Multiple sequence alignment - TraesCS6A01G243700

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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 TraesCS6A01G243700 chr6A 100.000 4521 0 0 1 4521 455042197 455046717 0.000000e+00 8349.0
1 TraesCS6A01G243700 chr6A 97.773 494 10 1 1 493 133639342 133639835 0.000000e+00 850.0
2 TraesCS6A01G243700 chr6D 94.627 3964 149 38 592 4521 317485101 317489034 0.000000e+00 6082.0
3 TraesCS6A01G243700 chr6B 94.493 2506 105 13 1444 3939 506710301 506707819 0.000000e+00 3832.0
4 TraesCS6A01G243700 chr6B 91.667 744 44 7 712 1452 506711149 506710421 0.000000e+00 1014.0
5 TraesCS6A01G243700 chr6B 92.204 372 19 7 3937 4301 506707658 506707290 6.700000e-143 518.0
6 TraesCS6A01G243700 chr6B 86.695 233 15 7 4304 4521 506707249 506707018 1.260000e-60 244.0
7 TraesCS6A01G243700 chr6B 98.246 57 1 0 491 547 73535116 73535172 2.880000e-17 100.0
8 TraesCS6A01G243700 chr7B 99.187 492 4 0 1 492 448463536 448464027 0.000000e+00 887.0
9 TraesCS6A01G243700 chr7B 98.980 490 4 1 1 490 448466191 448466679 0.000000e+00 876.0
10 TraesCS6A01G243700 chr7B 92.982 57 4 0 492 548 509593888 509593944 2.900000e-12 84.2
11 TraesCS6A01G243700 chr7B 95.833 48 2 0 499 546 611520797 611520844 1.350000e-10 78.7
12 TraesCS6A01G243700 chr1B 98.783 493 6 0 1 493 169529607 169529115 0.000000e+00 878.0
13 TraesCS6A01G243700 chr1B 98.384 495 7 1 1 494 628612852 628612358 0.000000e+00 869.0
14 TraesCS6A01G243700 chr5A 98.381 494 7 1 1 494 404326968 404326476 0.000000e+00 867.0
15 TraesCS6A01G243700 chr5A 95.335 493 21 1 1 493 194718844 194719334 0.000000e+00 782.0
16 TraesCS6A01G243700 chr1A 97.773 494 8 3 1 494 542149173 542149663 0.000000e+00 848.0
17 TraesCS6A01G243700 chr7A 95.335 493 20 3 1 493 25887976 25888465 0.000000e+00 780.0
18 TraesCS6A01G243700 chrUn 91.525 118 10 0 2657 2774 273323043 273322926 3.620000e-36 163.0
19 TraesCS6A01G243700 chrUn 91.525 118 10 0 2657 2774 366017937 366017820 3.620000e-36 163.0
20 TraesCS6A01G243700 chrUn 91.525 118 10 0 2657 2774 432254614 432254497 3.620000e-36 163.0
21 TraesCS6A01G243700 chr4D 91.525 118 10 0 2657 2774 123380326 123380443 3.620000e-36 163.0
22 TraesCS6A01G243700 chr4D 91.525 118 10 0 2657 2774 123591111 123591228 3.620000e-36 163.0
23 TraesCS6A01G243700 chr2D 91.525 118 10 0 2657 2774 635049756 635049873 3.620000e-36 163.0
24 TraesCS6A01G243700 chr2D 91.525 118 10 0 2657 2774 637323869 637323752 3.620000e-36 163.0
25 TraesCS6A01G243700 chr5D 93.548 62 4 0 488 549 280378720 280378781 4.820000e-15 93.5
26 TraesCS6A01G243700 chr4A 93.548 62 3 1 492 552 192622702 192622641 1.730000e-14 91.6


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 TraesCS6A01G243700 chr6A 455042197 455046717 4520 False 8349.0 8349 100.00000 1 4521 1 chr6A.!!$F2 4520
1 TraesCS6A01G243700 chr6D 317485101 317489034 3933 False 6082.0 6082 94.62700 592 4521 1 chr6D.!!$F1 3929
2 TraesCS6A01G243700 chr6B 506707018 506711149 4131 True 1402.0 3832 91.26475 712 4521 4 chr6B.!!$R1 3809
3 TraesCS6A01G243700 chr7B 448463536 448466679 3143 False 881.5 887 99.08350 1 492 2 chr7B.!!$F3 491

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
542 543 0.038744 AAATCCACTCCCACCTGCAG 59.961 55.000 6.78 6.78 0.00 4.41 F
1197 1201 0.034186 TTCTGCCCCTGTTAGCATGG 60.034 55.000 0.00 0.00 38.56 3.66 F
