Multiple sequence alignment - TraesCS6B01G473400

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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 TraesCS6B01G473400 chr6B 100.000 2857 0 0 1 2857 720558758 720561614 0.000000e+00 5276
1 TraesCS6B01G473400 chr6A 95.516 892 36 2 1966 2857 615432143 615431256 0.000000e+00 1423
2 TraesCS6B01G473400 chr6A 83.889 540 47 19 986 1510 615433700 615433186 1.990000e-131 479
3 TraesCS6B01G473400 chr6A 99.234 261 2 0 1595 1855 615433184 615432924 3.330000e-129 472
4 TraesCS6B01G473400 chr6A 80.439 501 41 31 230 705 615434394 615433926 2.120000e-86 329
5 TraesCS6B01G473400 chr6A 80.303 198 20 15 1 184 615434594 615434402 6.420000e-27 132
6 TraesCS6B01G473400 chr6A 91.892 74 6 0 1862 1935 615432538 615432465 1.400000e-18 104
7 TraesCS6B01G473400 chr6D 94.955 892 35 4 1966 2857 470574862 470573981 0.000000e+00 1389
8 TraesCS6B01G473400 chr6D 82.748 939 73 38 606 1510 470603322 470602439 0.000000e+00 754
9 TraesCS6B01G473400 chr6D 97.378 267 7 0 1595 1861 470602437 470602171 3.360000e-124 455
10 TraesCS6B01G473400 chr6D 91.463 82 7 0 4 85 470603875 470603794 2.330000e-21 113
11 TraesCS6B01G473400 chr5D 96.842 95 2 1 606 700 113386820 113386913 1.060000e-34 158
12 TraesCS6B01G473400 chr5A 96.809 94 3 0 607 700 118666166 118666259 1.060000e-34 158
13 TraesCS6B01G473400 chr4A 94.898 98 3 2 602 699 504218908 504218813 4.930000e-33 152
14 TraesCS6B01G473400 chr7A 94.000 100 5 1 601 700 549000448 549000546 1.770000e-32 150
15 TraesCS6B01G473400 chr7A 91.818 110 5 4 606 713 731255728 731255835 1.770000e-32 150
16 TraesCS6B01G473400 chr1A 94.000 100 5 1 619 718 119739095 119738997 1.770000e-32 150
17 TraesCS6B01G473400 chr1D 93.000 100 6 1 619 718 112632847 112632749 8.250000e-31 145


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 TraesCS6B01G473400 chr6B 720558758 720561614 2856 False 5276.000000 5276 100.000000 1 2857 1 chr6B.!!$F1 2856
1 TraesCS6B01G473400 chr6A 615431256 615434594 3338 True 489.833333 1423 88.545500 1 2857 6 chr6A.!!$R1 2856
2 TraesCS6B01G473400 chr6D 470573981 470574862 881 True 1389.000000 1389 94.955000 1966 2857 1 chr6D.!!$R1 891
3 TraesCS6B01G473400 chr6D 470602171 470603875 1704 True 440.666667 754 90.529667 4 1861 3 chr6D.!!$R2 1857

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
136 186 0.173481 TCCTCTGAAGCAATCGACCG 59.827 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 2559 0.109643 TAATTTGCTGTGCTGCGCAG 60.11 50.0 32.69 32.69 43.89 5.18 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
29 30 2.595463 CACTGGTGTGGCTGTGGG 60.595 66.667 0.00 0.00 40.33 4.61
59 60 0.598065 CGCAAGCCTACCAAAAAGCT 59.402 50.000 0.00 0.00 37.10 3.74
62 67 3.305064 CGCAAGCCTACCAAAAAGCTAAA 60.305 43.478 0.00 0.00 34.49 1.85
87 118 2.630995 GGGGATTTCCTCCTCTTCTCCT 60.631 54.545 0.00 0.00 41.91 3.69
97 128 4.344104 CTCCTCTTCTCCTCTTCTGAACT 58.656 47.826 0.00 0.00 0.00 3.01
114 149 2.233305 ACTTTCCTTCTCGCCCTCTA 57.767 50.000 0.00 0.00 0.00 2.43
127 177 1.408969 CCCTCTACCTCCTCTGAAGC 58.591 60.000 0.00 0.00 0.00 3.86
135 185 1.472376 CCTCCTCTGAAGCAATCGACC 60.472 57.143 0.00 0.00 0.00 4.79
136 186 0.173481 TCCTCTGAAGCAATCGACCG 59.827 55.000 0.00 0.00 0.00 4.79
137 187 0.173481 CCTCTGAAGCAATCGACCGA 59.827 55.000 0.00 0.00 0.00 4.69
138 188 1.554392 CTCTGAAGCAATCGACCGAG 58.446 55.000 0.00 0.00 0.00 4.63
144 194 0.249238 AGCAATCGACCGAGCATCTC 60.249 55.000 6.46 0.00 0.00 2.75
148 205 1.175983 ATCGACCGAGCATCTCCTCC 61.176 60.000 0.00 0.00 0.00 4.30
151 208 1.456705 ACCGAGCATCTCCTCCTCC 60.457 63.158 0.00 0.00 0.00 4.30
186 243 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
194 268 8.600449 TTCTTCTTCTTCTTCTTCTTAAGCAG 57.400 34.615 0.00 0.00 0.00 4.24
196 270 7.655328 TCTTCTTCTTCTTCTTCTTAAGCAGTG 59.345 37.037 1.97 0.00 0.00 3.66
198 272 5.552870 TCTTCTTCTTCTTAAGCAGTGGT 57.447 39.130 1.97 0.00 0.00 4.16
272 356 5.678955 AAGCTTCCGAGGTAAGTAGAAAT 57.321 39.130 0.00 0.00 32.23 2.17
320 404 2.183679 CTCAGCTCTCCTGGGTAAACT 58.816 52.381 0.00 0.00 42.05 2.66
328 412 3.720002 TCTCCTGGGTAAACTTGGTTTCT 59.280 43.478 0.00 0.00 37.01 2.52
330 414 4.211920 TCCTGGGTAAACTTGGTTTCTTG 58.788 43.478 0.00 0.00 37.01 3.02
337 421 6.651643 GGGTAAACTTGGTTTCTTGTTTGTTT 59.348 34.615 0.00 0.00 37.01 2.83
338 422 7.360522 GGGTAAACTTGGTTTCTTGTTTGTTTG 60.361 37.037 0.00 0.00 37.01 2.93
340 424 6.538189 AACTTGGTTTCTTGTTTGTTTGTG 57.462 33.333 0.00 0.00 0.00 3.33
346 430 7.189512 TGGTTTCTTGTTTGTTTGTGTTTTTG 58.810 30.769 0.00 0.00 0.00 2.44
348 432 6.927294 TTCTTGTTTGTTTGTGTTTTTGGT 57.073 29.167 0.00 0.00 0.00 3.67
371 455 9.432982 TGGTTGCCAATTATTCCTTTAGATTAT 57.567 29.630 0.00 0.00 0.00 1.28
