Multiple sequence alignment - TraesCS2D01G559400

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 TraesCS2D01G559400 chr2D 100.000 5392 0 0 1 5392 631956689 631962080 0.000000e+00 9958.0
1 TraesCS2D01G559400 chr2D 86.207 58 1 5 623 678 424041006 424040954 7.540000e-04 56.5
2 TraesCS2D01G559400 chr2A 93.951 4629 140 55 658 5213 759817655 759813094 0.000000e+00 6868.0
3 TraesCS2D01G559400 chr2B 90.718 2327 101 44 1132 3392 775367578 775369855 0.000000e+00 2994.0
4 TraesCS2D01G559400 chr2B 92.680 1899 102 20 3391 5268 775370116 775371998 0.000000e+00 2702.0
5 TraesCS2D01G559400 chr2B 91.739 460 20 8 654 1095 775366779 775367238 1.650000e-174 623.0
6 TraesCS2D01G559400 chr2B 91.406 384 27 6 1 384 782440650 782441027 6.190000e-144 521.0
7 TraesCS2D01G559400 chr2B 94.000 150 9 0 449 598 782454493 782454642 1.510000e-55 228.0
8 TraesCS2D01G559400 chr2B 92.727 55 2 2 5218 5271 357946062 357946009 1.610000e-10 78.7
9 TraesCS2D01G559400 chr2B 97.297 37 1 0 625 661 672021791 672021755 4.510000e-06 63.9
10 TraesCS2D01G559400 chr2B 86.792 53 3 3 622 673 503219958 503220007 7.540000e-04 56.5
11 TraesCS2D01G559400 chr6D 95.395 456 16 5 1 454 272855421 272854969 0.000000e+00 721.0
12 TraesCS2D01G559400 chr6D 93.833 454 24 4 1 454 23829531 23829980 0.000000e+00 680.0
13 TraesCS2D01G559400 chr6D 93.919 148 8 1 451 598 272854447 272854301 7.030000e-54 222.0
14 TraesCS2D01G559400 chr4A 94.923 453 20 3 1 452 560753139 560752689 0.000000e+00 706.0
15 TraesCS2D01G559400 chr4A 91.503 153 13 0 449 601 560745626 560745474 1.520000e-50 211.0
16 TraesCS2D01G559400 chr4A 78.231 147 28 4 5160 5304 183700470 183700326 2.070000e-14 91.6
17 TraesCS2D01G559400 chr4D 94.725 455 20 4 1 454 39594722 39595173 0.000000e+00 704.0
18 TraesCS2D01G559400 chr4D 93.333 150 10 0 449 598 39595693 39595842 7.030000e-54 222.0
19 TraesCS2D01G559400 chr4D 97.297 37 1 0 625 661 9744798 9744834 4.510000e-06 63.9
20 TraesCS2D01G559400 chr3D 94.505 455 19 6 1 454 589434153 589433704 0.000000e+00 697.0
21 TraesCS2D01G559400 chr3D 93.333 150 10 0 449 598 589433185 589433036 7.030000e-54 222.0
22 TraesCS2D01G559400 chr4B 94.318 264 11 4 1 262 579389517 579389778 8.410000e-108 401.0
23 TraesCS2D01G559400 chr1B 87.948 307 18 7 1 290 301772996 301773300 1.440000e-90 344.0
24 TraesCS2D01G559400 chr1B 84.146 246 30 5 3077 3322 152860253 152860489 4.200000e-56 230.0
25 TraesCS2D01G559400 chr1B 92.667 150 11 0 449 598 301776209 301776358 3.270000e-52 217.0
26 TraesCS2D01G559400 chr1B 93.590 78 5 0 5315 5392 296807262 296807339 3.410000e-22 117.0
27 TraesCS2D01G559400 chr5D 84.266 286 42 2 157 441 117196966 117197249 5.320000e-70 276.0
28 TraesCS2D01G559400 chr5D 88.667 150 17 0 449 598 3014114 3013965 3.320000e-42 183.0
29 TraesCS2D01G559400 chr5D 90.909 55 4 1 5230 5283 513665180 513665126 7.490000e-09 73.1
30 TraesCS2D01G559400 chr6A 93.243 148 10 0 449 596 577847411 577847264 9.090000e-53 219.0
31 TraesCS2D01G559400 chr6A 97.222 36 1 0 625 660 363892681 363892716 1.620000e-05 62.1
32 TraesCS2D01G559400 chr1D 87.500 160 19 1 449 607 416541890 416542049 3.320000e-42 183.0
33 TraesCS2D01G559400 chr1D 97.143 35 1 0 625 659 150938097 150938131 5.830000e-05 60.2
34 TraesCS2D01G559400 chr5B 94.340 53 2 1 5230 5282 672595017 672595068 4.480000e-11 80.5
35 TraesCS2D01G559400 chr5B 93.182 44 1 2 625 667 531648857 531648899 4.510000e-06 63.9
