Multiple sequence alignment - TraesCS6B01G134900

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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 TraesCS6B01G134900 chr6B 100.000 3065 0 0 1 3065 132283062 132286126 0.000000e+00 5661.0
1 TraesCS6B01G134900 chr6B 90.102 586 45 5 2480 3065 143603101 143602529 0.000000e+00 749.0
2 TraesCS6B01G134900 chr6B 76.963 573 105 21 1385 1951 132144775 132145326 4.970000e-78 302.0
3 TraesCS6B01G134900 chr6A 92.697 1698 90 14 795 2481 73844622 73846296 0.000000e+00 2418.0
4 TraesCS6B01G134900 chr6A 95.567 564 18 3 2 559 73843947 73844509 0.000000e+00 896.0
5 TraesCS6B01G134900 chr6A 94.068 118 4 2 646 763 73844508 73844622 3.140000e-40 176.0
6 TraesCS6B01G134900 chr6D 90.206 1215 62 23 1271 2481 58687537 58688698 0.000000e+00 1531.0
7 TraesCS6B01G134900 chr6D 93.858 635 28 7 646 1279 58673015 58673639 0.000000e+00 946.0
8 TraesCS6B01G134900 chr6D 95.307 554 23 1 2 552 58672451 58673004 0.000000e+00 876.0
9 TraesCS6B01G134900 chr3D 91.809 586 41 4 2482 3065 584458248 584458828 0.000000e+00 809.0
10 TraesCS6B01G134900 chr3D 90.801 587 49 5 2482 3065 13887355 13886771 0.000000e+00 780.0
11 TraesCS6B01G134900 chr3B 91.252 583 48 3 2483 3065 759071896 759071317 0.000000e+00 791.0
12 TraesCS6B01G134900 chr3B 88.660 97 8 3 557 652 71348591 71348685 6.940000e-22 115.0
13 TraesCS6B01G134900 chr4A 90.427 585 41 4 2482 3065 691250822 691251392 0.000000e+00 756.0
14 TraesCS6B01G134900 chr4A 90.526 95 5 4 554 647 67268356 67268447 4.150000e-24 122.0
15 TraesCS6B01G134900 chr1B 89.420 586 59 3 2481 3065 130582749 130583332 0.000000e+00 736.0
16 TraesCS6B01G134900 chr1B 89.231 585 47 9 2482 3065 63944584 63945153 0.000000e+00 717.0
17 TraesCS6B01G134900 chr1B 88.889 585 49 10 2482 3065 63937038 63937607 0.000000e+00 706.0
18 TraesCS6B01G134900 chr1B 88.889 585 49 9 2482 3065 63951574 63952143 0.000000e+00 706.0
19 TraesCS6B01G134900 chr1B 89.777 538 43 6 2482 3016 298755090 298754562 0.000000e+00 678.0
20 TraesCS6B01G134900 chr1B 92.222 90 7 0 558 647 655433782 655433693 8.920000e-26 128.0
21 TraesCS6B01G134900 chrUn 88.889 585 49 9 2482 3065 339391155 339390586 0.000000e+00 706.0
22 TraesCS6B01G134900 chrUn 88.205 585 53 9 2482 3065 65746483 65745914 0.000000e+00 684.0
23 TraesCS6B01G134900 chr2B 94.565 92 4 1 557 648 79676090 79676180 1.150000e-29 141.0
24 TraesCS6B01G134900 chr2B 90.099 101 5 3 555 651 26724667 26724766 3.210000e-25 126.0
25 TraesCS6B01G134900 chr2B 87.619 105 7 5 550 649 26724771 26724668 1.930000e-22 117.0
26 TraesCS6B01G134900 chr7D 96.053 76 3 0 575 650 277549129 277549204 1.150000e-24 124.0
27 TraesCS6B01G134900 chr7B 91.111 90 8 0 558 647 622580820 622580731 4.150000e-24 122.0
28 TraesCS6B01G134900 chr1A 85.714 119 8 4 539 652 30289486 30289372 1.930000e-22 117.0
29 TraesCS6B01G134900 chr2A 91.489 47 2 2 546 592 763018400 763018356 2.550000e-06 63.9


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 TraesCS6B01G134900 chr6B 132283062 132286126 3064 False 5661.000000 5661 100.000000 1 3065 1 chr6B.!!$F2 3064
1 TraesCS6B01G134900 chr6B 143602529 143603101 572 True 749.000000 749 90.102000 2480 3065 1 chr6B.!!$R1 585
