Multiple sequence alignment - TraesCS6D01G305600

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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 TraesCS6D01G305600 chr6D 100.000 3683 0 0 1 3683 414463882 414467564 0 6802
1 TraesCS6D01G305600 chr6A 85.747 1747 146 47 1 1707 559400473 559402156 0 1751
2 TraesCS6D01G305600 chr6A 87.828 953 66 18 2192 3129 559402181 559403098 0 1072
3 TraesCS6D01G305600 chr6A 92.522 575 27 6 3113 3678 559403115 559403682 0 809
4 TraesCS6D01G305600 chr6B 84.090 1653 122 60 130 1709 624780494 624782078 0 1465
5 TraesCS6D01G305600 chr6B 87.689 1259 77 31 2460 3675 624785067 624786290 0 1395
6 TraesCS6D01G305600 chr6B 84.190 759 56 28 1753 2476 624784323 624785052 0 678


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 TraesCS6D01G305600 chr6D 414463882 414467564 3682 False 6802.000000 6802 100.000 1 3683 1 chr6D.!!$F1 3682
1 TraesCS6D01G305600 chr6A 559400473 559403682 3209 False 1210.666667 1751 88.699 1 3678 3 chr6A.!!$F1 3677
2 TraesCS6D01G305600 chr6B 624780494 624786290 5796 False 1179.333333 1465 85.323 130 3675 3 chr6B.!!$F1 3545

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
56 57 0.098728 CCGTGGGATTTCGATTGTGC 59.901 55.0 0.0 0.0 0.00 4.57 F
1863 4167 0.038744 ACTGCTTGGTGCTTGCCTAT 59.961 50.0 0.0 0.0 43.37 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 4261 0.03438 ACTAGCAGGTCGTAGCTGGA 60.034 55.0 13.39 0.0 43.49 3.86 R
3518 5973 0.46546 CAGACTCCTCCTCCTCCTCG 60.465 65.0 0.00 0.0 0.00 4.63 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
23 24 4.278956 ACGAAAGTGTGGGATCGC 57.721 55.556 2.14 2.14 46.97 4.58
25 26 2.452813 CGAAAGTGTGGGATCGCCG 61.453 63.158 7.38 0.00 33.83 6.46
26 27 2.046314 AAAGTGTGGGATCGCCGG 60.046 61.111 7.38 0.00 33.83 6.13
38 39 4.570663 CGCCGGATCGTCTCCACC 62.571 72.222 5.05 0.00 45.24 4.61
48 49 0.739813 CGTCTCCACCGTGGGATTTC 60.740 60.000 17.76 3.90 38.32 2.17
52 53 0.616371 TCCACCGTGGGATTTCGATT 59.384 50.000 17.76 0.00 38.32 3.34
56 57 0.098728 CCGTGGGATTTCGATTGTGC 59.901 55.000 0.00 0.00 0.00 4.57
63 64 3.191371 GGGATTTCGATTGTGCTGTCTTT 59.809 43.478 0.00 0.00 0.00 2.52
72 73 1.016653 GTGCTGTCTTTCTCTCGCCC 61.017 60.000 0.00 0.00 0.00 6.13
73 74 1.448717 GCTGTCTTTCTCTCGCCCC 60.449 63.158 0.00 0.00 0.00 5.80
87 88 2.892425 CCCCGCGCTCAATGACTC 60.892 66.667 5.56 0.00 0.00 3.36
103 104 2.032528 TCCGCTCAGCTTTGGGTG 59.967 61.111 0.00 0.00 41.77 4.61
107 108 1.294659 CGCTCAGCTTTGGGTGACTC 61.295 60.000 0.00 0.00 43.82 3.36
112 113 0.905357 AGCTTTGGGTGACTCGCTAT 59.095 50.000 0.00 0.00 0.00 2.97
144 145 2.095567 GTGTGCATGATTTTCAGCTCGT 60.096 45.455 0.00 0.00 0.00 4.18
162 163 4.380233 GCTCGTGTGGCTAAACTTCTACTA 60.380 45.833 0.00 0.00 0.00 1.82
166 167 6.810182 TCGTGTGGCTAAACTTCTACTATTTC 59.190 38.462 0.00 0.00 0.00 2.17
244 254 1.785208 AGGCCTGGATCTATTGGCAAT 59.215 47.619 18.01 18.01 46.53 3.56
314 324 0.463474 GTCATCCTCTTGGCTGCTCC 60.463 60.000 0.00 0.00 30.03 4.70
336 346 3.115892 GGCCGCGATCGTTGAACA 61.116 61.111 17.81 0.00 0.00 3.18
347 357 3.226346 TCGTTGAACAGGACCTTATCG 57.774 47.619 0.00 0.00 0.00 2.92
349 359 3.256383 TCGTTGAACAGGACCTTATCGAA 59.744 43.478 0.00 0.00 0.00 3.71
399 409 1.081892 CCGAGAACATTGACCTGCTG 58.918 55.000 0.00 0.00 0.00 4.41
417 431 2.039084 GCTGGACGGGATCATTTCCTAT 59.961 50.000 0.00 0.00 44.75 2.57
419 433 4.822026 CTGGACGGGATCATTTCCTATAC 58.178 47.826 0.00 0.00 44.75 1.47
420 434 3.257375 TGGACGGGATCATTTCCTATACG 59.743 47.826 0.00 0.00 44.75 3.06
421 435 3.368116 GGACGGGATCATTTCCTATACGG 60.368 52.174 0.00 0.00 44.75 4.02
422 436 2.028385 ACGGGATCATTTCCTATACGGC 60.028 50.000 0.00 0.00 44.75 5.68
423 437 2.233922 CGGGATCATTTCCTATACGGCT 59.766 50.000 0.00 0.00 44.75 5.52
530 544 2.351336 GAATCCCGATCGACCACGCT 62.351 60.000 18.66 0.00 39.58 5.07
551 565 2.370445 AACAGGATCCAGAGCCCCG 61.370 63.158 15.82 0.00 37.67 5.73
592 606 2.578786 CATGCATGATGGGCAGAAGTA 58.421 47.619 22.59 0.00 45.68 2.24
624 643 3.837146 ACTCCATGCCATAGATCCTACAG 59.163 47.826 0.00 0.00 0.00 2.74
625 644 2.568956 TCCATGCCATAGATCCTACAGC 59.431 50.000 0.00 0.00 0.00 4.40
626 645 2.303890 CCATGCCATAGATCCTACAGCA 59.696 50.000 0.00 0.00 0.00 4.41
627 646 3.332919 CATGCCATAGATCCTACAGCAC 58.667 50.000 0.00 0.00 0.00 4.40
628 647 2.397597 TGCCATAGATCCTACAGCACA 58.602 47.619 0.00 0.00 0.00 4.57
629 648 2.974794 TGCCATAGATCCTACAGCACAT 59.025 45.455 0.00 0.00 0.00 3.21