1399 1405 0.527565 ACATTTCTGGTCAATGCGCC 59.472 50.000 4.18 0.00 35.36 6.53 F
1415 1421 0.684153 CGCCAGAAAATGATGGGGGT 60.684 55.000 0.64 0.00 43.75 4.95 F
1494 1629 1.270785 TGTGCATGACATCCGTCTTGT 60.271 47.619 0.00 0.00 44.93 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1406 1412 0.178828 TGTTTCCCCTACCCCCATCA 60.179 55.000 0.0 0.0 0.00 3.07 R
3070 3694 1.222113 GCTTCCTCCACCACTAGGC 59.778 63.158 0.0 0.0 39.06 3.93 R
3271 3895 4.264083 CCCTCCATTGCATATGGGTCTTAT 60.264 45.833 20.7 0.0 39.60 1.73 R
3284 3908 4.705023 AGTATTTACACAACCCTCCATTGC 59.295 41.667 0.0 0.0 0.00 3.56 R
3582 4213 1.935873 CCAGAAACATCGCATCATCGT 59.064 47.619 0.0 0.0 0.00 3.73 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
40 41 3.869065 TCCGTTGATTTGGCTAAGGTAG 58.131 45.455 0.00 0.00 0.00 3.18
189 190 3.850752 TGATTTGGCCAAGGTAGGAAAA 58.149 40.909 19.48 0.00 0.00 2.29
500 501 8.251383 TCCATTAGGAGTAGAGATTTAAGTGG 57.749 38.462 0.00 0.00 39.61 4.00
501 502 7.290248 TCCATTAGGAGTAGAGATTTAAGTGGG 59.710 40.741 0.00 0.00 39.61 4.61
502 503 7.290248 CCATTAGGAGTAGAGATTTAAGTGGGA 59.710 40.741 0.00 0.00 36.89 4.37
503 504 8.875168 CATTAGGAGTAGAGATTTAAGTGGGAT 58.125 37.037 0.00 0.00 0.00 3.85
504 505 6.739331 AGGAGTAGAGATTTAAGTGGGATG 57.261 41.667 0.00 0.00 0.00 3.51
505 506 6.444704 AGGAGTAGAGATTTAAGTGGGATGA 58.555 40.000 0.00 0.00 0.00 2.92
507 508 6.239458 GGAGTAGAGATTTAAGTGGGATGAGG 60.239 46.154 0.00 0.00 0.00 3.86
508 509 6.206042 AGTAGAGATTTAAGTGGGATGAGGT 58.794 40.000 0.00 0.00 0.00 3.85
509 510 7.363031 AGTAGAGATTTAAGTGGGATGAGGTA 58.637 38.462 0.00 0.00 0.00 3.08
513 514 7.844779 AGAGATTTAAGTGGGATGAGGTAGTTA 59.155 37.037 0.00 0.00 0.00 2.24
514 515 8.024145 AGATTTAAGTGGGATGAGGTAGTTAG 57.976 38.462 0.00 0.00 0.00 2.34
515 516 7.624077 AGATTTAAGTGGGATGAGGTAGTTAGT 59.376 37.037 0.00 0.00 0.00 2.24
516 517 6.786967 TTAAGTGGGATGAGGTAGTTAGTC 57.213 41.667 0.00 0.00 0.00 2.59
518 519 2.699321 GTGGGATGAGGTAGTTAGTCCC 59.301 54.545 1.32 1.32 44.43 4.46
519 520 3.042059 GGGATGAGGTAGTTAGTCCCA 57.958 52.381 3.46 0.00 43.78 4.37
520 521 2.699321 GGGATGAGGTAGTTAGTCCCAC 59.301 54.545 3.46 0.00 43.78 4.61
521 522 3.630311 GGGATGAGGTAGTTAGTCCCACT 60.630 52.174 3.46 0.00 43.78 4.00
522 523 4.031611 GGATGAGGTAGTTAGTCCCACTT 58.968 47.826 0.00 0.00 0.00 3.16
523 524 5.206587 GGATGAGGTAGTTAGTCCCACTTA 58.793 45.833 0.00 0.00 0.00 2.24
525 526 6.155737 GGATGAGGTAGTTAGTCCCACTTAAA 59.844 42.308 0.00 0.00 0.00 1.52
526 527 7.147532 GGATGAGGTAGTTAGTCCCACTTAAAT 60.148 40.741 0.00 0.00 0.00 1.40
527 528 7.179076 TGAGGTAGTTAGTCCCACTTAAATC 57.821 40.000 0.00 0.00 0.00 2.17
528 529 6.155737 TGAGGTAGTTAGTCCCACTTAAATCC 59.844 42.308 0.00 0.00 0.00 3.01
530 531 6.070366 AGGTAGTTAGTCCCACTTAAATCCAC 60.070 42.308 0.00 0.00 0.00 4.02
531 532 6.070366 GGTAGTTAGTCCCACTTAAATCCACT 60.070 42.308 0.00 0.00 0.00 4.00
532 533 6.051179 AGTTAGTCCCACTTAAATCCACTC 57.949 41.667 0.00 0.00 0.00 3.51
533 534 5.045797 AGTTAGTCCCACTTAAATCCACTCC 60.046 44.000 0.00 0.00 0.00 3.85
534 535 2.576648 AGTCCCACTTAAATCCACTCCC 59.423 50.000 0.00 0.00 0.00 4.30
536 537 2.307686 TCCCACTTAAATCCACTCCCAC 59.692 50.000 0.00 0.00 0.00 4.61
537 538 2.620627 CCCACTTAAATCCACTCCCACC 60.621 54.545 0.00 0.00 0.00 4.61
538 539 2.308866 CCACTTAAATCCACTCCCACCT 59.691 50.000 0.00 0.00 0.00 4.00
540 541 2.290960 ACTTAAATCCACTCCCACCTGC 60.291 50.000 0.00 0.00 0.00 4.85
