Multiple sequence alignment - TraesCS6A01G190900

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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 TraesCS6A01G190900 chr6A 100.000 4930 0 0 1 4930 255323277 255328206 0.000000e+00 9105.0
1 TraesCS6A01G190900 chr6A 94.340 106 4 2 1754 1858 362228911 362228807 1.420000e-35 161.0
2 TraesCS6A01G190900 chr6D 98.115 2705 44 5 1958 4661 199144772 199142074 0.000000e+00 4706.0
3 TraesCS6A01G190900 chr6D 97.770 1480 30 2 1 1480 199146662 199145186 0.000000e+00 2547.0
4 TraesCS6A01G190900 chr6D 98.210 447 8 0 1496 1942 199145202 199144756 0.000000e+00 782.0
5 TraesCS6A01G190900 chr6D 94.286 105 4 2 1754 1857 246435969 246436072 5.110000e-35 159.0
6 TraesCS6A01G190900 chr6D 84.507 71 10 1 20 89 27973256 27973326 8.860000e-08 69.4
7 TraesCS6A01G190900 chr6B 97.381 2444 55 6 1958 4396 320550964 320548525 0.000000e+00 4150.0
8 TraesCS6A01G190900 chr6B 93.920 921 19 13 1 912 320552859 320551967 0.000000e+00 1356.0
9 TraesCS6A01G190900 chr6B 96.667 570 11 1 911 1480 320551938 320551377 0.000000e+00 941.0
10 TraesCS6A01G190900 chr6B 96.606 442 14 1 1496 1937 320551393 320550953 0.000000e+00 732.0
11 TraesCS6A01G190900 chr6B 94.828 116 4 1 4380 4495 320517551 320517438 3.920000e-41 180.0
12 TraesCS6A01G190900 chr3A 88.131 396 40 4 4536 4930 54458597 54458208 9.670000e-127 464.0
13 TraesCS6A01G190900 chr3A 97.778 90 2 0 1772 1861 492755878 492755967 6.610000e-34 156.0
14 TraesCS6A01G190900 chr2B 87.879 396 41 4 4536 4930 756350769 756350380 4.500000e-125 459.0
15 TraesCS6A01G190900 chr1B 84.487 419 36 20 4536 4930 18383408 18382995 2.150000e-103 387.0
16 TraesCS6A01G190900 chr1B 92.188 64 5 0 4690 4753 18383172 18383109 1.890000e-14 91.6
17 TraesCS6A01G190900 chr7A 84.010 419 38 4 4536 4930 105247712 105248125 4.660000e-100 375.0
18 TraesCS6A01G190900 chr7A 92.188 64 5 0 4690 4753 105247948 105248011 1.890000e-14 91.6
19 TraesCS6A01G190900 chr4D 87.500 200 24 1 4536 4735 3394764 3394566 3.840000e-56 230.0
20 TraesCS6A01G190900 chr7D 91.837 147 11 1 4561 4707 631675246 631675101 2.330000e-48 204.0
21 TraesCS6A01G190900 chr7D 83.505 194 22 5 4550 4733 445900229 445900422 6.560000e-39 172.0
22 TraesCS6A01G190900 chr7D 82.524 206 17 9 4536 4738 638520186 638519997 3.950000e-36 163.0
23 TraesCS6A01G190900 chr1A 88.485 165 17 2 4581 4744 30317577 30317740 1.080000e-46 198.0
24 TraesCS6A01G190900 chr2D 95.876 97 4 0 1763 1859 627553776 627553872 1.840000e-34 158.0
25 TraesCS6A01G190900 chr7B 95.789 95 4 0 1763 1857 458527873 458527967 2.380000e-33 154.0
26 TraesCS6A01G190900 chr4B 95.745 94 4 0 1763 1856 548118247 548118340 8.550000e-33 152.0
27 TraesCS6A01G190900 chr3D 93.069 101 7 0 1763 1863 263991631 263991731 1.110000e-31 148.0


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 TraesCS6A01G190900 chr6A 255323277 255328206 4929 False 9105.000000 9105 100.000000 1 4930 1 chr6A.!!$F1 4929
1 TraesCS6A01G190900 chr6D 199142074 199146662 4588 True 2678.333333 4706 98.031667 1 4661 3 chr6D.!!$R1 4660
2 TraesCS6A01G190900 chr6B 320548525 320552859 4334 True 1794.750000 4150 96.143500 1 4396 4 chr6B.!!$R2 4395

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
679 689 0.195096 ACTTACCTGGGGGTTGGAGA 59.805 55.0 0.0 0.0 44.73 3.71 F
1475 1515 0.102481 GCCTGCCAAGCAATGATCTG 59.898 55.0 0.0 0.0 38.41 2.90 F
1476 1516 0.102481 CCTGCCAAGCAATGATCTGC 59.898 55.0 0.0 0.0 38.41 4.26 F
1965 2005 0.395586 TTTGCGGGGGATTCTCATGG 60.396 55.0 0.0 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 1986 0.395586 CCATGAGAATCCCCCGCAAA 60.396 55.000 0.0 0.0 0.00 3.68 R
3466 3510 0.690192 TCCATTCAGAACCAGCGGAA 59.310 50.000 1.5 0.0 0.00 4.30 R
3636 3680 9.731819 AATAGTGTCATGAAGTATTAGTACACG 57.268 33.333 0.0 0.0 40.58 4.49 R
4117 4161 2.114616 AGATCTCGGCAGGAAATGACT 58.885 47.619 0.0 0.0 33.15 3.41 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
34 35 9.410556 GACTTTGTAAACATGCTGATAACAAAT 57.589 29.630 0.00 0.00 0.00 2.32
67 68 1.893919 GCGTGCCTTCCTCTCCTCTT 61.894 60.000 0.00 0.00 0.00 2.85
69 70 0.980423 GTGCCTTCCTCTCCTCTTGT 59.020 55.000 0.00 0.00 0.00 3.16
97 98 6.953101 TGCATTCCTATGTAACTTCTGGTAA 58.047 36.000 0.00 0.00 34.12 2.85
138 139 4.378046 GGCCGTGTAACACTTTGAGTAATG 60.378 45.833 0.00 0.00 35.74 1.90
255 256 3.133542 CCTGCCTCACATAGATTGACAGA 59.866 47.826 0.00 0.00 0.00 3.41
257 258 4.026052 TGCCTCACATAGATTGACAGAGA 58.974 43.478 0.00 0.00 0.00 3.10
295 297 9.624697 TTAATCAGTTCATGAATAGCACAAAAC 57.375 29.630 12.12 0.00 42.53 2.43
350 360 2.096248 ACCAAAATTGTGTGTGTCGGT 58.904 42.857 0.00 0.00 0.00 4.69
444 454 0.900647 CAGACTCAGACTCCCGGGTT 60.901 60.000 22.86 9.04 0.00 4.11
679 689 0.195096 ACTTACCTGGGGGTTGGAGA 59.805 55.000 0.00 0.00 44.73 3.71
859 869 0.721718 GACCTTGCGATTTGAGACCG 59.278 55.000 0.00 0.00 0.00 4.79
1080 1120 1.194781 AGGTGGAGTTGTGCCTCGAT 61.195 55.000 0.00 0.00 31.98 3.59
1186 1226 2.758327 CAGTCGACCCCCGGATCA 60.758 66.667 13.01 0.00 39.14 2.92
1371 1411 4.695606 TGGTCCCATCTTACTTACCTCTT 58.304 43.478 0.00 0.00 0.00 2.85
1469 1509 3.064324 GTCCGCCTGCCAAGCAAT 61.064 61.111 0.00 0.00 38.41 3.56
1470 1510 3.063704 TCCGCCTGCCAAGCAATG 61.064 61.111 0.00 0.00 38.41 2.82
1471 1511 3.063704 CCGCCTGCCAAGCAATGA 61.064 61.111 0.00 0.00 38.41 2.57
1472 1512 2.420568 CCGCCTGCCAAGCAATGAT 61.421 57.895 0.00 0.00 38.41 2.45
1473 1513 1.065273 CGCCTGCCAAGCAATGATC 59.935 57.895 0.00 0.00 38.41 2.92
