Multiple sequence alignment - TraesCS6B01G122400

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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 TraesCS6B01G122400 chr6B 100.000 2171 0 0 301 2471 117630074 117632244 0.000000e+00 4010.0
1 TraesCS6B01G122400 chr6B 83.589 847 89 24 734 1562 117588637 117589451 0.000000e+00 749.0
2 TraesCS6B01G122400 chr6B 84.091 792 84 19 751 1523 117540922 117541690 0.000000e+00 726.0
3 TraesCS6B01G122400 chr6B 92.671 423 25 3 1905 2324 117542019 117542438 2.720000e-169 604.0
4 TraesCS6B01G122400 chr6B 92.941 170 8 4 1706 1874 117541855 117542021 6.830000e-61 244.0
5 TraesCS6B01G122400 chr6B 100.000 46 0 0 1 46 117629774 117629819 4.380000e-13 86.1
6 TraesCS6B01G122400 chr6D 86.936 1041 83 31 594 1616 53850579 53849574 0.000000e+00 1120.0
7 TraesCS6B01G122400 chr6D 90.625 640 50 4 1715 2351 53848953 53848321 0.000000e+00 841.0
8 TraesCS6B01G122400 chr6D 85.965 228 29 2 303 527 53852002 53851775 8.830000e-60 241.0
9 TraesCS6B01G122400 chr6A 92.535 710 38 8 758 1455 61185477 61186183 0.000000e+00 1003.0
10 TraesCS6B01G122400 chr6A 88.970 825 52 14 1627 2430 61186362 61187168 0.000000e+00 983.0
11 TraesCS6B01G122400 chr6A 83.888 751 72 27 734 1455 61136469 61137199 0.000000e+00 671.0
12 TraesCS6B01G122400 chr6A 83.750 320 29 5 1627 1926 61137374 61137690 5.200000e-72 281.0


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 TraesCS6B01G122400 chr6B 117629774 117632244 2470 False 2048.050000 4010 100.0000 1 2471 2 chr6B.!!$F3 2470
1 TraesCS6B01G122400 chr6B 117588637 117589451 814 False 749.000000 749 83.5890 734 1562 1 chr6B.!!$F1 828
2 TraesCS6B01G122400 chr6B 117540922 117542438 1516 False 524.666667 726 89.9010 751 2324 3 chr6B.!!$F2 1573
3 TraesCS6B01G122400 chr6D 53848321 53852002 3681 True 734.000000 1120 87.8420 303 2351 3 chr6D.!!$R1 2048
4 TraesCS6B01G122400 chr6A 61185477 61187168 1691 False 993.000000 1003 90.7525 758 2430 2 chr6A.!!$F2 1672
5 TraesCS6B01G122400 chr6A 61136469 61137690 1221 False 476.000000 671 83.8190 734 1926 2 chr6A.!!$F1 1192

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
414 415 0.034186 AGCGGGGCAATCTTCAATGA 60.034 50.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 3073 0.179086 GACAGGCTAGGAGCAAGAGC 60.179 60.0 0.21 0.0 44.75 4.09 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
30 31 8.824159 TGAATAATTGTAAATTTGTGTGTGGG 57.176 30.769 0.00 0.00 0.00 4.61
31 32 7.386299 TGAATAATTGTAAATTTGTGTGTGGGC 59.614 33.333 0.00 0.00 0.00 5.36
32 33 3.460857 TTGTAAATTTGTGTGTGGGCC 57.539 42.857 0.00 0.00 0.00 5.80
33 34 1.689273 TGTAAATTTGTGTGTGGGCCC 59.311 47.619 17.59 17.59 0.00 5.80
34 35 0.962489 TAAATTTGTGTGTGGGCCCG 59.038 50.000 19.37 0.00 0.00 6.13
35 36 2.376228 AAATTTGTGTGTGGGCCCGC 62.376 55.000 29.34 29.34 0.00 6.13
36 37 4.822628 TTTGTGTGTGGGCCCGCA 62.823 61.111 34.47 34.47 0.00 5.69
37 38 4.822628 TTGTGTGTGGGCCCGCAA 62.823 61.111 39.02 25.07 38.24 4.85
38 39 4.594854 TGTGTGTGGGCCCGCAAT 62.595 61.111 39.02 0.00 38.24 3.56
39 40 2.360600 GTGTGTGGGCCCGCAATA 60.361 61.111 39.02 27.20 38.24 1.90
40 41 1.752694 GTGTGTGGGCCCGCAATAT 60.753 57.895 39.02 0.00 38.24 1.28
41 42 0.464735 GTGTGTGGGCCCGCAATATA 60.465 55.000 39.02 22.12 38.24 0.86
42 43 0.256177 TGTGTGGGCCCGCAATATAA 59.744 50.000 39.02 19.18 38.24 0.98
43 44 0.951558 GTGTGGGCCCGCAATATAAG 59.048 55.000 39.02 0.00 38.24 1.73
44 45 0.179004 TGTGGGCCCGCAATATAAGG 60.179 55.000 35.86 0.00 33.12 2.69
45 46 0.109723 GTGGGCCCGCAATATAAGGA 59.890 55.000 30.93 0.00 0.00 3.36
