Multiple sequence alignment - TraesCS1A01G324000

Loading Multiple Alignment...

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 TraesCS1A01G324000 chr1A 100.000 3934 0 0 1 3934 514689294 514693227 0.000000e+00 7265.0
1 TraesCS1A01G324000 chr1B 91.676 2583 114 26 713 3244 564907158 564909690 0.000000e+00 3485.0
2 TraesCS1A01G324000 chr1B 81.173 972 121 26 2119 3059 565371563 565372503 0.000000e+00 725.0
3 TraesCS1A01G324000 chr1B 89.414 529 36 4 3240 3767 564909738 564910247 0.000000e+00 649.0
4 TraesCS1A01G324000 chr1B 85.135 592 66 14 3344 3934 565515468 565516038 1.570000e-163 586.0
5 TraesCS1A01G324000 chr1B 88.608 158 7 3 3080 3226 565514874 565515031 8.680000e-42 182.0
6 TraesCS1A01G324000 chr1D 89.645 2588 129 41 724 3247 418043684 418046196 0.000000e+00 3166.0
7 TraesCS1A01G324000 chr1D 91.667 696 29 7 3240 3934 418046236 418046903 0.000000e+00 937.0
8 TraesCS1A01G324000 chr4A 80.183 656 101 22 13 654 538832199 538832839 7.700000e-127 464.0
9 TraesCS1A01G324000 chr2B 82.505 503 62 17 146 636 632159188 632159676 6.080000e-113 418.0
10 TraesCS1A01G324000 chr3D 81.095 402 54 8 178 559 579591045 579591444 6.390000e-78 302.0
11 TraesCS1A01G324000 chr3D 88.489 139 11 4 7 141 579590914 579591051 3.150000e-36 163.0
12 TraesCS1A01G324000 chr3D 72.555 685 121 37 1 646 68394460 68395116 1.130000e-35 161.0
13 TraesCS1A01G324000 chr3D 86.567 67 8 1 6 71 353225710 353225776 5.450000e-09 73.1
14 TraesCS1A01G324000 chr5A 77.344 512 77 21 1726 2233 69023378 69023854 2.330000e-67 267.0
15 TraesCS1A01G324000 chr5A 83.333 102 12 5 1 97 552223291 552223392 5.410000e-14 89.8
16 TraesCS1A01G324000 chr3A 74.648 639 121 31 7 626 688950007 688949391 1.090000e-60 244.0
17 TraesCS1A01G324000 chr3A 73.153 406 67 27 293 662 427204258 427203859 1.490000e-19 108.0
18 TraesCS1A01G324000 chr3A 84.932 73 8 2 19 88 714649206 714649278 1.960000e-08 71.3
19 TraesCS1A01G324000 chr5D 82.096 229 39 1 1753 1979 425086615 425086843 1.120000e-45 195.0
20 TraesCS1A01G324000 chr3B 78.409 264 33 10 293 534 773906197 773906458 2.450000e-32 150.0
21 TraesCS1A01G324000 chr3B 95.455 44 0 2 8 49 718370233 718370190 7.050000e-08 69.4
22 TraesCS1A01G324000 chr4D 78.824 170 36 0 487 656 365516619 365516450 8.930000e-22 115.0
23 TraesCS1A01G324000 chr2A 74.411 297 63 8 1 290 709194626 709194916 8.930000e-22 115.0
24 TraesCS1A01G324000 chr2D 91.935 62 5 0 601 662 331460559 331460620 1.950000e-13 87.9
25 TraesCS1A01G324000 chr6A 78.689 122 24 2 544 664 572588355 572588235 3.260000e-11 80.5
26 TraesCS1A01G324000 chr4B 74.725 182 30 10 14 184 183565770 183565946 2.540000e-07 67.6


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G324000 chr1A 514689294 514693227 3933 False 7265.0 7265 100.0000 1 3934 1 chr1A.!!$F1 3933
1 TraesCS1A01G324000 chr1B 564907158 564910247 3089 False 2067.0 3485 90.5450 713 3767 2 chr1B.!!$F2 3054
2 TraesCS1A01G324000 chr1B 565371563 565372503 940 False 725.0 725 81.1730 2119 3059 1 chr1B.!!$F1 940
3 TraesCS1A01G324000 chr1B 565514874 565516038 1164 False 384.0 586 86.8715 3080 3934 2 chr1B.!!$F3 854
4 TraesCS1A01G324000 chr1D 418043684 418046903 3219 False 2051.5 3166 90.6560 724 3934 2 chr1D.!!$F1 3210
5 TraesCS1A01G324000 chr4A 538832199 538832839 640 False 464.0 464 80.1830 13 654 1 chr4A.!!$F1 641
6 TraesCS1A01G324000 chr3D 579590914 579591444 530 False 232.5 302 84.7920 7 559 2 chr3D.!!$F3 552
7 TraesCS1A01G324000 chr3A 688949391 688950007 616 True 244.0 244 74.6480 7 626 1 chr3A.!!$R2 619

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
