Multiple sequence alignment - TraesCS4A01G110100

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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 TraesCS4A01G110100 chr4A 100.000 3622 0 0 1 3622 134207245 134210866 0.000000e+00 6689.0
1 TraesCS4A01G110100 chr4D 95.258 2446 78 17 619 3050 337936951 337934530 0.000000e+00 3840.0
2 TraesCS4A01G110100 chr4D 85.714 511 58 9 3 499 337937920 337937411 3.200000e-145 525.0
3 TraesCS4A01G110100 chr4B 94.700 2264 95 9 619 2870 417139848 417137598 0.000000e+00 3493.0
4 TraesCS4A01G110100 chr4B 86.028 501 56 10 3 499 417140465 417139975 3.200000e-145 525.0
5 TraesCS4A01G110100 chr4B 94.565 184 8 2 2869 3050 417137437 417137254 2.130000e-72 283.0
6 TraesCS4A01G110100 chr7A 97.207 537 15 0 3086 3622 62758189 62758725 0.000000e+00 909.0
7 TraesCS4A01G110100 chr7A 95.194 541 26 0 3081 3621 666430161 666429621 0.000000e+00 856.0
8 TraesCS4A01G110100 chr5B 95.564 541 24 0 3081 3621 493602818 493603358 0.000000e+00 867.0
9 TraesCS4A01G110100 chr5B 95.336 536 25 0 3086 3621 531694810 531694275 0.000000e+00 852.0
10 TraesCS4A01G110100 chr5B 80.208 96 12 4 294 384 341524231 341524138 8.390000e-07 65.8
11 TraesCS4A01G110100 chr2B 95.221 544 26 0 3078 3621 196017041 196016498 0.000000e+00 861.0
12 TraesCS4A01G110100 chr6D 95.221 544 25 1 3079 3622 471320373 471320915 0.000000e+00 859.0
13 TraesCS4A01G110100 chr6D 89.815 108 10 1 516 623 12329383 12329277 1.750000e-28 137.0
14 TraesCS4A01G110100 chr1A 95.522 536 24 0 3086 3621 61253903 61254438 0.000000e+00 857.0
15 TraesCS4A01G110100 chr1B 95.194 541 24 2 3082 3621 286318799 286318260 0.000000e+00 854.0
16 TraesCS4A01G110100 chr5A 95.336 536 25 0 3086 3621 494399309 494399844 0.000000e+00 852.0
17 TraesCS4A01G110100 chr5A 88.991 109 9 3 516 622 527398269 527398376 8.160000e-27 132.0
18 TraesCS4A01G110100 chr3D 90.598 117 9 2 509 624 29607128 29607013 1.740000e-33 154.0
19 TraesCS4A01G110100 chrUn 90.826 109 8 2 518 625 12497582 12497689 1.050000e-30 145.0
20 TraesCS4A01G110100 chr7D 91.429 105 7 2 516 619 11414093 11413990 3.770000e-30 143.0
21 TraesCS4A01G110100 chr7D 87.719 114 9 5 513 625 7206095 7206204 1.060000e-25 128.0
22 TraesCS4A01G110100 chr5D 88.288 111 10 3 510 619 456591354 456591462 2.930000e-26 130.0
23 TraesCS4A01G110100 chr5D 79.310 116 17 4 294 404 299923339 299923226 1.390000e-09 75.0
24 TraesCS4A01G110100 chr2A 86.957 115 13 2 510 624 29159146 29159258 1.060000e-25 128.0
25 TraesCS4A01G110100 chr3B 86.325 117 14 2 509 624 50261633 50261518 3.800000e-25 126.0


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 TraesCS4A01G110100 chr4A 134207245 134210866 3621 False 6689.000000 6689 100.000000 1 3622 1 chr4A.!!$F1 3621
1 TraesCS4A01G110100 chr4D 337934530 337937920 3390 True 2182.500000 3840 90.486000 3 3050 2 chr4D.!!$R1 3047
2 TraesCS4A01G110100 chr4B 417137254 417140465 3211 True 1433.666667 3493 91.764333 3 3050 3 chr4B.!!$R1 3047
3 TraesCS4A01G110100 chr7A 62758189 62758725 536 False 909.000000 909 97.207000 3086 3622 1 chr7A.!!$F1 536
4 TraesCS4A01G110100 chr7A 666429621 666430161 540 True 856.000000 856 95.194000 3081 3621 1 chr7A.!!$R1 540
5 TraesCS4A01G110100 chr5B 493602818 493603358 540 False 867.000000 867 95.564000 3081 3621 1 chr5B.!!$F1 540