320 321 3.778954 ACTTTTGGAGGAGTTGGAGAG 57.221 47.619 0.00 0.00 0.00 3.20
324 325 1.220477 GGAGGAGTTGGAGAGCTGC 59.780 63.158 0.00 0.00 0.00 5.25
327 328 1.744741 GGAGTTGGAGAGCTGCTGC 60.745 63.158 7.01 7.62 40.05 5.25
332 333 2.188994 GGAGAGCTGCTGCCGAAT 59.811 61.111 7.01 0.00 40.80 3.34
374 375 1.996191 GATCTTCGTCAGGTGTTGCTC 59.004 52.381 0.00 0.00 0.00 4.26
379 380 2.022129 GTCAGGTGTTGCTCGACGG 61.022 63.158 0.00 0.00 0.00 4.79
380 381 2.197605 TCAGGTGTTGCTCGACGGA 61.198 57.895 0.00 0.00 0.00 4.69
390 391 2.672651 TCGACGGAGGCGTTGGTA 60.673 61.111 0.00 0.00 0.00 3.25
401 402 4.235731 GTTGGTAATCCAGCGGGG 57.764 61.111 2.05 0.00 45.22 5.73
414 415 0.034186 AGCGGGGCAATCTTCAATGA 60.034 50.000 0.00 0.00 0.00 2.57
416 417 0.378257 CGGGGCAATCTTCAATGACG 59.622 55.000 0.00 0.00 0.00 4.35
418 419 0.101219 GGGCAATCTTCAATGACGGC 59.899 55.000 0.00 0.00 0.00 5.68
419 420 0.101219 GGCAATCTTCAATGACGGCC 59.899 55.000 0.00 0.00 33.45 6.13
421 422 0.740737 CAATCTTCAATGACGGCCCC 59.259 55.000 0.00 0.00 0.00 5.80
422 423 0.748005 AATCTTCAATGACGGCCCCG 60.748 55.000 4.96 4.96 46.03 5.73
453 456 2.036089 GTCACCAGAAAAGAGAGTCGGT 59.964 50.000 0.00 0.00 0.00 4.69
458 461 3.458189 CAGAAAAGAGAGTCGGTGTGTT 58.542 45.455 0.00 0.00 0.00 3.32
464 467 0.389391 AGAGTCGGTGTGTTGTCCTG 59.611 55.000 0.00 0.00 0.00 3.86
468 471 1.954146 CGGTGTGTTGTCCTGGACG 60.954 63.158 21.15 3.60 34.95 4.79
473 476 2.032071 GTTGTCCTGGACGGTGGG 59.968 66.667 21.15 0.00 34.95 4.61
474 477 2.122769 TTGTCCTGGACGGTGGGA 60.123 61.111 21.15 0.09 34.95 4.37
487 490 0.179000 GGTGGGAAGCTCGACATCAT 59.821 55.000 0.00 0.00 0.00 2.45
508 511 1.372997 ACTAACCTGTCGTGCAGCG 60.373 57.895 0.00 0.00 43.71 5.18
527 530 2.861935 GCGGCATGATTGATTTTTCAGG 59.138 45.455 0.00 0.00 0.00 3.86
528 531 3.676873 GCGGCATGATTGATTTTTCAGGT 60.677 43.478 0.00 0.00 0.00 4.00
529 532 4.497300 CGGCATGATTGATTTTTCAGGTT 58.503 39.130 0.00 0.00 0.00 3.50
530 533 4.931002 CGGCATGATTGATTTTTCAGGTTT 59.069 37.500 0.00 0.00 0.00 3.27
531 534 5.409214 CGGCATGATTGATTTTTCAGGTTTT 59.591 36.000 0.00 0.00 0.00 2.43
532 535 6.401367 CGGCATGATTGATTTTTCAGGTTTTC 60.401 38.462 0.00 0.00 0.00 2.29
533 536 6.652062 GGCATGATTGATTTTTCAGGTTTTCT 59.348 34.615 0.00 0.00 0.00 2.52
534 537 7.173735 GGCATGATTGATTTTTCAGGTTTTCTT 59.826 33.333 0.00 0.00 0.00 2.52
535 538 8.562052 GCATGATTGATTTTTCAGGTTTTCTTT 58.438 29.630 0.00 0.00 0.00 2.52
538 541 9.108284 TGATTGATTTTTCAGGTTTTCTTTTCC 57.892 29.630 0.00 0.00 0.00 3.13
539 542 9.330063 GATTGATTTTTCAGGTTTTCTTTTCCT 57.670 29.630 0.00 0.00 0.00 3.36
540 543 8.716646 TTGATTTTTCAGGTTTTCTTTTCCTC 57.283 30.769 0.00 0.00 0.00 3.71
541 544 7.846066 TGATTTTTCAGGTTTTCTTTTCCTCA 58.154 30.769 0.00 0.00 0.00 3.86
542 545 8.317679 TGATTTTTCAGGTTTTCTTTTCCTCAA 58.682 29.630 0.00 0.00 0.00 3.02
543 546 8.722480 ATTTTTCAGGTTTTCTTTTCCTCAAG 57.278 30.769 0.00 0.00 0.00 3.02
544 547 6.850752 TTTCAGGTTTTCTTTTCCTCAAGT 57.149 33.333 0.00 0.00 0.00 3.16
545 548 6.850752 TTCAGGTTTTCTTTTCCTCAAGTT 57.149 33.333 0.00 0.00 0.00 2.66
546 549 6.850752 TCAGGTTTTCTTTTCCTCAAGTTT 57.149 33.333 0.00 0.00 0.00 2.66
547 550 6.630071 TCAGGTTTTCTTTTCCTCAAGTTTG 58.370 36.000 0.00 0.00 0.00 2.93
548 551 5.812127 CAGGTTTTCTTTTCCTCAAGTTTGG 59.188 40.000 0.00 0.00 0.00 3.28
549 552 5.483937 AGGTTTTCTTTTCCTCAAGTTTGGT 59.516 36.000 0.00 0.00 0.00 3.67
550 553 6.013725 AGGTTTTCTTTTCCTCAAGTTTGGTT 60.014 34.615 0.00 0.00 0.00 3.67
551 554 6.653320 GGTTTTCTTTTCCTCAAGTTTGGTTT 59.347 34.615 0.00 0.00 0.00 3.27
552 555 7.360861 GGTTTTCTTTTCCTCAAGTTTGGTTTG 60.361 37.037 0.00 0.00 0.00 2.93
