Multiple sequence alignment - TraesCS3B01G122600

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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 TraesCS3B01G122600 chr3B 100.000 2809 0 0 1 2809 92603624 92606432 0.000000e+00 5188.0
1 TraesCS3B01G122600 chr3B 99.275 138 1 0 536 673 92604020 92604157 1.670000e-62 250.0
2 TraesCS3B01G122600 chr3B 99.275 138 1 0 397 534 92604159 92604296 1.670000e-62 250.0
3 TraesCS3B01G122600 chr3B 85.294 170 21 4 350 516 662460595 662460427 3.720000e-39 172.0
4 TraesCS3B01G122600 chr3D 95.978 1964 41 11 856 2809 58428173 58430108 0.000000e+00 3155.0
5 TraesCS3B01G122600 chr3D 85.271 258 36 2 2 258 58404831 58405087 5.970000e-67 265.0
6 TraesCS3B01G122600 chr3D 86.905 168 20 2 360 525 614921202 614921369 1.330000e-43 187.0
7 TraesCS3B01G122600 chr3D 94.118 102 5 1 764 864 58427896 58427997 1.350000e-33 154.0
8 TraesCS3B01G122600 chr3A 96.529 1700 53 3 1116 2809 67383503 67385202 0.000000e+00 2808.0
9 TraesCS3B01G122600 chr3A 96.821 346 9 1 776 1119 67382725 67383070 6.750000e-161 577.0
10 TraesCS3B01G122600 chr3A 82.068 474 57 16 1 474 67382008 67382453 2.040000e-101 379.0
11 TraesCS3B01G122600 chr7A 85.083 181 26 1 353 532 134625442 134625622 1.720000e-42 183.0
12 TraesCS3B01G122600 chr5A 86.826 167 18 4 353 516 299294870 299295035 1.720000e-42 183.0
13 TraesCS3B01G122600 chr5A 84.571 175 25 2 353 525 139485648 139485822 3.720000e-39 172.0
14 TraesCS3B01G122600 chr5A 82.692 156 25 2 536 689 139485692 139485847 1.360000e-28 137.0
15 TraesCS3B01G122600 chr1B 85.311 177 25 1 353 528 589545624 589545448 6.180000e-42 182.0
16 TraesCS3B01G122600 chr1B 86.111 72 10 0 575 646 885670 885741 8.340000e-11 78.7
17 TraesCS3B01G122600 chr6A 85.965 171 21 3 353 521 610949723 610949892 2.220000e-41 180.0
18 TraesCS3B01G122600 chr6A 83.471 121 19 1 536 655 108887802 108887922 8.230000e-21 111.0
19 TraesCS3B01G122600 chr6A 84.932 73 8 3 574 644 425705085 425705014 1.400000e-08 71.3
20 TraesCS3B01G122600 chr2A 85.549 173 24 1 354 525 459017076 459017248 2.220000e-41 180.0
21 TraesCS3B01G122600 chr2B 83.916 143 21 2 352 493 159482840 159482981 4.880000e-28 135.0
22 TraesCS3B01G122600 chrUn 81.295 139 21 5 533 667 8168907 8168770 1.060000e-19 108.0
23 TraesCS3B01G122600 chr5D 89.535 86 7 2 576 660 424830329 424830245 1.060000e-19 108.0
24 TraesCS3B01G122600 chr6B 80.282 142 25 3 533 671 705377566 705377425 1.380000e-18 104.0
25 TraesCS3B01G122600 chr4B 77.844 167 30 6 533 694 622426385 622426549 2.300000e-16 97.1
26 TraesCS3B01G122600 chr7B 85.542 83 11 1 540 621 74606715 74606633 4.990000e-13 86.1


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 TraesCS3B01G122600 chr3B 92603624 92606432 2808 False 1896.000000 5188 99.516667 1 2809 3 chr3B.!!$F1 2808
1 TraesCS3B01G122600 chr3D 58427896 58430108 2212 False 1654.500000 3155 95.048000 764 2809 2 chr3D.!!$F3 2045
2 TraesCS3B01G122600 chr3A 67382008 67385202 3194 False 1254.666667 2808 91.806000 1 2809 3 chr3A.!!$F1 2808

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
69 70 0.241481 GAAGACCAGAACTCGTCGCT 59.759 55.0 0.0 0.0 34.10 4.93 F
89 90 0.250381 GTCTAGATCGAGGAGGCCGA 60.250 60.0 0.0 0.0 40.53 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1749 2395 2.183478 TTGTACACCATCCAGCAGTG 57.817 50.000 0.0 0.0 37.53 3.66 R
