Multiple sequence alignment - TraesCS6D01G393000

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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 TraesCS6D01G393000 chr6D 100.000 2285 0 0 1 2285 467041435 467043719 0.000000e+00 4220
1 TraesCS6D01G393000 chr6D 89.796 98 10 0 1626 1723 348647197 348647294 2.380000e-25 126
2 TraesCS6D01G393000 chr6A 88.609 1510 96 39 165 1638 613337383 613338852 0.000000e+00 1766
3 TraesCS6D01G393000 chr6A 95.455 176 8 0 1 176 613337187 613337362 4.810000e-72 281
4 TraesCS6D01G393000 chr6A 79.381 291 25 13 1810 2085 613339062 613339332 3.020000e-39 172
5 TraesCS6D01G393000 chr6A 80.383 209 11 16 2083 2274 613339641 613339836 5.120000e-27 132
6 TraesCS6D01G393000 chr6A 90.625 96 7 2 1629 1723 93892398 93892304 2.380000e-25 126
7 TraesCS6D01G393000 chr6B 87.209 1548 91 54 1 1480 712245279 712246787 0.000000e+00 1663
8 TraesCS6D01G393000 chr3D 82.234 197 19 7 1809 2003 505790907 505790725 3.040000e-34 156
9 TraesCS6D01G393000 chr7B 92.553 94 7 0 1630 1723 162120908 162120815 3.960000e-28 135
10 TraesCS6D01G393000 chr4B 91.489 94 7 1 1630 1723 576192221 576192129 6.630000e-26 128
11 TraesCS6D01G393000 chr4B 88.889 99 10 1 1625 1723 511163809 511163712 1.110000e-23 121
12 TraesCS6D01G393000 chr5D 90.426 94 9 0 1630 1723 481427106 481427199 8.570000e-25 124
13 TraesCS6D01G393000 chr4D 89.000 100 9 2 1625 1723 414999663 414999565 3.080000e-24 122
14 TraesCS6D01G393000 chr5B 89.474 95 10 0 1629 1723 695476059 695475965 1.110000e-23 121
15 TraesCS6D01G393000 chr5B 88.119 101 11 1 1630 1730 378998971 378998872 3.990000e-23 119


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 TraesCS6D01G393000 chr6D 467041435 467043719 2284 False 4220.00 4220 100.000 1 2285 1 chr6D.!!$F2 2284
1 TraesCS6D01G393000 chr6A 613337187 613339836 2649 False 587.75 1766 85.957 1 2274 4 chr6A.!!$F1 2273
2 TraesCS6D01G393000 chr6B 712245279 712246787 1508 False 1663.00 1663 87.209 1 1480 1 chr6B.!!$F1 1479

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
389 422 0.106268 TCCTTTGGTTGCTTGGCTGA 60.106 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2219 0.034089 TCAGCCAGTCCATCTCTCGA 60.034 55.0 0.0 0.0 0.0 4.04 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
81 82 2.580601 GGTGTGGGGTCTACGCTGT 61.581 63.158 0.00 0.00 0.00 4.40
92 93 1.207089 TCTACGCTGTTGGGGAATCTG 59.793 52.381 0.00 0.00 0.00 2.90
138 139 0.963856 ACCACCATGCATGCACTGAG 60.964 55.000 25.37 14.97 0.00 3.35
143 144 1.015109 CATGCATGCACTGAGAGTCC 58.985 55.000 25.37 0.00 0.00 3.85
179 180 8.437575 GGACATTTCCTTTCACCCTATTAGATA 58.562 37.037 0.00 0.00 39.13 1.98
180 181 9.495572 GACATTTCCTTTCACCCTATTAGATAG 57.504 37.037 0.00 0.00 0.00 2.08
184 185 7.798710 TCCTTTCACCCTATTAGATAGATGG 57.201 40.000 0.00 0.00 34.77 3.51
187 188 8.263640 CCTTTCACCCTATTAGATAGATGGATG 58.736 40.741 0.00 0.00 34.77 3.51
188 189 8.972662 TTTCACCCTATTAGATAGATGGATGA 57.027 34.615 0.00 0.00 34.77 2.92
189 190 8.972662 TTCACCCTATTAGATAGATGGATGAA 57.027 34.615 0.00 0.00 34.77 2.57
190 191 8.367660 TCACCCTATTAGATAGATGGATGAAC 57.632 38.462 0.00 0.00 34.77 3.18
208 237 8.977412 TGGATGAACAGATAACTTGTGTCTATA 58.023 33.333 0.00 0.00 0.00 1.31
315 348 3.706594 GACATCTCCATTCACCCTACAGA 59.293 47.826 0.00 0.00 0.00 3.41
317 350 4.102210 ACATCTCCATTCACCCTACAGATG 59.898 45.833 0.00 0.00 40.98 2.90
331 364 3.272574 ACAGATGACTTGTGCCTATGG 57.727 47.619 0.00 0.00 0.00 2.74
355 388 1.228862 GGCATGGGGTTCCTGTTGT 60.229 57.895 0.00 0.00 0.00 3.32
389 422 0.106268 TCCTTTGGTTGCTTGGCTGA 60.106 50.000 0.00 0.00 0.00 4.26
404 437 1.012841 GCTGAGCAGGCTAACATGAC 58.987 55.000 0.00 0.00 0.00 3.06
409 442 1.982073 GCAGGCTAACATGACGGCAC 61.982 60.000 0.00 0.00 36.20 5.01
538 587 2.787473 TGCATGTAGCCTAAAGTGCT 57.213 45.000 0.00 0.00 44.83 4.40
539 588 3.071874 TGCATGTAGCCTAAAGTGCTT 57.928 42.857 0.00 0.00 44.83 3.91
541 590 3.826157 TGCATGTAGCCTAAAGTGCTTTT 59.174 39.130 2.32 0.00 44.83 2.27
542 591 5.007034 TGCATGTAGCCTAAAGTGCTTTTA 58.993 37.500 2.32 0.00 44.83 1.52
545 594 6.693113 GCATGTAGCCTAAAGTGCTTTTATTC 59.307 38.462 2.32 0.00 40.23 1.75
548 597 7.165485 TGTAGCCTAAAGTGCTTTTATTCTCA 58.835 34.615 2.32 0.00 40.23 3.27
549 598 6.749923 AGCCTAAAGTGCTTTTATTCTCAG 57.250 37.500 2.32 0.00 34.87 3.35
550 599 6.476378 AGCCTAAAGTGCTTTTATTCTCAGA 58.524 36.000 2.32 0.00 34.87 3.27
553 602 8.246871 GCCTAAAGTGCTTTTATTCTCAGAAAT 58.753 33.333 2.32 0.00 34.23 2.17
554 603 9.780413 CCTAAAGTGCTTTTATTCTCAGAAATC 57.220 33.333 2.32 0.00 34.23 2.17
595 652 3.452627 ACTAGATCACCAAGTCCATGGAC 59.547 47.826 33.72 33.72 43.54 4.02
682 739 3.444742 TGCATGCTTTTCTCCTAACCATG 59.555 43.478 20.33 0.00 33.60 3.66
