Multiple sequence alignment - TraesCS4B01G208100

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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 TraesCS4B01G208100 chr4B 100.000 2300 0 0 1 2300 445239604 445241903 0.000000e+00 4248.0
1 TraesCS4B01G208100 chr4B 100.000 44 0 0 628 671 33742725 33742682 5.270000e-12 82.4
2 TraesCS4B01G208100 chr4B 100.000 44 0 0 628 671 70484384 70484427 5.270000e-12 82.4
3 TraesCS4B01G208100 chr4B 100.000 31 0 0 705 735 88371376 88371406 8.880000e-05 58.4
4 TraesCS4B01G208100 chr4B 87.755 49 2 3 705 751 660751702 660751656 1.000000e-03 54.7
5 TraesCS4B01G208100 chr4D 91.050 1419 62 27 767 2137 360467483 360468884 0.000000e+00 1857.0
6 TraesCS4B01G208100 chr4D 88.991 109 5 4 2181 2285 360469150 360469255 6.670000e-26 128.0
7 TraesCS4B01G208100 chr4D 100.000 45 0 0 627 671 464227339 464227295 1.460000e-12 84.2
8 TraesCS4B01G208100 chr4A 88.693 1592 77 44 756 2285 104391869 104390319 0.000000e+00 1847.0
9 TraesCS4B01G208100 chr4A 100.000 31 0 0 705 735 494458979 494459009 8.880000e-05 58.4
10 TraesCS4B01G208100 chr3B 94.612 631 32 2 1 629 155596365 155596995 0.000000e+00 976.0
11 TraesCS4B01G208100 chr3B 93.839 633 36 3 1 631 150272555 150271924 0.000000e+00 950.0
12 TraesCS4B01G208100 chr3B 93.810 630 36 3 1 628 154443183 154442555 0.000000e+00 944.0
13 TraesCS4B01G208100 chr1B 94.603 630 32 2 1 628 272894328 272894957 0.000000e+00 974.0
14 TraesCS4B01G208100 chr1B 94.089 626 34 3 1 624 26831273 26831897 0.000000e+00 948.0
15 TraesCS4B01G208100 chr1B 100.000 45 0 0 626 670 644547511 644547555 1.460000e-12 84.2
16 TraesCS4B01G208100 chr1B 93.023 43 2 1 705 747 644292064 644292105 6.860000e-06 62.1
17 TraesCS4B01G208100 chr1B 94.595 37 2 0 706 742 333785976 333786012 8.880000e-05 58.4
18 TraesCS4B01G208100 chr1B 86.538 52 3 4 705 756 500697187 500697140 1.000000e-03 54.7
19 TraesCS4B01G208100 chr2B 94.595 629 31 3 1 626 123153461 123152833 0.000000e+00 970.0
20 TraesCS4B01G208100 chr2B 100.000 45 0 0 627 671 36692742 36692786 1.460000e-12 84.2
21 TraesCS4B01G208100 chr2B 95.833 48 1 1 625 672 691182673 691182719 2.450000e-10 76.8
22 TraesCS4B01G208100 chr2B 96.970 33 1 0 705 737 31429651 31429683 3.190000e-04 56.5
23 TraesCS4B01G208100 chrUn 93.839 633 36 3 1 631 233141592 233140961 0.000000e+00 950.0
24 TraesCS4B01G208100 chr7B 93.939 627 35 2 1 624 376805962 376805336 0.000000e+00 944.0
25 TraesCS4B01G208100 chr7B 92.331 652 46 4 1 649 47731480 47732130 0.000000e+00 924.0
26 TraesCS4B01G208100 chr3A 97.872 47 1 0 625 671 625037784 625037830 5.270000e-12 82.4
27 TraesCS4B01G208100 chr3A 100.000 31 0 0 705 735 65962997 65963027 8.880000e-05 58.4
28 TraesCS4B01G208100 chr1A 97.872 47 1 0 625 671 557124510 557124556 5.270000e-12 82.4
29 TraesCS4B01G208100 chr5D 86.486 74 8 2 1226 1297 99418595 99418522 1.890000e-11 80.5
30 TraesCS4B01G208100 chr5A 86.301 73 10 0 1220 1292 103569263 103569335 1.890000e-11 80.5
31 TraesCS4B01G208100 chr2A 94.444 36 1 1 703 737 429933209 429933174 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 TraesCS4B01G208100 chr4B 445239604 445241903 2299 False 4248.0 4248 100.0000 1 2300 1 chr4B.!!$F3 2299
1 TraesCS4B01G208100 chr4D 360467483 360469255 1772 False 992.5 1857 90.0205 767 2285 2 chr4D.!!$F1 1518
2 TraesCS4B01G208100 chr4A 104390319 104391869 1550 True 1847.0 1847 88.6930 756 2285 1 chr4A.!!$R1 1529
3 TraesCS4B01G208100 chr3B 155596365 155596995 630 False 976.0 976 94.6120 1 629 1 chr3B.!!$F1 628
4 TraesCS4B01G208100 chr3B 150271924 150272555 631 True 950.0 950 93.8390 1 631 1 chr3B.!!$R1 630
