Multiple sequence alignment - TraesCS4A01G183700

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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 TraesCS4A01G183700 chr4A 100.000 3533 0 0 1 3533 462200615 462204147 0.000000e+00 6525
1 TraesCS4A01G183700 chr4A 92.259 956 34 13 2567 3518 611200497 611199578 0.000000e+00 1319
2 TraesCS4A01G183700 chr4D 94.480 2192 91 14 813 2993 115125603 115123431 0.000000e+00 3350
3 TraesCS4A01G183700 chr4D 89.937 954 35 30 2567 3518 447980693 447979799 0.000000e+00 1173
4 TraesCS4A01G183700 chr4D 95.273 550 20 3 2977 3520 115122902 115122353 0.000000e+00 867
5 TraesCS4A01G183700 chr4D 90.196 102 10 0 730 831 115132118 115132017 2.210000e-27 134
6 TraesCS4A01G183700 chr4B 94.605 1520 57 7 1923 3420 175563662 175562146 0.000000e+00 2329
7 TraesCS4A01G183700 chr4B 93.417 1200 42 12 728 1924 175564940 175563775 0.000000e+00 1744
8 TraesCS4A01G183700 chr3D 91.635 1040 50 5 2481 3520 554393038 554392036 0.000000e+00 1404
9 TraesCS4A01G183700 chr3D 85.366 697 95 4 1 695 531454614 531453923 0.000000e+00 715
10 TraesCS4A01G183700 chr2B 92.767 954 33 12 2567 3518 654361610 654362529 0.000000e+00 1347
11 TraesCS4A01G183700 chr2B 86.944 697 86 5 1 695 405268208 405268901 0.000000e+00 778
12 TraesCS4A01G183700 chr7B 92.042 955 36 19 2567 3518 686930324 686929407 0.000000e+00 1306
13 TraesCS4A01G183700 chr7B 93.832 535 30 3 2987 3520 109171770 109172302 0.000000e+00 802
14 TraesCS4A01G183700 chr7B 91.022 323 23 4 2481 2802 109180449 109180132 7.010000e-117 431
15 TraesCS4A01G183700 chr7A 91.824 954 35 15 2567 3518 284785628 284784716 0.000000e+00 1290
16 TraesCS4A01G183700 chr7A 88.092 697 77 6 1 693 607613669 607612975 0.000000e+00 822
17 TraesCS4A01G183700 chr5B 91.824 954 35 15 2567 3518 629972436 629973348 0.000000e+00 1290
18 TraesCS4A01G183700 chr5B 91.632 956 39 11 2567 3518 614980458 614981376 0.000000e+00 1284
19 TraesCS4A01G183700 chr6D 88.958 969 37 20 2567 3533 163353967 163353067 0.000000e+00 1133
20 TraesCS4A01G183700 chr6D 88.976 635 63 5 1 633 378264868 378264239 0.000000e+00 778
21 TraesCS4A01G183700 chr2D 88.169 710 81 3 1 708 496332195 496331487 0.000000e+00 843
22 TraesCS4A01G183700 chr5D 87.857 700 76 6 1 695 446263208 446263903 0.000000e+00 813
23 TraesCS4A01G183700 chr5D 85.694 706 97 4 1 703 273065524 273064820 0.000000e+00 741
24 TraesCS4A01G183700 chr2A 91.809 586 25 7 2567 3151 711071723 711071160 0.000000e+00 795
25 TraesCS4A01G183700 chr3A 86.733 701 86 7 1 698 82445417 82444721 0.000000e+00 773
26 TraesCS4A01G183700 chr1B 85.960 698 93 5 1 695 582523940 582524635 0.000000e+00 741


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 TraesCS4A01G183700 chr4A 462200615 462204147 3532 False 6525.0 6525 100.0000 1 3533 1 chr4A.!!$F1 3532
1 TraesCS4A01G183700 chr4A 611199578 611200497 919 True 1319.0 1319 92.2590 2567 3518 1 chr4A.!!$R1 951
