Multiple sequence alignment - TraesCS1B01G136900

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 TraesCS1B01G136900 chr1B 100.000 2378 0 0 1 2378 174785265 174782888 0.000000e+00 4392.0
1 TraesCS1B01G136900 chr1B 80.930 645 120 3 57 700 445661423 445662065 7.580000e-140 507.0
2 TraesCS1B01G136900 chr1B 81.340 418 34 21 968 1379 174763524 174763145 1.380000e-77 300.0
3 TraesCS1B01G136900 chr1B 85.714 287 20 7 1093 1379 175275786 175275521 1.390000e-72 283.0
4 TraesCS1B01G136900 chr1A 83.051 1652 165 62 753 2344 124190411 124188815 0.000000e+00 1393.0
5 TraesCS1B01G136900 chr1A 82.821 390 30 14 1001 1389 124787261 124786908 4.930000e-82 315.0
6 TraesCS1B01G136900 chr1A 78.555 429 47 23 968 1389 124181623 124181233 8.490000e-60 241.0
7 TraesCS1B01G136900 chr1D 84.652 1251 84 41 753 1944 114083891 114082690 0.000000e+00 1147.0
8 TraesCS1B01G136900 chr1D 86.957 414 33 8 1943 2344 114082350 114081946 1.680000e-121 446.0
9 TraesCS1B01G136900 chr1D 82.297 418 33 21 968 1379 114065179 114064797 8.200000e-85 324.0
10 TraesCS1B01G136900 chr1D 82.741 394 34 19 990 1379 114313705 114313342 1.060000e-83 320.0
11 TraesCS1B01G136900 chr2D 93.913 690 42 0 58 747 25073566 25074255 0.000000e+00 1042.0
12 TraesCS1B01G136900 chr2D 90.883 691 62 1 58 747 19388162 19388852 0.000000e+00 926.0
13 TraesCS1B01G136900 chr2D 86.036 666 91 2 78 742 625460969 625461633 0.000000e+00 713.0
14 TraesCS1B01G136900 chr7B 93.245 681 46 0 65 745 417554936 417555616 0.000000e+00 1003.0
15 TraesCS1B01G136900 chr7B 95.000 60 3 0 1 60 417553718 417553777 7.000000e-16 95.3
16 TraesCS1B01G136900 chr7D 91.172 691 60 1 58 747 61142943 61143633 0.000000e+00 937.0
17 TraesCS1B01G136900 chr2B 90.630 683 41 9 65 747 718635255 718635914 0.000000e+00 885.0
18 TraesCS1B01G136900 chr2A 85.277 686 100 1 57 742 369205529 369204845 0.000000e+00 706.0
19 TraesCS1B01G136900 chrUn 91.142 508 45 0 64 571 64824838 64824331 0.000000e+00 689.0
20 TraesCS1B01G136900 chrUn 91.713 181 15 0 567 747 64822610 64822430 3.920000e-63 252.0
21 TraesCS1B01G136900 chr3D 82.278 237 30 11 1139 1366 86237044 86237277 6.710000e-46 195.0
22 TraesCS1B01G136900 chr6A 100.000 29 0 0 20 48 502918542 502918514 1.000000e-03 54.7


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 TraesCS1B01G136900 chr1B 174782888 174785265 2377 True 4392.00 4392 100.0000 1 2378 1 chr1B.!!$R2 2377
1 TraesCS1B01G136900 chr1B 445661423 445662065 642 False 507.00 507 80.9300 57 700 1 chr1B.!!$F1 643
2 TraesCS1B01G136900 chr1A 124188815 124190411 1596 True 1393.00 1393 83.0510 753 2344 1 chr1A.!!$R2 1591
3 TraesCS1B01G136900 chr1D 114081946 114083891 1945 True 796.50 1147 85.8045 753 2344 2 chr1D.!!$R3 1591
4 TraesCS1B01G136900 chr2D 25073566 25074255 689 False 1042.00 1042 93.9130 58 747 1 chr2D.!!$F2 689
5 TraesCS1B01G136900 chr2D 19388162 19388852 690 False 926.00 926 90.8830 58 747 1 chr2D.!!$F1 689
6 TraesCS1B01G136900 chr2D 625460969 625461633 664 False 713.00 713 86.0360 78 742 1 chr2D.!!$F3 664
7 TraesCS1B01G136900 chr7B 417553718 417555616 1898 False 549.15 1003 94.1225 1 745 2 chr7B.!!$F1 744
8 TraesCS1B01G136900 chr7D 61142943 61143633 690 False 937.00 937 91.1720 58 747 1 chr7D.!!$F1 689
