Multiple sequence alignment - TraesCS4D01G167600

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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 TraesCS4D01G167600 chr4D 100.000 2916 0 0 1 2916 291738026 291735111 0.000000e+00 5385.0
1 TraesCS4D01G167600 chr4B 84.669 1709 100 69 1 1638 273687398 273689015 0.000000e+00 1555.0
2 TraesCS4D01G167600 chr4B 85.759 646 43 24 724 1359 565111773 565112379 3.170000e-179 638.0
3 TraesCS4D01G167600 chr4B 92.978 413 27 2 1720 2131 273689014 273689425 4.160000e-168 601.0
4 TraesCS4D01G167600 chr4B 84.704 523 34 22 727 1239 10622139 10621653 5.650000e-132 481.0
5 TraesCS4D01G167600 chr4B 92.920 226 12 4 2338 2559 273689654 273689879 2.800000e-85 326.0
6 TraesCS4D01G167600 chr4B 93.506 77 5 0 2266 2342 273689544 273689620 6.600000e-22 115.0
7 TraesCS4D01G167600 chr4B 88.462 52 0 1 2871 2916 273689881 273689932 1.130000e-04 58.4
8 TraesCS4D01G167600 chr4A 85.528 1610 87 49 50 1592 210999129 211000659 0.000000e+00 1548.0
9 TraesCS4D01G167600 chr4A 87.942 622 45 18 1749 2342 211000682 211001301 0.000000e+00 706.0
10 TraesCS4D01G167600 chr4A 79.849 531 46 29 2339 2838 211001357 211001857 6.020000e-87 331.0
11 TraesCS4D01G167600 chr6B 85.692 643 43 24 727 1359 387720016 387719413 1.470000e-177 632.0
12 TraesCS4D01G167600 chr7B 85.294 646 46 24 724 1359 709128763 709129369 3.190000e-174 621.0
13 TraesCS4D01G167600 chr7B 84.914 643 48 24 727 1359 613375552 613374949 3.210000e-169 604.0
14 TraesCS4D01G167600 chr7B 83.270 526 55 12 2339 2838 591953482 591954000 1.230000e-123 453.0
15 TraesCS4D01G167600 chr7B 82.890 526 57 12 2339 2838 592345910 592345392 2.670000e-120 442.0
16 TraesCS4D01G167600 chr2B 85.381 643 45 24 727 1359 29006026 29005423 3.190000e-174 621.0
17 TraesCS4D01G167600 chr3B 84.783 644 47 26 727 1359 16180627 16180024 1.500000e-167 599.0
18 TraesCS4D01G167600 chr7D 82.765 528 55 17 2339 2838 548774203 548773684 3.450000e-119 438.0
19 TraesCS4D01G167600 chr7D 85.922 206 19 6 1834 2034 548774977 548774777 8.190000e-51 211.0
20 TraesCS4D01G167600 chr7D 96.591 88 3 0 1637 1724 87228036 87228123 2.340000e-31 147.0
21 TraesCS4D01G167600 chr7D 94.681 94 5 0 1632 1725 458728558 458728465 2.340000e-31 147.0
22 TraesCS4D01G167600 chr7D 93.750 96 6 0 1629 1724 386508007 386507912 8.420000e-31 145.0
23 TraesCS4D01G167600 chr7D 90.385 104 7 3 1636 1739 119063563 119063463 1.820000e-27 134.0
24 TraesCS4D01G167600 chr7A 81.818 528 59 17 2339 2838 632548933 632548415 2.700000e-110 409.0
25 TraesCS4D01G167600 chr7A 83.182 220 21 9 1876 2086 632549685 632549473 1.380000e-43 187.0
26 TraesCS4D01G167600 chr3D 94.565 92 5 0 1633 1724 424478026 424477935 3.030000e-30 143.0
27 TraesCS4D01G167600 chr2D 94.565 92 5 0 1631 1722 79051098 79051007 3.030000e-30 143.0
28 TraesCS4D01G167600 chr1D 93.684 95 5 1 1629 1722 340660132 340660038 1.090000e-29 141.0
29 TraesCS4D01G167600 chr1D 94.444 90 5 0 1633 1722 64326006 64325917 3.920000e-29 139.0
30 TraesCS4D01G167600 chr5B 88.991 109 11 1 1637 1744 183255760 183255868 1.820000e-27 134.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G167600 chr4D 291735111 291738026 2915 True 5385.000000 5385 100.000000 1 2916 1 chr4D.!!$R1 2915
1 TraesCS4D01G167600 chr4B 565111773 565112379 606 False 638.000000 638 85.759000 724 1359 1 chr4B.!!$F1 635
2 TraesCS4D01G167600 chr4B 273687398 273689932 2534 False 531.080000 1555 90.507000 1 2916 5 chr4B.!!$F2 2915
3 TraesCS4D01G167600 chr4A 210999129 211001857 2728 False 861.666667 1548 84.439667 50 2838 3 chr4A.!!$F1 2788
4 TraesCS4D01G167600 chr6B 387719413 387720016 603 True 632.000000 632 85.692000 727 1359 1 chr6B.!!$R1 632
5 TraesCS4D01G167600 chr7B 709128763 709129369 606 False 621.000000 621 85.294000 724 1359 1 chr7B.!!$F2 635
6 TraesCS4D01G167600 chr7B 613374949 613375552 603 True 604.000000 604 84.914000 727 1359 1 chr7B.!!$R2 632
7 TraesCS4D01G167600 chr7B 591953482 591954000 518 False 453.000000 453 83.270000 2339 2838 1 chr7B.!!$F1 499
8 TraesCS4D01G167600 chr7B 592345392 592345910 518 True 442.000000 442 82.890000 2339 2838 1 chr7B.!!$R1 499
9 TraesCS4D01G167600 chr2B 29005423 29006026 603 True 621.000000 621 85.381000 727 1359 1 chr2B.!!$R1 632
10 TraesCS4D01G167600 chr3B 16180024 16180627 603 True 599.000000 599 84.783000 727 1359 1 chr3B.!!$R1 632
11 TraesCS4D01G167600 chr7D 548773684 548774977 1293 True 324.500000 438 84.343500 1834 2838 2 chr7D.!!$R4 1004
12 TraesCS4D01G167600 chr7A 632548415 632549685 1270 True 298.000000 409 82.500000 1876 2838 2 chr7A.!!$R1 962

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
431 448 0.106708 TGGCCGCTCCTGCTATAAAG 59.893 55.0 0.0 0.0 36.97 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2365 2900 0.179163 GCAAACGGCAAGATAGCACC 60.179 55.0 0.0 0.0 43.97 5.01 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