683 740 3.181483 GCATGCTTTTCTCCTAACCATGG 60.181 47.826 11.19 11.19 31.73 3.66
684 741 2.446435 TGCTTTTCTCCTAACCATGGC 58.554 47.619 13.04 0.00 0.00 4.40
685 742 2.224992 TGCTTTTCTCCTAACCATGGCA 60.225 45.455 13.04 0.00 0.00 4.92
797 864 3.701532 TGCCAAACTTTTAGTGAACCG 57.298 42.857 0.00 0.00 0.00 4.44
881 953 0.901124 GGATGGAGGATGGAGGATCG 59.099 60.000 0.00 0.00 34.37 3.69
885 957 0.829602 GGAGGATGGAGGATCGCTCA 60.830 60.000 11.73 0.00 33.36 4.26
987 1062 0.468029 CCCTGCTCCTCTCTCTCTCC 60.468 65.000 0.00 0.00 0.00 3.71
1051 1133 1.383664 CCCTGCATCCTCCTCCTCA 60.384 63.158 0.00 0.00 0.00 3.86
1059 1141 0.105760 TCCTCCTCCTCATGCTCCTC 60.106 60.000 0.00 0.00 0.00 3.71
1128 1213 2.101233 GGAAGAAGAAGCGGTCGGC 61.101 63.158 0.00 0.00 44.05 5.54
1291 1376 0.969149 TCTGCACAACTGACGAGGAT 59.031 50.000 0.00 0.00 0.00 3.24
1292 1377 1.067565 TCTGCACAACTGACGAGGATC 60.068 52.381 0.00 0.00 0.00 3.36
1293 1378 0.678950 TGCACAACTGACGAGGATCA 59.321 50.000 0.00 0.00 33.17 2.92
1294 1379 1.069978 TGCACAACTGACGAGGATCAA 59.930 47.619 0.00 0.00 33.17 2.57
1295 1380 1.461127 GCACAACTGACGAGGATCAAC 59.539 52.381 0.00 0.00 33.17 3.18
1296 1381 1.721389 CACAACTGACGAGGATCAACG 59.279 52.381 8.76 8.76 33.17 4.10
1297 1382 0.716108 CAACTGACGAGGATCAACGC 59.284 55.000 9.96 5.04 33.17 4.84
1298 1383 0.317160 AACTGACGAGGATCAACGCA 59.683 50.000 9.96 8.42 33.17 5.24
1299 1384 0.109086 ACTGACGAGGATCAACGCAG 60.109 55.000 20.70 20.70 38.50 5.18
1300 1385 0.803768 CTGACGAGGATCAACGCAGG 60.804 60.000 17.68 5.75 33.64 4.85
1301 1386 1.519455 GACGAGGATCAACGCAGGG 60.519 63.158 9.96 0.00 33.17 4.45
1302 1387 2.227089 GACGAGGATCAACGCAGGGT 62.227 60.000 9.96 0.00 33.17 4.34
1303 1388 1.519455 CGAGGATCAACGCAGGGTC 60.519 63.158 0.00 0.00 33.17 4.46
1304 1389 1.596934 GAGGATCAACGCAGGGTCA 59.403 57.895 0.00 0.00 33.17 4.02
1305 1390 0.741221 GAGGATCAACGCAGGGTCAC 60.741 60.000 0.00 0.00 33.17 3.67
1306 1391 2.100631 GGATCAACGCAGGGTCACG 61.101 63.158 0.00 0.00 0.00 4.35
1307 1392 1.080093 GATCAACGCAGGGTCACGA 60.080 57.895 0.00 0.00 0.00 4.35
1472 1572 3.181473 GCCGTAGTACCACCATTGATGTA 60.181 47.826 0.00 0.00 0.00 2.29
1476 1576 6.239092 CCGTAGTACCACCATTGATGTATGTA 60.239 42.308 0.00 0.00 0.00 2.29
1480 1580 8.257602 AGTACCACCATTGATGTATGTATGTA 57.742 34.615 0.00 0.00 0.00 2.29
1481 1581 8.880244 AGTACCACCATTGATGTATGTATGTAT 58.120 33.333 0.00 0.00 0.00 2.29
1482 1582 7.984422 ACCACCATTGATGTATGTATGTATG 57.016 36.000 0.00 0.00 0.00 2.39
1483 1583 6.430925 ACCACCATTGATGTATGTATGTATGC 59.569 38.462 0.00 0.00 0.00 3.14
1495 1595 8.815912 TGTATGTATGTATGCTCATCAATACCT 58.184 33.333 10.08 5.73 31.96 3.08
1496 1596 9.091784 GTATGTATGTATGCTCATCAATACCTG 57.908 37.037 10.08 0.00 0.00 4.00
1497 1597 7.066307 TGTATGTATGCTCATCAATACCTGT 57.934 36.000 10.08 0.00 0.00 4.00
1498 1598 6.930722 TGTATGTATGCTCATCAATACCTGTG 59.069 38.462 10.08 0.00 0.00 3.66
1499 1599 4.707105 TGTATGCTCATCAATACCTGTGG 58.293 43.478 0.00 0.00 0.00 4.17
1500 1600 2.715749 TGCTCATCAATACCTGTGGG 57.284 50.000 0.00 0.00 38.88 4.61
1501 1601 1.312815 GCTCATCAATACCTGTGGGC 58.687 55.000 0.00 0.00 35.63 5.36
1502 1602 1.133976 GCTCATCAATACCTGTGGGCT 60.134 52.381 0.00 0.00 35.63 5.19
1503 1603 2.569059 CTCATCAATACCTGTGGGCTG 58.431 52.381 0.00 0.00 35.63 4.85
1504 1604 1.915489 TCATCAATACCTGTGGGCTGT 59.085 47.619 0.00 0.00 35.63 4.40
1505 1605 2.019249 CATCAATACCTGTGGGCTGTG 58.981 52.381 0.00 0.00 35.63 3.66
1506 1606 1.064003 TCAATACCTGTGGGCTGTGT 58.936 50.000 0.00 0.00 35.63 3.72
1507 1607 1.167851 CAATACCTGTGGGCTGTGTG 58.832 55.000 0.00 0.00 35.63 3.82
1508 1608 0.771127 AATACCTGTGGGCTGTGTGT 59.229 50.000 0.00 0.00 35.63 3.72
1509 1609 0.036732 ATACCTGTGGGCTGTGTGTG 59.963 55.000 0.00 0.00 35.63 3.82
1510 1610 1.341913 TACCTGTGGGCTGTGTGTGT 61.342 55.000 0.00 0.00 35.63 3.72
1511 1611 2.188829 CCTGTGGGCTGTGTGTGTG 61.189 63.158 0.00 0.00 0.00 3.82
1512 1612 1.451927 CTGTGGGCTGTGTGTGTGT 60.452 57.895 0.00 0.00 0.00 3.72
1529 1629 3.940480 TGTGGCTCCCTCCCTCCA 61.940 66.667 0.00 0.00 0.00 3.86
1531 1631 2.003548 GTGGCTCCCTCCCTCCATT 61.004 63.158 0.00 0.00 0.00 3.16
1533 1633 2.456443 GGCTCCCTCCCTCCATTCC 61.456 68.421 0.00 0.00 0.00 3.01
1541 1650 0.253347 TCCCTCCATTCCTGCTTCCT 60.253 55.000 0.00 0.00 0.00 3.36
1555 1664 4.132336 CTGCTTCCTTGCATGATTAGCTA 58.868 43.478 15.90 0.00 42.48 3.32
1556 1665 3.879295 TGCTTCCTTGCATGATTAGCTAC 59.121 43.478 15.90 0.00 38.12 3.58
1558 1667 4.024218 GCTTCCTTGCATGATTAGCTACAG 60.024 45.833 0.00 0.00 0.00 2.74
1560 1669 2.551459 CCTTGCATGATTAGCTACAGCC 59.449 50.000 0.00 0.00 43.38 4.85
1563 1672 2.224378 TGCATGATTAGCTACAGCCCTC 60.224 50.000 0.00 0.00 43.38 4.30