485 533 0.389391 GCTAATGTCCAGCTAGGCGA 59.611 55.0 0.0 0.0 36.07 5.54 F
1507 1597 0.316841 TGGCCGAAAGAAACCATTGC 59.683 50.0 0.0 0.0 0.00 3.56 F
2004 2107 0.464036 AACTTGCACGTCTCACAGGA 59.536 50.0 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2129 0.317160 TAGAATAGATGCACGGCCGG 59.683 55.000 31.76 19.49 0.00 6.13 R
2489 2598 0.322975 AGTACTTGCACTGCCTCCTG 59.677 55.000 0.00 0.00 0.00 3.86 R
2982 3116 1.059122 CCACACGACGATTTCACATCG 59.941 52.381 0.00 2.73 46.02 3.84 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
112 120 4.685165 TGGCATTTTGAAATCGTTCACATG 59.315 37.500 0.00 0.00 43.52 3.21
116 128 7.095857 GGCATTTTGAAATCGTTCACATGTTTA 60.096 33.333 0.00 0.00 43.52 2.01
172 185 7.948357 AGTGTTTACATATATGAACGCTCCTA 58.052 34.615 19.63 0.00 0.00 2.94
174 187 9.850628 GTGTTTACATATATGAACGCTCCTATA 57.149 33.333 19.63 0.00 0.00 1.31
194 207 7.040201 TCCTATATGTTCTTATTAAGGTCGCGT 60.040 37.037 5.77 0.00 0.00 6.01
213 226 3.632189 CGTCATCTATCGTCATGAGCAA 58.368 45.455 0.00 0.00 29.46 3.91
223 236 1.736681 GTCATGAGCAACCTTCAGAGC 59.263 52.381 0.00 0.00 0.00 4.09
247 261 3.084579 CTAGTTGCAGGCGCTTCG 58.915 61.111 7.64 0.00 39.64 3.79
269 283 1.546029 TGCGATATCCCGAGATTGAGG 59.454 52.381 0.00 0.00 33.67 3.86
285 299 2.536066 TGAGGCCTGTAAAGCACTCTA 58.464 47.619 12.00 0.00 32.24 2.43
291 305 4.434520 GCCTGTAAAGCACTCTAGTTAGG 58.565 47.826 0.00 0.00 0.00 2.69
479 527 3.136763 CGATTCATGCTAATGTCCAGCT 58.863 45.455 0.00 0.00 39.83 4.24
482 530 3.758755 TCATGCTAATGTCCAGCTAGG 57.241 47.619 0.00 0.00 39.83 3.02
485 533 0.389391 GCTAATGTCCAGCTAGGCGA 59.611 55.000 0.00 0.00 36.07 5.54
499 547 1.982660 AGGCGATCAACGATCCTAGA 58.017 50.000 0.00 0.00 45.77 2.43
518 566 5.183713 CCTAGAATTTGACTTGCCACATCAA 59.816 40.000 0.00 0.00 0.00 2.57
524 572 2.884012 TGACTTGCCACATCAACGAATT 59.116 40.909 0.00 0.00 0.00 2.17
525 573 3.317711 TGACTTGCCACATCAACGAATTT 59.682 39.130 0.00 0.00 0.00 1.82
534 582 6.324819 CCACATCAACGAATTTCAGCTAAAT 58.675 36.000 0.00 0.00 39.56 1.40
560 608 4.564821 CCTGAAGGTTCAAAATAGACCGGA 60.565 45.833 9.46 0.00 36.64 5.14
564 612 4.189231 AGGTTCAAAATAGACCGGAATCG 58.811 43.478 9.46 0.00 0.00 3.34
565 613 4.081309 AGGTTCAAAATAGACCGGAATCGA 60.081 41.667 9.46 0.00 39.00 3.59
615 663 8.047310 AGATTACAAACTCAGGGTTCGATTTAT 58.953 33.333 0.00 0.00 37.12 1.40
632 680 8.752766 TCGATTTATCTTTCGTCTACAAGTTT 57.247 30.769 0.00 0.00 36.74 2.66
637 685 8.801715 TTATCTTTCGTCTACAAGTTTAACGT 57.198 30.769 0.00 0.00 35.04 3.99
638 686 9.891828 TTATCTTTCGTCTACAAGTTTAACGTA 57.108 29.630 0.00 0.00 35.04 3.57
644 692 8.351495 TCGTCTACAAGTTTAACGTATGTTTT 57.649 30.769 5.48 0.00 39.54 2.43
648 696 9.107177 TCTACAAGTTTAACGTATGTTTTGGAA 57.893 29.630 5.48 0.00 39.54 3.53
689 737 9.804758 ATTAAAGGAATACTCTTAGTTGTCTCG 57.195 33.333 0.00 0.00 0.00 4.04
690 738 5.838531 AGGAATACTCTTAGTTGTCTCGG 57.161 43.478 0.00 0.00 0.00 4.63
691 739 5.507637 AGGAATACTCTTAGTTGTCTCGGA 58.492 41.667 0.00 0.00 0.00 4.55
692 740 5.950549 AGGAATACTCTTAGTTGTCTCGGAA 59.049 40.000 0.00 0.00 0.00 4.30
693 741 6.436532 AGGAATACTCTTAGTTGTCTCGGAAA 59.563 38.462 0.00 0.00 0.00 3.13
694 742 7.039223 AGGAATACTCTTAGTTGTCTCGGAAAA 60.039 37.037 0.00 0.00 0.00 2.29
695 743 7.275999 GGAATACTCTTAGTTGTCTCGGAAAAG 59.724 40.741 0.00 0.00 0.00 2.27
696 744 5.786264 ACTCTTAGTTGTCTCGGAAAAGA 57.214 39.130 0.00 0.00 0.00 2.52
697 745 6.158023 ACTCTTAGTTGTCTCGGAAAAGAA 57.842 37.500 0.00 0.00 0.00 2.52
698 746 6.579865 ACTCTTAGTTGTCTCGGAAAAGAAA 58.420 36.000 0.00 0.00 0.00 2.52
699 747 7.046033 ACTCTTAGTTGTCTCGGAAAAGAAAA 58.954 34.615 0.00 0.00 0.00 2.29
