Multiple sequence alignment - TraesCS7B01G166000

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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 TraesCS7B01G166000 chr7B 100.000 3676 0 0 1 3676 228913968 228917643 0.000000e+00 6789.0
1 TraesCS7B01G166000 chr7B 95.588 68 3 0 3498 3565 228917389 228917456 3.880000e-20 110.0
2 TraesCS7B01G166000 chr7B 95.588 68 3 0 3422 3489 228917465 228917532 3.880000e-20 110.0
3 TraesCS7B01G166000 chr7B 87.778 90 9 2 647 735 322042554 322042466 1.810000e-18 104.0
4 TraesCS7B01G166000 chr7A 91.506 3002 159 32 732 3676 268868089 268865127 0.000000e+00 4043.0
5 TraesCS7B01G166000 chr7A 90.079 504 39 4 1 496 268888910 268888410 0.000000e+00 643.0
6 TraesCS7B01G166000 chr7A 95.775 71 3 0 3422 3492 268865304 268865234 8.340000e-22 115.0
7 TraesCS7B01G166000 chr7A 94.444 72 4 0 3498 3569 268865380 268865309 1.080000e-20 111.0
8 TraesCS7B01G166000 chr7D 91.350 1607 106 19 2084 3676 252239939 252241526 0.000000e+00 2167.0
9 TraesCS7B01G166000 chr7D 87.853 1276 57 28 740 2003 252238710 252239899 0.000000e+00 1408.0
10 TraesCS7B01G166000 chr7D 90.782 499 31 5 1 484 252237790 252238288 0.000000e+00 652.0
11 TraesCS7B01G166000 chr7D 94.444 72 4 0 3498 3569 252241274 252241345 1.080000e-20 111.0
12 TraesCS7B01G166000 chr7D 97.561 41 1 0 2036 2076 390899833 390899873 1.830000e-08 71.3
13 TraesCS7B01G166000 chr3A 89.773 88 8 1 649 736 330891318 330891232 1.080000e-20 111.0
14 TraesCS7B01G166000 chr3D 84.746 118 9 4 495 604 614292063 614292179 3.880000e-20 110.0
15 TraesCS7B01G166000 chr3D 86.000 100 14 0 396 495 548637129 548637228 1.400000e-19 108.0
16 TraesCS7B01G166000 chr3D 88.764 89 9 1 647 735 607700404 607700317 1.400000e-19 108.0
17 TraesCS7B01G166000 chr6B 88.764 89 9 1 647 735 125482875 125482962 1.400000e-19 108.0
18 TraesCS7B01G166000 chr6A 88.764 89 9 1 647 735 564880341 564880254 1.400000e-19 108.0
19 TraesCS7B01G166000 chr6A 82.000 100 12 2 495 588 601315721 601315820 3.040000e-11 80.5
20 TraesCS7B01G166000 chr2A 87.234 94 12 0 642 735 641080640 641080733 1.400000e-19 108.0
21 TraesCS7B01G166000 chr1B 88.764 89 9 1 647 735 77674761 77674674 1.400000e-19 108.0
22 TraesCS7B01G166000 chr6D 88.636 88 9 1 649 736 26515637 26515551 5.020000e-19 106.0
23 TraesCS7B01G166000 chr2B 87.778 90 10 1 646 735 767690689 767690601 1.810000e-18 104.0
24 TraesCS7B01G166000 chr1D 95.556 45 1 1 2033 2076 452753099 452753055 1.830000e-08 71.3
25 TraesCS7B01G166000 chr3B 94.872 39 2 0 2036 2074 12906433 12906395 1.100000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G166000 chr7B 228913968 228917643 3675 False 2336.333333 6789 97.058667 1 3676 3 chr7B.!!$F1 3675
1 TraesCS7B01G166000 chr7A 268865127 268868089 2962 True 1423.000000 4043 93.908333 732 3676 3 chr7A.!!$R2 2944
2 TraesCS7B01G166000 chr7A 268888410 268888910 500 True 643.000000 643 90.079000 1 496 1 chr7A.!!$R1 495
3 TraesCS7B01G166000 chr7D 252237790 252241526 3736 False 1084.500000 2167 91.107250 1 3676 4 chr7D.!!$F2 3675

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
770 1059 0.390124 AAGCGTCCCGTACAAGAACA 59.610 50.0 0.00 0.0 0.0 3.18 F
1870 2191 0.392461 ACATATTCCGTGTTGGCGCT 60.392 50.0 7.64 0.0 37.8 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1917 2239 0.468648 ATGTAGAGGCCGGGCTAAAC 59.531 55.0 32.93 29.03 0.0 2.01 R
3234 3597 1.328279 TGTCCTCTCTGCGTTCTTCA 58.672 50.0 0.00 0.00 0.0 3.02 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
47 48 4.041815 AGCTATGAGTGATGATGCCTGAAT 59.958 41.667 0.00 0.00 0.00 2.57