2 TraesCS6B01G134900 chr6B 132144775 132145326 551 False 302.000000 302 76.963000 1385 1951 1 chr6B.!!$F1 566
3 TraesCS6B01G134900 chr6A 73843947 73846296 2349 False 1163.333333 2418 94.110667 2 2481 3 chr6A.!!$F1 2479
4 TraesCS6B01G134900 chr6D 58687537 58688698 1161 False 1531.000000 1531 90.206000 1271 2481 1 chr6D.!!$F1 1210
5 TraesCS6B01G134900 chr6D 58672451 58673639 1188 False 911.000000 946 94.582500 2 1279 2 chr6D.!!$F2 1277
6 TraesCS6B01G134900 chr3D 584458248 584458828 580 False 809.000000 809 91.809000 2482 3065 1 chr3D.!!$F1 583
7 TraesCS6B01G134900 chr3D 13886771 13887355 584 True 780.000000 780 90.801000 2482 3065 1 chr3D.!!$R1 583
8 TraesCS6B01G134900 chr3B 759071317 759071896 579 True 791.000000 791 91.252000 2483 3065 1 chr3B.!!$R1 582
9 TraesCS6B01G134900 chr4A 691250822 691251392 570 False 756.000000 756 90.427000 2482 3065 1 chr4A.!!$F2 583
10 TraesCS6B01G134900 chr1B 130582749 130583332 583 False 736.000000 736 89.420000 2481 3065 1 chr1B.!!$F4 584
11 TraesCS6B01G134900 chr1B 63944584 63945153 569 False 717.000000 717 89.231000 2482 3065 1 chr1B.!!$F2 583
12 TraesCS6B01G134900 chr1B 63937038 63937607 569 False 706.000000 706 88.889000 2482 3065 1 chr1B.!!$F1 583
13 TraesCS6B01G134900 chr1B 63951574 63952143 569 False 706.000000 706 88.889000 2482 3065 1 chr1B.!!$F3 583
14 TraesCS6B01G134900 chr1B 298754562 298755090 528 True 678.000000 678 89.777000 2482 3016 1 chr1B.!!$R1 534
15 TraesCS6B01G134900 chrUn 339390586 339391155 569 True 706.000000 706 88.889000 2482 3065 1 chrUn.!!$R2 583
16 TraesCS6B01G134900 chrUn 65745914 65746483 569 True 684.000000 684 88.205000 2482 3065 1 chrUn.!!$R1 583

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
694 701 0.032952 ACGACAAACTAAGCCTGCGA 59.967 50.0 0.0 0.0 0.0 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2458 2480 1.196354 GAGCTATGCCGATGATTGCAC 59.804 52.381 0.0 0.0 40.88 4.57 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
72 73 1.111277 GTTTTGGCCACACAGGAGTT 58.889 50.000 3.88 0.00 41.22 3.01
221 225 6.762187 TCATGTGTGTTTCAGCAAAATTTGAT 59.238 30.769 10.26 0.00 0.00 2.57
263 270 2.858868 GAGCTGTGCTTGTGCTCG 59.141 61.111 0.00 0.00 42.70 5.03
274 281 4.006682 GCTTGTGCTCGAGGAAACTTCC 62.007 54.545 15.58 0.00 40.94 3.46
327 334 5.968848 TGCTCACGTTATTTTCTGTTGAAAC 59.031 36.000 0.00 0.00 41.34 2.78
383 390 5.221303 ACCATCAACCAAACATCTGAAACTG 60.221 40.000 0.00 0.00 0.00 3.16
439 446 0.389426 GCCTTTGCAGCAGTGATTGG 60.389 55.000 0.00 0.00 37.47 3.16
567 574 6.461110 TTCAGTTAGTTTATACTCCCTCCG 57.539 41.667 0.00 0.00 35.78 4.63
568 575 5.513233 TCAGTTAGTTTATACTCCCTCCGT 58.487 41.667 0.00 0.00 35.78 4.69
569 576 5.591877 TCAGTTAGTTTATACTCCCTCCGTC 59.408 44.000 0.00 0.00 35.78 4.79
570 577 4.892345 AGTTAGTTTATACTCCCTCCGTCC 59.108 45.833 0.00 0.00 35.78 4.79
571 578 2.675583 AGTTTATACTCCCTCCGTCCC 58.324 52.381 0.00 0.00 0.00 4.46
572 579 2.023695 AGTTTATACTCCCTCCGTCCCA 60.024 50.000 0.00 0.00 0.00 4.37
573 580 2.767960 GTTTATACTCCCTCCGTCCCAA 59.232 50.000 0.00 0.00 0.00 4.12
574 581 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
575 582 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
576 583 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