432 516 7.070571 TCAGGTTTGTTTAATTCCTCCATTTGT 59.929 33.333 0.00 0.00 0.00 2.83
455 540 0.889186 GTGTGGTTGCGTGGAGGATT 60.889 55.000 0.00 0.00 0.00 3.01
480 576 8.640063 TTCCATCCATCCATATATTTGTTCTG 57.360 34.615 0.00 0.00 0.00 3.02
486 582 9.013229 TCCATCCATATATTTGTTCTGTATTGC 57.987 33.333 0.00 0.00 0.00 3.56
515 615 3.517100 AGCACCATACTGAGAGTGTTCAT 59.483 43.478 0.00 0.00 32.75 2.57
528 628 3.876914 GAGTGTTCATCAGTGTGTTTGGA 59.123 43.478 0.00 0.00 0.00 3.53
537 692 4.843728 TCAGTGTGTTTGGAAGAAGAGTT 58.156 39.130 0.00 0.00 0.00 3.01
575 730 4.265893 TGTTGTGTTCTTACATGTGGTGT 58.734 39.130 9.11 0.00 44.95 4.16
581 736 2.058705 TCTTACATGTGGTGTGGGGAA 58.941 47.619 9.11 0.00 42.24 3.97
582 737 2.159382 CTTACATGTGGTGTGGGGAAC 58.841 52.381 9.11 0.00 42.24 3.62
587 742 0.182537 TGTGGTGTGGGGAACAAGAG 59.817 55.000 0.00 0.00 41.57 2.85
588 743 0.182775 GTGGTGTGGGGAACAAGAGT 59.817 55.000 0.00 0.00 41.57 3.24
590 745 2.128535 TGGTGTGGGGAACAAGAGTTA 58.871 47.619 0.00 0.00 41.57 2.24
591 746 2.510382 TGGTGTGGGGAACAAGAGTTAA 59.490 45.455 0.00 0.00 41.57 2.01
592 747 3.053544 TGGTGTGGGGAACAAGAGTTAAA 60.054 43.478 0.00 0.00 41.57 1.52
593 748 3.955551 GGTGTGGGGAACAAGAGTTAAAA 59.044 43.478 0.00 0.00 41.57 1.52
594 749 4.403113 GGTGTGGGGAACAAGAGTTAAAAA 59.597 41.667 0.00 0.00 41.57 1.94
595 750 5.451381 GGTGTGGGGAACAAGAGTTAAAAAG 60.451 44.000 0.00 0.00 41.57 2.27
597 752 5.952947 TGTGGGGAACAAGAGTTAAAAAGAA 59.047 36.000 0.00 0.00 38.30 2.52
598 753 6.609616 TGTGGGGAACAAGAGTTAAAAAGAAT 59.390 34.615 0.00 0.00 38.30 2.40
599 754 7.125053 TGTGGGGAACAAGAGTTAAAAAGAATT 59.875 33.333 0.00 0.00 38.30 2.17
600 755 7.438160 GTGGGGAACAAGAGTTAAAAAGAATTG 59.562 37.037 0.00 0.00 38.30 2.32
601 756 7.343316 TGGGGAACAAGAGTTAAAAAGAATTGA 59.657 33.333 0.00 0.00 38.30 2.57
603 758 9.249457 GGGAACAAGAGTTAAAAAGAATTGAAG 57.751 33.333 0.00 0.00 38.30 3.02
604 759 9.249457 GGAACAAGAGTTAAAAAGAATTGAAGG 57.751 33.333 0.00 0.00 38.30 3.46
700 859 2.755103 CCACTAGACCAAATGCCCTTTC 59.245 50.000 0.00 0.00 0.00 2.62
709 868 2.298163 CAAATGCCCTTTCTTGTGCTCT 59.702 45.455 0.00 0.00 0.00 4.09
713 872 4.568072 TGCCCTTTCTTGTGCTCTATTA 57.432 40.909 0.00 0.00 0.00 0.98
715 874 4.261801 GCCCTTTCTTGTGCTCTATTACA 58.738 43.478 0.00 0.00 0.00 2.41
717 876 5.008118 GCCCTTTCTTGTGCTCTATTACATC 59.992 44.000 0.00 0.00 0.00 3.06
726 919 7.603180 TGTGCTCTATTACATCCTCACTTAT 57.397 36.000 0.00 0.00 0.00 1.73
759 952 3.838317 TCAGTACAGTTGGCCAAGATAGT 59.162 43.478 21.21 16.75 0.00 2.12
760 953 3.935203 CAGTACAGTTGGCCAAGATAGTG 59.065 47.826 21.21 18.87 0.00 2.74
761 954 1.826385 ACAGTTGGCCAAGATAGTGC 58.174 50.000 21.21 4.99 0.00 4.40
762 955 1.352352 ACAGTTGGCCAAGATAGTGCT 59.648 47.619 21.21 7.64 0.00 4.40
764 957 1.630369 AGTTGGCCAAGATAGTGCTGA 59.370 47.619 21.21 0.00 0.00 4.26
767 972 2.923121 TGGCCAAGATAGTGCTGATTC 58.077 47.619 0.61 0.00 0.00 2.52
783 988 2.834549 TGATTCCAGACTCCTCTGTTCC 59.165 50.000 0.00 0.00 42.36 3.62
788 993 3.716872 TCCAGACTCCTCTGTTCCTTTTT 59.283 43.478 0.00 0.00 42.36 1.94
861 1067 3.829886 ATATTGTGGTTGTGCTTCGTG 57.170 42.857 0.00 0.00 0.00 4.35
869 1075 1.002468 GTTGTGCTTCGTGCTGACAAT 60.002 47.619 10.27 0.00 38.96 2.71
870 1076 2.162319 TGTGCTTCGTGCTGACAATA 57.838 45.000 5.00 0.00 43.37 1.90
871 1077 2.068519 TGTGCTTCGTGCTGACAATAG 58.931 47.619 5.00 0.00 43.37 1.73
872 1078 1.078709 TGCTTCGTGCTGACAATAGC 58.921 50.000 5.00 0.00 43.95 2.97
873 1079 0.375106 GCTTCGTGCTGACAATAGCC 59.625 55.000 0.00 0.00 43.02 3.93
875 1081 1.929836 CTTCGTGCTGACAATAGCCTC 59.070 52.381 0.00 0.00 43.02 4.70
876 1082 0.175760 TCGTGCTGACAATAGCCTCC 59.824 55.000 0.00 0.00 43.02 4.30
877 1083 0.811616 CGTGCTGACAATAGCCTCCC 60.812 60.000 0.00 0.00 43.02 4.30
878 1084 0.464554 GTGCTGACAATAGCCTCCCC 60.465 60.000 0.00 0.00 43.02 4.81
879 1085 1.227674 GCTGACAATAGCCTCCCCG 60.228 63.158 0.00 0.00 37.73 5.73
882 1088 0.251916 TGACAATAGCCTCCCCGTTG 59.748 55.000 0.00 0.00 0.00 4.10
884 1090 0.252197 ACAATAGCCTCCCCGTTGAC 59.748 55.000 0.00 0.00 0.00 3.18
885 1091 0.251916 CAATAGCCTCCCCGTTGACA 59.748 55.000 0.00 0.00 0.00 3.58
886 1092 0.988832 AATAGCCTCCCCGTTGACAA 59.011 50.000 0.00 0.00 0.00 3.18
887 1093 1.213296 ATAGCCTCCCCGTTGACAAT 58.787 50.000 0.00 0.00 0.00 2.71
888 1094 1.868713 TAGCCTCCCCGTTGACAATA 58.131 50.000 0.00 0.00 0.00 1.90
889 1095 0.541863 AGCCTCCCCGTTGACAATAG 59.458 55.000 0.00 0.00 0.00 1.73
890 1096 0.252197 GCCTCCCCGTTGACAATAGT 59.748 55.000 0.00 0.00 0.00 2.12
891 1097 1.742750 GCCTCCCCGTTGACAATAGTC 60.743 57.143 0.00 0.00 45.19 2.59
909 1115 1.075970 CGTCCCTCCATCCTCCAGA 60.076 63.158 0.00 0.00 0.00 3.86
