Multiple sequence alignment - TraesCS1A01G101600

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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 TraesCS1A01G101600 chr1A 100.000 4373 0 0 1 4373 97955682 97951310 0.000000e+00 8076.0
1 TraesCS1A01G101600 chr1A 87.556 1575 186 9 772 2339 97806905 97805334 0.000000e+00 1814.0
2 TraesCS1A01G101600 chr1A 87.529 1307 146 8 2330 3630 97803711 97802416 0.000000e+00 1495.0
3 TraesCS1A01G101600 chr1A 89.079 467 51 0 1 467 97808417 97807951 8.150000e-162 580.0
4 TraesCS1A01G101600 chr1A 99.468 188 1 0 585 772 333878910 333878723 4.190000e-90 342.0
5 TraesCS1A01G101600 chr1A 91.346 104 9 0 482 585 97807002 97806899 4.560000e-30 143.0
6 TraesCS1A01G101600 chr1B 91.086 3646 274 24 772 4373 130354373 130350735 0.000000e+00 4885.0
7 TraesCS1A01G101600 chr1B 86.837 2150 231 20 1503 3626 130021454 130019331 0.000000e+00 2355.0
8 TraesCS1A01G101600 chr1B 95.264 739 35 0 772 1510 130022693 130021955 0.000000e+00 1171.0
9 TraesCS1A01G101600 chr1B 96.928 586 18 0 1 586 130354951 130354366 0.000000e+00 983.0
10 TraesCS1A01G101600 chr1B 92.308 585 45 0 1 585 130023271 130022687 0.000000e+00 832.0
11 TraesCS1A01G101600 chr1B 100.000 188 0 0 585 772 288394445 288394632 9.000000e-92 348.0
12 TraesCS1A01G101600 chr1B 100.000 186 0 0 586 771 80964017 80963832 1.160000e-90 344.0
13 TraesCS1A01G101600 chr1D 89.882 3647 303 35 772 4369 79140423 79136794 0.000000e+00 4630.0
14 TraesCS1A01G101600 chr1D 99.319 587 4 0 1 587 79141001 79140415 0.000000e+00 1062.0
15 TraesCS1A01G101600 chr1D 78.157 293 51 9 3164 3456 79136398 79136119 1.620000e-39 174.0
16 TraesCS1A01G101600 chr2B 74.840 1093 231 38 772 1836 693336698 693337774 5.160000e-124 455.0
17 TraesCS1A01G101600 chr2B 80.000 545 96 9 22 558 754921919 754922458 1.470000e-104 390.0
18 TraesCS1A01G101600 chr2B 100.000 187 0 0 587 773 66807541 66807727 3.240000e-91 346.0
19 TraesCS1A01G101600 chr6D 81.272 566 99 5 26 586 83163694 83164257 6.670000e-123 451.0
20 TraesCS1A01G101600 chr6D 78.090 178 37 2 3169 3345 83171883 83172059 1.290000e-20 111.0
21 TraesCS1A01G101600 chr6B 82.424 495 80 5 26 515 158167668 158168160 4.040000e-115 425.0
22 TraesCS1A01G101600 chr6B 99.468 188 1 0 587 774 259290048 259289861 4.190000e-90 342.0
23 TraesCS1A01G101600 chr6B 75.342 219 52 2 3136 3353 51760162 51760379 2.150000e-18 104.0
24 TraesCS1A01G101600 chr6B 88.525 61 7 0 3290 3350 51950635 51950695 1.690000e-09 75.0
25 TraesCS1A01G101600 chr4D 78.621 580 115 7 12 585 3346843 3346267 4.130000e-100 375.0
26 TraesCS1A01G101600 chr3D 80.156 514 89 10 22 527 600155096 600155604 5.340000e-99 372.0
27 TraesCS1A01G101600 chr3D 93.617 47 3 0 2685 2731 613569699 613569653 2.180000e-08 71.3
28 TraesCS1A01G101600 chr5A 100.000 187 0 0 586 772 340131891 340131705 3.240000e-91 346.0
29 TraesCS1A01G101600 chr7B 100.000 186 0 0 586 771 51073830 51073645 1.160000e-90 344.0
30 TraesCS1A01G101600 chr3A 100.000 186 0 0 586 771 329511538 329511723 1.160000e-90 344.0
31 TraesCS1A01G101600 chr6A 99.468 188 1 0 585 772 272125493 272125306 4.190000e-90 342.0
32 TraesCS1A01G101600 chr6A 79.096 177 37 0 3169 3345 100299807 100299983 5.940000e-24 122.0
33 TraesCS1A01G101600 chr2D 72.040 1191 280 44 773 1929 577128211 577129382 5.490000e-79 305.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G101600 chr1A 97951310 97955682 4372 True 8076.000000 8076 100.000000 1 4373 1 chr1A.!!$R1 4372
1 TraesCS1A01G101600 chr1A 97802416 97808417 6001 True 1008.000000 1814 88.877500 1 3630 4 chr1A.!!$R3 3629
