Multiple sequence alignment - TraesCS5B01G252300

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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 TraesCS5B01G252300 chr5B 100.000 2860 0 0 1 2860 434910054 434912913 0.000000e+00 5282.0
1 TraesCS5B01G252300 chr5D 91.354 879 56 14 1993 2860 433994398 433995267 0.000000e+00 1184.0
2 TraesCS5B01G252300 chr5D 92.668 791 34 11 1 777 367515297 367516077 0.000000e+00 1118.0
3 TraesCS5B01G252300 chr5D 95.122 41 1 1 818 858 367659000 367659039 2.380000e-06 63.9
4 TraesCS5B01G252300 chr7D 90.524 897 48 13 1997 2860 625619523 625618631 0.000000e+00 1151.0
5 TraesCS5B01G252300 chr7D 88.636 880 74 18 1992 2859 182034599 182033734 0.000000e+00 1048.0
6 TraesCS5B01G252300 chr7D 93.478 46 0 2 1529 1573 323407810 323407853 6.610000e-07 65.8
7 TraesCS5B01G252300 chr2B 92.222 810 49 10 1992 2794 594852403 594853205 0.000000e+00 1134.0
8 TraesCS5B01G252300 chr2B 91.566 166 14 0 1992 2157 431166110 431166275 2.220000e-56 230.0
9 TraesCS5B01G252300 chr1B 89.605 885 65 10 1995 2860 462800771 462801647 0.000000e+00 1099.0
10 TraesCS5B01G252300 chr2D 89.420 879 68 17 1997 2860 587275322 587276190 0.000000e+00 1085.0
11 TraesCS5B01G252300 chr1A 88.827 904 60 23 1984 2860 566580746 566579857 0.000000e+00 1072.0
12 TraesCS5B01G252300 chr3B 90.886 790 58 10 2078 2860 166332942 166332160 0.000000e+00 1048.0
13 TraesCS5B01G252300 chr3B 82.297 209 37 0 1222 1430 814229316 814229108 6.290000e-42 182.0
14 TraesCS5B01G252300 chr3A 88.155 878 74 23 1997 2860 517937161 517938022 0.000000e+00 1018.0
15 TraesCS5B01G252300 chr3A 97.619 42 1 0 1531 1572 138831032 138831073 3.950000e-09 73.1
16 TraesCS5B01G252300 chr5A 92.624 583 26 5 187 760 469272798 469273372 0.000000e+00 822.0
17 TraesCS5B01G252300 chr5A 94.340 424 23 1 1002 1425 469489450 469489872 0.000000e+00 649.0
18 TraesCS5B01G252300 chr5A 88.866 485 20 14 1 482 456265155 456265608 1.490000e-157 566.0
19 TraesCS5B01G252300 chr5A 95.312 192 7 2 1 191 469272274 469272464 1.290000e-78 303.0
20 TraesCS5B01G252300 chr5A 86.404 228 23 7 540 761 456278439 456278664 2.850000e-60 243.0
21 TraesCS5B01G252300 chr5A 86.700 203 21 4 478 674 456265893 456266095 1.330000e-53 220.0
22 TraesCS5B01G252300 chr5A 85.167 209 31 0 1222 1430 705301658 705301450 6.210000e-52 215.0
23 TraesCS5B01G252300 chr5A 80.000 270 51 1 1126 1395 705932088 705932354 2.250000e-46 196.0
24 TraesCS5B01G252300 chr5A 89.908 109 5 1 905 1007 469488858 469488966 4.970000e-28 135.0
25 TraesCS5B01G252300 chr5A 88.608 79 9 0 577 655 456265926 456266004 2.350000e-16 97.1
26 TraesCS5B01G252300 chr5A 98.182 55 1 0 842 896 469488822 469488876 2.350000e-16 97.1
27 TraesCS5B01G252300 chr5A 95.652 46 2 0 1527 1572 119071318 119071273 1.100000e-09 75.0
28 TraesCS5B01G252300 chr2A 93.608 485 23 7 1 482 393513119 393512640 0.000000e+00 717.0
29 TraesCS5B01G252300 chr2A 91.954 87 7 0 511 597 393512238 393512152 3.870000e-24 122.0
30 TraesCS5B01G252300 chr2A 93.750 48 1 2 1527 1572 2930354 2930307 1.420000e-08 71.3
31 TraesCS5B01G252300 chr2A 100.000 28 0 0 780 807 735871381 735871408 5.000000e-03 52.8
32 TraesCS5B01G252300 chr7A 92.105 418 22 7 1527 1939 546277148 546277559 1.910000e-161 579.0
33 TraesCS5B01G252300 chr7A 100.000 28 0 0 1966 1993 546277649 546277676 5.000000e-03 52.8
34 TraesCS5B01G252300 chr6A 91.827 416 22 8 1529 1939 270753788 270753380 1.150000e-158 569.0
35 TraesCS5B01G252300 chr6A 96.000 50 1 1 1524 1572 180185185 180185234 2.360000e-11 80.5
36 TraesCS5B01G252300 chr6A 100.000 28 0 0 1966 1993 270753290 270753263 5.000000e-03 52.8
37 TraesCS5B01G252300 chr7B 91.566 415 23 8 1530 1939 723895784 723895377 1.920000e-156 562.0
38 TraesCS5B01G252300 chr7B 82.857 210 35 1 1222 1430 742248098 742248307 1.350000e-43 187.0
39 TraesCS5B01G252300 chr6B 90.698 430 27 9 1516 1939 430559499 430559077 6.920000e-156 560.0
40 TraesCS5B01G252300 chr6B 100.000 28 0 0 1966 1993 430558987 430558960 5.000000e-03 52.8
41 TraesCS5B01G252300 chr1D 91.444 187 11 3 1594 1778 415638896 415639079 4.730000e-63 252.0
42 TraesCS5B01G252300 chr1D 90.303 165 10 2 1774 1933 415645033 415645196 8.030000e-51 211.0
43 TraesCS5B01G252300 chr1D 90.303 165 10 2 1774 1933 415661637 415661800 8.030000e-51 211.0
44 TraesCS5B01G252300 chrUn 86.124 209 29 0 1222 1430 108697168 108697376 2.870000e-55 226.0
45 TraesCS5B01G252300 chrUn 88.889 162 18 0 1236 1397 108291847 108291686 1.740000e-47 200.0
46 TraesCS5B01G252300 chr4D 86.310 168 15 5 1777 1939 318331320 318331156 2.930000e-40 176.0
47 TraesCS5B01G252300 chr4B 85.321 109 16 0 1222 1330 665455712 665455820 2.330000e-21 113.0