9 TraesCS1B01G136900 chr2B 718635255 718635914 659 False 885.00 885 90.6300 65 747 1 chr2B.!!$F1 682
10 TraesCS1B01G136900 chr2A 369204845 369205529 684 True 706.00 706 85.2770 57 742 1 chr2A.!!$R1 685
11 TraesCS1B01G136900 chrUn 64822430 64824838 2408 True 470.50 689 91.4275 64 747 2 chrUn.!!$R1 683

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
772 3653 0.250209 GCATGAGTCCAGGCGATCAT 60.25 55.0 0.0 0.0 40.39 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 5286 0.037017 TGGTGGGTGGTAATGGTTCG 59.963 55.0 0.0 0.0 0.0 3.95 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
61 1216 1.069227 GTTCGACACAGTGAAATGGCC 60.069 52.381 7.81 0.00 0.00 5.36
62 1217 0.605319 TCGACACAGTGAAATGGCCC 60.605 55.000 7.81 0.00 0.00 5.80
85 1240 0.319728 CTACATGGGATCCAGCTCCG 59.680 60.000 15.23 0.00 36.75 4.63
405 1560 1.328279 TTGGAGAACTCTGTGCTCGA 58.672 50.000 1.86 0.00 39.04 4.04
565 1720 2.350388 GGAATGCAATTGTGTTCGACGT 60.350 45.455 7.40 0.00 36.07 4.34
603 3483 0.322456 GCAGGTAGTTGGGCACATCA 60.322 55.000 0.00 0.00 0.00 3.07
640 3520 2.250237 GGCAGCAGGCGAGCTTATC 61.250 63.158 4.73 0.00 43.70 1.75
680 3560 2.437085 TGCTCGATCTTCTGGTAGGA 57.563 50.000 0.00 0.00 0.00 2.94
688 3568 4.742012 GATCTTCTGGTAGGATGGGTAGA 58.258 47.826 0.00 0.00 0.00 2.59
709 3589 1.136984 GTGAGTAGTCCCGACTGCG 59.863 63.158 7.63 0.00 46.57 5.18
747 3628 3.003275 GCGGTGGATTGTACATTATGTGG 59.997 47.826 8.26 0.00 0.00 4.17
748 3629 4.447290 CGGTGGATTGTACATTATGTGGA 58.553 43.478 8.26 0.00 0.00 4.02
749 3630 4.878971 CGGTGGATTGTACATTATGTGGAA 59.121 41.667 8.26 0.96 0.00 3.53
750 3631 5.355630 CGGTGGATTGTACATTATGTGGAAA 59.644 40.000 8.26 0.29 0.00 3.13
751 3632 6.127869 CGGTGGATTGTACATTATGTGGAAAA 60.128 38.462 8.26 0.00 0.00 2.29
762 3643 5.581126 TTATGTGGAAAATGCATGAGTCC 57.419 39.130 14.00 14.00 0.00 3.85
764 3645 2.821378 TGTGGAAAATGCATGAGTCCAG 59.179 45.455 20.87 0.00 39.02 3.86
765 3646 2.165030 GTGGAAAATGCATGAGTCCAGG 59.835 50.000 20.87 0.00 39.02 4.45
772 3653 0.250209 GCATGAGTCCAGGCGATCAT 60.250 55.000 0.00 0.00 40.39 2.45
773 3654 1.509703 CATGAGTCCAGGCGATCATG 58.490 55.000 11.70 11.70 42.04 3.07
805 3686 2.909965 GAAAAGCGCACCCCCACA 60.910 61.111 11.47 0.00 0.00 4.17
848 3729 4.898265 TCCTATCCACTCTTCATCCTCTTG 59.102 45.833 0.00 0.00 0.00 3.02
864 3759 5.445964 TCCTCTTGCCCTGGTTATAAATTC 58.554 41.667 0.00 0.00 0.00 2.17
867 3762 4.017037 TCTTGCCCTGGTTATAAATTCCCA 60.017 41.667 0.00 0.00 0.00 4.37
898 3793 0.897621 TCTCCATCTCGCAAGCTCAA 59.102 50.000 0.00 0.00 37.18 3.02
899 3794 1.005340 CTCCATCTCGCAAGCTCAAC 58.995 55.000 0.00 0.00 37.18 3.18
900 3795 0.391661 TCCATCTCGCAAGCTCAACC 60.392 55.000 0.00 0.00 37.18 3.77
921 3816 4.036734 ACCAGCATTCACAGTTTACAACAG 59.963 41.667 0.00 0.00 0.00 3.16
925 3820 4.275936 GCATTCACAGTTTACAACAGTCCT 59.724 41.667 0.00 0.00 0.00 3.85
928 3823 4.439057 TCACAGTTTACAACAGTCCTCAC 58.561 43.478 0.00 0.00 0.00 3.51
981 3877 3.058363 CCCGTAGTAGAATCTTACGAGCC 60.058 52.174 14.08 0.00 36.38 4.70
1015 3911 1.453745 CTAATGGCCATGGCACCGT 60.454 57.895 36.56 19.59 41.84 4.83
1017 3913 2.203549 TAATGGCCATGGCACCGTCA 62.204 55.000 36.56 24.92 41.84 4.35
1401 4319 3.923864 AGCCAACTCGCCGACACA 61.924 61.111 0.00 0.00 0.00 3.72