5 TraesCS4B01G208100 chr3B 154442555 154443183 628 True 944.0 944 93.8100 1 628 1 chr3B.!!$R2 627
6 TraesCS4B01G208100 chr1B 272894328 272894957 629 False 974.0 974 94.6030 1 628 1 chr1B.!!$F2 627
7 TraesCS4B01G208100 chr1B 26831273 26831897 624 False 948.0 948 94.0890 1 624 1 chr1B.!!$F1 623
8 TraesCS4B01G208100 chr2B 123152833 123153461 628 True 970.0 970 94.5950 1 626 1 chr2B.!!$R1 625
9 TraesCS4B01G208100 chrUn 233140961 233141592 631 True 950.0 950 93.8390 1 631 1 chrUn.!!$R1 630
10 TraesCS4B01G208100 chr7B 376805336 376805962 626 True 944.0 944 93.9390 1 624 1 chr7B.!!$R1 623
11 TraesCS4B01G208100 chr7B 47731480 47732130 650 False 924.0 924 92.3310 1 649 1 chr7B.!!$F1 648

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
740 746 0.036388 CGACCAGCCTTAAGCCTCAA 60.036 55.0 0.0 0.0 45.47 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2256 0.036294 GAACTGTGGAGGGCCTGTAC 60.036 60.0 12.95 10.58 34.31 2.9 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
37 38 6.710597 TCGGATTAGACTAGTTGTGCTAAT 57.289 37.500 12.15 12.15 34.66 1.73
200 201 5.366768 TGTTGTTAGATTAGAGGCTAGGCAT 59.633 40.000 19.70 9.13 0.00 4.40
330 332 2.427506 CCAACTCAAGGGAGCAGTTAC 58.572 52.381 0.00 0.00 45.42 2.50
573 579 1.078347 ATTGCCCACCCAAACGGAT 59.922 52.632 0.00 0.00 34.64 4.18
593 599 5.368989 GGATAGAATCCGGACAAAACAGAT 58.631 41.667 6.12 0.00 40.13 2.90
605 611 5.997385 GACAAAACAGATGTCCGTTTATGT 58.003 37.500 0.00 3.35 41.02 2.29
633 639 2.488153 GGTGGAGTTGGCTTTATGACAC 59.512 50.000 0.00 0.00 30.21 3.67
634 640 2.488153 GTGGAGTTGGCTTTATGACACC 59.512 50.000 0.00 0.00 30.21 4.16
639 645 4.265073 AGTTGGCTTTATGACACCTCATC 58.735 43.478 0.00 0.00 38.21 2.92
641 647 4.299586 TGGCTTTATGACACCTCATCAA 57.700 40.909 0.00 0.00 38.21 2.57
643 649 5.076182 TGGCTTTATGACACCTCATCAAAA 58.924 37.500 0.00 0.00 38.21 2.44
644 650 5.716228 TGGCTTTATGACACCTCATCAAAAT 59.284 36.000 0.00 0.00 38.21 1.82
649 655 5.733620 ATGACACCTCATCAAAATTGCTT 57.266 34.783 0.00 0.00 30.64 3.91
650 656 6.839124 ATGACACCTCATCAAAATTGCTTA 57.161 33.333 0.00 0.00 30.64 3.09
651 657 6.258230 TGACACCTCATCAAAATTGCTTAG 57.742 37.500 0.00 0.00 0.00 2.18
652 658 5.769662 TGACACCTCATCAAAATTGCTTAGT 59.230 36.000 0.00 0.00 0.00 2.24
653 659 6.265196 TGACACCTCATCAAAATTGCTTAGTT 59.735 34.615 0.00 0.00 0.00 2.24
654 660 6.449698 ACACCTCATCAAAATTGCTTAGTTG 58.550 36.000 0.00 0.00 0.00 3.16
655 661 5.865552 CACCTCATCAAAATTGCTTAGTTGG 59.134 40.000 0.00 0.00 0.00 3.77
656 662 4.866486 CCTCATCAAAATTGCTTAGTTGGC 59.134 41.667 0.00 0.00 0.00 4.52
657 663 5.465532 TCATCAAAATTGCTTAGTTGGCA 57.534 34.783 0.00 0.00 37.97 4.92
658 664 6.040209 TCATCAAAATTGCTTAGTTGGCAT 57.960 33.333 0.00 0.00 39.54 4.40
659 665 5.870433 TCATCAAAATTGCTTAGTTGGCATG 59.130 36.000 0.00 0.00 39.54 4.06
660 666 3.995705 TCAAAATTGCTTAGTTGGCATGC 59.004 39.130 9.90 9.90 39.54 4.06
661 667 3.681593 AAATTGCTTAGTTGGCATGCA 57.318 38.095 21.36 2.54 39.54 3.96
662 668 3.899052 AATTGCTTAGTTGGCATGCAT 57.101 38.095 21.36 4.57 39.54 3.96
663 669 2.658373 TTGCTTAGTTGGCATGCATG 57.342 45.000 22.70 22.70 39.54 4.06
664 670 1.836802 TGCTTAGTTGGCATGCATGA 58.163 45.000 30.64 7.50 34.56 3.07
665 671 2.380941 TGCTTAGTTGGCATGCATGAT 58.619 42.857 30.64 11.73 34.56 2.45
666 672 3.553904 TGCTTAGTTGGCATGCATGATA 58.446 40.909 30.64 14.66 34.56 2.15
667 673 3.316029 TGCTTAGTTGGCATGCATGATAC 59.684 43.478 30.64 21.28 34.56 2.24
668 674 3.567164 GCTTAGTTGGCATGCATGATACT 59.433 43.478 30.64 26.11 0.00 2.12
669 675 4.756642 GCTTAGTTGGCATGCATGATACTA 59.243 41.667 30.64 25.19 0.00 1.82
670 676 5.334414 GCTTAGTTGGCATGCATGATACTAC 60.334 44.000 30.64 22.16 0.00 2.73