541 542 1.367346 TAAATCCACTCCCACCTGCA 58.633 50.000 0.00 0.00 0.00 4.41
542 543 0.038744 AAATCCACTCCCACCTGCAG 59.961 55.000 6.78 6.78 0.00 4.41
543 544 2.490270 AATCCACTCCCACCTGCAGC 62.490 60.000 8.66 0.00 0.00 5.25
544 545 4.729918 CCACTCCCACCTGCAGCC 62.730 72.222 8.66 0.00 0.00 4.85
545 546 3.644606 CACTCCCACCTGCAGCCT 61.645 66.667 8.66 0.00 0.00 4.58
546 547 3.644606 ACTCCCACCTGCAGCCTG 61.645 66.667 8.66 5.38 0.00 4.85
547 548 3.324930 CTCCCACCTGCAGCCTGA 61.325 66.667 8.66 0.68 0.00 3.86
548 549 2.853542 TCCCACCTGCAGCCTGAA 60.854 61.111 8.66 0.00 0.00 3.02
549 550 2.207501 CTCCCACCTGCAGCCTGAAT 62.208 60.000 8.66 0.00 0.00 2.57
550 551 2.050350 CCCACCTGCAGCCTGAATG 61.050 63.158 8.66 0.00 0.00 2.67
551 552 1.303888 CCACCTGCAGCCTGAATGT 60.304 57.895 8.66 0.00 0.00 2.71
552 553 0.896940 CCACCTGCAGCCTGAATGTT 60.897 55.000 8.66 0.00 0.00 2.71
553 554 0.242825 CACCTGCAGCCTGAATGTTG 59.757 55.000 8.66 0.00 0.00 3.33
554 555 0.178981 ACCTGCAGCCTGAATGTTGT 60.179 50.000 8.66 0.00 0.00 3.32
555 556 0.524862 CCTGCAGCCTGAATGTTGTC 59.475 55.000 8.66 0.00 0.00 3.18
556 557 1.531423 CTGCAGCCTGAATGTTGTCT 58.469 50.000 0.00 0.00 0.00 3.41
557 558 1.884579 CTGCAGCCTGAATGTTGTCTT 59.115 47.619 0.00 0.00 0.00 3.01
558 559 2.295349 CTGCAGCCTGAATGTTGTCTTT 59.705 45.455 0.00 0.00 0.00 2.52
559 560 2.694628 TGCAGCCTGAATGTTGTCTTTT 59.305 40.909 0.00 0.00 0.00 2.27
560 561 3.054878 GCAGCCTGAATGTTGTCTTTTG 58.945 45.455 0.00 0.00 0.00 2.44
561 562 3.491447 GCAGCCTGAATGTTGTCTTTTGT 60.491 43.478 0.00 0.00 0.00 2.83
562 563 4.046462 CAGCCTGAATGTTGTCTTTTGTG 58.954 43.478 0.00 0.00 0.00 3.33
563 564 2.796593 GCCTGAATGTTGTCTTTTGTGC 59.203 45.455 0.00 0.00 0.00 4.57
564 565 3.737663 GCCTGAATGTTGTCTTTTGTGCA 60.738 43.478 0.00 0.00 0.00 4.57
565 566 3.798337 CCTGAATGTTGTCTTTTGTGCAC 59.202 43.478 10.75 10.75 0.00 4.57
566 567 3.779759 TGAATGTTGTCTTTTGTGCACC 58.220 40.909 15.69 0.00 0.00 5.01
567 568 3.194329 TGAATGTTGTCTTTTGTGCACCA 59.806 39.130 15.69 0.00 0.00 4.17
568 569 3.883830 ATGTTGTCTTTTGTGCACCAA 57.116 38.095 15.69 6.86 0.00 3.67
569 570 3.667497 TGTTGTCTTTTGTGCACCAAA 57.333 38.095 15.69 15.11 41.25 3.28
583 584 7.798596 TGTGCACCAAAAATTTAATTGATGT 57.201 28.000 15.69 0.00 0.00 3.06
584 585 8.218338 TGTGCACCAAAAATTTAATTGATGTT 57.782 26.923 15.69 0.00 0.00 2.71
585 586 9.330063 TGTGCACCAAAAATTTAATTGATGTTA 57.670 25.926 15.69 0.00 0.00 2.41
586 587 9.592720 GTGCACCAAAAATTTAATTGATGTTAC 57.407 29.630 5.22 0.00 0.00 2.50
587 588 9.330063 TGCACCAAAAATTTAATTGATGTTACA 57.670 25.926 4.50 0.00 0.00 2.41
588 589 9.592720 GCACCAAAAATTTAATTGATGTTACAC 57.407 29.630 4.50 0.00 0.00 2.90
589 590 9.790433 CACCAAAAATTTAATTGATGTTACACG 57.210 29.630 4.50 0.00 0.00 4.49
590 591 8.983724 ACCAAAAATTTAATTGATGTTACACGG 58.016 29.630 4.50 0.00 0.00 4.94
601 602 1.301087 TTACACGGGTCACAAGCGG 60.301 57.895 0.00 0.00 0.00 5.52
606 607 1.079405 CGGGTCACAAGCGGTACAT 60.079 57.895 0.00 0.00 0.00 2.29
681 682 6.210078 ACACAAACTTTTTGTCTGAAAACGA 58.790 32.000 1.25 0.00 0.00 3.85
709 710 0.311790 TCACGCGAGTTTCTACGGTT 59.688 50.000 15.93 0.00 46.40 4.44
857 860 5.660864 TCAACTCCAGGGAAAACAGAAAAAT 59.339 36.000 0.00 0.00 0.00 1.82
1128 1131 3.431766 CCGGAATCGAAGGTATTGGTTCT 60.432 47.826 0.00 0.00 39.00 3.01
1129 1132 3.802685 CGGAATCGAAGGTATTGGTTCTC 59.197 47.826 0.00 0.00 39.00 2.87
