Multiple sequence alignment - TraesCS1D01G397400

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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 TraesCS1D01G397400 chr1D 100.000 4973 0 0 1 4973 465097246 465102218 0.000000e+00 9184.0
1 TraesCS1D01G397400 chr1D 78.571 154 20 9 1578 1718 381017459 381017612 6.860000e-14 89.8
2 TraesCS1D01G397400 chr1A 92.598 2256 91 19 2770 4973 557425451 557427682 0.000000e+00 3171.0
3 TraesCS1D01G397400 chr1A 91.431 1062 58 13 1717 2771 557424303 557425338 0.000000e+00 1426.0
4 TraesCS1D01G397400 chr1A 84.996 1413 91 60 205 1542 557422943 557424309 0.000000e+00 1323.0
5 TraesCS1D01G397400 chr1A 83.333 234 22 10 1 223 557422659 557422886 3.040000e-47 200.0
6 TraesCS1D01G397400 chr1A 85.149 202 14 9 3939 4135 557427918 557428108 5.080000e-45 193.0
7 TraesCS1D01G397400 chr4B 92.944 1063 48 8 1717 2771 111779675 111780718 0.000000e+00 1522.0
8 TraesCS1D01G397400 chr4B 94.942 771 27 5 3148 3918 111781096 111781854 0.000000e+00 1197.0
9 TraesCS1D01G397400 chr4B 88.750 720 50 18 848 1542 111778968 111779681 0.000000e+00 852.0
10 TraesCS1D01G397400 chr4B 83.043 861 52 35 1 830 111778182 111778979 0.000000e+00 695.0
11 TraesCS1D01G397400 chr4B 92.135 445 18 11 4406 4836 111783149 111783590 3.290000e-171 612.0
12 TraesCS1D01G397400 chr4B 95.890 292 12 0 2770 3061 111780809 111781100 1.620000e-129 473.0
13 TraesCS1D01G397400 chr4B 87.500 216 10 5 4198 4413 111782337 111782535 2.990000e-57 233.0
14 TraesCS1D01G397400 chr4B 96.923 130 4 0 4844 4973 111783753 111783882 8.380000e-53 219.0
15 TraesCS1D01G397400 chr4B 93.388 121 8 0 3939 4059 111781921 111782041 3.960000e-41 180.0
16 TraesCS1D01G397400 chr4B 82.243 107 16 3 1289 1395 96191236 96191339 6.860000e-14 89.8
17 TraesCS1D01G397400 chr1B 97.025 706 16 3 3148 3850 642061338 642062041 0.000000e+00 1182.0
18 TraesCS1D01G397400 chr1B 94.165 497 10 1 2565 3061 642060865 642061342 0.000000e+00 739.0
19 TraesCS1D01G397400 chr1B 93.039 431 22 2 2077 2505 642060430 642060854 1.520000e-174 623.0
20 TraesCS1D01G397400 chr1B 85.063 395 27 5 3844 4209 642062592 642062983 1.690000e-99 374.0
21 TraesCS1D01G397400 chr1B 84.091 176 13 7 4198 4369 642063030 642063194 6.670000e-34 156.0
22 TraesCS1D01G397400 chr1B 83.721 86 11 3 1586 1670 652481080 652480997 1.480000e-10 78.7
23 TraesCS1D01G397400 chr5D 91.600 250 14 5 4724 4973 35871937 35872179 6.170000e-89 339.0
24 TraesCS1D01G397400 chr5A 91.532 248 14 3 4724 4971 324964170 324963930 7.980000e-88 335.0
25 TraesCS1D01G397400 chr5A 82.432 74 12 1 1323 1396 379400064 379399992 4.160000e-06 63.9
26 TraesCS1D01G397400 chr6D 91.200 250 15 3 4724 4973 435548729 435548971 2.870000e-87 333.0
27 TraesCS1D01G397400 chr6D 89.683 252 14 7 4724 4973 461003937 461004178 1.340000e-80 311.0
28 TraesCS1D01G397400 chr6D 79.630 108 15 6 1289 1393 14294815 14294918 2.480000e-08 71.3
29 TraesCS1D01G397400 chr3D 81.481 324 56 4 3148 3469 120147316 120146995 3.820000e-66 263.0
30 TraesCS1D01G397400 chr3A 80.556 324 59 4 3148 3469 127089207 127088886 3.840000e-61 246.0
31 TraesCS1D01G397400 chr3A 79.649 285 30 20 1 267 22228488 22228762 3.960000e-41 180.0
32 TraesCS1D01G397400 chr3A 80.263 152 18 7 1570 1718 670750118 670750260 2.450000e-18 104.0
33 TraesCS1D01G397400 chr3A 83.117 77 10 3 1311 1385 63467127 63467052 3.210000e-07 67.6
34 TraesCS1D01G397400 chr7D 83.495 206 32 2 1872 2076 159736614 159736818 1.830000e-44 191.0
35 TraesCS1D01G397400 chr7A 83.495 206 32 2 1872 2076 158395273 158395477 1.830000e-44 191.0
36 TraesCS1D01G397400 chr7A 92.857 42 3 0 4863 4904 580480432 580480473 1.490000e-05 62.1
37 TraesCS1D01G397400 chr7B 83.010 206 33 2 1872 2076 120586995 120587199 8.500000e-43 185.0
38 TraesCS1D01G397400 chr7B 79.259 135 23 5 1578 1707 517623186 517623320 6.860000e-14 89.8
39 TraesCS1D01G397400 chr7B 78.505 107 15 4 4862 4960 537731943 537732049 4.160000e-06 63.9
40 TraesCS1D01G397400 chr4A 79.151 259 31 16 1288 1541 215251325 215251085 1.850000e-34 158.0
41 TraesCS1D01G397400 chr4A 81.395 86 12 3 1600 1684 576039892 576039810 3.210000e-07 67.6
42 TraesCS1D01G397400 chr5B 75.776 322 62 6 3148 3466 507795349 507795657 1.120000e-31 148.0
43 TraesCS1D01G397400 chr5B 78.977 176 25 11 1289 1456 533479439 533479610 5.260000e-20 110.0
44 TraesCS1D01G397400 chr5B 87.640 89 5 3 1578 1664 61147968 61148052 1.140000e-16 99.0
45 TraesCS1D01G397400 chr2D 89.583 96 8 2 1571 1666 57167741 57167648 2.430000e-23 121.0
46 TraesCS1D01G397400 chr2A 98.000 50 1 0 1578 1627 608252262 608252213 2.470000e-13 87.9
47 TraesCS1D01G397400 chr6B 81.481 108 14 5 1289 1393 26036946 26036842 3.190000e-12 84.2
48 TraesCS1D01G397400 chr3B 83.696 92 12 3 1302 1391 617418082 617417992 3.190000e-12 84.2
49 TraesCS1D01G397400 chrUn 81.609 87 12 4 1578 1660 99865456 99865542 8.930000e-08 69.4


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 TraesCS1D01G397400 chr1D 465097246 465102218 4972 False 9184.000000 9184 100.000000 1 4973 1 chr1D.!!$F2 4972