1474 1514 1.381928 CGCCTGCCAAGCAATGATCT 61.382 55.000 0.00 0.00 38.41 2.75
1475 1515 0.102481 GCCTGCCAAGCAATGATCTG 59.898 55.000 0.00 0.00 38.41 2.90
1476 1516 0.102481 CCTGCCAAGCAATGATCTGC 59.898 55.000 0.00 0.00 38.41 4.26
1477 1517 0.815095 CTGCCAAGCAATGATCTGCA 59.185 50.000 9.38 0.00 45.18 4.41
1478 1518 1.203758 CTGCCAAGCAATGATCTGCAA 59.796 47.619 9.38 0.00 45.18 4.08
1479 1519 1.828595 TGCCAAGCAATGATCTGCAAT 59.171 42.857 9.38 0.00 45.18 3.56
1480 1520 2.235155 TGCCAAGCAATGATCTGCAATT 59.765 40.909 9.38 0.00 45.18 2.32
1481 1521 3.447944 TGCCAAGCAATGATCTGCAATTA 59.552 39.130 9.38 0.00 45.18 1.40
1482 1522 4.100344 TGCCAAGCAATGATCTGCAATTAT 59.900 37.500 9.38 0.00 45.18 1.28
1483 1523 4.684703 GCCAAGCAATGATCTGCAATTATC 59.315 41.667 9.38 0.00 45.18 1.75
1484 1524 5.227908 CCAAGCAATGATCTGCAATTATCC 58.772 41.667 9.38 0.00 45.18 2.59
1485 1525 4.761235 AGCAATGATCTGCAATTATCCG 57.239 40.909 9.38 0.00 45.18 4.18
1486 1526 3.057736 AGCAATGATCTGCAATTATCCGC 60.058 43.478 9.38 0.00 45.18 5.54
1487 1527 3.304861 GCAATGATCTGCAATTATCCGCA 60.305 43.478 2.23 0.00 42.17 5.69
1488 1528 4.793678 GCAATGATCTGCAATTATCCGCAA 60.794 41.667 2.23 0.00 42.17 4.85
1489 1529 5.283294 CAATGATCTGCAATTATCCGCAAA 58.717 37.500 0.00 0.00 37.76 3.68
1490 1530 4.979943 TGATCTGCAATTATCCGCAAAA 57.020 36.364 0.00 0.00 37.76 2.44
1491 1531 5.321959 TGATCTGCAATTATCCGCAAAAA 57.678 34.783 0.00 0.00 37.76 1.94
1760 1800 6.909550 TTTACATGAAGGCAACCTTACATT 57.090 33.333 0.00 0.98 44.82 2.71
1788 1828 6.400568 TGTTAAATACTCCCTCCGTAAACTG 58.599 40.000 0.00 0.00 0.00 3.16
1920 1960 7.500892 TCTTAAACTTTGCTGTGTTATTCCTGA 59.499 33.333 0.00 0.00 0.00 3.86
1938 1978 8.655935 ATTCCTGAAATTTTCTCATGGTAAGT 57.344 30.769 10.33 0.00 0.00 2.24
1939 1979 9.753674 ATTCCTGAAATTTTCTCATGGTAAGTA 57.246 29.630 10.33 0.00 0.00 2.24
1940 1980 9.581289 TTCCTGAAATTTTCTCATGGTAAGTAA 57.419 29.630 10.33 0.00 0.00 2.24
1941 1981 9.753674 TCCTGAAATTTTCTCATGGTAAGTAAT 57.246 29.630 10.33 0.00 0.00 1.89
1962 2002 3.755810 TTTTTGCGGGGGATTCTCA 57.244 47.368 0.00 0.00 0.00 3.27
1963 2003 2.230130 TTTTTGCGGGGGATTCTCAT 57.770 45.000 0.00 0.00 0.00 2.90
1964 2004 1.473258 TTTTGCGGGGGATTCTCATG 58.527 50.000 0.00 0.00 0.00 3.07
1965 2005 0.395586 TTTGCGGGGGATTCTCATGG 60.396 55.000 0.00 0.00 0.00 3.66
1966 2006 1.570857 TTGCGGGGGATTCTCATGGT 61.571 55.000 0.00 0.00 0.00 3.55
1967 2007 0.692756 TGCGGGGGATTCTCATGGTA 60.693 55.000 0.00 0.00 0.00 3.25
1968 2008 0.472471 GCGGGGGATTCTCATGGTAA 59.528 55.000 0.00 0.00 0.00 2.85
1969 2009 1.543429 GCGGGGGATTCTCATGGTAAG 60.543 57.143 0.00 0.00 0.00 2.34
2188 2228 4.345859 TGAGTTGTCGTCCTTAAATGGT 57.654 40.909 0.00 0.00 0.00 3.55
2811 2851 8.715190 TTAACCAGGTAGCATGATACTACATA 57.285 34.615 19.77 5.78 41.49 2.29
3207 3251 4.707563 TCAATCTCACGTTTTATGTTGCG 58.292 39.130 0.00 0.00 0.00 4.85
3290 3334 3.290710 AGTGTGACATCCAAAGTGCTTT 58.709 40.909 0.00 0.00 0.00 3.51
3380 3424 1.795170 CTGGGTGTTTTCCTGTGCCG 61.795 60.000 0.00 0.00 0.00 5.69
3396 3440 1.542030 TGCCGCGTTTGATTTACCATT 59.458 42.857 4.92 0.00 0.00 3.16
4117 4161 1.415672 AAGGCCCGTCCTGAAGTTGA 61.416 55.000 0.00 0.00 46.94 3.18
4377 4421 4.100498 ACCTTACCGTGAGAAACTCTTGAA 59.900 41.667 0.00 0.00 0.00 2.69
4470 4514 3.690460 AGTTGAGACATTGGGAATCCAC 58.310 45.455 0.09 0.00 43.94 4.02
4481 4525 2.101582 TGGGAATCCACAAAACCAAACG 59.898 45.455 0.09 0.00 38.32 3.60
4516 4561 3.945346 TGCTTTATTCCAGGTCGCTAAA 58.055 40.909 0.00 0.00 0.00 1.85
4517 4562 4.328536 TGCTTTATTCCAGGTCGCTAAAA 58.671 39.130 0.00 0.00 0.00 1.52
4518 4563 4.762765 TGCTTTATTCCAGGTCGCTAAAAA 59.237 37.500 0.00 0.00 0.00 1.94
4522 4567 6.490566 TTATTCCAGGTCGCTAAAAACTTC 57.509 37.500 0.00 0.00 0.00 3.01
4542 4587 3.869065 TCCACGGTTTCATAAGATGACC 58.131 45.455 0.00 0.00 39.39 4.02
4567 4612 0.600557 CGCCCATGGTGTAAAAAGCA 59.399 50.000 11.73 0.00 0.00 3.91
4668 4713 7.931015 ATGGTACCATGATAGACTAAAAGGA 57.069 36.000 26.82 0.00 35.03 3.36
4669 4714 7.743116 TGGTACCATGATAGACTAAAAGGAA 57.257 36.000 11.60 0.00 0.00 3.36
4670 4715 7.792032 TGGTACCATGATAGACTAAAAGGAAG 58.208 38.462 11.60 0.00 0.00 3.46
4671 4716 7.402071 TGGTACCATGATAGACTAAAAGGAAGT 59.598 37.037 11.60 0.00 0.00 3.01
4672 4717 8.921205 GGTACCATGATAGACTAAAAGGAAGTA 58.079 37.037 7.15 0.00 0.00 2.24
4675 4720 9.838339 ACCATGATAGACTAAAAGGAAGTAATG 57.162 33.333 0.00 0.00 0.00 1.90
4683 4728 8.816894 AGACTAAAAGGAAGTAATGAGATCACA 58.183 33.333 0.00 0.00 0.00 3.58
4684 4729 9.606631 GACTAAAAGGAAGTAATGAGATCACAT 57.393 33.333 0.00 0.00 0.00 3.21
4685 4730 9.388506 ACTAAAAGGAAGTAATGAGATCACATG 57.611 33.333 6.39 0.00 0.00 3.21
4686 4731 9.605275 CTAAAAGGAAGTAATGAGATCACATGA 57.395 33.333 6.39 0.00 0.00 3.07
4687 4732 7.856145 AAAGGAAGTAATGAGATCACATGAC 57.144 36.000 11.62 11.62 33.19 3.06
4688 4733 6.550938 AGGAAGTAATGAGATCACATGACA 57.449 37.500 19.35 1.86 34.90 3.58
4689 4734 6.950842 AGGAAGTAATGAGATCACATGACAA 58.049 36.000 19.35 0.04 34.90 3.18
4690 4735 7.397221 AGGAAGTAATGAGATCACATGACAAA 58.603 34.615 19.35 0.00 34.90 2.83
4691 4736 8.051535 AGGAAGTAATGAGATCACATGACAAAT 58.948 33.333 19.35 7.93 34.90 2.32
4692 4737 9.330063 GGAAGTAATGAGATCACATGACAAATA 57.670 33.333 19.35 0.77 34.90 1.40
4694 4739 8.375608 AGTAATGAGATCACATGACAAATAGC 57.624 34.615 19.35 0.00 34.90 2.97
4695 4740 7.989170 AGTAATGAGATCACATGACAAATAGCA 59.011 33.333 19.35 0.00 34.90 3.49
4696 4741 7.818997 AATGAGATCACATGACAAATAGCAT 57.181 32.000 6.39 0.00 0.00 3.79
