Multiple sequence alignment - TraesCS1A01G402500

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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 TraesCS1A01G402500 chr1A 100.000 4042 0 0 1 4042 566108671 566112712 0.000000e+00 7465.0
1 TraesCS1A01G402500 chr1B 90.616 3879 188 87 262 4020 655846965 655850787 0.000000e+00 4985.0
2 TraesCS1A01G402500 chr1B 82.750 400 49 12 443 833 24503698 24504086 5.000000e-89 339.0
3 TraesCS1A01G402500 chr1D 91.958 3320 160 49 266 3529 471839101 471842369 0.000000e+00 4553.0
4 TraesCS1A01G402500 chr1D 93.313 329 15 5 1 323 471838702 471839029 2.830000e-131 479.0
5 TraesCS1A01G402500 chr1D 93.605 172 11 0 3642 3813 471842362 471842533 1.440000e-64 257.0
6 TraesCS1A01G402500 chr1D 95.000 40 2 0 2414 2453 3630681 3630720 3.370000e-06 63.9
7 TraesCS1A01G402500 chr5D 90.821 207 19 0 2516 2722 406333758 406333964 1.110000e-70 278.0
8 TraesCS1A01G402500 chr5A 90.821 207 19 0 2516 2722 511906069 511906275 1.110000e-70 278.0
9 TraesCS1A01G402500 chr5B 90.338 207 20 0 2516 2722 487222795 487223001 5.150000e-69 272.0
10 TraesCS1A01G402500 chr2D 97.561 41 1 0 2413 2453 423275689 423275729 2.020000e-08 71.3
11 TraesCS1A01G402500 chr2D 97.500 40 1 0 2414 2453 351970687 351970726 7.250000e-08 69.4
12 TraesCS1A01G402500 chr2D 97.500 40 1 0 2414 2453 563968847 563968886 7.250000e-08 69.4
13 TraesCS1A01G402500 chr7D 97.500 40 1 0 2414 2453 98878801 98878762 7.250000e-08 69.4
14 TraesCS1A01G402500 chr4B 93.617 47 2 1 2407 2453 89458246 89458291 7.250000e-08 69.4
15 TraesCS1A01G402500 chr6D 97.368 38 1 0 2416 2453 46838650 46838613 9.380000e-07 65.8


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 TraesCS1A01G402500 chr1A 566108671 566112712 4041 False 7465 7465 100.000000 1 4042 1 chr1A.!!$F1 4041
1 TraesCS1A01G402500 chr1B 655846965 655850787 3822 False 4985 4985 90.616000 262 4020 1 chr1B.!!$F2 3758
2 TraesCS1A01G402500 chr1D 471838702 471842533 3831 False 1763 4553 92.958667 1 3813 3 chr1D.!!$F2 3812

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
45 46 0.035439 ACCCGCCAACCATACAGAAG 60.035 55.0 0.00 0.00 0.00 2.85 F
508 643 0.251354 ATGGCCACAGCTGACTACAG 59.749 55.0 23.35 2.95 45.91 2.74 F
1143 1292 0.320771 GATCCCATATTGCTCGCCGT 60.321 55.0 0.00 0.00 0.00 5.68 F
1866 2041 0.389556 CCTCGAGCGCATGCATCTAT 60.390 55.0 19.57 0.00 46.23 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1101 1250 0.179020 TGAAACCACCAGCTCCAGTG 60.179 55.000 1.80 1.8 0.00 3.66 R
2013 2190 0.744414 TCTTGCGGCTGAATGGTAGC 60.744 55.000 0.00 0.0 40.41 3.58 R
2017 2194 1.065273 GCATCTTGCGGCTGAATGG 59.935 57.895 0.00 0.0 31.71 3.16 R
3609 3840 0.040204 AGCCTTGGTTTGCAGCCTAT 59.960 50.000 10.19 0.0 0.00 2.57 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
45 46 0.035439 ACCCGCCAACCATACAGAAG 60.035 55.000 0.00 0.00 0.00 2.85
65 70 5.299531 AGAAGGTTTCAGGTTTAGCTTGTTC 59.700 40.000 0.00 0.00 30.47 3.18
66 71 4.532834 AGGTTTCAGGTTTAGCTTGTTCA 58.467 39.130 0.00 0.00 0.00 3.18
100 107 2.758979 TGAGAATACCTCCAAGTCGTCC 59.241 50.000 0.00 0.00 41.25 4.79
154 161 4.450419 GTCAAAGGAGGATATCGCATTCAG 59.550 45.833 0.00 0.00 0.00 3.02
191 198 5.036737 CCTGGCATAAAAAGAGTTATTGCG 58.963 41.667 0.00 0.00 0.00 4.85