1410 4328 1.667830 CGCCGACACAACCAGACAT 60.668 57.895 0.00 0.00 0.00 3.06
1415 4333 0.239347 GACACAACCAGACATGCTGC 59.761 55.000 10.54 0.00 43.50 5.25
1442 4360 1.717645 CGTGCGTGTACCTAGTTGTTC 59.282 52.381 0.00 0.00 0.00 3.18
1459 4377 0.541863 TTCCCTCTTTCGATCTGGGC 59.458 55.000 8.01 0.00 37.83 5.36
1464 4382 2.208431 CTCTTTCGATCTGGGCATCAC 58.792 52.381 0.00 0.00 0.00 3.06
1492 4426 6.439058 AGTCCTTTCTGTGTTAGAGCTTAGAT 59.561 38.462 0.00 0.00 36.61 1.98
1499 4433 6.887002 TCTGTGTTAGAGCTTAGATGAGAGAA 59.113 38.462 0.00 0.00 0.00 2.87
1516 4450 5.420421 TGAGAGAAGTCGGAAATGAGATCTT 59.580 40.000 0.00 0.00 0.00 2.40
1542 4476 2.577970 AGGGTTGATCCATTCCCTTCT 58.422 47.619 7.89 0.00 46.99 2.85
1601 4535 3.266510 AGAGGCGCAGATGTTTCAATA 57.733 42.857 10.83 0.00 0.00 1.90
1629 4598 0.812811 CGCATGTCCCAGATCTGTGG 60.813 60.000 21.11 19.93 37.34 4.17
1637 4606 3.767673 GTCCCAGATCTGTGGTACTTGTA 59.232 47.826 21.11 2.43 35.60 2.41
1640 4609 4.954202 CCCAGATCTGTGGTACTTGTACTA 59.046 45.833 21.11 2.21 35.60 1.82
1642 4611 5.450688 CCAGATCTGTGGTACTTGTACTAGC 60.451 48.000 21.11 0.00 32.32 3.42
1644 4613 5.894393 AGATCTGTGGTACTTGTACTAGCAT 59.106 40.000 4.10 0.00 0.00 3.79
1645 4614 5.995565 TCTGTGGTACTTGTACTAGCATT 57.004 39.130 4.10 0.00 0.00 3.56
1646 4615 5.720202 TCTGTGGTACTTGTACTAGCATTG 58.280 41.667 4.10 0.00 0.00 2.82
1647 4616 5.245301 TCTGTGGTACTTGTACTAGCATTGT 59.755 40.000 4.10 0.00 0.00 2.71
1650 4619 6.425721 TGTGGTACTTGTACTAGCATTGTTTC 59.574 38.462 4.10 0.00 0.00 2.78
1651 4620 6.649557 GTGGTACTTGTACTAGCATTGTTTCT 59.350 38.462 4.10 0.00 0.00 2.52
1652 4621 6.649141 TGGTACTTGTACTAGCATTGTTTCTG 59.351 38.462 4.10 0.00 0.00 3.02
1653 4622 6.649557 GGTACTTGTACTAGCATTGTTTCTGT 59.350 38.462 4.10 0.00 0.00 3.41
1654 4623 6.545504 ACTTGTACTAGCATTGTTTCTGTG 57.454 37.500 4.10 0.00 0.00 3.66
1655 4624 6.055588 ACTTGTACTAGCATTGTTTCTGTGT 58.944 36.000 4.10 0.00 0.00 3.72
1656 4625 6.542370 ACTTGTACTAGCATTGTTTCTGTGTT 59.458 34.615 4.10 0.00 0.00 3.32
1657 4626 7.713507 ACTTGTACTAGCATTGTTTCTGTGTTA 59.286 33.333 4.10 0.00 0.00 2.41
1658 4627 8.439993 TTGTACTAGCATTGTTTCTGTGTTAA 57.560 30.769 0.00 0.00 0.00 2.01
1659 4628 8.439993 TGTACTAGCATTGTTTCTGTGTTAAA 57.560 30.769 0.00 0.00 0.00 1.52
1660 4629 9.062524 TGTACTAGCATTGTTTCTGTGTTAAAT 57.937 29.630 0.00 0.00 0.00 1.40
1661 4630 9.543018 GTACTAGCATTGTTTCTGTGTTAAATC 57.457 33.333 0.00 0.00 0.00 2.17
1662 4631 8.396272 ACTAGCATTGTTTCTGTGTTAAATCT 57.604 30.769 0.00 0.00 0.00 2.40
1663 4632 8.292448 ACTAGCATTGTTTCTGTGTTAAATCTG 58.708 33.333 0.00 0.00 0.00 2.90
1664 4633 6.449698 AGCATTGTTTCTGTGTTAAATCTGG 58.550 36.000 0.00 0.00 0.00 3.86
1665 4634 6.265196 AGCATTGTTTCTGTGTTAAATCTGGA 59.735 34.615 0.00 0.00 0.00 3.86
1666 4635 7.039504 AGCATTGTTTCTGTGTTAAATCTGGAT 60.040 33.333 0.00 0.00 0.00 3.41
1667 4636 7.274250 GCATTGTTTCTGTGTTAAATCTGGATC 59.726 37.037 0.00 0.00 0.00 3.36
1668 4637 8.517878 CATTGTTTCTGTGTTAAATCTGGATCT 58.482 33.333 0.00 0.00 0.00 2.75
1669 4638 7.439157 TGTTTCTGTGTTAAATCTGGATCTG 57.561 36.000 0.00 0.00 0.00 2.90
1670 4639 7.223584 TGTTTCTGTGTTAAATCTGGATCTGA 58.776 34.615 0.00 0.00 0.00 3.27
1671 4640 7.719193 TGTTTCTGTGTTAAATCTGGATCTGAA 59.281 33.333 0.00 0.00 0.00 3.02
