Multiple sequence alignment - TraesCS5D01G231900

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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 TraesCS5D01G231900 chr5D 100.000 3557 0 0 1 3557 339068951 339065395 0.000000e+00 6569
1 TraesCS5D01G231900 chr5D 87.273 550 56 7 1492 2040 339086495 339085959 1.810000e-172 616
2 TraesCS5D01G231900 chr5D 81.239 549 76 11 1492 2039 339092340 339091818 5.490000e-113 418
3 TraesCS5D01G231900 chr5A 93.645 2030 88 12 821 2847 439774054 439772063 0.000000e+00 2996
4 TraesCS5D01G231900 chr5A 87.455 550 61 7 1492 2040 439825852 439825310 8.380000e-176 627
5 TraesCS5D01G231900 chr5A 84.925 597 60 9 169 739 439777649 439777057 8.560000e-161 577
6 TraesCS5D01G231900 chr5A 83.091 550 79 9 1492 2040 439854688 439854152 4.130000e-134 488
7 TraesCS5D01G231900 chr5A 94.231 156 8 1 2841 2995 439771888 439771733 1.650000e-58 237
8 TraesCS5D01G231900 chr5B 90.158 1839 116 34 495 2324 397967146 397965364 0.000000e+00 2333
9 TraesCS5D01G231900 chr5B 88.022 551 59 7 1492 2040 398059696 398059151 0.000000e+00 645
10 TraesCS5D01G231900 chr5B 83.485 551 75 12 1492 2040 398064163 398063627 1.910000e-137 499
11 TraesCS5D01G231900 chr5B 89.124 331 34 2 168 497 397967515 397967186 9.190000e-111 411
12 TraesCS5D01G231900 chr5B 92.857 280 20 0 2563 2842 397965351 397965072 1.190000e-109 407
13 TraesCS5D01G231900 chr3D 97.865 562 12 0 2996 3557 167377912 167377351 0.000000e+00 972
14 TraesCS5D01G231900 chr3D 97.513 563 14 0 2995 3557 527120777 527120215 0.000000e+00 963
15 TraesCS5D01G231900 chr3D 97.513 563 14 0 2995 3557 527126231 527125669 0.000000e+00 963
16 TraesCS5D01G231900 chr4D 97.687 562 12 1 2996 3557 73331769 73332329 0.000000e+00 965
17 TraesCS5D01G231900 chr4D 97.513 563 13 1 2995 3557 73345773 73346334 0.000000e+00 961
18 TraesCS5D01G231900 chr4D 90.230 174 12 5 1 172 489955301 489955471 4.620000e-54 222
19 TraesCS5D01G231900 chr4D 80.851 235 33 8 261 493 8196498 8196274 1.310000e-39 174
20 TraesCS5D01G231900 chrUn 97.513 563 14 0 2995 3557 27176982 27177544 0.000000e+00 963
21 TraesCS5D01G231900 chr7D 97.513 563 14 0 2995 3557 106381693 106381131 0.000000e+00 963
22 TraesCS5D01G231900 chr7D 97.513 563 14 0 2995 3557 133218239 133217677 0.000000e+00 963
23 TraesCS5D01G231900 chr2D 97.183 568 16 0 2990 3557 571223172 571223739 0.000000e+00 961
24 TraesCS5D01G231900 chr2A 83.171 410 57 8 1630 2039 236918916 236918519 7.260000e-97 364
25 TraesCS5D01G231900 chr2A 90.588 170 13 3 1 167 4904875 4904706 4.620000e-54 222
26 TraesCS5D01G231900 chr1A 91.860 172 10 4 1 168 544732253 544732082 1.650000e-58 237
27 TraesCS5D01G231900 chr1D 91.765 170 11 3 1 168 338270326 338270494 2.140000e-57 233
28 TraesCS5D01G231900 chr1D 91.176 170 10 3 1 168 254053540 254053374 3.570000e-55 226
29 TraesCS5D01G231900 chr1D 89.714 175 14 4 1 173 373113738 373113910 1.660000e-53 220
30 TraesCS5D01G231900 chr7A 91.228 171 12 2 1 168 730830846 730830676 2.760000e-56 230
31 TraesCS5D01G231900 chr1B 91.018 167 14 1 1 166 409847361 409847527 1.290000e-54 224
32 TraesCS5D01G231900 chr6A 90.588 170 13 3 1 168 70223694 70223526 4.620000e-54 222


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 TraesCS5D01G231900 chr5D 339065395 339068951 3556 True 6569.000000 6569 100.000000 1 3557 1 chr5D.!!$R1 3556