638 657 6.240894 AGATCCTACAGCACATTTTTCTGAA 58.759 36.000 0.00 0.00 0.00 3.02
646 665 5.987347 CAGCACATTTTTCTGAAATCTTGGT 59.013 36.000 3.31 2.73 0.00 3.67
649 668 6.258507 GCACATTTTTCTGAAATCTTGGTGTT 59.741 34.615 3.31 0.00 0.00 3.32
653 672 8.881743 CATTTTTCTGAAATCTTGGTGTTTGAA 58.118 29.630 3.31 0.00 0.00 2.69
658 677 6.376864 TCTGAAATCTTGGTGTTTGAACTGAA 59.623 34.615 0.00 0.00 0.00 3.02
665 684 3.256879 TGGTGTTTGAACTGAACTTTGCA 59.743 39.130 0.00 0.00 0.00 4.08
667 686 4.688413 GGTGTTTGAACTGAACTTTGCAAA 59.312 37.500 12.14 12.14 0.00 3.68
669 688 4.384247 TGTTTGAACTGAACTTTGCAAACG 59.616 37.500 8.05 7.39 44.65 3.60
670 689 3.840890 TGAACTGAACTTTGCAAACGT 57.159 38.095 8.05 8.04 0.00 3.99
671 690 3.753842 TGAACTGAACTTTGCAAACGTC 58.246 40.909 8.05 8.93 0.00 4.34
672 691 3.189495 TGAACTGAACTTTGCAAACGTCA 59.811 39.130 8.05 12.97 0.00 4.35
692 717 5.266242 GTCATCACTGACTGTCAAACAAAC 58.734 41.667 12.16 3.07 46.84 2.93
701 726 6.436261 TGACTGTCAAACAAACAAACGTTTA 58.564 32.000 14.20 0.00 34.82 2.01
704 729 4.615961 TGTCAAACAAACAAACGTTTACGG 59.384 37.500 14.20 4.17 44.95 4.02
758 783 1.092921 GGCCACCAATTATCGTCGCA 61.093 55.000 0.00 0.00 0.00 5.10
769 794 4.470170 CGTCGCACATCGGACGGA 62.470 66.667 5.73 0.00 37.74 4.69
819 855 0.249120 ATGGATCCGTGTCGCTTTCA 59.751 50.000 5.41 0.00 0.00 2.69
890 926 1.109920 TGATGCTCCTCGCCCTCTAC 61.110 60.000 0.00 0.00 38.05 2.59
893 929 1.323271 TGCTCCTCGCCCTCTACAAG 61.323 60.000 0.00 0.00 38.05 3.16
933 981 3.268603 CTTCCACACGCGCACACA 61.269 61.111 5.73 0.00 0.00 3.72
1059 1122 1.915769 AGAGCAGAACGAGGGCCTT 60.916 57.895 7.89 0.00 0.00 4.35
1100 1169 3.201494 GCTCTGCGCTAGTCTGGA 58.799 61.111 9.73 0.00 35.14 3.86
1120 1189 2.360439 CTACGGGGAGGAGGAGGAGG 62.360 70.000 0.00 0.00 0.00 4.30
1121 1190 2.870597 TACGGGGAGGAGGAGGAGGA 62.871 65.000 0.00 0.00 0.00 3.71
1122 1191 2.612251 GGGGAGGAGGAGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
1123 1192 2.612251 GGGAGGAGGAGGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
1124 1193 2.015726 GGGAGGAGGAGGAGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
1125 1194 1.541672 GGAGGAGGAGGAGGAGGAG 59.458 68.421 0.00 0.00 0.00 3.69
1129 1198 1.585651 GGAGGAGGAGGAGGAGGTGA 61.586 65.000 0.00 0.00 0.00 4.02
1135 1204 1.304217 GAGGAGGAGGTGACACGGA 60.304 63.158 0.00 0.00 0.00 4.69
1164 1233 1.503542 GCTCAACTTCGGCATGGTG 59.496 57.895 0.00 0.00 0.00 4.17
1264 1333 1.001248 TGAGTCCCCTTCCCTACCG 59.999 63.158 0.00 0.00 0.00 4.02
1265 1334 1.001376 GAGTCCCCTTCCCTACCGT 59.999 63.158 0.00 0.00 0.00 4.83
1268 1337 1.045350 GTCCCCTTCCCTACCGTACC 61.045 65.000 0.00 0.00 0.00 3.34
1280 1349 0.808453 ACCGTACCATGCCGAAATCG 60.808 55.000 0.00 0.00 39.44 3.34
1282 1351 1.003851 CGTACCATGCCGAAATCGTT 58.996 50.000 1.79 0.00 37.74 3.85
1299 1368 4.992740 TGGCCACCATGCACCCAC 62.993 66.667 0.00 0.00 0.00 4.61
1311 1380 0.246635 GCACCCACGCTTCTCTCTTA 59.753 55.000 0.00 0.00 0.00 2.10
1313 1382 2.544685 CACCCACGCTTCTCTCTTATG 58.455 52.381 0.00 0.00 0.00 1.90
1314 1383 2.093973 CACCCACGCTTCTCTCTTATGT 60.094 50.000 0.00 0.00 0.00 2.29
1315 1384 2.567615 ACCCACGCTTCTCTCTTATGTT 59.432 45.455 0.00 0.00 0.00 2.71
1316 1385 3.190874 CCCACGCTTCTCTCTTATGTTC 58.809 50.000 0.00 0.00 0.00 3.18
1317 1386 3.118956 CCCACGCTTCTCTCTTATGTTCT 60.119 47.826 0.00 0.00 0.00 3.01
1318 1387 4.109050 CCACGCTTCTCTCTTATGTTCTC 58.891 47.826 0.00 0.00 0.00 2.87
1319 1388 4.380973 CCACGCTTCTCTCTTATGTTCTCA 60.381 45.833 0.00 0.00 0.00 3.27
1330 1404 3.723348 GTTCTCAACGCCCCGTGC 61.723 66.667 0.00 0.00 39.99 5.34
1341 1415 4.047059 CCCGTGCTGCTTGCTTGG 62.047 66.667 0.00 5.46 43.37 3.61
1347 1421 1.372623 GCTGCTTGCTTGGTTGCTC 60.373 57.895 0.00 0.00 38.95 4.26
1466 1553 4.082026 AGGTATGAACAATTCAGCCTTTGC 60.082 41.667 10.09 0.00 42.53 3.68
1521 1608 1.669502 GCATCGACCTGCATTTTTGCA 60.670 47.619 6.13 0.23 41.87 4.08
1523 1610 3.734597 GCATCGACCTGCATTTTTGCATA 60.735 43.478 6.13 0.00 44.47 3.14
1525 1612 5.761003 CATCGACCTGCATTTTTGCATATA 58.239 37.500 0.53 0.00 44.47 0.86
1526 1613 5.826601 TCGACCTGCATTTTTGCATATAA 57.173 34.783 0.53 0.00 44.47 0.98
1527 1614 6.201226 TCGACCTGCATTTTTGCATATAAA 57.799 33.333 0.53 0.00 44.47 1.40
1528 1615 6.033341 TCGACCTGCATTTTTGCATATAAAC 58.967 36.000 0.53 0.00 44.47 2.01
1548 1653 2.283298 CGTGGCAGCAGTAAATGATCT 58.717 47.619 0.00 0.00 0.00 2.75
1551 1656 4.418392 GTGGCAGCAGTAAATGATCTTTG 58.582 43.478 0.00 0.00 0.00 2.77
1553 1658 3.696051 GGCAGCAGTAAATGATCTTTGGA 59.304 43.478 0.00 0.00 0.00 3.53
