.73 3.32
2404 2587 0.036732 TGTCCAAAGGCCACAGCTAG 59.963 55.000 5.01 0.00 39.73 3.42
2405 2588 0.324943 GTCCAAAGGCCACAGCTAGA 59.675 55.000 5.01 0.00 39.73 2.43
2406 2589 0.615331 TCCAAAGGCCACAGCTAGAG 59.385 55.000 5.01 0.00 39.73 2.43
2407 2590 1.028868 CCAAAGGCCACAGCTAGAGC 61.029 60.000 5.01 0.00 39.73 4.09
2429 2612 3.733236 GGTTGGCCGGCTAAAATTC 57.267 52.632 28.04 14.44 0.00 2.17
2430 2613 0.174845 GGTTGGCCGGCTAAAATTCC 59.825 55.000 28.04 19.73 0.00 3.01
2431 2614 0.179148 GTTGGCCGGCTAAAATTCCG 60.179 55.000 28.04 0.00 44.89 4.30
2435 2618 2.024163 CGGCTAAAATTCCGGCGC 59.976 61.111 0.00 0.00 41.82 6.53
2436 2619 2.756025 CGGCTAAAATTCCGGCGCA 61.756 57.895 10.83 0.00 41.82 6.09
2437 2620 1.733526 GGCTAAAATTCCGGCGCAT 59.266 52.632 10.83 0.00 0.00 4.73
2438 2621 0.594796 GGCTAAAATTCCGGCGCATG 60.595 55.000 10.83 0.00 0.00 4.06
2439 2622 0.594796 GCTAAAATTCCGGCGCATGG 60.595 55.000 10.83 11.17 0.00 3.66
2440 2623 0.030638 CTAAAATTCCGGCGCATGGG 59.969 55.000 16.77 11.14 0.00 4.00
2441 2624 1.388065 TAAAATTCCGGCGCATGGGG 61.388 55.000 16.77 8.67 0.00 4.96
2451 2634 2.747855 GCATGGGGCGGCTATAGC 60.748 66.667 16.78 16.78 41.14 2.97
2464 2647 3.305398 GCTATAGCCGCTCATTACACT 57.695 47.619 14.13 0.00 34.31 3.55
2465 2648 4.436242 GCTATAGCCGCTCATTACACTA 57.564 45.455 14.13 0.00 34.31 2.74
2466 2649 4.167268 GCTATAGCCGCTCATTACACTAC 58.833 47.826 14.13 0.00 34.31 2.73
2467 2650 4.321008 GCTATAGCCGCTCATTACACTACA 60.321 45.833 14.13 0.00 34.31 2.74
2468 2651 4.873746 ATAGCCGCTCATTACACTACAT 57.126 40.909 0.00 0.00 0.00 2.29
2469 2652 3.543680 AGCCGCTCATTACACTACATT 57.456 42.857 0.00 0.00 0.00 2.71
2470 2653 4.665833 AGCCGCTCATTACACTACATTA 57.334 40.909 0.00 0.00 0.00 1.90
2471 2654 5.215252 AGCCGCTCATTACACTACATTAT 57.785 39.130 0.00 0.00 0.00 1.28
2472 2655 5.230942 AGCCGCTCATTACACTACATTATC 58.769 41.667 0.00 0.00 0.00 1.75
2473 2656 4.389077 GCCGCTCATTACACTACATTATCC 59.611 45.833 0.00 0.00 0.00 2.59
2474 2657 5.784177 CCGCTCATTACACTACATTATCCT 58.216 41.667 0.00 0.00 0.00 3.24
2475 2658 5.635280 CCGCTCATTACACTACATTATCCTG 59.365 44.000 0.00 0.00 0.00 3.86
2476 2659 6.216569 CGCTCATTACACTACATTATCCTGT 58.783 40.000 0.00 0.00 0.00 4.00
2477 2660 7.368059 CGCTCATTACACTACATTATCCTGTA 58.632 38.462 0.00 0.00 0.00 2.74
2478 2661 8.029522 CGCTCATTACACTACATTATCCTGTAT 58.970 37.037 0.00 0.00 31.49 2.29
2496 2679 9.920946 ATCCTGTATATGCTTTTTAAGAGGAAA 57.079 29.630 0.00 0.00 29.01 3.13
2497 2680 9.747898 TCCTGTATATGCTTTTTAAGAGGAAAA 57.252 29.630 0.00 0.00 0.00 2.29
2530 2713 9.948964 AAAGACCTGTAAAATAATAGTTACGGT 57.051 29.630 8.68 8.68 38.56 4.83