36 TraesCS2D01G559400 chr1A 94.872 39 2 0 625 663 102451821 102451859 1.620000e-05 62.1
37 TraesCS2D01G559400 chr3A 89.130 46 4 1 625 669 741036460 741036415 7.540000e-04 56.5


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 TraesCS2D01G559400 chr2D 631956689 631962080 5391 False 9958.000000 9958 100.000000 1 5392 1 chr2D.!!$F1 5391
1 TraesCS2D01G559400 chr2A 759813094 759817655 4561 True 6868.000000 6868 93.951000 658 5213 1 chr2A.!!$R1 4555
2 TraesCS2D01G559400 chr2B 775366779 775371998 5219 False 2106.333333 2994 91.712333 654 5268 3 chr2B.!!$F4 4614
3 TraesCS2D01G559400 chr6D 272854301 272855421 1120 True 471.500000 721 94.657000 1 598 2 chr6D.!!$R1 597
4 TraesCS2D01G559400 chr4D 39594722 39595842 1120 False 463.000000 704 94.029000 1 598 2 chr4D.!!$F2 597
5 TraesCS2D01G559400 chr3D 589433036 589434153 1117 True 459.500000 697 93.919000 1 598 2 chr3D.!!$R1 597
6 TraesCS2D01G559400 chr1B 301772996 301776358 3362 False 280.500000 344 90.307500 1 598 2 chr1B.!!$F3 597

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
653 3423 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20 F
1363 4474 0.034059 CCGGTGATCTGGTCTATGCC 59.966 60.000 0.00 0.00 35.48 4.40 F
1364 4475 0.752658 CGGTGATCTGGTCTATGCCA 59.247 55.000 0.00 0.00 36.97 4.92 F
2087 5253 0.936297 GTTTGGCTGTTTCTGCTGCG 60.936 55.000 0.00 0.00 34.71 5.18 F
3323 6506 1.000060 CACCACCATTGCTTGTGAAGG 60.000 52.381 0.00 0.00 34.37 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1991 5157 0.625316 TGAATAGCCACCCACTGCAT 59.375 50.000 0.0 0.0 0.00 3.96 R
3323 6506 0.596600 TTCGACAAGTCTGGTGCGAC 60.597 55.000 0.0 0.0 0.00 5.19 R
3331 6514 2.175202 AGATCCTGCTTCGACAAGTCT 58.825 47.619 0.0 0.0 31.45 3.24 R
3883 7332 4.932200 CACTTGTTCATGAGGGAGAGTTAC 59.068 45.833 0.0 0.0 0.00 2.50 R
5288 8768 0.107993 GTTACCTACCGTCAAGGGCC 60.108 60.000 0.0 0.0 46.96 5.80 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
31 32 2.028112 AGAATCCTGCGACACTAGCAAA 60.028 45.455 0.00 0.00 44.67 3.68
39 40 5.391950 CCTGCGACACTAGCAAATAACAAAT 60.392 40.000 0.00 0.00 44.67 2.32
40 41 5.389778 TGCGACACTAGCAAATAACAAATG 58.610 37.500 0.00 0.00 42.18 2.32
41 42 5.180304 TGCGACACTAGCAAATAACAAATGA 59.820 36.000 0.00 0.00 42.18 2.57
134 136 2.564721 GCTCACCAACCAAGCCCAC 61.565 63.158 0.00 0.00 0.00 4.61
379 2398 2.159000 TGCACAGAAGATGATGCGAGAT 60.159 45.455 0.00 0.00 38.20 2.75
416 2435 3.187699 CTACGCGCTCGATCCAGCT 62.188 63.158 5.73 0.00 37.25 4.24
557 3327 0.527565 GCAATGAGCACGTTTGGGAT 59.472 50.000 0.00 0.00 44.79 3.85
572 3342 3.973206 TGGGATGAGAAGCTAAAACGA 57.027 42.857 0.00 0.00 0.00 3.85
598 3368 4.574828 CACGTTCGGGATTTATTGATTCCT 59.425 41.667 0.00 0.00 0.00 3.36
599 3369 5.065988 CACGTTCGGGATTTATTGATTCCTT 59.934 40.000 0.00 0.00 0.00 3.36
600 3370 5.650703 ACGTTCGGGATTTATTGATTCCTTT 59.349 36.000 0.00 0.00 0.00 3.11
601 3371 6.152154 ACGTTCGGGATTTATTGATTCCTTTT 59.848 34.615 0.00 0.00 0.00 2.27
602 3372 7.033185 CGTTCGGGATTTATTGATTCCTTTTT 58.967 34.615 0.00 0.00 0.00 1.94
631 3401 3.398954 GCGAAATGCATCGTTTTAGGA 57.601 42.857 11.09 0.00 44.49 2.94
632 3402 3.098636 GCGAAATGCATCGTTTTAGGAC 58.901 45.455 11.09 0.00 44.49 3.85
633 3403 3.425625 GCGAAATGCATCGTTTTAGGACA 60.426 43.478 11.09 0.00 44.49 4.02
634 3404 4.717991 CGAAATGCATCGTTTTAGGACAA 58.282 39.130 0.00 0.00 38.01 3.18
635 3405 4.788100 CGAAATGCATCGTTTTAGGACAAG 59.212 41.667 0.00 0.00 38.01 3.16
636 3406 5.616866 CGAAATGCATCGTTTTAGGACAAGT 60.617 40.000 0.00 0.00 38.01 3.16