4697 4742 8.913487 AATGAGATCACATGACAAATAGCATA 57.087 30.769 6.39 0.00 0.00 3.14
4698 4743 7.719778 TGAGATCACATGACAAATAGCATAC 57.280 36.000 0.00 0.00 0.00 2.39
4699 4744 7.274447 TGAGATCACATGACAAATAGCATACA 58.726 34.615 0.00 0.00 0.00 2.29
4700 4745 7.935210 TGAGATCACATGACAAATAGCATACAT 59.065 33.333 0.00 0.00 0.00 2.29
4701 4746 8.687292 AGATCACATGACAAATAGCATACATT 57.313 30.769 0.00 0.00 0.00 2.71
4702 4747 8.565416 AGATCACATGACAAATAGCATACATTG 58.435 33.333 0.00 0.00 0.00 2.82
4703 4748 7.030075 TCACATGACAAATAGCATACATTGG 57.970 36.000 0.00 0.00 0.00 3.16
4704 4749 6.602803 TCACATGACAAATAGCATACATTGGT 59.397 34.615 0.00 0.00 39.88 3.67
4705 4750 7.122501 TCACATGACAAATAGCATACATTGGTT 59.877 33.333 0.00 0.00 37.26 3.67
4706 4751 7.760794 CACATGACAAATAGCATACATTGGTTT 59.239 33.333 0.00 0.00 37.26 3.27
4707 4752 8.313292 ACATGACAAATAGCATACATTGGTTTT 58.687 29.630 0.00 0.00 37.26 2.43
4708 4753 9.800433 CATGACAAATAGCATACATTGGTTTTA 57.200 29.630 0.00 0.00 37.26 1.52
4714 4759 9.965824 AAATAGCATACATTGGTTTTATACAGC 57.034 29.630 0.00 0.00 37.26 4.40
4715 4760 8.690203 ATAGCATACATTGGTTTTATACAGCA 57.310 30.769 0.00 0.00 37.26 4.41
4716 4761 7.403312 AGCATACATTGGTTTTATACAGCAA 57.597 32.000 0.00 0.00 36.15 3.91
4717 4762 7.483307 AGCATACATTGGTTTTATACAGCAAG 58.517 34.615 0.00 0.00 35.22 4.01
4718 4763 6.198966 GCATACATTGGTTTTATACAGCAAGC 59.801 38.462 0.00 0.00 35.22 4.01
4719 4764 5.982890 ACATTGGTTTTATACAGCAAGCT 57.017 34.783 0.00 0.00 35.22 3.74
4720 4765 8.620416 CATACATTGGTTTTATACAGCAAGCTA 58.380 33.333 0.00 0.00 35.22 3.32
4721 4766 6.852664 ACATTGGTTTTATACAGCAAGCTAC 58.147 36.000 0.00 0.00 35.22 3.58
4722 4767 6.432783 ACATTGGTTTTATACAGCAAGCTACA 59.567 34.615 0.00 0.00 35.22 2.74
4723 4768 6.494893 TTGGTTTTATACAGCAAGCTACAG 57.505 37.500 0.00 0.00 0.00 2.74
4724 4769 5.556915 TGGTTTTATACAGCAAGCTACAGT 58.443 37.500 0.00 0.00 0.00 3.55
4725 4770 6.703319 TGGTTTTATACAGCAAGCTACAGTA 58.297 36.000 0.00 0.00 0.00 2.74
4726 4771 6.816640 TGGTTTTATACAGCAAGCTACAGTAG 59.183 38.462 2.85 2.85 0.00 2.57
4750 4795 6.232139 CAAAGATGCATTGTATATCTGCGA 57.768 37.500 0.00 0.00 38.75 5.10
4751 4796 6.661669 CAAAGATGCATTGTATATCTGCGAA 58.338 36.000 0.00 0.00 38.75 4.70
4752 4797 5.852738 AGATGCATTGTATATCTGCGAAC 57.147 39.130 0.00 0.00 38.75 3.95
4753 4798 5.299949 AGATGCATTGTATATCTGCGAACA 58.700 37.500 0.00 0.00 38.75 3.18
4754 4799 5.759763 AGATGCATTGTATATCTGCGAACAA 59.240 36.000 0.00 0.00 38.75 2.83
4755 4800 6.429078 AGATGCATTGTATATCTGCGAACAAT 59.571 34.615 0.00 0.00 41.87 2.71
4756 4801 7.603784 AGATGCATTGTATATCTGCGAACAATA 59.396 33.333 0.00 0.00 39.80 1.90
4757 4802 7.120789 TGCATTGTATATCTGCGAACAATAG 57.879 36.000 0.00 0.00 39.80 1.73
4758 4803 6.017933 GCATTGTATATCTGCGAACAATAGC 58.982 40.000 0.00 0.00 39.80 2.97
4759 4804 6.347644 GCATTGTATATCTGCGAACAATAGCA 60.348 38.462 0.00 0.00 39.80 3.49
4760 4805 7.624974 GCATTGTATATCTGCGAACAATAGCAT 60.625 37.037 0.00 0.00 42.95 3.79
4761 4806 8.872845 CATTGTATATCTGCGAACAATAGCATA 58.127 33.333 0.00 0.00 42.95 3.14
4762 4807 7.812309 TGTATATCTGCGAACAATAGCATAC 57.188 36.000 0.00 0.00 42.95 2.39
4763 4808 7.375053 TGTATATCTGCGAACAATAGCATACA 58.625 34.615 0.00 0.00 42.95 2.29
4764 4809 8.034804 TGTATATCTGCGAACAATAGCATACAT 58.965 33.333 0.00 0.00 42.95 2.29
4765 4810 7.912056 ATATCTGCGAACAATAGCATACATT 57.088 32.000 0.00 0.00 42.95 2.71
4766 4811 5.408204 TCTGCGAACAATAGCATACATTG 57.592 39.130 0.00 0.00 42.95 2.82
4767 4812 4.273235 TCTGCGAACAATAGCATACATTGG 59.727 41.667 0.00 0.00 42.95 3.16
4768 4813 3.944650 TGCGAACAATAGCATACATTGGT 59.055 39.130 0.00 0.00 38.59 3.67
4769 4814 4.397730 TGCGAACAATAGCATACATTGGTT 59.602 37.500 0.00 0.00 38.59 3.67
4770 4815 5.105957 TGCGAACAATAGCATACATTGGTTT 60.106 36.000 0.00 0.00 38.59 3.27
4771 4816 5.804979 GCGAACAATAGCATACATTGGTTTT 59.195 36.000 0.00 0.00 37.64 2.43
4772 4817 6.970043 GCGAACAATAGCATACATTGGTTTTA 59.030 34.615 0.00 0.00 37.64 1.52
4773 4818 7.647715 GCGAACAATAGCATACATTGGTTTTAT 59.352 33.333 0.00 0.00 37.64 1.40
4774 4819 8.957028 CGAACAATAGCATACATTGGTTTTATG 58.043 33.333 0.00 0.00 37.64 1.90
4778 4823 8.971321 CAATAGCATACATTGGTTTTATGAAGC 58.029 33.333 0.00 0.00 37.26 3.86
4779 4824 6.528537 AGCATACATTGGTTTTATGAAGCA 57.471 33.333 0.00 0.00 29.87 3.91
4780 4825 6.934056 AGCATACATTGGTTTTATGAAGCAA 58.066 32.000 9.66 9.66 41.14 3.91
4781 4826 7.037438 AGCATACATTGGTTTTATGAAGCAAG 58.963 34.615 11.95 8.06 40.38 4.01
4782 4827 6.237915 GCATACATTGGTTTTATGAAGCAAGC 60.238 38.462 11.95 7.33 40.38 4.01
4783 4828 5.473066 ACATTGGTTTTATGAAGCAAGCT 57.527 34.783 11.95 0.00 40.38 3.74
4784 4829 6.588719 ACATTGGTTTTATGAAGCAAGCTA 57.411 33.333 11.95 0.00 40.38 3.32
4785 4830 6.389906 ACATTGGTTTTATGAAGCAAGCTAC 58.610 36.000 11.95 0.00 40.38 3.58
4786 4831 6.015519 ACATTGGTTTTATGAAGCAAGCTACA 60.016 34.615 11.95 0.00 40.38 2.74
4787 4832 5.627499 TGGTTTTATGAAGCAAGCTACAG 57.373 39.130 0.00 0.00 0.00 2.74
4788 4833 5.070001 TGGTTTTATGAAGCAAGCTACAGT 58.930 37.500 0.00 0.00 0.00 3.55
4789 4834 6.234920 TGGTTTTATGAAGCAAGCTACAGTA 58.765 36.000 0.00 0.00 0.00 2.74
4790 4835 6.371548 TGGTTTTATGAAGCAAGCTACAGTAG 59.628 38.462 2.85 2.85 0.00 2.57
4815 4860 7.734924 CAAAGATGCATTCTATAGCTACCAA 57.265 36.000 0.00 0.00 33.05 3.67
4816 4861 8.332996 CAAAGATGCATTCTATAGCTACCAAT 57.667 34.615 0.00 0.00 33.05 3.16
4817 4862 8.790718 CAAAGATGCATTCTATAGCTACCAATT 58.209 33.333 0.00 0.00 33.05 2.32