6 TraesCS4A01G110100 chr5B 531694275 531694810 535 True 852.000000 852 95.336000 3086 3621 1 chr5B.!!$R2 535
7 TraesCS4A01G110100 chr2B 196016498 196017041 543 True 861.000000 861 95.221000 3078 3621 1 chr2B.!!$R1 543
8 TraesCS4A01G110100 chr6D 471320373 471320915 542 False 859.000000 859 95.221000 3079 3622 1 chr6D.!!$F1 543
9 TraesCS4A01G110100 chr1A 61253903 61254438 535 False 857.000000 857 95.522000 3086 3621 1 chr1A.!!$F1 535
10 TraesCS4A01G110100 chr1B 286318260 286318799 539 True 854.000000 854 95.194000 3082 3621 1 chr1B.!!$R1 539
11 TraesCS4A01G110100 chr5A 494399309 494399844 535 False 852.000000 852 95.336000 3086 3621 1 chr5A.!!$F1 535

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
215 223 0.477597 TCTCCCCACCACCCTTTCAT 60.478 55.0 0.0 0.0 0.0 2.57 F
1258 1621 0.458543 GTCGATGCTCAAGAGGCGAA 60.459 55.0 0.0 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 2132 0.620556 TCTTCACAGCCCCCTCAATC 59.379 55.0 0.0 0.0 0.00 2.67 R
2992 3525 0.032815 TTTGATGTGTCGGCTGTCGA 59.967 50.0 0.0 0.0 46.77 4.20 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
74 75 3.763360 TGCTAGCTGTAAATTGGCATGTT 59.237 39.130 17.23 0.00 0.00 2.71
80 81 2.160615 TGTAAATTGGCATGTTCCGACG 59.839 45.455 0.00 0.00 0.00 5.12
87 88 1.553308 GCATGTTCCGACGGTACTAC 58.447 55.000 22.07 12.90 0.00 2.73
112 113 7.440255 ACCTTACGATATATTTCAAAACGGAGG 59.560 37.037 0.00 0.00 35.03 4.30
115 116 7.242914 ACGATATATTTCAAAACGGAGGAAC 57.757 36.000 0.00 0.00 0.00 3.62
178 186 5.839621 TGTATCTCCGCTAACATAAGGTTC 58.160 41.667 0.00 0.00 40.96 3.62
190 198 7.121315 GCTAACATAAGGTTCCATCTTTCACTT 59.879 37.037 0.00 0.00 40.96 3.16
192 200 8.934023 AACATAAGGTTCCATCTTTCACTTAA 57.066 30.769 0.00 0.00 33.35 1.85
210 218 1.167033 AATTTTCTCCCCACCACCCT 58.833 50.000 0.00 0.00 0.00 4.34
214 222 0.699577 TTCTCCCCACCACCCTTTCA 60.700 55.000 0.00 0.00 0.00 2.69
215 223 0.477597 TCTCCCCACCACCCTTTCAT 60.478 55.000 0.00 0.00 0.00 2.57
227 235 4.284178 CACCCTTTCATCCAATCTTCCAT 58.716 43.478 0.00 0.00 0.00 3.41
291 303 9.565090 TTTTCATCAAACTAGATCATCTATGGG 57.435 33.333 0.00 0.00 0.00 4.00
320 332 9.383519 AGCAATAAATTCACGGTCCATATATAG 57.616 33.333 0.00 0.00 0.00 1.31
437 450 6.357367 ACGAATCTCTTATATTTGGCAACCT 58.643 36.000 0.00 0.00 0.00 3.50
445 458 8.391075 TCTTATATTTGGCAACCTAATACAGC 57.609 34.615 0.00 0.00 35.00 4.40
456 469 7.355778 GCAACCTAATACAGCAGATAAATCAC 58.644 38.462 0.00 0.00 0.00 3.06
462 475 2.016318 CAGCAGATAAATCACGGGCAA 58.984 47.619 0.00 0.00 0.00 4.52
471 484 7.822334 CAGATAAATCACGGGCAAATACCTATA 59.178 37.037 0.00 0.00 0.00 1.31
474 487 7.833285 AAATCACGGGCAAATACCTATATTT 57.167 32.000 0.00 0.00 40.91 1.40
475 488 8.927675 AAATCACGGGCAAATACCTATATTTA 57.072 30.769 0.00 0.00 38.67 1.40
476 489 7.916914 ATCACGGGCAAATACCTATATTTAC 57.083 36.000 0.00 0.00 38.67 2.01
479 492 5.999600 ACGGGCAAATACCTATATTTACCAC 59.000 40.000 9.99 1.75 42.62 4.16
501 515 9.914131 ACCACTTTAAGAAATAGCTGAAAAATC 57.086 29.630 0.00 0.00 0.00 2.17
502 516 9.912634 CCACTTTAAGAAATAGCTGAAAAATCA 57.087 29.630 0.00 0.00 0.00 2.57
504 518 9.612620 ACTTTAAGAAATAGCTGAAAAATCACG 57.387 29.630 0.00 0.00 0.00 4.35
505 519 9.612620 CTTTAAGAAATAGCTGAAAAATCACGT 57.387 29.630 0.00 0.00 0.00 4.49
506 520 9.607285 TTTAAGAAATAGCTGAAAAATCACGTC 57.393 29.630 0.00 0.00 0.00 4.34
507 521 5.858475 AGAAATAGCTGAAAAATCACGTCG 58.142 37.500 0.00 0.00 0.00 5.12