1 TraesCS1D01G397400 chr1A 557422659 557428108 5449 False 1262.600000 3171 87.501400 1 4973 5 chr1A.!!$F1 4972
2 TraesCS1D01G397400 chr4B 111778182 111783882 5700 False 664.777778 1522 91.723889 1 4973 9 chr4B.!!$F2 4972
3 TraesCS1D01G397400 chr1B 642060430 642063194 2764 False 614.800000 1182 90.676600 2077 4369 5 chr1B.!!$F1 2292

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
998 1143 0.382158 GGCGCCCTTTTGAGCTATTC 59.618 55.0 18.11 0.00 0.00 1.75 F
2178 2389 0.181350 GCGTTGATCCCCAGAATCCT 59.819 55.0 0.00 0.00 0.00 3.24 F
2330 2550 0.883814 GATTCCGCAGCCTGATCTGG 60.884 60.0 14.07 14.07 34.74 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 2773 0.299895 GTCAGAATGCATGCGTCTCG 59.700 55.0 18.17 14.16 34.76 4.04 R
3562 3913 1.134530 CGTCACGTTCTGCTCGATCC 61.135 60.0 0.00 0.00 0.00 3.36 R
4288 5439 0.806102 CTGCATGCAGCTCAAATGGC 60.806 55.0 33.18 0.00 45.94 4.40 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
59 64 3.497227 GGCCTACTTGGTTGTGGTTTCTA 60.497 47.826 0.00 0.00 38.35 2.10
95 107 9.146984 ACAAAATCAATGAATCACTTGCATAAG 57.853 29.630 0.00 0.00 39.86 1.73
96 108 7.766219 AAATCAATGAATCACTTGCATAAGC 57.234 32.000 0.00 0.00 37.43 3.09
165 178 5.222079 TCAACAGTACCATACACACACAT 57.778 39.130 0.00 0.00 0.00 3.21
197 210 9.738832 TGCATGTGTGATAATCAATTTCATAAG 57.261 29.630 0.00 0.00 0.00 1.73
198 211 9.955208 GCATGTGTGATAATCAATTTCATAAGA 57.045 29.630 0.00 0.00 0.00 2.10
280 370 7.478044 CGCGGAAAATAATTAGAACGTAACAAA 59.522 33.333 0.00 0.00 0.00 2.83
375 467 3.635734 GACGACAGTGTGCATGCGC 62.636 63.158 24.25 24.25 39.24 6.09
383 475 1.077858 TGTGCATGCGCCTATTCCA 60.078 52.632 27.42 4.89 37.32 3.53
384 476 1.096967 TGTGCATGCGCCTATTCCAG 61.097 55.000 27.42 0.00 37.32 3.86
385 477 2.188829 TGCATGCGCCTATTCCAGC 61.189 57.895 14.09 0.00 37.32 4.85
386 478 2.912624 GCATGCGCCTATTCCAGCC 61.913 63.158 4.18 0.00 0.00 4.85
466 566 2.668632 GACTTGGTGCCGGATGGA 59.331 61.111 5.05 0.00 37.49 3.41
467 567 1.224592 GACTTGGTGCCGGATGGAT 59.775 57.895 5.05 0.00 37.49 3.41
468 568 1.077501 ACTTGGTGCCGGATGGATG 60.078 57.895 5.05 0.00 37.49 3.51
560 671 3.786368 TTCACACATGATGAACCAGGA 57.214 42.857 0.00 0.00 33.85 3.86
564 675 4.278170 TCACACATGATGAACCAGGAAAAC 59.722 41.667 0.00 0.00 0.00 2.43
565 676 3.253188 ACACATGATGAACCAGGAAAACG 59.747 43.478 0.00 0.00 0.00 3.60
613 726 2.939460 AACAAACAGAACCACACAGC 57.061 45.000 0.00 0.00 0.00 4.40
636 749 6.992063 CTTCCAAGCTAAATTAGAGAGCAA 57.008 37.500 3.88 0.00 38.73 3.91
637 750 7.383102 CTTCCAAGCTAAATTAGAGAGCAAA 57.617 36.000 3.88 0.00 38.73 3.68
638 751 6.743575 TCCAAGCTAAATTAGAGAGCAAAC 57.256 37.500 3.88 0.00 38.73 2.93
652 765 5.063817 AGAGAGCAAACATGCAAACAAAAAC 59.936 36.000 3.41 0.00 37.25 2.43
704 821 4.299547 TGCGTCTCTGCTGCCGTT 62.300 61.111 0.00 0.00 35.36 4.44
728 845 4.473199 CATCGCATATTCAATTCCTGCTG 58.527 43.478 0.00 0.00 0.00 4.41
729 846 2.291465 TCGCATATTCAATTCCTGCTGC 59.709 45.455 0.00 0.00 0.00 5.25
731 848 2.288640 GCATATTCAATTCCTGCTGCCC 60.289 50.000 0.00 0.00 0.00 5.36
786 917 4.218852 CCTCCTCTCCGTAATAATCAGGAC 59.781 50.000 0.00 0.00 0.00 3.85
787 918 4.800023 TCCTCTCCGTAATAATCAGGACA 58.200 43.478 0.00 0.00 0.00 4.02
793 924 5.617252 TCCGTAATAATCAGGACAATTCCC 58.383 41.667 0.00 0.00 44.10 3.97
817 957 2.176364 AGTACGTGATTAGGAGGGCCTA 59.824 50.000 5.73 0.00 44.74 3.93
827 967 3.130734 AGGAGGGCCTAAGTAACATGA 57.869 47.619 5.73 0.00 44.74 3.07
828 968 2.772515 AGGAGGGCCTAAGTAACATGAC 59.227 50.000 5.73 0.00 44.74 3.06
829 969 2.158798 GGAGGGCCTAAGTAACATGACC 60.159 54.545 5.73 0.00 0.00 4.02
830 970 2.504175 GAGGGCCTAAGTAACATGACCA 59.496 50.000 5.73 0.00 0.00 4.02
831 971 3.123273 AGGGCCTAAGTAACATGACCAT 58.877 45.455 2.82 0.00 0.00 3.55
832 972 3.136626 AGGGCCTAAGTAACATGACCATC 59.863 47.826 2.82 0.00 0.00 3.51
833 973 3.118038 GGGCCTAAGTAACATGACCATCA 60.118 47.826 0.84 0.00 0.00 3.07
834 974 4.130118 GGCCTAAGTAACATGACCATCAG 58.870 47.826 0.00 0.00 0.00 2.90
835 975 3.561725 GCCTAAGTAACATGACCATCAGC 59.438 47.826 0.00 0.00 0.00 4.26
836 976 4.684485 GCCTAAGTAACATGACCATCAGCT 60.684 45.833 0.00 0.00 0.00 4.24
837 977 5.431765 CCTAAGTAACATGACCATCAGCTT 58.568 41.667 0.00 0.00 0.00 3.74
838 978 6.582636 CCTAAGTAACATGACCATCAGCTTA 58.417 40.000 0.00 0.00 0.00 3.09
839 979 7.047891 CCTAAGTAACATGACCATCAGCTTAA 58.952 38.462 0.00 0.00 0.00 1.85
840 980 7.552687 CCTAAGTAACATGACCATCAGCTTAAA 59.447 37.037 0.00 0.00 0.00 1.52
841 981 7.759489 AAGTAACATGACCATCAGCTTAAAA 57.241 32.000 0.00 0.00 0.00 1.52
842 982 7.759489 AGTAACATGACCATCAGCTTAAAAA 57.241 32.000 0.00 0.00 0.00 1.94
998 1143 0.382158 GGCGCCCTTTTGAGCTATTC 59.618 55.000 18.11 0.00 0.00 1.75
999 1144 0.382158 GCGCCCTTTTGAGCTATTCC 59.618 55.000 0.00 0.00 0.00 3.01
1001 1146 1.408822 CGCCCTTTTGAGCTATTCCCT 60.409 52.381 0.00 0.00 0.00 4.20
1108 1279 0.832135 TCTTCGGTCTCCTGGCACTT 60.832 55.000 0.00 0.00 0.00 3.16
1111 1282 2.431683 GGTCTCCTGGCACTTGCA 59.568 61.111 3.15 0.00 44.36 4.08