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 TraesCS5B01G252300 chr5B 434910054 434912913 2859 False 5282.000000 5282 100.000000 1 2860 1 chr5B.!!$F1 2859
1 TraesCS5B01G252300 chr5D 433994398 433995267 869 False 1184.000000 1184 91.354000 1993 2860 1 chr5D.!!$F3 867
2 TraesCS5B01G252300 chr5D 367515297 367516077 780 False 1118.000000 1118 92.668000 1 777 1 chr5D.!!$F1 776
3 TraesCS5B01G252300 chr7D 625618631 625619523 892 True 1151.000000 1151 90.524000 1997 2860 1 chr7D.!!$R2 863
4 TraesCS5B01G252300 chr7D 182033734 182034599 865 True 1048.000000 1048 88.636000 1992 2859 1 chr7D.!!$R1 867
5 TraesCS5B01G252300 chr2B 594852403 594853205 802 False 1134.000000 1134 92.222000 1992 2794 1 chr2B.!!$F2 802
6 TraesCS5B01G252300 chr1B 462800771 462801647 876 False 1099.000000 1099 89.605000 1995 2860 1 chr1B.!!$F1 865
7 TraesCS5B01G252300 chr2D 587275322 587276190 868 False 1085.000000 1085 89.420000 1997 2860 1 chr2D.!!$F1 863
8 TraesCS5B01G252300 chr1A 566579857 566580746 889 True 1072.000000 1072 88.827000 1984 2860 1 chr1A.!!$R1 876
9 TraesCS5B01G252300 chr3B 166332160 166332942 782 True 1048.000000 1048 90.886000 2078 2860 1 chr3B.!!$R1 782
10 TraesCS5B01G252300 chr3A 517937161 517938022 861 False 1018.000000 1018 88.155000 1997 2860 1 chr3A.!!$F2 863
11 TraesCS5B01G252300 chr5A 469272274 469273372 1098 False 562.500000 822 93.968000 1 760 2 chr5A.!!$F4 759
12 TraesCS5B01G252300 chr5A 456265155 456266095 940 False 294.366667 566 88.058000 1 674 3 chr5A.!!$F3 673
13 TraesCS5B01G252300 chr5A 469488822 469489872 1050 False 293.700000 649 94.143333 842 1425 3 chr5A.!!$F5 583
14 TraesCS5B01G252300 chr2A 393512152 393513119 967 True 419.500000 717 92.781000 1 597 2 chr2A.!!$R2 596
15 TraesCS5B01G252300 chr7A 546277148 546277676 528 False 315.900000 579 96.052500 1527 1993 2 chr7A.!!$F1 466
16 TraesCS5B01G252300 chr6A 270753263 270753788 525 True 310.900000 569 95.913500 1529 1993 2 chr6A.!!$R1 464
17 TraesCS5B01G252300 chr6B 430558960 430559499 539 True 306.400000 560 95.349000 1516 1993 2 chr6B.!!$R1 477

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
958 1637 0.248743 TCTCCGTATTTACAGCCGCG 60.249 55.0 0.0 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2161 3407 0.95104 CAGGTGTTGGCCGAAGAGTC 60.951 60.0 0.0 0.0 0.0 3.36 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
288 639 9.678941 TGCACTTCTATATCTACGTTTAGATTG 57.321 33.333 6.17 0.00 41.59 2.67
312 664 5.259832 ACTCGTATAAGTAAGAACAGGCC 57.740 43.478 0.00 0.00 0.00 5.19
347 700 1.283029 AGGGCATACACAAGTGCAGAT 59.717 47.619 0.00 0.00 43.00 2.90
378 731 2.187946 CCTGATCCACCGGCTGAC 59.812 66.667 0.00 0.00 0.00 3.51
456 809 6.895782 TGGGAGACGAATAACCAAAGATATT 58.104 36.000 0.00 0.00 0.00 1.28
473 826 2.127271 ATTTCATGGCGTGATGTGGA 57.873 45.000 10.74 0.00 36.54 4.02
482 1142 1.156736 CGTGATGTGGACTGAAACCC 58.843 55.000 0.00 0.00 0.00 4.11
529 1189 4.798682 ACCGGCGGGGAGGAAGAT 62.799 66.667 31.78 1.72 39.97 2.40
579 1239 0.466124 GAGGTGGCCATAGGACTGAC 59.534 60.000 9.72 0.00 0.00 3.51
606 1272 0.592754 GAGGAAGACGATTCGCCGAG 60.593 60.000 5.86 0.00 0.00 4.63
633 1299 0.969894 CAGGAAGAAGACGAGGTGGT 59.030 55.000 0.00 0.00 0.00 4.16
700 1378 4.947147 CGTGGTGGTGGGTGGGTG 62.947 72.222 0.00 0.00 0.00 4.61
701 1379 4.596585 GTGGTGGTGGGTGGGTGG 62.597 72.222 0.00 0.00 0.00 4.61
740 1419 3.726782 CGGCGAAACTAATACAAACCTGC 60.727 47.826 0.00 0.00 0.00 4.85
743 1422 3.181514 CGAAACTAATACAAACCTGCCCG 60.182 47.826 0.00 0.00 0.00 6.13
777 1456 1.377229 CCTGGCCTGGGTTAAACGA 59.623 57.895 20.77 0.00 0.00 3.85
778 1457 0.676782 CCTGGCCTGGGTTAAACGAG 60.677 60.000 20.77 0.00 0.00 4.18
779 1458 0.676782 CTGGCCTGGGTTAAACGAGG 60.677 60.000 16.76 16.76 0.00 4.63
780 1459 1.378119 GGCCTGGGTTAAACGAGGG 60.378 63.158 21.62 7.12 0.00 4.30
781 1460 1.681076 GCCTGGGTTAAACGAGGGA 59.319 57.895 21.62 0.00 0.00 4.20
782 1461 0.255033 GCCTGGGTTAAACGAGGGAT 59.745 55.000 21.62 0.00 0.00 3.85
783 1462 2.017113 GCCTGGGTTAAACGAGGGATG 61.017 57.143 21.62 0.00 0.00 3.51
784 1463 1.379527 CTGGGTTAAACGAGGGATGC 58.620 55.000 0.00 0.00 0.00 3.91
785 1464 0.693622 TGGGTTAAACGAGGGATGCA 59.306 50.000 0.00 0.00 0.00 3.96
786 1465 1.283613 TGGGTTAAACGAGGGATGCAT 59.716 47.619 0.00 0.00 0.00 3.96
787 1466 2.506231 TGGGTTAAACGAGGGATGCATA 59.494 45.455 0.00 0.00 0.00 3.14
788 1467 3.139077 GGGTTAAACGAGGGATGCATAG 58.861 50.000 0.00 0.00 0.00 2.23
789 1468 3.181458 GGGTTAAACGAGGGATGCATAGA 60.181 47.826 0.00 0.00 0.00 1.98
790 1469 4.058817 GGTTAAACGAGGGATGCATAGAG 58.941 47.826 0.00 0.00 0.00 2.43
791 1470 4.202223 GGTTAAACGAGGGATGCATAGAGA 60.202 45.833 0.00 0.00 0.00 3.10
