Multiple sequence alignment - TraesCS7A01G100500

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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 TraesCS7A01G100500 chr7A 100.000 3976 0 0 1 3976 61797319 61793344 0.000000e+00 7343
1 TraesCS7A01G100500 chr4A 93.127 2590 112 29 596 3144 673974918 673977482 0.000000e+00 3736
2 TraesCS7A01G100500 chr4A 93.969 829 33 7 3161 3976 674353488 674354312 0.000000e+00 1238
3 TraesCS7A01G100500 chr4A 87.193 937 98 12 675 1594 674350673 674351604 0.000000e+00 1046
4 TraesCS7A01G100500 chr4A 93.720 621 34 2 2541 3160 674352690 674353306 0.000000e+00 926
5 TraesCS7A01G100500 chr4A 88.814 742 69 8 817 1552 676546329 676547062 0.000000e+00 898
6 TraesCS7A01G100500 chr4A 86.617 807 83 9 1628 2412 676547156 676547959 0.000000e+00 869
7 TraesCS7A01G100500 chr4A 90.396 656 39 13 3161 3800 673977860 673978507 0.000000e+00 841
8 TraesCS7A01G100500 chr4A 89.822 619 55 5 2541 3156 676548048 676548661 0.000000e+00 787
9 TraesCS7A01G100500 chr4A 86.612 732 64 18 3161 3874 676548696 676549411 0.000000e+00 778
10 TraesCS7A01G100500 chr4A 93.089 463 21 9 1 461 673974011 673974464 0.000000e+00 667
11 TraesCS7A01G100500 chr4A 84.535 666 87 8 1643 2293 674351797 674352461 0.000000e+00 645
12 TraesCS7A01G100500 chr4A 89.308 159 5 1 3830 3976 673978500 673978658 5.250000e-44 189
13 TraesCS7A01G100500 chr7D 92.949 2340 106 19 847 3145 56991164 56988843 0.000000e+00 3352
14 TraesCS7A01G100500 chr7D 96.695 817 24 3 3161 3976 56988511 56987697 0.000000e+00 1356
15 TraesCS7A01G100500 chr3D 92.460 2321 131 21 847 3131 545231681 545229369 0.000000e+00 3277
16 TraesCS7A01G100500 chr3D 95.125 718 19 6 3272 3976 545228983 545228269 0.000000e+00 1118
17 TraesCS7A01G100500 chr3D 97.674 86 2 0 3161 3246 545229059 545228974 8.900000e-32 148


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 TraesCS7A01G100500 chr7A 61793344 61797319 3975 True 7343.000000 7343 100.000000 1 3976 1 chr7A.!!$R1 3975
1 TraesCS7A01G100500 chr4A 673974011 673978658 4647 False 1358.250000 3736 91.480000 1 3976 4 chr4A.!!$F1 3975
2 TraesCS7A01G100500 chr4A 674350673 674354312 3639 False 963.750000 1238 89.854250 675 3976 4 chr4A.!!$F2 3301
3 TraesCS7A01G100500 chr4A 676546329 676549411 3082 False 833.000000 898 87.966250 817 3874 4 chr4A.!!$F3 3057
4 TraesCS7A01G100500 chr7D 56987697 56991164 3467 True 2354.000000 3352 94.822000 847 3976 2 chr7D.!!$R1 3129
5 TraesCS7A01G100500 chr3D 545228269 545231681 3412 True 1514.333333 3277 95.086333 847 3976 3 chr3D.!!$R1 3129

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
554 557 0.108615 ATCAAGACCGCCTCAACTCG 60.109 55.0 0.00 0.00 0.00 4.18 F
562 565 0.652592 CGCCTCAACTCGGCTTTATG 59.347 55.0 0.00 0.00 45.37 1.90 F
1488 1839 0.107081 ATGAGATGAGCAGCTCCAGC 59.893 55.0 20.16 10.55 42.79 4.85 F
2246 2800 0.537143 AAGAGGCATGTGCGTTGGAA 60.537 50.0 1.44 0.00 43.26 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 1839 0.306840 CATTAGATGCTGCACTGGCG 59.693 55.000 3.57 0.00 45.35 5.69 R
2279 2833 1.982958 TCTTGGGTTACCTCCTGGTTC 59.017 52.381 0.00 0.00 46.05 3.62 R
2889 3495 1.341089 TGTCCTAGCACGAGAGGATGT 60.341 52.381 0.00 0.00 43.71 3.06 R
3156 3764 3.305267 GCACTGTTCCATTAATGCACACA 60.305 43.478 10.11 10.32 33.27 3.72 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.105310 AGTGCTATTGGTAGTACTCCAAGTG 60.105 44.000 22.71 19.07 46.75 3.16