671 677 4.428294 AGTTGGCATGCATGATACTACT 57.572 40.909 30.64 23.73 0.00 2.57
672 678 4.384056 AGTTGGCATGCATGATACTACTC 58.616 43.478 30.64 9.40 0.00 2.59
673 679 4.129380 GTTGGCATGCATGATACTACTCA 58.871 43.478 30.64 10.71 0.00 3.41
674 680 3.732212 TGGCATGCATGATACTACTCAC 58.268 45.455 30.64 7.92 0.00 3.51
675 681 3.070018 GGCATGCATGATACTACTCACC 58.930 50.000 30.64 13.33 0.00 4.02
676 682 3.070018 GCATGCATGATACTACTCACCC 58.930 50.000 30.64 3.61 0.00 4.61
677 683 3.244353 GCATGCATGATACTACTCACCCT 60.244 47.826 30.64 0.00 0.00 4.34
678 684 4.564041 CATGCATGATACTACTCACCCTC 58.436 47.826 22.59 0.00 0.00 4.30
679 685 3.916035 TGCATGATACTACTCACCCTCT 58.084 45.455 0.00 0.00 0.00 3.69
680 686 4.290093 TGCATGATACTACTCACCCTCTT 58.710 43.478 0.00 0.00 0.00 2.85
681 687 5.454966 TGCATGATACTACTCACCCTCTTA 58.545 41.667 0.00 0.00 0.00 2.10
682 688 5.897250 TGCATGATACTACTCACCCTCTTAA 59.103 40.000 0.00 0.00 0.00 1.85
683 689 6.382859 TGCATGATACTACTCACCCTCTTAAA 59.617 38.462 0.00 0.00 0.00 1.52
684 690 7.093068 TGCATGATACTACTCACCCTCTTAAAA 60.093 37.037 0.00 0.00 0.00 1.52
685 691 7.934120 GCATGATACTACTCACCCTCTTAAAAT 59.066 37.037 0.00 0.00 0.00 1.82
694 700 8.943909 ACTCACCCTCTTAAAATATTAGAACG 57.056 34.615 0.00 0.00 0.00 3.95
695 701 8.537858 ACTCACCCTCTTAAAATATTAGAACGT 58.462 33.333 0.00 0.00 0.00 3.99
696 702 9.379791 CTCACCCTCTTAAAATATTAGAACGTT 57.620 33.333 0.00 0.00 0.00 3.99
697 703 9.729281 TCACCCTCTTAAAATATTAGAACGTTT 57.271 29.630 0.46 0.00 0.00 3.60
713 719 9.701098 TTAGAACGTTTTTGACACTATGATACT 57.299 29.630 0.46 0.00 0.00 2.12
715 721 9.136952 AGAACGTTTTTGACACTATGATACTAC 57.863 33.333 0.46 0.00 0.00 2.73
716 722 7.823149 ACGTTTTTGACACTATGATACTACC 57.177 36.000 0.00 0.00 0.00 3.18
717 723 7.380536 ACGTTTTTGACACTATGATACTACCA 58.619 34.615 0.00 0.00 0.00 3.25
718 724 8.038944 ACGTTTTTGACACTATGATACTACCAT 58.961 33.333 0.00 0.00 0.00 3.55
719 725 8.879759 CGTTTTTGACACTATGATACTACCATT 58.120 33.333 0.00 0.00 0.00 3.16
722 728 9.524106 TTTTGACACTATGATACTACCATTACG 57.476 33.333 0.00 0.00 0.00 3.18
723 729 8.454570 TTGACACTATGATACTACCATTACGA 57.545 34.615 0.00 0.00 0.00 3.43
724 730 7.868775 TGACACTATGATACTACCATTACGAC 58.131 38.462 0.00 0.00 0.00 4.34
725 731 7.040892 TGACACTATGATACTACCATTACGACC 60.041 40.741 0.00 0.00 0.00 4.79
726 732 6.774170 ACACTATGATACTACCATTACGACCA 59.226 38.462 0.00 0.00 0.00 4.02
727 733 7.040617 ACACTATGATACTACCATTACGACCAG 60.041 40.741 0.00 0.00 0.00 4.00
728 734 4.579454 TGATACTACCATTACGACCAGC 57.421 45.455 0.00 0.00 0.00 4.85
729 735 3.319972 TGATACTACCATTACGACCAGCC 59.680 47.826 0.00 0.00 0.00 4.85
730 736 1.861982 ACTACCATTACGACCAGCCT 58.138 50.000 0.00 0.00 0.00 4.58
731 737 2.185387 ACTACCATTACGACCAGCCTT 58.815 47.619 0.00 0.00 0.00 4.35
732 738 3.368248 ACTACCATTACGACCAGCCTTA 58.632 45.455 0.00 0.00 0.00 2.69
733 739 3.770933 ACTACCATTACGACCAGCCTTAA 59.229 43.478 0.00 0.00 0.00 1.85
734 740 3.261981 ACCATTACGACCAGCCTTAAG 57.738 47.619 0.00 0.00 0.00 1.85
735 741 1.940613 CCATTACGACCAGCCTTAAGC 59.059 52.381 0.00 0.00 44.25 3.09
736 742 1.940613 CATTACGACCAGCCTTAAGCC 59.059 52.381 0.00 0.00 45.47 4.35
737 743 1.272807 TTACGACCAGCCTTAAGCCT 58.727 50.000 0.00 0.00 45.47 4.58
738 744 0.822164 TACGACCAGCCTTAAGCCTC 59.178 55.000 0.00 0.00 45.47 4.70
739 745 1.192146 ACGACCAGCCTTAAGCCTCA 61.192 55.000 0.00 0.00 45.47 3.86
740 746 0.036388 CGACCAGCCTTAAGCCTCAA 60.036 55.000 0.00 0.00 45.47 3.02
741 747 1.743996 GACCAGCCTTAAGCCTCAAG 58.256 55.000 0.00 0.00 45.47 3.02
742 748 1.279271 GACCAGCCTTAAGCCTCAAGA 59.721 52.381 0.00 0.00 45.47 3.02