1 TraesCS5D01G231900 chr5D 339085959 339086495 536 True 616.000000 616 87.273000 1492 2040 1 chr5D.!!$R2 548
2 TraesCS5D01G231900 chr5D 339091818 339092340 522 True 418.000000 418 81.239000 1492 2039 1 chr5D.!!$R3 547
3 TraesCS5D01G231900 chr5A 439771733 439777649 5916 True 1270.000000 2996 90.933667 169 2995 3 chr5A.!!$R3 2826
4 TraesCS5D01G231900 chr5A 439825310 439825852 542 True 627.000000 627 87.455000 1492 2040 1 chr5A.!!$R1 548
5 TraesCS5D01G231900 chr5A 439854152 439854688 536 True 488.000000 488 83.091000 1492 2040 1 chr5A.!!$R2 548
6 TraesCS5D01G231900 chr5B 397965072 397967515 2443 True 1050.333333 2333 90.713000 168 2842 3 chr5B.!!$R1 2674
7 TraesCS5D01G231900 chr5B 398059151 398064163 5012 True 572.000000 645 85.753500 1492 2040 2 chr5B.!!$R2 548
8 TraesCS5D01G231900 chr3D 167377351 167377912 561 True 972.000000 972 97.865000 2996 3557 1 chr3D.!!$R1 561
9 TraesCS5D01G231900 chr3D 527120215 527120777 562 True 963.000000 963 97.513000 2995 3557 1 chr3D.!!$R2 562
10 TraesCS5D01G231900 chr3D 527125669 527126231 562 True 963.000000 963 97.513000 2995 3557 1 chr3D.!!$R3 562
11 TraesCS5D01G231900 chr4D 73331769 73332329 560 False 965.000000 965 97.687000 2996 3557 1 chr4D.!!$F1 561
12 TraesCS5D01G231900 chr4D 73345773 73346334 561 False 961.000000 961 97.513000 2995 3557 1 chr4D.!!$F2 562
13 TraesCS5D01G231900 chrUn 27176982 27177544 562 False 963.000000 963 97.513000 2995 3557 1 chrUn.!!$F1 562
14 TraesCS5D01G231900 chr7D 106381131 106381693 562 True 963.000000 963 97.513000 2995 3557 1 chr7D.!!$R1 562
15 TraesCS5D01G231900 chr7D 133217677 133218239 562 True 963.000000 963 97.513000 2995 3557 1 chr7D.!!$R2 562
16 TraesCS5D01G231900 chr2D 571223172 571223739 567 False 961.000000 961 97.183000 2990 3557 1 chr2D.!!$F1 567

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
758 3749 0.034574 TCACATGGGTGGGTGTATGC 60.035 55.0 0.0 0.0 45.32 3.14 F
2228 5222 0.320771 GAGTGGTGGACATCGTTGCT 60.321 55.0 0.0 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 5347 0.035152 CAGGGGCATTGCTCACTACA 60.035 55.0 11.32 0.0 0.0 2.74 R
3287 10206 0.464373 ATCATCACCATGTCCACCGC 60.464 55.0 0.00 0.0 0.0 5.68 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
46 47 8.643324 AGTTATGTCACATCTAACCTAATCTCC 58.357 37.037 0.00 0.00 0.00 3.71
47 48 8.421784 GTTATGTCACATCTAACCTAATCTCCA 58.578 37.037 0.00 0.00 0.00 3.86
48 49 6.222038 TGTCACATCTAACCTAATCTCCAC 57.778 41.667 0.00 0.00 0.00 4.02
49 50 5.958380 TGTCACATCTAACCTAATCTCCACT 59.042 40.000 0.00 0.00 0.00 4.00
50 51 7.123383 TGTCACATCTAACCTAATCTCCACTA 58.877 38.462 0.00 0.00 0.00 2.74
51 52 7.785028 TGTCACATCTAACCTAATCTCCACTAT 59.215 37.037 0.00 0.00 0.00 2.12
52 53 8.085296 GTCACATCTAACCTAATCTCCACTATG 58.915 40.741 0.00 0.00 0.00 2.23
53 54 7.785028 TCACATCTAACCTAATCTCCACTATGT 59.215 37.037 0.00 0.00 0.00 2.29
54 55 8.424918 CACATCTAACCTAATCTCCACTATGTT 58.575 37.037 0.00 0.00 0.00 2.71
55 56 8.993424 ACATCTAACCTAATCTCCACTATGTTT 58.007 33.333 0.00 0.00 0.00 2.83
56 57 9.265901 CATCTAACCTAATCTCCACTATGTTTG 57.734 37.037 0.00 0.00 0.00 2.93
57 58 8.375493 TCTAACCTAATCTCCACTATGTTTGT 57.625 34.615 0.00 0.00 0.00 2.83
58 59 8.258007 TCTAACCTAATCTCCACTATGTTTGTG 58.742 37.037 0.00 0.00 35.39 3.33
