Multiple sequence alignment - TraesCS5B01G531300

Loading Multiple Alignment...

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 TraesCS5B01G531300 chr5B 100.000 5471 0 0 1 5471 689369166 689374636 0.000000e+00 10104
1 TraesCS5B01G531300 chr5B 86.532 594 72 6 1 588 585265595 585265004 0.000000e+00 647
2 TraesCS5B01G531300 chr5B 85.859 594 77 5 1 589 118912590 118911999 4.650000e-175 625
3 TraesCS5B01G531300 chr5B 85.246 610 63 13 1 586 545810163 545810769 2.180000e-168 603
4 TraesCS5B01G531300 chr5B 80.028 716 97 31 4135 4846 527840764 527840091 6.370000e-134 488
5 TraesCS5B01G531300 chr5D 90.857 4856 266 79 704 5471 546080388 546085153 0.000000e+00 6344
6 TraesCS5B01G531300 chr4A 88.942 4811 311 97 617 5351 623322007 623317342 0.000000e+00 5733
7 TraesCS5B01G531300 chr4A 79.832 714 100 29 4135 4846 655565818 655565147 1.070000e-131 481
8 TraesCS5B01G531300 chr2B 84.810 790 60 21 938 1691 67122061 67122826 0.000000e+00 739
9 TraesCS5B01G531300 chr2B 85.427 597 70 12 1 588 656349216 656349804 6.060000e-169 604
10 TraesCS5B01G531300 chr2B 80.252 714 97 29 4135 4846 35129583 35130254 1.060000e-136 497
11 TraesCS5B01G531300 chrUn 84.171 796 67 22 940 1698 49201421 49200648 0.000000e+00 717
12 TraesCS5B01G531300 chr7A 85.500 600 68 14 1 586 146912690 146912096 4.690000e-170 608
13 TraesCS5B01G531300 chr2D 85.216 602 64 19 1 586 398457080 398457672 3.650000e-166 595
14 TraesCS5B01G531300 chr2D 84.253 616 70 18 1 598 499719223 499718617 4.750000e-160 575
15 TraesCS5B01G531300 chr6D 84.808 599 72 15 1 586 457702242 457701650 7.900000e-163 584
16 TraesCS5B01G531300 chr3B 84.307 599 71 15 1 586 191142285 191142873 1.030000e-156 564
17 TraesCS5B01G531300 chr3B 84.599 474 41 7 1 466 670537405 670536956 5.030000e-120 442
18 TraesCS5B01G531300 chr7D 79.739 612 76 17 2324 2925 528059047 528058474 3.070000e-107 399
19 TraesCS5B01G531300 chr4B 83.114 456 59 13 4135 4590 90860697 90861134 3.070000e-107 399
20 TraesCS5B01G531300 chr2A 79.541 567 64 25 2265 2821 64333192 64333716 1.870000e-94 357
21 TraesCS5B01G531300 chr3D 81.221 213 32 7 4355 4566 592170796 592170591 1.220000e-36 165
22 TraesCS5B01G531300 chr3D 81.221 213 32 7 4355 4566 592239026 592238821 1.220000e-36 165
23 TraesCS5B01G531300 chr3D 80.282 213 34 7 4355 4566 592319312 592319107 2.640000e-33 154


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 TraesCS5B01G531300 chr5B 689369166 689374636 5470 False 10104 10104 100.000 1 5471 1 chr5B.!!$F2 5470
1 TraesCS5B01G531300 chr5B 585265004 585265595 591 True 647 647 86.532 1 588 1 chr5B.!!$R3 587
2 TraesCS5B01G531300 chr5B 118911999 118912590 591 True 625 625 85.859 1 589 1 chr5B.!!$R1 588
3 TraesCS5B01G531300 chr5B 545810163 545810769 606 False 603 603 85.246 1 586 1 chr5B.!!$F1 585
4 TraesCS5B01G531300 chr5B 527840091 527840764 673 True 488 488 80.028 4135 4846 1 chr5B.!!$R2 711
5 TraesCS5B01G531300 chr5D 546080388 546085153 4765 False 6344 6344 90.857 704 5471 1 chr5D.!!$F1 4767
6 TraesCS5B01G531300 chr4A 623317342 623322007 4665 True 5733 5733 88.942 617 5351 1 chr4A.!!$R1 4734
7 TraesCS5B01G531300 chr4A 655565147 655565818 671 True 481 481 79.832 4135 4846 1 chr4A.!!$R2 711
8 TraesCS5B01G531300 chr2B 67122061 67122826 765 False 739 739 84.810 938 1691 1 chr2B.!!$F2 753
9 TraesCS5B01G531300 chr2B 656349216 656349804 588 False 604 604 85.427 1 588 1 chr2B.!!$F3 587
10 TraesCS5B01G531300 chr2B 35129583 35130254 671 False 497 497 80.252 4135 4846 1 chr2B.!!$F1 711
11 TraesCS5B01G531300 chrUn 49200648 49201421 773 True 717 717 84.171 940 1698 1 chrUn.!!$R1 758
12 TraesCS5B01G531300 chr7A 146912096 146912690 594 True 608 608 85.500 1 586 1 chr7A.!!$R1 585
13 TraesCS5B01G531300 chr2D 398457080 398457672 592 False 595 595 85.216 1 586 1 chr2D.!!$F1 585
14 TraesCS5B01G531300 chr2D 499718617 499719223 606 True 575 575 84.253 1 598 1 chr2D.!!$R1 597
15 TraesCS5B01G531300 chr6D 457701650 457702242 592 True 584 584 84.808 1 586 1 chr6D.!!$R1 585
16 TraesCS5B01G531300 chr3B 191142285 191142873 588 False 564 564 84.307 1 586 1 chr3B.!!$F1 585
17 TraesCS5B01G531300 chr7D 528058474 528059047 573 True 399 399 79.739 2324 2925 1 chr7D.!!$R1 601
18 TraesCS5B01G531300 chr2A 64333192 64333716 524 False 357 357 79.541 2265 2821 1 chr2A.!!$F1 556

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
817 869 0.028505 CTGAAATGAAGATGGCGCGG 59.971 55.000 8.83 0.00 0.00 6.46 F