69 70 2.096417 CGTCGCTTCCAACTTAAAGTGG 60.096 50.000 0.00 0.00 34.52 4.00
71 72 2.875933 TCGCTTCCAACTTAAAGTGGTG 59.124 45.455 4.44 1.64 34.52 4.17
72 73 2.875933 CGCTTCCAACTTAAAGTGGTGA 59.124 45.455 4.44 0.00 31.03 4.02
145 146 1.177401 GAAATGACAGGGAGTTGGCC 58.823 55.000 0.00 0.00 0.00 5.36
177 178 7.746703 ACAAACTCATAAGTATATCTTCCCCC 58.253 38.462 0.00 0.00 37.56 5.40
178 179 7.572861 ACAAACTCATAAGTATATCTTCCCCCT 59.427 37.037 0.00 0.00 37.56 4.79
179 180 9.101325 CAAACTCATAAGTATATCTTCCCCCTA 57.899 37.037 0.00 0.00 37.56 3.53
236 238 3.313526 CGAAATTCTCTTCGGCCATTCAT 59.686 43.478 2.24 0.00 43.51 2.57
254 256 7.576477 GCCATTCATTTTCCTAGATAAGCATCC 60.576 40.741 0.00 0.00 0.00 3.51
267 269 5.475909 AGATAAGCATCCCACATAAGCATTG 59.524 40.000 0.00 0.00 0.00 2.82
277 279 4.082081 CCACATAAGCATTGAAAGGAGCAA 60.082 41.667 0.00 0.00 0.00 3.91
305 308 7.467623 AGAGCGAGTCAAAAGCATAATTTAAG 58.532 34.615 0.00 0.00 0.00 1.85
378 381 8.907885 ACTAAAATCCTCTCTGGCAATTTTATC 58.092 33.333 11.04 0.00 35.63 1.75
431 434 3.077359 GGGGAGCATGATTAATTCCTCG 58.923 50.000 0.00 0.00 0.00 4.63
452 455 3.414269 GACGGAAATGTCCCTTACCAAA 58.586 45.455 0.00 0.00 41.44 3.28
461 464 6.894339 ATGTCCCTTACCAAAGTTTGTTAG 57.106 37.500 14.36 8.04 0.00 2.34
462 465 6.003859 TGTCCCTTACCAAAGTTTGTTAGA 57.996 37.500 14.36 0.00 0.00 2.10
463 466 6.424883 TGTCCCTTACCAAAGTTTGTTAGAA 58.575 36.000 14.36 2.52 0.00 2.10
464 467 6.544564 TGTCCCTTACCAAAGTTTGTTAGAAG 59.455 38.462 14.36 10.66 0.00 2.85
465 468 6.769341 GTCCCTTACCAAAGTTTGTTAGAAGA 59.231 38.462 14.36 2.33 0.00 2.87
467 470 8.002459 TCCCTTACCAAAGTTTGTTAGAAGATT 58.998 33.333 14.36 0.00 0.00 2.40
468 471 8.638873 CCCTTACCAAAGTTTGTTAGAAGATTT 58.361 33.333 14.36 0.00 0.00 2.17
472 475 6.695713 ACCAAAGTTTGTTAGAAGATTTTCGC 59.304 34.615 14.36 0.00 38.38 4.70
474 477 8.073768 CCAAAGTTTGTTAGAAGATTTTCGCTA 58.926 33.333 14.36 0.00 38.38 4.26
475 478 9.107367 CAAAGTTTGTTAGAAGATTTTCGCTAG 57.893 33.333 7.48 0.00 38.38 3.42
477 480 9.485206 AAGTTTGTTAGAAGATTTTCGCTAGTA 57.515 29.630 0.00 0.00 38.38 1.82
478 481 8.923683 AGTTTGTTAGAAGATTTTCGCTAGTAC 58.076 33.333 0.00 0.00 38.38 2.73
479 482 8.706035 GTTTGTTAGAAGATTTTCGCTAGTACA 58.294 33.333 0.00 0.00 38.38 2.90
480 483 8.821147 TTGTTAGAAGATTTTCGCTAGTACAA 57.179 30.769 0.00 0.00 38.38 2.41
481 484 8.462143 TGTTAGAAGATTTTCGCTAGTACAAG 57.538 34.615 0.00 0.00 38.38 3.16
483 486 6.282199 AGAAGATTTTCGCTAGTACAAGGA 57.718 37.500 0.00 0.00 38.38 3.36
485 488 8.008513 AGAAGATTTTCGCTAGTACAAGGATA 57.991 34.615 0.00 0.00 38.38 2.59
486 489 8.643324 AGAAGATTTTCGCTAGTACAAGGATAT 58.357 33.333 0.00 0.00 38.38 1.63
487 490 9.909644 GAAGATTTTCGCTAGTACAAGGATATA 57.090 33.333 0.00 0.00 0.00 0.86
488 491 9.694137 AAGATTTTCGCTAGTACAAGGATATAC 57.306 33.333 0.00 0.00 0.00 1.47
489 492 9.080097 AGATTTTCGCTAGTACAAGGATATACT 57.920 33.333 0.00 0.00 35.76 2.12
502 505 8.422577 ACAAGGATATACTATATGTCACTGCA 57.577 34.615 0.00 0.00 0.00 4.41
503 506 8.870116 ACAAGGATATACTATATGTCACTGCAA 58.130 33.333 0.00 0.00 0.00 4.08
504 507 9.710900 CAAGGATATACTATATGTCACTGCAAA 57.289 33.333 0.00 0.00 0.00 3.68
507 510 8.926710 GGATATACTATATGTCACTGCAAACAC 58.073 37.037 0.00 0.00 0.00 3.32
508 511 9.698309 GATATACTATATGTCACTGCAAACACT 57.302 33.333 0.00 0.00 0.00 3.55
510 513 6.727824 ACTATATGTCACTGCAAACACTTC 57.272 37.500 0.00 0.00 0.00 3.01
511 514 6.467677 ACTATATGTCACTGCAAACACTTCT 58.532 36.000 0.00 0.00 0.00 2.85