2 TraesCS4A01G183700 chr4D 115122353 115125603 3250 True 2108.5 3350 94.8765 813 3520 2 chr4D.!!$R3 2707
3 TraesCS4A01G183700 chr4D 447979799 447980693 894 True 1173.0 1173 89.9370 2567 3518 1 chr4D.!!$R2 951
4 TraesCS4A01G183700 chr4B 175562146 175564940 2794 True 2036.5 2329 94.0110 728 3420 2 chr4B.!!$R1 2692
5 TraesCS4A01G183700 chr3D 554392036 554393038 1002 True 1404.0 1404 91.6350 2481 3520 1 chr3D.!!$R2 1039
6 TraesCS4A01G183700 chr3D 531453923 531454614 691 True 715.0 715 85.3660 1 695 1 chr3D.!!$R1 694
7 TraesCS4A01G183700 chr2B 654361610 654362529 919 False 1347.0 1347 92.7670 2567 3518 1 chr2B.!!$F2 951
8 TraesCS4A01G183700 chr2B 405268208 405268901 693 False 778.0 778 86.9440 1 695 1 chr2B.!!$F1 694
9 TraesCS4A01G183700 chr7B 686929407 686930324 917 True 1306.0 1306 92.0420 2567 3518 1 chr7B.!!$R2 951
10 TraesCS4A01G183700 chr7B 109171770 109172302 532 False 802.0 802 93.8320 2987 3520 1 chr7B.!!$F1 533
11 TraesCS4A01G183700 chr7A 284784716 284785628 912 True 1290.0 1290 91.8240 2567 3518 1 chr7A.!!$R1 951
12 TraesCS4A01G183700 chr7A 607612975 607613669 694 True 822.0 822 88.0920 1 693 1 chr7A.!!$R2 692
13 TraesCS4A01G183700 chr5B 629972436 629973348 912 False 1290.0 1290 91.8240 2567 3518 1 chr5B.!!$F2 951
14 TraesCS4A01G183700 chr5B 614980458 614981376 918 False 1284.0 1284 91.6320 2567 3518 1 chr5B.!!$F1 951
15 TraesCS4A01G183700 chr6D 163353067 163353967 900 True 1133.0 1133 88.9580 2567 3533 1 chr6D.!!$R1 966
16 TraesCS4A01G183700 chr6D 378264239 378264868 629 True 778.0 778 88.9760 1 633 1 chr6D.!!$R2 632
17 TraesCS4A01G183700 chr2D 496331487 496332195 708 True 843.0 843 88.1690 1 708 1 chr2D.!!$R1 707
18 TraesCS4A01G183700 chr5D 446263208 446263903 695 False 813.0 813 87.8570 1 695 1 chr5D.!!$F1 694
19 TraesCS4A01G183700 chr5D 273064820 273065524 704 True 741.0 741 85.6940 1 703 1 chr5D.!!$R1 702
20 TraesCS4A01G183700 chr2A 711071160 711071723 563 True 795.0 795 91.8090 2567 3151 1 chr2A.!!$R1 584
21 TraesCS4A01G183700 chr3A 82444721 82445417 696 True 773.0 773 86.7330 1 698 1 chr3A.!!$R1 697
22 TraesCS4A01G183700 chr1B 582523940 582524635 695 False 741.0 741 85.9600 1 695 1 chr1B.!!$F1 694

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
742 750 0.039180 GGGGAAGGGGTTAAGTGGTG 59.961 60.0 0.0 0.0 0.00 4.17 F
1459 1468 0.108585 ATCGGTGATTGGGGGAATCG 59.891 55.0 0.0 0.0 43.22 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2075 0.327591 CAGAGCCCTGCTTCCTTCTT 59.672 55.000 0.0 0.0 39.88 2.52 R
2832 2990 1.064208 CGCTAGACATAGACTGTGCGT 59.936 52.381 0.0 0.0 38.54 5.24 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 28 2.746277 GACGAGGGGTTGCGCAAT 60.746 61.111 27.79 10.36 0.00 3.56
53 54 2.289882 CCATTGAGGTGAGAAGAGCACA 60.290 50.000 0.00 0.00 37.99 4.57
61 62 2.747460 GAAGAGCACATGCCGCCA 60.747 61.111 0.00 0.00 43.38 5.69