577 584 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
578 585 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
579 586 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
580 587 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
581 588 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
582 589 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
583 590 2.890945 CCTCCGTCCCAAAATTCTTGTT 59.109 45.455 0.00 0.00 0.00 2.83
584 591 3.320826 CCTCCGTCCCAAAATTCTTGTTT 59.679 43.478 0.00 0.00 0.00 2.83
585 592 4.202212 CCTCCGTCCCAAAATTCTTGTTTT 60.202 41.667 0.00 0.00 0.00 2.43
586 593 5.010213 CCTCCGTCCCAAAATTCTTGTTTTA 59.990 40.000 0.00 0.00 30.56 1.52
587 594 6.079424 TCCGTCCCAAAATTCTTGTTTTAG 57.921 37.500 0.00 0.00 30.56 1.85
588 595 5.595133 TCCGTCCCAAAATTCTTGTTTTAGT 59.405 36.000 0.00 0.00 30.56 2.24
589 596 6.771749 TCCGTCCCAAAATTCTTGTTTTAGTA 59.228 34.615 0.00 0.00 30.56 1.82
590 597 7.449086 TCCGTCCCAAAATTCTTGTTTTAGTAT 59.551 33.333 0.00 0.00 30.56 2.12
591 598 8.085909 CCGTCCCAAAATTCTTGTTTTAGTATT 58.914 33.333 0.00 0.00 30.56 1.89
620 627 7.367159 ACATCCGTATCTAGACGAATCTAAG 57.633 40.000 5.60 0.00 45.82 2.18
621 628 7.160049 ACATCCGTATCTAGACGAATCTAAGA 58.840 38.462 5.60 0.00 45.82 2.10
622 629 7.118101 ACATCCGTATCTAGACGAATCTAAGAC 59.882 40.741 5.60 0.00 45.82 3.01
623 630 6.519382 TCCGTATCTAGACGAATCTAAGACA 58.481 40.000 5.60 0.00 45.82 3.41
624 631 6.988580 TCCGTATCTAGACGAATCTAAGACAA 59.011 38.462 5.60 0.00 45.82 3.18
625 632 7.171167 TCCGTATCTAGACGAATCTAAGACAAG 59.829 40.741 5.60 0.00 45.82 3.16
626 633 7.171167 CCGTATCTAGACGAATCTAAGACAAGA 59.829 40.741 5.60 0.00 45.82 3.02
627 634 8.549548 CGTATCTAGACGAATCTAAGACAAGAA 58.450 37.037 0.00 0.00 45.82 2.52
633 640 8.833231 AGACGAATCTAAGACAAGAATTTTGA 57.167 30.769 0.00 0.00 31.46 2.69
634 641 8.930760 AGACGAATCTAAGACAAGAATTTTGAG 58.069 33.333 0.00 0.00 31.46 3.02
635 642 8.833231 ACGAATCTAAGACAAGAATTTTGAGA 57.167 30.769 0.00 1.83 0.00 3.27
636 643 8.713271 ACGAATCTAAGACAAGAATTTTGAGAC 58.287 33.333 0.00 0.00 0.00 3.36
637 644 7.895259 CGAATCTAAGACAAGAATTTTGAGACG 59.105 37.037 7.18 0.00 0.00 4.18
638 645 7.602517 ATCTAAGACAAGAATTTTGAGACGG 57.397 36.000 7.18 0.00 0.00 4.79
639 646 6.755206 TCTAAGACAAGAATTTTGAGACGGA 58.245 36.000 7.18 0.00 0.00 4.69
640 647 5.931441 AAGACAAGAATTTTGAGACGGAG 57.069 39.130 7.18 0.00 0.00 4.63
641 648 4.319177 AGACAAGAATTTTGAGACGGAGG 58.681 43.478 7.18 0.00 0.00 4.30
642 649 3.412386 ACAAGAATTTTGAGACGGAGGG 58.588 45.455 7.18 0.00 0.00 4.30
643 650 3.072476 ACAAGAATTTTGAGACGGAGGGA 59.928 43.478 7.18 0.00 0.00 4.20
644 651 3.618690 AGAATTTTGAGACGGAGGGAG 57.381 47.619 0.00 0.00 0.00 4.30
691 698 1.873591 AGCAACGACAAACTAAGCCTG 59.126 47.619 0.00 0.00 0.00 4.85
693 700 0.865769 AACGACAAACTAAGCCTGCG 59.134 50.000 0.00 0.00 0.00 5.18
694 701 0.032952 ACGACAAACTAAGCCTGCGA 59.967 50.000 0.00 0.00 0.00 5.10
695 702 1.337823 ACGACAAACTAAGCCTGCGAT 60.338 47.619 0.00 0.00 0.00 4.58
757 764 2.811431 CACGTGCTTTGTGGGATCTTTA 59.189 45.455 0.82 0.00 33.69 1.85
778 786 9.556030 TCTTTATCATATCTCATACGCGTTAAG 57.444 33.333 20.78 13.02 0.00 1.85
807 815 1.078848 ACACGAGCTGATGCCTTCC 60.079 57.895 0.00 0.00 40.80 3.46