1982 2628 4.213270 TCACTTTGTAAAGGCAACATCTCG 59.787 41.667 9.0 0.0 40.31 4.04 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
44 45 0.249405 CGCCAAGAGCTGAGATCTCC 60.249 60.000 20.03 5.58 40.39 3.71
47 48 1.337703 CCAAGAGCTGAGATCTCCGAG 59.662 57.143 20.03 12.45 0.00 4.63
68 69 0.733223 GGAAGACCAGAACTCGTCGC 60.733 60.000 0.00 0.00 34.10 5.19
69 70 0.241481 GAAGACCAGAACTCGTCGCT 59.759 55.000 0.00 0.00 34.10 4.93
73 74 1.173444 ACCAGAACTCGTCGCTGTCT 61.173 55.000 0.00 0.00 0.00 3.41
89 90 0.250381 GTCTAGATCGAGGAGGCCGA 60.250 60.000 0.00 0.00 40.53 5.54
94 95 2.691674 GATCGAGGAGGCCGAAGCAG 62.692 65.000 0.00 0.00 42.56 4.24
98 99 1.680522 GAGGAGGCCGAAGCAGATCA 61.681 60.000 0.00 0.00 42.56 2.92
105 106 2.414691 GGCCGAAGCAGATCAAAGTTTC 60.415 50.000 0.00 0.00 42.56 2.78
127 128 2.100605 AGATCGAAGAACAACAGGGC 57.899 50.000 0.00 0.00 43.58 5.19
134 135 1.119684 AGAACAACAGGGCCAAAACC 58.880 50.000 6.18 0.00 0.00 3.27
162 163 4.815973 CCCCTGGACCCCGATGGA 62.816 72.222 0.00 0.00 38.00 3.41
178 179 3.501349 GATGGACTAGATCTGGGCAGTA 58.499 50.000 14.66 0.00 0.00 2.74
179 180 3.398318 TGGACTAGATCTGGGCAGTAA 57.602 47.619 14.66 0.00 0.00 2.24
217 218 1.071471 AACCAGCTCTCCACAACCG 59.929 57.895 0.00 0.00 0.00 4.44
219 220 2.583441 CCAGCTCTCCACAACCGGA 61.583 63.158 9.46 0.00 0.00 5.14
238 239 3.003480 GGAATGAAGAACCGAAGACTGG 58.997 50.000 0.00 0.00 0.00 4.00
239 240 3.557264 GGAATGAAGAACCGAAGACTGGT 60.557 47.826 0.00 0.00 42.98 4.00
246 247 1.122019 ACCGAAGACTGGTTGCCTCT 61.122 55.000 0.00 0.00 35.82 3.69
253 254 0.835543 ACTGGTTGCCTCTGAGCTCT 60.836 55.000 16.19 0.00 0.00 4.09
258 259 3.082701 GCCTCTGAGCTCTGCCCT 61.083 66.667 16.19 0.00 0.00 5.19
259 260 2.901813 CCTCTGAGCTCTGCCCTG 59.098 66.667 16.19 5.68 0.00 4.45
261 262 3.388703 CTCTGAGCTCTGCCCTGGC 62.389 68.421 16.19 0.00 42.35 4.85
262 263 4.834453 CTGAGCTCTGCCCTGGCG 62.834 72.222 16.19 0.00 45.51 5.69
280 281 3.697747 CCGTCACGCCCTAACCCA 61.698 66.667 0.00 0.00 0.00 4.51
281 282 2.344500 CGTCACGCCCTAACCCAA 59.656 61.111 0.00 0.00 0.00 4.12
282 283 2.030958 CGTCACGCCCTAACCCAAC 61.031 63.158 0.00 0.00 0.00 3.77
283 284 2.030958 GTCACGCCCTAACCCAACG 61.031 63.158 0.00 0.00 0.00 4.10
284 285 3.428282 CACGCCCTAACCCAACGC 61.428 66.667 0.00 0.00 0.00 4.84
285 286 3.633116 ACGCCCTAACCCAACGCT 61.633 61.111 0.00 0.00 0.00 5.07
286 287 3.124921 CGCCCTAACCCAACGCTG 61.125 66.667 0.00 0.00 0.00 5.18
287 288 2.750237 GCCCTAACCCAACGCTGG 60.750 66.667 0.00 0.00 43.10 4.85
308 309 4.473520 CCCGCCCAAGATCGCTGT 62.474 66.667 0.00 0.00 0.00 4.40
311 312 2.514824 GCCCAAGATCGCTGTCCC 60.515 66.667 0.00 0.00 0.00 4.46
313 314 2.579201 CCAAGATCGCTGTCCCGT 59.421 61.111 0.00 0.00 0.00 5.28
314 315 1.811266 CCAAGATCGCTGTCCCGTG 60.811 63.158 0.00 0.00 0.00 4.94
322 323 2.048503 CTGTCCCGTGTCGAACCC 60.049 66.667 0.00 0.00 0.00 4.11
369 370 1.764854 CCGCACACCCTACCCCTAT 60.765 63.158 0.00 0.00 0.00 2.57
370 371 1.445942 CGCACACCCTACCCCTATG 59.554 63.158 0.00 0.00 0.00 2.23
379 380 1.417890 CCTACCCCTATGAGCACCTTG 59.582 57.143 0.00 0.00 0.00 3.61
382 383 1.561542 ACCCCTATGAGCACCTTGAAG 59.438 52.381 0.00 0.00 0.00 3.02
385 386 2.768527 CCCTATGAGCACCTTGAAGAGA 59.231 50.000 0.00 0.00 0.00 3.10
409 410 3.390311 TGAGCCAGCATATCATCTTGAGT 59.610 43.478 0.00 0.00 0.00 3.41
413 414 5.067413 AGCCAGCATATCATCTTGAGTTTTG 59.933 40.000 0.00 0.00 0.00 2.44
415 416 5.163591 CCAGCATATCATCTTGAGTTTTGCA 60.164 40.000 0.00 0.00 0.00 4.08