63 64 1.865788 GAAGAGCACATGCCGCCAAA 61.866 55.000 0.00 0.00 43.38 3.28
194 196 2.909006 TCTTGAAGAGGAGGATGCTTGT 59.091 45.455 0.00 0.00 36.27 3.16
257 259 4.605183 TCGGGATTTGGAACCAATATTGT 58.395 39.130 14.25 0.00 35.70 2.71
319 322 0.108520 GGGAACAAGTGTCGGCGATA 60.109 55.000 14.79 7.84 0.00 2.92
370 374 1.301716 GGTGCGGAGTGAAGAGCAA 60.302 57.895 0.00 0.00 41.56 3.91
386 390 5.113446 AGAGCAACAAGATGATCAAGGAT 57.887 39.130 0.00 0.00 38.17 3.24
426 431 2.884639 AGTCCTTTTGCGTTTGTGCTAT 59.115 40.909 0.00 0.00 35.36 2.97
483 488 8.816144 TGTTTTAGCATTTGAATTTGAAGTCAC 58.184 29.630 0.00 0.00 32.15 3.67
489 494 6.476380 GCATTTGAATTTGAAGTCACTTGTCA 59.524 34.615 0.00 0.00 32.15 3.58
516 522 6.552859 TCACTGTCAAATTCGCTTATTGAA 57.447 33.333 0.00 0.00 35.07 2.69
532 538 3.489180 TTGAAGTTTTTCGGTTTGCGA 57.511 38.095 0.00 0.00 36.04 5.10
533 539 3.489180 TGAAGTTTTTCGGTTTGCGAA 57.511 38.095 0.00 0.00 36.04 4.70
572 579 1.828660 CAGACTCGGGGTAGCCGAT 60.829 63.158 4.56 0.00 39.01 4.18
633 641 1.676014 CCGTTTGTGGGATCTGACTCC 60.676 57.143 0.00 0.00 34.31 3.85
661 669 2.739671 GCGCCGACCCGTAAAGTT 60.740 61.111 0.00 0.00 0.00 2.66
662 670 2.319841 GCGCCGACCCGTAAAGTTT 61.320 57.895 0.00 0.00 0.00 2.66
708 716 3.186047 CGGGCCGTCGTTTGCTAG 61.186 66.667 19.97 0.00 0.00 3.42
709 717 2.263540 GGGCCGTCGTTTGCTAGA 59.736 61.111 0.00 0.00 0.00 2.43
710 718 1.810030 GGGCCGTCGTTTGCTAGAG 60.810 63.158 0.00 0.00 0.00 2.43
711 719 1.214589 GGCCGTCGTTTGCTAGAGA 59.785 57.895 0.00 0.00 0.00 3.10
712 720 0.179108 GGCCGTCGTTTGCTAGAGAT 60.179 55.000 0.00 0.00 0.00 2.75
713 721 0.924090 GCCGTCGTTTGCTAGAGATG 59.076 55.000 0.00 0.00 0.00 2.90
714 722 0.924090 CCGTCGTTTGCTAGAGATGC 59.076 55.000 0.00 0.00 0.00 3.91
715 723 1.469940 CCGTCGTTTGCTAGAGATGCT 60.470 52.381 0.00 0.00 0.00 3.79
716 724 1.849219 CGTCGTTTGCTAGAGATGCTC 59.151 52.381 0.00 0.00 0.00 4.26
717 725 2.478709 CGTCGTTTGCTAGAGATGCTCT 60.479 50.000 0.00 2.22 43.83 4.09
718 726 3.242772 CGTCGTTTGCTAGAGATGCTCTA 60.243 47.826 0.00 4.30 41.50 2.43
719 727 4.673441 GTCGTTTGCTAGAGATGCTCTAA 58.327 43.478 5.75 0.00 41.74 2.10
720 728 5.285651 GTCGTTTGCTAGAGATGCTCTAAT 58.714 41.667 5.75 0.00 41.74 1.73
721 729 5.174761 GTCGTTTGCTAGAGATGCTCTAATG 59.825 44.000 5.75 0.00 41.74 1.90
722 730 5.067805 TCGTTTGCTAGAGATGCTCTAATGA 59.932 40.000 5.75 1.80 41.74 2.57
723 731 5.401972 CGTTTGCTAGAGATGCTCTAATGAG 59.598 44.000 5.75 0.00 41.74 2.90
724 732 5.465532 TTGCTAGAGATGCTCTAATGAGG 57.534 43.478 5.75 0.00 41.74 3.86
725 733 3.831333 TGCTAGAGATGCTCTAATGAGGG 59.169 47.826 5.75 0.00 41.74 4.30
726 734 3.195396 GCTAGAGATGCTCTAATGAGGGG 59.805 52.174 5.75 0.00 41.74 4.79
741 749 0.103554 AGGGGAAGGGGTTAAGTGGT 60.104 55.000 0.00 0.00 0.00 4.16
742 750 0.039180 GGGGAAGGGGTTAAGTGGTG 59.961 60.000 0.00 0.00 0.00 4.17
754 762 5.246307 GGTTAAGTGGTGAGTTAGCAATCT 58.754 41.667 0.00 0.00 38.75 2.40