916 1122 0.684479 TCCATCCTCCAGACAGACCG 60.684 60.000 0.00 0.00 0.00 4.79
942 1148 1.821753 GTCGATCGATCCATCCATCCT 59.178 52.381 22.50 0.00 0.00 3.24
943 1149 1.821136 TCGATCGATCCATCCATCCTG 59.179 52.381 19.51 1.80 0.00 3.86
947 1153 2.182827 TCGATCCATCCATCCTGATCC 58.817 52.381 0.00 0.00 31.94 3.36
980 1186 0.738975 TCCAGTCGTGGTGATCGATC 59.261 55.000 18.72 18.72 45.28 3.69
981 1187 0.592500 CCAGTCGTGGTGATCGATCG 60.593 60.000 20.03 9.36 39.30 3.69
982 1188 0.377203 CAGTCGTGGTGATCGATCGA 59.623 55.000 21.86 21.86 39.45 3.59
983 1189 1.002359 CAGTCGTGGTGATCGATCGAT 60.002 52.381 29.76 29.76 39.45 3.59
984 1190 5.965851 CCAGTCGTGGTGATCGATCGATC 62.966 56.522 38.90 38.90 42.01 3.69
1038 1244 2.526110 GGCAACCCCCAGAACCTT 59.474 61.111 0.00 0.00 0.00 3.50
1044 1250 0.912487 ACCCCCAGAACCTTCGCATA 60.912 55.000 0.00 0.00 0.00 3.14
1104 1319 4.504916 CGGAGCAGCTCGTCCCAG 62.505 72.222 16.47 0.00 0.00 4.45
1113 1328 3.691744 CTCGTCCCAGCTCGCACTC 62.692 68.421 0.00 0.00 0.00 3.51
1115 1330 2.581354 GTCCCAGCTCGCACTCAT 59.419 61.111 0.00 0.00 0.00 2.90
1117 1332 2.584418 CCCAGCTCGCACTCATCG 60.584 66.667 0.00 0.00 0.00 3.84
1119 1334 2.507769 CAGCTCGCACTCATCGCA 60.508 61.111 0.00 0.00 0.00 5.10
1120 1335 2.096442 CAGCTCGCACTCATCGCAA 61.096 57.895 0.00 0.00 0.00 4.85
1152 1367 1.225704 CACCAGGAGGCCATCTTCC 59.774 63.158 5.01 2.28 39.06 3.46
1285 1506 3.354467 AGAAAAGACGACGAGGAGGTAT 58.646 45.455 0.00 0.00 0.00 2.73
1340 1573 2.616969 TGACGAACAGAAAGCTGGC 58.383 52.632 0.00 0.00 46.60 4.85
1343 1576 0.106708 ACGAACAGAAAGCTGGCTGA 59.893 50.000 19.55 0.00 46.60 4.26
1506 1742 3.248171 GACGTGACGCTCATCCGC 61.248 66.667 4.25 0.00 0.00 5.54
1508 1744 2.809174 CGTGACGCTCATCCGCAA 60.809 61.111 0.00 0.00 0.00 4.85
1509 1745 2.792290 CGTGACGCTCATCCGCAAG 61.792 63.158 0.00 0.00 0.00 4.01
1521 1757 3.642755 CGCAAGGTCAGGACACAC 58.357 61.111 1.41 0.00 0.00 3.82
1522 1758 1.961277 CGCAAGGTCAGGACACACC 60.961 63.158 1.41 0.00 39.35 4.16
1533 1769 2.325583 GGACACACCTTTCTCACACA 57.674 50.000 0.00 0.00 35.41 3.72
1534 1770 2.213499 GGACACACCTTTCTCACACAG 58.787 52.381 0.00 0.00 35.41 3.66
1535 1771 2.158957 GGACACACCTTTCTCACACAGA 60.159 50.000 0.00 0.00 35.41 3.41
1536 1772 3.126831 GACACACCTTTCTCACACAGAG 58.873 50.000 0.00 0.00 46.14 3.35
1537 1773 2.158900 ACACACCTTTCTCACACAGAGG 60.159 50.000 0.00 0.00 44.81 3.69
1538 1774 2.103094 CACACCTTTCTCACACAGAGGA 59.897 50.000 0.00 0.00 44.81 3.71
1539 1775 2.771943 ACACCTTTCTCACACAGAGGAA 59.228 45.455 0.00 0.00 44.81 3.36
1540 1776 3.392616 ACACCTTTCTCACACAGAGGAAT 59.607 43.478 0.00 0.00 41.06 3.01
1541 1777 4.141390 ACACCTTTCTCACACAGAGGAATT 60.141 41.667 0.00 0.00 41.06 2.17
1542 1778 4.823989 CACCTTTCTCACACAGAGGAATTT 59.176 41.667 0.00 0.00 41.06 1.82
1543 1779 4.823989 ACCTTTCTCACACAGAGGAATTTG 59.176 41.667 0.00 0.00 41.06 2.32
1544 1780 4.217118 CCTTTCTCACACAGAGGAATTTGG 59.783 45.833 0.00 0.00 41.06 3.28
1545 1781 4.705110 TTCTCACACAGAGGAATTTGGA 57.295 40.909 0.00 0.00 44.81 3.53
1546 1782 4.705110 TCTCACACAGAGGAATTTGGAA 57.295 40.909 0.00 0.00 44.81 3.53
1547 1783 4.645535 TCTCACACAGAGGAATTTGGAAG 58.354 43.478 0.00 0.00 44.81 3.46
1548 1784 3.149196 TCACACAGAGGAATTTGGAAGC 58.851 45.455 0.00 0.00 0.00 3.86
1549 1785 2.886523 CACACAGAGGAATTTGGAAGCA 59.113 45.455 0.00 0.00 0.00 3.91
1550 1786 3.318839 CACACAGAGGAATTTGGAAGCAA 59.681 43.478 0.00 0.00 0.00 3.91
1551 1787 3.319122 ACACAGAGGAATTTGGAAGCAAC 59.681 43.478 0.00 0.00 0.00 4.17
1552 1788 3.318839 CACAGAGGAATTTGGAAGCAACA 59.681 43.478 0.00 0.00 0.00 3.33
1553 1789 4.021719 CACAGAGGAATTTGGAAGCAACAT 60.022 41.667 0.00 0.00 0.00 2.71
1554 1790 5.183713 CACAGAGGAATTTGGAAGCAACATA 59.816 40.000 0.00 0.00 0.00 2.29
1555 1791 5.183904 ACAGAGGAATTTGGAAGCAACATAC 59.816 40.000 0.00 0.00 0.00 2.39
1556 1792 4.396166 AGAGGAATTTGGAAGCAACATACG 59.604 41.667 0.00 0.00 0.00 3.06
1557 1793 4.331968 AGGAATTTGGAAGCAACATACGA 58.668 39.130 0.00 0.00 0.00 3.43
1558 1794 4.949856 AGGAATTTGGAAGCAACATACGAT 59.050 37.500 0.00 0.00 0.00 3.73
1559 1795 6.119536 AGGAATTTGGAAGCAACATACGATA 58.880 36.000 0.00 0.00 0.00 2.92
1560 1796 6.601613 AGGAATTTGGAAGCAACATACGATAA 59.398 34.615 0.00 0.00 0.00 1.75
1561 1797 7.285401 AGGAATTTGGAAGCAACATACGATAAT 59.715 33.333 0.00 0.00 0.00 1.28
1562 1798 7.379529 GGAATTTGGAAGCAACATACGATAATG 59.620 37.037 0.00 0.00 0.00 1.90
1563 1799 5.749596 TTGGAAGCAACATACGATAATGG 57.250 39.130 0.00 0.00 0.00 3.16
1564 1800 5.029807 TGGAAGCAACATACGATAATGGA 57.970 39.130 0.00 0.00 0.00 3.41
1565 1801 5.056480 TGGAAGCAACATACGATAATGGAG 58.944 41.667 0.00 0.00 0.00 3.86
1566 1802 4.452455 GGAAGCAACATACGATAATGGAGG 59.548 45.833 0.00 0.00 0.00 4.30