1268 1439 4.637771 GCAAGGCCAACGGAGTAT 57.362 55.556 5.01 0.00 45.00 2.12
1270 1441 1.993369 GCAAGGCCAACGGAGTATGC 61.993 60.000 5.01 0.00 45.00 3.14
1279 1452 4.497507 GCCAACGGAGTATGCCTATTTTTC 60.498 45.833 0.00 0.00 45.00 2.29
1295 1468 7.614583 GCCTATTTTTCTTTTTACCTACTCCCT 59.385 37.037 0.00 0.00 0.00 4.20
1298 1471 7.500720 TTTTTCTTTTTACCTACTCCCTTCG 57.499 36.000 0.00 0.00 0.00 3.79
1299 1472 6.423776 TTTCTTTTTACCTACTCCCTTCGA 57.576 37.500 0.00 0.00 0.00 3.71
1371 1554 4.953579 AGTTTGGCCAACTCTTGAAAAGTA 59.046 37.500 20.35 0.00 42.62 2.24
1382 1565 8.669243 CAACTCTTGAAAAGTATGGTAAGATCC 58.331 37.037 0.00 0.00 46.34 3.36
1390 1573 5.099042 AGTATGGTAAGATCCACAACACC 57.901 43.478 0.00 0.00 40.51 4.16
1402 1590 3.936453 TCCACAACACCAAATACGATAGC 59.064 43.478 0.00 0.00 42.67 2.97
1448 1636 9.920946 AATAATCTCATGGTACTAATTGGTGTT 57.079 29.630 4.47 0.00 0.00 3.32
1449 1637 7.865706 AATCTCATGGTACTAATTGGTGTTC 57.134 36.000 4.47 0.00 0.00 3.18
1450 1638 6.367374 TCTCATGGTACTAATTGGTGTTCA 57.633 37.500 4.47 0.94 0.00 3.18
1453 1641 5.937540 TCATGGTACTAATTGGTGTTCAGTG 59.062 40.000 4.47 0.00 0.00 3.66
1454 1642 5.298989 TGGTACTAATTGGTGTTCAGTGT 57.701 39.130 4.47 0.00 0.00 3.55
1456 1644 5.761234 TGGTACTAATTGGTGTTCAGTGTTC 59.239 40.000 4.47 0.00 0.00 3.18
1457 1645 5.995897 GGTACTAATTGGTGTTCAGTGTTCT 59.004 40.000 4.47 0.00 0.00 3.01
1458 1646 6.073222 GGTACTAATTGGTGTTCAGTGTTCTG 60.073 42.308 4.47 0.00 42.54 3.02
1503 1697 7.825270 TGTAGACTTGGTCAAACTTAAACAAGA 59.175 33.333 7.12 0.00 38.80 3.02
1504 1698 7.696992 AGACTTGGTCAAACTTAAACAAGAA 57.303 32.000 7.12 0.00 38.80 2.52
1505 1699 7.535997 AGACTTGGTCAAACTTAAACAAGAAC 58.464 34.615 7.12 1.82 38.80 3.01
1506 1700 7.393515 AGACTTGGTCAAACTTAAACAAGAACT 59.606 33.333 7.12 3.77 38.80 3.01
1507 1701 7.535997 ACTTGGTCAAACTTAAACAAGAACTC 58.464 34.615 7.12 0.00 38.80 3.01
1508 1702 7.175990 ACTTGGTCAAACTTAAACAAGAACTCA 59.824 33.333 7.12 0.00 38.80 3.41
1509 1703 7.083875 TGGTCAAACTTAAACAAGAACTCAG 57.916 36.000 0.00 0.00 0.00 3.35
1510 1704 6.094881 TGGTCAAACTTAAACAAGAACTCAGG 59.905 38.462 0.00 0.00 0.00 3.86
1512 1706 7.187480 GTCAAACTTAAACAAGAACTCAGGAC 58.813 38.462 0.00 0.00 0.00 3.85
1513 1707 6.882140 TCAAACTTAAACAAGAACTCAGGACA 59.118 34.615 0.00 0.00 0.00 4.02
1518 1714 3.644966 ACAAGAACTCAGGACAAACCA 57.355 42.857 0.00 0.00 42.04 3.67
1520 1716 3.947834 ACAAGAACTCAGGACAAACCAAG 59.052 43.478 0.00 0.00 42.04 3.61
1521 1717 4.199310 CAAGAACTCAGGACAAACCAAGA 58.801 43.478 0.00 0.00 42.04 3.02
1559 1755 9.950680 TTTTGAAAATAGTCTTGCTAAGTCTTG 57.049 29.630 0.00 0.00 32.72 3.02
1560 1756 7.672983 TGAAAATAGTCTTGCTAAGTCTTGG 57.327 36.000 0.00 0.00 32.72 3.61
1561 1757 7.224297 TGAAAATAGTCTTGCTAAGTCTTGGT 58.776 34.615 0.00 0.00 32.72 3.67
1562 1758 7.387948 TGAAAATAGTCTTGCTAAGTCTTGGTC 59.612 37.037 0.00 0.00 32.72 4.02
1563 1759 3.305398 AGTCTTGCTAAGTCTTGGTCG 57.695 47.619 0.00 0.00 0.00 4.79
1564 1760 2.891580 AGTCTTGCTAAGTCTTGGTCGA 59.108 45.455 0.00 0.00 0.00 4.20
1565 1761 2.987821 GTCTTGCTAAGTCTTGGTCGAC 59.012 50.000 7.13 7.13 0.00 4.20
1566 1762 2.029290 TCTTGCTAAGTCTTGGTCGACC 60.029 50.000 28.17 28.17 34.46 4.79
1567 1763 0.242825 TGCTAAGTCTTGGTCGACCG 59.757 55.000 28.70 16.15 39.43 4.79
1568 1764 0.524862 GCTAAGTCTTGGTCGACCGA 59.475 55.000 28.70 26.03 39.43 4.69
1569 1765 1.467713 GCTAAGTCTTGGTCGACCGAG 60.468 57.143 36.89 36.89 46.81 4.63
1577 1773 3.731652 TTGGTCGACCGAGACTTAAAA 57.268 42.857 28.70 11.81 40.76 1.52
1578 1774 3.017265 TGGTCGACCGAGACTTAAAAC 57.983 47.619 28.70 1.37 40.76 2.43
1579 1775 2.624838 TGGTCGACCGAGACTTAAAACT 59.375 45.455 28.70 0.00 40.76 2.66
1580 1776 3.068590 TGGTCGACCGAGACTTAAAACTT 59.931 43.478 28.70 0.00 40.76 2.66
1581 1777 3.672397 GGTCGACCGAGACTTAAAACTTC 59.328 47.826 20.85 0.00 40.76 3.01
1582 1778 3.360168 GTCGACCGAGACTTAAAACTTCG 59.640 47.826 3.51 0.00 38.09 3.79
1583 1779 3.003689 TCGACCGAGACTTAAAACTTCGT 59.996 43.478 0.00 0.00 0.00 3.85
1584 1780 3.732721 CGACCGAGACTTAAAACTTCGTT 59.267 43.478 0.00 0.00 0.00 3.85
1585 1781 4.911610 CGACCGAGACTTAAAACTTCGTTA 59.088 41.667 0.00 0.00 0.00 3.18
1586 1782 5.399301 CGACCGAGACTTAAAACTTCGTTAA 59.601 40.000 0.00 0.00 0.00 2.01
1587 1783 6.398309 CGACCGAGACTTAAAACTTCGTTAAG 60.398 42.308 3.07 3.07 42.03 1.85
1595 1791 8.350238 ACTTAAAACTTCGTTAAGTCTCAGTC 57.650 34.615 4.20 0.00 44.62 3.51
1596 1792 5.885020 AAAACTTCGTTAAGTCTCAGTCG 57.115 39.130 0.00 0.00 45.37 4.18
1597 1793 4.825546 AACTTCGTTAAGTCTCAGTCGA 57.174 40.909 0.00 0.00 45.37 4.20
1598 1794 5.373981 AACTTCGTTAAGTCTCAGTCGAT 57.626 39.130 0.00 0.00 45.37 3.59
1599 1795 6.492007 AACTTCGTTAAGTCTCAGTCGATA 57.508 37.500 0.00 0.00 45.37 2.92
1600 1796 5.867166 ACTTCGTTAAGTCTCAGTCGATAC 58.133 41.667 0.00 0.00 42.42 2.24
1601 1797 5.642919 ACTTCGTTAAGTCTCAGTCGATACT 59.357 40.000 0.00 0.00 42.42 2.12
1602 1798 6.815641 ACTTCGTTAAGTCTCAGTCGATACTA 59.184 38.462 0.00 0.00 42.42 1.82