1672 4641 7.672983 TTCTGTGTTAAATCTGGATCTGAAC 57.327 36.000 0.00 0.00 0.00 3.18
1673 4642 6.768483 TCTGTGTTAAATCTGGATCTGAACA 58.232 36.000 0.00 0.00 0.00 3.18
1674 4643 6.650807 TCTGTGTTAAATCTGGATCTGAACAC 59.349 38.462 18.19 18.19 43.35 3.32
1675 4644 6.533730 TGTGTTAAATCTGGATCTGAACACT 58.466 36.000 21.69 0.00 43.42 3.55
1676 4645 6.427853 TGTGTTAAATCTGGATCTGAACACTG 59.572 38.462 21.69 0.00 43.42 3.66
1677 4646 6.650807 GTGTTAAATCTGGATCTGAACACTGA 59.349 38.462 17.96 0.00 41.09 3.41
1678 4647 7.335422 GTGTTAAATCTGGATCTGAACACTGAT 59.665 37.037 17.96 0.00 41.09 2.90
1679 4648 7.884877 TGTTAAATCTGGATCTGAACACTGATT 59.115 33.333 0.00 0.00 34.40 2.57
1680 4649 9.383519 GTTAAATCTGGATCTGAACACTGATTA 57.616 33.333 0.00 0.00 33.20 1.75
1681 4650 9.958180 TTAAATCTGGATCTGAACACTGATTAA 57.042 29.630 0.00 0.00 33.20 1.40
1682 4651 8.868522 AAATCTGGATCTGAACACTGATTAAA 57.131 30.769 0.00 0.00 33.20 1.52
1683 4652 9.471702 AAATCTGGATCTGAACACTGATTAAAT 57.528 29.630 0.00 0.00 33.20 1.40
1684 4653 8.674263 ATCTGGATCTGAACACTGATTAAATC 57.326 34.615 0.00 0.00 0.00 2.17
1687 4656 7.397221 TGGATCTGAACACTGATTAAATCTGT 58.603 34.615 0.00 0.00 41.36 3.41
1720 4689 6.595682 ACCGATTAAATCTGGATCTGAACAT 58.404 36.000 0.00 0.00 0.00 2.71
1723 4692 9.224267 CCGATTAAATCTGGATCTGAACATTAT 57.776 33.333 0.00 0.00 0.00 1.28
1790 4764 6.653320 TGCTTCTGTGTTATTTACCCTAACAG 59.347 38.462 0.00 0.00 39.17 3.16
1800 4774 8.557029 GTTATTTACCCTAACAGTATGATGCAC 58.443 37.037 0.00 0.00 39.69 4.57
1805 4784 5.221722 ACCCTAACAGTATGATGCACCTATG 60.222 44.000 0.00 0.00 39.69 2.23
1819 4798 8.747471 TGATGCACCTATGAATCAAAAACATTA 58.253 29.630 0.00 0.00 46.35 1.90
1886 4873 2.523168 GTTGGGTTGGGGTGGGTG 60.523 66.667 0.00 0.00 0.00 4.61
1922 4909 1.587054 AGGAACTCCTCGCTTGTCG 59.413 57.895 0.00 0.00 44.77 4.35
1923 4910 2.095252 GGAACTCCTCGCTTGTCGC 61.095 63.158 0.00 0.00 38.27 5.19
1924 4911 1.080434 GAACTCCTCGCTTGTCGCT 60.080 57.895 0.00 0.00 38.27 4.93
1952 5286 8.835160 GCGTTACATTATATACTACGAACTGAC 58.165 37.037 0.00 0.00 0.00 3.51
1983 5322 0.742990 ACCCACCATGATACGCAACG 60.743 55.000 0.00 0.00 0.00 4.10
1998 5337 2.123342 GCAACGATCTCCAGATCTTCG 58.877 52.381 13.51 11.29 46.58 3.79
1999 5338 2.480416 GCAACGATCTCCAGATCTTCGT 60.480 50.000 12.47 12.47 46.58 3.85
2000 5339 3.243101 GCAACGATCTCCAGATCTTCGTA 60.243 47.826 17.24 0.00 46.58 3.43
2001 5340 4.557695 GCAACGATCTCCAGATCTTCGTAT 60.558 45.833 17.24 7.47 46.58 3.06
2008 5347 9.841880 CGATCTCCAGATCTTCGTATTTAATTA 57.158 33.333 13.51 0.00 46.58 1.40
2027 5366 6.803154 AATTACACAAAGTACTCTGCCTTC 57.197 37.500 0.00 0.00 30.91 3.46
2029 5368 4.150897 ACACAAAGTACTCTGCCTTCAA 57.849 40.909 0.00 0.00 0.00 2.69
2042 5381 1.338200 GCCTTCAATCAGTCGACCAGT 60.338 52.381 13.01 0.00 0.00 4.00
2043 5382 2.872038 GCCTTCAATCAGTCGACCAGTT 60.872 50.000 13.01 1.27 0.00 3.16
2044 5383 3.616560 GCCTTCAATCAGTCGACCAGTTA 60.617 47.826 13.01 0.00 0.00 2.24
2045 5384 3.927142 CCTTCAATCAGTCGACCAGTTAC 59.073 47.826 13.01 0.00 0.00 2.50
2046 5385 3.211803 TCAATCAGTCGACCAGTTACG 57.788 47.619 13.01 0.00 0.00 3.18
2047 5386 1.654105 CAATCAGTCGACCAGTTACGC 59.346 52.381 13.01 0.00 0.00 4.42