416 417 6.327154 CAGCATATCATCTTGAGTTTTGCAA 58.673 36.000 0.00 0.00 0.00 4.08
420 421 7.008992 GCATATCATCTTGAGTTTTGCAAAGTC 59.991 37.037 12.41 13.32 0.00 3.01
422 423 5.581605 TCATCTTGAGTTTTGCAAAGTCAC 58.418 37.500 20.23 13.31 0.00 3.67
430 431 2.284754 TTGCAAAGTCACCATAGGCA 57.715 45.000 0.00 0.00 0.00 4.75
436 437 1.781786 AGTCACCATAGGCATCTCGT 58.218 50.000 0.00 0.00 0.00 4.18
466 467 3.223435 AGAACGTCTCCTCTCACTGAAA 58.777 45.455 0.00 0.00 0.00 2.69
470 471 2.252714 GTCTCCTCTCACTGAAAGGGT 58.747 52.381 0.00 0.00 39.54 4.34
474 475 3.024547 TCCTCTCACTGAAAGGGTATCG 58.975 50.000 0.00 0.00 39.54 2.92
475 476 2.482142 CCTCTCACTGAAAGGGTATCGC 60.482 54.545 0.00 0.00 39.54 4.58
479 480 0.899720 ACTGAAAGGGTATCGCCGAA 59.100 50.000 0.00 0.00 39.30 4.30
480 481 1.276989 ACTGAAAGGGTATCGCCGAAA 59.723 47.619 0.00 0.00 39.30 3.46
481 482 2.289819 ACTGAAAGGGTATCGCCGAAAA 60.290 45.455 0.00 0.00 39.30 2.29
482 483 2.943033 CTGAAAGGGTATCGCCGAAAAT 59.057 45.455 0.00 0.00 38.44 1.82
483 484 3.349022 TGAAAGGGTATCGCCGAAAATT 58.651 40.909 0.00 0.00 38.44 1.82
485 486 3.277142 AAGGGTATCGCCGAAAATTCT 57.723 42.857 0.00 0.00 38.44 2.40
486 487 4.411256 AAGGGTATCGCCGAAAATTCTA 57.589 40.909 0.00 0.00 38.44 2.10
487 488 4.411256 AGGGTATCGCCGAAAATTCTAA 57.589 40.909 0.00 0.00 38.44 2.10
488 489 4.773013 AGGGTATCGCCGAAAATTCTAAA 58.227 39.130 0.00 0.00 38.44 1.85
490 491 5.826208 AGGGTATCGCCGAAAATTCTAAAAT 59.174 36.000 0.00 0.00 38.44 1.82
492 493 7.499895 AGGGTATCGCCGAAAATTCTAAAATAA 59.500 33.333 0.00 0.00 38.44 1.40
493 494 8.130469 GGGTATCGCCGAAAATTCTAAAATAAA 58.870 33.333 0.00 0.00 38.44 1.40
494 495 9.673454 GGTATCGCCGAAAATTCTAAAATAAAT 57.327 29.630 0.00 0.00 0.00 1.40
498 499 9.627395 TCGCCGAAAATTCTAAAATAAATCAAA 57.373 25.926 0.00 0.00 0.00 2.69
522 523 6.494893 AAAAATGCGAGCATCAGTACTTAA 57.505 33.333 11.26 0.00 35.31 1.85
523 524 6.494893 AAAATGCGAGCATCAGTACTTAAA 57.505 33.333 11.26 0.00 35.31 1.52
526 527 4.174009 TGCGAGCATCAGTACTTAAACTC 58.826 43.478 0.00 0.00 33.17 3.01
527 528 4.082190 TGCGAGCATCAGTACTTAAACTCT 60.082 41.667 0.00 0.00 33.17 3.24
529 530 5.641709 CGAGCATCAGTACTTAAACTCTCA 58.358 41.667 0.00 0.00 33.17 3.27
530 531 6.269315 CGAGCATCAGTACTTAAACTCTCAT 58.731 40.000 0.00 0.00 33.17 2.90
531 532 6.198029 CGAGCATCAGTACTTAAACTCTCATG 59.802 42.308 0.00 0.00 33.17 3.07
532 533 5.814705 AGCATCAGTACTTAAACTCTCATGC 59.185 40.000 0.00 0.00 35.84 4.06
533 534 5.276584 GCATCAGTACTTAAACTCTCATGCG 60.277 44.000 0.00 0.00 30.41 4.73
548 572 6.094193 TCTCATGCGAATATCATCTTGAGT 57.906 37.500 0.00 0.00 0.00 3.41
552 576 7.412063 TCATGCGAATATCATCTTGAGTTTTG 58.588 34.615 0.00 0.00 0.00 2.44
554 578 5.123661 TGCGAATATCATCTTGAGTTTTGCA 59.876 36.000 10.64 10.64 38.32 4.08
561 585 6.206395 TCATCTTGAGTTTTGCAAAGTCAA 57.794 33.333 25.60 25.60 0.00 3.18
569 593 4.099266 AGTTTTGCAAAGTCAACATAGGCA 59.901 37.500 12.41 0.00 0.00 4.75
573 597 3.691118 TGCAAAGTCAACATAGGCATCTC 59.309 43.478 0.00 0.00 0.00 2.75
601 625 1.444836 CGAGAACGTCTCCTCTCACT 58.555 55.000 13.79 0.00 40.34 3.41
604 628 2.814919 GAGAACGTCTCCTCTCACTGAA 59.185 50.000 9.58 0.00 37.55 3.02
605 629 3.223435 AGAACGTCTCCTCTCACTGAAA 58.777 45.455 0.00 0.00 0.00 2.69
606 630 3.254657 AGAACGTCTCCTCTCACTGAAAG 59.745 47.826 0.00 0.00 42.29 2.62
607 631 1.889829 ACGTCTCCTCTCACTGAAAGG 59.110 52.381 0.00 0.00 39.30 3.11