1569 1674 1.847328 TGGATTCAGAGTAGCCGTGA 58.153 50.000 0.00 0.00 0.00 4.35
1586 1691 1.812922 GAGCTGTGGCGTGGATGAG 60.813 63.158 0.00 0.00 44.37 2.90
1587 1692 3.503363 GCTGTGGCGTGGATGAGC 61.503 66.667 0.00 0.00 0.00 4.26
1589 1694 1.450848 CTGTGGCGTGGATGAGCAT 60.451 57.895 0.00 0.00 34.54 3.79
1590 1695 1.712018 CTGTGGCGTGGATGAGCATG 61.712 60.000 0.00 0.00 34.54 4.06
1591 1696 2.825387 TGGCGTGGATGAGCATGC 60.825 61.111 10.51 10.51 34.54 4.06
1592 1697 3.589881 GGCGTGGATGAGCATGCC 61.590 66.667 15.66 6.65 44.87 4.40
1593 1698 2.825387 GCGTGGATGAGCATGCCA 60.825 61.111 15.66 12.73 0.00 4.92
1626 1731 4.459337 GCATTTGCCTTTTCTACCACTACT 59.541 41.667 0.00 0.00 34.31 2.57
1627 1732 5.646360 GCATTTGCCTTTTCTACCACTACTA 59.354 40.000 0.00 0.00 34.31 1.82
1703 1808 6.367422 CCAGTCTCTTTCATGAGAAACAGTAC 59.633 42.308 0.00 0.00 43.68 2.73
1707 1812 9.593134 GTCTCTTTCATGAGAAACAGTACATAT 57.407 33.333 0.00 0.00 43.68 1.78
1712 1817 9.476202 TTTCATGAGAAACAGTACATATATCCG 57.524 33.333 0.00 0.00 38.76 4.18
1714 1819 8.297426 TCATGAGAAACAGTACATATATCCGAC 58.703 37.037 0.00 0.00 0.00 4.79
1715 1820 6.978338 TGAGAAACAGTACATATATCCGACC 58.022 40.000 0.00 0.00 0.00 4.79
1716 1821 6.548251 TGAGAAACAGTACATATATCCGACCA 59.452 38.462 0.00 0.00 0.00 4.02
1718 1823 6.550108 AGAAACAGTACATATATCCGACCACT 59.450 38.462 0.00 0.00 0.00 4.00
1719 1824 6.726490 AACAGTACATATATCCGACCACTT 57.274 37.500 0.00 0.00 0.00 3.16
1720 1825 6.726490 ACAGTACATATATCCGACCACTTT 57.274 37.500 0.00 0.00 0.00 2.66
1721 1826 6.746120 ACAGTACATATATCCGACCACTTTC 58.254 40.000 0.00 0.00 0.00 2.62
1722 1827 6.322969 ACAGTACATATATCCGACCACTTTCA 59.677 38.462 0.00 0.00 0.00 2.69
1723 1828 6.641314 CAGTACATATATCCGACCACTTTCAC 59.359 42.308 0.00 0.00 0.00 3.18
1724 1829 5.871396 ACATATATCCGACCACTTTCACT 57.129 39.130 0.00 0.00 0.00 3.41
1732 2912 2.878406 CGACCACTTTCACTTCCATGTT 59.122 45.455 0.00 0.00 0.00 2.71
1738 2918 5.221501 CCACTTTCACTTCCATGTTTTCCAT 60.222 40.000 0.00 0.00 0.00 3.41
1739 2919 5.922544 CACTTTCACTTCCATGTTTTCCATC 59.077 40.000 0.00 0.00 0.00 3.51
1740 2920 5.598005 ACTTTCACTTCCATGTTTTCCATCA 59.402 36.000 0.00 0.00 0.00 3.07
1741 2921 5.710513 TTCACTTCCATGTTTTCCATCAG 57.289 39.130 0.00 0.00 0.00 2.90
1742 2922 4.984295 TCACTTCCATGTTTTCCATCAGA 58.016 39.130 0.00 0.00 0.00 3.27
1746 2926 2.041485 TCCATGTTTTCCATCAGAGGCA 59.959 45.455 0.00 0.00 0.00 4.75
1747 2927 3.028850 CCATGTTTTCCATCAGAGGCAT 58.971 45.455 0.00 0.00 0.00 4.40
1749 2929 4.646040 CCATGTTTTCCATCAGAGGCATTA 59.354 41.667 0.00 0.00 0.00 1.90
1750 2930 5.450965 CCATGTTTTCCATCAGAGGCATTAC 60.451 44.000 0.00 0.00 0.00 1.89
1751 2931 4.661222 TGTTTTCCATCAGAGGCATTACA 58.339 39.130 0.00 0.00 0.00 2.41
1752 2932 5.263599 TGTTTTCCATCAGAGGCATTACAT 58.736 37.500 0.00 0.00 0.00 2.29
1753 2933 5.125900 TGTTTTCCATCAGAGGCATTACATG 59.874 40.000 0.00 0.00 0.00 3.21
1754 2934 4.776435 TTCCATCAGAGGCATTACATGA 57.224 40.909 0.00 0.00 0.00 3.07
1755 2935 4.987963 TCCATCAGAGGCATTACATGAT 57.012 40.909 0.00 0.00 0.00 2.45
1756 2936 4.903054 TCCATCAGAGGCATTACATGATC 58.097 43.478 0.00 0.00 0.00 2.92
1757 2937 3.683340 CCATCAGAGGCATTACATGATCG 59.317 47.826 0.00 0.00 0.00 3.69
1766 4070 3.721035 CATTACATGATCGACCAGCTCA 58.279 45.455 0.00 0.00 0.00 4.26
1773 4077 2.003301 GATCGACCAGCTCACCTTTTC 58.997 52.381 0.00 0.00 0.00 2.29
1788 4092 1.474077 CTTTTCACCTGCCATGCTACC 59.526 52.381 0.00 0.00 0.00 3.18
1799 4103 2.553904 GCCATGCTACCCTCTGCATTAT 60.554 50.000 0.00 0.00 46.29 1.28
1801 4105 3.504906 CCATGCTACCCTCTGCATTATTG 59.495 47.826 0.00 0.00 46.29 1.90
1823 4127 7.889589 TTGCTATATACATGTCTGCATACAC 57.110 36.000 7.12 0.00 33.30 2.90
1824 4128 6.991938 TGCTATATACATGTCTGCATACACA 58.008 36.000 7.12 1.32 33.30 3.72
1832 4136 5.712004 CATGTCTGCATACACATGGAAAAA 58.288 37.500 19.06 0.00 44.19 1.94
1833 4137 5.119931 TGTCTGCATACACATGGAAAAAC 57.880 39.130 0.00 0.00 31.42 2.43
1840 4144 5.708948 CATACACATGGAAAAACGGATGTT 58.291 37.500 0.00 0.00 40.98 2.71
1841 4145 3.976169 ACACATGGAAAAACGGATGTTG 58.024 40.909 0.00 0.00 38.62 3.33
1842 4146 2.730928 CACATGGAAAAACGGATGTTGC 59.269 45.455 0.00 0.00 38.62 4.17
1843 4147 2.627699 ACATGGAAAAACGGATGTTGCT 59.372 40.909 0.00 0.00 38.62 3.91
1844 4148 3.823873 ACATGGAAAAACGGATGTTGCTA 59.176 39.130 0.00 0.00 38.62 3.49
1845 4149 3.907894 TGGAAAAACGGATGTTGCTAC 57.092 42.857 0.00 0.00 38.62 3.58