2048 5387 0.885879 ATCAGTCGACCAGTTACGCA 59.114 50.000 13.01 0.00 0.00 5.24
2049 5388 0.669619 TCAGTCGACCAGTTACGCAA 59.330 50.000 13.01 0.00 0.00 4.85
2106 5457 2.165641 GCCGGCAGCTTTACCTTAAATT 59.834 45.455 24.80 0.00 38.99 1.82
2133 5484 1.029408 AGTGTGCTTTGTTGCCGTGA 61.029 50.000 0.00 0.00 0.00 4.35
2144 5495 6.565999 GCTTTGTTGCCGTGATATACTATTCC 60.566 42.308 0.00 0.00 0.00 3.01
2156 5507 9.461312 GTGATATACTATTCCCAAATGGCATTA 57.539 33.333 14.05 0.00 0.00 1.90
2177 5528 1.599047 CGATCCAGTGGCTGAACCT 59.401 57.895 3.51 0.00 40.22 3.50
2202 5553 0.110509 CTGCGCCATATCATTCGTGC 60.111 55.000 4.18 0.00 0.00 5.34
2244 5595 0.040425 GCACTTGCTAAACCGTGTGG 60.040 55.000 0.00 0.00 38.67 4.17
2272 5623 0.039888 GTTGTGCGCCGGTGTTTTAT 60.040 50.000 17.91 0.00 0.00 1.40
2273 5624 0.669077 TTGTGCGCCGGTGTTTTATT 59.331 45.000 17.91 0.00 0.00 1.40
2310 5661 2.764269 AGCATCCTAGTAAAGGGCTCA 58.236 47.619 0.00 0.00 46.55 4.26
2323 5674 1.003003 AGGGCTCAGCTGAAGAACTTC 59.997 52.381 18.85 7.51 39.91 3.01
2331 5682 3.077359 AGCTGAAGAACTTCGGAAATGG 58.923 45.455 22.55 4.37 46.23 3.16
2344 5695 2.556622 CGGAAATGGCTACAGTTTTGGT 59.443 45.455 0.00 0.00 34.65 3.67
2345 5696 3.611530 CGGAAATGGCTACAGTTTTGGTG 60.612 47.826 0.00 0.00 34.65 4.17
2346 5697 3.320826 GGAAATGGCTACAGTTTTGGTGT 59.679 43.478 0.00 0.00 34.65 4.16
2347 5698 4.521256 GGAAATGGCTACAGTTTTGGTGTA 59.479 41.667 0.00 0.00 34.65 2.90
2348 5699 5.335661 GGAAATGGCTACAGTTTTGGTGTAG 60.336 44.000 5.99 5.99 46.92 2.74
2358 5709 7.823745 ACAGTTTTGGTGTAGAGAATGATTT 57.176 32.000 0.00 0.00 0.00 2.17
2359 5710 7.651808 ACAGTTTTGGTGTAGAGAATGATTTG 58.348 34.615 0.00 0.00 0.00 2.32
2360 5711 7.086376 CAGTTTTGGTGTAGAGAATGATTTGG 58.914 38.462 0.00 0.00 0.00 3.28
2361 5712 6.777580 AGTTTTGGTGTAGAGAATGATTTGGT 59.222 34.615 0.00 0.00 0.00 3.67
2362 5713 7.287696 AGTTTTGGTGTAGAGAATGATTTGGTT 59.712 33.333 0.00 0.00 0.00 3.67
2363 5714 6.817765 TTGGTGTAGAGAATGATTTGGTTC 57.182 37.500 0.00 0.00 0.00 3.62
2364 5715 5.875224 TGGTGTAGAGAATGATTTGGTTCA 58.125 37.500 0.00 0.00 0.00 3.18
2365 5716 6.484288 TGGTGTAGAGAATGATTTGGTTCAT 58.516 36.000 0.00 0.00 37.96 2.57
2366 5717 6.599244 TGGTGTAGAGAATGATTTGGTTCATC 59.401 38.462 0.00 0.00 35.29 2.92
2367 5718 6.238211 GGTGTAGAGAATGATTTGGTTCATCG 60.238 42.308 0.00 0.00 35.29 3.84
2368 5719 6.535150 GTGTAGAGAATGATTTGGTTCATCGA 59.465 38.462 0.00 0.00 35.29 3.59
2369 5720 7.225538 GTGTAGAGAATGATTTGGTTCATCGAT 59.774 37.037 0.00 0.00 35.29 3.59
2370 5721 8.421002 TGTAGAGAATGATTTGGTTCATCGATA 58.579 33.333 0.00 0.00 35.29 2.92
2371 5722 9.261180 GTAGAGAATGATTTGGTTCATCGATAA 57.739 33.333 0.00 0.00 35.29 1.75
2372 5723 8.915057 AGAGAATGATTTGGTTCATCGATAAT 57.085 30.769 0.00 0.00 35.29 1.28
2373 5724 9.347240 AGAGAATGATTTGGTTCATCGATAATT 57.653 29.630 0.00 0.00 35.29 1.40
2374 5725 9.390795 GAGAATGATTTGGTTCATCGATAATTG 57.609 33.333 0.00 0.00 35.29 2.32
2375 5726 9.123902 AGAATGATTTGGTTCATCGATAATTGA 57.876 29.630 0.00 0.00 35.29 2.57
2376 5727 9.903682 GAATGATTTGGTTCATCGATAATTGAT 57.096 29.630 0.00 0.00 35.29 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.159338 CCAACTTGATCATCAAAGCCGG 60.159 50.000 0.75 0.00 35.73 6.13
41 42 1.069227 GGCCATTTCACTGTGTCGAAC 60.069 52.381 7.79 0.00 0.00 3.95