1567 1803 4.955811 AGCAACATACGATAATGGAGGA 57.044 40.909 0.00 0.00 0.00 3.71
1568 1804 5.290493 AGCAACATACGATAATGGAGGAA 57.710 39.130 0.00 0.00 0.00 3.36
1569 1805 5.300752 AGCAACATACGATAATGGAGGAAG 58.699 41.667 0.00 0.00 0.00 3.46
1570 1806 4.083802 GCAACATACGATAATGGAGGAAGC 60.084 45.833 0.00 0.00 0.00 3.86
1571 1807 5.300752 CAACATACGATAATGGAGGAAGCT 58.699 41.667 0.00 0.00 0.00 3.74
1572 1808 4.887748 ACATACGATAATGGAGGAAGCTG 58.112 43.478 0.00 0.00 0.00 4.24
1573 1809 2.246719 ACGATAATGGAGGAAGCTGC 57.753 50.000 0.00 0.00 0.00 5.25
1574 1810 1.486310 ACGATAATGGAGGAAGCTGCA 59.514 47.619 1.02 0.00 0.00 4.41
1575 1811 1.869767 CGATAATGGAGGAAGCTGCAC 59.130 52.381 1.02 0.00 0.00 4.57
1576 1812 2.484417 CGATAATGGAGGAAGCTGCACT 60.484 50.000 1.02 0.00 0.00 4.40
1577 1813 2.408271 TAATGGAGGAAGCTGCACTG 57.592 50.000 1.02 0.00 0.00 3.66
1578 1814 0.964358 AATGGAGGAAGCTGCACTGC 60.964 55.000 1.02 2.99 0.00 4.40
1579 1815 2.033141 GGAGGAAGCTGCACTGCA 59.967 61.111 3.11 3.11 36.92 4.41
1580 1816 1.601759 GGAGGAAGCTGCACTGCAA 60.602 57.895 4.99 0.00 38.41 4.08
1581 1817 1.578423 GAGGAAGCTGCACTGCAAC 59.422 57.895 4.99 0.07 38.41 4.17
1582 1818 0.888285 GAGGAAGCTGCACTGCAACT 60.888 55.000 4.99 2.83 38.41 3.16
1583 1819 1.170919 AGGAAGCTGCACTGCAACTG 61.171 55.000 7.70 0.00 38.41 3.16
1584 1820 1.371389 GAAGCTGCACTGCAACTGC 60.371 57.895 7.70 6.66 38.41 4.40
1609 1845 1.923395 AGGAGTTCATGGGGCGGAA 60.923 57.895 0.00 0.00 0.00 4.30
1691 1927 2.496817 GAGTACCTGCTCCGCCTG 59.503 66.667 0.00 0.00 0.00 4.85
1891 2506 5.934043 TCCTGAATTCAAGACCATATATGCG 59.066 40.000 9.88 3.71 0.00 4.73
1894 2509 6.287525 TGAATTCAAGACCATATATGCGTGA 58.712 36.000 5.45 6.11 0.00 4.35
1910 2525 1.059692 CGTGAAGCAGACTACATTGCG 59.940 52.381 0.00 0.00 44.80 4.85
1919 2534 2.930040 AGACTACATTGCGTACACATGC 59.070 45.455 0.00 0.00 37.19 4.06
1922 2537 0.721154 ACATTGCGTACACATGCTCG 59.279 50.000 0.00 0.00 37.58 5.03
1935 2550 3.440151 GCTCGTATAGCCGGACCA 58.560 61.111 5.05 0.00 46.25 4.02
1936 2551 1.737816 GCTCGTATAGCCGGACCAA 59.262 57.895 5.05 0.00 46.25 3.67
1938 2553 1.270147 GCTCGTATAGCCGGACCAAAT 60.270 52.381 5.05 0.00 46.25 2.32
1939 2554 2.404215 CTCGTATAGCCGGACCAAATG 58.596 52.381 5.05 0.00 0.00 2.32
1941 2556 2.631062 TCGTATAGCCGGACCAAATGAT 59.369 45.455 5.05 0.00 0.00 2.45
1942 2557 3.070446 TCGTATAGCCGGACCAAATGATT 59.930 43.478 5.05 0.00 0.00 2.57
1943 2558 3.432252 CGTATAGCCGGACCAAATGATTC 59.568 47.826 5.05 0.00 0.00 2.52
1944 2559 2.341846 TAGCCGGACCAAATGATTCC 57.658 50.000 5.05 0.00 0.00 3.01
1945 2560 0.625849 AGCCGGACCAAATGATTCCT 59.374 50.000 5.05 0.00 0.00 3.36
1946 2561 0.740737 GCCGGACCAAATGATTCCTG 59.259 55.000 5.05 0.00 0.00 3.86
1947 2562 0.740737 CCGGACCAAATGATTCCTGC 59.259 55.000 0.00 0.00 0.00 4.85
1948 2563 0.378257 CGGACCAAATGATTCCTGCG 59.622 55.000 0.00 0.00 0.00 5.18
1949 2564 0.101219 GGACCAAATGATTCCTGCGC 59.899 55.000 0.00 0.00 0.00 6.09
1950 2565 0.810648 GACCAAATGATTCCTGCGCA 59.189 50.000 10.98 10.98 0.00 6.09
1951 2566 0.813184 ACCAAATGATTCCTGCGCAG 59.187 50.000 30.52 30.52 0.00 5.18
2000 2906 7.922278 GCCTACATGCTGAATTATGAAATCAAA 59.078 33.333 0.00 0.00 0.00 2.69
2054 2960 7.122650 AGCAGTACAAAGGCAACAAACATATAT 59.877 33.333 0.00 0.00 41.41 0.86
2109 3015 1.347707 CTACAGGTTCAGAAGGTGCCA 59.652 52.381 0.00 0.00 0.00 4.92
2152 3058 7.119699 CACAGAGAACAATATCTAAAGCACCAA 59.880 37.037 0.00 0.00 0.00 3.67
2153 3059 7.335422 ACAGAGAACAATATCTAAAGCACCAAG 59.665 37.037 0.00 0.00 0.00 3.61
2154 3060 6.317391 AGAGAACAATATCTAAAGCACCAAGC 59.683 38.462 0.00 0.00 46.19 4.01
2172 3078 4.334759 CCAAGCTAGAGGTGAATTGTGATG 59.665 45.833 0.00 0.00 0.00 3.07
2189 3095 7.905604 TTGTGATGATAAAGAAGTGGTACAG 57.094 36.000 0.00 0.00 41.80 2.74
2314 3220 2.237143 TCTATCTTGTGCCCTGAACCAG 59.763 50.000 0.00 0.00 0.00 4.00
2325 3231 1.610102 CCTGAACCAGAGGAACTGCTG 60.610 57.143 0.00 0.00 44.52 4.41
2333 3239 1.346068 AGAGGAACTGCTGGAGTCAAC 59.654 52.381 1.22 0.00 41.55 3.18
2364 3270 2.788786 GCACATGAAGAAACACAAACGG 59.211 45.455 0.00 0.00 0.00 4.44
2382 3288 5.485662 AACGGCTAATAGATTTCAAGTGC 57.514 39.130 0.00 0.00 0.00 4.40
2394 3300 5.973565 AGATTTCAAGTGCAAGAAGAAAACG 59.026 36.000 8.35 0.00 32.65 3.60
2408 3314 8.936864 CAAGAAGAAAACGATAACTTATCACCT 58.063 33.333 9.08 0.00 34.87 4.00
2413 3319 6.422776 AAACGATAACTTATCACCTGCTTG 57.577 37.500 9.08 0.00 34.87 4.01
2439 3345 2.778299 GACAACATACTGTCCCAAGCA 58.222 47.619 0.00 0.00 39.93 3.91
2551 3457 1.450531 CCTTCTTCATCGCCATGCCC 61.451 60.000 0.00 0.00 0.00 5.36
2616 3522 0.908198 ATCAGACCCTTGACAGCCTC 59.092 55.000 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 118 3.555168 GGCGAGAAGGAAAGTTCAGAAGA 60.555 47.826 0.00 0.00 0.00 2.87