193 194 4.498520 CCGCCGCTCATCGACAGT 62.499 66.667 0.00 0.00 41.67 3.55
245 260 2.575455 GAAGAGGAGGAGCGGGAGGA 62.575 65.000 0.00 0.00 0.00 3.71
250 265 0.393132 GGAGGAGCGGGAGGAAAAAG 60.393 60.000 0.00 0.00 0.00 2.27
255 270 2.030185 GGAGCGGGAGGAAAAAGAAAAC 60.030 50.000 0.00 0.00 0.00 2.43
256 271 1.607148 AGCGGGAGGAAAAAGAAAACG 59.393 47.619 0.00 0.00 0.00 3.60
257 272 1.335597 GCGGGAGGAAAAAGAAAACGG 60.336 52.381 0.00 0.00 0.00 4.44
258 273 1.268625 CGGGAGGAAAAAGAAAACGGG 59.731 52.381 0.00 0.00 0.00 5.28
267 282 0.251209 AAGAAAACGGGAAGGAGGGC 60.251 55.000 0.00 0.00 0.00 5.19
315 330 2.426406 GGCCCAGCCCAATAACAGC 61.426 63.158 0.00 0.00 44.06 4.40
336 351 4.101448 CCACGGCCCAAGGAGGAG 62.101 72.222 0.00 0.00 41.22 3.69
340 355 4.120755 GGCCCAAGGAGGAGGCTG 62.121 72.222 0.00 0.00 46.31 4.85
341 356 4.811364 GCCCAAGGAGGAGGCTGC 62.811 72.222 0.00 0.00 43.62 5.25
342 357 4.479993 CCCAAGGAGGAGGCTGCG 62.480 72.222 0.00 0.00 41.22 5.18
343 358 3.710722 CCAAGGAGGAGGCTGCGT 61.711 66.667 0.00 0.00 41.22 5.24
344 359 2.348998 CAAGGAGGAGGCTGCGTT 59.651 61.111 0.00 0.00 0.00 4.84
345 360 2.037136 CAAGGAGGAGGCTGCGTTG 61.037 63.158 0.00 2.49 0.00 4.10
346 361 3.909086 AAGGAGGAGGCTGCGTTGC 62.909 63.158 0.00 0.00 0.00 4.17
347 362 4.704833 GGAGGAGGCTGCGTTGCA 62.705 66.667 0.00 0.00 36.92 4.08
348 363 2.669569 GAGGAGGCTGCGTTGCAA 60.670 61.111 0.00 0.00 38.41 4.08
349 364 2.670934 AGGAGGCTGCGTTGCAAG 60.671 61.111 0.00 0.00 38.41 4.01
350 365 4.410743 GGAGGCTGCGTTGCAAGC 62.411 66.667 0.00 6.66 38.41 4.01
351 366 4.748679 GAGGCTGCGTTGCAAGCG 62.749 66.667 0.00 8.25 38.41 4.68
431 448 0.106708 TGGCCGCTCCTGCTATAAAG 59.893 55.000 0.00 0.00 36.97 1.85
482 500 1.743252 CCGCACCAGCTTCTCTTCC 60.743 63.158 0.00 0.00 39.10 3.46
530 548 0.250513 GAGATCAAGGTGCGTCCCTT 59.749 55.000 0.00 2.34 45.85 3.95
531 549 0.250513 AGATCAAGGTGCGTCCCTTC 59.749 55.000 4.95 0.00 43.04 3.46
532 550 0.744771 GATCAAGGTGCGTCCCTTCC 60.745 60.000 4.95 0.00 43.04 3.46
539 572 4.344865 GCGTCCCTTCCCTGCCAA 62.345 66.667 0.00 0.00 0.00 4.52
570 603 3.557595 GGTAATCTGTTGCTCGATCTTGG 59.442 47.826 0.00 0.00 0.00 3.61
693 733 3.030291 CAGGATCTATGGCTAGCCTAGG 58.970 54.545 33.07 21.41 36.94 3.02
708 748 1.302366 CTAGGATGCGATGCTTTGCA 58.698 50.000 16.20 16.20 46.23 4.08
725 789 0.940126 GCATACCGCAAGATGGACTG 59.060 55.000 0.00 0.00 41.79 3.51
773 837 5.614324 TGTGTCCCAGATCCTGTTATTAG 57.386 43.478 0.00 0.00 0.00 1.73
778 842 5.753921 GTCCCAGATCCTGTTATTAGTTTCG 59.246 44.000 0.00 0.00 0.00 3.46
779 843 5.424252 TCCCAGATCCTGTTATTAGTTTCGT 59.576 40.000 0.00 0.00 0.00 3.85
780 844 6.608405 TCCCAGATCCTGTTATTAGTTTCGTA 59.392 38.462 0.00 0.00 0.00 3.43
781 845 6.924060 CCCAGATCCTGTTATTAGTTTCGTAG 59.076 42.308 0.00 0.00 0.00 3.51
811 875 3.032017 AGTAGGAATCGATTCATGCCG 57.968 47.619 32.92 0.00 38.53 5.69
823 891 1.529226 TCATGCCGTTTGTTAGGGTG 58.471 50.000 0.00 0.00 34.18 4.61
824 892 1.072489 TCATGCCGTTTGTTAGGGTGA 59.928 47.619 0.00 0.00 34.18 4.02
860 934 4.313277 TGATGTCGCTAGATTCTTGGAG 57.687 45.455 0.00 0.00 0.00 3.86
877 951 2.116983 GAGACAAGGCTGTGGCTGGA 62.117 60.000 9.35 0.00 36.83 3.86
878 952 1.968540 GACAAGGCTGTGGCTGGAC 60.969 63.158 2.44 0.00 38.81 4.02
880 954 1.303888 CAAGGCTGTGGCTGGACAT 60.304 57.895 0.00 0.00 38.81 3.06
896 970 1.207089 GACATGACCGACTTCCCATGA 59.793 52.381 0.00 0.00 38.83 3.07
901 975 1.141881 CCGACTTCCCATGACCTCG 59.858 63.158 0.00 0.00 0.00 4.63
949 1032 3.763897 AGTTTGTGCCTCAACTGTTTCTT 59.236 39.130 0.00 0.00 35.61 2.52
950 1033 4.105486 GTTTGTGCCTCAACTGTTTCTTC 58.895 43.478 0.00 0.00 35.61 2.87
951 1034 3.281727 TGTGCCTCAACTGTTTCTTCT 57.718 42.857 0.00 0.00 0.00 2.85
952 1035 3.620488 TGTGCCTCAACTGTTTCTTCTT 58.380 40.909 0.00 0.00 0.00 2.52
972 1055 0.311790 CCATTTGCAGTCGCTGTTGT 59.688 50.000 8.32 0.00 39.64 3.32
1063 1146 2.159043 AGGAAGTGGTATGTCTCATGCG 60.159 50.000 0.00 0.00 0.00 4.73
1065 1148 0.826715 AGTGGTATGTCTCATGCGCT 59.173 50.000 9.73 0.00 0.00 5.92
1084 1167 3.716601 GCTCTCTCTTTAGTCTGATGGC 58.283 50.000 0.00 0.00 0.00 4.40
1087 1170 4.524053 TCTCTCTTTAGTCTGATGGCGTA 58.476 43.478 0.00 0.00 0.00 4.42
1099 1182 2.556189 TGATGGCGTATGTTTTGCACTT 59.444 40.909 0.00 0.00 0.00 3.16
1284 1373 6.371548 GTGCTCAGGTAATCATCTTTGTTGTA 59.628 38.462 0.00 0.00 0.00 2.41
1367 1456 5.405269 CAGTGATCGTGTTACTGTTGATGAA 59.595 40.000 2.70 0.00 39.06 2.57
1374 1463 8.683550 TCGTGTTACTGTTGATGAAATAGTAG 57.316 34.615 0.00 0.00 41.70 2.57
1386 1475 9.871238 TTGATGAAATAGTAGTAAACTCAGTCC 57.129 33.333 0.00 0.00 39.80 3.85
1408 1499 6.659242 GTCCTATCTTTGAGGAAATGGAACAA 59.341 38.462 0.00 0.00 43.81 2.83
1432 1523 8.863049 CAAGTGTTTGATATTTTCTATTGGTGC 58.137 33.333 0.00 0.00 36.36 5.01
1436 1527 5.422666 TGATATTTTCTATTGGTGCTGCG 57.577 39.130 0.00 0.00 0.00 5.18
1479 1579 8.627208 ACCTGATAATATTGACCATGAACATC 57.373 34.615 0.00 0.00 0.00 3.06