757 765 4.199432 AGTGGTGAGTTAGCAATCTCAG 57.801 45.455 5.27 0.00 40.63 3.35
779 787 1.485124 TTCATCTCTGCCCTTCGCTA 58.515 50.000 0.00 0.00 38.78 4.26
786 794 2.036992 CTCTGCCCTTCGCTATTGATCT 59.963 50.000 0.00 0.00 38.78 2.75
798 806 4.633126 CGCTATTGATCTAATGACCCATGG 59.367 45.833 4.14 4.14 0.00 3.66
808 816 6.194235 TCTAATGACCCATGGCATTAGTTTT 58.806 36.000 30.93 15.96 42.80 2.43
812 820 4.016444 GACCCATGGCATTAGTTTTCAGA 58.984 43.478 6.09 0.00 0.00 3.27
813 821 4.613437 ACCCATGGCATTAGTTTTCAGAT 58.387 39.130 6.09 0.00 0.00 2.90
814 822 5.025453 ACCCATGGCATTAGTTTTCAGATT 58.975 37.500 6.09 0.00 0.00 2.40
815 823 5.484998 ACCCATGGCATTAGTTTTCAGATTT 59.515 36.000 6.09 0.00 0.00 2.17
816 824 6.013466 ACCCATGGCATTAGTTTTCAGATTTT 60.013 34.615 6.09 0.00 0.00 1.82
817 825 6.536224 CCCATGGCATTAGTTTTCAGATTTTC 59.464 38.462 6.09 0.00 0.00 2.29
818 826 7.098477 CCATGGCATTAGTTTTCAGATTTTCA 58.902 34.615 0.00 0.00 0.00 2.69
819 827 7.767198 CCATGGCATTAGTTTTCAGATTTTCAT 59.233 33.333 0.00 0.00 0.00 2.57
820 828 8.814235 CATGGCATTAGTTTTCAGATTTTCATC 58.186 33.333 0.00 0.00 0.00 2.92
821 829 7.028962 TGGCATTAGTTTTCAGATTTTCATCG 58.971 34.615 0.00 0.00 34.17 3.84
944 952 1.536073 CGACAGCACAAGGGAGGAGA 61.536 60.000 0.00 0.00 0.00 3.71
952 960 2.760092 CACAAGGGAGGAGAAGAGAGAG 59.240 54.545 0.00 0.00 0.00 3.20
953 961 2.652348 ACAAGGGAGGAGAAGAGAGAGA 59.348 50.000 0.00 0.00 0.00 3.10
954 962 3.290710 CAAGGGAGGAGAAGAGAGAGAG 58.709 54.545 0.00 0.00 0.00 3.20
955 963 2.858644 AGGGAGGAGAAGAGAGAGAGA 58.141 52.381 0.00 0.00 0.00 3.10
956 964 2.780010 AGGGAGGAGAAGAGAGAGAGAG 59.220 54.545 0.00 0.00 0.00 3.20
957 965 2.777692 GGGAGGAGAAGAGAGAGAGAGA 59.222 54.545 0.00 0.00 0.00 3.10
958 966 3.181450 GGGAGGAGAAGAGAGAGAGAGAG 60.181 56.522 0.00 0.00 0.00 3.20
959 967 3.711704 GGAGGAGAAGAGAGAGAGAGAGA 59.288 52.174 0.00 0.00 0.00 3.10
1175 1184 1.679305 TCAGAGCCGGTCACTCCTC 60.679 63.158 1.90 0.00 34.56 3.71
1320 1329 0.182061 CCTCAGCCATGTATGTGCCT 59.818 55.000 0.00 0.00 0.00 4.75
1412 1421 1.315690 TAACTGTAGCGGGGATCGAG 58.684 55.000 0.00 0.00 42.43 4.04
1459 1468 0.108585 ATCGGTGATTGGGGGAATCG 59.891 55.000 0.00 0.00 43.22 3.34
1502 1511 1.524008 TTCTCTTGGCGTGCTCTCGA 61.524 55.000 0.00 0.00 0.00 4.04
1514 1523 2.600867 GTGCTCTCGAAAGATTCTTCCG 59.399 50.000 0.00 0.00 40.84 4.30
1569 1578 7.658261 TGCTATAAGTGCTAACGTATCTTGAT 58.342 34.615 0.00 0.00 33.67 2.57
1570 1579 8.141909 TGCTATAAGTGCTAACGTATCTTGATT 58.858 33.333 0.00 0.00 33.67 2.57
1571 1580 8.640291 GCTATAAGTGCTAACGTATCTTGATTC 58.360 37.037 0.00 0.00 33.67 2.52
1572 1581 9.900710 CTATAAGTGCTAACGTATCTTGATTCT 57.099 33.333 0.00 0.00 33.67 2.40
1574 1583 6.893958 AGTGCTAACGTATCTTGATTCTTG 57.106 37.500 0.00 0.00 0.00 3.02
1575 1584 6.631016 AGTGCTAACGTATCTTGATTCTTGA 58.369 36.000 0.00 0.00 0.00 3.02
1626 1635 8.548025 TGATAGAAAAATTGGATGTCCTAGTGA 58.452 33.333 0.09 0.00 36.82 3.41
1683 1692 1.069765 AGAGTGTTGACGGCTGTGG 59.930 57.895 0.80 0.00 0.00 4.17