2531 2714 9.591792 AAGACCTGTAAAATAATAGTTACGGTC 57.408 33.333 18.88 18.88 44.00 4.79
2532 2715 8.752187 AGACCTGTAAAATAATAGTTACGGTCA 58.248 33.333 23.46 4.60 44.82 4.02
2533 2716 9.369904 GACCTGTAAAATAATAGTTACGGTCAA 57.630 33.333 20.22 0.00 43.65 3.18
2534 2717 9.895138 ACCTGTAAAATAATAGTTACGGTCAAT 57.105 29.630 0.00 0.00 34.76 2.57
2571 2754 2.221169 GGATGCGACATATGCCAAAGA 58.779 47.619 1.58 0.00 0.00 2.52
2875 3060 3.522343 CTGGGGGTTTATATAGGCCTACC 59.478 52.174 16.61 13.48 0.00 3.18
2876 3061 3.115882 TGGGGGTTTATATAGGCCTACCA 60.116 47.826 16.61 11.74 39.06 3.25
2950 3137 2.754658 GGCCTCCGTCTTCTCCGA 60.755 66.667 0.00 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.439507 ACCAATCCGGAGATTATGCTGT 59.560 45.455 11.34 0.00 40.89 4.40
38 39 0.970937 TGCTAGGTCGAAGGAGGTGG 60.971 60.000 0.00 0.00 0.00 4.61
59 61 4.082845 CAGGATCATATAGGACCGACACT 58.917 47.826 0.00 0.00 0.00 3.55
81 83 5.470845 AAAAGCGACATATCTACAACAGC 57.529 39.130 0.00 0.00 0.00 4.40
132 134 8.615878 TCTACATAACTAAAATGCACACAACT 57.384 30.769 0.00 0.00 0.00 3.16
134 136 7.361713 GCCTCTACATAACTAAAATGCACACAA 60.362 37.037 0.00 0.00 0.00 3.33
138 140 5.277345 CGGCCTCTACATAACTAAAATGCAC 60.277 44.000 0.00 0.00 0.00 4.57
144 146 4.897076 TCATCCGGCCTCTACATAACTAAA 59.103 41.667 0.00 0.00 0.00 1.85
154 156 2.971901 TGAGTATCATCCGGCCTCTA 57.028 50.000 0.00 0.00 42.56 2.43
174 176 6.035843 GCAATCAATCGGATACAAAACATGT 58.964 36.000 0.00 0.00 46.36 3.21
196 198 9.421806 CCATTTTTATTGACTCAAAATGTAGCA 57.578 29.630 13.00 0.00 42.54 3.49
197 199 9.423061 ACCATTTTTATTGACTCAAAATGTAGC 57.577 29.630 13.00 0.00 42.54 3.58
223 225 5.620429 GCCCGGTTTCAATTTTCGATAAAGA 60.620 40.000 0.00 0.00 0.00 2.52
236 239 1.679153 GAAAACTCTGCCCGGTTTCAA 59.321 47.619 0.00 0.00 35.02 2.69
240 243 2.552373 CCTTAGAAAACTCTGCCCGGTT 60.552 50.000 0.00 0.00 0.00 4.44
243 246 2.076863 CACCTTAGAAAACTCTGCCCG 58.923 52.381 0.00 0.00 0.00 6.13
244 247 2.437413 CCACCTTAGAAAACTCTGCCC 58.563 52.381 0.00 0.00 0.00 5.36
303 322 1.271762 GGAAAAGGTTAGGCGGGTTCT 60.272 52.381 0.00 0.00 0.00 3.01
304 323 1.171308 GGAAAAGGTTAGGCGGGTTC 58.829 55.000 0.00 0.00 0.00 3.62
305 324 0.251474 GGGAAAAGGTTAGGCGGGTT 60.251 55.000 0.00 0.00 0.00 4.11
306 325 1.381463 GGGAAAAGGTTAGGCGGGT 59.619 57.895 0.00 0.00 0.00 5.28
307 326 0.963856 GTGGGAAAAGGTTAGGCGGG 60.964 60.000 0.00 0.00 0.00 6.13
310 329 1.162698 GACGTGGGAAAAGGTTAGGC 58.837 55.000 0.00 0.00 0.00 3.93
420 439 1.795286 GTGCTTGAGACTCGAACAAGG 59.205 52.381 16.86 0.00 40.57 3.61
421 440 2.473816 TGTGCTTGAGACTCGAACAAG 58.526 47.619 13.29 13.29 42.33 3.16
422 441 2.595124 TGTGCTTGAGACTCGAACAA 57.405 45.000 0.00 0.00 0.00 2.83
