Multiple sequence alignment - TraesCS5A01G252400

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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 TraesCS5A01G252400 chr5A 100.000 3194 0 0 1 3194 468803965 468807158 0.000000e+00 5899.0
1 TraesCS5A01G252400 chr5A 90.570 456 34 5 1387 1833 468805309 468805764 2.120000e-166 595.0
2 TraesCS5A01G252400 chr5A 90.570 456 34 5 1345 1800 468805351 468805797 2.120000e-166 595.0
3 TraesCS5A01G252400 chr5A 87.527 465 38 13 1389 1834 468805269 468805732 1.310000e-143 520.0
4 TraesCS5A01G252400 chr5A 87.527 465 38 13 1305 1768 468805353 468805798 1.310000e-143 520.0
5 TraesCS5A01G252400 chr5A 95.652 276 12 0 1559 1834 468805424 468805699 8.130000e-121 444.0
6 TraesCS5A01G252400 chr5A 95.370 108 5 0 1463 1570 468805691 468805798 4.240000e-39 172.0
7 TraesCS5A01G252400 chr5A 94.667 75 4 0 1463 1537 468805724 468805798 2.010000e-22 117.0
8 TraesCS5A01G252400 chr5B 92.985 1568 67 21 1657 3194 433799820 433801374 0.000000e+00 2246.0
9 TraesCS5A01G252400 chr5B 95.661 945 38 2 726 1669 433798490 433799432 0.000000e+00 1515.0
10 TraesCS5A01G252400 chr5B 89.815 540 53 1 1 540 690991585 690992122 0.000000e+00 691.0
11 TraesCS5A01G252400 chr5B 89.834 541 49 3 1 540 581833699 581833164 0.000000e+00 689.0
12 TraesCS5A01G252400 chr5B 97.523 323 8 0 1628 1950 433799226 433799548 1.290000e-153 553.0
13 TraesCS5A01G252400 chr5D 93.840 1250 59 9 1387 2620 366502130 366503377 0.000000e+00 1866.0
14 TraesCS5A01G252400 chr5D 95.907 1075 42 1 726 1800 366501513 366502585 0.000000e+00 1740.0
15 TraesCS5A01G252400 chr5D 89.858 424 34 5 1345 1768 366502172 366502586 1.300000e-148 536.0
16 TraesCS5A01G252400 chr5D 86.910 466 39 15 1389 1834 366502090 366502553 1.320000e-138 503.0
17 TraesCS5A01G252400 chr7D 97.222 540 15 0 1 540 369382502 369383041 0.000000e+00 915.0
18 TraesCS5A01G252400 chr7D 89.074 540 59 0 1 540 159650779 159651318 0.000000e+00 671.0
19 TraesCS5A01G252400 chr7A 94.981 538 27 0 1 538 229837173 229836636 0.000000e+00 845.0
20 TraesCS5A01G252400 chr7A 96.970 33 0 1 2713 2744 725442933 725442965 2.000000e-03 54.7
21 TraesCS5A01G252400 chr3B 94.259 540 20 2 1 540 616306412 616306940 0.000000e+00 815.0
22 TraesCS5A01G252400 chr2A 90.556 540 51 0 1 540 362431192 362430653 0.000000e+00 715.0
23 TraesCS5A01G252400 chr4D 89.834 541 53 2 1 540 196238492 196239031 0.000000e+00 693.0
24 TraesCS5A01G252400 chr1D 88.764 534 59 1 7 540 248252180 248251648 0.000000e+00 652.0
25 TraesCS5A01G252400 chr2B 89.815 108 9 2 2007 2112 682194417 682194524 1.550000e-28 137.0
26 TraesCS5A01G252400 chr2B 92.222 90 5 2 2062 2150 682194559 682194647 3.340000e-25 126.0
27 TraesCS5A01G252400 chr2B 100.000 29 0 0 2718 2746 77774421 77774393 2.000000e-03 54.7
28 TraesCS5A01G252400 chr4B 97.143 35 0 1 2713 2746 147699458 147699424 1.240000e-04 58.4
29 TraesCS5A01G252400 chr2D 97.143 35 0 1 2713 2746 590937989 590937955 1.240000e-04 58.4
30 TraesCS5A01G252400 chr2D 100.000 29 0 0 2718 2746 597962526 597962498 2.000000e-03 54.7
31 TraesCS5A01G252400 chr2D 100.000 29 0 0 2718 2746 641974768 641974740 2.000000e-03 54.7
32 TraesCS5A01G252400 chr1B 100.000 30 0 0 2717 2746 569514600 569514571 4.450000e-04 56.5
33 TraesCS5A01G252400 chr7B 100.000 29 0 0 2718 2746 428922178 428922150 2.000000e-03 54.7