846 898 0.099968 CTAGATCGAACGGCGTGGAA 59.900 55.000 15.70 1.41 41.80 3.53 F
1634 1738 0.761187 ACTGATGGGGTCGGATCATG 59.239 55.000 0.00 0.00 36.66 3.07 F
1881 1988 0.976641 TCTGCCACTCTTACCTGGTG 59.023 55.000 10.23 0.00 0.00 4.17 F
1894 2001 1.420138 ACCTGGTGAGGATCGTGTTTT 59.580 47.619 0.00 0.00 42.93 2.43 F
1923 2030 1.843851 TCCAGTGGGTTGACTTGTTCT 59.156 47.619 9.92 0.00 34.93 3.01 F
2275 2392 1.884235 AGGCTGTTGTACTGCTTGTC 58.116 50.000 8.28 0.00 41.90 3.18 F
3863 4004 0.250234 CATCCCTTGCTCGAGGAACA 59.750 55.000 16.06 0.67 39.25 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 2035 0.037697 CAGACCCGTCGAATCACCAA 60.038 55.000 0.00 0.00 34.09 3.67 R
2344 2462 1.276421 AGTAACAGGAGATTGTGCGCT 59.724 47.619 9.73 0.00 0.00 5.92 R
3101 3238 0.722676 TGGTGGGGGAGAACCTAGAT 59.277 55.000 0.00 0.00 40.03 1.98 R
3105 3242 2.303660 AATATGGTGGGGGAGAACCT 57.696 50.000 0.00 0.00 40.03 3.50 R
3106 3243 3.296854 GAAAATATGGTGGGGGAGAACC 58.703 50.000 0.00 0.00 36.96 3.62 R
3522 3660 3.320610 TCCAGAAGAGCTATGCTACCT 57.679 47.619 0.00 0.00 39.88 3.08 R
4261 4404 0.896923 TGGTACACGGCCGTTTCTAT 59.103 50.000 32.11 14.36 0.00 1.98 R
4924 5089 1.061131 CGATCACAAGGCACTAAAGCG 59.939 52.381 0.00 0.00 38.49 4.68 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
27 29 1.514678 AATTGCCGAACAGCTTGCGA 61.515 50.000 1.55 0.00 0.00 5.10
153 174 2.264794 CGAGGCGCCTACTTGGTT 59.735 61.111 32.97 4.00 38.35 3.67
266 293 2.742856 CGGCATTGCTCAGAGGATGTTA 60.743 50.000 8.82 0.00 0.00 2.41
270 298 1.557099 TGCTCAGAGGATGTTACGGT 58.443 50.000 0.00 0.00 0.00 4.83
308 338 4.669809 ACCGGAAAATGGGCGGCA 62.670 61.111 9.46 0.00 0.00 5.69
336 372 4.424711 GGAGGCGGGCATGGTTGA 62.425 66.667 3.78 0.00 0.00 3.18
347 388 2.101783 GCATGGTTGATGTTGGATGGA 58.898 47.619 0.00 0.00 34.14 3.41
355 396 1.987807 ATGTTGGATGGAGGGAGGCG 61.988 60.000 0.00 0.00 0.00 5.52
420 463 2.729862 GCGCGTCTGTCTCGTGTT 60.730 61.111 8.43 0.00 40.28 3.32
504 549 2.968156 CGCGTCCGTTTGGGTTGA 60.968 61.111 0.00 0.00 37.00 3.18
507 552 1.884004 CGTCCGTTTGGGTTGACGT 60.884 57.895 0.00 0.00 44.00 4.34
512 557 0.727970 CGTTTGGGTTGACGTGTTGA 59.272 50.000 0.00 0.00 34.75 3.18
515 560 0.107410 TTGGGTTGACGTGTTGAGCT 60.107 50.000 0.00 0.00 0.00 4.09
590 635 1.293924 CGTTGGAGCTGCTCTTATGG 58.706 55.000 27.09 10.86 0.00 2.74
593 638 2.408271 TGGAGCTGCTCTTATGGTTG 57.592 50.000 27.09 0.00 0.00 3.77
598 643 3.722147 AGCTGCTCTTATGGTTGATACG 58.278 45.455 0.00 0.00 0.00 3.06
599 644 3.384789 AGCTGCTCTTATGGTTGATACGA 59.615 43.478 0.00 0.00 0.00 3.43
600 645 3.738282 GCTGCTCTTATGGTTGATACGAG 59.262 47.826 0.00 0.00 36.45 4.18
601 646 4.737946 GCTGCTCTTATGGTTGATACGAGT 60.738 45.833 0.00 0.00 35.99 4.18
602 647 5.339008 TGCTCTTATGGTTGATACGAGTT 57.661 39.130 0.00 0.00 35.99 3.01
603 648 5.730550 TGCTCTTATGGTTGATACGAGTTT 58.269 37.500 0.00 0.00 35.99 2.66
604 649 5.580691 TGCTCTTATGGTTGATACGAGTTTG 59.419 40.000 0.00 0.00 35.99 2.93
605 650 5.502544 GCTCTTATGGTTGATACGAGTTTGC 60.503 44.000 0.00 0.00 35.99 3.68
606 651 5.483811 TCTTATGGTTGATACGAGTTTGCA 58.516 37.500 0.00 0.00 0.00 4.08
607 652 5.935206 TCTTATGGTTGATACGAGTTTGCAA 59.065 36.000 0.00 0.00 0.00 4.08
608 653 6.428465 TCTTATGGTTGATACGAGTTTGCAAA 59.572 34.615 8.05 8.05 0.00 3.68
609 654 5.643379 ATGGTTGATACGAGTTTGCAAAT 57.357 34.783 16.21 4.49 0.00 2.32
610 655 6.751514 ATGGTTGATACGAGTTTGCAAATA 57.248 33.333 16.21 3.82 0.00 1.40
611 656 5.933790 TGGTTGATACGAGTTTGCAAATAC 58.066 37.500 16.21 11.28 0.00 1.89
612 657 5.470437 TGGTTGATACGAGTTTGCAAATACA 59.530 36.000 16.21 5.63 0.00 2.29
613 658 6.017026 TGGTTGATACGAGTTTGCAAATACAA 60.017 34.615 16.21 10.71 0.00 2.41
614 659 6.858993 GGTTGATACGAGTTTGCAAATACAAA 59.141 34.615 16.21 2.14 37.20 2.83
615 660 7.540745 GGTTGATACGAGTTTGCAAATACAAAT 59.459 33.333 16.21 7.04 41.31 2.32
619 664 9.123709 GATACGAGTTTGCAAATACAAATGAAA 57.876 29.630 16.21 0.00 41.31 2.69
629 674 9.638239 TGCAAATACAAATGAAATCTTTAGGAC 57.362 29.630 0.00 0.00 0.00 3.85
636 681 7.290014 ACAAATGAAATCTTTAGGACCAAACCT 59.710 33.333 0.00 0.00 43.32 3.50
649 694 0.447801 CAAACCTTGGATTCGAGCCG 59.552 55.000 0.00 0.00 0.00 5.52
655 700 1.927174 CTTGGATTCGAGCCGTGTAAG 59.073 52.381 2.48 0.00 0.00 2.34
658 703 1.925185 GGATTCGAGCCGTGTAAGAAC 59.075 52.381 0.00 0.00 0.00 3.01
661 706 1.774639 TCGAGCCGTGTAAGAACAAC 58.225 50.000 0.00 0.00 37.36 3.32
662 707 0.788391 CGAGCCGTGTAAGAACAACC 59.212 55.000 0.00 0.00 37.36 3.77