1502 1613 4.525912 ATTTTCATCTTGTCCTTGCACC 57.474 40.909 0.00 0.00 0.00 5.01
1562 1673 9.296400 GTTCTGAGTGTTCTAGTTATCTGATTC 57.704 37.037 0.00 0.00 0.00 2.52
1563 1674 8.581253 TCTGAGTGTTCTAGTTATCTGATTCA 57.419 34.615 0.00 0.00 0.00 2.57
1564 1675 9.025041 TCTGAGTGTTCTAGTTATCTGATTCAA 57.975 33.333 0.00 0.00 0.00 2.69
1565 1676 9.645059 CTGAGTGTTCTAGTTATCTGATTCAAA 57.355 33.333 0.00 0.00 0.00 2.69
1568 1679 9.388506 AGTGTTCTAGTTATCTGATTCAAATGG 57.611 33.333 0.00 0.00 0.00 3.16
1569 1680 9.383519 GTGTTCTAGTTATCTGATTCAAATGGA 57.616 33.333 0.00 0.00 0.00 3.41
1572 1683 8.613060 TCTAGTTATCTGATTCAAATGGATGC 57.387 34.615 0.00 0.00 0.00 3.91
1573 1684 8.435187 TCTAGTTATCTGATTCAAATGGATGCT 58.565 33.333 0.00 0.00 0.00 3.79
1574 1685 7.507733 AGTTATCTGATTCAAATGGATGCTC 57.492 36.000 0.00 0.00 0.00 4.26
1575 1686 7.058525 AGTTATCTGATTCAAATGGATGCTCA 58.941 34.615 0.00 0.00 0.00 4.26
1576 1687 7.228906 AGTTATCTGATTCAAATGGATGCTCAG 59.771 37.037 0.00 0.00 34.13 3.35
1577 1688 4.851843 TCTGATTCAAATGGATGCTCAGT 58.148 39.130 0.00 0.00 34.32 3.41
1578 1689 4.638865 TCTGATTCAAATGGATGCTCAGTG 59.361 41.667 0.00 0.00 34.32 3.66
1579 1690 4.338012 TGATTCAAATGGATGCTCAGTGT 58.662 39.130 0.00 0.00 0.00 3.55
1580 1691 4.397103 TGATTCAAATGGATGCTCAGTGTC 59.603 41.667 0.00 0.00 0.00 3.67
1581 1692 3.421919 TCAAATGGATGCTCAGTGTCA 57.578 42.857 0.00 0.00 0.00 3.58
1582 1693 3.959293 TCAAATGGATGCTCAGTGTCAT 58.041 40.909 0.00 0.00 0.00 3.06
1583 1694 3.943381 TCAAATGGATGCTCAGTGTCATC 59.057 43.478 15.17 15.17 38.60 2.92
1584 1695 3.639672 AATGGATGCTCAGTGTCATCA 57.360 42.857 21.01 12.50 40.50 3.07
1585 1696 3.859061 ATGGATGCTCAGTGTCATCAT 57.141 42.857 21.01 13.59 40.50 2.45
1586 1697 2.914059 TGGATGCTCAGTGTCATCATG 58.086 47.619 21.01 0.00 40.50 3.07
1587 1698 2.237893 TGGATGCTCAGTGTCATCATGT 59.762 45.455 21.01 0.00 40.50 3.21
1588 1699 3.276857 GGATGCTCAGTGTCATCATGTT 58.723 45.455 21.01 0.00 40.50 2.71
1589 1700 4.080975 TGGATGCTCAGTGTCATCATGTTA 60.081 41.667 21.01 7.03 40.50 2.41
1590 1701 5.061853 GGATGCTCAGTGTCATCATGTTAT 58.938 41.667 21.01 0.00 40.50 1.89
1611 1757 9.056005 TGTTATCAAATGGATGCTCAGTATTAC 57.944 33.333 0.00 0.00 36.72 1.89
1637 1783 9.130661 CCATGTTATCCACTTTGGTTATTGATA 57.869 33.333 0.00 0.00 39.03 2.15
1638 1784 9.950680 CATGTTATCCACTTTGGTTATTGATAC 57.049 33.333 0.00 0.00 39.03 2.24
1639 1785 9.920946 ATGTTATCCACTTTGGTTATTGATACT 57.079 29.630 0.00 0.00 39.03 2.12
1640 1786 9.747898 TGTTATCCACTTTGGTTATTGATACTT 57.252 29.630 0.00 0.00 39.03 2.24
1642 1788 7.881775 ATCCACTTTGGTTATTGATACTTCC 57.118 36.000 0.00 0.00 39.03 3.46
1643 1789 7.027874 TCCACTTTGGTTATTGATACTTCCT 57.972 36.000 0.00 0.00 39.03 3.36
1644 1790 7.110155 TCCACTTTGGTTATTGATACTTCCTC 58.890 38.462 0.00 0.00 39.03 3.71
1645 1791 7.037586 TCCACTTTGGTTATTGATACTTCCTCT 60.038 37.037 0.00 0.00 39.03 3.69
1646 1792 7.066284 CCACTTTGGTTATTGATACTTCCTCTG 59.934 40.741 0.00 0.00 31.35 3.35
1647 1793 7.607991 CACTTTGGTTATTGATACTTCCTCTGT 59.392 37.037 0.00 0.00 0.00 3.41
1648 1794 8.822805 ACTTTGGTTATTGATACTTCCTCTGTA 58.177 33.333 0.00 0.00 0.00 2.74
1649 1795 9.667107 CTTTGGTTATTGATACTTCCTCTGTAA 57.333 33.333 0.00 0.00 0.00 2.41
1651 1797 9.444600 TTGGTTATTGATACTTCCTCTGTAAAC 57.555 33.333 0.00 0.00 0.00 2.01
1652 1798 8.822805 TGGTTATTGATACTTCCTCTGTAAACT 58.177 33.333 0.00 0.00 0.00 2.66
1653 1799 9.668497 GGTTATTGATACTTCCTCTGTAAACTT 57.332 33.333 0.00 0.00 0.00 2.66
1663 1809 8.035984 ACTTCCTCTGTAAACTTGTATAAGAGC 58.964 37.037 6.19 0.00 37.36 4.09
1664 1810 6.561614 TCCTCTGTAAACTTGTATAAGAGCG 58.438 40.000 6.19 0.00 37.36 5.03
1665 1811 6.152323 TCCTCTGTAAACTTGTATAAGAGCGT 59.848 38.462 6.19 0.00 37.36 5.07
1666 1812 6.812160 CCTCTGTAAACTTGTATAAGAGCGTT 59.188 38.462 6.19 0.00 37.36 4.84
1667 1813 7.331193 CCTCTGTAAACTTGTATAAGAGCGTTT 59.669 37.037 6.19 0.04 37.36 3.60
1668 1814 9.350357 CTCTGTAAACTTGTATAAGAGCGTTTA 57.650 33.333 6.19 0.00 37.36 2.01
1669 1815 9.350357 TCTGTAAACTTGTATAAGAGCGTTTAG 57.650 33.333 6.19 0.00 37.36 1.85
1670 1816 9.350357 CTGTAAACTTGTATAAGAGCGTTTAGA 57.650 33.333 6.19 0.10 37.36 2.10
1671 1817 9.865321 TGTAAACTTGTATAAGAGCGTTTAGAT 57.135 29.630 6.19 0.00 37.36 1.98
1673 1819 8.997621 AAACTTGTATAAGAGCGTTTAGATCA 57.002 30.769 6.19 0.00 37.82 2.92
1674 1820 7.988904 ACTTGTATAAGAGCGTTTAGATCAC 57.011 36.000 6.19 0.00 37.82 3.06
1675 1821 7.773149 ACTTGTATAAGAGCGTTTAGATCACT 58.227 34.615 6.19 0.00 37.82 3.41
1676 1822 8.900781 ACTTGTATAAGAGCGTTTAGATCACTA 58.099 33.333 6.19 0.00 37.82 2.74
1677 1823 9.731819 CTTGTATAAGAGCGTTTAGATCACTAA 57.268 33.333 0.00 0.00 37.82 2.24
1679 1825 9.731819 TGTATAAGAGCGTTTAGATCACTAAAG 57.268 33.333 0.00 0.00 45.42 1.85
1680 1826 9.733219 GTATAAGAGCGTTTAGATCACTAAAGT 57.267 33.333 0.00 0.00 45.42 2.66
1682 1828 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
1683 1829 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