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 TraesCS5A01G252400 chr5A 468803965 468807158 3193 False 1107.75 5899 92.735375 1 3194 8 chr5A.!!$F1 3193
1 TraesCS5A01G252400 chr5B 433798490 433801374 2884 False 1438.00 2246 95.389667 726 3194 3 chr5B.!!$F2 2468
2 TraesCS5A01G252400 chr5B 690991585 690992122 537 False 691.00 691 89.815000 1 540 1 chr5B.!!$F1 539
3 TraesCS5A01G252400 chr5B 581833164 581833699 535 True 689.00 689 89.834000 1 540 1 chr5B.!!$R1 539
4 TraesCS5A01G252400 chr5D 366501513 366503377 1864 False 1161.25 1866 91.628750 726 2620 4 chr5D.!!$F1 1894
5 TraesCS5A01G252400 chr7D 369382502 369383041 539 False 915.00 915 97.222000 1 540 1 chr7D.!!$F2 539
6 TraesCS5A01G252400 chr7D 159650779 159651318 539 False 671.00 671 89.074000 1 540 1 chr7D.!!$F1 539
7 TraesCS5A01G252400 chr7A 229836636 229837173 537 True 845.00 845 94.981000 1 538 1 chr7A.!!$R1 537
8 TraesCS5A01G252400 chr3B 616306412 616306940 528 False 815.00 815 94.259000 1 540 1 chr3B.!!$F1 539
9 TraesCS5A01G252400 chr2A 362430653 362431192 539 True 715.00 715 90.556000 1 540 1 chr2A.!!$R1 539
10 TraesCS5A01G252400 chr4D 196238492 196239031 539 False 693.00 693 89.834000 1 540 1 chr4D.!!$F1 539
11 TraesCS5A01G252400 chr1D 248251648 248252180 532 True 652.00 652 88.764000 7 540 1 chr1D.!!$R1 533

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
547 558 0.31777 CGTGCCATTTGCGTTTGAGT 60.318 50.0 0.0 0.0 45.6 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2244 2656 0.539051 ATTGCCCTCCAGAGTTCGAG 59.461 55.0 0.0 0.0 0.0 4.04 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
41 42 1.747367 CTCGTCCTCGGTCTCTGCT 60.747 63.158 0.00 0.00 37.69 4.24
87 88 4.892934 TGGCAAAGTTCACTTTAAGACCAT 59.107 37.500 4.61 0.00 43.72 3.55
255 266 1.429148 CGCCTTCACAACGATAGCCC 61.429 60.000 0.00 0.00 42.67 5.19
456 467 4.821805 ACACTTCGAACAAGAATGTCCATT 59.178 37.500 0.00 0.00 39.40 3.16
540 551 1.153978 AATGAGCGTGCCATTTGCG 60.154 52.632 3.66 0.00 45.60 4.85
541 552 1.865788 AATGAGCGTGCCATTTGCGT 61.866 50.000 3.66 0.00 45.60 5.24
542 553 1.865788 ATGAGCGTGCCATTTGCGTT 61.866 50.000 0.00 0.00 45.60 4.84
543 554 1.371635 GAGCGTGCCATTTGCGTTT 60.372 52.632 0.00 0.00 45.60 3.60
544 555 1.608093 GAGCGTGCCATTTGCGTTTG 61.608 55.000 0.00 0.00 45.60 2.93
545 556 1.659954 GCGTGCCATTTGCGTTTGA 60.660 52.632 0.00 0.00 45.60 2.69
546 557 1.608093 GCGTGCCATTTGCGTTTGAG 61.608 55.000 0.00 0.00 45.60 3.02
547 558 0.317770 CGTGCCATTTGCGTTTGAGT 60.318 50.000 0.00 0.00 45.60 3.41
548 559 1.851658 GTGCCATTTGCGTTTGAGTT 58.148 45.000 0.00 0.00 45.60 3.01
549 560 2.603412 CGTGCCATTTGCGTTTGAGTTA 60.603 45.455 0.00 0.00 45.60 2.24
550 561 2.724174 GTGCCATTTGCGTTTGAGTTAC 59.276 45.455 0.00 0.00 45.60 2.50
551 562 2.359214 TGCCATTTGCGTTTGAGTTACA 59.641 40.909 0.00 0.00 45.60 2.41
552 563 2.724174 GCCATTTGCGTTTGAGTTACAC 59.276 45.455 0.00 0.00 0.00 2.90
553 564 3.793801 GCCATTTGCGTTTGAGTTACACA 60.794 43.478 0.00 0.00 0.00 3.72
554 565 3.974401 CCATTTGCGTTTGAGTTACACAG 59.026 43.478 0.00 0.00 0.00 3.66
555 566 3.684103 TTTGCGTTTGAGTTACACAGG 57.316 42.857 0.00 0.00 0.00 4.00
556 567 1.588674 TGCGTTTGAGTTACACAGGG 58.411 50.000 0.00 0.00 0.00 4.45
557 568 1.134340 TGCGTTTGAGTTACACAGGGT 60.134 47.619 0.00 0.00 0.00 4.34
558 569 1.944709 GCGTTTGAGTTACACAGGGTT 59.055 47.619 0.00 0.00 0.00 4.11
559 570 2.356695 GCGTTTGAGTTACACAGGGTTT 59.643 45.455 0.00 0.00 0.00 3.27