700 748 7.224949 ACTCTTAGTTGTCTCGGAAAAGAAAAG 59.775 37.037 0.00 0.00 0.00 2.27
701 749 6.482308 TCTTAGTTGTCTCGGAAAAGAAAAGG 59.518 38.462 0.00 0.00 0.00 3.11
702 750 3.883489 AGTTGTCTCGGAAAAGAAAAGGG 59.117 43.478 0.00 0.00 0.00 3.95
703 751 3.849563 TGTCTCGGAAAAGAAAAGGGA 57.150 42.857 0.00 0.00 0.00 4.20
704 752 4.159244 TGTCTCGGAAAAGAAAAGGGAA 57.841 40.909 0.00 0.00 0.00 3.97
705 753 4.725490 TGTCTCGGAAAAGAAAAGGGAAT 58.275 39.130 0.00 0.00 0.00 3.01
706 754 5.871834 TGTCTCGGAAAAGAAAAGGGAATA 58.128 37.500 0.00 0.00 0.00 1.75
707 755 5.704053 TGTCTCGGAAAAGAAAAGGGAATAC 59.296 40.000 0.00 0.00 0.00 1.89
708 756 5.123502 GTCTCGGAAAAGAAAAGGGAATACC 59.876 44.000 0.00 0.00 40.67 2.73
709 757 4.988029 TCGGAAAAGAAAAGGGAATACCA 58.012 39.130 0.00 0.00 43.89 3.25
710 758 5.007682 TCGGAAAAGAAAAGGGAATACCAG 58.992 41.667 0.00 0.00 43.89 4.00
711 759 4.765339 CGGAAAAGAAAAGGGAATACCAGT 59.235 41.667 0.00 0.00 43.89 4.00
844 903 2.355837 GAGCACGTCACTGCGGAA 60.356 61.111 0.00 0.00 42.42 4.30
1068 1133 2.239681 TTGTTCTCCTCTCCCTCTCC 57.760 55.000 0.00 0.00 0.00 3.71
1076 1141 2.015726 TCTCCCTCTCCCTCTCCCC 61.016 68.421 0.00 0.00 0.00 4.81
1101 1166 1.517832 CTCGGTTCCGGATCAGCTT 59.482 57.895 4.15 0.00 0.00 3.74
1331 1420 6.490721 TGTGGTTAAAACGGAAACTGGAATAT 59.509 34.615 0.00 0.00 0.00 1.28
1332 1421 7.664731 TGTGGTTAAAACGGAAACTGGAATATA 59.335 33.333 0.00 0.00 0.00 0.86
1333 1422 7.964559 GTGGTTAAAACGGAAACTGGAATATAC 59.035 37.037 0.00 0.00 0.00 1.47
1391 1481 1.881973 CCCAATCATGATAACGGCCAG 59.118 52.381 9.04 0.00 0.00 4.85
1412 1502 4.575236 CAGCATGAAAGCAGATCACAGTAT 59.425 41.667 0.00 0.00 39.69 2.12
1450 1540 2.186903 GCTCCGGGCGATTCTTGA 59.813 61.111 0.00 0.00 0.00 3.02
1467 1557 1.080434 GACTTCTTGCTCTCGCCGT 60.080 57.895 0.00 0.00 34.43 5.68
1501 1591 1.807142 CTCCTCTTGGCCGAAAGAAAC 59.193 52.381 6.94 0.00 35.79 2.78
1503 1593 1.604604 CTCTTGGCCGAAAGAAACCA 58.395 50.000 6.94 0.00 35.79 3.67
1507 1597 0.316841 TGGCCGAAAGAAACCATTGC 59.683 50.000 0.00 0.00 0.00 3.56
1534 1624 1.267121 ATCGGTCACTGTGCTAAGGT 58.733 50.000 2.12 0.00 0.00 3.50
1535 1625 1.045407 TCGGTCACTGTGCTAAGGTT 58.955 50.000 2.12 0.00 0.00 3.50
1536 1626 2.241160 TCGGTCACTGTGCTAAGGTTA 58.759 47.619 2.12 0.00 0.00 2.85
1537 1627 2.029649 TCGGTCACTGTGCTAAGGTTAC 60.030 50.000 2.12 0.00 0.00 2.50
1658 1759 9.559732 TCAGTTACACCATAATTCATGATTAGG 57.440 33.333 0.00 0.00 36.69 2.69
1659 1760 9.559732 CAGTTACACCATAATTCATGATTAGGA 57.440 33.333 0.00 0.00 34.69 2.94
1660 1761 9.784531 AGTTACACCATAATTCATGATTAGGAG 57.215 33.333 0.00 0.00 34.69 3.69
1675 1776 6.178324 TGATTAGGAGTAGTTGAACGAGAGA 58.822 40.000 0.00 0.00 0.00 3.10
1987 2090 2.877335 CCTCTACAAGGTGCGTCTAAC 58.123 52.381 0.00 0.00 40.67 2.34
2004 2107 0.464036 AACTTGCACGTCTCACAGGA 59.536 50.000 0.00 0.00 0.00 3.86
2005 2108 0.464036 ACTTGCACGTCTCACAGGAA 59.536 50.000 0.00 0.00 0.00 3.36
2026 2129 5.277731 GGAAAAATCTGCTCAAGGATCGATC 60.278 44.000 17.36 17.36 0.00 3.69
2039 2142 4.592192 CGATCCGGCCGTGCATCT 62.592 66.667 26.12 0.79 0.00 2.90
2172 2275 0.744771 GGAAGATCACCAAGACGGCC 60.745 60.000 0.00 0.00 39.03 6.13
2341 2444 5.359576 AGGTTACTGAAACTTTTGATGTGCA 59.640 36.000 0.00 0.00 38.23 4.57
2489 2598 1.453762 GATCAAGCAGGGCAGGCATC 61.454 60.000 0.00 0.00 0.00 3.91
2575 2708 2.034376 AGTGAGCTCGGTCCGACT 59.966 61.111 10.71 12.69 0.00 4.18
2617 2750 6.071728 CCTTTGATATTGGCTTGAGTTTCACT 60.072 38.462 0.00 0.00 0.00 3.41
2719 2852 3.118112 AGTTAGATGCATTCAGGGACCAG 60.118 47.826 0.00 0.00 0.00 4.00
2744 2877 3.153735 GCTTGTTGATTCGTTACTTCGC 58.846 45.455 0.00 0.00 0.00 4.70