1569 1678 1.386533 TAGCTACAGCCCTCGTGTAC 58.613 55.000 0.00 0.00 43.38 2.90
1588 1697 6.424683 GTGTACATATGCAGTGATTGATGTG 58.575 40.000 1.58 0.00 0.00 3.21
1589 1698 5.528320 TGTACATATGCAGTGATTGATGTGG 59.472 40.000 1.58 0.00 0.00 4.17
1591 1700 1.108776 ATGCAGTGATTGATGTGGCC 58.891 50.000 0.00 0.00 0.00 5.36
1595 1704 1.475280 CAGTGATTGATGTGGCCAAGG 59.525 52.381 7.24 0.00 0.00 3.61
1597 1706 1.314534 TGATTGATGTGGCCAAGGCG 61.315 55.000 7.24 0.00 43.06 5.52
1601 1710 1.750399 GATGTGGCCAAGGCGTGAT 60.750 57.895 7.24 0.00 43.06 3.06
1604 1713 1.078426 GTGGCCAAGGCGTGATAGT 60.078 57.895 7.24 0.00 43.06 2.12
1613 1722 2.858745 AGGCGTGATAGTTTGTTGGTT 58.141 42.857 0.00 0.00 0.00 3.67
1614 1723 4.010667 AGGCGTGATAGTTTGTTGGTTA 57.989 40.909 0.00 0.00 0.00 2.85
1624 1733 8.018520 TGATAGTTTGTTGGTTAAGCATTTACG 58.981 33.333 8.40 0.00 0.00 3.18
1626 1735 7.261829 AGTTTGTTGGTTAAGCATTTACGTA 57.738 32.000 8.40 0.00 0.00 3.57
1628 1737 5.266756 TGTTGGTTAAGCATTTACGTACG 57.733 39.130 15.01 15.01 0.00 3.67
1630 1739 5.923114 TGTTGGTTAAGCATTTACGTACGTA 59.077 36.000 23.60 23.60 0.00 3.57
1638 1747 3.793465 GCATTTACGTACGTACTCCCTCC 60.793 52.174 26.83 8.79 0.00 4.30
1640 1749 0.821517 TACGTACGTACTCCCTCCGA 59.178 55.000 23.60 0.00 0.00 4.55
1641 1750 0.179000 ACGTACGTACTCCCTCCGAT 59.821 55.000 21.41 0.00 0.00 4.18
1643 1752 1.233919 GTACGTACTCCCTCCGATCC 58.766 60.000 18.47 0.00 0.00 3.36
1644 1753 0.839277 TACGTACTCCCTCCGATCCA 59.161 55.000 0.00 0.00 0.00 3.41
1649 1758 4.263639 ACGTACTCCCTCCGATCCATAATA 60.264 45.833 0.00 0.00 0.00 0.98
1650 1759 4.703575 CGTACTCCCTCCGATCCATAATAA 59.296 45.833 0.00 0.00 0.00 1.40
1651 1760 5.163642 CGTACTCCCTCCGATCCATAATAAG 60.164 48.000 0.00 0.00 0.00 1.73
1652 1761 4.753186 ACTCCCTCCGATCCATAATAAGT 58.247 43.478 0.00 0.00 0.00 2.24
1654 1763 4.489737 TCCCTCCGATCCATAATAAGTGT 58.510 43.478 0.00 0.00 0.00 3.55
1658 1767 4.866921 TCCGATCCATAATAAGTGTCGTG 58.133 43.478 0.00 0.00 0.00 4.35
1659 1768 3.987868 CCGATCCATAATAAGTGTCGTGG 59.012 47.826 0.00 0.00 0.00 4.94
1662 1771 5.522460 CGATCCATAATAAGTGTCGTGGTTT 59.478 40.000 0.00 0.00 0.00 3.27
1663 1772 6.036735 CGATCCATAATAAGTGTCGTGGTTTT 59.963 38.462 0.00 0.00 0.00 2.43
1664 1773 6.489127 TCCATAATAAGTGTCGTGGTTTTG 57.511 37.500 0.00 0.00 0.00 2.44
1665 1774 6.231951 TCCATAATAAGTGTCGTGGTTTTGA 58.768 36.000 0.00 0.00 0.00 2.69
1666 1775 6.711194 TCCATAATAAGTGTCGTGGTTTTGAA 59.289 34.615 0.00 0.00 0.00 2.69
1667 1776 6.799925 CCATAATAAGTGTCGTGGTTTTGAAC 59.200 38.462 0.00 0.00 0.00 3.18
1668 1777 7.308348 CCATAATAAGTGTCGTGGTTTTGAACT 60.308 37.037 0.00 0.00 0.00 3.01
1671 1780 5.479716 AAGTGTCGTGGTTTTGAACTAAG 57.520 39.130 0.00 0.00 0.00 2.18
1672 1781 3.875134 AGTGTCGTGGTTTTGAACTAAGG 59.125 43.478 0.00 0.00 0.00 2.69
1674 1783 4.095334 GTGTCGTGGTTTTGAACTAAGGTT 59.905 41.667 0.00 0.00 38.52 3.50
1675 1784 4.095185 TGTCGTGGTTTTGAACTAAGGTTG 59.905 41.667 0.00 0.00 35.58 3.77
1676 1785 3.628487 TCGTGGTTTTGAACTAAGGTTGG 59.372 43.478 0.00 0.00 35.58 3.77
1677 1786 3.628487 CGTGGTTTTGAACTAAGGTTGGA 59.372 43.478 0.00 0.00 35.58 3.53
1678 1787 4.277423 CGTGGTTTTGAACTAAGGTTGGAT 59.723 41.667 0.00 0.00 35.58 3.41
1679 1788 5.221165 CGTGGTTTTGAACTAAGGTTGGATT 60.221 40.000 0.00 0.00 35.58 3.01
1680 1789 6.016943 CGTGGTTTTGAACTAAGGTTGGATTA 60.017 38.462 0.00 0.00 35.58 1.75
1682 1791 7.865889 GTGGTTTTGAACTAAGGTTGGATTAAG 59.134 37.037 0.00 0.00 35.58 1.85
1683 1792 6.866770 GGTTTTGAACTAAGGTTGGATTAAGC 59.133 38.462 0.00 0.00 35.58 3.09
1694 1803 6.779860 AGGTTGGATTAAGCTTAGTTCAGAA 58.220 36.000 9.66 4.77 44.32 3.02
1695 1804 6.655425 AGGTTGGATTAAGCTTAGTTCAGAAC 59.345 38.462 9.66 5.00 44.32 3.01
1696 1805 6.127980 GGTTGGATTAAGCTTAGTTCAGAACC 60.128 42.308 20.98 20.98 34.01 3.62
1697 1806 5.175859 TGGATTAAGCTTAGTTCAGAACCG 58.824 41.667 9.85 0.46 0.00 4.44
1698 1807 4.034163 GGATTAAGCTTAGTTCAGAACCGC 59.966 45.833 9.85 10.16 0.00 5.68
1700 1809 0.601558 AGCTTAGTTCAGAACCGCGA 59.398 50.000 8.23 0.00 0.00 5.87
1701 1810 0.714439 GCTTAGTTCAGAACCGCGAC 59.286 55.000 8.23 0.00 0.00 5.19
1702 1811 1.933500 GCTTAGTTCAGAACCGCGACA 60.934 52.381 8.23 0.00 0.00 4.35
1703 1812 1.719780 CTTAGTTCAGAACCGCGACAC 59.280 52.381 8.23 0.00 0.00 3.67
1704 1813 0.956633 TAGTTCAGAACCGCGACACT 59.043 50.000 8.23 0.00 0.00 3.55
1705 1814 0.104304 AGTTCAGAACCGCGACACTT 59.896 50.000 8.23 0.00 0.00 3.16
1707 1816 2.029290 AGTTCAGAACCGCGACACTTAT 60.029 45.455 8.23 0.00 0.00 1.73
1708 1817 2.735134 GTTCAGAACCGCGACACTTATT 59.265 45.455 8.23 0.00 0.00 1.40
1709 1818 3.034721 TCAGAACCGCGACACTTATTT 57.965 42.857 8.23 0.00 0.00 1.40