122 123 6.042638 TGAGAAATAGAGAAACAGACCCTG 57.957 41.667 0.00 0.00 37.52 4.45
145 152 2.245582 CCATACCTAACGACCTAGGGG 58.754 57.143 14.81 7.16 42.57 4.79
167 174 1.002315 GGGGGTTGTACGTTGCTTAGA 59.998 52.381 0.00 0.00 0.00 2.10
217 224 1.552337 GCAGACAAGGAGGATGAGACA 59.448 52.381 0.00 0.00 0.00 3.41
245 252 0.827368 GACGAAGGGGAGAAGCATCT 59.173 55.000 0.00 0.00 39.10 2.90
269 276 1.218047 CCGGAGATTGAAGTCGCCA 59.782 57.895 0.00 0.00 37.88 5.69
313 320 2.494777 ATCTGAGTCACCGGGGTCGA 62.495 60.000 2.12 0.00 39.00 4.20
343 350 1.602377 GAACTGAGGTTGGGTTTGTCG 59.398 52.381 0.00 0.00 35.58 4.35
408 425 1.674322 CCCGCTTGGAATCGGTGTT 60.674 57.895 1.36 0.00 43.87 3.32
437 454 9.723601 TTTTTACACCCGTATTTATTCTACAGT 57.276 29.630 0.00 0.00 0.00 3.55
488 505 2.288640 ACCGAGAAAGAAAACGACGGAT 60.289 45.455 0.00 0.00 41.09 4.18
496 513 2.094338 AGAAAACGACGGATGGAGGTAC 60.094 50.000 0.00 0.00 0.00 3.34
498 515 2.425143 AACGACGGATGGAGGTACTA 57.575 50.000 0.00 0.00 41.55 1.82
499 516 1.673168 ACGACGGATGGAGGTACTAC 58.327 55.000 0.00 0.00 41.55 2.73
509 526 3.833304 GGTACTACCTCCGTCCGG 58.167 66.667 0.00 0.00 34.73 5.14
510 527 1.224592 GGTACTACCTCCGTCCGGA 59.775 63.158 0.00 0.00 42.90 5.14
511 528 0.394352 GGTACTACCTCCGTCCGGAA 60.394 60.000 5.23 0.00 44.66 4.30
512 529 1.463674 GTACTACCTCCGTCCGGAAA 58.536 55.000 5.23 0.00 44.66 3.13
513 530 2.027385 GTACTACCTCCGTCCGGAAAT 58.973 52.381 5.23 3.48 44.66 2.17
514 531 2.442236 ACTACCTCCGTCCGGAAATA 57.558 50.000 5.23 4.45 44.66 1.40
515 532 2.027385 ACTACCTCCGTCCGGAAATAC 58.973 52.381 5.23 0.00 44.66 1.89
516 533 2.305009 CTACCTCCGTCCGGAAATACT 58.695 52.381 5.23 0.00 44.66 2.12
517 534 1.565067 ACCTCCGTCCGGAAATACTT 58.435 50.000 5.23 0.00 44.66 2.24
518 535 1.206371 ACCTCCGTCCGGAAATACTTG 59.794 52.381 5.23 0.00 44.66 3.16
519 536 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
520 537 2.268298 CTCCGTCCGGAAATACTTGTG 58.732 52.381 5.23 0.00 44.66 3.33
521 538 1.894466 TCCGTCCGGAAATACTTGTGA 59.106 47.619 5.23 0.00 42.05 3.58
522 539 2.498481 TCCGTCCGGAAATACTTGTGAT 59.502 45.455 5.23 0.00 42.05 3.06
523 540 2.607635 CCGTCCGGAAATACTTGTGATG 59.392 50.000 5.23 0.00 37.50 3.07
524 541 2.607635 CGTCCGGAAATACTTGTGATGG 59.392 50.000 5.23 0.00 0.00 3.51
525 542 3.606687 GTCCGGAAATACTTGTGATGGT 58.393 45.455 5.23 0.00 0.00 3.55
526 543 4.007659 GTCCGGAAATACTTGTGATGGTT 58.992 43.478 5.23 0.00 0.00 3.67
527 544 4.006989 TCCGGAAATACTTGTGATGGTTG 58.993 43.478 0.00 0.00 0.00 3.77
528 545 3.756434 CCGGAAATACTTGTGATGGTTGT 59.244 43.478 0.00 0.00 0.00 3.32
529 546 4.938832 CCGGAAATACTTGTGATGGTTGTA 59.061 41.667 0.00 0.00 0.00 2.41
530 547 5.588648 CCGGAAATACTTGTGATGGTTGTAT 59.411 40.000 0.00 0.00 0.00 2.29
531 548 6.238374 CCGGAAATACTTGTGATGGTTGTATC 60.238 42.308 0.00 0.00 0.00 2.24
532 549 6.538742 CGGAAATACTTGTGATGGTTGTATCT 59.461 38.462 0.00 0.00 0.00 1.98
533 550 7.709182 CGGAAATACTTGTGATGGTTGTATCTA 59.291 37.037 0.00 0.00 0.00 1.98
534 551 9.046296 GGAAATACTTGTGATGGTTGTATCTAG 57.954 37.037 0.00 0.00 0.00 2.43
535 552 9.817809 GAAATACTTGTGATGGTTGTATCTAGA 57.182 33.333 0.00 0.00 0.00 2.43
536 553 9.601217 AAATACTTGTGATGGTTGTATCTAGAC 57.399 33.333 0.00 0.00 0.00 2.59
537 554 6.859112 ACTTGTGATGGTTGTATCTAGACT 57.141 37.500 0.00 0.00 0.00 3.24
538 555 7.246171 ACTTGTGATGGTTGTATCTAGACTT 57.754 36.000 0.00 0.00 0.00 3.01
539 556 8.362464 ACTTGTGATGGTTGTATCTAGACTTA 57.638 34.615 0.00 0.00 0.00 2.24
540 557 8.982723 ACTTGTGATGGTTGTATCTAGACTTAT 58.017 33.333 0.00 0.00 0.00 1.73
541 558 9.823647 CTTGTGATGGTTGTATCTAGACTTATT 57.176 33.333 0.00 0.00 0.00 1.40