608 632 1.203523 CGTCTCCTCTCACTGAAAGGG 59.796 57.143 0.00 0.00 40.34 3.95
609 633 2.252714 GTCTCCTCTCACTGAAAGGGT 58.747 52.381 0.00 0.00 39.54 4.34
625 649 4.411256 AAGGGTATCGCCGAAAATTCTA 57.589 40.909 0.00 0.00 38.44 2.10
628 652 5.187687 AGGGTATCGCCGAAAATTCTAAAA 58.812 37.500 0.00 0.00 38.44 1.52
637 661 9.627395 TCGCCGAAAATTCTAAAATAAATCAAA 57.373 25.926 0.00 0.00 0.00 2.69
661 685 6.494893 AAAAATGCGAGCATCAGTACTTAA 57.505 33.333 11.26 0.00 35.31 1.85
662 686 6.494893 AAAATGCGAGCATCAGTACTTAAA 57.505 33.333 11.26 0.00 35.31 1.52
663 687 5.470845 AATGCGAGCATCAGTACTTAAAC 57.529 39.130 11.26 0.00 35.31 2.01
664 688 4.188247 TGCGAGCATCAGTACTTAAACT 57.812 40.909 0.00 0.00 33.17 2.66
665 689 4.174009 TGCGAGCATCAGTACTTAAACTC 58.826 43.478 0.00 0.00 33.17 3.01
666 690 4.082190 TGCGAGCATCAGTACTTAAACTCT 60.082 41.667 0.00 0.00 33.17 3.24
667 691 4.501198 GCGAGCATCAGTACTTAAACTCTC 59.499 45.833 0.00 0.00 33.17 3.20
668 692 5.641709 CGAGCATCAGTACTTAAACTCTCA 58.358 41.667 0.00 0.00 33.17 3.27
669 693 6.269315 CGAGCATCAGTACTTAAACTCTCAT 58.731 40.000 0.00 0.00 33.17 2.90
670 694 6.198029 CGAGCATCAGTACTTAAACTCTCATG 59.802 42.308 0.00 0.00 33.17 3.07
671 695 5.814705 AGCATCAGTACTTAAACTCTCATGC 59.185 40.000 0.00 0.00 35.84 4.06
672 696 5.276584 GCATCAGTACTTAAACTCTCATGCG 60.277 44.000 0.00 0.00 30.41 4.73
673 697 4.174009 TCAGTACTTAAACTCTCATGCGC 58.826 43.478 0.00 0.00 0.00 6.09
674 698 4.082190 TCAGTACTTAAACTCTCATGCGCT 60.082 41.667 9.73 0.00 0.00 5.92
675 699 4.266502 CAGTACTTAAACTCTCATGCGCTC 59.733 45.833 9.73 0.00 0.00 5.03
676 700 2.263077 ACTTAAACTCTCATGCGCTCG 58.737 47.619 9.73 0.00 0.00 5.03
677 701 1.590238 CTTAAACTCTCATGCGCTCGG 59.410 52.381 9.73 0.00 0.00 4.63
678 702 0.815095 TAAACTCTCATGCGCTCGGA 59.185 50.000 9.73 2.18 0.00 4.55
689 713 1.000607 TGCGCTCGGAATACCACTATC 60.001 52.381 9.73 0.00 35.59 2.08
693 717 3.243771 CGCTCGGAATACCACTATCCTTT 60.244 47.826 0.00 0.00 35.59 3.11
696 720 6.465084 GCTCGGAATACCACTATCCTTTTAT 58.535 40.000 0.00 0.00 35.59 1.40
697 721 6.369065 GCTCGGAATACCACTATCCTTTTATG 59.631 42.308 0.00 0.00 35.59 1.90
698 722 6.765403 TCGGAATACCACTATCCTTTTATGG 58.235 40.000 0.00 0.00 36.46 2.74
699 723 6.328148 TCGGAATACCACTATCCTTTTATGGT 59.672 38.462 0.00 0.00 45.56 3.55
700 724 6.996282 CGGAATACCACTATCCTTTTATGGTT 59.004 38.462 0.00 0.00 40.86 3.67
701 725 7.501225 CGGAATACCACTATCCTTTTATGGTTT 59.499 37.037 0.00 0.00 40.86 3.27
702 726 9.197306 GGAATACCACTATCCTTTTATGGTTTT 57.803 33.333 0.00 0.00 40.86 2.43
735 759 4.750098 CCACATGTTGATTCGATACTACCC 59.250 45.833 0.00 0.00 0.00 3.69
744 768 6.749139 TGATTCGATACTACCCTGAGAATTG 58.251 40.000 0.00 0.00 0.00 2.32
748 772 6.068670 TCGATACTACCCTGAGAATTGATCA 58.931 40.000 0.00 0.00 0.00 2.92
750 774 6.642950 CGATACTACCCTGAGAATTGATCAAC 59.357 42.308 11.07 0.00 0.00 3.18
759 783 6.654161 CCTGAGAATTGATCAACAGAGAAGTT 59.346 38.462 19.93 5.99 37.09 2.66
760 784 7.148440 CCTGAGAATTGATCAACAGAGAAGTTC 60.148 40.741 19.93 13.28 37.09 3.01
761 785 7.448420 TGAGAATTGATCAACAGAGAAGTTCT 58.552 34.615 11.07 12.72 36.25 3.01
762 786 7.601886 TGAGAATTGATCAACAGAGAAGTTCTC 59.398 37.037 24.31 24.31 43.70 2.87
872 1080 2.029380 GCGAATTTACAAAACAGGGGCT 60.029 45.455 0.00 0.00 0.00 5.19
928 1136 1.536496 CGTGTCGTGTAACAGGAACCA 60.536 52.381 0.00 0.00 37.24 3.67
1404 2050 1.740585 CTCATCGTCTTCCTCGTCTGT 59.259 52.381 0.00 0.00 0.00 3.41