4818 4863 7.918536 AGATGCATTCTATAGCTACCAATTG 57.081 36.000 0.00 0.00 30.96 2.32
4819 4864 6.883217 AGATGCATTCTATAGCTACCAATTGG 59.117 38.462 23.31 23.31 35.26 3.16
4820 4865 6.186420 TGCATTCTATAGCTACCAATTGGA 57.814 37.500 31.22 13.31 38.94 3.53
4821 4866 6.600388 TGCATTCTATAGCTACCAATTGGAA 58.400 36.000 31.22 11.46 38.94 3.53
4822 4867 6.712095 TGCATTCTATAGCTACCAATTGGAAG 59.288 38.462 31.22 14.39 38.94 3.46
4823 4868 6.936900 GCATTCTATAGCTACCAATTGGAAGA 59.063 38.462 31.22 16.17 38.94 2.87
4824 4869 7.095017 GCATTCTATAGCTACCAATTGGAAGAC 60.095 40.741 31.22 15.97 38.94 3.01
4825 4870 6.420913 TCTATAGCTACCAATTGGAAGACC 57.579 41.667 31.22 13.19 38.94 3.85
4826 4871 2.403252 AGCTACCAATTGGAAGACCG 57.597 50.000 31.22 12.14 39.42 4.79
4827 4872 1.065418 AGCTACCAATTGGAAGACCGG 60.065 52.381 31.22 0.00 39.42 5.28
4828 4873 2.017113 GCTACCAATTGGAAGACCGGG 61.017 57.143 31.22 11.28 39.42 5.73
4829 4874 1.557832 CTACCAATTGGAAGACCGGGA 59.442 52.381 31.22 0.00 39.42 5.14
4830 4875 0.037734 ACCAATTGGAAGACCGGGAC 59.962 55.000 31.22 0.00 39.42 4.46
4831 4876 0.037590 CCAATTGGAAGACCGGGACA 59.962 55.000 20.50 0.00 39.42 4.02
4832 4877 1.340991 CCAATTGGAAGACCGGGACAT 60.341 52.381 20.50 0.00 39.42 3.06
4833 4878 1.745087 CAATTGGAAGACCGGGACATG 59.255 52.381 6.32 0.00 39.42 3.21
4834 4879 0.255890 ATTGGAAGACCGGGACATGG 59.744 55.000 6.32 0.00 39.42 3.66
4835 4880 0.838554 TTGGAAGACCGGGACATGGA 60.839 55.000 6.32 0.00 39.42 3.41
4836 4881 0.838554 TGGAAGACCGGGACATGGAA 60.839 55.000 6.32 0.00 39.42 3.53
4837 4882 0.107654 GGAAGACCGGGACATGGAAG 60.108 60.000 6.32 0.00 0.00 3.46
4838 4883 0.613777 GAAGACCGGGACATGGAAGT 59.386 55.000 6.32 0.00 0.00 3.01
4839 4884 0.324943 AAGACCGGGACATGGAAGTG 59.675 55.000 6.32 0.00 0.00 3.16
4840 4885 0.544357 AGACCGGGACATGGAAGTGA 60.544 55.000 6.32 0.00 0.00 3.41
4841 4886 0.541863 GACCGGGACATGGAAGTGAT 59.458 55.000 6.32 0.00 0.00 3.06
4842 4887 0.253044 ACCGGGACATGGAAGTGATG 59.747 55.000 6.32 0.00 0.00 3.07
4843 4888 0.464373 CCGGGACATGGAAGTGATGG 60.464 60.000 0.00 0.00 0.00 3.51
4844 4889 0.253044 CGGGACATGGAAGTGATGGT 59.747 55.000 0.00 0.00 0.00 3.55
4845 4890 1.484653 CGGGACATGGAAGTGATGGTA 59.515 52.381 0.00 0.00 0.00 3.25
4846 4891 2.104792 CGGGACATGGAAGTGATGGTAT 59.895 50.000 0.00 0.00 0.00 2.73
4847 4892 3.433598 CGGGACATGGAAGTGATGGTATT 60.434 47.826 0.00 0.00 0.00 1.89
4848 4893 4.202315 CGGGACATGGAAGTGATGGTATTA 60.202 45.833 0.00 0.00 0.00 0.98
4849 4894 5.513094 CGGGACATGGAAGTGATGGTATTAT 60.513 44.000 0.00 0.00 0.00 1.28
4850 4895 5.707298 GGGACATGGAAGTGATGGTATTATG 59.293 44.000 0.00 0.00 0.00 1.90
4851 4896 5.182001 GGACATGGAAGTGATGGTATTATGC 59.818 44.000 0.00 0.00 0.00 3.14
4852 4897 5.693961 ACATGGAAGTGATGGTATTATGCA 58.306 37.500 0.00 0.00 0.00 3.96
4853 4898 5.766670 ACATGGAAGTGATGGTATTATGCAG 59.233 40.000 0.00 0.00 0.00 4.41
4854 4899 5.628797 TGGAAGTGATGGTATTATGCAGA 57.371 39.130 0.00 0.00 0.00 4.26
4855 4900 5.614308 TGGAAGTGATGGTATTATGCAGAG 58.386 41.667 0.00 0.00 0.00 3.35
4856 4901 4.453819 GGAAGTGATGGTATTATGCAGAGC 59.546 45.833 0.00 0.00 0.00 4.09
4857 4902 3.657634 AGTGATGGTATTATGCAGAGCG 58.342 45.455 0.00 0.00 0.00 5.03
4858 4903 3.321968 AGTGATGGTATTATGCAGAGCGA 59.678 43.478 0.00 0.00 0.00 4.93
4859 4904 3.677121 GTGATGGTATTATGCAGAGCGAG 59.323 47.826 0.00 0.00 0.00 5.03
4860 4905 2.154854 TGGTATTATGCAGAGCGAGC 57.845 50.000 0.00 0.00 0.00 5.03
4866 4911 4.699626 TGCAGAGCGAGCATTCAA 57.300 50.000 0.00 0.00 37.02 2.69
4867 4912 2.931246 TGCAGAGCGAGCATTCAAA 58.069 47.368 0.00 0.00 37.02 2.69
4868 4913 0.518636 TGCAGAGCGAGCATTCAAAC 59.481 50.000 0.00 0.00 37.02 2.93
4869 4914 0.179179 GCAGAGCGAGCATTCAAACC 60.179 55.000 0.00 0.00 0.00 3.27
4870 4915 1.159285 CAGAGCGAGCATTCAAACCA 58.841 50.000 0.00 0.00 0.00 3.67
4871 4916 1.741706 CAGAGCGAGCATTCAAACCAT 59.258 47.619 0.00 0.00 0.00 3.55
4872 4917 1.741706 AGAGCGAGCATTCAAACCATG 59.258 47.619 0.00 0.00 0.00 3.66
4873 4918 0.171903 AGCGAGCATTCAAACCATGC 59.828 50.000 0.00 0.00 46.39 4.06
4878 4923 2.443887 GCATTCAAACCATGCACACT 57.556 45.000 0.00 0.00 45.50 3.55
4879 4924 3.574284 GCATTCAAACCATGCACACTA 57.426 42.857 0.00 0.00 45.50 2.74
4880 4925 3.244976 GCATTCAAACCATGCACACTAC 58.755 45.455 0.00 0.00 45.50 2.73
4881 4926 3.305267 GCATTCAAACCATGCACACTACA 60.305 43.478 0.00 0.00 45.50 2.74
4882 4927 4.795635 GCATTCAAACCATGCACACTACAA 60.796 41.667 0.00 0.00 45.50 2.41
4883 4928 5.472148 CATTCAAACCATGCACACTACAAT 58.528 37.500 0.00 0.00 0.00 2.71
4884 4929 6.619744 CATTCAAACCATGCACACTACAATA 58.380 36.000 0.00 0.00 0.00 1.90
4885 4930 6.832520 TTCAAACCATGCACACTACAATAT 57.167 33.333 0.00 0.00 0.00 1.28
4886 4931 6.832520 TCAAACCATGCACACTACAATATT 57.167 33.333 0.00 0.00 0.00 1.28
4887 4932 7.225784 TCAAACCATGCACACTACAATATTT 57.774 32.000 0.00 0.00 0.00 1.40
4888 4933 8.341892 TCAAACCATGCACACTACAATATTTA 57.658 30.769 0.00 0.00 0.00 1.40
4889 4934 8.458052 TCAAACCATGCACACTACAATATTTAG 58.542 33.333 0.00 0.00 0.00 1.85
4890 4935 8.458052 CAAACCATGCACACTACAATATTTAGA 58.542 33.333 0.00 0.00 0.00 2.10
4891 4936 8.752005 AACCATGCACACTACAATATTTAGAT 57.248 30.769 0.00 0.00 0.00 1.98
4892 4937 8.158169 ACCATGCACACTACAATATTTAGATG 57.842 34.615 0.00 8.86 0.00 2.90
4893 4938 7.080099 CCATGCACACTACAATATTTAGATGC 58.920 38.462 18.20 18.20 35.02 3.91
4894 4939 7.255208 CCATGCACACTACAATATTTAGATGCA 60.255 37.037 23.12 23.12 41.74 3.96