792 1471 5.357257 GTTAAACGAGGGATGCATAGAGAA 58.643 41.667 0.00 0.00 0.00 2.87
793 1472 3.742433 AACGAGGGATGCATAGAGAAG 57.258 47.619 0.00 0.00 0.00 2.85
794 1473 1.967066 ACGAGGGATGCATAGAGAAGG 59.033 52.381 0.00 0.00 0.00 3.46
795 1474 2.242926 CGAGGGATGCATAGAGAAGGA 58.757 52.381 0.00 0.00 0.00 3.36
796 1475 2.630098 CGAGGGATGCATAGAGAAGGAA 59.370 50.000 0.00 0.00 0.00 3.36
797 1476 3.070159 CGAGGGATGCATAGAGAAGGAAA 59.930 47.826 0.00 0.00 0.00 3.13
798 1477 4.640364 GAGGGATGCATAGAGAAGGAAAG 58.360 47.826 0.00 0.00 0.00 2.62
799 1478 4.302067 AGGGATGCATAGAGAAGGAAAGA 58.698 43.478 0.00 0.00 0.00 2.52
800 1479 4.723789 AGGGATGCATAGAGAAGGAAAGAA 59.276 41.667 0.00 0.00 0.00 2.52
801 1480 5.192522 AGGGATGCATAGAGAAGGAAAGAAA 59.807 40.000 0.00 0.00 0.00 2.52
802 1481 6.067350 GGGATGCATAGAGAAGGAAAGAAAT 58.933 40.000 0.00 0.00 0.00 2.17
803 1482 6.206438 GGGATGCATAGAGAAGGAAAGAAATC 59.794 42.308 0.00 0.00 0.00 2.17
804 1483 6.073331 GGATGCATAGAGAAGGAAAGAAATCG 60.073 42.308 0.00 0.00 0.00 3.34
805 1484 5.734720 TGCATAGAGAAGGAAAGAAATCGT 58.265 37.500 0.00 0.00 0.00 3.73
806 1485 6.173339 TGCATAGAGAAGGAAAGAAATCGTT 58.827 36.000 0.00 0.00 0.00 3.85
807 1486 6.655003 TGCATAGAGAAGGAAAGAAATCGTTT 59.345 34.615 0.00 0.00 0.00 3.60
808 1487 7.174946 TGCATAGAGAAGGAAAGAAATCGTTTT 59.825 33.333 0.00 0.00 0.00 2.43
809 1488 8.023706 GCATAGAGAAGGAAAGAAATCGTTTTT 58.976 33.333 0.00 0.00 0.00 1.94
881 1560 0.309612 ACCGCGTCAACAACCAAATC 59.690 50.000 4.92 0.00 0.00 2.17
882 1561 0.309302 CCGCGTCAACAACCAAATCA 59.691 50.000 4.92 0.00 0.00 2.57
883 1562 1.268794 CCGCGTCAACAACCAAATCAA 60.269 47.619 4.92 0.00 0.00 2.57
884 1563 2.606795 CCGCGTCAACAACCAAATCAAT 60.607 45.455 4.92 0.00 0.00 2.57
885 1564 2.404693 CGCGTCAACAACCAAATCAATG 59.595 45.455 0.00 0.00 0.00 2.82
886 1565 2.155539 GCGTCAACAACCAAATCAATGC 59.844 45.455 0.00 0.00 0.00 3.56
887 1566 2.730928 CGTCAACAACCAAATCAATGCC 59.269 45.455 0.00 0.00 0.00 4.40
888 1567 2.730928 GTCAACAACCAAATCAATGCCG 59.269 45.455 0.00 0.00 0.00 5.69
889 1568 2.067766 CAACAACCAAATCAATGCCGG 58.932 47.619 0.00 0.00 0.00 6.13
890 1569 1.337118 ACAACCAAATCAATGCCGGT 58.663 45.000 1.90 0.00 0.00 5.28
891 1570 2.520069 ACAACCAAATCAATGCCGGTA 58.480 42.857 1.90 0.00 0.00 4.02
892 1571 2.894126 ACAACCAAATCAATGCCGGTAA 59.106 40.909 1.90 0.00 0.00 2.85
893 1572 3.513515 ACAACCAAATCAATGCCGGTAAT 59.486 39.130 1.90 0.00 0.00 1.89
894 1573 4.707448 ACAACCAAATCAATGCCGGTAATA 59.293 37.500 1.90 0.00 0.00 0.98
895 1574 5.186021 ACAACCAAATCAATGCCGGTAATAA 59.814 36.000 1.90 0.00 0.00 1.40
896 1575 5.257082 ACCAAATCAATGCCGGTAATAAC 57.743 39.130 1.90 0.00 0.00 1.89
897 1576 4.201970 ACCAAATCAATGCCGGTAATAACG 60.202 41.667 1.90 0.00 0.00 3.18
953 1632 6.653183 CATGCTGAATTCTCCGTATTTACAG 58.347 40.000 7.05 0.00 0.00 2.74
954 1633 4.570772 TGCTGAATTCTCCGTATTTACAGC 59.429 41.667 7.05 0.00 45.21 4.40
958 1637 0.248743 TCTCCGTATTTACAGCCGCG 60.249 55.000 0.00 0.00 0.00 6.46
969 1648 1.732941 ACAGCCGCGAATTAACATGA 58.267 45.000 8.23 0.00 0.00 3.07
990 1675 2.216920 GCGATCAATGCAAACGCCG 61.217 57.895 12.64 6.09 42.79 6.46
1039 2213 0.394938 TAATGACACCACGGCACAGT 59.605 50.000 0.00 0.00 0.00 3.55
1063 2237 2.100631 CACAGCGTCCGTCCATTCC 61.101 63.158 0.00 0.00 0.00 3.01
1072 2246 3.279875 GTCCATTCCCATCGCCGC 61.280 66.667 0.00 0.00 0.00 6.53
1095 2269 2.531206 GTGGCTAGTCGATCAACAGAC 58.469 52.381 0.00 0.00 37.63 3.51
1103 2277 1.272490 TCGATCAACAGACACCAGACC 59.728 52.381 0.00 0.00 0.00 3.85
1112 2286 2.361610 CACCAGACCACCATGGCC 60.362 66.667 13.04 0.00 42.67 5.36
1169 2343 2.811317 GTCCTTGCAGTCGCCTCG 60.811 66.667 0.00 0.00 37.32 4.63
1196 2370 1.066858 ACTGTTGTCTATCCACAGCCG 60.067 52.381 0.00 0.00 32.16 5.52
1289 2463 2.730524 GCAGGTCCTCCAGGCTCTC 61.731 68.421 0.00 0.00 34.78 3.20
1317 2491 1.868997 GACGTGCACATCACCAAGG 59.131 57.895 18.64 0.00 42.69 3.61
1330 2504 3.123620 CAAGGACTGCTGCGAGGC 61.124 66.667 0.00 0.00 0.00 4.70
1365 2539 1.446907 CGAAGAAACCTGCAGCATCT 58.553 50.000 8.66 8.23 0.00 2.90
1366 2540 1.129998 CGAAGAAACCTGCAGCATCTG 59.870 52.381 8.66 0.00 34.12 2.90
1406 2580 3.954904 TCGGCTAGCTACTTCTCAAGATT 59.045 43.478 15.72 0.00 0.00 2.40
1425 2599 3.744559 GGTTCAGCTTCACCGCAA 58.255 55.556 0.00 0.00 0.00 4.85
1426 2600 1.576421 GGTTCAGCTTCACCGCAAG 59.424 57.895 0.00 0.00 0.00 4.01
1427 2601 0.884704 GGTTCAGCTTCACCGCAAGA 60.885 55.000 0.00 0.00 43.02 3.02
1428 2602 1.160137 GTTCAGCTTCACCGCAAGAT 58.840 50.000 0.00 0.00 43.02 2.40
1429 2603 2.346803 GTTCAGCTTCACCGCAAGATA 58.653 47.619 0.00 0.00 43.02 1.98
1430 2604 2.742053 GTTCAGCTTCACCGCAAGATAA 59.258 45.455 0.00 0.00 43.02 1.75