61 1216 0.681733 CTGGATCCCATGTAGTCGGG 59.318 60.000 9.90 0.00 44.60 5.14
62 1217 0.034059 GCTGGATCCCATGTAGTCGG 59.966 60.000 9.90 0.00 30.82 4.79
308 1463 2.042831 GCAGAACGGGCAAGCATCT 61.043 57.895 0.00 0.00 0.00 2.90
343 1498 1.629861 TCAGCAGGATGTGGTCAATGA 59.370 47.619 0.00 0.00 39.31 2.57
565 1720 0.457443 CTGTAGTGATGGAGCAGCGA 59.543 55.000 0.00 0.00 0.00 4.93
603 3483 0.962356 CAAGCCTTGCCTTCCGTGAT 60.962 55.000 0.00 0.00 0.00 3.06
640 3520 0.876342 GCTATCCACTTCGCCCTTCG 60.876 60.000 0.00 0.00 40.15 3.79
680 3560 3.117436 GGGACTACTCACTCTCTACCCAT 60.117 52.174 0.00 0.00 35.41 4.00
688 3568 1.951424 GCAGTCGGGACTACTCACTCT 60.951 57.143 0.21 0.00 40.20 3.24
709 3589 2.388232 CGCTCCACCTACAAACGCC 61.388 63.158 0.00 0.00 0.00 5.68
747 3628 1.202222 CGCCTGGACTCATGCATTTTC 60.202 52.381 0.00 0.00 34.78 2.29
748 3629 0.813184 CGCCTGGACTCATGCATTTT 59.187 50.000 0.00 0.00 34.78 1.82
749 3630 0.035152 TCGCCTGGACTCATGCATTT 60.035 50.000 0.00 0.00 34.78 2.32
750 3631 0.182061 ATCGCCTGGACTCATGCATT 59.818 50.000 0.00 0.00 34.78 3.56
751 3632 0.250209 GATCGCCTGGACTCATGCAT 60.250 55.000 0.00 0.00 34.78 3.96
762 3643 2.863853 CGTGACGCATGATCGCCTG 61.864 63.158 0.00 0.00 0.00 4.85
813 3694 4.524318 ATAGGAACGGCGCGTGGG 62.524 66.667 6.90 0.00 39.99 4.61
848 3729 2.963101 GGTGGGAATTTATAACCAGGGC 59.037 50.000 0.00 0.00 32.84 5.19
864 3759 1.694133 GGAGAGCTGGAGATGGTGGG 61.694 65.000 0.00 0.00 0.00 4.61
867 3762 1.062275 AGATGGAGAGCTGGAGATGGT 60.062 52.381 0.00 0.00 0.00 3.55
898 3793 4.568152 GTTGTAAACTGTGAATGCTGGT 57.432 40.909 0.00 0.00 45.32 4.00
921 3816 1.561643 TGGTGAGAGATGGTGAGGAC 58.438 55.000 0.00 0.00 0.00 3.85
925 3820 1.001974 CGGTTTGGTGAGAGATGGTGA 59.998 52.381 0.00 0.00 0.00 4.02
928 3823 2.472695 TTCGGTTTGGTGAGAGATGG 57.527 50.000 0.00 0.00 0.00 3.51
981 3877 1.014044 TTAGCTCGGTCGCTTGCTTG 61.014 55.000 0.00 0.00 41.30 4.01
1017 3913 3.077556 AAGGAGACGGCGGATGCT 61.078 61.111 13.24 6.85 42.25 3.79
1050 3946 1.586028 CCCGAAAGTCGTTCCCGTA 59.414 57.895 0.00 0.00 38.40 4.02
1226 4128 1.313129 GCCTTCTCCTCCTCCTCCT 59.687 63.158 0.00 0.00 0.00 3.69
1415 4333 3.411351 GTACACGCACGGGCACAG 61.411 66.667 11.77 0.00 41.24 3.66
1459 4377 2.430465 CACAGAAAGGACTGGGTGATG 58.570 52.381 0.00 0.00 41.59 3.07
1464 4382 3.866449 GCTCTAACACAGAAAGGACTGGG 60.866 52.174 0.00 0.00 45.62 4.45
1471 4389 7.542890 TCTCATCTAAGCTCTAACACAGAAAG 58.457 38.462 0.00 0.00 31.12 2.62
1473 4391 6.887002 TCTCTCATCTAAGCTCTAACACAGAA 59.113 38.462 0.00 0.00 31.12 3.02
1492 4426 4.952957 AGATCTCATTTCCGACTTCTCTCA 59.047 41.667 0.00 0.00 0.00 3.27
1499 4433 6.595716 CCTAAAACAAGATCTCATTTCCGACT 59.404 38.462 0.00 0.00 0.00 4.18
1516 4450 4.349365 GGGAATGGATCAACCCTAAAACA 58.651 43.478 0.00 0.00 39.28 2.83
1565 4499 2.870435 GCCTCTAAAACAAGCAGACCGA 60.870 50.000 0.00 0.00 0.00 4.69
1601 4535 1.151450 GGGACATGCGGGGAATCAT 59.849 57.895 0.00 0.00 0.00 2.45
1629 4598 7.170998 ACACAGAAACAATGCTAGTACAAGTAC 59.829 37.037 2.18 2.18 36.35 2.73
1637 4606 8.292448 CAGATTTAACACAGAAACAATGCTAGT 58.708 33.333 0.00 0.00 0.00 2.57
1640 4609 6.265196 TCCAGATTTAACACAGAAACAATGCT 59.735 34.615 0.00 0.00 0.00 3.79
1642 4611 8.517878 AGATCCAGATTTAACACAGAAACAATG 58.482 33.333 0.00 0.00 0.00 2.82