667 712 1.259507 CCGTGTAAGAACAACCGTGTG 59.740 52.381 0.00 0.00 38.27 3.82
670 716 3.181518 CGTGTAAGAACAACCGTGTGTTT 60.182 43.478 2.84 0.00 41.78 2.83
679 725 3.757493 ACAACCGTGTGTTTACTTTTGGA 59.243 39.130 0.00 0.00 36.31 3.53
685 731 5.204833 CGTGTGTTTACTTTTGGATGTGAG 58.795 41.667 0.00 0.00 0.00 3.51
686 732 4.976116 GTGTGTTTACTTTTGGATGTGAGC 59.024 41.667 0.00 0.00 0.00 4.26
689 735 2.107950 TACTTTTGGATGTGAGCCCG 57.892 50.000 0.00 0.00 0.00 6.13
697 743 1.899814 GGATGTGAGCCCGGTGATATA 59.100 52.381 0.00 0.00 0.00 0.86
702 748 3.135712 TGTGAGCCCGGTGATATATTTGT 59.864 43.478 0.00 0.00 0.00 2.83
707 753 4.288626 AGCCCGGTGATATATTTGTGGTAT 59.711 41.667 0.00 0.00 0.00 2.73
708 754 4.394920 GCCCGGTGATATATTTGTGGTATG 59.605 45.833 0.00 0.00 0.00 2.39
711 757 6.072728 CCCGGTGATATATTTGTGGTATGTTG 60.073 42.308 0.00 0.00 0.00 3.33
712 758 6.370593 CGGTGATATATTTGTGGTATGTTGC 58.629 40.000 0.00 0.00 0.00 4.17
724 771 7.377766 TGTGGTATGTTGCTCTTTTTATCTC 57.622 36.000 0.00 0.00 0.00 2.75
729 776 8.730680 GGTATGTTGCTCTTTTTATCTCTTGAA 58.269 33.333 0.00 0.00 0.00 2.69
734 781 9.286946 GTTGCTCTTTTTATCTCTTGAATGATG 57.713 33.333 0.00 0.00 0.00 3.07
752 799 9.558648 TGAATGATGAATGTTCAAATTTAGACG 57.441 29.630 0.00 0.00 41.13 4.18
768 816 7.778470 ATTTAGACGCAAAATAAGAGAGAGG 57.222 36.000 0.00 0.00 0.00 3.69
804 856 8.987890 CCAAAACGGAAAATATGTTTCTGAAAT 58.012 29.630 18.25 0.00 38.00 2.17
807 859 9.757227 AAACGGAAAATATGTTTCTGAAATGAA 57.243 25.926 18.25 0.00 38.00 2.57
817 869 0.028505 CTGAAATGAAGATGGCGCGG 59.971 55.000 8.83 0.00 0.00 6.46
829 881 3.661131 GCGCGGATCTCGAGGCTA 61.661 66.667 13.56 0.00 42.43 3.93
846 898 0.099968 CTAGATCGAACGGCGTGGAA 59.900 55.000 15.70 1.41 41.80 3.53
913 972 2.580601 CCACCCGTTCCGTCCTCTT 61.581 63.158 0.00 0.00 0.00 2.85
915 974 2.281295 ACCCGTTCCGTCCTCTTCC 61.281 63.158 0.00 0.00 0.00 3.46
931 990 3.330720 CCTCCCAGTGACCCACCC 61.331 72.222 0.00 0.00 34.49 4.61
1139 1204 2.037238 AATCCCCATCCCCTCCCC 60.037 66.667 0.00 0.00 0.00 4.81
1189 1273 5.479375 AGTCAGTTTGGCATCAAGATTGATT 59.521 36.000 5.32 0.00 45.13 2.57
1236 1320 7.979444 ACTCTTCTTATTTTCCGTTGATGAA 57.021 32.000 0.00 0.00 0.00 2.57
1258 1343 5.276461 ACAAAAATGTTGAAAGGGGACTC 57.724 39.130 0.00 0.00 42.68 3.36
1281 1366 4.450082 AAAAACGGACATTATTCCCAGC 57.550 40.909 0.00 0.00 31.03 4.85
1320 1405 9.788960 AAGTTGTTCTTCATTTTAGTCAGAAAC 57.211 29.630 0.00 0.00 0.00 2.78
1329 1414 3.396260 TTAGTCAGAAACGGGGAGTTG 57.604 47.619 0.00 0.00 43.37 3.16
1358 1459 2.947938 ATCAGGGTATGTGCTGCCGC 62.948 60.000 0.00 0.00 0.00 6.53
1385 1489 2.308570 TCCTCACATACTTGGCACCATT 59.691 45.455 0.00 0.00 0.00 3.16
1437 1541 2.783135 ACATCCAACGTCAAGCAGAAT 58.217 42.857 0.00 0.00 0.00 2.40
1470 1574 5.107065 CGTGAAATTCTGGAAGGTACTGTTC 60.107 44.000 0.00 0.00 40.86 3.18
1530 1634 3.920446 AGACGAGAGAGAAAAGAAAGGC 58.080 45.455 0.00 0.00 0.00 4.35
1536 1640 2.887152 GAGAGAAAAGAAAGGCCAGCAA 59.113 45.455 5.01 0.00 0.00 3.91
1537 1641 3.504375 AGAGAAAAGAAAGGCCAGCAAT 58.496 40.909 5.01 0.00 0.00 3.56
1538 1642 3.899980 AGAGAAAAGAAAGGCCAGCAATT 59.100 39.130 5.01 0.00 0.00 2.32
1547 1651 3.188159 AGGCCAGCAATTGCATTATTG 57.812 42.857 30.89 19.44 45.16 1.90
1588 1692 3.119637 GGTCCCATCGTTACAATTTGTGG 60.120 47.826 12.30 3.67 0.00 4.17
1634 1738 0.761187 ACTGATGGGGTCGGATCATG 59.239 55.000 0.00 0.00 36.66 3.07
1646 1750 2.234661 TCGGATCATGGGATGCATCTAC 59.765 50.000 25.28 18.45 41.53 2.59
1666 1770 3.403038 ACTGCCACTTGTGTTCAGATAC 58.597 45.455 19.46 0.00 32.17 2.24
1756 1863 6.473758 ACTATCTTACCCTTGTTTTCAGGAC 58.526 40.000 0.00 0.00 0.00 3.85
1776 1883 4.319549 GGACTACGAAAGGAAGCAAACAAG 60.320 45.833 0.00 0.00 0.00 3.16
1814 1921 2.100749 ACCAGGTTCCGCAAAAAGAAAG 59.899 45.455 0.00 0.00 0.00 2.62
1834 1941 2.239907 AGTAATGAAGGAGGTGCTTCCC 59.760 50.000 8.57 0.00 38.02 3.97
1843 1950 2.100631 GGTGCTTCCCGATGACACG 61.101 63.158 0.00 0.00 32.00 4.49
1881 1988 0.976641 TCTGCCACTCTTACCTGGTG 59.023 55.000 10.23 0.00 0.00 4.17
1885 1992 1.938585 CCACTCTTACCTGGTGAGGA 58.061 55.000 17.48 8.10 42.93 3.71
1887 1994 2.432510 CCACTCTTACCTGGTGAGGATC 59.567 54.545 17.48 0.00 42.93 3.36
1890 1997 2.099921 CTCTTACCTGGTGAGGATCGTG 59.900 54.545 17.48 0.00 42.93 4.35
1894 2001 1.420138 ACCTGGTGAGGATCGTGTTTT 59.580 47.619 0.00 0.00 42.93 2.43
1905 2012 6.538742 TGAGGATCGTGTTTTCTTTCATATCC 59.461 38.462 0.00 0.00 38.61 2.59