1711 1820 3.185594 TCAGAACCGCGACACTTATTTTG 59.814 43.478 8.23 0.00 0.00 2.44
1712 1821 2.482721 AGAACCGCGACACTTATTTTGG 59.517 45.455 8.23 0.00 0.00 3.28
1715 1870 2.676342 ACCGCGACACTTATTTTGGATC 59.324 45.455 8.23 0.00 0.00 3.36
1719 1874 4.578601 GCGACACTTATTTTGGATCGAAG 58.421 43.478 0.00 0.00 0.00 3.79
1723 1878 4.941873 ACACTTATTTTGGATCGAAGGGAC 59.058 41.667 0.00 0.00 0.00 4.46
1745 1900 4.948621 ACGGAGTACTAAATAGCAGTGTCT 59.051 41.667 0.00 0.00 41.94 3.41
1746 1901 5.418209 ACGGAGTACTAAATAGCAGTGTCTT 59.582 40.000 0.00 0.00 41.94 3.01
1747 1902 6.071503 ACGGAGTACTAAATAGCAGTGTCTTT 60.072 38.462 0.00 0.00 41.94 2.52
1748 1903 7.121759 ACGGAGTACTAAATAGCAGTGTCTTTA 59.878 37.037 0.00 0.00 41.94 1.85
1749 1904 7.431668 CGGAGTACTAAATAGCAGTGTCTTTAC 59.568 40.741 0.00 0.00 0.00 2.01
1750 1905 8.248945 GGAGTACTAAATAGCAGTGTCTTTACA 58.751 37.037 0.00 0.00 0.00 2.41
1751 1906 9.635520 GAGTACTAAATAGCAGTGTCTTTACAA 57.364 33.333 0.00 0.00 37.36 2.41
1754 1909 8.186178 ACTAAATAGCAGTGTCTTTACAATCG 57.814 34.615 0.00 0.00 37.36 3.34
1756 1911 6.408858 AATAGCAGTGTCTTTACAATCGTG 57.591 37.500 0.00 0.00 37.36 4.35
1757 1912 3.728845 AGCAGTGTCTTTACAATCGTGT 58.271 40.909 0.00 0.00 42.09 4.49
1758 1913 4.878439 AGCAGTGTCTTTACAATCGTGTA 58.122 39.130 0.00 0.00 39.30 2.90
1763 1919 6.419710 CAGTGTCTTTACAATCGTGTAGTTGA 59.580 38.462 0.00 0.00 41.25 3.18
1764 1920 6.641314 AGTGTCTTTACAATCGTGTAGTTGAG 59.359 38.462 0.00 0.00 41.25 3.02
1766 1922 7.592533 GTGTCTTTACAATCGTGTAGTTGAGTA 59.407 37.037 0.00 0.00 41.25 2.59
1773 1929 6.827251 ACAATCGTGTAGTTGAGTAGGATCTA 59.173 38.462 0.00 0.00 35.72 1.98
1778 1934 8.188799 TCGTGTAGTTGAGTAGGATCTAAAATG 58.811 37.037 0.00 0.00 0.00 2.32
1783 1939 7.271511 AGTTGAGTAGGATCTAAAATGCTGAG 58.728 38.462 0.00 0.00 0.00 3.35
1787 1943 7.070447 TGAGTAGGATCTAAAATGCTGAGATGT 59.930 37.037 0.00 0.00 30.01 3.06
1789 1945 6.939132 AGGATCTAAAATGCTGAGATGTTG 57.061 37.500 0.00 0.00 30.01 3.33
1793 1949 5.702865 TCTAAAATGCTGAGATGTTGTTGC 58.297 37.500 0.00 0.00 0.00 4.17
1798 1954 2.291465 TGCTGAGATGTTGTTGCTGTTC 59.709 45.455 0.00 0.00 0.00 3.18
1799 1955 2.551459 GCTGAGATGTTGTTGCTGTTCT 59.449 45.455 0.00 0.00 0.00 3.01
1800 1956 3.004106 GCTGAGATGTTGTTGCTGTTCTT 59.996 43.478 0.00 0.00 0.00 2.52
1801 1957 4.781071 CTGAGATGTTGTTGCTGTTCTTC 58.219 43.478 0.00 0.00 0.00 2.87
1802 1958 4.454678 TGAGATGTTGTTGCTGTTCTTCT 58.545 39.130 0.00 0.00 0.00 2.85
1803 1959 4.883585 TGAGATGTTGTTGCTGTTCTTCTT 59.116 37.500 0.00 0.00 0.00 2.52
1804 1960 5.357878 TGAGATGTTGTTGCTGTTCTTCTTT 59.642 36.000 0.00 0.00 0.00 2.52
1805 1961 6.127647 TGAGATGTTGTTGCTGTTCTTCTTTT 60.128 34.615 0.00 0.00 0.00 2.27
1806 1962 6.633856 AGATGTTGTTGCTGTTCTTCTTTTT 58.366 32.000 0.00 0.00 0.00 1.94
1807 1963 6.753744 AGATGTTGTTGCTGTTCTTCTTTTTC 59.246 34.615 0.00 0.00 0.00 2.29
1808 1964 6.024552 TGTTGTTGCTGTTCTTCTTTTTCT 57.975 33.333 0.00 0.00 0.00 2.52
1809 1965 6.454795 TGTTGTTGCTGTTCTTCTTTTTCTT 58.545 32.000 0.00 0.00 0.00 2.52
1876 2038 4.396166 GTGATATCTTGTGGTTGTTGGAGG 59.604 45.833 3.98 0.00 0.00 4.30
1889 2051 4.224105 GGAGGGCTCCCATCTAGG 57.776 66.667 7.82 0.00 43.94 3.02
1901 2063 5.570205 TCCCATCTAGGAGTAGTAGAGTG 57.430 47.826 0.00 0.00 41.22 3.51
1922 2084 6.696411 AGTGGTATCTGCTGATCTATAAAGC 58.304 40.000 9.62 2.07 37.46 3.51
1923 2085 6.268617 AGTGGTATCTGCTGATCTATAAAGCA 59.731 38.462 9.62 4.65 44.36 3.91
1929 2094 5.859205 TGCTGATCTATAAAGCAGAGTCA 57.141 39.130 0.00 0.00 41.83 3.41
1930 2095 6.416631 TGCTGATCTATAAAGCAGAGTCAT 57.583 37.500 0.00 0.00 41.83 3.06
1964 2133 2.107950 TGCTTAATCAACCCCGTGAG 57.892 50.000 0.00 0.00 0.00 3.51
1965 2134 0.733150 GCTTAATCAACCCCGTGAGC 59.267 55.000 0.00 0.00 0.00 4.26
1966 2135 1.006832 CTTAATCAACCCCGTGAGCG 58.993 55.000 0.00 0.00 37.95 5.03
1995 2164 5.587443 AGGTGTTAATTACTTAATCACGGGC 59.413 40.000 0.00 0.00 33.91 6.13
2026 2195 2.551071 CGCCTCCTCTCCTTTTTCTTGT 60.551 50.000 0.00 0.00 0.00 3.16
2042 2211 9.487790 CTTTTTCTTGTAAATATTTTGGGAGCA 57.512 29.630 5.91 0.00 0.00 4.26
2058 2229 4.195416 GGGAGCAATCTTTTTCGAGAGAT 58.805 43.478 3.13 3.13 41.60 2.75
2063 2234 4.633565 GCAATCTTTTTCGAGAGATGGACT 59.366 41.667 11.82 0.00 41.60 3.85
2065 2236 4.193826 TCTTTTTCGAGAGATGGACTGG 57.806 45.455 0.00 0.00 41.60 4.00
2085 2256 2.554032 GGCTGAAGCAAAGCAGAGTAAA 59.446 45.455 4.43 0.00 42.69 2.01
2086 2257 3.192212 GGCTGAAGCAAAGCAGAGTAAAT 59.808 43.478 4.43 0.00 42.69 1.40
2116 2598 0.325933 AATGTCTGCAGCTGGCTGTA 59.674 50.000 21.34 16.92 45.24 2.74
2120 2602 1.153489 CTGCAGCTGGCTGTACGAT 60.153 57.895 21.34 0.00 45.24 3.73
2129 2611 6.676943 GCAGCTGGCTGTACGATTTTATTTTA 60.677 38.462 21.34 0.00 45.24 1.52