97 128 1.192428 GGTAGAGGGCGAGAAGGAAA 58.808 55.000 0.00 0.00 0.00 3.13
114 149 1.205893 GTCGATTGCTTCAGAGGAGGT 59.794 52.381 0.00 0.00 0.00 3.85
127 177 0.387202 AGGAGATGCTCGGTCGATTG 59.613 55.000 0.00 0.00 0.00 2.67
135 185 1.178534 GGAGGAGGAGGAGATGCTCG 61.179 65.000 0.00 0.00 46.85 5.03
136 186 0.188342 AGGAGGAGGAGGAGATGCTC 59.812 60.000 0.00 0.00 45.25 4.26
137 187 0.188342 GAGGAGGAGGAGGAGATGCT 59.812 60.000 0.00 0.00 0.00 3.79
138 188 0.188342 AGAGGAGGAGGAGGAGATGC 59.812 60.000 0.00 0.00 0.00 3.91
144 194 2.846665 AGAAGAAGAGGAGGAGGAGG 57.153 55.000 0.00 0.00 0.00 4.30
148 205 5.716703 AGAAGAAGAAGAAGAAGAGGAGGAG 59.283 44.000 0.00 0.00 0.00 3.69
151 208 7.232118 AGAAGAAGAAGAAGAAGAAGAGGAG 57.768 40.000 0.00 0.00 0.00 3.69
239 319 3.753272 CCTCGGAAGCTTTTTCAGATCAA 59.247 43.478 0.00 0.00 0.00 2.57
272 356 3.951563 ATTAATCAGGCAGCCAGGTAA 57.048 42.857 15.80 8.62 0.00 2.85
320 404 6.927294 AAACACAAACAAACAAGAAACCAA 57.073 29.167 0.00 0.00 0.00 3.67
328 412 5.273944 GCAACCAAAAACACAAACAAACAA 58.726 33.333 0.00 0.00 0.00 2.83
330 414 4.222886 GGCAACCAAAAACACAAACAAAC 58.777 39.130 0.00 0.00 0.00 2.93
371 455 6.655078 TGCTGATGCAGATATACTAGTGAA 57.345 37.500 5.39 0.00 45.31 3.18
405 489 7.610580 AATGGAGGAATTAAACAAACCTGAA 57.389 32.000 0.00 0.00 0.00 3.02
408 492 7.373617 ACAAATGGAGGAATTAAACAAACCT 57.626 32.000 0.00 0.00 0.00 3.50
432 516 0.813610 CTCCACGCAACCACACTGAA 60.814 55.000 0.00 0.00 0.00 3.02
455 540 8.226810 ACAGAACAAATATATGGATGGATGGAA 58.773 33.333 0.00 0.00 0.00 3.53
465 550 7.650890 TGCAGCAATACAGAACAAATATATGG 58.349 34.615 0.00 0.00 0.00 2.74
495 591 5.077134 TGATGAACACTCTCAGTATGGTG 57.923 43.478 0.00 0.00 36.16 4.17
502 598 3.987547 ACACACTGATGAACACTCTCAG 58.012 45.455 0.00 0.00 41.69 3.35
503 599 4.406648 AACACACTGATGAACACTCTCA 57.593 40.909 0.00 0.00 0.00 3.27
515 615 4.487714 ACTCTTCTTCCAAACACACTGA 57.512 40.909 0.00 0.00 0.00 3.41
544 699 9.077885 ACATGTAAGAACACAACAAAGGATATT 57.922 29.630 0.00 0.00 38.78 1.28
545 700 8.514594 CACATGTAAGAACACAACAAAGGATAT 58.485 33.333 0.00 0.00 38.78 1.63
546 701 7.040755 CCACATGTAAGAACACAACAAAGGATA 60.041 37.037 0.00 0.00 38.78 2.59
548 703 5.067153 CCACATGTAAGAACACAACAAAGGA 59.933 40.000 0.00 0.00 38.78 3.36
549 704 5.163561 ACCACATGTAAGAACACAACAAAGG 60.164 40.000 0.00 0.00 38.78 3.11
550 705 5.743398 CACCACATGTAAGAACACAACAAAG 59.257 40.000 0.00 0.00 38.78 2.77
551 706 5.184096 ACACCACATGTAAGAACACAACAAA 59.816 36.000 0.00 0.00 40.88 2.83
552 707 4.702612 ACACCACATGTAAGAACACAACAA 59.297 37.500 0.00 0.00 40.88 2.83
553 708 4.095632 CACACCACATGTAAGAACACAACA 59.904 41.667 0.00 0.00 40.64 3.33
554 709 4.497340 CCACACCACATGTAAGAACACAAC 60.497 45.833 0.00 0.00 40.64 3.32
555 710 3.629855 CCACACCACATGTAAGAACACAA 59.370 43.478 0.00 0.00 40.64 3.33
556 711 3.210227 CCACACCACATGTAAGAACACA 58.790 45.455 0.00 0.00 40.64 3.72
557 712 2.552315 CCCACACCACATGTAAGAACAC 59.448 50.000 0.00 0.00 40.64 3.32
558 713 2.488167 CCCCACACCACATGTAAGAACA 60.488 50.000 0.00 0.00 40.64 3.18
559 714 2.159382 CCCCACACCACATGTAAGAAC 58.841 52.381 0.00 0.00 40.64 3.01
560 715 2.058705 TCCCCACACCACATGTAAGAA 58.941 47.619 0.00 0.00 40.64 2.52
561 716 1.735926 TCCCCACACCACATGTAAGA 58.264 50.000 0.00 0.00 40.64 2.10
562 717 2.159382 GTTCCCCACACCACATGTAAG 58.841 52.381 0.00 0.00 40.64 2.34
563 718 1.495148 TGTTCCCCACACCACATGTAA 59.505 47.619 0.00 0.00 40.64 2.41
564 719 1.141185 TGTTCCCCACACCACATGTA 58.859 50.000 0.00 0.00 40.64 2.29
565 720 0.260230 TTGTTCCCCACACCACATGT 59.740 50.000 0.00 0.00 44.81 3.21
566 721 0.961019 CTTGTTCCCCACACCACATG 59.039 55.000 0.00 0.00 33.98 3.21
567 722 0.850100 TCTTGTTCCCCACACCACAT 59.150 50.000 0.00 0.00 33.98 3.21
575 730 7.343316 TCAATTCTTTTTAACTCTTGTTCCCCA 59.657 33.333 0.00 0.00 37.59 4.96
603 758 8.682710 GCCCCCAATTTTATTTTATCTTTTTCC 58.317 33.333 0.00 0.00 0.00 3.13
604 759 9.237187 TGCCCCCAATTTTATTTTATCTTTTTC 57.763 29.630 0.00 0.00 0.00 2.29
613 768 4.226168 TCGGAATGCCCCCAATTTTATTTT 59.774 37.500 0.00 0.00 0.00 1.82
617 772 2.024846 TCTCGGAATGCCCCCAATTTTA 60.025 45.455 0.00 0.00 0.00 1.52
622 777 0.334676 AATTCTCGGAATGCCCCCAA 59.665 50.000 0.70 0.00 0.00 4.12
623 778 0.395586 CAATTCTCGGAATGCCCCCA 60.396 55.000 0.70 0.00 0.00 4.96
700 859 5.911752 AGTGAGGATGTAATAGAGCACAAG 58.088 41.667 0.00 0.00 0.00 3.16
713 872 7.343057 TGACACTGAAGATATAAGTGAGGATGT 59.657 37.037 8.90 0.00 43.22 3.06
715 874 7.563188 ACTGACACTGAAGATATAAGTGAGGAT 59.437 37.037 8.90 0.00 43.22 3.24
717 876 7.106439 ACTGACACTGAAGATATAAGTGAGG 57.894 40.000 8.90 1.91 43.22 3.86
726 919 5.566826 GCCAACTGTACTGACACTGAAGATA 60.567 44.000 6.77 0.00 0.00 1.98