1603 1799 7.495279 ACTTCGTTAAGTCTCAGTCGATACTAT 59.505 37.037 0.00 0.00 42.42 2.12
1604 1800 8.877808 TTCGTTAAGTCTCAGTCGATACTATA 57.122 34.615 0.00 0.00 33.48 1.31
1605 1801 9.486497 TTCGTTAAGTCTCAGTCGATACTATAT 57.514 33.333 0.00 0.00 33.48 0.86
1606 1802 9.138062 TCGTTAAGTCTCAGTCGATACTATATC 57.862 37.037 0.00 0.00 33.48 1.63
1607 1803 8.382130 CGTTAAGTCTCAGTCGATACTATATCC 58.618 40.741 0.00 0.00 33.48 2.59
1608 1804 9.217278 GTTAAGTCTCAGTCGATACTATATCCA 57.783 37.037 0.00 0.00 33.48 3.41
1609 1805 9.961264 TTAAGTCTCAGTCGATACTATATCCAT 57.039 33.333 0.00 0.00 33.48 3.41
1610 1806 7.857734 AGTCTCAGTCGATACTATATCCATG 57.142 40.000 0.00 0.00 33.48 3.66
1611 1807 7.625469 AGTCTCAGTCGATACTATATCCATGA 58.375 38.462 0.00 0.00 33.48 3.07
1612 1808 7.768582 AGTCTCAGTCGATACTATATCCATGAG 59.231 40.741 0.00 10.49 33.48 2.90
1613 1809 7.766738 GTCTCAGTCGATACTATATCCATGAGA 59.233 40.741 13.20 13.20 33.48 3.27
1614 1810 8.490311 TCTCAGTCGATACTATATCCATGAGAT 58.510 37.037 13.20 0.00 35.04 2.75
1615 1811 8.669946 TCAGTCGATACTATATCCATGAGATC 57.330 38.462 0.00 0.00 33.53 2.75
1616 1812 8.490311 TCAGTCGATACTATATCCATGAGATCT 58.510 37.037 0.00 0.00 33.53 2.75
1617 1813 9.119418 CAGTCGATACTATATCCATGAGATCTT 57.881 37.037 0.00 0.00 33.53 2.40
1638 1834 6.837992 TCTTACATTAAGATCCGCACAAAAC 58.162 36.000 0.00 0.00 39.73 2.43
1639 1835 6.428465 TCTTACATTAAGATCCGCACAAAACA 59.572 34.615 0.00 0.00 39.73 2.83
1640 1836 5.643379 ACATTAAGATCCGCACAAAACAT 57.357 34.783 0.00 0.00 0.00 2.71
1641 1837 6.024552 ACATTAAGATCCGCACAAAACATT 57.975 33.333 0.00 0.00 0.00 2.71
1642 1838 6.454795 ACATTAAGATCCGCACAAAACATTT 58.545 32.000 0.00 0.00 0.00 2.32
1643 1839 6.928492 ACATTAAGATCCGCACAAAACATTTT 59.072 30.769 0.00 0.00 0.00 1.82
1644 1840 7.440856 ACATTAAGATCCGCACAAAACATTTTT 59.559 29.630 0.00 0.00 0.00 1.94
1681 1877 8.561738 ACTTTTTCTCACTTACTGAAACTTGA 57.438 30.769 0.00 0.00 30.66 3.02
1682 1878 9.178758 ACTTTTTCTCACTTACTGAAACTTGAT 57.821 29.630 0.00 0.00 30.66 2.57
1702 1898 9.561069 ACTTGATTAAATGTAAGTCAACTGAGT 57.439 29.630 0.00 0.00 0.00 3.41
1704 1900 8.547967 TGATTAAATGTAAGTCAACTGAGTCC 57.452 34.615 0.00 0.00 0.00 3.85
1705 1901 8.375506 TGATTAAATGTAAGTCAACTGAGTCCT 58.624 33.333 0.00 0.00 0.00 3.85
1706 1902 9.871238 GATTAAATGTAAGTCAACTGAGTCCTA 57.129 33.333 0.00 0.00 0.00 2.94
1707 1903 9.877178 ATTAAATGTAAGTCAACTGAGTCCTAG 57.123 33.333 0.00 0.00 0.00 3.02
1708 1904 6.919775 AATGTAAGTCAACTGAGTCCTAGT 57.080 37.500 0.00 0.00 0.00 2.57
1709 1905 5.961396 TGTAAGTCAACTGAGTCCTAGTC 57.039 43.478 0.00 0.00 0.00 2.59
1710 1906 5.382616 TGTAAGTCAACTGAGTCCTAGTCA 58.617 41.667 0.00 0.00 0.00 3.41
1711 1907 4.857509 AAGTCAACTGAGTCCTAGTCAC 57.142 45.455 0.00 0.00 0.00 3.67
1712 1908 3.833732 AGTCAACTGAGTCCTAGTCACA 58.166 45.455 0.00 0.00 0.00 3.58
1713 1909 3.570550 AGTCAACTGAGTCCTAGTCACAC 59.429 47.826 0.00 0.00 0.00 3.82
1714 1910 2.891580 TCAACTGAGTCCTAGTCACACC 59.108 50.000 0.00 0.00 0.00 4.16
1715 1911 1.926108 ACTGAGTCCTAGTCACACCC 58.074 55.000 0.00 0.00 0.00 4.61
1716 1912 1.429687 ACTGAGTCCTAGTCACACCCT 59.570 52.381 0.00 0.00 0.00 4.34
1717 1913 2.158295 ACTGAGTCCTAGTCACACCCTT 60.158 50.000 0.00 0.00 0.00 3.95
1718 1914 2.232452 CTGAGTCCTAGTCACACCCTTG 59.768 54.545 0.00 0.00 0.00 3.61
1724 1920 2.105821 CCTAGTCACACCCTTGGAAACA 59.894 50.000 0.00 0.00 39.83 2.83
1777 1976 9.716531 TCAAAACATAATGCCATTTGTTTATGA 57.283 25.926 20.60 20.33 40.39 2.15
1785 1988 5.271598 TGCCATTTGTTTATGATCCTTCCT 58.728 37.500 0.00 0.00 0.00 3.36
1786 1989 6.430864 TGCCATTTGTTTATGATCCTTCCTA 58.569 36.000 0.00 0.00 0.00 2.94
1787 1990 7.068702 TGCCATTTGTTTATGATCCTTCCTAT 58.931 34.615 0.00 0.00 0.00 2.57
1788 1991 8.224025 TGCCATTTGTTTATGATCCTTCCTATA 58.776 33.333 0.00 0.00 0.00 1.31
1835 2038 0.248012 CTGCCATTGCCATGCTTTCA 59.752 50.000 0.00 0.00 36.33 2.69
1853 2056 1.913262 ACCTGATGGAGTGTCCGCA 60.913 57.895 0.00 0.00 40.17 5.69
1866 2077 1.121240 GTCCGCACGATCTTGTATCG 58.879 55.000 5.89 5.89 46.02 2.92
2178 2389 0.181350 GCGTTGATCCCCAGAATCCT 59.819 55.000 0.00 0.00 0.00 3.24
2193 2404 2.611964 ATCCTGGATCGGACCTGGCT 62.612 60.000 2.57 7.29 44.95 4.75
2202 2413 1.610673 GGACCTGGCTGGAGAGACA 60.611 63.158 18.12 0.00 39.71 3.41
2294 2505 3.629142 ACATTCTAAGCAGGTGGGTAC 57.371 47.619 0.00 0.00 0.00 3.34
2311 2531 1.064952 GTACATTTTGGCCCGATTCCG 59.935 52.381 0.00 0.00 0.00 4.30
2330 2550 0.883814 GATTCCGCAGCCTGATCTGG 60.884 60.000 14.07 14.07 34.74 3.86
2440 2662 3.384532 GCCGACAAGTACCGGGGA 61.385 66.667 6.32 0.00 45.42 4.81
2446 2668 2.167075 CGACAAGTACCGGGGAAAGTAT 59.833 50.000 6.32 0.00 0.00 2.12
2524 2746 6.879458 GGGTAATAAGCAACTCTCTCTGAAAA 59.121 38.462 0.00 0.00 0.00 2.29
2534 2756 2.167281 TCTCTCTGAAAAGAGATGCGGG 59.833 50.000 5.93 0.00 45.31 6.13
2557 2779 1.066152 TCAGAATCAGATGGCGAGACG 59.934 52.381 0.00 0.00 0.00 4.18
2608 2830 3.127533 GATGGTGCGGTGCAGGAC 61.128 66.667 0.00 0.00 40.08 3.85
2935 3271 1.226746 GGAACAACCTCCAGTTCGTG 58.773 55.000 0.00 0.00 43.79 4.35