1130 1133 4.127907 GGAATCGAAGGTATTGGTTCTCC 58.872 47.826 0.00 0.00 0.00 3.71
1132 1135 2.542550 TCGAAGGTATTGGTTCTCCCA 58.457 47.619 0.00 0.00 43.27 4.37
1148 1151 0.977627 CCCATTCCCCTTCCCTTTGC 60.978 60.000 0.00 0.00 0.00 3.68
1150 1153 1.188863 CATTCCCCTTCCCTTTGCTG 58.811 55.000 0.00 0.00 0.00 4.41
1197 1201 0.034186 TTCTGCCCCTGTTAGCATGG 60.034 55.000 0.00 0.00 38.56 3.66
1198 1202 0.913934 TCTGCCCCTGTTAGCATGGA 60.914 55.000 2.38 0.00 38.56 3.41
1205 1209 2.138320 CCTGTTAGCATGGATACGCTG 58.862 52.381 0.00 0.00 39.30 5.18
1206 1210 2.138320 CTGTTAGCATGGATACGCTGG 58.862 52.381 0.00 0.00 39.30 4.85
1236 1242 2.071540 CTGAGATGCGAGCTGTTTCAA 58.928 47.619 0.00 0.00 0.00 2.69
1279 1285 7.713750 TGGTTACGGTGATTTTTGAACAATTA 58.286 30.769 0.00 0.00 0.00 1.40
1308 1314 7.807977 ATTATCGTTGCTGTTTTAGGATCAT 57.192 32.000 0.00 0.00 0.00 2.45
1343 1349 3.615224 TCTGGTTACCCCAATCGTAAC 57.385 47.619 0.00 2.90 44.65 2.50
1360 1366 5.812652 TCGTAACAGTGAATTTTGTTGGAC 58.187 37.500 0.00 5.05 37.98 4.02
1361 1367 5.354513 TCGTAACAGTGAATTTTGTTGGACA 59.645 36.000 0.00 0.00 37.98 4.02
1363 1369 6.528423 CGTAACAGTGAATTTTGTTGGACAAA 59.472 34.615 0.00 2.34 45.37 2.83
1399 1405 0.527565 ACATTTCTGGTCAATGCGCC 59.472 50.000 4.18 0.00 35.36 6.53
1405 1411 2.725811 TGGTCAATGCGCCAGAAAA 58.274 47.368 4.18 0.00 0.00 2.29
1406 1412 1.255882 TGGTCAATGCGCCAGAAAAT 58.744 45.000 4.18 0.00 0.00 1.82
1407 1413 1.067706 TGGTCAATGCGCCAGAAAATG 60.068 47.619 4.18 0.00 0.00 2.32
1408 1414 1.202114 GGTCAATGCGCCAGAAAATGA 59.798 47.619 4.18 0.00 0.00 2.57
1409 1415 2.159198 GGTCAATGCGCCAGAAAATGAT 60.159 45.455 4.18 0.00 0.00 2.45
1415 1421 0.684153 CGCCAGAAAATGATGGGGGT 60.684 55.000 0.64 0.00 43.75 4.95
1431 1439 3.052490 TGGGGGTAGGGGAAACAAATATG 60.052 47.826 0.00 0.00 0.00 1.78
1432 1440 3.052414 GGGGGTAGGGGAAACAAATATGT 60.052 47.826 0.00 0.00 43.14 2.29
1494 1629 1.270785 TGTGCATGACATCCGTCTTGT 60.271 47.619 0.00 0.00 44.93 3.16
1561 1697 5.365403 TTGGCGTACACTAAAATTCAAGG 57.635 39.130 0.00 0.00 0.00 3.61
1660 1796 3.685139 TGTGGAACATCTCTTCTCACC 57.315 47.619 0.00 0.00 45.67 4.02
1678 1814 6.346096 TCTCACCTATGTTTGCTATGGTTAC 58.654 40.000 0.00 0.00 0.00 2.50
2436 3060 1.882623 CCTTGTTGCTCCTTGGAGTTC 59.117 52.381 16.95 8.98 0.00 3.01
2540 3164 4.649218 AGTGCCATCAACCTTAAAGTGTTT 59.351 37.500 0.00 0.00 0.00 2.83
2564 3188 2.030893 CACACTGGTAACTTGCACATGG 60.031 50.000 0.00 0.00 37.61 3.66
2700 3324 3.120321 TGCAATACGTTCACCAGTCTT 57.880 42.857 0.00 0.00 0.00 3.01
2722 3346 4.072131 TGGATCTTCAGAAAAAGGAACCG 58.928 43.478 0.00 0.00 0.00 4.44
2756 3380 3.944015 GCACTCTTTAGATGCCATCACTT 59.056 43.478 7.56 0.00 33.06 3.16
2827 3451 8.260114 TCTTATGAGAATGCTTCACAACAGATA 58.740 33.333 0.00 0.00 34.05 1.98
3070 3694 5.766670 TGGCTATATGCTTTGATCAGGAAAG 59.233 40.000 0.00 0.00 42.39 2.62
3127 3751 9.290988 TGGTTGTCAGTTGTATAACATTATGTT 57.709 29.630 15.22 15.22 43.88 2.71
3264 3888 9.010029 CATCTAAGTTACCATTGTAAACAACCT 57.990 33.333 0.00 0.00 38.62 3.50
3265 3889 8.983702 TCTAAGTTACCATTGTAAACAACCTT 57.016 30.769 0.00 0.00 38.62 3.50
3610 4241 1.339929 GCGATGTTTCTGGGTGGTTTT 59.660 47.619 0.00 0.00 0.00 2.43
3710 4341 4.411869 TGTACAGATAGGAATTGGCCATCA 59.588 41.667 6.09 0.00 0.00 3.07
3807 4438 2.284190 GAGCCTGGAACTGATGTTAGC 58.716 52.381 0.00 0.00 36.39 3.09
3831 4462 9.991906 AGCCTGTATATTTTATTAAACGAGCTA 57.008 29.630 0.00 0.00 0.00 3.32