553 556 6.597832 TTCTTTTCCTCAAGTTTGGTTTGA 57.402 33.333 0.00 0.00 33.76 2.69
554 557 6.790232 TCTTTTCCTCAAGTTTGGTTTGAT 57.210 33.333 0.00 0.00 34.33 2.57
555 558 6.572519 TCTTTTCCTCAAGTTTGGTTTGATG 58.427 36.000 0.00 0.00 34.33 3.07
556 559 4.935352 TTCCTCAAGTTTGGTTTGATGG 57.065 40.909 0.00 0.00 34.33 3.51
557 560 3.230134 TCCTCAAGTTTGGTTTGATGGG 58.770 45.455 0.00 0.00 34.33 4.00
558 561 2.299867 CCTCAAGTTTGGTTTGATGGGG 59.700 50.000 0.00 0.00 34.33 4.96
559 562 2.965147 CTCAAGTTTGGTTTGATGGGGT 59.035 45.455 0.00 0.00 34.33 4.95
560 563 2.697751 TCAAGTTTGGTTTGATGGGGTG 59.302 45.455 0.00 0.00 30.03 4.61
561 564 2.697751 CAAGTTTGGTTTGATGGGGTGA 59.302 45.455 0.00 0.00 0.00 4.02
562 565 3.039252 AGTTTGGTTTGATGGGGTGAA 57.961 42.857 0.00 0.00 0.00 3.18
563 566 2.965147 AGTTTGGTTTGATGGGGTGAAG 59.035 45.455 0.00 0.00 0.00 3.02
564 567 1.337118 TTGGTTTGATGGGGTGAAGC 58.663 50.000 0.00 0.00 0.00 3.86
565 568 0.187117 TGGTTTGATGGGGTGAAGCA 59.813 50.000 0.00 0.00 0.00 3.91
566 569 1.337118 GGTTTGATGGGGTGAAGCAA 58.663 50.000 0.00 0.00 0.00 3.91
573 576 0.179004 TGGGGTGAAGCAACGATGTT 60.179 50.000 0.00 0.00 0.00 2.71
577 580 2.604614 GGGTGAAGCAACGATGTTGTTC 60.605 50.000 10.96 12.36 0.00 3.18
582 585 5.404366 GTGAAGCAACGATGTTGTTCTAGTA 59.596 40.000 10.96 0.00 0.00 1.82
585 588 7.488150 TGAAGCAACGATGTTGTTCTAGTATAG 59.512 37.037 10.96 0.00 41.04 1.31
652 1824 9.814899 TCTAAATTCAAAATTGTCATGTTGTGT 57.185 25.926 0.00 0.00 30.34 3.72
695 1870 4.629634 TGTCATGCTGTAACGAGTAATTGG 59.370 41.667 0.00 0.00 0.00 3.16
716 1891 2.155732 GCACGCCAATATACATCTGACG 59.844 50.000 0.00 0.00 0.00 4.35
718 1893 1.726791 CGCCAATATACATCTGACGCC 59.273 52.381 0.00 0.00 0.00 5.68
731 1906 4.937201 TCTGACGCCTGATGTATATTGT 57.063 40.909 0.00 0.00 0.00 2.71
746 1923 2.434658 ATTGTGGTGTGCTCGCTCGA 62.435 55.000 0.00 0.00 0.00 4.04
747 1924 2.807045 GTGGTGTGCTCGCTCGAG 60.807 66.667 8.45 8.45 44.56 4.04
791 1968 2.636647 ATGGCAAAGGTTTGTTTGGG 57.363 45.000 4.45 0.00 40.24 4.12
801 1994 0.658897 TTTGTTTGGGTTCGCTCGTC 59.341 50.000 0.00 0.00 0.00 4.20
806 1999 0.878523 TTGGGTTCGCTCGTCACAAG 60.879 55.000 2.38 0.00 0.00 3.16
847 2040 0.905337 CGGGAAACTCCAGGAGGTCT 60.905 60.000 21.31 5.18 38.64 3.85
856 2063 1.270414 CCAGGAGGTCTCACATGGCT 61.270 60.000 0.00 0.00 0.00 4.75
865 2072 5.407049 AGGTCTCACATGGCTATATAAGGT 58.593 41.667 0.00 0.00 0.00 3.50
958 2175 4.473520 CAATCAGGTCGGCCGCCT 62.474 66.667 28.43 28.43 40.50 5.52
968 2190 2.671963 GGCCGCCTCTTTTCGGTT 60.672 61.111 0.71 0.00 46.79 4.44
972 2194 1.574702 CCGCCTCTTTTCGGTTGTCC 61.575 60.000 0.00 0.00 40.72 4.02
976 2198 2.846193 CCTCTTTTCGGTTGTCCAAGA 58.154 47.619 0.00 0.00 0.00 3.02
1059 2281 2.487428 CAGCTCCTGTCCGACTCG 59.513 66.667 0.00 0.00 0.00 4.18
1177 2402 1.626654 TTACGACGACGACGAGGACC 61.627 60.000 25.15 0.00 42.66 4.46
1198 2423 2.359107 ACGACTCGGGCGTCTACA 60.359 61.111 2.98 0.00 37.42 2.74
1234 2459 1.802636 CAGCACATAAGCCCCGTTG 59.197 57.895 0.00 0.00 34.23 4.10
1451 2677 3.442996 GGGACCATGAACTCAGACG 57.557 57.895 0.00 0.00 0.00 4.18
1452 2678 0.608640 GGGACCATGAACTCAGACGT 59.391 55.000 0.00 0.00 0.00 4.34
1453 2679 1.404315 GGGACCATGAACTCAGACGTC 60.404 57.143 7.70 7.70 0.00 4.34
1454 2680 1.618861 GACCATGAACTCAGACGTCG 58.381 55.000 10.46 5.48 0.00 5.12
1455 2681 0.243907 ACCATGAACTCAGACGTCGG 59.756 55.000 10.46 10.03 0.00 4.79
1456 2682 1.078759 CCATGAACTCAGACGTCGGC 61.079 60.000 11.11 0.00 0.00 5.54
1457 2683 1.154016 ATGAACTCAGACGTCGGCG 60.154 57.895 8.42 8.42 44.93 6.46
1458 2684 3.173240 GAACTCAGACGTCGGCGC 61.173 66.667 10.50 0.00 42.83 6.53