2 TraesCS1A01G101600 chr1B 130350735 130354951 4216 True 2934.000000 4885 94.007000 1 4373 2 chr1B.!!$R3 4372
3 TraesCS1A01G101600 chr1B 130019331 130023271 3940 True 1452.666667 2355 91.469667 1 3626 3 chr1B.!!$R2 3625
4 TraesCS1A01G101600 chr1D 79136119 79141001 4882 True 1955.333333 4630 89.119333 1 4369 3 chr1D.!!$R1 4368
5 TraesCS1A01G101600 chr2B 693336698 693337774 1076 False 455.000000 455 74.840000 772 1836 1 chr2B.!!$F2 1064
6 TraesCS1A01G101600 chr2B 754921919 754922458 539 False 390.000000 390 80.000000 22 558 1 chr2B.!!$F3 536
7 TraesCS1A01G101600 chr6D 83163694 83164257 563 False 451.000000 451 81.272000 26 586 1 chr6D.!!$F1 560
8 TraesCS1A01G101600 chr4D 3346267 3346843 576 True 375.000000 375 78.621000 12 585 1 chr4D.!!$R1 573
9 TraesCS1A01G101600 chr3D 600155096 600155604 508 False 372.000000 372 80.156000 22 527 1 chr3D.!!$F1 505
10 TraesCS1A01G101600 chr2D 577128211 577129382 1171 False 305.000000 305 72.040000 773 1929 1 chr2D.!!$F1 1156

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
763 1701 0.108041 CGCCTTAGGGACGCCTTTAA 60.108 55.0 0.00 0.0 33.58 1.52 F
2227 3691 0.034767 ACGGATCGAGGACTGTGGTA 60.035 55.0 0.00 0.0 0.00 3.25 F
2815 5932 0.035820 GGGCCACCTCACACGATTAA 60.036 55.0 4.39 0.0 0.00 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2517 5616 0.106769 TGTCCTTGCCAAGTGAAGCA 60.107 50.0 3.37 0.0 37.18 3.91 R
3178 6295 0.034059 AGAGAACTTGGCAGTCCGTG 59.966 55.0 0.00 0.0 34.14 4.94 R
3632 6773 0.390492 GCTTTCAAGGGCAGCAACTT 59.610 50.0 0.00 0.0 33.45 2.66 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
300 301 8.435931 ACTAGGCATTATAAGGTCACATGATA 57.564 34.615 4.36 0.00 0.00 2.15
319 320 4.766891 TGATAAGGCCAAAAGAACAGAAGG 59.233 41.667 5.01 0.00 0.00 3.46
518 1456 4.245660 CATCTGTACGTCACTTGTCCATT 58.754 43.478 0.00 0.00 0.00 3.16
586 1524 4.568152 ACAACAGTTATTTGAGTGCACC 57.432 40.909 14.63 5.76 0.00 5.01
587 1525 4.207165 ACAACAGTTATTTGAGTGCACCT 58.793 39.130 14.63 0.04 0.00 4.00
588 1526 5.373222 ACAACAGTTATTTGAGTGCACCTA 58.627 37.500 14.63 0.00 0.00 3.08
589 1527 6.003950 ACAACAGTTATTTGAGTGCACCTAT 58.996 36.000 14.63 4.59 0.00 2.57
590 1528 6.072508 ACAACAGTTATTTGAGTGCACCTATG 60.073 38.462 14.63 6.15 0.00 2.23
591 1529 5.560724 ACAGTTATTTGAGTGCACCTATGT 58.439 37.500 14.63 3.20 0.00 2.29
592 1530 6.003950 ACAGTTATTTGAGTGCACCTATGTT 58.996 36.000 14.63 0.00 0.00 2.71
593 1531 6.490040 ACAGTTATTTGAGTGCACCTATGTTT 59.510 34.615 14.63 0.00 0.00 2.83
594 1532 7.014230 ACAGTTATTTGAGTGCACCTATGTTTT 59.986 33.333 14.63 0.00 0.00 2.43
595 1533 7.867403 CAGTTATTTGAGTGCACCTATGTTTTT 59.133 33.333 14.63 0.00 0.00 1.94
596 1534 9.073475 AGTTATTTGAGTGCACCTATGTTTTTA 57.927 29.630 14.63 0.00 0.00 1.52
597 1535 9.685828 GTTATTTGAGTGCACCTATGTTTTTAA 57.314 29.630 14.63 0.00 0.00 1.52
598 1536 9.906660 TTATTTGAGTGCACCTATGTTTTTAAG 57.093 29.630 14.63 0.00 0.00 1.85
599 1537 5.957842 TGAGTGCACCTATGTTTTTAAGG 57.042 39.130 14.63 0.00 36.42 2.69
600 1538 4.217550 TGAGTGCACCTATGTTTTTAAGGC 59.782 41.667 14.63 0.00 33.42 4.35
601 1539 3.190535 AGTGCACCTATGTTTTTAAGGCG 59.809 43.478 14.63 0.00 33.42 5.52
602 1540 3.189702 GTGCACCTATGTTTTTAAGGCGA 59.810 43.478 5.22 0.00 33.42 5.54
603 1541 3.189702 TGCACCTATGTTTTTAAGGCGAC 59.810 43.478 0.00 0.00 33.42 5.19
604 1542 3.726782 GCACCTATGTTTTTAAGGCGACG 60.727 47.826 0.00 0.00 33.42 5.12
605 1543 2.417586 ACCTATGTTTTTAAGGCGACGC 59.582 45.455 12.43 12.43 33.42 5.19
617 1555 2.491152 CGACGCCTTACCGCCTTA 59.509 61.111 0.00 0.00 0.00 2.69
618 1556 1.588139 CGACGCCTTACCGCCTTAG 60.588 63.158 0.00 0.00 0.00 2.18