1431 2605 2.346803 TCAGCTTCACCGCAAGATAAC 58.653 47.619 0.00 0.00 43.02 1.89
1432 2606 2.028112 TCAGCTTCACCGCAAGATAACT 60.028 45.455 0.00 0.00 43.02 2.24
1433 2607 2.349886 CAGCTTCACCGCAAGATAACTC 59.650 50.000 0.00 0.00 43.02 3.01
1434 2608 2.234908 AGCTTCACCGCAAGATAACTCT 59.765 45.455 0.00 0.00 43.02 3.24
1435 2609 2.349886 GCTTCACCGCAAGATAACTCTG 59.650 50.000 0.00 0.00 43.02 3.35
1436 2610 2.672961 TCACCGCAAGATAACTCTGG 57.327 50.000 0.00 0.00 43.02 3.86
1437 2611 1.207089 TCACCGCAAGATAACTCTGGG 59.793 52.381 0.00 0.00 43.02 4.45
1438 2612 1.066143 CACCGCAAGATAACTCTGGGT 60.066 52.381 0.00 0.00 43.02 4.51
1439 2613 1.066143 ACCGCAAGATAACTCTGGGTG 60.066 52.381 0.00 0.00 43.02 4.61
1440 2614 1.066143 CCGCAAGATAACTCTGGGTGT 60.066 52.381 0.00 0.00 43.02 4.16
1441 2615 2.002586 CGCAAGATAACTCTGGGTGTG 58.997 52.381 0.00 0.00 43.02 3.82
1442 2616 1.740025 GCAAGATAACTCTGGGTGTGC 59.260 52.381 0.00 0.00 0.00 4.57
1443 2617 2.002586 CAAGATAACTCTGGGTGTGCG 58.997 52.381 0.00 0.00 0.00 5.34
1444 2618 1.267121 AGATAACTCTGGGTGTGCGT 58.733 50.000 0.00 0.00 0.00 5.24
1445 2619 1.066858 AGATAACTCTGGGTGTGCGTG 60.067 52.381 0.00 0.00 0.00 5.34
1446 2620 0.685097 ATAACTCTGGGTGTGCGTGT 59.315 50.000 0.00 0.00 0.00 4.49
1447 2621 1.330234 TAACTCTGGGTGTGCGTGTA 58.670 50.000 0.00 0.00 0.00 2.90
1448 2622 0.685097 AACTCTGGGTGTGCGTGTAT 59.315 50.000 0.00 0.00 0.00 2.29
1449 2623 1.552578 ACTCTGGGTGTGCGTGTATA 58.447 50.000 0.00 0.00 0.00 1.47
1450 2624 1.203994 ACTCTGGGTGTGCGTGTATAC 59.796 52.381 0.00 0.00 0.00 1.47
1451 2625 1.203758 CTCTGGGTGTGCGTGTATACA 59.796 52.381 0.08 0.08 0.00 2.29
1452 2626 1.828595 TCTGGGTGTGCGTGTATACAT 59.171 47.619 9.18 0.00 0.00 2.29
1453 2627 2.235155 TCTGGGTGTGCGTGTATACATT 59.765 45.455 9.18 0.00 0.00 2.71
1454 2628 2.351418 CTGGGTGTGCGTGTATACATTG 59.649 50.000 9.18 6.29 0.00 2.82
1455 2629 1.668751 GGGTGTGCGTGTATACATTGG 59.331 52.381 9.18 3.20 0.00 3.16
1456 2630 1.668751 GGTGTGCGTGTATACATTGGG 59.331 52.381 9.18 0.72 0.00 4.12
1457 2631 1.063469 GTGTGCGTGTATACATTGGGC 59.937 52.381 9.18 10.81 0.00 5.36
1458 2632 0.303493 GTGCGTGTATACATTGGGCG 59.697 55.000 9.18 8.55 0.00 6.13
1459 2633 0.108089 TGCGTGTATACATTGGGCGT 60.108 50.000 9.18 0.00 0.00 5.68
1460 2634 0.303493 GCGTGTATACATTGGGCGTG 59.697 55.000 9.18 0.00 0.00 5.34
1461 2635 1.647346 CGTGTATACATTGGGCGTGT 58.353 50.000 9.18 0.00 0.00 4.49
1462 2636 1.326245 CGTGTATACATTGGGCGTGTG 59.674 52.381 9.18 0.00 0.00 3.82
1463 2637 1.063469 GTGTATACATTGGGCGTGTGC 59.937 52.381 9.18 0.00 41.71 4.57
1464 2638 1.339151 TGTATACATTGGGCGTGTGCA 60.339 47.619 0.08 0.00 45.35 4.57
1484 2658 5.162000 GCACATGCACCTATTAGTCTTTC 57.838 43.478 0.00 0.00 41.59 2.62
1485 2659 4.035675 GCACATGCACCTATTAGTCTTTCC 59.964 45.833 0.00 0.00 41.59 3.13
1486 2660 5.185454 CACATGCACCTATTAGTCTTTCCA 58.815 41.667 0.00 0.00 0.00 3.53
1487 2661 5.824624 CACATGCACCTATTAGTCTTTCCAT 59.175 40.000 0.00 0.00 0.00 3.41
1488 2662 6.017605 CACATGCACCTATTAGTCTTTCCATC 60.018 42.308 0.00 0.00 0.00 3.51
1489 2663 5.957771 TGCACCTATTAGTCTTTCCATCT 57.042 39.130 0.00 0.00 0.00 2.90
1490 2664 6.313519 TGCACCTATTAGTCTTTCCATCTT 57.686 37.500 0.00 0.00 0.00 2.40
1491 2665 6.115446 TGCACCTATTAGTCTTTCCATCTTG 58.885 40.000 0.00 0.00 0.00 3.02
1492 2666 6.070251 TGCACCTATTAGTCTTTCCATCTTGA 60.070 38.462 0.00 0.00 0.00 3.02
1493 2667 6.481644 GCACCTATTAGTCTTTCCATCTTGAG 59.518 42.308 0.00 0.00 0.00 3.02
1494 2668 6.481644 CACCTATTAGTCTTTCCATCTTGAGC 59.518 42.308 0.00 0.00 0.00 4.26
1495 2669 6.385467 ACCTATTAGTCTTTCCATCTTGAGCT 59.615 38.462 0.00 0.00 0.00 4.09
1496 2670 6.928492 CCTATTAGTCTTTCCATCTTGAGCTC 59.072 42.308 6.82 6.82 0.00 4.09
1497 2671 5.745312 TTAGTCTTTCCATCTTGAGCTCA 57.255 39.130 13.74 13.74 0.00 4.26
1498 2672 3.936564 AGTCTTTCCATCTTGAGCTCAC 58.063 45.455 18.03 0.00 0.00 3.51
1499 2673 2.670414 GTCTTTCCATCTTGAGCTCACG 59.330 50.000 18.03 15.70 0.00 4.35
1500 2674 2.005451 CTTTCCATCTTGAGCTCACGG 58.995 52.381 18.03 14.55 0.00 4.94
1501 2675 1.266178 TTCCATCTTGAGCTCACGGA 58.734 50.000 18.03 17.66 0.00 4.69
1502 2676 1.266178 TCCATCTTGAGCTCACGGAA 58.734 50.000 18.03 0.00 0.00 4.30
1503 2677 1.623311 TCCATCTTGAGCTCACGGAAA 59.377 47.619 18.03 0.00 0.00 3.13
1504 2678 2.038426 TCCATCTTGAGCTCACGGAAAA 59.962 45.455 18.03 0.00 0.00 2.29
1505 2679 2.813754 CCATCTTGAGCTCACGGAAAAA 59.186 45.455 18.03 0.00 0.00 1.94
1506 2680 3.365364 CCATCTTGAGCTCACGGAAAAAC 60.365 47.826 18.03 0.00 0.00 2.43
1507 2681 2.912771 TCTTGAGCTCACGGAAAAACA 58.087 42.857 18.03 0.00 0.00 2.83
1508 2682 3.275143 TCTTGAGCTCACGGAAAAACAA 58.725 40.909 18.03 0.00 0.00 2.83