423 442 2.820059 ATGTGCTTGAGACTCGAACA 57.180 45.000 0.00 0.00 0.00 3.18
513 532 1.826921 TGGTAGGAGACGATCGGGC 60.827 63.158 20.98 11.08 0.00 6.13
522 541 0.179076 CATGCGCATGTGGTAGGAGA 60.179 55.000 36.45 0.00 34.23 3.71
565 635 3.414700 GCAGGTCAGAACACGCCG 61.415 66.667 0.00 0.00 0.00 6.46
596 666 2.358737 GGTGGACTGGTCAAGCGG 60.359 66.667 3.10 0.00 0.00 5.52
597 667 2.738521 CGGTGGACTGGTCAAGCG 60.739 66.667 13.90 13.90 46.12 4.68
598 668 1.374758 CTCGGTGGACTGGTCAAGC 60.375 63.158 3.10 0.37 0.00 4.01
599 669 0.679505 TTCTCGGTGGACTGGTCAAG 59.320 55.000 3.10 0.00 0.00 3.02
636 706 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
637 707 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
638 708 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
639 709 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
640 710 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
641 711 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
642 712 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
643 713 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
644 714 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
645 715 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
646 716 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
647 717 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
648 718 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
649 719 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
650 720 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
651 721 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
652 722 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
653 723 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
654 724 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
655 725 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
656 726 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
657 727 9.546428 AAGAAGAAGAAGAAGAAGAAGAAGAAG 57.454 33.333 0.00 0.00 0.00 2.85
658 728 9.541143 GAAGAAGAAGAAGAAGAAGAAGAAGAA 57.459 33.333 0.00 0.00 0.00 2.52
659 729 8.923270 AGAAGAAGAAGAAGAAGAAGAAGAAGA 58.077 33.333 0.00 0.00 0.00 2.87
738 811 3.567797 GATGCCCGCTTCACTCGC 61.568 66.667 0.00 0.00 0.00 5.03
788 866 2.480419 CCGTGTCACCAAAAGAAGCTAG 59.520 50.000 0.00 0.00 0.00 3.42
789 867 2.489971 CCGTGTCACCAAAAGAAGCTA 58.510 47.619 0.00 0.00 0.00 3.32
790 868 1.308998 CCGTGTCACCAAAAGAAGCT 58.691 50.000 0.00 0.00 0.00 3.74
791 869 0.317854 GCCGTGTCACCAAAAGAAGC 60.318 55.000 0.00 0.00 0.00 3.86
792 870 0.310854 GGCCGTGTCACCAAAAGAAG 59.689 55.000 0.00 0.00 0.00 2.85
