Multiple sequence alignment - TraesCS6D01G057400

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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 TraesCS6D01G057400 chr6D 100.000 2492 0 0 1 2492 27323003 27325494 0.000000e+00 4602.0
1 TraesCS6D01G057400 chr6D 75.534 609 106 25 939 1529 27204752 27205335 2.460000e-65 259.0
2 TraesCS6D01G057400 chr6A 88.201 1712 142 30 795 2492 31049441 31047776 0.000000e+00 1988.0
3 TraesCS6D01G057400 chrUn 86.842 988 88 21 1520 2492 76769742 76768782 0.000000e+00 1066.0
4 TraesCS6D01G057400 chrUn 91.678 733 33 10 794 1524 76816879 76816173 0.000000e+00 990.0
5 TraesCS6D01G057400 chrUn 92.955 511 35 1 1 511 76817685 76817176 0.000000e+00 743.0
6 TraesCS6D01G057400 chrUn 89.965 578 37 11 1522 2095 76816144 76815584 0.000000e+00 726.0
7 TraesCS6D01G057400 chrUn 86.126 555 40 16 1559 2095 76794865 76794330 4.650000e-157 564.0
8 TraesCS6D01G057400 chrUn 98.387 186 3 0 2128 2313 76815583 76815398 6.650000e-86 327.0
9 TraesCS6D01G057400 chrUn 91.099 191 13 4 2200 2386 76789048 76788858 3.180000e-64 255.0
10 TraesCS6D01G057400 chrUn 92.568 148 7 1 794 941 76821854 76821711 2.510000e-50 209.0
11 TraesCS6D01G057400 chrUn 94.656 131 4 2 569 696 76817165 76817035 1.510000e-47 200.0
12 TraesCS6D01G057400 chrUn 90.541 148 11 2 1377 1524 76788861 76788717 2.530000e-45 193.0
13 TraesCS6D01G057400 chrUn 98.701 77 1 0 2128 2204 76794329 76794253 1.200000e-28 137.0
14 TraesCS6D01G057400 chr7A 82.123 179 23 6 15 191 63705378 63705207 7.180000e-31 145.0
15 TraesCS6D01G057400 chr7A 96.970 33 1 0 708 740 200703738 200703706 3.460000e-04 56.5
16 TraesCS6D01G057400 chr3A 85.542 83 9 3 228 309 562199568 562199488 1.590000e-12 84.2
17 TraesCS6D01G057400 chr3A 100.000 29 0 0 713 741 38139268 38139240 1.000000e-03 54.7
18 TraesCS6D01G057400 chr1D 83.951 81 10 3 229 308 233337290 233337368 9.560000e-10 75.0
19 TraesCS6D01G057400 chr2D 100.000 33 0 0 708 740 639125956 639125924 7.440000e-06 62.1
20 TraesCS6D01G057400 chr5A 100.000 32 0 0 709 740 572702062 572702031 2.680000e-05 60.2
21 TraesCS6D01G057400 chr2B 100.000 32 0 0 709 740 413670894 413670863 2.680000e-05 60.2
22 TraesCS6D01G057400 chr2B 100.000 30 0 0 711 740 35046339 35046368 3.460000e-04 56.5
23 TraesCS6D01G057400 chr7B 100.000 31 0 0 805 835 154353175 154353205 9.630000e-05 58.4
24 TraesCS6D01G057400 chr7B 96.970 33 1 0 708 740 468195983 468195951 3.460000e-04 56.5
25 TraesCS6D01G057400 chr2A 100.000 28 0 0 213 240 757026742 757026715 4.000000e-03 52.8


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 TraesCS6D01G057400 chr6D 27323003 27325494 2491 False 4602.0 4602 100.0000 1 2492 1 chr6D.!!$F2 2491
1 TraesCS6D01G057400 chr6D 27204752 27205335 583 False 259.0 259 75.5340 939 1529 1 chr6D.!!$F1 590
2 TraesCS6D01G057400 chr6A 31047776 31049441 1665 True 1988.0 1988 88.2010 795 2492 1 chr6A.!!$R1 1697
3 TraesCS6D01G057400 chrUn 76768782 76769742 960 True 1066.0 1066 86.8420 1520 2492 1 chrUn.!!$R1 972
4 TraesCS6D01G057400 chrUn 76815398 76817685 2287 True 597.2 990 93.5282 1 2313 5 chrUn.!!$R5 2312
5 TraesCS6D01G057400 chrUn 76794253 76794865 612 True 350.5 564 92.4135 1559 2204 2 chrUn.!!$R4 645