2815 2949 5.365314 TGATGTGCATGTATGTAGGAGGTTA 59.635 40.000 0.00 0.00 0.00 2.85
2816 2950 5.887214 TGTGCATGTATGTAGGAGGTTAT 57.113 39.130 0.00 0.00 0.00 1.89
2817 2951 5.610398 TGTGCATGTATGTAGGAGGTTATG 58.390 41.667 0.00 0.00 0.00 1.90
2818 2952 5.130311 TGTGCATGTATGTAGGAGGTTATGT 59.870 40.000 0.00 0.00 0.00 2.29
2819 2953 6.325286 TGTGCATGTATGTAGGAGGTTATGTA 59.675 38.462 0.00 0.00 0.00 2.29
2820 2954 6.868864 GTGCATGTATGTAGGAGGTTATGTAG 59.131 42.308 0.00 0.00 0.00 2.74
2821 2955 6.014584 TGCATGTATGTAGGAGGTTATGTAGG 60.015 42.308 0.00 0.00 0.00 3.18
2822 2956 6.210784 GCATGTATGTAGGAGGTTATGTAGGA 59.789 42.308 0.00 0.00 0.00 2.94
2823 2957 7.577807 GCATGTATGTAGGAGGTTATGTAGGAG 60.578 44.444 0.00 0.00 0.00 3.69
2824 2958 6.312529 TGTATGTAGGAGGTTATGTAGGAGG 58.687 44.000 0.00 0.00 0.00 4.30
2825 2959 4.894252 TGTAGGAGGTTATGTAGGAGGT 57.106 45.455 0.00 0.00 0.00 3.85
2826 2960 5.216665 TGTAGGAGGTTATGTAGGAGGTT 57.783 43.478 0.00 0.00 0.00 3.50
2942 3076 3.245990 GTGGTTTCAGTTTTGAATGCAGC 59.754 43.478 0.00 0.00 42.60 5.25
2982 3116 4.725790 ATGCTTAATTTGACCTCCTTGC 57.274 40.909 0.00 0.00 0.00 4.01
2993 3127 2.352960 GACCTCCTTGCGATGTGAAATC 59.647 50.000 0.00 0.00 0.00 2.17
2997 3131 1.267038 CCTTGCGATGTGAAATCGTCG 60.267 52.381 6.89 4.30 45.82 5.12
3170 3318 6.464895 CTTGAGAGCAAGTAAAAGAGACAG 57.535 41.667 0.00 0.00 45.10 3.51
3404 3888 3.066291 ACAGTATGGATTTCAACGCCA 57.934 42.857 0.00 0.00 43.62 5.69
3441 3925 1.522676 GCTCTTTTTGAAACCAAGCGC 59.477 47.619 0.00 0.00 0.00 5.92
3475 3959 0.182775 CCCAACCCTTCCTATTCCCG 59.817 60.000 0.00 0.00 0.00 5.14
3492 3976 0.744874 CCGGCCGACTTCTCTTGATA 59.255 55.000 30.73 0.00 0.00 2.15
3500 3984 6.273825 GCCGACTTCTCTTGATACTGAAATA 58.726 40.000 0.00 0.00 0.00 1.40
3501 3985 6.199342 GCCGACTTCTCTTGATACTGAAATAC 59.801 42.308 0.00 0.00 0.00 1.89
3502 3986 7.484975 CCGACTTCTCTTGATACTGAAATACT 58.515 38.462 0.00 0.00 0.00 2.12
3503 3987 7.646130 CCGACTTCTCTTGATACTGAAATACTC 59.354 40.741 0.00 0.00 0.00 2.59
3504 3988 7.646130 CGACTTCTCTTGATACTGAAATACTCC 59.354 40.741 0.00 0.00 0.00 3.85
3505 3989 8.602472 ACTTCTCTTGATACTGAAATACTCCT 57.398 34.615 0.00 0.00 0.00 3.69
3506 3990 8.691797 ACTTCTCTTGATACTGAAATACTCCTC 58.308 37.037 0.00 0.00 0.00 3.71
3507 3991 8.830915 TTCTCTTGATACTGAAATACTCCTCT 57.169 34.615 0.00 0.00 0.00 3.69
3508 3992 8.830915 TCTCTTGATACTGAAATACTCCTCTT 57.169 34.615 0.00 0.00 0.00 2.85
3509 3993 9.261035 TCTCTTGATACTGAAATACTCCTCTTT 57.739 33.333 0.00 0.00 0.00 2.52
3510 3994 9.528018 CTCTTGATACTGAAATACTCCTCTTTC 57.472 37.037 0.00 0.00 33.06 2.62
3511 3995 8.478877 TCTTGATACTGAAATACTCCTCTTTCC 58.521 37.037 0.00 0.00 31.74 3.13
3512 3996 7.125792 TGATACTGAAATACTCCTCTTTCCC 57.874 40.000 0.00 0.00 31.74 3.97
3513 3997 4.846168 ACTGAAATACTCCTCTTTCCCC 57.154 45.455 0.00 0.00 31.74 4.81
3514 3998 3.523972 ACTGAAATACTCCTCTTTCCCCC 59.476 47.826 0.00 0.00 31.74 5.40
3515 3999 3.783082 CTGAAATACTCCTCTTTCCCCCT 59.217 47.826 0.00 0.00 31.74 4.79
3516 4000 3.780850 TGAAATACTCCTCTTTCCCCCTC 59.219 47.826 0.00 0.00 31.74 4.30
3528 4012 6.187727 TCTTTCCCCCTCATATGTTACATC 57.812 41.667 0.00 0.00 0.00 3.06
3656 4140 2.174424 GCTCATCCTCTTTCTTCCCCAT 59.826 50.000 0.00 0.00 0.00 4.00
3742 4226 6.046593 ACACTTTTCACGTACATGAAGAAGA 58.953 36.000 21.95 2.76 39.68 2.87
3762 4246 1.810151 ACACAAGTTTGCGAACTGTGT 59.190 42.857 29.73 29.73 45.18 3.72
3768 4252 5.514914 ACAAGTTTGCGAACTGTGTTTTATG 59.485 36.000 20.15 13.54 45.18 1.90
3774 4258 3.794536 CGAACTGTGTTTTATGGACGTG 58.205 45.455 0.00 0.00 0.00 4.49
3812 4296 2.260822 TGCTCCTAGCTTCTCCAACTT 58.739 47.619 0.00 0.00 42.97 2.66