3055 3391 1.808411 TCCTCGCATTTGTCAAGTCC 58.192 50.000 0.00 0.00 0.00 3.85
3099 3435 2.933906 CAACATTCCAATTCTGCCATGC 59.066 45.455 0.00 0.00 0.00 4.06
3122 3458 5.273944 CCTGCTGTTTACTTTCAGAAACAC 58.726 41.667 0.00 0.00 39.88 3.32
3123 3459 5.066505 CCTGCTGTTTACTTTCAGAAACACT 59.933 40.000 0.00 0.00 39.88 3.55
3124 3460 5.879237 TGCTGTTTACTTTCAGAAACACTG 58.121 37.500 0.00 0.00 46.97 3.66
3135 3471 2.571212 AGAAACACTGACGGCATTTCA 58.429 42.857 16.12 0.00 32.78 2.69
3562 3913 3.636231 TCGGCACCCTCACCTTGG 61.636 66.667 0.00 0.00 0.00 3.61
3594 3945 3.770040 TGACGAGGACATGGGCGG 61.770 66.667 0.00 0.00 0.00 6.13
3785 4142 0.252197 GGAGCGTCAGGTTTGGGTAT 59.748 55.000 0.00 0.00 0.00 2.73
3845 4202 2.418368 ACAAGCTGGTGTGAGTGAAA 57.582 45.000 0.00 0.00 0.00 2.69
3846 4203 2.017049 ACAAGCTGGTGTGAGTGAAAC 58.983 47.619 0.00 0.00 0.00 2.78
3847 4204 3.118408 TACAAGCTGGTGTGAGTGAAACT 60.118 43.478 3.21 0.00 41.03 2.66
3879 4796 4.111577 TCCATGTTTGAGGTCCTAGGATT 58.888 43.478 16.27 6.61 0.00 3.01
3964 4939 8.239998 GGAAGGAGTGAAGAGATTAAAAATGTG 58.760 37.037 0.00 0.00 0.00 3.21
3994 4969 0.333312 TCCTCTTCCTTCCGAGAGCT 59.667 55.000 0.00 0.00 38.43 4.09
4106 5187 3.123273 AGATACAAGGCATTACCCCAGT 58.877 45.455 0.00 0.00 40.58 4.00
4182 5263 5.298527 TCCTATCATTTGAGCTGCATTCTTG 59.701 40.000 1.02 0.00 0.00 3.02
4265 5408 3.426426 GCTGCATTTTCAGAGCTGAGAAG 60.426 47.826 9.00 0.25 41.13 2.85
4270 5413 3.601443 TTTCAGAGCTGAGAAGGCTAC 57.399 47.619 0.00 0.00 41.13 3.58
4288 5439 0.389948 ACGAAGCTAAGAAGGCACGG 60.390 55.000 0.00 0.00 36.63 4.94
4331 5482 6.426328 AGTTTCAGAGCTAAAGAGAATGTGTG 59.574 38.462 0.00 0.00 0.00 3.82
4404 6178 5.303078 ACTGACTGCTGTCTAAAAAGAGAGA 59.697 40.000 22.31 0.00 43.29 3.10
4405 6179 5.777802 TGACTGCTGTCTAAAAAGAGAGAG 58.222 41.667 22.31 0.00 43.29 3.20
4537 6311 2.007360 TGGCAAACAAGCAACACAAG 57.993 45.000 0.00 0.00 35.83 3.16
4651 6444 0.664767 GAGCAGTGCTTCTTCGACGT 60.665 55.000 20.80 0.00 39.88 4.34
4753 6546 0.438830 GACGAAAAGCCTGCGTACAG 59.561 55.000 0.00 0.00 44.05 2.74
4837 6630 4.037923 ACAACACACTGATAGGCAAAAAGG 59.962 41.667 0.00 0.00 0.00 3.11
4857 6808 3.082548 GGCTAAAAAGAAGGGGACTGAC 58.917 50.000 0.00 0.00 42.68 3.51
4891 6842 9.166173 CTGAATATGACTGAAGAAATAACACCA 57.834 33.333 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.522569 CTCCGGGCGGAAAAGAGAT 59.477 57.895 0.00 0.00 44.66 2.75
59 64 6.409524 TTCATTGATTTTGTTTCAGGAGCT 57.590 33.333 0.00 0.00 0.00 4.09
96 108 2.336945 TCTTACCTCCAGCATGCATG 57.663 50.000 22.70 22.70 31.97 4.06
97 109 2.860009 CATCTTACCTCCAGCATGCAT 58.140 47.619 21.98 1.69 31.97 3.96
98 110 1.748244 GCATCTTACCTCCAGCATGCA 60.748 52.381 21.98 0.00 37.24 3.96
106 118 8.457238 AGATAAAGAAAATGCATCTTACCTCC 57.543 34.615 0.00 0.00 36.14 4.30
139 152 8.068892 TGTGTGTGTATGGTACTGTTGATATA 57.931 34.615 0.00 0.00 0.00 0.86
151 164 3.689161 GCATGTGTATGTGTGTGTATGGT 59.311 43.478 0.00 0.00 36.65 3.55
155 168 4.322567 ACATGCATGTGTATGTGTGTGTA 58.677 39.130 30.92 0.00 46.87 2.90
280 370 7.114095 TGGGTAAACGAGCCTCTTTAATATTT 58.886 34.615 0.00 0.00 46.76 1.40
285 375 3.307199 CCTGGGTAAACGAGCCTCTTTAA 60.307 47.826 0.00 0.00 46.76 1.52
286 376 2.235402 CCTGGGTAAACGAGCCTCTTTA 59.765 50.000 0.00 0.00 46.76 1.85
287 377 1.003233 CCTGGGTAAACGAGCCTCTTT 59.997 52.381 0.00 0.00 46.76 2.52
288 378 0.613777 CCTGGGTAAACGAGCCTCTT 59.386 55.000 0.00 0.00 46.76 2.85
289 379 0.544595 ACCTGGGTAAACGAGCCTCT 60.545 55.000 0.00 0.00 46.76 3.69
290 380 0.323957 AACCTGGGTAAACGAGCCTC 59.676 55.000 0.00 0.00 46.76 4.70
375 467 4.626081 CCGGCCGGCTGGAATAGG 62.626 72.222 46.02 20.38 45.10 2.57
466 566 1.209019 CAGCACTAGCAGAGGTTCCAT 59.791 52.381 0.00 0.00 45.49 3.41
467 567 0.610174 CAGCACTAGCAGAGGTTCCA 59.390 55.000 0.00 0.00 45.49 3.53
468 568 0.742635 GCAGCACTAGCAGAGGTTCC 60.743 60.000 0.00 0.00 45.49 3.62
541 652 3.786368 TTCCTGGTTCATCATGTGTGA 57.214 42.857 0.00 0.00 39.04 3.58
560 671 3.509967 GGATCTCACCATTTTCCCGTTTT 59.490 43.478 0.00 0.00 0.00 2.43
564 675 2.717639 AGGATCTCACCATTTTCCCG 57.282 50.000 0.00 0.00 0.00 5.14
565 676 3.181439 CCCTAGGATCTCACCATTTTCCC 60.181 52.174 11.48 0.00 0.00 3.97
595 708 2.128771 AGCTGTGTGGTTCTGTTTGT 57.871 45.000 0.00 0.00 0.00 2.83
613 726 6.992063 TTGCTCTCTAATTTAGCTTGGAAG 57.008 37.500 0.00 0.00 37.16 3.46
635 748 3.600388 TCCCGTTTTTGTTTGCATGTTT 58.400 36.364 0.00 0.00 0.00 2.83
636 749 3.252974 TCCCGTTTTTGTTTGCATGTT 57.747 38.095 0.00 0.00 0.00 2.71
637 750 2.969628 TCCCGTTTTTGTTTGCATGT 57.030 40.000 0.00 0.00 0.00 3.21
638 751 3.868077 TCTTTCCCGTTTTTGTTTGCATG 59.132 39.130 0.00 0.00 0.00 4.06
652 765 3.744426 AGTTTTACACACGATCTTTCCCG 59.256 43.478 0.00 0.00 0.00 5.14
704 821 3.304861 GCAGGAATTGAATATGCGATGCA 60.305 43.478 0.00 0.00 44.86 3.96
709 826 2.606308 GGCAGCAGGAATTGAATATGCG 60.606 50.000 0.00 2.70 41.69 4.73
763 894 4.218852 GTCCTGATTATTACGGAGAGGAGG 59.781 50.000 0.00 0.00 0.00 4.30
786 917 5.303589 TCCTAATCACGTACTAGGGGAATTG 59.696 44.000 13.84 0.00 34.16 2.32