1509 2683 3.692101 TCTTGAGCTCACGGAAAAACAAA 59.308 39.130 18.03 0.00 0.00 2.83
1510 2684 4.156922 TCTTGAGCTCACGGAAAAACAAAA 59.843 37.500 18.03 0.00 0.00 2.44
1511 2685 4.442375 TGAGCTCACGGAAAAACAAAAA 57.558 36.364 13.74 0.00 0.00 1.94
1512 2686 5.004922 TGAGCTCACGGAAAAACAAAAAT 57.995 34.783 13.74 0.00 0.00 1.82
1513 2687 5.040635 TGAGCTCACGGAAAAACAAAAATC 58.959 37.500 13.74 0.00 0.00 2.17
1514 2688 5.163561 TGAGCTCACGGAAAAACAAAAATCT 60.164 36.000 13.74 0.00 0.00 2.40
1520 2694 9.848172 CTCACGGAAAAACAAAAATCTTTTATG 57.152 29.630 0.00 0.00 0.00 1.90
1758 2932 5.584251 TGCATACAATGTGTATACCACTGTG 59.416 40.000 14.63 0.00 41.28 3.66
1774 2948 4.487948 CACTGTGTGCTTCCCATTATTTG 58.512 43.478 0.00 0.00 0.00 2.32
1779 2953 4.567959 GTGTGCTTCCCATTATTTGCAATC 59.432 41.667 0.00 0.00 32.10 2.67
1825 2999 7.867445 TGCATAAAAGCACTTAACTAAAAGC 57.133 32.000 0.00 0.00 40.11 3.51
1903 3077 1.251251 CCTTTCTTTGGCACTCAGGG 58.749 55.000 0.00 0.00 0.00 4.45
1939 3118 2.744741 GCCTTTCTCTAACTCCTGTTGC 59.255 50.000 0.00 0.00 37.59 4.17
1941 3120 3.999663 CCTTTCTCTAACTCCTGTTGCAG 59.000 47.826 0.00 0.00 37.59 4.41
1942 3121 4.262635 CCTTTCTCTAACTCCTGTTGCAGA 60.263 45.833 0.00 0.00 37.59 4.26
1943 3122 4.955811 TTCTCTAACTCCTGTTGCAGAA 57.044 40.909 0.00 0.00 37.59 3.02
1944 3123 4.955811 TCTCTAACTCCTGTTGCAGAAA 57.044 40.909 0.00 0.00 37.59 2.52
1945 3124 5.290493 TCTCTAACTCCTGTTGCAGAAAA 57.710 39.130 0.00 0.00 37.59 2.29
1946 3125 5.680619 TCTCTAACTCCTGTTGCAGAAAAA 58.319 37.500 0.00 0.00 37.59 1.94
1947 3126 6.299141 TCTCTAACTCCTGTTGCAGAAAAAT 58.701 36.000 0.00 0.00 37.59 1.82
1949 3128 6.970484 TCTAACTCCTGTTGCAGAAAAATTC 58.030 36.000 0.00 0.00 37.59 2.17
1950 3129 4.228912 ACTCCTGTTGCAGAAAAATTCG 57.771 40.909 0.00 0.00 32.44 3.34
1951 3130 3.882888 ACTCCTGTTGCAGAAAAATTCGA 59.117 39.130 0.00 0.00 32.44 3.71
1952 3131 4.338118 ACTCCTGTTGCAGAAAAATTCGAA 59.662 37.500 0.00 0.00 32.44 3.71
1953 3132 5.163561 ACTCCTGTTGCAGAAAAATTCGAAA 60.164 36.000 0.00 0.00 32.44 3.46
1954 3133 5.841810 TCCTGTTGCAGAAAAATTCGAAAT 58.158 33.333 0.00 0.00 32.44 2.17
1955 3134 5.920273 TCCTGTTGCAGAAAAATTCGAAATC 59.080 36.000 0.00 0.00 32.44 2.17
1956 3135 5.691305 CCTGTTGCAGAAAAATTCGAAATCA 59.309 36.000 0.00 0.00 32.44 2.57
1957 3136 6.129009 CCTGTTGCAGAAAAATTCGAAATCAG 60.129 38.462 0.00 0.00 32.44 2.90
1959 3138 6.198778 TGTTGCAGAAAAATTCGAAATCAGTG 59.801 34.615 0.00 0.00 34.02 3.66
1961 3140 6.502652 TGCAGAAAAATTCGAAATCAGTGAA 58.497 32.000 0.00 0.00 34.02 3.18
1963 3142 6.129088 GCAGAAAAATTCGAAATCAGTGAACC 60.129 38.462 0.00 0.00 34.02 3.62
1964 3143 6.363357 CAGAAAAATTCGAAATCAGTGAACCC 59.637 38.462 0.00 0.00 34.02 4.11
1993 3235 9.726232 AGACGACAATTATTTGATCAATGAATG 57.274 29.630 9.40 7.89 36.64 2.67
2069 3313 8.646900 ACCCTAATGCAGAAAAATCAAAAGTAA 58.353 29.630 0.00 0.00 0.00 2.24
2160 3406 1.659794 CAACCGTTGGCCAAAGAGG 59.340 57.895 30.02 27.55 41.84 3.69
2161 3407 1.530655 AACCGTTGGCCAAAGAGGG 60.531 57.895 30.02 23.98 38.09 4.30
2162 3408 2.002018 AACCGTTGGCCAAAGAGGGA 62.002 55.000 30.02 0.00 38.09 4.20
2179 3425 1.371558 GACTCTTCGGCCAACACCT 59.628 57.895 2.24 0.00 0.00 4.00
2306 3553 9.283768 TCATGTTTGACTAGATTTGAAAGCTTA 57.716 29.630 0.00 0.00 0.00 3.09
2412 3659 7.561021 TTGCTACATGTTCTTTGTGACTTTA 57.439 32.000 2.30 0.00 0.00 1.85
2414 3661 8.840833 TGCTACATGTTCTTTGTGACTTTATA 57.159 30.769 2.30 0.00 0.00 0.98
2423 3670 9.922305 GTTCTTTGTGACTTTATATATCAGTGC 57.078 33.333 2.82 0.00 0.00 4.40
2646 3903 2.413310 TCCTCCATTTACTTTCCCGC 57.587 50.000 0.00 0.00 0.00 6.13
2648 3905 1.340600 CCTCCATTTACTTTCCCGCCA 60.341 52.381 0.00 0.00 0.00 5.69
2651 3908 2.757868 TCCATTTACTTTCCCGCCATTG 59.242 45.455 0.00 0.00 0.00 2.82
2668 3925 4.263025 GCCATTGTTTCCCTCCATTTTCTT 60.263 41.667 0.00 0.00 0.00 2.52
2673 3930 0.695924 TCCCTCCATTTTCTTCCGCA 59.304 50.000 0.00 0.00 0.00 5.69
2741 4037 0.108662 CCTGCCATTTTCTTTCCCGC 60.109 55.000 0.00 0.00 0.00 6.13
2794 4090 5.993748 TTTTCTCCCGCCATTTTATTTCT 57.006 34.783 0.00 0.00 0.00 2.52
2796 4092 4.503714 TCTCCCGCCATTTTATTTCTCT 57.496 40.909 0.00 0.00 0.00 3.10
2826 4135 2.002505 TTCCGCCATTTTCTTTCCCA 57.997 45.000 0.00 0.00 0.00 4.37
2834 4143 4.466015 GCCATTTTCTTTCCCACCATTCTA 59.534 41.667 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 121 1.000396 AGGGATTTGCCTGGTGAGC 60.000 57.895 0.00 0.00 36.66 4.26
288 639 6.183360 TGGCCTGTTCTTACTTATACGAGTAC 60.183 42.308 3.32 0.00 32.12 2.73
291 642 5.041940 GTGGCCTGTTCTTACTTATACGAG 58.958 45.833 3.32 0.00 0.00 4.18
292 643 4.142093 GGTGGCCTGTTCTTACTTATACGA 60.142 45.833 3.32 0.00 0.00 3.43
293 644 4.117685 GGTGGCCTGTTCTTACTTATACG 58.882 47.826 3.32 0.00 0.00 3.06