513 516 8.094548 ACTATATGTCACTGCAAACACTTCTTA 58.905 33.333 0.00 0.00 0.00 2.10
514 517 4.875544 TGTCACTGCAAACACTTCTTAC 57.124 40.909 0.00 0.00 0.00 2.34
515 518 4.257731 TGTCACTGCAAACACTTCTTACA 58.742 39.130 0.00 0.00 0.00 2.41
516 519 4.332543 TGTCACTGCAAACACTTCTTACAG 59.667 41.667 0.00 0.00 0.00 2.74
517 520 3.876914 TCACTGCAAACACTTCTTACAGG 59.123 43.478 0.00 0.00 0.00 4.00
518 521 3.876914 CACTGCAAACACTTCTTACAGGA 59.123 43.478 0.00 0.00 0.00 3.86
519 522 4.335315 CACTGCAAACACTTCTTACAGGAA 59.665 41.667 0.00 0.00 0.00 3.36
520 523 4.947388 ACTGCAAACACTTCTTACAGGAAA 59.053 37.500 0.00 0.00 0.00 3.13
521 524 5.066505 ACTGCAAACACTTCTTACAGGAAAG 59.933 40.000 0.00 0.00 0.00 2.62
523 526 4.202010 GCAAACACTTCTTACAGGAAAGCA 60.202 41.667 0.00 0.00 0.00 3.91
524 527 5.514279 CAAACACTTCTTACAGGAAAGCAG 58.486 41.667 0.00 0.00 0.00 4.24
525 528 4.689612 ACACTTCTTACAGGAAAGCAGA 57.310 40.909 0.00 0.00 0.00 4.26
527 530 3.434984 CACTTCTTACAGGAAAGCAGAGC 59.565 47.826 0.00 0.00 0.00 4.09
528 531 3.071602 ACTTCTTACAGGAAAGCAGAGCA 59.928 43.478 0.00 0.00 0.00 4.26
529 532 3.325293 TCTTACAGGAAAGCAGAGCAG 57.675 47.619 0.00 0.00 0.00 4.24
530 533 2.027745 TCTTACAGGAAAGCAGAGCAGG 60.028 50.000 0.00 0.00 0.00 4.85
531 534 0.615331 TACAGGAAAGCAGAGCAGGG 59.385 55.000 0.00 0.00 0.00 4.45
534 537 1.003580 CAGGAAAGCAGAGCAGGGTTA 59.996 52.381 0.00 0.00 0.00 2.85
535 538 1.705186 AGGAAAGCAGAGCAGGGTTAA 59.295 47.619 0.00 0.00 0.00 2.01
536 539 2.310052 AGGAAAGCAGAGCAGGGTTAAT 59.690 45.455 0.00 0.00 0.00 1.40
538 541 3.347216 GAAAGCAGAGCAGGGTTAATCA 58.653 45.455 0.00 0.00 0.00 2.57
539 542 3.439857 AAGCAGAGCAGGGTTAATCAA 57.560 42.857 0.00 0.00 0.00 2.57
540 543 2.996631 AGCAGAGCAGGGTTAATCAAG 58.003 47.619 0.00 0.00 0.00 3.02
541 544 2.573462 AGCAGAGCAGGGTTAATCAAGA 59.427 45.455 0.00 0.00 0.00 3.02
542 545 2.680339 GCAGAGCAGGGTTAATCAAGAC 59.320 50.000 0.00 0.00 0.00 3.01
543 546 3.274288 CAGAGCAGGGTTAATCAAGACC 58.726 50.000 0.00 0.00 35.14 3.85
544 547 2.093447 AGAGCAGGGTTAATCAAGACCG 60.093 50.000 0.00 0.00 36.78 4.79
545 548 0.733150 GCAGGGTTAATCAAGACCGC 59.267 55.000 0.00 0.00 36.78 5.68
546 549 1.379527 CAGGGTTAATCAAGACCGCC 58.620 55.000 0.00 0.00 36.78 6.13
548 551 1.209747 AGGGTTAATCAAGACCGCCTC 59.790 52.381 0.00 0.00 36.78 4.70
549 552 1.065709 GGGTTAATCAAGACCGCCTCA 60.066 52.381 0.00 0.00 36.78 3.86
550 553 2.617021 GGGTTAATCAAGACCGCCTCAA 60.617 50.000 0.00 0.00 36.78 3.02
551 554 2.418976 GGTTAATCAAGACCGCCTCAAC 59.581 50.000 0.00 0.00 0.00 3.18
553 556 2.100605 AATCAAGACCGCCTCAACTC 57.899 50.000 0.00 0.00 0.00 3.01
554 557 0.108615 ATCAAGACCGCCTCAACTCG 60.109 55.000 0.00 0.00 0.00 4.18
559 562 2.358737 CCGCCTCAACTCGGCTTT 60.359 61.111 0.00 0.00 45.37 3.51
560 563 1.079405 CCGCCTCAACTCGGCTTTA 60.079 57.895 0.00 0.00 45.37 1.85
562 565 0.652592 CGCCTCAACTCGGCTTTATG 59.347 55.000 0.00 0.00 45.37 1.90
564 567 1.737838 CCTCAACTCGGCTTTATGCA 58.262 50.000 0.00 0.00 45.15 3.96
565 568 1.398390 CCTCAACTCGGCTTTATGCAC 59.602 52.381 0.00 0.00 45.15 4.57
566 569 2.076100 CTCAACTCGGCTTTATGCACA 58.924 47.619 0.00 0.00 45.15 4.57
567 570 1.804151 TCAACTCGGCTTTATGCACAC 59.196 47.619 0.00 0.00 45.15 3.82
568 571 1.806542 CAACTCGGCTTTATGCACACT 59.193 47.619 0.00 0.00 45.15 3.55
569 572 3.000041 CAACTCGGCTTTATGCACACTA 59.000 45.455 0.00 0.00 45.15 2.74
570 573 2.893637 ACTCGGCTTTATGCACACTAG 58.106 47.619 0.00 0.00 45.15 2.57
