Multiple sequence alignment - TraesCS6B01G321700

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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 TraesCS6B01G321700 chr6B 100.000 2468 0 0 1 2468 569880277 569882744 0.000000e+00 4558.0
1 TraesCS6B01G321700 chr6B 93.440 625 31 6 2 624 280914147 280913531 0.000000e+00 918.0
2 TraesCS6B01G321700 chr6B 84.656 189 17 4 2180 2364 131179445 131179625 7.010000e-41 178.0
3 TraesCS6B01G321700 chr4B 93.936 874 51 2 623 1494 119382592 119383465 0.000000e+00 1319.0
4 TraesCS6B01G321700 chr3B 93.936 874 51 2 623 1494 767245613 767244740 0.000000e+00 1319.0
5 TraesCS6B01G321700 chr7A 93.651 882 54 2 623 1503 648084200 648083320 0.000000e+00 1317.0
6 TraesCS6B01G321700 chr5B 93.356 873 56 2 623 1494 273864243 273865114 0.000000e+00 1290.0
7 TraesCS6B01G321700 chr5B 93.450 626 28 7 1 622 130105521 130106137 0.000000e+00 917.0
8 TraesCS6B01G321700 chrUn 93.612 861 51 2 623 1482 119076577 119077434 0.000000e+00 1282.0
9 TraesCS6B01G321700 chr7D 93.135 874 57 3 623 1494 590148123 590148995 0.000000e+00 1279.0
10 TraesCS6B01G321700 chr7D 93.127 873 56 3 623 1493 449520698 449521568 0.000000e+00 1277.0
11 TraesCS6B01G321700 chr6A 93.403 864 55 2 623 1485 592596047 592595185 0.000000e+00 1279.0
12 TraesCS6B01G321700 chr3D 91.533 874 70 4 623 1494 269278545 269279416 0.000000e+00 1201.0
13 TraesCS6B01G321700 chr3D 93.312 628 33 8 1 625 602178121 602177500 0.000000e+00 918.0
14 TraesCS6B01G321700 chr3D 90.511 137 12 1 2180 2316 26213390 26213255 1.950000e-41 180.0
15 TraesCS6B01G321700 chr3D 90.179 112 10 1 2181 2292 425122640 425122750 7.110000e-31 145.0
16 TraesCS6B01G321700 chr3D 97.297 37 0 1 2287 2323 425137340 425137375 7.370000e-06 62.1
17 TraesCS6B01G321700 chr1B 95.981 622 19 5 1 621 503687880 503688496 0.000000e+00 1005.0
18 TraesCS6B01G321700 chr1B 94.921 630 25 6 1 628 503703218 503703842 0.000000e+00 979.0
19 TraesCS6B01G321700 chr1B 93.610 626 28 7 1 624 312231151 312230536 0.000000e+00 924.0
20 TraesCS6B01G321700 chr2B 93.930 626 30 7 1 624 375018118 375017499 0.000000e+00 939.0
21 TraesCS6B01G321700 chr2B 93.641 629 28 7 1 627 20269004 20268386 0.000000e+00 929.0
22 TraesCS6B01G321700 chr2B 93.301 627 28 9 1 624 452730203 452729588 0.000000e+00 913.0
23 TraesCS6B01G321700 chr2B 90.511 137 12 1 2180 2316 112599247 112599112 1.950000e-41 180.0
24 TraesCS6B01G321700 chr6D 84.061 458 27 16 1735 2179 381362908 381362484 1.370000e-107 399.0
25 TraesCS6B01G321700 chr6D 92.617 149 11 0 1497 1645 381363334 381363186 5.350000e-52 215.0
26 TraesCS6B01G321700 chr6D 95.192 104 5 0 2365 2468 381362491 381362388 5.460000e-37 165.0
27 TraesCS6B01G321700 chr1A 90.909 132 11 1 2180 2311 20272765 20272895 2.520000e-40 176.0
28 TraesCS6B01G321700 chr2D 86.957 138 16 2 2180 2316 46004000 46004136 1.180000e-33 154.0
29 TraesCS6B01G321700 chr2D 86.232 138 17 2 2180 2316 46039423 46039559 5.500000e-32 148.0
30 TraesCS6B01G321700 chr2D 86.029 136 17 2 2182 2316 45956958 45957092 7.110000e-31 145.0
31 TraesCS6B01G321700 chr2D 85.507 138 18 2 2180 2316 46020704 46020840 2.560000e-30 143.0


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 TraesCS6B01G321700 chr6B 569880277 569882744 2467 False 4558.000000 4558 100.000000 1 2468 1 chr6B.!!$F2 2467
1 TraesCS6B01G321700 chr6B 280913531 280914147 616 True 918.000000 918 93.440000 2 624 1 chr6B.!!$R1 622
2 TraesCS6B01G321700 chr4B 119382592 119383465 873 False 1319.000000 1319 93.936000 623 1494 1 chr4B.!!$F1 871
3 TraesCS6B01G321700 chr3B 767244740 767245613 873 True 1319.000000 1319 93.936000 623 1494 1 chr3B.!!$R1 871
4 TraesCS6B01G321700 chr7A 648083320 648084200 880 True 1317.000000 1317 93.651000 623 1503 1 chr7A.!!$R1 880
5 TraesCS6B01G321700 chr5B 273864243 273865114 871 False 1290.000000 1290 93.356000 623 1494 1 chr5B.!!$F2 871
6 TraesCS6B01G321700 chr5B 130105521 130106137 616 False 917.000000 917 93.450000 1 622 1 chr5B.!!$F1 621
7 TraesCS6B01G321700 chrUn 119076577 119077434 857 False 1282.000000 1282 93.612000 623 1482 1 chrUn.!!$F1 859
8 TraesCS6B01G321700 chr7D 590148123 590148995 872 False 1279.000000 1279 93.135000 623 1494 1 chr7D.!!$F2 871
9 TraesCS6B01G321700 chr7D 449520698 449521568 870 False 1277.000000 1277 93.127000 623 1493 1 chr7D.!!$F1 870
10 TraesCS6B01G321700 chr6A 592595185 592596047 862 True 1279.000000 1279 93.403000 623 1485 1 chr6A.!!$R1 862
11 TraesCS6B01G321700 chr3D 269278545 269279416 871 False 1201.000000 1201 91.533000 623 1494 1 chr3D.!!$F1 871
12 TraesCS6B01G321700 chr3D 602177500 602178121 621 True 918.000000 918 93.312000 1 625 1 chr3D.!!$R2 624
13 TraesCS6B01G321700 chr1B 503687880 503688496 616 False 1005.000000 1005 95.981000 1 621 1 chr1B.!!$F1 620
14 TraesCS6B01G321700 chr1B 503703218 503703842 624 False 979.000000 979 94.921000 1 628 1 chr1B.!!$F2 627
15 TraesCS6B01G321700 chr1B 312230536 312231151 615 True 924.000000 924 93.610000 1 624 1 chr1B.!!$R1 623
16 TraesCS6B01G321700 chr2B 375017499 375018118 619 True 939.000000 939 93.930000 1 624 1 chr2B.!!$R3 623
17 TraesCS6B01G321700 chr2B 20268386 20269004 618 True 929.000000 929 93.641000 1 627 1 chr2B.!!$R1 626
18 TraesCS6B01G321700 chr2B 452729588 452730203 615 True 913.000000 913 93.301000 1 624 1 chr2B.!!$R4 623
19 TraesCS6B01G321700 chr6D 381362388 381363334 946 True 259.666667 399 90.623333 1497 2468 3 chr6D.!!$R1 971