4895 4940 7.250445 TGCACACTACAATATTTAGATGCAG 57.750 36.000 20.61 4.71 37.32 4.41
4896 4941 6.138761 GCACACTACAATATTTAGATGCAGC 58.861 40.000 19.03 0.00 34.79 5.25
4897 4942 6.662616 CACACTACAATATTTAGATGCAGCC 58.337 40.000 0.00 0.00 0.00 4.85
4898 4943 5.466728 ACACTACAATATTTAGATGCAGCCG 59.533 40.000 0.00 0.00 0.00 5.52
4899 4944 5.696270 CACTACAATATTTAGATGCAGCCGA 59.304 40.000 0.00 0.00 0.00 5.54
4900 4945 6.369890 CACTACAATATTTAGATGCAGCCGAT 59.630 38.462 0.00 0.00 0.00 4.18
4901 4946 7.545615 CACTACAATATTTAGATGCAGCCGATA 59.454 37.037 0.00 0.00 0.00 2.92
4902 4947 6.727824 ACAATATTTAGATGCAGCCGATAC 57.272 37.500 0.00 0.00 0.00 2.24
4903 4948 6.230472 ACAATATTTAGATGCAGCCGATACA 58.770 36.000 0.00 0.00 0.00 2.29
4904 4949 6.881065 ACAATATTTAGATGCAGCCGATACAT 59.119 34.615 0.00 0.00 0.00 2.29
4905 4950 8.040727 ACAATATTTAGATGCAGCCGATACATA 58.959 33.333 0.00 0.00 0.00 2.29
4906 4951 8.546244 CAATATTTAGATGCAGCCGATACATAG 58.454 37.037 0.00 0.00 0.00 2.23
4907 4952 2.376808 AGATGCAGCCGATACATAGC 57.623 50.000 0.00 0.00 0.00 2.97
4908 4953 1.620323 AGATGCAGCCGATACATAGCA 59.380 47.619 0.00 0.00 36.34 3.49
4909 4954 2.235650 AGATGCAGCCGATACATAGCAT 59.764 45.455 0.00 0.00 44.50 3.79
4910 4955 2.549064 TGCAGCCGATACATAGCATT 57.451 45.000 0.00 0.00 0.00 3.56
4911 4956 3.676291 TGCAGCCGATACATAGCATTA 57.324 42.857 0.00 0.00 0.00 1.90
4912 4957 3.325870 TGCAGCCGATACATAGCATTAC 58.674 45.455 0.00 0.00 0.00 1.89
4913 4958 3.244044 TGCAGCCGATACATAGCATTACA 60.244 43.478 0.00 0.00 0.00 2.41
4914 4959 3.745975 GCAGCCGATACATAGCATTACAA 59.254 43.478 0.00 0.00 0.00 2.41
4915 4960 4.143030 GCAGCCGATACATAGCATTACAAG 60.143 45.833 0.00 0.00 0.00 3.16
4916 4961 5.230182 CAGCCGATACATAGCATTACAAGA 58.770 41.667 0.00 0.00 0.00 3.02
4917 4962 5.347093 CAGCCGATACATAGCATTACAAGAG 59.653 44.000 0.00 0.00 0.00 2.85
4918 4963 5.243954 AGCCGATACATAGCATTACAAGAGA 59.756 40.000 0.00 0.00 0.00 3.10
4919 4964 5.574830 GCCGATACATAGCATTACAAGAGAG 59.425 44.000 0.00 0.00 0.00 3.20
4920 4965 5.574830 CCGATACATAGCATTACAAGAGAGC 59.425 44.000 0.00 0.00 0.00 4.09
4921 4966 5.574830 CGATACATAGCATTACAAGAGAGCC 59.425 44.000 0.00 0.00 0.00 4.70
4922 4967 4.760530 ACATAGCATTACAAGAGAGCCA 57.239 40.909 0.00 0.00 0.00 4.75
4923 4968 4.446371 ACATAGCATTACAAGAGAGCCAC 58.554 43.478 0.00 0.00 0.00 5.01
4924 4969 4.080919 ACATAGCATTACAAGAGAGCCACA 60.081 41.667 0.00 0.00 0.00 4.17
4925 4970 3.423539 AGCATTACAAGAGAGCCACAA 57.576 42.857 0.00 0.00 0.00 3.33
4926 4971 3.341823 AGCATTACAAGAGAGCCACAAG 58.658 45.455 0.00 0.00 0.00 3.16
4927 4972 3.008375 AGCATTACAAGAGAGCCACAAGA 59.992 43.478 0.00 0.00 0.00 3.02
4928 4973 3.944015 GCATTACAAGAGAGCCACAAGAT 59.056 43.478 0.00 0.00 0.00 2.40
4929 4974 4.034975 GCATTACAAGAGAGCCACAAGATC 59.965 45.833 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 7.119699 CAGAAGTTACATAGGAATGCAAGAACA 59.880 37.037 0.00 0.00 36.50 3.18
69 70 6.599244 CCAGAAGTTACATAGGAATGCAAGAA 59.401 38.462 0.00 0.00 36.50 2.52
97 98 0.538746 CCAAGGCCGGTTACAAGGTT 60.539 55.000 1.90 0.00 0.00 3.50
350 360 5.295787 CCTGCCTATTTTAGTTCATGCGTAA 59.704 40.000 0.00 0.00 0.00 3.18
444 454 2.573869 GTACGCTCTGCAGCTCCA 59.426 61.111 9.47 0.00 44.40 3.86
636 646 4.351054 CCCCCTTGCACGCTTCCT 62.351 66.667 0.00 0.00 0.00 3.36
859 869 0.108138 AAGCCCATGTACAGCGACTC 60.108 55.000 0.33 0.00 0.00 3.36
930 970 4.202264 GGGAGAAGAAGAAGAATATGCCGA 60.202 45.833 0.00 0.00 0.00 5.54
1101 1141 2.907458 TCTCCACCTCACTCAGATCA 57.093 50.000 0.00 0.00 0.00 2.92
1371 1411 8.518430 ACAATAGGACACATGCATATAACAAA 57.482 30.769 0.00 0.00 0.00 2.83
1469 1509 4.979943 TTTTGCGGATAATTGCAGATCA 57.020 36.364 0.00 0.00 42.89 2.92
1492 1532 4.630069 GCTCATTGCAGATCATTGCTTTTT 59.370 37.500 8.27 0.00 44.38 1.94
1493 1533 4.181578 GCTCATTGCAGATCATTGCTTTT 58.818 39.130 8.27 0.00 44.38 2.27
1494 1534 3.782046 GCTCATTGCAGATCATTGCTTT 58.218 40.909 8.27 0.00 44.38 3.51
1495 1535 3.438297 GCTCATTGCAGATCATTGCTT 57.562 42.857 8.27 0.00 44.38 3.91
1760 1800 5.750352 ACGGAGGGAGTATTTAACAAAGA 57.250 39.130 0.00 0.00 0.00 2.52
1944 1984 1.824230 CATGAGAATCCCCCGCAAAAA 59.176 47.619 0.00 0.00 0.00 1.94
1945 1985 1.473258 CATGAGAATCCCCCGCAAAA 58.527 50.000 0.00 0.00 0.00 2.44
1946 1986 0.395586 CCATGAGAATCCCCCGCAAA 60.396 55.000 0.00 0.00 0.00 3.68
1947 1987 1.227102 CCATGAGAATCCCCCGCAA 59.773 57.895 0.00 0.00 0.00 4.85
1948 1988 0.692756 TACCATGAGAATCCCCCGCA 60.693 55.000 0.00 0.00 0.00 5.69
1949 1989 0.472471 TTACCATGAGAATCCCCCGC 59.528 55.000 0.00 0.00 0.00 6.13
1950 1990 1.768870 ACTTACCATGAGAATCCCCCG 59.231 52.381 0.00 0.00 0.00 5.73
1951 1991 3.953542 AACTTACCATGAGAATCCCCC 57.046 47.619 0.00 0.00 0.00 5.40
1952 1992 5.073144 TGGATAACTTACCATGAGAATCCCC 59.927 44.000 0.00 0.00 33.34 4.81
1953 1993 6.187727 TGGATAACTTACCATGAGAATCCC 57.812 41.667 0.00 0.00 33.34 3.85
1962 2002 5.132648 TCAGAAGGCATGGATAACTTACCAT 59.867 40.000 0.00 0.00 46.22 3.55
1963 2003 4.473196 TCAGAAGGCATGGATAACTTACCA 59.527 41.667 0.00 0.00 40.57 3.25
1964 2004 4.816925 GTCAGAAGGCATGGATAACTTACC 59.183 45.833 0.00 0.00 0.00 2.85
1965 2005 5.428253 TGTCAGAAGGCATGGATAACTTAC 58.572 41.667 0.00 0.00 0.00 2.34
1966 2006 5.692115 TGTCAGAAGGCATGGATAACTTA 57.308 39.130 0.00 0.00 0.00 2.24
1967 2007 4.574674 TGTCAGAAGGCATGGATAACTT 57.425 40.909 0.00 0.00 0.00 2.66
1968 2008 4.574674 TTGTCAGAAGGCATGGATAACT 57.425 40.909 0.00 0.00 0.00 2.24
1969 2009 4.702131 ACTTTGTCAGAAGGCATGGATAAC 59.298 41.667 0.00 0.00 0.00 1.89