736 929 2.543777 TCTTGGCCAACTGTACTGAC 57.456 50.000 16.05 0.00 0.00 3.51
759 952 1.829849 CAGAGGAGTCTGGAATCAGCA 59.170 52.381 0.69 0.00 45.85 4.41
760 953 2.600470 CAGAGGAGTCTGGAATCAGC 57.400 55.000 0.69 0.00 45.85 4.26
828 1033 9.720667 CACAACCACAATATATGTATGAACAAG 57.279 33.333 0.00 0.00 41.46 3.16
839 1044 4.201910 GCACGAAGCACAACCACAATATAT 60.202 41.667 0.00 0.00 44.79 0.86
861 1067 1.227674 CGGGGAGGCTATTGTCAGC 60.228 63.158 0.00 0.00 41.02 4.26
869 1075 1.760613 CTATTGTCAACGGGGAGGCTA 59.239 52.381 0.00 0.00 0.00 3.93
870 1076 0.541863 CTATTGTCAACGGGGAGGCT 59.458 55.000 0.00 0.00 0.00 4.58
871 1077 0.252197 ACTATTGTCAACGGGGAGGC 59.748 55.000 0.00 0.00 0.00 4.70
872 1078 1.470979 CGACTATTGTCAACGGGGAGG 60.471 57.143 8.04 0.00 43.06 4.30
873 1079 1.203994 ACGACTATTGTCAACGGGGAG 59.796 52.381 8.04 0.00 43.06 4.30
875 1081 1.636988 GACGACTATTGTCAACGGGG 58.363 55.000 8.04 0.00 43.06 5.73
876 1082 1.636988 GGACGACTATTGTCAACGGG 58.363 55.000 8.04 0.00 43.06 5.28
877 1083 1.203994 AGGGACGACTATTGTCAACGG 59.796 52.381 8.04 0.00 43.06 4.44
878 1084 2.527100 GAGGGACGACTATTGTCAACG 58.473 52.381 8.04 0.00 43.06 4.10
879 1085 2.232941 TGGAGGGACGACTATTGTCAAC 59.767 50.000 8.04 0.97 43.06 3.18
882 1088 2.036089 GGATGGAGGGACGACTATTGTC 59.964 54.545 0.00 0.00 39.70 3.18
884 1090 2.297597 GAGGATGGAGGGACGACTATTG 59.702 54.545 0.00 0.00 0.00 1.90
885 1091 2.599677 GAGGATGGAGGGACGACTATT 58.400 52.381 0.00 0.00 0.00 1.73
886 1092 1.203075 GGAGGATGGAGGGACGACTAT 60.203 57.143 0.00 0.00 0.00 2.12
887 1093 0.185416 GGAGGATGGAGGGACGACTA 59.815 60.000 0.00 0.00 0.00 2.59
888 1094 1.075896 GGAGGATGGAGGGACGACT 60.076 63.158 0.00 0.00 0.00 4.18
889 1095 1.381327 TGGAGGATGGAGGGACGAC 60.381 63.158 0.00 0.00 0.00 4.34
890 1096 1.075970 CTGGAGGATGGAGGGACGA 60.076 63.158 0.00 0.00 0.00 4.20
891 1097 1.075970 TCTGGAGGATGGAGGGACG 60.076 63.158 0.00 0.00 0.00 4.79
892 1098 0.325671 TGTCTGGAGGATGGAGGGAC 60.326 60.000 0.00 0.00 0.00 4.46
893 1099 0.031716 CTGTCTGGAGGATGGAGGGA 60.032 60.000 0.00 0.00 0.00 4.20
894 1100 0.031716 TCTGTCTGGAGGATGGAGGG 60.032 60.000 0.00 0.00 0.00 4.30
895 1101 1.118838 GTCTGTCTGGAGGATGGAGG 58.881 60.000 0.00 0.00 0.00 4.30
898 1104 1.680522 CCGGTCTGTCTGGAGGATGG 61.681 65.000 0.00 0.00 45.09 3.51
900 1106 1.697910 TCCGGTCTGTCTGGAGGAT 59.302 57.895 0.00 0.00 45.77 3.24
909 1115 0.526662 GATCGACTTGTCCGGTCTGT 59.473 55.000 0.00 0.00 34.59 3.41
916 1122 2.608261 GGATGGATCGATCGACTTGTCC 60.608 54.545 22.06 22.53 0.00 4.02
942 1148 0.475632 ACAGGACAACCCCAGGATCA 60.476 55.000 0.00 0.00 36.73 2.92
943 1149 0.253327 GACAGGACAACCCCAGGATC 59.747 60.000 0.00 0.00 36.73 3.36
947 1153 1.376466 CTGGACAGGACAACCCCAG 59.624 63.158 0.00 0.00 37.01 4.45
985 1191 0.600557 ATCATGGAGCTCGACCGATC 59.399 55.000 7.83 0.00 0.00 3.69
986 1192 0.316522 CATCATGGAGCTCGACCGAT 59.683 55.000 7.83 7.12 0.00 4.18
987 1193 0.751643 TCATCATGGAGCTCGACCGA 60.752 55.000 7.83 4.88 0.00 4.69
988 1194 0.103026 TTCATCATGGAGCTCGACCG 59.897 55.000 7.83 0.00 0.00 4.79
989 1195 2.141517 CATTCATCATGGAGCTCGACC 58.858 52.381 7.83 0.00 0.00 4.79
990 1196 2.543012 CACATTCATCATGGAGCTCGAC 59.457 50.000 7.83 0.00 37.17 4.20
991 1197 2.830104 CACATTCATCATGGAGCTCGA 58.170 47.619 7.83 3.70 37.17 4.04
1024 1230 1.789576 ATGCGAAGGTTCTGGGGGTT 61.790 55.000 0.00 0.00 0.00 4.11
1038 1244 1.488393 TGGTGGTGATGGATTATGCGA 59.512 47.619 0.00 0.00 0.00 5.10
1044 1250 3.091545 GTGTTGATGGTGGTGATGGATT 58.908 45.455 0.00 0.00 0.00 3.01
1098 1313 1.520342 GATGAGTGCGAGCTGGGAC 60.520 63.158 12.50 12.50 0.00 4.46
1099 1314 2.895680 GATGAGTGCGAGCTGGGA 59.104 61.111 0.00 0.00 0.00 4.37
1100 1315 2.584418 CGATGAGTGCGAGCTGGG 60.584 66.667 0.00 0.00 0.00 4.45
1104 1319 0.315706 GATTTGCGATGAGTGCGAGC 60.316 55.000 0.00 0.00 34.24 5.03
1111 1326 2.411904 GCTAGGAGGATTTGCGATGAG 58.588 52.381 0.00 0.00 0.00 2.90
1113 1328 1.517242 GGCTAGGAGGATTTGCGATG 58.483 55.000 0.00 0.00 0.00 3.84
1115 1330 1.441729 CGGCTAGGAGGATTTGCGA 59.558 57.895 0.00 0.00 0.00 5.10
1117 1332 1.153168 TGCGGCTAGGAGGATTTGC 60.153 57.895 0.00 0.00 0.00 3.68
1119 1334 1.271840 TGGTGCGGCTAGGAGGATTT 61.272 55.000 0.00 0.00 0.00 2.17
1120 1335 1.689233 TGGTGCGGCTAGGAGGATT 60.689 57.895 0.00 0.00 0.00 3.01
1243 1458 1.068472 TCGCTTCTTCTCTTGGTCGTC 60.068 52.381 0.00 0.00 0.00 4.20
1244 1459 0.959553 TCGCTTCTTCTCTTGGTCGT 59.040 50.000 0.00 0.00 0.00 4.34
1245 1460 1.989165 CTTCGCTTCTTCTCTTGGTCG 59.011 52.381 0.00 0.00 0.00 4.79
1285 1506 3.855379 CGCACGCAACAAGATTAGTAGTA 59.145 43.478 0.00 0.00 0.00 1.82
1332 1558 0.737219 GCAATCGATCAGCCAGCTTT 59.263 50.000 10.73 0.00 0.00 3.51
1333 1559 0.393402 TGCAATCGATCAGCCAGCTT 60.393 50.000 17.08 0.00 0.00 3.74