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
700 704 0.400594 ACCAGTTGCCAACTACTCCC 59.599 55.0 10.26 0.0 40.46 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2308 2480 0.534412 CCTCCTATGCCCGCTGATAG 59.466 60.0 0.0 0.0 0.0 2.08 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
26 27 6.622549 ACCAAACTCTAGAATTCGAGTAGTG 58.377 40.000 14.29 14.16 39.44 2.74
50 51 5.963594 AGGTCACTAGTTTAGGAAATCGTC 58.036 41.667 0.00 0.00 0.00 4.20
58 59 9.245962 ACTAGTTTAGGAAATCGTCGAAATATG 57.754 33.333 0.00 0.00 0.00 1.78
99 100 6.621316 TTGTTCGCTGGTCACTATTAAAAA 57.379 33.333 0.00 0.00 0.00 1.94
108 109 7.327032 GCTGGTCACTATTAAAAAGAGCAAAAG 59.673 37.037 0.00 0.00 36.44 2.27
167 168 4.225942 TCAACTGATCATAGCAGGTCCTTT 59.774 41.667 0.00 0.00 37.69 3.11
180 181 2.238646 AGGTCCTTTGACAGACACAACA 59.761 45.455 0.00 0.00 43.65 3.33
217 218 7.766738 TGAAACGTATAAGAATAGGCAATGTGA 59.233 33.333 0.00 0.00 0.00 3.58
255 256 9.442047 TTTGTTTATTTGTGAAGATTGTTGGTT 57.558 25.926 0.00 0.00 0.00 3.67
256 257 8.641499 TGTTTATTTGTGAAGATTGTTGGTTC 57.359 30.769 0.00 0.00 0.00 3.62
269 270 2.687425 TGTTGGTTCCACATGTGAACTG 59.313 45.455 27.46 10.37 0.00 3.16
271 272 0.598065 GGTTCCACATGTGAACTGGC 59.402 55.000 27.46 12.05 0.00 4.85
293 294 4.879545 GCCATCGACTCCAACCTTTATAAA 59.120 41.667 0.00 0.00 0.00 1.40
301 302 9.169592 CGACTCCAACCTTTATAAATAGGAAAA 57.830 33.333 9.74 0.00 35.45 2.29
338 339 3.191371 CCAAACCATTTGTCAGCTACCTC 59.809 47.826 0.00 0.00 38.98 3.85
352 353 1.266175 CTACCTCGTCGTGACTTGTGT 59.734 52.381 0.00 0.00 0.00 3.72
368 369 6.092944 TGACTTGTGTCGTTTCAAATTAGTGT 59.907 34.615 0.00 0.00 45.70 3.55
399 400 4.569943 CCAGCTACATTTACCATCGCTAT 58.430 43.478 0.00 0.00 0.00 2.97
419 420 6.234177 GCTATCTAACCAGTTGCCATCTATT 58.766 40.000 0.00 0.00 0.00 1.73
424 425 7.398829 TCTAACCAGTTGCCATCTATTTTGTA 58.601 34.615 0.00 0.00 0.00 2.41
469 470 2.434336 TGCCAGCTACATTTATCGTCCT 59.566 45.455 0.00 0.00 0.00 3.85
478 479 4.504858 ACATTTATCGTCCTCACTGAACC 58.495 43.478 0.00 0.00 0.00 3.62
484 485 1.873903 CGTCCTCACTGAACCTGTTGG 60.874 57.143 0.00 0.00 39.83 3.77
505 506 3.525537 GTCATCAACCTCGTCATCACAT 58.474 45.455 0.00 0.00 0.00 3.21
508 509 2.687370 TCAACCTCGTCATCACATGTG 58.313 47.619 20.18 20.18 0.00 3.21
511 512 1.066858 ACCTCGTCATCACATGTGTCC 60.067 52.381 24.63 10.45 0.00 4.02
513 514 2.354103 CCTCGTCATCACATGTGTCCTT 60.354 50.000 24.63 6.63 0.00 3.36
514 515 3.329386 CTCGTCATCACATGTGTCCTTT 58.671 45.455 24.63 4.26 0.00 3.11
515 516 3.325870 TCGTCATCACATGTGTCCTTTC 58.674 45.455 24.63 10.93 0.00 2.62
516 517 3.066380 CGTCATCACATGTGTCCTTTCA 58.934 45.455 24.63 4.64 0.00 2.69
518 519 4.024133 CGTCATCACATGTGTCCTTTCAAA 60.024 41.667 24.63 3.11 0.00 2.69
519 520 5.335113 CGTCATCACATGTGTCCTTTCAAAT 60.335 40.000 24.63 5.45 0.00 2.32
521 522 7.572910 CGTCATCACATGTGTCCTTTCAAATTA 60.573 37.037 24.63 1.60 0.00 1.40
522 523 8.081633 GTCATCACATGTGTCCTTTCAAATTAA 58.918 33.333 24.63 1.15 0.00 1.40
523 524 8.805175 TCATCACATGTGTCCTTTCAAATTAAT 58.195 29.630 24.63 3.58 0.00 1.40
524 525 8.865978 CATCACATGTGTCCTTTCAAATTAATG 58.134 33.333 24.63 11.89 0.00 1.90
525 526 7.950512 TCACATGTGTCCTTTCAAATTAATGT 58.049 30.769 24.63 0.00 0.00 2.71