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
39 40 0.759346 CCGAAATGGACTAGGGAGGG 59.241 60.0 0.0 0.0 42.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1650 1670 0.037447 TGACGATTGTGGAATGGCCA 59.963 50.0 8.56 8.56 46.96 5.36 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
38 39 1.789523 TCCGAAATGGACTAGGGAGG 58.210 55.000 0.00 0.00 43.74 4.30
39 40 0.759346 CCGAAATGGACTAGGGAGGG 59.241 60.000 0.00 0.00 42.00 4.30
40 41 0.759346 CGAAATGGACTAGGGAGGGG 59.241 60.000 0.00 0.00 0.00 4.79
350 362 2.736995 CACCGTCATCACGCCGTT 60.737 61.111 0.00 0.00 45.29 4.44
465 478 1.440476 GGTACTTGGATCGGTCGGG 59.560 63.158 0.00 0.00 0.00 5.14
592 607 2.279741 GATCTTGCATGTGCGTAGGAA 58.720 47.619 0.01 0.00 45.83 3.36
593 608 1.438651 TCTTGCATGTGCGTAGGAAC 58.561 50.000 0.01 0.00 45.83 3.62
687 702 3.633986 CCAAGATCAAAAGAGGTATGGCC 59.366 47.826 0.00 0.00 37.58 5.36
790 805 2.930826 TGGAGGAAACTGAAGTCCAC 57.069 50.000 0.00 0.00 44.43 4.02
809 824 3.010138 CCACATCCTAGGTCTTCCCAAAA 59.990 47.826 9.08 0.00 34.66 2.44
833 848 4.189580 AGGTTGTGGCCACTGCGT 62.190 61.111 34.75 24.24 38.85 5.24
841 856 1.815421 GGCCACTGCGTCATGGTAG 60.815 63.158 0.00 0.00 38.34 3.18
858 874 3.329520 TGGTAGCTATGGTTTGAACACCT 59.670 43.478 0.00 0.00 37.75 4.00
871 889 9.144298 TGGTTTGAACACCTAAAAATTACCATA 57.856 29.630 0.00 0.00 37.75 2.74
899 917 2.235155 ACACCCAAAAACCCTCACAAAC 59.765 45.455 0.00 0.00 0.00 2.93
940 958 8.212317 AGGACTCTCGACTAACTTTACTATTC 57.788 38.462 0.00 0.00 0.00 1.75
961 979 3.117663 TCCTTGTTCCACTAAGGCAAAGT 60.118 43.478 0.00 0.00 42.52 2.66
1005 1023 2.936993 GCCGATGCAGGGGTATATGAAG 60.937 54.545 8.52 0.00 37.47 3.02
1044 1062 4.460382 GGCTTTGACCATGATCTTCTTGAA 59.540 41.667 0.00 0.00 0.00 2.69
1080 1098 5.297547 GCAGTAATCCGAGATTACAATGGA 58.702 41.667 25.43 0.00 37.05 3.41
1091 1109 9.801873 CCGAGATTACAATGGAAAATTTATTGT 57.198 29.630 17.53 17.53 44.54 2.71
1152 1170 3.818787 GCAGAGGCATTGGCGGTG 61.819 66.667 4.38 7.44 42.47 4.94
1268 1286 0.106918 TCCTTTTCGGTGGCAAGTGT 60.107 50.000 0.00 0.00 0.00 3.55
1271 1289 2.287368 CCTTTTCGGTGGCAAGTGTAAC 60.287 50.000 0.00 0.00 0.00 2.50
1316 1336 9.425893 CATGTCGTCAGATTTTAATCATGTAAC 57.574 33.333 5.36 0.00 37.89 2.50
1477 1497 5.978814 TGCTAAGTGAATAAAGGAGGAGAC 58.021 41.667 0.00 0.00 0.00 3.36
1494 1514 4.766007 GGAGACGTTCCGTAAAGAAAAAC 58.234 43.478 0.00 0.00 41.37 2.43
1495 1515 4.509230 GGAGACGTTCCGTAAAGAAAAACT 59.491 41.667 0.00 0.00 41.37 2.66
1505 1525 6.198966 TCCGTAAAGAAAAACTACTTGTCGAC 59.801 38.462 9.11 9.11 0.00 4.20
1539 1559 3.772025 TCCTTGTCTTTCTCCTCATCCTC 59.228 47.826 0.00 0.00 0.00 3.71
1542 1562 3.729108 TGTCTTTCTCCTCATCCTCCAT 58.271 45.455 0.00 0.00 0.00 3.41
1545 1565 5.907662 TGTCTTTCTCCTCATCCTCCATAAT 59.092 40.000 0.00 0.00 0.00 1.28
1559 1579 5.253564 TCCTCCATAATGGCATATTCATCCA 59.746 40.000 0.00 0.00 37.47 3.41
1579 1599 1.827969 ACATCCTCCTCTTTCTCCACG 59.172 52.381 0.00 0.00 0.00 4.94
1586 1606 1.070134 CCTCTTTCTCCACGAACACCA 59.930 52.381 0.00 0.00 0.00 4.17
1594 1614 1.276989 TCCACGAACACCAGAATACCC 59.723 52.381 0.00 0.00 0.00 3.69
1597 1617 1.553704 ACGAACACCAGAATACCCCTC 59.446 52.381 0.00 0.00 0.00 4.30
1609 1629 0.690762 TACCCCTCACAAGTGGCTTC 59.309 55.000 0.00 0.00 0.00 3.86
1618 1638 0.798776 CAAGTGGCTTCGTGATGTCC 59.201 55.000 0.00 0.00 0.00 4.02
1645 1665 4.104086 TGACCTTCACCCTCATGTATTCT 58.896 43.478 0.00 0.00 0.00 2.40
1646 1666 4.162320 TGACCTTCACCCTCATGTATTCTC 59.838 45.833 0.00 0.00 0.00 2.87
1647 1667 3.456277 ACCTTCACCCTCATGTATTCTCC 59.544 47.826 0.00 0.00 0.00 3.71
1648 1668 3.181450 CCTTCACCCTCATGTATTCTCCC 60.181 52.174 0.00 0.00 0.00 4.30
1649 1669 3.129262 TCACCCTCATGTATTCTCCCA 57.871 47.619 0.00 0.00 0.00 4.37
1650 1670 3.668821 TCACCCTCATGTATTCTCCCAT 58.331 45.455 0.00 0.00 0.00 4.00
1651 1671 3.392285 TCACCCTCATGTATTCTCCCATG 59.608 47.826 0.00 0.00 39.82 3.66
1652 1672 2.713167 ACCCTCATGTATTCTCCCATGG 59.287 50.000 4.14 4.14 39.12 3.66
1653 1673 2.553904 CCCTCATGTATTCTCCCATGGC 60.554 54.545 6.09 0.00 39.12 4.40
1654 1674 2.553904 CCTCATGTATTCTCCCATGGCC 60.554 54.545 6.09 0.00 39.12 5.36
1655 1675 2.107031 CTCATGTATTCTCCCATGGCCA 59.893 50.000 8.56 8.56 39.12 5.36
1656 1676 2.718062 TCATGTATTCTCCCATGGCCAT 59.282 45.455 14.09 14.09 39.12 4.40
1657 1677 3.140707 TCATGTATTCTCCCATGGCCATT 59.859 43.478 17.92 1.58 39.12 3.16
1658 1678 3.228188 TGTATTCTCCCATGGCCATTC 57.772 47.619 17.92 0.00 0.00 2.67
1659 1679 2.158475 TGTATTCTCCCATGGCCATTCC 60.158 50.000 17.92 0.00 0.00 3.01
1668 1688 2.866872 TGGCCATTCCACAATCGTC 58.133 52.632 0.00 0.00 40.72 4.20
1669 1689 0.037447 TGGCCATTCCACAATCGTCA 59.963 50.000 0.00 0.00 40.72 4.35
1670 1690 1.173043 GGCCATTCCACAATCGTCAA 58.827 50.000 0.00 0.00 34.01 3.18
1671 1691 1.135402 GGCCATTCCACAATCGTCAAC 60.135 52.381 0.00 0.00 34.01 3.18
1672 1692 1.539388 GCCATTCCACAATCGTCAACA 59.461 47.619 0.00 0.00 0.00 3.33
1673 1693 2.164219 GCCATTCCACAATCGTCAACAT 59.836 45.455 0.00 0.00 0.00 2.71
1674 1694 3.731867 GCCATTCCACAATCGTCAACATC 60.732 47.826 0.00 0.00 0.00 3.06
1675 1695 3.181497 CCATTCCACAATCGTCAACATCC 60.181 47.826 0.00 0.00 0.00 3.51
1676 1696 2.849294 TCCACAATCGTCAACATCCA 57.151 45.000 0.00 0.00 0.00 3.41
1677 1697 2.422597 TCCACAATCGTCAACATCCAC 58.577 47.619 0.00 0.00 0.00 4.02
1678 1698 1.128507 CCACAATCGTCAACATCCACG 59.871 52.381 0.00 0.00 37.36 4.94