560 571 3.790789 GCGTTTGAGTTACACAGGGTTTG 60.791 47.826 0.00 0.00 0.00 2.93
561 572 3.242936 CGTTTGAGTTACACAGGGTTTGG 60.243 47.826 0.00 0.00 0.00 3.28
562 573 1.975660 TGAGTTACACAGGGTTTGGC 58.024 50.000 0.00 0.00 0.00 4.52
563 574 1.493022 TGAGTTACACAGGGTTTGGCT 59.507 47.619 0.00 0.00 0.00 4.75
564 575 1.880027 GAGTTACACAGGGTTTGGCTG 59.120 52.381 0.00 0.00 0.00 4.85
565 576 1.493022 AGTTACACAGGGTTTGGCTGA 59.507 47.619 0.00 0.00 0.00 4.26
566 577 2.092103 AGTTACACAGGGTTTGGCTGAA 60.092 45.455 0.00 0.00 0.00 3.02
567 578 2.890945 GTTACACAGGGTTTGGCTGAAT 59.109 45.455 0.00 0.00 0.00 2.57
568 579 1.331214 ACACAGGGTTTGGCTGAATG 58.669 50.000 0.00 0.00 0.00 2.67
569 580 1.133513 ACACAGGGTTTGGCTGAATGA 60.134 47.619 0.00 0.00 0.00 2.57
570 581 1.542915 CACAGGGTTTGGCTGAATGAG 59.457 52.381 0.00 0.00 0.00 2.90
580 591 3.483954 CTGAATGAGCACCCCGAAT 57.516 52.632 0.00 0.00 0.00 3.34
581 592 1.019673 CTGAATGAGCACCCCGAATG 58.980 55.000 0.00 0.00 0.00 2.67
582 593 0.327924 TGAATGAGCACCCCGAATGT 59.672 50.000 0.00 0.00 0.00 2.71
583 594 1.557371 TGAATGAGCACCCCGAATGTA 59.443 47.619 0.00 0.00 0.00 2.29
584 595 2.172505 TGAATGAGCACCCCGAATGTAT 59.827 45.455 0.00 0.00 0.00 2.29
585 596 3.214328 GAATGAGCACCCCGAATGTATT 58.786 45.455 0.00 0.00 0.00 1.89
586 597 2.325583 TGAGCACCCCGAATGTATTC 57.674 50.000 0.00 0.00 0.00 1.75
587 598 1.837439 TGAGCACCCCGAATGTATTCT 59.163 47.619 3.40 0.00 34.69 2.40
588 599 2.213499 GAGCACCCCGAATGTATTCTG 58.787 52.381 3.40 0.00 34.69 3.02
589 600 0.663153 GCACCCCGAATGTATTCTGC 59.337 55.000 3.40 2.77 34.69 4.26
590 601 2.016604 GCACCCCGAATGTATTCTGCA 61.017 52.381 10.06 0.00 35.55 4.41
591 602 2.364632 CACCCCGAATGTATTCTGCAA 58.635 47.619 3.40 0.00 34.69 4.08
592 603 2.355756 CACCCCGAATGTATTCTGCAAG 59.644 50.000 3.40 0.00 34.69 4.01
593 604 2.026262 ACCCCGAATGTATTCTGCAAGT 60.026 45.455 3.40 0.00 34.69 3.16
594 605 3.016736 CCCCGAATGTATTCTGCAAGTT 58.983 45.455 3.40 0.00 34.69 2.66
595 606 3.181497 CCCCGAATGTATTCTGCAAGTTG 60.181 47.826 0.00 0.00 34.69 3.16
596 607 3.440173 CCCGAATGTATTCTGCAAGTTGT 59.560 43.478 4.48 0.00 34.69 3.32
597 608 4.634004 CCCGAATGTATTCTGCAAGTTGTA 59.366 41.667 4.48 0.00 34.69 2.41
598 609 5.296780 CCCGAATGTATTCTGCAAGTTGTAT 59.703 40.000 4.48 0.00 34.69 2.29
599 610 6.422223 CCGAATGTATTCTGCAAGTTGTATC 58.578 40.000 4.48 0.00 34.69 2.24
600 611 6.037062 CCGAATGTATTCTGCAAGTTGTATCA 59.963 38.462 4.48 0.00 34.69 2.15
601 612 7.121911 CGAATGTATTCTGCAAGTTGTATCAG 58.878 38.462 4.48 3.82 34.69 2.90
602 613 7.010460 CGAATGTATTCTGCAAGTTGTATCAGA 59.990 37.037 4.48 6.19 34.69 3.27
603 614 8.743085 AATGTATTCTGCAAGTTGTATCAGAT 57.257 30.769 11.09 6.09 35.74 2.90
604 615 7.543947 TGTATTCTGCAAGTTGTATCAGATG 57.456 36.000 11.09 0.00 35.74 2.90
605 616 7.330262 TGTATTCTGCAAGTTGTATCAGATGA 58.670 34.615 11.09 0.90 35.74 2.92
606 617 7.823799 TGTATTCTGCAAGTTGTATCAGATGAA 59.176 33.333 11.09 3.77 35.74 2.57
607 618 7.692460 ATTCTGCAAGTTGTATCAGATGAAA 57.308 32.000 11.09 0.04 35.74 2.69
608 619 7.692460 TTCTGCAAGTTGTATCAGATGAAAT 57.308 32.000 11.09 0.00 35.74 2.17
609 620 7.312657 TCTGCAAGTTGTATCAGATGAAATC 57.687 36.000 4.48 0.00 38.53 2.17
610 621 6.317140 TCTGCAAGTTGTATCAGATGAAATCC 59.683 38.462 4.48 0.00 38.91 3.01
611 622 8.545984 TCTGCAAGTTGTATCAGATGAAATCCC 61.546 40.741 4.48 0.00 38.91 3.85