743 749 1.705186 ACCAGCCTTAAGCCTCAAGAA 59.295 47.619 0.00 0.00 45.47 2.52
744 750 2.087646 CCAGCCTTAAGCCTCAAGAAC 58.912 52.381 0.00 0.00 45.47 3.01
745 751 2.553028 CCAGCCTTAAGCCTCAAGAACA 60.553 50.000 0.00 0.00 45.47 3.18
746 752 3.149196 CAGCCTTAAGCCTCAAGAACAA 58.851 45.455 0.00 0.00 45.47 2.83
747 753 3.190118 CAGCCTTAAGCCTCAAGAACAAG 59.810 47.826 0.00 0.00 45.47 3.16
748 754 2.095008 GCCTTAAGCCTCAAGAACAAGC 60.095 50.000 0.00 0.00 34.35 4.01
749 755 3.149196 CCTTAAGCCTCAAGAACAAGCA 58.851 45.455 0.00 0.00 0.00 3.91
750 756 3.760684 CCTTAAGCCTCAAGAACAAGCAT 59.239 43.478 0.00 0.00 0.00 3.79
751 757 4.380233 CCTTAAGCCTCAAGAACAAGCATG 60.380 45.833 0.00 0.00 0.00 4.06
752 758 2.574006 AGCCTCAAGAACAAGCATGA 57.426 45.000 0.00 0.00 0.00 3.07
753 759 3.083122 AGCCTCAAGAACAAGCATGAT 57.917 42.857 0.00 0.00 0.00 2.45
754 760 3.428532 AGCCTCAAGAACAAGCATGATT 58.571 40.909 0.00 0.00 0.00 2.57
783 789 1.068895 TGCAAAATCAACAGGTGCCAG 59.931 47.619 0.00 0.00 34.25 4.85
799 806 4.307432 GTGCCAGCATAATCTGTATACGT 58.693 43.478 0.00 0.00 32.32 3.57
803 810 7.117812 GTGCCAGCATAATCTGTATACGTAAAT 59.882 37.037 0.00 0.00 32.32 1.40
928 950 1.450312 CCTCGCACTCCCCACATTC 60.450 63.158 0.00 0.00 0.00 2.67
966 989 2.125225 ACTTCACCCTCCCCTCCC 59.875 66.667 0.00 0.00 0.00 4.30
967 990 2.692741 CTTCACCCTCCCCTCCCC 60.693 72.222 0.00 0.00 0.00 4.81
968 991 4.364686 TTCACCCTCCCCTCCCCC 62.365 72.222 0.00 0.00 0.00 5.40
980 1003 1.819632 CTCCCCCGCAAGCATACAC 60.820 63.158 0.00 0.00 0.00 2.90
982 1005 2.272146 CCCCGCAAGCATACACCT 59.728 61.111 0.00 0.00 0.00 4.00
984 1007 1.078497 CCCGCAAGCATACACCTCA 60.078 57.895 0.00 0.00 0.00 3.86
985 1008 1.091771 CCCGCAAGCATACACCTCAG 61.092 60.000 0.00 0.00 0.00 3.35
986 1009 1.091771 CCGCAAGCATACACCTCAGG 61.092 60.000 0.00 0.00 0.00 3.86
987 1010 1.091771 CGCAAGCATACACCTCAGGG 61.092 60.000 0.00 0.00 38.88 4.45
1013 1041 3.270877 GCAAATCCATGGAGTTCTACGT 58.729 45.455 24.05 0.00 29.47 3.57
1136 1167 2.833913 CCAGCACAAGGGACCAGGT 61.834 63.158 0.00 0.00 0.00 4.00
1209 1243 2.881352 CCTTCGTTCTCGAGCCGC 60.881 66.667 7.81 0.00 46.81 6.53
1260 1294 1.835483 GCTTCTACATCATGCGCCGG 61.835 60.000 4.18 0.00 0.00 6.13
1633 1689 3.885976 TGGGGGATCTTGTTGTTGTTA 57.114 42.857 0.00 0.00 0.00 2.41
1731 1800 7.047271 GCTGAAATCTAGTGGATCTTCTTCTT 58.953 38.462 0.00 0.00 32.76 2.52
1734 1803 9.480861 TGAAATCTAGTGGATCTTCTTCTTCTA 57.519 33.333 0.00 0.00 32.76 2.10
1806 1885 9.817809 GATGTATAGGTAAAGAAATGAGACACA 57.182 33.333 0.00 0.00 0.00 3.72
1814 1893 7.920682 GGTAAAGAAATGAGACACAACAACATT 59.079 33.333 0.00 0.00 33.50 2.71
1815 1894 7.992180 AAAGAAATGAGACACAACAACATTC 57.008 32.000 0.00 0.00 32.02 2.67
1816 1895 6.949352 AGAAATGAGACACAACAACATTCT 57.051 33.333 0.00 0.00 32.02 2.40
1817 1896 6.732154 AGAAATGAGACACAACAACATTCTG 58.268 36.000 0.00 0.00 32.02 3.02
1819 1898 4.880886 TGAGACACAACAACATTCTGTG 57.119 40.909 0.08 0.08 44.81 3.66
1820 1899 3.065233 TGAGACACAACAACATTCTGTGC 59.935 43.478 1.50 0.00 43.42 4.57
1822 1901 3.313526 AGACACAACAACATTCTGTGCTC 59.686 43.478 1.50 0.22 43.42 4.26
1826 1909 2.191128 ACAACATTCTGTGCTCCTCC 57.809 50.000 0.00 0.00 0.00 4.30
1857 1940 4.142071 CCTCCTCGATCTTGTCATTTCTCA 60.142 45.833 0.00 0.00 0.00 3.27
1911 1996 1.364626 GAGAGGCGCAAGTGGACATG 61.365 60.000 10.83 0.00 41.68 3.21
1917 2002 0.036952 CGCAAGTGGACATGAGAGGT 60.037 55.000 0.00 0.00 0.00 3.85
1930 2015 6.464892 GGACATGAGAGGTATCAAATGGATGA 60.465 42.308 0.00 0.00 36.72 2.92
1931 2016 6.294473 ACATGAGAGGTATCAAATGGATGAC 58.706 40.000 0.00 0.00 36.72 3.06
1971 2056 1.638529 AGAGAAGAGTGGTGGTGAGG 58.361 55.000 0.00 0.00 0.00 3.86