508 522 5.637810 AGAAATAGCTGAAAAATCACGTCGA 59.362 36.000 0.00 0.00 0.00 4.20
509 523 4.842139 ATAGCTGAAAAATCACGTCGAC 57.158 40.909 5.18 5.18 0.00 4.20
510 524 1.455786 AGCTGAAAAATCACGTCGACG 59.544 47.619 34.58 34.58 46.33 5.12
511 525 1.853230 CTGAAAAATCACGTCGACGC 58.147 50.000 35.92 18.18 44.43 5.19
512 526 0.509499 TGAAAAATCACGTCGACGCC 59.491 50.000 35.92 15.45 44.43 5.68
514 528 0.511221 AAAAATCACGTCGACGCCAG 59.489 50.000 35.92 25.31 44.43 4.85
515 529 0.599204 AAAATCACGTCGACGCCAGT 60.599 50.000 35.92 19.89 44.43 4.00
516 530 1.282248 AAATCACGTCGACGCCAGTG 61.282 55.000 35.92 25.90 44.43 3.66
517 531 3.626680 ATCACGTCGACGCCAGTGG 62.627 63.158 35.92 18.58 44.43 4.00
518 532 4.640855 CACGTCGACGCCAGTGGT 62.641 66.667 35.92 13.60 44.43 4.16
519 533 4.338539 ACGTCGACGCCAGTGGTC 62.339 66.667 35.92 0.00 44.43 4.02
524 538 3.103911 GACGCCAGTGGTCGTTCG 61.104 66.667 25.38 16.31 36.12 3.95
525 539 4.657824 ACGCCAGTGGTCGTTCGG 62.658 66.667 21.08 2.51 33.33 4.30
527 541 3.041940 GCCAGTGGTCGTTCGGTG 61.042 66.667 11.74 0.00 0.00 4.94
528 542 2.357034 CCAGTGGTCGTTCGGTGG 60.357 66.667 0.00 0.00 0.00 4.61
529 543 2.420043 CAGTGGTCGTTCGGTGGT 59.580 61.111 0.00 0.00 0.00 4.16
530 544 1.661480 CAGTGGTCGTTCGGTGGTA 59.339 57.895 0.00 0.00 0.00 3.25
532 546 1.473677 CAGTGGTCGTTCGGTGGTATA 59.526 52.381 0.00 0.00 0.00 1.47
534 548 2.100252 AGTGGTCGTTCGGTGGTATATG 59.900 50.000 0.00 0.00 0.00 1.78
535 549 1.409790 TGGTCGTTCGGTGGTATATGG 59.590 52.381 0.00 0.00 0.00 2.74
536 550 1.682854 GGTCGTTCGGTGGTATATGGA 59.317 52.381 0.00 0.00 0.00 3.41
537 551 2.101249 GGTCGTTCGGTGGTATATGGAA 59.899 50.000 0.00 0.00 0.00 3.53
538 552 3.118542 GTCGTTCGGTGGTATATGGAAC 58.881 50.000 0.00 0.00 34.99 3.62
539 553 2.101249 TCGTTCGGTGGTATATGGAACC 59.899 50.000 0.00 0.00 34.89 3.62
541 555 3.463944 GTTCGGTGGTATATGGAACCTG 58.536 50.000 0.00 0.00 37.91 4.00
544 558 3.323691 TCGGTGGTATATGGAACCTGATG 59.676 47.826 0.00 0.00 37.91 3.07
546 560 4.282449 CGGTGGTATATGGAACCTGATGTA 59.718 45.833 0.00 0.00 37.91 2.29
547 561 5.221561 CGGTGGTATATGGAACCTGATGTAA 60.222 44.000 0.00 0.00 37.91 2.41
548 562 6.520061 CGGTGGTATATGGAACCTGATGTAAT 60.520 42.308 0.00 0.00 37.91 1.89
549 563 7.231467 GGTGGTATATGGAACCTGATGTAATT 58.769 38.462 0.00 0.00 37.91 1.40
551 565 9.131791 GTGGTATATGGAACCTGATGTAATTTT 57.868 33.333 0.00 0.00 37.91 1.82
552 566 9.707957 TGGTATATGGAACCTGATGTAATTTTT 57.292 29.630 0.00 0.00 37.91 1.94
575 589 9.968870 TTTTATTATGTTTGAGGTGTTTGGTAC 57.031 29.630 0.00 0.00 0.00 3.34
576 590 8.927675 TTATTATGTTTGAGGTGTTTGGTACT 57.072 30.769 0.00 0.00 0.00 2.73
578 592 5.767816 ATGTTTGAGGTGTTTGGTACTTC 57.232 39.130 0.00 0.00 0.00 3.01
579 593 3.949113 TGTTTGAGGTGTTTGGTACTTCC 59.051 43.478 0.00 0.00 0.00 3.46
580 594 2.536761 TGAGGTGTTTGGTACTTCCG 57.463 50.000 0.00 0.00 39.52 4.30
584 598 1.202675 GGTGTTTGGTACTTCCGGTGA 60.203 52.381 0.00 0.00 39.52 4.02
585 599 2.563702 GTGTTTGGTACTTCCGGTGAA 58.436 47.619 0.00 0.00 39.52 3.18
586 600 3.143728 GTGTTTGGTACTTCCGGTGAAT 58.856 45.455 0.00 0.00 39.52 2.57
587 601 3.187842 GTGTTTGGTACTTCCGGTGAATC 59.812 47.826 0.00 0.00 39.52 2.52
588 602 2.745821 GTTTGGTACTTCCGGTGAATCC 59.254 50.000 0.00 0.88 39.52 3.01
589 603 1.946984 TGGTACTTCCGGTGAATCCT 58.053 50.000 0.00 0.00 39.52 3.24