2188 2228 3.826157 CTGTGCTGGAAACCTTGGATAAA 59.174 43.478 0.00 0.00 0.00 1.40
2381 2421 7.710676 AGAGTAGAACATGTGAGAACATAGT 57.289 36.000 0.00 0.00 0.00 2.12
2764 2804 4.871933 TGGCTCAATATCTTCGATAGCA 57.128 40.909 0.00 0.00 0.00 3.49
3207 3251 6.215845 ACTTCAACAATATGCACCAACTTTC 58.784 36.000 0.00 0.00 0.00 2.62
3356 3400 2.127708 ACAGGAAAACACCCAGAGACT 58.872 47.619 0.00 0.00 0.00 3.24
3380 3424 8.132362 TCATAATGGTAATGGTAAATCAAACGC 58.868 33.333 0.00 0.00 0.00 4.84
3396 3440 5.360649 TGTCCATTTCGGTCATAATGGTA 57.639 39.130 12.18 2.86 46.98 3.25
3450 3494 3.119137 AGCGGAAGTGCTTCAAACTTTTT 60.119 39.130 13.16 0.00 44.46 1.94
3466 3510 0.690192 TCCATTCAGAACCAGCGGAA 59.310 50.000 1.50 0.00 0.00 4.30
3636 3680 9.731819 AATAGTGTCATGAAGTATTAGTACACG 57.268 33.333 0.00 0.00 40.58 4.49
4117 4161 2.114616 AGATCTCGGCAGGAAATGACT 58.885 47.619 0.00 0.00 33.15 3.41
4377 4421 6.307031 TCAAGTTTGTGCGTTGTATGTTAT 57.693 33.333 0.00 0.00 0.00 1.89
4507 4552 1.196127 CCGTGGAAGTTTTTAGCGACC 59.804 52.381 0.00 0.00 0.00 4.79
4510 4555 3.242804 TGAAACCGTGGAAGTTTTTAGCG 60.243 43.478 0.00 0.00 37.55 4.26
4516 4561 6.001460 TCATCTTATGAAACCGTGGAAGTTT 58.999 36.000 0.00 0.00 40.07 2.66
4517 4562 5.411669 GTCATCTTATGAAACCGTGGAAGTT 59.588 40.000 0.00 0.00 41.69 2.66
4518 4563 4.935808 GTCATCTTATGAAACCGTGGAAGT 59.064 41.667 0.00 0.00 41.69 3.01
4522 4567 2.943033 GGGTCATCTTATGAAACCGTGG 59.057 50.000 7.19 0.00 41.69 4.94
4559 4604 1.890876 TGGCTCGCTCTTGCTTTTTA 58.109 45.000 0.00 0.00 36.97 1.52
4567 4612 3.334583 TTGAATACTTGGCTCGCTCTT 57.665 42.857 0.00 0.00 0.00 2.85
4661 4706 9.383519 GTCATGTGATCTCATTACTTCCTTTTA 57.616 33.333 7.53 0.00 0.00 1.52
4662 4707 7.884877 TGTCATGTGATCTCATTACTTCCTTTT 59.115 33.333 18.11 0.00 0.00 2.27
4663 4708 7.397221 TGTCATGTGATCTCATTACTTCCTTT 58.603 34.615 18.11 0.00 0.00 3.11
4664 4709 6.950842 TGTCATGTGATCTCATTACTTCCTT 58.049 36.000 18.11 0.00 0.00 3.36
4665 4710 6.550938 TGTCATGTGATCTCATTACTTCCT 57.449 37.500 18.11 0.00 0.00 3.36
4666 4711 7.615582 TTTGTCATGTGATCTCATTACTTCC 57.384 36.000 18.11 0.00 0.00 3.46
4668 4713 8.834465 GCTATTTGTCATGTGATCTCATTACTT 58.166 33.333 18.11 9.28 0.00 2.24
4669 4714 7.989170 TGCTATTTGTCATGTGATCTCATTACT 59.011 33.333 18.11 5.90 0.00 2.24
4670 4715 8.146479 TGCTATTTGTCATGTGATCTCATTAC 57.854 34.615 12.91 12.91 0.00 1.89
4671 4716 8.913487 ATGCTATTTGTCATGTGATCTCATTA 57.087 30.769 7.53 0.00 0.00 1.90
4672 4717 7.818997 ATGCTATTTGTCATGTGATCTCATT 57.181 32.000 7.53 0.00 0.00 2.57
4673 4718 7.935210 TGTATGCTATTTGTCATGTGATCTCAT 59.065 33.333 4.42 4.42 0.00 2.90
4674 4719 7.274447 TGTATGCTATTTGTCATGTGATCTCA 58.726 34.615 0.00 0.00 0.00 3.27
4675 4720 7.719778 TGTATGCTATTTGTCATGTGATCTC 57.280 36.000 0.00 0.00 0.00 2.75
4676 4721 8.565416 CAATGTATGCTATTTGTCATGTGATCT 58.435 33.333 0.00 0.00 0.00 2.75
4677 4722 7.806487 CCAATGTATGCTATTTGTCATGTGATC 59.194 37.037 0.00 0.00 0.00 2.92
4678 4723 7.286087 ACCAATGTATGCTATTTGTCATGTGAT 59.714 33.333 0.00 0.00 0.00 3.06
4679 4724 6.602803 ACCAATGTATGCTATTTGTCATGTGA 59.397 34.615 0.00 0.00 0.00 3.58
4680 4725 6.798482 ACCAATGTATGCTATTTGTCATGTG 58.202 36.000 0.00 0.00 0.00 3.21
4681 4726 7.408756 AACCAATGTATGCTATTTGTCATGT 57.591 32.000 0.00 0.00 0.00 3.21
4682 4727 8.706492 AAAACCAATGTATGCTATTTGTCATG 57.294 30.769 0.00 0.00 0.00 3.07
4688 4733 9.965824 GCTGTATAAAACCAATGTATGCTATTT 57.034 29.630 0.00 0.00 0.00 1.40
4689 4734 9.130661 TGCTGTATAAAACCAATGTATGCTATT 57.869 29.630 0.00 0.00 0.00 1.73
4690 4735 8.690203 TGCTGTATAAAACCAATGTATGCTAT 57.310 30.769 0.00 0.00 0.00 2.97
4691 4736 8.512966 TTGCTGTATAAAACCAATGTATGCTA 57.487 30.769 0.00 0.00 0.00 3.49
4692 4737 7.403312 TTGCTGTATAAAACCAATGTATGCT 57.597 32.000 0.00 0.00 0.00 3.79
4693 4738 6.198966 GCTTGCTGTATAAAACCAATGTATGC 59.801 38.462 0.00 0.00 0.00 3.14
4694 4739 7.483307 AGCTTGCTGTATAAAACCAATGTATG 58.517 34.615 0.00 0.00 0.00 2.39
4695 4740 7.645058 AGCTTGCTGTATAAAACCAATGTAT 57.355 32.000 0.00 0.00 0.00 2.29
4696 4741 7.608376 TGTAGCTTGCTGTATAAAACCAATGTA 59.392 33.333 5.26 0.00 0.00 2.29
4697 4742 5.982890 AGCTTGCTGTATAAAACCAATGT 57.017 34.783 0.00 0.00 0.00 2.71
4698 4743 6.851609 TGTAGCTTGCTGTATAAAACCAATG 58.148 36.000 5.26 0.00 0.00 2.82
4699 4744 6.659242 ACTGTAGCTTGCTGTATAAAACCAAT 59.341 34.615 5.26 0.00 0.00 3.16
4700 4745 6.001460 ACTGTAGCTTGCTGTATAAAACCAA 58.999 36.000 5.26 0.00 0.00 3.67
4701 4746 5.556915 ACTGTAGCTTGCTGTATAAAACCA 58.443 37.500 5.26 0.00 0.00 3.67
4702 4747 7.235430 CTACTGTAGCTTGCTGTATAAAACC 57.765 40.000 5.26 0.00 0.00 3.27
4725 4770 8.857243 TTCGCAGATATACAATGCATCTTTGCT 61.857 37.037 0.00 0.00 43.38 3.91
4726 4771 6.785044 TTCGCAGATATACAATGCATCTTTGC 60.785 38.462 0.00 1.60 43.31 3.68
4727 4772 6.232139 TCGCAGATATACAATGCATCTTTG 57.768 37.500 0.00 0.00 39.97 2.77
4728 4773 6.260714 TGTTCGCAGATATACAATGCATCTTT 59.739 34.615 0.00 0.00 39.97 2.52
4729 4774 5.759763 TGTTCGCAGATATACAATGCATCTT 59.240 36.000 0.00 0.00 39.97 2.40
4730 4775 5.299949 TGTTCGCAGATATACAATGCATCT 58.700 37.500 0.00 0.00 39.97 2.90
4731 4776 5.596268 TGTTCGCAGATATACAATGCATC 57.404 39.130 0.00 0.00 39.97 3.91
4732 4777 6.564709 ATTGTTCGCAGATATACAATGCAT 57.435 33.333 0.00 0.00 41.93 3.96
4733 4778 6.347644 GCTATTGTTCGCAGATATACAATGCA 60.348 38.462 8.79 0.00 42.94 3.96
4734 4779 6.017933 GCTATTGTTCGCAGATATACAATGC 58.982 40.000 8.79 7.18 42.94 3.56
4735 4780 7.120789 TGCTATTGTTCGCAGATATACAATG 57.879 36.000 8.79 2.62 42.94 2.82