2011 2097 1.414866 GGATCAGGGAGGGAGAAGGC 61.415 65.000 0.00 0.00 0.00 4.35
2119 2219 0.740737 GCCACTCCATTATTGCGCTT 59.259 50.000 9.73 0.00 0.00 4.68
2120 2220 1.534595 GCCACTCCATTATTGCGCTTG 60.535 52.381 9.73 0.00 0.00 4.01
2121 2221 1.534595 CCACTCCATTATTGCGCTTGC 60.535 52.381 9.73 0.00 39.78 4.01
2122 2222 1.402968 CACTCCATTATTGCGCTTGCT 59.597 47.619 9.73 0.00 40.12 3.91
2123 2223 1.402968 ACTCCATTATTGCGCTTGCTG 59.597 47.619 9.73 0.00 40.12 4.41
2124 2224 0.101040 TCCATTATTGCGCTTGCTGC 59.899 50.000 9.73 0.00 40.12 5.25
2125 2225 0.872881 CCATTATTGCGCTTGCTGCC 60.873 55.000 9.73 0.00 40.12 4.85
2126 2226 0.872881 CATTATTGCGCTTGCTGCCC 60.873 55.000 9.73 0.00 40.12 5.36
2127 2227 2.019897 ATTATTGCGCTTGCTGCCCC 62.020 55.000 9.73 0.00 40.12 5.80
2147 2247 1.599576 GTCCCTCACCCTCAGCTTC 59.400 63.158 0.00 0.00 0.00 3.86
2152 2252 0.534412 CTCACCCTCAGCTTCGACAT 59.466 55.000 0.00 0.00 0.00 3.06
2153 2253 0.247460 TCACCCTCAGCTTCGACATG 59.753 55.000 0.00 0.00 0.00 3.21
2154 2254 1.078848 ACCCTCAGCTTCGACATGC 60.079 57.895 0.00 0.00 0.00 4.06
2155 2255 1.078918 CCCTCAGCTTCGACATGCA 60.079 57.895 0.00 0.00 0.00 3.96
2156 2256 1.088340 CCCTCAGCTTCGACATGCAG 61.088 60.000 0.00 0.00 0.00 4.41
2157 2257 0.390866 CCTCAGCTTCGACATGCAGT 60.391 55.000 0.00 0.00 0.00 4.40
2158 2258 1.134995 CCTCAGCTTCGACATGCAGTA 60.135 52.381 0.00 0.00 0.00 2.74
2159 2259 1.923204 CTCAGCTTCGACATGCAGTAC 59.077 52.381 0.00 0.00 0.00 2.73
2160 2260 1.272212 TCAGCTTCGACATGCAGTACA 59.728 47.619 0.00 0.00 0.00 2.90
2161 2261 1.657594 CAGCTTCGACATGCAGTACAG 59.342 52.381 0.00 0.00 0.00 2.74
2162 2262 1.002366 GCTTCGACATGCAGTACAGG 58.998 55.000 0.00 0.00 35.74 4.00
2163 2263 1.002366 CTTCGACATGCAGTACAGGC 58.998 55.000 0.00 0.00 31.69 4.85
2164 2264 0.391130 TTCGACATGCAGTACAGGCC 60.391 55.000 0.00 0.00 31.69 5.19
2166 2266 1.604378 GACATGCAGTACAGGCCCT 59.396 57.895 0.00 0.00 31.69 5.19
2167 2267 0.462759 GACATGCAGTACAGGCCCTC 60.463 60.000 0.00 0.00 31.69 4.30
2168 2268 1.153086 CATGCAGTACAGGCCCTCC 60.153 63.158 0.00 0.00 0.00 4.30
2170 2270 1.915078 ATGCAGTACAGGCCCTCCAC 61.915 60.000 0.00 0.00 33.74 4.02
2171 2271 2.592993 GCAGTACAGGCCCTCCACA 61.593 63.158 0.00 0.00 33.74 4.17
2172 2272 1.599047 CAGTACAGGCCCTCCACAG 59.401 63.158 0.00 0.00 33.74 3.66
2174 2274 0.473886 AGTACAGGCCCTCCACAGTT 60.474 55.000 0.00 0.00 33.74 3.16
2175 2275 0.036294 GTACAGGCCCTCCACAGTTC 60.036 60.000 0.00 0.00 33.74 3.01
2212 2541 6.380079 AAACAGAGTGACCCAGAGAAATAT 57.620 37.500 0.00 0.00 0.00 1.28
2218 2551 4.009675 GTGACCCAGAGAAATATGCACAA 58.990 43.478 0.00 0.00 0.00 3.33
2228 2561 4.891168 AGAAATATGCACAATCAGCCATGA 59.109 37.500 0.00 0.00 40.50 3.07
2230 2563 4.783764 ATATGCACAATCAGCCATGATG 57.216 40.909 0.00 0.00 45.67 3.07
2244 2577 2.355412 CCATGATGAGTGCCTCACTTGA 60.355 50.000 7.00 0.00 45.44 3.02
2245 2578 2.756840 TGATGAGTGCCTCACTTGAG 57.243 50.000 7.00 0.00 45.44 3.02
2246 2579 2.250924 TGATGAGTGCCTCACTTGAGA 58.749 47.619 7.87 0.00 45.44 3.27
2286 2622 3.620785 GATCTGAGGCCGGCCGAT 61.621 66.667 38.88 32.95 41.95 4.18
2287 2623 3.873026 GATCTGAGGCCGGCCGATG 62.873 68.421 38.88 29.70 41.95 3.84
2294 2630 4.179579 GCCGGCCGATGCAGTTTC 62.180 66.667 30.73 0.00 40.13 2.78
2295 2631 2.745884 CCGGCCGATGCAGTTTCA 60.746 61.111 30.73 0.00 40.13 2.69
2296 2632 2.331893 CCGGCCGATGCAGTTTCAA 61.332 57.895 30.73 0.00 40.13 2.69
2297 2633 1.578926 CGGCCGATGCAGTTTCAAA 59.421 52.632 24.07 0.00 40.13 2.69
2298 2634 0.171007 CGGCCGATGCAGTTTCAAAT 59.829 50.000 24.07 0.00 40.13 2.32