543 560 9.599866 TGTGATGGTTGTATCTAGACTTATTTG 57.400 33.333 0.00 0.00 0.00 2.32
544 561 9.817809 GTGATGGTTGTATCTAGACTTATTTGA 57.182 33.333 0.00 0.00 0.00 2.69
568 585 9.778741 TGAGTTATAGATACATTCCATTTGTCC 57.221 33.333 0.00 0.00 0.00 4.02
569 586 9.778741 GAGTTATAGATACATTCCATTTGTCCA 57.221 33.333 0.00 0.00 0.00 4.02
574 591 9.872684 ATAGATACATTCCATTTGTCCATTTCT 57.127 29.630 0.00 0.00 0.00 2.52
576 593 9.347240 AGATACATTCCATTTGTCCATTTCTAG 57.653 33.333 0.00 0.00 0.00 2.43
577 594 6.780457 ACATTCCATTTGTCCATTTCTAGG 57.220 37.500 0.00 0.00 0.00 3.02
578 595 6.493166 ACATTCCATTTGTCCATTTCTAGGA 58.507 36.000 0.00 0.00 0.00 2.94
590 607 7.843490 TCCATTTCTAGGACAAGTATTTTCG 57.157 36.000 0.00 0.00 0.00 3.46
591 608 6.821665 TCCATTTCTAGGACAAGTATTTTCGG 59.178 38.462 0.00 0.00 0.00 4.30
592 609 6.821665 CCATTTCTAGGACAAGTATTTTCGGA 59.178 38.462 0.00 0.00 0.00 4.55
593 610 7.011482 CCATTTCTAGGACAAGTATTTTCGGAG 59.989 40.741 0.00 0.00 0.00 4.63
594 611 6.845758 TTCTAGGACAAGTATTTTCGGAGA 57.154 37.500 0.00 0.00 0.00 3.71
595 612 6.845758 TCTAGGACAAGTATTTTCGGAGAA 57.154 37.500 0.00 0.00 45.90 2.87
596 613 6.864342 TCTAGGACAAGTATTTTCGGAGAAG 58.136 40.000 0.00 0.00 45.90 2.85
597 614 4.833390 AGGACAAGTATTTTCGGAGAAGG 58.167 43.478 0.00 0.00 45.90 3.46
598 615 3.939592 GGACAAGTATTTTCGGAGAAGGG 59.060 47.826 0.00 0.00 45.90 3.95
599 616 4.323257 GGACAAGTATTTTCGGAGAAGGGA 60.323 45.833 0.00 0.00 45.90 4.20
600 617 4.833390 ACAAGTATTTTCGGAGAAGGGAG 58.167 43.478 0.00 0.00 45.90 4.30
601 618 4.286291 ACAAGTATTTTCGGAGAAGGGAGT 59.714 41.667 0.00 0.00 45.90 3.85
602 619 5.482878 ACAAGTATTTTCGGAGAAGGGAGTA 59.517 40.000 0.00 0.00 45.90 2.59
603 620 6.156429 ACAAGTATTTTCGGAGAAGGGAGTAT 59.844 38.462 0.00 0.00 45.90 2.12
604 621 6.163135 AGTATTTTCGGAGAAGGGAGTATG 57.837 41.667 0.00 0.00 45.90 2.39
605 622 5.661759 AGTATTTTCGGAGAAGGGAGTATGT 59.338 40.000 0.00 0.00 45.90 2.29
606 623 6.837568 AGTATTTTCGGAGAAGGGAGTATGTA 59.162 38.462 0.00 0.00 45.90 2.29
611 628 6.158023 TCGGAGAAGGGAGTATGTATTTTC 57.842 41.667 0.00 0.00 0.00 2.29
657 859 0.815734 GTAGACTGCGAGGTGCCTAA 59.184 55.000 0.00 0.00 45.60 2.69
661 863 1.448540 CTGCGAGGTGCCTAAGGTG 60.449 63.158 0.00 0.00 45.60 4.00
666 868 4.820903 GCGAGGTGCCTAAGGTGACTTT 62.821 54.545 0.00 0.00 43.36 2.66
696 898 9.542462 AAATCTCAAAATGATATGCCATTTCAG 57.458 29.630 4.22 0.00 43.61 3.02
700 902 8.070034 TCAAAATGATATGCCATTTCAGTCTT 57.930 30.769 4.22 0.00 43.61 3.01
710 912 3.403038 CATTTCAGTCTTTCGGAGGTGT 58.597 45.455 0.00 0.00 0.00 4.16
725 927 1.368558 AGGTGTTCATAGGGGTAGGGT 59.631 52.381 0.00 0.00 0.00 4.34
729 931 1.134189 GTTCATAGGGGTAGGGTGTGC 60.134 57.143 0.00 0.00 0.00 4.57
734 993 1.378514 GGGGTAGGGTGTGCATGTG 60.379 63.158 0.00 0.00 0.00 3.21
770 1059 0.390124 AAGCGTCCCGTACAAGAACA 59.610 50.000 0.00 0.00 0.00 3.18
1195 1506 3.749064 GCGGAGGAGCTGACGACA 61.749 66.667 0.00 0.00 0.00 4.35
1251 1565 4.083862 GTGGCTCTCGGGGTGTCC 62.084 72.222 0.00 0.00 0.00 4.02
1254 1568 3.462678 GCTCTCGGGGTGTCCTCC 61.463 72.222 0.00 0.00 0.00 4.30
1263 1577 2.342648 GTGTCCTCCTCCGCGTTT 59.657 61.111 4.92 0.00 0.00 3.60
1374 1688 2.173964 GAAAATGTACGTTCGCCATGC 58.826 47.619 0.00 0.00 0.00 4.06
1382 1696 2.361104 TTCGCCATGCCCCACTTC 60.361 61.111 0.00 0.00 0.00 3.01
1450 1764 2.767394 CAAAATCCATGGAATCAGGCCA 59.233 45.455 20.67 0.00 40.24 5.36
1454 1768 1.288633 TCCATGGAATCAGGCCACAAT 59.711 47.619 13.46 0.00 38.44 2.71
1578 1892 1.351350 GGTGCTCACCCTTACCTCTTT 59.649 52.381 7.82 0.00 45.68 2.52
1579 1893 2.615747 GGTGCTCACCCTTACCTCTTTC 60.616 54.545 7.82 0.00 45.68 2.62