619 1557 1.227176 GACGCCTTACCGCCTTAGG 60.227 63.158 0.00 0.00 37.30 2.69
620 1558 2.108362 CGCCTTACCGCCTTAGGG 59.892 66.667 0.00 0.00 35.02 3.53
621 1559 2.428925 CGCCTTACCGCCTTAGGGA 61.429 63.158 0.00 0.00 35.02 4.20
622 1560 1.446366 GCCTTACCGCCTTAGGGAG 59.554 63.158 0.00 0.00 35.02 4.30
668 1606 4.467084 CTAGGCGGGCGCTTTGGA 62.467 66.667 7.64 0.00 41.60 3.53
669 1607 4.770874 TAGGCGGGCGCTTTGGAC 62.771 66.667 7.64 0.00 41.60 4.02
677 1615 3.195698 CGCTTTGGACGCCTAGGC 61.196 66.667 24.75 24.75 37.85 3.93
695 1633 3.274067 GCCCAAAGCGGTCGATTT 58.726 55.556 0.55 0.55 33.72 2.17
696 1634 1.584495 GCCCAAAGCGGTCGATTTT 59.416 52.632 3.79 0.00 30.80 1.82
697 1635 0.456142 GCCCAAAGCGGTCGATTTTC 60.456 55.000 3.79 0.00 30.80 2.29
698 1636 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.00 30.80 3.13
699 1637 0.878416 CCAAAGCGGTCGATTTTCCA 59.122 50.000 3.79 0.00 30.80 3.53
700 1638 1.268352 CCAAAGCGGTCGATTTTCCAA 59.732 47.619 3.79 0.00 30.80 3.53
701 1639 2.287909 CCAAAGCGGTCGATTTTCCAAA 60.288 45.455 3.79 0.00 30.80 3.28
702 1640 2.979813 CAAAGCGGTCGATTTTCCAAAG 59.020 45.455 3.79 0.00 30.80 2.77
703 1641 0.521735 AGCGGTCGATTTTCCAAAGC 59.478 50.000 0.00 0.00 0.00 3.51
704 1642 0.793104 GCGGTCGATTTTCCAAAGCG 60.793 55.000 0.54 0.54 0.00 4.68
705 1643 0.179200 CGGTCGATTTTCCAAAGCGG 60.179 55.000 7.00 0.00 0.00 5.52
706 1644 1.161843 GGTCGATTTTCCAAAGCGGA 58.838 50.000 7.00 0.00 44.40 5.54
713 1651 3.009115 TCCAAAGCGGAGGGGGAG 61.009 66.667 0.00 0.00 39.64 4.30
714 1652 4.803908 CCAAAGCGGAGGGGGAGC 62.804 72.222 0.00 0.00 36.56 4.70
722 1660 4.516195 GAGGGGGAGCGCTTCGAC 62.516 72.222 13.26 5.82 0.00 4.20
759 1697 3.459063 GTCGCCTTAGGGACGCCT 61.459 66.667 0.00 0.00 44.82 5.52
760 1698 2.682494 TCGCCTTAGGGACGCCTT 60.682 61.111 0.00 0.00 34.09 4.35
761 1699 2.267961 CGCCTTAGGGACGCCTTT 59.732 61.111 0.00 0.00 33.58 3.11
762 1700 0.971959 TCGCCTTAGGGACGCCTTTA 60.972 55.000 0.00 0.00 34.09 1.85
763 1701 0.108041 CGCCTTAGGGACGCCTTTAA 60.108 55.000 0.00 0.00 33.58 1.52
764 1702 1.676615 CGCCTTAGGGACGCCTTTAAA 60.677 52.381 0.00 0.00 33.58 1.52
765 1703 2.439409 GCCTTAGGGACGCCTTTAAAA 58.561 47.619 0.00 0.00 33.58 1.52
766 1704 2.163010 GCCTTAGGGACGCCTTTAAAAC 59.837 50.000 0.00 0.00 33.58 2.43
767 1705 3.414269 CCTTAGGGACGCCTTTAAAACA 58.586 45.455 0.00 0.00 33.58 2.83
768 1706 4.014406 CCTTAGGGACGCCTTTAAAACAT 58.986 43.478 0.00 0.00 33.58 2.71
769 1707 5.187687 CCTTAGGGACGCCTTTAAAACATA 58.812 41.667 0.00 0.00 33.58 2.29
770 1708 5.296035 CCTTAGGGACGCCTTTAAAACATAG 59.704 44.000 0.00 0.00 33.58 2.23
888 1826 3.914426 TTTAGGGAAGCTAGAGCCTTG 57.086 47.619 0.00 0.00 43.38 3.61
927 1865 3.544684 TGGTGCATCATATTCTGTGGAC 58.455 45.455 0.00 0.00 32.95 4.02
1650 3108 7.967890 AAGTTTCCATATTTTGAAAAGGCTG 57.032 32.000 0.00 0.00 32.68 4.85
1918 3382 5.645067 CCATGCTCAGTTGAGATAGAACAAA 59.355 40.000 13.13 0.00 44.74 2.83
1978 3442 7.444183 AGAACTACAAATCGGAATTGAGTTTGA 59.556 33.333 12.50 0.00 32.97 2.69
1995 3459 6.127730 TGAGTTTGAAAGTTGAGGGAAAAGAC 60.128 38.462 0.00 0.00 0.00 3.01
1996 3460 5.952347 AGTTTGAAAGTTGAGGGAAAAGACT 59.048 36.000 0.00 0.00 0.00 3.24
2007 3471 2.508526 GGAAAAGACTGTCAGCATGGT 58.491 47.619 10.88 0.00 36.16 3.55
2009 3473 1.242076 AAAGACTGTCAGCATGGTGC 58.758 50.000 20.07 14.89 45.46 5.01
2028 3492 1.907807 GTTGTGGAATGGGCTGGCA 60.908 57.895 2.88 0.00 0.00 4.92
2094 3558 0.549950 CTCCCCTGCCACTGATTCAT 59.450 55.000 0.00 0.00 0.00 2.57
2100 3564 2.562635 CTGCCACTGATTCATCTCCAG 58.437 52.381 0.00 0.00 0.00 3.86
2124 3588 5.096443 AGCTAAAATCTCTCAAGTCCCTG 57.904 43.478 0.00 0.00 0.00 4.45