2299 2635 1.402720 CGGCCGATGCAGTTTCAAATT 60.403 47.619 24.07 0.00 40.13 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.710597 TTAGCACAACTAGTCTAATCCGAT 57.289 37.500 0.00 0.00 30.79 4.18
111 112 7.307493 GTGCATGAACATGTACTAGATTTCA 57.693 36.000 21.98 0.00 46.42 2.69
130 131 4.202305 CCTCTAGGCTAGCTAAAAGTGCAT 60.202 45.833 16.85 0.00 0.00 3.96
181 182 7.185565 AGTATCATGCCTAGCCTCTAATCTAA 58.814 38.462 0.00 0.00 0.00 2.10
200 201 3.086282 TGCTTCCTCACACGTAGTATCA 58.914 45.455 0.00 0.00 41.61 2.15
348 350 6.748132 ACAAGAACCACAAGAATACATTTGG 58.252 36.000 0.00 0.00 0.00 3.28
443 446 8.474006 TTTTCTTTGCAAGTCCTTAAACTTTC 57.526 30.769 0.00 0.00 37.38 2.62
573 579 5.160607 ACATCTGTTTTGTCCGGATTCTA 57.839 39.130 7.81 0.00 0.00 2.10
593 599 1.782807 GCGCGAACATAAACGGACA 59.217 52.632 12.10 0.00 0.00 4.02
602 608 3.876589 AACTCCACCGCGCGAACAT 62.877 57.895 34.63 11.00 0.00 2.71
603 609 4.595538 AACTCCACCGCGCGAACA 62.596 61.111 34.63 11.07 0.00 3.18
624 630 7.230849 AGCAATTTTGATGAGGTGTCATAAA 57.769 32.000 0.00 0.00 43.92 1.40
633 639 4.866486 GCCAACTAAGCAATTTTGATGAGG 59.134 41.667 0.00 0.00 29.13 3.86
634 640 5.472148 TGCCAACTAAGCAATTTTGATGAG 58.528 37.500 0.00 0.00 37.28 2.90
639 645 3.747010 TGCATGCCAACTAAGCAATTTTG 59.253 39.130 16.68 0.00 44.83 2.44
641 647 3.681593 TGCATGCCAACTAAGCAATTT 57.318 38.095 16.68 0.00 44.83 1.82
643 649 2.761767 TCATGCATGCCAACTAAGCAAT 59.238 40.909 22.25 0.00 44.83 3.56
644 650 2.169330 TCATGCATGCCAACTAAGCAA 58.831 42.857 22.25 0.00 44.83 3.91
649 655 5.070313 TGAGTAGTATCATGCATGCCAACTA 59.930 40.000 22.25 21.88 0.00 2.24
650 656 4.141642 TGAGTAGTATCATGCATGCCAACT 60.142 41.667 22.25 22.78 0.00 3.16
651 657 4.024556 GTGAGTAGTATCATGCATGCCAAC 60.025 45.833 22.25 17.59 0.00 3.77
652 658 4.129380 GTGAGTAGTATCATGCATGCCAA 58.871 43.478 22.25 5.34 0.00 4.52
653 659 3.494924 GGTGAGTAGTATCATGCATGCCA 60.495 47.826 22.25 8.84 0.00 4.92
654 660 3.070018 GGTGAGTAGTATCATGCATGCC 58.930 50.000 22.25 11.72 0.00 4.40
655 661 3.070018 GGGTGAGTAGTATCATGCATGC 58.930 50.000 22.25 11.82 0.00 4.06
656 662 4.282957 AGAGGGTGAGTAGTATCATGCATG 59.717 45.833 21.07 21.07 0.00 4.06
657 663 4.487804 AGAGGGTGAGTAGTATCATGCAT 58.512 43.478 0.00 0.00 0.00 3.96
658 664 3.916035 AGAGGGTGAGTAGTATCATGCA 58.084 45.455 0.00 0.00 0.00 3.96
659 665 4.946478 AAGAGGGTGAGTAGTATCATGC 57.054 45.455 0.00 0.00 0.00 4.06
669 675 8.537858 ACGTTCTAATATTTTAAGAGGGTGAGT 58.462 33.333 0.00 0.00 0.00 3.41
670 676 8.943909 ACGTTCTAATATTTTAAGAGGGTGAG 57.056 34.615 0.00 0.00 0.00 3.51
671 677 9.729281 AAACGTTCTAATATTTTAAGAGGGTGA 57.271 29.630 0.00 0.00 0.00 4.02
687 693 9.701098 AGTATCATAGTGTCAAAAACGTTCTAA 57.299 29.630 0.00 0.00 0.00 2.10
689 695 9.136952 GTAGTATCATAGTGTCAAAAACGTTCT 57.863 33.333 0.00 0.00 0.00 3.01
690 696 8.378421 GGTAGTATCATAGTGTCAAAAACGTTC 58.622 37.037 0.00 0.00 0.00 3.95
691 697 7.874016 TGGTAGTATCATAGTGTCAAAAACGTT 59.126 33.333 0.00 0.00 0.00 3.99
692 698 7.380536 TGGTAGTATCATAGTGTCAAAAACGT 58.619 34.615 0.00 0.00 0.00 3.99
693 699 7.821595 TGGTAGTATCATAGTGTCAAAAACG 57.178 36.000 0.00 0.00 0.00 3.60
696 702 9.524106 CGTAATGGTAGTATCATAGTGTCAAAA 57.476 33.333 0.00 0.00 0.00 2.44
697 703 8.905850 TCGTAATGGTAGTATCATAGTGTCAAA 58.094 33.333 0.00 0.00 0.00 2.69
698 704 8.347771 GTCGTAATGGTAGTATCATAGTGTCAA 58.652 37.037 0.00 0.00 0.00 3.18
699 705 7.040892 GGTCGTAATGGTAGTATCATAGTGTCA 60.041 40.741 0.00 0.00 0.00 3.58
700 706 7.040892 TGGTCGTAATGGTAGTATCATAGTGTC 60.041 40.741 0.00 0.00 0.00 3.67
701 707 6.774170 TGGTCGTAATGGTAGTATCATAGTGT 59.226 38.462 0.00 0.00 0.00 3.55
702 708 7.210718 TGGTCGTAATGGTAGTATCATAGTG 57.789 40.000 0.00 0.00 0.00 2.74