1908 2015 6.316390 GGATCGTGTTTTCTTTCATATCCAGT 59.684 38.462 0.00 0.00 33.32 4.00
1909 2016 6.480524 TCGTGTTTTCTTTCATATCCAGTG 57.519 37.500 0.00 0.00 0.00 3.66
1913 2020 6.015434 GTGTTTTCTTTCATATCCAGTGGGTT 60.015 38.462 9.92 0.00 34.93 4.11
1914 2021 6.015519 TGTTTTCTTTCATATCCAGTGGGTTG 60.016 38.462 9.92 3.84 34.93 3.77
1915 2022 5.512942 TTCTTTCATATCCAGTGGGTTGA 57.487 39.130 9.92 6.28 34.93 3.18
1916 2023 4.843728 TCTTTCATATCCAGTGGGTTGAC 58.156 43.478 9.92 0.00 34.93 3.18
1917 2024 4.536090 TCTTTCATATCCAGTGGGTTGACT 59.464 41.667 9.92 0.00 34.93 3.41
1918 2025 4.927267 TTCATATCCAGTGGGTTGACTT 57.073 40.909 9.92 0.00 34.93 3.01
1919 2026 4.220693 TCATATCCAGTGGGTTGACTTG 57.779 45.455 9.92 0.00 34.93 3.16
1920 2027 3.587061 TCATATCCAGTGGGTTGACTTGT 59.413 43.478 9.92 0.00 34.93 3.16
1921 2028 4.042809 TCATATCCAGTGGGTTGACTTGTT 59.957 41.667 9.92 0.00 34.93 2.83
1922 2029 2.341846 TCCAGTGGGTTGACTTGTTC 57.658 50.000 9.92 0.00 34.93 3.18
1923 2030 1.843851 TCCAGTGGGTTGACTTGTTCT 59.156 47.619 9.92 0.00 34.93 3.01
1928 2035 3.458487 AGTGGGTTGACTTGTTCTTAGGT 59.542 43.478 0.00 0.00 0.00 3.08
1942 2049 2.094390 TCTTAGGTTGGTGATTCGACGG 60.094 50.000 0.00 0.00 0.00 4.79
2074 2181 8.518702 GGAAAGCTTAAGAGTGATTTCTTGAAT 58.481 33.333 6.67 0.00 37.91 2.57
2147 2254 2.064014 GTGCAGTACGAGGTTTGTACC 58.936 52.381 0.00 0.00 42.46 3.34
2161 2268 6.887626 GGTTTGTACCAGAGGATTAAACAA 57.112 37.500 0.00 0.00 44.36 2.83
2162 2269 7.279750 GGTTTGTACCAGAGGATTAAACAAA 57.720 36.000 0.00 0.00 44.36 2.83
2164 2271 7.937649 GTTTGTACCAGAGGATTAAACAAACT 58.062 34.615 16.66 0.00 45.75 2.66
2218 2326 5.580297 TCAAACAAAAAGAAAGGTCACATGC 59.420 36.000 0.00 0.00 0.00 4.06
2219 2327 4.734398 ACAAAAAGAAAGGTCACATGCA 57.266 36.364 0.00 0.00 0.00 3.96
2226 2343 3.504906 AGAAAGGTCACATGCATCAACTG 59.495 43.478 0.00 0.00 0.00 3.16
2235 2352 4.092529 CACATGCATCAACTGTACTGTCTC 59.907 45.833 5.81 0.00 0.00 3.36
2244 2361 3.134458 ACTGTACTGTCTCTTTTGCTGC 58.866 45.455 0.00 0.00 0.00 5.25
2273 2390 3.599343 TGATAGGCTGTTGTACTGCTTG 58.401 45.455 0.00 0.00 41.90 4.01
2275 2392 1.884235 AGGCTGTTGTACTGCTTGTC 58.116 50.000 8.28 0.00 41.90 3.18
2385 2506 4.167268 CTCTCTAAGACCGTAACTGCAAC 58.833 47.826 0.00 0.00 0.00 4.17
2502 2623 2.477863 GGTATTTGACGCTGCATTGTCC 60.478 50.000 13.93 1.14 34.18 4.02
2509 2630 2.879907 CTGCATTGTCCGGGCAAG 59.120 61.111 27.63 18.94 37.06 4.01
2552 2673 7.696992 ATAAAGGGTAAGGTATTGTTGTGTG 57.303 36.000 0.00 0.00 0.00 3.82
2553 2674 4.717279 AGGGTAAGGTATTGTTGTGTGT 57.283 40.909 0.00 0.00 0.00 3.72
2558 2679 6.882678 GGGTAAGGTATTGTTGTGTGTTAGAT 59.117 38.462 0.00 0.00 0.00 1.98
2617 2738 2.768253 TTCCGTCAGATGTTGATGCT 57.232 45.000 0.00 0.00 40.78 3.79
2835 2962 3.330701 AGAATGCCCCAGAGTTCTTTGTA 59.669 43.478 0.00 0.00 0.00 2.41
2845 2972 7.310734 CCCCAGAGTTCTTTGTAGATTAGTTCT 60.311 40.741 0.00 0.00 38.57 3.01
2940 3072 8.974060 AGGATTGTGTCACTAAAAGTCTAAAA 57.026 30.769 4.27 0.00 0.00 1.52
3034 3166 2.942804 TGCCCAACTGTTCAAATCTCA 58.057 42.857 0.00 0.00 0.00 3.27
3101 3238 3.261643 TCTGAAATTGCTGCACTCTAGGA 59.738 43.478 0.00 0.00 0.00 2.94
3102 3239 4.080695 TCTGAAATTGCTGCACTCTAGGAT 60.081 41.667 0.00 0.00 0.00 3.24
3103 3240 4.194640 TGAAATTGCTGCACTCTAGGATC 58.805 43.478 0.00 0.00 0.00 3.36
3104 3241 4.080695 TGAAATTGCTGCACTCTAGGATCT 60.081 41.667 0.00 0.00 0.00 2.75
3105 3242 5.129320 TGAAATTGCTGCACTCTAGGATCTA 59.871 40.000 0.00 0.00 0.00 1.98
3106 3243 4.870123 ATTGCTGCACTCTAGGATCTAG 57.130 45.455 0.00 0.00 0.00 2.43
3107 3244 2.591923 TGCTGCACTCTAGGATCTAGG 58.408 52.381 0.00 0.00 0.00 3.02
3196 3333 4.336433 ACATGCATAGCACCAATAAGTGAC 59.664 41.667 0.00 0.00 43.04 3.67
3197 3334 4.220693 TGCATAGCACCAATAAGTGACT 57.779 40.909 0.00 0.00 40.34 3.41
3377 3514 3.130869 TGGAGCAACAATTATCACATGGC 59.869 43.478 0.00 0.00 0.00 4.40
3452 3590 3.954200 ACATTCATGTACCAGCATGTGA 58.046 40.909 6.04 0.00 44.68 3.58
3522 3660 6.228258 ACTGGAAACACTAGAAAATTCGCTA 58.772 36.000 0.00 0.00 35.60 4.26
3567 3705 4.607239 ACAGATCATTGCCTTCCAAAGAT 58.393 39.130 0.00 0.00 42.68 2.40
3570 3708 6.837568 ACAGATCATTGCCTTCCAAAGATATT 59.162 34.615 0.00 0.00 40.76 1.28
3636 3775 9.528489 AAAATAATAGGTGTGGTCATTTGTAGT 57.472 29.630 0.00 0.00 0.00 2.73
3749 3890 8.899427 ATTACTCTTGATGATCTAACACATGG 57.101 34.615 0.00 0.00 0.00 3.66
3815 3956 9.205719 CTAAAAGACTGGTTAAAGAGGTTAGTC 57.794 37.037 0.00 0.00 34.75 2.59