571 574 1.594862 CTCGGCTTTATGCACACTAGC 59.405 52.381 0.00 0.00 45.15 3.42
572 575 1.207089 TCGGCTTTATGCACACTAGCT 59.793 47.619 10.54 0.00 45.15 3.32
573 576 1.328680 CGGCTTTATGCACACTAGCTG 59.671 52.381 0.00 8.52 45.15 4.24
574 577 1.064654 GGCTTTATGCACACTAGCTGC 59.935 52.381 0.00 6.12 45.15 5.25
579 582 3.327600 TGCACACTAGCTGCACATT 57.672 47.368 10.87 0.00 39.76 2.71
584 914 3.425359 GCACACTAGCTGCACATTAACAG 60.425 47.826 1.02 0.00 34.56 3.16
606 936 8.516811 ACAGTTTACAAGAGTACAAAGTATCG 57.483 34.615 0.00 0.00 0.00 2.92
607 937 8.355169 ACAGTTTACAAGAGTACAAAGTATCGA 58.645 33.333 0.00 0.00 0.00 3.59
608 938 8.851416 CAGTTTACAAGAGTACAAAGTATCGAG 58.149 37.037 0.00 0.00 0.00 4.04
633 963 1.810151 CACGGGAGTTACAAACCATGG 59.190 52.381 11.19 11.19 44.67 3.66
649 979 3.056322 ACCATGGAGCTGAAAAATCAAGC 60.056 43.478 21.47 0.00 0.00 4.01
723 1053 1.250328 TTGGGAACTTGCATGCTCAG 58.750 50.000 20.33 16.67 0.00 3.35
751 1081 4.576463 ACTGGATGATTTACATTTCCGCTC 59.424 41.667 0.00 0.00 39.56 5.03
806 1145 3.127030 GGGAGCGTGAAGAATCGAAAAAT 59.873 43.478 0.00 0.00 0.00 1.82
834 1173 6.038825 AGAGTTTGAGTCATATACTGAGGACG 59.961 42.308 7.55 0.00 39.07 4.79
835 1174 5.652891 AGTTTGAGTCATATACTGAGGACGT 59.347 40.000 0.00 0.00 39.07 4.34
838 1177 5.677567 TGAGTCATATACTGAGGACGTGTA 58.322 41.667 0.00 0.00 39.07 2.90
1371 1719 2.280592 GTGTTGAAGGGCGACGGT 60.281 61.111 0.00 0.00 33.27 4.83
1488 1839 0.107081 ATGAGATGAGCAGCTCCAGC 59.893 55.000 20.16 10.55 42.79 4.85
1580 1931 1.453155 CTCGGTAGCTGCAATGGTTT 58.547 50.000 3.61 0.00 0.00 3.27
1585 1936 3.317150 GGTAGCTGCAATGGTTTTGTTC 58.683 45.455 3.61 0.00 0.00 3.18
1604 1955 8.887264 TTTGTTCTTTAGATAATAGCCCCAAA 57.113 30.769 0.00 0.00 0.00 3.28
1656 2032 9.051027 GTTGTTATTTGTGAAGTAATCGTCATG 57.949 33.333 0.00 0.00 34.93 3.07
1664 2198 5.465724 GTGAAGTAATCGTCATGTAATCCCC 59.534 44.000 0.00 0.00 34.93 4.81
1701 2235 4.845387 CATGCAATGCAGCTAGAAACTAG 58.155 43.478 14.98 0.00 43.65 2.57
1736 2271 4.333372 TGTTTAGAAGTTGTCCACCGAAAC 59.667 41.667 0.00 0.00 0.00 2.78
1758 2293 2.798976 TCATGCACTGGAAAACTTGC 57.201 45.000 0.00 0.00 35.45 4.01
1878 2422 1.025647 AGACGAGTCCAGGTAGTCGC 61.026 60.000 13.18 8.30 44.37 5.19
1923 2473 4.390129 TTTTATGGACCACTAAAGGGCA 57.610 40.909 0.00 0.00 38.98 5.36
1950 2503 7.646314 TCCTGTAATCTACGCTAACTGATAAC 58.354 38.462 0.00 0.00 0.00 1.89
1963 2516 6.314896 GCTAACTGATAACATCAAACTGCTCT 59.685 38.462 0.00 0.00 39.11 4.09
2139 2693 8.996024 TTTTTATTTTCTAGCCCTGTAATTGC 57.004 30.769 0.00 0.00 0.00 3.56
2141 2695 2.729028 TTCTAGCCCTGTAATTGCCC 57.271 50.000 0.00 0.00 0.00 5.36
2190 2744 1.280421 AGGTGGAAGAGCTCAATGTCC 59.720 52.381 17.77 16.22 0.00 4.02
2246 2800 0.537143 AAGAGGCATGTGCGTTGGAA 60.537 50.000 1.44 0.00 43.26 3.53
2279 2833 4.925646 GGAAAAGCTGCCATTAAAGAACTG 59.074 41.667 0.00 0.00 0.00 3.16
2365 2920 3.373439 GTCAAGAAATGCGCTTCTCAGAT 59.627 43.478 9.73 0.00 34.49 2.90
2834 3440 1.349357 AGAAAAGGGAGAGACAGTGCC 59.651 52.381 0.00 0.00 0.00 5.01
2839 3445 1.671742 GGAGAGACAGTGCCCGAAA 59.328 57.895 0.00 0.00 0.00 3.46
2889 3495 3.618594 GCAGCAACTTCGAGTCATATCAA 59.381 43.478 0.00 0.00 0.00 2.57
2914 3520 1.066303 CTCTCGTGCTAGGACATGGTC 59.934 57.143 15.20 0.00 0.00 4.02
2989 3595 5.913137 AGGATCTGACTAAGTTCTCACAG 57.087 43.478 0.00 0.00 0.00 3.66
3003 3609 2.563179 TCTCACAGTTTCCCAGACTAGC 59.437 50.000 0.00 0.00 0.00 3.42