629 640 3.864789 CCCTAGCATGGGTTGAATAGT 57.135 47.619 5.93 0.00 42.25 2.12
630 641 4.974645 CCCTAGCATGGGTTGAATAGTA 57.025 45.455 5.93 0.00 42.25 1.82
631 642 4.899502 CCCTAGCATGGGTTGAATAGTAG 58.100 47.826 5.93 0.00 42.25 2.57
632 643 4.593206 CCCTAGCATGGGTTGAATAGTAGA 59.407 45.833 5.93 0.00 42.25 2.59
633 644 5.279708 CCCTAGCATGGGTTGAATAGTAGAG 60.280 48.000 5.93 0.00 42.25 2.43
634 645 5.305644 CCTAGCATGGGTTGAATAGTAGAGT 59.694 44.000 0.00 0.00 0.00 3.24
635 646 5.028549 AGCATGGGTTGAATAGTAGAGTG 57.971 43.478 0.00 0.00 0.00 3.51
636 647 4.716784 AGCATGGGTTGAATAGTAGAGTGA 59.283 41.667 0.00 0.00 0.00 3.41
637 648 5.189736 AGCATGGGTTGAATAGTAGAGTGAA 59.810 40.000 0.00 0.00 0.00 3.18
638 649 5.880332 GCATGGGTTGAATAGTAGAGTGAAA 59.120 40.000 0.00 0.00 0.00 2.69
639 650 6.183360 GCATGGGTTGAATAGTAGAGTGAAAC 60.183 42.308 0.00 0.00 0.00 2.78
692 703 4.353383 AAAAAGAAGGCCTACTCGAAGT 57.647 40.909 5.16 0.00 0.00 3.01
693 704 3.596310 AAAGAAGGCCTACTCGAAGTC 57.404 47.619 5.16 0.00 0.00 3.01
694 705 2.517998 AGAAGGCCTACTCGAAGTCT 57.482 50.000 5.16 0.00 0.00 3.24
695 706 2.371306 AGAAGGCCTACTCGAAGTCTC 58.629 52.381 5.16 0.00 0.00 3.36
696 707 1.064357 GAAGGCCTACTCGAAGTCTCG 59.936 57.143 5.16 0.00 46.87 4.04
708 719 1.996191 GAAGTCTCGAACAGTCCATGC 59.004 52.381 0.00 0.00 0.00 4.06
709 720 0.969149 AGTCTCGAACAGTCCATGCA 59.031 50.000 0.00 0.00 0.00 3.96
710 721 1.552337 AGTCTCGAACAGTCCATGCAT 59.448 47.619 0.00 0.00 0.00 3.96
711 722 2.027745 AGTCTCGAACAGTCCATGCATT 60.028 45.455 0.00 0.00 0.00 3.56
712 723 2.744202 GTCTCGAACAGTCCATGCATTT 59.256 45.455 0.00 0.00 0.00 2.32
713 724 3.932710 GTCTCGAACAGTCCATGCATTTA 59.067 43.478 0.00 0.00 0.00 1.40
714 725 4.033358 GTCTCGAACAGTCCATGCATTTAG 59.967 45.833 0.00 0.00 0.00 1.85
715 726 2.677836 TCGAACAGTCCATGCATTTAGC 59.322 45.455 0.00 0.00 45.96 3.09
765 776 1.929714 GTTGCAATCGATCGCACGC 60.930 57.895 11.29 12.51 38.00 5.34
851 862 2.953821 CGCCACCGCTGTCAAATT 59.046 55.556 0.00 0.00 0.00 1.82
858 869 3.941483 CCACCGCTGTCAAATTAAGATCT 59.059 43.478 0.00 0.00 0.00 2.75
878 889 1.752501 CGACGCCAAAGATAGCCACG 61.753 60.000 0.00 0.00 0.00 4.94
942 954 2.127383 GTCAAAAGTTCGCCGCGG 60.127 61.111 24.05 24.05 0.00 6.46
944 956 2.426752 CAAAAGTTCGCCGCGGTG 60.427 61.111 32.48 32.48 0.00 4.94
1046 1058 3.017323 CATCCTCATCGTTGCCGC 58.983 61.111 0.00 0.00 0.00 6.53
1121 1133 0.175989 CCGGAGAAGTCTAAGGCCAC 59.824 60.000 5.01 0.00 0.00 5.01
1218 1230 2.597903 GGGACCCTTGGGATGCTC 59.402 66.667 13.39 0.00 0.00 4.26
1220 1232 1.225704 GGACCCTTGGGATGCTCAG 59.774 63.158 13.39 0.00 0.00 3.35
1239 1251 3.941657 GAGCACTCTGGGCGGACAC 62.942 68.421 0.00 0.00 36.08 3.67
1882 2294 3.740764 GCACAAAGCTTTCACCATGGAAA 60.741 43.478 21.47 8.67 41.15 3.13
2004 2416 2.030562 AAGGTCACCAGTTCGGCG 59.969 61.111 0.00 0.00 39.03 6.46
2198 2610 0.173708 GTGGGTGCTCTCTAAGACGG 59.826 60.000 0.00 0.00 0.00 4.79
2202 2614 2.278923 GCTCTCTAAGACGGCCGC 60.279 66.667 28.58 18.62 0.00 6.53
2236 2648 3.854669 CACCCTAGGCCGGCTCAG 61.855 72.222 28.56 22.17 0.00 3.35
2361 2774 3.766591 TGGAGGAGCACACAAAAAGAAAA 59.233 39.130 0.00 0.00 0.00 2.29
2376 2789 8.527810 ACAAAAAGAAAAGATGTGGTCACTTAA 58.472 29.630 2.66 0.00 0.00 1.85
2466 2885 7.042321 TGTTGTGTTATCGTTTCAAGTAAGAGG 60.042 37.037 0.00 0.00 0.00 3.69
2475 2894 1.623811 TCAAGTAAGAGGTGCAGGTCC 59.376 52.381 0.00 0.00 0.00 4.46