206 213 0.512518 TTGCGAATCAAGCTCGTGTG 59.487 50.000 0.00 0.00 38.57 3.82
210 217 1.795768 GAATCAAGCTCGTGTGGACA 58.204 50.000 0.00 0.00 0.00 4.02
285 420 8.352201 CAACTGTTTTTCAAGGATAACTGATGA 58.648 33.333 0.00 0.00 29.84 2.92
288 423 8.634335 TGTTTTTCAAGGATAACTGATGATGA 57.366 30.769 0.00 0.00 0.00 2.92
291 426 9.912634 TTTTTCAAGGATAACTGATGATGAAAC 57.087 29.630 0.00 0.00 35.85 2.78
292 427 8.868522 TTTCAAGGATAACTGATGATGAAACT 57.131 30.769 0.00 0.00 32.42 2.66
293 428 7.854557 TCAAGGATAACTGATGATGAAACTG 57.145 36.000 0.00 0.00 0.00 3.16
294 429 7.623630 TCAAGGATAACTGATGATGAAACTGA 58.376 34.615 0.00 0.00 0.00 3.41
295 430 8.102676 TCAAGGATAACTGATGATGAAACTGAA 58.897 33.333 0.00 0.00 0.00 3.02
296 431 7.856145 AGGATAACTGATGATGAAACTGAAC 57.144 36.000 0.00 0.00 0.00 3.18
297 432 6.825721 AGGATAACTGATGATGAAACTGAACC 59.174 38.462 0.00 0.00 0.00 3.62
312 447 1.742831 TGAACCAACACACTGCAGAAC 59.257 47.619 23.35 0.00 0.00 3.01
339 474 3.904571 TGTATAATCGTACATGGCGGTC 58.095 45.455 11.10 0.00 30.00 4.79
350 485 5.506815 CGTACATGGCGGTCTAGAAAGATTA 60.507 44.000 0.00 0.00 33.30 1.75
359 494 5.176590 CGGTCTAGAAAGATTAGCAATGCTC 59.823 44.000 12.53 0.00 35.53 4.26
361 496 5.980116 GTCTAGAAAGATTAGCAATGCTCGA 59.020 40.000 12.53 1.74 35.53 4.04
362 497 6.477033 GTCTAGAAAGATTAGCAATGCTCGAA 59.523 38.462 12.53 1.05 35.53 3.71
389 524 1.573829 TTTGAGGCCGCATCGACAAC 61.574 55.000 10.98 0.00 0.00 3.32
392 527 3.047280 GGCCGCATCGACAACACA 61.047 61.111 0.00 0.00 0.00 3.72
394 529 2.476051 CCGCATCGACAACACAGC 59.524 61.111 0.00 0.00 0.00 4.40
396 531 3.549467 GCATCGACAACACAGCGA 58.451 55.556 0.00 0.00 38.51 4.93
416 551 3.253677 CGAGACTAGTGACCTTGACAGTT 59.746 47.826 0.00 0.00 0.00 3.16
417 552 4.261656 CGAGACTAGTGACCTTGACAGTTT 60.262 45.833 0.00 0.00 0.00 2.66
418 553 5.048921 CGAGACTAGTGACCTTGACAGTTTA 60.049 44.000 0.00 0.00 0.00 2.01
419 554 6.334102 AGACTAGTGACCTTGACAGTTTAG 57.666 41.667 0.00 0.00 0.00 1.85
420 555 5.244178 AGACTAGTGACCTTGACAGTTTAGG 59.756 44.000 0.00 1.29 35.14 2.69
421 556 3.127425 AGTGACCTTGACAGTTTAGGC 57.873 47.619 2.54 0.00 32.08 3.93
422 557 2.152016 GTGACCTTGACAGTTTAGGCC 58.848 52.381 0.00 0.00 32.08 5.19
423 558 2.054799 TGACCTTGACAGTTTAGGCCT 58.945 47.619 11.78 11.78 32.08 5.19
424 559 2.038557 TGACCTTGACAGTTTAGGCCTC 59.961 50.000 9.68 0.00 32.08 4.70
425 560 2.303311 GACCTTGACAGTTTAGGCCTCT 59.697 50.000 9.68 0.00 32.08 3.69
426 561 2.711547 ACCTTGACAGTTTAGGCCTCTT 59.288 45.455 9.68 0.00 32.08 2.85
427 562 3.138468 ACCTTGACAGTTTAGGCCTCTTT 59.862 43.478 9.68 0.00 32.08 2.52
428 563 4.145052 CCTTGACAGTTTAGGCCTCTTTT 58.855 43.478 9.68 0.00 0.00 2.27
429 564 4.022849 CCTTGACAGTTTAGGCCTCTTTTG 60.023 45.833 9.68 7.15 0.00 2.44
430 565 3.486383 TGACAGTTTAGGCCTCTTTTGG 58.514 45.455 9.68 0.00 0.00 3.28
431 566 3.117663 TGACAGTTTAGGCCTCTTTTGGT 60.118 43.478 9.68 1.27 0.00 3.67
432 567 3.889538 GACAGTTTAGGCCTCTTTTGGTT 59.110 43.478 9.68 0.00 0.00 3.67
433 568 3.889538 ACAGTTTAGGCCTCTTTTGGTTC 59.110 43.478 9.68 0.00 0.00 3.62
434 569 3.058224 CAGTTTAGGCCTCTTTTGGTTCG 60.058 47.826 9.68 0.00 0.00 3.95
435 570 2.882761 GTTTAGGCCTCTTTTGGTTCGT 59.117 45.455 9.68 0.00 0.00 3.85
436 571 4.067192 GTTTAGGCCTCTTTTGGTTCGTA 58.933 43.478 9.68 0.00 0.00 3.43