703 709 6.072064 GCTGGTCGTAATGGTAGTATCATAGT 60.072 42.308 0.00 0.00 0.00 2.12
704 710 6.323266 GCTGGTCGTAATGGTAGTATCATAG 58.677 44.000 0.00 0.00 0.00 2.23
705 711 5.184479 GGCTGGTCGTAATGGTAGTATCATA 59.816 44.000 0.00 0.00 0.00 2.15
706 712 4.021368 GGCTGGTCGTAATGGTAGTATCAT 60.021 45.833 0.00 0.00 0.00 2.45
707 713 3.319972 GGCTGGTCGTAATGGTAGTATCA 59.680 47.826 0.00 0.00 0.00 2.15
708 714 3.573110 AGGCTGGTCGTAATGGTAGTATC 59.427 47.826 0.00 0.00 0.00 2.24
709 715 3.573695 AGGCTGGTCGTAATGGTAGTAT 58.426 45.455 0.00 0.00 0.00 2.12
710 716 3.022557 AGGCTGGTCGTAATGGTAGTA 57.977 47.619 0.00 0.00 0.00 1.82
711 717 1.861982 AGGCTGGTCGTAATGGTAGT 58.138 50.000 0.00 0.00 0.00 2.73
712 718 2.981859 AAGGCTGGTCGTAATGGTAG 57.018 50.000 0.00 0.00 0.00 3.18
713 719 3.431207 GCTTAAGGCTGGTCGTAATGGTA 60.431 47.826 4.29 0.00 38.06 3.25
714 720 2.679930 GCTTAAGGCTGGTCGTAATGGT 60.680 50.000 4.29 0.00 38.06 3.55
715 721 1.940613 GCTTAAGGCTGGTCGTAATGG 59.059 52.381 4.29 0.00 38.06 3.16
716 722 1.940613 GGCTTAAGGCTGGTCGTAATG 59.059 52.381 21.08 0.00 41.46 1.90
717 723 2.327200 GGCTTAAGGCTGGTCGTAAT 57.673 50.000 21.08 0.00 41.46 1.89
718 724 3.846955 GGCTTAAGGCTGGTCGTAA 57.153 52.632 21.08 0.00 41.46 3.18
727 733 2.095008 GCTTGTTCTTGAGGCTTAAGGC 60.095 50.000 20.84 20.84 41.43 4.35
728 734 3.149196 TGCTTGTTCTTGAGGCTTAAGG 58.851 45.455 17.77 3.91 0.00 2.69
729 735 4.456911 TCATGCTTGTTCTTGAGGCTTAAG 59.543 41.667 12.50 12.50 0.00 1.85
730 736 4.397420 TCATGCTTGTTCTTGAGGCTTAA 58.603 39.130 0.00 0.00 0.00 1.85
731 737 4.019792 TCATGCTTGTTCTTGAGGCTTA 57.980 40.909 0.00 0.00 0.00 3.09
732 738 2.867624 TCATGCTTGTTCTTGAGGCTT 58.132 42.857 0.00 0.00 0.00 4.35
733 739 2.574006 TCATGCTTGTTCTTGAGGCT 57.426 45.000 0.00 0.00 0.00 4.58
734 740 3.863142 AATCATGCTTGTTCTTGAGGC 57.137 42.857 0.00 0.00 0.00 4.70
762 768 1.693062 TGGCACCTGTTGATTTTGCAT 59.307 42.857 0.00 0.00 34.76 3.96
803 810 7.342769 TGGATTTCTAGTAATTGCGAGTCTA 57.657 36.000 3.79 0.00 0.00 2.59
855 875 0.046242 TGGAGAGGATGGGGGTGAAT 59.954 55.000 0.00 0.00 0.00 2.57
928 950 1.190643 GTGGAGACTGAGAGAAGGGG 58.809 60.000 0.00 0.00 0.00 4.79
966 989 1.078497 TGAGGTGTATGCTTGCGGG 60.078 57.895 0.00 0.00 0.00 6.13
967 990 1.091771 CCTGAGGTGTATGCTTGCGG 61.092 60.000 0.00 0.00 0.00 5.69
968 991 1.091771 CCCTGAGGTGTATGCTTGCG 61.092 60.000 0.00 0.00 0.00 4.85
969 992 0.253044 TCCCTGAGGTGTATGCTTGC 59.747 55.000 0.00 0.00 0.00 4.01
970 993 2.636830 CTTCCCTGAGGTGTATGCTTG 58.363 52.381 0.00 0.00 0.00 4.01
980 1003 1.379642 GGATTTGCGCTTCCCTGAGG 61.380 60.000 9.73 0.00 0.00 3.86
982 1005 0.034186 ATGGATTTGCGCTTCCCTGA 60.034 50.000 9.73 0.00 0.00 3.86
984 1007 1.039233 CCATGGATTTGCGCTTCCCT 61.039 55.000 5.56 2.73 0.00 4.20
985 1008 1.037030 TCCATGGATTTGCGCTTCCC 61.037 55.000 11.44 5.32 0.00 3.97
986 1009 0.383231 CTCCATGGATTTGCGCTTCC 59.617 55.000 16.63 13.10 0.00 3.46
987 1010 1.098050 ACTCCATGGATTTGCGCTTC 58.902 50.000 16.63 2.73 0.00 3.86
1013 1041 3.243771 GGAGAACTTCCACTTCTCGTCAA 60.244 47.826 0.00 0.00 46.01 3.18
1215 1249 2.853542 TGCTCCTTCACCAGCCCA 60.854 61.111 0.00 0.00 34.47 5.36
1260 1294 2.730672 GACGAGCATGGTGACGCAC 61.731 63.158 0.00 1.92 0.00 5.34
1363 1399 3.762407 TGCTTCTGTACTGTGGCTAAA 57.238 42.857 15.56 0.00 0.00 1.85
1493 1542 5.510861 GCACTAGTAGTTTCTCCAAGAACCA 60.511 44.000 0.00 0.00 33.26 3.67
1613 1669 2.765689 AACAACAACAAGATCCCCCA 57.234 45.000 0.00 0.00 0.00 4.96
1731 1800 4.386867 GCACTGGCAGTACAATAGTAGA 57.613 45.455 21.59 0.00 40.72 2.59
1814 1893 1.000993 GGAGGAGGAGGAGCACAGA 59.999 63.158 0.00 0.00 0.00 3.41
1815 1894 1.001503 AGGAGGAGGAGGAGCACAG 59.998 63.158 0.00 0.00 0.00 3.66