111 112 9.606631 TTTTTGTTCCTTGTTGCTATGTTATTT 57.393 25.926 0.00 0.00 0.00 1.40
112 113 8.586570 TTTGTTCCTTGTTGCTATGTTATTTG 57.413 30.769 0.00 0.00 0.00 2.32
113 114 7.283625 TGTTCCTTGTTGCTATGTTATTTGT 57.716 32.000 0.00 0.00 0.00 2.83
114 115 7.144661 TGTTCCTTGTTGCTATGTTATTTGTG 58.855 34.615 0.00 0.00 0.00 3.33
115 116 6.266168 TCCTTGTTGCTATGTTATTTGTGG 57.734 37.500 0.00 0.00 0.00 4.17
116 117 5.184864 TCCTTGTTGCTATGTTATTTGTGGG 59.815 40.000 0.00 0.00 0.00 4.61
117 118 5.184864 CCTTGTTGCTATGTTATTTGTGGGA 59.815 40.000 0.00 0.00 0.00 4.37
118 119 5.895636 TGTTGCTATGTTATTTGTGGGAG 57.104 39.130 0.00 0.00 0.00 4.30
119 120 5.321102 TGTTGCTATGTTATTTGTGGGAGT 58.679 37.500 0.00 0.00 0.00 3.85
120 121 5.772672 TGTTGCTATGTTATTTGTGGGAGTT 59.227 36.000 0.00 0.00 0.00 3.01
121 122 6.266558 TGTTGCTATGTTATTTGTGGGAGTTT 59.733 34.615 0.00 0.00 0.00 2.66
122 123 7.448777 TGTTGCTATGTTATTTGTGGGAGTTTA 59.551 33.333 0.00 0.00 0.00 2.01
123 124 7.624360 TGCTATGTTATTTGTGGGAGTTTAG 57.376 36.000 0.00 0.00 0.00 1.85
124 125 7.398829 TGCTATGTTATTTGTGGGAGTTTAGA 58.601 34.615 0.00 0.00 0.00 2.10
125 126 8.052748 TGCTATGTTATTTGTGGGAGTTTAGAT 58.947 33.333 0.00 0.00 0.00 1.98
126 127 8.345565 GCTATGTTATTTGTGGGAGTTTAGATG 58.654 37.037 0.00 0.00 0.00 2.90
127 128 9.396022 CTATGTTATTTGTGGGAGTTTAGATGT 57.604 33.333 0.00 0.00 0.00 3.06
128 129 7.447374 TGTTATTTGTGGGAGTTTAGATGTG 57.553 36.000 0.00 0.00 0.00 3.21
129 130 7.227873 TGTTATTTGTGGGAGTTTAGATGTGA 58.772 34.615 0.00 0.00 0.00 3.58
130 131 7.174253 TGTTATTTGTGGGAGTTTAGATGTGAC 59.826 37.037 0.00 0.00 0.00 3.67
131 132 4.698201 TTGTGGGAGTTTAGATGTGACA 57.302 40.909 0.00 0.00 0.00 3.58
132 133 4.908601 TGTGGGAGTTTAGATGTGACAT 57.091 40.909 0.00 0.00 0.00 3.06
133 134 4.832248 TGTGGGAGTTTAGATGTGACATC 58.168 43.478 17.46 17.46 0.00 3.06
134 135 4.192317 GTGGGAGTTTAGATGTGACATCC 58.808 47.826 21.05 6.28 0.00 3.51
135 136 4.080863 GTGGGAGTTTAGATGTGACATCCT 60.081 45.833 21.05 11.37 0.00 3.24
136 137 4.536090 TGGGAGTTTAGATGTGACATCCTT 59.464 41.667 21.05 7.22 0.00 3.36
137 138 5.724370 TGGGAGTTTAGATGTGACATCCTTA 59.276 40.000 21.05 6.22 0.00 2.69
138 139 6.127054 TGGGAGTTTAGATGTGACATCCTTAG 60.127 42.308 21.05 0.00 0.00 2.18
139 140 6.098409 GGGAGTTTAGATGTGACATCCTTAGA 59.902 42.308 21.05 1.88 0.00 2.10
140 141 7.364762 GGGAGTTTAGATGTGACATCCTTAGAA 60.365 40.741 21.05 7.16 0.00 2.10
141 142 8.041323 GGAGTTTAGATGTGACATCCTTAGAAA 58.959 37.037 21.05 11.24 0.00 2.52
142 143 9.436957 GAGTTTAGATGTGACATCCTTAGAAAA 57.563 33.333 21.05 9.88 0.00 2.29
143 144 9.965902 AGTTTAGATGTGACATCCTTAGAAAAT 57.034 29.630 21.05 10.60 0.00 1.82
195 196 9.507280 AAATGATAACGTGATTGCTTAAATGAG 57.493 29.630 0.00 0.00 0.00 2.90
206 207 3.142174 GCTTAAATGAGAGGGGAATCGG 58.858 50.000 0.00 0.00 0.00 4.18
257 258 6.554334 AACTAGTAATGTGAACGTGCAATT 57.446 33.333 0.00 3.56 0.00 2.32
259 260 3.564511 AGTAATGTGAACGTGCAATTGC 58.435 40.909 23.69 23.69 42.50 3.56
408 413 5.932303 GCTCGCCATTTGATTAATCTAGGTA 59.068 40.000 16.24 0.00 0.00 3.08
409 414 6.091441 GCTCGCCATTTGATTAATCTAGGTAG 59.909 42.308 16.24 13.14 0.00 3.18
420 425 9.213777 TGATTAATCTAGGTAGTTGGATTGACT 57.786 33.333 16.24 0.00 31.89 3.41
431 436 9.444600 GGTAGTTGGATTGACTTAGTTTTATGA 57.555 33.333 0.00 0.00 0.00 2.15
582 629 1.802337 TACTTGACGCTGGTGCTCGT 61.802 55.000 0.00 0.00 42.09 4.18