437 572 2.474410 AGGCCTCTTTTGGTTCGTAG 57.526 50.000 0.00 0.00 0.00 3.51
438 573 1.003233 AGGCCTCTTTTGGTTCGTAGG 59.997 52.381 0.00 0.00 0.00 3.18
439 574 1.002773 GGCCTCTTTTGGTTCGTAGGA 59.997 52.381 0.00 0.00 0.00 2.94
440 575 2.355818 GGCCTCTTTTGGTTCGTAGGAT 60.356 50.000 0.00 0.00 0.00 3.24
441 576 3.118519 GGCCTCTTTTGGTTCGTAGGATA 60.119 47.826 0.00 0.00 0.00 2.59
458 593 9.085645 TCGTAGGATATTACTGGTAAATCATGT 57.914 33.333 0.00 0.00 0.00 3.21
484 619 9.817809 TTAATTCAGCTTATTAGTACTGTCCAG 57.182 33.333 5.39 0.00 0.00 3.86
504 639 2.774234 AGTTATATGGCCACAGCTGACT 59.226 45.455 23.35 6.11 39.73 3.41
505 640 3.967326 AGTTATATGGCCACAGCTGACTA 59.033 43.478 23.35 7.71 39.73 2.59
506 641 2.918712 ATATGGCCACAGCTGACTAC 57.081 50.000 23.35 8.46 39.73 2.73
507 642 1.567357 TATGGCCACAGCTGACTACA 58.433 50.000 23.35 14.05 39.73 2.74
508 643 0.251354 ATGGCCACAGCTGACTACAG 59.749 55.000 23.35 2.95 45.91 2.74
509 644 1.078848 GGCCACAGCTGACTACAGG 60.079 63.158 23.35 12.47 43.62 4.00
511 646 0.539051 GCCACAGCTGACTACAGGAT 59.461 55.000 23.35 0.00 43.62 3.24
523 659 4.100035 TGACTACAGGATGAGGCAATACAG 59.900 45.833 0.00 0.00 39.69 2.74
528 664 5.371526 ACAGGATGAGGCAATACAGTAATG 58.628 41.667 0.00 0.00 39.69 1.90
595 731 7.416213 CGAAGCAAGTTGGATATTTTATTCCCA 60.416 37.037 4.75 0.00 0.00 4.37
609 745 1.706995 TTCCCAACGGTGTTGGCCTA 61.707 55.000 20.60 7.63 38.23 3.93
632 769 3.002348 CAGTAGGTTTAATTAGCGGCTGC 59.998 47.826 13.86 10.33 43.24 5.25
679 818 2.664402 CCCCCATGCTTTACTATGCT 57.336 50.000 0.00 0.00 0.00 3.79
686 825 1.480545 TGCTTTACTATGCTCGCCAGA 59.519 47.619 0.00 0.00 0.00 3.86
711 850 2.832129 AGATCCCTGTAAAAGCTGTCGA 59.168 45.455 0.00 0.00 0.00 4.20
712 851 3.452627 AGATCCCTGTAAAAGCTGTCGAT 59.547 43.478 0.00 0.00 0.00 3.59
715 854 3.132289 TCCCTGTAAAAGCTGTCGATAGG 59.868 47.826 11.42 0.00 0.00 2.57
721 860 2.370281 AAGCTGTCGATAGGTGTGTG 57.630 50.000 14.86 0.00 0.00 3.82
737 876 4.216257 GGTGTGTGTGCTGAACATAGATTT 59.784 41.667 0.00 0.00 41.97 2.17
821 964 0.469070 ATGAGCAGCCCTCTAAGCAG 59.531 55.000 3.93 0.00 41.35 4.24
829 972 1.065126 GCCCTCTAAGCAGTGGATGTT 60.065 52.381 0.00 0.00 37.59 2.71
924 1073 5.601662 TCGAATTAAGTGCCTATCTGAAGG 58.398 41.667 0.00 2.66 39.87 3.46
963 1112 8.886719 TGCTTCATATCAATTTGACTTCTAGTG 58.113 33.333 0.15 0.00 0.00 2.74
964 1113 8.887717 GCTTCATATCAATTTGACTTCTAGTGT 58.112 33.333 0.15 0.00 0.00 3.55
1101 1250 2.425312 TGAGAAGCTGAGAATCTCGGTC 59.575 50.000 19.20 10.57 41.96 4.79
1143 1292 0.320771 GATCCCATATTGCTCGCCGT 60.321 55.000 0.00 0.00 0.00 5.68
1278 1427 1.427368 TGCCTTAAGGTCACCACCAAT 59.573 47.619 22.55 0.00 46.68 3.16
1335 1484 1.341383 GGCATGGGGTTCATTCAGTCT 60.341 52.381 0.00 0.00 32.92 3.24
1435 1584 7.229907 TGAAGAGGTTTGTAACTTCATTTACCC 59.770 37.037 0.00 0.00 42.05 3.69
1440 1589 8.387813 AGGTTTGTAACTTCATTTACCCATCTA 58.612 33.333 0.00 0.00 31.87 1.98
1461 1610 2.027377 AGCTGAAGTGTGCTATGAGCTT 60.027 45.455 0.00 0.00 42.97 3.74
1472 1621 3.453717 TGCTATGAGCTTGTCCAGAGATT 59.546 43.478 0.00 0.00 42.97 2.40
1474 1623 4.987912 GCTATGAGCTTGTCCAGAGATTAC 59.012 45.833 0.00 0.00 38.45 1.89
1478 1650 4.528206 TGAGCTTGTCCAGAGATTACTTGA 59.472 41.667 0.00 0.00 0.00 3.02