526 527 8.081633 TCACATGTGTCCTTTCAAATTAATGTC 58.918 33.333 24.63 0.00 0.00 3.06
527 528 7.329226 CACATGTGTCCTTTCAAATTAATGTCC 59.671 37.037 18.03 0.00 0.00 4.02
528 529 7.233348 ACATGTGTCCTTTCAAATTAATGTCCT 59.767 33.333 0.00 0.00 0.00 3.85
529 530 6.980593 TGTGTCCTTTCAAATTAATGTCCTG 58.019 36.000 0.00 0.00 0.00 3.86
530 531 6.015519 TGTGTCCTTTCAAATTAATGTCCTGG 60.016 38.462 0.00 0.00 0.00 4.45
531 532 6.015434 GTGTCCTTTCAAATTAATGTCCTGGT 60.015 38.462 0.00 0.00 0.00 4.00
532 533 6.015519 TGTCCTTTCAAATTAATGTCCTGGTG 60.016 38.462 0.00 0.00 0.00 4.17
533 534 6.015434 GTCCTTTCAAATTAATGTCCTGGTGT 60.015 38.462 0.00 0.00 0.00 4.16
534 535 6.208599 TCCTTTCAAATTAATGTCCTGGTGTC 59.791 38.462 0.00 0.00 0.00 3.67
535 536 6.015519 CCTTTCAAATTAATGTCCTGGTGTCA 60.016 38.462 0.00 0.00 0.00 3.58
536 537 6.573664 TTCAAATTAATGTCCTGGTGTCAG 57.426 37.500 0.00 0.00 40.59 3.51
537 538 4.458989 TCAAATTAATGTCCTGGTGTCAGC 59.541 41.667 0.00 0.00 39.61 4.26
538 539 4.307032 AATTAATGTCCTGGTGTCAGCT 57.693 40.909 3.30 0.00 39.61 4.24
539 540 5.435686 AATTAATGTCCTGGTGTCAGCTA 57.564 39.130 3.30 0.00 39.61 3.32
540 541 2.770164 AATGTCCTGGTGTCAGCTAC 57.230 50.000 3.30 0.35 39.61 3.58
541 542 1.644509 ATGTCCTGGTGTCAGCTACA 58.355 50.000 3.30 5.85 39.61 2.74
542 543 1.644509 TGTCCTGGTGTCAGCTACAT 58.355 50.000 3.30 0.00 41.10 2.29
543 544 1.977854 TGTCCTGGTGTCAGCTACATT 59.022 47.619 3.30 0.00 41.10 2.71
544 545 2.371841 TGTCCTGGTGTCAGCTACATTT 59.628 45.455 3.30 0.00 41.10 2.32
545 546 3.580895 TGTCCTGGTGTCAGCTACATTTA 59.419 43.478 3.30 0.00 41.10 1.40
546 547 3.933332 GTCCTGGTGTCAGCTACATTTAC 59.067 47.826 3.30 0.00 41.10 2.01
547 548 3.055385 TCCTGGTGTCAGCTACATTTACC 60.055 47.826 3.30 0.00 41.10 2.85
548 549 3.307410 CCTGGTGTCAGCTACATTTACCA 60.307 47.826 3.30 0.00 41.10 3.25
549 550 3.670625 TGGTGTCAGCTACATTTACCAC 58.329 45.455 3.30 0.00 41.10 4.16
550 551 3.007635 GGTGTCAGCTACATTTACCACC 58.992 50.000 0.00 0.00 41.10 4.61
551 552 2.671396 GTGTCAGCTACATTTACCACCG 59.329 50.000 0.00 0.00 41.10 4.94
552 553 2.300723 TGTCAGCTACATTTACCACCGT 59.699 45.455 0.00 0.00 31.43 4.83
553 554 3.244284 TGTCAGCTACATTTACCACCGTT 60.244 43.478 0.00 0.00 31.43 4.44
554 555 3.749609 GTCAGCTACATTTACCACCGTTT 59.250 43.478 0.00 0.00 0.00 3.60
555 556 4.931002 GTCAGCTACATTTACCACCGTTTA 59.069 41.667 0.00 0.00 0.00 2.01
556 557 5.409214 GTCAGCTACATTTACCACCGTTTAA 59.591 40.000 0.00 0.00 0.00 1.52
557 558 5.996513 TCAGCTACATTTACCACCGTTTAAA 59.003 36.000 0.00 0.00 0.00 1.52
558 559 6.655848 TCAGCTACATTTACCACCGTTTAAAT 59.344 34.615 0.00 0.00 0.00 1.40
559 560 7.175293 TCAGCTACATTTACCACCGTTTAAATT 59.825 33.333 0.00 0.00 0.00 1.82
560 561 8.452534 CAGCTACATTTACCACCGTTTAAATTA 58.547 33.333 0.00 0.00 0.00 1.40
561 562 9.012161 AGCTACATTTACCACCGTTTAAATTAA 57.988 29.630 0.00 0.00 0.00 1.40
562 563 9.791820 GCTACATTTACCACCGTTTAAATTAAT 57.208 29.630 0.00 0.00 0.00 1.40
615 616 2.230660 GAGCCAGTTGCCAACTAAACT 58.769 47.619 10.26 7.77 40.46 2.66
638 642 2.348498 CGTCCTGACATGTGTTGTTTCG 60.348 50.000 1.15 0.00 39.18 3.46
643 647 4.676471 CCTGACATGTGTTGTTTCGAAATG 59.324 41.667 14.69 8.75 39.18 2.32
677 681 2.427095 GAGCAACATTTACCATCCCCAC 59.573 50.000 0.00 0.00 0.00 4.61