2125 3589 4.534103 AGCTAAAATCTCTCAAGTCCCTGT 59.466 41.667 0.00 0.00 0.00 4.00
2148 3612 3.181469 GGATAACCGGTATGAGCAACTCA 60.181 47.826 8.00 0.00 44.99 3.41
2209 3673 3.560068 CCCGCTTCCAGTTGAACATATAC 59.440 47.826 0.00 0.00 0.00 1.47
2227 3691 0.034767 ACGGATCGAGGACTGTGGTA 60.035 55.000 0.00 0.00 0.00 3.25
2235 3699 2.457598 GAGGACTGTGGTACTGATGGA 58.542 52.381 0.00 0.00 36.63 3.41
2249 3713 3.392616 ACTGATGGAAAGGAACTGACACT 59.607 43.478 0.00 0.00 40.86 3.55
2256 3720 4.511826 GGAAAGGAACTGACACTACTGTTG 59.488 45.833 0.00 0.00 40.86 3.33
2260 3724 4.406003 AGGAACTGACACTACTGTTGTCTT 59.594 41.667 12.39 1.81 37.18 3.01
2279 3743 3.260884 TCTTATTTCCCGAAGCTCACTGT 59.739 43.478 0.00 0.00 0.00 3.55
2283 3747 1.334160 TCCCGAAGCTCACTGTGTTA 58.666 50.000 7.79 0.00 0.00 2.41
2285 3749 1.000955 CCCGAAGCTCACTGTGTTAGT 59.999 52.381 7.79 0.00 41.36 2.24
2287 3751 3.305813 CCCGAAGCTCACTGTGTTAGTAA 60.306 47.826 7.79 0.00 37.60 2.24
2319 3783 4.284490 TGTGAGAAGATAACAGAGCTTGGT 59.716 41.667 0.00 0.00 32.64 3.67
2460 5559 0.396417 GAGGAGGTCTGCTGCTCCTA 60.396 60.000 16.29 0.00 45.39 2.94
2466 5565 2.105930 CTGCTGCTCCTACCTCGC 59.894 66.667 0.00 0.00 0.00 5.03
2492 5591 2.350522 ACAGGAGTTGAACATCGATGC 58.649 47.619 25.11 10.54 0.00 3.91
2493 5592 2.289631 ACAGGAGTTGAACATCGATGCA 60.290 45.455 25.11 13.14 0.00 3.96
2498 5597 2.488937 AGTTGAACATCGATGCATGCAA 59.511 40.909 26.68 18.91 0.00 4.08
2517 5616 1.551452 AAGAGCTGCGGTTACTCTCT 58.449 50.000 0.00 0.00 39.84 3.10
2519 5618 0.804156 GAGCTGCGGTTACTCTCTGC 60.804 60.000 0.00 0.00 37.66 4.26
2627 5744 1.604755 CCTCTCGTCCTATTCGTCCTG 59.395 57.143 0.00 0.00 0.00 3.86
2674 5791 1.171308 CTCCCTGCAACAACTCATGG 58.829 55.000 0.00 0.00 0.00 3.66
2680 5797 3.871775 CAACAACTCATGGTGTGGC 57.128 52.632 0.00 0.00 42.09 5.01
2734 5851 5.267587 TCTCAAATCTCATCTCTCTCACCA 58.732 41.667 0.00 0.00 0.00 4.17
2735 5852 5.360429 TCTCAAATCTCATCTCTCTCACCAG 59.640 44.000 0.00 0.00 0.00 4.00
2741 5858 8.774546 AATCTCATCTCTCTCACCAGTTTATA 57.225 34.615 0.00 0.00 0.00 0.98
2743 5860 7.119387 TCTCATCTCTCTCACCAGTTTATACA 58.881 38.462 0.00 0.00 0.00 2.29
2747 5864 5.023533 TCTCTCACCAGTTTATACATGCC 57.976 43.478 0.00 0.00 0.00 4.40
2749 5866 4.769688 TCTCACCAGTTTATACATGCCTG 58.230 43.478 0.00 0.00 0.00 4.85
2778 5895 1.000394 GATCTAAGAGGCGAGGGCTTC 60.000 57.143 0.00 0.00 44.99 3.86
2815 5932 0.035820 GGGCCACCTCACACGATTAA 60.036 55.000 4.39 0.00 0.00 1.40
2822 5939 4.093408 CCACCTCACACGATTAAACATCTG 59.907 45.833 0.00 0.00 0.00 2.90
2860 5977 0.617413 CACTGGTTCAGAGCCCTCAT 59.383 55.000 0.00 0.00 35.18 2.90
2905 6022 4.617253 TCCTCTTCATCCAAACTCGAAA 57.383 40.909 0.00 0.00 0.00 3.46
2910 6027 6.402983 CCTCTTCATCCAAACTCGAAAATCTG 60.403 42.308 0.00 0.00 0.00 2.90
2912 6029 5.862924 TCATCCAAACTCGAAAATCTGTC 57.137 39.130 0.00 0.00 0.00 3.51
2968 6085 0.455410 CTGCAGACTCCTCTCTTCCG 59.545 60.000 8.42 0.00 0.00 4.30
2976 6093 1.684049 CCTCTCTTCCGCCCTCACT 60.684 63.158 0.00 0.00 0.00 3.41
2977 6094 1.515020 CTCTCTTCCGCCCTCACTG 59.485 63.158 0.00 0.00 0.00 3.66
2979 6096 0.967887 TCTCTTCCGCCCTCACTGAG 60.968 60.000 0.00 0.00 0.00 3.35
2984 6101 1.344065 TCCGCCCTCACTGAGTTAAA 58.656 50.000 5.32 0.00 0.00 1.52
2992 6109 5.163550 GCCCTCACTGAGTTAAACTTTTGTT 60.164 40.000 5.32 0.00 45.94 2.83
2998 6115 7.958567 TCACTGAGTTAAACTTTTGTTACAACG 59.041 33.333 0.00 0.00 42.67 4.10
3015 6132 1.248785 ACGAAGAGGTGGAGCGCTTA 61.249 55.000 13.26 0.05 0.00 3.09
3052 6169 3.046374 GAGGCCCTTTACCTCCTCAATA 58.954 50.000 0.00 0.00 46.81 1.90
3053 6170 3.049344 AGGCCCTTTACCTCCTCAATAG 58.951 50.000 0.00 0.00 28.76 1.73