1717 1863 8.777578 TGCTCTTATATTAGTTTACAGAGGGA 57.222 34.615 0.00 0.00 0.00 4.20
1718 1864 8.861086 TGCTCTTATATTAGTTTACAGAGGGAG 58.139 37.037 0.00 0.00 0.00 4.30
1719 1865 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
1733 1879 6.784031 ACAGAGGGAGTACTTTGAATTCAAT 58.216 36.000 21.10 10.31 35.55 2.57
1734 1880 7.234355 ACAGAGGGAGTACTTTGAATTCAATT 58.766 34.615 21.10 13.59 35.55 2.32
1738 1884 8.250143 AGGGAGTACTTTGAATTCAATTTGTT 57.750 30.769 21.10 8.00 35.55 2.83
1740 1886 7.384932 GGGAGTACTTTGAATTCAATTTGTTGG 59.615 37.037 21.10 8.48 35.55 3.77
1741 1887 8.141268 GGAGTACTTTGAATTCAATTTGTTGGA 58.859 33.333 21.10 3.45 35.55 3.53
1746 1892 9.829507 ACTTTGAATTCAATTTGTTGGATTACA 57.170 25.926 21.10 0.93 35.55 2.41
1748 1894 9.605275 TTTGAATTCAATTTGTTGGATTACACA 57.395 25.926 21.10 0.00 35.55 3.72
1809 1955 4.201950 GGGTGCATTCATGTCTTGTATCAC 60.202 45.833 0.00 0.00 0.00 3.06
1812 1958 6.405065 GGTGCATTCATGTCTTGTATCACATT 60.405 38.462 0.00 0.00 30.48 2.71
1829 1975 6.252599 TCACATTCATTACTGGGCTCTTAT 57.747 37.500 0.00 0.00 0.00 1.73
1830 1976 6.291377 TCACATTCATTACTGGGCTCTTATC 58.709 40.000 0.00 0.00 0.00 1.75
1946 2099 6.147328 GCTAGTAGTTTTACCTGGAACTTGTG 59.853 42.308 0.00 0.00 37.32 3.33
1999 2152 1.476085 TGTGGTTGGTTTCAGTTGCTG 59.524 47.619 0.00 0.00 0.00 4.41
2038 2191 2.107378 TGATGTCACTTGGCCTGGTTTA 59.893 45.455 3.32 0.00 0.00 2.01
2105 2300 5.552870 ATGTCCCTTATCTCGTTGCTTAT 57.447 39.130 0.00 0.00 0.00 1.73
2132 2327 7.665559 TGTTATACTGATGATTTGGCCCTTATC 59.334 37.037 0.00 0.64 0.00 1.75
2134 2329 4.723309 ACTGATGATTTGGCCCTTATCTC 58.277 43.478 0.00 1.65 0.00 2.75
2135 2330 3.743521 TGATGATTTGGCCCTTATCTCG 58.256 45.455 0.00 0.00 0.00 4.04
2136 2331 3.136443 TGATGATTTGGCCCTTATCTCGT 59.864 43.478 0.00 0.00 0.00 4.18
2138 2333 3.278574 TGATTTGGCCCTTATCTCGTTG 58.721 45.455 0.00 0.00 0.00 4.10
2141 2336 0.618458 TGGCCCTTATCTCGTTGCTT 59.382 50.000 0.00 0.00 0.00 3.91
2150 2345 7.155328 CCCTTATCTCGTTGCTTAATCTGTAT 58.845 38.462 0.00 0.00 0.00 2.29
2151 2346 7.657761 CCCTTATCTCGTTGCTTAATCTGTATT 59.342 37.037 0.00 0.00 0.00 1.89
2152 2347 8.491152 CCTTATCTCGTTGCTTAATCTGTATTG 58.509 37.037 0.00 0.00 0.00 1.90
2154 2349 7.706281 ATCTCGTTGCTTAATCTGTATTGAG 57.294 36.000 0.00 0.00 33.06 3.02
2155 2350 6.631016 TCTCGTTGCTTAATCTGTATTGAGT 58.369 36.000 0.00 0.00 32.62 3.41
2197 2520 9.979578 ATTCTTTACTTCAAAATGCATGTACAA 57.020 25.926 0.00 0.00 0.00 2.41
2208 2531 7.510549 AAATGCATGTACAAGAGTAACAACT 57.489 32.000 0.00 0.00 30.67 3.16
2218 2541 7.568199 ACAAGAGTAACAACTGTAGCAAATT 57.432 32.000 0.00 0.00 0.00 1.82
2219 2542 7.639945 ACAAGAGTAACAACTGTAGCAAATTC 58.360 34.615 0.00 0.00 0.00 2.17
2220 2543 6.467723 AGAGTAACAACTGTAGCAAATTCG 57.532 37.500 0.00 0.00 0.00 3.34
2223 2546 3.896648 ACAACTGTAGCAAATTCGTGG 57.103 42.857 0.00 0.00 0.00 4.94
2227 2550 3.067106 ACTGTAGCAAATTCGTGGACAG 58.933 45.455 0.00 0.00 38.96 3.51
2228 2551 1.804151 TGTAGCAAATTCGTGGACAGC 59.196 47.619 0.00 0.00 0.00 4.40
2229 2552 1.804151 GTAGCAAATTCGTGGACAGCA 59.196 47.619 0.00 0.00 0.00 4.41
2230 2553 1.317613 AGCAAATTCGTGGACAGCAA 58.682 45.000 0.00 0.00 0.00 3.91
2231 2554 1.001378 AGCAAATTCGTGGACAGCAAC 60.001 47.619 0.00 0.00 0.00 4.17
2257 2655 4.083908 CGTTTTGGCCAATTGAAATCCTTG 60.084 41.667 21.26 0.00 0.00 3.61
2272 2670 6.371548 TGAAATCCTTGGATTTCTAAGACGTG 59.628 38.462 35.32 0.00 46.28 4.49
2316 2732 7.969536 ATCTTATTCCATCACACTATTTCCG 57.030 36.000 0.00 0.00 0.00 4.30
2347 2882 3.372206 GCTGACGATTGATGCTGTAAACT 59.628 43.478 0.00 0.00 0.00 2.66
2354 2889 2.507484 TGATGCTGTAAACTGCTTGCT 58.493 42.857 12.34 0.00 40.79 3.91
2365 2900 5.429957 AAACTGCTTGCTAAGAAACTCTG 57.570 39.130 0.00 0.00 0.00 3.35
2408 2943 2.125106 CGGGTAGAAGCCACCAGC 60.125 66.667 0.00 0.00 44.25 4.85
2592 3157 2.342279 CTGGTTTCTCGTGGCGGA 59.658 61.111 0.00 0.00 0.00 5.54
2729 3294 3.316283 AGTTGCAACAAATACAATGGCG 58.684 40.909 30.11 0.00 0.00 5.69
2732 3297 2.258755 GCAACAAATACAATGGCGTCC 58.741 47.619 0.00 0.00 0.00 4.79
2733 3298 2.094752 GCAACAAATACAATGGCGTCCT 60.095 45.455 0.00 0.00 0.00 3.85
2735 3300 3.848272 ACAAATACAATGGCGTCCTTG 57.152 42.857 3.32 3.32 0.00 3.61
2736 3301 3.153919 ACAAATACAATGGCGTCCTTGT 58.846 40.909 14.98 14.98 38.95 3.16
2737 3302 3.572255 ACAAATACAATGGCGTCCTTGTT 59.428 39.130 15.78 2.12 36.92 2.83
2741 3306 1.202830 ACAATGGCGTCCTTGTTACCA 60.203 47.619 4.75 0.00 31.74 3.25
2743 3308 1.530323 ATGGCGTCCTTGTTACCAAC 58.470 50.000 0.00 0.00 33.30 3.77
2746 3311 2.303600 TGGCGTCCTTGTTACCAACTAT 59.696 45.455 0.00 0.00 0.00 2.12
2747 3312 2.676342 GGCGTCCTTGTTACCAACTATG 59.324 50.000 0.00 0.00 0.00 2.23
2750 3315 4.634443 GCGTCCTTGTTACCAACTATGAAT 59.366 41.667 0.00 0.00 0.00 2.57
2751 3316 5.447279 GCGTCCTTGTTACCAACTATGAATG 60.447 44.000 0.00 0.00 0.00 2.67
2785 3361 3.469008 TGGATACGATGTTGGATGGTC 57.531 47.619 0.00 0.00 42.51 4.02