2131 2613 8.556194 CAGCTGGCTGTACGATTTTATTTTATA 58.444 33.333 13.76 0.00 39.10 0.98
2132 2614 9.284968 AGCTGGCTGTACGATTTTATTTTATAT 57.715 29.630 0.00 0.00 0.00 0.86
2133 2615 9.893305 GCTGGCTGTACGATTTTATTTTATATT 57.107 29.630 0.00 0.00 0.00 1.28
2168 2650 4.087892 AGCTGGGCTGGCTGTACG 62.088 66.667 0.00 0.00 37.57 3.67
2169 2651 4.394712 GCTGGGCTGGCTGTACGT 62.395 66.667 0.00 0.00 0.00 3.57
2170 2652 2.434884 CTGGGCTGGCTGTACGTG 60.435 66.667 0.00 0.00 0.00 4.49
2171 2653 3.958147 CTGGGCTGGCTGTACGTGG 62.958 68.421 0.00 0.00 0.00 4.94
2179 2661 1.670083 GCTGTACGTGGGTTGGGTC 60.670 63.158 0.00 0.00 0.00 4.46
2180 2662 1.373748 CTGTACGTGGGTTGGGTCG 60.374 63.158 0.00 0.00 0.00 4.79
2181 2663 2.739671 GTACGTGGGTTGGGTCGC 60.740 66.667 0.00 0.00 0.00 5.19
2204 2686 4.899239 CAGCGATGTCCCCGGAGC 62.899 72.222 0.73 0.00 0.00 4.70
2229 2726 1.511305 CGCAGGACGTACAGGTGAT 59.489 57.895 0.00 0.00 36.87 3.06
2260 2759 3.680786 TCGGTGGTGGACTCGCAG 61.681 66.667 0.00 0.00 0.00 5.18
2266 2765 1.293498 GGTGGACTCGCAGACACAT 59.707 57.895 0.00 0.00 35.62 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 1.679977 GCAGCAGCAGATTCCCCAA 60.680 57.895 0.00 0.00 41.58 4.12
138 139 1.580059 TGTCCCCTACCATTGGACTC 58.420 55.000 10.37 0.00 46.97 3.36
143 144 3.669939 AGGAAATGTCCCCTACCATTG 57.330 47.619 0.00 0.00 46.30 2.82
179 180 6.715280 ACACAAGTTATCTGTTCATCCATCT 58.285 36.000 0.00 0.00 0.00 2.90
180 181 6.820656 AGACACAAGTTATCTGTTCATCCATC 59.179 38.462 0.00 0.00 0.00 3.51
183 184 9.817809 TTATAGACACAAGTTATCTGTTCATCC 57.182 33.333 0.00 0.00 0.00 3.51
190 191 9.751542 CCTTAGGTTATAGACACAAGTTATCTG 57.248 37.037 0.00 0.00 0.00 2.90
208 237 1.615262 GAGCCCCATGCCTTAGGTT 59.385 57.895 0.00 0.00 42.71 3.50
355 388 0.486879 AAGGAAACCAATGGCCCTGA 59.513 50.000 0.00 0.00 0.00 3.86
389 422 1.450312 GCCGTCATGTTAGCCTGCT 60.450 57.895 0.00 0.00 0.00 4.24
409 442 2.743928 GTGGCAGCAAGTCCTCCG 60.744 66.667 0.00 0.00 0.00 4.63
538 587 8.950210 CAGGTGCTAAGATTTCTGAGAATAAAA 58.050 33.333 0.00 0.00 0.00 1.52
539 588 7.066284 GCAGGTGCTAAGATTTCTGAGAATAAA 59.934 37.037 0.00 0.00 38.21 1.40
541 590 6.051717 GCAGGTGCTAAGATTTCTGAGAATA 58.948 40.000 0.00 0.00 38.21 1.75
542 591 4.880696 GCAGGTGCTAAGATTTCTGAGAAT 59.119 41.667 0.00 0.00 38.21 2.40
573 630 3.452627 GTCCATGGACTTGGTGATCTAGT 59.547 47.826 33.47 0.00 41.57 2.57
595 652 6.853720 TCTTTAGTATCTTCCAAGTGTCTCG 58.146 40.000 0.00 0.00 0.00 4.04
597 654 7.891183 TCTCTCTTTAGTATCTTCCAAGTGTCT 59.109 37.037 0.00 0.00 0.00 3.41
797 864 7.045416 TGACTACATGGTATGGTAATGTGTTC 58.955 38.462 0.00 0.00 36.08 3.18
881 953 6.091441 CAGGTAACAAGAAATAGACACTGAGC 59.909 42.308 0.00 0.00 41.41 4.26
885 957 6.827727 ACACAGGTAACAAGAAATAGACACT 58.172 36.000 0.00 0.00 41.41 3.55
1059 1141 3.434319 GGCAGGTGTGACATGGCG 61.434 66.667 0.00 0.00 44.93 5.69
1128 1213 1.712977 GCTGGCCTTTGATGAGCTCG 61.713 60.000 9.64 0.00 0.00 5.03
1161 1246 3.033659 TCTTGAGTAGGGGAGATGGTC 57.966 52.381 0.00 0.00 0.00 4.02
1291 1376 2.338620 CTCGTGACCCTGCGTTGA 59.661 61.111 0.00 0.00 0.00 3.18
1292 1377 2.507110 ATCCTCGTGACCCTGCGTTG 62.507 60.000 0.00 0.00 0.00 4.10
1293 1378 2.227089 GATCCTCGTGACCCTGCGTT 62.227 60.000 0.00 0.00 0.00 4.84
1294 1379 2.680352 ATCCTCGTGACCCTGCGT 60.680 61.111 0.00 0.00 0.00 5.24
1295 1380 2.105128 GATCCTCGTGACCCTGCG 59.895 66.667 0.00 0.00 0.00 5.18
1296 1381 2.105128 CGATCCTCGTGACCCTGC 59.895 66.667 0.00 0.00 34.72 4.85
1305 1390 1.371022 CTGATGCCGACGATCCTCG 60.371 63.158 7.09 7.09 46.93 4.63
1306 1391 1.663074 GCTGATGCCGACGATCCTC 60.663 63.158 0.00 0.00 0.00 3.71
1307 1392 2.081425 GAGCTGATGCCGACGATCCT 62.081 60.000 0.00 0.00 40.80 3.24
1317 1402 1.596477 GATCCACCGGAGCTGATGC 60.596 63.158 9.46 0.00 34.95 3.91
1472 1572 7.605309 CACAGGTATTGATGAGCATACATACAT 59.395 37.037 11.01 0.00 0.00 2.29
1476 1576 5.311265 CCACAGGTATTGATGAGCATACAT 58.689 41.667 0.00 0.00 0.00 2.29
1480 1580 2.750807 GCCCACAGGTATTGATGAGCAT 60.751 50.000 0.00 0.00 34.57 3.79
1481 1581 1.408683 GCCCACAGGTATTGATGAGCA 60.409 52.381 0.00 0.00 34.57 4.26
1482 1582 1.133976 AGCCCACAGGTATTGATGAGC 60.134 52.381 0.00 0.00 34.57 4.26
1483 1583 2.092753 ACAGCCCACAGGTATTGATGAG 60.093 50.000 0.00 0.00 34.57 2.90
1495 1595 1.748500 CACACACACACAGCCCACA 60.749 57.895 0.00 0.00 0.00 4.17
1496 1596 1.748879 ACACACACACACAGCCCAC 60.749 57.895 0.00 0.00 0.00 4.61
1497 1597 1.748500 CACACACACACACAGCCCA 60.749 57.895 0.00 0.00 0.00 5.36
1498 1598 2.480610 CCACACACACACACAGCCC 61.481 63.158 0.00 0.00 0.00 5.19
1499 1599 3.110139 CCACACACACACACAGCC 58.890 61.111 0.00 0.00 0.00 4.85
1500 1600 2.051804 GAGCCACACACACACACAGC 62.052 60.000 0.00 0.00 0.00 4.40