1846 4150 3.482436 TGGAAAAACGGATGTTGCTACT 58.518 40.909 0.00 0.00 38.62 2.57
1847 4151 3.252215 TGGAAAAACGGATGTTGCTACTG 59.748 43.478 0.00 0.00 38.62 2.74
1848 4152 2.989422 AAAACGGATGTTGCTACTGC 57.011 45.000 0.00 0.00 38.62 4.40
1849 4153 2.185004 AAACGGATGTTGCTACTGCT 57.815 45.000 0.00 0.00 38.62 4.24
1850 4154 2.185004 AACGGATGTTGCTACTGCTT 57.815 45.000 0.00 0.00 36.81 3.91
1851 4155 1.442769 ACGGATGTTGCTACTGCTTG 58.557 50.000 0.00 0.00 40.48 4.01
1852 4156 0.729116 CGGATGTTGCTACTGCTTGG 59.271 55.000 0.00 0.00 40.48 3.61
1853 4157 1.826385 GGATGTTGCTACTGCTTGGT 58.174 50.000 0.00 0.00 40.48 3.67
1854 4158 1.470098 GGATGTTGCTACTGCTTGGTG 59.530 52.381 0.00 0.00 40.48 4.17
1855 4159 0.883833 ATGTTGCTACTGCTTGGTGC 59.116 50.000 0.00 0.00 40.48 5.01
1856 4160 0.179020 TGTTGCTACTGCTTGGTGCT 60.179 50.000 0.00 0.00 43.37 4.40
1857 4161 0.954452 GTTGCTACTGCTTGGTGCTT 59.046 50.000 0.00 0.00 43.37 3.91
1858 4162 0.953727 TTGCTACTGCTTGGTGCTTG 59.046 50.000 0.00 0.00 43.37 4.01
1859 4163 1.211190 GCTACTGCTTGGTGCTTGC 59.789 57.895 0.00 0.00 43.37 4.01
1860 4164 1.878775 CTACTGCTTGGTGCTTGCC 59.121 57.895 0.00 0.00 43.37 4.52
1861 4165 0.607489 CTACTGCTTGGTGCTTGCCT 60.607 55.000 0.00 0.00 43.37 4.75
1862 4166 0.690192 TACTGCTTGGTGCTTGCCTA 59.310 50.000 0.00 0.00 43.37 3.93
1863 4167 0.038744 ACTGCTTGGTGCTTGCCTAT 59.961 50.000 0.00 0.00 43.37 2.57
1867 4171 2.173356 TGCTTGGTGCTTGCCTATCTAT 59.827 45.455 0.00 0.00 43.37 1.98
1869 4173 3.495806 GCTTGGTGCTTGCCTATCTATCT 60.496 47.826 0.00 0.00 38.95 1.98
1881 4185 4.740695 GCCTATCTATCTTCACGTGTCAAC 59.259 45.833 16.51 0.00 0.00 3.18
1889 4193 3.067601 TCTTCACGTGTCAACAGCTCTAA 59.932 43.478 16.51 0.00 0.00 2.10
1890 4194 3.446310 TCACGTGTCAACAGCTCTAAA 57.554 42.857 16.51 0.00 0.00 1.85
1893 4197 4.447724 TCACGTGTCAACAGCTCTAAATTC 59.552 41.667 16.51 0.00 0.00 2.17
1900 4204 7.010923 GTGTCAACAGCTCTAAATTCTATCTGG 59.989 40.741 0.00 0.00 0.00 3.86
1905 4209 8.719645 ACAGCTCTAAATTCTATCTGGTATCT 57.280 34.615 0.00 0.00 0.00 1.98
1952 4256 4.161565 ACATATTCCACTGTCGGCTCTTTA 59.838 41.667 0.00 0.00 0.00 1.85
1957 4261 2.093973 CCACTGTCGGCTCTTTACTCAT 60.094 50.000 0.00 0.00 0.00 2.90
1959 4263 2.166664 ACTGTCGGCTCTTTACTCATCC 59.833 50.000 0.00 0.00 0.00 3.51
1965 4269 3.723260 GGCTCTTTACTCATCCAGCTAC 58.277 50.000 0.00 0.00 0.00 3.58
1968 4272 4.602995 CTCTTTACTCATCCAGCTACGAC 58.397 47.826 0.00 0.00 0.00 4.34
1985 4289 2.492484 ACGACCTGCTAGTTAGTGGAAG 59.508 50.000 0.00 4.24 0.00 3.46
1988 4292 1.834263 CCTGCTAGTTAGTGGAAGGCT 59.166 52.381 0.00 0.00 0.00 4.58
2056 4360 2.223226 TGTCGGCGATTAACAATGCATG 60.223 45.455 14.79 0.00 0.00 4.06
2058 4362 1.533547 CGGCGATTAACAATGCATGCA 60.534 47.619 25.04 25.04 0.00 3.96
2059 4363 2.746269 GGCGATTAACAATGCATGCAT 58.254 42.857 27.46 27.46 38.46 3.96
2062 4366 3.551454 GCGATTAACAATGCATGCATCCT 60.551 43.478 32.25 20.89 35.31 3.24
2063 4367 4.320421 GCGATTAACAATGCATGCATCCTA 60.320 41.667 32.25 19.93 35.31 2.94
2064 4368 5.620654 GCGATTAACAATGCATGCATCCTAT 60.621 40.000 32.25 19.99 35.31 2.57
2065 4369 5.798434 CGATTAACAATGCATGCATCCTATG 59.202 40.000 32.25 26.79 35.31 2.23
2066 4370 5.456548 TTAACAATGCATGCATCCTATGG 57.543 39.130 32.25 18.81 35.31 2.74
2067 4371 2.953453 ACAATGCATGCATCCTATGGT 58.047 42.857 32.25 19.38 35.31 3.55
2068 4372 2.626266 ACAATGCATGCATCCTATGGTG 59.374 45.455 32.25 25.11 35.31 4.17
2103 4407 8.517878 CAACTTTAGTTCAGAATCATCCATGTT 58.482 33.333 0.00 0.00 35.83 2.71
2129 4433 2.144482 GCAACTGCAATGCAAACTCT 57.856 45.000 9.92 0.00 43.29 3.24
2136 4440 4.098349 ACTGCAATGCAAACTCTCTTTTGA 59.902 37.500 9.92 0.00 38.41 2.69
2147 4452 7.534239 GCAAACTCTCTTTTGAAAACCTATACG 59.466 37.037 0.00 0.00 38.54 3.06
2152 4457 8.475331 TCTCTTTTGAAAACCTATACGATGTC 57.525 34.615 0.00 0.00 0.00 3.06
2164 4469 0.391661 ACGATGTCTGCGAAATGCCT 60.392 50.000 0.00 0.00 45.60 4.75
2190 4504 2.844122 AACTGAAACCTTGTTGCGAC 57.156 45.000 0.00 0.00 0.00 5.19
2312 4629 1.154035 CGAAGGCCGCAAAATCACC 60.154 57.895 0.00 0.00 0.00 4.02
2318 4635 0.814457 GCCGCAAAATCACCCACATA 59.186 50.000 0.00 0.00 0.00 2.29
2322 4639 2.730715 CGCAAAATCACCCACATAACCG 60.731 50.000 0.00 0.00 0.00 4.44
2336 4653 3.865745 ACATAACCGCTTGAAATCTCTCG 59.134 43.478 0.00 0.00 0.00 4.04
2351 4668 8.021973 TGAAATCTCTCGTTCTCTAACTAACAC 58.978 37.037 0.00 0.00 33.15 3.32
2443 4786 3.262842 AGGCCTCCATTGATCATCCATA 58.737 45.455 0.00 0.00 0.00 2.74
2448 4791 6.837568 GGCCTCCATTGATCATCCATATATTT 59.162 38.462 0.00 0.00 0.00 1.40