2792 3369 2.935849 CGATGTTGGATGGTCGATTTGA 59.064 45.455 0.00 0.00 36.25 2.69
2793 3370 3.373748 CGATGTTGGATGGTCGATTTGAA 59.626 43.478 0.00 0.00 36.25 2.69
2794 3371 4.035558 CGATGTTGGATGGTCGATTTGAAT 59.964 41.667 0.00 0.00 36.25 2.57
2795 3372 5.449041 CGATGTTGGATGGTCGATTTGAATT 60.449 40.000 0.00 0.00 36.25 2.17
2796 3373 5.720371 TGTTGGATGGTCGATTTGAATTT 57.280 34.783 0.00 0.00 0.00 1.82
2797 3374 5.468592 TGTTGGATGGTCGATTTGAATTTG 58.531 37.500 0.00 0.00 0.00 2.32
2798 3375 5.242615 TGTTGGATGGTCGATTTGAATTTGA 59.757 36.000 0.00 0.00 0.00 2.69
2803 3380 7.121907 TGGATGGTCGATTTGAATTTGATTACA 59.878 33.333 0.00 0.00 0.00 2.41
2838 3415 1.520192 CGTCGATGATGGGGTTGGA 59.480 57.895 0.00 0.00 0.00 3.53
2839 3416 0.107897 CGTCGATGATGGGGTTGGAA 60.108 55.000 0.00 0.00 0.00 3.53
2840 3417 1.668419 GTCGATGATGGGGTTGGAAG 58.332 55.000 0.00 0.00 0.00 3.46
2841 3418 1.065418 GTCGATGATGGGGTTGGAAGT 60.065 52.381 0.00 0.00 0.00 3.01
2842 3419 1.633432 TCGATGATGGGGTTGGAAGTT 59.367 47.619 0.00 0.00 0.00 2.66
2843 3420 1.745087 CGATGATGGGGTTGGAAGTTG 59.255 52.381 0.00 0.00 0.00 3.16
2844 3421 2.617788 CGATGATGGGGTTGGAAGTTGA 60.618 50.000 0.00 0.00 0.00 3.18
2845 3422 2.584835 TGATGGGGTTGGAAGTTGAG 57.415 50.000 0.00 0.00 0.00 3.02
2846 3423 1.075374 TGATGGGGTTGGAAGTTGAGG 59.925 52.381 0.00 0.00 0.00 3.86
2847 3424 0.409484 ATGGGGTTGGAAGTTGAGGG 59.591 55.000 0.00 0.00 0.00 4.30
2848 3425 1.606601 GGGGTTGGAAGTTGAGGGC 60.607 63.158 0.00 0.00 0.00 5.19
2849 3426 1.152830 GGGTTGGAAGTTGAGGGCA 59.847 57.895 0.00 0.00 0.00 5.36
2850 3427 0.469144 GGGTTGGAAGTTGAGGGCAA 60.469 55.000 0.00 0.00 0.00 4.52
2851 3428 1.408969 GGTTGGAAGTTGAGGGCAAA 58.591 50.000 0.00 0.00 35.42 3.68
2852 3429 1.341209 GGTTGGAAGTTGAGGGCAAAG 59.659 52.381 0.00 0.00 35.42 2.77
2853 3430 2.031870 GTTGGAAGTTGAGGGCAAAGT 58.968 47.619 0.00 0.00 35.42 2.66
2854 3431 2.430694 GTTGGAAGTTGAGGGCAAAGTT 59.569 45.455 0.00 0.00 35.42 2.66
2855 3432 2.031120 TGGAAGTTGAGGGCAAAGTTG 58.969 47.619 0.00 0.00 35.42 3.16
2856 3433 2.031870 GGAAGTTGAGGGCAAAGTTGT 58.968 47.619 0.00 0.00 35.42 3.32
2857 3434 2.430694 GGAAGTTGAGGGCAAAGTTGTT 59.569 45.455 0.00 0.00 35.42 2.83
2858 3435 3.447742 GAAGTTGAGGGCAAAGTTGTTG 58.552 45.455 0.00 0.00 35.42 3.33
2859 3436 1.756538 AGTTGAGGGCAAAGTTGTTGG 59.243 47.619 0.00 0.00 35.42 3.77
2860 3437 0.463620 TTGAGGGCAAAGTTGTTGGC 59.536 50.000 4.19 4.19 43.30 4.52
2861 3438 1.007387 GAGGGCAAAGTTGTTGGCG 60.007 57.895 6.55 0.00 44.74 5.69
2862 3439 2.661537 GGGCAAAGTTGTTGGCGC 60.662 61.111 0.00 0.00 44.74 6.53
2863 3440 2.417097 GGCAAAGTTGTTGGCGCT 59.583 55.556 7.64 0.00 32.68 5.92
2864 3441 1.661509 GGCAAAGTTGTTGGCGCTC 60.662 57.895 7.64 0.00 32.68 5.03
2865 3442 1.065600 GCAAAGTTGTTGGCGCTCA 59.934 52.632 7.64 0.00 0.00 4.26
2866 3443 0.936297 GCAAAGTTGTTGGCGCTCAG 60.936 55.000 7.64 0.00 0.00 3.35
2867 3444 0.318107 CAAAGTTGTTGGCGCTCAGG 60.318 55.000 7.64 0.00 0.00 3.86
2868 3445 0.751643 AAAGTTGTTGGCGCTCAGGT 60.752 50.000 7.64 0.00 0.00 4.00
2869 3446 1.166531 AAGTTGTTGGCGCTCAGGTC 61.167 55.000 7.64 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 194 3.545124 AACGCGACAGGCCATGGAA 62.545 57.895 18.40 0.00 38.94 3.53
245 260 2.963101 CCCTCCTTCCCGTTTTCTTTTT 59.037 45.455 0.00 0.00 0.00 1.94
250 265 2.038837 CGCCCTCCTTCCCGTTTTC 61.039 63.158 0.00 0.00 0.00 2.29
281 296 2.510906 CCCCAGCCCAATACTCCG 59.489 66.667 0.00 0.00 0.00 4.63
334 349 4.748679 CGCTTGCAACGCAGCCTC 62.749 66.667 17.22 0.00 40.61 4.70
341 356 2.127496 CAGACAGCGCTTGCAACG 60.127 61.111 7.50 14.44 42.66 4.10
342 357 1.082496 GACAGACAGCGCTTGCAAC 60.082 57.895 7.50 0.00 42.66 4.17
343 358 1.224069 GAGACAGACAGCGCTTGCAA 61.224 55.000 7.50 0.00 42.66 4.08
344 359 1.665916 GAGACAGACAGCGCTTGCA 60.666 57.895 7.50 0.00 42.66 4.08
345 360 2.724708 CGAGACAGACAGCGCTTGC 61.725 63.158 7.50 1.77 39.58 4.01
346 361 2.724708 GCGAGACAGACAGCGCTTG 61.725 63.158 7.50 6.61 45.41 4.01
347 362 2.431601 GCGAGACAGACAGCGCTT 60.432 61.111 7.50 0.00 45.41 4.68
350 365 3.177920 GCAGCGAGACAGACAGCG 61.178 66.667 0.00 0.00 34.34 5.18
351 366 2.813042 GGCAGCGAGACAGACAGC 60.813 66.667 0.00 0.00 0.00 4.40
352 367 2.505777 CGGCAGCGAGACAGACAG 60.506 66.667 0.00 0.00 0.00 3.51
353 368 4.056125 CCGGCAGCGAGACAGACA 62.056 66.667 0.00 0.00 0.00 3.41
354 369 4.057428 ACCGGCAGCGAGACAGAC 62.057 66.667 0.00 0.00 0.00 3.51
388 403 4.850822 GGGCTCGTAAACCCTAGC 57.149 61.111 0.00 0.00 43.36 3.42
431 448 4.699522 GGTGTGTGAGGCCGGGAC 62.700 72.222 2.18 0.00 0.00 4.46
530 548 1.374947 CGAAAGGAGTTGGCAGGGA 59.625 57.895 0.00 0.00 0.00 4.20
531 549 3.987404 CGAAAGGAGTTGGCAGGG 58.013 61.111 0.00 0.00 0.00 4.45
570 603 1.021390 CACGCAGGAAGGTGGACATC 61.021 60.000 0.00 0.00 0.00 3.06
708 748 0.833287 AGCAGTCCATCTTGCGGTAT 59.167 50.000 0.00 0.00 0.00 2.73
725 789 0.373716 CGCTTAACCACGAATCCAGC 59.626 55.000 0.00 0.00 0.00 4.85