1501 1601 1.439353 GGAGCCACACACACACACAG 61.439 60.000 0.00 0.00 0.00 3.66
1502 1602 1.451207 GGAGCCACACACACACACA 60.451 57.895 0.00 0.00 0.00 3.72
1503 1603 2.186826 GGGAGCCACACACACACAC 61.187 63.158 0.00 0.00 0.00 3.82
1504 1604 2.191908 GGGAGCCACACACACACA 59.808 61.111 0.00 0.00 0.00 3.72
1505 1605 1.598130 GAGGGAGCCACACACACAC 60.598 63.158 0.00 0.00 0.00 3.82
1506 1606 2.818169 GGAGGGAGCCACACACACA 61.818 63.158 0.00 0.00 0.00 3.72
1507 1607 2.032681 GGAGGGAGCCACACACAC 59.967 66.667 0.00 0.00 0.00 3.82
1508 1608 3.249189 GGGAGGGAGCCACACACA 61.249 66.667 0.00 0.00 0.00 3.72
1509 1609 2.930562 AGGGAGGGAGCCACACAC 60.931 66.667 0.00 0.00 0.00 3.82
1510 1610 2.607750 GAGGGAGGGAGCCACACA 60.608 66.667 0.00 0.00 0.00 3.72
1511 1611 3.403558 GGAGGGAGGGAGCCACAC 61.404 72.222 0.00 0.00 0.00 3.82
1512 1612 2.788230 AATGGAGGGAGGGAGCCACA 62.788 60.000 0.00 0.00 32.42 4.17
1541 1650 2.173356 AGGGCTGTAGCTAATCATGCAA 59.827 45.455 0.00 0.00 41.70 4.08
1555 1664 1.202533 GCATATGTACACGAGGGCTGT 60.203 52.381 0.00 0.00 0.00 4.40
1556 1665 1.202521 TGCATATGTACACGAGGGCTG 60.203 52.381 0.00 0.00 0.00 4.85
1558 1667 1.202533 ACTGCATATGTACACGAGGGC 60.203 52.381 0.00 0.00 0.00 5.19
1560 1669 3.436700 TCACTGCATATGTACACGAGG 57.563 47.619 0.00 0.00 0.00 4.63
1563 1672 5.234972 ACATCAATCACTGCATATGTACACG 59.765 40.000 0.00 0.00 0.00 4.49
1569 1678 3.305131 GGCCACATCAATCACTGCATATG 60.305 47.826 0.00 0.00 0.00 1.78
1588 1697 0.451783 CAAACTATCACGCCTTGGCC 59.548 55.000 6.02 0.00 0.00 5.36
1589 1698 1.165270 ACAAACTATCACGCCTTGGC 58.835 50.000 0.75 0.75 0.00 4.52
1591 1700 2.552315 ACCAACAAACTATCACGCCTTG 59.448 45.455 0.00 0.00 0.00 3.61
1595 1704 4.156182 GCTTAACCAACAAACTATCACGC 58.844 43.478 0.00 0.00 0.00 5.34
1597 1706 9.124807 GTAAATGCTTAACCAACAAACTATCAC 57.875 33.333 0.00 0.00 0.00 3.06
1601 1710 7.261829 ACGTAAATGCTTAACCAACAAACTA 57.738 32.000 0.00 0.00 0.00 2.24
1604 1713 6.134730 CGTACGTAAATGCTTAACCAACAAA 58.865 36.000 7.22 0.00 0.00 2.83
1613 1722 4.640201 AGGGAGTACGTACGTAAATGCTTA 59.360 41.667 28.34 4.30 31.86 3.09
1614 1723 3.445096 AGGGAGTACGTACGTAAATGCTT 59.555 43.478 28.34 18.32 31.86 3.91
1624 1733 1.233919 GGATCGGAGGGAGTACGTAC 58.766 60.000 18.10 18.10 0.00 3.67
1626 1735 0.185416 ATGGATCGGAGGGAGTACGT 59.815 55.000 0.00 0.00 0.00 3.57
1628 1737 5.715753 ACTTATTATGGATCGGAGGGAGTAC 59.284 44.000 0.00 0.00 0.00 2.73
1630 1739 4.528596 CACTTATTATGGATCGGAGGGAGT 59.471 45.833 0.00 0.00 0.00 3.85
1638 1747 4.617959 ACCACGACACTTATTATGGATCG 58.382 43.478 0.00 0.00 0.00 3.69
1640 1749 6.882140 TCAAAACCACGACACTTATTATGGAT 59.118 34.615 0.00 0.00 0.00 3.41
1641 1750 6.231951 TCAAAACCACGACACTTATTATGGA 58.768 36.000 0.00 0.00 0.00 3.41
1643 1752 7.581476 AGTTCAAAACCACGACACTTATTATG 58.419 34.615 0.00 0.00 0.00 1.90
1644 1753 7.739498 AGTTCAAAACCACGACACTTATTAT 57.261 32.000 0.00 0.00 0.00 1.28
1649 1758 4.334481 CCTTAGTTCAAAACCACGACACTT 59.666 41.667 0.00 0.00 0.00 3.16
1650 1759 3.875134 CCTTAGTTCAAAACCACGACACT 59.125 43.478 0.00 0.00 0.00 3.55
1651 1760 3.624410 ACCTTAGTTCAAAACCACGACAC 59.376 43.478 0.00 0.00 0.00 3.67
1652 1761 3.876341 ACCTTAGTTCAAAACCACGACA 58.124 40.909 0.00 0.00 0.00 4.35
1654 1763 3.628487 CCAACCTTAGTTCAAAACCACGA 59.372 43.478 0.00 0.00 32.45 4.35
1658 1767 6.866770 GCTTAATCCAACCTTAGTTCAAAACC 59.133 38.462 0.00 0.00 32.45 3.27
1659 1768 7.658261 AGCTTAATCCAACCTTAGTTCAAAAC 58.342 34.615 0.00 0.00 32.45 2.43
1662 1771 8.161425 ACTAAGCTTAATCCAACCTTAGTTCAA 58.839 33.333 7.74 0.00 40.44 2.69
1663 1772 7.686434 ACTAAGCTTAATCCAACCTTAGTTCA 58.314 34.615 7.74 0.00 40.44 3.18
1664 1773 8.563123 AACTAAGCTTAATCCAACCTTAGTTC 57.437 34.615 14.77 0.00 44.77 3.01
1666 1775 7.686434 TGAACTAAGCTTAATCCAACCTTAGT 58.314 34.615 7.74 5.75 43.13 2.24
1667 1776 8.041323 TCTGAACTAAGCTTAATCCAACCTTAG 58.959 37.037 7.74 0.00 37.98 2.18
1668 1777 7.913789 TCTGAACTAAGCTTAATCCAACCTTA 58.086 34.615 7.74 0.00 0.00 2.69
1671 1780 6.127980 GGTTCTGAACTAAGCTTAATCCAACC 60.128 42.308 19.05 20.48 0.00 3.77
1672 1781 6.402226 CGGTTCTGAACTAAGCTTAATCCAAC 60.402 42.308 19.05 12.56 0.00 3.77
1674 1783 5.175859 CGGTTCTGAACTAAGCTTAATCCA 58.824 41.667 19.05 4.68 0.00 3.41
1675 1784 4.034163 GCGGTTCTGAACTAAGCTTAATCC 59.966 45.833 19.05 0.00 0.00 3.01
1676 1785 4.259850 CGCGGTTCTGAACTAAGCTTAATC 60.260 45.833 19.05 9.43 0.00 1.75
1677 1786 3.617263 CGCGGTTCTGAACTAAGCTTAAT 59.383 43.478 19.05 0.00 0.00 1.40
1678 1787 2.991190 CGCGGTTCTGAACTAAGCTTAA 59.009 45.455 19.05 0.00 0.00 1.85
1679 1788 2.229543 TCGCGGTTCTGAACTAAGCTTA 59.770 45.455 19.05 5.94 0.00 3.09
1680 1789 1.000506 TCGCGGTTCTGAACTAAGCTT 59.999 47.619 19.05 3.48 0.00 3.74