2476 4850 4.695455 CCCTACACCTCATACAACACTTTG 59.305 45.833 0.00 0.00 38.83 2.77
2505 4879 7.315142 TGAAAATCATAACCATGTGCTTCTTC 58.685 34.615 0.00 0.00 33.57 2.87
2664 5038 0.445436 CGTCAAGCTTGGTGCATCTC 59.555 55.000 25.73 6.27 45.94 2.75
2665 5039 1.818642 GTCAAGCTTGGTGCATCTCT 58.181 50.000 25.73 0.00 45.94 3.10
2673 5047 1.300963 GGTGCATCTCTTGGCCTCA 59.699 57.895 3.32 0.00 0.00 3.86
2715 5093 4.102649 CGTTTTTCGTTTCTCTTTTGGCT 58.897 39.130 0.00 0.00 34.52 4.75
2857 5239 6.214191 TGAGAGATGTACTCCTTGAATGAC 57.786 41.667 0.00 0.00 45.96 3.06
2907 5289 7.992008 TGTATGACACAATATCGTTACTCTCA 58.008 34.615 0.00 0.00 32.95 3.27
2967 5355 8.428852 TGATAGGATTTCCGAGATGTTATTTCA 58.571 33.333 0.00 0.00 42.08 2.69
3016 5411 7.701539 TTACTGATGCCATTTGACAACTAAT 57.298 32.000 0.00 0.00 0.00 1.73
3031 5426 6.874134 TGACAACTAATTACTTCTCCAGCTTC 59.126 38.462 0.00 0.00 0.00 3.86
3132 5573 5.396213 GGTGAGTCTAGCCAGAAAGATGAAT 60.396 44.000 0.00 0.00 30.85 2.57
3143 5584 5.359756 CAGAAAGATGAATGATGGACCGTA 58.640 41.667 0.00 0.00 0.00 4.02
3177 5618 2.036256 AAGTGGACATGGGCCTGC 59.964 61.111 4.53 0.00 0.00 4.85
3194 5640 1.153168 GCTAAGCCCGAATGCCTCA 60.153 57.895 0.00 0.00 0.00 3.86
3245 5691 3.714798 ACGCTGATATTTTCCTTCCCCTA 59.285 43.478 0.00 0.00 0.00 3.53
3548 6009 3.023832 GGAGGAGTCTGAAGAGGAAGAG 58.976 54.545 0.00 0.00 0.00 2.85
3623 6084 1.770324 CCCCAAGAACAAGCCTCCT 59.230 57.895 0.00 0.00 0.00 3.69
3678 6139 0.467290 CGAGGAGGAGGAAGAGGAGG 60.467 65.000 0.00 0.00 0.00 4.30
3679 6140 0.930726 GAGGAGGAGGAAGAGGAGGA 59.069 60.000 0.00 0.00 0.00 3.71
3680 6141 0.933700 AGGAGGAGGAAGAGGAGGAG 59.066 60.000 0.00 0.00 0.00 3.69
3681 6142 0.105709 GGAGGAGGAAGAGGAGGAGG 60.106 65.000 0.00 0.00 0.00 4.30
3682 6143 0.930726 GAGGAGGAAGAGGAGGAGGA 59.069 60.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.392710 ATCCCACGGTGGAGACGATC 61.393 60.000 28.36 0.00 40.96 3.69
33 34 0.616371 AATCGAAATCCCACGGTGGA 59.384 50.000 28.36 14.46 40.96 4.02
38 39 1.086696 AGCACAATCGAAATCCCACG 58.913 50.000 0.00 0.00 0.00 4.94
48 49 2.343843 CGAGAGAAAGACAGCACAATCG 59.656 50.000 0.00 0.00 0.00 3.34
52 53 0.319900 GGCGAGAGAAAGACAGCACA 60.320 55.000 0.00 0.00 0.00 4.57
56 57 1.153745 CGGGGCGAGAGAAAGACAG 60.154 63.158 0.00 0.00 0.00 3.51
72 73 3.257561 CGGAGTCATTGAGCGCGG 61.258 66.667 8.83 0.00 0.00 6.46
73 74 3.918220 GCGGAGTCATTGAGCGCG 61.918 66.667 0.00 0.00 0.00 6.86
77 78 0.175302 AGCTGAGCGGAGTCATTGAG 59.825 55.000 0.00 0.00 0.00 3.02
84 85 2.348998 CCCAAAGCTGAGCGGAGT 59.651 61.111 0.00 0.00 0.00 3.85
86 87 2.032528 CACCCAAAGCTGAGCGGA 59.967 61.111 0.00 0.00 0.00 5.54
87 88 2.032528 TCACCCAAAGCTGAGCGG 59.967 61.111 0.00 0.00 0.00 5.52
103 104 2.484264 ACACCAAGCAAAATAGCGAGTC 59.516 45.455 0.00 0.00 40.15 3.36
107 108 2.318578 CACACACCAAGCAAAATAGCG 58.681 47.619 0.00 0.00 40.15 4.26
112 113 1.479730 TCATGCACACACCAAGCAAAA 59.520 42.857 0.00 0.00 42.15 2.44
174 175 3.307480 CCGGTGACCTAGAAATTCAAGGT 60.307 47.826 0.00 6.13 35.30 3.50
178 179 4.837093 AATCCGGTGACCTAGAAATTCA 57.163 40.909 0.00 0.00 0.00 2.57
221 231 2.024080 TGCCAATAGATCCAGGCCTTTT 60.024 45.455 0.00 0.00 46.45 2.27
325 335 3.797256 CGATAAGGTCCTGTTCAACGATC 59.203 47.826 0.00 0.00 0.00 3.69
347 357 3.129109 AGAACTTCCGGTTTCGTTCTTC 58.871 45.455 17.94 4.76 42.29 2.87
349 359 2.870411 CAAGAACTTCCGGTTTCGTTCT 59.130 45.455 17.94 17.94 45.64 3.01
417 431 1.174712 GGGGAGCACGTATAGCCGTA 61.175 60.000 0.00 0.00 39.45 4.02
419 433 2.338984 GGGGAGCACGTATAGCCG 59.661 66.667 0.00 0.00 0.00 5.52
420 434 2.024590 AACGGGGAGCACGTATAGCC 62.025 60.000 0.00 0.00 44.83 3.93
421 435 0.670162 TAACGGGGAGCACGTATAGC 59.330 55.000 0.00 0.00 44.83 2.97
422 436 1.677576 TGTAACGGGGAGCACGTATAG 59.322 52.381 0.00 0.00 44.83 1.31
423 437 1.405105 GTGTAACGGGGAGCACGTATA 59.595 52.381 0.00 0.00 44.83 1.47
496 510 3.466791 ATTCCGGGCCATCTCGCTG 62.467 63.158 4.39 0.00 0.00 5.18
530 544 1.204146 GGGCTCTGGATCCTGTTGTA 58.796 55.000 14.23 0.00 0.00 2.41
592 606 0.176680 GGCATGGAGTGACACTCGAT 59.823 55.000 25.47 24.23 45.96 3.59
624 643 5.754890 ACACCAAGATTTCAGAAAAATGTGC 59.245 36.000 0.00 0.00 0.00 4.57
625 644 7.775397 AACACCAAGATTTCAGAAAAATGTG 57.225 32.000 0.00 6.33 0.00 3.21
626 645 8.040132 TCAAACACCAAGATTTCAGAAAAATGT 58.960 29.630 0.00 0.00 0.00 2.71
627 646 8.422973 TCAAACACCAAGATTTCAGAAAAATG 57.577 30.769 0.00 0.00 0.00 2.32
628 647 8.882736 GTTCAAACACCAAGATTTCAGAAAAAT 58.117 29.630 0.00 0.00 0.00 1.82