600 647 8.068380 GGTGCTCGTATTTTTCTGGATTATTAC 58.932 37.037 0.00 0.00 0.00 1.89
627 674 4.084507 GTCTTTTCAGCGATGTTCATTCG 58.915 43.478 0.00 0.00 39.55 3.34
662 709 1.683943 CCGTCGACTATAGGGGAACA 58.316 55.000 14.70 0.00 0.00 3.18
694 741 6.455647 ACTTCGTCAATCTTCAGATGTTGTA 58.544 36.000 0.00 0.00 34.49 2.41
696 743 7.276658 ACTTCGTCAATCTTCAGATGTTGTATC 59.723 37.037 0.00 0.00 34.49 2.24
699 746 6.042777 GTCAATCTTCAGATGTTGTATCGGA 58.957 40.000 0.00 0.00 34.49 4.55
703 750 6.220726 TCTTCAGATGTTGTATCGGATCAA 57.779 37.500 0.00 0.00 0.00 2.57
711 758 4.578928 TGTTGTATCGGATCAATCTCTCGA 59.421 41.667 0.00 0.00 0.00 4.04
722 773 5.977489 TCAATCTCTCGAAAGTGTAAGGA 57.023 39.130 0.00 0.00 0.00 3.36
739 790 1.740296 GATAGGGTGTGCGTGCGTT 60.740 57.895 0.00 0.00 0.00 4.84
741 792 2.443260 ATAGGGTGTGCGTGCGTTCA 62.443 55.000 0.00 0.00 0.00 3.18
742 793 4.307908 GGGTGTGCGTGCGTTCAC 62.308 66.667 10.68 10.68 39.78 3.18
743 794 3.568743 GGTGTGCGTGCGTTCACA 61.569 61.111 16.93 10.56 43.28 3.58
747 3738 3.353029 TGCGTGCGTTCACATGGG 61.353 61.111 0.00 0.00 43.28 4.00
750 3741 2.953821 GTGCGTTCACATGGGTGG 59.046 61.111 0.00 0.00 45.32 4.61
758 3749 0.034574 TCACATGGGTGGGTGTATGC 60.035 55.000 0.00 0.00 45.32 3.14
769 3760 3.751175 GTGGGTGTATGCGCATATGTATT 59.249 43.478 31.14 8.09 33.93 1.89
770 3761 4.215399 GTGGGTGTATGCGCATATGTATTT 59.785 41.667 31.14 7.28 33.93 1.40
774 3765 4.612614 GTGTATGCGCATATGTATTTGTGC 59.387 41.667 31.14 15.38 46.76 4.57
788 3779 0.602638 TTGTGCCTGCGTCCTTGTAG 60.603 55.000 0.00 0.00 0.00 2.74
791 3782 1.004918 GCCTGCGTCCTTGTAGTGT 60.005 57.895 0.00 0.00 0.00 3.55
795 3786 2.288579 CCTGCGTCCTTGTAGTGTGTTA 60.289 50.000 0.00 0.00 0.00 2.41
848 3841 8.659925 ATCTCACAACTATCAAAAGATAGCAG 57.340 34.615 11.35 7.51 38.40 4.24
1101 4095 3.702048 CCACCACCGACGGTCCAT 61.702 66.667 18.72 2.00 37.07 3.41
1142 4136 2.751913 CGACGAGGAGGAGGACGTG 61.752 68.421 0.00 0.00 39.04 4.49
1337 4331 3.928992 CGCCGCATCAAGTCATAGATATT 59.071 43.478 0.00 0.00 0.00 1.28
1364 4358 9.828039 GATGATAATGATAGGCATGAAGTCATA 57.172 33.333 0.00 0.00 37.28 2.15
1373 4367 6.931790 AGGCATGAAGTCATAGATGTAGAT 57.068 37.500 0.00 0.00 34.26 1.98
1406 4400 4.224594 AGCCTGATCTTCATCAAAGAGACA 59.775 41.667 0.00 0.00 46.95 3.41
1844 4838 3.033764 GCGCTCACGAACGTGGAA 61.034 61.111 23.50 7.82 45.43 3.53
1873 4867 2.325082 GCAACCGGATGTTCTGCGT 61.325 57.895 9.46 0.00 36.91 5.24
1980 4974 2.989253 TGAGGAAGGTCGCGCAGA 60.989 61.111 8.75 2.49 0.00 4.26
2051 5045 3.138798 GGCTGCCAGCACATGAGG 61.139 66.667 19.95 0.00 44.75 3.86
2122 5116 5.685511 ACAAGAAAATTACGTTCATGTGCAC 59.314 36.000 10.75 10.75 36.03 4.57
2228 5222 0.320771 GAGTGGTGGACATCGTTGCT 60.321 55.000 0.00 0.00 0.00 3.91
2254 5248 2.099921 CAGGCGTACTGCTTACTGATCT 59.900 50.000 9.06 0.00 45.43 2.75
2256 5250 1.855360 GCGTACTGCTTACTGATCTGC 59.145 52.381 0.00 0.00 41.73 4.26
2257 5251 2.735444 GCGTACTGCTTACTGATCTGCA 60.735 50.000 0.00 0.00 41.73 4.41
2258 5252 3.711086 CGTACTGCTTACTGATCTGCAT 58.289 45.455 0.00 0.00 34.79 3.96
2260 5254 4.677378 CGTACTGCTTACTGATCTGCATAC 59.323 45.833 0.00 0.00 34.79 2.39
2342 5343 5.816258 GGAAGGAAATTACTACTACCAGTGC 59.184 44.000 0.00 0.00 0.00 4.40
2346 5347 6.384305 AGGAAATTACTACTACCAGTGCTGAT 59.616 38.462 0.02 0.00 0.00 2.90
2347 5348 6.480320 GGAAATTACTACTACCAGTGCTGATG 59.520 42.308 0.02 0.00 0.00 3.07