1464 2690 4.849329 AGACGTCGGCGCGGATTC 62.849 66.667 21.12 18.62 42.83 2.52
1468 2694 2.890474 GTCGGCGCGGATTCACAT 60.890 61.111 21.12 0.00 0.00 3.21
1469 2695 2.889988 TCGGCGCGGATTCACATG 60.890 61.111 14.27 0.00 0.00 3.21
1470 2696 2.889988 CGGCGCGGATTCACATGA 60.890 61.111 9.72 0.00 0.00 3.07
1471 2697 2.246739 CGGCGCGGATTCACATGAT 61.247 57.895 9.72 0.00 0.00 2.45
1472 2698 1.280746 GGCGCGGATTCACATGATG 59.719 57.895 8.83 0.00 0.00 3.07
1473 2699 1.159713 GGCGCGGATTCACATGATGA 61.160 55.000 8.83 0.00 34.65 2.92
1474 2700 0.870393 GCGCGGATTCACATGATGAT 59.130 50.000 8.83 0.00 37.11 2.45
1475 2701 1.265095 GCGCGGATTCACATGATGATT 59.735 47.619 8.83 0.00 37.11 2.57
1476 2702 2.287188 GCGCGGATTCACATGATGATTT 60.287 45.455 8.83 0.00 37.11 2.17
1477 2703 3.058983 GCGCGGATTCACATGATGATTTA 60.059 43.478 8.83 0.00 37.11 1.40
1478 2704 4.457810 CGCGGATTCACATGATGATTTAC 58.542 43.478 0.00 0.00 37.11 2.01
1479 2705 4.024977 CGCGGATTCACATGATGATTTACA 60.025 41.667 0.00 0.00 37.11 2.41
1480 2706 5.446709 GCGGATTCACATGATGATTTACAG 58.553 41.667 0.00 0.00 37.11 2.74
1481 2707 5.561532 GCGGATTCACATGATGATTTACAGG 60.562 44.000 0.00 0.00 37.11 4.00
1482 2708 5.561532 CGGATTCACATGATGATTTACAGGC 60.562 44.000 0.00 0.00 37.11 4.85
1486 2735 4.122046 CACATGATGATTTACAGGCTCGA 58.878 43.478 0.00 0.00 0.00 4.04
1496 2772 0.687354 ACAGGCTCGATCCAACAAGT 59.313 50.000 8.23 0.00 0.00 3.16
1503 2779 2.480419 CTCGATCCAACAAGTGTGGAAC 59.520 50.000 0.00 0.00 35.13 3.62
1518 2794 4.647291 GTGGAACAATGTGAAGACGTAG 57.353 45.455 0.00 0.00 44.16 3.51
1523 2799 7.500883 TGGAACAATGTGAAGACGTAGTTAGC 61.501 42.308 0.00 0.00 35.95 3.09
1567 2845 2.969628 TTTGGCGTGACAACCAATTT 57.030 40.000 11.04 0.00 45.08 1.82
1570 2848 4.592485 TTGGCGTGACAACCAATTTATT 57.408 36.364 7.03 0.00 40.98 1.40
1571 2849 3.906998 TGGCGTGACAACCAATTTATTG 58.093 40.909 0.00 0.00 37.52 1.90
1583 2863 4.647424 CAATTTATTGGGCGGTGTGTAT 57.353 40.909 0.00 0.00 34.22 2.29
1584 2864 5.004922 CAATTTATTGGGCGGTGTGTATT 57.995 39.130 0.00 0.00 34.22 1.89
1585 2865 5.415221 CAATTTATTGGGCGGTGTGTATTT 58.585 37.500 0.00 0.00 34.22 1.40
1590 2876 1.248101 GGGCGGTGTGTATTTGGCTT 61.248 55.000 0.00 0.00 0.00 4.35
1616 2902 2.572290 AGTGCTTGGAGTTGTTGGTAC 58.428 47.619 0.00 0.00 0.00 3.34
1617 2903 2.172717 AGTGCTTGGAGTTGTTGGTACT 59.827 45.455 0.00 0.00 0.00 2.73
1619 2905 4.131596 GTGCTTGGAGTTGTTGGTACTAA 58.868 43.478 0.00 0.00 0.00 2.24
1621 2907 5.935789 GTGCTTGGAGTTGTTGGTACTAATA 59.064 40.000 0.00 0.00 0.00 0.98
1622 2908 5.935789 TGCTTGGAGTTGTTGGTACTAATAC 59.064 40.000 0.00 0.00 0.00 1.89
1623 2909 5.935789 GCTTGGAGTTGTTGGTACTAATACA 59.064 40.000 0.00 0.00 32.40 2.29
1624 2910 6.598064 GCTTGGAGTTGTTGGTACTAATACAT 59.402 38.462 0.00 0.00 32.40 2.29
1625 2911 7.414098 GCTTGGAGTTGTTGGTACTAATACATG 60.414 40.741 0.00 0.00 32.40 3.21
1732 3073 3.192001 CAGGTGTTCCAAGTGGATGAATG 59.808 47.826 0.00 0.00 44.98 2.67
1828 3645 5.162075 GCCCTAATCATAGTACTTACAGCG 58.838 45.833 0.00 0.00 0.00 5.18
1833 3650 4.713824 TCATAGTACTTACAGCGCAAGT 57.286 40.909 11.47 13.66 39.50 3.16
1834 3651 4.669318 TCATAGTACTTACAGCGCAAGTC 58.331 43.478 14.15 7.42 37.42 3.01
1880 3697 3.233355 GGATTTGCTCCTGTCACGT 57.767 52.632 0.00 0.00 41.29 4.49
1906 3723 5.243730 GGAATCAGAAATTCAGAAACCACCA 59.756 40.000 0.00 0.00 0.00 4.17
2111 3931 1.734477 CCGGAGTCGTCAGTGCAAG 60.734 63.158 0.00 0.00 33.95 4.01
2181 4001 4.139420 CGCGCGGAGAGTTTGCAG 62.139 66.667 24.84 0.00 0.00 4.41
2251 4071 1.005984 TACGCAGGCTTGTTACGCA 60.006 52.632 0.00 0.00 0.00 5.24