629 648 8.093927 AGTTCAAACACCAAGATTTCAGAAAAA 58.906 29.630 0.00 0.00 0.00 1.94
638 657 6.530019 AAGTTCAGTTCAAACACCAAGATT 57.470 33.333 0.00 0.00 0.00 2.40
646 665 4.384247 CGTTTGCAAAGTTCAGTTCAAACA 59.616 37.500 13.26 0.00 41.69 2.83
649 668 4.162812 GACGTTTGCAAAGTTCAGTTCAA 58.837 39.130 13.26 0.00 0.00 2.69
653 672 3.376859 TGATGACGTTTGCAAAGTTCAGT 59.623 39.130 21.27 13.46 0.00 3.41
658 677 2.942376 TCAGTGATGACGTTTGCAAAGT 59.058 40.909 13.26 12.63 0.00 2.66
665 684 3.452755 TGACAGTCAGTGATGACGTTT 57.547 42.857 0.00 0.00 43.15 3.60
667 686 3.123804 GTTTGACAGTCAGTGATGACGT 58.876 45.455 2.82 0.00 43.15 4.34
669 688 5.163764 TGTTTGTTTGACAGTCAGTGATGAC 60.164 40.000 2.82 0.06 39.00 3.06
670 689 4.940654 TGTTTGTTTGACAGTCAGTGATGA 59.059 37.500 2.82 0.00 0.00 2.92
671 690 5.233957 TGTTTGTTTGACAGTCAGTGATG 57.766 39.130 2.82 0.00 0.00 3.07
672 691 5.895636 TTGTTTGTTTGACAGTCAGTGAT 57.104 34.783 2.82 0.00 0.00 3.06
692 717 1.081708 GGCTGGCCGTAAACGTTTG 60.082 57.895 23.46 8.10 37.74 2.93
704 729 2.107953 GGATGAGACGAGGCTGGC 59.892 66.667 0.00 0.00 0.00 4.85
808 844 5.758924 AGAAATTTTAGGTGAAAGCGACAC 58.241 37.500 0.00 0.00 40.95 3.67
819 855 3.713826 TGGCGAGGAGAAATTTTAGGT 57.286 42.857 0.00 0.00 0.00 3.08
890 926 0.928229 GCGATACGGCAGGTTACTTG 59.072 55.000 0.00 0.00 0.00 3.16
893 929 3.609258 CGCGATACGGCAGGTTAC 58.391 61.111 0.00 0.00 38.44 2.50
933 981 0.598680 GTTGAGTGCGAGAGTGTGCT 60.599 55.000 0.00 0.00 0.00 4.40
935 983 1.135046 CAGTTGAGTGCGAGAGTGTG 58.865 55.000 0.00 0.00 0.00 3.82
1059 1122 2.356278 GGGTGCTTCCATGCCTCA 59.644 61.111 0.00 0.00 38.11 3.86
1100 1169 1.621822 TCCTCCTCCTCCCCGTAGT 60.622 63.158 0.00 0.00 0.00 2.73
1120 1189 1.258445 ACCATCCGTGTCACCTCCTC 61.258 60.000 0.00 0.00 0.00 3.71
1121 1190 1.229209 ACCATCCGTGTCACCTCCT 60.229 57.895 0.00 0.00 0.00 3.69
1122 1191 1.079127 CACCATCCGTGTCACCTCC 60.079 63.158 0.00 0.00 37.73 4.30
1123 1192 1.741770 GCACCATCCGTGTCACCTC 60.742 63.158 0.00 0.00 44.97 3.85
1124 1193 2.347490 GCACCATCCGTGTCACCT 59.653 61.111 0.00 0.00 44.97 4.00
1125 1194 2.746277 GGCACCATCCGTGTCACC 60.746 66.667 0.00 0.00 46.90 4.02
1264 1333 1.063469 CCAACGATTTCGGCATGGTAC 59.937 52.381 4.84 0.00 44.95 3.34
1265 1334 1.374560 CCAACGATTTCGGCATGGTA 58.625 50.000 4.84 0.00 44.95 3.25
1268 1337 4.382728 GCCAACGATTTCGGCATG 57.617 55.556 4.84 0.00 45.52 4.06
1280 1349 3.694538 GGGTGCATGGTGGCCAAC 61.695 66.667 15.99 15.99 36.95 3.77
1282 1351 4.992740 GTGGGTGCATGGTGGCCA 62.993 66.667 0.00 0.00 38.19 5.36
1299 1368 4.264145 CGTTGAGAACATAAGAGAGAAGCG 59.736 45.833 0.00 0.00 0.00 4.68
1300 1369 4.032331 GCGTTGAGAACATAAGAGAGAAGC 59.968 45.833 0.00 0.00 0.00 3.86
1311 1380 1.671054 CACGGGGCGTTGAGAACAT 60.671 57.895 0.00 0.00 38.32 2.71
1313 1382 3.723348 GCACGGGGCGTTGAGAAC 61.723 66.667 0.00 0.00 38.32 3.01
1330 1404 1.288127 GGAGCAACCAAGCAAGCAG 59.712 57.895 0.00 0.00 38.79 4.24
1407 1488 1.066573 CGAAGTGGTGGAGCTTGATCT 60.067 52.381 0.00 0.00 0.00 2.75
1466 1553 0.804989 GTCCTGGGAAATGCACGAAG 59.195 55.000 0.00 0.00 0.00 3.79
1480 1567 4.637771 GATGGTTTCCCCGTCCTG 57.362 61.111 0.00 0.00 42.63 3.86
1488 1575 2.159379 GGTCGATGCAAAGATGGTTTCC 60.159 50.000 0.00 0.00 0.00 3.13
1521 1608 5.820423 TCATTTACTGCTGCCACGTTTATAT 59.180 36.000 0.00 0.00 0.00 0.86
1523 1610 4.006989 TCATTTACTGCTGCCACGTTTAT 58.993 39.130 0.00 0.00 0.00 1.40
1525 1612 2.226330 TCATTTACTGCTGCCACGTTT 58.774 42.857 0.00 0.00 0.00 3.60
1526 1613 1.890876 TCATTTACTGCTGCCACGTT 58.109 45.000 0.00 0.00 0.00 3.99
1527 1614 2.009774 GATCATTTACTGCTGCCACGT 58.990 47.619 0.00 0.00 0.00 4.49
1528 1615 2.283298 AGATCATTTACTGCTGCCACG 58.717 47.619 0.00 0.00 0.00 4.94
1548 1653 2.565391 TCACGGCTACTCTGAATCCAAA 59.435 45.455 0.00 0.00 0.00 3.28
1551 1656 1.537135 GCTCACGGCTACTCTGAATCC 60.537 57.143 0.00 0.00 38.06 3.01
1569 1674 2.267006 CTCATCCACGCCACAGCT 59.733 61.111 0.00 0.00 36.60 4.24
1591 1696 1.010419 GCAAATGCTGCCGAAAGTGG 61.010 55.000 0.00 0.00 46.13 4.00
1592 1697 2.437850 GCAAATGCTGCCGAAAGTG 58.562 52.632 0.00 0.00 46.13 3.16
1593 1698 4.972591 GCAAATGCTGCCGAAAGT 57.027 50.000 0.00 0.00 46.13 2.66
1606 1711 6.429521 AGTAGTAGTGGTAGAAAAGGCAAA 57.570 37.500 0.00 0.00 0.00 3.68
1619 1724 2.084546 GCCCAAGCAAAGTAGTAGTGG 58.915 52.381 0.00 0.00 39.53 4.00
1695 1800 6.726490 AGTGGTCGGATATATGTACTGTTT 57.274 37.500 0.00 0.00 0.00 2.83
1703 1808 5.696724 GGAAGTGAAAGTGGTCGGATATATG 59.303 44.000 0.00 0.00 0.00 1.78