685 689 1.268992 TACCATCCCCACCGAACCAG 61.269 60.000 0.00 0.00 0.00 4.00
696 700 0.872388 CCGAACCAGTTGCCAACTAC 59.128 55.000 10.26 1.99 40.46 2.73
697 701 1.542547 CCGAACCAGTTGCCAACTACT 60.543 52.381 10.26 0.00 40.46 2.57
698 702 1.798813 CGAACCAGTTGCCAACTACTC 59.201 52.381 10.26 6.26 40.46 2.59
700 704 0.400594 ACCAGTTGCCAACTACTCCC 59.599 55.000 10.26 0.00 40.46 4.30
701 705 0.693049 CCAGTTGCCAACTACTCCCT 59.307 55.000 10.26 0.00 40.46 4.20
702 706 1.906574 CCAGTTGCCAACTACTCCCTA 59.093 52.381 10.26 0.00 40.46 3.53
703 707 2.304761 CCAGTTGCCAACTACTCCCTAA 59.695 50.000 10.26 0.00 40.46 2.69
705 709 2.028385 AGTTGCCAACTACTCCCTAACG 60.028 50.000 8.67 0.00 40.69 3.18
706 710 0.899720 TGCCAACTACTCCCTAACGG 59.100 55.000 0.00 0.00 0.00 4.44
707 711 0.900421 GCCAACTACTCCCTAACGGT 59.100 55.000 0.00 0.00 0.00 4.83
709 713 2.497273 GCCAACTACTCCCTAACGGTAA 59.503 50.000 0.00 0.00 0.00 2.85
711 715 4.498241 CCAACTACTCCCTAACGGTAAAC 58.502 47.826 0.00 0.00 0.00 2.01
729 733 8.743470 CGGTAAACGCTCTTATATTTGTTTAC 57.257 34.615 14.22 14.22 45.25 2.01
730 734 7.576602 CGGTAAACGCTCTTATATTTGTTTACG 59.423 37.037 15.43 9.72 46.15 3.18
731 735 8.594687 GGTAAACGCTCTTATATTTGTTTACGA 58.405 33.333 15.43 0.00 46.15 3.43
732 736 9.956797 GTAAACGCTCTTATATTTGTTTACGAA 57.043 29.630 9.24 0.00 40.64 3.85
734 738 7.230466 ACGCTCTTATATTTGTTTACGAAGG 57.770 36.000 0.00 0.00 0.00 3.46
735 739 6.257193 ACGCTCTTATATTTGTTTACGAAGGG 59.743 38.462 0.00 0.00 0.00 3.95
736 740 6.477688 CGCTCTTATATTTGTTTACGAAGGGA 59.522 38.462 0.00 0.00 0.00 4.20
749 753 8.938906 TGTTTACGAAGGGAGTATCAAAATAAC 58.061 33.333 0.00 0.00 36.25 1.89
750 754 9.159364 GTTTACGAAGGGAGTATCAAAATAACT 57.841 33.333 0.00 0.00 36.25 2.24
752 756 9.807649 TTACGAAGGGAGTATCAAAATAACTAC 57.192 33.333 0.00 0.00 36.25 2.73
754 758 6.704937 CGAAGGGAGTATCAAAATAACTACCC 59.295 42.308 0.00 0.00 36.25 3.69
759 815 7.344134 GGAGTATCAAAATAACTACCCCAACT 58.656 38.462 0.00 0.00 36.25 3.16
784 840 3.067180 AGGTGTGCAGTTTTCAGTTGATG 59.933 43.478 0.00 0.00 0.00 3.07
797 853 1.303561 TTGATGTGTCCTGGCCAGC 60.304 57.895 28.39 15.38 0.00 4.85
872 954 1.100510 CTTCTCACCACCCATGCATG 58.899 55.000 20.19 20.19 0.00 4.06
873 955 0.966875 TTCTCACCACCCATGCATGC 60.967 55.000 21.69 11.82 0.00 4.06
874 956 1.679641 CTCACCACCCATGCATGCA 60.680 57.895 25.04 25.04 0.00 3.96
875 957 1.000612 TCACCACCCATGCATGCAT 59.999 52.632 27.46 27.46 37.08 3.96
917 999 1.106944 ACAAAGGCTGAACCCCAACG 61.107 55.000 0.00 0.00 40.58 4.10
935 1018 2.954753 GCTCGTCCGCCACAACTTG 61.955 63.158 0.00 0.00 0.00 3.16
950 1033 2.595463 TTGGCACTCCACAGCAGC 60.595 61.111 0.00 0.00 43.33 5.25
959 1042 1.676967 CCACAGCAGCTCCCTTTCC 60.677 63.158 0.00 0.00 0.00 3.13
1056 1143 2.161486 GTGCGTGCTCCTCGTCATC 61.161 63.158 0.00 0.00 0.00 2.92
1161 1254 1.344438 TGGATCTGCAAAGTCGACTGT 59.656 47.619 20.85 11.54 0.00 3.55
1190 1283 3.659183 ATGCAAGGAAGAAGGCTACAT 57.341 42.857 0.00 0.00 0.00 2.29
1237 1332 3.695606 TCTGCAGCACCGACTCCC 61.696 66.667 9.47 0.00 0.00 4.30
1238 1333 4.767255 CTGCAGCACCGACTCCCC 62.767 72.222 0.00 0.00 0.00 4.81
1332 1430 5.046529 CGTTTATGGATGAACTCTCCTGAG 58.953 45.833 0.00 0.00 45.43 3.35