1762 1771 9.297037 GAATATAATGGGGCATAACACTAGTTT 57.703 33.333 0.00 0.00 39.15 2.66
1769 1778 4.438744 GGGCATAACACTAGTTTGATGTGC 60.439 45.833 7.97 6.14 39.15 4.57
1789 1799 2.610727 GCAGTCTGTCGCCTTAGTTCTT 60.611 50.000 0.93 0.00 0.00 2.52
1797 1807 4.096081 TGTCGCCTTAGTTCTTCTACTAGC 59.904 45.833 0.00 0.00 32.54 3.42
1799 1810 4.575645 TCGCCTTAGTTCTTCTACTAGCTC 59.424 45.833 0.00 0.00 32.54 4.09
1949 2075 1.391933 ATGCTCACCCGTGCTCGATA 61.392 55.000 10.21 0.00 39.71 2.92
1964 2090 1.139058 TCGATAAGAAGGAAGCAGGGC 59.861 52.381 0.00 0.00 0.00 5.19
1987 2122 6.347240 GGCTCTGAGTAATATTCTGAATTGCG 60.347 42.308 8.38 0.00 0.00 4.85
2298 2433 1.446792 ATGCTCGCCTGAAGTGTCG 60.447 57.895 0.00 0.00 0.00 4.35
2304 2439 0.453793 CGCCTGAAGTGTCGAGATCT 59.546 55.000 0.00 0.00 0.00 2.75
2307 2442 2.733858 GCCTGAAGTGTCGAGATCTGAC 60.734 54.545 0.00 9.05 36.88 3.51
2437 2573 2.170607 TCGGAGGATCAGGGAAACAATC 59.829 50.000 0.00 0.00 36.25 2.67
2490 2626 4.911390 AGAATAACAACCAGACAGGGAAG 58.089 43.478 0.00 0.00 43.89 3.46
2514 2650 2.616634 ACATAGAGAGTCCTCGCGTA 57.383 50.000 5.77 0.00 44.08 4.42
2708 2845 7.755373 GGTTTCTTCTTAAAGCACCACATTATC 59.245 37.037 0.00 0.00 36.37 1.75
2761 2898 2.698274 TCACACTCAAGTACTCAGGCAA 59.302 45.455 0.00 0.00 0.00 4.52
2832 2990 4.202461 ACTGGGAAGTGCTTAATCAGACAA 60.202 41.667 12.26 0.00 0.00 3.18
2841 2999 3.423645 GCTTAATCAGACAACGCACAGTC 60.424 47.826 0.00 0.00 35.02 3.51
2851 3009 2.853731 ACGCACAGTCTATGTCTAGC 57.146 50.000 0.00 0.00 41.41 3.42
3040 3748 3.963665 TGCAACAATCACTTGTAACTGC 58.036 40.909 6.66 6.66 44.83 4.40
3055 3763 4.513692 TGTAACTGCACCACTGTTATTGAC 59.486 41.667 0.00 0.00 42.46 3.18
3118 3836 1.819632 GCAGACACTATTGCCCCCG 60.820 63.158 0.00 0.00 34.28 5.73
3156 3874 6.058553 TCATCATTCAACACAGAAGGATCT 57.941 37.500 1.39 0.00 43.23 2.75
3351 4105 5.468746 TGAAATTTGCCTACACTACACACTC 59.531 40.000 0.00 0.00 0.00 3.51
3352 4106 4.617253 ATTTGCCTACACTACACACTCA 57.383 40.909 0.00 0.00 0.00 3.41
3353 4107 3.380479 TTGCCTACACTACACACTCAC 57.620 47.619 0.00 0.00 0.00 3.51
3354 4108 2.312390 TGCCTACACTACACACTCACA 58.688 47.619 0.00 0.00 0.00 3.58
3355 4109 2.897326 TGCCTACACTACACACTCACAT 59.103 45.455 0.00 0.00 0.00 3.21
3356 4110 3.056821 TGCCTACACTACACACTCACATC 60.057 47.826 0.00 0.00 0.00 3.06
3357 4111 3.056821 GCCTACACTACACACTCACATCA 60.057 47.826 0.00 0.00 0.00 3.07
3358 4112 4.560716 GCCTACACTACACACTCACATCAA 60.561 45.833 0.00 0.00 0.00 2.57
3359 4113 5.724328 CCTACACTACACACTCACATCAAT 58.276 41.667 0.00 0.00 0.00 2.57
3360 4114 5.578336 CCTACACTACACACTCACATCAATG 59.422 44.000 0.00 0.00 0.00 2.82
3361 4115 4.960938 ACACTACACACTCACATCAATGT 58.039 39.130 0.00 0.00 42.84 2.71
3362 4116 6.096673 ACACTACACACTCACATCAATGTA 57.903 37.500 0.00 0.00 39.39 2.29
3363 4117 6.701340 ACACTACACACTCACATCAATGTAT 58.299 36.000 0.00 0.00 39.39 2.29