3842 4473 9.555727 TTTATTAAACGAGCTAGAATAGGCATT 57.444 29.630 0.00 0.00 39.70 3.56
3893 4524 3.067320 GCCTGAGCCTGGTAATGAAATTC 59.933 47.826 0.00 0.00 37.87 2.17
3919 4550 1.550524 TCCATGCTATCATAGACCCGC 59.449 52.381 0.00 0.00 0.00 6.13
4007 4801 2.771943 ACTAAGATGCATCCGGGAGAAA 59.228 45.455 23.06 0.00 0.00 2.52
4012 4806 0.617935 TGCATCCGGGAGAAATGTGA 59.382 50.000 0.00 0.00 0.00 3.58
4097 4894 7.318141 ACTCCTATGTGATTGCAAATTTTGAG 58.682 34.615 13.26 5.25 0.00 3.02
4252 5053 6.545666 ACAAACATTCCTGTTGTGATCAGTTA 59.454 34.615 0.00 0.00 44.83 2.24
4266 5067 7.726216 TGTGATCAGTTACTTTTCTTCAGAGA 58.274 34.615 0.00 0.00 0.00 3.10
4445 6016 5.450965 GCCATCAGGTTTGTCAAATATCAGG 60.451 44.000 0.40 2.00 37.19 3.86
4466 6047 3.264574 TGCCTTTGCACCAGTATCC 57.735 52.632 0.00 0.00 44.23 2.59
4490 6071 2.723209 CGACGTTTCCCCTTGAAAAAC 58.277 47.619 0.00 0.00 44.30 2.43
4491 6072 2.356695 CGACGTTTCCCCTTGAAAAACT 59.643 45.455 0.00 0.00 44.30 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.471233 TCAACGGATCTCTCTCATTAATGT 57.529 37.500 14.97 0.00 0.00 2.71
189 190 9.775854 CTAATGACAAAGGATCACAGATCTAAT 57.224 33.333 0.00 0.00 0.00 1.73
492 493 6.155737 GGACTAACTACCTCATCCCACTTAAA 59.844 42.308 0.00 0.00 0.00 1.52
494 495 5.206587 GGACTAACTACCTCATCCCACTTA 58.793 45.833 0.00 0.00 0.00 2.24
495 496 4.031611 GGACTAACTACCTCATCCCACTT 58.968 47.826 0.00 0.00 0.00 3.16
497 498 2.699321 GGGACTAACTACCTCATCCCAC 59.301 54.545 2.15 0.00 44.53 4.61
498 499 3.042059 GGGACTAACTACCTCATCCCA 57.958 52.381 2.15 0.00 44.53 4.37
499 500 2.699321 GTGGGACTAACTACCTCATCCC 59.301 54.545 0.00 0.00 45.24 3.85
500 501 3.644335 AGTGGGACTAACTACCTCATCC 58.356 50.000 0.00 0.00 0.00 3.51
501 502 6.786967 TTAAGTGGGACTAACTACCTCATC 57.213 41.667 0.00 0.00 0.00 2.92
502 503 7.147532 GGATTTAAGTGGGACTAACTACCTCAT 60.148 40.741 0.00 0.00 0.00 2.90
503 504 6.155737 GGATTTAAGTGGGACTAACTACCTCA 59.844 42.308 0.00 0.00 0.00 3.86
504 505 6.155737 TGGATTTAAGTGGGACTAACTACCTC 59.844 42.308 0.00 0.00 0.00 3.85
505 506 6.027482 TGGATTTAAGTGGGACTAACTACCT 58.973 40.000 0.00 0.00 0.00 3.08
507 508 6.944096 AGTGGATTTAAGTGGGACTAACTAC 58.056 40.000 0.00 0.00 0.00 2.73
508 509 6.155737 GGAGTGGATTTAAGTGGGACTAACTA 59.844 42.308 0.00 0.00 0.00 2.24
509 510 5.045797 GGAGTGGATTTAAGTGGGACTAACT 60.046 44.000 0.00 0.00 0.00 2.24
513 514 2.576648 GGGAGTGGATTTAAGTGGGACT 59.423 50.000 0.00 0.00 0.00 3.85
514 515 2.307686 TGGGAGTGGATTTAAGTGGGAC 59.692 50.000 0.00 0.00 0.00 4.46
515 516 2.307686 GTGGGAGTGGATTTAAGTGGGA 59.692 50.000 0.00 0.00 0.00 4.37
516 517 2.620627 GGTGGGAGTGGATTTAAGTGGG 60.621 54.545 0.00 0.00 0.00 4.61
518 519 3.347216 CAGGTGGGAGTGGATTTAAGTG 58.653 50.000 0.00 0.00 0.00 3.16
519 520 2.290960 GCAGGTGGGAGTGGATTTAAGT 60.291 50.000 0.00 0.00 0.00 2.24
520 521 2.290896 TGCAGGTGGGAGTGGATTTAAG 60.291 50.000 0.00 0.00 0.00 1.85
521 522 1.707989 TGCAGGTGGGAGTGGATTTAA 59.292 47.619 0.00 0.00 0.00 1.52
522 523 1.281867 CTGCAGGTGGGAGTGGATTTA 59.718 52.381 5.57 0.00 0.00 1.40
523 524 0.038744 CTGCAGGTGGGAGTGGATTT 59.961 55.000 5.57 0.00 0.00 2.17
525 526 2.976490 GCTGCAGGTGGGAGTGGAT 61.976 63.158 17.12 0.00 37.27 3.41
526 527 3.640407 GCTGCAGGTGGGAGTGGA 61.640 66.667 17.12 0.00 37.27 4.02
527 528 4.729918 GGCTGCAGGTGGGAGTGG 62.730 72.222 17.12 0.00 37.27 4.00
528 529 3.644606 AGGCTGCAGGTGGGAGTG 61.645 66.667 17.12 0.00 37.27 3.51