2285 4105 4.379243 CCGTCGGTTGCCTCTGCT 62.379 66.667 2.08 0.00 38.71 4.24
2326 4146 2.668457 CCACACGAGCAAACACTAGATC 59.332 50.000 0.00 0.00 0.00 2.75
2348 4168 9.579932 AGATCTTTGTTCCTCTATCTTTTGTTT 57.420 29.630 0.00 0.00 0.00 2.83
2391 4213 5.609423 TCATCTTTTGTTGATTGGTTTGGG 58.391 37.500 0.00 0.00 0.00 4.12
2442 4264 8.940768 TTTCATGATAATACGTGTCTCATTCA 57.059 30.769 0.00 0.00 0.00 2.57
2443 4265 9.546428 TTTCATGATAATACGTGTCTCATTCAT 57.454 29.630 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 9.434420 CCCACACACAAATTTACAATTATTCAT 57.566 29.630 0.00 0.00 0.00 2.57
5 6 7.386299 GCCCACACACAAATTTACAATTATTCA 59.614 33.333 0.00 0.00 0.00 2.57
6 7 7.148490 GGCCCACACACAAATTTACAATTATTC 60.148 37.037 0.00 0.00 0.00 1.75
7 8 6.652900 GGCCCACACACAAATTTACAATTATT 59.347 34.615 0.00 0.00 0.00 1.40
8 9 6.169800 GGCCCACACACAAATTTACAATTAT 58.830 36.000 0.00 0.00 0.00 1.28
9 10 5.511545 GGGCCCACACACAAATTTACAATTA 60.512 40.000 19.95 0.00 0.00 1.40
10 11 4.384940 GGCCCACACACAAATTTACAATT 58.615 39.130 0.00 0.00 0.00 2.32
11 12 3.244387 GGGCCCACACACAAATTTACAAT 60.244 43.478 19.95 0.00 0.00 2.71
12 13 2.103263 GGGCCCACACACAAATTTACAA 59.897 45.455 19.95 0.00 0.00 2.41
13 14 1.689273 GGGCCCACACACAAATTTACA 59.311 47.619 19.95 0.00 0.00 2.41
14 15 1.336424 CGGGCCCACACACAAATTTAC 60.336 52.381 24.92 0.00 0.00 2.01
15 16 0.962489 CGGGCCCACACACAAATTTA 59.038 50.000 24.92 0.00 0.00 1.40
16 17 1.745264 CGGGCCCACACACAAATTT 59.255 52.632 24.92 0.00 0.00 1.82
17 18 2.866726 GCGGGCCCACACACAAATT 61.867 57.895 24.92 0.00 0.00 1.82
18 19 3.302344 GCGGGCCCACACACAAAT 61.302 61.111 24.92 0.00 0.00 2.32
19 20 4.822628 TGCGGGCCCACACACAAA 62.823 61.111 24.92 0.00 0.00 2.83
20 21 2.698776 TATTGCGGGCCCACACACAA 62.699 55.000 24.92 17.21 0.00 3.33
21 22 2.491770 ATATTGCGGGCCCACACACA 62.492 55.000 24.92 8.55 0.00 3.72
22 23 0.464735 TATATTGCGGGCCCACACAC 60.465 55.000 24.92 5.64 0.00 3.82
23 24 0.256177 TTATATTGCGGGCCCACACA 59.744 50.000 24.92 14.30 0.00 3.72
24 25 0.951558 CTTATATTGCGGGCCCACAC 59.048 55.000 24.92 11.40 0.00 3.82
25 26 0.179004 CCTTATATTGCGGGCCCACA 60.179 55.000 24.92 17.37 0.00 4.17
26 27 0.109723 TCCTTATATTGCGGGCCCAC 59.890 55.000 24.92 14.12 0.00 4.61
27 28 2.545969 TCCTTATATTGCGGGCCCA 58.454 52.632 24.92 1.51 0.00 5.36
300 301 2.224646 GCTCTCCAACTCCTCCAAAAGT 60.225 50.000 0.00 0.00 0.00 2.66
301 302 2.039613 AGCTCTCCAACTCCTCCAAAAG 59.960 50.000 0.00 0.00 0.00 2.27
302 303 2.057922 AGCTCTCCAACTCCTCCAAAA 58.942 47.619 0.00 0.00 0.00 2.44
303 304 1.349026 CAGCTCTCCAACTCCTCCAAA 59.651 52.381 0.00 0.00 0.00 3.28
304 305 0.979665 CAGCTCTCCAACTCCTCCAA 59.020 55.000 0.00 0.00 0.00 3.53
305 306 1.548357 GCAGCTCTCCAACTCCTCCA 61.548 60.000 0.00 0.00 0.00 3.86
306 307 1.220477 GCAGCTCTCCAACTCCTCC 59.780 63.158 0.00 0.00 0.00 4.30
319 320 2.786539 TTCGTCATTCGGCAGCAGCT 62.787 55.000 0.00 0.00 41.70 4.24
320 321 2.301902 CTTCGTCATTCGGCAGCAGC 62.302 60.000 0.00 0.00 40.32 5.25
324 325 0.173481 TCTCCTTCGTCATTCGGCAG 59.827 55.000 0.00 0.00 40.32 4.85
327 328 1.212616 GCATCTCCTTCGTCATTCGG 58.787 55.000 0.00 0.00 40.32 4.30
332 333 0.171231 CACTCGCATCTCCTTCGTCA 59.829 55.000 0.00 0.00 0.00 4.35
379 380 1.429148 CGCTGGATTACCAACGCCTC 61.429 60.000 0.00 0.00 46.15 4.70
380 381 1.449601 CGCTGGATTACCAACGCCT 60.450 57.895 0.00 0.00 46.15 5.52
390 391 0.753111 GAAGATTGCCCCGCTGGATT 60.753 55.000 0.00 0.00 35.39 3.01
398 399 0.740737 CCGTCATTGAAGATTGCCCC 59.259 55.000 0.82 0.00 0.00 5.80
399 400 0.101219 GCCGTCATTGAAGATTGCCC 59.899 55.000 0.82 0.00 0.00 5.36