294 645 5.093849 TGGTGGCCTGTTCTTACTTATAC 57.906 43.478 3.32 0.00 0.00 1.47
295 646 5.765576 TTGGTGGCCTGTTCTTACTTATA 57.234 39.130 3.32 0.00 0.00 0.98
312 664 0.391263 GCCCTACCTCTCGTTTGGTG 60.391 60.000 0.00 0.00 37.74 4.17
347 700 1.964223 GATCAGGTCGGAGGCAGATTA 59.036 52.381 0.00 0.00 29.02 1.75
378 731 0.662619 TGCTTGTTTCGCTTCAGGTG 59.337 50.000 0.00 0.00 0.00 4.00
456 809 0.324614 AGTCCACATCACGCCATGAA 59.675 50.000 0.00 0.00 41.93 2.57
473 826 5.591067 TGAAAGAAAATACGTGGGTTTCAGT 59.409 36.000 17.34 8.43 34.40 3.41
482 1142 4.088648 GTCGCCATGAAAGAAAATACGTG 58.911 43.478 0.00 0.00 0.00 4.49
606 1272 3.793144 CTTCTTCCTGCACGCCGC 61.793 66.667 0.00 0.00 42.89 6.53
633 1299 3.770040 CGCCGGTCAGTCCCATGA 61.770 66.667 1.90 0.00 0.00 3.07
761 1440 1.377229 CCTCGTTTAACCCAGGCCA 59.623 57.895 5.01 0.00 0.00 5.36
769 1448 4.945246 TCTCTATGCATCCCTCGTTTAAC 58.055 43.478 0.19 0.00 0.00 2.01
777 1456 4.302067 TCTTTCCTTCTCTATGCATCCCT 58.698 43.478 0.19 0.00 0.00 4.20
778 1457 4.696479 TCTTTCCTTCTCTATGCATCCC 57.304 45.455 0.19 0.00 0.00 3.85
779 1458 6.073331 CGATTTCTTTCCTTCTCTATGCATCC 60.073 42.308 0.19 0.00 0.00 3.51
780 1459 6.481644 ACGATTTCTTTCCTTCTCTATGCATC 59.518 38.462 0.19 0.00 0.00 3.91
781 1460 6.352516 ACGATTTCTTTCCTTCTCTATGCAT 58.647 36.000 3.79 3.79 0.00 3.96
782 1461 5.734720 ACGATTTCTTTCCTTCTCTATGCA 58.265 37.500 0.00 0.00 0.00 3.96
783 1462 6.670077 AACGATTTCTTTCCTTCTCTATGC 57.330 37.500 0.00 0.00 0.00 3.14
806 1485 7.085746 GCTAATTAAGCCGGTTTGTCTAAAAA 58.914 34.615 14.54 0.00 46.25 1.94
807 1486 6.614160 GCTAATTAAGCCGGTTTGTCTAAAA 58.386 36.000 14.54 0.00 46.25 1.52
808 1487 6.185852 GCTAATTAAGCCGGTTTGTCTAAA 57.814 37.500 14.54 0.00 46.25 1.85
809 1488 5.806366 GCTAATTAAGCCGGTTTGTCTAA 57.194 39.130 14.54 0.00 46.25 2.10
835 1514 1.994916 TAGTAGCGCCGGTTAACAAC 58.005 50.000 2.29 0.00 0.00 3.32
836 1515 2.965572 ATAGTAGCGCCGGTTAACAA 57.034 45.000 2.29 0.00 0.00 2.83
837 1516 2.034558 GGTATAGTAGCGCCGGTTAACA 59.965 50.000 2.29 0.00 0.00 2.41
838 1517 2.294512 AGGTATAGTAGCGCCGGTTAAC 59.705 50.000 2.29 0.00 0.00 2.01
839 1518 2.586425 AGGTATAGTAGCGCCGGTTAA 58.414 47.619 2.29 0.00 0.00 2.01
840 1519 2.276732 AGGTATAGTAGCGCCGGTTA 57.723 50.000 2.29 0.00 0.00 2.85
847 1526 1.662309 CGCGGTGAAGGTATAGTAGCG 60.662 57.143 0.00 0.00 39.14 4.26
887 1566 7.462200 GCATTGATTTTTGAACCGTTATTACCG 60.462 37.037 0.00 0.00 0.00 4.02
888 1567 7.201487 GGCATTGATTTTTGAACCGTTATTACC 60.201 37.037 0.00 0.00 0.00 2.85
889 1568 7.462200 CGGCATTGATTTTTGAACCGTTATTAC 60.462 37.037 0.00 0.00 34.83 1.89
890 1569 6.528423 CGGCATTGATTTTTGAACCGTTATTA 59.472 34.615 0.00 0.00 34.83 0.98
891 1570 5.347364 CGGCATTGATTTTTGAACCGTTATT 59.653 36.000 0.00 0.00 34.83 1.40
892 1571 4.862018 CGGCATTGATTTTTGAACCGTTAT 59.138 37.500 0.00 0.00 34.83 1.89
893 1572 4.230657 CGGCATTGATTTTTGAACCGTTA 58.769 39.130 0.00 0.00 34.83 3.18
894 1573 3.056304 CGGCATTGATTTTTGAACCGTT 58.944 40.909 0.00 0.00 34.83 4.44
895 1574 2.609244 CCGGCATTGATTTTTGAACCGT 60.609 45.455 0.00 0.00 37.74 4.83
896 1575 1.991965 CCGGCATTGATTTTTGAACCG 59.008 47.619 0.00 0.00 39.11 4.44
897 1576 3.038788 ACCGGCATTGATTTTTGAACC 57.961 42.857 0.00 0.00 0.00 3.62
898 1577 7.820044 TTATTACCGGCATTGATTTTTGAAC 57.180 32.000 0.00 0.00 0.00 3.18
899 1578 7.062371 CGTTTATTACCGGCATTGATTTTTGAA 59.938 33.333 0.00 0.00 0.00 2.69
900 1579 6.528423 CGTTTATTACCGGCATTGATTTTTGA 59.472 34.615 0.00 0.00 0.00 2.69
901 1580 6.309251 ACGTTTATTACCGGCATTGATTTTTG 59.691 34.615 0.00 0.00 0.00 2.44
902 1581 6.391537 ACGTTTATTACCGGCATTGATTTTT 58.608 32.000 0.00 0.00 0.00 1.94
903 1582 5.956642 ACGTTTATTACCGGCATTGATTTT 58.043 33.333 0.00 0.00 0.00 1.82
904 1583 5.570234 ACGTTTATTACCGGCATTGATTT 57.430 34.783 0.00 0.00 0.00 2.17
905 1584 5.336744 CAACGTTTATTACCGGCATTGATT 58.663 37.500 0.00 0.00 0.00 2.57
906 1585 4.732355 GCAACGTTTATTACCGGCATTGAT 60.732 41.667 0.00 0.00 0.00 2.57
907 1586 3.426426 GCAACGTTTATTACCGGCATTGA 60.426 43.478 0.00 0.00 0.00 2.57
953 1632 1.856014 GCTGTCATGTTAATTCGCGGC 60.856 52.381 6.13 0.00 0.00 6.53
954 1633 1.592110 CGCTGTCATGTTAATTCGCGG 60.592 52.381 6.13 0.00 36.16 6.46
958 1637 5.397534 GCATTGATCGCTGTCATGTTAATTC 59.602 40.000 0.00 0.00 0.00 2.17
969 1648 0.454957 GCGTTTGCATTGATCGCTGT 60.455 50.000 5.33 0.00 42.88 4.40
990 1675 5.706369 TGTCGCTATTTATAGAGAGGGAGAC 59.294 44.000 5.09 0.00 39.34 3.36
1039 2213 0.108992 GGACGGACGCTGTGATGTTA 60.109 55.000 0.00 0.00 0.00 2.41
1072 2246 1.269166 GTTGATCGACTAGCCACGTG 58.731 55.000 9.08 9.08 0.00 4.49
1077 2251 2.531206 GTGTCTGTTGATCGACTAGCC 58.469 52.381 14.27 1.44 0.00 3.93
1078 2252 2.094700 TGGTGTCTGTTGATCGACTAGC 60.095 50.000 14.27 8.13 0.00 3.42