787 918 5.461327 TCCTAATCACGTACTAGGGGAATT 58.539 41.667 13.84 0.00 34.16 2.17
793 924 2.557490 GCCCTCCTAATCACGTACTAGG 59.443 54.545 9.48 9.48 34.60 3.02
817 957 7.759489 TTTTAAGCTGATGGTCATGTTACTT 57.241 32.000 0.00 0.00 0.00 2.24
818 958 7.759489 TTTTTAAGCTGATGGTCATGTTACT 57.241 32.000 0.00 0.00 0.00 2.24
840 980 7.830099 AAAGATGGTCATGAGACTTCTTTTT 57.170 32.000 22.50 11.47 44.80 1.94
841 981 7.830099 AAAAGATGGTCATGAGACTTCTTTT 57.170 32.000 27.32 27.32 46.86 2.27
842 982 8.954350 CATAAAAGATGGTCATGAGACTTCTTT 58.046 33.333 22.50 22.50 46.61 2.52
843 983 7.555554 CCATAAAAGATGGTCATGAGACTTCTT 59.444 37.037 16.53 16.53 42.99 2.52
844 984 7.052873 CCATAAAAGATGGTCATGAGACTTCT 58.947 38.462 0.00 2.86 44.36 2.85
845 985 7.011857 GTCCATAAAAGATGGTCATGAGACTTC 59.988 40.741 0.00 0.39 44.36 3.01
846 986 6.825721 GTCCATAAAAGATGGTCATGAGACTT 59.174 38.462 0.00 0.00 44.36 3.01
851 991 6.064060 GGATGTCCATAAAAGATGGTCATGA 58.936 40.000 17.32 0.00 44.08 3.07
998 1143 0.256177 GGCTTTGGAGGGAGTTAGGG 59.744 60.000 0.00 0.00 0.00 3.53
999 1144 0.991920 TGGCTTTGGAGGGAGTTAGG 59.008 55.000 0.00 0.00 0.00 2.69
1001 1146 2.490168 GGTTTGGCTTTGGAGGGAGTTA 60.490 50.000 0.00 0.00 0.00 2.24
1108 1279 0.171679 CAAGCTTCGCCATTGATGCA 59.828 50.000 0.00 0.00 40.43 3.96
1111 1282 1.133790 GAAGCAAGCTTCGCCATTGAT 59.866 47.619 17.88 0.00 42.23 2.57
1132 1303 1.516161 CCATGGCATAGTCATGTCCG 58.484 55.000 10.31 0.00 43.25 4.79
1153 1324 4.619679 AGTAGAGGAGGCTCTTCTTCAAT 58.380 43.478 30.67 13.19 34.48 2.57
1268 1439 7.395206 GGGAGTAGGTAAAAAGAAAAATAGGCA 59.605 37.037 0.00 0.00 0.00 4.75
1270 1441 9.529823 AAGGGAGTAGGTAAAAAGAAAAATAGG 57.470 33.333 0.00 0.00 0.00 2.57
1279 1452 6.877322 TGAAATCGAAGGGAGTAGGTAAAAAG 59.123 38.462 0.00 0.00 0.00 2.27
1371 1554 4.380843 TTGGTGTTGTGGATCTTACCAT 57.619 40.909 0.00 0.00 42.17 3.55
1382 1565 4.153296 TGTGCTATCGTATTTGGTGTTGTG 59.847 41.667 0.00 0.00 0.00 3.33
1435 1623 6.822442 TCAGAACACTGAACACCAATTAGTA 58.178 36.000 0.00 0.00 37.66 1.82
1473 1667 9.874215 GTTTAAGTTTGACCAAGTCTACATAAC 57.126 33.333 0.00 0.00 33.15 1.89
1476 1670 8.514330 TTGTTTAAGTTTGACCAAGTCTACAT 57.486 30.769 0.00 0.00 33.15 2.29
1503 1697 4.600062 AGTTTCTTGGTTTGTCCTGAGTT 58.400 39.130 0.00 0.00 37.07 3.01
1504 1698 4.236527 AGTTTCTTGGTTTGTCCTGAGT 57.763 40.909 0.00 0.00 37.07 3.41
1505 1699 5.582689 AAAGTTTCTTGGTTTGTCCTGAG 57.417 39.130 0.00 0.00 37.07 3.35
1506 1700 7.654022 ATTAAAGTTTCTTGGTTTGTCCTGA 57.346 32.000 0.00 0.00 37.07 3.86
1507 1701 9.981114 ATAATTAAAGTTTCTTGGTTTGTCCTG 57.019 29.630 0.00 0.00 37.07 3.86
1538 1734 6.369065 CGACCAAGACTTAGCAAGACTATTTT 59.631 38.462 3.37 0.00 33.26 1.82
1539 1735 5.869888 CGACCAAGACTTAGCAAGACTATTT 59.130 40.000 3.37 0.00 33.26 1.40
1540 1736 5.185249 TCGACCAAGACTTAGCAAGACTATT 59.815 40.000 3.37 0.00 33.26 1.73
1541 1737 4.705507 TCGACCAAGACTTAGCAAGACTAT 59.294 41.667 3.37 0.00 33.26 2.12
1542 1738 4.077108 TCGACCAAGACTTAGCAAGACTA 58.923 43.478 3.37 0.00 33.26 2.59
1543 1739 2.891580 TCGACCAAGACTTAGCAAGACT 59.108 45.455 3.37 0.28 35.05 3.24
1544 1740 2.987821 GTCGACCAAGACTTAGCAAGAC 59.012 50.000 3.51 0.00 38.09 3.01
1545 1741 2.029290 GGTCGACCAAGACTTAGCAAGA 60.029 50.000 29.75 0.00 40.76 3.02
1546 1742 2.338500 GGTCGACCAAGACTTAGCAAG 58.662 52.381 29.75 0.00 40.76 4.01
1547 1743 1.336517 CGGTCGACCAAGACTTAGCAA 60.337 52.381 32.80 0.00 40.76 3.91
1548 1744 0.242825 CGGTCGACCAAGACTTAGCA 59.757 55.000 32.80 0.00 40.76 3.49
1549 1745 0.524862 TCGGTCGACCAAGACTTAGC 59.475 55.000 32.80 3.24 40.76 3.09
1550 1746 2.082231 TCTCGGTCGACCAAGACTTAG 58.918 52.381 32.80 14.79 40.76 2.18
1551 1747 1.808945 GTCTCGGTCGACCAAGACTTA 59.191 52.381 37.32 12.46 40.76 2.24
1552 1748 0.597072 GTCTCGGTCGACCAAGACTT 59.403 55.000 37.32 0.00 40.76 3.01
1553 1749 0.250814 AGTCTCGGTCGACCAAGACT 60.251 55.000 40.27 40.27 40.76 3.24
1554 1750 0.597072 AAGTCTCGGTCGACCAAGAC 59.403 55.000 37.66 37.66 40.25 3.01
1555 1751 2.189594 TAAGTCTCGGTCGACCAAGA 57.810 50.000 32.80 27.44 34.46 3.02
1556 1752 3.293311 TTTAAGTCTCGGTCGACCAAG 57.707 47.619 32.80 25.45 34.46 3.61
1557 1753 3.068590 AGTTTTAAGTCTCGGTCGACCAA 59.931 43.478 32.80 16.12 34.46 3.67
1558 1754 2.624838 AGTTTTAAGTCTCGGTCGACCA 59.375 45.455 32.80 19.01 34.46 4.02
1559 1755 3.294816 AGTTTTAAGTCTCGGTCGACC 57.705 47.619 25.28 25.28 34.46 4.79
1560 1756 3.360168 CGAAGTTTTAAGTCTCGGTCGAC 59.640 47.826 7.13 7.13 0.00 4.20
1561 1757 3.003689 ACGAAGTTTTAAGTCTCGGTCGA 59.996 43.478 0.00 0.00 37.78 4.20
1562 1758 3.303406 ACGAAGTTTTAAGTCTCGGTCG 58.697 45.455 0.00 0.00 37.78 4.79
1574 1770 7.325579 GTATCGACTGAGACTTAACGAAGTTTT 59.674 37.037 0.00 0.00 46.23 2.43
1575 1771 6.800892 GTATCGACTGAGACTTAACGAAGTTT 59.199 38.462 0.00 0.00 46.23 2.66
1576 1772 6.149142 AGTATCGACTGAGACTTAACGAAGTT 59.851 38.462 0.00 0.00 43.97 2.66
1577 1773 5.642919 AGTATCGACTGAGACTTAACGAAGT 59.357 40.000 0.00 0.00 43.97 3.01
1578 1774 6.109320 AGTATCGACTGAGACTTAACGAAG 57.891 41.667 0.00 0.00 43.97 3.79