3830 4314 5.124297 CCAACTTTATCATGTCAGATGTGCA 59.876 40.000 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.849804 TTGAAAATCCAAACATTTTCCGAAA 57.150 28.000 13.48 0.00 46.03 3.46
1 2 7.849804 TTTGAAAATCCAAACATTTTCCGAA 57.150 28.000 13.48 7.76 46.03 4.30
2 3 7.849804 TTTTGAAAATCCAAACATTTTCCGA 57.150 28.000 13.48 3.30 46.03 4.55
3 4 9.513727 AATTTTTGAAAATCCAAACATTTTCCG 57.486 25.926 13.48 0.00 46.03 4.30
97 105 8.563732 TCTTGAATAAACATGTGAACGATTTCA 58.436 29.630 0.00 0.18 39.55 2.69
98 106 8.948853 TCTTGAATAAACATGTGAACGATTTC 57.051 30.769 0.00 0.00 0.00 2.17
103 111 8.506140 ACATTTCTTGAATAAACATGTGAACG 57.494 30.769 0.00 0.00 0.00 3.95
141 153 9.769093 GCGTTCATATATGTAAACACTTCTTTT 57.231 29.630 12.42 0.00 0.00 2.27
142 154 9.162764 AGCGTTCATATATGTAAACACTTCTTT 57.837 29.630 12.42 0.00 0.00 2.52
143 155 8.718102 AGCGTTCATATATGTAAACACTTCTT 57.282 30.769 12.42 0.00 0.00 2.52
144 156 7.438459 GGAGCGTTCATATATGTAAACACTTCT 59.562 37.037 12.42 5.67 0.00 2.85
145 157 7.438459 AGGAGCGTTCATATATGTAAACACTTC 59.562 37.037 12.42 8.55 0.00 3.01
148 160 8.758633 ATAGGAGCGTTCATATATGTAAACAC 57.241 34.615 12.42 5.17 29.05 3.32
165 178 7.485277 CGACCTTAATAAGAACATATAGGAGCG 59.515 40.741 0.83 0.00 0.00 5.03
172 185 6.509656 TGACGCGACCTTAATAAGAACATAT 58.490 36.000 15.93 0.00 0.00 1.78
174 187 4.751060 TGACGCGACCTTAATAAGAACAT 58.249 39.130 15.93 0.00 0.00 2.71
185 198 1.002684 GACGATAGATGACGCGACCTT 60.003 52.381 15.93 1.79 41.38 3.50
194 207 3.638627 AGGTTGCTCATGACGATAGATGA 59.361 43.478 0.00 0.00 41.38 2.92
213 226 2.659610 GCCACTCGCTCTGAAGGT 59.340 61.111 0.00 0.00 0.00 3.50
223 236 2.103042 GCCTGCAACTAGCCACTCG 61.103 63.158 0.00 0.00 44.83 4.18
247 261 1.272490 TCAATCTCGGGATATCGCACC 59.728 52.381 18.74 3.74 0.00 5.01
254 268 1.342074 CAGGCCTCAATCTCGGGATA 58.658 55.000 0.00 0.00 0.00 2.59
269 283 4.434520 CCTAACTAGAGTGCTTTACAGGC 58.565 47.826 0.00 0.00 0.00 4.85
445 493 2.124320 AATCGGACCGGCCCATTG 60.124 61.111 15.25 0.00 0.00 2.82
479 527 3.136009 TCTAGGATCGTTGATCGCCTA 57.864 47.619 0.00 0.00 39.72 3.93
482 530 4.745125 TCAAATTCTAGGATCGTTGATCGC 59.255 41.667 0.50 0.00 39.72 4.58
485 533 6.037610 GCAAGTCAAATTCTAGGATCGTTGAT 59.962 38.462 2.17 0.00 0.00 2.57
499 547 3.317711 TCGTTGATGTGGCAAGTCAAATT 59.682 39.130 14.91 0.00 34.04 1.82
518 566 3.129287 CAGGGCATTTAGCTGAAATTCGT 59.871 43.478 0.00 0.00 44.79 3.85
524 572 2.041620 ACCTTCAGGGCATTTAGCTGAA 59.958 45.455 0.00 0.00 44.79 3.02
525 573 1.635487 ACCTTCAGGGCATTTAGCTGA 59.365 47.619 0.00 0.00 44.79 4.26
534 582 4.079253 GTCTATTTTGAACCTTCAGGGCA 58.921 43.478 0.00 0.00 38.61 5.36
586 634 4.994852 CGAACCCTGAGTTTGTAATCTCAA 59.005 41.667 6.79 0.00 39.40 3.02
589 637 4.884668 TCGAACCCTGAGTTTGTAATCT 57.115 40.909 0.00 0.00 39.40 2.40
598 646 5.109903 CGAAAGATAAATCGAACCCTGAGT 58.890 41.667 0.00 0.00 41.43 3.41
599 647 5.109903 ACGAAAGATAAATCGAACCCTGAG 58.890 41.667 1.84 0.00 41.43 3.35
615 663 7.862372 ACATACGTTAAACTTGTAGACGAAAGA 59.138 33.333 0.00 0.00 37.20 2.52
663 711 9.804758 CGAGACAACTAAGAGTATTCCTTTAAT 57.195 33.333 0.00 0.00 0.00 1.40
664 712 8.248945 CCGAGACAACTAAGAGTATTCCTTTAA 58.751 37.037 0.00 0.00 0.00 1.52
665 713 7.613022 TCCGAGACAACTAAGAGTATTCCTTTA 59.387 37.037 0.00 0.00 0.00 1.85
666 714 6.436532 TCCGAGACAACTAAGAGTATTCCTTT 59.563 38.462 0.00 0.00 0.00 3.11
667 715 5.950549 TCCGAGACAACTAAGAGTATTCCTT 59.049 40.000 0.00 0.00 0.00 3.36
668 716 5.507637 TCCGAGACAACTAAGAGTATTCCT 58.492 41.667 0.00 0.00 0.00 3.36
669 717 5.831702 TCCGAGACAACTAAGAGTATTCC 57.168 43.478 0.00 0.00 0.00 3.01