842 850 1.800655 CGTGATGTGCTAGGAGTCTGC 60.801 57.143 0.00 0.00 0.00 4.26
851 859 2.552315 GCTAGGAGTCTGCTACAGCTAG 59.448 54.545 8.48 0.00 42.66 3.42
859 867 4.035792 AGTCTGCTACAGCTAGTCAATACG 59.964 45.833 2.44 0.00 42.66 3.06
882 891 7.655490 ACGGACACATATAAACTGTATCCTAC 58.345 38.462 1.81 0.00 37.93 3.18
883 892 7.504911 ACGGACACATATAAACTGTATCCTACT 59.495 37.037 1.81 0.00 37.93 2.57
884 893 9.006839 CGGACACATATAAACTGTATCCTACTA 57.993 37.037 1.81 0.00 37.93 1.82
940 953 4.156622 GTTAGGAAACCGCGCGCC 62.157 66.667 27.36 20.54 0.00 6.53
1031 1044 3.360340 GACCTCGTCGACGGTGGT 61.360 66.667 37.17 37.17 44.31 4.16
1078 1091 0.613777 GGTTACTGGTCACTCCCTGG 59.386 60.000 0.00 0.00 34.77 4.45
1145 1158 2.224281 GCCATCACGACTGGAATATCCA 60.224 50.000 0.00 0.00 45.98 3.41
1146 1159 3.393800 CCATCACGACTGGAATATCCAC 58.606 50.000 0.00 0.00 42.67 4.02
1199 1212 2.559668 ACGATCAGTTCACCTCGGTTTA 59.440 45.455 0.00 0.00 35.52 2.01
1324 1340 1.269831 ACAAGTTCGTGCCTGAGTCTC 60.270 52.381 0.00 0.00 0.00 3.36
1326 1342 1.079750 GTTCGTGCCTGAGTCTCCC 60.080 63.158 0.00 0.00 0.00 4.30
1349 1365 1.603739 GGGGTGTCTCCAGGTTTGC 60.604 63.158 0.00 0.00 38.11 3.68
1352 1368 0.951040 GGTGTCTCCAGGTTTGCGAG 60.951 60.000 0.00 0.00 35.97 5.03
1371 1387 2.032634 TAAAGCTGACTTGGCCGCG 61.033 57.895 0.00 0.00 35.85 6.46
1426 1442 2.688507 AGTGCACCGTCAGAGTTATTG 58.311 47.619 14.63 0.00 0.00 1.90
1449 1465 3.154489 CTCTAAACTCAACGACGACGAG 58.846 50.000 15.32 9.24 42.66 4.18
1660 1676 0.663867 CGCGATGATGGAGAGCAGAG 60.664 60.000 0.00 0.00 0.00 3.35
1746 1762 3.094572 CAATGATTGCCTCCCTGAGTTT 58.905 45.455 0.00 0.00 0.00 2.66
1797 1813 5.181690 ACATGACGCAACATTTGTTAGTT 57.818 34.783 0.00 0.00 36.32 2.24
1849 1865 3.498774 AGCTTATATGTGAGGGCAAGG 57.501 47.619 0.00 0.00 0.00 3.61
1872 1888 1.303309 GCAAGGCGCTAGATGTCAAT 58.697 50.000 7.64 0.00 37.77 2.57
1952 1968 8.038944 GGATTACTGTCTCAAGTACATGGTAAA 58.961 37.037 0.00 0.00 32.39 2.01
1959 1975 6.929606 GTCTCAAGTACATGGTAAAAGACAGT 59.070 38.462 10.36 0.00 32.78 3.55
2076 2092 0.179129 AGCTGTAATTGCATTGCCGC 60.179 50.000 6.12 0.00 35.87 6.53
2077 2093 1.147557 GCTGTAATTGCATTGCCGCC 61.148 55.000 6.12 0.00 31.11 6.13
2078 2094 0.866906 CTGTAATTGCATTGCCGCCG 60.867 55.000 6.12 0.00 0.00 6.46
2086 2102 1.137404 CATTGCCGCCGAGAAAAGG 59.863 57.895 0.00 0.00 0.00 3.11
2142 2158 9.157104 TCTGTAAACTGATTATTTCGTAATGCA 57.843 29.630 0.00 0.00 33.16 3.96
2144 2160 9.715123 TGTAAACTGATTATTTCGTAATGCATG 57.285 29.630 0.00 0.00 33.16 4.06
2145 2161 9.169468 GTAAACTGATTATTTCGTAATGCATGG 57.831 33.333 0.00 0.00 33.16 3.66
2150 2166 7.635423 TGATTATTTCGTAATGCATGGTGTAC 58.365 34.615 0.00 0.00 33.16 2.90
2151 2169 7.497579 TGATTATTTCGTAATGCATGGTGTACT 59.502 33.333 0.00 0.00 33.16 2.73
2160 2178 4.182693 TGCATGGTGTACTGTGTACTAC 57.817 45.455 8.94 5.92 0.00 2.73
2197 2215 5.874895 TCTTTGATGCATCACTCTTTCAG 57.125 39.130 28.72 14.74 36.36 3.02
2215 2233 1.798223 CAGCTTAACACAAGCACGCTA 59.202 47.619 11.24 0.00 45.30 4.26
2254 2272 8.541899 TTTAAAGACAGTTTTTATGAACCCCT 57.458 30.769 0.00 0.00 0.00 4.79
2290 2308 4.152759 TCTTGGTTACTGCGAATTTAACGG 59.847 41.667 0.00 0.00 0.00 4.44
2316 2335 2.676121 CAAACGCATGGGCCAGGA 60.676 61.111 24.47 0.00 36.38 3.86