1679 1699 1.798223 CACAATCGTCAACATCCACGT 59.202 47.619 0.00 0.00 37.30 4.49
1680 1700 2.066262 ACAATCGTCAACATCCACGTC 58.934 47.619 0.00 0.00 37.30 4.34
1681 1701 2.288825 ACAATCGTCAACATCCACGTCT 60.289 45.455 0.00 0.00 37.30 4.18
1682 1702 3.057104 ACAATCGTCAACATCCACGTCTA 60.057 43.478 0.00 0.00 37.30 2.59
1683 1703 3.861276 ATCGTCAACATCCACGTCTAA 57.139 42.857 0.00 0.00 37.30 2.10
1684 1704 3.211803 TCGTCAACATCCACGTCTAAG 57.788 47.619 0.00 0.00 37.30 2.18
1685 1705 2.815503 TCGTCAACATCCACGTCTAAGA 59.184 45.455 0.00 0.00 37.30 2.10
1686 1706 3.253921 TCGTCAACATCCACGTCTAAGAA 59.746 43.478 0.00 0.00 37.30 2.52
1687 1707 3.608506 CGTCAACATCCACGTCTAAGAAG 59.391 47.826 0.00 0.00 0.00 2.85
1688 1708 4.557205 GTCAACATCCACGTCTAAGAAGT 58.443 43.478 0.00 0.00 0.00 3.01
1689 1709 4.621886 GTCAACATCCACGTCTAAGAAGTC 59.378 45.833 0.00 0.00 0.00 3.01
1690 1710 4.279922 TCAACATCCACGTCTAAGAAGTCA 59.720 41.667 0.00 0.00 0.00 3.41
1691 1711 5.047306 TCAACATCCACGTCTAAGAAGTCAT 60.047 40.000 0.00 0.00 0.00 3.06
1692 1712 5.000012 ACATCCACGTCTAAGAAGTCATC 58.000 43.478 0.00 0.00 0.00 2.92
1693 1713 4.462834 ACATCCACGTCTAAGAAGTCATCA 59.537 41.667 0.00 0.00 0.00 3.07
1694 1714 5.047306 ACATCCACGTCTAAGAAGTCATCAA 60.047 40.000 0.00 0.00 0.00 2.57
1695 1715 5.661056 TCCACGTCTAAGAAGTCATCAAT 57.339 39.130 0.00 0.00 0.00 2.57
1696 1716 6.037786 TCCACGTCTAAGAAGTCATCAATT 57.962 37.500 0.00 0.00 0.00 2.32
1697 1717 6.464222 TCCACGTCTAAGAAGTCATCAATTT 58.536 36.000 0.00 0.00 0.00 1.82
1698 1718 6.590292 TCCACGTCTAAGAAGTCATCAATTTC 59.410 38.462 0.00 0.00 0.00 2.17
1699 1719 6.368791 CCACGTCTAAGAAGTCATCAATTTCA 59.631 38.462 0.00 0.00 0.00 2.69
1700 1720 7.065085 CCACGTCTAAGAAGTCATCAATTTCAT 59.935 37.037 0.00 0.00 0.00 2.57
1701 1721 9.087424 CACGTCTAAGAAGTCATCAATTTCATA 57.913 33.333 0.00 0.00 0.00 2.15
1702 1722 9.823647 ACGTCTAAGAAGTCATCAATTTCATAT 57.176 29.630 0.00 0.00 0.00 1.78
1726 1746 5.592587 TTTTCCCCTATTTCTTCACCTGA 57.407 39.130 0.00 0.00 0.00 3.86
1727 1747 5.796502 TTTCCCCTATTTCTTCACCTGAT 57.203 39.130 0.00 0.00 0.00 2.90
1728 1748 5.796502 TTCCCCTATTTCTTCACCTGATT 57.203 39.130 0.00 0.00 0.00 2.57
1729 1749 5.373812 TCCCCTATTTCTTCACCTGATTC 57.626 43.478 0.00 0.00 0.00 2.52
1730 1750 4.166144 TCCCCTATTTCTTCACCTGATTCC 59.834 45.833 0.00 0.00 0.00 3.01
1731 1751 4.166919 CCCCTATTTCTTCACCTGATTCCT 59.833 45.833 0.00 0.00 0.00 3.36
1732 1752 5.340360 CCCCTATTTCTTCACCTGATTCCTT 60.340 44.000 0.00 0.00 0.00 3.36
1733 1753 5.591877 CCCTATTTCTTCACCTGATTCCTTG 59.408 44.000 0.00 0.00 0.00 3.61
1759 1967 3.949586 TGACCCCATCAATAGATTGCA 57.050 42.857 0.00 0.00 37.68 4.08
1793 2001 9.377312 GAATTCATATTCATCTAGGGTCTTAGC 57.623 37.037 0.00 0.00 39.96 3.09
1824 2032 0.819259 TGTCCAGCACCAGCAAACTC 60.819 55.000 0.00 0.00 45.49 3.01
1825 2033 0.536006 GTCCAGCACCAGCAAACTCT 60.536 55.000 0.00 0.00 45.49 3.24
1840 2048 8.134895 CCAGCAAACTCTTGTATTGTCTAAAAA 58.865 33.333 0.00 0.00 34.79 1.94
1869 2084 3.078097 TGTTTAACATCCACGGACCATG 58.922 45.455 0.00 0.00 0.00 3.66
1881 2096 0.912486 GGACCATGGTCTAGTGCCTT 59.088 55.000 37.26 4.25 44.04 4.35
1882 2097 1.134371 GGACCATGGTCTAGTGCCTTC 60.134 57.143 37.26 18.25 44.04 3.46
1883 2098 1.834263 GACCATGGTCTAGTGCCTTCT 59.166 52.381 33.47 0.00 41.57 2.85
1884 2099 2.237392 GACCATGGTCTAGTGCCTTCTT 59.763 50.000 33.47 0.00 41.57 2.52
1885 2100 2.237392 ACCATGGTCTAGTGCCTTCTTC 59.763 50.000 13.00 0.00 0.00 2.87
1886 2101 2.503356 CCATGGTCTAGTGCCTTCTTCT 59.497 50.000 2.57 0.00 0.00 2.85
1887 2102 3.054802 CCATGGTCTAGTGCCTTCTTCTT 60.055 47.826 2.57 0.00 0.00 2.52
1888 2103 3.963428 TGGTCTAGTGCCTTCTTCTTC 57.037 47.619 7.42 0.00 0.00 2.87
1889 2104 2.567615 TGGTCTAGTGCCTTCTTCTTCC 59.432 50.000 7.42 0.00 0.00 3.46
1890 2105 2.417515 GGTCTAGTGCCTTCTTCTTCCG 60.418 54.545 0.00 0.00 0.00 4.30
1891 2106 2.231721 GTCTAGTGCCTTCTTCTTCCGT 59.768 50.000 0.00 0.00 0.00 4.69
1892 2107 2.231478 TCTAGTGCCTTCTTCTTCCGTG 59.769 50.000 0.00 0.00 0.00 4.94
1893 2108 0.603975 AGTGCCTTCTTCTTCCGTGC 60.604 55.000 0.00 0.00 0.00 5.34
1894 2109 0.603975 GTGCCTTCTTCTTCCGTGCT 60.604 55.000 0.00 0.00 0.00 4.40
1895 2110 0.108585 TGCCTTCTTCTTCCGTGCTT 59.891 50.000 0.00 0.00 0.00 3.91
1896 2111 0.799393 GCCTTCTTCTTCCGTGCTTC 59.201 55.000 0.00 0.00 0.00 3.86
1897 2112 1.443802 CCTTCTTCTTCCGTGCTTCC 58.556 55.000 0.00 0.00 0.00 3.46
1898 2113 1.002544 CCTTCTTCTTCCGTGCTTCCT 59.997 52.381 0.00 0.00 0.00 3.36
1899 2114 2.342179 CTTCTTCTTCCGTGCTTCCTC 58.658 52.381 0.00 0.00 0.00 3.71
1900 2115 0.243907 TCTTCTTCCGTGCTTCCTCG 59.756 55.000 0.00 0.00 0.00 4.63
1901 2116 1.355066 CTTCTTCCGTGCTTCCTCGC 61.355 60.000 0.00 0.00 0.00 5.03
1902 2117 3.181967 CTTCCGTGCTTCCTCGCG 61.182 66.667 0.00 0.00 39.43 5.87
1941 2157 1.005805 CATCCCCTTGAATGGACACCA 59.994 52.381 0.00 0.00 38.19 4.17
1946 2162 2.283298 CCTTGAATGGACACCAGATCG 58.717 52.381 0.00 0.00 36.75 3.69
1975 2195 5.730296 AAGTGCTTACTACTCTCACATGT 57.270 39.130 0.00 0.00 0.00 3.21
2084 2308 0.984995 AGGGGAGACAACAGCTAACC 59.015 55.000 0.00 0.00 0.00 2.85
2087 2311 1.610886 GGGAGACAACAGCTAACCCAC 60.611 57.143 0.00 0.00 36.27 4.61
2106 2330 0.835941 CTGCCTACATCTTCCCAGCT 59.164 55.000 0.00 0.00 0.00 4.24
2107 2331 0.833287 TGCCTACATCTTCCCAGCTC 59.167 55.000 0.00 0.00 0.00 4.09
2108 2332 0.107643 GCCTACATCTTCCCAGCTCC 59.892 60.000 0.00 0.00 0.00 4.70
2109 2333 1.799933 CCTACATCTTCCCAGCTCCT 58.200 55.000 0.00 0.00 0.00 3.69