1437 2083 0.907486 TCGTCCTCTACTTCCTCCGA 59.093 55.000 0.00 0.00 0.00 4.55
1629 2275 2.466846 GAGGACAACGTTGACGAAGAA 58.533 47.619 33.66 0.00 43.02 2.52
1749 2395 3.013921 TGTATGCATTTCGGTTCTTCCC 58.986 45.455 3.54 0.00 0.00 3.97
1803 2449 2.736721 TCTTGCTGTGCTATTGTCGTTC 59.263 45.455 0.00 0.00 0.00 3.95
1804 2450 1.438651 TGCTGTGCTATTGTCGTTCC 58.561 50.000 0.00 0.00 0.00 3.62
1820 2466 3.567585 TCGTTCCTGAACATGAATGCAAA 59.432 39.130 10.38 0.00 41.20 3.68
1821 2467 3.916172 CGTTCCTGAACATGAATGCAAAG 59.084 43.478 10.38 0.00 41.20 2.77
1822 2468 4.320421 CGTTCCTGAACATGAATGCAAAGA 60.320 41.667 10.38 0.00 41.20 2.52
1862 2508 6.150474 CCCGAATTTTACCTGTGTAGTTGATT 59.850 38.462 0.00 0.00 0.00 2.57
1912 2558 1.195448 CTCAAACAGTCACGGTCATGC 59.805 52.381 0.00 0.00 0.00 4.06
1917 2563 1.002366 CAGTCACGGTCATGCTAAGC 58.998 55.000 0.00 0.00 0.00 3.09
2199 2845 5.079689 TGATTGACAGAGTTTGCGGTATA 57.920 39.130 0.00 0.00 0.00 1.47
2200 2846 4.868171 TGATTGACAGAGTTTGCGGTATAC 59.132 41.667 0.00 0.00 0.00 1.47
2331 2983 6.519761 CGTGTATCTATGTGCTTGTTTTTCAC 59.480 38.462 0.00 0.00 0.00 3.18
2600 3252 5.298777 AGTTTTAGAGCTCAATCATCATGCC 59.701 40.000 17.77 0.00 0.00 4.40
2607 3259 4.581824 AGCTCAATCATCATGCCGTAAAAT 59.418 37.500 0.00 0.00 0.00 1.82
2614 3266 8.605746 CAATCATCATGCCGTAAAATTCATTTT 58.394 29.630 3.13 3.13 42.21 1.82
2621 3273 4.752604 GCCGTAAAATTCATTTTGGTGGTT 59.247 37.500 7.63 0.00 40.00 3.67
2629 3281 4.927978 TCATTTTGGTGGTTGGTACTTG 57.072 40.909 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 2.422235 GGTCTTCCTCTCGGAGATCTCA 60.422 54.545 23.85 3.80 41.25 3.27
44 45 1.131504 CGAGTTCTGGTCTTCCTCTCG 59.868 57.143 0.00 0.00 36.33 4.04
47 48 1.135632 CGACGAGTTCTGGTCTTCCTC 60.136 57.143 11.78 0.00 34.23 3.71
57 58 2.096220 TCTAGACAGCGACGAGTTCT 57.904 50.000 0.00 0.00 0.00 3.01
58 59 2.597971 CGATCTAGACAGCGACGAGTTC 60.598 54.545 0.00 0.00 0.00 3.01
68 69 1.243902 GGCCTCCTCGATCTAGACAG 58.756 60.000 0.00 0.00 0.00 3.51
69 70 0.535328 CGGCCTCCTCGATCTAGACA 60.535 60.000 0.00 0.00 0.00 3.41
73 74 1.173444 GCTTCGGCCTCCTCGATCTA 61.173 60.000 0.00 0.00 36.49 1.98
89 90 5.163913 CGATCTTCGAAACTTTGATCTGCTT 60.164 40.000 17.28 0.00 43.74 3.91
105 106 2.668457 CCCTGTTGTTCTTCGATCTTCG 59.332 50.000 0.00 0.00 42.10 3.79
143 144 3.164269 CATCGGGGTCCAGGGGAG 61.164 72.222 0.00 0.00 29.39 4.30
153 154 1.261480 CCAGATCTAGTCCATCGGGG 58.739 60.000 0.00 0.00 33.31 5.73
157 158 2.324541 ACTGCCCAGATCTAGTCCATC 58.675 52.381 0.00 0.00 0.00 3.51
159 160 3.398318 TTACTGCCCAGATCTAGTCCA 57.602 47.619 0.00 0.00 0.00 4.02
162 163 3.243724 GGGATTACTGCCCAGATCTAGT 58.756 50.000 0.00 0.00 45.31 2.57
199 200 1.071471 CGGTTGTGGAGAGCTGGTT 59.929 57.895 0.00 0.00 0.00 3.67
205 206 2.028112 TCTTCATTCCGGTTGTGGAGAG 60.028 50.000 0.00 0.00 39.72 3.20
206 207 1.974957 TCTTCATTCCGGTTGTGGAGA 59.025 47.619 0.00 5.87 39.72 3.71
217 218 3.003480 CCAGTCTTCGGTTCTTCATTCC 58.997 50.000 0.00 0.00 0.00 3.01
219 220 3.771577 ACCAGTCTTCGGTTCTTCATT 57.228 42.857 0.00 0.00 30.53 2.57
238 239 1.744741 GGCAGAGCTCAGAGGCAAC 60.745 63.158 17.77 0.00 34.17 4.17
239 240 2.667418 GGCAGAGCTCAGAGGCAA 59.333 61.111 17.77 0.00 34.17 4.52
263 264 3.242897 TTGGGTTAGGGCGTGACGG 62.243 63.158 7.25 0.00 0.00 4.79
264 265 2.030958 GTTGGGTTAGGGCGTGACG 61.031 63.158 0.00 0.00 0.00 4.35
265 266 2.030958 CGTTGGGTTAGGGCGTGAC 61.031 63.158 0.00 0.00 0.00 3.67