670 718 8.027771 TCTTTTCCGAGACAACTAAGAGTATTC 58.972 37.037 0.00 0.00 0.00 1.75
671 719 7.893658 TCTTTTCCGAGACAACTAAGAGTATT 58.106 34.615 0.00 0.00 0.00 1.89
672 720 7.463961 TCTTTTCCGAGACAACTAAGAGTAT 57.536 36.000 0.00 0.00 0.00 2.12
673 721 6.889301 TCTTTTCCGAGACAACTAAGAGTA 57.111 37.500 0.00 0.00 0.00 2.59
674 722 5.786264 TCTTTTCCGAGACAACTAAGAGT 57.214 39.130 0.00 0.00 0.00 3.24
675 723 7.307455 CCTTTTCTTTTCCGAGACAACTAAGAG 60.307 40.741 0.00 0.00 0.00 2.85
676 724 6.482308 CCTTTTCTTTTCCGAGACAACTAAGA 59.518 38.462 0.00 0.00 0.00 2.10
677 725 6.293462 CCCTTTTCTTTTCCGAGACAACTAAG 60.293 42.308 0.00 0.00 0.00 2.18
678 726 5.529800 CCCTTTTCTTTTCCGAGACAACTAA 59.470 40.000 0.00 0.00 0.00 2.24
679 727 5.061179 CCCTTTTCTTTTCCGAGACAACTA 58.939 41.667 0.00 0.00 0.00 2.24
680 728 3.883489 CCCTTTTCTTTTCCGAGACAACT 59.117 43.478 0.00 0.00 0.00 3.16
681 729 3.881089 TCCCTTTTCTTTTCCGAGACAAC 59.119 43.478 0.00 0.00 0.00 3.32
682 730 4.159244 TCCCTTTTCTTTTCCGAGACAA 57.841 40.909 0.00 0.00 0.00 3.18
683 731 3.849563 TCCCTTTTCTTTTCCGAGACA 57.150 42.857 0.00 0.00 0.00 3.41
684 732 5.123502 GGTATTCCCTTTTCTTTTCCGAGAC 59.876 44.000 0.00 0.00 0.00 3.36
685 733 5.221966 TGGTATTCCCTTTTCTTTTCCGAGA 60.222 40.000 0.00 0.00 0.00 4.04
686 734 5.007682 TGGTATTCCCTTTTCTTTTCCGAG 58.992 41.667 0.00 0.00 0.00 4.63
687 735 4.988029 TGGTATTCCCTTTTCTTTTCCGA 58.012 39.130 0.00 0.00 0.00 4.55
688 736 4.765339 ACTGGTATTCCCTTTTCTTTTCCG 59.235 41.667 0.00 0.00 0.00 4.30
689 737 6.717997 TGTACTGGTATTCCCTTTTCTTTTCC 59.282 38.462 0.00 0.00 0.00 3.13
690 738 7.754851 TGTACTGGTATTCCCTTTTCTTTTC 57.245 36.000 0.00 0.00 0.00 2.29
691 739 7.120726 CGATGTACTGGTATTCCCTTTTCTTTT 59.879 37.037 0.00 0.00 0.00 2.27
692 740 6.598064 CGATGTACTGGTATTCCCTTTTCTTT 59.402 38.462 0.00 0.00 0.00 2.52
693 741 6.113411 CGATGTACTGGTATTCCCTTTTCTT 58.887 40.000 0.00 0.00 0.00 2.52
694 742 5.671493 CGATGTACTGGTATTCCCTTTTCT 58.329 41.667 0.00 0.00 0.00 2.52
695 743 4.272748 GCGATGTACTGGTATTCCCTTTTC 59.727 45.833 0.00 0.00 0.00 2.29
696 744 4.196971 GCGATGTACTGGTATTCCCTTTT 58.803 43.478 0.00 0.00 0.00 2.27
697 745 3.199071 TGCGATGTACTGGTATTCCCTTT 59.801 43.478 0.00 0.00 0.00 3.11
698 746 2.769663 TGCGATGTACTGGTATTCCCTT 59.230 45.455 0.00 0.00 0.00 3.95
699 747 2.102588 GTGCGATGTACTGGTATTCCCT 59.897 50.000 0.00 0.00 0.00 4.20
700 748 2.159014 TGTGCGATGTACTGGTATTCCC 60.159 50.000 0.00 0.00 0.00 3.97
701 749 3.173668 TGTGCGATGTACTGGTATTCC 57.826 47.619 0.00 0.00 0.00 3.01
702 750 3.059597 GCATGTGCGATGTACTGGTATTC 60.060 47.826 0.00 0.00 0.00 1.75
703 751 2.872245 GCATGTGCGATGTACTGGTATT 59.128 45.455 0.00 0.00 0.00 1.89
704 752 2.483876 GCATGTGCGATGTACTGGTAT 58.516 47.619 0.00 0.00 0.00 2.73
705 753 1.934589 GCATGTGCGATGTACTGGTA 58.065 50.000 0.00 0.00 0.00 3.25
706 754 2.767536 GCATGTGCGATGTACTGGT 58.232 52.632 0.00 0.00 0.00 4.00
738 786 3.325201 AACTCCGTCCCGATTGGCC 62.325 63.158 0.00 0.00 0.00 5.36
752 800 1.126296 GGCGTTTAACGAGCTCAACTC 59.874 52.381 22.15 5.37 46.05 3.01
964 1023 3.972328 AAGGGAGGGAAGAGGGGGC 62.972 68.421 0.00 0.00 0.00 5.80
965 1024 1.694525 GAAGGGAGGGAAGAGGGGG 60.695 68.421 0.00 0.00 0.00 5.40
966 1025 1.694525 GGAAGGGAGGGAAGAGGGG 60.695 68.421 0.00 0.00 0.00 4.79
967 1026 1.694525 GGGAAGGGAGGGAAGAGGG 60.695 68.421 0.00 0.00 0.00 4.30
968 1027 1.082954 TGGGAAGGGAGGGAAGAGG 59.917 63.158 0.00 0.00 0.00 3.69
972 1031 2.204244 GGGTGGGAAGGGAGGGAA 60.204 66.667 0.00 0.00 0.00 3.97
1078 1143 3.447025 GATCCGGAACCGAGGCTGG 62.447 68.421 9.01 0.00 42.83 4.85
1083 1148 0.528684 GAAGCTGATCCGGAACCGAG 60.529 60.000 9.01 0.72 42.83 4.63