1644 4613 7.719193 TCAGATCCAGATTTAACACAGAAACAA 59.281 33.333 0.00 0.00 0.00 2.83
1645 4614 7.223584 TCAGATCCAGATTTAACACAGAAACA 58.776 34.615 0.00 0.00 0.00 2.83
1646 4615 7.672983 TCAGATCCAGATTTAACACAGAAAC 57.327 36.000 0.00 0.00 0.00 2.78
1647 4616 7.719193 TGTTCAGATCCAGATTTAACACAGAAA 59.281 33.333 0.00 0.00 0.00 2.52
1650 4619 6.652481 AGTGTTCAGATCCAGATTTAACACAG 59.348 38.462 22.24 0.00 44.66 3.66
1651 4620 6.427853 CAGTGTTCAGATCCAGATTTAACACA 59.572 38.462 22.24 6.58 44.66 3.72
1652 4621 6.650807 TCAGTGTTCAGATCCAGATTTAACAC 59.349 38.462 17.35 17.35 43.32 3.32
1653 4622 6.768483 TCAGTGTTCAGATCCAGATTTAACA 58.232 36.000 0.00 0.00 0.00 2.41
1654 4623 7.856145 ATCAGTGTTCAGATCCAGATTTAAC 57.144 36.000 0.00 0.00 0.00 2.01
1655 4624 9.958180 TTAATCAGTGTTCAGATCCAGATTTAA 57.042 29.630 0.00 0.00 0.00 1.52
1656 4625 9.958180 TTTAATCAGTGTTCAGATCCAGATTTA 57.042 29.630 0.00 0.00 0.00 1.40
1657 4626 8.868522 TTTAATCAGTGTTCAGATCCAGATTT 57.131 30.769 0.00 0.00 0.00 2.17
1658 4627 9.118300 GATTTAATCAGTGTTCAGATCCAGATT 57.882 33.333 0.00 0.00 0.00 2.40
1659 4628 8.492782 AGATTTAATCAGTGTTCAGATCCAGAT 58.507 33.333 7.74 0.00 0.00 2.90
1660 4629 7.767659 CAGATTTAATCAGTGTTCAGATCCAGA 59.232 37.037 7.74 0.00 0.00 3.86
1661 4630 7.551974 ACAGATTTAATCAGTGTTCAGATCCAG 59.448 37.037 7.74 0.00 0.00 3.86
1662 4631 7.397221 ACAGATTTAATCAGTGTTCAGATCCA 58.603 34.615 7.74 0.00 0.00 3.41
1663 4632 7.856145 ACAGATTTAATCAGTGTTCAGATCC 57.144 36.000 7.74 0.00 0.00 3.36
1666 4635 9.591792 CAGATACAGATTTAATCAGTGTTCAGA 57.408 33.333 12.27 0.00 31.17 3.27
1667 4636 9.591792 TCAGATACAGATTTAATCAGTGTTCAG 57.408 33.333 12.27 7.09 31.17 3.02
1668 4637 9.942850 TTCAGATACAGATTTAATCAGTGTTCA 57.057 29.630 12.27 0.00 31.17 3.18
1672 4641 9.994432 GGTTTTCAGATACAGATTTAATCAGTG 57.006 33.333 12.27 3.43 31.17 3.66
1673 4642 8.883731 CGGTTTTCAGATACAGATTTAATCAGT 58.116 33.333 7.74 7.89 33.38 3.41
1674 4643 9.098355 TCGGTTTTCAGATACAGATTTAATCAG 57.902 33.333 7.74 1.67 0.00 2.90
1675 4644 9.613428 ATCGGTTTTCAGATACAGATTTAATCA 57.387 29.630 7.74 0.00 33.29 2.57
1682 4651 9.838339 AGATTTAATCGGTTTTCAGATACAGAT 57.162 29.630 0.00 0.00 33.89 2.90
1683 4652 9.098355 CAGATTTAATCGGTTTTCAGATACAGA 57.902 33.333 0.00 0.00 33.89 3.41
1684 4653 8.338259 CCAGATTTAATCGGTTTTCAGATACAG 58.662 37.037 4.57 0.00 33.89 2.74
1687 4656 9.273016 GATCCAGATTTAATCGGTTTTCAGATA 57.727 33.333 12.76 0.00 33.89 1.98
1695 4664 6.414732 TGTTCAGATCCAGATTTAATCGGTT 58.585 36.000 12.76 7.17 0.00 4.44
1705 4674 4.321718 CGCCATAATGTTCAGATCCAGAT 58.678 43.478 0.00 0.00 0.00 2.90
1735 4709 7.607250 AGTATAGTTTGTTGAGGAGAAGACAG 58.393 38.462 0.00 0.00 0.00 3.51
1781 4755 3.115390 AGGTGCATCATACTGTTAGGGT 58.885 45.455 0.00 0.00 0.00 4.34
1790 4764 8.190122 TGTTTTTGATTCATAGGTGCATCATAC 58.810 33.333 0.00 0.00 37.73 2.39
1800 4774 9.403110 GCAGCTATAATGTTTTTGATTCATAGG 57.597 33.333 0.00 0.00 0.00 2.57
1805 4784 8.481132 CGTAGCAGCTATAATGTTTTTGATTC 57.519 34.615 5.14 0.00 0.00 2.52
1839 4822 5.067283 ACAATCAACTTGTGAAGGTTGGTAC 59.933 40.000 0.00 0.00 46.37 3.34
1886 4873 6.879400 AGTTCCTTTCACATAGACATAGTCC 58.121 40.000 0.00 0.00 32.18 3.85
1918 4905 6.210796 AGTATATAATGTAACGCAAGCGACA 58.789 36.000 22.30 15.80 42.83 4.35