3863 4004 0.250234 CATCCCTTGCTCGAGGAACA 59.750 55.000 16.06 0.67 39.25 3.18
3868 4009 1.734465 CCTTGCTCGAGGAACAATGTC 59.266 52.381 16.06 0.00 39.25 3.06
4035 4177 3.369242 TGCATGATTCATCTGTCCCAA 57.631 42.857 0.00 0.00 0.00 4.12
4192 4335 7.011295 CAGATAAAAGAATCAGAACTGGAGCTC 59.989 40.741 4.71 4.71 0.00 4.09
4261 4404 1.971167 GCATCCAGGCGAAACCACA 60.971 57.895 0.00 0.00 43.14 4.17
4286 4429 0.105408 ACGGCCGTGTACCATATTCC 59.895 55.000 33.75 0.00 0.00 3.01
4350 4493 3.323751 CCAATCTTTTTGGGCTTCCTG 57.676 47.619 0.00 0.00 35.96 3.86
4541 4685 2.034066 TTGGCAAGAGAAGGGCGG 59.966 61.111 0.00 0.00 0.00 6.13
4542 4686 3.567579 TTGGCAAGAGAAGGGCGGG 62.568 63.158 0.00 0.00 0.00 6.13
4598 4745 1.603802 AGCACATCAACTGACGTTTGG 59.396 47.619 0.00 0.00 0.00 3.28
4600 4747 2.602217 GCACATCAACTGACGTTTGGTC 60.602 50.000 0.00 0.00 46.27 4.02
4601 4748 2.032030 CACATCAACTGACGTTTGGTCC 60.032 50.000 0.00 0.00 45.46 4.46
4602 4749 2.217750 CATCAACTGACGTTTGGTCCA 58.782 47.619 0.00 0.00 45.46 4.02
4603 4750 2.631160 TCAACTGACGTTTGGTCCAT 57.369 45.000 0.00 0.00 45.46 3.41
4604 4751 3.755112 TCAACTGACGTTTGGTCCATA 57.245 42.857 0.00 0.00 45.46 2.74
4605 4752 3.659786 TCAACTGACGTTTGGTCCATAG 58.340 45.455 0.00 0.00 45.46 2.23
4606 4753 2.094762 ACTGACGTTTGGTCCATAGC 57.905 50.000 0.00 0.00 45.46 2.97
4625 4776 0.982852 CCCATAGGTCAGAGGTGCCA 60.983 60.000 0.00 0.00 0.00 4.92
4637 4788 3.898509 GTGCCAACTGCGCCAACA 61.899 61.111 4.18 0.00 44.91 3.33
4656 4807 1.076850 TGGTGCGGCCATGATGATT 60.077 52.632 2.24 0.00 43.61 2.57
4665 4816 2.032550 GGCCATGATGATTGTCAACGAG 59.967 50.000 0.00 0.00 0.00 4.18
4673 4824 1.197721 GATTGTCAACGAGGGCAACAG 59.802 52.381 0.61 0.00 39.74 3.16
4676 4827 2.281761 CAACGAGGGCAACAGGCT 60.282 61.111 0.00 0.00 44.01 4.58
4677 4828 2.281761 AACGAGGGCAACAGGCTG 60.282 61.111 14.16 14.16 44.01 4.85
4678 4829 2.818169 AACGAGGGCAACAGGCTGA 61.818 57.895 23.66 0.00 44.01 4.26
4679 4830 2.129555 AACGAGGGCAACAGGCTGAT 62.130 55.000 23.66 6.45 44.01 2.90
4680 4831 1.817099 CGAGGGCAACAGGCTGATC 60.817 63.158 23.66 9.07 44.01 2.92
4702 4853 2.833582 ATGCTGATGCTGGCTGGC 60.834 61.111 0.00 0.00 40.48 4.85
4715 4866 1.287442 TGGCTGGCATTATGGAAAGGA 59.713 47.619 0.00 0.00 0.00 3.36
4725 4876 5.525012 GCATTATGGAAAGGAAAAATCTGGC 59.475 40.000 0.00 0.00 0.00 4.85
4734 4885 3.054361 AGGAAAAATCTGGCCATCGTAGT 60.054 43.478 5.51 0.00 0.00 2.73
4748 4899 4.870426 CCATCGTAGTGAAGCAGTTTGTAT 59.130 41.667 0.00 0.00 0.00 2.29
4751 4902 6.505044 TCGTAGTGAAGCAGTTTGTATAGA 57.495 37.500 0.00 0.00 0.00 1.98
4752 4903 6.552629 TCGTAGTGAAGCAGTTTGTATAGAG 58.447 40.000 0.00 0.00 0.00 2.43
4753 4904 6.373495 TCGTAGTGAAGCAGTTTGTATAGAGA 59.627 38.462 0.00 0.00 0.00 3.10
4759 4910 3.964031 AGCAGTTTGTATAGAGAGGGAGG 59.036 47.826 0.00 0.00 0.00 4.30
4862 5027 8.499403 AGAAATGTAAAGTAGCTGAATTCCTC 57.501 34.615 2.27 0.00 0.00 3.71
4888 5053 5.163519 CGGGGCTGATGAAAAAGAATATGTT 60.164 40.000 0.00 0.00 0.00 2.71
4943 5108 1.398390 CCGCTTTAGTGCCTTGTGATC 59.602 52.381 0.00 0.00 0.00 2.92
5262 5440 1.377994 CTGGCTCCCTGCTTGACTT 59.622 57.895 0.00 0.00 42.39 3.01
5411 5590 3.254166 CACAAATGCCCAGGTCTATATGC 59.746 47.826 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 15 4.139420 CGCTCGCAAGCTGTTCGG 62.139 66.667 0.00 0.00 46.91 4.30
27 29 0.179161 CCGTCTTCTTCATCGACGCT 60.179 55.000 5.60 0.00 46.49 5.07
65 67 1.372997 CTAGTTGGTCTGTGCGCGT 60.373 57.895 8.43 0.00 0.00 6.01
143 164 2.388232 GCGACCGCAACCAAGTAGG 61.388 63.158 9.73 0.00 41.75 3.18
249 276 2.501723 ACCGTAACATCCTCTGAGCAAT 59.498 45.455 0.00 0.00 0.00 3.56
336 372 1.925888 GCCTCCCTCCATCCAACAT 59.074 57.895 0.00 0.00 0.00 2.71
355 396 2.690778 GCTGGTCGGTGGCACATTC 61.691 63.158 20.82 8.20 44.52 2.67
504 549 2.095853 CACAAAAGTCAGCTCAACACGT 59.904 45.455 0.00 0.00 0.00 4.49
507 552 2.682856 GGACACAAAAGTCAGCTCAACA 59.317 45.455 0.00 0.00 40.29 3.33
515 560 2.539338 GGCGCGGACACAAAAGTCA 61.539 57.895 8.83 0.00 40.29 3.41
579 624 4.938080 ACTCGTATCAACCATAAGAGCAG 58.062 43.478 4.94 0.00 43.71 4.24
590 635 7.845617 TTTGTATTTGCAAACTCGTATCAAC 57.154 32.000 15.41 2.86 33.91 3.18
593 638 8.667987 TTCATTTGTATTTGCAAACTCGTATC 57.332 30.769 15.41 1.16 40.58 2.24
603 648 9.638239 GTCCTAAAGATTTCATTTGTATTTGCA 57.362 29.630 0.00 0.00 0.00 4.08
604 649 9.087424 GGTCCTAAAGATTTCATTTGTATTTGC 57.913 33.333 0.00 0.00 0.00 3.68
609 654 8.581578 GGTTTGGTCCTAAAGATTTCATTTGTA 58.418 33.333 0.00 0.00 0.00 2.41