3103 6220 1.903877 GAAGCTGCAGCACCTCCCTA 61.904 60.000 38.24 0.00 45.16 3.53
3104 6221 1.277580 AAGCTGCAGCACCTCCCTAT 61.278 55.000 38.24 13.55 45.16 2.57
3145 6262 5.486526 CCAGCCTCAAGATATTACAGATCC 58.513 45.833 0.00 0.00 0.00 3.36
3165 6282 0.962356 GGTGGTGTCCAGCCATTCAG 60.962 60.000 6.71 0.00 45.22 3.02
3198 6315 1.272490 CACGGACTGCCAAGTTCTCTA 59.728 52.381 0.00 0.00 36.52 2.43
3208 6325 7.398024 ACTGCCAAGTTCTCTACAAGAATTAT 58.602 34.615 0.00 0.00 45.57 1.28
3210 6327 9.553064 CTGCCAAGTTCTCTACAAGAATTATAT 57.447 33.333 0.00 0.00 45.57 0.86
3282 6399 8.767085 CCAAGTTCACTACGAAAATTACAAGTA 58.233 33.333 0.00 0.00 34.69 2.24
3358 6478 8.859236 AACCATTCCAATCATCATAGACTATG 57.141 34.615 15.25 15.25 37.52 2.23
3359 6479 6.883217 ACCATTCCAATCATCATAGACTATGC 59.117 38.462 16.38 0.00 36.14 3.14
3362 6482 6.631763 TCCAATCATCATAGACTATGCCAT 57.368 37.500 16.38 4.51 36.14 4.40
3364 6484 6.442885 TCCAATCATCATAGACTATGCCATCT 59.557 38.462 16.38 0.16 36.14 2.90
3411 6540 3.281727 TGATGGCTTGTACTCATTCCC 57.718 47.619 0.00 0.00 0.00 3.97
3432 6561 2.562738 CCACTTTCCCACCCTCAAATTC 59.437 50.000 0.00 0.00 0.00 2.17
3449 6578 7.749126 CCTCAAATTCACGTTACTTTCCATAAC 59.251 37.037 0.00 0.00 0.00 1.89
3557 6694 3.446442 AATCTTCTGAATGTGCAGGGT 57.554 42.857 0.00 0.00 36.55 4.34
3564 6701 2.746362 CTGAATGTGCAGGGTTCTTCTC 59.254 50.000 0.00 0.00 32.26 2.87
3632 6773 4.824479 TCTATCCAAGCACAGTTCATGA 57.176 40.909 0.00 0.00 0.00 3.07
3647 6788 1.202915 TCATGAAGTTGCTGCCCTTGA 60.203 47.619 6.42 0.00 0.00 3.02
3758 6905 1.959042 ACACCACTTCTTCAGCACTG 58.041 50.000 0.00 0.00 0.00 3.66
3772 6919 8.850454 TCTTCAGCACTGTTTACAAATTTAAC 57.150 30.769 0.00 0.00 0.00 2.01
3773 6920 8.462811 TCTTCAGCACTGTTTACAAATTTAACA 58.537 29.630 5.21 5.21 0.00 2.41
3778 6925 6.343616 GCACTGTTTACAAATTTAACACGTCG 60.344 38.462 1.68 0.00 0.00 5.12
3814 6966 7.033530 TGTGTCTTGTTATTTTGGTTACCTG 57.966 36.000 2.07 0.00 0.00 4.00
3950 7110 2.356382 TCCCACACACGTCAACATTTTC 59.644 45.455 0.00 0.00 0.00 2.29
4077 7242 0.461548 TGCACAATTTTGGACGCCAA 59.538 45.000 7.15 7.15 42.29 4.52
4094 7259 0.518636 CAAGACCTTGTGTGGCATCG 59.481 55.000 0.00 0.00 35.92 3.84
4147 7312 2.890945 CACCACTTTACCCCTTTGGAAG 59.109 50.000 0.00 0.00 38.00 3.46
4257 7422 3.031013 TCAATCTACTTCGCAGGGATCA 58.969 45.455 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
300 301 2.695147 CACCTTCTGTTCTTTTGGCCTT 59.305 45.455 3.32 0.00 0.00 4.35
518 1456 9.878667 TCTTTGACATCGGTATTTTCTACAATA 57.121 29.630 0.00 0.00 0.00 1.90
586 1524 3.047613 GGCGTCGCCTTAAAAACATAG 57.952 47.619 28.98 0.00 46.69 2.23
605 1543 1.408453 CCCTCCCTAAGGCGGTAAGG 61.408 65.000 0.00 0.00 44.71 2.69
606 1544 1.408453 CCCCTCCCTAAGGCGGTAAG 61.408 65.000 0.00 0.00 44.71 2.34
607 1545 1.383525 CCCCTCCCTAAGGCGGTAA 60.384 63.158 0.00 0.00 44.71 2.85
608 1546 2.284493 CCCCTCCCTAAGGCGGTA 59.716 66.667 0.00 0.00 44.71 4.02
609 1547 4.817909 CCCCCTCCCTAAGGCGGT 62.818 72.222 0.00 0.00 44.71 5.68
651 1589 4.467084 TCCAAAGCGCCCGCCTAG 62.467 66.667 2.29 0.00 43.17 3.02
652 1590 4.770874 GTCCAAAGCGCCCGCCTA 62.771 66.667 2.29 0.00 43.17 3.93
660 1598 3.195698 GCCTAGGCGTCCAAAGCG 61.196 66.667 20.16 0.00 35.00 4.68
678 1616 0.456142 GAAAATCGACCGCTTTGGGC 60.456 55.000 0.00 0.00 45.45 5.36
679 1617 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.000 0.00 0.00 44.64 4.12
680 1618 0.878416 TGGAAAATCGACCGCTTTGG 59.122 50.000 0.00 0.00 46.41 3.28
681 1619 2.697431 TTGGAAAATCGACCGCTTTG 57.303 45.000 0.00 0.00 0.00 2.77
682 1620 2.607038 GCTTTGGAAAATCGACCGCTTT 60.607 45.455 0.00 0.00 0.00 3.51