2500 2919 7.661437 CCTATGCAAATAGGTGTATGTGTATGT 59.339 37.037 5.35 0.00 39.03 2.29
2554 2973 2.404215 GCTGAGAGCGTGAACTGTTTA 58.596 47.619 0.00 0.00 0.00 2.01
2604 3023 1.464687 CCAGATGAAAGCTTTGCGACG 60.465 52.381 18.30 2.01 0.00 5.12
2622 3041 4.201990 GCGACGGAAGAGAAATACTTAGGA 60.202 45.833 0.00 0.00 0.00 2.94
2629 3048 6.408662 GGAAGAGAAATACTTAGGATGTGGCT 60.409 42.308 0.00 0.00 0.00 4.75
2641 3060 3.640967 AGGATGTGGCTTAGATCTCAGTC 59.359 47.826 0.00 0.00 30.16 3.51
2642 3061 3.551863 GGATGTGGCTTAGATCTCAGTCG 60.552 52.174 0.00 0.00 30.16 4.18
2643 3062 2.447443 TGTGGCTTAGATCTCAGTCGT 58.553 47.619 0.00 0.00 0.00 4.34
2644 3063 2.423892 TGTGGCTTAGATCTCAGTCGTC 59.576 50.000 0.00 0.00 0.00 4.20
2696 3141 2.890808 ATATGCACGGATCTTCACGT 57.109 45.000 0.00 0.00 45.25 4.49
2699 3144 2.442212 TGCACGGATCTTCACGTAAA 57.558 45.000 0.00 0.00 42.04 2.01
2707 3152 4.027621 CGGATCTTCACGTAAAATCTCACG 60.028 45.833 0.00 0.00 43.63 4.35
2714 3159 8.188799 TCTTCACGTAAAATCTCACGAATATCT 58.811 33.333 0.62 0.00 40.56 1.98
2796 3241 3.275617 ACCAAGCACGGAATATTAGCA 57.724 42.857 0.00 0.00 0.00 3.49
2797 3242 3.820557 ACCAAGCACGGAATATTAGCAT 58.179 40.909 0.00 0.00 0.00 3.79
2903 3349 0.040499 GACAGGTCTCTCCACCCTCT 59.960 60.000 0.00 0.00 37.09 3.69
2920 3366 2.667199 TGACGACTGCTCCGACGA 60.667 61.111 0.00 0.00 0.00 4.20
2990 3437 1.066430 AGGGCTAGTTTTTCGATCGCA 60.066 47.619 11.09 0.00 0.00 5.10
3011 3458 1.133407 TGTTGTTTCGGTTTGGACAGC 59.867 47.619 0.00 0.00 0.00 4.40
3021 3468 2.476852 TTTGGACAGCTATGGCGGCA 62.477 55.000 16.34 16.34 44.37 5.69
3022 3469 2.124736 GGACAGCTATGGCGGCAA 60.125 61.111 18.31 4.62 44.37 4.52
3042 3489 3.134574 ACGTTGAATAAAGGTGCTCCA 57.865 42.857 7.70 0.00 35.59 3.86
3094 3541 0.456142 CGTCGACGAATCTGGAAGCA 60.456 55.000 33.35 0.00 43.02 3.91
3116 3563 2.742589 GGTTTCCTAAGTGAGAAAGGCG 59.257 50.000 0.00 0.00 32.86 5.52
3120 3567 1.002087 CCTAAGTGAGAAAGGCGTGGT 59.998 52.381 0.00 0.00 0.00 4.16
3123 3570 1.227853 GTGAGAAAGGCGTGGTGGT 60.228 57.895 0.00 0.00 0.00 4.16
3124 3571 1.227823 TGAGAAAGGCGTGGTGGTG 60.228 57.895 0.00 0.00 0.00 4.17
3125 3572 1.966451 GAGAAAGGCGTGGTGGTGG 60.966 63.158 0.00 0.00 0.00 4.61
3142 3589 4.481112 GCCGCCGCCTTGTGATTG 62.481 66.667 0.00 0.00 0.00 2.67
3170 3618 0.249911 CTATGGCTTCACTACCGGGC 60.250 60.000 6.32 0.00 0.00 6.13
3175 3623 1.515954 CTTCACTACCGGGCGATGT 59.484 57.895 6.32 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.069978 TCTGCGGCAATTATGATCCGA 59.930 47.619 3.44 0.00 44.23 4.55
87 88 1.138859 CACCATCTTCGGAGTGGCATA 59.861 52.381 11.07 0.00 36.47 3.14
255 266 1.742761 ATTGCCATGGACGTTCTCAG 58.257 50.000 18.40 0.00 0.00 3.35
307 318 0.741221 GCACGCTAAAGGTCTGAGGG 60.741 60.000 0.00 0.00 0.00 4.30
456 467 1.149101 AAAGCCTTTGACTCCCTGGA 58.851 50.000 0.00 0.00 0.00 3.86
540 551 3.490249 GCCAAACCCTGTGTAACTCAAAC 60.490 47.826 0.00 0.00 38.04 2.93
541 552 2.691011 GCCAAACCCTGTGTAACTCAAA 59.309 45.455 0.00 0.00 38.04 2.69
542 553 2.092103 AGCCAAACCCTGTGTAACTCAA 60.092 45.455 0.00 0.00 38.04 3.02
543 554 1.493022 AGCCAAACCCTGTGTAACTCA 59.507 47.619 0.00 0.00 38.04 3.41
544 555 1.880027 CAGCCAAACCCTGTGTAACTC 59.120 52.381 0.00 0.00 38.04 3.01
545 556 1.493022 TCAGCCAAACCCTGTGTAACT 59.507 47.619 0.00 0.00 38.04 2.24
546 557 1.975660 TCAGCCAAACCCTGTGTAAC 58.024 50.000 0.00 0.00 37.35 2.50
547 558 2.738587 TTCAGCCAAACCCTGTGTAA 57.261 45.000 0.00 0.00 0.00 2.41