1919 4906 6.686130 AGTATATAATGTAACGCAAGCGAC 57.314 37.500 22.30 10.30 42.83 5.19
1920 4907 6.520790 CGTAGTATATAATGTAACGCAAGCGA 59.479 38.462 22.30 0.00 42.83 4.93
1921 4908 6.520790 TCGTAGTATATAATGTAACGCAAGCG 59.479 38.462 13.50 13.50 46.03 4.68
1922 4909 7.786305 TCGTAGTATATAATGTAACGCAAGC 57.214 36.000 0.00 0.00 45.62 4.01
1924 4911 9.172820 CAGTTCGTAGTATATAATGTAACGCAA 57.827 33.333 0.00 0.00 0.00 4.85
1952 5286 0.037017 TGGTGGGTGGTAATGGTTCG 59.963 55.000 0.00 0.00 0.00 3.95
1998 5337 9.983804 GGCAGAGTACTTTGTGTAATTAAATAC 57.016 33.333 14.34 0.00 32.25 1.89
1999 5338 9.953565 AGGCAGAGTACTTTGTGTAATTAAATA 57.046 29.630 14.34 0.00 32.25 1.40
2000 5339 8.863872 AGGCAGAGTACTTTGTGTAATTAAAT 57.136 30.769 14.34 0.00 32.25 1.40
2001 5340 8.685838 AAGGCAGAGTACTTTGTGTAATTAAA 57.314 30.769 14.34 0.00 32.25 1.52
2008 5347 3.838244 TGAAGGCAGAGTACTTTGTGT 57.162 42.857 14.34 0.22 0.00 3.72
2027 5366 1.654105 GCGTAACTGGTCGACTGATTG 59.346 52.381 16.46 4.13 0.00 2.67
2029 5368 0.885879 TGCGTAACTGGTCGACTGAT 59.114 50.000 16.46 6.34 0.00 2.90
2047 5386 3.078837 ACTACTACCGGGCAAACAATTG 58.921 45.455 6.32 3.24 39.65 2.32
2048 5387 3.428413 ACTACTACCGGGCAAACAATT 57.572 42.857 6.32 0.00 0.00 2.32
2049 5388 4.162698 TGATACTACTACCGGGCAAACAAT 59.837 41.667 6.32 0.00 0.00 2.71
2133 5484 8.525290 GCTAATGCCATTTGGGAATAGTATAT 57.475 34.615 12.91 0.00 40.07 0.86
2159 5510 0.742281 CAGGTTCAGCCACTGGATCG 60.742 60.000 0.00 0.00 40.61 3.69
2161 5512 0.037303 CACAGGTTCAGCCACTGGAT 59.963 55.000 0.00 0.00 40.61 3.41
2163 5514 1.601759 CCACAGGTTCAGCCACTGG 60.602 63.158 0.00 0.00 40.61 4.00
2166 5517 2.985847 GCCCACAGGTTCAGCCAC 60.986 66.667 0.00 0.00 40.61 5.01
2214 5565 2.945984 CAAGTGCCATCGTGCGTT 59.054 55.556 0.00 0.00 0.00 4.84
2220 5571 0.096976 CGGTTTAGCAAGTGCCATCG 59.903 55.000 0.00 0.00 43.38 3.84
2225 5576 0.040425 CCACACGGTTTAGCAAGTGC 60.040 55.000 0.00 0.00 38.08 4.40
2244 5595 1.369568 GGCGCACAACGGTTAACAC 60.370 57.895 10.83 0.00 43.93 3.32
2254 5605 0.669077 AATAAAACACCGGCGCACAA 59.331 45.000 10.83 0.00 0.00 3.33
2272 5623 1.792949 GCTTCGCGAGACAGAAGAAAA 59.207 47.619 9.59 0.00 44.76 2.29
2273 5624 1.269569 TGCTTCGCGAGACAGAAGAAA 60.270 47.619 9.59 0.00 44.76 2.52
2302 5653 1.063183 AGTTCTTCAGCTGAGCCCTT 58.937 50.000 17.43 1.41 0.00 3.95
2304 5655 1.447945 GAAGTTCTTCAGCTGAGCCC 58.552 55.000 17.43 6.58 0.00 5.19
2310 5661 3.077359 CCATTTCCGAAGTTCTTCAGCT 58.923 45.455 12.15 0.00 0.00 4.24
2323 5674 2.556622 ACCAAAACTGTAGCCATTTCCG 59.443 45.455 0.00 0.00 0.00 4.30
2331 5682 5.932303 TCATTCTCTACACCAAAACTGTAGC 59.068 40.000 1.41 0.00 40.62 3.58
2344 5695 6.639563 TCGATGAACCAAATCATTCTCTACA 58.360 36.000 0.00 0.00 40.08 2.74
2345 5696 7.721286 ATCGATGAACCAAATCATTCTCTAC 57.279 36.000 0.00 0.00 40.08 2.59
2347 5698 8.915057 ATTATCGATGAACCAAATCATTCTCT 57.085 30.769 8.54 0.00 40.08 3.10
2348 5699 9.390795 CAATTATCGATGAACCAAATCATTCTC 57.609 33.333 8.54 0.00 40.08 2.87
2349 5700 9.123902 TCAATTATCGATGAACCAAATCATTCT 57.876 29.630 8.54 0.00 40.08 2.40
2350 5701 9.903682 ATCAATTATCGATGAACCAAATCATTC 57.096 29.630 8.54 0.00 40.08 2.67


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

AutoCloner maintained by Alex Coulton.