683 1621 1.068541 GCTTTGGAAAATCGACCGCTT 60.069 47.619 0.00 0.00 0.00 4.68
684 1622 0.521735 GCTTTGGAAAATCGACCGCT 59.478 50.000 0.00 0.00 0.00 5.52
685 1623 0.793104 CGCTTTGGAAAATCGACCGC 60.793 55.000 0.00 0.00 0.00 5.68
686 1624 0.179200 CCGCTTTGGAAAATCGACCG 60.179 55.000 0.00 0.00 42.00 4.79
687 1625 1.161843 TCCGCTTTGGAAAATCGACC 58.838 50.000 0.00 0.00 46.38 4.79
697 1635 4.803908 GCTCCCCCTCCGCTTTGG 62.804 72.222 0.00 0.00 40.09 3.28
705 1643 4.516195 GTCGAAGCGCTCCCCCTC 62.516 72.222 12.06 2.47 0.00 4.30
742 1680 2.517484 AAAGGCGTCCCTAAGGCGAC 62.517 60.000 0.00 0.00 41.90 5.19
743 1681 0.971959 TAAAGGCGTCCCTAAGGCGA 60.972 55.000 0.00 0.00 41.90 5.54
744 1682 0.108041 TTAAAGGCGTCCCTAAGGCG 60.108 55.000 0.00 0.00 41.90 5.52
745 1683 2.118313 TTTAAAGGCGTCCCTAAGGC 57.882 50.000 0.00 0.00 41.90 4.35
746 1684 3.414269 TGTTTTAAAGGCGTCCCTAAGG 58.586 45.455 0.00 0.00 41.90 2.69
747 1685 5.296035 CCTATGTTTTAAAGGCGTCCCTAAG 59.704 44.000 0.00 0.00 41.90 2.18
748 1686 5.045724 TCCTATGTTTTAAAGGCGTCCCTAA 60.046 40.000 0.00 0.00 41.90 2.69
749 1687 4.470664 TCCTATGTTTTAAAGGCGTCCCTA 59.529 41.667 0.00 0.00 41.90 3.53
750 1688 3.264964 TCCTATGTTTTAAAGGCGTCCCT 59.735 43.478 0.00 0.00 45.77 4.20
751 1689 3.613030 TCCTATGTTTTAAAGGCGTCCC 58.387 45.455 0.00 0.00 0.00 4.46
752 1690 4.094442 CACTCCTATGTTTTAAAGGCGTCC 59.906 45.833 0.00 0.00 0.00 4.79
753 1691 4.436986 GCACTCCTATGTTTTAAAGGCGTC 60.437 45.833 0.00 0.00 0.00 5.19
754 1692 3.439129 GCACTCCTATGTTTTAAAGGCGT 59.561 43.478 0.00 0.00 0.00 5.68
755 1693 3.438781 TGCACTCCTATGTTTTAAAGGCG 59.561 43.478 0.00 0.00 0.00 5.52
756 1694 4.459337 AGTGCACTCCTATGTTTTAAAGGC 59.541 41.667 15.25 0.00 0.00 4.35
757 1695 6.316390 CCTAGTGCACTCCTATGTTTTAAAGG 59.684 42.308 25.56 15.52 0.00 3.11
758 1696 6.879458 ACCTAGTGCACTCCTATGTTTTAAAG 59.121 38.462 25.56 10.03 0.00 1.85
759 1697 6.775708 ACCTAGTGCACTCCTATGTTTTAAA 58.224 36.000 25.56 0.00 0.00 1.52
760 1698 6.368779 ACCTAGTGCACTCCTATGTTTTAA 57.631 37.500 25.56 0.00 0.00 1.52
761 1699 7.484993 TTACCTAGTGCACTCCTATGTTTTA 57.515 36.000 25.56 0.00 0.00 1.52
762 1700 4.910458 ACCTAGTGCACTCCTATGTTTT 57.090 40.909 25.56 0.00 0.00 2.43
763 1701 6.368779 TTTACCTAGTGCACTCCTATGTTT 57.631 37.500 25.56 0.00 0.00 2.83
764 1702 6.212791 TCTTTTACCTAGTGCACTCCTATGTT 59.787 38.462 25.56 4.51 0.00 2.71
765 1703 5.720041 TCTTTTACCTAGTGCACTCCTATGT 59.280 40.000 25.56 15.91 0.00 2.29
766 1704 6.222038 TCTTTTACCTAGTGCACTCCTATG 57.778 41.667 25.56 10.78 0.00 2.23
767 1705 7.125811 TCAATCTTTTACCTAGTGCACTCCTAT 59.874 37.037 25.56 10.27 0.00 2.57
768 1706 6.439375 TCAATCTTTTACCTAGTGCACTCCTA 59.561 38.462 25.56 4.90 0.00 2.94
769 1707 5.248477 TCAATCTTTTACCTAGTGCACTCCT 59.752 40.000 25.56 9.36 0.00 3.69
770 1708 5.488341 TCAATCTTTTACCTAGTGCACTCC 58.512 41.667 25.56 0.00 0.00 3.85
888 1826 2.484264 ACCAGACAGAAAAATAGTGCGC 59.516 45.455 0.00 0.00 0.00 6.09
927 1865 0.381801 AAAAGTCCAGCAACACAGCG 59.618 50.000 0.00 0.00 40.15 5.18
1800 3261 7.549488 AGTTTAGGAAACCAAGACATATTCTCG 59.451 37.037 0.00 0.00 42.34 4.04
1918 3382 2.290960 GCTTCCCAAATACTGGTCCTGT 60.291 50.000 6.64 6.64 44.76 4.00
1978 3442 4.855340 TGACAGTCTTTTCCCTCAACTTT 58.145 39.130 1.31 0.00 0.00 2.66
1995 3459 1.208358 CAACGCACCATGCTGACAG 59.792 57.895 0.00 0.00 42.25 3.51
1996 3460 1.525765 ACAACGCACCATGCTGACA 60.526 52.632 0.00 0.00 42.25 3.58
2007 3471 2.115052 AGCCCATTCCACAACGCA 59.885 55.556 0.00 0.00 0.00 5.24
2009 3473 2.993471 GCCAGCCCATTCCACAACG 61.993 63.158 0.00 0.00 0.00 4.10