548 559 2.107378 TCATTCAGCCAAACCCTGTGTA 59.893 45.455 0.00 0.00 0.00 2.90
549 560 1.133513 TCATTCAGCCAAACCCTGTGT 60.134 47.619 0.00 0.00 0.00 3.72
550 561 1.542915 CTCATTCAGCCAAACCCTGTG 59.457 52.381 0.00 0.00 0.00 3.66
551 562 1.915141 CTCATTCAGCCAAACCCTGT 58.085 50.000 0.00 0.00 0.00 4.00
552 563 0.529378 GCTCATTCAGCCAAACCCTG 59.471 55.000 0.00 0.00 43.17 4.45
553 564 2.967270 GCTCATTCAGCCAAACCCT 58.033 52.632 0.00 0.00 43.17 4.34
562 573 1.019673 CATTCGGGGTGCTCATTCAG 58.980 55.000 0.00 0.00 0.00 3.02
563 574 0.327924 ACATTCGGGGTGCTCATTCA 59.672 50.000 0.00 0.00 0.00 2.57
564 575 2.325583 TACATTCGGGGTGCTCATTC 57.674 50.000 0.00 0.00 0.00 2.67
565 576 3.117888 AGAATACATTCGGGGTGCTCATT 60.118 43.478 0.00 0.00 41.56 2.57
566 577 2.439507 AGAATACATTCGGGGTGCTCAT 59.560 45.455 0.00 0.00 41.56 2.90
567 578 1.837439 AGAATACATTCGGGGTGCTCA 59.163 47.619 0.00 0.00 41.56 4.26
568 579 2.213499 CAGAATACATTCGGGGTGCTC 58.787 52.381 0.00 0.00 41.56 4.26
569 580 1.747206 GCAGAATACATTCGGGGTGCT 60.747 52.381 4.61 0.00 41.56 4.40
570 581 0.663153 GCAGAATACATTCGGGGTGC 59.337 55.000 4.61 2.25 41.56 5.01
571 582 2.036958 TGCAGAATACATTCGGGGTG 57.963 50.000 4.61 0.00 41.56 4.61
572 583 2.026262 ACTTGCAGAATACATTCGGGGT 60.026 45.455 4.61 0.00 41.56 4.95
573 584 2.643551 ACTTGCAGAATACATTCGGGG 58.356 47.619 4.61 0.00 41.56 5.73
574 585 3.440173 ACAACTTGCAGAATACATTCGGG 59.560 43.478 4.61 0.00 41.56 5.14
575 586 4.685169 ACAACTTGCAGAATACATTCGG 57.315 40.909 0.00 0.00 41.56 4.30
576 587 7.003939 TGATACAACTTGCAGAATACATTCG 57.996 36.000 0.00 0.00 41.56 3.34
577 588 8.201554 TCTGATACAACTTGCAGAATACATTC 57.798 34.615 0.00 0.00 34.71 2.67
578 589 8.618677 CATCTGATACAACTTGCAGAATACATT 58.381 33.333 0.00 0.00 40.38 2.71
579 590 7.989170 TCATCTGATACAACTTGCAGAATACAT 59.011 33.333 0.00 0.00 40.38 2.29
580 591 7.330262 TCATCTGATACAACTTGCAGAATACA 58.670 34.615 0.00 0.00 40.38 2.29
581 592 7.776933 TCATCTGATACAACTTGCAGAATAC 57.223 36.000 0.00 0.00 40.38 1.89
582 593 8.791327 TTTCATCTGATACAACTTGCAGAATA 57.209 30.769 0.00 0.00 40.38 1.75
583 594 7.692460 TTTCATCTGATACAACTTGCAGAAT 57.308 32.000 0.00 0.00 40.38 2.40
584 595 7.148188 GGATTTCATCTGATACAACTTGCAGAA 60.148 37.037 0.00 0.00 40.38 3.02
585 596 6.317140 GGATTTCATCTGATACAACTTGCAGA 59.683 38.462 0.00 0.00 41.14 4.26
586 597 6.459298 GGGATTTCATCTGATACAACTTGCAG 60.459 42.308 0.00 0.00 0.00 4.41
587 598 5.357878 GGGATTTCATCTGATACAACTTGCA 59.642 40.000 0.00 0.00 0.00 4.08
588 599 5.591877 AGGGATTTCATCTGATACAACTTGC 59.408 40.000 0.00 0.00 0.00 4.01
589 600 7.041508 GCTAGGGATTTCATCTGATACAACTTG 60.042 40.741 0.00 0.00 0.00 3.16
590 601 6.995091 GCTAGGGATTTCATCTGATACAACTT 59.005 38.462 0.00 0.00 0.00 2.66
591 602 6.100279 TGCTAGGGATTTCATCTGATACAACT 59.900 38.462 0.00 0.00 0.00 3.16
592 603 6.291377 TGCTAGGGATTTCATCTGATACAAC 58.709 40.000 0.00 0.00 0.00 3.32
593 604 6.499106 TGCTAGGGATTTCATCTGATACAA 57.501 37.500 0.00 0.00 0.00 2.41
594 605 6.470278 CATGCTAGGGATTTCATCTGATACA 58.530 40.000 0.00 0.00 0.00 2.29
595 606 5.879223 CCATGCTAGGGATTTCATCTGATAC 59.121 44.000 0.00 0.00 0.00 2.24
596 607 6.058553 CCATGCTAGGGATTTCATCTGATA 57.941 41.667 0.00 0.00 0.00 2.15
597 608 4.919793 CCATGCTAGGGATTTCATCTGAT 58.080 43.478 0.00 0.00 0.00 2.90
598 609 4.362470 CCATGCTAGGGATTTCATCTGA 57.638 45.455 0.00 0.00 0.00 3.27