2392 5393 6.111382 TCTCTGATGCCATTTTGAGAAGTAG 58.889 40.000 3.77 0.00 0.00 2.57
2393 5394 5.809001 TCTGATGCCATTTTGAGAAGTAGT 58.191 37.500 0.00 0.00 0.00 2.73
2394 5395 6.240894 TCTGATGCCATTTTGAGAAGTAGTT 58.759 36.000 0.00 0.00 0.00 2.24
2397 5398 9.330063 CTGATGCCATTTTGAGAAGTAGTTATA 57.670 33.333 0.00 0.00 0.00 0.98
2398 5399 9.330063 TGATGCCATTTTGAGAAGTAGTTATAG 57.670 33.333 0.00 0.00 0.00 1.31
2402 5404 7.621991 CCATTTTGAGAAGTAGTTATAGCACG 58.378 38.462 0.00 0.00 0.00 5.34
2495 5497 1.068434 GGAGCTACTAGAAGGCAGCTG 59.932 57.143 10.11 10.11 44.17 4.24
2521 5523 3.133362 TGGTCCTATATCGTGGGAAACAC 59.867 47.826 0.00 0.00 46.78 3.32
2534 5536 3.117322 TGGGAAACACTCTTGGATTTGGA 60.117 43.478 0.00 0.00 0.00 3.53
2558 5560 2.791383 TGAAATTCCACGCAACCTTG 57.209 45.000 0.00 0.00 0.00 3.61
2569 5571 0.242017 GCAACCTTGTGGCAGATGTC 59.758 55.000 0.00 0.00 31.84 3.06
2607 5610 5.940192 TTTTGTGTGTGTGGATCTATGAC 57.060 39.130 0.00 0.00 0.00 3.06
2611 5614 2.766263 TGTGTGTGGATCTATGACCTCC 59.234 50.000 0.00 0.00 0.00 4.30
2625 5628 4.356405 TGACCTCCCAATATGCAGTATG 57.644 45.455 0.00 0.00 40.87 2.39
2632 5635 4.639755 TCCCAATATGCAGTATGTTGTGTG 59.360 41.667 7.12 0.00 36.48 3.82
2693 5696 0.627469 ATCCCCTAGTGCCACCCAAT 60.627 55.000 0.00 0.00 0.00 3.16
2702 5705 3.698765 CCACCCAATGGCTCAACC 58.301 61.111 0.00 0.00 43.24 3.77
2708 5711 1.095228 CCAATGGCTCAACCGCGTAT 61.095 55.000 4.92 0.00 43.94 3.06
2769 5772 7.012610 ACCTTTCTTGAATTCCAAATTGCAAAG 59.987 33.333 1.71 0.00 33.76 2.77
2796 5799 7.112452 AGTTTCCTTTTAAGCAAGTGTTCAT 57.888 32.000 0.00 0.00 0.00 2.57
2814 5817 3.717707 TCATATCGCAGTAGGTTTGAGC 58.282 45.455 0.00 0.00 0.00 4.26
2829 5832 5.827797 AGGTTTGAGCAGTTGTATTCTTTGA 59.172 36.000 0.00 0.00 0.00 2.69
2842 5845 7.440523 TGTATTCTTTGAAAGGAGAGCTTTC 57.559 36.000 4.94 0.00 40.22 2.62
2853 6038 3.067320 AGGAGAGCTTTCAAAAGTGCAAC 59.933 43.478 6.59 0.00 38.28 4.17
2856 6041 4.427312 AGAGCTTTCAAAAGTGCAACAAG 58.573 39.130 4.54 0.00 41.43 3.16
2887 6072 6.674037 GCAATACATACTGTGCACTCTTTCTG 60.674 42.308 19.41 10.25 36.97 3.02
2941 6126 2.745884 TGGCATGCTACACGGTGC 60.746 61.111 18.92 0.00 36.88 5.01
2975 6160 1.629861 CCATTTGCCAAAATCCCTGGT 59.370 47.619 0.00 0.00 33.59 4.00
2986 6171 2.556840 ATCCCTGGTCCAACATGGCG 62.557 60.000 0.00 0.00 37.47 5.69
2999 6184 1.134640 ACATGGCGCGGTATCTTGTTA 60.135 47.619 8.83 0.00 0.00 2.41
3078 8193 6.021468 GCATTGACACAAATAAACGCATACTC 60.021 38.462 0.00 0.00 0.00 2.59
3080 8195 5.922546 TGACACAAATAAACGCATACTCAC 58.077 37.500 0.00 0.00 0.00 3.51
3169 8978 1.968493 ACAGAAAACAGTAGGAGCGGA 59.032 47.619 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 8.643324 GGAGATTAGGTTAGATGTGACATAACT 58.357 37.037 10.13 1.17 31.53 2.24
21 22 8.421784 TGGAGATTAGGTTAGATGTGACATAAC 58.578 37.037 0.00 0.00 0.00 1.89
22 23 8.421784 GTGGAGATTAGGTTAGATGTGACATAA 58.578 37.037 0.00 0.00 0.00 1.90
23 24 7.785028 AGTGGAGATTAGGTTAGATGTGACATA 59.215 37.037 0.00 0.00 0.00 2.29
24 25 6.613271 AGTGGAGATTAGGTTAGATGTGACAT 59.387 38.462 0.00 0.00 0.00 3.06
25 26 5.958380 AGTGGAGATTAGGTTAGATGTGACA 59.042 40.000 0.00 0.00 0.00 3.58
26 27 6.472686 AGTGGAGATTAGGTTAGATGTGAC 57.527 41.667 0.00 0.00 0.00 3.67
27 28 7.785028 ACATAGTGGAGATTAGGTTAGATGTGA 59.215 37.037 0.00 0.00 0.00 3.58