1434 1535 0.599728 GCGTTGGCCATTTTGCAGAA 60.600 50.000 6.09 0.00 0.00 3.02
1459 1560 1.813753 GGCGCTGCGGATTGTAAGA 60.814 57.895 24.61 0.00 0.00 2.10
1537 1669 0.798776 GAGATGTTGAACGGCTGTGG 59.201 55.000 0.00 0.00 0.00 4.17
1623 1758 1.739466 TCTCAAAGCGGCATGTTCATC 59.261 47.619 1.45 0.00 0.00 2.92
1632 1767 3.561310 GCGGCATGTTCATCTCATAAGAA 59.439 43.478 0.00 0.00 34.49 2.52
1641 1776 6.531594 TGTTCATCTCATAAGAAGCTAACACG 59.468 38.462 0.00 0.00 34.49 4.49
1732 1884 7.939039 TCAACTTTGATTAGTCAGAACCAGATT 59.061 33.333 0.00 0.00 35.39 2.40
1747 1900 4.134563 ACCAGATTAAAAACAGACACGCT 58.865 39.130 0.00 0.00 0.00 5.07
1776 1934 4.460382 GGACAGGAGAAGAAATTTGATGCA 59.540 41.667 0.00 0.00 0.00 3.96
1784 1942 8.033626 GGAGAAGAAATTTGATGCAGAATTCTT 58.966 33.333 4.86 10.52 0.00 2.52
1853 2021 0.946528 TGAGCACACACAGAATGCAC 59.053 50.000 0.00 0.00 42.53 4.57
2077 2247 0.955428 GCATCTCAGCCACCGAAACA 60.955 55.000 0.00 0.00 0.00 2.83
2096 2268 3.384168 ACATAACTGATACCTGCAGGGA 58.616 45.455 35.42 30.13 40.27 4.20
2163 2335 7.520453 GCCATCAAATTGATATCTGCGACTTTA 60.520 37.037 8.29 0.00 34.28 1.85
2308 2480 5.552870 TCTGATCCCAATAGAGGCTAAAC 57.447 43.478 0.00 0.00 0.00 2.01
2315 2487 5.012148 TCCCAATAGAGGCTAAACTATCAGC 59.988 44.000 0.00 0.00 37.05 4.26
2323 2495 2.996621 GCTAAACTATCAGCGGGCATAG 59.003 50.000 0.00 0.00 0.00 2.23
2360 2532 8.221944 TGGAGTAGGAAATAAGAAAAACCTCAA 58.778 33.333 0.00 0.00 0.00 3.02
2361 2533 8.731605 GGAGTAGGAAATAAGAAAAACCTCAAG 58.268 37.037 0.00 0.00 0.00 3.02
2363 2535 6.346477 AGGAAATAAGAAAAACCTCAAGGC 57.654 37.500 0.00 0.00 39.32 4.35
2364 2536 5.838521 AGGAAATAAGAAAAACCTCAAGGCA 59.161 36.000 0.00 0.00 39.32 4.75
2459 2640 8.097038 GTGAGTAAGGGATCATGCATCTTATTA 58.903 37.037 0.00 0.00 0.00 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 5.963594 ACGATTTCCTAAACTAGTGACCTC 58.036 41.667 0.00 0.00 0.00 3.85
42 43 4.904116 TGCCAACATATTTCGACGATTTC 58.096 39.130 0.00 0.00 0.00 2.17
50 51 3.967401 TGCATGATGCCAACATATTTCG 58.033 40.909 15.70 0.00 44.23 3.46
72 73 1.166531 AGTGACCAGCGAACAAAGGC 61.167 55.000 0.00 0.00 0.00 4.35
75 76 6.621316 TTTTAATAGTGACCAGCGAACAAA 57.379 33.333 0.00 0.00 0.00 2.83
78 79 6.476243 TCTTTTTAATAGTGACCAGCGAAC 57.524 37.500 0.00 0.00 0.00 3.95
99 100 9.066892 TGTGATCTTTTGTTATACTTTTGCTCT 57.933 29.630 0.00 0.00 0.00 4.09
108 109 5.163652 GCCCAGGTGTGATCTTTTGTTATAC 60.164 44.000 0.00 0.00 0.00 1.47
148 149 4.125703 GTCAAAGGACCTGCTATGATCAG 58.874 47.826 0.09 0.00 38.12 2.90
152 153 3.055819 GTCTGTCAAAGGACCTGCTATGA 60.056 47.826 0.00 0.00 43.65 2.15
167 168 8.628280 TCATAATTTGAAATGTTGTGTCTGTCA 58.372 29.630 0.00 0.00 0.00 3.58
255 256 0.405198 ATGGCCAGTTCACATGTGGA 59.595 50.000 25.16 15.19 32.60 4.02
256 257 0.813184 GATGGCCAGTTCACATGTGG 59.187 55.000 25.16 10.39 0.00 4.17
269 270 0.322546 AAAGGTTGGAGTCGATGGCC 60.323 55.000 0.00 0.00 0.00 5.36
271 272 7.387948 CCTATTTATAAAGGTTGGAGTCGATGG 59.612 40.741 3.94 0.00 0.00 3.51
293 294 9.713684 TTGGTGAGGATGATAAATTTTTCCTAT 57.286 29.630 0.00 0.00 36.95 2.57
301 302 7.738437 AATGGTTTGGTGAGGATGATAAATT 57.262 32.000 0.00 0.00 0.00 1.82
338 339 0.918619 AAACGACACAAGTCACGACG 59.081 50.000 0.00 0.00 45.23 5.12