637 3407 6.401688 CGAAATGCATCGTTTTAGGACAAGTA 60.402 38.462 0.00 0.00 38.01 2.24
638 3408 7.391148 AAATGCATCGTTTTAGGACAAGTAT 57.609 32.000 0.00 0.00 0.00 2.12
639 3409 7.391148 AATGCATCGTTTTAGGACAAGTATT 57.609 32.000 0.00 0.00 0.00 1.89
640 3410 6.811253 TGCATCGTTTTAGGACAAGTATTT 57.189 33.333 0.00 0.00 0.00 1.40
641 3411 6.837992 TGCATCGTTTTAGGACAAGTATTTC 58.162 36.000 0.00 0.00 0.00 2.17
642 3412 6.128117 TGCATCGTTTTAGGACAAGTATTTCC 60.128 38.462 0.00 0.00 0.00 3.13
643 3413 6.475207 CATCGTTTTAGGACAAGTATTTCCG 58.525 40.000 0.00 0.00 36.95 4.30
644 3414 4.931002 TCGTTTTAGGACAAGTATTTCCGG 59.069 41.667 0.00 0.00 36.95 5.14
645 3415 4.931002 CGTTTTAGGACAAGTATTTCCGGA 59.069 41.667 0.00 0.00 36.95 5.14
646 3416 5.163923 CGTTTTAGGACAAGTATTTCCGGAC 60.164 44.000 1.83 0.00 36.95 4.79
647 3417 2.667473 AGGACAAGTATTTCCGGACG 57.333 50.000 1.83 0.00 36.95 4.79
648 3418 1.206371 AGGACAAGTATTTCCGGACGG 59.794 52.381 1.83 3.96 36.95 4.79
649 3419 1.205417 GGACAAGTATTTCCGGACGGA 59.795 52.381 1.83 9.76 43.52 4.69
650 3420 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
651 3421 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
652 3422 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
653 3423 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
654 3424 0.826062 GTATTTCCGGACGGAGGGAA 59.174 55.000 13.64 6.20 46.06 3.97
655 3425 1.415289 GTATTTCCGGACGGAGGGAAT 59.585 52.381 13.64 12.81 46.06 3.01
743 3513 1.197721 CTTGCTTCCCAAGTTGTAGCG 59.802 52.381 13.72 0.00 44.74 4.26
744 3514 1.234615 TGCTTCCCAAGTTGTAGCGC 61.235 55.000 0.00 0.00 34.65 5.92
746 3516 1.453155 CTTCCCAAGTTGTAGCGCAT 58.547 50.000 11.47 0.00 0.00 4.73
1252 4363 4.447989 GCTGCGCTCTGCTCCTCA 62.448 66.667 9.73 0.00 46.63 3.86
1314 4425 0.672091 TGTTTTAGATGCCGCGCTCA 60.672 50.000 5.56 3.36 0.00 4.26
1363 4474 0.034059 CCGGTGATCTGGTCTATGCC 59.966 60.000 0.00 0.00 35.48 4.40
1364 4475 0.752658 CGGTGATCTGGTCTATGCCA 59.247 55.000 0.00 0.00 36.97 4.92
1365 4476 1.539065 CGGTGATCTGGTCTATGCCAC 60.539 57.143 0.00 0.00 34.36 5.01
1418 4555 5.296035 GTGACCTTTTGTAGCACAGTTACTT 59.704 40.000 0.00 0.00 0.00 2.24
1422 4559 6.704937 ACCTTTTGTAGCACAGTTACTTACTC 59.295 38.462 0.00 0.00 33.85 2.59
1424 4561 5.443185 TTGTAGCACAGTTACTTACTCGT 57.557 39.130 0.00 0.00 33.85 4.18
1448 4588 4.201990 GCTCTGTCCCATCATGATTTGAAC 60.202 45.833 5.16 3.15 38.03 3.18
1462 4603 8.420222 TCATGATTTGAACACAAATACAAAGGT 58.580 29.630 7.93 0.00 42.08 3.50
1464 4605 6.983307 TGATTTGAACACAAATACAAAGGTGG 59.017 34.615 7.93 0.00 42.08 4.61
1506 4647 6.385176 TGATGTTCCTGTAGATGGAGAATCTT 59.615 38.462 0.00 0.00 43.52 2.40
1507 4648 7.565029 TGATGTTCCTGTAGATGGAGAATCTTA 59.435 37.037 0.00 0.00 43.52 2.10
1508 4649 7.113658 TGTTCCTGTAGATGGAGAATCTTAC 57.886 40.000 0.00 0.00 43.52 2.34
1598 4749 7.871853 TCTTAAATTAGTTGCTTGTGAAGGAC 58.128 34.615 0.00 0.00 0.00 3.85
1888 5053 3.434309 AGGTGCTTGAAATAGCCACAAT 58.566 40.909 0.00 0.00 40.49 2.71
1889 5054 3.834231 AGGTGCTTGAAATAGCCACAATT 59.166 39.130 0.00 0.00 40.49 2.32
1931 5097 3.340034 TGTTCCTGCTTATTTGTACCCG 58.660 45.455 0.00 0.00 0.00 5.28
1953 5119 5.048991 CCGTTTTTGGCTACAACTATCAACT 60.049 40.000 0.00 0.00 36.06 3.16
1954 5120 6.148150 CCGTTTTTGGCTACAACTATCAACTA 59.852 38.462 0.00 0.00 36.06 2.24
1991 5157 4.753516 ATGGATACGACCTTTGTGATCA 57.246 40.909 0.00 0.00 42.51 2.92
2004 5170 1.378911 TGATCATGCAGTGGGTGGC 60.379 57.895 0.00 0.00 0.00 5.01