28 29 7.957002 ACATAGTGGAGATTAGGTTAGATGTG 58.043 38.462 0.00 0.00 0.00 3.21
29 30 8.554490 AACATAGTGGAGATTAGGTTAGATGT 57.446 34.615 0.00 0.00 0.00 3.06
30 31 9.265901 CAAACATAGTGGAGATTAGGTTAGATG 57.734 37.037 0.00 0.00 0.00 2.90
31 32 8.993424 ACAAACATAGTGGAGATTAGGTTAGAT 58.007 33.333 0.00 0.00 0.00 1.98
32 33 8.258007 CACAAACATAGTGGAGATTAGGTTAGA 58.742 37.037 0.00 0.00 33.43 2.10
33 34 8.425577 CACAAACATAGTGGAGATTAGGTTAG 57.574 38.462 0.00 0.00 33.43 2.34
85 86 9.606631 AAATAACATAGCAACAAGGAACAAAAA 57.393 25.926 0.00 0.00 0.00 1.94
86 87 9.039870 CAAATAACATAGCAACAAGGAACAAAA 57.960 29.630 0.00 0.00 0.00 2.44
87 88 8.200792 ACAAATAACATAGCAACAAGGAACAAA 58.799 29.630 0.00 0.00 0.00 2.83
88 89 7.651304 CACAAATAACATAGCAACAAGGAACAA 59.349 33.333 0.00 0.00 0.00 2.83
89 90 7.144661 CACAAATAACATAGCAACAAGGAACA 58.855 34.615 0.00 0.00 0.00 3.18
90 91 6.586082 CCACAAATAACATAGCAACAAGGAAC 59.414 38.462 0.00 0.00 0.00 3.62
91 92 6.295011 CCCACAAATAACATAGCAACAAGGAA 60.295 38.462 0.00 0.00 0.00 3.36
92 93 5.184864 CCCACAAATAACATAGCAACAAGGA 59.815 40.000 0.00 0.00 0.00 3.36
93 94 5.184864 TCCCACAAATAACATAGCAACAAGG 59.815 40.000 0.00 0.00 0.00 3.61
94 95 6.071952 ACTCCCACAAATAACATAGCAACAAG 60.072 38.462 0.00 0.00 0.00 3.16
95 96 5.772672 ACTCCCACAAATAACATAGCAACAA 59.227 36.000 0.00 0.00 0.00 2.83
96 97 5.321102 ACTCCCACAAATAACATAGCAACA 58.679 37.500 0.00 0.00 0.00 3.33
97 98 5.897377 ACTCCCACAAATAACATAGCAAC 57.103 39.130 0.00 0.00 0.00 4.17
98 99 6.909550 AAACTCCCACAAATAACATAGCAA 57.090 33.333 0.00 0.00 0.00 3.91
99 100 7.398829 TCTAAACTCCCACAAATAACATAGCA 58.601 34.615 0.00 0.00 0.00 3.49
100 101 7.859325 TCTAAACTCCCACAAATAACATAGC 57.141 36.000 0.00 0.00 0.00 2.97
101 102 9.396022 ACATCTAAACTCCCACAAATAACATAG 57.604 33.333 0.00 0.00 0.00 2.23
102 103 9.173021 CACATCTAAACTCCCACAAATAACATA 57.827 33.333 0.00 0.00 0.00 2.29
103 104 7.888021 TCACATCTAAACTCCCACAAATAACAT 59.112 33.333 0.00 0.00 0.00 2.71
104 105 7.174253 GTCACATCTAAACTCCCACAAATAACA 59.826 37.037 0.00 0.00 0.00 2.41
105 106 7.174253 TGTCACATCTAAACTCCCACAAATAAC 59.826 37.037 0.00 0.00 0.00 1.89
106 107 7.227873 TGTCACATCTAAACTCCCACAAATAA 58.772 34.615 0.00 0.00 0.00 1.40
107 108 6.774673 TGTCACATCTAAACTCCCACAAATA 58.225 36.000 0.00 0.00 0.00 1.40
108 109 5.630121 TGTCACATCTAAACTCCCACAAAT 58.370 37.500 0.00 0.00 0.00 2.32
109 110 5.042463 TGTCACATCTAAACTCCCACAAA 57.958 39.130 0.00 0.00 0.00 2.83
110 111 4.698201 TGTCACATCTAAACTCCCACAA 57.302 40.909 0.00 0.00 0.00 3.33
111 112 4.323485 GGATGTCACATCTAAACTCCCACA 60.323 45.833 17.46 0.00 0.00 4.17
112 113 4.080863 AGGATGTCACATCTAAACTCCCAC 60.081 45.833 17.46 0.00 0.00 4.61
113 114 4.104086 AGGATGTCACATCTAAACTCCCA 58.896 43.478 17.46 0.00 0.00 4.37
114 115 4.762289 AGGATGTCACATCTAAACTCCC 57.238 45.455 17.46 0.00 0.00 4.30
115 116 7.113658 TCTAAGGATGTCACATCTAAACTCC 57.886 40.000 17.46 0.18 0.00 3.85
116 117 9.436957 TTTTCTAAGGATGTCACATCTAAACTC 57.563 33.333 17.46 0.00 0.00 3.01
117 118 9.965902 ATTTTCTAAGGATGTCACATCTAAACT 57.034 29.630 17.46 3.19 0.00 2.66
155 156 9.825972 CACGTTATCATTTTCAGTTTGTCTAAT 57.174 29.630 0.00 0.00 0.00 1.73
156 157 9.047371 TCACGTTATCATTTTCAGTTTGTCTAA 57.953 29.630 0.00 0.00 0.00 2.10
157 158 8.596271 TCACGTTATCATTTTCAGTTTGTCTA 57.404 30.769 0.00 0.00 0.00 2.59