1707 1812 2.901192 TGGAAGTGAAAGTGGTCGGATA 59.099 45.455 0.00 0.00 0.00 2.59
1710 1815 1.806542 CATGGAAGTGAAAGTGGTCGG 59.193 52.381 0.00 0.00 0.00 4.79
1712 1817 4.918810 AAACATGGAAGTGAAAGTGGTC 57.081 40.909 0.00 0.00 0.00 4.02
1714 1819 4.099266 TGGAAAACATGGAAGTGAAAGTGG 59.901 41.667 0.00 0.00 0.00 4.00
1715 1820 5.261209 TGGAAAACATGGAAGTGAAAGTG 57.739 39.130 0.00 0.00 0.00 3.16
1716 1821 5.598005 TGATGGAAAACATGGAAGTGAAAGT 59.402 36.000 0.00 0.00 40.72 2.66
1718 1823 5.832595 TCTGATGGAAAACATGGAAGTGAAA 59.167 36.000 0.00 0.00 40.72 2.69
1719 1824 5.384336 TCTGATGGAAAACATGGAAGTGAA 58.616 37.500 0.00 0.00 40.72 3.18
1720 1825 4.984295 TCTGATGGAAAACATGGAAGTGA 58.016 39.130 0.00 0.00 40.72 3.41
1721 1826 4.157289 CCTCTGATGGAAAACATGGAAGTG 59.843 45.833 0.00 0.00 40.72 3.16
1722 1827 4.338879 CCTCTGATGGAAAACATGGAAGT 58.661 43.478 0.00 0.00 40.72 3.01
1723 1828 3.129988 GCCTCTGATGGAAAACATGGAAG 59.870 47.826 0.00 0.00 40.72 3.46
1724 1829 3.091545 GCCTCTGATGGAAAACATGGAA 58.908 45.455 0.00 0.00 40.72 3.53
1732 2912 5.114764 TCATGTAATGCCTCTGATGGAAA 57.885 39.130 0.00 0.00 46.21 3.13
1738 2918 3.243873 GGTCGATCATGTAATGCCTCTGA 60.244 47.826 0.00 0.00 46.21 3.27
1739 2919 3.062763 GGTCGATCATGTAATGCCTCTG 58.937 50.000 0.00 0.00 46.21 3.35
1740 2920 2.700371 TGGTCGATCATGTAATGCCTCT 59.300 45.455 0.00 0.00 46.21 3.69
1741 2921 3.062763 CTGGTCGATCATGTAATGCCTC 58.937 50.000 0.00 0.00 46.21 4.70
1742 2922 2.808202 GCTGGTCGATCATGTAATGCCT 60.808 50.000 0.00 0.00 46.21 4.75
1746 2926 3.493350 GGTGAGCTGGTCGATCATGTAAT 60.493 47.826 0.00 0.00 40.63 1.89
1747 2927 2.159099 GGTGAGCTGGTCGATCATGTAA 60.159 50.000 0.00 0.00 40.63 2.41
1749 2929 0.176680 GGTGAGCTGGTCGATCATGT 59.823 55.000 0.00 0.00 40.63 3.21
1750 2930 0.463204 AGGTGAGCTGGTCGATCATG 59.537 55.000 0.00 0.00 40.63 3.07
1751 2931 1.198713 AAGGTGAGCTGGTCGATCAT 58.801 50.000 0.00 0.00 40.63 2.45
1752 2932 0.976641 AAAGGTGAGCTGGTCGATCA 59.023 50.000 0.00 0.00 35.28 2.92
1753 2933 2.003301 GAAAAGGTGAGCTGGTCGATC 58.997 52.381 0.00 0.00 0.00 3.69
1754 2934 1.347707 TGAAAAGGTGAGCTGGTCGAT 59.652 47.619 0.00 0.00 0.00 3.59
1755 2935 0.756294 TGAAAAGGTGAGCTGGTCGA 59.244 50.000 0.00 0.00 0.00 4.20
1756 2936 0.868406 GTGAAAAGGTGAGCTGGTCG 59.132 55.000 0.00 0.00 0.00 4.79
1757 2937 1.202818 AGGTGAAAAGGTGAGCTGGTC 60.203 52.381 0.00 0.00 0.00 4.02
1766 4070 0.178953 AGCATGGCAGGTGAAAAGGT 60.179 50.000 0.00 0.00 0.00 3.50
1773 4077 1.153086 GAGGGTAGCATGGCAGGTG 60.153 63.158 0.00 0.00 0.00 4.00
1799 4103 7.441017 TGTGTATGCAGACATGTATATAGCAA 58.559 34.615 18.45 0.00 36.55 3.91
1801 4105 7.903062 CATGTGTATGCAGACATGTATATAGC 58.097 38.462 18.45 1.68 46.33 2.97
1823 4127 3.302365 AGCAACATCCGTTTTTCCATG 57.698 42.857 0.00 0.00 31.13 3.66
1824 4128 4.079253 AGTAGCAACATCCGTTTTTCCAT 58.921 39.130 0.00 0.00 31.13 3.41
1832 4136 1.442769 CAAGCAGTAGCAACATCCGT 58.557 50.000 0.00 0.00 45.49 4.69
1833 4137 0.729116 CCAAGCAGTAGCAACATCCG 59.271 55.000 0.00 0.00 45.49 4.18
1847 4151 2.332063 TAGATAGGCAAGCACCAAGC 57.668 50.000 0.00 0.00 46.19 4.01
1848 4152 4.348863 AGATAGATAGGCAAGCACCAAG 57.651 45.455 0.00 0.00 0.00 3.61
1849 4153 4.164030 TGAAGATAGATAGGCAAGCACCAA 59.836 41.667 0.00 0.00 0.00 3.67
1850 4154 3.711190 TGAAGATAGATAGGCAAGCACCA 59.289 43.478 0.00 0.00 0.00 4.17
1851 4155 4.061596 GTGAAGATAGATAGGCAAGCACC 58.938 47.826 0.00 0.00 0.00 5.01
1852 4156 3.738282 CGTGAAGATAGATAGGCAAGCAC 59.262 47.826 0.00 0.00 0.00 4.40
1853 4157 3.384789 ACGTGAAGATAGATAGGCAAGCA 59.615 43.478 0.00 0.00 0.00 3.91
1854 4158 3.738282 CACGTGAAGATAGATAGGCAAGC 59.262 47.826 10.90 0.00 0.00 4.01
1855 4159 4.938080 ACACGTGAAGATAGATAGGCAAG 58.062 43.478 25.01 0.00 0.00 4.01
1856 4160 4.401202 TGACACGTGAAGATAGATAGGCAA 59.599 41.667 25.01 0.00 0.00 4.52
1857 4161 3.951680 TGACACGTGAAGATAGATAGGCA 59.048 43.478 25.01 0.00 0.00 4.75
1858 4162 4.569761 TGACACGTGAAGATAGATAGGC 57.430 45.455 25.01 0.00 0.00 3.93
1859 4163 5.891451 TGTTGACACGTGAAGATAGATAGG 58.109 41.667 25.01 0.00 0.00 2.57
1860 4164 5.457148 GCTGTTGACACGTGAAGATAGATAG 59.543 44.000 25.01 9.12 0.00 2.08
1861 4165 5.125578 AGCTGTTGACACGTGAAGATAGATA 59.874 40.000 25.01 0.00 0.00 1.98
1862 4166 4.081972 AGCTGTTGACACGTGAAGATAGAT 60.082 41.667 25.01 10.43 0.00 1.98
1863 4167 3.255888 AGCTGTTGACACGTGAAGATAGA 59.744 43.478 25.01 0.33 0.00 1.98
1867 4171 1.409064 AGAGCTGTTGACACGTGAAGA 59.591 47.619 25.01 4.48 0.00 2.87