799 877 2.203139 CAACAGGCCGTGTCACCA 60.203 61.111 8.09 0.00 39.03 4.17
803 881 1.525077 TGAACCAACAGGCCGTGTC 60.525 57.895 8.09 0.00 39.03 3.67
810 888 3.190535 CCTAATTTCCGTGAACCAACAGG 59.809 47.826 0.00 0.00 0.00 4.00
812 890 3.150767 CCCTAATTTCCGTGAACCAACA 58.849 45.455 0.00 0.00 0.00 3.33
813 891 3.414269 TCCCTAATTTCCGTGAACCAAC 58.586 45.455 0.00 0.00 0.00 3.77
814 892 3.791953 TCCCTAATTTCCGTGAACCAA 57.208 42.857 0.00 0.00 0.00 3.67
815 893 4.384427 GGTATCCCTAATTTCCGTGAACCA 60.384 45.833 0.00 0.00 0.00 3.67
830 912 1.393468 AGGGCCAAAAAGGTATCCCT 58.607 50.000 6.18 0.00 45.63 4.20
912 994 4.582656 AGAGTGCTAGTATTAGGTGAGCAG 59.417 45.833 0.00 0.00 43.43 4.24
945 1040 7.978414 CAGCTGATTTCTAATTCAGTAGACTCA 59.022 37.037 8.42 0.00 41.16 3.41
946 1041 7.437862 CCAGCTGATTTCTAATTCAGTAGACTC 59.562 40.741 17.39 0.67 41.16 3.36
947 1042 7.124901 TCCAGCTGATTTCTAATTCAGTAGACT 59.875 37.037 17.39 3.16 41.16 3.24
948 1043 7.268586 TCCAGCTGATTTCTAATTCAGTAGAC 58.731 38.462 17.39 1.45 41.16 2.59
1007 1140 0.960364 GCCGCCTTTTCCAGTCATGA 60.960 55.000 0.00 0.00 0.00 3.07
1029 1162 0.463833 GATAGTTGGGGACGGGCTTG 60.464 60.000 0.00 0.00 0.00 4.01
1118 1251 0.772124 TTGGGTCCTTGGAGCTTCCT 60.772 55.000 16.95 0.00 37.46 3.36
1119 1252 0.609406 GTTGGGTCCTTGGAGCTTCC 60.609 60.000 16.95 2.60 36.96 3.46
1120 1253 0.609406 GGTTGGGTCCTTGGAGCTTC 60.609 60.000 16.95 8.66 0.00 3.86
1132 1265 4.227583 CCGGGGTTTGGGTTGGGT 62.228 66.667 0.00 0.00 0.00 4.51
1173 1306 4.021102 TCTCTTTTGGTTCTGGTCATCC 57.979 45.455 0.00 0.00 0.00 3.51
1185 1318 2.276732 TGACCAGCCTTCTCTTTTGG 57.723 50.000 0.00 0.00 35.07 3.28
1186 1319 2.555757 CCTTGACCAGCCTTCTCTTTTG 59.444 50.000 0.00 0.00 0.00 2.44
1187 1320 2.175715 ACCTTGACCAGCCTTCTCTTTT 59.824 45.455 0.00 0.00 0.00 2.27
1188 1321 1.777272 ACCTTGACCAGCCTTCTCTTT 59.223 47.619 0.00 0.00 0.00 2.52
1189 1322 1.439543 ACCTTGACCAGCCTTCTCTT 58.560 50.000 0.00 0.00 0.00 2.85
1190 1323 1.903183 GTACCTTGACCAGCCTTCTCT 59.097 52.381 0.00 0.00 0.00 3.10
1224 1357 2.479049 GCTGAAATCTACGACACGCCTA 60.479 50.000 0.00 0.00 0.00 3.93
1235 1368 3.410631 TGTCGGGTTTGCTGAAATCTA 57.589 42.857 0.00 0.00 0.00 1.98
1331 1470 2.108566 CATCGGCAGGAGCAGGAG 59.891 66.667 0.00 0.00 44.61 3.69
1341 1480 0.394192 GATGAGATGGTCCATCGGCA 59.606 55.000 23.38 23.65 44.67 5.69
1385 1530 1.010046 TCCCCTTCATCACATCCCTCT 59.990 52.381 0.00 0.00 0.00 3.69
1387 1532 1.985622 TTCCCCTTCATCACATCCCT 58.014 50.000 0.00 0.00 0.00 4.20
1388 1533 2.760650 GTTTTCCCCTTCATCACATCCC 59.239 50.000 0.00 0.00 0.00 3.85
1389 1534 3.193479 GTGTTTTCCCCTTCATCACATCC 59.807 47.826 0.00 0.00 0.00 3.51
1553 1713 0.324285 CTCTGTTCTCTTGCCAGCCT 59.676 55.000 0.00 0.00 0.00 4.58