590 604 2.262637 TGGTACTTCCGGTGAATCCTT 58.737 47.619 0.00 0.00 39.52 3.36
591 605 3.443052 TGGTACTTCCGGTGAATCCTTA 58.557 45.455 0.00 0.00 39.52 2.69
592 606 4.035112 TGGTACTTCCGGTGAATCCTTAT 58.965 43.478 0.00 0.00 39.52 1.73
593 607 5.210430 TGGTACTTCCGGTGAATCCTTATA 58.790 41.667 0.00 0.00 39.52 0.98
594 608 5.662208 TGGTACTTCCGGTGAATCCTTATAA 59.338 40.000 0.00 0.00 39.52 0.98
596 610 7.510001 TGGTACTTCCGGTGAATCCTTATAATA 59.490 37.037 0.00 0.00 39.52 0.98
597 611 8.033626 GGTACTTCCGGTGAATCCTTATAATAG 58.966 40.741 0.00 0.00 0.00 1.73
598 612 7.850935 ACTTCCGGTGAATCCTTATAATAGA 57.149 36.000 0.00 0.00 0.00 1.98
599 613 8.437274 ACTTCCGGTGAATCCTTATAATAGAT 57.563 34.615 0.00 0.00 0.00 1.98
602 616 9.763837 TTCCGGTGAATCCTTATAATAGATCTA 57.236 33.333 4.57 4.57 0.00 1.98
603 617 9.763837 TCCGGTGAATCCTTATAATAGATCTAA 57.236 33.333 6.52 0.00 0.00 2.10
657 1012 2.297597 CACTACTATGGCACTAGGGAGC 59.702 54.545 0.00 0.00 0.00 4.70
662 1017 2.109229 ATGGCACTAGGGAGCAGTAT 57.891 50.000 0.00 0.00 0.00 2.12
663 1018 2.767644 TGGCACTAGGGAGCAGTATA 57.232 50.000 0.00 0.00 0.00 1.47
702 1060 4.333372 GGAAATGTTGCCCAATAATTGCAG 59.667 41.667 0.00 0.00 36.21 4.41
776 1134 4.806640 ACATTAAGAAACAATGGCCCTG 57.193 40.909 0.00 0.00 37.64 4.45
821 1179 2.187946 CCTAGGGCCAAGCGAGTG 59.812 66.667 6.18 0.00 0.00 3.51
822 1180 2.187946 CTAGGGCCAAGCGAGTGG 59.812 66.667 6.18 0.57 42.05 4.00
1041 1404 3.453679 AGCTCGCCGGTCTTCTCC 61.454 66.667 1.90 0.00 0.00 3.71
1107 1470 3.812019 CCCGAGTCCGTCTCCGTG 61.812 72.222 0.00 0.00 39.84 4.94
1108 1471 3.054503 CCGAGTCCGTCTCCGTGT 61.055 66.667 0.00 0.00 39.84 4.49
1109 1472 2.479650 CGAGTCCGTCTCCGTGTC 59.520 66.667 0.41 0.00 39.84 3.67
1110 1473 2.876219 GAGTCCGTCTCCGTGTCC 59.124 66.667 0.00 0.00 37.22 4.02
1111 1474 3.036783 GAGTCCGTCTCCGTGTCCG 62.037 68.421 0.00 0.00 37.22 4.79
1112 1475 3.360340 GTCCGTCTCCGTGTCCGT 61.360 66.667 0.00 0.00 0.00 4.69
1257 1620 1.139734 GTCGATGCTCAAGAGGCGA 59.860 57.895 0.00 0.00 0.00 5.54
1258 1621 0.458543 GTCGATGCTCAAGAGGCGAA 60.459 55.000 0.00 0.00 0.00 4.70
1761 2132 0.318441 ACGGTGGTGACAGTGATGAG 59.682 55.000 0.00 0.00 44.46 2.90
2022 2393 7.549134 AGATCTTGTATGCTTCGAATGTGTTTA 59.451 33.333 0.00 0.00 0.00 2.01
2056 2427 5.858581 GTGACAATTGTAGTTTGAAGGATGC 59.141 40.000 11.95 0.00 0.00 3.91
2258 2629 4.342378 TCTGTGACTTATGTGCTCTATCCC 59.658 45.833 0.00 0.00 0.00 3.85
2263 2634 7.016563 TGTGACTTATGTGCTCTATCCCATTAT 59.983 37.037 0.00 0.00 0.00 1.28
2279 2650 3.055458 CCATTATTTTTCAGGGCGGGTTT 60.055 43.478 0.00 0.00 0.00 3.27
2342 2713 1.078848 AGTGTCAAGAGGCATCGGC 60.079 57.895 0.00 0.00 40.13 5.54
2688 3059 0.902531 AACAGAGTGGTGTATCGGGG 59.097 55.000 0.00 0.00 0.00 5.73
2689 3060 0.252103 ACAGAGTGGTGTATCGGGGT 60.252 55.000 0.00 0.00 0.00 4.95
2767 3138 1.608542 GCACCATTTTGCAGGCATTCA 60.609 47.619 0.00 0.00 42.49 2.57
2778 3149 2.030805 GCAGGCATTCAACTCTTTTCGT 60.031 45.455 0.00 0.00 0.00 3.85
2780 3151 4.670221 GCAGGCATTCAACTCTTTTCGTAG 60.670 45.833 0.00 0.00 0.00 3.51
2832 3203 6.927416 TCCATTCATTCATTCTTTGGTTCTG 58.073 36.000 0.00 0.00 0.00 3.02
2908 3441 3.688694 TGTACATGGTTGACTGGGTAC 57.311 47.619 0.00 0.00 33.53 3.34
2944 3477 7.515684 GCATAATTGCCTCTTTGCTTATTTTCG 60.516 37.037 0.00 0.00 43.38 3.46
2979 3512 5.048504 ACTCTTGAAGTGCATGTGGTTTATG 60.049 40.000 0.00 0.00 36.65 1.90