158 159 7.490962 TCACGTTATCATTTTCAGTTTGTCT 57.509 32.000 0.00 0.00 0.00 3.41
159 160 8.629986 CAATCACGTTATCATTTTCAGTTTGTC 58.370 33.333 0.00 0.00 0.00 3.18
160 161 7.114811 GCAATCACGTTATCATTTTCAGTTTGT 59.885 33.333 0.00 0.00 0.00 2.83
161 162 7.326789 AGCAATCACGTTATCATTTTCAGTTTG 59.673 33.333 0.00 0.00 0.00 2.93
162 163 7.370383 AGCAATCACGTTATCATTTTCAGTTT 58.630 30.769 0.00 0.00 0.00 2.66
163 164 6.913170 AGCAATCACGTTATCATTTTCAGTT 58.087 32.000 0.00 0.00 0.00 3.16
164 165 6.500684 AGCAATCACGTTATCATTTTCAGT 57.499 33.333 0.00 0.00 0.00 3.41
165 166 8.894409 TTAAGCAATCACGTTATCATTTTCAG 57.106 30.769 0.00 0.00 0.00 3.02
166 167 9.853555 ATTTAAGCAATCACGTTATCATTTTCA 57.146 25.926 0.00 0.00 0.00 2.69
195 196 1.694696 AGATGTTAGCCGATTCCCCTC 59.305 52.381 0.00 0.00 0.00 4.30
206 207 3.831715 GGAAACCACACAGATGTTAGC 57.168 47.619 0.00 0.00 36.72 3.09
365 369 4.326278 CGAGCGTCAACATGTTTAGTATGT 59.674 41.667 8.77 0.00 40.30 2.29
369 373 1.459592 GCGAGCGTCAACATGTTTAGT 59.540 47.619 8.77 0.00 0.00 2.24
408 413 7.119262 CGGTCATAAAACTAAGTCAATCCAACT 59.881 37.037 0.00 0.00 0.00 3.16
409 414 7.118680 TCGGTCATAAAACTAAGTCAATCCAAC 59.881 37.037 0.00 0.00 0.00 3.77
418 423 9.367444 CAACTAATCTCGGTCATAAAACTAAGT 57.633 33.333 0.00 0.00 0.00 2.24
420 425 8.533657 TCCAACTAATCTCGGTCATAAAACTAA 58.466 33.333 0.00 0.00 0.00 2.24
431 436 8.980481 AATGAATAAATCCAACTAATCTCGGT 57.020 30.769 0.00 0.00 0.00 4.69
519 566 1.136110 CACCACAAAGAACCCAACCAC 59.864 52.381 0.00 0.00 0.00 4.16
553 600 2.092211 CAGCGTCAAGTATCGAAACACC 59.908 50.000 0.00 0.00 0.00 4.16
555 602 2.288579 ACCAGCGTCAAGTATCGAAACA 60.289 45.455 0.00 0.00 0.00 2.83
600 647 6.228273 TGAACATCGCTGAAAAGACTAAAG 57.772 37.500 0.00 0.00 0.00 1.85
613 660 1.202533 CCCTACCGAATGAACATCGCT 60.203 52.381 0.00 0.00 38.93 4.93
694 741 4.098654 ACACTTTCGAGAGATTGATCCGAT 59.901 41.667 10.37 0.00 41.60 4.18
696 743 3.775202 ACACTTTCGAGAGATTGATCCG 58.225 45.455 10.37 0.00 41.60 4.18
699 746 6.531503 TCCTTACACTTTCGAGAGATTGAT 57.468 37.500 10.37 0.00 41.60 2.57
703 750 5.536916 CCCTATCCTTACACTTTCGAGAGAT 59.463 44.000 10.37 0.00 41.60 2.75
711 758 3.618997 CGCACACCCTATCCTTACACTTT 60.619 47.826 0.00 0.00 0.00 2.66
722 773 1.740296 GAACGCACGCACACCCTAT 60.740 57.895 0.00 0.00 0.00 2.57
739 790 0.034574 GCATACACCCACCCATGTGA 60.035 55.000 0.00 0.00 45.76 3.58
741 792 1.077787 CGCATACACCCACCCATGT 60.078 57.895 0.00 0.00 0.00 3.21
742 793 2.480610 GCGCATACACCCACCCATG 61.481 63.158 0.30 0.00 0.00 3.66
743 794 2.124320 GCGCATACACCCACCCAT 60.124 61.111 0.30 0.00 0.00 4.00
747 3738 1.593196 ACATATGCGCATACACCCAC 58.407 50.000 31.17 0.00 0.00 4.61
750 3741 5.146460 CACAAATACATATGCGCATACACC 58.854 41.667 31.17 0.00 0.00 4.16
758 3749 2.653890 GCAGGCACAAATACATATGCG 58.346 47.619 1.58 0.00 39.02 4.73
769 3760 0.602638 CTACAAGGACGCAGGCACAA 60.603 55.000 0.00 0.00 0.00 3.33
770 3761 1.005037 CTACAAGGACGCAGGCACA 60.005 57.895 0.00 0.00 0.00 4.57
774 3765 0.033504 ACACACTACAAGGACGCAGG 59.966 55.000 0.00 0.00 0.00 4.85
1055 4049 2.125912 ATGACAGGCGACGAGTGC 60.126 61.111 0.00 0.00 0.00 4.40
1101 4095 3.706389 TGAGATGTAGATGGGGAAGGA 57.294 47.619 0.00 0.00 0.00 3.36
1142 4136 2.270527 GAGGAGCCAAGGACTGCC 59.729 66.667 0.00 0.00 0.00 4.85
1172 4166 0.317799 CCTGCTGGATCTGGATCTCG 59.682 60.000 2.92 3.77 37.92 4.04