266 267 2.344500 CGTTGGGTTAGGGCGTGA 59.656 61.111 0.00 0.00 0.00 4.35
267 268 3.428282 GCGTTGGGTTAGGGCGTG 61.428 66.667 0.00 0.00 0.00 5.34
268 269 3.633116 AGCGTTGGGTTAGGGCGT 61.633 61.111 0.00 0.00 0.00 5.68
269 270 3.124921 CAGCGTTGGGTTAGGGCG 61.125 66.667 0.00 0.00 0.00 6.13
270 271 2.750237 CCAGCGTTGGGTTAGGGC 60.750 66.667 10.99 0.00 41.05 5.19
291 292 4.473520 ACAGCGATCTTGGGCGGG 62.474 66.667 0.00 0.00 0.00 6.13
294 295 2.514824 GGGACAGCGATCTTGGGC 60.515 66.667 0.00 0.00 0.00 5.36
297 298 1.078759 GACACGGGACAGCGATCTTG 61.079 60.000 0.00 0.00 0.00 3.02
298 299 1.215647 GACACGGGACAGCGATCTT 59.784 57.895 0.00 0.00 0.00 2.40
305 306 2.048503 GGGTTCGACACGGGACAG 60.049 66.667 0.00 0.00 0.00 3.51
308 309 4.938074 TGGGGGTTCGACACGGGA 62.938 66.667 0.00 0.00 0.00 5.14
311 312 2.663852 GTGTGGGGGTTCGACACG 60.664 66.667 0.00 0.00 43.26 4.49
313 314 2.446994 AGGTGTGGGGGTTCGACA 60.447 61.111 0.00 0.00 0.00 4.35
314 315 2.032071 CAGGTGTGGGGGTTCGAC 59.968 66.667 0.00 0.00 0.00 4.20
322 323 0.975040 CTCTCCTCTCCAGGTGTGGG 60.975 65.000 9.31 3.99 45.11 4.61
369 370 2.298446 CTCAGTCTCTTCAAGGTGCTCA 59.702 50.000 0.00 0.00 0.00 4.26
370 371 2.930455 GCTCAGTCTCTTCAAGGTGCTC 60.930 54.545 0.00 0.00 0.00 4.26
379 380 3.069300 TGATATGCTGGCTCAGTCTCTTC 59.931 47.826 4.45 0.00 33.43 2.87
382 383 3.258872 AGATGATATGCTGGCTCAGTCTC 59.741 47.826 4.45 0.00 33.43 3.36
385 386 3.390311 TCAAGATGATATGCTGGCTCAGT 59.610 43.478 4.45 0.00 33.43 3.41
409 410 2.961741 TGCCTATGGTGACTTTGCAAAA 59.038 40.909 13.84 0.00 0.00 2.44
413 414 2.615912 GAGATGCCTATGGTGACTTTGC 59.384 50.000 0.00 0.00 0.00 3.68
415 416 2.501723 ACGAGATGCCTATGGTGACTTT 59.498 45.455 0.00 0.00 0.00 2.66
416 417 2.111384 ACGAGATGCCTATGGTGACTT 58.889 47.619 0.00 0.00 0.00 3.01
420 421 2.350868 CGACTACGAGATGCCTATGGTG 60.351 54.545 0.00 0.00 42.66 4.17
422 423 2.152016 TCGACTACGAGATGCCTATGG 58.848 52.381 0.00 0.00 43.81 2.74
459 460 0.174845 TCGGCGATACCCTTTCAGTG 59.825 55.000 4.99 0.00 33.26 3.66
466 467 4.411256 TTAGAATTTTCGGCGATACCCT 57.589 40.909 11.76 7.46 33.26 4.34
500 501 6.149474 AGTTTAAGTACTGATGCTCGCATTTT 59.851 34.615 5.79 0.00 36.70 1.82
501 502 5.643777 AGTTTAAGTACTGATGCTCGCATTT 59.356 36.000 5.79 0.00 36.70 2.32
503 504 4.759782 AGTTTAAGTACTGATGCTCGCAT 58.240 39.130 3.70 3.70 39.69 4.73
504 505 4.082190 AGAGTTTAAGTACTGATGCTCGCA 60.082 41.667 0.00 0.00 0.00 5.10
506 507 5.641709 TGAGAGTTTAAGTACTGATGCTCG 58.358 41.667 0.00 0.00 0.00 5.03
508 509 5.814705 GCATGAGAGTTTAAGTACTGATGCT 59.185 40.000 15.70 0.00 33.38 3.79
511 512 6.208988 TCGCATGAGAGTTTAAGTACTGAT 57.791 37.500 0.00 0.00 0.00 2.90
512 513 5.638596 TCGCATGAGAGTTTAAGTACTGA 57.361 39.130 0.00 0.00 0.00 3.41
514 515 8.414003 TGATATTCGCATGAGAGTTTAAGTACT 58.586 33.333 0.00 0.00 0.00 2.73
515 516 8.575565 TGATATTCGCATGAGAGTTTAAGTAC 57.424 34.615 0.00 0.00 0.00 2.73
517 518 8.147058 AGATGATATTCGCATGAGAGTTTAAGT 58.853 33.333 0.00 0.00 0.00 2.24
519 520 8.768019 CAAGATGATATTCGCATGAGAGTTTAA 58.232 33.333 0.00 0.00 0.00 1.52
520 521 8.143835 TCAAGATGATATTCGCATGAGAGTTTA 58.856 33.333 0.00 0.00 0.00 2.01
522 523 6.519382 TCAAGATGATATTCGCATGAGAGTT 58.481 36.000 0.00 0.00 0.00 3.01
523 524 6.094193 TCAAGATGATATTCGCATGAGAGT 57.906 37.500 0.00 0.00 0.00 3.24
526 527 6.782298 AACTCAAGATGATATTCGCATGAG 57.218 37.500 0.00 0.00 0.00 2.90