610 655 7.290014 AGGTTTGGTCCTAAAGATTTCATTTGT 59.710 33.333 0.00 0.00 35.87 2.83
611 656 7.670364 AGGTTTGGTCCTAAAGATTTCATTTG 58.330 34.615 0.00 0.00 35.87 2.32
612 657 7.855784 AGGTTTGGTCCTAAAGATTTCATTT 57.144 32.000 0.00 0.00 35.87 2.32
613 658 7.256296 CCAAGGTTTGGTCCTAAAGATTTCATT 60.256 37.037 0.00 0.00 45.93 2.57
614 659 6.211384 CCAAGGTTTGGTCCTAAAGATTTCAT 59.789 38.462 0.00 0.00 45.93 2.57
615 660 5.538433 CCAAGGTTTGGTCCTAAAGATTTCA 59.462 40.000 0.00 0.00 45.93 2.69
631 676 0.036306 ACGGCTCGAATCCAAGGTTT 59.964 50.000 1.50 0.00 0.00 3.27
633 678 1.079127 CACGGCTCGAATCCAAGGT 60.079 57.895 1.50 0.00 0.00 3.50
636 681 1.546923 TCTTACACGGCTCGAATCCAA 59.453 47.619 1.50 0.00 0.00 3.53
645 690 0.105408 ACGGTTGTTCTTACACGGCT 59.895 50.000 0.00 0.00 32.98 5.52
647 692 1.259507 CACACGGTTGTTCTTACACGG 59.740 52.381 0.00 0.00 31.66 4.94
649 694 4.345271 AAACACACGGTTGTTCTTACAC 57.655 40.909 4.57 0.00 38.82 2.90
655 700 4.559643 CCAAAAGTAAACACACGGTTGTTC 59.440 41.667 4.57 0.00 38.82 3.18
658 703 4.358494 TCCAAAAGTAAACACACGGTTG 57.642 40.909 0.00 0.00 40.35 3.77
661 706 4.035792 TCACATCCAAAAGTAAACACACGG 59.964 41.667 0.00 0.00 0.00 4.94
662 707 5.163302 TCACATCCAAAAGTAAACACACG 57.837 39.130 0.00 0.00 0.00 4.49
667 712 3.365969 CGGGCTCACATCCAAAAGTAAAC 60.366 47.826 0.00 0.00 0.00 2.01
670 716 1.339631 CCGGGCTCACATCCAAAAGTA 60.340 52.381 0.00 0.00 0.00 2.24
679 725 4.202461 ACAAATATATCACCGGGCTCACAT 60.202 41.667 6.32 0.00 0.00 3.21
685 731 2.858745 ACCACAAATATATCACCGGGC 58.141 47.619 6.32 0.00 0.00 6.13
686 732 5.556915 ACATACCACAAATATATCACCGGG 58.443 41.667 6.32 0.00 0.00 5.73
689 735 7.445402 AGAGCAACATACCACAAATATATCACC 59.555 37.037 0.00 0.00 0.00 4.02
697 743 8.806146 AGATAAAAAGAGCAACATACCACAAAT 58.194 29.630 0.00 0.00 0.00 2.32
702 748 7.882791 TCAAGAGATAAAAAGAGCAACATACCA 59.117 33.333 0.00 0.00 0.00 3.25
707 753 8.394971 TCATTCAAGAGATAAAAAGAGCAACA 57.605 30.769 0.00 0.00 0.00 3.33
708 754 9.286946 CATCATTCAAGAGATAAAAAGAGCAAC 57.713 33.333 0.00 0.00 0.00 4.17
729 776 7.537715 TGCGTCTAAATTTGAACATTCATCAT 58.462 30.769 0.00 0.00 37.00 2.45
752 799 7.539022 GCTTACAAAACCTCTCTCTTATTTTGC 59.461 37.037 7.47 0.00 41.70 3.68
789 837 7.198390 CGCCATCTTCATTTCAGAAACATATT 58.802 34.615 0.00 0.00 0.00 1.28
804 856 1.068083 GAGATCCGCGCCATCTTCA 59.932 57.895 17.08 0.00 30.30 3.02
807 859 2.907407 TCGAGATCCGCGCCATCT 60.907 61.111 16.26 16.26 38.37 2.90
817 869 2.159761 CGTTCGATCTAGCCTCGAGATC 60.160 54.545 15.71 7.76 45.00 2.75
828 880 0.099968 CTTCCACGCCGTTCGATCTA 59.900 55.000 0.00 0.00 41.67 1.98
829 881 1.153823 CTTCCACGCCGTTCGATCT 60.154 57.895 0.00 0.00 41.67 2.75
846 898 2.049063 GCGAGCACGTTCCTGTCT 60.049 61.111 5.23 0.00 41.98 3.41
906 964 0.899019 GTCACTGGGAGGAAGAGGAC 59.101 60.000 0.00 0.00 0.00 3.85
913 972 2.203938 GGTGGGTCACTGGGAGGA 60.204 66.667 0.00 0.00 34.40 3.71
915 974 2.471084 TAGGGGTGGGTCACTGGGAG 62.471 65.000 0.00 0.00 34.40 4.30
1139 1204 1.776667 TCTAGGGGGATTGATTGCAGG 59.223 52.381 0.00 0.00 0.00 4.85
1236 1320 4.714308 TGAGTCCCCTTTCAACATTTTTGT 59.286 37.500 0.00 0.00 0.00 2.83
1305 1390 4.324267 ACTCCCCGTTTCTGACTAAAATG 58.676 43.478 0.00 0.00 0.00 2.32
1320 1405 3.118408 TGATTCAAGATACCAACTCCCCG 60.118 47.826 0.00 0.00 0.00 5.73
1329 1414 4.757149 GCACATACCCTGATTCAAGATACC 59.243 45.833 0.00 0.00 0.00 2.73
1358 1459 0.806102 CAAGTATGTGAGGACGGCCG 60.806 60.000 26.86 26.86 39.96 6.13
1362 1463 1.359848 GTGCCAAGTATGTGAGGACG 58.640 55.000 0.00 0.00 0.00 4.79
1385 1489 2.975799 GCCGGTCGACCTGCAAAA 60.976 61.111 36.85 0.00 44.38 2.44
1437 1541 3.769300 TCCAGAATTTCACGATCCTCAGA 59.231 43.478 0.00 0.00 0.00 3.27
1481 1585 2.508526 ACTGAAACTGAATGCAGGGAC 58.491 47.619 5.47 0.00 46.60 4.46
1483 1587 2.886523 TGAACTGAAACTGAATGCAGGG 59.113 45.455 5.47 0.00 46.60 4.45
1646 1750 2.413112 CGTATCTGAACACAAGTGGCAG 59.587 50.000 14.99 14.99 37.98 4.85
1666 1770 2.987149 ACGCTGTTACAAGATTCAGACG 59.013 45.455 0.00 0.00 35.45 4.18
1756 1863 3.555518 GCTTGTTTGCTTCCTTTCGTAG 58.444 45.455 0.00 0.00 0.00 3.51
1814 1921 2.644676 GGGAAGCACCTCCTTCATTAC 58.355 52.381 4.54 0.00 42.31 1.89
1834 1941 1.395954 TCGTAGAAGTCCGTGTCATCG 59.604 52.381 0.00 0.00 0.00 3.84
1843 1950 1.750206 GAAGGGTCCTCGTAGAAGTCC 59.250 57.143 0.00 0.00 34.09 3.85
1881 1988 6.538742 TGGATATGAAAGAAAACACGATCCTC 59.461 38.462 0.00 0.00 35.08 3.71
1885 1992 6.094048 CCACTGGATATGAAAGAAAACACGAT 59.906 38.462 0.00 0.00 0.00 3.73