2991 3524 6.434596 CATGTGGTTTATGTTCGTCAAGAAA 58.565 36.000 0.00 0.00 41.10 2.52
2992 3525 6.627395 TGTGGTTTATGTTCGTCAAGAAAT 57.373 33.333 0.00 0.00 41.10 2.17
3033 3568 9.258826 TCAAAATAATTTGCAAATATAGCGCAT 57.741 25.926 24.35 9.27 44.52 4.73
3047 3582 1.895131 AGCGCATGAAGGTTCCAAAAT 59.105 42.857 11.47 0.00 0.00 1.82
3049 3584 3.509575 AGCGCATGAAGGTTCCAAAATTA 59.490 39.130 11.47 0.00 0.00 1.40
3050 3585 3.859386 GCGCATGAAGGTTCCAAAATTAG 59.141 43.478 0.30 0.00 0.00 1.73
3051 3586 4.380444 GCGCATGAAGGTTCCAAAATTAGA 60.380 41.667 0.30 0.00 0.00 2.10
3052 3587 5.095490 CGCATGAAGGTTCCAAAATTAGAC 58.905 41.667 0.00 0.00 0.00 2.59
3053 3588 5.106157 CGCATGAAGGTTCCAAAATTAGACT 60.106 40.000 0.00 0.00 0.00 3.24
3054 3589 6.570378 CGCATGAAGGTTCCAAAATTAGACTT 60.570 38.462 0.00 0.00 0.00 3.01
3055 3590 6.587608 GCATGAAGGTTCCAAAATTAGACTTG 59.412 38.462 0.00 0.00 0.00 3.16
3056 3591 6.648879 TGAAGGTTCCAAAATTAGACTTGG 57.351 37.500 0.84 0.84 43.00 3.61
3057 3592 6.133356 TGAAGGTTCCAAAATTAGACTTGGT 58.867 36.000 6.54 0.00 42.37 3.67
3058 3593 6.609616 TGAAGGTTCCAAAATTAGACTTGGTT 59.390 34.615 6.54 0.00 42.37 3.67
3059 3594 7.125053 TGAAGGTTCCAAAATTAGACTTGGTTT 59.875 33.333 6.54 0.00 42.37 3.27
3060 3595 6.816136 AGGTTCCAAAATTAGACTTGGTTTG 58.184 36.000 6.54 0.00 42.37 2.93
3061 3596 5.989168 GGTTCCAAAATTAGACTTGGTTTGG 59.011 40.000 13.45 13.45 46.28 3.28
3065 3600 6.648879 CAAAATTAGACTTGGTTTGGAGGA 57.351 37.500 0.00 0.00 0.00 3.71
3066 3601 6.681777 CAAAATTAGACTTGGTTTGGAGGAG 58.318 40.000 0.00 0.00 0.00 3.69
3067 3602 5.843019 AATTAGACTTGGTTTGGAGGAGA 57.157 39.130 0.00 0.00 0.00 3.71
3068 3603 5.843019 ATTAGACTTGGTTTGGAGGAGAA 57.157 39.130 0.00 0.00 0.00 2.87
3069 3604 5.843019 TTAGACTTGGTTTGGAGGAGAAT 57.157 39.130 0.00 0.00 0.00 2.40
3070 3605 4.731313 AGACTTGGTTTGGAGGAGAATT 57.269 40.909 0.00 0.00 0.00 2.17
3071 3606 4.401925 AGACTTGGTTTGGAGGAGAATTG 58.598 43.478 0.00 0.00 0.00 2.32
3072 3607 4.104738 AGACTTGGTTTGGAGGAGAATTGA 59.895 41.667 0.00 0.00 0.00 2.57
3073 3608 4.401925 ACTTGGTTTGGAGGAGAATTGAG 58.598 43.478 0.00 0.00 0.00 3.02
3074 3609 4.104738 ACTTGGTTTGGAGGAGAATTGAGA 59.895 41.667 0.00 0.00 0.00 3.27
3075 3610 4.292186 TGGTTTGGAGGAGAATTGAGAG 57.708 45.455 0.00 0.00 0.00 3.20
3076 3611 3.009473 TGGTTTGGAGGAGAATTGAGAGG 59.991 47.826 0.00 0.00 0.00 3.69
3077 3612 3.264450 GGTTTGGAGGAGAATTGAGAGGA 59.736 47.826 0.00 0.00 0.00 3.71
3078 3613 4.512484 GTTTGGAGGAGAATTGAGAGGAG 58.488 47.826 0.00 0.00 0.00 3.69
3079 3614 3.765432 TGGAGGAGAATTGAGAGGAGA 57.235 47.619 0.00 0.00 0.00 3.71
3080 3615 4.277788 TGGAGGAGAATTGAGAGGAGAT 57.722 45.455 0.00 0.00 0.00 2.75
3081 3616 4.629122 TGGAGGAGAATTGAGAGGAGATT 58.371 43.478 0.00 0.00 0.00 2.40
3082 3617 5.035556 TGGAGGAGAATTGAGAGGAGATTT 58.964 41.667 0.00 0.00 0.00 2.17
3083 3618 5.490357 TGGAGGAGAATTGAGAGGAGATTTT 59.510 40.000 0.00 0.00 0.00 1.82
3084 3619 6.054941 GGAGGAGAATTGAGAGGAGATTTTC 58.945 44.000 0.00 0.00 0.00 2.29
3222 3757 1.019278 TTCCCTAGCTTTCTTGCGCG 61.019 55.000 0.00 0.00 38.13 6.86
3319 3854 3.662247 ACTCGGACGTTTCTCTCATTT 57.338 42.857 0.00 0.00 0.00 2.32
3434 3969 2.742053 GTTGCTTCTAACTGCCAATCGA 59.258 45.455 0.00 0.00 0.00 3.59
3524 4059 2.626785 TGACAAAGAGGTGTATCCCCA 58.373 47.619 0.00 0.00 36.75 4.96
3574 4110 4.275781 CCACAGTTTGGCCAACCT 57.724 55.556 20.35 15.10 39.07 3.50