1584 1898 4.827835 GCTCACCCTTACCTCTTTCTTTTT 59.172 41.667 0.00 0.00 0.00 1.94
1594 1908 5.689835 ACCTCTTTCTTTTTGCTCTCTCTT 58.310 37.500 0.00 0.00 0.00 2.85
1595 1909 6.125719 ACCTCTTTCTTTTTGCTCTCTCTTT 58.874 36.000 0.00 0.00 0.00 2.52
1596 1910 6.262049 ACCTCTTTCTTTTTGCTCTCTCTTTC 59.738 38.462 0.00 0.00 0.00 2.62
1597 1911 6.292389 TCTTTCTTTTTGCTCTCTCTTTCG 57.708 37.500 0.00 0.00 0.00 3.46
1598 1912 4.474226 TTCTTTTTGCTCTCTCTTTCGC 57.526 40.909 0.00 0.00 0.00 4.70
1610 1924 1.986378 CTCTTTCGCTTCGACGATTGT 59.014 47.619 0.00 0.00 42.54 2.71
1615 1929 1.344226 CGCTTCGACGATTGTCTGCA 61.344 55.000 11.37 0.00 43.21 4.41
1619 1933 1.859383 TCGACGATTGTCTGCAAACA 58.141 45.000 11.37 0.00 43.21 2.83
1639 1953 4.632153 ACACGTAAGCTTCTTGATCACTT 58.368 39.130 0.00 0.00 45.62 3.16
1644 1958 7.219154 CACGTAAGCTTCTTGATCACTTACTAG 59.781 40.741 21.47 14.01 40.18 2.57
1645 1959 7.094291 ACGTAAGCTTCTTGATCACTTACTAGT 60.094 37.037 21.47 14.43 40.18 2.57
1646 1960 7.755822 CGTAAGCTTCTTGATCACTTACTAGTT 59.244 37.037 21.47 4.50 40.18 2.24
1648 1962 8.989653 AAGCTTCTTGATCACTTACTAGTTAC 57.010 34.615 0.00 0.00 30.26 2.50
1649 1963 8.356000 AGCTTCTTGATCACTTACTAGTTACT 57.644 34.615 0.00 0.00 30.26 2.24
1650 1964 9.463902 AGCTTCTTGATCACTTACTAGTTACTA 57.536 33.333 0.00 0.00 30.26 1.82
1654 1968 9.524496 TCTTGATCACTTACTAGTTACTAACCA 57.476 33.333 0.00 0.00 30.26 3.67
1655 1969 9.570488 CTTGATCACTTACTAGTTACTAACCAC 57.430 37.037 0.00 0.00 30.26 4.16
1814 2135 5.047306 CAGTAACACTCTTACCATGTCCTGA 60.047 44.000 0.00 0.00 31.68 3.86
1870 2191 0.392461 ACATATTCCGTGTTGGCGCT 60.392 50.000 7.64 0.00 37.80 5.92
1917 2239 3.752796 CATTGCATGCCCCTCTTTG 57.247 52.632 16.68 0.00 0.00 2.77
1921 2243 2.300956 TGCATGCCCCTCTTTGTTTA 57.699 45.000 16.68 0.00 0.00 2.01
1933 2268 0.985760 TTTGTTTAGCCCGGCCTCTA 59.014 50.000 5.55 0.00 0.00 2.43
1940 2275 1.227674 GCCCGGCCTCTACATCAAG 60.228 63.158 0.00 0.00 0.00 3.02
1983 2319 5.163923 GGAAGTGACGACTAAAATTAACCCG 60.164 44.000 0.00 0.00 0.00 5.28
2003 2339 3.935203 CCGTACAGCTGTGAATTGATCTT 59.065 43.478 29.57 0.00 0.00 2.40
2004 2340 4.033358 CCGTACAGCTGTGAATTGATCTTC 59.967 45.833 29.57 4.28 0.00 2.87
2006 2342 5.292834 CGTACAGCTGTGAATTGATCTTCAT 59.707 40.000 29.57 0.00 37.47 2.57
2020 2367 8.922058 ATTGATCTTCATTGTTTATTGACAGC 57.078 30.769 0.00 0.00 0.00 4.40
2047 2394 5.634439 TCCGCATTCATCTTCATTGTTTTTG 59.366 36.000 0.00 0.00 0.00 2.44
2069 2416 4.041938 TGATATAGCTCACCATTCATGCCA 59.958 41.667 0.00 0.00 0.00 4.92
2081 2428 0.322366 TCATGCCAAATGGTCTCGCA 60.322 50.000 0.71 0.00 37.57 5.10
2125 2472 6.879400 ACCCTTTGTTTTAATTGTAGCACAA 58.121 32.000 4.56 4.56 42.95 3.33
2164 2512 6.735130 TGCTCATCTTTATCATCTGCAATTG 58.265 36.000 0.00 0.00 0.00 2.32
2194 2544 3.164028 GCAGTTTTGCCTCGTTGTC 57.836 52.632 0.00 0.00 44.74 3.18
2303 2653 8.750515 TCTTCTCATTCATATGTTTGGCAATA 57.249 30.769 0.00 0.00 33.34 1.90
2364 2714 3.256383 TGAAAGTTGGAGGATTACGTCGA 59.744 43.478 0.00 0.00 0.00 4.20
2376 2726 5.533903 AGGATTACGTCGATTGTACATACCT 59.466 40.000 0.00 0.00 0.00 3.08
2410 2760 3.654414 AGTCTTGCCTTGTCGAGTTTAG 58.346 45.455 0.00 0.00 0.00 1.85
2484 2840 6.650427 AACTTTACCTTTTCCTCCAATGAC 57.350 37.500 0.00 0.00 0.00 3.06
2663 3019 4.553330 ATTGTTCGTACCTGGTCTTGAT 57.447 40.909 0.63 0.00 0.00 2.57
2674 3030 3.381590 CCTGGTCTTGATGACGATGAGTA 59.618 47.826 0.00 0.00 46.24 2.59
2699 3055 5.909621 AGCATCATCTTGCAACTTTACAT 57.090 34.783 0.00 0.00 45.23 2.29
2706 3062 3.503363 TCTTGCAACTTTACATGAGGCAG 59.497 43.478 0.00 0.00 0.00 4.85