610 621 5.305644 ACTCTACTATTCAACCCATGCTAGG 59.694 44.000 0.00 0.00 0.00 3.02
611 622 6.040955 TCACTCTACTATTCAACCCATGCTAG 59.959 42.308 0.00 0.00 0.00 3.42
612 623 5.897250 TCACTCTACTATTCAACCCATGCTA 59.103 40.000 0.00 0.00 0.00 3.49
613 624 4.716784 TCACTCTACTATTCAACCCATGCT 59.283 41.667 0.00 0.00 0.00 3.79
614 625 5.023533 TCACTCTACTATTCAACCCATGC 57.976 43.478 0.00 0.00 0.00 4.06
615 626 7.065085 CAGTTTCACTCTACTATTCAACCCATG 59.935 40.741 0.00 0.00 0.00 3.66
616 627 7.038302 TCAGTTTCACTCTACTATTCAACCCAT 60.038 37.037 0.00 0.00 0.00 4.00
617 628 6.269077 TCAGTTTCACTCTACTATTCAACCCA 59.731 38.462 0.00 0.00 0.00 4.51
618 629 6.698380 TCAGTTTCACTCTACTATTCAACCC 58.302 40.000 0.00 0.00 0.00 4.11
619 630 8.779354 AATCAGTTTCACTCTACTATTCAACC 57.221 34.615 0.00 0.00 0.00 3.77
620 631 9.424319 TGAATCAGTTTCACTCTACTATTCAAC 57.576 33.333 0.00 0.00 39.44 3.18
621 632 9.996554 TTGAATCAGTTTCACTCTACTATTCAA 57.003 29.630 0.00 0.00 43.99 2.69
622 633 9.996554 TTTGAATCAGTTTCACTCTACTATTCA 57.003 29.630 0.00 0.00 43.99 2.57
671 682 4.040584 AGACTTCGAGTAGGCCTTCTTTTT 59.959 41.667 12.58 0.00 0.00 1.94
672 683 3.579151 AGACTTCGAGTAGGCCTTCTTTT 59.421 43.478 12.58 0.00 0.00 2.27
673 684 3.166679 AGACTTCGAGTAGGCCTTCTTT 58.833 45.455 12.58 0.00 0.00 2.52
674 685 2.756207 GAGACTTCGAGTAGGCCTTCTT 59.244 50.000 12.58 0.00 0.00 2.52
675 686 2.371306 GAGACTTCGAGTAGGCCTTCT 58.629 52.381 12.58 12.45 0.00 2.85
676 687 2.855660 GAGACTTCGAGTAGGCCTTC 57.144 55.000 12.58 5.68 0.00 3.46
688 699 1.996191 GCATGGACTGTTCGAGACTTC 59.004 52.381 0.00 0.00 0.00 3.01
689 700 1.344438 TGCATGGACTGTTCGAGACTT 59.656 47.619 0.00 0.00 0.00 3.01
690 701 0.969149 TGCATGGACTGTTCGAGACT 59.031 50.000 0.00 0.00 0.00 3.24
691 702 2.015736 ATGCATGGACTGTTCGAGAC 57.984 50.000 0.00 0.00 0.00 3.36
692 703 2.768253 AATGCATGGACTGTTCGAGA 57.232 45.000 0.00 0.00 0.00 4.04
693 704 3.242543 GCTAAATGCATGGACTGTTCGAG 60.243 47.826 0.00 0.00 42.31 4.04
694 705 2.677836 GCTAAATGCATGGACTGTTCGA 59.322 45.455 0.00 0.00 42.31 3.71
695 706 3.056952 GCTAAATGCATGGACTGTTCG 57.943 47.619 0.00 0.00 42.31 3.95
719 730 1.671845 GGAGTGTGCACGTACCAAAAA 59.328 47.619 13.13 0.00 36.20 1.94
720 731 1.301423 GGAGTGTGCACGTACCAAAA 58.699 50.000 13.13 0.00 36.20 2.44
721 732 0.178301 TGGAGTGTGCACGTACCAAA 59.822 50.000 20.70 4.67 33.72 3.28
722 733 0.531090 GTGGAGTGTGCACGTACCAA 60.531 55.000 23.26 10.42 36.41 3.67
723 734 1.068417 GTGGAGTGTGCACGTACCA 59.932 57.895 19.61 19.61 36.20 3.25
724 735 3.946907 GTGGAGTGTGCACGTACC 58.053 61.111 13.13 14.72 36.20 3.34
765 776 0.460987 GAGTGGAGGAAGATGGTGCG 60.461 60.000 0.00 0.00 0.00 5.34
771 782 2.427245 CGCCGGAGTGGAGGAAGAT 61.427 63.158 5.05 0.00 42.00 2.40
851 862 4.556898 GCTATCTTTGGCGTCGAGATCTTA 60.557 45.833 8.73 0.00 32.68 2.10
858 869 0.459585 GTGGCTATCTTTGGCGTCGA 60.460 55.000 0.00 0.00 0.00 4.20
942 954 2.186125 GTGGGTAGGTAGCGCCAC 59.814 66.667 2.29 0.00 40.61 5.01
944 956 1.456331 TAGGTGGGTAGGTAGCGCC 60.456 63.158 2.29 0.00 37.58 6.53
1100 1112 1.192428 GGCCTTAGACTTCTCCGGAA 58.808 55.000 5.23 0.00 0.00 4.30
1218 1230 4.463879 CCGCCCAGAGTGCTCCTG 62.464 72.222 0.00 0.00 0.00 3.86
1220 1232 4.459089 GTCCGCCCAGAGTGCTCC 62.459 72.222 0.00 0.00 0.00 4.70
1242 1254 2.124695 GCGGAGGCCTTACCCTTG 60.125 66.667 6.77 0.00 40.58 3.61
1244 1256 3.083997 CAGCGGAGGCCTTACCCT 61.084 66.667 6.77 0.95 40.58 4.34