1591 1764 7.012989 GGTGGTCTTTAGAAGCTTTGTTAAAGA 59.987 37.037 23.58 23.58 41.02 2.52
1592 1765 8.568794 GTGGTCTTTAGAAGCTTTGTTAAAGAT 58.431 33.333 26.73 0.00 41.48 2.40
1593 1766 8.567948 TGGTCTTTAGAAGCTTTGTTAAAGATG 58.432 33.333 26.73 12.89 41.48 2.90
1594 1767 7.539022 GGTCTTTAGAAGCTTTGTTAAAGATGC 59.461 37.037 26.73 20.13 41.48 3.91
1665 1839 6.128929 TGTTTCTTGTCGAGTTGATATTGACG 60.129 38.462 0.00 0.00 34.34 4.35
1689 1863 7.148205 ACGCTACCAAACTGAACTTAAGAAAAA 60.148 33.333 10.09 0.00 0.00 1.94
1747 1921 7.093992 TGTTTTCCTTTCGAATTGTTTCAAGT 58.906 30.769 0.00 0.00 0.00 3.16
1805 1979 9.886132 ATCCAAATAACTTACGTATCCCATATC 57.114 33.333 0.00 0.00 0.00 1.63
1811 1985 6.829229 ACTTACGTATCCCATATCGATTCA 57.171 37.500 1.71 0.00 0.00 2.57
1866 2041 0.389556 CCTCGAGCGCATGCATCTAT 60.390 55.000 19.57 0.00 46.23 1.98
1881 2056 7.485810 CATGCATCTATCCTGAATTCAAACAA 58.514 34.615 9.88 0.00 0.00 2.83
2027 2204 0.391661 ACTGTGCTACCATTCAGCCG 60.392 55.000 0.00 0.00 38.29 5.52
2099 2276 4.821805 CACTACACCAAGGACTTTGACATT 59.178 41.667 0.00 0.00 39.21 2.71
2228 2405 0.519961 GCAATTTGTTAGGCGGTCGT 59.480 50.000 0.00 0.00 0.00 4.34
2405 2582 8.820933 CACATTATACCAGACAGAACTACATTG 58.179 37.037 0.00 0.00 0.00 2.82
2673 2853 1.436195 GCCGCAACTCTGACAACACA 61.436 55.000 0.00 0.00 0.00 3.72
2725 2905 3.019564 ACAATGAGGCTCAAGGTAATGC 58.980 45.455 22.84 0.00 0.00 3.56
2757 2938 4.285807 TCAAACACTGACAATTCCAACG 57.714 40.909 0.00 0.00 0.00 4.10
2766 2947 2.164219 GACAATTCCAACGCCACATGAT 59.836 45.455 0.00 0.00 0.00 2.45
2840 3021 5.178096 TGATGGCTTCAGTAAAATCCTCA 57.822 39.130 0.00 0.00 0.00 3.86
2859 3040 7.655521 TCCTCAGGAAGTCGAAGATAATTAA 57.344 36.000 0.00 0.00 40.67 1.40
3081 3268 1.237285 GCCTATTATGCCACTGCCCG 61.237 60.000 0.00 0.00 36.33 6.13
3098 3285 1.509463 CGTCGAACGGATCCTTCCA 59.491 57.895 10.75 0.00 42.74 3.53
3108 3295 2.477863 CGGATCCTTCCATGCGAAAAAC 60.478 50.000 10.75 0.00 42.74 2.43
3142 3330 1.383248 CAGCCTGCCCTACCTACCT 60.383 63.158 0.00 0.00 0.00 3.08
3147 3335 1.413082 CCTGCCCTACCTACCTCATGA 60.413 57.143 0.00 0.00 0.00 3.07
3166 3355 5.761726 TCATGAGCGATTTTAGCAGATTCAT 59.238 36.000 0.00 0.00 37.01 2.57
3168 3357 4.217497 GAGCGATTTTAGCAGATTCATGC 58.783 43.478 0.00 0.00 46.88 4.06
3237 3452 5.324832 TTGGATGAAGAATAAGATCCCCC 57.675 43.478 0.00 0.00 34.54 5.40
3274 3489 3.669023 GCTGAGCTGTATTGTGTGCTTTC 60.669 47.826 0.00 0.00 35.76 2.62
3331 3546 0.647410 CTAGATGACTTGTTGCGCCG 59.353 55.000 4.18 0.00 0.00 6.46
3361 3577 8.062448 GCATCGACTATAACCAAAACTTATGTC 58.938 37.037 0.00 0.00 0.00 3.06
3365 3581 8.601476 CGACTATAACCAAAACTTATGTCCTTC 58.399 37.037 0.00 0.00 0.00 3.46
3439 3664 7.189512 GCCAGCTTAAAGTTCTTACATGTATG 58.810 38.462 6.36 9.39 0.00 2.39
3487 3712 3.055819 GCTCCATTGAGTAGGTGAACAGA 60.056 47.826 0.00 0.00 40.95 3.41
3489 3714 5.738909 CTCCATTGAGTAGGTGAACAGAAT 58.261 41.667 0.00 0.00 33.70 2.40
3596 3827 6.621596 GCCTATTAGCTTCCAATTAATCTGCG 60.622 42.308 0.00 0.00 0.00 5.18
3629 3864 0.695924 TAGGCTGCAAACCAAGGCTA 59.304 50.000 8.09 4.57 38.20 3.93
3649 3884 3.191078 AGCAGTCCTTATAGCAAGCAG 57.809 47.619 0.00 0.00 0.00 4.24
3716 3951 6.238842 CCAATGCAGTTACAATCTATGAAGGG 60.239 42.308 0.00 0.00 0.00 3.95
3720 3955 5.294552 GCAGTTACAATCTATGAAGGGTGAC 59.705 44.000 0.00 0.00 0.00 3.67