4736 4781 7.912056 ATGCTATTGTTCGCAGATATACAAT 57.088 32.000 0.00 0.00 44.49 2.71
4737 4782 7.870445 TGTATGCTATTGTTCGCAGATATACAA 59.130 33.333 0.00 0.00 38.81 2.41
4738 4783 7.375053 TGTATGCTATTGTTCGCAGATATACA 58.625 34.615 0.00 0.00 39.82 2.29
4739 4784 7.812309 TGTATGCTATTGTTCGCAGATATAC 57.188 36.000 0.00 0.00 39.82 1.47
4740 4785 8.872845 CAATGTATGCTATTGTTCGCAGATATA 58.127 33.333 0.00 0.00 39.82 0.86
4741 4786 7.148356 CCAATGTATGCTATTGTTCGCAGATAT 60.148 37.037 0.00 0.00 39.82 1.63
4742 4787 6.147656 CCAATGTATGCTATTGTTCGCAGATA 59.852 38.462 0.00 0.00 39.82 1.98
4743 4788 5.049198 CCAATGTATGCTATTGTTCGCAGAT 60.049 40.000 0.00 0.00 39.82 2.90
4744 4789 4.273235 CCAATGTATGCTATTGTTCGCAGA 59.727 41.667 0.00 0.00 39.82 4.26
4745 4790 4.035558 ACCAATGTATGCTATTGTTCGCAG 59.964 41.667 0.00 0.00 39.82 5.18
4746 4791 3.944650 ACCAATGTATGCTATTGTTCGCA 59.055 39.130 0.00 0.00 40.87 5.10
4747 4792 4.552166 ACCAATGTATGCTATTGTTCGC 57.448 40.909 0.00 0.00 34.51 4.70
4748 4793 8.957028 CATAAAACCAATGTATGCTATTGTTCG 58.043 33.333 0.00 0.00 34.51 3.95
4752 4797 8.971321 GCTTCATAAAACCAATGTATGCTATTG 58.029 33.333 0.00 0.00 35.75 1.90
4753 4798 8.694540 TGCTTCATAAAACCAATGTATGCTATT 58.305 29.630 0.00 0.00 0.00 1.73
4754 4799 8.236585 TGCTTCATAAAACCAATGTATGCTAT 57.763 30.769 0.00 0.00 0.00 2.97
4755 4800 7.637631 TGCTTCATAAAACCAATGTATGCTA 57.362 32.000 0.00 0.00 0.00 3.49
4756 4801 6.528537 TGCTTCATAAAACCAATGTATGCT 57.471 33.333 0.00 0.00 0.00 3.79
4757 4802 6.237915 GCTTGCTTCATAAAACCAATGTATGC 60.238 38.462 0.00 0.00 0.00 3.14
4758 4803 7.037438 AGCTTGCTTCATAAAACCAATGTATG 58.963 34.615 0.00 0.00 0.00 2.39
4759 4804 7.174107 AGCTTGCTTCATAAAACCAATGTAT 57.826 32.000 0.00 0.00 0.00 2.29
4760 4805 6.588719 AGCTTGCTTCATAAAACCAATGTA 57.411 33.333 0.00 0.00 0.00 2.29
4761 4806 5.473066 AGCTTGCTTCATAAAACCAATGT 57.527 34.783 0.00 0.00 0.00 2.71
4762 4807 6.389091 TGTAGCTTGCTTCATAAAACCAATG 58.611 36.000 0.00 0.00 0.00 2.82
4763 4808 6.209391 ACTGTAGCTTGCTTCATAAAACCAAT 59.791 34.615 0.00 0.00 0.00 3.16
4764 4809 5.534654 ACTGTAGCTTGCTTCATAAAACCAA 59.465 36.000 0.00 0.00 0.00 3.67
4765 4810 5.070001 ACTGTAGCTTGCTTCATAAAACCA 58.930 37.500 0.00 0.00 0.00 3.67
4766 4811 5.629079 ACTGTAGCTTGCTTCATAAAACC 57.371 39.130 0.00 0.00 0.00 3.27
4791 4836 7.734924 TTGGTAGCTATAGAATGCATCTTTG 57.265 36.000 3.21 0.00 39.71 2.77
4792 4837 8.790718 CAATTGGTAGCTATAGAATGCATCTTT 58.209 33.333 3.21 0.00 39.71 2.52
4793 4838 7.392673 CCAATTGGTAGCTATAGAATGCATCTT 59.607 37.037 16.90 0.00 39.71 2.40
4794 4839 6.883217 CCAATTGGTAGCTATAGAATGCATCT 59.117 38.462 16.90 1.57 42.48 2.90
4795 4840 6.881065 TCCAATTGGTAGCTATAGAATGCATC 59.119 38.462 23.76 0.00 36.34 3.91
4796 4841 6.782986 TCCAATTGGTAGCTATAGAATGCAT 58.217 36.000 23.76 0.00 36.34 3.96
4797 4842 6.186420 TCCAATTGGTAGCTATAGAATGCA 57.814 37.500 23.76 0.00 36.34 3.96
4798 4843 6.936900 TCTTCCAATTGGTAGCTATAGAATGC 59.063 38.462 23.76 0.00 33.22 3.56
4799 4844 7.389053 GGTCTTCCAATTGGTAGCTATAGAATG 59.611 40.741 23.76 3.59 33.22 2.67
4800 4845 7.454225 GGTCTTCCAATTGGTAGCTATAGAAT 58.546 38.462 23.76 0.00 33.22 2.40
4801 4846 6.462487 CGGTCTTCCAATTGGTAGCTATAGAA 60.462 42.308 23.76 6.81 33.22 2.10
4802 4847 5.010719 CGGTCTTCCAATTGGTAGCTATAGA 59.989 44.000 23.76 12.48 33.22 1.98
4803 4848 5.230942 CGGTCTTCCAATTGGTAGCTATAG 58.769 45.833 23.76 10.02 33.22 1.31
4804 4849 4.039973 CCGGTCTTCCAATTGGTAGCTATA 59.960 45.833 23.76 5.33 33.22 1.31
4805 4850 3.181454 CCGGTCTTCCAATTGGTAGCTAT 60.181 47.826 23.76 0.00 33.22 2.97
4806 4851 2.169769 CCGGTCTTCCAATTGGTAGCTA 59.830 50.000 23.76 6.40 33.22 3.32
4807 4852 1.065418 CCGGTCTTCCAATTGGTAGCT 60.065 52.381 23.76 0.00 33.22 3.32
4808 4853 1.379527 CCGGTCTTCCAATTGGTAGC 58.620 55.000 23.76 17.62 33.22 3.58
4809 4854 1.557832 TCCCGGTCTTCCAATTGGTAG 59.442 52.381 23.76 22.69 36.34 3.18
4810 4855 1.279846 GTCCCGGTCTTCCAATTGGTA 59.720 52.381 23.76 13.96 36.34 3.25
4811 4856 0.037734 GTCCCGGTCTTCCAATTGGT 59.962 55.000 23.76 0.00 36.34 3.67
4812 4857 0.037590 TGTCCCGGTCTTCCAATTGG 59.962 55.000 19.08 19.08 0.00 3.16
4813 4858 1.745087 CATGTCCCGGTCTTCCAATTG 59.255 52.381 0.00 0.00 0.00 2.32
4814 4859 1.340991 CCATGTCCCGGTCTTCCAATT 60.341 52.381 0.00 0.00 0.00 2.32
4815 4860 0.255890 CCATGTCCCGGTCTTCCAAT 59.744 55.000 0.00 0.00 0.00 3.16
4816 4861 0.838554 TCCATGTCCCGGTCTTCCAA 60.839 55.000 0.00 0.00 0.00 3.53
4817 4862 0.838554 TTCCATGTCCCGGTCTTCCA 60.839 55.000 0.00 0.00 0.00 3.53
4818 4863 0.107654 CTTCCATGTCCCGGTCTTCC 60.108 60.000 0.00 0.00 0.00 3.46
4819 4864 0.613777 ACTTCCATGTCCCGGTCTTC 59.386 55.000 0.00 0.00 0.00 2.87
4820 4865 0.324943 CACTTCCATGTCCCGGTCTT 59.675 55.000 0.00 0.00 0.00 3.01
4821 4866 0.544357 TCACTTCCATGTCCCGGTCT 60.544 55.000 0.00 0.00 0.00 3.85
4822 4867 0.541863 ATCACTTCCATGTCCCGGTC 59.458 55.000 0.00 0.00 0.00 4.79
4823 4868 0.253044 CATCACTTCCATGTCCCGGT 59.747 55.000 0.00 0.00 0.00 5.28
4824 4869 0.464373 CCATCACTTCCATGTCCCGG 60.464 60.000 0.00 0.00 0.00 5.73
4825 4870 0.253044 ACCATCACTTCCATGTCCCG 59.747 55.000 0.00 0.00 0.00 5.14
4826 4871 3.864789 ATACCATCACTTCCATGTCCC 57.135 47.619 0.00 0.00 0.00 4.46
4827 4872 5.182001 GCATAATACCATCACTTCCATGTCC 59.818 44.000 0.00 0.00 0.00 4.02
4828 4873 5.764686 TGCATAATACCATCACTTCCATGTC 59.235 40.000 0.00 0.00 0.00 3.06
4829 4874 5.693961 TGCATAATACCATCACTTCCATGT 58.306 37.500 0.00 0.00 0.00 3.21