1564 1724 3.244249 GGTGGCTTTACACTCTCTGTTCT 60.244 47.826 0.00 0.00 41.09 3.01
1565 1725 3.067833 GGTGGCTTTACACTCTCTGTTC 58.932 50.000 0.00 0.00 41.09 3.18
1566 1726 2.548067 CGGTGGCTTTACACTCTCTGTT 60.548 50.000 0.00 0.00 41.09 3.16
1567 1727 1.000955 CGGTGGCTTTACACTCTCTGT 59.999 52.381 0.00 0.00 41.09 3.41
1568 1728 1.272490 TCGGTGGCTTTACACTCTCTG 59.728 52.381 0.00 0.00 41.09 3.35
1569 1729 1.629043 TCGGTGGCTTTACACTCTCT 58.371 50.000 0.00 0.00 41.09 3.10
1570 1730 2.450609 TTCGGTGGCTTTACACTCTC 57.549 50.000 0.00 0.00 41.09 3.20
1571 1731 2.767505 CTTTCGGTGGCTTTACACTCT 58.232 47.619 0.00 0.00 41.09 3.24
1572 1732 1.197036 GCTTTCGGTGGCTTTACACTC 59.803 52.381 0.00 0.00 41.09 3.51
1573 1733 1.235724 GCTTTCGGTGGCTTTACACT 58.764 50.000 0.00 0.00 41.09 3.55
1574 1734 0.110373 CGCTTTCGGTGGCTTTACAC 60.110 55.000 0.00 0.00 40.60 2.90
1575 1735 0.249953 TCGCTTTCGGTGGCTTTACA 60.250 50.000 0.00 0.00 36.13 2.41
1576 1736 0.869730 TTCGCTTTCGGTGGCTTTAC 59.130 50.000 0.00 0.00 36.13 2.01
1577 1737 1.153353 CTTCGCTTTCGGTGGCTTTA 58.847 50.000 0.00 0.00 36.13 1.85
1578 1738 0.534203 TCTTCGCTTTCGGTGGCTTT 60.534 50.000 0.00 0.00 36.13 3.51
1579 1739 0.534203 TTCTTCGCTTTCGGTGGCTT 60.534 50.000 0.00 0.00 36.13 4.35
1580 1740 0.534203 TTTCTTCGCTTTCGGTGGCT 60.534 50.000 0.00 0.00 36.13 4.75
1581 1741 0.385598 GTTTCTTCGCTTTCGGTGGC 60.386 55.000 0.00 0.00 36.13 5.01
1584 1744 0.179040 TGGGTTTCTTCGCTTTCGGT 60.179 50.000 0.00 0.00 36.13 4.69
1593 1753 1.541588 GGCAGTGTCATGGGTTTCTTC 59.458 52.381 0.00 0.00 0.00 2.87
1600 1760 2.436646 GACGGGCAGTGTCATGGG 60.437 66.667 0.00 0.00 36.37 4.00
1603 1763 0.250124 TTTTCGACGGGCAGTGTCAT 60.250 50.000 0.00 0.00 36.11 3.06
1604 1764 1.144276 TTTTCGACGGGCAGTGTCA 59.856 52.632 0.00 0.00 36.11 3.58
1609 1769 0.882927 TCCTTGTTTTCGACGGGCAG 60.883 55.000 0.00 0.00 0.00 4.85
1645 1805 3.149196 CCTGCTTAACATCACCAGTTGT 58.851 45.455 0.00 0.00 0.00 3.32
1651 1814 2.290960 ACTTCCCCTGCTTAACATCACC 60.291 50.000 0.00 0.00 0.00 4.02
1652 1815 3.010420 GACTTCCCCTGCTTAACATCAC 58.990 50.000 0.00 0.00 0.00 3.06
1662 1825 1.066787 GTGTAGAGTGACTTCCCCTGC 60.067 57.143 0.00 0.00 0.00 4.85
1686 1849 0.601046 CAGCACGCTCTTCTTGGTCA 60.601 55.000 0.00 0.00 0.00 4.02
1792 1970 1.448893 TGGCCGAGTTATTGGTCGC 60.449 57.895 0.00 0.00 37.40 5.19
1796 1974 1.339631 TGAAGGTGGCCGAGTTATTGG 60.340 52.381 0.00 0.00 0.00 3.16
1800 1978 0.321298 GCTTGAAGGTGGCCGAGTTA 60.321 55.000 0.00 0.00 0.00 2.24
1846 2024 0.902531 TCTTGTTCGGATGGGAGGAC 59.097 55.000 0.00 0.00 0.00 3.85
1996 2174 3.041940 CGTCAACTCCGGCACCAC 61.042 66.667 0.00 0.00 0.00 4.16