530 531 2.207501 ATTCAGGCTGCAGGTGGGAG 62.208 60.000 17.12 0.00 38.13 4.30
531 532 2.233566 ATTCAGGCTGCAGGTGGGA 61.234 57.895 17.12 0.00 0.00 4.37
532 533 2.050350 CATTCAGGCTGCAGGTGGG 61.050 63.158 17.12 0.00 0.00 4.61
533 534 0.896940 AACATTCAGGCTGCAGGTGG 60.897 55.000 17.12 0.00 0.00 4.61
534 535 0.242825 CAACATTCAGGCTGCAGGTG 59.757 55.000 17.12 6.96 0.00 4.00
536 537 0.524862 GACAACATTCAGGCTGCAGG 59.475 55.000 17.12 2.77 0.00 4.85
537 538 1.531423 AGACAACATTCAGGCTGCAG 58.469 50.000 10.11 10.11 0.00 4.41
538 539 1.985473 AAGACAACATTCAGGCTGCA 58.015 45.000 10.34 0.00 0.00 4.41
540 541 4.046462 CACAAAAGACAACATTCAGGCTG 58.954 43.478 8.58 8.58 0.00 4.85
541 542 3.491447 GCACAAAAGACAACATTCAGGCT 60.491 43.478 0.00 0.00 0.00 4.58
542 543 2.796593 GCACAAAAGACAACATTCAGGC 59.203 45.455 0.00 0.00 0.00 4.85
543 544 3.798337 GTGCACAAAAGACAACATTCAGG 59.202 43.478 13.17 0.00 0.00 3.86
544 545 3.798337 GGTGCACAAAAGACAACATTCAG 59.202 43.478 20.43 0.00 0.00 3.02
545 546 3.194329 TGGTGCACAAAAGACAACATTCA 59.806 39.130 20.43 0.00 0.00 2.57
546 547 3.779759 TGGTGCACAAAAGACAACATTC 58.220 40.909 20.43 0.00 0.00 2.67
547 548 3.883830 TGGTGCACAAAAGACAACATT 57.116 38.095 20.43 0.00 0.00 2.71
548 549 3.883830 TTGGTGCACAAAAGACAACAT 57.116 38.095 20.43 0.00 35.79 2.71
549 550 3.667497 TTTGGTGCACAAAAGACAACA 57.333 38.095 20.43 0.37 45.59 3.33
557 558 8.680903 ACATCAATTAAATTTTTGGTGCACAAA 58.319 25.926 20.43 11.67 46.82 2.83
558 559 8.218338 ACATCAATTAAATTTTTGGTGCACAA 57.782 26.923 20.43 3.78 37.45 3.33
559 560 7.798596 ACATCAATTAAATTTTTGGTGCACA 57.201 28.000 20.43 1.62 37.45 4.57
560 561 9.592720 GTAACATCAATTAAATTTTTGGTGCAC 57.407 29.630 8.80 8.80 37.45 4.57
561 562 9.330063 TGTAACATCAATTAAATTTTTGGTGCA 57.670 25.926 13.42 4.13 37.45 4.57
562 563 9.592720 GTGTAACATCAATTAAATTTTTGGTGC 57.407 29.630 13.42 2.09 37.45 5.01
563 564 9.790433 CGTGTAACATCAATTAAATTTTTGGTG 57.210 29.630 12.34 12.34 39.36 4.17
564 565 8.983724 CCGTGTAACATCAATTAAATTTTTGGT 58.016 29.630 0.00 0.00 35.74 3.67
565 566 8.439286 CCCGTGTAACATCAATTAAATTTTTGG 58.561 33.333 0.00 0.00 35.74 3.28
566 567 8.983724 ACCCGTGTAACATCAATTAAATTTTTG 58.016 29.630 0.00 0.00 35.74 2.44
567 568 9.198837 GACCCGTGTAACATCAATTAAATTTTT 57.801 29.630 0.00 0.00 35.74 1.94
568 569 8.361139 TGACCCGTGTAACATCAATTAAATTTT 58.639 29.630 0.00 0.00 35.74 1.82
569 570 7.810759 GTGACCCGTGTAACATCAATTAAATTT 59.189 33.333 0.00 0.00 35.74 1.82
570 571 7.040340 TGTGACCCGTGTAACATCAATTAAATT 60.040 33.333 0.00 0.00 35.74 1.82
571 572 6.431543 TGTGACCCGTGTAACATCAATTAAAT 59.568 34.615 0.00 0.00 35.74 1.40
572 573 5.763698 TGTGACCCGTGTAACATCAATTAAA 59.236 36.000 0.00 0.00 35.74 1.52
573 574 5.306394 TGTGACCCGTGTAACATCAATTAA 58.694 37.500 0.00 0.00 35.74 1.40
574 575 4.895961 TGTGACCCGTGTAACATCAATTA 58.104 39.130 0.00 0.00 35.74 1.40
575 576 3.745799 TGTGACCCGTGTAACATCAATT 58.254 40.909 0.00 0.00 35.74 2.32
576 577 3.410631 TGTGACCCGTGTAACATCAAT 57.589 42.857 0.00 0.00 35.74 2.57
577 578 2.912690 TGTGACCCGTGTAACATCAA 57.087 45.000 0.00 0.00 35.74 2.57
578 579 2.761559 CTTGTGACCCGTGTAACATCA 58.238 47.619 0.00 0.00 35.71 3.07
579 580 1.463444 GCTTGTGACCCGTGTAACATC 59.537 52.381 0.00 0.00 35.71 3.06
580 581 1.519408 GCTTGTGACCCGTGTAACAT 58.481 50.000 0.00 0.00 35.71 2.71
581 582 0.876777 CGCTTGTGACCCGTGTAACA 60.877 55.000 0.00 0.00 33.81 2.41