1334 1560 0.814410 CTGCAATCGATCAGCCAGCT 60.814 55.000 17.08 0.00 0.00 4.24
1335 1561 1.647629 CTGCAATCGATCAGCCAGC 59.352 57.895 17.08 7.78 0.00 4.85
1339 1570 1.146930 TCCCCTGCAATCGATCAGC 59.853 57.895 14.01 14.01 0.00 4.26
1340 1573 0.877649 CGTCCCCTGCAATCGATCAG 60.878 60.000 0.00 2.44 0.00 2.90
1343 1576 1.144057 GACGTCCCCTGCAATCGAT 59.856 57.895 3.51 0.00 0.00 3.59
1479 1715 2.576317 GTCACGTCGTAGCTCCGC 60.576 66.667 0.00 0.00 0.00 5.54
1513 1749 6.249168 CTCTGTGTGAGAAAGGTGTGTCCT 62.249 50.000 0.00 0.00 46.36 3.85
1514 1750 2.158957 TCTGTGTGAGAAAGGTGTGTCC 60.159 50.000 0.00 0.00 0.00 4.02
1515 1751 3.126831 CTCTGTGTGAGAAAGGTGTGTC 58.873 50.000 0.00 0.00 45.39 3.67
1516 1752 2.158900 CCTCTGTGTGAGAAAGGTGTGT 60.159 50.000 0.00 0.00 45.39 3.72
1517 1753 2.103094 TCCTCTGTGTGAGAAAGGTGTG 59.897 50.000 0.00 0.00 45.39 3.82
1518 1754 2.398588 TCCTCTGTGTGAGAAAGGTGT 58.601 47.619 0.00 0.00 45.39 4.16
1519 1755 3.475566 TTCCTCTGTGTGAGAAAGGTG 57.524 47.619 0.00 0.00 45.39 4.00
1520 1756 4.713792 AATTCCTCTGTGTGAGAAAGGT 57.286 40.909 0.00 0.00 45.39 3.50
1521 1757 4.217118 CCAAATTCCTCTGTGTGAGAAAGG 59.783 45.833 0.00 0.00 45.39 3.11
1522 1758 5.065914 TCCAAATTCCTCTGTGTGAGAAAG 58.934 41.667 0.00 0.00 45.39 2.62
1523 1759 5.047566 TCCAAATTCCTCTGTGTGAGAAA 57.952 39.130 0.00 0.00 45.39 2.52
1524 1760 4.705110 TCCAAATTCCTCTGTGTGAGAA 57.295 40.909 0.00 0.00 45.39 2.87
1525 1761 4.645535 CTTCCAAATTCCTCTGTGTGAGA 58.354 43.478 0.00 0.00 45.39 3.27
1526 1762 3.190118 GCTTCCAAATTCCTCTGTGTGAG 59.810 47.826 0.00 0.00 42.30 3.51
1527 1763 3.149196 GCTTCCAAATTCCTCTGTGTGA 58.851 45.455 0.00 0.00 0.00 3.58
1528 1764 2.886523 TGCTTCCAAATTCCTCTGTGTG 59.113 45.455 0.00 0.00 0.00 3.82
1529 1765 3.228188 TGCTTCCAAATTCCTCTGTGT 57.772 42.857 0.00 0.00 0.00 3.72
1530 1766 3.318839 TGTTGCTTCCAAATTCCTCTGTG 59.681 43.478 0.00 0.00 31.68 3.66
1531 1767 3.565307 TGTTGCTTCCAAATTCCTCTGT 58.435 40.909 0.00 0.00 31.68 3.41
1532 1768 4.796038 ATGTTGCTTCCAAATTCCTCTG 57.204 40.909 0.00 0.00 31.68 3.35
1533 1769 4.396166 CGTATGTTGCTTCCAAATTCCTCT 59.604 41.667 0.00 0.00 31.68 3.69
1534 1770 4.394920 TCGTATGTTGCTTCCAAATTCCTC 59.605 41.667 0.00 0.00 31.68 3.71
1535 1771 4.331968 TCGTATGTTGCTTCCAAATTCCT 58.668 39.130 0.00 0.00 31.68 3.36
1536 1772 4.695217 TCGTATGTTGCTTCCAAATTCC 57.305 40.909 0.00 0.00 31.68 3.01
1537 1773 7.379529 CCATTATCGTATGTTGCTTCCAAATTC 59.620 37.037 0.00 0.00 31.68 2.17
1538 1774 7.068103 TCCATTATCGTATGTTGCTTCCAAATT 59.932 33.333 0.00 0.00 31.68 1.82
1539 1775 6.545666 TCCATTATCGTATGTTGCTTCCAAAT 59.454 34.615 0.00 0.00 31.68 2.32
1540 1776 5.883115 TCCATTATCGTATGTTGCTTCCAAA 59.117 36.000 0.00 0.00 31.68 3.28
1541 1777 5.432645 TCCATTATCGTATGTTGCTTCCAA 58.567 37.500 0.00 0.00 0.00 3.53
1542 1778 5.029807 TCCATTATCGTATGTTGCTTCCA 57.970 39.130 0.00 0.00 0.00 3.53
1543 1779 4.452455 CCTCCATTATCGTATGTTGCTTCC 59.548 45.833 0.00 0.00 0.00 3.46
1544 1780 5.297547 TCCTCCATTATCGTATGTTGCTTC 58.702 41.667 0.00 0.00 0.00 3.86
1545 1781 5.290493 TCCTCCATTATCGTATGTTGCTT 57.710 39.130 0.00 0.00 0.00 3.91
1546 1782 4.955811 TCCTCCATTATCGTATGTTGCT 57.044 40.909 0.00 0.00 0.00 3.91
1547 1783 4.083802 GCTTCCTCCATTATCGTATGTTGC 60.084 45.833 0.00 0.00 0.00 4.17
1548 1784 5.178252 CAGCTTCCTCCATTATCGTATGTTG 59.822 44.000 0.00 0.00 0.00 3.33
1549 1785 5.300752 CAGCTTCCTCCATTATCGTATGTT 58.699 41.667 0.00 0.00 0.00 2.71
1550 1786 4.800914 GCAGCTTCCTCCATTATCGTATGT 60.801 45.833 0.00 0.00 0.00 2.29
1551 1787 3.681897 GCAGCTTCCTCCATTATCGTATG 59.318 47.826 0.00 0.00 0.00 2.39
1552 1788 3.324846 TGCAGCTTCCTCCATTATCGTAT 59.675 43.478 0.00 0.00 0.00 3.06
1553 1789 2.698274 TGCAGCTTCCTCCATTATCGTA 59.302 45.455 0.00 0.00 0.00 3.43
1554 1790 1.486310 TGCAGCTTCCTCCATTATCGT 59.514 47.619 0.00 0.00 0.00 3.73
1555 1791 1.869767 GTGCAGCTTCCTCCATTATCG 59.130 52.381 0.00 0.00 0.00 2.92
1556 1792 2.877168 CAGTGCAGCTTCCTCCATTATC 59.123 50.000 0.00 0.00 0.00 1.75
1557 1793 2.928334 CAGTGCAGCTTCCTCCATTAT 58.072 47.619 0.00 0.00 0.00 1.28
1558 1794 1.679944 GCAGTGCAGCTTCCTCCATTA 60.680 52.381 11.09 0.00 0.00 1.90
1559 1795 0.964358 GCAGTGCAGCTTCCTCCATT 60.964 55.000 11.09 0.00 0.00 3.16
1560 1796 1.378250 GCAGTGCAGCTTCCTCCAT 60.378 57.895 11.09 0.00 0.00 3.41
1561 1797 2.033141 GCAGTGCAGCTTCCTCCA 59.967 61.111 11.09 0.00 0.00 3.86
1562 1798 1.601759 TTGCAGTGCAGCTTCCTCC 60.602 57.895 18.81 0.00 40.61 4.30
1563 1799 1.578423 GTTGCAGTGCAGCTTCCTC 59.422 57.895 23.09 4.29 40.61 3.71
1564 1800 3.755434 GTTGCAGTGCAGCTTCCT 58.245 55.556 23.09 0.00 40.61 3.36
1582 1818 1.241165 CATGAACTCCTGCAGTTGCA 58.759 50.000 13.81 6.63 46.10 4.08