2004 2182 2.029844 GTGCCTCAGCGTCAACTCC 61.030 63.158 0.00 0.00 44.31 3.85
2008 2186 0.749818 TTTTGGTGCCTCAGCGTCAA 60.750 50.000 0.00 0.00 44.31 3.18
2061 2239 2.422479 CGTCTCCTCGATCAGGTTGTTA 59.578 50.000 9.98 0.00 43.95 2.41
2090 2268 2.932194 TCCTGCTCTTGGCCAGCT 60.932 61.111 15.70 0.00 40.92 4.24
2108 2286 2.671682 GGGACTTGACCCTGCTCC 59.328 66.667 0.00 0.00 45.90 4.70
2127 2305 2.493675 GAGAGATTCAAAAGCCCCAACC 59.506 50.000 0.00 0.00 0.00 3.77
2160 2338 1.271379 GCTGCTGAACCCTACTTTCCA 60.271 52.381 0.00 0.00 0.00 3.53
2185 2363 3.186119 ACAAAACGAAACATTGGTGCAG 58.814 40.909 0.00 0.00 0.00 4.41
2194 2372 4.238514 CCAAGGACAAACAAAACGAAACA 58.761 39.130 0.00 0.00 0.00 2.83
2199 2377 2.926838 CAACCCAAGGACAAACAAAACG 59.073 45.455 0.00 0.00 0.00 3.60
2213 2391 5.248248 TGTCATCACTCTAGAATCAACCCAA 59.752 40.000 0.00 0.00 0.00 4.12
2224 2402 2.360483 ACAGCGGATGTCATCACTCTAG 59.640 50.000 14.72 3.10 37.75 2.43
2225 2403 2.379005 ACAGCGGATGTCATCACTCTA 58.621 47.619 14.72 0.00 37.75 2.43
2226 2404 1.189752 ACAGCGGATGTCATCACTCT 58.810 50.000 14.72 5.25 37.75 3.24
2227 2405 2.015736 AACAGCGGATGTCATCACTC 57.984 50.000 14.72 3.11 43.00 3.51
2228 2406 2.027745 AGAAACAGCGGATGTCATCACT 60.028 45.455 14.72 8.27 43.00 3.41
2229 2407 2.094894 CAGAAACAGCGGATGTCATCAC 59.905 50.000 14.72 6.12 43.00 3.06
2230 2408 2.349590 CAGAAACAGCGGATGTCATCA 58.650 47.619 14.72 0.00 43.00 3.07
2231 2409 1.063174 GCAGAAACAGCGGATGTCATC 59.937 52.381 0.00 4.06 43.00 2.92
2232 2410 1.089920 GCAGAAACAGCGGATGTCAT 58.910 50.000 0.00 0.00 43.00 3.06
2233 2411 0.035317 AGCAGAAACAGCGGATGTCA 59.965 50.000 0.00 0.00 43.00 3.58
2234 2412 1.929836 CTAGCAGAAACAGCGGATGTC 59.070 52.381 0.00 0.00 43.00 3.06
2235 2413 1.276421 ACTAGCAGAAACAGCGGATGT 59.724 47.619 0.00 0.00 46.97 3.06
2236 2414 2.015736 ACTAGCAGAAACAGCGGATG 57.984 50.000 0.00 0.00 37.01 3.51
2237 2415 2.028112 TGAACTAGCAGAAACAGCGGAT 60.028 45.455 0.00 0.00 37.01 4.18
2238 2416 1.343142 TGAACTAGCAGAAACAGCGGA 59.657 47.619 0.00 0.00 37.01 5.54
2239 2417 1.795768 TGAACTAGCAGAAACAGCGG 58.204 50.000 0.00 0.00 37.01 5.52
2240 2418 3.433274 TGATTGAACTAGCAGAAACAGCG 59.567 43.478 0.00 0.00 37.01 5.18
2241 2419 4.142730 CCTGATTGAACTAGCAGAAACAGC 60.143 45.833 3.49 0.00 0.00 4.40
2270 2448 7.818930 AGAGAAAACATCAACTTTTGCTTTCAA 59.181 29.630 0.00 0.00 0.00 2.69
2281 2459 8.416329 ACAAAATGCTTAGAGAAAACATCAACT 58.584 29.630 0.00 0.00 0.00 3.16
2282 2460 8.579682 ACAAAATGCTTAGAGAAAACATCAAC 57.420 30.769 0.00 0.00 0.00 3.18
2320 2498 9.069078 CCATGCAATCATCGAACATATAATTTC 57.931 33.333 0.00 0.00 0.00 2.17
2326 2504 6.431852 TGATTCCATGCAATCATCGAACATAT 59.568 34.615 8.01 0.00 37.77 1.78