3770 4005 6.280643 TCATAACATTAGTGAGGATTGGTCG 58.719 40.000 0.00 0.00 0.00 4.79
3775 4010 2.751166 AGTGAGGATTGGTCGAACTG 57.249 50.000 0.33 0.00 0.00 3.16
3816 4067 3.819337 GTGGATCATCATCACCAGATTGG 59.181 47.826 0.00 0.00 45.02 3.16
3850 4101 1.566231 CCCAGATAATCCTATGCCCCC 59.434 57.143 0.00 0.00 0.00 5.40
3853 4104 3.184628 CAGATAATCCTATGCCCCCTGA 58.815 50.000 0.00 0.00 0.00 3.86
3854 4105 3.784763 CAGATAATCCTATGCCCCCTGAT 59.215 47.826 0.00 0.00 0.00 2.90
3860 4111 2.584965 TCCTATGCCCCCTGATTTTCAA 59.415 45.455 0.00 0.00 0.00 2.69
3910 4161 0.687354 AAAGAGGAAGAGCCAAGCGA 59.313 50.000 0.00 0.00 40.02 4.93
3919 4170 1.550524 AGAGCCAAGCGACTGATACAA 59.449 47.619 0.00 0.00 0.00 2.41
3926 4177 2.875080 GCGACTGATACAACGCTTTT 57.125 45.000 0.00 0.00 46.06 2.27
3928 4179 2.156891 GCGACTGATACAACGCTTTTCA 59.843 45.455 0.00 0.00 46.06 2.69
3949 4200 2.158827 AGCATACAGTTCACACACCACA 60.159 45.455 0.00 0.00 0.00 4.17
3957 4208 3.938963 AGTTCACACACCACAACTACAAG 59.061 43.478 0.00 0.00 0.00 3.16
3965 4216 3.312421 CACCACAACTACAAGGACACAAG 59.688 47.826 0.00 0.00 0.00 3.16
3968 4219 3.002656 CACAACTACAAGGACACAAGCAG 59.997 47.826 0.00 0.00 0.00 4.24
4020 4271 0.247736 GACGAGGCATGGTTCAGACT 59.752 55.000 0.00 0.00 0.00 3.24
4021 4272 0.036952 ACGAGGCATGGTTCAGACTG 60.037 55.000 0.00 0.00 0.00 3.51
4022 4273 0.036952 CGAGGCATGGTTCAGACTGT 60.037 55.000 1.59 0.00 0.00 3.55
4023 4274 1.609061 CGAGGCATGGTTCAGACTGTT 60.609 52.381 1.59 0.00 0.00 3.16
4024 4275 2.353704 CGAGGCATGGTTCAGACTGTTA 60.354 50.000 1.59 0.00 0.00 2.41
4025 4276 3.674997 GAGGCATGGTTCAGACTGTTAA 58.325 45.455 1.59 0.00 0.00 2.01
4026 4277 4.072131 GAGGCATGGTTCAGACTGTTAAA 58.928 43.478 1.59 0.00 0.00 1.52
4027 4278 4.666512 AGGCATGGTTCAGACTGTTAAAT 58.333 39.130 1.59 0.00 0.00 1.40
4028 4279 4.460382 AGGCATGGTTCAGACTGTTAAATG 59.540 41.667 1.59 4.79 0.00 2.32
4029 4280 4.218417 GGCATGGTTCAGACTGTTAAATGT 59.782 41.667 1.59 0.00 0.00 2.71
4030 4281 5.414454 GGCATGGTTCAGACTGTTAAATGTA 59.586 40.000 1.59 0.00 0.00 2.29
4031 4282 6.072175 GGCATGGTTCAGACTGTTAAATGTAA 60.072 38.462 1.59 0.00 0.00 2.41
4032 4283 7.362920 GGCATGGTTCAGACTGTTAAATGTAAT 60.363 37.037 1.59 0.00 0.00 1.89
4033 4284 8.028938 GCATGGTTCAGACTGTTAAATGTAATT 58.971 33.333 1.59 0.00 38.98 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.053650 GGTACCTTCGGCTTAGAAAATATGT 58.946 40.000 4.06 0.00 0.00 2.29
25 26 1.208535 CTTCTGTATGGTTGGCGGGTA 59.791 52.381 0.00 0.00 0.00 3.69
26 27 0.035439 CTTCTGTATGGTTGGCGGGT 60.035 55.000 0.00 0.00 0.00 5.28
30 31 3.153919 TGAAACCTTCTGTATGGTTGGC 58.846 45.455 0.00 0.00 44.83 4.52
31 32 3.758554 CCTGAAACCTTCTGTATGGTTGG 59.241 47.826 0.00 0.00 44.83 3.77
45 46 4.338400 ACTGAACAAGCTAAACCTGAAACC 59.662 41.667 0.00 0.00 0.00 3.27
65 70 4.932200 GGTATTCTCAGGTTCTCACAACTG 59.068 45.833 0.00 0.00 0.00 3.16
66 71 4.841246 AGGTATTCTCAGGTTCTCACAACT 59.159 41.667 0.00 0.00 0.00 3.16
100 107 7.330946 TCGAAAACACAATAGTTAGACAGATGG 59.669 37.037 0.00 0.00 0.00 3.51
154 161 1.810532 CCAGGAGTGTCGCCTCTAC 59.189 63.158 0.00 0.00 29.38 2.59
191 198 1.795768 TGTCCACACGAGCTTGATTC 58.204 50.000 8.31 0.00 0.00 2.52
215 222 3.896888 TGAAATGGCAGGTCAAAACTGAT 59.103 39.130 0.00 0.00 38.20 2.90