1583 1819 0.524862 CCATGAACTCCTGCAGTTGC 59.475 55.000 13.81 0.00 46.10 4.17
1584 1820 1.171308 CCCATGAACTCCTGCAGTTG 58.829 55.000 13.81 7.31 46.10 3.16
1586 1822 1.687612 CCCCATGAACTCCTGCAGT 59.312 57.895 13.81 0.00 36.64 4.40
1587 1823 1.751927 GCCCCATGAACTCCTGCAG 60.752 63.158 6.78 6.78 0.00 4.41
1588 1824 2.356278 GCCCCATGAACTCCTGCA 59.644 61.111 0.00 0.00 0.00 4.41
1589 1825 2.825836 CGCCCCATGAACTCCTGC 60.826 66.667 0.00 0.00 0.00 4.85
1590 1826 2.124570 CCGCCCCATGAACTCCTG 60.125 66.667 0.00 0.00 0.00 3.86
1593 1829 1.749258 GGTTCCGCCCCATGAACTC 60.749 63.158 0.00 0.00 40.50 3.01
1609 1845 2.434884 CGTTCATCGCCAGCAGGT 60.435 61.111 0.00 0.00 37.19 4.00
1691 1927 3.343421 GTGTTGGCCACGTCGTCC 61.343 66.667 3.88 0.00 33.61 4.79
1891 2506 2.069273 ACGCAATGTAGTCTGCTTCAC 58.931 47.619 0.00 0.00 36.38 3.18
1894 2509 2.993899 GTGTACGCAATGTAGTCTGCTT 59.006 45.455 0.39 0.00 36.38 3.91
1906 2521 2.287393 ATACGAGCATGTGTACGCAA 57.713 45.000 14.03 0.00 0.00 4.85
1919 2534 2.035449 TCATTTGGTCCGGCTATACGAG 59.965 50.000 0.00 0.00 35.47 4.18
1922 2537 3.751698 GGAATCATTTGGTCCGGCTATAC 59.248 47.826 0.00 0.00 0.00 1.47
1935 2550 0.171903 GTGCTGCGCAGGAATCATTT 59.828 50.000 36.47 0.00 40.08 2.32
1936 2551 0.961857 TGTGCTGCGCAGGAATCATT 60.962 50.000 36.47 0.00 40.08 2.57
1938 2553 2.032376 TGTGCTGCGCAGGAATCA 59.968 55.556 36.47 26.21 40.08 2.57
1939 2554 2.789917 CTGTGCTGCGCAGGAATC 59.210 61.111 36.47 23.94 40.08 2.52
1941 2556 4.933563 TGCTGTGCTGCGCAGGAA 62.934 61.111 35.71 22.87 39.20 3.36
1942 2557 4.933563 TTGCTGTGCTGCGCAGGA 62.934 61.111 35.71 32.80 41.66 3.86
1943 2558 2.758770 AATTTGCTGTGCTGCGCAGG 62.759 55.000 35.71 21.74 41.66 4.85
1944 2559 0.109643 TAATTTGCTGTGCTGCGCAG 60.110 50.000 32.69 32.69 43.89 5.18
1945 2560 0.527113 ATAATTTGCTGTGCTGCGCA 59.473 45.000 15.86 15.86 35.60 6.09
1946 2561 1.585214 GAATAATTTGCTGTGCTGCGC 59.415 47.619 6.19 6.19 35.36 6.09
1947 2562 3.103738 GAGAATAATTTGCTGTGCTGCG 58.896 45.455 0.00 0.00 35.36 5.18
1948 2563 3.855950 GTGAGAATAATTTGCTGTGCTGC 59.144 43.478 0.00 0.00 0.00 5.25
1949 2564 4.093514 CGTGAGAATAATTTGCTGTGCTG 58.906 43.478 0.00 0.00 0.00 4.41
1950 2565 3.426695 GCGTGAGAATAATTTGCTGTGCT 60.427 43.478 0.00 0.00 0.00 4.40
1951 2566 2.848302 GCGTGAGAATAATTTGCTGTGC 59.152 45.455 0.00 0.00 0.00 4.57
1952 2567 4.082274 TGCGTGAGAATAATTTGCTGTG 57.918 40.909 0.00 0.00 0.00 3.66
1953 2568 3.426695 GCTGCGTGAGAATAATTTGCTGT 60.427 43.478 0.00 0.00 0.00 4.40
1954 2569 3.103738 GCTGCGTGAGAATAATTTGCTG 58.896 45.455 0.00 0.00 0.00 4.41
1955 2570 2.098117 GGCTGCGTGAGAATAATTTGCT 59.902 45.455 0.00 0.00 0.00 3.91
1956 2571 2.098117 AGGCTGCGTGAGAATAATTTGC 59.902 45.455 0.00 0.00 0.00 3.68
1957 2572 4.332543 TGTAGGCTGCGTGAGAATAATTTG 59.667 41.667 4.91 0.00 0.00 2.32
1958 2573 4.513442 TGTAGGCTGCGTGAGAATAATTT 58.487 39.130 4.91 0.00 0.00 1.82
1959 2574 4.137116 TGTAGGCTGCGTGAGAATAATT 57.863 40.909 4.91 0.00 0.00 1.40
1962 2577 2.803133 GCATGTAGGCTGCGTGAGAATA 60.803 50.000 26.13 0.00 0.00 1.75
2000 2906 5.982890 AAAGGATTGAATCAACCGATTGT 57.017 34.783 7.56 0.00 42.06 2.71
2054 2960 5.510430 TCCAAGCACTATAGAGAGAAGTCA 58.490 41.667 6.78 0.00 0.00 3.41
2109 3015 3.118038 TCTGTGTAACTTTGGGAGCAGTT 60.118 43.478 0.00 0.00 38.04 3.16
2152 3058 5.627182 ATCATCACAATTCACCTCTAGCT 57.373 39.130 0.00 0.00 0.00 3.32
2153 3059 7.712639 TCTTTATCATCACAATTCACCTCTAGC 59.287 37.037 0.00 0.00 0.00 3.42
2154 3060 9.605275 TTCTTTATCATCACAATTCACCTCTAG 57.395 33.333 0.00 0.00 0.00 2.43
2155 3061 9.605275 CTTCTTTATCATCACAATTCACCTCTA 57.395 33.333 0.00 0.00 0.00 2.43
2172 3078 5.479306 TGCAGTCTGTACCACTTCTTTATC 58.521 41.667 0.93 0.00 0.00 1.75
2189 3095 3.931578 ACTTCAGTTACCAGATGCAGTC 58.068 45.455 0.00 0.00 0.00 3.51
2304 3210 0.322008 GCAGTTCCTCTGGTTCAGGG 60.322 60.000 0.00 0.00 43.78 4.45
2314 3220 1.609320 GGTTGACTCCAGCAGTTCCTC 60.609 57.143 0.00 0.00 34.41 3.71
2325 3231 1.966451 CTTGTGGCCGGTTGACTCC 60.966 63.158 1.90 0.00 0.00 3.85
2333 3239 2.203972 CTTCATGTGCTTGTGGCCGG 62.204 60.000 0.00 0.00 40.92 6.13
2364 3270 7.978982 TCTTCTTGCACTTGAAATCTATTAGC 58.021 34.615 0.00 0.00 0.00 3.09
2382 3288 8.936864 AGGTGATAAGTTATCGTTTTCTTCTTG 58.063 33.333 16.29 0.00 38.02 3.02
2394 3300 5.415415 CTGCAAGCAGGTGATAAGTTATC 57.585 43.478 14.10 14.86 40.17 1.75
2408 3314 0.605050 TATGTTGTCGCCTGCAAGCA 60.605 50.000 8.26 0.00 0.00 3.91
2445 3351 1.846782 CCGAGATGAAAGCGTAACTCG 59.153 52.381 0.00 0.00 44.05 4.18
2551 3457 0.963856 TGAAGCATGCCAAGGAGCTG 60.964 55.000 15.66 0.00 37.41 4.24
2658 3564 2.538141 TTTGTCCCTGCCCTGGAGG 61.538 63.158 0.00 0.00 39.47 4.30


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

AutoCloner maintained by Alex Coulton.