2320 2339 3.136123 CGCATGGGCCAGGAAGTG 61.136 66.667 24.47 11.36 36.38 3.16
2363 2382 0.943835 GTTTTCCACAATGCCCACGC 60.944 55.000 0.00 0.00 0.00 5.34
2381 2400 2.287608 ACGCACTTAAAAGCTGAAAGGC 60.288 45.455 7.60 6.96 0.00 4.35
2382 2401 2.287547 CGCACTTAAAAGCTGAAAGGCA 60.288 45.455 7.60 0.00 34.17 4.75
2393 2412 2.877300 GCTGAAAGGCATGGAGAACTGA 60.877 50.000 0.00 0.00 0.00 3.41
2402 2421 6.529220 AGGCATGGAGAACTGAAGAATATAC 58.471 40.000 0.00 0.00 0.00 1.47
2403 2422 5.703130 GGCATGGAGAACTGAAGAATATACC 59.297 44.000 0.00 0.00 0.00 2.73
2404 2423 6.465035 GGCATGGAGAACTGAAGAATATACCT 60.465 42.308 0.00 0.00 0.00 3.08
2405 2424 7.256332 GGCATGGAGAACTGAAGAATATACCTA 60.256 40.741 0.00 0.00 0.00 3.08
2406 2425 7.600752 GCATGGAGAACTGAAGAATATACCTAC 59.399 40.741 0.00 0.00 0.00 3.18
2407 2426 8.865090 CATGGAGAACTGAAGAATATACCTACT 58.135 37.037 0.00 0.00 0.00 2.57
2408 2427 8.466617 TGGAGAACTGAAGAATATACCTACTC 57.533 38.462 0.00 0.00 0.00 2.59
2409 2428 8.282982 TGGAGAACTGAAGAATATACCTACTCT 58.717 37.037 0.00 0.00 0.00 3.24
2410 2429 9.796180 GGAGAACTGAAGAATATACCTACTCTA 57.204 37.037 0.00 0.00 0.00 2.43
2419 2438 8.411991 AGAATATACCTACTCTACCTTTGAGC 57.588 38.462 0.00 0.00 35.12 4.26
2439 2458 7.624360 TGAGCATACAAAATAAATTCCGTCT 57.376 32.000 0.00 0.00 0.00 4.18
2440 2459 8.725405 TGAGCATACAAAATAAATTCCGTCTA 57.275 30.769 0.00 0.00 0.00 2.59
2458 2480 4.380655 CGTCTACTGTTAACTTCCAGGAGG 60.381 50.000 7.22 0.00 39.65 4.30
2759 2789 2.064581 CCCTTCCTTCCCCGATCGT 61.065 63.158 15.09 0.00 0.00 3.73
2773 2803 3.385749 ATCGTCGCCATGTCCACCC 62.386 63.158 0.00 0.00 0.00 4.61
2820 2850 3.012722 CAAACCTCCGGGGCCCTA 61.013 66.667 24.38 7.74 39.10 3.53
2827 2857 1.616930 TCCGGGGCCCTAATCAACA 60.617 57.895 24.38 0.00 0.00 3.33
2828 2858 1.453197 CCGGGGCCCTAATCAACAC 60.453 63.158 24.38 0.00 0.00 3.32
2829 2859 1.453197 CGGGGCCCTAATCAACACC 60.453 63.158 24.38 0.00 0.00 4.16
2830 2860 1.694856 GGGGCCCTAATCAACACCA 59.305 57.895 24.38 0.00 0.00 4.17
2831 2861 0.683179 GGGGCCCTAATCAACACCAC 60.683 60.000 24.38 0.00 0.00 4.16
2832 2862 0.683179 GGGCCCTAATCAACACCACC 60.683 60.000 17.04 0.00 0.00 4.61
2833 2863 0.331616 GGCCCTAATCAACACCACCT 59.668 55.000 0.00 0.00 0.00 4.00
2834 2864 1.682087 GGCCCTAATCAACACCACCTC 60.682 57.143 0.00 0.00 0.00 3.85
2835 2865 1.682087 GCCCTAATCAACACCACCTCC 60.682 57.143 0.00 0.00 0.00 4.30
2836 2866 1.406887 CCCTAATCAACACCACCTCCG 60.407 57.143 0.00 0.00 0.00 4.63
2837 2867 1.369625 CTAATCAACACCACCTCCGC 58.630 55.000 0.00 0.00 0.00 5.54
2838 2868 0.035820 TAATCAACACCACCTCCGCC 60.036 55.000 0.00 0.00 0.00 6.13
2839 2869 3.605749 ATCAACACCACCTCCGCCG 62.606 63.158 0.00 0.00 0.00 6.46
2943 2997 1.153765 CGTCCTCGATCTGCAGCAA 60.154 57.895 9.47 0.00 39.71 3.91
2958 3012 1.539388 CAGCAATCCAACTACGCCAAA 59.461 47.619 0.00 0.00 0.00 3.28
2962 3016 2.491693 CAATCCAACTACGCCAAATGGT 59.508 45.455 0.71 0.00 37.57 3.55
3025 3079 3.371063 ACATCTCCGCCGTCACGT 61.371 61.111 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.463585 TCGGCCGGCGGATAAGTT 61.464 61.111 33.44 0.00 0.00 2.66
31 32 3.905493 TTGAAAAGGTGGGGGTTATGA 57.095 42.857 0.00 0.00 0.00 2.15
91 92 6.972328 GTGTGGTTAAAATATGCATGTGGTAG 59.028 38.462 10.16 0.00 0.00 3.18