3004 3610 2.564947 CTCACAGTTTCCCAGACTAGCT 59.435 50.000 0.00 0.00 0.00 3.32
3005 3611 3.764434 CTCACAGTTTCCCAGACTAGCTA 59.236 47.826 0.00 0.00 0.00 3.32
3006 3612 3.764434 TCACAGTTTCCCAGACTAGCTAG 59.236 47.826 19.44 19.44 0.00 3.42
3054 3662 4.760530 TCTCTATGTAAGCATGCACCTT 57.239 40.909 21.98 8.25 36.58 3.50
3094 3702 6.378710 TTCATATGGTCTTCTCACTACTCG 57.621 41.667 2.13 0.00 0.00 4.18
3156 3764 4.098349 TCATTCAACTTGCAGCTCTTTTGT 59.902 37.500 0.00 0.00 0.00 2.83
3350 4319 6.283694 TGAAGCCTGACACTCATACATTATC 58.716 40.000 0.00 0.00 0.00 1.75
3559 4530 3.767673 GGGTTCCCCTTTTAGGAAATGAC 59.232 47.826 0.00 0.00 44.84 3.06
3575 4547 4.701956 AATGACATTGGTAGCGGAAAAG 57.298 40.909 0.00 0.00 0.00 2.27
3629 4616 9.750882 GTTCCTTAAACAGTCATAATAACGAAC 57.249 33.333 0.00 0.00 37.82 3.95
3638 4625 6.018751 CAGTCATAATAACGAACACTGGATGG 60.019 42.308 0.00 0.00 0.00 3.51
3681 4668 8.579682 CTTGAGAAACAAGGGTTTATTTCTTG 57.420 34.615 0.00 0.00 46.84 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.331166 TGCCACTTGGAGTACTACCAA 58.669 47.619 19.35 19.35 43.84 3.67
37 38 1.525619 GGAAGCGACGTATACAATGCC 59.474 52.381 3.32 0.00 0.00 4.40
93 94 7.712204 TGATTACGCCTGATGGTTATCTATA 57.288 36.000 0.00 0.00 34.31 1.31
94 95 6.605471 TGATTACGCCTGATGGTTATCTAT 57.395 37.500 0.00 0.00 34.31 1.98
136 137 1.544724 TTGTTATGCTGGCCAACTCC 58.455 50.000 7.01 0.00 0.00 3.85
226 228 5.335191 GCTTATCTAGGAAAATGAATGGCCG 60.335 44.000 0.00 0.00 0.00 6.13
227 229 5.536161 TGCTTATCTAGGAAAATGAATGGCC 59.464 40.000 0.00 0.00 0.00 5.36
236 238 5.708736 TGTGGGATGCTTATCTAGGAAAA 57.291 39.130 0.00 0.00 0.00 2.29
254 256 3.444742 TGCTCCTTTCAATGCTTATGTGG 59.555 43.478 0.00 0.00 0.00 4.17
267 269 1.462670 CTCGCTCTTGTTGCTCCTTTC 59.537 52.381 0.00 0.00 0.00 2.62
277 279 1.953559 TGCTTTTGACTCGCTCTTGT 58.046 45.000 0.00 0.00 0.00 3.16
348 351 3.198635 TGCCAGAGAGGATTTTAGTGAGG 59.801 47.826 0.00 0.00 41.22 3.86
360 363 6.521151 AACAAGATAAAATTGCCAGAGAGG 57.479 37.500 0.00 0.00 41.84 3.69
378 381 7.907045 GCTGTCATGTGAAGATTATGTAACAAG 59.093 37.037 0.00 0.00 0.00 3.16
391 394 2.030540 CCCAACTTGCTGTCATGTGAAG 60.031 50.000 0.00 0.00 31.85 3.02
431 434 2.773993 TGGTAAGGGACATTTCCGTC 57.226 50.000 0.00 0.00 43.94 4.79
452 455 7.964604 ACTAGCGAAAATCTTCTAACAAACT 57.035 32.000 0.00 0.00 0.00 2.66
461 464 8.819643 ATATCCTTGTACTAGCGAAAATCTTC 57.180 34.615 0.00 0.00 0.00 2.87
462 465 9.694137 GTATATCCTTGTACTAGCGAAAATCTT 57.306 33.333 0.00 0.00 0.00 2.40
463 466 9.080097 AGTATATCCTTGTACTAGCGAAAATCT 57.920 33.333 0.00 0.00 28.95 2.40
475 478 9.790389 GCAGTGACATATAGTATATCCTTGTAC 57.210 37.037 0.00 0.00 0.00 2.90
477 480 8.422577 TGCAGTGACATATAGTATATCCTTGT 57.577 34.615 0.00 0.00 0.00 3.16
478 481 9.710900 TTTGCAGTGACATATAGTATATCCTTG 57.289 33.333 0.00 0.00 0.00 3.61
479 482 9.712305 GTTTGCAGTGACATATAGTATATCCTT 57.288 33.333 0.00 0.00 0.00 3.36
480 483 8.870116 TGTTTGCAGTGACATATAGTATATCCT 58.130 33.333 0.00 0.00 0.00 3.24
481 484 8.926710 GTGTTTGCAGTGACATATAGTATATCC 58.073 37.037 0.00 0.00 0.00 2.59
485 488 8.260818 AGAAGTGTTTGCAGTGACATATAGTAT 58.739 33.333 0.00 0.00 0.00 2.12
486 489 7.611770 AGAAGTGTTTGCAGTGACATATAGTA 58.388 34.615 0.00 0.00 0.00 1.82
487 490 6.467677 AGAAGTGTTTGCAGTGACATATAGT 58.532 36.000 0.00 0.00 0.00 2.12
488 491 6.974932 AGAAGTGTTTGCAGTGACATATAG 57.025 37.500 0.00 0.00 0.00 1.31
489 492 7.875554 TGTAAGAAGTGTTTGCAGTGACATATA 59.124 33.333 0.00 0.00 0.00 0.86