2730 3086 8.509690 CAGCTGAAGAGAATGATTTTCTGTTTA 58.490 33.333 8.42 0.00 33.01 2.01
2780 3137 4.407818 TGTTTTCGGCAGCAAATTATACG 58.592 39.130 0.00 0.00 0.00 3.06
2942 3300 0.674895 AGTGTCAGATTTGCTCGCCC 60.675 55.000 0.00 0.00 0.00 6.13
3020 3380 5.539582 TCAATAAATACACGGTTCTGTGC 57.460 39.130 11.14 0.00 43.74 4.57
3042 3402 4.814147 CTTTTCCTTTTTGAGGGATCTGC 58.186 43.478 0.00 0.00 46.31 4.26
3123 3483 4.684242 GGTTTGTGCAATTAAGCCAACTAC 59.316 41.667 0.00 0.00 0.00 2.73
3133 3496 7.489113 GCAATTAAGCCAACTACTAACGTACTA 59.511 37.037 0.00 0.00 0.00 1.82
3134 3497 9.357652 CAATTAAGCCAACTACTAACGTACTAA 57.642 33.333 0.00 0.00 0.00 2.24
3150 3513 8.891671 AACGTACTAAATTGGTGAGTCTTTTA 57.108 30.769 0.00 0.00 0.00 1.52
3198 3561 6.048073 TGTCAGATTGTCTTTGTTTCTTCG 57.952 37.500 0.00 0.00 0.00 3.79
3234 3597 9.236691 CTGCTAAATACGCATCATTTTGTATTT 57.763 29.630 12.21 12.21 44.89 1.40
3320 3683 1.055849 GGCCCCAGACCAAAACAAAT 58.944 50.000 0.00 0.00 0.00 2.32
3414 3777 5.585445 CAGCTTCTTAATCAGATTGACAGCT 59.415 40.000 5.85 9.78 0.00 4.24
3419 3782 9.322773 CTTCTTAATCAGATTGACAGCTTATCA 57.677 33.333 5.85 0.00 0.00 2.15
3492 3855 0.690762 GCACCTGTAGACCCCAGAAA 59.309 55.000 0.00 0.00 31.38 2.52
3560 3923 2.224426 ACAAACATCCGCACCTGTAGAA 60.224 45.455 0.00 0.00 0.00 2.10
3565 3928 1.375523 CCGCACCTGTAGAACCCAC 60.376 63.158 0.00 0.00 0.00 4.61
3573 3936 3.201266 ACCTGTAGAACCCACAAGAACAA 59.799 43.478 0.00 0.00 0.00 2.83
3608 3972 5.242838 CAGAAGGAAGACTAGACAACTGACT 59.757 44.000 0.00 0.00 0.00 3.41
3619 3983 5.599999 AGACAACTGACTGTAACTTGAGT 57.400 39.130 0.00 0.00 0.00 3.41
3625 3989 4.218852 ACTGACTGTAACTTGAGTAGCCTC 59.781 45.833 0.00 0.00 38.27 4.70
3633 3997 0.895530 TTGAGTAGCCTCGAACCCTG 59.104 55.000 0.00 0.00 40.85 4.45
3634 3998 0.251653 TGAGTAGCCTCGAACCCTGT 60.252 55.000 0.00 0.00 40.85 4.00
3664 4028 6.232581 AGGCTATATACTTGCTGATGATCC 57.767 41.667 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.984230 TGTGATTCAGGTCTGGGTCC 59.016 55.000 0.00 0.00 0.00 4.46
47 48 3.500680 GGACGAACAAATGAAGCTGGTTA 59.499 43.478 0.00 0.00 0.00 2.85
103 104 4.327680 GTGCAGGGTCTGTTTCTCTATTT 58.672 43.478 0.00 0.00 33.43 1.40
122 123 2.035576 CCTAGGTCGTTAGGTATGGTGC 59.964 54.545 0.00 0.00 36.29 5.01
157 164 2.009774 CTCCAATGGGTCTAAGCAACG 58.990 52.381 0.00 0.00 34.93 4.10
197 204 1.552337 TGTCTCATCCTCCTTGTCTGC 59.448 52.381 0.00 0.00 0.00 4.26
217 224 2.362632 CCCTTCGTCTCCGACCCT 60.363 66.667 0.00 0.00 44.13 4.34
245 252 1.745115 CTTCAATCTCCGGCGGCAA 60.745 57.895 23.83 12.23 0.00 4.52
313 320 0.687354 ACCTCAGTTCTTGCCACGAT 59.313 50.000 0.00 0.00 0.00 3.73
343 350 2.099427 ACTAGCTCACCTTTAGCGCTAC 59.901 50.000 18.63 2.67 44.87 3.58
453 470 9.613428 TTTCTTTCTCGGTTGATAATCACATAT 57.387 29.630 0.00 0.00 0.00 1.78
463 480 3.183775 CGTCGTTTTCTTTCTCGGTTGAT 59.816 43.478 0.00 0.00 0.00 2.57
496 513 2.305009 AGTATTTCCGGACGGAGGTAG 58.695 52.381 13.64 0.00 46.06 3.18
497 514 2.428171 CAAGTATTTCCGGACGGAGGTA 59.572 50.000 13.64 8.09 46.06 3.08
498 515 1.206371 CAAGTATTTCCGGACGGAGGT 59.794 52.381 13.64 9.03 46.06 3.85
499 516 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
501 518 1.894466 TCACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
502 519 2.373540 TCACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
503 520 2.607635 CCATCACAAGTATTTCCGGACG 59.392 50.000 1.83 0.00 0.00 4.79
504 521 3.606687 ACCATCACAAGTATTTCCGGAC 58.393 45.455 1.83 0.00 0.00 4.79
505 522 3.992943 ACCATCACAAGTATTTCCGGA 57.007 42.857 0.00 0.00 0.00 5.14
506 523 3.756434 ACAACCATCACAAGTATTTCCGG 59.244 43.478 0.00 0.00 0.00 5.14