582 583 1.562575 CCGCTTGTGACCCGTGTAAC 61.563 60.000 0.00 0.00 0.00 2.50
583 584 1.301087 CCGCTTGTGACCCGTGTAA 60.301 57.895 0.00 0.00 0.00 2.41
584 585 1.177895 TACCGCTTGTGACCCGTGTA 61.178 55.000 0.00 0.00 0.00 2.90
585 586 2.500714 TACCGCTTGTGACCCGTGT 61.501 57.895 0.00 0.00 0.00 4.49
586 587 2.025418 GTACCGCTTGTGACCCGTG 61.025 63.158 0.00 0.00 0.00 4.94
587 588 1.823169 ATGTACCGCTTGTGACCCGT 61.823 55.000 0.00 0.00 0.00 5.28
588 589 0.672401 AATGTACCGCTTGTGACCCG 60.672 55.000 0.00 0.00 0.00 5.28
589 590 1.084289 GAATGTACCGCTTGTGACCC 58.916 55.000 0.00 0.00 0.00 4.46
590 591 1.732259 CAGAATGTACCGCTTGTGACC 59.268 52.381 0.00 0.00 0.00 4.02
660 661 8.484008 TCTTTTCGTTTTCAGACAAAAAGTTTG 58.516 29.630 0.00 0.00 35.95 2.93
664 665 6.528072 AGCTCTTTTCGTTTTCAGACAAAAAG 59.472 34.615 0.00 0.00 35.87 2.27
665 666 6.386654 AGCTCTTTTCGTTTTCAGACAAAAA 58.613 32.000 0.00 0.00 0.00 1.94
666 667 5.949735 AGCTCTTTTCGTTTTCAGACAAAA 58.050 33.333 0.00 0.00 0.00 2.44
667 668 5.560966 AGCTCTTTTCGTTTTCAGACAAA 57.439 34.783 0.00 0.00 0.00 2.83
670 671 4.964555 GTGAAGCTCTTTTCGTTTTCAGAC 59.035 41.667 0.00 0.00 0.00 3.51
671 672 4.260212 CGTGAAGCTCTTTTCGTTTTCAGA 60.260 41.667 0.00 0.00 0.00 3.27
672 673 3.962481 CGTGAAGCTCTTTTCGTTTTCAG 59.038 43.478 0.00 0.00 0.00 3.02
681 682 1.583054 AACTCGCGTGAAGCTCTTTT 58.417 45.000 16.04 0.00 45.59 2.27
709 710 4.919168 CGACGGTACAGTTCAGTAAATCAA 59.081 41.667 0.00 0.00 0.00 2.57
821 822 6.758254 TCCCTGGAGTTGATTTTTGATTTTC 58.242 36.000 0.00 0.00 0.00 2.29
822 823 6.745794 TCCCTGGAGTTGATTTTTGATTTT 57.254 33.333 0.00 0.00 0.00 1.82
823 824 6.745794 TTCCCTGGAGTTGATTTTTGATTT 57.254 33.333 0.00 0.00 0.00 2.17
837 838 7.726216 AGTTTATTTTTCTGTTTTCCCTGGAG 58.274 34.615 0.00 0.00 0.00 3.86
857 860 1.274167 AGACGGTGGCAATCGAGTTTA 59.726 47.619 16.52 0.00 0.00 2.01
1029 1032 4.988598 ACGTTGAGCAGCACCGGG 62.989 66.667 6.32 0.00 36.65 5.73
1128 1131 0.709992 CAAAGGGAAGGGGAATGGGA 59.290 55.000 0.00 0.00 0.00 4.37
1129 1132 0.977627 GCAAAGGGAAGGGGAATGGG 60.978 60.000 0.00 0.00 0.00 4.00
1130 1133 0.041684 AGCAAAGGGAAGGGGAATGG 59.958 55.000 0.00 0.00 0.00 3.16
1132 1135 0.786435 ACAGCAAAGGGAAGGGGAAT 59.214 50.000 0.00 0.00 0.00 3.01
1197 1201 4.439057 TCAGTTAAATCCACCAGCGTATC 58.561 43.478 0.00 0.00 0.00 2.24
1198 1202 4.161565 TCTCAGTTAAATCCACCAGCGTAT 59.838 41.667 0.00 0.00 0.00 3.06
1205 1209 3.531538 TCGCATCTCAGTTAAATCCACC 58.468 45.455 0.00 0.00 0.00 4.61
1206 1210 3.001736 GCTCGCATCTCAGTTAAATCCAC 59.998 47.826 0.00 0.00 0.00 4.02
1236 1242 9.047371 CCGTAACCAAATTGTTTTTAGGAAAAT 57.953 29.630 0.00 0.00 37.12 1.82
1279 1285 8.500753 TCCTAAAACAGCAACGATAATAACAT 57.499 30.769 0.00 0.00 0.00 2.71
1288 1294 5.957842 AAATGATCCTAAAACAGCAACGA 57.042 34.783 0.00 0.00 0.00 3.85
1379 1385 1.067635 GGCGCATTGACCAGAAATGTT 60.068 47.619 10.83 0.00 37.35 2.71
1389 1395 2.634982 TCATTTTCTGGCGCATTGAC 57.365 45.000 10.83 0.00 0.00 3.18
1399 1405 2.424812 CCCCTACCCCCATCATTTTCTG 60.425 54.545 0.00 0.00 0.00 3.02
1405 1411 1.231963 GTTTCCCCTACCCCCATCAT 58.768 55.000 0.00 0.00 0.00 2.45
1406 1412 0.178828 TGTTTCCCCTACCCCCATCA 60.179 55.000 0.00 0.00 0.00 3.07
1407 1413 1.004436 TTGTTTCCCCTACCCCCATC 58.996 55.000 0.00 0.00 0.00 3.51
1408 1414 1.473550 TTTGTTTCCCCTACCCCCAT 58.526 50.000 0.00 0.00 0.00 4.00
1409 1415 1.473550 ATTTGTTTCCCCTACCCCCA 58.526 50.000 0.00 0.00 0.00 4.96