1579 1775 7.783090 ATAGTATCGACTGAGACTTAACGAA 57.217 36.000 0.00 0.00 43.97 3.85
1580 1776 9.138062 GATATAGTATCGACTGAGACTTAACGA 57.862 37.037 0.00 0.00 43.97 3.85
1581 1777 8.382130 GGATATAGTATCGACTGAGACTTAACG 58.618 40.741 0.00 0.00 43.97 3.18
1582 1778 9.217278 TGGATATAGTATCGACTGAGACTTAAC 57.783 37.037 0.00 0.00 43.97 2.01
1583 1779 9.961264 ATGGATATAGTATCGACTGAGACTTAA 57.039 33.333 0.00 0.00 43.97 1.85
1584 1780 9.384764 CATGGATATAGTATCGACTGAGACTTA 57.615 37.037 0.00 0.00 43.97 2.24
1585 1781 8.103935 TCATGGATATAGTATCGACTGAGACTT 58.896 37.037 0.00 0.00 43.97 3.01
1587 1783 7.766738 TCTCATGGATATAGTATCGACTGAGAC 59.233 40.741 14.22 0.00 36.28 3.36
1588 1784 7.852263 TCTCATGGATATAGTATCGACTGAGA 58.148 38.462 14.22 14.22 36.28 3.27
1589 1785 8.675705 ATCTCATGGATATAGTATCGACTGAG 57.324 38.462 0.00 11.66 33.24 3.35
1590 1786 8.490311 AGATCTCATGGATATAGTATCGACTGA 58.510 37.037 0.00 0.00 34.33 3.41
1591 1787 8.675705 AGATCTCATGGATATAGTATCGACTG 57.324 38.462 0.00 0.00 34.33 3.51
1615 1811 6.607689 TGTTTTGTGCGGATCTTAATGTAAG 58.392 36.000 0.00 0.00 37.13 2.34
1616 1812 6.561737 TGTTTTGTGCGGATCTTAATGTAA 57.438 33.333 0.00 0.00 0.00 2.41
1617 1813 6.751514 ATGTTTTGTGCGGATCTTAATGTA 57.248 33.333 0.00 0.00 0.00 2.29
1618 1814 5.643379 ATGTTTTGTGCGGATCTTAATGT 57.357 34.783 0.00 0.00 0.00 2.71
1619 1815 6.949578 AAATGTTTTGTGCGGATCTTAATG 57.050 33.333 0.00 0.00 0.00 1.90
1620 1816 7.961325 AAAAATGTTTTGTGCGGATCTTAAT 57.039 28.000 0.00 0.00 0.00 1.40
1655 1851 9.661563 TCAAGTTTCAGTAAGTGAGAAAAAGTA 57.338 29.630 0.00 0.00 36.21 2.24
1656 1852 8.561738 TCAAGTTTCAGTAAGTGAGAAAAAGT 57.438 30.769 0.00 0.00 36.21 2.66
1676 1872 9.561069 ACTCAGTTGACTTACATTTAATCAAGT 57.439 29.630 2.27 2.27 34.11 3.16
1678 1874 8.999431 GGACTCAGTTGACTTACATTTAATCAA 58.001 33.333 0.00 0.00 0.00 2.57
1679 1875 8.375506 AGGACTCAGTTGACTTACATTTAATCA 58.624 33.333 0.00 0.00 0.00 2.57
1680 1876 8.779354 AGGACTCAGTTGACTTACATTTAATC 57.221 34.615 0.00 0.00 0.00 1.75
1681 1877 9.877178 CTAGGACTCAGTTGACTTACATTTAAT 57.123 33.333 0.00 0.00 0.00 1.40
1682 1878 8.867097 ACTAGGACTCAGTTGACTTACATTTAA 58.133 33.333 0.00 0.00 0.00 1.52
1683 1879 8.418597 ACTAGGACTCAGTTGACTTACATTTA 57.581 34.615 0.00 0.00 0.00 1.40
1684 1880 7.015292 TGACTAGGACTCAGTTGACTTACATTT 59.985 37.037 0.00 0.00 0.00 2.32
1685 1881 6.493802 TGACTAGGACTCAGTTGACTTACATT 59.506 38.462 0.00 0.00 0.00 2.71
1686 1882 6.010850 TGACTAGGACTCAGTTGACTTACAT 58.989 40.000 0.00 0.00 0.00 2.29
1687 1883 5.241064 GTGACTAGGACTCAGTTGACTTACA 59.759 44.000 0.00 0.00 0.00 2.41
1688 1884 5.241064 TGTGACTAGGACTCAGTTGACTTAC 59.759 44.000 0.00 0.00 0.00 2.34
1689 1885 5.241064 GTGTGACTAGGACTCAGTTGACTTA 59.759 44.000 0.00 0.00 0.00 2.24
1690 1886 4.038162 GTGTGACTAGGACTCAGTTGACTT 59.962 45.833 0.00 0.00 0.00 3.01
1691 1887 3.570550 GTGTGACTAGGACTCAGTTGACT 59.429 47.826 0.00 0.00 0.00 3.41
1692 1888 3.305471 GGTGTGACTAGGACTCAGTTGAC 60.305 52.174 0.00 0.00 0.00 3.18
1693 1889 2.891580 GGTGTGACTAGGACTCAGTTGA 59.108 50.000 0.00 0.00 0.00 3.18
1694 1890 2.028930 GGGTGTGACTAGGACTCAGTTG 60.029 54.545 0.00 0.00 0.00 3.16
1695 1891 2.158295 AGGGTGTGACTAGGACTCAGTT 60.158 50.000 0.00 0.00 0.00 3.16
1696 1892 1.429687 AGGGTGTGACTAGGACTCAGT 59.570 52.381 0.00 0.00 0.00 3.41
1697 1893 2.223803 AGGGTGTGACTAGGACTCAG 57.776 55.000 0.00 0.00 0.00 3.35
1698 1894 2.248248 CAAGGGTGTGACTAGGACTCA 58.752 52.381 0.00 0.00 0.00 3.41
1699 1895 1.550976 CCAAGGGTGTGACTAGGACTC 59.449 57.143 0.00 0.00 0.00 3.36
1700 1896 1.149288 TCCAAGGGTGTGACTAGGACT 59.851 52.381 0.00 0.00 0.00 3.85
1701 1897 1.640917 TCCAAGGGTGTGACTAGGAC 58.359 55.000 0.00 0.00 0.00 3.85
1702 1898 2.370849 GTTTCCAAGGGTGTGACTAGGA 59.629 50.000 0.00 0.00 0.00 2.94
1703 1899 2.105821 TGTTTCCAAGGGTGTGACTAGG 59.894 50.000 0.00 0.00 0.00 3.02
1704 1900 3.071023 TCTGTTTCCAAGGGTGTGACTAG 59.929 47.826 0.00 0.00 0.00 2.57
1705 1901 3.042682 TCTGTTTCCAAGGGTGTGACTA 58.957 45.455 0.00 0.00 0.00 2.59
1706 1902 1.843851 TCTGTTTCCAAGGGTGTGACT 59.156 47.619 0.00 0.00 0.00 3.41
1707 1903 2.222027 CTCTGTTTCCAAGGGTGTGAC 58.778 52.381 0.00 0.00 0.00 3.67
1708 1904 1.142870 CCTCTGTTTCCAAGGGTGTGA 59.857 52.381 0.00 0.00 0.00 3.58
1709 1905 1.133792 ACCTCTGTTTCCAAGGGTGTG 60.134 52.381 0.00 0.00 34.31 3.82
1710 1906 1.222567 ACCTCTGTTTCCAAGGGTGT 58.777 50.000 0.00 0.00 34.31 4.16
1711 1907 2.372172 AGTACCTCTGTTTCCAAGGGTG 59.628 50.000 0.00 0.00 34.31 4.61
1712 1908 2.702748 AGTACCTCTGTTTCCAAGGGT 58.297 47.619 0.00 0.00 34.31 4.34
1713 1909 3.838903 ACTAGTACCTCTGTTTCCAAGGG 59.161 47.826 0.00 0.00 34.31 3.95
1714 1910 5.479375 TGTACTAGTACCTCTGTTTCCAAGG 59.521 44.000 26.41 0.00 35.26 3.61
1715 1911 6.585695 TGTACTAGTACCTCTGTTTCCAAG 57.414 41.667 26.41 0.00 35.26 3.61
1716 1912 7.892241 AGTATGTACTAGTACCTCTGTTTCCAA 59.108 37.037 26.41 7.09 34.13 3.53
1717 1913 7.408543 AGTATGTACTAGTACCTCTGTTTCCA 58.591 38.462 26.41 7.62 34.13 3.53
1718 1914 7.878547 AGTATGTACTAGTACCTCTGTTTCC 57.121 40.000 26.41 7.48 34.13 3.13