400 401 0.101219 GGCCGTCATTGAAGATTGCC 59.899 55.000 0.82 2.35 32.42 4.52
401 402 0.101219 GGGCCGTCATTGAAGATTGC 59.899 55.000 0.00 0.00 0.00 3.56
439 440 3.195661 ACAACACACCGACTCTCTTTTC 58.804 45.455 0.00 0.00 0.00 2.29
441 442 2.483188 GGACAACACACCGACTCTCTTT 60.483 50.000 0.00 0.00 0.00 2.52
453 456 1.145156 CACCGTCCAGGACAACACA 59.855 57.895 20.13 0.00 45.00 3.72
458 461 2.122769 TTCCCACCGTCCAGGACA 60.123 61.111 20.13 0.00 45.00 4.02
464 467 3.379445 TCGAGCTTCCCACCGTCC 61.379 66.667 0.00 0.00 0.00 4.79
468 471 0.179000 ATGATGTCGAGCTTCCCACC 59.821 55.000 0.00 0.00 0.00 4.61
473 476 4.740695 GGTTAGTGTATGATGTCGAGCTTC 59.259 45.833 0.00 0.00 0.00 3.86
474 477 4.402793 AGGTTAGTGTATGATGTCGAGCTT 59.597 41.667 0.00 0.00 0.00 3.74
487 490 2.717580 CTGCACGACAGGTTAGTGTA 57.282 50.000 0.00 5.63 43.19 2.90
508 511 6.652062 AGAAAACCTGAAAAATCAATCATGCC 59.348 34.615 0.00 0.00 0.00 4.40
527 530 7.386573 TCAAACCAAACTTGAGGAAAAGAAAAC 59.613 33.333 0.00 0.00 0.00 2.43
528 531 7.445945 TCAAACCAAACTTGAGGAAAAGAAAA 58.554 30.769 0.00 0.00 0.00 2.29
529 532 6.998802 TCAAACCAAACTTGAGGAAAAGAAA 58.001 32.000 0.00 0.00 0.00 2.52
530 533 6.597832 TCAAACCAAACTTGAGGAAAAGAA 57.402 33.333 0.00 0.00 0.00 2.52
531 534 6.406849 CCATCAAACCAAACTTGAGGAAAAGA 60.407 38.462 0.00 0.00 36.86 2.52
532 535 5.754890 CCATCAAACCAAACTTGAGGAAAAG 59.245 40.000 0.00 0.00 36.86 2.27
533 536 5.396213 CCCATCAAACCAAACTTGAGGAAAA 60.396 40.000 0.00 0.00 36.86 2.29
534 537 4.100808 CCCATCAAACCAAACTTGAGGAAA 59.899 41.667 0.00 0.00 36.86 3.13
535 538 3.640967 CCCATCAAACCAAACTTGAGGAA 59.359 43.478 0.00 0.00 36.86 3.36
536 539 3.230134 CCCATCAAACCAAACTTGAGGA 58.770 45.455 0.00 0.00 36.86 3.71
537 540 2.299867 CCCCATCAAACCAAACTTGAGG 59.700 50.000 0.00 0.00 36.30 3.86
538 541 2.965147 ACCCCATCAAACCAAACTTGAG 59.035 45.455 0.00 0.00 36.30 3.02
539 542 2.697751 CACCCCATCAAACCAAACTTGA 59.302 45.455 0.00 0.00 37.22 3.02
540 543 2.697751 TCACCCCATCAAACCAAACTTG 59.302 45.455 0.00 0.00 0.00 3.16
541 544 3.039252 TCACCCCATCAAACCAAACTT 57.961 42.857 0.00 0.00 0.00 2.66
542 545 2.765689 TCACCCCATCAAACCAAACT 57.234 45.000 0.00 0.00 0.00 2.66
543 546 2.547855 GCTTCACCCCATCAAACCAAAC 60.548 50.000 0.00 0.00 0.00 2.93
544 547 1.691434 GCTTCACCCCATCAAACCAAA 59.309 47.619 0.00 0.00 0.00 3.28
545 548 1.337118 GCTTCACCCCATCAAACCAA 58.663 50.000 0.00 0.00 0.00 3.67
546 549 0.187117 TGCTTCACCCCATCAAACCA 59.813 50.000 0.00 0.00 0.00 3.67
547 550 1.000843 GTTGCTTCACCCCATCAAACC 59.999 52.381 0.00 0.00 0.00 3.27
548 551 1.335872 CGTTGCTTCACCCCATCAAAC 60.336 52.381 0.00 0.00 0.00 2.93
549 552 0.958091 CGTTGCTTCACCCCATCAAA 59.042 50.000 0.00 0.00 0.00 2.69
550 553 0.109532 TCGTTGCTTCACCCCATCAA 59.890 50.000 0.00 0.00 0.00 2.57
551 554 0.327924 ATCGTTGCTTCACCCCATCA 59.672 50.000 0.00 0.00 0.00 3.07
552 555 0.734889 CATCGTTGCTTCACCCCATC 59.265 55.000 0.00 0.00 0.00 3.51
553 556 0.038166 ACATCGTTGCTTCACCCCAT 59.962 50.000 0.00 0.00 0.00 4.00
554 557 0.179004 AACATCGTTGCTTCACCCCA 60.179 50.000 0.00 0.00 0.00 4.96
555 558 0.240945 CAACATCGTTGCTTCACCCC 59.759 55.000 0.00 0.00 0.00 4.95
556 559 0.951558 ACAACATCGTTGCTTCACCC 59.048 50.000 6.77 0.00 0.00 4.61
557 560 2.290641 AGAACAACATCGTTGCTTCACC 59.709 45.455 6.77 0.00 0.00 4.02
558 561 3.609103 AGAACAACATCGTTGCTTCAC 57.391 42.857 6.77 0.00 0.00 3.18
559 562 4.377021 ACTAGAACAACATCGTTGCTTCA 58.623 39.130 6.77 2.44 0.00 3.02
560 563 4.992381 ACTAGAACAACATCGTTGCTTC 57.008 40.909 6.77 9.46 0.00 3.86
561 564 6.757010 CCTATACTAGAACAACATCGTTGCTT 59.243 38.462 6.77 1.49 0.00 3.91