3585 4121 1.743252 GCCAACCTCGCTTCTCCAG 60.743 63.158 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 9.056005 CCAATTTACAGCTAGCATATTTACTCA 57.944 33.333 18.83 0.00 0.00 3.41
55 56 3.376859 CGGAACATGCCAATTTACAGCTA 59.623 43.478 0.00 0.00 0.00 3.32
74 75 1.206132 TCGTAAGGTAGTACCGTCGGA 59.794 52.381 20.51 14.90 44.90 4.55
87 88 7.654520 TCCTCCGTTTTGAAATATATCGTAAGG 59.345 37.037 0.00 0.00 38.47 2.69
112 113 5.591643 ATTTATGTGTCGCGATATGGTTC 57.408 39.130 14.06 0.00 0.00 3.62
115 116 7.987268 ATAGTATTTATGTGTCGCGATATGG 57.013 36.000 14.06 0.00 0.00 2.74
156 164 5.221382 TGGAACCTTATGTTAGCGGAGATAC 60.221 44.000 0.00 0.00 37.29 2.24
178 186 6.437162 TGGGGAGAAAATTAAGTGAAAGATGG 59.563 38.462 0.00 0.00 0.00 3.51
190 198 2.364190 AGGGTGGTGGGGAGAAAATTA 58.636 47.619 0.00 0.00 0.00 1.40
192 200 1.167033 AAGGGTGGTGGGGAGAAAAT 58.833 50.000 0.00 0.00 0.00 1.82
210 218 4.230272 TGGAGGATGGAAGATTGGATGAAA 59.770 41.667 0.00 0.00 0.00 2.69
214 222 4.249490 AGATGGAGGATGGAAGATTGGAT 58.751 43.478 0.00 0.00 0.00 3.41
215 223 3.673343 AGATGGAGGATGGAAGATTGGA 58.327 45.455 0.00 0.00 0.00 3.53
243 254 9.108284 GAAAATCAAAAGAGGATGAAAAACCAA 57.892 29.630 0.00 0.00 0.00 3.67
291 303 3.942748 TGGACCGTGAATTTATTGCTACC 59.057 43.478 0.00 0.00 0.00 3.18
320 332 7.970061 GGTACCGGATTTACCATAAAAAGAAAC 59.030 37.037 9.46 0.00 39.17 2.78
324 336 8.913487 ATAGGTACCGGATTTACCATAAAAAG 57.087 34.615 19.02 0.00 41.48 2.27
414 427 6.867662 AGGTTGCCAAATATAAGAGATTCG 57.132 37.500 0.00 0.00 0.00 3.34
437 450 4.994852 GCCCGTGATTTATCTGCTGTATTA 59.005 41.667 0.00 0.00 0.00 0.98
442 455 1.667236 TGCCCGTGATTTATCTGCTG 58.333 50.000 0.00 0.00 0.00 4.41
445 458 4.821805 AGGTATTTGCCCGTGATTTATCTG 59.178 41.667 0.00 0.00 0.00 2.90
475 488 9.914131 GATTTTTCAGCTATTTCTTAAAGTGGT 57.086 29.630 0.00 0.00 0.00 4.16
476 489 9.912634 TGATTTTTCAGCTATTTCTTAAAGTGG 57.087 29.630 0.00 0.00 0.00 4.00
479 492 9.612620 ACGTGATTTTTCAGCTATTTCTTAAAG 57.387 29.630 0.00 0.00 0.00 1.85
495 509 0.511221 CTGGCGTCGACGTGATTTTT 59.489 50.000 35.48 0.00 42.22 1.94
501 515 4.640855 ACCACTGGCGTCGACGTG 62.641 66.667 35.48 25.66 42.22 4.49
502 516 4.338539 GACCACTGGCGTCGACGT 62.339 66.667 35.48 16.87 42.22 4.34
507 521 3.103911 CGAACGACCACTGGCGTC 61.104 66.667 15.09 9.59 35.28 5.19
508 522 4.657824 CCGAACGACCACTGGCGT 62.658 66.667 10.59 10.59 37.13 5.68
509 523 4.657824 ACCGAACGACCACTGGCG 62.658 66.667 9.51 9.51 0.00 5.69
510 524 3.041940 CACCGAACGACCACTGGC 61.042 66.667 0.00 0.00 0.00 4.85
511 525 1.808531 TACCACCGAACGACCACTGG 61.809 60.000 0.00 0.00 0.00 4.00
512 526 0.245539 ATACCACCGAACGACCACTG 59.754 55.000 0.00 0.00 0.00 3.66
514 528 2.466846 CATATACCACCGAACGACCAC 58.533 52.381 0.00 0.00 0.00 4.16
515 529 1.409790 CCATATACCACCGAACGACCA 59.590 52.381 0.00 0.00 0.00 4.02
516 530 1.682854 TCCATATACCACCGAACGACC 59.317 52.381 0.00 0.00 0.00 4.79
517 531 3.118542 GTTCCATATACCACCGAACGAC 58.881 50.000 0.00 0.00 0.00 4.34
518 532 2.101249 GGTTCCATATACCACCGAACGA 59.899 50.000 0.00 0.00 34.89 3.85
519 533 2.101917 AGGTTCCATATACCACCGAACG 59.898 50.000 0.00 0.00 38.16 3.95
520 534 3.133362 TCAGGTTCCATATACCACCGAAC 59.867 47.826 0.00 0.00 38.16 3.95
521 535 3.376636 TCAGGTTCCATATACCACCGAA 58.623 45.455 0.00 0.00 38.16 4.30
523 537 3.071023 ACATCAGGTTCCATATACCACCG 59.929 47.826 0.00 0.00 38.16 4.94