352 353 6.567701 GCATCAGGAACACTAATTTGAAACGA 60.568 38.462 0.00 0.00 0.00 3.85
368 369 3.370840 AAATGTAGCTGGCATCAGGAA 57.629 42.857 0.00 0.00 41.19 3.36
399 400 6.245408 ACAAAATAGATGGCAACTGGTTAGA 58.755 36.000 7.62 0.00 37.61 2.10
469 470 2.437651 TGATGACCAACAGGTTCAGTGA 59.562 45.455 0.00 0.00 35.25 3.41
484 485 2.959516 TGTGATGACGAGGTTGATGAC 58.040 47.619 0.00 0.00 0.00 3.06
499 500 8.587608 ACATTAATTTGAAAGGACACATGTGAT 58.412 29.630 31.94 16.02 0.00 3.06
505 506 6.015519 CCAGGACATTAATTTGAAAGGACACA 60.016 38.462 0.00 0.00 0.00 3.72
508 509 6.015434 ACACCAGGACATTAATTTGAAAGGAC 60.015 38.462 0.00 0.00 0.00 3.85
511 512 6.980593 TGACACCAGGACATTAATTTGAAAG 58.019 36.000 0.00 0.00 0.00 2.62
513 514 5.048083 GCTGACACCAGGACATTAATTTGAA 60.048 40.000 0.00 0.00 40.72 2.69
514 515 4.458989 GCTGACACCAGGACATTAATTTGA 59.541 41.667 0.00 0.00 40.72 2.69
515 516 4.460382 AGCTGACACCAGGACATTAATTTG 59.540 41.667 0.00 0.00 40.72 2.32
516 517 4.666512 AGCTGACACCAGGACATTAATTT 58.333 39.130 0.00 0.00 40.72 1.82
518 519 4.225042 TGTAGCTGACACCAGGACATTAAT 59.775 41.667 0.00 0.00 40.72 1.40
519 520 3.580895 TGTAGCTGACACCAGGACATTAA 59.419 43.478 0.00 0.00 40.72 1.40
521 522 1.977854 TGTAGCTGACACCAGGACATT 59.022 47.619 0.00 0.00 40.72 2.71
522 523 1.644509 TGTAGCTGACACCAGGACAT 58.355 50.000 0.00 0.00 40.72 3.06
523 524 1.644509 ATGTAGCTGACACCAGGACA 58.355 50.000 0.00 0.00 42.17 4.02
524 525 2.770164 AATGTAGCTGACACCAGGAC 57.230 50.000 0.00 0.00 42.17 3.85
525 526 3.055385 GGTAAATGTAGCTGACACCAGGA 60.055 47.826 0.00 0.00 42.17 3.86
526 527 3.270877 GGTAAATGTAGCTGACACCAGG 58.729 50.000 0.00 0.00 42.17 4.45
527 528 3.684788 GTGGTAAATGTAGCTGACACCAG 59.315 47.826 0.00 0.00 42.17 4.00
528 529 3.558321 GGTGGTAAATGTAGCTGACACCA 60.558 47.826 0.00 0.00 44.80 4.17
529 530 3.007635 GGTGGTAAATGTAGCTGACACC 58.992 50.000 0.00 0.00 42.17 4.16
530 531 2.671396 CGGTGGTAAATGTAGCTGACAC 59.329 50.000 0.00 0.00 42.17 3.67
531 532 2.300723 ACGGTGGTAAATGTAGCTGACA 59.699 45.455 0.00 0.00 43.97 3.58
532 533 2.968675 ACGGTGGTAAATGTAGCTGAC 58.031 47.619 0.00 0.00 0.00 3.51
533 534 3.688694 AACGGTGGTAAATGTAGCTGA 57.311 42.857 0.00 0.00 0.00 4.26
534 535 5.866335 TTAAACGGTGGTAAATGTAGCTG 57.134 39.130 0.00 0.00 0.00 4.24
535 536 7.457024 AATTTAAACGGTGGTAAATGTAGCT 57.543 32.000 9.55 0.00 31.79 3.32
536 537 9.791820 ATTAATTTAAACGGTGGTAAATGTAGC 57.208 29.630 9.55 0.00 31.79 3.58
545 546 8.354426 GCACCATATATTAATTTAAACGGTGGT 58.646 33.333 20.95 13.64 40.38 4.16
546 547 7.810759 GGCACCATATATTAATTTAAACGGTGG 59.189 37.037 20.95 13.22 40.38 4.61
547 548 8.353684 TGGCACCATATATTAATTTAAACGGTG 58.646 33.333 18.19 18.19 42.40 4.94
548 549 8.466617 TGGCACCATATATTAATTTAAACGGT 57.533 30.769 0.00 0.00 0.00 4.83
549 550 9.187455 GTTGGCACCATATATTAATTTAAACGG 57.813 33.333 0.00 0.00 0.00 4.44
550 551 9.959749 AGTTGGCACCATATATTAATTTAAACG 57.040 29.630 0.00 0.00 0.00 3.60
562 563 9.899661 GATGGTAAATATAGTTGGCACCATATA 57.100 33.333 15.38 0.00 43.50 0.86
563 564 7.834181 GGATGGTAAATATAGTTGGCACCATAT 59.166 37.037 15.38 0.63 43.50 1.78
564 565 7.172342 GGATGGTAAATATAGTTGGCACCATA 58.828 38.462 15.38 0.00 43.50 2.74
565 566 6.010219 GGATGGTAAATATAGTTGGCACCAT 58.990 40.000 15.35 15.35 45.52 3.55