490 493 6.710295 TGTAAGAAGTGTTTGCAGTGACATAT 59.290 34.615 0.00 0.00 0.00 1.78
491 494 6.052360 TGTAAGAAGTGTTTGCAGTGACATA 58.948 36.000 0.00 0.00 0.00 2.29
492 495 4.881273 TGTAAGAAGTGTTTGCAGTGACAT 59.119 37.500 0.00 0.00 0.00 3.06
493 496 4.257731 TGTAAGAAGTGTTTGCAGTGACA 58.742 39.130 0.00 0.00 0.00 3.58
494 497 4.260784 CCTGTAAGAAGTGTTTGCAGTGAC 60.261 45.833 0.00 0.00 36.79 3.67
495 498 3.876914 CCTGTAAGAAGTGTTTGCAGTGA 59.123 43.478 0.00 0.00 36.79 3.41
496 499 3.876914 TCCTGTAAGAAGTGTTTGCAGTG 59.123 43.478 0.00 0.00 36.79 3.66
497 500 4.150897 TCCTGTAAGAAGTGTTTGCAGT 57.849 40.909 0.00 0.00 36.79 4.40
498 501 5.499139 TTTCCTGTAAGAAGTGTTTGCAG 57.501 39.130 0.00 0.00 37.81 4.41
500 503 4.202010 TGCTTTCCTGTAAGAAGTGTTTGC 60.202 41.667 0.00 0.00 34.07 3.68
502 505 5.437060 TCTGCTTTCCTGTAAGAAGTGTTT 58.563 37.500 0.00 0.00 34.07 2.83
503 506 5.036117 TCTGCTTTCCTGTAAGAAGTGTT 57.964 39.130 0.00 0.00 34.07 3.32
504 507 4.636249 CTCTGCTTTCCTGTAAGAAGTGT 58.364 43.478 0.00 0.00 34.07 3.55
507 510 3.668447 TGCTCTGCTTTCCTGTAAGAAG 58.332 45.455 0.00 0.00 34.07 2.85
508 511 3.557898 CCTGCTCTGCTTTCCTGTAAGAA 60.558 47.826 0.00 0.00 34.07 2.52
509 512 2.027745 CCTGCTCTGCTTTCCTGTAAGA 60.028 50.000 0.00 0.00 34.07 2.10
510 513 2.354259 CCTGCTCTGCTTTCCTGTAAG 58.646 52.381 0.00 0.00 0.00 2.34
511 514 1.003580 CCCTGCTCTGCTTTCCTGTAA 59.996 52.381 0.00 0.00 0.00 2.41
513 516 1.377994 CCCTGCTCTGCTTTCCTGT 59.622 57.895 0.00 0.00 0.00 4.00
514 517 0.251077 AACCCTGCTCTGCTTTCCTG 60.251 55.000 0.00 0.00 0.00 3.86
515 518 1.362224 TAACCCTGCTCTGCTTTCCT 58.638 50.000 0.00 0.00 0.00 3.36
516 519 2.200373 TTAACCCTGCTCTGCTTTCC 57.800 50.000 0.00 0.00 0.00 3.13
517 520 3.347216 TGATTAACCCTGCTCTGCTTTC 58.653 45.455 0.00 0.00 0.00 2.62
518 521 3.439857 TGATTAACCCTGCTCTGCTTT 57.560 42.857 0.00 0.00 0.00 3.51
519 522 3.009473 TCTTGATTAACCCTGCTCTGCTT 59.991 43.478 0.00 0.00 0.00 3.91
520 523 2.573462 TCTTGATTAACCCTGCTCTGCT 59.427 45.455 0.00 0.00 0.00 4.24
521 524 2.680339 GTCTTGATTAACCCTGCTCTGC 59.320 50.000 0.00 0.00 0.00 4.26
523 526 2.093447 CGGTCTTGATTAACCCTGCTCT 60.093 50.000 0.00 0.00 31.49 4.09
524 527 2.280628 CGGTCTTGATTAACCCTGCTC 58.719 52.381 0.00 0.00 31.49 4.26
525 528 1.679032 GCGGTCTTGATTAACCCTGCT 60.679 52.381 0.00 0.00 31.49 4.24
527 530 1.065418 AGGCGGTCTTGATTAACCCTG 60.065 52.381 0.00 0.00 31.49 4.45
528 531 1.209747 GAGGCGGTCTTGATTAACCCT 59.790 52.381 0.00 0.00 31.49 4.34
529 532 1.065709 TGAGGCGGTCTTGATTAACCC 60.066 52.381 0.00 0.00 31.49 4.11
530 533 2.396590 TGAGGCGGTCTTGATTAACC 57.603 50.000 0.00 0.00 0.00 2.85
531 534 3.335579 AGTTGAGGCGGTCTTGATTAAC 58.664 45.455 0.00 0.00 0.00 2.01
534 537 1.673033 CGAGTTGAGGCGGTCTTGATT 60.673 52.381 0.00 0.00 0.00 2.57
535 538 0.108615 CGAGTTGAGGCGGTCTTGAT 60.109 55.000 0.00 0.00 0.00 2.57
536 539 1.289066 CGAGTTGAGGCGGTCTTGA 59.711 57.895 0.00 0.00 0.00 3.02
538 541 2.657237 CCGAGTTGAGGCGGTCTT 59.343 61.111 0.00 0.00 42.49 3.01
545 548 1.398390 GTGCATAAAGCCGAGTTGAGG 59.602 52.381 0.00 0.00 44.83 3.86
546 549 2.076100 TGTGCATAAAGCCGAGTTGAG 58.924 47.619 0.00 0.00 44.83 3.02
548 551 1.806542 AGTGTGCATAAAGCCGAGTTG 59.193 47.619 0.00 0.00 44.83 3.16
549 552 2.185004 AGTGTGCATAAAGCCGAGTT 57.815 45.000 0.00 0.00 44.83 3.01
550 553 2.893637 CTAGTGTGCATAAAGCCGAGT 58.106 47.619 0.00 0.00 44.83 4.18
551 554 1.594862 GCTAGTGTGCATAAAGCCGAG 59.405 52.381 7.57 0.00 44.83 4.63