507 524 6.538742 AGATACAACCATCACAAGTATTTCCG 59.461 38.462 0.00 0.00 0.00 4.30
508 525 7.865706 AGATACAACCATCACAAGTATTTCC 57.134 36.000 0.00 0.00 0.00 3.13
509 526 9.817809 TCTAGATACAACCATCACAAGTATTTC 57.182 33.333 0.00 0.00 0.00 2.17
510 527 9.601217 GTCTAGATACAACCATCACAAGTATTT 57.399 33.333 0.00 0.00 0.00 1.40
511 528 8.982723 AGTCTAGATACAACCATCACAAGTATT 58.017 33.333 0.00 0.00 0.00 1.89
512 529 8.540507 AGTCTAGATACAACCATCACAAGTAT 57.459 34.615 0.00 0.00 0.00 2.12
513 530 7.956328 AGTCTAGATACAACCATCACAAGTA 57.044 36.000 0.00 0.00 0.00 2.24
514 531 6.859112 AGTCTAGATACAACCATCACAAGT 57.141 37.500 0.00 0.00 0.00 3.16
515 532 9.823647 AATAAGTCTAGATACAACCATCACAAG 57.176 33.333 0.00 0.00 0.00 3.16
517 534 9.599866 CAAATAAGTCTAGATACAACCATCACA 57.400 33.333 0.00 0.00 0.00 3.58
518 535 9.817809 TCAAATAAGTCTAGATACAACCATCAC 57.182 33.333 0.00 0.00 0.00 3.06
542 559 9.778741 GGACAAATGGAATGTATCTATAACTCA 57.221 33.333 0.00 0.00 0.00 3.41
543 560 9.778741 TGGACAAATGGAATGTATCTATAACTC 57.221 33.333 0.00 0.00 0.00 3.01
548 565 9.872684 AGAAATGGACAAATGGAATGTATCTAT 57.127 29.630 0.00 0.00 0.00 1.98
550 567 9.347240 CTAGAAATGGACAAATGGAATGTATCT 57.653 33.333 0.00 0.00 0.00 1.98
551 568 8.571336 CCTAGAAATGGACAAATGGAATGTATC 58.429 37.037 0.00 0.00 0.00 2.24
552 569 8.281531 TCCTAGAAATGGACAAATGGAATGTAT 58.718 33.333 0.00 0.00 0.00 2.29
553 570 7.638444 TCCTAGAAATGGACAAATGGAATGTA 58.362 34.615 0.00 0.00 0.00 2.29
554 571 6.493166 TCCTAGAAATGGACAAATGGAATGT 58.507 36.000 0.00 0.00 0.00 2.71
566 583 6.821665 CCGAAAATACTTGTCCTAGAAATGGA 59.178 38.462 0.00 0.00 0.00 3.41
567 584 6.821665 TCCGAAAATACTTGTCCTAGAAATGG 59.178 38.462 0.00 0.00 0.00 3.16
568 585 7.764443 TCTCCGAAAATACTTGTCCTAGAAATG 59.236 37.037 0.00 0.00 0.00 2.32
569 586 7.848128 TCTCCGAAAATACTTGTCCTAGAAAT 58.152 34.615 0.00 0.00 0.00 2.17
570 587 7.235935 TCTCCGAAAATACTTGTCCTAGAAA 57.764 36.000 0.00 0.00 0.00 2.52
571 588 6.845758 TCTCCGAAAATACTTGTCCTAGAA 57.154 37.500 0.00 0.00 0.00 2.10
572 589 6.127423 CCTTCTCCGAAAATACTTGTCCTAGA 60.127 42.308 0.00 0.00 0.00 2.43
573 590 6.043411 CCTTCTCCGAAAATACTTGTCCTAG 58.957 44.000 0.00 0.00 0.00 3.02
574 591 5.105064 CCCTTCTCCGAAAATACTTGTCCTA 60.105 44.000 0.00 0.00 0.00 2.94
575 592 4.323562 CCCTTCTCCGAAAATACTTGTCCT 60.324 45.833 0.00 0.00 0.00 3.85
576 593 3.939592 CCCTTCTCCGAAAATACTTGTCC 59.060 47.826 0.00 0.00 0.00 4.02
577 594 4.828829 TCCCTTCTCCGAAAATACTTGTC 58.171 43.478 0.00 0.00 0.00 3.18
578 595 4.286291 ACTCCCTTCTCCGAAAATACTTGT 59.714 41.667 0.00 0.00 0.00 3.16
579 596 4.833390 ACTCCCTTCTCCGAAAATACTTG 58.167 43.478 0.00 0.00 0.00 3.16
580 597 6.156429 ACATACTCCCTTCTCCGAAAATACTT 59.844 38.462 0.00 0.00 0.00 2.24
581 598 5.661759 ACATACTCCCTTCTCCGAAAATACT 59.338 40.000 0.00 0.00 0.00 2.12
582 599 5.915175 ACATACTCCCTTCTCCGAAAATAC 58.085 41.667 0.00 0.00 0.00 1.89
583 600 7.850935 ATACATACTCCCTTCTCCGAAAATA 57.149 36.000 0.00 0.00 0.00 1.40
584 601 6.749036 ATACATACTCCCTTCTCCGAAAAT 57.251 37.500 0.00 0.00 0.00 1.82
585 602 6.555463 AATACATACTCCCTTCTCCGAAAA 57.445 37.500 0.00 0.00 0.00 2.29
586 603 6.555463 AAATACATACTCCCTTCTCCGAAA 57.445 37.500 0.00 0.00 0.00 3.46
587 604 6.383147 AGAAAATACATACTCCCTTCTCCGAA 59.617 38.462 0.00 0.00 0.00 4.30
588 605 5.897824 AGAAAATACATACTCCCTTCTCCGA 59.102 40.000 0.00 0.00 0.00 4.55
589 606 6.163135 AGAAAATACATACTCCCTTCTCCG 57.837 41.667 0.00 0.00 0.00 4.63
595 612 9.448587 ACACCTATAAGAAAATACATACTCCCT 57.551 33.333 0.00 0.00 0.00 4.20
630 647 2.288886 ACCTCGCAGTCTACTGTTTTCC 60.289 50.000 11.54 0.00 45.45 3.13