527 528 7.412063 CAAAACTCAAGATGATATTCGCATGA 58.588 34.615 0.00 0.00 0.00 3.07
529 530 6.183360 TGCAAAACTCAAGATGATATTCGCAT 60.183 34.615 0.00 0.00 0.00 4.73
530 531 5.123661 TGCAAAACTCAAGATGATATTCGCA 59.876 36.000 0.00 0.00 0.00 5.10
531 532 5.572211 TGCAAAACTCAAGATGATATTCGC 58.428 37.500 0.00 0.00 0.00 4.70
532 533 7.752239 ACTTTGCAAAACTCAAGATGATATTCG 59.248 33.333 13.84 0.00 0.00 3.34
533 534 8.976986 ACTTTGCAAAACTCAAGATGATATTC 57.023 30.769 13.84 0.00 0.00 1.75
548 572 4.662468 TGCCTATGTTGACTTTGCAAAA 57.338 36.364 13.84 0.00 0.00 2.44
552 576 3.242543 CGAGATGCCTATGTTGACTTTGC 60.243 47.826 0.00 0.00 0.00 3.68
554 578 4.207891 ACGAGATGCCTATGTTGACTTT 57.792 40.909 0.00 0.00 0.00 2.66
561 585 2.847441 TCGACTACGAGATGCCTATGT 58.153 47.619 0.00 0.00 43.81 2.29
585 609 3.570559 CTTTCAGTGAGAGGAGACGTTC 58.429 50.000 2.68 0.00 0.00 3.95
587 611 1.889829 CCTTTCAGTGAGAGGAGACGT 59.110 52.381 22.50 0.00 36.19 4.34
589 613 2.252714 ACCCTTTCAGTGAGAGGAGAC 58.747 52.381 27.29 0.00 36.19 3.36
594 618 2.482142 GGCGATACCCTTTCAGTGAGAG 60.482 54.545 3.66 3.66 0.00 3.20
595 619 1.480954 GGCGATACCCTTTCAGTGAGA 59.519 52.381 0.00 0.00 0.00 3.27
597 621 0.174845 CGGCGATACCCTTTCAGTGA 59.825 55.000 0.00 0.00 33.26 3.41
598 622 0.174845 TCGGCGATACCCTTTCAGTG 59.825 55.000 4.99 0.00 33.26 3.66
601 625 2.476126 TTTTCGGCGATACCCTTTCA 57.524 45.000 11.76 0.00 33.26 2.69
604 628 3.277142 AGAATTTTCGGCGATACCCTT 57.723 42.857 11.76 0.07 33.26 3.95
605 629 4.411256 TTAGAATTTTCGGCGATACCCT 57.589 40.909 11.76 7.46 33.26 4.34
606 630 5.488645 TTTTAGAATTTTCGGCGATACCC 57.511 39.130 11.76 0.00 33.26 3.69
607 631 9.673454 ATTTATTTTAGAATTTTCGGCGATACC 57.327 29.630 11.76 0.00 0.00 2.73
644 668 4.425520 AGAGTTTAAGTACTGATGCTCGC 58.574 43.478 0.00 0.00 0.00 5.03
645 669 5.641709 TGAGAGTTTAAGTACTGATGCTCG 58.358 41.667 0.00 0.00 0.00 5.03
650 674 4.806247 GCGCATGAGAGTTTAAGTACTGAT 59.194 41.667 0.30 0.00 0.00 2.90
651 675 4.082190 AGCGCATGAGAGTTTAAGTACTGA 60.082 41.667 11.47 0.00 0.00 3.41
652 676 4.177026 AGCGCATGAGAGTTTAAGTACTG 58.823 43.478 11.47 0.00 0.00 2.74
653 677 4.425520 GAGCGCATGAGAGTTTAAGTACT 58.574 43.478 11.47 0.00 0.00 2.73
654 678 3.240861 CGAGCGCATGAGAGTTTAAGTAC 59.759 47.826 11.47 0.00 0.00 2.73
655 679 3.435566 CGAGCGCATGAGAGTTTAAGTA 58.564 45.455 11.47 0.00 0.00 2.24
656 680 2.263077 CGAGCGCATGAGAGTTTAAGT 58.737 47.619 11.47 0.00 0.00 2.24
657 681 1.590238 CCGAGCGCATGAGAGTTTAAG 59.410 52.381 11.47 0.00 0.00 1.85
658 682 1.203758 TCCGAGCGCATGAGAGTTTAA 59.796 47.619 11.47 0.00 0.00 1.52
659 683 0.815095 TCCGAGCGCATGAGAGTTTA 59.185 50.000 11.47 0.00 0.00 2.01
660 684 0.037326 TTCCGAGCGCATGAGAGTTT 60.037 50.000 11.47 0.00 0.00 2.66
661 685 0.176680 ATTCCGAGCGCATGAGAGTT 59.823 50.000 11.47 0.00 0.00 3.01
662 686 1.032794 TATTCCGAGCGCATGAGAGT 58.967 50.000 11.47 0.00 0.00 3.24
663 687 1.413382 GTATTCCGAGCGCATGAGAG 58.587 55.000 11.47 0.00 0.00 3.20
664 688 0.032130 GGTATTCCGAGCGCATGAGA 59.968 55.000 11.47 0.00 0.00 3.27
665 689 0.249447 TGGTATTCCGAGCGCATGAG 60.249 55.000 11.47 0.00 36.30 2.90
666 690 0.529773 GTGGTATTCCGAGCGCATGA 60.530 55.000 11.47 0.00 36.30 3.07
667 691 0.530650 AGTGGTATTCCGAGCGCATG 60.531 55.000 11.47 0.00 36.30 4.06
668 692 1.037493 TAGTGGTATTCCGAGCGCAT 58.963 50.000 11.47 0.00 36.30 4.73
669 693 1.000607 GATAGTGGTATTCCGAGCGCA 60.001 52.381 11.47 0.00 36.30 6.09