553 556 1.328680 CAGCTAGTGTGCATAAAGCCG 59.671 52.381 13.36 2.56 44.83 5.52
554 557 1.064654 GCAGCTAGTGTGCATAAAGCC 59.935 52.381 13.36 0.00 44.83 4.35
555 558 1.739466 TGCAGCTAGTGTGCATAAAGC 59.261 47.619 15.51 10.09 45.96 3.51
562 565 2.483877 TGTTAATGTGCAGCTAGTGTGC 59.516 45.455 11.19 11.19 41.59 4.57
564 567 4.008074 ACTGTTAATGTGCAGCTAGTGT 57.992 40.909 0.00 0.00 36.26 3.55
565 568 5.362556 AAACTGTTAATGTGCAGCTAGTG 57.637 39.130 0.00 0.00 36.26 2.74
566 569 5.995282 TGTAAACTGTTAATGTGCAGCTAGT 59.005 36.000 0.00 0.00 36.26 2.57
567 570 6.480524 TGTAAACTGTTAATGTGCAGCTAG 57.519 37.500 0.00 0.00 36.26 3.42
568 571 6.708502 TCTTGTAAACTGTTAATGTGCAGCTA 59.291 34.615 0.00 0.00 36.26 3.32
569 572 5.530915 TCTTGTAAACTGTTAATGTGCAGCT 59.469 36.000 0.00 0.00 36.26 4.24
570 573 5.757886 TCTTGTAAACTGTTAATGTGCAGC 58.242 37.500 0.00 0.00 36.26 5.25
571 574 6.959361 ACTCTTGTAAACTGTTAATGTGCAG 58.041 36.000 0.00 0.00 38.58 4.41
572 575 6.935741 ACTCTTGTAAACTGTTAATGTGCA 57.064 33.333 0.00 0.00 0.00 4.57
573 576 7.857569 TGTACTCTTGTAAACTGTTAATGTGC 58.142 34.615 0.00 0.00 0.00 4.57
584 914 8.739649 ACTCGATACTTTGTACTCTTGTAAAC 57.260 34.615 0.00 0.00 0.00 2.01
601 931 5.466728 TGTAACTCCCGTGTATACTCGATAC 59.533 44.000 24.67 17.95 40.90 2.24
602 932 5.610398 TGTAACTCCCGTGTATACTCGATA 58.390 41.667 24.67 13.05 35.14 2.92
603 933 4.454678 TGTAACTCCCGTGTATACTCGAT 58.545 43.478 24.67 10.37 35.14 3.59
604 934 3.872696 TGTAACTCCCGTGTATACTCGA 58.127 45.455 24.67 8.37 35.14 4.04
605 935 4.621068 TTGTAACTCCCGTGTATACTCG 57.379 45.455 18.05 18.05 0.00 4.18
606 936 5.105063 GGTTTGTAACTCCCGTGTATACTC 58.895 45.833 4.17 0.00 0.00 2.59
607 937 4.527816 TGGTTTGTAACTCCCGTGTATACT 59.472 41.667 4.17 0.00 0.00 2.12
608 938 4.819769 TGGTTTGTAACTCCCGTGTATAC 58.180 43.478 0.00 0.00 0.00 1.47
633 963 2.589014 CGTGGCTTGATTTTTCAGCTC 58.411 47.619 0.00 0.00 0.00 4.09
649 979 2.178912 ACCATACTTTGTCACCGTGG 57.821 50.000 0.00 0.00 0.00 4.94
723 1053 6.573434 GGAAATGTAAATCATCCAGTTTCCC 58.427 40.000 0.00 0.00 34.70 3.97
735 1065 8.665685 TCTTTCTTAAGAGCGGAAATGTAAATC 58.334 33.333 5.12 0.00 35.49 2.17
751 1081 7.006564 CGCGCAAATTTAACTCTCTTTCTTAAG 59.993 37.037 8.75 0.00 0.00 1.85
789 1128 8.934973 AACTCTTTATTTTTCGATTCTTCACG 57.065 30.769 0.00 0.00 0.00 4.35
806 1145 9.475620 TCCTCAGTATATGACTCAAACTCTTTA 57.524 33.333 0.00 0.00 35.64 1.85
828 1167 2.882927 TGTGCCATATACACGTCCTC 57.117 50.000 0.00 0.00 41.03 3.71
834 1173 4.881273 TGTTCAGGATTGTGCCATATACAC 59.119 41.667 1.91 1.91 38.55 2.90
835 1174 5.109500 TGTTCAGGATTGTGCCATATACA 57.891 39.130 0.00 0.00 0.00 2.29
838 1177 4.340097 CACATGTTCAGGATTGTGCCATAT 59.660 41.667 0.00 0.00 33.78 1.78
849 1188 0.770499 TCCTTGGCACATGTTCAGGA 59.230 50.000 0.00 1.61 39.30 3.86
1022 1369 1.269569 ACACGACAATCTTCTGCACGA 60.270 47.619 0.00 0.00 0.00 4.35
1082 1429 4.815269 TGCTTTCTCTTCAGAAGCTCTAC 58.185 43.478 5.15 0.00 39.90 2.59
1083 1430 4.769488 TCTGCTTTCTCTTCAGAAGCTCTA 59.231 41.667 5.15 0.00 39.90 2.43
1371 1719 4.019950 TGCAGGATTGAACTTCTCTGATCA 60.020 41.667 0.00 0.00 0.00 2.92
1488 1839 0.306840 CATTAGATGCTGCACTGGCG 59.693 55.000 3.57 0.00 45.35 5.69
1580 1931 7.891183 TGTTTGGGGCTATTATCTAAAGAACAA 59.109 33.333 0.00 0.00 0.00 2.83
1585 1936 6.126409 TGGTGTTTGGGGCTATTATCTAAAG 58.874 40.000 0.00 0.00 0.00 1.85
1604 1955 9.431887 CTATGTACTGTATTTTGTAGTTGGTGT 57.568 33.333 0.00 0.00 0.00 4.16