225 232 6.205270 CAGCTTTTTATTTTGAAATGGCAGGT 59.795 34.615 0.00 0.00 0.00 4.00
278 413 5.009010 GTGTTGGTTCAGTTTCATCATCAGT 59.991 40.000 0.00 0.00 0.00 3.41
285 420 3.181487 GCAGTGTGTTGGTTCAGTTTCAT 60.181 43.478 0.00 0.00 0.00 2.57
288 423 2.164219 CTGCAGTGTGTTGGTTCAGTTT 59.836 45.455 5.25 0.00 0.00 2.66
291 426 1.667236 TCTGCAGTGTGTTGGTTCAG 58.333 50.000 14.67 0.00 0.00 3.02
292 427 1.742831 GTTCTGCAGTGTGTTGGTTCA 59.257 47.619 14.67 0.00 0.00 3.18
293 428 2.017049 AGTTCTGCAGTGTGTTGGTTC 58.983 47.619 14.67 0.00 0.00 3.62
294 429 2.128771 AGTTCTGCAGTGTGTTGGTT 57.871 45.000 14.67 0.00 0.00 3.67
295 430 2.128771 AAGTTCTGCAGTGTGTTGGT 57.871 45.000 14.67 0.00 0.00 3.67
296 431 3.508744 AAAAGTTCTGCAGTGTGTTGG 57.491 42.857 14.67 0.00 0.00 3.77
318 453 3.570975 AGACCGCCATGTACGATTATACA 59.429 43.478 6.92 0.00 39.35 2.29
325 460 1.753930 TTCTAGACCGCCATGTACGA 58.246 50.000 6.92 0.00 0.00 3.43
327 462 3.795623 TCTTTCTAGACCGCCATGTAC 57.204 47.619 0.00 0.00 0.00 2.90
339 474 6.834959 TTCGAGCATTGCTAATCTTTCTAG 57.165 37.500 11.96 0.00 39.88 2.43
366 501 1.135402 GTCGATGCGGCCTCAAATTTT 60.135 47.619 0.00 0.00 0.00 1.82
372 507 2.434185 GTTGTCGATGCGGCCTCA 60.434 61.111 0.00 0.00 0.00 3.86
373 508 2.434185 TGTTGTCGATGCGGCCTC 60.434 61.111 0.00 0.00 0.00 4.70
374 509 2.742372 GTGTTGTCGATGCGGCCT 60.742 61.111 0.00 0.00 0.00 5.19
375 510 3.027170 CTGTGTTGTCGATGCGGCC 62.027 63.158 0.00 0.00 0.00 6.13
389 524 1.169577 AGGTCACTAGTCTCGCTGTG 58.830 55.000 0.00 0.00 0.00 3.66
392 527 1.813786 GTCAAGGTCACTAGTCTCGCT 59.186 52.381 0.00 0.00 0.00 4.93
394 529 2.814919 ACTGTCAAGGTCACTAGTCTCG 59.185 50.000 0.00 0.00 0.00 4.04
396 531 5.244178 CCTAAACTGTCAAGGTCACTAGTCT 59.756 44.000 0.00 0.00 0.00 3.24
416 551 2.943036 ACGAACCAAAAGAGGCCTAA 57.057 45.000 4.42 0.00 0.00 2.69
417 552 2.235402 CCTACGAACCAAAAGAGGCCTA 59.765 50.000 4.42 0.00 0.00 3.93
418 553 1.003233 CCTACGAACCAAAAGAGGCCT 59.997 52.381 3.86 3.86 0.00 5.19
419 554 1.002773 TCCTACGAACCAAAAGAGGCC 59.997 52.381 0.00 0.00 0.00 5.19
420 555 2.467566 TCCTACGAACCAAAAGAGGC 57.532 50.000 0.00 0.00 0.00 4.70
421 556 7.438459 CAGTAATATCCTACGAACCAAAAGAGG 59.562 40.741 0.00 0.00 0.00 3.69
422 557 7.438459 CCAGTAATATCCTACGAACCAAAAGAG 59.562 40.741 0.00 0.00 0.00 2.85
423 558 7.093201 ACCAGTAATATCCTACGAACCAAAAGA 60.093 37.037 0.00 0.00 0.00 2.52
424 559 7.046033 ACCAGTAATATCCTACGAACCAAAAG 58.954 38.462 0.00 0.00 0.00 2.27
425 560 6.949715 ACCAGTAATATCCTACGAACCAAAA 58.050 36.000 0.00 0.00 0.00 2.44
426 561 6.549433 ACCAGTAATATCCTACGAACCAAA 57.451 37.500 0.00 0.00 0.00 3.28
427 562 7.658525 TTACCAGTAATATCCTACGAACCAA 57.341 36.000 0.00 0.00 0.00 3.67
428 563 7.658525 TTTACCAGTAATATCCTACGAACCA 57.341 36.000 0.00 0.00 0.00 3.67
429 564 8.362639 TGATTTACCAGTAATATCCTACGAACC 58.637 37.037 0.00 0.00 0.00 3.62
430 565 9.924650 ATGATTTACCAGTAATATCCTACGAAC 57.075 33.333 0.00 0.00 0.00 3.95
431 566 9.923143 CATGATTTACCAGTAATATCCTACGAA 57.077 33.333 0.00 0.00 0.00 3.85
432 567 9.085645 ACATGATTTACCAGTAATATCCTACGA 57.914 33.333 0.00 0.00 0.00 3.43
433 568 9.706691 AACATGATTTACCAGTAATATCCTACG 57.293 33.333 0.00 0.00 0.00 3.51
458 593 9.817809 CTGGACAGTACTAATAAGCTGAATTAA 57.182 33.333 0.00 0.00 33.57 1.40