2028 3492 8.878211 TCTTTCAGATCAGCTAGATTATGGAAT 58.122 33.333 0.00 0.00 37.00 3.01
2055 3519 0.951040 GGCACTTCGTCACCTTCAGG 60.951 60.000 0.00 0.00 42.17 3.86
2066 3530 4.785453 GCAGGGGAGGGCACTTCG 62.785 72.222 0.00 0.00 0.00 3.79
2094 3558 6.212388 ACTTGAGAGATTTTAGCTTCTGGAGA 59.788 38.462 0.00 0.00 0.00 3.71
2100 3564 5.584251 CAGGGACTTGAGAGATTTTAGCTTC 59.416 44.000 0.00 0.00 34.60 3.86
2124 3588 2.870411 GTTGCTCATACCGGTTATCCAC 59.130 50.000 15.04 0.00 0.00 4.02
2125 3589 2.769663 AGTTGCTCATACCGGTTATCCA 59.230 45.455 15.04 0.93 0.00 3.41
2148 3612 2.309613 TCACCTTCAAACAGCAGCAAT 58.690 42.857 0.00 0.00 0.00 3.56
2209 3673 0.381089 GTACCACAGTCCTCGATCCG 59.619 60.000 0.00 0.00 0.00 4.18
2227 3691 3.392616 AGTGTCAGTTCCTTTCCATCAGT 59.607 43.478 0.00 0.00 0.00 3.41
2235 3699 5.099042 ACAACAGTAGTGTCAGTTCCTTT 57.901 39.130 3.07 0.00 35.08 3.11
2249 3713 4.933400 GCTTCGGGAAATAAGACAACAGTA 59.067 41.667 0.00 0.00 0.00 2.74
2256 3720 3.619038 CAGTGAGCTTCGGGAAATAAGAC 59.381 47.826 0.00 0.00 0.00 3.01
2260 3724 2.301870 ACACAGTGAGCTTCGGGAAATA 59.698 45.455 7.81 0.00 0.00 1.40
2279 3743 8.638873 TCTTCTCACAACTTCTCATTACTAACA 58.361 33.333 0.00 0.00 0.00 2.41
2283 3747 9.646427 GTTATCTTCTCACAACTTCTCATTACT 57.354 33.333 0.00 0.00 0.00 2.24
2285 3749 9.645059 CTGTTATCTTCTCACAACTTCTCATTA 57.355 33.333 0.00 0.00 0.00 1.90
2287 3751 7.901029 TCTGTTATCTTCTCACAACTTCTCAT 58.099 34.615 0.00 0.00 0.00 2.90
2319 3783 2.280797 GTCTGAAGCACCGCCACA 60.281 61.111 0.00 0.00 0.00 4.17
2371 5467 4.300803 TCTTGTGCATGCTCAATTTCAAC 58.699 39.130 29.39 12.85 0.00 3.18
2460 5559 0.542232 ACTCCTGTAGTTGGCGAGGT 60.542 55.000 0.00 0.00 33.35 3.85
2483 5582 1.065102 GCTCTTTGCATGCATCGATGT 59.935 47.619 23.37 4.92 42.31 3.06
2488 5587 0.866061 CGCAGCTCTTTGCATGCATC 60.866 55.000 23.37 8.60 44.28 3.91
2489 5588 1.138883 CGCAGCTCTTTGCATGCAT 59.861 52.632 23.37 1.46 44.28 3.96
2492 5591 0.804364 TAACCGCAGCTCTTTGCATG 59.196 50.000 0.00 0.00 44.28 4.06
2493 5592 0.804989 GTAACCGCAGCTCTTTGCAT 59.195 50.000 0.00 0.00 44.28 3.96
2498 5597 1.203523 CAGAGAGTAACCGCAGCTCTT 59.796 52.381 0.00 0.00 39.43 2.85
2517 5616 0.106769 TGTCCTTGCCAAGTGAAGCA 60.107 50.000 3.37 0.00 37.18 3.91
2519 5618 0.595095 GCTGTCCTTGCCAAGTGAAG 59.405 55.000 3.37 0.00 0.00 3.02
2565 5664 2.877975 CAACCATTGGAGGGAGCAG 58.122 57.895 10.37 0.00 0.00 4.24
2594 5711 1.002011 GAGAGGAACCTGGGGCAAC 60.002 63.158 0.00 0.00 0.00 4.17
2627 5744 1.657751 GGGGAAACAAGATGAGGCGC 61.658 60.000 0.00 0.00 0.00 6.53
2734 5851 4.889409 CCCACAATCAGGCATGTATAAACT 59.111 41.667 0.00 0.00 0.00 2.66
2735 5852 4.037923 CCCCACAATCAGGCATGTATAAAC 59.962 45.833 0.00 0.00 0.00 2.01
2741 5858 0.632835 ATCCCCACAATCAGGCATGT 59.367 50.000 0.00 0.00 0.00 3.21
2743 5860 1.229131 AGATCCCCACAATCAGGCAT 58.771 50.000 0.00 0.00 0.00 4.40
2747 5864 3.495806 GCCTCTTAGATCCCCACAATCAG 60.496 52.174 0.00 0.00 0.00 2.90
2749 5866 2.548920 CGCCTCTTAGATCCCCACAATC 60.549 54.545 0.00 0.00 0.00 2.67
2801 5918 4.690748 CACAGATGTTTAATCGTGTGAGGT 59.309 41.667 9.26 0.00 38.00 3.85
2815 5932 2.765689 TTTGGGGTTCCACAGATGTT 57.234 45.000 0.00 0.00 43.94 2.71
2822 5939 3.641436 AGTGAAGAATTTTGGGGTTCCAC 59.359 43.478 0.00 0.00 43.94 4.02
2860 5977 1.913951 ATCTCTTGGTCATGCGGCCA 61.914 55.000 2.24 0.00 0.00 5.36
2910 6027 1.517257 CGCCCAGTCATCTGTCGAC 60.517 63.158 9.11 9.11 39.82 4.20
2912 6029 2.202797 CCGCCCAGTCATCTGTCG 60.203 66.667 0.00 0.00 39.82 4.35
2924 6041 1.988406 ACAGTAAGGACTCCCGCCC 60.988 63.158 0.00 0.00 37.58 6.13
2940 6057 1.297689 GAGTCTGCAGATGGGCACA 59.702 57.895 21.47 0.00 39.25 4.57