2110 2334 2.122768 CCTACATCTTCCCAGCTCCTT 58.877 52.381 0.00 0.00 0.00 3.36
2179 2403 2.545731 GATTTCAGCTTCCTCTCGACC 58.454 52.381 0.00 0.00 0.00 4.79
2180 2404 1.338107 TTTCAGCTTCCTCTCGACCA 58.662 50.000 0.00 0.00 0.00 4.02
2181 2405 0.891373 TTCAGCTTCCTCTCGACCAG 59.109 55.000 0.00 0.00 0.00 4.00
2182 2406 0.251386 TCAGCTTCCTCTCGACCAGT 60.251 55.000 0.00 0.00 0.00 4.00
2183 2407 0.108898 CAGCTTCCTCTCGACCAGTG 60.109 60.000 0.00 0.00 0.00 3.66
2184 2408 1.216710 GCTTCCTCTCGACCAGTGG 59.783 63.158 7.91 7.91 37.14 4.00
2185 2409 1.216710 CTTCCTCTCGACCAGTGGC 59.783 63.158 9.78 0.82 35.92 5.01
2186 2410 2.549611 CTTCCTCTCGACCAGTGGCG 62.550 65.000 9.78 14.14 35.92 5.69
2187 2411 4.135153 CCTCTCGACCAGTGGCGG 62.135 72.222 20.79 9.44 0.00 6.13
2188 2412 3.062466 CTCTCGACCAGTGGCGGA 61.062 66.667 20.79 12.81 0.00 5.54
2189 2413 3.057547 CTCTCGACCAGTGGCGGAG 62.058 68.421 19.32 19.32 0.00 4.63
2208 2432 6.030548 CGGAGCTTGATCAGAATTATAGGA 57.969 41.667 0.00 0.00 0.00 2.94
2209 2433 6.098679 CGGAGCTTGATCAGAATTATAGGAG 58.901 44.000 0.00 0.00 0.00 3.69
2210 2434 6.405538 GGAGCTTGATCAGAATTATAGGAGG 58.594 44.000 0.00 0.00 0.00 4.30
2211 2435 6.371595 AGCTTGATCAGAATTATAGGAGGG 57.628 41.667 0.00 0.00 0.00 4.30
2212 2436 5.250313 AGCTTGATCAGAATTATAGGAGGGG 59.750 44.000 0.00 0.00 0.00 4.79
2213 2437 5.495640 CTTGATCAGAATTATAGGAGGGGC 58.504 45.833 0.00 0.00 0.00 5.80
2214 2438 4.767908 TGATCAGAATTATAGGAGGGGCT 58.232 43.478 0.00 0.00 0.00 5.19
2215 2439 5.915628 TGATCAGAATTATAGGAGGGGCTA 58.084 41.667 0.00 0.00 0.00 3.93
2216 2440 6.331032 TGATCAGAATTATAGGAGGGGCTAA 58.669 40.000 0.00 0.00 0.00 3.09
2217 2441 6.213600 TGATCAGAATTATAGGAGGGGCTAAC 59.786 42.308 0.00 0.00 0.00 2.34
2218 2442 4.844655 TCAGAATTATAGGAGGGGCTAACC 59.155 45.833 0.00 0.00 39.11 2.85
2234 2458 0.623617 AACCCATGTAGGAGGGGGTC 60.624 60.000 1.04 0.00 45.13 4.46
2235 2459 1.004230 CCCATGTAGGAGGGGGTCA 59.996 63.158 0.00 0.00 42.62 4.02
2236 2460 0.401979 CCCATGTAGGAGGGGGTCAT 60.402 60.000 0.00 0.00 42.62 3.06
2237 2461 1.522900 CCATGTAGGAGGGGGTCATT 58.477 55.000 0.00 0.00 41.22 2.57
2238 2462 1.421646 CCATGTAGGAGGGGGTCATTC 59.578 57.143 0.00 0.00 41.22 2.67
2239 2463 2.126882 CATGTAGGAGGGGGTCATTCA 58.873 52.381 0.00 0.00 0.00 2.57
2240 2464 2.352561 TGTAGGAGGGGGTCATTCAA 57.647 50.000 0.00 0.00 0.00 2.69
2241 2465 2.858644 TGTAGGAGGGGGTCATTCAAT 58.141 47.619 0.00 0.00 0.00 2.57
2242 2466 2.777692 TGTAGGAGGGGGTCATTCAATC 59.222 50.000 0.00 0.00 0.00 2.67
2243 2467 1.226311 AGGAGGGGGTCATTCAATCC 58.774 55.000 0.00 0.00 0.00 3.01
2244 2468 0.926293 GGAGGGGGTCATTCAATCCA 59.074 55.000 0.00 0.00 0.00 3.41
2245 2469 1.287739 GGAGGGGGTCATTCAATCCAA 59.712 52.381 0.00 0.00 0.00 3.53
2246 2470 2.659428 GAGGGGGTCATTCAATCCAAG 58.341 52.381 0.00 0.00 0.00 3.61
2247 2471 2.242196 GAGGGGGTCATTCAATCCAAGA 59.758 50.000 0.00 0.00 0.00 3.02
2248 2472 2.861317 AGGGGGTCATTCAATCCAAGAT 59.139 45.455 0.00 0.00 0.00 2.40
2249 2473 3.273084 AGGGGGTCATTCAATCCAAGATT 59.727 43.478 0.00 0.00 0.00 2.40
2250 2474 3.385755 GGGGGTCATTCAATCCAAGATTG 59.614 47.826 10.42 10.42 0.00 2.67
2251 2475 3.181472 GGGGTCATTCAATCCAAGATTGC 60.181 47.826 11.60 0.00 0.00 3.56
2252 2476 3.489738 GGGTCATTCAATCCAAGATTGCG 60.490 47.826 11.60 4.34 0.00 4.85
2253 2477 3.111098 GTCATTCAATCCAAGATTGCGC 58.889 45.455 11.60 0.00 0.00 6.09
2254 2478 2.754002 TCATTCAATCCAAGATTGCGCA 59.246 40.909 5.66 5.66 0.00 6.09
2255 2479 3.193056 TCATTCAATCCAAGATTGCGCAA 59.807 39.130 27.24 27.24 0.00 4.85
2256 2480 3.657015 TTCAATCCAAGATTGCGCAAA 57.343 38.095 28.81 9.99 0.00 3.68
2257 2481 3.657015 TCAATCCAAGATTGCGCAAAA 57.343 38.095 28.81 5.32 0.00 2.44
2258 2482 3.316283 TCAATCCAAGATTGCGCAAAAC 58.684 40.909 28.81 22.69 0.00 2.43
2259 2483 3.058450 CAATCCAAGATTGCGCAAAACA 58.942 40.909 28.81 3.91 0.00 2.83
2260 2484 2.132740 TCCAAGATTGCGCAAAACAC 57.867 45.000 28.81 17.75 0.00 3.32
2261 2485 1.139163 CCAAGATTGCGCAAAACACC 58.861 50.000 28.81 13.50 0.00 4.16
2262 2486 1.537776 CCAAGATTGCGCAAAACACCA 60.538 47.619 28.81 1.57 0.00 4.17
2263 2487 2.406130 CAAGATTGCGCAAAACACCAT 58.594 42.857 28.81 8.63 0.00 3.55
2264 2488 2.801679 CAAGATTGCGCAAAACACCATT 59.198 40.909 28.81 7.75 0.00 3.16
2265 2489 3.932545 AGATTGCGCAAAACACCATTA 57.067 38.095 28.81 0.00 0.00 1.90
2266 2490 4.454728 AGATTGCGCAAAACACCATTAT 57.545 36.364 28.81 6.02 0.00 1.28
2267 2491 4.819769 AGATTGCGCAAAACACCATTATT 58.180 34.783 28.81 5.41 0.00 1.40
2268 2492 4.864247 AGATTGCGCAAAACACCATTATTC 59.136 37.500 28.81 14.96 0.00 1.75
2269 2493 2.953020 TGCGCAAAACACCATTATTCC 58.047 42.857 8.16 0.00 0.00 3.01
2270 2494 2.560542 TGCGCAAAACACCATTATTCCT 59.439 40.909 8.16 0.00 0.00 3.36
2271 2495 2.923020 GCGCAAAACACCATTATTCCTG 59.077 45.455 0.30 0.00 0.00 3.86
2272 2496 3.613910 GCGCAAAACACCATTATTCCTGT 60.614 43.478 0.30 0.00 0.00 4.00
2273 2497 4.555262 CGCAAAACACCATTATTCCTGTT 58.445 39.130 0.00 0.00 0.00 3.16
2274 2498 4.987912 CGCAAAACACCATTATTCCTGTTT 59.012 37.500 0.00 0.00 38.24 2.83
2275 2499 6.153067 CGCAAAACACCATTATTCCTGTTTA 58.847 36.000 0.00 0.00 36.13 2.01
2276 2500 6.642950 CGCAAAACACCATTATTCCTGTTTAA 59.357 34.615 0.00 0.00 36.13 1.52
2277 2501 7.330700 CGCAAAACACCATTATTCCTGTTTAAT 59.669 33.333 0.00 0.00 36.13 1.40
2278 2502 8.998377 GCAAAACACCATTATTCCTGTTTAATT 58.002 29.630 0.00 0.00 36.13 1.40
2284 2508 9.248291 CACCATTATTCCTGTTTAATTATGTGC 57.752 33.333 0.00 0.00 0.00 4.57