566 567 5.103898 TGGATGGTAAATATAGTTGGCACCA 60.104 40.000 8.14 8.14 38.82 4.17
567 568 5.240844 GTGGATGGTAAATATAGTTGGCACC 59.759 44.000 0.00 0.00 0.00 5.01
615 616 2.613026 ACAACACATGTCAGGACGAA 57.387 45.000 0.00 0.00 37.96 3.85
638 642 6.073058 TGTTGCTCACACTAGAACATCATTTC 60.073 38.462 0.00 0.00 0.00 2.17
643 647 5.869753 AATGTTGCTCACACTAGAACATC 57.130 39.130 0.00 0.00 38.61 3.06
677 681 0.872388 GTAGTTGGCAACTGGTTCGG 59.128 55.000 36.40 0.00 42.84 4.30
685 689 2.344025 CGTTAGGGAGTAGTTGGCAAC 58.656 52.381 22.48 22.48 0.00 4.17
696 700 1.475682 AGAGCGTTTACCGTTAGGGAG 59.524 52.381 0.00 0.00 43.47 4.30
697 701 1.549203 AGAGCGTTTACCGTTAGGGA 58.451 50.000 0.00 0.00 43.47 4.20
698 702 2.375173 AAGAGCGTTTACCGTTAGGG 57.625 50.000 0.00 0.00 43.47 3.53
700 704 8.123445 ACAAATATAAGAGCGTTTACCGTTAG 57.877 34.615 0.00 0.00 39.32 2.34
701 705 8.477984 AACAAATATAAGAGCGTTTACCGTTA 57.522 30.769 0.00 0.00 39.32 3.18
702 706 6.973229 ACAAATATAAGAGCGTTTACCGTT 57.027 33.333 0.00 0.00 39.32 4.44
703 707 6.973229 AACAAATATAAGAGCGTTTACCGT 57.027 33.333 0.00 0.00 39.32 4.83
705 709 8.594687 TCGTAAACAAATATAAGAGCGTTTACC 58.405 33.333 14.09 2.01 42.57 2.85
706 710 9.956797 TTCGTAAACAAATATAAGAGCGTTTAC 57.043 29.630 11.17 11.17 42.32 2.01
709 713 7.201582 CCCTTCGTAAACAAATATAAGAGCGTT 60.202 37.037 0.00 0.00 0.00 4.84
711 715 6.477688 TCCCTTCGTAAACAAATATAAGAGCG 59.522 38.462 0.00 0.00 0.00 5.03
713 717 8.943909 ACTCCCTTCGTAAACAAATATAAGAG 57.056 34.615 0.00 0.00 0.00 2.85
718 722 9.675464 TTTGATACTCCCTTCGTAAACAAATAT 57.325 29.630 0.00 0.00 30.40 1.28
719 723 9.504708 TTTTGATACTCCCTTCGTAAACAAATA 57.495 29.630 0.00 0.00 32.77 1.40
720 724 7.989416 TTTGATACTCCCTTCGTAAACAAAT 57.011 32.000 0.00 0.00 30.40 2.32
721 725 7.804843 TTTTGATACTCCCTTCGTAAACAAA 57.195 32.000 0.00 0.00 31.84 2.83
722 726 7.989416 ATTTTGATACTCCCTTCGTAAACAA 57.011 32.000 0.00 0.00 0.00 2.83
723 727 8.938906 GTTATTTTGATACTCCCTTCGTAAACA 58.061 33.333 0.00 0.00 0.00 2.83
724 728 9.159364 AGTTATTTTGATACTCCCTTCGTAAAC 57.841 33.333 0.00 0.00 0.00 2.01
726 730 9.807649 GTAGTTATTTTGATACTCCCTTCGTAA 57.192 33.333 0.00 0.00 0.00 3.18
727 731 8.416329 GGTAGTTATTTTGATACTCCCTTCGTA 58.584 37.037 0.00 0.00 0.00 3.43
728 732 7.270779 GGTAGTTATTTTGATACTCCCTTCGT 58.729 38.462 0.00 0.00 0.00 3.85
729 733 6.704937 GGGTAGTTATTTTGATACTCCCTTCG 59.295 42.308 0.00 0.00 31.82 3.79
730 734 6.996879 GGGGTAGTTATTTTGATACTCCCTTC 59.003 42.308 0.00 0.00 33.40 3.46
731 735 6.449041 TGGGGTAGTTATTTTGATACTCCCTT 59.551 38.462 0.00 0.00 37.89 3.95
732 736 5.974370 TGGGGTAGTTATTTTGATACTCCCT 59.026 40.000 0.00 0.00 37.89 4.20
733 737 6.256643 TGGGGTAGTTATTTTGATACTCCC 57.743 41.667 0.00 0.00 37.89 4.30
734 738 7.344134 AGTTGGGGTAGTTATTTTGATACTCC 58.656 38.462 0.00 0.00 38.94 3.85
735 739 8.803397 AAGTTGGGGTAGTTATTTTGATACTC 57.197 34.615 0.00 0.00 0.00 2.59
739 743 8.174757 ACCTAAAGTTGGGGTAGTTATTTTGAT 58.825 33.333 0.00 0.00 32.31 2.57
749 753 2.224670 TGCACACCTAAAGTTGGGGTAG 60.225 50.000 0.00 0.00 39.56 3.18
750 754 1.775459 TGCACACCTAAAGTTGGGGTA 59.225 47.619 0.00 0.00 39.56 3.69
751 755 0.553819 TGCACACCTAAAGTTGGGGT 59.446 50.000 0.00 0.00 42.87 4.95