1869 4173 3.446310 TTAGAGCTGTTGACACGTGAA 57.554 42.857 25.01 7.12 0.00 3.18
1889 4193 7.148641 CGTTGCAGTAGATACCAGATAGAATT 58.851 38.462 0.00 0.00 0.00 2.17
1890 4194 6.294787 CCGTTGCAGTAGATACCAGATAGAAT 60.295 42.308 0.00 0.00 0.00 2.40
1893 4197 4.278669 ACCGTTGCAGTAGATACCAGATAG 59.721 45.833 0.00 0.00 0.00 2.08
1900 4204 3.436496 GAGTCACCGTTGCAGTAGATAC 58.564 50.000 0.00 0.00 0.00 2.24
1905 4209 0.039798 GTCGAGTCACCGTTGCAGTA 60.040 55.000 0.00 0.00 0.00 2.74
1952 4256 1.107114 CAGGTCGTAGCTGGATGAGT 58.893 55.000 0.00 0.00 39.87 3.41
1957 4261 0.034380 ACTAGCAGGTCGTAGCTGGA 60.034 55.000 13.39 0.00 43.49 3.86
1959 4263 2.683867 ACTAACTAGCAGGTCGTAGCTG 59.316 50.000 0.00 8.95 45.86 4.24
1965 4269 2.159226 CCTTCCACTAACTAGCAGGTCG 60.159 54.545 0.00 0.00 0.00 4.79
1968 4272 1.834263 AGCCTTCCACTAACTAGCAGG 59.166 52.381 0.00 0.00 0.00 4.85
1988 4292 2.126228 CAGCGTCGACGGCCTTTA 60.126 61.111 36.13 0.00 40.23 1.85
2056 4360 0.761187 TGAGCTCCACCATAGGATGC 59.239 55.000 12.15 0.00 36.99 3.91
2066 4370 3.127425 ACTAAAGTTGGTGAGCTCCAC 57.873 47.619 12.15 9.37 44.95 4.02
2067 4371 3.135712 TGAACTAAAGTTGGTGAGCTCCA 59.864 43.478 12.15 0.00 38.56 3.86
2068 4372 3.740115 TGAACTAAAGTTGGTGAGCTCC 58.260 45.455 12.15 2.19 38.56 4.70
2129 4433 7.148474 GCAGACATCGTATAGGTTTTCAAAAGA 60.148 37.037 0.00 0.00 0.00 2.52
2136 4440 4.380841 TCGCAGACATCGTATAGGTTTT 57.619 40.909 0.00 0.00 0.00 2.43
2147 4452 2.279741 TGTAGGCATTTCGCAGACATC 58.720 47.619 0.00 0.00 45.17 3.06
2152 4457 5.030295 CAGTTATTTGTAGGCATTTCGCAG 58.970 41.667 0.00 0.00 45.17 5.18
2164 4469 6.038382 TCGCAACAAGGTTTCAGTTATTTGTA 59.962 34.615 0.00 0.00 0.00 2.41
2190 4504 1.569493 CGACAAACGGTTCCTGCAG 59.431 57.895 6.78 6.78 38.46 4.41
2281 4598 2.557317 GGCCTTCGATCGGTGAAAATA 58.443 47.619 16.41 0.00 0.00 1.40
2284 4601 1.447140 CGGCCTTCGATCGGTGAAA 60.447 57.895 16.41 0.61 42.43 2.69
2312 4629 3.941483 AGAGATTTCAAGCGGTTATGTGG 59.059 43.478 0.00 0.00 0.00 4.17
2318 4635 2.457366 ACGAGAGATTTCAAGCGGTT 57.543 45.000 0.00 0.00 0.00 4.44
2322 4639 6.096695 AGTTAGAGAACGAGAGATTTCAAGC 58.903 40.000 0.00 0.00 40.76 4.01
2336 4653 6.015265 ACAGGGAGAAGTGTTAGTTAGAGAAC 60.015 42.308 0.00 0.00 35.64 3.01
2443 4786 4.584638 TGAGGTGTAGGGTGCAAAATAT 57.415 40.909 0.00 0.00 0.00 1.28
2448 4791 2.261729 TGTATGAGGTGTAGGGTGCAA 58.738 47.619 0.00 0.00 0.00 4.08
2476 4850 8.931385 AAGCACATGGTTATGATTTTCATTAC 57.069 30.769 0.00 0.00 38.26 1.89
2640 5014 1.436195 GCACCAAGCTTGACGTGTCA 61.436 55.000 28.05 0.00 41.15 3.58
2664 5038 1.538512 CATCAACACTGTGAGGCCAAG 59.461 52.381 15.86 0.00 0.00 3.61
2665 5039 1.142667 TCATCAACACTGTGAGGCCAA 59.857 47.619 15.86 0.00 0.00 4.52
2673 5047 1.671261 GCTCGCTCTCATCAACACTGT 60.671 52.381 0.00 0.00 0.00 3.55
2715 5093 2.668632 GTGGCAGGATCGGGACAA 59.331 61.111 0.00 0.00 0.00 3.18
2823 5202 2.122768 ACATCTCTCATTGGTCCCCTC 58.877 52.381 0.00 0.00 0.00 4.30
2825 5204 3.041946 AGTACATCTCTCATTGGTCCCC 58.958 50.000 0.00 0.00 0.00 4.81
2826 5205 3.070302 GGAGTACATCTCTCATTGGTCCC 59.930 52.174 0.00 0.00 42.40 4.46
2827 5206 3.964031 AGGAGTACATCTCTCATTGGTCC 59.036 47.826 0.00 0.00 42.40 4.46
2893 5275 9.314321 CTACCATTTTTGTGAGAGTAACGATAT 57.686 33.333 0.00 0.00 0.00 1.63
2928 5315 6.475076 GGAAATCCTATCAGATCGATCATTCG 59.525 42.308 26.47 12.12 46.87 3.34
2967 5355 3.243359 TCAGTCCAGCCCAGAATTTTT 57.757 42.857 0.00 0.00 0.00 1.94
2973 5361 1.067295 AACATTCAGTCCAGCCCAGA 58.933 50.000 0.00 0.00 0.00 3.86
3016 5411 4.152647 TCACTCAGAAGCTGGAGAAGTAA 58.847 43.478 15.02 0.00 31.51 2.24
3099 5507 0.820871 CTAGACTCACCCACAGCTCC 59.179 60.000 0.00 0.00 0.00 4.70
3108 5516 3.449018 TCATCTTTCTGGCTAGACTCACC 59.551 47.826 0.00 0.00 31.21 4.02
3132 5573 1.796017 TGGCCTTATACGGTCCATCA 58.204 50.000 3.32 0.00 0.00 3.07
3194 5640 3.442076 ACGATAACCCTTTCTCTCCTGT 58.558 45.455 0.00 0.00 0.00 4.00
3232 5678 5.343715 GGGGTTTATTTAGGGGAAGGAAAA 58.656 41.667 0.00 0.00 0.00 2.29
3245 5691 3.835395 TCTCGCAATTTGGGGGTTTATTT 59.165 39.130 12.51 0.00 32.00 1.40
3306 5752 1.633945 GCTAGGGTTTGGGAGAGGAAA 59.366 52.381 0.00 0.00 0.00 3.13
3310 5756 2.696187 GACTAGCTAGGGTTTGGGAGAG 59.304 54.545 24.35 0.00 0.00 3.20
3515 5970 3.024356 TCCTCCTCCTCCTCGCCT 61.024 66.667 0.00 0.00 0.00 5.52
3518 5973 0.465460 CAGACTCCTCCTCCTCCTCG 60.465 65.000 0.00 0.00 0.00 4.63
3548 6009 1.216678 TCATCAGACTCCTCCTCCTCC 59.783 57.143 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.