2087 5253 0.936297 GTTTGGCTGTTTCTGCTGCG 60.936 55.000 0.00 0.00 34.71 5.18
2415 5582 6.380095 TGTTGTGTGGTGGTTTCTTATAAC 57.620 37.500 0.00 0.00 0.00 1.89
2432 5599 7.136119 TCTTATAACGGTGTTTTCTTGCTTTG 58.864 34.615 0.00 0.00 0.00 2.77
2575 5742 2.346541 GCAAGGAGGGAAAGCAGGC 61.347 63.158 0.00 0.00 0.00 4.85
2662 5829 2.411547 GCAAGGAGTTCATTCGTTGTCG 60.412 50.000 9.34 0.00 42.16 4.35
2712 5891 7.435068 TCTTTTGCTGTTACAAGATAACCTC 57.565 36.000 0.00 0.00 0.00 3.85
2713 5892 6.995686 TCTTTTGCTGTTACAAGATAACCTCA 59.004 34.615 0.00 0.00 0.00 3.86
2714 5893 6.554334 TTTGCTGTTACAAGATAACCTCAC 57.446 37.500 0.00 0.00 0.00 3.51
2715 5894 5.222079 TGCTGTTACAAGATAACCTCACA 57.778 39.130 0.00 0.00 0.00 3.58
2716 5895 5.804639 TGCTGTTACAAGATAACCTCACAT 58.195 37.500 0.00 0.00 0.00 3.21
2717 5896 6.941857 TGCTGTTACAAGATAACCTCACATA 58.058 36.000 0.00 0.00 0.00 2.29
2718 5897 7.390823 TGCTGTTACAAGATAACCTCACATAA 58.609 34.615 0.00 0.00 0.00 1.90
2719 5898 7.333423 TGCTGTTACAAGATAACCTCACATAAC 59.667 37.037 0.00 0.00 0.00 1.89
2720 5899 7.333423 GCTGTTACAAGATAACCTCACATAACA 59.667 37.037 0.00 0.00 31.35 2.41
2721 5900 8.542497 TGTTACAAGATAACCTCACATAACAC 57.458 34.615 0.00 0.00 29.10 3.32
2722 5901 7.329962 TGTTACAAGATAACCTCACATAACACG 59.670 37.037 0.00 0.00 29.10 4.49
2723 5902 5.790593 ACAAGATAACCTCACATAACACGT 58.209 37.500 0.00 0.00 0.00 4.49
2872 6051 8.114331 AGTAAACTGATGCATTTCTTGAATGA 57.886 30.769 0.00 0.00 46.59 2.57
2878 6057 7.876068 ACTGATGCATTTCTTGAATGATTTGTT 59.124 29.630 0.00 0.00 46.59 2.83
2909 6088 3.517100 ACACTGTACTTCATGATGGCTCT 59.483 43.478 12.76 0.00 0.00 4.09
3323 6506 1.000060 CACCACCATTGCTTGTGAAGG 60.000 52.381 0.00 0.00 34.37 3.46
3331 6514 1.891919 GCTTGTGAAGGTCGCACCA 60.892 57.895 7.86 0.00 41.95 4.17
3367 6550 2.641305 GATCTTGAGGACATTGCTGCT 58.359 47.619 0.00 0.00 0.00 4.24
3550 6995 5.823045 GCACTGACTAGCATAACCCTAATTT 59.177 40.000 0.00 0.00 0.00 1.82
3620 7065 6.762108 ACTGTTTGCTTATTCTTTATCGACG 58.238 36.000 0.00 0.00 0.00 5.12
3883 7332 6.913673 GCTACTATTTCTTTACTGGAGTCTCG 59.086 42.308 0.00 0.00 0.00 4.04
4105 7560 0.817634 AGCTTTACACCGCACTTGCA 60.818 50.000 1.48 0.00 42.21 4.08
4188 7648 1.888512 AGCTTACAAGTTGCACCCATG 59.111 47.619 1.81 0.00 0.00 3.66
4200 7660 3.681593 TGCACCCATGTTTCTAGTTACC 58.318 45.455 0.00 0.00 0.00 2.85
4204 7664 4.695455 CACCCATGTTTCTAGTTACCACAG 59.305 45.833 0.00 0.00 0.00 3.66
4205 7665 4.261801 CCCATGTTTCTAGTTACCACAGG 58.738 47.826 0.00 0.00 0.00 4.00
4279 7749 4.637534 GCCTGCTCTATGTCTGAATTGAAA 59.362 41.667 0.00 0.00 0.00 2.69
4293 7763 6.039382 TCTGAATTGAAATCTGATGCTGATGG 59.961 38.462 0.00 0.00 0.00 3.51
4398 7868 1.242076 CTTGAAGGCCTGAACACCAG 58.758 55.000 5.69 0.00 42.55 4.00
4415 7885 0.179062 CAGCCGAGATCCTCCTTTGG 60.179 60.000 0.00 0.00 0.00 3.28
4420 7890 0.466124 GAGATCCTCCTTTGGGACGG 59.534 60.000 0.00 0.00 36.57 4.79
4486 7956 0.731514 CGGACGCTACTCGAAAAGCA 60.732 55.000 16.38 0.00 41.67 3.91
4939 8419 4.612264 AGTTATAACTGTGGTGGTCGTT 57.388 40.909 17.35 0.00 37.98 3.85
4940 8420 4.563061 AGTTATAACTGTGGTGGTCGTTC 58.437 43.478 17.35 0.00 37.98 3.95
4964 8444 2.555325 CAGCATGGAAGCTTTTGTCTGA 59.445 45.455 0.00 0.00 43.70 3.27
5089 8569 3.829026 TCTGCTACTGTGTTGAGACATCT 59.171 43.478 0.00 0.00 38.23 2.90
5090 8570 3.917988 TGCTACTGTGTTGAGACATCTG 58.082 45.455 0.00 0.00 38.23 2.90
5091 8571 3.321968 TGCTACTGTGTTGAGACATCTGT 59.678 43.478 0.00 0.00 38.23 3.41
5107 8587 4.274214 ACATCTGTGAACCATAATCATGCG 59.726 41.667 0.00 0.00 0.00 4.73