752 756 1.247567 CTGCACACCTAAAGTTGGGG 58.752 55.000 0.00 0.00 32.31 4.96
754 758 4.142271 TGAAAACTGCACACCTAAAGTTGG 60.142 41.667 0.00 0.00 33.30 3.77
759 815 4.702612 TCAACTGAAAACTGCACACCTAAA 59.297 37.500 0.00 0.00 0.00 1.85
763 819 3.181487 ACATCAACTGAAAACTGCACACC 60.181 43.478 0.00 0.00 0.00 4.16
784 840 2.359230 GACAGCTGGCCAGGACAC 60.359 66.667 33.46 17.07 0.00 3.67
797 853 2.432628 GTTCGACCCGGCTGACAG 60.433 66.667 0.00 0.00 0.00 3.51
872 954 1.877637 TATGGGTGCGTGATGTATGC 58.122 50.000 0.00 0.00 41.83 3.14
873 955 4.631377 CCTTATATGGGTGCGTGATGTATG 59.369 45.833 0.00 0.00 0.00 2.39
874 956 4.323485 CCCTTATATGGGTGCGTGATGTAT 60.323 45.833 14.41 0.00 42.25 2.29
875 957 3.007506 CCCTTATATGGGTGCGTGATGTA 59.992 47.826 14.41 0.00 42.25 2.29
917 999 2.665185 AAGTTGTGGCGGACGAGC 60.665 61.111 0.00 0.00 0.00 5.03
935 1018 2.745492 GAGCTGCTGTGGAGTGCC 60.745 66.667 7.01 0.00 0.00 5.01
950 1033 3.177228 TGAGAAGAGAAGGGAAAGGGAG 58.823 50.000 0.00 0.00 0.00 4.30
959 1042 3.870419 GTGCAAGCTATGAGAAGAGAAGG 59.130 47.826 0.00 0.00 0.00 3.46
1161 1254 3.401033 TCTTCCTTGCATTTCTCGACA 57.599 42.857 0.00 0.00 0.00 4.35
1208 1301 2.203832 TGCAGACCCAGAGGCAGA 60.204 61.111 0.00 0.00 36.11 4.26
1280 1375 4.445452 AATGCAATGCAAGTAAGGTGAG 57.555 40.909 13.45 0.00 43.62 3.51
1368 1468 5.406780 ACAGACGATTCTTCTTTGTGTCATC 59.593 40.000 0.00 0.00 0.00 2.92
1369 1469 5.300752 ACAGACGATTCTTCTTTGTGTCAT 58.699 37.500 0.00 0.00 0.00 3.06
1370 1470 4.693283 ACAGACGATTCTTCTTTGTGTCA 58.307 39.130 0.00 0.00 0.00 3.58
1459 1560 0.036952 CACCTCTTGTGGCACTCGAT 60.037 55.000 19.83 0.00 41.52 3.59
1537 1669 5.637387 ACATTTTATTGATTGGTTCGGCAAC 59.363 36.000 0.00 0.00 0.00 4.17
1623 1758 8.462143 TCTTTTACGTGTTAGCTTCTTATGAG 57.538 34.615 0.00 0.00 0.00 2.90
1632 1767 6.314400 TGTTTGAGTTCTTTTACGTGTTAGCT 59.686 34.615 0.00 0.00 0.00 3.32
1641 1776 9.899226 AGATTGCTAATGTTTGAGTTCTTTTAC 57.101 29.630 0.00 0.00 0.00 2.01
1732 1884 3.252215 CCCATTCAGCGTGTCTGTTTTTA 59.748 43.478 0.00 0.00 43.32 1.52
1740 1893 1.021390 CCTGTCCCATTCAGCGTGTC 61.021 60.000 0.00 0.00 0.00 3.67
1747 1900 4.934797 ATTTCTTCTCCTGTCCCATTCA 57.065 40.909 0.00 0.00 0.00 2.57
1748 1901 5.711976 TCAAATTTCTTCTCCTGTCCCATTC 59.288 40.000 0.00 0.00 0.00 2.67
1762 1915 7.330208 CGGAAAGAATTCTGCATCAAATTTCTT 59.670 33.333 9.17 0.00 35.26 2.52
1776 1934 5.577164 CGTTGTATCTGACGGAAAGAATTCT 59.423 40.000 0.88 0.88 35.79 2.40
1784 1942 1.887854 TCCACGTTGTATCTGACGGAA 59.112 47.619 0.00 0.00 43.16 4.30
1837 1995 1.727022 GCGTGCATTCTGTGTGTGC 60.727 57.895 0.00 0.00 39.26 4.57
1853 2021 2.975410 TCAGTTGATCTTTGCTTGCG 57.025 45.000 0.00 0.00 0.00 4.85
1983 2151 1.802960 CAGTGGTCAGATGTGAAGTGC 59.197 52.381 0.00 0.00 33.27 4.40
2077 2247 5.653255 ATTTCCCTGCAGGTATCAGTTAT 57.347 39.130 30.63 9.72 36.75 1.89
2308 2480 0.534412 CCTCCTATGCCCGCTGATAG 59.466 60.000 0.00 0.00 0.00 2.08
2315 2487 1.418908 ATGAACCCCTCCTATGCCCG 61.419 60.000 0.00 0.00 0.00 6.13
2323 2495 1.132500 CCTACTCCATGAACCCCTCC 58.868 60.000 0.00 0.00 0.00 4.30
2400 2576 8.866093 TGCATGAATTTGATTAGATTCATCCAT 58.134 29.630 11.85 0.00 45.19 3.41
2429 2605 3.519107 TGCATGATCCCTTACTCACTTCA 59.481 43.478 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.