2329 2507 3.946558 TGATTCCATGCAATCATCGAACA 59.053 39.130 8.01 0.00 37.77 3.18
2330 2508 4.036027 AGTGATTCCATGCAATCATCGAAC 59.964 41.667 14.99 2.45 43.17 3.95
2340 2518 4.591929 TGAAGATGAAGTGATTCCATGCA 58.408 39.130 0.00 0.00 0.00 3.96
2349 2527 3.243873 ACAAGACGCTGAAGATGAAGTGA 60.244 43.478 0.00 0.00 0.00 3.41
2352 2530 5.809562 AGATTACAAGACGCTGAAGATGAAG 59.190 40.000 0.00 0.00 0.00 3.02
2364 2542 5.243207 ACAAGGGGTTAAGATTACAAGACG 58.757 41.667 0.00 0.00 0.00 4.18
2368 2551 5.586155 TGGACAAGGGGTTAAGATTACAA 57.414 39.130 0.00 0.00 0.00 2.41
2371 2554 5.576128 CCTTTGGACAAGGGGTTAAGATTA 58.424 41.667 5.37 0.00 34.28 1.75
2374 2557 2.490168 GCCTTTGGACAAGGGGTTAAGA 60.490 50.000 14.06 0.00 37.94 2.10
2388 2571 1.028868 GCTCTAGCTGTGGCCTTTGG 61.029 60.000 3.32 0.00 39.73 3.28
2395 2578 4.880537 CCGGCGCTCTAGCTGTGG 62.881 72.222 7.64 0.00 41.72 4.17
2396 2579 3.649277 AACCGGCGCTCTAGCTGTG 62.649 63.158 7.64 0.00 41.72 3.66
2397 2580 3.382832 AACCGGCGCTCTAGCTGT 61.383 61.111 7.64 0.00 41.72 4.40
2398 2581 2.887568 CAACCGGCGCTCTAGCTG 60.888 66.667 7.64 0.00 42.86 4.24
2399 2582 4.148825 CCAACCGGCGCTCTAGCT 62.149 66.667 7.64 0.00 39.32 3.32
2411 2594 0.174845 GGAATTTTAGCCGGCCAACC 59.825 55.000 26.15 9.74 0.00 3.77
2412 2595 0.179148 CGGAATTTTAGCCGGCCAAC 60.179 55.000 26.15 3.23 43.67 3.77
2413 2596 2.185238 CGGAATTTTAGCCGGCCAA 58.815 52.632 26.15 14.66 43.67 4.52
2414 2597 3.912614 CGGAATTTTAGCCGGCCA 58.087 55.556 26.15 6.66 43.67 5.36
2418 2601 2.024163 GCGCCGGAATTTTAGCCG 59.976 61.111 5.05 0.00 46.80 5.52
2419 2602 0.594796 CATGCGCCGGAATTTTAGCC 60.595 55.000 5.05 0.00 0.00 3.93
2420 2603 0.594796 CCATGCGCCGGAATTTTAGC 60.595 55.000 5.05 0.00 0.00 3.09
2421 2604 0.030638 CCCATGCGCCGGAATTTTAG 59.969 55.000 5.05 0.00 0.00 1.85
2422 2605 1.388065 CCCCATGCGCCGGAATTTTA 61.388 55.000 5.05 0.00 0.00 1.52
2423 2606 2.720134 CCCCATGCGCCGGAATTTT 61.720 57.895 5.05 0.00 0.00 1.82
2424 2607 3.146913 CCCCATGCGCCGGAATTT 61.147 61.111 5.05 0.00 0.00 1.82
2434 2617 2.747855 GCTATAGCCGCCCCATGC 60.748 66.667 14.13 0.00 34.31 4.06
2444 2627 3.305398 AGTGTAATGAGCGGCTATAGC 57.695 47.619 16.78 16.78 41.14 2.97
2445 2628 5.372547 TGTAGTGTAATGAGCGGCTATAG 57.627 43.478 0.60 0.00 0.00 1.31
2446 2629 5.977489 ATGTAGTGTAATGAGCGGCTATA 57.023 39.130 0.60 0.00 0.00 1.31
2447 2630 4.873746 ATGTAGTGTAATGAGCGGCTAT 57.126 40.909 0.60 0.00 0.00 2.97
2448 2631 4.665833 AATGTAGTGTAATGAGCGGCTA 57.334 40.909 0.60 0.00 0.00 3.93
2449 2632 3.543680 AATGTAGTGTAATGAGCGGCT 57.456 42.857 0.00 0.00 0.00 5.52
2450 2633 4.389077 GGATAATGTAGTGTAATGAGCGGC 59.611 45.833 0.00 0.00 0.00 6.53