2285 2509 8.976353 ACCATTATTCCTGTTTAATTATGTGCA 58.024 29.630 0.00 0.00 0.00 4.57
2286 2510 9.814899 CCATTATTCCTGTTTAATTATGTGCAA 57.185 29.630 0.00 0.00 0.00 4.08
2314 2538 5.705609 ATAACAAAACTACACAAGCTGGG 57.294 39.130 0.00 0.00 0.00 4.45
2315 2539 2.306847 ACAAAACTACACAAGCTGGGG 58.693 47.619 0.00 0.00 0.00 4.96
2316 2540 1.000274 CAAAACTACACAAGCTGGGGC 60.000 52.381 0.00 0.00 39.06 5.80
2317 2541 0.184933 AAACTACACAAGCTGGGGCA 59.815 50.000 0.00 0.00 41.70 5.36
2318 2542 0.250901 AACTACACAAGCTGGGGCAG 60.251 55.000 0.00 0.00 41.70 4.85
2319 2543 1.377725 CTACACAAGCTGGGGCAGG 60.378 63.158 0.00 0.00 41.70 4.85
2320 2544 2.826777 CTACACAAGCTGGGGCAGGG 62.827 65.000 0.00 0.00 41.70 4.45
2340 2564 4.828296 GGGGGTGGCATGGCTCAG 62.828 72.222 21.08 0.00 0.00 3.35
2341 2565 4.828296 GGGGTGGCATGGCTCAGG 62.828 72.222 21.08 0.00 0.00 3.86
2342 2566 4.052518 GGGTGGCATGGCTCAGGT 62.053 66.667 21.08 0.00 0.00 4.00
2343 2567 2.036256 GGTGGCATGGCTCAGGTT 59.964 61.111 21.08 0.00 0.00 3.50
2344 2568 2.345760 GGTGGCATGGCTCAGGTTG 61.346 63.158 21.08 0.00 0.00 3.77
2345 2569 2.036098 TGGCATGGCTCAGGTTGG 59.964 61.111 21.08 0.00 0.00 3.77
2346 2570 3.455469 GGCATGGCTCAGGTTGGC 61.455 66.667 12.86 0.00 0.00 4.52
2350 2574 1.619363 ATGGCTCAGGTTGGCCCTA 60.619 57.895 0.00 0.00 43.86 3.53
2351 2575 1.214305 ATGGCTCAGGTTGGCCCTAA 61.214 55.000 0.00 0.00 43.86 2.69
2352 2576 1.077429 GGCTCAGGTTGGCCCTAAG 60.077 63.158 0.00 0.00 43.86 2.18
2353 2577 1.750780 GCTCAGGTTGGCCCTAAGC 60.751 63.158 0.00 0.00 43.86 3.09
2354 2578 1.994463 CTCAGGTTGGCCCTAAGCT 59.006 57.895 0.00 0.00 43.86 3.74
2355 2579 0.107459 CTCAGGTTGGCCCTAAGCTC 60.107 60.000 0.00 0.00 43.86 4.09
2356 2580 1.077429 CAGGTTGGCCCTAAGCTCC 60.077 63.158 0.00 0.00 43.86 4.70
2357 2581 2.124695 GGTTGGCCCTAAGCTCCG 60.125 66.667 0.00 0.00 43.05 4.63
2358 2582 2.824489 GTTGGCCCTAAGCTCCGC 60.824 66.667 0.00 0.00 43.05 5.54
2359 2583 4.109675 TTGGCCCTAAGCTCCGCC 62.110 66.667 0.00 6.41 43.05 6.13
2361 2585 4.858680 GGCCCTAAGCTCCGCCAC 62.859 72.222 8.09 0.00 43.05 5.01
2362 2586 3.787001 GCCCTAAGCTCCGCCACT 61.787 66.667 0.00 0.00 38.99 4.00
2363 2587 2.187946 CCCTAAGCTCCGCCACTG 59.812 66.667 0.00 0.00 0.00 3.66
2364 2588 2.512515 CCTAAGCTCCGCCACTGC 60.513 66.667 0.00 0.00 0.00 4.40
2365 2589 2.581354 CTAAGCTCCGCCACTGCT 59.419 61.111 0.00 0.00 38.87 4.24
2366 2590 1.520342 CTAAGCTCCGCCACTGCTC 60.520 63.158 0.00 0.00 35.85 4.26
2367 2591 1.954362 CTAAGCTCCGCCACTGCTCT 61.954 60.000 0.00 0.00 35.85 4.09
2368 2592 1.949847 TAAGCTCCGCCACTGCTCTC 61.950 60.000 0.00 0.00 35.85 3.20
2370 2594 3.443925 CTCCGCCACTGCTCTCGA 61.444 66.667 0.00 0.00 34.43 4.04
2371 2595 3.691744 CTCCGCCACTGCTCTCGAC 62.692 68.421 0.00 0.00 34.43 4.20
2392 2616 1.882352 GCCTTCCATCGAAACACCACT 60.882 52.381 0.00 0.00 0.00 4.00
2393 2617 1.806542 CCTTCCATCGAAACACCACTG 59.193 52.381 0.00 0.00 0.00 3.66
2409 2633 2.826128 CCACTGTACTAGCACCTCTCAA 59.174 50.000 0.00 0.00 0.00 3.02
2441 2665 8.472007 TGTGACCAACCAAAGTATAAAGAAAT 57.528 30.769 0.00 0.00 0.00 2.17
2453 2677 7.978099 AGTATAAAGAAATGCAGGGGAAATT 57.022 32.000 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 182 3.335579 CGTATATAAAGGAGCAAGGGGC 58.664 50.000 0.00 0.00 45.30 5.80
261 273 2.039418 CGAGGTGGAATATGGTGGAGA 58.961 52.381 0.00 0.00 0.00 3.71
350 362 1.666011 GGAGAGTTCCGTCAGCACA 59.334 57.895 0.00 0.00 32.79 4.57
455 468 1.226603 CTTCACGACCCGACCGATC 60.227 63.158 0.00 0.00 0.00 3.69
603 618 7.255001 CCATATTGTTGGGGAACGTAGTAATTC 60.255 40.741 0.00 0.00 33.83 2.17
654 669 4.320608 TTTGATCTTGGGCACTCAAAAC 57.679 40.909 0.00 0.00 35.35 2.43
687 702 2.498481 ACATCAATCAGCCCCAATTGTG 59.502 45.455 4.43 0.00 35.02 3.33
720 735 7.523293 TCACCTGATTTGAATTGTGTACATT 57.477 32.000 0.00 0.00 0.00 2.71
790 805 5.116084 TCATTTTGGGAAGACCTAGGATG 57.884 43.478 17.98 4.57 41.11 3.51
809 824 0.251341 GTGGCCACAACCTCCTTCAT 60.251 55.000 31.23 0.00 0.00 2.57
833 848 4.941263 GTGTTCAAACCATAGCTACCATGA 59.059 41.667 0.00 0.00 0.00 3.07
841 856 9.135843 GTAATTTTTAGGTGTTCAAACCATAGC 57.864 33.333 0.00 0.00 43.20 2.97
858 874 8.171400 TGGGTGTCCTCTTTATGGTAATTTTTA 58.829 33.333 0.00 0.00 0.00 1.52
871 889 2.023404 AGGGTTTTTGGGTGTCCTCTTT 60.023 45.455 0.00 0.00 0.00 2.52
924 942 8.933807 GTGGAACAAGGAATAGTAAAGTTAGTC 58.066 37.037 0.00 0.00 44.16 2.59
940 958 3.222603 ACTTTGCCTTAGTGGAACAAGG 58.777 45.455 0.00 0.00 44.16 3.61
961 979 4.545208 TCTCCCATGAATCAACACGTAA 57.455 40.909 0.00 0.00 0.00 3.18
990 1008 8.154856 TCTACATTTAACTTCATATACCCCTGC 58.845 37.037 0.00 0.00 0.00 4.85
1005 1023 6.030228 GTCAAAGCCAGCATCTACATTTAAC 58.970 40.000 0.00 0.00 0.00 2.01
1044 1062 0.253160 TTACTGCCCCCACTGATCCT 60.253 55.000 0.00 0.00 0.00 3.24
1080 1098 7.063308 CGTTCATTAGCTGCCACAATAAATTTT 59.937 33.333 0.00 0.00 0.00 1.82
1091 1109 1.675714 CCACTCGTTCATTAGCTGCCA 60.676 52.381 0.00 0.00 0.00 4.92
1271 1289 8.501580 ACGACATGAAATAGCAATCATCAATAG 58.498 33.333 0.00 0.00 34.12 1.73
1404 1424 1.518572 CAGTACATCCGGTGCCGAC 60.519 63.158 12.71 1.77 42.83 4.79
1482 1502 7.158243 AGTCGACAAGTAGTTTTTCTTTACG 57.842 36.000 19.50 0.00 0.00 3.18
1488 1508 5.530712 AGGAGAGTCGACAAGTAGTTTTTC 58.469 41.667 19.50 2.03 0.00 2.29
1494 1514 7.446013 AGGATAATAAGGAGAGTCGACAAGTAG 59.554 40.741 19.50 0.00 0.00 2.57
1495 1515 7.288560 AGGATAATAAGGAGAGTCGACAAGTA 58.711 38.462 19.50 1.30 0.00 2.24