562 565 6.096423 TCCTATACTAGAACAACATCGTTGCT 59.904 38.462 6.77 0.00 0.00 3.91
563 566 6.270815 TCCTATACTAGAACAACATCGTTGC 58.729 40.000 6.77 0.00 0.00 4.17
564 567 8.873215 ATTCCTATACTAGAACAACATCGTTG 57.127 34.615 5.34 5.34 0.00 4.10
653 1825 9.881529 GCATGACAATTGTTTTGACAAATATTT 57.118 25.926 13.36 0.00 32.94 1.40
654 1826 9.275398 AGCATGACAATTGTTTTGACAAATATT 57.725 25.926 13.36 0.34 32.94 1.28
655 1827 8.714179 CAGCATGACAATTGTTTTGACAAATAT 58.286 29.630 13.36 0.00 39.69 1.28
658 1830 5.873712 ACAGCATGACAATTGTTTTGACAAA 59.126 32.000 13.36 0.00 39.69 2.83
659 1831 5.417811 ACAGCATGACAATTGTTTTGACAA 58.582 33.333 13.36 0.00 39.69 3.18
660 1832 5.008619 ACAGCATGACAATTGTTTTGACA 57.991 34.783 13.36 5.95 39.69 3.58
661 1833 6.344936 CGTTACAGCATGACAATTGTTTTGAC 60.345 38.462 13.36 9.46 39.69 3.18
695 1870 2.155732 CGTCAGATGTATATTGGCGTGC 59.844 50.000 0.00 0.00 35.41 5.34
716 1891 3.003689 GCACACCACAATATACATCAGGC 59.996 47.826 0.00 0.00 0.00 4.85
718 1893 4.209911 CGAGCACACCACAATATACATCAG 59.790 45.833 0.00 0.00 0.00 2.90
731 1906 4.056125 CCTCGAGCGAGCACACCA 62.056 66.667 14.05 0.00 40.69 4.17
746 1923 4.129737 CGGCGTCCGTGTCATCCT 62.130 66.667 9.69 0.00 42.73 3.24
791 1968 1.462541 GCATTCTTGTGACGAGCGAAC 60.463 52.381 0.00 0.00 0.00 3.95
801 1994 3.916172 CGAAACTGAATGGCATTCTTGTG 59.084 43.478 33.21 23.48 39.96 3.33
806 1999 4.406943 GAGTTCGAAACTGAATGGCATTC 58.593 43.478 28.92 28.92 43.03 2.67
847 2040 6.554982 ACTCTTGACCTTATATAGCCATGTGA 59.445 38.462 0.00 0.00 0.00 3.58
856 2063 3.305131 CGGCGCACTCTTGACCTTATATA 60.305 47.826 10.83 0.00 0.00 0.86
865 2072 4.742201 GGAGCGGCGCACTCTTGA 62.742 66.667 35.02 0.00 34.46 3.02
919 2128 4.025480 TGCAATTGATTGATCGATGTCTCG 60.025 41.667 10.34 0.00 41.98 4.04
932 2141 2.159198 GCCGACCTGATTGCAATTGATT 60.159 45.455 14.33 0.00 0.00 2.57
958 2175 2.159071 TCGTCTTGGACAACCGAAAAGA 60.159 45.455 0.00 0.00 39.42 2.52
968 2190 3.362262 CGGAGGTCGTCTTGGACA 58.638 61.111 0.00 0.00 38.70 4.02
1198 2423 2.516923 CTGCGTCGTCGTCTCTAATTT 58.483 47.619 3.66 0.00 39.49 1.82
1234 2459 2.202756 CTTCGCGAGCACCCTACC 60.203 66.667 9.59 0.00 0.00 3.18
1438 2664 1.406219 CGCCGACGTCTGAGTTCATG 61.406 60.000 14.70 0.00 33.53 3.07
1447 2673 4.849329 GAATCCGCGCCGACGTCT 62.849 66.667 14.70 0.00 42.83 4.18
1451 2677 2.890474 ATGTGAATCCGCGCCGAC 60.890 61.111 0.00 0.00 0.00 4.79
1452 2678 2.642996 ATCATGTGAATCCGCGCCGA 62.643 55.000 0.00 0.00 0.00 5.54
1453 2679 2.246739 ATCATGTGAATCCGCGCCG 61.247 57.895 0.00 0.00 0.00 6.46
1454 2680 1.159713 TCATCATGTGAATCCGCGCC 61.160 55.000 0.00 0.00 32.78 6.53
1455 2681 0.870393 ATCATCATGTGAATCCGCGC 59.130 50.000 0.00 0.00 40.97 6.86
1456 2682 3.614159 AAATCATCATGTGAATCCGCG 57.386 42.857 0.00 0.00 40.97 6.46
1457 2683 5.422666 TGTAAATCATCATGTGAATCCGC 57.577 39.130 0.00 0.00 40.97 5.54
1458 2684 5.561532 GCCTGTAAATCATCATGTGAATCCG 60.562 44.000 0.00 0.00 40.97 4.18
1459 2685 5.533903 AGCCTGTAAATCATCATGTGAATCC 59.466 40.000 0.00 0.00 40.97 3.01
1460 2686 6.565435 CGAGCCTGTAAATCATCATGTGAATC 60.565 42.308 0.00 0.00 40.97 2.52
1461 2687 5.237996 CGAGCCTGTAAATCATCATGTGAAT 59.762 40.000 0.00 0.00 40.97 2.57
1462 2688 4.571984 CGAGCCTGTAAATCATCATGTGAA 59.428 41.667 0.00 0.00 40.97 3.18
1463 2689 4.122046 CGAGCCTGTAAATCATCATGTGA 58.878 43.478 0.00 0.00 42.06 3.58
1464 2690 4.122046 TCGAGCCTGTAAATCATCATGTG 58.878 43.478 0.00 0.00 0.00 3.21
1465 2691 4.406648 TCGAGCCTGTAAATCATCATGT 57.593 40.909 0.00 0.00 0.00 3.21
1466 2692 4.391216 GGATCGAGCCTGTAAATCATCATG 59.609 45.833 13.71 0.00 0.00 3.07
1467 2693 4.040829 TGGATCGAGCCTGTAAATCATCAT 59.959 41.667 22.18 0.00 0.00 2.45