5181 8661 4.035091 GCAAATTTGGTGTTTTGACCCTTC 59.965 41.667 19.47 0.00 35.34 3.46
5182 8662 4.415881 AATTTGGTGTTTTGACCCTTCC 57.584 40.909 0.00 0.00 34.79 3.46
5192 8672 5.360144 TGTTTTGACCCTTCCGTGAAAATTA 59.640 36.000 0.00 0.00 32.67 1.40
5201 8681 5.449177 CCTTCCGTGAAAATTAAGCCAGATC 60.449 44.000 0.00 0.00 0.00 2.75
5210 8690 7.773690 TGAAAATTAAGCCAGATCTAACCCTAC 59.226 37.037 0.00 0.00 0.00 3.18
5213 8693 8.562949 AATTAAGCCAGATCTAACCCTACTTA 57.437 34.615 0.00 0.00 0.00 2.24
5214 8694 7.983166 TTAAGCCAGATCTAACCCTACTTAA 57.017 36.000 0.00 0.24 0.00 1.85
5217 8697 7.266905 AGCCAGATCTAACCCTACTTAAAAA 57.733 36.000 0.00 0.00 0.00 1.94
5268 8748 3.925090 GGGTCGATGGCGGTAGGG 61.925 72.222 0.00 0.00 38.28 3.53
5269 8749 3.152400 GGTCGATGGCGGTAGGGT 61.152 66.667 0.00 0.00 38.28 4.34
5270 8750 1.829533 GGTCGATGGCGGTAGGGTA 60.830 63.158 0.00 0.00 38.28 3.69
5271 8751 1.183676 GGTCGATGGCGGTAGGGTAT 61.184 60.000 0.00 0.00 38.28 2.73
5272 8752 0.038526 GTCGATGGCGGTAGGGTATG 60.039 60.000 0.00 0.00 38.28 2.39
5273 8753 1.374252 CGATGGCGGTAGGGTATGC 60.374 63.158 0.00 0.00 0.00 3.14
5276 8756 2.426023 GGCGGTAGGGTATGCCAG 59.574 66.667 1.04 0.00 46.76 4.85
5277 8757 2.280865 GCGGTAGGGTATGCCAGC 60.281 66.667 1.04 0.00 36.17 4.85
5278 8758 2.426023 CGGTAGGGTATGCCAGCC 59.574 66.667 1.04 0.00 45.89 4.85
5286 8766 2.257207 GGGTATGCCAGCCTACTATCA 58.743 52.381 1.04 0.00 41.95 2.15
5287 8767 2.637872 GGGTATGCCAGCCTACTATCAA 59.362 50.000 1.04 0.00 41.95 2.57
5288 8768 3.307059 GGGTATGCCAGCCTACTATCAAG 60.307 52.174 1.04 0.00 41.95 3.02
5289 8769 3.307059 GGTATGCCAGCCTACTATCAAGG 60.307 52.174 0.00 0.00 34.29 3.61
5301 8781 4.218856 TCAAGGCCCTTGACGGTA 57.781 55.556 22.25 0.00 44.27 4.02
5302 8782 1.980052 TCAAGGCCCTTGACGGTAG 59.020 57.895 22.25 0.00 44.27 3.18
5303 8783 1.078426 CAAGGCCCTTGACGGTAGG 60.078 63.158 19.04 0.00 43.42 3.18
5304 8784 1.538135 AAGGCCCTTGACGGTAGGT 60.538 57.895 0.00 0.00 0.00 3.08
5305 8785 0.252375 AAGGCCCTTGACGGTAGGTA 60.252 55.000 0.00 0.00 0.00 3.08
5306 8786 0.252375 AGGCCCTTGACGGTAGGTAA 60.252 55.000 0.00 0.00 0.00 2.85
5307 8787 0.107993 GGCCCTTGACGGTAGGTAAC 60.108 60.000 0.00 0.00 0.00 2.50
5359 8839 9.624697 TGATGCAAATTAGACAAGATTAACAAC 57.375 29.630 0.00 0.00 0.00 3.32
5360 8840 9.624697 GATGCAAATTAGACAAGATTAACAACA 57.375 29.630 0.00 0.00 0.00 3.33
5361 8841 9.979578 ATGCAAATTAGACAAGATTAACAACAA 57.020 25.926 0.00 0.00 0.00 2.83
5362 8842 9.243637 TGCAAATTAGACAAGATTAACAACAAC 57.756 29.630 0.00 0.00 0.00 3.32
5363 8843 9.243637 GCAAATTAGACAAGATTAACAACAACA 57.756 29.630 0.00 0.00 0.00 3.33
5370 8850 9.651913 AGACAAGATTAACAACAACAAAACAAT 57.348 25.926 0.00 0.00 0.00 2.71
5387 8867 9.744468 ACAAAACAATTAGAACTAATTCACCAC 57.256 29.630 14.43 0.00 42.11 4.16
5388 8868 9.743057 CAAAACAATTAGAACTAATTCACCACA 57.257 29.630 14.43 0.00 42.11 4.17
5390 8870 9.965824 AAACAATTAGAACTAATTCACCACAAG 57.034 29.630 14.43 6.29 42.11 3.16
5391 8871 8.691661 ACAATTAGAACTAATTCACCACAAGT 57.308 30.769 14.43 6.77 42.11 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 96 0.960364 GATCTTGCGCTGGGGTTCAA 60.960 55.000 9.73 0.00 0.00 2.69
134 136 3.335356 ATCTTGCGCTGGGGTCTGG 62.335 63.158 9.73 0.00 0.00 3.86
279 299 3.555324 TGTCGCCTCCTGCACCAA 61.555 61.111 0.00 0.00 41.33 3.67
348 2367 2.854963 TCTTCTGTGCAAGCAAGTCAT 58.145 42.857 0.00 0.00 0.00 3.06
349 2368 2.330440 TCTTCTGTGCAAGCAAGTCA 57.670 45.000 0.00 0.00 0.00 3.41