3364 4118 7.161404 ACACTACACACTCACATCAATGTATT 58.839 34.615 0.00 0.00 39.39 1.89
3398 4156 6.614160 TGTTCATGATCATGTTGCTTGTAAG 58.386 36.000 30.01 5.39 39.72 2.34
3415 4173 2.990066 AAGCTTACTGATCCCTTCGG 57.010 50.000 0.00 0.00 36.72 4.30
3462 4220 3.110178 CCACGAAGTTCGCCGTCC 61.110 66.667 24.64 0.00 45.12 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.975536 CGCAACCCCTCGTCCTTA 59.024 61.111 0.00 0.00 0.00 2.69
27 28 2.046023 CTCACCTCAATGGCCGCA 60.046 61.111 0.00 0.00 40.22 5.69
41 42 1.742880 GCGGCATGTGCTCTTCTCA 60.743 57.895 4.84 0.00 41.70 3.27
53 54 0.884259 GGCTTTGTTTTTGGCGGCAT 60.884 50.000 14.32 0.00 0.00 4.40
61 62 3.118298 AGCTTGGACATGGCTTTGTTTTT 60.118 39.130 0.00 0.00 31.81 1.94
63 64 2.041701 AGCTTGGACATGGCTTTGTTT 58.958 42.857 0.00 0.00 31.81 2.83
160 162 3.251484 TCTTCAAGATGTCCCTCCTTGT 58.749 45.455 0.00 0.00 38.61 3.16
194 196 0.668096 GTAACACACATCGGCCGACA 60.668 55.000 33.75 10.24 0.00 4.35
215 217 2.455674 TGAGGAAACATCACCGACAG 57.544 50.000 0.00 0.00 0.00 3.51
230 232 1.064758 TGGTTCCAAATCCCGATGAGG 60.065 52.381 0.00 0.00 40.63 3.86
257 259 0.538584 AGGCTCACTGAATGCATCGA 59.461 50.000 0.00 0.00 0.00 3.59
319 322 3.227276 ATCGCCGCCCTCGAATCT 61.227 61.111 0.00 0.00 39.54 2.40
370 374 4.521146 GACCACATCCTTGATCATCTTGT 58.479 43.478 0.00 0.00 0.00 3.16
386 390 1.369839 TTGCAAAAGCGACGACCACA 61.370 50.000 0.00 0.00 0.00 4.17
426 431 5.003967 GCGCGCAAATAAAAGCATAGTTTTA 59.996 36.000 29.10 0.00 36.55 1.52
479 484 4.371786 TGACAGTGATTCTGACAAGTGAC 58.628 43.478 0.00 0.00 46.27 3.67
489 494 6.992063 ATAAGCGAATTTGACAGTGATTCT 57.008 33.333 0.00 0.00 0.00 2.40
550 556 2.052690 GCTACCCCGAGTCTGCTCA 61.053 63.158 0.00 0.00 41.71 4.26
594 601 9.403583 ACAAACGGACACATATAAAGGATATTT 57.596 29.630 0.00 0.00 0.00 1.40
610 618 1.052617 TCAGATCCCACAAACGGACA 58.947 50.000 0.00 0.00 30.39 4.02
710 718 2.039613 CCCTTCCCCTCATTAGAGCATC 59.960 54.545 0.00 0.00 40.68 3.91
711 719 2.061061 CCCTTCCCCTCATTAGAGCAT 58.939 52.381 0.00 0.00 40.68 3.79
712 720 1.511613 CCCTTCCCCTCATTAGAGCA 58.488 55.000 0.00 0.00 40.68 4.26
713 721 0.767998 CCCCTTCCCCTCATTAGAGC 59.232 60.000 0.00 0.00 40.68 4.09
714 722 2.198334 ACCCCTTCCCCTCATTAGAG 57.802 55.000 0.00 0.00 41.72 2.43
715 723 2.680439 AACCCCTTCCCCTCATTAGA 57.320 50.000 0.00 0.00 0.00 2.10
716 724 3.786450 ACTTAACCCCTTCCCCTCATTAG 59.214 47.826 0.00 0.00 0.00 1.73
717 725 3.526019 CACTTAACCCCTTCCCCTCATTA 59.474 47.826 0.00 0.00 0.00 1.90
718 726 2.311841 CACTTAACCCCTTCCCCTCATT 59.688 50.000 0.00 0.00 0.00 2.57
719 727 1.923148 CACTTAACCCCTTCCCCTCAT 59.077 52.381 0.00 0.00 0.00 2.90
720 728 1.368374 CACTTAACCCCTTCCCCTCA 58.632 55.000 0.00 0.00 0.00 3.86
721 729 0.624254 CCACTTAACCCCTTCCCCTC 59.376 60.000 0.00 0.00 0.00 4.30
722 730 0.103554 ACCACTTAACCCCTTCCCCT 60.104 55.000 0.00 0.00 0.00 4.79
723 731 0.039180 CACCACTTAACCCCTTCCCC 59.961 60.000 0.00 0.00 0.00 4.81