524 538 4.706842 ACATCAGGTTCCATATACCACC 57.293 45.455 0.00 0.00 38.16 4.61
525 539 8.691661 AAATTACATCAGGTTCCATATACCAC 57.308 34.615 0.00 0.00 38.16 4.16
549 563 9.968870 GTACCAAACACCTCAAACATAATAAAA 57.031 29.630 0.00 0.00 0.00 1.52
551 565 8.927675 AGTACCAAACACCTCAAACATAATAA 57.072 30.769 0.00 0.00 0.00 1.40
552 566 8.927675 AAGTACCAAACACCTCAAACATAATA 57.072 30.769 0.00 0.00 0.00 0.98
556 570 4.583073 GGAAGTACCAAACACCTCAAACAT 59.417 41.667 0.00 0.00 38.79 2.71
558 572 3.002965 CGGAAGTACCAAACACCTCAAAC 59.997 47.826 0.00 0.00 38.90 2.93
559 573 3.207778 CGGAAGTACCAAACACCTCAAA 58.792 45.455 0.00 0.00 38.90 2.69
561 575 1.071071 CCGGAAGTACCAAACACCTCA 59.929 52.381 0.00 0.00 38.90 3.86
562 576 1.071228 ACCGGAAGTACCAAACACCTC 59.929 52.381 9.46 0.00 38.90 3.85
565 579 2.243602 TCACCGGAAGTACCAAACAC 57.756 50.000 9.46 0.00 38.90 3.32
566 580 3.404899 GATTCACCGGAAGTACCAAACA 58.595 45.455 9.46 0.00 36.25 2.83
567 581 2.745821 GGATTCACCGGAAGTACCAAAC 59.254 50.000 9.46 0.00 36.25 2.93
571 585 4.684484 ATAAGGATTCACCGGAAGTACC 57.316 45.455 9.46 6.02 44.74 3.34
572 586 8.800332 TCTATTATAAGGATTCACCGGAAGTAC 58.200 37.037 9.46 0.00 44.74 2.73
573 587 8.945195 TCTATTATAAGGATTCACCGGAAGTA 57.055 34.615 9.46 0.00 44.74 2.24
574 588 7.850935 TCTATTATAAGGATTCACCGGAAGT 57.149 36.000 9.46 0.00 44.74 3.01
575 589 8.754080 AGATCTATTATAAGGATTCACCGGAAG 58.246 37.037 9.46 0.00 44.74 3.46
576 590 8.666129 AGATCTATTATAAGGATTCACCGGAA 57.334 34.615 9.46 0.00 44.74 4.30
607 621 6.787986 CGTGAAACTTTTTCTTTTTGCGAAAA 59.212 30.769 11.37 11.37 38.26 2.29
608 622 6.144080 TCGTGAAACTTTTTCTTTTTGCGAAA 59.856 30.769 0.00 0.00 31.75 3.46
609 623 5.629849 TCGTGAAACTTTTTCTTTTTGCGAA 59.370 32.000 0.00 0.00 31.75 4.70
610 624 5.154932 TCGTGAAACTTTTTCTTTTTGCGA 58.845 33.333 0.00 0.00 31.75 5.10
612 626 7.422462 GTGAATCGTGAAACTTTTTCTTTTTGC 59.578 33.333 0.68 0.00 31.75 3.68
614 628 8.757164 AGTGAATCGTGAAACTTTTTCTTTTT 57.243 26.923 0.68 0.00 31.75 1.94
617 631 8.209917 AGTAGTGAATCGTGAAACTTTTTCTT 57.790 30.769 0.68 0.00 31.75 2.52
619 633 9.530129 CATAGTAGTGAATCGTGAAACTTTTTC 57.470 33.333 0.00 0.00 31.75 2.29
624 979 5.109903 GCCATAGTAGTGAATCGTGAAACT 58.890 41.667 0.00 0.00 31.75 2.66
662 1017 9.762933 CAACATTTCCTTCCTTGAAGAAAATTA 57.237 29.630 5.43 0.00 35.10 1.40
663 1018 7.227314 GCAACATTTCCTTCCTTGAAGAAAATT 59.773 33.333 5.43 2.50 35.10 1.82
685 1043 2.273557 CTGCTGCAATTATTGGGCAAC 58.726 47.619 3.02 0.00 37.06 4.17
702 1060 2.989166 GCACAGGTAGAAAATTTGCTGC 59.011 45.455 9.11 7.35 0.00 5.25
762 1120 0.244721 GACTGCAGGGCCATTGTTTC 59.755 55.000 19.93 0.00 0.00 2.78
772 1130 0.179020 TTGTGAACTGGACTGCAGGG 60.179 55.000 19.93 7.63 0.00 4.45
776 1134 1.664016 CGCAATTGTGAACTGGACTGC 60.664 52.381 13.88 0.00 0.00 4.40
821 1179 4.452733 CGCTCCCGTGGGAACTCC 62.453 72.222 9.34 0.00 44.66 3.85
822 1180 4.452733 CCGCTCCCGTGGGAACTC 62.453 72.222 9.34 0.64 44.66 3.01
862 1225 3.670625 TGAACGGGCTTATATATGGTGC 58.329 45.455 0.00 0.00 0.00 5.01
973 1336 1.078143 CTTCTTCGGCCTTGGGAGG 60.078 63.158 0.00 0.00 46.50 4.30
1243 1606 1.451028 GCCTTCGCCTCTTGAGCAT 60.451 57.895 0.00 0.00 0.00 3.79
1549 1913 1.659022 TCCATCCCGGGTTTAGTCAA 58.341 50.000 22.86 0.00 34.36 3.18
1555 1919 3.184382 AGAAATTTCCATCCCGGGTTT 57.816 42.857 22.86 11.85 34.36 3.27