1682 1791 0.714439 GTCGCGGTTCTGAACTAAGC 59.286 55.000 19.05 18.81 0.00 3.09
1683 1792 1.719780 GTGTCGCGGTTCTGAACTAAG 59.280 52.381 19.05 12.16 0.00 2.18
1684 1793 1.338973 AGTGTCGCGGTTCTGAACTAA 59.661 47.619 19.05 1.37 0.00 2.24
1685 1794 0.956633 AGTGTCGCGGTTCTGAACTA 59.043 50.000 19.05 1.67 0.00 2.24
1687 1796 1.774639 TAAGTGTCGCGGTTCTGAAC 58.225 50.000 12.05 12.05 0.00 3.18
1688 1797 2.736144 ATAAGTGTCGCGGTTCTGAA 57.264 45.000 6.13 0.00 0.00 3.02
1690 1799 3.479006 CAAAATAAGTGTCGCGGTTCTG 58.521 45.455 6.13 0.00 0.00 3.02
1691 1800 2.482721 CCAAAATAAGTGTCGCGGTTCT 59.517 45.455 6.13 0.00 0.00 3.01
1692 1801 2.481185 TCCAAAATAAGTGTCGCGGTTC 59.519 45.455 6.13 0.00 0.00 3.62
1694 1803 2.172851 TCCAAAATAAGTGTCGCGGT 57.827 45.000 6.13 0.00 0.00 5.68
1695 1804 2.285602 CGATCCAAAATAAGTGTCGCGG 60.286 50.000 6.13 0.00 0.00 6.46
1696 1805 2.601314 TCGATCCAAAATAAGTGTCGCG 59.399 45.455 0.00 0.00 0.00 5.87
1697 1806 4.494199 CCTTCGATCCAAAATAAGTGTCGC 60.494 45.833 0.00 0.00 0.00 5.19
1698 1807 4.034048 CCCTTCGATCCAAAATAAGTGTCG 59.966 45.833 0.00 0.00 0.00 4.35
1700 1809 4.941873 GTCCCTTCGATCCAAAATAAGTGT 59.058 41.667 0.00 0.00 0.00 3.55
1701 1810 4.034048 CGTCCCTTCGATCCAAAATAAGTG 59.966 45.833 0.00 0.00 0.00 3.16
1702 1811 4.189231 CGTCCCTTCGATCCAAAATAAGT 58.811 43.478 0.00 0.00 0.00 2.24
1703 1812 3.560068 CCGTCCCTTCGATCCAAAATAAG 59.440 47.826 0.00 0.00 0.00 1.73
1704 1813 3.198200 TCCGTCCCTTCGATCCAAAATAA 59.802 43.478 0.00 0.00 0.00 1.40
1705 1814 2.767394 TCCGTCCCTTCGATCCAAAATA 59.233 45.455 0.00 0.00 0.00 1.40
1707 1816 0.978151 TCCGTCCCTTCGATCCAAAA 59.022 50.000 0.00 0.00 0.00 2.44
1708 1817 0.535335 CTCCGTCCCTTCGATCCAAA 59.465 55.000 0.00 0.00 0.00 3.28
1709 1818 0.613853 ACTCCGTCCCTTCGATCCAA 60.614 55.000 0.00 0.00 0.00 3.53
1711 1820 0.667453 GTACTCCGTCCCTTCGATCC 59.333 60.000 0.00 0.00 0.00 3.36
1712 1821 1.677942 AGTACTCCGTCCCTTCGATC 58.322 55.000 0.00 0.00 0.00 3.69
1715 1870 4.556302 GCTATTTAGTACTCCGTCCCTTCG 60.556 50.000 0.00 0.00 0.00 3.79
1719 1874 3.635836 ACTGCTATTTAGTACTCCGTCCC 59.364 47.826 0.00 0.00 0.00 4.46
1723 1878 5.502153 AGACACTGCTATTTAGTACTCCG 57.498 43.478 0.00 0.00 0.00 4.63
1730 1885 8.110612 CACGATTGTAAAGACACTGCTATTTAG 58.889 37.037 0.00 0.00 34.48 1.85
1733 1888 5.932303 ACACGATTGTAAAGACACTGCTATT 59.068 36.000 0.00 0.00 34.48 1.73
1738 1893 6.419710 TCAACTACACGATTGTAAAGACACTG 59.580 38.462 0.00 0.00 37.77 3.66
1741 1896 6.509656 ACTCAACTACACGATTGTAAAGACA 58.490 36.000 0.00 0.00 37.77 3.41
1743 1898 7.175467 TCCTACTCAACTACACGATTGTAAAGA 59.825 37.037 0.00 0.00 37.77 2.52
1745 1900 7.218228 TCCTACTCAACTACACGATTGTAAA 57.782 36.000 0.00 0.00 37.77 2.01
1746 1901 6.822667 TCCTACTCAACTACACGATTGTAA 57.177 37.500 0.00 0.00 37.77 2.41
1747 1902 6.827251 AGATCCTACTCAACTACACGATTGTA 59.173 38.462 0.00 0.00 37.15 2.41
1748 1903 5.652891 AGATCCTACTCAACTACACGATTGT 59.347 40.000 0.00 0.00 40.02 2.71
1749 1904 6.137794 AGATCCTACTCAACTACACGATTG 57.862 41.667 0.00 0.00 0.00 2.67
1750 1905 7.876936 TTAGATCCTACTCAACTACACGATT 57.123 36.000 0.00 0.00 0.00 3.34
1751 1906 7.876936 TTTAGATCCTACTCAACTACACGAT 57.123 36.000 0.00 0.00 0.00 3.73
1753 1908 7.043325 GCATTTTAGATCCTACTCAACTACACG 60.043 40.741 0.00 0.00 0.00 4.49
1754 1909 7.982354 AGCATTTTAGATCCTACTCAACTACAC 59.018 37.037 0.00 0.00 0.00 2.90
1756 1911 8.198109 TCAGCATTTTAGATCCTACTCAACTAC 58.802 37.037 0.00 0.00 0.00 2.73
1757 1912 8.306313 TCAGCATTTTAGATCCTACTCAACTA 57.694 34.615 0.00 0.00 0.00 2.24
1758 1913 7.124901 TCTCAGCATTTTAGATCCTACTCAACT 59.875 37.037 0.00 0.00 0.00 3.16
1763 1919 7.372260 ACATCTCAGCATTTTAGATCCTACT 57.628 36.000 0.00 0.00 0.00 2.57
1764 1920 7.497249 ACAACATCTCAGCATTTTAGATCCTAC 59.503 37.037 0.00 0.00 0.00 3.18
1766 1922 6.421485 ACAACATCTCAGCATTTTAGATCCT 58.579 36.000 0.00 0.00 0.00 3.24
1773 1929 4.202182 ACAGCAACAACATCTCAGCATTTT 60.202 37.500 0.00 0.00 0.00 1.82
1778 1934 2.551459 AGAACAGCAACAACATCTCAGC 59.449 45.455 0.00 0.00 0.00 4.26
1783 1939 6.753744 AGAAAAAGAAGAACAGCAACAACATC 59.246 34.615 0.00 0.00 0.00 3.06
1787 1943 7.961325 AAAAGAAAAAGAAGAACAGCAACAA 57.039 28.000 0.00 0.00 0.00 2.83
1814 1970 9.114952 AGCTTACTTAATTTCTTCAGATAAGGC 57.885 33.333 0.00 0.00 0.00 4.35
1850 2006 4.156556 CCAACAACCACAAGATATCACTGG 59.843 45.833 5.32 8.42 0.00 4.00
1851 2007 5.003160 TCCAACAACCACAAGATATCACTG 58.997 41.667 5.32 4.47 0.00 3.66
1852 2008 5.241403 TCCAACAACCACAAGATATCACT 57.759 39.130 5.32 0.00 0.00 3.41
1853 2009 4.396166 CCTCCAACAACCACAAGATATCAC 59.604 45.833 5.32 0.00 0.00 3.06
1854 2010 4.567537 CCCTCCAACAACCACAAGATATCA 60.568 45.833 5.32 0.00 0.00 2.15