1086 1151 0.806492 GTCGAAGCTGATCCGGAACC 60.806 60.000 9.01 3.91 0.00 3.62
1088 1153 1.138883 CGTCGAAGCTGATCCGGAA 59.861 57.895 9.01 0.00 0.00 4.30
1093 1158 1.493950 CCATGCCGTCGAAGCTGATC 61.494 60.000 9.82 0.00 0.00 2.92
1117 1182 1.229658 CCTCTTGGAGGGTGGAGGT 60.230 63.158 5.73 0.00 45.43 3.85
1127 1192 3.077556 GCCGCCTCTCCTCTTGGA 61.078 66.667 0.00 0.00 40.69 3.53
1156 1221 0.833949 GATCCTTCCTCTCCACACCC 59.166 60.000 0.00 0.00 0.00 4.61
1159 1224 2.630889 ACAGATCCTTCCTCTCCACA 57.369 50.000 0.00 0.00 0.00 4.17
1161 1226 2.472029 GGAACAGATCCTTCCTCTCCA 58.528 52.381 11.14 0.00 45.56 3.86
1294 1376 7.664731 TCCGTTTTAACCACAATAAATCCACTA 59.335 33.333 0.00 0.00 0.00 2.74
1391 1481 5.496133 AATACTGTGATCTGCTTTCATGC 57.504 39.130 0.00 0.00 0.00 4.06
1412 1502 3.679639 GCCGACGGAAAAGTAGGGAATAA 60.680 47.826 20.50 0.00 37.37 1.40
1467 1557 4.763793 CCAAGAGGAGCAAAGAAGATTTGA 59.236 41.667 4.59 0.00 36.89 2.69
1501 1591 2.628106 CGATTCGGCGAGCAATGG 59.372 61.111 10.46 0.00 0.00 3.16
1578 1675 1.071567 GTAAGCACGCAGGTCGACTC 61.072 60.000 16.46 5.70 41.67 3.36
1579 1676 1.080705 GTAAGCACGCAGGTCGACT 60.081 57.895 16.46 0.00 41.67 4.18
1580 1677 1.080705 AGTAAGCACGCAGGTCGAC 60.081 57.895 7.13 7.13 41.67 4.20
1581 1678 1.080772 CAGTAAGCACGCAGGTCGA 60.081 57.895 0.00 0.00 41.67 4.20
1582 1679 0.666274 TTCAGTAAGCACGCAGGTCG 60.666 55.000 0.00 0.00 45.38 4.79
1583 1680 1.394917 CATTCAGTAAGCACGCAGGTC 59.605 52.381 0.00 0.00 0.00 3.85
1584 1681 1.001974 TCATTCAGTAAGCACGCAGGT 59.998 47.619 0.00 0.00 0.00 4.00
1585 1682 1.725641 TCATTCAGTAAGCACGCAGG 58.274 50.000 0.00 0.00 0.00 4.85
1586 1683 5.007039 ACATAATCATTCAGTAAGCACGCAG 59.993 40.000 0.00 0.00 0.00 5.18
1699 1800 6.030228 CGTTTGCAGGGAAAAATATTCTCTC 58.970 40.000 0.00 0.00 0.00 3.20
1701 1802 5.709966 ACGTTTGCAGGGAAAAATATTCTC 58.290 37.500 0.00 0.00 0.00 2.87
1704 1805 7.438564 ACTTAACGTTTGCAGGGAAAAATATT 58.561 30.769 5.91 0.00 0.00 1.28
1707 1808 5.270893 ACTTAACGTTTGCAGGGAAAAAT 57.729 34.783 5.91 0.00 0.00 1.82
1892 1995 3.581770 TGAAGGATCTGATGGCCTCTATG 59.418 47.826 3.32 0.00 0.00 2.23
1985 2088 0.464036 TCCTGTGAGACGTGCAAGTT 59.536 50.000 6.76 0.00 0.00 2.66
1987 2090 1.581934 TTTCCTGTGAGACGTGCAAG 58.418 50.000 0.00 0.00 0.00 4.01
1994 2097 4.067896 TGAGCAGATTTTTCCTGTGAGAC 58.932 43.478 0.00 0.00 34.29 3.36
2004 2107 4.578105 GGATCGATCCTTGAGCAGATTTTT 59.422 41.667 32.91 0.00 43.73 1.94
2005 2108 4.133078 GGATCGATCCTTGAGCAGATTTT 58.867 43.478 32.91 0.00 43.73 1.82
2026 2129 0.317160 TAGAATAGATGCACGGCCGG 59.683 55.000 31.76 19.49 0.00 6.13
2028 2131 2.143925 GGTTAGAATAGATGCACGGCC 58.856 52.381 0.00 0.00 0.00 6.13
2029 2132 2.802816 CAGGTTAGAATAGATGCACGGC 59.197 50.000 0.00 0.00 0.00 5.68
2030 2133 4.322080 TCAGGTTAGAATAGATGCACGG 57.678 45.455 0.00 0.00 0.00 4.94
2031 2134 7.093354 ACATATCAGGTTAGAATAGATGCACG 58.907 38.462 0.00 0.00 0.00 5.34
2032 2135 8.310382 AGACATATCAGGTTAGAATAGATGCAC 58.690 37.037 0.00 0.00 0.00 4.57
2341 2444 2.897326 GCCAAGGTTACCCTGTGAAATT 59.103 45.455 0.00 0.00 41.56 1.82
2489 2598 0.322975 AGTACTTGCACTGCCTCCTG 59.677 55.000 0.00 0.00 0.00 3.86
2575 2708 2.779755 AGGGCGATGAAACATGTGTA 57.220 45.000 0.00 0.00 0.00 2.90
2617 2750 6.061441 GTCTAGTCTCTCCATGATCTCTTCA 58.939 44.000 0.00 0.00 39.12 3.02
2686 2819 5.791336 ATGCATCTAACTCCTCGAATACA 57.209 39.130 0.00 0.00 0.00 2.29
2719 2852 4.946784 AGTAACGAATCAACAAGCCATC 57.053 40.909 0.00 0.00 0.00 3.51
2744 2877 7.687005 TGCACGTTAAAAGATTAAAAACTGG 57.313 32.000 0.00 0.00 32.98 4.00
2815 2949 4.657814 ACATCCACAAAACCTCCTACAT 57.342 40.909 0.00 0.00 0.00 2.29