221 225 9.947433 TCCTCGTTATATTTTCACCTTTCTTTA 57.053 29.630 0.00 0.00 0.00 1.85
262 269 0.882927 TTGCCACGGAAGTTTCCTCG 60.883 55.000 9.11 0.00 46.40 4.63
263 270 1.001706 GTTTGCCACGGAAGTTTCCTC 60.002 52.381 9.11 0.00 46.40 3.71
274 281 0.040514 TGCGAATCAAGTTTGCCACG 60.041 50.000 0.00 0.00 45.10 4.94
383 390 9.846248 ATGATCTGAGCTTGTAAAAATACAAAC 57.154 29.630 3.35 0.00 39.19 2.93
439 446 2.410730 AGTACGTGCGTATCAAACTTGC 59.589 45.455 7.72 0.00 32.82 4.01
544 551 5.954150 ACGGAGGGAGTATAAACTAACTGAA 59.046 40.000 0.00 0.00 35.56 3.02
552 559 2.391678 TGGGACGGAGGGAGTATAAAC 58.608 52.381 0.00 0.00 0.00 2.01
554 561 2.852714 TTGGGACGGAGGGAGTATAA 57.147 50.000 0.00 0.00 0.00 0.98
557 564 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
558 565 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
559 566 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
561 568 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
562 569 2.514803 ACAAGAATTTTGGGACGGAGG 58.485 47.619 0.00 0.00 0.00 4.30
563 570 4.584327 AAACAAGAATTTTGGGACGGAG 57.416 40.909 0.00 0.00 0.00 4.63
564 571 5.595133 ACTAAAACAAGAATTTTGGGACGGA 59.405 36.000 0.00 0.00 35.11 4.69
565 572 5.838529 ACTAAAACAAGAATTTTGGGACGG 58.161 37.500 0.00 0.00 35.11 4.79
594 601 9.100554 CTTAGATTCGTCTAGATACGGATGTAT 57.899 37.037 2.64 0.00 41.14 2.29
595 602 8.309656 TCTTAGATTCGTCTAGATACGGATGTA 58.690 37.037 2.64 1.02 41.14 2.29
596 603 7.118101 GTCTTAGATTCGTCTAGATACGGATGT 59.882 40.741 2.64 1.92 41.14 3.06
597 604 7.117956 TGTCTTAGATTCGTCTAGATACGGATG 59.882 40.741 2.64 0.00 41.14 3.51
598 605 7.160049 TGTCTTAGATTCGTCTAGATACGGAT 58.840 38.462 0.00 0.00 43.73 4.18
599 606 6.519382 TGTCTTAGATTCGTCTAGATACGGA 58.481 40.000 0.00 0.00 43.05 4.69
600 607 6.782298 TGTCTTAGATTCGTCTAGATACGG 57.218 41.667 0.00 0.00 43.05 4.02
601 608 8.074474 TCTTGTCTTAGATTCGTCTAGATACG 57.926 38.462 0.00 0.00 44.19 3.06
607 614 9.923143 TCAAAATTCTTGTCTTAGATTCGTCTA 57.077 29.630 0.00 0.00 0.00 2.59
608 615 8.833231 TCAAAATTCTTGTCTTAGATTCGTCT 57.167 30.769 0.00 0.00 0.00 4.18
609 616 8.926710 TCTCAAAATTCTTGTCTTAGATTCGTC 58.073 33.333 0.00 0.00 0.00 4.20
610 617 8.713271 GTCTCAAAATTCTTGTCTTAGATTCGT 58.287 33.333 0.00 0.00 0.00 3.85
611 618 7.895259 CGTCTCAAAATTCTTGTCTTAGATTCG 59.105 37.037 0.00 0.00 0.00 3.34
612 619 8.171840 CCGTCTCAAAATTCTTGTCTTAGATTC 58.828 37.037 0.00 0.00 0.00 2.52
613 620 7.878127 TCCGTCTCAAAATTCTTGTCTTAGATT 59.122 33.333 0.00 0.00 0.00 2.40
614 621 7.386851 TCCGTCTCAAAATTCTTGTCTTAGAT 58.613 34.615 0.00 0.00 0.00 1.98
615 622 6.755206 TCCGTCTCAAAATTCTTGTCTTAGA 58.245 36.000 0.00 0.00 0.00 2.10
616 623 6.091441 CCTCCGTCTCAAAATTCTTGTCTTAG 59.909 42.308 0.00 0.00 0.00 2.18
617 624 5.932303 CCTCCGTCTCAAAATTCTTGTCTTA 59.068 40.000 0.00 0.00 0.00 2.10
618 625 4.757149 CCTCCGTCTCAAAATTCTTGTCTT 59.243 41.667 0.00 0.00 0.00 3.01
619 626 4.319177 CCTCCGTCTCAAAATTCTTGTCT 58.681 43.478 0.00 0.00 0.00 3.41
620 627 3.437049 CCCTCCGTCTCAAAATTCTTGTC 59.563 47.826 0.00 0.00 0.00 3.18
621 628 3.072476 TCCCTCCGTCTCAAAATTCTTGT 59.928 43.478 0.00 0.00 0.00 3.16
622 629 3.674997 TCCCTCCGTCTCAAAATTCTTG 58.325 45.455 0.00 0.00 0.00 3.02
623 630 3.328050 ACTCCCTCCGTCTCAAAATTCTT 59.672 43.478 0.00 0.00 0.00 2.52