1816 1895 1.000993 GAGGAGGAGGAGGAGCACA 59.999 63.158 0.00 0.00 0.00 4.57
1817 1896 1.760480 GGAGGAGGAGGAGGAGCAC 60.760 68.421 0.00 0.00 0.00 4.40
1819 1898 1.152546 GAGGAGGAGGAGGAGGAGC 60.153 68.421 0.00 0.00 0.00 4.70
1820 1899 0.998945 AGGAGGAGGAGGAGGAGGAG 60.999 65.000 0.00 0.00 0.00 3.69
1822 1901 1.541672 GAGGAGGAGGAGGAGGAGG 59.458 68.421 0.00 0.00 0.00 4.30
1826 1909 0.771127 AGATCGAGGAGGAGGAGGAG 59.229 60.000 0.00 0.00 0.00 3.69
1886 1969 1.476891 CCACTTGCGCCTCTCTACTTA 59.523 52.381 4.18 0.00 0.00 2.24
1887 1970 0.247736 CCACTTGCGCCTCTCTACTT 59.752 55.000 4.18 0.00 0.00 2.24
1888 1971 0.612174 TCCACTTGCGCCTCTCTACT 60.612 55.000 4.18 0.00 0.00 2.57
1911 1996 4.747108 CACGTCATCCATTTGATACCTCTC 59.253 45.833 0.00 0.00 30.56 3.20
1917 2002 3.198853 TCCACCACGTCATCCATTTGATA 59.801 43.478 0.00 0.00 30.56 2.15
1930 2015 1.111116 TTCGTCTTCCTCCACCACGT 61.111 55.000 0.00 0.00 0.00 4.49
1931 2016 0.388649 CTTCGTCTTCCTCCACCACG 60.389 60.000 0.00 0.00 0.00 4.94
1971 2056 1.462670 CAAAGCAACGCTCTTCCTCTC 59.537 52.381 0.00 0.00 38.25 3.20
2011 2097 0.106719 ACCATCCCCATTTACTGCCG 60.107 55.000 0.00 0.00 0.00 5.69
2125 2225 4.715130 TGAGGGTGAGGGACGGGG 62.715 72.222 0.00 0.00 0.00 5.73
2126 2226 3.077556 CTGAGGGTGAGGGACGGG 61.078 72.222 0.00 0.00 0.00 5.28
2127 2227 3.775654 GCTGAGGGTGAGGGACGG 61.776 72.222 0.00 0.00 0.00 4.79
2128 2228 2.232298 GAAGCTGAGGGTGAGGGACG 62.232 65.000 0.00 0.00 0.00 4.79
2129 2229 1.599576 GAAGCTGAGGGTGAGGGAC 59.400 63.158 0.00 0.00 0.00 4.46
2147 2247 1.815421 GGGCCTGTACTGCATGTCG 60.815 63.158 0.84 0.00 0.00 4.35
2152 2252 2.203922 TGGAGGGCCTGTACTGCA 60.204 61.111 12.95 0.00 32.44 4.41
2153 2253 2.269241 GTGGAGGGCCTGTACTGC 59.731 66.667 12.95 0.00 34.31 4.40
2154 2254 1.194781 ACTGTGGAGGGCCTGTACTG 61.195 60.000 12.95 15.72 34.31 2.74
2155 2255 0.473886 AACTGTGGAGGGCCTGTACT 60.474 55.000 12.95 0.00 34.31 2.73
2156 2256 0.036294 GAACTGTGGAGGGCCTGTAC 60.036 60.000 12.95 10.58 34.31 2.90
2157 2257 0.472925 TGAACTGTGGAGGGCCTGTA 60.473 55.000 12.95 0.00 34.31 2.74
2158 2258 1.770110 TGAACTGTGGAGGGCCTGT 60.770 57.895 12.95 0.00 34.31 4.00
2159 2259 1.302832 GTGAACTGTGGAGGGCCTG 60.303 63.158 12.95 0.00 34.31 4.85
2160 2260 1.770110 TGTGAACTGTGGAGGGCCT 60.770 57.895 5.25 5.25 34.31 5.19
2161 2261 1.600916 GTGTGAACTGTGGAGGGCC 60.601 63.158 0.00 0.00 0.00 5.80
2162 2262 1.148273 TGTGTGAACTGTGGAGGGC 59.852 57.895 0.00 0.00 0.00 5.19
2163 2263 0.180171 TGTGTGTGAACTGTGGAGGG 59.820 55.000 0.00 0.00 0.00 4.30
2164 2264 2.036958 TTGTGTGTGAACTGTGGAGG 57.963 50.000 0.00 0.00 0.00 4.30
2166 2266 1.735018 CGTTTGTGTGTGAACTGTGGA 59.265 47.619 0.00 0.00 0.00 4.02
2167 2267 1.793714 GCGTTTGTGTGTGAACTGTGG 60.794 52.381 0.00 0.00 0.00 4.17
2168 2268 1.135831 TGCGTTTGTGTGTGAACTGTG 60.136 47.619 0.00 0.00 0.00 3.66
2170 2270 2.254918 TTGCGTTTGTGTGTGAACTG 57.745 45.000 0.00 0.00 0.00 3.16
2171 2271 2.983803 GTTTTGCGTTTGTGTGTGAACT 59.016 40.909 0.00 0.00 0.00 3.01
2172 2272 2.726760 TGTTTTGCGTTTGTGTGTGAAC 59.273 40.909 0.00 0.00 0.00 3.18
2174 2274 2.226674 TCTGTTTTGCGTTTGTGTGTGA 59.773 40.909 0.00 0.00 0.00 3.58
2175 2275 2.590073 TCTGTTTTGCGTTTGTGTGTG 58.410 42.857 0.00 0.00 0.00 3.82
2212 2541 2.021457 CTCATCATGGCTGATTGTGCA 58.979 47.619 0.00 0.00 40.20 4.57
2218 2551 3.416253 GGCACTCATCATGGCTGAT 57.584 52.632 0.00 0.00 43.02 2.90
2244 2577 2.224354 GCGTCCTAGCTACTCCTACTCT 60.224 54.545 0.00 0.00 0.00 3.24
2245 2578 2.145536 GCGTCCTAGCTACTCCTACTC 58.854 57.143 0.00 0.00 0.00 2.59
2246 2579 2.259266 GCGTCCTAGCTACTCCTACT 57.741 55.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.