1505 1525 8.147704 GGAGAAAGACAAGGATAATAAGGAGAG 58.852 40.741 0.00 0.00 0.00 3.20
1539 1559 6.183360 GGATGTGGATGAATATGCCATTATGG 60.183 42.308 6.92 6.92 41.55 2.74
1542 1562 6.143551 AGGATGTGGATGAATATGCCATTA 57.856 37.500 0.00 0.00 33.66 1.90
1545 1565 3.245016 GGAGGATGTGGATGAATATGCCA 60.245 47.826 0.00 0.00 0.00 4.92
1559 1579 1.827969 CGTGGAGAAAGAGGAGGATGT 59.172 52.381 0.00 0.00 0.00 3.06
1579 1599 2.304761 TGTGAGGGGTATTCTGGTGTTC 59.695 50.000 0.00 0.00 0.00 3.18
1594 1614 0.249868 TCACGAAGCCACTTGTGAGG 60.250 55.000 1.89 0.00 36.50 3.86
1597 1617 1.195448 GACATCACGAAGCCACTTGTG 59.805 52.381 0.00 0.00 0.00 3.33
1609 1629 2.680312 AGGTCAGATTGGACATCACG 57.320 50.000 0.00 0.00 39.59 4.35
1618 1638 3.276857 CATGAGGGTGAAGGTCAGATTG 58.723 50.000 0.00 0.00 0.00 2.67
1650 1670 0.037447 TGACGATTGTGGAATGGCCA 59.963 50.000 8.56 8.56 46.96 5.36
1651 1671 1.135402 GTTGACGATTGTGGAATGGCC 60.135 52.381 0.00 0.00 37.10 5.36
1652 1672 1.539388 TGTTGACGATTGTGGAATGGC 59.461 47.619 0.00 0.00 0.00 4.40
1653 1673 3.181497 GGATGTTGACGATTGTGGAATGG 60.181 47.826 0.00 0.00 0.00 3.16
1654 1674 3.439825 TGGATGTTGACGATTGTGGAATG 59.560 43.478 0.00 0.00 0.00 2.67
1655 1675 3.440173 GTGGATGTTGACGATTGTGGAAT 59.560 43.478 0.00 0.00 0.00 3.01
1656 1676 2.811431 GTGGATGTTGACGATTGTGGAA 59.189 45.455 0.00 0.00 0.00 3.53
1657 1677 2.422597 GTGGATGTTGACGATTGTGGA 58.577 47.619 0.00 0.00 0.00 4.02
1658 1678 1.128507 CGTGGATGTTGACGATTGTGG 59.871 52.381 0.00 0.00 37.81 4.17
1659 1679 1.798223 ACGTGGATGTTGACGATTGTG 59.202 47.619 0.00 0.00 38.94 3.33
1660 1680 2.066262 GACGTGGATGTTGACGATTGT 58.934 47.619 0.00 0.00 38.94 2.71
1661 1681 2.337583 AGACGTGGATGTTGACGATTG 58.662 47.619 0.00 0.00 38.94 2.67
1662 1682 2.743636 AGACGTGGATGTTGACGATT 57.256 45.000 0.00 0.00 38.94 3.34
1663 1683 3.442625 TCTTAGACGTGGATGTTGACGAT 59.557 43.478 0.00 0.00 38.94 3.73
1664 1684 2.815503 TCTTAGACGTGGATGTTGACGA 59.184 45.455 0.00 0.00 38.94 4.20
1665 1685 3.211803 TCTTAGACGTGGATGTTGACG 57.788 47.619 0.00 0.00 41.41 4.35
1666 1686 4.557205 ACTTCTTAGACGTGGATGTTGAC 58.443 43.478 0.00 0.00 0.00 3.18
1667 1687 4.279922 TGACTTCTTAGACGTGGATGTTGA 59.720 41.667 0.00 0.00 0.00 3.18
1668 1688 4.556233 TGACTTCTTAGACGTGGATGTTG 58.444 43.478 0.00 0.00 0.00 3.33
1669 1689 4.866508 TGACTTCTTAGACGTGGATGTT 57.133 40.909 0.00 0.00 0.00 2.71
1670 1690 4.462834 TGATGACTTCTTAGACGTGGATGT 59.537 41.667 0.00 0.00 0.00 3.06
1671 1691 4.998788 TGATGACTTCTTAGACGTGGATG 58.001 43.478 0.00 0.00 0.00 3.51
1672 1692 5.661056 TTGATGACTTCTTAGACGTGGAT 57.339 39.130 0.00 0.00 0.00 3.41
1673 1693 5.661056 ATTGATGACTTCTTAGACGTGGA 57.339 39.130 0.00 0.00 0.00 4.02
1674 1694 6.368791 TGAAATTGATGACTTCTTAGACGTGG 59.631 38.462 0.00 0.00 0.00 4.94
1675 1695 7.351414 TGAAATTGATGACTTCTTAGACGTG 57.649 36.000 0.00 0.00 0.00 4.49
1676 1696 9.823647 ATATGAAATTGATGACTTCTTAGACGT 57.176 29.630 0.00 0.00 0.00 4.34
1703 1723 5.959512 TCAGGTGAAGAAATAGGGGAAAAA 58.040 37.500 0.00 0.00 0.00 1.94
1704 1724 5.592587 TCAGGTGAAGAAATAGGGGAAAA 57.407 39.130 0.00 0.00 0.00 2.29
1705 1725 5.796502 ATCAGGTGAAGAAATAGGGGAAA 57.203 39.130 0.00 0.00 0.00 3.13
1706 1726 5.340027 GGAATCAGGTGAAGAAATAGGGGAA 60.340 44.000 0.00 0.00 0.00 3.97
1707 1727 4.166144 GGAATCAGGTGAAGAAATAGGGGA 59.834 45.833 0.00 0.00 0.00 4.81
1708 1728 4.166919 AGGAATCAGGTGAAGAAATAGGGG 59.833 45.833 0.00 0.00 0.00 4.79
1709 1729 5.379706 AGGAATCAGGTGAAGAAATAGGG 57.620 43.478 0.00 0.00 0.00 3.53
1710 1730 6.183347 ACAAGGAATCAGGTGAAGAAATAGG 58.817 40.000 0.00 0.00 0.00 2.57
1711 1731 7.391554 TGAACAAGGAATCAGGTGAAGAAATAG 59.608 37.037 0.00 0.00 0.00 1.73
1712 1732 7.230747 TGAACAAGGAATCAGGTGAAGAAATA 58.769 34.615 0.00 0.00 0.00 1.40
1713 1733 6.070656 TGAACAAGGAATCAGGTGAAGAAAT 58.929 36.000 0.00 0.00 0.00 2.17
1714 1734 5.445069 TGAACAAGGAATCAGGTGAAGAAA 58.555 37.500 0.00 0.00 0.00 2.52
1715 1735 5.047566 TGAACAAGGAATCAGGTGAAGAA 57.952 39.130 0.00 0.00 0.00 2.52
1716 1736 4.705110 TGAACAAGGAATCAGGTGAAGA 57.295 40.909 0.00 0.00 0.00 2.87
1717 1737 5.474532 TCAATGAACAAGGAATCAGGTGAAG 59.525 40.000 0.00 0.00 0.00 3.02
1718 1738 5.241506 GTCAATGAACAAGGAATCAGGTGAA 59.758 40.000 0.00 0.00 30.14 3.18
1719 1739 4.761739 GTCAATGAACAAGGAATCAGGTGA 59.238 41.667 0.00 0.00 0.00 4.02
1720 1740 4.082571 GGTCAATGAACAAGGAATCAGGTG 60.083 45.833 0.00 0.00 0.00 4.00
1721 1741 4.082125 GGTCAATGAACAAGGAATCAGGT 58.918 43.478 0.00 0.00 0.00 4.00
1722 1742 3.445096 GGGTCAATGAACAAGGAATCAGG 59.555 47.826 0.00 0.00 0.00 3.86
1723 1743 3.445096 GGGGTCAATGAACAAGGAATCAG 59.555 47.826 0.00 0.00 0.00 2.90
1724 1744 3.181424 TGGGGTCAATGAACAAGGAATCA 60.181 43.478 0.00 0.00 0.00 2.57
1725 1745 3.430453 TGGGGTCAATGAACAAGGAATC 58.570 45.455 0.00 0.00 0.00 2.52
1726 1746 3.541242 TGGGGTCAATGAACAAGGAAT 57.459 42.857 0.00 0.00 0.00 3.01
1727 1747 3.181424 TGATGGGGTCAATGAACAAGGAA 60.181 43.478 0.00 0.00 32.78 3.36
1728 1748 2.378208 TGATGGGGTCAATGAACAAGGA 59.622 45.455 0.00 0.00 32.78 3.36
1729 1749 2.806434 TGATGGGGTCAATGAACAAGG 58.194 47.619 0.00 0.00 32.78 3.61
1781 1989 2.467880 TCAACCCTGCTAAGACCCTAG 58.532 52.381 0.00 0.00 0.00 3.02
1791 1999 0.550914 TGGACAAGTTCAACCCTGCT 59.449 50.000 0.00 0.00 0.00 4.24
1793 2001 0.954452 GCTGGACAAGTTCAACCCTG 59.046 55.000 0.00 0.00 0.00 4.45
1840 2048 6.532302 GTCCGTGGATGTTAAACAAAAGTTTT 59.468 34.615 0.00 0.00 0.00 2.43