638 655 0.815734 TTAGGCACCTCGCAGTCTAC 59.184 55.000 0.00 0.00 45.17 2.59
639 656 1.103803 CTTAGGCACCTCGCAGTCTA 58.896 55.000 0.00 0.00 45.17 2.59
641 658 1.153549 CCTTAGGCACCTCGCAGTC 60.154 63.158 0.00 0.00 45.17 3.51
642 659 1.913762 ACCTTAGGCACCTCGCAGT 60.914 57.895 0.00 0.00 45.17 4.40
644 661 1.911269 TCACCTTAGGCACCTCGCA 60.911 57.895 0.00 0.00 45.17 5.10
645 662 1.448013 GTCACCTTAGGCACCTCGC 60.448 63.158 0.00 0.00 41.28 5.03
650 852 5.761165 TTTTACAAAGTCACCTTAGGCAC 57.239 39.130 0.00 0.00 0.00 5.01
657 859 8.912988 TCATTTTGAGATTTTACAAAGTCACCT 58.087 29.630 0.00 0.00 37.32 4.00
674 876 7.713750 AGACTGAAATGGCATATCATTTTGAG 58.286 34.615 0.00 0.00 44.48 3.02
688 890 2.744202 CACCTCCGAAAGACTGAAATGG 59.256 50.000 0.00 0.00 0.00 3.16
691 893 3.118555 TGAACACCTCCGAAAGACTGAAA 60.119 43.478 0.00 0.00 0.00 2.69
692 894 2.432874 TGAACACCTCCGAAAGACTGAA 59.567 45.455 0.00 0.00 0.00 3.02
696 898 3.522553 CCTATGAACACCTCCGAAAGAC 58.477 50.000 0.00 0.00 0.00 3.01
700 902 1.200519 CCCCTATGAACACCTCCGAA 58.799 55.000 0.00 0.00 0.00 4.30
710 912 1.209621 GCACACCCTACCCCTATGAA 58.790 55.000 0.00 0.00 0.00 2.57
778 1067 3.308866 GTGTTAAATCAACGCCGCTAGAT 59.691 43.478 0.00 0.00 41.01 1.98
897 1193 0.920664 GCAAATTAAATCCGCGGTGC 59.079 50.000 27.15 20.80 0.00 5.01
898 1194 2.097466 AGAGCAAATTAAATCCGCGGTG 59.903 45.455 27.15 14.55 0.00 4.94
899 1195 2.365582 AGAGCAAATTAAATCCGCGGT 58.634 42.857 27.15 8.80 0.00 5.68
900 1196 4.378459 GGATAGAGCAAATTAAATCCGCGG 60.378 45.833 22.12 22.12 0.00 6.46
901 1197 4.213270 TGGATAGAGCAAATTAAATCCGCG 59.787 41.667 0.00 0.00 36.49 6.46
902 1198 5.239525 AGTGGATAGAGCAAATTAAATCCGC 59.760 40.000 4.88 4.88 41.94 5.54
1062 1367 2.291457 GAAGACAGGCCCTCGAGCTC 62.291 65.000 6.99 2.73 0.00 4.09
1173 1484 2.989253 TCAGCTCCTCCGCGTTGA 60.989 61.111 4.92 0.00 34.40 3.18
1177 1488 4.838486 GTCGTCAGCTCCTCCGCG 62.838 72.222 0.00 0.00 34.40 6.46
1238 1552 1.755008 GAGGAGGACACCCCGAGAG 60.755 68.421 0.00 0.00 40.87 3.20
1251 1565 2.358737 AGGCAAAACGCGGAGGAG 60.359 61.111 12.47 0.00 43.84 3.69
1254 1568 3.599792 CTGCAGGCAAAACGCGGAG 62.600 63.158 12.47 0.00 43.84 4.63
1382 1696 1.261989 CGAAATGCTGCATTCCAACG 58.738 50.000 26.40 22.54 32.43 4.10
1460 1774 1.181098 GGCAGCTGAAAAGGCAGGAA 61.181 55.000 20.43 0.00 36.41 3.36
1467 1781 2.421424 GTCACCATAGGCAGCTGAAAAG 59.579 50.000 20.43 2.48 0.00 2.27
1568 1882 6.934083 AGAGAGAGCAAAAAGAAAGAGGTAAG 59.066 38.462 0.00 0.00 0.00 2.34
1578 1892 3.733337 AGCGAAAGAGAGAGCAAAAAGA 58.267 40.909 0.00 0.00 0.00 2.52
1579 1893 4.462307 GAAGCGAAAGAGAGAGCAAAAAG 58.538 43.478 0.00 0.00 0.00 2.27
1584 1898 0.881796 TCGAAGCGAAAGAGAGAGCA 59.118 50.000 0.00 0.00 31.06 4.26
1610 1924 2.833794 AGAAGCTTACGTGTTTGCAGA 58.166 42.857 0.00 0.00 0.00 4.26
1615 1929 5.057149 AGTGATCAAGAAGCTTACGTGTTT 58.943 37.500 0.00 0.00 0.00 2.83
1619 1933 6.026947 AGTAAGTGATCAAGAAGCTTACGT 57.973 37.500 19.46 0.00 43.44 3.57
1639 1953 5.048782 CACACACGGTGGTTAGTAACTAGTA 60.049 44.000 13.48 0.00 44.04 1.82
1654 1968 0.531974 CAGCAACCTACACACACGGT 60.532 55.000 0.00 0.00 0.00 4.83
1655 1969 1.841663 GCAGCAACCTACACACACGG 61.842 60.000 0.00 0.00 0.00 4.94
1814 2135 1.283793 GCGAGCTGCACAACAACAT 59.716 52.632 1.02 0.00 45.45 2.71
1870 2191 2.355716 GCCTGCAGTAAATACCTGTCCA 60.356 50.000 13.81 0.00 0.00 4.02
1917 2239 0.468648 ATGTAGAGGCCGGGCTAAAC 59.531 55.000 32.93 29.03 0.00 2.01
1921 2243 1.689233 TTGATGTAGAGGCCGGGCT 60.689 57.895 33.40 33.40 0.00 5.19
1933 2268 1.470285 GGCATGCAAATCGCTTGATGT 60.470 47.619 21.36 0.00 46.19 3.06