4830 4875 5.999600 TCTGCATAATACCATCACTTCCATG 59.000 40.000 0.00 0.00 0.00 3.66
4831 4876 6.191657 TCTGCATAATACCATCACTTCCAT 57.808 37.500 0.00 0.00 0.00 3.41
4832 4877 5.614308 CTCTGCATAATACCATCACTTCCA 58.386 41.667 0.00 0.00 0.00 3.53
4833 4878 4.453819 GCTCTGCATAATACCATCACTTCC 59.546 45.833 0.00 0.00 0.00 3.46
4834 4879 4.151335 CGCTCTGCATAATACCATCACTTC 59.849 45.833 0.00 0.00 0.00 3.01
4835 4880 4.060900 CGCTCTGCATAATACCATCACTT 58.939 43.478 0.00 0.00 0.00 3.16
4836 4881 3.321968 TCGCTCTGCATAATACCATCACT 59.678 43.478 0.00 0.00 0.00 3.41
4837 4882 3.653344 TCGCTCTGCATAATACCATCAC 58.347 45.455 0.00 0.00 0.00 3.06
4838 4883 3.862264 GCTCGCTCTGCATAATACCATCA 60.862 47.826 0.00 0.00 0.00 3.07
4839 4884 2.670414 GCTCGCTCTGCATAATACCATC 59.330 50.000 0.00 0.00 0.00 3.51
4840 4885 2.037641 TGCTCGCTCTGCATAATACCAT 59.962 45.455 0.00 0.00 35.31 3.55
4841 4886 1.412343 TGCTCGCTCTGCATAATACCA 59.588 47.619 0.00 0.00 35.31 3.25
4842 4887 2.154854 TGCTCGCTCTGCATAATACC 57.845 50.000 0.00 0.00 35.31 2.73
4849 4894 0.518636 GTTTGAATGCTCGCTCTGCA 59.481 50.000 0.00 0.00 44.95 4.41
4850 4895 0.179179 GGTTTGAATGCTCGCTCTGC 60.179 55.000 0.00 0.00 0.00 4.26
4851 4896 1.159285 TGGTTTGAATGCTCGCTCTG 58.841 50.000 0.00 0.00 0.00 3.35
4852 4897 1.741706 CATGGTTTGAATGCTCGCTCT 59.258 47.619 0.00 0.00 0.00 4.09
4853 4898 1.796617 GCATGGTTTGAATGCTCGCTC 60.797 52.381 0.00 0.00 45.62 5.03
4854 4899 0.171903 GCATGGTTTGAATGCTCGCT 59.828 50.000 0.00 0.00 45.62 4.93
4855 4900 2.657336 GCATGGTTTGAATGCTCGC 58.343 52.632 0.00 0.00 45.62 5.03
4860 4905 4.502171 TGTAGTGTGCATGGTTTGAATG 57.498 40.909 0.00 0.00 0.00 2.67
4861 4906 5.726980 ATTGTAGTGTGCATGGTTTGAAT 57.273 34.783 0.00 0.00 0.00 2.57
4862 4907 6.832520 ATATTGTAGTGTGCATGGTTTGAA 57.167 33.333 0.00 0.00 0.00 2.69
4863 4908 6.832520 AATATTGTAGTGTGCATGGTTTGA 57.167 33.333 0.00 0.00 0.00 2.69
4864 4909 8.458052 TCTAAATATTGTAGTGTGCATGGTTTG 58.542 33.333 0.00 0.00 0.00 2.93
4865 4910 8.574251 TCTAAATATTGTAGTGTGCATGGTTT 57.426 30.769 0.00 0.00 0.00 3.27
4866 4911 8.623903 CATCTAAATATTGTAGTGTGCATGGTT 58.376 33.333 0.00 0.00 0.00 3.67
4867 4912 7.255242 GCATCTAAATATTGTAGTGTGCATGGT 60.255 37.037 18.43 0.00 34.46 3.55
4868 4913 7.080099 GCATCTAAATATTGTAGTGTGCATGG 58.920 38.462 18.43 0.00 34.46 3.66
4869 4914 7.641760 TGCATCTAAATATTGTAGTGTGCATG 58.358 34.615 19.99 0.00 36.89 4.06
4870 4915 7.521099 GCTGCATCTAAATATTGTAGTGTGCAT 60.521 37.037 21.68 0.00 38.87 3.96
4871 4916 6.238456 GCTGCATCTAAATATTGTAGTGTGCA 60.238 38.462 21.04 21.04 38.11 4.57
4872 4917 6.138761 GCTGCATCTAAATATTGTAGTGTGC 58.861 40.000 17.61 17.61 34.67 4.57
4873 4918 6.564686 CGGCTGCATCTAAATATTGTAGTGTG 60.565 42.308 0.50 0.50 0.00 3.82
4874 4919 5.466728 CGGCTGCATCTAAATATTGTAGTGT 59.533 40.000 0.50 0.00 0.00 3.55
4875 4920 5.696270 TCGGCTGCATCTAAATATTGTAGTG 59.304 40.000 0.50 0.00 0.00 2.74
4876 4921 5.853936 TCGGCTGCATCTAAATATTGTAGT 58.146 37.500 0.50 0.00 0.00 2.73
4877 4922 6.974932 ATCGGCTGCATCTAAATATTGTAG 57.025 37.500 0.50 0.00 0.00 2.74
4878 4923 7.382898 TGTATCGGCTGCATCTAAATATTGTA 58.617 34.615 0.50 0.00 0.00 2.41
4879 4924 6.230472 TGTATCGGCTGCATCTAAATATTGT 58.770 36.000 0.50 0.00 0.00 2.71
4880 4925 6.726258 TGTATCGGCTGCATCTAAATATTG 57.274 37.500 0.50 0.00 0.00 1.90
4881 4926 7.225538 GCTATGTATCGGCTGCATCTAAATATT 59.774 37.037 0.50 0.00 32.00 1.28
4882 4927 6.703607 GCTATGTATCGGCTGCATCTAAATAT 59.296 38.462 0.50 0.00 32.00 1.28
4883 4928 6.042777 GCTATGTATCGGCTGCATCTAAATA 58.957 40.000 0.50 0.00 32.00 1.40
4884 4929 4.872691 GCTATGTATCGGCTGCATCTAAAT 59.127 41.667 0.50 0.00 32.00 1.40
4885 4930 4.245660 GCTATGTATCGGCTGCATCTAAA 58.754 43.478 0.50 0.00 32.00 1.85
4886 4931 3.258123 TGCTATGTATCGGCTGCATCTAA 59.742 43.478 0.50 0.00 32.00 2.10
4887 4932 2.825532 TGCTATGTATCGGCTGCATCTA 59.174 45.455 0.50 0.00 32.00 1.98
4888 4933 1.620323 TGCTATGTATCGGCTGCATCT 59.380 47.619 0.50 0.00 32.00 2.90
4889 4934 2.084610 TGCTATGTATCGGCTGCATC 57.915 50.000 0.50 0.00 32.00 3.91
4890 4935 2.775911 ATGCTATGTATCGGCTGCAT 57.224 45.000 0.50 0.00 36.48 3.96
4891 4936 2.549064 AATGCTATGTATCGGCTGCA 57.451 45.000 0.50 0.00 34.88 4.41
4892 4937 3.325870 TGTAATGCTATGTATCGGCTGC 58.674 45.455 0.00 0.00 0.00 5.25
4893 4938 5.230182 TCTTGTAATGCTATGTATCGGCTG 58.770 41.667 0.00 0.00 0.00 4.85
4894 4939 5.243954 TCTCTTGTAATGCTATGTATCGGCT 59.756 40.000 0.00 0.00 0.00 5.52
4895 4940 5.470368 TCTCTTGTAATGCTATGTATCGGC 58.530 41.667 0.00 0.00 0.00 5.54
4896 4941 5.574830 GCTCTCTTGTAATGCTATGTATCGG 59.425 44.000 0.00 0.00 0.00 4.18
4897 4942 5.574830 GGCTCTCTTGTAATGCTATGTATCG 59.425 44.000 0.00 0.00 0.00 2.92
4898 4943 6.367422 GTGGCTCTCTTGTAATGCTATGTATC 59.633 42.308 0.00 0.00 0.00 2.24
4899 4944 6.183361 TGTGGCTCTCTTGTAATGCTATGTAT 60.183 38.462 0.00 0.00 0.00 2.29
4900 4945 5.128663 TGTGGCTCTCTTGTAATGCTATGTA 59.871 40.000 0.00 0.00 0.00 2.29
4901 4946 4.080919 TGTGGCTCTCTTGTAATGCTATGT 60.081 41.667 0.00 0.00 0.00 2.29
4902 4947 4.445453 TGTGGCTCTCTTGTAATGCTATG 58.555 43.478 0.00 0.00 0.00 2.23
4903 4948 4.760530 TGTGGCTCTCTTGTAATGCTAT 57.239 40.909 0.00 0.00 0.00 2.97
4904 4949 4.222810 TCTTGTGGCTCTCTTGTAATGCTA 59.777 41.667 0.00 0.00 0.00 3.49
4905 4950 3.008375 TCTTGTGGCTCTCTTGTAATGCT 59.992 43.478 0.00 0.00 0.00 3.79
4906 4951 3.338249 TCTTGTGGCTCTCTTGTAATGC 58.662 45.455 0.00 0.00 0.00 3.56
4907 4952 5.731599 GATCTTGTGGCTCTCTTGTAATG 57.268 43.478 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.