1850 2065 2.040545 ACCATGGTCCGTGGATGTTAAA 59.959 45.455 33.12 0.00 42.73 1.52
1852 2067 1.208535 GACCATGGTCCGTGGATGTTA 59.791 52.381 33.12 0.00 42.73 2.41
1862 2077 0.912486 AAGGCACTAGACCATGGTCC 59.088 55.000 36.09 23.04 42.03 4.46
1869 2084 2.417515 CGGAAGAAGAAGGCACTAGACC 60.418 54.545 0.00 0.00 38.49 3.85
1881 2096 0.243907 CGAGGAAGCACGGAAGAAGA 59.756 55.000 0.00 0.00 0.00 2.87
1882 2097 1.355066 GCGAGGAAGCACGGAAGAAG 61.355 60.000 0.00 0.00 37.05 2.85
1883 2098 1.374252 GCGAGGAAGCACGGAAGAA 60.374 57.895 0.00 0.00 37.05 2.52
1884 2099 2.261671 GCGAGGAAGCACGGAAGA 59.738 61.111 0.00 0.00 37.05 2.87
1885 2100 3.181967 CGCGAGGAAGCACGGAAG 61.182 66.667 0.00 0.00 36.85 3.46
1897 2112 2.034685 TGTAAGGATCTCATTCCGCGAG 59.965 50.000 8.23 0.00 40.94 5.03
1898 2113 2.028876 TGTAAGGATCTCATTCCGCGA 58.971 47.619 8.23 0.00 40.94 5.87
1899 2114 2.128035 GTGTAAGGATCTCATTCCGCG 58.872 52.381 0.00 0.00 40.94 6.46
1900 2115 3.181475 TGAGTGTAAGGATCTCATTCCGC 60.181 47.826 0.00 0.00 40.94 5.54
1901 2116 4.655762 TGAGTGTAAGGATCTCATTCCG 57.344 45.455 0.00 0.00 40.94 4.30
1902 2117 5.546526 GGATGAGTGTAAGGATCTCATTCC 58.453 45.833 8.04 7.39 45.21 3.01
1903 2118 5.512232 GGGGATGAGTGTAAGGATCTCATTC 60.512 48.000 8.04 6.31 45.21 2.67
1904 2119 4.349342 GGGGATGAGTGTAAGGATCTCATT 59.651 45.833 8.04 0.00 45.21 2.57
1905 2120 3.906846 GGGGATGAGTGTAAGGATCTCAT 59.093 47.826 6.60 6.60 46.99 2.90
1906 2121 3.051803 AGGGGATGAGTGTAAGGATCTCA 60.052 47.826 0.00 0.00 41.43 3.27
1907 2122 3.582164 AGGGGATGAGTGTAAGGATCTC 58.418 50.000 0.00 0.00 0.00 2.75
1908 2123 3.713764 CAAGGGGATGAGTGTAAGGATCT 59.286 47.826 0.00 0.00 0.00 2.75
1909 2124 3.711704 TCAAGGGGATGAGTGTAAGGATC 59.288 47.826 0.00 0.00 0.00 3.36
1910 2125 3.736094 TCAAGGGGATGAGTGTAAGGAT 58.264 45.455 0.00 0.00 0.00 3.24
1911 2126 3.199442 TCAAGGGGATGAGTGTAAGGA 57.801 47.619 0.00 0.00 0.00 3.36
1941 2157 2.770164 AAGCACTTTAGGCACGATCT 57.230 45.000 0.00 0.00 0.00 2.75
1946 2162 5.074584 AGAGTAGTAAGCACTTTAGGCAC 57.925 43.478 0.00 0.00 36.14 5.01
1975 2195 1.980036 AGCCAAGGTACGGAAGGTAAA 59.020 47.619 0.00 0.00 31.61 2.01
2023 2244 0.384309 GCTAATGCCCGGCCTTAAAC 59.616 55.000 7.03 0.00 0.00 2.01
2084 2308 0.911769 TGGGAAGATGTAGGCAGTGG 59.088 55.000 0.00 0.00 0.00 4.00
2087 2311 0.835941 AGCTGGGAAGATGTAGGCAG 59.164 55.000 0.00 0.00 0.00 4.85
2106 2330 1.181098 GCAAGCCAGCAAGGAAAGGA 61.181 55.000 0.00 0.00 41.22 3.36
2107 2331 1.291272 GCAAGCCAGCAAGGAAAGG 59.709 57.895 0.00 0.00 41.22 3.11
2108 2332 2.043625 TGCAAGCCAGCAAGGAAAG 58.956 52.632 0.00 0.00 42.46 2.62
2109 2333 4.274012 TGCAAGCCAGCAAGGAAA 57.726 50.000 0.00 0.00 42.46 3.13
2179 2403 1.078918 TGATCAAGCTCCGCCACTG 60.079 57.895 0.00 0.00 0.00 3.66
2180 2404 1.220206 CTGATCAAGCTCCGCCACT 59.780 57.895 0.00 0.00 0.00 4.00
2181 2405 0.391661 TTCTGATCAAGCTCCGCCAC 60.392 55.000 0.00 0.00 0.00 5.01
2182 2406 0.543277 ATTCTGATCAAGCTCCGCCA 59.457 50.000 0.00 0.00 0.00 5.69
2183 2407 1.673168 AATTCTGATCAAGCTCCGCC 58.327 50.000 0.00 0.00 0.00 6.13
2184 2408 4.629200 CCTATAATTCTGATCAAGCTCCGC 59.371 45.833 0.00 0.00 0.00 5.54
2185 2409 6.030548 TCCTATAATTCTGATCAAGCTCCG 57.969 41.667 0.00 0.00 0.00 4.63
2186 2410 6.405538 CCTCCTATAATTCTGATCAAGCTCC 58.594 44.000 0.00 0.00 0.00 4.70
2187 2411 6.405538 CCCTCCTATAATTCTGATCAAGCTC 58.594 44.000 0.00 0.00 0.00 4.09
2188 2412 5.250313 CCCCTCCTATAATTCTGATCAAGCT 59.750 44.000 0.00 0.00 0.00 3.74
2189 2413 5.495640 CCCCTCCTATAATTCTGATCAAGC 58.504 45.833 0.00 0.00 0.00 4.01
2190 2414 5.250313 AGCCCCTCCTATAATTCTGATCAAG 59.750 44.000 0.00 0.00 0.00 3.02
2191 2415 5.165652 AGCCCCTCCTATAATTCTGATCAA 58.834 41.667 0.00 0.00 0.00 2.57
2192 2416 4.767908 AGCCCCTCCTATAATTCTGATCA 58.232 43.478 0.00 0.00 0.00 2.92
2193 2417 6.352308 GGTTAGCCCCTCCTATAATTCTGATC 60.352 46.154 0.00 0.00 0.00 2.92
2194 2418 5.489278 GGTTAGCCCCTCCTATAATTCTGAT 59.511 44.000 0.00 0.00 0.00 2.90
2195 2419 4.844655 GGTTAGCCCCTCCTATAATTCTGA 59.155 45.833 0.00 0.00 0.00 3.27
2196 2420 5.167303 GGTTAGCCCCTCCTATAATTCTG 57.833 47.826 0.00 0.00 0.00 3.02
2211 2435 0.765510 CCCTCCTACATGGGTTAGCC 59.234 60.000 0.00 0.00 38.65 3.93
2212 2436 0.765510 CCCCTCCTACATGGGTTAGC 59.234 60.000 0.00 0.00 41.82 3.09
2213 2437 1.435256 CCCCCTCCTACATGGGTTAG 58.565 60.000 0.00 0.00 41.82 2.34
2214 2438 3.666876 CCCCCTCCTACATGGGTTA 57.333 57.895 0.00 0.00 41.82 2.85
2215 2439 4.520063 CCCCCTCCTACATGGGTT 57.480 61.111 0.00 0.00 41.82 4.11
2216 2440 3.222522 ACCCCCTCCTACATGGGT 58.777 61.111 0.00 0.00 46.50 4.51
2217 2441 0.401979 ATGACCCCCTCCTACATGGG 60.402 60.000 0.00 0.00 44.03 4.00
2218 2442 1.421646 GAATGACCCCCTCCTACATGG 59.578 57.143 0.00 0.00 37.10 3.66
2219 2443 2.126882 TGAATGACCCCCTCCTACATG 58.873 52.381 0.00 0.00 0.00 3.21
2220 2444 2.587060 TGAATGACCCCCTCCTACAT 57.413 50.000 0.00 0.00 0.00 2.29
2221 2445 2.352561 TTGAATGACCCCCTCCTACA 57.647 50.000 0.00 0.00 0.00 2.74
2222 2446 2.106684 GGATTGAATGACCCCCTCCTAC 59.893 54.545 0.00 0.00 0.00 3.18
2223 2447 2.294195 TGGATTGAATGACCCCCTCCTA 60.294 50.000 0.00 0.00 0.00 2.94
2224 2448 1.226311 GGATTGAATGACCCCCTCCT 58.774 55.000 0.00 0.00 0.00 3.69
2225 2449 0.926293 TGGATTGAATGACCCCCTCC 59.074 55.000 0.00 0.00 0.00 4.30
2226 2450 2.242196 TCTTGGATTGAATGACCCCCTC 59.758 50.000 0.00 0.00 0.00 4.30
2227 2451 2.287584 TCTTGGATTGAATGACCCCCT 58.712 47.619 0.00 0.00 0.00 4.79
2228 2452 2.826674 TCTTGGATTGAATGACCCCC 57.173 50.000 0.00 0.00 0.00 5.40