399 2418 3.209812 AGCTGGATCGAGCGCGTA 61.210 61.111 22.01 0.00 44.24 4.42
450 2469 4.377760 AGGGCGAAGTCTCCCGGA 62.378 66.667 0.73 0.00 45.44 5.14
552 3322 3.369471 CCTCGTTTTAGCTTCTCATCCCA 60.369 47.826 0.00 0.00 0.00 4.37
557 3327 2.413837 GTGCCTCGTTTTAGCTTCTCA 58.586 47.619 0.00 0.00 0.00 3.27
572 3342 2.014128 CAATAAATCCCGAACGTGCCT 58.986 47.619 0.00 0.00 0.00 4.75
611 3381 3.098636 GTCCTAAAACGATGCATTTCGC 58.901 45.455 9.55 0.00 42.82 4.70
612 3382 4.335082 TGTCCTAAAACGATGCATTTCG 57.665 40.909 8.13 8.13 44.56 3.46
613 3383 5.699839 ACTTGTCCTAAAACGATGCATTTC 58.300 37.500 0.00 0.00 0.00 2.17
614 3384 5.705609 ACTTGTCCTAAAACGATGCATTT 57.294 34.783 0.00 0.00 0.00 2.32
615 3385 7.391148 AATACTTGTCCTAAAACGATGCATT 57.609 32.000 0.00 0.00 0.00 3.56
616 3386 7.391148 AAATACTTGTCCTAAAACGATGCAT 57.609 32.000 0.00 0.00 0.00 3.96
617 3387 6.128117 GGAAATACTTGTCCTAAAACGATGCA 60.128 38.462 0.00 0.00 0.00 3.96
618 3388 6.255950 GGAAATACTTGTCCTAAAACGATGC 58.744 40.000 0.00 0.00 0.00 3.91
619 3389 6.456449 CCGGAAATACTTGTCCTAAAACGATG 60.456 42.308 0.00 0.00 0.00 3.84
620 3390 5.583457 CCGGAAATACTTGTCCTAAAACGAT 59.417 40.000 0.00 0.00 0.00 3.73
621 3391 4.931002 CCGGAAATACTTGTCCTAAAACGA 59.069 41.667 0.00 0.00 0.00 3.85
622 3392 4.931002 TCCGGAAATACTTGTCCTAAAACG 59.069 41.667 0.00 0.00 0.00 3.60
623 3393 5.163923 CGTCCGGAAATACTTGTCCTAAAAC 60.164 44.000 5.23 0.00 0.00 2.43
624 3394 4.931002 CGTCCGGAAATACTTGTCCTAAAA 59.069 41.667 5.23 0.00 0.00 1.52
625 3395 4.497300 CGTCCGGAAATACTTGTCCTAAA 58.503 43.478 5.23 0.00 0.00 1.85
626 3396 3.119029 CCGTCCGGAAATACTTGTCCTAA 60.119 47.826 5.23 0.00 37.50 2.69
627 3397 2.428171 CCGTCCGGAAATACTTGTCCTA 59.572 50.000 5.23 0.00 37.50 2.94
628 3398 1.206371 CCGTCCGGAAATACTTGTCCT 59.794 52.381 5.23 0.00 37.50 3.85
629 3399 1.205417 TCCGTCCGGAAATACTTGTCC 59.795 52.381 5.23 0.00 42.05 4.02
630 3400 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
631 3401 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
632 3402 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
633 3403 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
634 3404 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
635 3405 0.826062 TTCCCTCCGTCCGGAAATAC 59.174 55.000 5.23 0.00 44.66 1.89
636 3406 1.797320 ATTCCCTCCGTCCGGAAATA 58.203 50.000 5.23 0.00 44.66 1.40
637 3407 1.415289 GTATTCCCTCCGTCCGGAAAT 59.585 52.381 5.23 9.21 44.66 2.17
638 3408 0.826062 GTATTCCCTCCGTCCGGAAA 59.174 55.000 5.23 1.92 44.66 3.13
639 3409 0.032813 AGTATTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
640 3410 0.032813 AAGTATTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
641 3411 0.104304 CAAGTATTCCCTCCGTCCGG 59.896 60.000 0.00 0.00 0.00 5.14
642 3412 0.529992 GCAAGTATTCCCTCCGTCCG 60.530 60.000 0.00 0.00 0.00 4.79
643 3413 0.831307 AGCAAGTATTCCCTCCGTCC 59.169 55.000 0.00 0.00 0.00 4.79
644 3414 3.574826 AGATAGCAAGTATTCCCTCCGTC 59.425 47.826 0.00 0.00 0.00 4.79
645 3415 3.574826 GAGATAGCAAGTATTCCCTCCGT 59.425 47.826 0.00 0.00 0.00 4.69
646 3416 3.574396 TGAGATAGCAAGTATTCCCTCCG 59.426 47.826 0.00 0.00 0.00 4.63
647 3417 5.146010 CTGAGATAGCAAGTATTCCCTCC 57.854 47.826 0.00 0.00 0.00 4.30
743 3513 5.675538 AGACCAGTAGAAATAACTCCATGC 58.324 41.667 0.00 0.00 0.00 4.06
744 3514 7.118496 AGAGACCAGTAGAAATAACTCCATG 57.882 40.000 0.00 0.00 0.00 3.66
746 3516 6.127703 CGAAGAGACCAGTAGAAATAACTCCA 60.128 42.308 0.00 0.00 0.00 3.86