1468 2694 3.387699 TGGATCGAGCCTGTAAATCATCA 59.612 43.478 22.18 0.00 0.00 3.07
1469 2695 3.995199 TGGATCGAGCCTGTAAATCATC 58.005 45.455 22.18 0.00 0.00 2.92
1470 2696 4.130118 GTTGGATCGAGCCTGTAAATCAT 58.870 43.478 22.18 0.00 0.00 2.45
1471 2697 3.055458 TGTTGGATCGAGCCTGTAAATCA 60.055 43.478 22.18 2.42 0.00 2.57
1472 2698 3.531538 TGTTGGATCGAGCCTGTAAATC 58.468 45.455 22.18 0.00 0.00 2.17
1473 2699 3.627395 TGTTGGATCGAGCCTGTAAAT 57.373 42.857 22.18 0.00 0.00 1.40
1474 2700 3.244422 ACTTGTTGGATCGAGCCTGTAAA 60.244 43.478 22.18 3.37 0.00 2.01
1475 2701 2.301870 ACTTGTTGGATCGAGCCTGTAA 59.698 45.455 22.18 11.50 0.00 2.41
1476 2702 1.899814 ACTTGTTGGATCGAGCCTGTA 59.100 47.619 22.18 3.67 0.00 2.74
1477 2703 0.687354 ACTTGTTGGATCGAGCCTGT 59.313 50.000 22.18 8.91 0.00 4.00
1478 2704 1.081892 CACTTGTTGGATCGAGCCTG 58.918 55.000 22.18 5.56 0.00 4.85
1479 2705 0.687354 ACACTTGTTGGATCGAGCCT 59.313 50.000 22.18 0.00 0.00 4.58
1480 2706 0.798776 CACACTTGTTGGATCGAGCC 59.201 55.000 14.17 14.17 0.00 4.70
1481 2707 0.798776 CCACACTTGTTGGATCGAGC 59.201 55.000 0.00 0.00 0.00 5.03
1482 2708 2.455674 TCCACACTTGTTGGATCGAG 57.544 50.000 0.00 0.00 0.00 4.04
1486 2735 3.960102 ACATTGTTCCACACTTGTTGGAT 59.040 39.130 0.00 0.00 0.00 3.41
1496 2772 2.912771 ACGTCTTCACATTGTTCCACA 58.087 42.857 0.00 0.00 0.00 4.17
1503 2779 4.091509 GTGGCTAACTACGTCTTCACATTG 59.908 45.833 0.00 0.00 0.00 2.82
1540 2816 2.325583 TGTCACGCCAAAAGTTCTCT 57.674 45.000 0.00 0.00 0.00 3.10
1541 2817 2.540973 GGTTGTCACGCCAAAAGTTCTC 60.541 50.000 0.00 0.00 0.00 2.87
1542 2818 1.404035 GGTTGTCACGCCAAAAGTTCT 59.596 47.619 0.00 0.00 0.00 3.01
1543 2819 1.133407 TGGTTGTCACGCCAAAAGTTC 59.867 47.619 0.00 0.00 0.00 3.01
1545 2821 1.178276 TTGGTTGTCACGCCAAAAGT 58.822 45.000 1.52 0.00 41.28 2.66
1546 2822 2.507339 ATTGGTTGTCACGCCAAAAG 57.493 45.000 7.60 0.00 46.34 2.27
1548 2824 2.969628 AAATTGGTTGTCACGCCAAA 57.030 40.000 7.60 0.00 46.34 3.28
1550 2826 3.906998 CAATAAATTGGTTGTCACGCCA 58.093 40.909 0.00 0.00 34.22 5.69
1567 2845 2.370349 CCAAATACACACCGCCCAATA 58.630 47.619 0.00 0.00 0.00 1.90
1570 2848 1.974343 GCCAAATACACACCGCCCA 60.974 57.895 0.00 0.00 0.00 5.36
1571 2849 1.248101 AAGCCAAATACACACCGCCC 61.248 55.000 0.00 0.00 0.00 6.13
1582 2862 3.256631 CCAAGCACTTGAGTAAGCCAAAT 59.743 43.478 11.94 0.00 42.93 2.32
1583 2863 2.622942 CCAAGCACTTGAGTAAGCCAAA 59.377 45.455 11.94 0.00 42.93 3.28
1584 2864 2.158682 TCCAAGCACTTGAGTAAGCCAA 60.159 45.455 11.94 0.00 42.93 4.52
1585 2865 1.419762 TCCAAGCACTTGAGTAAGCCA 59.580 47.619 11.94 0.00 42.93 4.75
1590 2876 3.838244 ACAACTCCAAGCACTTGAGTA 57.162 42.857 11.94 0.00 42.93 2.59
1732 3073 0.179086 GACAGGCTAGGAGCAAGAGC 60.179 60.000 0.21 0.00 44.75 4.09
1813 3630 3.797256 GGACTTGCGCTGTAAGTACTATG 59.203 47.826 9.73 0.00 38.49 2.23
1828 3645 1.105457 TTATGCATGCTGGGACTTGC 58.895 50.000 20.33 0.00 40.21 4.01
1873 3690 2.920724 TTTCTGATTCCCACGTGACA 57.079 45.000 19.30 7.99 0.00 3.58
1880 3697 5.243730 GTGGTTTCTGAATTTCTGATTCCCA 59.756 40.000 16.61 14.20 0.00 4.37
1906 3723 4.473520 CATCGCGAGGGCCAAGGT 62.474 66.667 16.66 0.00 35.02 3.50
2093 3913 1.734477 CTTGCACTGACGACTCCGG 60.734 63.158 0.00 0.00 40.78 5.14
2285 4105 1.938585 CACCTCCAGGACAGGTAAGA 58.061 55.000 0.00 0.00 42.85 2.10
2363 4185 9.695526 CAAACCAATCAACAAAAGATGATTCTA 57.304 29.630 0.00 0.00 42.72 2.10
2372 4194 4.379652 CCTCCCAAACCAATCAACAAAAG 58.620 43.478 0.00 0.00 0.00 2.27
2376 4198 2.008242 CCCTCCCAAACCAATCAACA 57.992 50.000 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.