484 619 3.199880 AGTCAGCTGTGGCCATATAAC 57.800 47.619 9.72 3.11 39.73 1.89
504 639 6.099701 ACATTACTGTATTGCCTCATCCTGTA 59.900 38.462 9.06 0.00 32.49 2.74
505 640 5.104360 ACATTACTGTATTGCCTCATCCTGT 60.104 40.000 9.06 0.00 32.49 4.00
506 641 5.237996 CACATTACTGTATTGCCTCATCCTG 59.762 44.000 9.06 0.00 33.14 3.86
507 642 5.371526 CACATTACTGTATTGCCTCATCCT 58.628 41.667 9.06 0.00 33.14 3.24
508 643 4.516698 CCACATTACTGTATTGCCTCATCC 59.483 45.833 9.06 0.00 33.14 3.51
509 644 5.237344 GTCCACATTACTGTATTGCCTCATC 59.763 44.000 9.06 0.00 33.14 2.92
511 646 4.019771 TGTCCACATTACTGTATTGCCTCA 60.020 41.667 9.06 3.00 33.14 3.86
523 659 1.806542 CACCAGCACTGTCCACATTAC 59.193 52.381 0.00 0.00 0.00 1.89
547 683 4.663140 CGAACAACACTAATGCTGTGTACG 60.663 45.833 0.00 2.03 46.46 3.67
595 731 1.001633 CTACTGTAGGCCAACACCGTT 59.998 52.381 5.01 0.00 33.69 4.44
609 745 4.189231 CAGCCGCTAATTAAACCTACTGT 58.811 43.478 0.00 0.00 0.00 3.55
632 769 0.111253 ACTGAAGGTTGGAAGGCCTG 59.889 55.000 5.69 0.00 34.90 4.85
679 818 1.305297 AGGGATCTGTGTCTGGCGA 60.305 57.895 0.00 0.00 0.00 5.54
711 850 2.928801 TGTTCAGCACACACACCTAT 57.071 45.000 0.00 0.00 0.00 2.57
712 851 2.928801 ATGTTCAGCACACACACCTA 57.071 45.000 0.00 0.00 38.61 3.08
715 854 5.149273 CAAATCTATGTTCAGCACACACAC 58.851 41.667 0.00 0.00 38.61 3.82
721 860 3.181493 CCAGCCAAATCTATGTTCAGCAC 60.181 47.826 0.00 0.00 0.00 4.40
821 964 6.398918 ACAGAGTACATCAGTAAACATCCAC 58.601 40.000 0.00 0.00 30.67 4.02
890 1039 4.927425 GCACTTAATTCGAACTAGGACACA 59.073 41.667 0.00 0.00 0.00 3.72
903 1052 5.930135 TCCCTTCAGATAGGCACTTAATTC 58.070 41.667 0.00 0.00 41.75 2.17
938 1087 8.887717 ACACTAGAAGTCAAATTGATATGAAGC 58.112 33.333 0.00 0.00 0.00 3.86
1101 1250 0.179020 TGAAACCACCAGCTCCAGTG 60.179 55.000 1.80 1.80 0.00 3.66
1143 1292 2.366469 GTGCCCCTCACTCTTCAGA 58.634 57.895 0.00 0.00 42.38 3.27
1176 1325 1.964223 TGCTCGTTCTTCTTCCAGTCT 59.036 47.619 0.00 0.00 0.00 3.24
1278 1427 3.673323 CGAGATTGAAGACATGGTCGACA 60.673 47.826 18.91 3.91 37.67 4.35
1335 1484 7.672240 TGTTGTACATGATAACAGAGTGGTTA 58.328 34.615 0.00 0.00 34.53 2.85
1435 1584 4.941657 TCATAGCACACTTCAGCTAGATG 58.058 43.478 0.24 0.24 45.53 2.90
1440 1589 1.554160 AGCTCATAGCACACTTCAGCT 59.446 47.619 1.22 0.00 45.56 4.24
1461 1610 5.073144 ACCCTTTTCAAGTAATCTCTGGACA 59.927 40.000 0.00 0.00 0.00 4.02
1472 1621 9.990360 GAATTCCAAATAAACCCTTTTCAAGTA 57.010 29.630 0.00 0.00 0.00 2.24
1474 1623 8.900983 TGAATTCCAAATAAACCCTTTTCAAG 57.099 30.769 2.27 0.00 0.00 3.02
1594 1767 9.036671 TGAATATATTTGTCAAATGCAAGCATG 57.963 29.630 19.10 0.00 36.68 4.06
1866 2041 5.885352 TGTCTCAAGTTGTTTGAATTCAGGA 59.115 36.000 8.41 0.00 44.84 3.86
1881 2056 4.454678 TCAAGCTCACATTTGTCTCAAGT 58.545 39.130 0.00 0.00 0.00 3.16
2009 2186 1.709147 GCGGCTGAATGGTAGCACAG 61.709 60.000 0.00 2.20 42.88 3.66
2013 2190 0.744414 TCTTGCGGCTGAATGGTAGC 60.744 55.000 0.00 0.00 40.41 3.58
2017 2194 1.065273 GCATCTTGCGGCTGAATGG 59.935 57.895 0.00 0.00 31.71 3.16
2523 2703 2.992114 ACGGGCTCGCAGAAGTCT 60.992 61.111 5.51 0.00 40.63 3.24
2673 2853 2.617532 GCCAAGCTTCTCCTTGATGAGT 60.618 50.000 0.00 0.00 43.79 3.41
2757 2938 5.506317 GCTTCAGGTGTTATTATCATGTGGC 60.506 44.000 0.00 0.00 0.00 5.01
2863 3044 7.373617 TCCTGCACAGAATTCATAGGTATTA 57.626 36.000 8.44 0.00 0.00 0.98