796 860 3.405170 ACAAACGGCATGAATCGATTC 57.595 42.857 27.59 27.59 37.31 2.52
806 870 2.279935 TTCACCCTAACAAACGGCAT 57.720 45.000 0.00 0.00 0.00 4.40
811 875 9.626045 CAGAAATTCTTATTCACCCTAACAAAC 57.374 33.333 0.00 0.00 0.00 2.93
823 891 7.467623 AGCGACATCAACAGAAATTCTTATTC 58.532 34.615 0.00 0.00 0.00 1.75
824 892 7.383102 AGCGACATCAACAGAAATTCTTATT 57.617 32.000 0.00 0.00 0.00 1.40
860 934 1.968540 GTCCAGCCACAGCCTTGTC 60.969 63.158 0.00 0.00 41.25 3.18
867 941 1.742880 CGGTCATGTCCAGCCACAG 60.743 63.158 9.71 0.00 0.00 3.66
877 951 1.066143 GTCATGGGAAGTCGGTCATGT 60.066 52.381 0.00 0.00 38.39 3.21
878 952 1.656652 GTCATGGGAAGTCGGTCATG 58.343 55.000 0.00 0.00 38.54 3.07
880 954 0.544357 AGGTCATGGGAAGTCGGTCA 60.544 55.000 0.00 0.00 0.00 4.02
949 1032 1.159285 CAGCGACTGCAAATGGAAGA 58.841 50.000 0.00 0.00 46.23 2.87
950 1033 0.877071 ACAGCGACTGCAAATGGAAG 59.123 50.000 6.74 0.00 46.23 3.46
951 1034 1.001487 CAACAGCGACTGCAAATGGAA 60.001 47.619 6.74 0.00 46.23 3.53
952 1035 0.592637 CAACAGCGACTGCAAATGGA 59.407 50.000 6.74 0.00 46.23 3.41
972 1055 3.256960 GGAGGGGGAGTGGCACAA 61.257 66.667 21.41 0.00 44.16 3.33
997 1080 1.021390 CCCACCTCGTTCTGCATGAC 61.021 60.000 0.00 0.00 0.00 3.06
998 1081 1.296392 CCCACCTCGTTCTGCATGA 59.704 57.895 0.00 0.00 0.00 3.07
1063 1146 3.716601 GCCATCAGACTAAAGAGAGAGC 58.283 50.000 0.00 0.00 0.00 4.09
1065 1148 3.357203 ACGCCATCAGACTAAAGAGAGA 58.643 45.455 0.00 0.00 0.00 3.10
1084 1167 3.296628 GTCCACAAGTGCAAAACATACG 58.703 45.455 0.00 0.00 0.00 3.06
1087 1170 1.535860 GCGTCCACAAGTGCAAAACAT 60.536 47.619 0.00 0.00 0.00 2.71
1099 1182 5.122239 CAGAAGAAAATGATTAGCGTCCACA 59.878 40.000 0.00 0.00 0.00 4.17
1374 1463 7.171630 TCCTCAAAGATAGGACTGAGTTTAC 57.828 40.000 0.00 0.00 38.24 2.01
1378 1467 6.352565 CCATTTCCTCAAAGATAGGACTGAGT 60.353 42.308 0.00 0.00 42.89 3.41
1386 1475 7.175641 ACACTTGTTCCATTTCCTCAAAGATAG 59.824 37.037 0.00 0.00 0.00 2.08
1394 1485 5.514274 TCAAACACTTGTTCCATTTCCTC 57.486 39.130 0.00 0.00 37.25 3.71
1408 1499 8.246180 CAGCACCAATAGAAAATATCAAACACT 58.754 33.333 0.00 0.00 0.00 3.55
1414 1505 4.881273 ACGCAGCACCAATAGAAAATATCA 59.119 37.500 0.00 0.00 0.00 2.15
1432 1523 5.793457 GGTTTTAACATAAGCAAGTACGCAG 59.207 40.000 0.00 0.00 0.00 5.18
1464 1557 9.417561 AGATGAAAATAGATGTTCATGGTCAAT 57.582 29.630 11.82 0.00 42.98 2.57
1479 1579 5.393461 GGGTGCAAGGACAAGATGAAAATAG 60.393 44.000 0.00 0.00 0.00 1.73
1502 1613 7.707104 AGACAAGTCTTCAAACAATTACTTGG 58.293 34.615 15.16 1.24 45.00 3.61
1562 1673 3.692593 TGATGACACTGAGCATCCATTTG 59.307 43.478 0.00 0.00 40.05 2.32
1563 1674 3.959293 TGATGACACTGAGCATCCATTT 58.041 40.909 0.00 0.00 40.05 2.32
1564 1675 3.639672 TGATGACACTGAGCATCCATT 57.360 42.857 0.00 0.00 40.05 3.16
1565 1676 3.118000 ACATGATGACACTGAGCATCCAT 60.118 43.478 0.00 0.00 40.05 3.41
1566 1677 2.237893 ACATGATGACACTGAGCATCCA 59.762 45.455 0.00 0.00 40.05 3.41
1567 1678 2.915349 ACATGATGACACTGAGCATCC 58.085 47.619 0.00 0.00 40.05 3.51
1568 1679 5.756833 TGATAACATGATGACACTGAGCATC 59.243 40.000 0.00 0.00 40.92 3.91
1569 1680 5.677567 TGATAACATGATGACACTGAGCAT 58.322 37.500 0.00 0.00 0.00 3.79
1570 1681 5.088680 TGATAACATGATGACACTGAGCA 57.911 39.130 0.00 0.00 0.00 4.26
1571 1682 6.426980 TTTGATAACATGATGACACTGAGC 57.573 37.500 0.00 0.00 0.00 4.26
1572 1683 7.281549 TCCATTTGATAACATGATGACACTGAG 59.718 37.037 0.00 0.00 0.00 3.35
1573 1684 7.111466 TCCATTTGATAACATGATGACACTGA 58.889 34.615 0.00 0.00 0.00 3.41
1574 1685 7.324354 TCCATTTGATAACATGATGACACTG 57.676 36.000 0.00 0.00 0.00 3.66
1575 1686 7.469594 GCATCCATTTGATAACATGATGACACT 60.470 37.037 0.00 0.00 30.56 3.55
1576 1687 6.639686 GCATCCATTTGATAACATGATGACAC 59.360 38.462 0.00 0.00 30.56 3.67
1577 1688 6.548251 AGCATCCATTTGATAACATGATGACA 59.452 34.615 0.00 0.00 30.56 3.58
1578 1689 6.978338 AGCATCCATTTGATAACATGATGAC 58.022 36.000 0.00 0.00 30.56 3.06
1579 1690 6.773685 TGAGCATCCATTTGATAACATGATGA 59.226 34.615 0.00 0.00 30.56 2.92
1580 1691 6.977213 TGAGCATCCATTTGATAACATGATG 58.023 36.000 0.00 0.00 30.56 3.07
1581 1692 6.776116 ACTGAGCATCCATTTGATAACATGAT 59.224 34.615 0.00 0.00 30.56 2.45
1582 1693 6.124340 ACTGAGCATCCATTTGATAACATGA 58.876 36.000 0.00 0.00 30.56 3.07
1583 1694 6.387041 ACTGAGCATCCATTTGATAACATG 57.613 37.500 0.00 0.00 30.56 3.21
1584 1695 8.701908 AATACTGAGCATCCATTTGATAACAT 57.298 30.769 0.00 0.00 30.56 2.71
1585 1696 9.056005 GTAATACTGAGCATCCATTTGATAACA 57.944 33.333 0.00 0.00 30.56 2.41
1586 1697 8.507249 GGTAATACTGAGCATCCATTTGATAAC 58.493 37.037 0.00 0.00 30.56 1.89
1587 1698 8.217111 TGGTAATACTGAGCATCCATTTGATAA 58.783 33.333 0.00 0.00 30.56 1.75
1588 1699 7.744733 TGGTAATACTGAGCATCCATTTGATA 58.255 34.615 0.00 0.00 30.56 2.15
1589 1700 6.604171 TGGTAATACTGAGCATCCATTTGAT 58.396 36.000 0.00 0.00 0.00 2.57
1590 1701 6.000246 TGGTAATACTGAGCATCCATTTGA 58.000 37.500 0.00 0.00 0.00 2.69
1611 1757 7.403312 TCAATAACCAAAGTGGATAACATGG 57.597 36.000 0.18 0.00 40.96 3.66