1920 2332 0.674895 CTTCTTCGCTGGACCCCTTG 60.675 60.000 0.00 0.00 0.00 3.61
1925 2337 2.815647 CGGCTTCTTCGCTGGACC 60.816 66.667 0.00 0.00 32.64 4.46
1982 2394 1.150536 GAACTGGTGACCTTGGCCA 59.849 57.895 0.00 0.00 0.00 5.36
2004 2416 3.179939 GCCGTCGAGCTTTCGTCC 61.180 66.667 0.00 0.00 0.00 4.79
2069 2481 3.966930 GAGTCGGGACCAGGAGCCT 62.967 68.421 0.00 0.00 0.00 4.58
2233 2645 4.742201 GTTCGAGCGCCAGCCTGA 62.742 66.667 2.29 0.00 46.67 3.86
2236 2648 4.443266 AGAGTTCGAGCGCCAGCC 62.443 66.667 2.29 0.00 46.67 4.85
2244 2656 0.539051 ATTGCCCTCCAGAGTTCGAG 59.461 55.000 0.00 0.00 0.00 4.04
2299 2711 2.359726 TGCATGCTTAGCACGGCA 60.360 55.556 24.84 24.84 45.31 5.69
2361 2774 4.894784 ACGATTGTTAAGTGACCACATCT 58.105 39.130 2.78 0.00 0.00 2.90
2475 2894 8.607441 ACATACACATACACCTATTTGCATAG 57.393 34.615 0.00 0.00 33.21 2.23
2500 2919 7.628366 GCATTTTCTATCCGATCACTGGAAAAA 60.628 37.037 11.67 6.60 39.39 1.94
2554 2973 9.090692 CATGAAACAACTGAATCTGAAAGTTTT 57.909 29.630 0.00 0.00 31.88 2.43
2604 3023 5.760743 GCCACATCCTAAGTATTTCTCTTCC 59.239 44.000 0.00 0.00 0.00 3.46
2622 3041 3.027412 ACGACTGAGATCTAAGCCACAT 58.973 45.455 7.04 0.00 0.00 3.21
2629 3048 5.122554 GTCACTTGAGACGACTGAGATCTAA 59.877 44.000 0.00 0.00 0.00 2.10
2642 3061 6.128661 TGTTTATATGTTGCGTCACTTGAGAC 60.129 38.462 0.00 0.00 35.19 3.36
2643 3062 5.929415 TGTTTATATGTTGCGTCACTTGAGA 59.071 36.000 0.00 0.00 0.00 3.27
2644 3063 6.090763 TCTGTTTATATGTTGCGTCACTTGAG 59.909 38.462 0.00 0.00 0.00 3.02
2678 3123 3.786516 TTACGTGAAGATCCGTGCATA 57.213 42.857 0.00 0.00 37.91 3.14
2691 3136 6.631636 CGAGATATTCGTGAGATTTTACGTGA 59.368 38.462 0.00 0.00 44.27 4.35
2707 3152 6.066410 CGAAGTCTTAGTCGACGAGATATTC 58.934 44.000 21.88 23.08 39.64 1.75
2714 3159 4.449068 ACTTAACGAAGTCTTAGTCGACGA 59.551 41.667 10.46 0.94 45.00 4.20
2738 3183 5.006165 GGAATTGCTAAATCTCACGACTGAG 59.994 44.000 0.00 0.00 44.94 3.35
2741 3186 5.091261 AGGAATTGCTAAATCTCACGACT 57.909 39.130 0.00 0.00 0.00 4.18
2760 3205 7.431249 CGTGCTTGGTAGATAAGTATTTAGGA 58.569 38.462 0.00 0.00 0.00 2.94
2796 3241 4.682021 AGAAGGGGAAAACAAGATCCAT 57.318 40.909 0.00 0.00 37.46 3.41
2797 3242 5.492524 AGATAGAAGGGGAAAACAAGATCCA 59.507 40.000 0.00 0.00 37.46 3.41
2879 3325 0.806241 GTGGAGAGACCTGTCGACTC 59.194 60.000 17.92 6.13 39.86 3.36
2903 3349 2.667199 TCGTCGGAGCAGTCGTCA 60.667 61.111 0.00 0.00 0.00 4.35
2920 3366 4.677151 GGTCCCCCACCCTCCAGT 62.677 72.222 0.00 0.00 39.69 4.00
2952 3399 2.897969 CCCTAACCTATCTACACGCCAT 59.102 50.000 0.00 0.00 0.00 4.40
2990 3437 2.223711 GCTGTCCAAACCGAAACAACAT 60.224 45.455 0.00 0.00 0.00 2.71
3011 3458 0.732571 ATTCAACGTTGCCGCCATAG 59.267 50.000 23.47 0.00 37.70 2.23
3021 3468 3.482436 TGGAGCACCTTTATTCAACGTT 58.518 40.909 0.71 0.00 37.04 3.99
3022 3469 3.074412 CTGGAGCACCTTTATTCAACGT 58.926 45.455 0.71 0.00 37.04 3.99
3025 3472 4.640771 AGTCTGGAGCACCTTTATTCAA 57.359 40.909 0.71 0.00 37.04 2.69
3086 3533 3.077359 CACTTAGGAAACCTGCTTCCAG 58.923 50.000 5.36 0.00 46.38 3.86
3094 3541 3.557264 CGCCTTTCTCACTTAGGAAACCT 60.557 47.826 0.00 0.00 37.71 3.50
3125 3572 4.481112 CAATCACAAGGCGGCGGC 62.481 66.667 27.24 27.24 38.90 6.53
3170 3618 2.029288 AACACTGGAGCGCACATCG 61.029 57.895 11.47 4.84 42.12 3.84
3175 3623 1.451207 ACAACAACACTGGAGCGCA 60.451 52.632 11.47 0.00 0.00 6.09


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

AutoCloner maintained by Alex Coulton.