2871 3052 2.029623 GCCATCCTGCACAGAATTCAT 58.970 47.619 8.44 0.00 0.00 2.57
3098 3285 6.127925 TGCTATTCTCTGAATGTTTTTCGCAT 60.128 34.615 3.35 0.00 0.00 4.73
3108 3295 3.560481 CAGGCTGTGCTATTCTCTGAATG 59.440 47.826 6.28 0.00 0.00 2.67
3142 3330 5.118286 TGAATCTGCTAAAATCGCTCATGA 58.882 37.500 0.00 0.00 0.00 3.07
3147 3335 3.303593 CGCATGAATCTGCTAAAATCGCT 60.304 43.478 0.00 0.00 40.06 4.93
3166 3355 2.093625 GTGACACAAAGATAATCGCGCA 59.906 45.455 8.75 0.00 0.00 6.09
3168 3357 2.285026 CGGTGACACAAAGATAATCGCG 60.285 50.000 8.08 0.00 0.00 5.87
3171 3360 6.316390 AGGAATTCGGTGACACAAAGATAATC 59.684 38.462 8.08 3.27 0.00 1.75
3331 3546 5.527582 AGTTTTGGTTATAGTCGATGCCATC 59.472 40.000 0.00 0.00 0.00 3.51
3361 3577 0.533308 TTCGGTGGGTTTCACGAAGG 60.533 55.000 0.00 0.00 46.96 3.46
3365 3581 1.096386 TGGTTTCGGTGGGTTTCACG 61.096 55.000 0.00 0.00 46.96 4.35
3475 3700 7.550906 AGCTTCTATTCAATTCTGTTCACCTAC 59.449 37.037 0.00 0.00 0.00 3.18
3487 3712 8.099537 TGAGTTCTTCAGAGCTTCTATTCAATT 58.900 33.333 0.00 0.00 35.71 2.32
3489 3714 6.870965 GTGAGTTCTTCAGAGCTTCTATTCAA 59.129 38.462 0.00 0.00 35.71 2.69
3579 3810 3.790123 GCACTCGCAGATTAATTGGAAGC 60.790 47.826 0.00 0.00 38.36 3.86
3596 3827 7.414540 GGTTTGCAGCCTATTATATATGCACTC 60.415 40.741 6.04 3.58 42.82 3.51
3604 3835 4.524328 GCCTTGGTTTGCAGCCTATTATAT 59.476 41.667 10.19 0.00 0.00 0.86
3606 3837 2.695147 GCCTTGGTTTGCAGCCTATTAT 59.305 45.455 10.19 0.00 0.00 1.28
3607 3838 2.099405 GCCTTGGTTTGCAGCCTATTA 58.901 47.619 10.19 0.00 0.00 0.98
3609 3840 0.040204 AGCCTTGGTTTGCAGCCTAT 59.960 50.000 10.19 0.00 0.00 2.57
3629 3864 2.158842 CCTGCTTGCTATAAGGACTGCT 60.159 50.000 0.00 0.00 30.92 4.24
3649 3884 2.096248 TCCCAATTTTGTATGACGCCC 58.904 47.619 0.00 0.00 0.00 6.13
3683 3918 7.062322 AGATTGTAACTGCATTGGGATGAATA 58.938 34.615 0.00 0.00 35.16 1.75
3754 3989 3.830178 TCAGTTCGACCAATCCTCACTAA 59.170 43.478 0.00 0.00 0.00 2.24
3770 4005 4.094887 TGCTTGAGGCGATAATTTCAGTTC 59.905 41.667 0.00 0.00 45.43 3.01
3775 4010 3.242870 CCACTGCTTGAGGCGATAATTTC 60.243 47.826 0.00 0.00 45.43 2.17
3816 4067 5.599999 TTATCTGGGCAGACTTAACTCTC 57.400 43.478 0.00 0.00 40.75 3.20
3850 4101 7.337689 TCTCCATTGTGTATCCTTGAAAATCAG 59.662 37.037 0.00 0.00 0.00 2.90
3853 4104 6.604795 CCTCTCCATTGTGTATCCTTGAAAAT 59.395 38.462 0.00 0.00 0.00 1.82
3854 4105 5.945784 CCTCTCCATTGTGTATCCTTGAAAA 59.054 40.000 0.00 0.00 0.00 2.29
3860 4111 3.454858 ACACCTCTCCATTGTGTATCCT 58.545 45.455 0.00 0.00 41.18 3.24
3910 4161 3.138304 TGCTGAAAAGCGTTGTATCAGT 58.862 40.909 12.22 0.00 39.68 3.41
3919 4170 3.058914 GTGAACTGTATGCTGAAAAGCGT 60.059 43.478 0.00 0.00 37.69 5.07
3926 4177 2.103941 TGGTGTGTGAACTGTATGCTGA 59.896 45.455 0.00 0.00 0.00 4.26
3928 4179 2.158827 TGTGGTGTGTGAACTGTATGCT 60.159 45.455 0.00 0.00 0.00 3.79
3949 4200 2.158755 AGCTGCTTGTGTCCTTGTAGTT 60.159 45.455 0.00 0.00 0.00 2.24
3957 4208 2.507110 TAGGCGAGCTGCTTGTGTCC 62.507 60.000 17.76 10.73 45.43 4.02
3965 4216 1.874466 GTTCGACTAGGCGAGCTGC 60.874 63.158 25.67 12.02 41.79 5.25
3968 4219 1.064458 GAGGTTCGACTAGGCGAGC 59.936 63.158 25.08 25.08 41.79 5.03


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

AutoCloner maintained by Alex Coulton.