2968 6085 4.338400 ACAAAAGTTTAACTCAGTGAGGGC 59.662 41.667 23.79 8.89 33.35 5.19
2976 6093 8.719648 TCTTCGTTGTAACAAAAGTTTAACTCA 58.280 29.630 0.00 0.00 0.00 3.41
2977 6094 9.207042 CTCTTCGTTGTAACAAAAGTTTAACTC 57.793 33.333 0.00 0.00 0.00 3.01
2979 6096 7.964559 ACCTCTTCGTTGTAACAAAAGTTTAAC 59.035 33.333 0.00 0.00 0.00 2.01
2984 6101 4.334481 CCACCTCTTCGTTGTAACAAAAGT 59.666 41.667 0.00 0.00 0.00 2.66
2992 6109 0.242825 CGCTCCACCTCTTCGTTGTA 59.757 55.000 0.00 0.00 0.00 2.41
2998 6115 1.337823 TGTTAAGCGCTCCACCTCTTC 60.338 52.381 12.06 0.00 0.00 2.87
3015 6132 1.274712 CCTCCTCTTGCTCCTCTGTT 58.725 55.000 0.00 0.00 0.00 3.16
3052 6169 2.736670 AACACAAGTTTCTGGAGGCT 57.263 45.000 0.00 0.00 33.11 4.58
3053 6170 3.381590 AGAAAACACAAGTTTCTGGAGGC 59.618 43.478 0.00 0.00 46.79 4.70
3145 6262 2.034066 AATGGCTGGACACCACCG 59.966 61.111 0.00 0.00 40.82 4.94
3178 6295 0.034059 AGAGAACTTGGCAGTCCGTG 59.966 55.000 0.00 0.00 34.14 4.94
3208 6325 3.035363 TGGCCGGACAGTTTCTGATATA 58.965 45.455 5.41 0.00 35.18 0.86
3210 6327 1.271856 TGGCCGGACAGTTTCTGATA 58.728 50.000 5.41 0.00 35.18 2.15
3282 6399 1.134007 TCCTCGCTGATGCCATCAAAT 60.134 47.619 9.00 0.00 39.11 2.32
3284 6401 0.179065 CTCCTCGCTGATGCCATCAA 60.179 55.000 9.00 0.00 39.11 2.57
3286 6403 1.960250 GCTCCTCGCTGATGCCATC 60.960 63.158 0.00 0.00 35.36 3.51
3345 6462 8.518430 AGTAGTAGATGGCATAGTCTATGATG 57.482 38.462 21.78 0.54 38.45 3.07
3357 6477 5.216622 ACCTTGGATTAGTAGTAGATGGCA 58.783 41.667 0.00 0.00 0.00 4.92
3358 6478 5.810080 ACCTTGGATTAGTAGTAGATGGC 57.190 43.478 0.00 0.00 0.00 4.40
3359 6479 8.361139 CAGTTACCTTGGATTAGTAGTAGATGG 58.639 40.741 0.00 0.00 0.00 3.51
3362 6482 8.111545 TGTCAGTTACCTTGGATTAGTAGTAGA 58.888 37.037 0.00 0.00 0.00 2.59
3364 6484 8.834004 ATGTCAGTTACCTTGGATTAGTAGTA 57.166 34.615 0.00 0.00 0.00 1.82
3384 6507 4.650734 TGAGTACAAGCCATCAAATGTCA 58.349 39.130 0.00 0.00 0.00 3.58
3411 6540 2.309136 ATTTGAGGGTGGGAAAGTGG 57.691 50.000 0.00 0.00 0.00 4.00
3432 6561 7.487189 ACGAGATTAGTTATGGAAAGTAACGTG 59.513 37.037 0.00 0.00 37.18 4.49
3449 6578 7.644490 ACTCTGATGCTTACTTACGAGATTAG 58.356 38.462 0.00 0.00 0.00 1.73
3461 6590 7.659652 AAAAGACAACTACTCTGATGCTTAC 57.340 36.000 0.00 0.00 0.00 2.34
3509 6638 2.624838 GTGGGTTATTCAGATGGCATGG 59.375 50.000 3.81 0.00 0.00 3.66
3511 6640 3.959495 AGTGGGTTATTCAGATGGCAT 57.041 42.857 0.00 0.00 0.00 4.40
3557 6694 7.386851 AGAAGAATGTACAAATCCGAGAAGAA 58.613 34.615 0.00 0.00 0.00 2.52
3564 6701 5.360591 AGGCTAGAAGAATGTACAAATCCG 58.639 41.667 0.00 0.00 0.00 4.18
3632 6773 0.390492 GCTTTCAAGGGCAGCAACTT 59.610 50.000 0.00 0.00 33.45 2.66
3673 6817 4.262894 CCAGTATAATAATGGACGGGTGCT 60.263 45.833 0.00 0.00 46.34 4.40
3758 6905 8.735837 ACAAATCGACGTGTTAAATTTGTAAAC 58.264 29.630 16.73 0.00 44.42 2.01
3772 6919 3.217608 CACATCACAACAAATCGACGTG 58.782 45.455 0.00 0.00 0.00 4.49
3773 6920 2.869801 ACACATCACAACAAATCGACGT 59.130 40.909 0.00 0.00 0.00 4.34
3778 6925 8.801715 AATAACAAGACACATCACAACAAATC 57.198 30.769 0.00 0.00 0.00 2.17
3814 6966 9.912634 TGAAACATATGAAATGGAAACTTTCTC 57.087 29.630 10.38 0.00 34.43 2.87
3856 7009 4.590222 AGGAAGCATTTGTTCAGTTCCAAT 59.410 37.500 0.00 0.00 36.67 3.16
3950 7110 4.728608 GCGGTAAGCGAAACAGATAAAATG 59.271 41.667 0.00 0.00 35.41 2.32
4055 7215 1.526464 GGCGTCCAAAATTGTGCAAAG 59.474 47.619 0.00 0.00 0.00 2.77
4077 7242 1.672356 GCGATGCCACACAAGGTCT 60.672 57.895 0.00 0.00 0.00 3.85
4147 7312 2.818751 TGGGGTCACCATGGATTAAC 57.181 50.000 21.47 10.14 46.80 2.01
4257 7422 7.982354 GCTATAAGAATGTACAACTCCAAGACT 59.018 37.037 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.