1887 1994 5.391950 CCCACTGGATATGAAAGAAAACACG 60.392 44.000 0.00 0.00 0.00 4.49
1890 1997 6.208599 TCAACCCACTGGATATGAAAGAAAAC 59.791 38.462 0.00 0.00 34.81 2.43
1894 2001 4.536090 AGTCAACCCACTGGATATGAAAGA 59.464 41.667 0.00 0.00 34.81 2.52
1905 2012 3.815401 CCTAAGAACAAGTCAACCCACTG 59.185 47.826 0.00 0.00 0.00 3.66
1908 2015 4.204012 CAACCTAAGAACAAGTCAACCCA 58.796 43.478 0.00 0.00 0.00 4.51
1909 2016 3.568430 CCAACCTAAGAACAAGTCAACCC 59.432 47.826 0.00 0.00 0.00 4.11
1913 2020 4.764050 TCACCAACCTAAGAACAAGTCA 57.236 40.909 0.00 0.00 0.00 3.41
1914 2021 5.107065 CGAATCACCAACCTAAGAACAAGTC 60.107 44.000 0.00 0.00 0.00 3.01
1915 2022 4.755123 CGAATCACCAACCTAAGAACAAGT 59.245 41.667 0.00 0.00 0.00 3.16
1916 2023 4.994852 TCGAATCACCAACCTAAGAACAAG 59.005 41.667 0.00 0.00 0.00 3.16
1917 2024 4.753107 GTCGAATCACCAACCTAAGAACAA 59.247 41.667 0.00 0.00 0.00 2.83
1918 2025 4.312443 GTCGAATCACCAACCTAAGAACA 58.688 43.478 0.00 0.00 0.00 3.18
1919 2026 3.367025 CGTCGAATCACCAACCTAAGAAC 59.633 47.826 0.00 0.00 0.00 3.01
1920 2027 3.581755 CGTCGAATCACCAACCTAAGAA 58.418 45.455 0.00 0.00 0.00 2.52
1921 2028 2.094390 CCGTCGAATCACCAACCTAAGA 60.094 50.000 0.00 0.00 0.00 2.10
1922 2029 2.268298 CCGTCGAATCACCAACCTAAG 58.732 52.381 0.00 0.00 0.00 2.18
1923 2030 1.066716 CCCGTCGAATCACCAACCTAA 60.067 52.381 0.00 0.00 0.00 2.69
1928 2035 0.037697 CAGACCCGTCGAATCACCAA 60.038 55.000 0.00 0.00 34.09 3.67
1942 2049 1.610522 ACAGCACAAATTCAGCAGACC 59.389 47.619 0.00 0.00 0.00 3.85
2074 2181 2.368439 CTCGCAATTCCTTGATTCCCA 58.632 47.619 0.00 0.00 34.04 4.37
2160 2267 8.945193 TCATAGCTGGACCCTAAATAATAGTTT 58.055 33.333 0.00 0.00 0.00 2.66
2161 2268 8.506196 TCATAGCTGGACCCTAAATAATAGTT 57.494 34.615 0.00 0.00 0.00 2.24
2162 2269 8.686739 ATCATAGCTGGACCCTAAATAATAGT 57.313 34.615 0.00 0.00 0.00 2.12
2163 2270 9.606631 GAATCATAGCTGGACCCTAAATAATAG 57.393 37.037 0.00 0.00 0.00 1.73
2164 2271 9.338968 AGAATCATAGCTGGACCCTAAATAATA 57.661 33.333 0.00 0.00 0.00 0.98
2170 2277 5.219739 AGAAGAATCATAGCTGGACCCTAA 58.780 41.667 0.00 0.00 0.00 2.69
2173 2280 4.141620 TGAAGAAGAATCATAGCTGGACCC 60.142 45.833 0.00 0.00 0.00 4.46
2177 2284 6.748333 TGTTTGAAGAAGAATCATAGCTGG 57.252 37.500 0.00 0.00 0.00 4.85
2218 2326 5.468072 AGCAAAAGAGACAGTACAGTTGATG 59.532 40.000 0.00 0.00 0.00 3.07
2219 2327 5.468072 CAGCAAAAGAGACAGTACAGTTGAT 59.532 40.000 0.00 0.00 0.00 2.57
2226 2343 4.810790 TCTAGCAGCAAAAGAGACAGTAC 58.189 43.478 0.00 0.00 0.00 2.73
2235 2352 5.448360 GCCTATCAGTTTCTAGCAGCAAAAG 60.448 44.000 0.00 0.00 0.00 2.27
2244 2361 6.754209 CAGTACAACAGCCTATCAGTTTCTAG 59.246 42.308 0.00 0.00 0.00 2.43
2273 2390 4.957296 TCTTTCACTACAAACCAGAGGAC 58.043 43.478 0.00 0.00 0.00 3.85
2275 2392 6.693315 TTTTCTTTCACTACAAACCAGAGG 57.307 37.500 0.00 0.00 0.00 3.69
2343 2461 1.661112 GTAACAGGAGATTGTGCGCTC 59.339 52.381 9.73 5.51 0.00 5.03
2344 2462 1.276421 AGTAACAGGAGATTGTGCGCT 59.724 47.619 9.73 0.00 0.00 5.92
2345 2463 1.661112 GAGTAACAGGAGATTGTGCGC 59.339 52.381 0.00 0.00 0.00 6.09
2346 2464 3.119316 AGAGAGTAACAGGAGATTGTGCG 60.119 47.826 0.00 0.00 0.00 5.34
2502 2623 1.301716 AGTGTGTGTAGCTTGCCCG 60.302 57.895 0.00 0.00 0.00 6.13
2509 2630 7.360946 CCCTTTATAAGTTTCAGTGTGTGTAGC 60.361 40.741 0.00 0.00 0.00 3.58
2546 2667 6.489700 ACATGTGGAAATGATCTAACACACAA 59.510 34.615 13.93 2.93 41.02 3.33
2558 2679 6.622679 GCGTCAATTTAGACATGTGGAAATGA 60.623 38.462 1.15 1.19 38.43 2.57
2648 2769 9.108284 CAACTAAAAAGGATGGTTGAAACATTT 57.892 29.630 0.00 0.00 39.39 2.32
2706 2829 2.174639 ACCACATCAACCCTGTTCAAGA 59.825 45.455 0.00 0.00 0.00 3.02
2784 2911 6.073058 TCAGTTCCATCTGATGAAAAACTTCG 60.073 38.462 18.92 12.66 39.20 3.79
2835 2962 6.582636 TGGCGTGAATTCATAGAACTAATCT 58.417 36.000 12.12 0.00 42.48 2.40
2940 3072 7.499232 ACTGACTCAGCTATTTTTACAAACAGT 59.501 33.333 5.92 0.00 34.37 3.55
2957 3089 2.547211 CTGCTGGTTGAAACTGACTCAG 59.453 50.000 4.36 4.36 37.52 3.35
3101 3238 0.722676 TGGTGGGGGAGAACCTAGAT 59.277 55.000 0.00 0.00 40.03 1.98
3102 3239 0.722676 ATGGTGGGGGAGAACCTAGA 59.277 55.000 0.00 0.00 40.03 2.43
3103 3240 2.489528 TATGGTGGGGGAGAACCTAG 57.510 55.000 0.00 0.00 40.03 3.02
3104 3241 3.448277 AATATGGTGGGGGAGAACCTA 57.552 47.619 0.00 0.00 40.03 3.08
3105 3242 2.303660 AATATGGTGGGGGAGAACCT 57.696 50.000 0.00 0.00 40.03 3.50
3106 3243 3.296854 GAAAATATGGTGGGGGAGAACC 58.703 50.000 0.00 0.00 36.96 3.62
3107 3244 3.976015 TGAAAATATGGTGGGGGAGAAC 58.024 45.455 0.00 0.00 0.00 3.01