724 732 1.004394 CTCACCACTTAACCCCTTCCC 59.996 57.143 0.00 0.00 0.00 3.97
725 733 1.703513 ACTCACCACTTAACCCCTTCC 59.296 52.381 0.00 0.00 0.00 3.46
726 734 3.503800 AACTCACCACTTAACCCCTTC 57.496 47.619 0.00 0.00 0.00 3.46
741 749 5.227569 TGAAACCTGAGATTGCTAACTCA 57.772 39.130 7.79 7.79 40.22 3.41
742 750 6.112058 AGATGAAACCTGAGATTGCTAACTC 58.888 40.000 0.00 0.00 0.00 3.01
754 762 1.661463 AGGGCAGAGATGAAACCTGA 58.339 50.000 0.00 0.00 0.00 3.86
757 765 1.373570 CGAAGGGCAGAGATGAAACC 58.626 55.000 0.00 0.00 0.00 3.27
779 787 4.458256 TGCCATGGGTCATTAGATCAAT 57.542 40.909 15.13 0.00 0.00 2.57
786 794 5.954752 TGAAAACTAATGCCATGGGTCATTA 59.045 36.000 15.13 17.22 33.78 1.90
798 806 8.673626 TTCGATGAAAATCTGAAAACTAATGC 57.326 30.769 0.00 0.00 0.00 3.56
808 816 5.902613 AAGGCAATTCGATGAAAATCTGA 57.097 34.783 0.00 0.00 0.00 3.27
812 820 5.178061 GGGAAAAGGCAATTCGATGAAAAT 58.822 37.500 0.00 0.00 0.00 1.82
813 821 4.039730 TGGGAAAAGGCAATTCGATGAAAA 59.960 37.500 0.00 0.00 0.00 2.29
814 822 3.576118 TGGGAAAAGGCAATTCGATGAAA 59.424 39.130 0.00 0.00 0.00 2.69
815 823 3.161067 TGGGAAAAGGCAATTCGATGAA 58.839 40.909 0.00 0.00 0.00 2.57
816 824 2.801483 TGGGAAAAGGCAATTCGATGA 58.199 42.857 0.00 0.00 0.00 2.92
817 825 3.591196 TTGGGAAAAGGCAATTCGATG 57.409 42.857 0.00 0.00 0.00 3.84
818 826 3.323403 TGTTTGGGAAAAGGCAATTCGAT 59.677 39.130 0.00 0.00 0.00 3.59
819 827 2.695666 TGTTTGGGAAAAGGCAATTCGA 59.304 40.909 0.00 0.00 0.00 3.71
820 828 3.104843 TGTTTGGGAAAAGGCAATTCG 57.895 42.857 0.00 0.00 0.00 3.34
821 829 5.588246 TCTTTTGTTTGGGAAAAGGCAATTC 59.412 36.000 0.00 0.00 39.75 2.17
944 952 4.100808 GCTCTCTCTCTCTCTCTCTCTCTT 59.899 50.000 0.00 0.00 0.00 2.85
952 960 1.498865 CGCGGCTCTCTCTCTCTCTC 61.499 65.000 0.00 0.00 0.00 3.20
953 961 1.523711 CGCGGCTCTCTCTCTCTCT 60.524 63.158 0.00 0.00 0.00 3.10
954 962 3.022287 CGCGGCTCTCTCTCTCTC 58.978 66.667 0.00 0.00 0.00 3.20
955 963 3.209097 GCGCGGCTCTCTCTCTCT 61.209 66.667 8.83 0.00 0.00 3.10
956 964 4.264638 GGCGCGGCTCTCTCTCTC 62.265 72.222 27.05 0.00 0.00 3.20
1502 1511 2.162681 CCTTGGCACGGAAGAATCTTT 58.837 47.619 3.47 0.00 0.00 2.52
1514 1523 8.220755 TCAAATATATACTTGTTCCTTGGCAC 57.779 34.615 4.01 0.00 0.00 5.01
1569 1578 1.871039 GTACCGCTGCTTGTTCAAGAA 59.129 47.619 15.52 5.00 0.00 2.52
1570 1579 1.202592 TGTACCGCTGCTTGTTCAAGA 60.203 47.619 15.52 1.78 0.00 3.02
1571 1580 1.195448 CTGTACCGCTGCTTGTTCAAG 59.805 52.381 8.04 8.04 0.00 3.02
1572 1581 1.225855 CTGTACCGCTGCTTGTTCAA 58.774 50.000 0.00 0.00 0.00 2.69
1573 1582 1.227999 GCTGTACCGCTGCTTGTTCA 61.228 55.000 1.52 0.00 38.75 3.18
1574 1583 1.497722 GCTGTACCGCTGCTTGTTC 59.502 57.895 1.52 0.00 38.75 3.18
1575 1584 2.317609 CGCTGTACCGCTGCTTGTT 61.318 57.895 7.70 0.00 39.51 2.83
1626 1635 3.320826 GGTTTGACTTAGGCACCAACATT 59.679 43.478 5.18 0.00 0.00 2.71
1683 1692 9.162764 TGGTTCAGTAGCAAAAATCTAGATAAC 57.837 33.333 5.46 2.16 0.00 1.89