1637 1783 8.035984 GCTCTTATACAAGTTTACAGAGGAAGT 58.964 37.037 0.00 0.00 33.20 3.01
1638 1784 7.221067 CGCTCTTATACAAGTTTACAGAGGAAG 59.779 40.741 0.00 0.00 33.20 3.46
1639 1785 7.033791 CGCTCTTATACAAGTTTACAGAGGAA 58.966 38.462 0.00 0.00 33.20 3.36
1640 1786 6.152323 ACGCTCTTATACAAGTTTACAGAGGA 59.848 38.462 0.00 0.00 33.20 3.71
1641 1787 6.331061 ACGCTCTTATACAAGTTTACAGAGG 58.669 40.000 0.00 0.00 33.20 3.69
1642 1788 7.813852 AACGCTCTTATACAAGTTTACAGAG 57.186 36.000 0.00 0.00 33.20 3.35
1643 1789 9.350357 CTAAACGCTCTTATACAAGTTTACAGA 57.650 33.333 0.00 0.00 34.29 3.41
1644 1790 9.350357 TCTAAACGCTCTTATACAAGTTTACAG 57.650 33.333 0.00 0.00 34.29 2.74
1645 1791 9.865321 ATCTAAACGCTCTTATACAAGTTTACA 57.135 29.630 0.00 0.00 34.29 2.41
1648 1794 8.870879 GTGATCTAAACGCTCTTATACAAGTTT 58.129 33.333 0.00 0.00 36.11 2.66
1649 1795 8.251721 AGTGATCTAAACGCTCTTATACAAGTT 58.748 33.333 0.00 0.00 33.20 2.66
1650 1796 7.773149 AGTGATCTAAACGCTCTTATACAAGT 58.227 34.615 0.00 0.00 33.20 3.16
1651 1797 9.731819 TTAGTGATCTAAACGCTCTTATACAAG 57.268 33.333 0.00 0.00 33.79 3.16
1653 1799 9.731819 CTTTAGTGATCTAAACGCTCTTATACA 57.268 33.333 0.00 0.00 40.05 2.29
1654 1800 9.733219 ACTTTAGTGATCTAAACGCTCTTATAC 57.267 33.333 0.00 0.00 40.05 1.47
1656 1802 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
1657 1803 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
1658 1804 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
1659 1805 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
1691 1837 9.381038 TCCCTCTGTAAACTAATATAAGAGCAT 57.619 33.333 0.00 0.00 0.00 3.79
1692 1838 8.777578 TCCCTCTGTAAACTAATATAAGAGCA 57.222 34.615 0.00 0.00 0.00 4.26
1693 1839 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
1700 1846 9.537852 TCAAAGTACTCCCTCTGTAAACTAATA 57.462 33.333 0.00 0.00 0.00 0.98
1701 1847 8.431910 TCAAAGTACTCCCTCTGTAAACTAAT 57.568 34.615 0.00 0.00 0.00 1.73
1702 1848 7.844493 TCAAAGTACTCCCTCTGTAAACTAA 57.156 36.000 0.00 0.00 0.00 2.24
1703 1849 7.844493 TTCAAAGTACTCCCTCTGTAAACTA 57.156 36.000 0.00 0.00 0.00 2.24
1704 1850 6.742559 TTCAAAGTACTCCCTCTGTAAACT 57.257 37.500 0.00 0.00 0.00 2.66
1705 1851 7.660208 TGAATTCAAAGTACTCCCTCTGTAAAC 59.340 37.037 5.45 0.00 0.00 2.01
1706 1852 7.741785 TGAATTCAAAGTACTCCCTCTGTAAA 58.258 34.615 5.45 0.00 0.00 2.01
1707 1853 7.311092 TGAATTCAAAGTACTCCCTCTGTAA 57.689 36.000 5.45 0.00 0.00 2.41
1708 1854 6.928348 TGAATTCAAAGTACTCCCTCTGTA 57.072 37.500 5.45 0.00 0.00 2.74
1709 1855 5.825593 TGAATTCAAAGTACTCCCTCTGT 57.174 39.130 5.45 0.00 0.00 3.41
1710 1856 7.693969 AATTGAATTCAAAGTACTCCCTCTG 57.306 36.000 23.91 0.00 39.55 3.35
1711 1857 7.725844 ACAAATTGAATTCAAAGTACTCCCTCT 59.274 33.333 23.91 0.99 39.55 3.69
1712 1858 7.886338 ACAAATTGAATTCAAAGTACTCCCTC 58.114 34.615 23.91 0.00 39.55 4.30
1713 1859 7.839680 ACAAATTGAATTCAAAGTACTCCCT 57.160 32.000 23.91 2.25 39.55 4.20
1714 1860 7.384932 CCAACAAATTGAATTCAAAGTACTCCC 59.615 37.037 23.91 0.00 39.55 4.30
1715 1861 8.141268 TCCAACAAATTGAATTCAAAGTACTCC 58.859 33.333 23.91 0.00 39.55 3.85
1716 1862 9.696917 ATCCAACAAATTGAATTCAAAGTACTC 57.303 29.630 23.91 0.00 39.55 2.59
1765 1911 5.304101 ACCCAACAATTATCAAAACAGCTCA 59.696 36.000 0.00 0.00 0.00 4.26
1766 1912 5.634859 CACCCAACAATTATCAAAACAGCTC 59.365 40.000 0.00 0.00 0.00 4.09
1768 1914 4.152223 GCACCCAACAATTATCAAAACAGC 59.848 41.667 0.00 0.00 0.00 4.40
1809 1955 4.153117 GCGATAAGAGCCCAGTAATGAATG 59.847 45.833 0.00 0.00 0.00 2.67
1812 1958 2.965831 AGCGATAAGAGCCCAGTAATGA 59.034 45.455 0.00 0.00 34.64 2.57
1829 1975 2.030363 CCTGCCAAAACATAACAAGCGA 60.030 45.455 0.00 0.00 0.00 4.93
1830 1976 2.327568 CCTGCCAAAACATAACAAGCG 58.672 47.619 0.00 0.00 0.00 4.68
1946 2099 2.365941 GCTAGGTAGACATGGGAAGGAC 59.634 54.545 0.00 0.00 0.00 3.85
1999 2152 5.465056 GACATCAAGTCTTAGCTTCCATAGC 59.535 44.000 0.00 0.00 46.01 2.97
2105 2300 5.765510 AGGGCCAAATCATCAGTATAACAA 58.234 37.500 6.18 0.00 0.00 2.83
2132 2327 6.893958 ACTCAATACAGATTAAGCAACGAG 57.106 37.500 0.00 0.00 0.00 4.18
2134 2329 6.831769 ACAACTCAATACAGATTAAGCAACG 58.168 36.000 0.00 0.00 0.00 4.10
2135 2330 8.905702 CAAACAACTCAATACAGATTAAGCAAC 58.094 33.333 0.00 0.00 0.00 4.17
2136 2331 8.629158 ACAAACAACTCAATACAGATTAAGCAA 58.371 29.630 0.00 0.00 0.00 3.91
2138 2333 7.750903 GGACAAACAACTCAATACAGATTAAGC 59.249 37.037 0.00 0.00 0.00 3.09
2141 2336 7.458397 AGGGACAAACAACTCAATACAGATTA 58.542 34.615 0.00 0.00 0.00 1.75
2150 2345 6.605594 AGAATAACAAGGGACAAACAACTCAA 59.394 34.615 0.00 0.00 0.00 3.02
2151 2346 6.126409 AGAATAACAAGGGACAAACAACTCA 58.874 36.000 0.00 0.00 0.00 3.41
2152 2347 6.635030 AGAATAACAAGGGACAAACAACTC 57.365 37.500 0.00 0.00 0.00 3.01
2154 2349 8.410912 AGTAAAGAATAACAAGGGACAAACAAC 58.589 33.333 0.00 0.00 0.00 3.32
2155 2350 8.528044 AGTAAAGAATAACAAGGGACAAACAA 57.472 30.769 0.00 0.00 0.00 2.83