2451 2634 5.635280 CAGGATAATGTAGTGTAATGAGCGG 59.365 44.000 0.00 0.00 0.00 5.52
2452 2635 6.216569 ACAGGATAATGTAGTGTAATGAGCG 58.783 40.000 0.00 0.00 0.00 5.03
2470 2653 9.920946 TTTCCTCTTAAAAAGCATATACAGGAT 57.079 29.630 0.00 0.00 0.00 3.24
2471 2654 9.747898 TTTTCCTCTTAAAAAGCATATACAGGA 57.252 29.630 0.00 0.00 0.00 3.86
2504 2687 9.948964 ACCGTAACTATTATTTTACAGGTCTTT 57.051 29.630 0.00 0.00 33.61 2.52
2505 2688 9.591792 GACCGTAACTATTATTTTACAGGTCTT 57.408 33.333 18.11 0.03 41.86 3.01
2506 2689 8.752187 TGACCGTAACTATTATTTTACAGGTCT 58.248 33.333 21.84 3.33 43.31 3.85
2507 2690 8.931385 TGACCGTAACTATTATTTTACAGGTC 57.069 34.615 18.33 18.33 43.27 3.85
2508 2691 9.895138 ATTGACCGTAACTATTATTTTACAGGT 57.105 29.630 0.00 0.00 37.58 4.00
2516 2699 9.391006 ACAATGTGATTGACCGTAACTATTATT 57.609 29.630 3.35 0.00 42.83 1.40
2517 2700 8.958119 ACAATGTGATTGACCGTAACTATTAT 57.042 30.769 3.35 0.00 42.83 1.28
2518 2701 7.221259 CGACAATGTGATTGACCGTAACTATTA 59.779 37.037 3.35 0.00 42.83 0.98
2519 2702 6.035650 CGACAATGTGATTGACCGTAACTATT 59.964 38.462 3.35 0.00 42.83 1.73
2520 2703 5.518847 CGACAATGTGATTGACCGTAACTAT 59.481 40.000 3.35 0.00 42.83 2.12
2521 2704 4.860352 CGACAATGTGATTGACCGTAACTA 59.140 41.667 3.35 0.00 42.83 2.24
2522 2705 3.678072 CGACAATGTGATTGACCGTAACT 59.322 43.478 3.35 0.00 42.83 2.24
2523 2706 3.181524 CCGACAATGTGATTGACCGTAAC 60.182 47.826 3.35 0.00 42.83 2.50
2524 2707 2.997303 CCGACAATGTGATTGACCGTAA 59.003 45.455 3.35 0.00 42.83 3.18
2525 2708 2.612604 CCGACAATGTGATTGACCGTA 58.387 47.619 3.35 0.00 42.83 4.02
2526 2709 1.438651 CCGACAATGTGATTGACCGT 58.561 50.000 3.35 0.00 42.83 4.83
2527 2710 0.726827 CCCGACAATGTGATTGACCG 59.273 55.000 3.35 6.21 42.83 4.79
2528 2711 1.094785 CCCCGACAATGTGATTGACC 58.905 55.000 3.35 0.00 42.83 4.02
2529 2712 1.094785 CCCCCGACAATGTGATTGAC 58.905 55.000 3.35 0.00 42.83 3.18
2530 2713 0.695924 ACCCCCGACAATGTGATTGA 59.304 50.000 3.35 0.00 42.83 2.57
2531 2714 1.202114 CAACCCCCGACAATGTGATTG 59.798 52.381 0.00 0.00 45.59 2.67
2532 2715 1.544724 CAACCCCCGACAATGTGATT 58.455 50.000 0.00 0.00 0.00 2.57
2533 2716 0.323360 CCAACCCCCGACAATGTGAT 60.323 55.000 0.00 0.00 0.00 3.06
2534 2717 1.074072 CCAACCCCCGACAATGTGA 59.926 57.895 0.00 0.00 0.00 3.58
2535 2718 0.323360 ATCCAACCCCCGACAATGTG 60.323 55.000 0.00 0.00 0.00 3.21
2536 2719 0.323360 CATCCAACCCCCGACAATGT 60.323 55.000 0.00 0.00 0.00 2.71
2571 2754 1.133072 CCCCCACCATGATAAGCCATT 60.133 52.381 0.00 0.00 0.00 3.16
2603 2786 3.508840 GTTTCCAGGCATCGGCGG 61.509 66.667 7.21 0.00 42.47 6.13


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.