1415 1421 9.535170 TTGTTCATTACATATTTGTTTCCCCTA 57.465 29.630 0.00 0.00 36.44 3.53
1431 1439 9.921637 TTCCCAAGAAAATACATTGTTCATTAC 57.078 29.630 0.00 0.00 0.00 1.89
1526 1661 5.993441 AGTGTACGCCAAAACTACACTTATT 59.007 36.000 1.98 0.00 45.36 1.40
1561 1697 6.929606 ACATAAACCTACAGTCAGTTTCAGTC 59.070 38.462 4.52 0.00 35.45 3.51
1650 1786 5.757320 CCATAGCAAACATAGGTGAGAAGAG 59.243 44.000 0.00 0.00 0.00 2.85
1651 1787 5.189736 ACCATAGCAAACATAGGTGAGAAGA 59.810 40.000 0.00 0.00 0.00 2.87
1652 1788 5.431765 ACCATAGCAAACATAGGTGAGAAG 58.568 41.667 0.00 0.00 0.00 2.85
1653 1789 5.435686 ACCATAGCAAACATAGGTGAGAA 57.564 39.130 0.00 0.00 0.00 2.87
1654 1790 5.435686 AACCATAGCAAACATAGGTGAGA 57.564 39.130 0.00 0.00 0.00 3.27
1660 1796 7.283127 AGGAACATGTAACCATAGCAAACATAG 59.717 37.037 19.54 0.00 0.00 2.23
1678 1814 4.508461 TGCACATGAGAAAAGGAACATG 57.492 40.909 0.00 0.00 43.56 3.21
1760 1901 3.998913 TCCATGCCATGAACTACTCAA 57.001 42.857 6.18 0.00 37.67 3.02
2329 2953 3.935203 ACAACATGTCATTCTTAGCCTCG 59.065 43.478 0.00 0.00 0.00 4.63
2436 3060 5.210715 GTGCAAGACAAAGTGAAATCTCTG 58.789 41.667 0.00 0.00 0.00 3.35
2540 3164 1.403679 GTGCAAGTTACCAGTGTGCAA 59.596 47.619 5.51 0.00 46.00 4.08
2700 3324 4.072131 CGGTTCCTTTTTCTGAAGATCCA 58.928 43.478 0.00 0.00 0.00 3.41
2722 3346 7.521261 GCATCTAAAGAGTGCCAAAATAGGATC 60.521 40.741 0.00 0.00 32.88 3.36
2827 3451 9.754382 GAAATGTGAAATGCCATATATGTTTCT 57.246 29.630 19.79 7.03 31.79 2.52
2954 3578 8.107095 ACTGGAATACCTTAGTTTTGCTCATTA 58.893 33.333 0.00 0.00 37.04 1.90
3070 3694 1.222113 GCTTCCTCCACCACTAGGC 59.778 63.158 0.00 0.00 39.06 3.93
3125 3749 8.931775 AGTTTTTAAGTGTCAATTTTGGTCAAC 58.068 29.630 0.00 0.00 0.00 3.18
3127 3751 9.575783 GTAGTTTTTAAGTGTCAATTTTGGTCA 57.424 29.630 0.00 0.00 0.00 4.02
3271 3895 4.264083 CCCTCCATTGCATATGGGTCTTAT 60.264 45.833 20.70 0.00 39.60 1.73
3284 3908 4.705023 AGTATTTACACAACCCTCCATTGC 59.295 41.667 0.00 0.00 0.00 3.56
3582 4213 1.935873 CCAGAAACATCGCATCATCGT 59.064 47.619 0.00 0.00 0.00 3.73
3610 4241 0.538057 ACGGTTCCGTCCTGTCACTA 60.538 55.000 11.27 0.00 38.35 2.74
3710 4341 8.611051 AGTAACTAGACCTATCTTTTGGACAT 57.389 34.615 0.00 0.00 36.29 3.06
3831 4462 5.028549 ACATTCTCGACAATGCCTATTCT 57.971 39.130 12.66 0.00 37.28 2.40
3842 4473 1.879380 CCAAGGCAAACATTCTCGACA 59.121 47.619 0.00 0.00 0.00 4.35
3893 4524 4.831674 TCTATGATAGCATGGACATGGG 57.168 45.455 13.63 0.00 37.13 4.00
4007 4801 5.048504 CAGTCTTTTGCACCAGTTATCACAT 60.049 40.000 0.00 0.00 0.00 3.21
4012 4806 5.852282 AAACAGTCTTTTGCACCAGTTAT 57.148 34.783 0.00 0.00 0.00 1.89
4102 4899 6.650390 ACATAGGCCACAAAAATGATGTTTTC 59.350 34.615 5.01 0.00 0.00 2.29
4196 4997 7.656542 TGAATGCTTGCACATTTCATAGAAAAA 59.343 29.630 4.24 0.00 40.31 1.94
4252 5053 8.916628 AGCTTAAGAATTCTCTGAAGAAAAGT 57.083 30.769 20.67 2.21 41.31 2.66
4344 5439 1.369091 ATCGCGTGGCAGAAATGACC 61.369 55.000 5.77 0.00 0.00 4.02
4413 5984 1.203052 CAAACCTGATGGCAAGCGATT 59.797 47.619 0.00 0.00 36.63 3.34
4461 6042 1.004595 GGGAAACGTCGCAAGGATAC 58.995 55.000 0.00 0.00 36.72 2.24
4466 6047 0.882927 TCAAGGGGAAACGTCGCAAG 60.883 55.000 0.00 0.00 38.45 4.01
4490 6071 1.343821 GTTGATACGTTGGCGCGAG 59.656 57.895 12.10 0.00 42.83 5.03
4491 6072 0.738063 ATGTTGATACGTTGGCGCGA 60.738 50.000 12.10 0.00 42.83 5.87


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

AutoCloner maintained by Alex Coulton.