3196 3333 6.314400 CACTCCATGCCCATTTGATTAAAAAG 59.686 38.462 0.00 0.00 0.00 2.27
3197 3334 6.171921 CACTCCATGCCCATTTGATTAAAAA 58.828 36.000 0.00 0.00 0.00 1.94
3377 3514 5.295431 TCATGAGGCAAAAACATACTTCG 57.705 39.130 0.00 0.00 0.00 3.79
3522 3660 3.320610 TCCAGAAGAGCTATGCTACCT 57.679 47.619 0.00 0.00 39.88 3.08
3539 3677 3.511146 GGAAGGCAATGATCTGTTTTCCA 59.489 43.478 11.39 0.00 34.12 3.53
3617 3756 5.541101 ACACTACTACAAATGACCACACCTA 59.459 40.000 0.00 0.00 0.00 3.08
3636 3775 8.589701 TCATCTAGTTCAGGTTGATAACACTA 57.410 34.615 0.00 0.00 0.00 2.74
3708 3849 9.322773 TCAAGAGTAATATCTGATGAAAAGCTG 57.677 33.333 0.00 0.00 0.00 4.24
3744 3885 6.463995 ACAAAACATACAACAAGACCATGT 57.536 33.333 0.00 0.00 34.24 3.21
3749 3890 6.435428 CACCCTACAAAACATACAACAAGAC 58.565 40.000 0.00 0.00 0.00 3.01
3815 3956 7.577979 TGGAAGCAAATTAGTAACAACTAACG 58.422 34.615 0.34 0.00 35.34 3.18
3858 3999 6.352516 AGATATCCAAGTCTGACATTGTTCC 58.647 40.000 10.88 0.00 0.00 3.62
3992 4133 1.760029 TGCCCCAAGTTTGACCTTTTC 59.240 47.619 0.00 0.00 0.00 2.29
4192 4335 2.065993 TTTCCTTCAGCTCTTCGTCG 57.934 50.000 0.00 0.00 0.00 5.12
4218 4361 7.360776 GCTCAAACTGAATAAGAAAGACTCTGG 60.361 40.741 0.00 0.00 33.37 3.86
4261 4404 0.896923 TGGTACACGGCCGTTTCTAT 59.103 50.000 32.11 14.36 0.00 1.98
4286 4429 6.170675 AGCAGCTATTTTGAGTTCTTAACG 57.829 37.500 0.00 0.00 36.23 3.18
4350 4493 3.319755 CAATGATGTTGACCTGCCAAAC 58.680 45.455 0.00 0.00 0.00 2.93
4516 4660 1.466167 CTTCTCTTGCCAACCGATGTG 59.534 52.381 0.00 0.00 0.00 3.21
4541 4685 9.232473 ACAAAAATATACACTTCTTCTCTTCCC 57.768 33.333 0.00 0.00 0.00 3.97
4598 4745 2.564947 CTCTGACCTATGGGCTATGGAC 59.435 54.545 0.00 0.00 35.63 4.02
4600 4747 1.905215 CCTCTGACCTATGGGCTATGG 59.095 57.143 0.00 0.00 35.63 2.74
4601 4748 2.301296 CACCTCTGACCTATGGGCTATG 59.699 54.545 0.00 0.00 35.63 2.23
4602 4749 2.614259 CACCTCTGACCTATGGGCTAT 58.386 52.381 0.00 0.00 35.63 2.97
4603 4750 2.034799 GCACCTCTGACCTATGGGCTA 61.035 57.143 0.00 0.00 35.63 3.93
4604 4751 1.341156 GCACCTCTGACCTATGGGCT 61.341 60.000 0.00 0.00 35.63 5.19
4605 4752 1.147153 GCACCTCTGACCTATGGGC 59.853 63.158 0.00 0.00 35.63 5.36
4606 4753 0.982852 TGGCACCTCTGACCTATGGG 60.983 60.000 0.00 0.00 38.88 4.00
4625 4776 3.041701 CACCATGTTGGCGCAGTT 58.958 55.556 10.83 0.00 42.67 3.16
4644 4795 2.016318 TCGTTGACAATCATCATGGCC 58.984 47.619 0.00 0.00 0.00 5.36
4645 4796 2.032550 CCTCGTTGACAATCATCATGGC 59.967 50.000 0.00 0.00 0.00 4.40
4656 4807 1.227823 CCTGTTGCCCTCGTTGACA 60.228 57.895 0.00 0.00 0.00 3.58
4665 4816 1.941999 GCTTGATCAGCCTGTTGCCC 61.942 60.000 0.00 0.00 43.65 5.36
4685 4836 2.833582 GCCAGCCAGCATCAGCAT 60.834 61.111 0.00 0.00 45.49 3.79
4686 4837 4.354162 TGCCAGCCAGCATCAGCA 62.354 61.111 0.00 0.00 45.49 4.41
4702 4853 6.051074 GGCCAGATTTTTCCTTTCCATAATG 58.949 40.000 0.00 0.00 0.00 1.90
4705 4856 4.682563 TGGCCAGATTTTTCCTTTCCATA 58.317 39.130 0.00 0.00 0.00 2.74
4715 4866 3.950397 TCACTACGATGGCCAGATTTTT 58.050 40.909 13.05 0.00 0.00 1.94
4725 4876 3.067106 ACAAACTGCTTCACTACGATGG 58.933 45.455 0.00 0.00 0.00 3.51
4734 4885 5.023452 TCCCTCTCTATACAAACTGCTTCA 58.977 41.667 0.00 0.00 0.00 3.02
4748 4899 3.011821 ACATTCTGTGACCTCCCTCTCTA 59.988 47.826 0.00 0.00 0.00 2.43
4751 4902 2.334006 ACATTCTGTGACCTCCCTCT 57.666 50.000 0.00 0.00 0.00 3.69
4752 4903 3.964031 AGATACATTCTGTGACCTCCCTC 59.036 47.826 0.00 0.00 31.79 4.30
4753 4904 3.964031 GAGATACATTCTGTGACCTCCCT 59.036 47.826 0.00 0.00 33.74 4.20
4786 4937 7.814107 GCAGGATTATGATCAAACAAACAGAAA 59.186 33.333 0.00 0.00 33.77 2.52
4788 4939 6.433716 TGCAGGATTATGATCAAACAAACAGA 59.566 34.615 0.00 0.00 33.77 3.41
4789 4940 6.623486 TGCAGGATTATGATCAAACAAACAG 58.377 36.000 0.00 0.00 33.77 3.16
4862 5027 1.137404 CTTTTTCATCAGCCCCGCG 59.863 57.895 0.00 0.00 0.00 6.46
4910 5075 5.673818 GCACTAAAGCGGTTCAGAAAATAGG 60.674 44.000 4.10 0.00 0.00 2.57
4924 5089 1.061131 CGATCACAAGGCACTAAAGCG 59.939 52.381 0.00 0.00 38.49 4.68
4967 5132 5.332130 CGAAGATTAATCTCACACGCATCAG 60.332 44.000 18.19 3.58 35.76 2.90
5056 5221 6.758254 AGAATAAATTCTTGTTTGTGGGGTG 58.242 36.000 0.00 0.00 44.28 4.61
5262 5440 6.288294 AGTGCTGTTACTGAACATACAAGAA 58.712 36.000 3.25 0.00 44.53 2.52
5322 5500 3.387699 ACAAATTGAACCTGGAACCTTGG 59.612 43.478 0.00 0.00 0.00 3.61
5411 5590 5.100751 AGAACAGATGAAAGAAAAGCGTG 57.899 39.130 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.