1650 2026 6.875948 TCATAAAATGGGGATTACATGACG 57.124 37.500 0.00 0.00 0.00 4.35
1656 2032 5.774690 TGCAGGATCATAAAATGGGGATTAC 59.225 40.000 0.00 0.00 0.00 1.89
1664 2198 6.466308 CATTGCATGCAGGATCATAAAATG 57.534 37.500 21.50 13.25 0.00 2.32
1701 2235 9.813080 GACAACTTCTAAACATAACAAGATCAC 57.187 33.333 0.00 0.00 0.00 3.06
1736 2271 3.581755 CAAGTTTTCCAGTGCATGATGG 58.418 45.455 0.00 8.80 37.97 3.51
1758 2293 7.009568 CAGCTTGAAGTAGTTTATTAGCTGG 57.990 40.000 15.89 3.84 46.41 4.85
1878 2422 3.543680 ATGGTAGACATCTTTGGTCGG 57.456 47.619 0.00 0.00 40.20 4.79
1923 2473 6.710597 TCAGTTAGCGTAGATTACAGGAAT 57.289 37.500 0.00 0.00 0.00 3.01
1936 2489 5.163854 GCAGTTTGATGTTATCAGTTAGCGT 60.164 40.000 0.00 0.00 40.94 5.07
1937 2490 5.063944 AGCAGTTTGATGTTATCAGTTAGCG 59.936 40.000 0.00 0.00 40.94 4.26
1950 2503 4.318332 TGACCTGTTAGAGCAGTTTGATG 58.682 43.478 0.00 0.00 34.84 3.07
1963 2516 6.127925 GCAAATGATCACAATCTGACCTGTTA 60.128 38.462 0.00 0.00 32.75 2.41
2115 2668 7.364320 GGGCAATTACAGGGCTAGAAAATAAAA 60.364 37.037 0.00 0.00 0.00 1.52
2139 2693 3.774216 AGAAAGAGACTTCAGATCCTGGG 59.226 47.826 0.00 0.00 31.51 4.45
2141 2695 5.657826 TGAGAAAGAGACTTCAGATCCTG 57.342 43.478 0.00 0.00 0.00 3.86
2190 2744 3.512724 TCCTGTTCTACTTCCTTTACCCG 59.487 47.826 0.00 0.00 0.00 5.28
2279 2833 1.982958 TCTTGGGTTACCTCCTGGTTC 59.017 52.381 0.00 0.00 46.05 3.62
2490 3061 6.978080 GTGCAAACTCAAGGATTTCAAACTTA 59.022 34.615 0.00 0.00 0.00 2.24
2521 3092 8.000780 AGAGATGTTTTCCTATTGCATTTACC 57.999 34.615 0.00 0.00 0.00 2.85
2834 3440 5.738370 CAGGCGTATCTTATTCTTTTTCGG 58.262 41.667 0.00 0.00 0.00 4.30
2839 3445 4.130118 CCAGCAGGCGTATCTTATTCTTT 58.870 43.478 0.00 0.00 0.00 2.52
2889 3495 1.341089 TGTCCTAGCACGAGAGGATGT 60.341 52.381 0.00 0.00 43.71 3.06
2914 3520 4.692625 ACAATCTTCCGTTCTGATCAACAG 59.307 41.667 0.00 0.00 46.97 3.16
2989 3595 6.294843 GGATATGTCTAGCTAGTCTGGGAAAC 60.295 46.154 20.10 9.03 0.00 2.78
3003 3609 3.835395 GGAACAGGGAGGGATATGTCTAG 59.165 52.174 0.00 0.00 0.00 2.43
3004 3610 3.439558 GGGAACAGGGAGGGATATGTCTA 60.440 52.174 0.00 0.00 0.00 2.59
3005 3611 2.695585 GGAACAGGGAGGGATATGTCT 58.304 52.381 0.00 0.00 0.00 3.41
3006 3612 1.700186 GGGAACAGGGAGGGATATGTC 59.300 57.143 0.00 0.00 0.00 3.06
3094 3702 3.604582 AGGCAGACAAACTAGATTCAGC 58.395 45.455 0.00 0.00 0.00 4.26
3156 3764 3.305267 GCACTGTTCCATTAATGCACACA 60.305 43.478 10.11 10.32 33.27 3.72
3254 4223 9.932207 TGTAAGTATCAAAAGTTTCCGAATAGA 57.068 29.630 0.00 0.00 0.00 1.98
3256 4225 9.158233 CCTGTAAGTATCAAAAGTTTCCGAATA 57.842 33.333 0.00 0.00 0.00 1.75
3257 4226 7.120726 CCCTGTAAGTATCAAAAGTTTCCGAAT 59.879 37.037 0.00 0.00 0.00 3.34
3260 4229 5.704053 ACCCTGTAAGTATCAAAAGTTTCCG 59.296 40.000 0.00 0.00 0.00 4.30
3262 4231 7.368059 CCAACCCTGTAAGTATCAAAAGTTTC 58.632 38.462 0.00 0.00 0.00 2.78
3263 4232 6.239204 GCCAACCCTGTAAGTATCAAAAGTTT 60.239 38.462 0.00 0.00 0.00 2.66
3350 4319 7.761249 AGGTTTCTGAATGTTTTGAGTTTTGAG 59.239 33.333 0.00 0.00 0.00 3.02
3559 4530 3.508744 ATTGCTTTTCCGCTACCAATG 57.491 42.857 0.00 0.00 0.00 2.82
3575 4547 8.642908 AGTTTGTAAGGTGTTTCTTAAATTGC 57.357 30.769 0.00 0.00 31.85 3.56
3629 4616 5.982890 AATGTTTAAAGGTCCATCCAGTG 57.017 39.130 0.00 0.00 39.02 3.66
3681 4668 4.903045 TGTTGCCTTATAGTATAGGGGC 57.097 45.455 17.56 19.15 39.93 5.80


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

AutoCloner maintained by Alex Coulton.