1855 2011 3.947834 CCCTCCAACAACCACAAGATATC 59.052 47.826 0.00 0.00 0.00 1.63
1862 2024 1.150536 GAGCCCTCCAACAACCACA 59.849 57.895 0.00 0.00 0.00 4.17
1889 2051 5.369833 TCAGCAGATACCACTCTACTACTC 58.630 45.833 0.00 0.00 0.00 2.59
1891 2053 6.001460 AGATCAGCAGATACCACTCTACTAC 58.999 44.000 0.00 0.00 33.72 2.73
1892 2054 6.194285 AGATCAGCAGATACCACTCTACTA 57.806 41.667 0.00 0.00 33.72 1.82
1893 2055 5.060427 AGATCAGCAGATACCACTCTACT 57.940 43.478 0.00 0.00 33.72 2.57
1894 2056 8.568676 TTATAGATCAGCAGATACCACTCTAC 57.431 38.462 0.00 0.00 33.72 2.59
1895 2057 9.237187 CTTTATAGATCAGCAGATACCACTCTA 57.763 37.037 0.00 0.00 33.72 2.43
1896 2058 7.309744 GCTTTATAGATCAGCAGATACCACTCT 60.310 40.741 0.00 0.00 33.72 3.24
1897 2059 6.811170 GCTTTATAGATCAGCAGATACCACTC 59.189 42.308 0.00 0.00 33.72 3.51
1898 2060 6.268617 TGCTTTATAGATCAGCAGATACCACT 59.731 38.462 0.77 0.00 38.65 4.00
1899 2061 6.459066 TGCTTTATAGATCAGCAGATACCAC 58.541 40.000 0.77 0.00 38.65 4.16
1900 2062 6.670695 TGCTTTATAGATCAGCAGATACCA 57.329 37.500 0.77 0.00 38.65 3.25
1922 2084 4.850822 ATGCGCCTCATGACTCTG 57.149 55.556 4.18 0.00 33.26 3.35
1929 2094 1.731700 GCATTCACATGCGCCTCAT 59.268 52.632 4.18 0.00 46.45 2.90
1930 2095 3.189921 GCATTCACATGCGCCTCA 58.810 55.556 4.18 0.00 46.45 3.86
1964 2133 2.629051 AGTAATTAACACCTGCTCCGC 58.371 47.619 0.00 0.00 0.00 5.54
1965 2134 6.537301 TGATTAAGTAATTAACACCTGCTCCG 59.463 38.462 0.00 0.00 0.00 4.63
1966 2135 7.465513 CGTGATTAAGTAATTAACACCTGCTCC 60.466 40.741 15.87 0.00 0.00 4.70
1967 2136 7.399523 CGTGATTAAGTAATTAACACCTGCTC 58.600 38.462 15.87 4.17 0.00 4.26
1968 2137 6.315393 CCGTGATTAAGTAATTAACACCTGCT 59.685 38.462 15.87 0.00 0.00 4.24
1969 2138 6.457799 CCCGTGATTAAGTAATTAACACCTGC 60.458 42.308 15.87 0.00 0.00 4.85
2026 2195 9.364989 CGAAAAAGATTGCTCCCAAAATATTTA 57.635 29.630 0.01 0.00 34.05 1.40
2034 2203 3.750371 TCTCGAAAAAGATTGCTCCCAA 58.250 40.909 0.00 0.00 35.01 4.12
2037 2206 4.034975 CCATCTCTCGAAAAAGATTGCTCC 59.965 45.833 2.71 0.00 29.77 4.70
2038 2207 4.872691 TCCATCTCTCGAAAAAGATTGCTC 59.127 41.667 2.71 0.00 29.77 4.26
2039 2208 4.633565 GTCCATCTCTCGAAAAAGATTGCT 59.366 41.667 2.71 0.00 29.77 3.91
2042 2211 5.181748 CCAGTCCATCTCTCGAAAAAGATT 58.818 41.667 2.71 0.00 29.77 2.40
2050 2219 0.034089 TCAGCCAGTCCATCTCTCGA 60.034 55.000 0.00 0.00 0.00 4.04
2051 2220 0.820226 TTCAGCCAGTCCATCTCTCG 59.180 55.000 0.00 0.00 0.00 4.04
2058 2229 1.174712 GCTTTGCTTCAGCCAGTCCA 61.175 55.000 0.00 0.00 41.18 4.02
2063 2234 0.179009 ACTCTGCTTTGCTTCAGCCA 60.179 50.000 0.00 0.00 41.18 4.75
2065 2236 3.904136 TTTACTCTGCTTTGCTTCAGC 57.096 42.857 0.00 0.00 42.50 4.26
2085 2256 9.754382 CCAGCTGCAGACATTTTATTTATTTAT 57.246 29.630 20.43 0.00 0.00 1.40
2086 2257 7.706179 GCCAGCTGCAGACATTTTATTTATTTA 59.294 33.333 20.43 0.00 40.77 1.40
2129 2611 9.603921 CAGCTGAATCACCCAAAAATTAAATAT 57.396 29.630 8.42 0.00 0.00 1.28
2131 2613 6.880529 CCAGCTGAATCACCCAAAAATTAAAT 59.119 34.615 17.39 0.00 0.00 1.40
2132 2614 6.229733 CCAGCTGAATCACCCAAAAATTAAA 58.770 36.000 17.39 0.00 0.00 1.52
2133 2615 5.279910 CCCAGCTGAATCACCCAAAAATTAA 60.280 40.000 17.39 0.00 0.00 1.40
2134 2616 4.222588 CCCAGCTGAATCACCCAAAAATTA 59.777 41.667 17.39 0.00 0.00 1.40
2135 2617 3.008266 CCCAGCTGAATCACCCAAAAATT 59.992 43.478 17.39 0.00 0.00 1.82
2136 2618 2.568509 CCCAGCTGAATCACCCAAAAAT 59.431 45.455 17.39 0.00 0.00 1.82
2137 2619 1.969923 CCCAGCTGAATCACCCAAAAA 59.030 47.619 17.39 0.00 0.00 1.94
2138 2620 1.631405 CCCAGCTGAATCACCCAAAA 58.369 50.000 17.39 0.00 0.00 2.44
2139 2621 0.899717 GCCCAGCTGAATCACCCAAA 60.900 55.000 17.39 0.00 0.00 3.28
2140 2622 1.304381 GCCCAGCTGAATCACCCAA 60.304 57.895 17.39 0.00 0.00 4.12
2141 2623 2.233566 AGCCCAGCTGAATCACCCA 61.234 57.895 17.39 0.00 37.57 4.51
2171 2653 4.612412 TGACACGGCGACCCAACC 62.612 66.667 16.62 0.00 0.00 3.77
2180 2662 3.188786 GGACATCGCTGACACGGC 61.189 66.667 0.00 0.00 0.00 5.68
2181 2663 2.509336 GGGACATCGCTGACACGG 60.509 66.667 0.00 0.00 0.00 4.94
2205 2687 4.849329 GTACGTCCTGCGGCTCCG 62.849 72.222 3.56 3.56 46.52 4.63
2206 2688 3.701604 CTGTACGTCCTGCGGCTCC 62.702 68.421 0.00 0.00 46.52 4.70
2207 2689 2.202623 CTGTACGTCCTGCGGCTC 60.203 66.667 0.00 0.00 46.52 4.70
2208 2690 3.760035 CCTGTACGTCCTGCGGCT 61.760 66.667 0.00 0.00 46.52 5.52
2210 2692 1.945354 ATCACCTGTACGTCCTGCGG 61.945 60.000 0.00 0.00 46.52 5.69
2213 2695 2.758979 ACCTAATCACCTGTACGTCCTG 59.241 50.000 0.00 0.00 0.00 3.86
2215 2697 2.756760 TCACCTAATCACCTGTACGTCC 59.243 50.000 0.00 0.00 0.00 4.79
2229 2726 1.531365 ACCGACCACCGTCACCTAA 60.531 57.895 0.00 0.00 39.11 2.69


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

AutoCloner maintained by Alex Coulton.