2816 2950 4.447138 AACATCCACAAAACCTCCTACA 57.553 40.909 0.00 0.00 0.00 2.74
2817 2951 5.310451 TGTAACATCCACAAAACCTCCTAC 58.690 41.667 0.00 0.00 0.00 3.18
2818 2952 5.514136 CCTGTAACATCCACAAAACCTCCTA 60.514 44.000 0.00 0.00 0.00 2.94
2819 2953 4.398319 CTGTAACATCCACAAAACCTCCT 58.602 43.478 0.00 0.00 0.00 3.69
2820 2954 3.506067 CCTGTAACATCCACAAAACCTCC 59.494 47.826 0.00 0.00 0.00 4.30
2821 2955 4.023193 CACCTGTAACATCCACAAAACCTC 60.023 45.833 0.00 0.00 0.00 3.85
2822 2956 3.888930 CACCTGTAACATCCACAAAACCT 59.111 43.478 0.00 0.00 0.00 3.50
2823 2957 3.634910 ACACCTGTAACATCCACAAAACC 59.365 43.478 0.00 0.00 0.00 3.27
2824 2958 4.336993 TCACACCTGTAACATCCACAAAAC 59.663 41.667 0.00 0.00 0.00 2.43
2825 2959 4.527944 TCACACCTGTAACATCCACAAAA 58.472 39.130 0.00 0.00 0.00 2.44
2826 2960 4.157849 TCACACCTGTAACATCCACAAA 57.842 40.909 0.00 0.00 0.00 2.83
2982 3116 1.059122 CCACACGACGATTTCACATCG 59.941 52.381 0.00 2.73 46.02 3.84
2993 3127 2.631418 AGTGAGTAATCCACACGACG 57.369 50.000 0.00 0.00 39.19 5.12
2997 3131 6.554334 TTAAAGCAAGTGAGTAATCCACAC 57.446 37.500 0.00 0.00 37.01 3.82
3170 3318 4.697514 TCTTATCTGTATTCAGCACCAGC 58.302 43.478 0.00 0.00 41.10 4.85
3311 3514 6.816640 GGTGCTTTGTACACATAGTGAGATTA 59.183 38.462 3.88 0.00 39.87 1.75
3404 3888 2.674220 GCTAGCCTGGCAAGTCCCT 61.674 63.158 22.65 0.00 0.00 4.20
3441 3925 2.289010 GGTTGGGAATTGAAGTTGCAGG 60.289 50.000 0.00 0.00 0.00 4.85
3475 3959 2.427453 TCAGTATCAAGAGAAGTCGGCC 59.573 50.000 0.00 0.00 0.00 6.13
3492 3976 3.523972 GGGGGAAAGAGGAGTATTTCAGT 59.476 47.826 0.00 0.00 35.88 3.41
3500 3984 3.311702 ACATATGAGGGGGAAAGAGGAGT 60.312 47.826 10.38 0.00 0.00 3.85
3501 3985 3.321950 ACATATGAGGGGGAAAGAGGAG 58.678 50.000 10.38 0.00 0.00 3.69
3502 3986 3.438131 ACATATGAGGGGGAAAGAGGA 57.562 47.619 10.38 0.00 0.00 3.71
3503 3987 4.412199 TGTAACATATGAGGGGGAAAGAGG 59.588 45.833 10.38 0.00 0.00 3.69
3504 3988 5.630415 TGTAACATATGAGGGGGAAAGAG 57.370 43.478 10.38 0.00 0.00 2.85
3505 3989 5.073144 GGATGTAACATATGAGGGGGAAAGA 59.927 44.000 10.38 0.00 0.00 2.52
3506 3990 5.163099 TGGATGTAACATATGAGGGGGAAAG 60.163 44.000 10.38 0.00 0.00 2.62
3507 3991 4.729370 TGGATGTAACATATGAGGGGGAAA 59.271 41.667 10.38 0.00 0.00 3.13
3508 3992 4.311613 TGGATGTAACATATGAGGGGGAA 58.688 43.478 10.38 0.00 0.00 3.97
3509 3993 3.909995 CTGGATGTAACATATGAGGGGGA 59.090 47.826 10.38 0.00 0.00 4.81
3510 3994 3.652869 ACTGGATGTAACATATGAGGGGG 59.347 47.826 10.38 0.00 0.00 5.40
3511 3995 4.982241 ACTGGATGTAACATATGAGGGG 57.018 45.455 10.38 0.00 0.00 4.79
3512 3996 6.356556 TGAAACTGGATGTAACATATGAGGG 58.643 40.000 10.38 0.00 0.00 4.30
3513 3997 7.521099 GCATGAAACTGGATGTAACATATGAGG 60.521 40.741 10.38 0.00 0.00 3.86
3514 3998 7.228108 AGCATGAAACTGGATGTAACATATGAG 59.772 37.037 10.38 0.00 0.00 2.90
3515 3999 7.056006 AGCATGAAACTGGATGTAACATATGA 58.944 34.615 10.38 0.00 0.00 2.15
3516 4000 7.012610 TGAGCATGAAACTGGATGTAACATATG 59.987 37.037 0.00 0.00 0.00 1.78
3607 4091 3.001533 GCATGAAGCAACAACCAAAACAG 59.998 43.478 0.00 0.00 44.79 3.16
3742 4226 1.810151 ACACAGTTCGCAAACTTGTGT 59.190 42.857 15.51 15.51 43.28 3.72
3762 4246 6.487331 AGTCCAATAACAACACGTCCATAAAA 59.513 34.615 0.00 0.00 0.00 1.52
3768 4252 4.823790 AAAGTCCAATAACAACACGTCC 57.176 40.909 0.00 0.00 0.00 4.79
3774 4258 7.158099 AGGAGCATTAAAGTCCAATAACAAC 57.842 36.000 4.45 0.00 32.23 3.32
3812 4296 6.035975 CGTACTTTGCACATCTGACATGATAA 59.964 38.462 0.00 0.00 0.00 1.75
3830 4314 3.665745 TTAAAGCCGAGTCCGTACTTT 57.334 42.857 0.00 0.00 40.72 2.66
3885 4369 1.929836 CTTAGAGCGAGATGTGTTGGC 59.070 52.381 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.