1079 2253 3.440522 TCTGGTGTCTGTTGATCGACTAG 59.559 47.826 14.27 9.74 0.00 2.57
1082 2256 2.329379 GTCTGGTGTCTGTTGATCGAC 58.671 52.381 6.11 6.11 0.00 4.20
1095 2269 2.361610 GGCCATGGTGGTCTGGTG 60.362 66.667 14.67 0.00 39.55 4.17
1169 2343 2.230508 TGGATAGACAACAGTGACGGAC 59.769 50.000 0.00 0.00 0.00 4.79
1203 2377 1.981256 TTCTGTTTTGGAGCTGGGAC 58.019 50.000 0.00 0.00 0.00 4.46
1270 2444 4.154347 GAGCCTGGAGGACCTGCG 62.154 72.222 8.65 3.39 38.79 5.18
1339 2513 1.627550 GCAGGTTTCTTCGCCGACTC 61.628 60.000 0.00 0.00 0.00 3.36
1340 2514 1.668151 GCAGGTTTCTTCGCCGACT 60.668 57.895 0.00 0.00 0.00 4.18
1365 2539 0.033894 ATGGATCTGCACATGTGGCA 60.034 50.000 26.55 21.62 39.32 4.92
1366 2540 0.666913 GATGGATCTGCACATGTGGC 59.333 55.000 26.55 18.47 0.00 5.01
1369 2543 0.816825 GCCGATGGATCTGCACATGT 60.817 55.000 0.00 0.00 37.06 3.21
1373 2547 0.948141 GCTAGCCGATGGATCTGCAC 60.948 60.000 2.29 0.00 39.16 4.57
1425 2599 1.066858 CACGCACACCCAGAGTTATCT 60.067 52.381 0.00 0.00 35.63 1.98
1426 2600 1.337823 ACACGCACACCCAGAGTTATC 60.338 52.381 0.00 0.00 0.00 1.75
1427 2601 0.685097 ACACGCACACCCAGAGTTAT 59.315 50.000 0.00 0.00 0.00 1.89
1428 2602 1.330234 TACACGCACACCCAGAGTTA 58.670 50.000 0.00 0.00 0.00 2.24
1429 2603 0.685097 ATACACGCACACCCAGAGTT 59.315 50.000 0.00 0.00 0.00 3.01
1430 2604 1.203994 GTATACACGCACACCCAGAGT 59.796 52.381 0.00 0.00 0.00 3.24
1431 2605 1.203758 TGTATACACGCACACCCAGAG 59.796 52.381 0.08 0.00 0.00 3.35
1432 2606 1.258676 TGTATACACGCACACCCAGA 58.741 50.000 0.08 0.00 0.00 3.86
1433 2607 2.309528 ATGTATACACGCACACCCAG 57.690 50.000 7.96 0.00 0.00 4.45
1434 2608 2.351455 CAATGTATACACGCACACCCA 58.649 47.619 7.96 0.00 0.00 4.51
1435 2609 1.668751 CCAATGTATACACGCACACCC 59.331 52.381 7.96 0.00 0.00 4.61
1436 2610 1.668751 CCCAATGTATACACGCACACC 59.331 52.381 7.96 0.00 0.00 4.16
1437 2611 1.063469 GCCCAATGTATACACGCACAC 59.937 52.381 7.96 0.00 0.00 3.82
1438 2612 1.374560 GCCCAATGTATACACGCACA 58.625 50.000 7.96 0.00 0.00 4.57
1439 2613 0.303493 CGCCCAATGTATACACGCAC 59.697 55.000 7.96 0.00 0.00 5.34
1440 2614 0.108089 ACGCCCAATGTATACACGCA 60.108 50.000 7.96 0.00 0.00 5.24
1441 2615 0.303493 CACGCCCAATGTATACACGC 59.697 55.000 7.96 6.83 0.00 5.34
1442 2616 1.326245 CACACGCCCAATGTATACACG 59.674 52.381 7.96 9.38 0.00 4.49
1443 2617 1.063469 GCACACGCCCAATGTATACAC 59.937 52.381 7.96 0.00 0.00 2.90
1444 2618 1.339151 TGCACACGCCCAATGTATACA 60.339 47.619 8.27 8.27 37.32 2.29
1445 2619 1.063469 GTGCACACGCCCAATGTATAC 59.937 52.381 13.17 0.00 37.32 1.47
1446 2620 1.339151 TGTGCACACGCCCAATGTATA 60.339 47.619 17.42 0.00 37.32 1.47
1447 2621 0.607762 TGTGCACACGCCCAATGTAT 60.608 50.000 17.42 0.00 37.32 2.29
1448 2622 0.607762 ATGTGCACACGCCCAATGTA 60.608 50.000 24.37 0.00 37.32 2.29
1449 2623 1.902918 ATGTGCACACGCCCAATGT 60.903 52.632 24.37 0.00 37.32 2.71
1450 2624 1.444724 CATGTGCACACGCCCAATG 60.445 57.895 24.37 11.02 37.32 2.82
1451 2625 2.964174 CATGTGCACACGCCCAAT 59.036 55.556 24.37 0.27 37.32 3.16
1452 2626 3.976000 GCATGTGCACACGCCCAA 61.976 61.111 26.62 0.00 41.59 4.12
1462 2636 4.035675 GGAAAGACTAATAGGTGCATGTGC 59.964 45.833 0.00 0.00 42.50 4.57
1463 2637 5.185454 TGGAAAGACTAATAGGTGCATGTG 58.815 41.667 0.00 0.00 0.00 3.21
1464 2638 5.435686 TGGAAAGACTAATAGGTGCATGT 57.564 39.130 0.00 0.00 0.00 3.21
1465 2639 6.294473 AGATGGAAAGACTAATAGGTGCATG 58.706 40.000 0.00 0.00 0.00 4.06
1466 2640 6.506538 AGATGGAAAGACTAATAGGTGCAT 57.493 37.500 0.00 0.00 0.00 3.96
1467 2641 5.957771 AGATGGAAAGACTAATAGGTGCA 57.042 39.130 0.00 0.00 0.00 4.57
1468 2642 6.349300 TCAAGATGGAAAGACTAATAGGTGC 58.651 40.000 0.00 0.00 0.00 5.01
1469 2643 6.481644 GCTCAAGATGGAAAGACTAATAGGTG 59.518 42.308 0.00 0.00 0.00 4.00
1470 2644 6.385467 AGCTCAAGATGGAAAGACTAATAGGT 59.615 38.462 0.00 0.00 0.00 3.08
1471 2645 6.825610 AGCTCAAGATGGAAAGACTAATAGG 58.174 40.000 0.00 0.00 0.00 2.57
1472 2646 7.437862 GTGAGCTCAAGATGGAAAGACTAATAG 59.562 40.741 20.19 0.00 0.00 1.73
1473 2647 7.268586 GTGAGCTCAAGATGGAAAGACTAATA 58.731 38.462 20.19 0.00 0.00 0.98
1474 2648 6.112058 GTGAGCTCAAGATGGAAAGACTAAT 58.888 40.000 20.19 0.00 0.00 1.73
1475 2649 5.482908 GTGAGCTCAAGATGGAAAGACTAA 58.517 41.667 20.19 0.00 0.00 2.24
1476 2650 4.380973 CGTGAGCTCAAGATGGAAAGACTA 60.381 45.833 23.33 0.00 0.00 2.59
1477 2651 3.616076 CGTGAGCTCAAGATGGAAAGACT 60.616 47.826 23.33 0.00 0.00 3.24
1478 2652 2.670414 CGTGAGCTCAAGATGGAAAGAC 59.330 50.000 23.33 3.24 0.00 3.01
1479 2653 2.354103 CCGTGAGCTCAAGATGGAAAGA 60.354 50.000 28.28 0.00 0.00 2.52
1480 2654 2.005451 CCGTGAGCTCAAGATGGAAAG 58.995 52.381 28.28 8.14 0.00 2.62
1481 2655 1.623311 TCCGTGAGCTCAAGATGGAAA 59.377 47.619 28.28 6.97 0.00 3.13