2196 2519 6.482308 ACGAATTTGCTACAGTTGTTACTCTT 59.518 34.615 0.00 0.00 30.26 2.85
2197 2520 5.989777 ACGAATTTGCTACAGTTGTTACTCT 59.010 36.000 0.00 0.00 30.26 3.24
2208 2531 1.804151 GCTGTCCACGAATTTGCTACA 59.196 47.619 0.00 0.00 0.00 2.74
2218 2541 2.661537 CGCAGTTGCTGTCCACGA 60.662 61.111 2.29 0.00 39.32 4.35
2219 2542 2.967076 ACGCAGTTGCTGTCCACG 60.967 61.111 2.29 0.00 37.78 4.94
2231 2554 1.863267 TTCAATTGGCCAAAACGCAG 58.137 45.000 24.71 8.90 0.00 5.18
2257 2655 2.853003 GCGTCTCACGTCTTAGAAATCC 59.147 50.000 0.00 0.00 44.73 3.01
2272 2670 1.811679 GGCCTAAGTGCAGCGTCTC 60.812 63.158 0.00 0.00 0.00 3.36
2316 2732 4.553547 GCATCAATCGTCAGCCAGAATAAC 60.554 45.833 0.00 0.00 0.00 1.89
2347 2882 3.141398 CACCAGAGTTTCTTAGCAAGCA 58.859 45.455 0.00 0.00 0.00 3.91
2354 2889 5.178797 GCAAGATAGCACCAGAGTTTCTTA 58.821 41.667 0.00 0.00 0.00 2.10
2365 2900 0.179163 GCAAACGGCAAGATAGCACC 60.179 55.000 0.00 0.00 43.97 5.01
2539 3092 0.768221 TCAAGGACAAGGGGCTCACT 60.768 55.000 0.00 0.00 0.00 3.41
2550 3103 2.391724 GAAGTGCGGGGTCAAGGACA 62.392 60.000 0.00 0.00 33.68 4.02
2592 3157 0.247736 GATCACCGTGGCAGAGTTCT 59.752 55.000 0.00 0.00 0.00 3.01
2707 3272 4.022762 ACGCCATTGTATTTGTTGCAACTA 60.023 37.500 28.61 19.86 32.44 2.24
2710 3275 3.312828 GACGCCATTGTATTTGTTGCAA 58.687 40.909 0.00 0.00 34.26 4.08
2735 3300 3.064820 CGGCACCATTCATAGTTGGTAAC 59.935 47.826 0.00 0.00 44.38 2.50
2736 3301 3.055021 TCGGCACCATTCATAGTTGGTAA 60.055 43.478 0.00 0.00 44.38 2.85
2737 3302 2.502130 TCGGCACCATTCATAGTTGGTA 59.498 45.455 0.00 0.00 44.38 3.25
2741 3306 2.945008 CACATCGGCACCATTCATAGTT 59.055 45.455 0.00 0.00 0.00 2.24
2743 3308 1.265095 GCACATCGGCACCATTCATAG 59.735 52.381 0.00 0.00 0.00 2.23
2746 3311 1.303155 TGCACATCGGCACCATTCA 60.303 52.632 0.00 0.00 39.25 2.57
2747 3312 3.589579 TGCACATCGGCACCATTC 58.410 55.556 0.00 0.00 39.25 2.67
2793 3370 8.893727 GCTACCAGACTAAACATGTAATCAAAT 58.106 33.333 0.00 0.00 0.00 2.32
2794 3371 7.335924 GGCTACCAGACTAAACATGTAATCAAA 59.664 37.037 0.00 0.00 0.00 2.69
2795 3372 6.821665 GGCTACCAGACTAAACATGTAATCAA 59.178 38.462 0.00 0.00 0.00 2.57
2796 3373 6.346096 GGCTACCAGACTAAACATGTAATCA 58.654 40.000 0.00 0.00 0.00 2.57
2797 3374 5.462398 CGGCTACCAGACTAAACATGTAATC 59.538 44.000 0.00 0.00 0.00 1.75
2798 3375 5.105064 ACGGCTACCAGACTAAACATGTAAT 60.105 40.000 0.00 0.00 0.00 1.89
2803 3380 2.159282 CGACGGCTACCAGACTAAACAT 60.159 50.000 0.00 0.00 0.00 2.71
2838 3415 2.168313 CCAACAACTTTGCCCTCAACTT 59.832 45.455 0.00 0.00 30.75 2.66
2839 3416 1.756538 CCAACAACTTTGCCCTCAACT 59.243 47.619 0.00 0.00 30.75 3.16
2840 3417 1.806247 GCCAACAACTTTGCCCTCAAC 60.806 52.381 0.00 0.00 30.75 3.18
2841 3418 0.463620 GCCAACAACTTTGCCCTCAA 59.536 50.000 0.00 0.00 0.00 3.02
2842 3419 1.733402 CGCCAACAACTTTGCCCTCA 61.733 55.000 0.00 0.00 0.00 3.86
2843 3420 1.007387 CGCCAACAACTTTGCCCTC 60.007 57.895 0.00 0.00 0.00 4.30
2844 3421 3.128375 CGCCAACAACTTTGCCCT 58.872 55.556 0.00 0.00 0.00 5.19
2845 3422 2.661537 GCGCCAACAACTTTGCCC 60.662 61.111 0.00 0.00 0.00 5.36
2846 3423 1.661509 GAGCGCCAACAACTTTGCC 60.662 57.895 2.29 0.00 0.00 4.52
2847 3424 0.936297 CTGAGCGCCAACAACTTTGC 60.936 55.000 2.29 0.00 0.00 3.68
2848 3425 0.318107 CCTGAGCGCCAACAACTTTG 60.318 55.000 2.29 0.00 0.00 2.77
2849 3426 0.751643 ACCTGAGCGCCAACAACTTT 60.752 50.000 2.29 0.00 0.00 2.66
2850 3427 1.152963 ACCTGAGCGCCAACAACTT 60.153 52.632 2.29 0.00 0.00 2.66
2851 3428 1.598130 GACCTGAGCGCCAACAACT 60.598 57.895 2.29 0.00 0.00 3.16
2852 3429 2.946762 GACCTGAGCGCCAACAAC 59.053 61.111 2.29 0.00 0.00 3.32
2853 3430 2.449031 ATCGACCTGAGCGCCAACAA 62.449 55.000 2.29 0.00 0.00 2.83
2854 3431 2.835701 GATCGACCTGAGCGCCAACA 62.836 60.000 2.29 0.93 0.00 3.33
2855 3432 2.125512 ATCGACCTGAGCGCCAAC 60.126 61.111 2.29 0.00 0.00 3.77
2856 3433 1.888436 AAGATCGACCTGAGCGCCAA 61.888 55.000 2.29 0.00 38.28 4.52
2857 3434 1.888436 AAAGATCGACCTGAGCGCCA 61.888 55.000 2.29 0.10 38.28 5.69
2858 3435 1.153549 AAAGATCGACCTGAGCGCC 60.154 57.895 2.29 0.00 38.28 6.53
2859 3436 1.424493 CCAAAGATCGACCTGAGCGC 61.424 60.000 0.00 0.00 38.28 5.92
2860 3437 1.424493 GCCAAAGATCGACCTGAGCG 61.424 60.000 0.00 0.00 38.28 5.03
2861 3438 1.092345 GGCCAAAGATCGACCTGAGC 61.092 60.000 0.00 0.00 0.00 4.26
2862 3439 0.539051 AGGCCAAAGATCGACCTGAG 59.461 55.000 5.01 0.00 0.00 3.35
2863 3440 1.757118 CTAGGCCAAAGATCGACCTGA 59.243 52.381 5.01 0.00 31.79 3.86
2864 3441 1.202580 CCTAGGCCAAAGATCGACCTG 60.203 57.143 5.01 0.00 31.79 4.00
2865 3442 1.123928 CCTAGGCCAAAGATCGACCT 58.876 55.000 5.01 0.00 34.42 3.85
2866 3443 0.106894 CCCTAGGCCAAAGATCGACC 59.893 60.000 5.01 0.00 0.00 4.79
2867 3444 1.120530 TCCCTAGGCCAAAGATCGAC 58.879 55.000 5.01 0.00 0.00 4.20
2868 3445 1.485066 GTTCCCTAGGCCAAAGATCGA 59.515 52.381 5.01 0.00 0.00 3.59
2869 3446 1.475213 GGTTCCCTAGGCCAAAGATCG 60.475 57.143 5.01 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.