869 3653 3.761218 TGGAAGAGAAGTAGCAGACTCTG 59.239 47.826 1.21 1.21 37.44 3.35
871 3655 3.426963 CGTGGAAGAGAAGTAGCAGACTC 60.427 52.174 0.00 0.00 37.44 3.36
909 3696 4.729918 AGCAAGCAGAAGGGGCGG 62.730 66.667 0.00 0.00 36.08 6.13
1199 4301 1.737236 GTGTATGCGTGAATGCCAAGA 59.263 47.619 0.00 0.00 0.00 3.02
1202 4304 0.035534 AGGTGTATGCGTGAATGCCA 60.036 50.000 0.00 0.00 0.00 4.92
1209 4311 2.788176 CGCGTGAGGTGTATGCGTG 61.788 63.158 0.00 0.00 45.62 5.34
1345 4456 0.752658 TGGCATAGACCAGATCACCG 59.247 55.000 0.00 0.00 33.75 4.94
1418 4555 4.834911 TGGGACAGAGCACGAGTA 57.165 55.556 0.00 0.00 0.00 2.59
1462 4603 6.419791 ACATCAAGTCCGGTTATTATTTCCA 58.580 36.000 0.00 0.00 0.00 3.53
1464 4605 7.282450 AGGAACATCAAGTCCGGTTATTATTTC 59.718 37.037 0.00 0.00 0.00 2.17
1474 4615 2.496070 TCTACAGGAACATCAAGTCCGG 59.504 50.000 0.00 0.00 0.00 5.14
1506 4647 6.782082 ATCTCAAGAATAGTGCAGTCAGTA 57.218 37.500 0.00 0.00 33.05 2.74
1507 4648 5.674052 ATCTCAAGAATAGTGCAGTCAGT 57.326 39.130 0.00 0.00 0.00 3.41
1508 4649 6.981762 AAATCTCAAGAATAGTGCAGTCAG 57.018 37.500 0.00 0.00 0.00 3.51
1675 4837 4.884668 ATTGACGAGGAACAAGGACTAA 57.115 40.909 0.00 0.00 0.00 2.24
1768 4933 1.890041 CCAAAACGTGGCCTCGTCA 60.890 57.895 30.87 0.00 43.38 4.35
1889 5054 9.793259 GGAACATATGAATTCCTAGAATACCAA 57.207 33.333 10.38 0.00 41.13 3.67
1931 5097 7.389607 TCCTAGTTGATAGTTGTAGCCAAAAAC 59.610 37.037 0.00 0.00 30.94 2.43
1953 5119 6.377429 CGTATCCATTAGTGAATAGGCTCCTA 59.623 42.308 0.00 0.00 0.00 2.94
1954 5120 5.186021 CGTATCCATTAGTGAATAGGCTCCT 59.814 44.000 0.00 0.00 0.00 3.69
1991 5157 0.625316 TGAATAGCCACCCACTGCAT 59.375 50.000 0.00 0.00 0.00 3.96
2004 5170 7.351414 TCACGAGTTCTGTTGATTTGAATAG 57.649 36.000 0.00 0.00 0.00 1.73
2415 5582 3.420839 AGACAAAGCAAGAAAACACCG 57.579 42.857 0.00 0.00 0.00 4.94
2432 5599 3.610242 CGATTGACTACAGCACTGAAGAC 59.390 47.826 4.31 0.00 0.00 3.01
2575 5742 0.704076 TGACTCCCAAAATCCCAGGG 59.296 55.000 0.00 0.00 44.22 4.45
2662 5829 3.199880 ACCAGGTAATCAGCATACTGC 57.800 47.619 0.00 0.00 44.10 4.40
2859 6038 9.805966 CATTGACAACAAATCATTCAAGAAATG 57.194 29.630 0.00 0.00 41.42 2.32
2872 6051 4.389890 ACAGTGTGCATTGACAACAAAT 57.610 36.364 0.00 0.00 39.54 2.32
2878 6057 3.802866 TGAAGTACAGTGTGCATTGACA 58.197 40.909 14.11 3.54 0.00 3.58
3323 6506 0.596600 TTCGACAAGTCTGGTGCGAC 60.597 55.000 0.00 0.00 0.00 5.19
3331 6514 2.175202 AGATCCTGCTTCGACAAGTCT 58.825 47.619 0.00 0.00 31.45 3.24
3367 6550 6.368779 AAGGCTTTAGTCCAGTATGTTACA 57.631 37.500 0.00 0.00 0.00 2.41
3550 6995 9.109393 GAGAAATACATATTTGCACAGGAGTTA 57.891 33.333 1.60 0.00 36.13 2.24
3883 7332 4.932200 CACTTGTTCATGAGGGAGAGTTAC 59.068 45.833 0.00 0.00 0.00 2.50
4105 7560 0.259065 TGAGAGCTGGACCTCCGTAT 59.741 55.000 0.00 0.00 39.43 3.06
4188 7648 3.036075 ACGCCTGTGGTAACTAGAAAC 57.964 47.619 0.00 0.00 37.61 2.78
4200 7660 1.995484 CTGAACAGTGATACGCCTGTG 59.005 52.381 0.00 0.00 40.91 3.66
4204 7664 4.868171 TCATTTACTGAACAGTGATACGCC 59.132 41.667 16.37 0.00 42.52 5.68
4205 7665 5.500931 GCTCATTTACTGAACAGTGATACGC 60.501 44.000 16.37 11.40 42.52 4.42
4279 7749 4.993584 GTCGAATAACCATCAGCATCAGAT 59.006 41.667 0.00 0.00 0.00 2.90
4293 7763 0.179108 AGCTCGGCCTGTCGAATAAC 60.179 55.000 0.00 0.00 38.77 1.89
4398 7868 1.147153 CCCAAAGGAGGATCTCGGC 59.853 63.158 0.00 0.00 33.47 5.54
4415 7885 2.422479 GGGAAAAATTCTGCTACCGTCC 59.578 50.000 0.00 0.00 0.00 4.79
4420 7890 4.676546 GCTCATGGGAAAAATTCTGCTAC 58.323 43.478 0.00 0.00 0.00 3.58