670 694 1.669211 GGATAGTGGTATTCCGAGCGC 60.669 57.143 0.00 0.00 36.30 5.92
671 695 1.887198 AGGATAGTGGTATTCCGAGCG 59.113 52.381 0.00 0.00 36.30 5.03
672 696 4.338379 AAAGGATAGTGGTATTCCGAGC 57.662 45.455 0.00 0.00 36.30 5.03
673 697 6.874134 CCATAAAAGGATAGTGGTATTCCGAG 59.126 42.308 0.00 0.00 36.30 4.63
674 698 6.328148 ACCATAAAAGGATAGTGGTATTCCGA 59.672 38.462 0.00 0.00 41.15 4.55
675 699 6.531021 ACCATAAAAGGATAGTGGTATTCCG 58.469 40.000 0.00 0.00 41.15 4.30
676 700 8.762481 AAACCATAAAAGGATAGTGGTATTCC 57.238 34.615 0.00 0.00 42.05 3.01
697 721 3.576550 ACATGTGGTTGGATGGTAAAACC 59.423 43.478 0.00 0.00 43.07 3.27
698 722 4.864704 ACATGTGGTTGGATGGTAAAAC 57.135 40.909 0.00 0.00 0.00 2.43
713 737 5.463392 CAGGGTAGTATCGAATCAACATGTG 59.537 44.000 0.00 0.00 0.00 3.21
714 738 5.362717 TCAGGGTAGTATCGAATCAACATGT 59.637 40.000 0.00 0.00 0.00 3.21
727 751 7.345653 TCTGTTGATCAATTCTCAGGGTAGTAT 59.654 37.037 18.52 0.00 32.19 2.12
735 759 7.603404 AGAACTTCTCTGTTGATCAATTCTCAG 59.397 37.037 12.12 13.62 31.12 3.35
766 790 4.334203 GCCGGTGTTTGGAAATTTCTTTTT 59.666 37.500 17.42 0.00 0.00 1.94
767 791 3.874543 GCCGGTGTTTGGAAATTTCTTTT 59.125 39.130 17.42 0.00 0.00 2.27
768 792 3.118592 TGCCGGTGTTTGGAAATTTCTTT 60.119 39.130 17.42 0.00 0.00 2.52
769 793 2.432510 TGCCGGTGTTTGGAAATTTCTT 59.567 40.909 17.42 0.00 0.00 2.52
770 794 2.035632 TGCCGGTGTTTGGAAATTTCT 58.964 42.857 17.42 0.00 0.00 2.52
771 795 2.131972 GTGCCGGTGTTTGGAAATTTC 58.868 47.619 9.83 9.83 0.00 2.17
772 796 1.202592 GGTGCCGGTGTTTGGAAATTT 60.203 47.619 1.90 0.00 0.00 1.82
773 797 0.391228 GGTGCCGGTGTTTGGAAATT 59.609 50.000 1.90 0.00 0.00 1.82
774 798 1.801309 CGGTGCCGGTGTTTGGAAAT 61.801 55.000 1.90 0.00 35.56 2.17
872 1080 1.141019 GGCATTCTAGACGGCGACA 59.859 57.895 16.62 0.00 0.00 4.35
1404 2050 2.758327 ACGAGCCAGCCGACCATA 60.758 61.111 7.38 0.00 0.00 2.74
1596 2242 3.241530 TCCTCCGCCTTGTGCAGT 61.242 61.111 0.00 0.00 41.33 4.40
1749 2395 2.183478 TTGTACACCATCCAGCAGTG 57.817 50.000 0.00 0.00 37.53 3.66
1803 2449 5.716094 TCATTCTTTGCATTCATGTTCAGG 58.284 37.500 0.00 0.00 0.00 3.86
1804 2450 6.237835 GCATCATTCTTTGCATTCATGTTCAG 60.238 38.462 0.00 0.00 38.72 3.02
1820 2466 4.963318 TCGGGAAGATAAGCATCATTCT 57.037 40.909 0.00 0.00 33.21 2.40
1821 2467 6.566197 AATTCGGGAAGATAAGCATCATTC 57.434 37.500 0.00 0.00 33.21 2.67
1822 2468 6.966534 AAATTCGGGAAGATAAGCATCATT 57.033 33.333 0.00 0.00 33.21 2.57
1912 2558 4.904116 TGACAAACAAACTGAACGCTTAG 58.096 39.130 0.00 0.00 0.00 2.18
1982 2628 4.213270 TCACTTTGTAAAGGCAACATCTCG 59.787 41.667 9.00 0.00 40.31 4.04
2199 2845 1.618837 ACAGCCTGATAGTGACAACGT 59.381 47.619 0.00 0.00 0.00 3.99
2200 2846 2.263077 GACAGCCTGATAGTGACAACG 58.737 52.381 0.00 0.00 0.00 4.10
2331 2983 2.620251 TACAATGATTCTGCCCTCCG 57.380 50.000 0.00 0.00 0.00 4.63
2575 3227 6.484643 GGCATGATGATTGAGCTCTAAAACTA 59.515 38.462 16.19 0.00 0.00 2.24
2600 3252 5.755861 ACCAACCACCAAAATGAATTTTACG 59.244 36.000 0.86 0.00 37.86 3.18
2607 3259 4.442192 GCAAGTACCAACCACCAAAATGAA 60.442 41.667 0.00 0.00 0.00 2.57
2614 3266 0.466555 GGTGCAAGTACCAACCACCA 60.467 55.000 14.25 0.00 44.07 4.17
2629 3281 0.179018 ACCCTTCAGAAGTGTGGTGC 60.179 55.000 9.41 0.00 0.00 5.01
2704 3359 8.920174 TGTTCCTCTAAATAATCGTAAGGATGA 58.080 33.333 0.00 0.00 34.93 2.92


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

AutoCloner maintained by Alex Coulton.