1482 2656 1.266178 TCCGTGAGCTCAAGATGGAA 58.734 50.000 28.28 10.96 0.00 3.53
1483 2657 1.266178 TTCCGTGAGCTCAAGATGGA 58.734 50.000 28.28 23.10 0.00 3.41
1484 2658 2.099141 TTTCCGTGAGCTCAAGATGG 57.901 50.000 28.28 21.41 0.00 3.51
1485 2659 3.250762 TGTTTTTCCGTGAGCTCAAGATG 59.749 43.478 28.28 14.22 0.00 2.90
1486 2660 3.476552 TGTTTTTCCGTGAGCTCAAGAT 58.523 40.909 28.28 0.00 0.00 2.40
1487 2661 2.912771 TGTTTTTCCGTGAGCTCAAGA 58.087 42.857 28.28 20.24 0.00 3.02
1488 2662 3.691049 TTGTTTTTCCGTGAGCTCAAG 57.309 42.857 20.19 20.75 0.00 3.02
1489 2663 4.442375 TTTTGTTTTTCCGTGAGCTCAA 57.558 36.364 20.19 0.00 0.00 3.02
1490 2664 4.442375 TTTTTGTTTTTCCGTGAGCTCA 57.558 36.364 13.74 13.74 0.00 4.26
1491 2665 5.281727 AGATTTTTGTTTTTCCGTGAGCTC 58.718 37.500 6.82 6.82 0.00 4.09
1492 2666 5.262588 AGATTTTTGTTTTTCCGTGAGCT 57.737 34.783 0.00 0.00 0.00 4.09
1493 2667 5.966636 AAGATTTTTGTTTTTCCGTGAGC 57.033 34.783 0.00 0.00 0.00 4.26
1494 2668 9.848172 CATAAAAGATTTTTGTTTTTCCGTGAG 57.152 29.630 0.00 0.00 0.00 3.51
1495 2669 9.587772 TCATAAAAGATTTTTGTTTTTCCGTGA 57.412 25.926 0.00 0.00 0.00 4.35
1524 2698 6.706270 CGGGCCATTTTGCTAGTATATATAGG 59.294 42.308 4.39 0.00 0.00 2.57
1525 2699 7.224753 CACGGGCCATTTTGCTAGTATATATAG 59.775 40.741 4.39 0.00 0.00 1.31
1746 2920 2.027561 TGGGAAGCACACAGTGGTATAC 60.028 50.000 5.31 0.00 43.73 1.47
1748 2922 1.064003 TGGGAAGCACACAGTGGTAT 58.936 50.000 5.31 0.00 43.73 2.73
1758 2932 4.757594 TGATTGCAAATAATGGGAAGCAC 58.242 39.130 1.71 0.00 0.00 4.40
1825 2999 6.146347 GGTAGTGACAAGCTTTAGAGTTCAAG 59.854 42.308 0.00 0.00 0.00 3.02
1882 3056 1.479389 CCTGAGTGCCAAAGAAAGGGT 60.479 52.381 0.00 0.00 0.00 4.34
1883 3057 1.251251 CCTGAGTGCCAAAGAAAGGG 58.749 55.000 0.00 0.00 0.00 3.95
1939 3118 6.363357 GGGTTCACTGATTTCGAATTTTTCTG 59.637 38.462 0.00 1.54 0.00 3.02
1941 3120 6.447162 AGGGTTCACTGATTTCGAATTTTTC 58.553 36.000 0.00 0.00 0.00 2.29
1942 3121 6.405278 AGGGTTCACTGATTTCGAATTTTT 57.595 33.333 0.00 0.00 0.00 1.94
1943 3122 6.405278 AAGGGTTCACTGATTTCGAATTTT 57.595 33.333 0.00 0.00 0.00 1.82
1944 3123 6.940298 TCTAAGGGTTCACTGATTTCGAATTT 59.060 34.615 0.00 0.00 0.00 1.82
1945 3124 6.371825 GTCTAAGGGTTCACTGATTTCGAATT 59.628 38.462 0.00 0.00 0.00 2.17
1946 3125 5.875359 GTCTAAGGGTTCACTGATTTCGAAT 59.125 40.000 0.00 0.00 0.00 3.34
1947 3126 5.235516 GTCTAAGGGTTCACTGATTTCGAA 58.764 41.667 0.00 0.00 0.00 3.71
1949 3128 3.612860 CGTCTAAGGGTTCACTGATTTCG 59.387 47.826 0.00 0.00 0.00 3.46
1950 3129 4.626172 GTCGTCTAAGGGTTCACTGATTTC 59.374 45.833 0.00 0.00 0.00 2.17
1951 3130 4.039973 TGTCGTCTAAGGGTTCACTGATTT 59.960 41.667 0.00 0.00 0.00 2.17
1952 3131 3.576982 TGTCGTCTAAGGGTTCACTGATT 59.423 43.478 0.00 0.00 0.00 2.57
1953 3132 3.162666 TGTCGTCTAAGGGTTCACTGAT 58.837 45.455 0.00 0.00 0.00 2.90
1954 3133 2.589720 TGTCGTCTAAGGGTTCACTGA 58.410 47.619 0.00 0.00 0.00 3.41
1955 3134 3.380479 TTGTCGTCTAAGGGTTCACTG 57.620 47.619 0.00 0.00 0.00 3.66
1956 3135 4.618920 AATTGTCGTCTAAGGGTTCACT 57.381 40.909 0.00 0.00 0.00 3.41
1957 3136 6.980051 AATAATTGTCGTCTAAGGGTTCAC 57.020 37.500 0.00 0.00 0.00 3.18
1959 3138 7.605410 TCAAATAATTGTCGTCTAAGGGTTC 57.395 36.000 0.00 0.00 37.79 3.62
1961 3140 7.335627 TGATCAAATAATTGTCGTCTAAGGGT 58.664 34.615 0.00 0.00 37.79 4.34
1963 3142 9.655769 CATTGATCAAATAATTGTCGTCTAAGG 57.344 33.333 13.09 0.00 37.79 2.69
2069 3313 4.640690 AGGAGGCCGACAGGGTGT 62.641 66.667 0.00 0.00 38.44 4.16
2160 3406 1.671379 GGTGTTGGCCGAAGAGTCC 60.671 63.158 0.00 0.00 0.00 3.85
2161 3407 0.951040 CAGGTGTTGGCCGAAGAGTC 60.951 60.000 0.00 0.00 0.00 3.36
2162 3408 1.071471 CAGGTGTTGGCCGAAGAGT 59.929 57.895 0.00 0.00 0.00 3.24
2381 3628 8.196771 TCACAAAGAACATGTAGCAAAAAGAAT 58.803 29.630 0.00 0.00 0.00 2.40
2637 3894 0.966179 GGAAACAATGGCGGGAAAGT 59.034 50.000 0.00 0.00 0.00 2.66
2646 3903 5.482006 GAAGAAAATGGAGGGAAACAATGG 58.518 41.667 0.00 0.00 0.00 3.16
2648 3905 4.220602 CGGAAGAAAATGGAGGGAAACAAT 59.779 41.667 0.00 0.00 0.00 2.71
2651 3908 2.094700 GCGGAAGAAAATGGAGGGAAAC 60.095 50.000 0.00 0.00 0.00 2.78
2673 3930 4.388485 AGAAAATGGCGGCAAAGAAAATT 58.612 34.783 18.31 0.00 0.00 1.82
2741 4037 3.795877 AGAATGGCGGCAAATAAAATGG 58.204 40.909 18.31 0.00 0.00 3.16
2794 4090 2.870175 TGGCGGAAAAGAAAATGGAGA 58.130 42.857 0.00 0.00 0.00 3.71
2796 4092 4.615588 AAATGGCGGAAAAGAAAATGGA 57.384 36.364 0.00 0.00 0.00 3.41
2808 4117 1.253100 GTGGGAAAGAAAATGGCGGA 58.747 50.000 0.00 0.00 0.00 5.54
2826 4135 1.734655 AGATGGCGGGATAGAATGGT 58.265 50.000 0.00 0.00 0.00 3.55
2834 4143 1.133976 CAGGAAAGAAGATGGCGGGAT 60.134 52.381 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.