1796 1999 5.048083 GGCAGTGGTTCATCAAGTTCATTAA 60.048 40.000 0.00 0.00 0.00 1.40
1800 2003 2.229792 GGCAGTGGTTCATCAAGTTCA 58.770 47.619 0.00 0.00 0.00 3.18
1835 2038 1.913262 TGCGGACACTCCATCAGGT 60.913 57.895 0.00 0.00 35.91 4.00
1855 2058 4.669318 TCGACCTGAAACGATACAAGATC 58.331 43.478 0.00 0.00 33.62 2.75
1861 2064 4.265556 CACAAGATCGACCTGAAACGATAC 59.734 45.833 0.00 0.00 46.71 2.24
1866 2077 2.076863 CCCACAAGATCGACCTGAAAC 58.923 52.381 0.00 0.00 0.00 2.78
1867 2078 1.974957 TCCCACAAGATCGACCTGAAA 59.025 47.619 0.00 0.00 0.00 2.69
2154 2365 1.153168 CTGGGGATCAACGCGGAAT 60.153 57.895 12.47 0.00 31.87 3.01
2178 2389 3.083349 CCAGCCAGGTCCGATCCA 61.083 66.667 0.00 0.00 0.00 3.41
2181 2392 1.760086 CTCTCCAGCCAGGTCCGAT 60.760 63.158 0.00 0.00 39.02 4.18
2230 2441 1.202533 CGGATAAGTGGTGCGGAAGAT 60.203 52.381 0.00 0.00 0.00 2.40
2294 2505 1.032014 ATCGGAATCGGGCCAAAATG 58.968 50.000 4.39 0.00 36.95 2.32
2311 2531 0.883814 CCAGATCAGGCTGCGGAATC 60.884 60.000 10.34 7.72 34.56 2.52
2330 2550 5.679734 TGTCAGATTTCTTCAAGTTGAGC 57.320 39.130 5.56 0.00 0.00 4.26
2333 2553 7.642978 CAGTTCTTGTCAGATTTCTTCAAGTTG 59.357 37.037 15.59 0.00 37.02 3.16
2531 2753 1.520494 CCATCTGATTCTGATGCCCG 58.480 55.000 21.72 9.69 38.11 6.13
2532 2754 1.245732 GCCATCTGATTCTGATGCCC 58.754 55.000 21.72 13.75 38.11 5.36
2534 2756 1.799403 CTCGCCATCTGATTCTGATGC 59.201 52.381 21.72 16.99 38.11 3.91
2539 2761 3.955291 CGTCTCGCCATCTGATTCT 57.045 52.632 0.00 0.00 0.00 2.40
2551 2773 0.299895 GTCAGAATGCATGCGTCTCG 59.700 55.000 18.17 14.16 34.76 4.04
2557 2779 3.795623 AAGGAATGTCAGAATGCATGC 57.204 42.857 11.82 11.82 34.10 4.06
2558 2780 5.319140 TGAAAGGAATGTCAGAATGCATG 57.681 39.130 0.00 0.00 34.10 4.06
2559 2781 5.244402 TGTTGAAAGGAATGTCAGAATGCAT 59.756 36.000 0.00 0.00 35.03 3.96
2560 2782 4.583907 TGTTGAAAGGAATGTCAGAATGCA 59.416 37.500 0.00 0.00 34.76 3.96
2561 2783 5.125100 TGTTGAAAGGAATGTCAGAATGC 57.875 39.130 0.00 0.00 34.76 3.56
2562 2784 7.115805 CACATTGTTGAAAGGAATGTCAGAATG 59.884 37.037 0.00 0.00 38.06 2.67
2563 2785 7.014518 TCACATTGTTGAAAGGAATGTCAGAAT 59.985 33.333 0.00 0.00 38.06 2.40
2935 3271 3.394836 AGGAAGGAGGCGCTGGTC 61.395 66.667 7.64 1.41 0.00 4.02
3043 3379 5.836024 TTACTACCTGGGACTTGACAAAT 57.164 39.130 0.00 0.00 0.00 2.32
3055 3391 2.034812 GGCTGTCGAGATTACTACCTGG 59.965 54.545 0.00 0.00 0.00 4.45
3099 3435 5.066505 AGTGTTTCTGAAAGTAAACAGCAGG 59.933 40.000 2.48 0.00 41.27 4.85
3122 3458 7.593273 TGTATAAAAAGTTTGAAATGCCGTCAG 59.407 33.333 0.00 0.00 0.00 3.51
3123 3459 7.426410 TGTATAAAAAGTTTGAAATGCCGTCA 58.574 30.769 0.00 0.00 0.00 4.35
3124 3460 7.061789 CCTGTATAAAAAGTTTGAAATGCCGTC 59.938 37.037 0.00 0.00 0.00 4.79
3127 3463 7.870445 TCACCTGTATAAAAAGTTTGAAATGCC 59.130 33.333 0.00 0.00 0.00 4.40
3562 3913 1.134530 CGTCACGTTCTGCTCGATCC 61.135 60.000 0.00 0.00 0.00 3.36
3594 3945 2.184579 GTAGGTCCTGCGCCTGAC 59.815 66.667 15.76 15.76 37.54 3.51
3879 4796 3.636300 CCACCAAAAACTCTGGATTGTCA 59.364 43.478 0.00 0.00 37.40 3.58
3964 4939 3.557228 AGGAAGAGGATGAGCACAATC 57.443 47.619 0.00 0.00 0.00 2.67
4079 5160 5.656859 GGGGTAATGCCTTGTATCTTCTTTT 59.343 40.000 0.00 0.00 37.43 2.27
4080 5161 5.201243 GGGGTAATGCCTTGTATCTTCTTT 58.799 41.667 0.00 0.00 37.43 2.52
4081 5162 4.229582 TGGGGTAATGCCTTGTATCTTCTT 59.770 41.667 0.00 0.00 37.43 2.52
4082 5163 3.785887 TGGGGTAATGCCTTGTATCTTCT 59.214 43.478 0.00 0.00 37.43 2.85
4083 5164 4.137543 CTGGGGTAATGCCTTGTATCTTC 58.862 47.826 0.00 0.00 37.43 2.87
4089 5170 2.694616 AAACTGGGGTAATGCCTTGT 57.305 45.000 0.00 0.00 37.43 3.16
4182 5263 2.227388 CAGTGTTTCAGGGCATTGACTC 59.773 50.000 0.00 0.00 0.00 3.36
4270 5413 1.696832 GCCGTGCCTTCTTAGCTTCG 61.697 60.000 0.00 0.00 0.00 3.79
4288 5439 0.806102 CTGCATGCAGCTCAAATGGC 60.806 55.000 33.18 0.00 45.94 4.40
4404 6178 1.486726 GTAGCTCACATAGTTGGGGCT 59.513 52.381 0.00 0.00 36.89 5.19
4405 6179 1.806623 CGTAGCTCACATAGTTGGGGC 60.807 57.143 0.00 0.00 0.00 5.80
4506 6280 9.676195 GTTGCTTGTTTGCCATAATTTATTTTT 57.324 25.926 0.00 0.00 0.00 1.94
4511 6285 6.283694 TGTGTTGCTTGTTTGCCATAATTTA 58.716 32.000 0.00 0.00 0.00 1.40
4512 6286 5.121811 TGTGTTGCTTGTTTGCCATAATTT 58.878 33.333 0.00 0.00 0.00 1.82
4686 6479 4.810191 AGTCTAACTTGAGGTCCACATC 57.190 45.455 0.00 0.00 0.00 3.06
4736 6529 0.716108 CTCTGTACGCAGGCTTTTCG 59.284 55.000 0.00 0.00 42.78 3.46
4753 6546 2.467962 GGCCTTACCAACGCTTCTC 58.532 57.895 0.00 0.00 38.86 2.87
4772 6565 2.373169 TCTTCTCTGCATCCCTGTGTTT 59.627 45.455 0.00 0.00 0.00 2.83
4837 6630 3.751518 TGTCAGTCCCCTTCTTTTTAGC 58.248 45.455 0.00 0.00 0.00 3.09
4842 6635 2.106684 GTTCCTGTCAGTCCCCTTCTTT 59.893 50.000 0.00 0.00 0.00 2.52
4843 6636 1.700186 GTTCCTGTCAGTCCCCTTCTT 59.300 52.381 0.00 0.00 0.00 2.52
4844 6637 1.353091 GTTCCTGTCAGTCCCCTTCT 58.647 55.000 0.00 0.00 0.00 2.85
4857 6808 6.401394 TCTTCAGTCATATTCAGTGTTCCTG 58.599 40.000 0.00 0.00 42.97 3.86


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

AutoCloner maintained by Alex Coulton.