1762 1771 1.374631 GGCGACAGACTGCACATCA 60.375 57.895 1.25 0.00 0.00 3.07
1769 1778 3.057174 AGAAGAACTAAGGCGACAGACTG 60.057 47.826 0.00 0.00 34.63 3.51
1949 2075 0.327591 CAGAGCCCTGCTTCCTTCTT 59.672 55.000 0.00 0.00 39.88 2.52
1964 2090 7.936950 TCGCAATTCAGAATATTACTCAGAG 57.063 36.000 0.00 0.00 0.00 3.35
2220 2355 0.609957 CATGCTTTCTGCCAGGGTCA 60.610 55.000 0.00 0.00 42.00 4.02
2256 2391 2.059541 GGAATTACTATCACCGCGCTC 58.940 52.381 5.56 0.00 0.00 5.03
2298 2433 1.596477 GCGGCATGGGTCAGATCTC 60.596 63.158 0.00 0.00 0.00 2.75
2437 2573 1.811266 CAACCTCAGATGGCGTCGG 60.811 63.158 0.13 0.03 0.00 4.79
2490 2626 3.440228 GCGAGGACTCTCTATGTTCAAC 58.560 50.000 0.00 0.00 37.86 3.18
2559 2695 2.551459 CAGACTGCAGGAAAAGGAACTG 59.449 50.000 19.93 8.73 40.86 3.16
2708 2845 3.136763 ACTGCTTGAGTGTGATCAACAG 58.863 45.455 0.00 12.95 40.26 3.16
2761 2898 1.251251 GGGAAGAAACTGTGCATGCT 58.749 50.000 20.33 0.00 0.00 3.79
2832 2990 1.064208 CGCTAGACATAGACTGTGCGT 59.936 52.381 0.00 0.00 38.54 5.24
2841 2999 4.385146 CACATGATGCTTCGCTAGACATAG 59.615 45.833 0.00 0.00 0.00 2.23
2851 3009 3.770263 AAATGGACACATGATGCTTCG 57.230 42.857 0.00 0.00 37.40 3.79
3040 3748 7.354025 TGTAAATACGTCAATAACAGTGGTG 57.646 36.000 0.00 0.00 0.00 4.17
3055 3763 7.275779 ACTGCTGACTGTTCTTATGTAAATACG 59.724 37.037 0.00 0.00 0.00 3.06
3118 3836 6.997655 TGAATGATGAGGTGGTGTAGATATC 58.002 40.000 0.00 0.00 0.00 1.63
3206 3924 4.639078 TGGATCCTTCTGTGTTGAATGA 57.361 40.909 14.23 0.00 0.00 2.57
3351 4105 7.988737 ACATAACAGGTGAATACATTGATGTG 58.011 34.615 6.87 0.00 41.89 3.21
3352 4106 8.579850 AACATAACAGGTGAATACATTGATGT 57.420 30.769 1.84 1.84 44.48 3.06
3353 4107 8.676401 TGAACATAACAGGTGAATACATTGATG 58.324 33.333 0.00 0.00 0.00 3.07
3354 4108 8.806429 TGAACATAACAGGTGAATACATTGAT 57.194 30.769 0.00 0.00 0.00 2.57
3355 4109 8.676401 CATGAACATAACAGGTGAATACATTGA 58.324 33.333 0.00 0.00 0.00 2.57
3356 4110 8.676401 TCATGAACATAACAGGTGAATACATTG 58.324 33.333 0.00 0.00 0.00 2.82
3357 4111 8.806429 TCATGAACATAACAGGTGAATACATT 57.194 30.769 0.00 0.00 0.00 2.71
3358 4112 8.985315 ATCATGAACATAACAGGTGAATACAT 57.015 30.769 0.00 0.00 0.00 2.29
3359 4113 8.046107 TGATCATGAACATAACAGGTGAATACA 58.954 33.333 0.00 0.00 0.00 2.29
3360 4114 8.437360 TGATCATGAACATAACAGGTGAATAC 57.563 34.615 0.00 0.00 0.00 1.89
3361 4115 9.059260 CATGATCATGAACATAACAGGTGAATA 57.941 33.333 28.37 0.00 41.20 1.75
3362 4116 7.558807 ACATGATCATGAACATAACAGGTGAAT 59.441 33.333 36.37 9.76 41.20 2.57
3363 4117 6.885918 ACATGATCATGAACATAACAGGTGAA 59.114 34.615 36.37 0.00 41.20 3.18
3364 4118 6.417258 ACATGATCATGAACATAACAGGTGA 58.583 36.000 36.37 0.00 41.20 4.02
3415 4173 1.312815 ACTGCCTGTTTCACTGAAGC 58.687 50.000 0.00 0.00 0.00 3.86
3462 4220 6.577103 TGTAGCTACTCCATTCAAATGAGAG 58.423 40.000 23.84 14.46 38.70 3.20


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

AutoCloner maintained by Alex Coulton.