2229 2453 3.181472 GCAATCTTGGATTGAATGACCCC 60.181 47.826 20.18 1.09 0.00 4.95
2230 2454 3.489738 CGCAATCTTGGATTGAATGACCC 60.490 47.826 20.18 3.98 0.00 4.46
2231 2455 3.699067 CGCAATCTTGGATTGAATGACC 58.301 45.455 20.18 4.54 0.00 4.02
2232 2456 3.111098 GCGCAATCTTGGATTGAATGAC 58.889 45.455 20.18 5.10 0.00 3.06
2233 2457 2.754002 TGCGCAATCTTGGATTGAATGA 59.246 40.909 20.18 2.43 0.00 2.57
2234 2458 3.153676 TGCGCAATCTTGGATTGAATG 57.846 42.857 20.18 11.61 0.00 2.67
2235 2459 3.872511 TTGCGCAATCTTGGATTGAAT 57.127 38.095 21.02 0.00 0.00 2.57
2236 2460 3.657015 TTTGCGCAATCTTGGATTGAA 57.343 38.095 25.64 0.36 0.00 2.69
2237 2461 3.243670 TGTTTTGCGCAATCTTGGATTGA 60.244 39.130 25.64 0.97 0.00 2.57
2238 2462 3.058450 TGTTTTGCGCAATCTTGGATTG 58.942 40.909 25.64 13.86 0.00 2.67
2239 2463 3.059166 GTGTTTTGCGCAATCTTGGATT 58.941 40.909 25.64 0.00 0.00 3.01
2240 2464 2.610232 GGTGTTTTGCGCAATCTTGGAT 60.610 45.455 25.64 0.00 0.00 3.41
2241 2465 1.269517 GGTGTTTTGCGCAATCTTGGA 60.270 47.619 25.64 4.45 0.00 3.53
2242 2466 1.139163 GGTGTTTTGCGCAATCTTGG 58.861 50.000 25.64 0.00 0.00 3.61
2243 2467 1.850377 TGGTGTTTTGCGCAATCTTG 58.150 45.000 25.64 0.00 0.00 3.02
2244 2468 2.818130 ATGGTGTTTTGCGCAATCTT 57.182 40.000 25.64 7.02 0.00 2.40
2245 2469 2.818130 AATGGTGTTTTGCGCAATCT 57.182 40.000 25.64 1.84 0.00 2.40
2246 2470 4.032786 GGAATAATGGTGTTTTGCGCAATC 59.967 41.667 25.64 19.65 0.00 2.67
2247 2471 3.932089 GGAATAATGGTGTTTTGCGCAAT 59.068 39.130 25.64 8.86 0.00 3.56
2248 2472 3.006323 AGGAATAATGGTGTTTTGCGCAA 59.994 39.130 21.02 21.02 0.00 4.85
2249 2473 2.560542 AGGAATAATGGTGTTTTGCGCA 59.439 40.909 5.66 5.66 0.00 6.09
2250 2474 2.923020 CAGGAATAATGGTGTTTTGCGC 59.077 45.455 0.00 0.00 0.00 6.09
2251 2475 4.173036 ACAGGAATAATGGTGTTTTGCG 57.827 40.909 0.00 0.00 0.00 4.85
2252 2476 7.954788 TTAAACAGGAATAATGGTGTTTTGC 57.045 32.000 4.77 0.00 41.93 3.68
2258 2482 9.248291 GCACATAATTAAACAGGAATAATGGTG 57.752 33.333 0.00 0.00 0.00 4.17
2259 2483 8.976353 TGCACATAATTAAACAGGAATAATGGT 58.024 29.630 0.00 0.00 0.00 3.55
2260 2484 9.814899 TTGCACATAATTAAACAGGAATAATGG 57.185 29.630 0.00 0.00 0.00 3.16
2288 2512 8.952278 CCCAGCTTGTGTAGTTTTGTTATATTA 58.048 33.333 0.00 0.00 0.00 0.98
2289 2513 7.093945 CCCCAGCTTGTGTAGTTTTGTTATATT 60.094 37.037 0.00 0.00 0.00 1.28
2290 2514 6.377146 CCCCAGCTTGTGTAGTTTTGTTATAT 59.623 38.462 0.00 0.00 0.00 0.86
2291 2515 5.708230 CCCCAGCTTGTGTAGTTTTGTTATA 59.292 40.000 0.00 0.00 0.00 0.98
2292 2516 4.522789 CCCCAGCTTGTGTAGTTTTGTTAT 59.477 41.667 0.00 0.00 0.00 1.89
2293 2517 3.886505 CCCCAGCTTGTGTAGTTTTGTTA 59.113 43.478 0.00 0.00 0.00 2.41
2294 2518 2.693074 CCCCAGCTTGTGTAGTTTTGTT 59.307 45.455 0.00 0.00 0.00 2.83
2295 2519 2.306847 CCCCAGCTTGTGTAGTTTTGT 58.693 47.619 0.00 0.00 0.00 2.83
2296 2520 1.000274 GCCCCAGCTTGTGTAGTTTTG 60.000 52.381 0.00 0.00 35.50 2.44
2297 2521 1.328279 GCCCCAGCTTGTGTAGTTTT 58.672 50.000 0.00 0.00 35.50 2.43
2298 2522 0.184933 TGCCCCAGCTTGTGTAGTTT 59.815 50.000 0.00 0.00 40.80 2.66
2299 2523 0.250901 CTGCCCCAGCTTGTGTAGTT 60.251 55.000 0.00 0.00 40.80 2.24
2300 2524 1.376466 CTGCCCCAGCTTGTGTAGT 59.624 57.895 0.00 0.00 40.80 2.73
2301 2525 1.377725 CCTGCCCCAGCTTGTGTAG 60.378 63.158 0.00 0.00 40.80 2.74
2302 2526 2.756400 CCTGCCCCAGCTTGTGTA 59.244 61.111 0.00 0.00 40.80 2.90
2303 2527 4.290622 CCCTGCCCCAGCTTGTGT 62.291 66.667 0.00 0.00 40.80 3.72
2323 2547 4.828296 CTGAGCCATGCCACCCCC 62.828 72.222 0.00 0.00 0.00 5.40
2324 2548 4.828296 CCTGAGCCATGCCACCCC 62.828 72.222 0.00 0.00 0.00 4.95
2325 2549 3.590466 AACCTGAGCCATGCCACCC 62.590 63.158 0.00 0.00 0.00 4.61
2326 2550 2.036256 AACCTGAGCCATGCCACC 59.964 61.111 0.00 0.00 0.00 4.61
2327 2551 2.345760 CCAACCTGAGCCATGCCAC 61.346 63.158 0.00 0.00 0.00 5.01
2328 2552 2.036098 CCAACCTGAGCCATGCCA 59.964 61.111 0.00 0.00 0.00 4.92
2329 2553 3.455469 GCCAACCTGAGCCATGCC 61.455 66.667 0.00 0.00 0.00 4.40
2340 2564 2.124695 CGGAGCTTAGGGCCAACC 60.125 66.667 6.18 0.00 43.05 3.77
2358 2582 3.288308 AAGGCGTCGAGAGCAGTGG 62.288 63.158 13.82 0.00 36.08 4.00
2359 2583 1.803519 GAAGGCGTCGAGAGCAGTG 60.804 63.158 13.82 0.00 36.08 3.66
2360 2584 2.569134 GAAGGCGTCGAGAGCAGT 59.431 61.111 13.82 1.90 36.08 4.40
2361 2585 2.202676 GGAAGGCGTCGAGAGCAG 60.203 66.667 13.82 0.00 36.08 4.24
2362 2586 2.284798 GATGGAAGGCGTCGAGAGCA 62.285 60.000 13.82 0.00 36.08 4.26
2363 2587 1.590259 GATGGAAGGCGTCGAGAGC 60.590 63.158 0.00 4.36 0.00 4.09
2364 2588 1.298713 CGATGGAAGGCGTCGAGAG 60.299 63.158 0.00 0.00 37.55 3.20
2365 2589 1.310216 TTCGATGGAAGGCGTCGAGA 61.310 55.000 0.00 0.00 44.08 4.04
2366 2590 0.457853 TTTCGATGGAAGGCGTCGAG 60.458 55.000 0.00 0.00 44.08 4.04
2367 2591 0.734942 GTTTCGATGGAAGGCGTCGA 60.735 55.000 0.00 0.00 42.01 4.20
2368 2592 1.011968 TGTTTCGATGGAAGGCGTCG 61.012 55.000 0.00 0.00 36.75 5.12
2369 2593 0.442699 GTGTTTCGATGGAAGGCGTC 59.557 55.000 0.00 0.00 32.80 5.19
2370 2594 0.953960 GGTGTTTCGATGGAAGGCGT 60.954 55.000 0.00 0.00 32.80 5.68
2371 2595 0.953471 TGGTGTTTCGATGGAAGGCG 60.953 55.000 0.00 0.00 32.80 5.52
2392 2616 5.546621 AAACTTTGAGAGGTGCTAGTACA 57.453 39.130 13.26 0.00 0.00 2.90
2393 2617 6.260271 ACAAAAACTTTGAGAGGTGCTAGTAC 59.740 38.462 1.77 1.77 0.00 2.73
2409 2633 5.222079 ACTTTGGTTGGTCACAAAAACTT 57.778 34.783 0.00 0.00 38.54 2.66


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

AutoCloner maintained by Alex Coulton.