624 631 2.907042 ACTCCCTCCGTCTCAAAATTCT 59.093 45.455 0.00 0.00 0.00 2.40
625 632 3.336138 ACTCCCTCCGTCTCAAAATTC 57.664 47.619 0.00 0.00 0.00 2.17
626 633 6.749036 ATATACTCCCTCCGTCTCAAAATT 57.251 37.500 0.00 0.00 0.00 1.82
627 634 7.509659 ACTTATATACTCCCTCCGTCTCAAAAT 59.490 37.037 0.00 0.00 0.00 1.82
628 635 6.837568 ACTTATATACTCCCTCCGTCTCAAAA 59.162 38.462 0.00 0.00 0.00 2.44
629 636 6.371278 ACTTATATACTCCCTCCGTCTCAAA 58.629 40.000 0.00 0.00 0.00 2.69
630 637 5.950023 ACTTATATACTCCCTCCGTCTCAA 58.050 41.667 0.00 0.00 0.00 3.02
631 638 5.579753 ACTTATATACTCCCTCCGTCTCA 57.420 43.478 0.00 0.00 0.00 3.27
632 639 6.002704 TGAACTTATATACTCCCTCCGTCTC 58.997 44.000 0.00 0.00 0.00 3.36
633 640 5.950023 TGAACTTATATACTCCCTCCGTCT 58.050 41.667 0.00 0.00 0.00 4.18
634 641 6.040166 TGTTGAACTTATATACTCCCTCCGTC 59.960 42.308 0.00 0.00 0.00 4.79
635 642 5.895534 TGTTGAACTTATATACTCCCTCCGT 59.104 40.000 0.00 0.00 0.00 4.69
636 643 6.183360 TGTGTTGAACTTATATACTCCCTCCG 60.183 42.308 0.00 0.00 0.00 4.63
637 644 7.120923 TGTGTTGAACTTATATACTCCCTCC 57.879 40.000 0.00 0.00 0.00 4.30
638 645 8.421784 TGATGTGTTGAACTTATATACTCCCTC 58.578 37.037 0.00 0.00 0.00 4.30
639 646 8.319057 TGATGTGTTGAACTTATATACTCCCT 57.681 34.615 0.00 0.00 0.00 4.20
667 674 3.497262 GGCTTAGTTTGTCGTTGCTAAGT 59.503 43.478 10.56 0.00 41.22 2.24
693 700 3.185246 ACAACTCACCCGATGATGATC 57.815 47.619 0.00 0.00 36.48 2.92
694 701 3.055167 TGAACAACTCACCCGATGATGAT 60.055 43.478 0.00 0.00 36.48 2.45
695 702 2.301583 TGAACAACTCACCCGATGATGA 59.698 45.455 0.00 0.00 36.48 2.92
757 764 7.865889 TCAAACTTAACGCGTATGAGATATGAT 59.134 33.333 14.46 0.00 0.00 2.45
770 777 2.154198 TGTCACGATCAAACTTAACGCG 59.846 45.455 3.53 3.53 0.00 6.01
842 850 4.095932 TGTGTCCGTATTGACTAGCTGTAG 59.904 45.833 0.00 0.00 36.21 2.74
851 859 7.766219 ACAGTTTATATGTGTCCGTATTGAC 57.234 36.000 0.00 0.00 35.77 3.18
940 953 3.612860 AGAAAAGAAATCGATCGTGGACG 59.387 43.478 15.94 0.00 41.45 4.79
1068 1081 2.359169 GCCGATGACCAGGGAGTGA 61.359 63.158 0.00 0.00 0.00 3.41
1078 1091 1.599542 GAAGGTATTGCTGCCGATGAC 59.400 52.381 0.00 0.00 31.34 3.06
1126 1139 4.327982 AGTGGATATTCCAGTCGTGATG 57.672 45.455 0.00 0.00 46.94 3.07
1145 1158 1.377202 TCGCCGTTCGGGTAGTAGT 60.377 57.895 13.16 0.00 39.05 2.73
1146 1159 1.063166 GTCGCCGTTCGGGTAGTAG 59.937 63.158 13.16 0.00 39.05 2.57
1199 1212 5.648092 GTGTTTATGTTTACCAGCCAGAGAT 59.352 40.000 0.00 0.00 0.00 2.75
1289 1302 1.076024 ACTTGTCGGTGTAGGGTCCTA 59.924 52.381 0.00 0.00 0.00 2.94
1326 1342 1.376466 CCTGGAGACACCCCAACTG 59.624 63.158 0.00 0.00 38.00 3.16
1349 1365 1.079503 GGCCAAGTCAGCTTTACTCG 58.920 55.000 0.00 0.00 31.49 4.18
1352 1368 1.502190 GCGGCCAAGTCAGCTTTAC 59.498 57.895 2.24 0.00 31.49 2.01
1371 1387 3.005578 AGTCGTCTTTAAGACACCCTGAC 59.994 47.826 22.70 19.31 45.30 3.51
1426 1442 1.984297 GTCGTCGTTGAGTTTAGAGGC 59.016 52.381 0.00 0.00 0.00 4.70
1449 1465 1.209640 GTCCTCACAGTCGTCGTCC 59.790 63.158 0.00 0.00 0.00 4.79
1660 1676 2.289002 CCTTGATGCGGATAGTGCTTTC 59.711 50.000 0.00 0.00 0.00 2.62
1746 1762 3.099905 CACTTCTGTGGTCTCCTCCATA 58.900 50.000 0.00 0.00 40.33 2.74
1797 1813 4.865761 GCGTACCGATCAGCCGCA 62.866 66.667 8.28 0.00 43.53 5.69