1761 2132 0.620556 TCTTCACAGCCCCCTCAATC 59.379 55.000 0.00 0.00 0.00 2.67
2056 2427 7.772332 AGGTCTAGTTTATTTATCAAGTGCG 57.228 36.000 0.00 0.00 0.00 5.34
2120 2491 6.375455 ACCAAGCAACAAGAATTATCCACTAG 59.625 38.462 0.00 0.00 0.00 2.57
2258 2629 3.885724 AACCCGCCCTGAAAAATAATG 57.114 42.857 0.00 0.00 0.00 1.90
2263 2634 1.134670 CAACAAACCCGCCCTGAAAAA 60.135 47.619 0.00 0.00 0.00 1.94
2342 2713 0.806868 ATTGCTTGAGGTGTGCATCG 59.193 50.000 0.00 0.00 36.55 3.84
2688 3059 2.300437 GGTATCAGTCTATCCTGCCCAC 59.700 54.545 0.00 0.00 32.32 4.61
2689 3060 2.609747 GGTATCAGTCTATCCTGCCCA 58.390 52.381 0.00 0.00 32.32 5.36
2760 3131 5.163884 GGTACTACGAAAAGAGTTGAATGCC 60.164 44.000 0.00 0.00 0.00 4.40
2767 3138 9.939802 ATAAAGAATGGTACTACGAAAAGAGTT 57.060 29.630 0.00 0.00 0.00 3.01
2827 3198 3.139077 CCCCGCCTTATTACATCAGAAC 58.861 50.000 0.00 0.00 0.00 3.01
2832 3203 2.651382 AACCCCCGCCTTATTACATC 57.349 50.000 0.00 0.00 0.00 3.06
2973 3506 6.586751 TGTCGATTTCTTGACGAACATAAAC 58.413 36.000 0.00 0.00 38.46 2.01
2979 3512 2.159827 GGCTGTCGATTTCTTGACGAAC 60.160 50.000 0.00 0.00 38.46 3.95
2992 3525 0.032815 TTTGATGTGTCGGCTGTCGA 59.967 50.000 0.00 0.00 46.77 4.20
3029 3563 5.095490 GTCTAATTTTGGAACCTTCATGCG 58.905 41.667 0.00 0.00 0.00 4.73
3033 3568 6.133356 ACCAAGTCTAATTTTGGAACCTTCA 58.867 36.000 12.56 0.00 45.32 3.02
3047 3582 5.843019 ATTCTCCTCCAAACCAAGTCTAA 57.157 39.130 0.00 0.00 0.00 2.10
3049 3584 4.104738 TCAATTCTCCTCCAAACCAAGTCT 59.895 41.667 0.00 0.00 0.00 3.24
3050 3585 4.398319 TCAATTCTCCTCCAAACCAAGTC 58.602 43.478 0.00 0.00 0.00 3.01
3051 3586 4.104738 TCTCAATTCTCCTCCAAACCAAGT 59.895 41.667 0.00 0.00 0.00 3.16
3052 3587 4.655963 TCTCAATTCTCCTCCAAACCAAG 58.344 43.478 0.00 0.00 0.00 3.61
3053 3588 4.507335 CCTCTCAATTCTCCTCCAAACCAA 60.507 45.833 0.00 0.00 0.00 3.67
3054 3589 3.009473 CCTCTCAATTCTCCTCCAAACCA 59.991 47.826 0.00 0.00 0.00 3.67
3055 3590 3.264450 TCCTCTCAATTCTCCTCCAAACC 59.736 47.826 0.00 0.00 0.00 3.27
3056 3591 4.223923 TCTCCTCTCAATTCTCCTCCAAAC 59.776 45.833 0.00 0.00 0.00 2.93
3057 3592 4.429505 TCTCCTCTCAATTCTCCTCCAAA 58.570 43.478 0.00 0.00 0.00 3.28
3058 3593 4.066578 TCTCCTCTCAATTCTCCTCCAA 57.933 45.455 0.00 0.00 0.00 3.53
3059 3594 3.765432 TCTCCTCTCAATTCTCCTCCA 57.235 47.619 0.00 0.00 0.00 3.86
3060 3595 5.628797 AAATCTCCTCTCAATTCTCCTCC 57.371 43.478 0.00 0.00 0.00 4.30
3061 3596 6.888105 AGAAAATCTCCTCTCAATTCTCCTC 58.112 40.000 0.00 0.00 0.00 3.71
3062 3597 6.889595 AGAAAATCTCCTCTCAATTCTCCT 57.110 37.500 0.00 0.00 0.00 3.69
3063 3598 7.936496 AAAGAAAATCTCCTCTCAATTCTCC 57.064 36.000 0.00 0.00 0.00 3.71
3148 3683 6.362283 GCTTATTTGTGAGTGCGTTGTAAAAT 59.638 34.615 0.00 0.00 0.00 1.82
3222 3757 3.818773 TGCTAAACTTTGGGTTACTGCTC 59.181 43.478 0.00 0.00 37.12 4.26
3305 3840 5.334105 CGACCATTTGAAATGAGAGAAACGT 60.334 40.000 18.82 5.77 0.00 3.99
3319 3854 3.629855 TGCTTGTTTCTTCGACCATTTGA 59.370 39.130 0.00 0.00 0.00 2.69
3434 3969 1.229428 CTCACGCACATGAACACCTT 58.771 50.000 0.00 0.00 0.00 3.50
3524 4059 5.232838 CGCTTTGCAAAAGAGAACAAGAAAT 59.767 36.000 13.84 0.00 0.00 2.17
3574 4110 1.715862 CCGATCGTCTGGAGAAGCGA 61.716 60.000 15.09 0.00 38.30 4.93
3585 4121 0.931005 GATTTGGACTGCCGATCGTC 59.069 55.000 15.09 0.47 36.79 4.20


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

AutoCloner maintained by Alex Coulton.