4486 7956 2.285977 AGTTTCGACTTGGTTTCGCTT 58.714 42.857 0.00 0.00 36.40 4.68
4933 8413 0.955428 TTCCATGCTGCAGAACGACC 60.955 55.000 20.43 0.00 0.00 4.79
4935 8415 1.300971 GCTTCCATGCTGCAGAACGA 61.301 55.000 20.43 3.11 0.00 3.85
4936 8416 1.136147 GCTTCCATGCTGCAGAACG 59.864 57.895 20.43 0.00 0.00 3.95
4937 8417 0.886563 AAGCTTCCATGCTGCAGAAC 59.113 50.000 20.43 0.12 43.24 3.01
4938 8418 1.624336 AAAGCTTCCATGCTGCAGAA 58.376 45.000 20.43 7.68 43.24 3.02
4939 8419 1.271379 CAAAAGCTTCCATGCTGCAGA 59.729 47.619 20.43 2.70 43.24 4.26
4940 8420 1.000506 ACAAAAGCTTCCATGCTGCAG 59.999 47.619 10.11 10.11 43.24 4.41
5089 8569 1.675483 GCCGCATGATTATGGTTCACA 59.325 47.619 0.00 0.00 34.79 3.58
5090 8570 1.001378 GGCCGCATGATTATGGTTCAC 60.001 52.381 0.00 0.00 34.79 3.18
5091 8571 1.317613 GGCCGCATGATTATGGTTCA 58.682 50.000 0.00 0.00 34.79 3.18
5181 8661 6.458342 GGTTAGATCTGGCTTAATTTTCACGG 60.458 42.308 5.18 0.00 0.00 4.94
5182 8662 6.458342 GGGTTAGATCTGGCTTAATTTTCACG 60.458 42.308 5.18 0.00 0.00 4.35
5192 8672 6.886178 TTTAAGTAGGGTTAGATCTGGCTT 57.114 37.500 5.18 2.18 0.00 4.35
5220 8700 9.244292 GGTAGGAAAAGGTCAGATTCTATTTTT 57.756 33.333 0.00 0.00 0.00 1.94
5221 8701 7.553044 CGGTAGGAAAAGGTCAGATTCTATTTT 59.447 37.037 0.00 0.00 0.00 1.82
5222 8702 7.048512 CGGTAGGAAAAGGTCAGATTCTATTT 58.951 38.462 0.00 0.00 0.00 1.40
5223 8703 6.583562 CGGTAGGAAAAGGTCAGATTCTATT 58.416 40.000 0.00 0.00 0.00 1.73
5224 8704 5.453480 GCGGTAGGAAAAGGTCAGATTCTAT 60.453 44.000 0.00 0.00 0.00 1.98
5228 8708 2.355818 GGCGGTAGGAAAAGGTCAGATT 60.356 50.000 0.00 0.00 0.00 2.40
5236 8716 2.124860 CCCCGGCGGTAGGAAAAG 60.125 66.667 26.32 6.37 0.00 2.27
5260 8740 2.280865 GCTGGCATACCCTACCGC 60.281 66.667 0.00 0.00 33.59 5.68
5264 8744 3.076937 TGATAGTAGGCTGGCATACCCTA 59.923 47.826 12.72 4.22 34.18 3.53
5268 8748 3.931578 CCTTGATAGTAGGCTGGCATAC 58.068 50.000 9.02 9.02 33.91 2.39
5284 8764 1.550130 CCTACCGTCAAGGGCCTTGA 61.550 60.000 38.53 38.53 46.50 3.02
5285 8765 1.078426 CCTACCGTCAAGGGCCTTG 60.078 63.158 35.44 35.44 46.96 3.61
5286 8766 0.252375 TACCTACCGTCAAGGGCCTT 60.252 55.000 14.48 14.48 46.96 4.35
5287 8767 0.252375 TTACCTACCGTCAAGGGCCT 60.252 55.000 0.00 0.00 46.96 5.19
5288 8768 0.107993 GTTACCTACCGTCAAGGGCC 60.108 60.000 0.00 0.00 46.96 5.80
5289 8769 0.900421 AGTTACCTACCGTCAAGGGC 59.100 55.000 0.00 0.00 46.96 5.19
5290 8770 3.511146 TGTTAGTTACCTACCGTCAAGGG 59.489 47.826 0.00 0.00 46.96 3.95
5333 8813 9.624697 GTTGTTAATCTTGTCTAATTTGCATCA 57.375 29.630 0.00 0.00 0.00 3.07
5334 8814 9.624697 TGTTGTTAATCTTGTCTAATTTGCATC 57.375 29.630 0.00 0.00 0.00 3.91
5335 8815 9.979578 TTGTTGTTAATCTTGTCTAATTTGCAT 57.020 25.926 0.00 0.00 0.00 3.96
5336 8816 9.243637 GTTGTTGTTAATCTTGTCTAATTTGCA 57.756 29.630 0.00 0.00 0.00 4.08
5337 8817 9.243637 TGTTGTTGTTAATCTTGTCTAATTTGC 57.756 29.630 0.00 0.00 0.00 3.68
5344 8824 9.651913 ATTGTTTTGTTGTTGTTAATCTTGTCT 57.348 25.926 0.00 0.00 0.00 3.41
5361 8841 9.744468 GTGGTGAATTAGTTCTAATTGTTTTGT 57.256 29.630 18.58 0.00 35.33 2.83
5362 8842 9.743057 TGTGGTGAATTAGTTCTAATTGTTTTG 57.257 29.630 18.58 0.00 35.33 2.44
5364 8844 9.965824 CTTGTGGTGAATTAGTTCTAATTGTTT 57.034 29.630 18.58 0.50 35.33 2.83
5365 8845 9.131791 ACTTGTGGTGAATTAGTTCTAATTGTT 57.868 29.630 18.58 0.81 35.33 2.83
5366 8846 8.691661 ACTTGTGGTGAATTAGTTCTAATTGT 57.308 30.769 18.58 8.06 35.33 2.71


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

AutoCloner maintained by Alex Coulton.