1940 2275 2.123428 AGAGGGGCATGCAAATCGC 61.123 57.895 21.36 10.26 42.89 4.58
1983 2319 6.674694 ATGAAGATCAATTCACAGCTGTAC 57.325 37.500 21.20 4.01 41.76 2.90
2003 2339 3.126858 GGAGCGCTGTCAATAAACAATGA 59.873 43.478 18.48 0.00 0.00 2.57
2004 2340 3.429085 GGAGCGCTGTCAATAAACAATG 58.571 45.455 18.48 0.00 0.00 2.82
2006 2342 1.463056 CGGAGCGCTGTCAATAAACAA 59.537 47.619 18.48 0.00 0.00 2.83
2047 2394 4.582869 TGGCATGAATGGTGAGCTATATC 58.417 43.478 0.00 0.00 0.00 1.63
2069 2416 4.264253 TGAAGATGAATGCGAGACCATTT 58.736 39.130 0.00 0.00 35.67 2.32
2116 2463 9.352784 GCATGAAATTAATTTAGTTGTGCTACA 57.647 29.630 13.34 4.13 0.00 2.74
2164 2512 3.372060 GCAAAACTGCTTGTTAGTCCAC 58.628 45.455 0.00 0.00 38.03 4.02
2193 2543 9.053472 TGACAAATTTAGATTTCCTAGGGTAGA 57.947 33.333 9.46 0.00 33.25 2.59
2194 2544 9.853177 ATGACAAATTTAGATTTCCTAGGGTAG 57.147 33.333 9.46 0.00 33.25 3.18
2303 2653 5.429762 TCATCAAGTCCCTTTATCACCTGAT 59.570 40.000 0.00 0.00 38.51 2.90
2331 2681 4.697352 CCTCCAACTTTCATCGACAAGATT 59.303 41.667 7.63 0.00 37.52 2.40
2364 2714 7.253905 ACTTACTTGACCAGGTATGTACAAT 57.746 36.000 0.00 0.00 32.30 2.71
2376 2726 4.267349 GGCAAGACTACTTACTTGACCA 57.733 45.455 0.00 0.00 43.77 4.02
2410 2760 0.785979 CGTTCTTGGCATTGCTTTGC 59.214 50.000 8.82 3.20 42.01 3.68
2423 2773 7.061789 CAGCTAGTTTTGTTTTGTTTCGTTCTT 59.938 33.333 0.00 0.00 0.00 2.52
2425 2775 6.307077 ACAGCTAGTTTTGTTTTGTTTCGTTC 59.693 34.615 0.00 0.00 0.00 3.95
2484 2840 0.592637 TGAAGAAACACAGCGCATGG 59.407 50.000 11.47 0.14 0.00 3.66
2663 3019 5.973651 GATGATGCTTTTACTCATCGTCA 57.026 39.130 15.54 0.00 46.85 4.35
2674 3030 6.514947 TGTAAAGTTGCAAGATGATGCTTTT 58.485 32.000 12.42 2.60 46.54 2.27
2699 3055 1.904537 TCATTCTCTTCAGCTGCCTCA 59.095 47.619 9.47 0.00 0.00 3.86
2706 3062 9.286946 CATAAACAGAAAATCATTCTCTTCAGC 57.713 33.333 0.00 0.00 0.00 4.26
2742 3098 6.037172 GCCGAAAACAATGTCACTCTACATAT 59.963 38.462 0.00 0.00 39.16 1.78
2791 3148 8.746052 AGGTTGCTATGCACTTAATACAAATA 57.254 30.769 0.00 0.00 38.71 1.40
2942 3300 3.318839 TGAGTGCTCCATGTTCCTTTTTG 59.681 43.478 0.00 0.00 0.00 2.44
3020 3380 8.018529 ATCGCAGATCCCTCAAAAAGGAAAAG 62.019 42.308 0.00 0.00 45.99 2.27
3042 3402 4.229876 GTCTTGCAAGAAAAAGGGAATCG 58.770 43.478 29.99 0.00 36.68 3.34
3083 3443 4.098807 ACAAACCACATGTTTTGGGACTAC 59.901 41.667 21.30 0.00 44.80 2.73
3115 3475 6.591448 ACCAATTTAGTACGTTAGTAGTTGGC 59.409 38.462 15.05 0.00 37.63 4.52
3123 3483 8.530269 AAAGACTCACCAATTTAGTACGTTAG 57.470 34.615 0.00 0.00 0.00 2.34
3169 3532 5.490139 ACAAAGACAATCTGACAAGTGTG 57.510 39.130 0.00 0.00 0.00 3.82
3177 3540 6.705825 TCATCGAAGAAACAAAGACAATCTGA 59.294 34.615 0.00 0.00 43.58 3.27
3198 3561 6.169419 TGCGTATTTAGCAGCATATTCATC 57.831 37.500 0.00 0.00 40.01 2.92
3234 3597 1.328279 TGTCCTCTCTGCGTTCTTCA 58.672 50.000 0.00 0.00 0.00 3.02
3320 3683 7.448777 TGGCCTTTGTATGTACAGATTGTTTTA 59.551 33.333 3.32 0.00 37.52 1.52
3414 3777 5.106317 GCAGATTCTTCGGGTTTGTTGATAA 60.106 40.000 0.00 0.00 0.00 1.75
3419 3782 2.582052 TGCAGATTCTTCGGGTTTGTT 58.418 42.857 0.00 0.00 0.00 2.83
3492 3855 6.271488 TGCAGATTCTTCGGATTTGAAAAT 57.729 33.333 0.00 0.00 0.00 1.82
3560 3923 5.738619 AGAAAAGTTTTGTTCTTGTGGGT 57.261 34.783 5.36 0.00 29.67 4.51
3565 3928 8.028938 TCCTTCTGAAGAAAAGTTTTGTTCTTG 58.971 33.333 28.31 22.41 42.67 3.02
3597 3961 5.599999 ACTCAAGTTACAGTCAGTTGTCT 57.400 39.130 2.83 0.00 32.56 3.41
3608 3972 3.057033 GGTTCGAGGCTACTCAAGTTACA 60.057 47.826 0.00 0.00 44.17 2.41
3619 3983 6.363065 CCTATATATACAGGGTTCGAGGCTA 58.637 44.000 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.