1820 1836 3.470709 TCACATATAAGCTTCAGCCTGC 58.529 45.455 0.00 0.00 43.38 4.85
1821 1837 4.063689 CCTCACATATAAGCTTCAGCCTG 58.936 47.826 0.00 0.00 43.38 4.85
1952 1968 3.391049 GCTCGTAACCTTTCACTGTCTT 58.609 45.455 0.00 0.00 0.00 3.01
1959 1975 3.134574 ACAATGGCTCGTAACCTTTCA 57.865 42.857 0.00 0.00 0.00 2.69
2076 2092 1.826385 AGTTGCATCCCTTTTCTCGG 58.174 50.000 0.00 0.00 0.00 4.63
2077 2093 3.568538 CAAAGTTGCATCCCTTTTCTCG 58.431 45.455 4.35 0.00 0.00 4.04
2101 2117 9.754382 TCAGTTTACAGAAAATAGACTTTACGT 57.246 29.630 0.00 0.00 0.00 3.57
2133 2149 3.258228 CACAGTACACCATGCATTACGA 58.742 45.455 0.00 0.00 0.00 3.43
2134 2150 3.000041 ACACAGTACACCATGCATTACG 59.000 45.455 0.00 0.00 0.00 3.18
2135 2151 5.175859 AGTACACAGTACACCATGCATTAC 58.824 41.667 0.00 0.00 0.00 1.89
2138 2154 3.981071 AGTACACAGTACACCATGCAT 57.019 42.857 9.68 0.00 0.00 3.96
2140 2156 3.194968 AGGTAGTACACAGTACACCATGC 59.805 47.826 20.47 4.02 32.94 4.06
2142 2158 6.893554 TGATTAGGTAGTACACAGTACACCAT 59.106 38.462 20.47 12.22 32.94 3.55
2144 2160 6.764308 TGATTAGGTAGTACACAGTACACC 57.236 41.667 9.68 12.92 32.94 4.16
2145 2161 8.464404 TGAATGATTAGGTAGTACACAGTACAC 58.536 37.037 9.68 5.93 32.94 2.90
2160 2178 8.936070 TGCATCAAAGAAAATGAATGATTAGG 57.064 30.769 0.00 0.00 0.00 2.69
2182 2200 4.214119 GTGTTAAGCTGAAAGAGTGATGCA 59.786 41.667 0.00 0.00 34.07 3.96
2197 2215 1.798813 ACTAGCGTGCTTGTGTTAAGC 59.201 47.619 8.12 4.77 43.29 3.09
2250 2268 1.693627 AGACGTACTATGCAGAGGGG 58.306 55.000 13.85 3.73 0.00 4.79
2254 2272 4.703575 AGTAACCAAGACGTACTATGCAGA 59.296 41.667 0.00 0.00 0.00 4.26
2307 2326 2.925706 TACGCACTTCCTGGCCCA 60.926 61.111 0.00 0.00 0.00 5.36
2363 2382 4.022068 TCCATGCCTTTCAGCTTTTAAGTG 60.022 41.667 0.00 0.00 0.00 3.16
2365 2384 4.460382 TCTCCATGCCTTTCAGCTTTTAAG 59.540 41.667 0.00 0.00 0.00 1.85
2381 2400 8.865090 AGTAGGTATATTCTTCAGTTCTCCATG 58.135 37.037 0.00 0.00 0.00 3.66
2382 2401 9.084533 GAGTAGGTATATTCTTCAGTTCTCCAT 57.915 37.037 0.00 0.00 0.00 3.41
2393 2412 8.862085 GCTCAAAGGTAGAGTAGGTATATTCTT 58.138 37.037 0.00 0.00 35.55 2.52
2402 2421 5.854010 TGTATGCTCAAAGGTAGAGTAGG 57.146 43.478 0.00 0.00 35.55 3.18
2403 2422 8.723942 ATTTTGTATGCTCAAAGGTAGAGTAG 57.276 34.615 0.00 0.00 38.32 2.57
2405 2424 9.515226 TTTATTTTGTATGCTCAAAGGTAGAGT 57.485 29.630 0.00 0.00 38.32 3.24
2410 2429 7.759433 CGGAATTTATTTTGTATGCTCAAAGGT 59.241 33.333 0.00 0.00 38.32 3.50
2411 2430 7.759433 ACGGAATTTATTTTGTATGCTCAAAGG 59.241 33.333 0.00 0.00 38.32 3.11
2439 2458 3.007614 GCACCTCCTGGAAGTTAACAGTA 59.992 47.826 8.61 0.00 37.04 2.74
2440 2459 2.224548 GCACCTCCTGGAAGTTAACAGT 60.225 50.000 8.61 0.00 37.04 3.55
2458 2480 1.196354 GAGCTATGCCGATGATTGCAC 59.804 52.381 0.00 0.00 40.88 4.57
2707 2734 4.369837 TTAGGGTTTGGGGCGGCC 62.370 66.667 22.00 22.00 0.00 6.13
2712 2739 2.754254 GCGCCTTAGGGTTTGGGG 60.754 66.667 0.00 0.00 36.95 4.96
2820 2850 1.303317 GGCGGAGGTGGTGTTGATT 60.303 57.895 0.00 0.00 0.00 2.57
2934 2988 1.725641 CGTAGTTGGATTGCTGCAGA 58.274 50.000 20.43 0.00 0.00 4.26
2943 2997 2.091541 CACCATTTGGCGTAGTTGGAT 58.908 47.619 0.00 0.00 39.32 3.41
2962 3016 1.450134 GGACGGTGATGAGCATGCA 60.450 57.895 21.98 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.