1224 4218 4.864334 GGAGGGCATGCCTGTCGG 62.864 72.222 34.70 0.00 36.10 4.79
1337 4331 7.682628 TGACTTCATGCCTATCATTATCATCA 58.317 34.615 0.00 0.00 31.79 3.07
1355 4349 7.445402 TCATCGTCATCTACATCTATGACTTCA 59.555 37.037 12.19 0.00 46.36 3.02
1364 4358 3.005261 GGCTGTCATCGTCATCTACATCT 59.995 47.826 0.00 0.00 0.00 2.90
1373 4367 1.478631 AGATCAGGCTGTCATCGTCA 58.521 50.000 15.27 0.00 0.00 4.35
1406 4400 3.710722 CTCCACTTCCCGCTGCCT 61.711 66.667 0.00 0.00 0.00 4.75
1446 4440 2.868999 GAACCTTCGCCGACCTCGAG 62.869 65.000 5.13 5.13 43.02 4.04
1448 4442 2.506438 GAACCTTCGCCGACCTCG 60.506 66.667 0.00 0.00 39.44 4.63
1747 4741 3.306472 TGAAGGGGCAGTAAAACTTGT 57.694 42.857 0.00 0.00 0.00 3.16
1754 4748 1.351017 CAGTCCTTGAAGGGGCAGTAA 59.649 52.381 11.99 0.00 35.59 2.24
1844 4838 2.985282 CGGTTGCAGTGTGGGCAT 60.985 61.111 0.00 0.00 41.58 4.40
1980 4974 0.689623 CACCTCTGCCACTTCCTCTT 59.310 55.000 0.00 0.00 0.00 2.85
2051 5045 9.038803 GTTAGTTGGTAGTTTATATACCTGCAC 57.961 37.037 3.98 0.00 42.73 4.57
2060 5054 7.398047 TCAGGCAGAGTTAGTTGGTAGTTTATA 59.602 37.037 0.00 0.00 0.00 0.98
2061 5055 6.212791 TCAGGCAGAGTTAGTTGGTAGTTTAT 59.787 38.462 0.00 0.00 0.00 1.40
2062 5056 5.541101 TCAGGCAGAGTTAGTTGGTAGTTTA 59.459 40.000 0.00 0.00 0.00 2.01
2063 5057 4.347000 TCAGGCAGAGTTAGTTGGTAGTTT 59.653 41.667 0.00 0.00 0.00 2.66
2122 5116 0.738412 CCTAGTTTGTACCCCGTGCG 60.738 60.000 0.00 0.00 0.00 5.34
2256 5250 5.061179 TCATTCACCATGCAGATCAGTATG 58.939 41.667 8.88 8.88 32.13 2.39
2257 5251 5.300411 TCATTCACCATGCAGATCAGTAT 57.700 39.130 0.00 0.00 32.13 2.12
2258 5252 4.758773 TCATTCACCATGCAGATCAGTA 57.241 40.909 0.00 0.00 32.13 2.74
2260 5254 4.214332 CAGATCATTCACCATGCAGATCAG 59.786 45.833 9.99 0.00 35.52 2.90
2342 5343 1.945394 GGGCATTGCTCACTACATCAG 59.055 52.381 8.82 0.00 0.00 2.90
2346 5347 0.035152 CAGGGGCATTGCTCACTACA 60.035 55.000 11.32 0.00 0.00 2.74
2347 5348 1.379642 GCAGGGGCATTGCTCACTAC 61.380 60.000 11.32 0.00 40.72 2.73
2402 5404 5.826586 AGTCTCAATCATGACACGATAGAC 58.173 41.667 0.00 6.39 41.38 2.59
2412 5414 3.432749 GCCCAAGCTAGTCTCAATCATGA 60.433 47.826 0.00 0.00 35.50 3.07
2495 5497 3.162666 TCCCACGATATAGGACCACATC 58.837 50.000 0.00 0.00 0.00 3.06
2521 5523 7.709613 GGAATTTCATTGATCCAAATCCAAGAG 59.290 37.037 0.00 0.00 32.08 2.85
2522 5524 7.180587 TGGAATTTCATTGATCCAAATCCAAGA 59.819 33.333 5.22 0.00 38.95 3.02
2527 5529 5.232838 GCGTGGAATTTCATTGATCCAAATC 59.767 40.000 8.68 0.00 43.21 2.17
2534 5536 3.511146 AGGTTGCGTGGAATTTCATTGAT 59.489 39.130 0.00 0.00 0.00 2.57
2558 5560 3.325293 TGAGAGAAAGACATCTGCCAC 57.675 47.619 0.00 0.00 0.00 5.01
2607 5610 4.276678 CACAACATACTGCATATTGGGAGG 59.723 45.833 0.00 0.00 0.00 4.30
2611 5614 4.639755 TCCACACAACATACTGCATATTGG 59.360 41.667 0.00 0.00 0.00 3.16
2625 5628 5.459762 CACATGATTTTGAACTCCACACAAC 59.540 40.000 0.00 0.00 0.00 3.32
2693 5696 0.747852 TATGATACGCGGTTGAGCCA 59.252 50.000 12.47 0.00 36.97 4.75
2702 5705 3.059188 GTCCATTGGGTTTATGATACGCG 60.059 47.826 3.53 3.53 34.93 6.01
2708 5711 4.627741 GCACCTAGTCCATTGGGTTTATGA 60.628 45.833 2.09 0.00 34.93 2.15
2769 5772 6.073327 ACACTTGCTTAAAAGGAAACTAGC 57.927 37.500 0.00 0.00 42.68 3.42
2796 5799 2.496070 ACTGCTCAAACCTACTGCGATA 59.504 45.455 0.00 0.00 0.00 2.92
2814 5817 6.429385 AGCTCTCCTTTCAAAGAATACAACTG 59.571 38.462 0.00 0.00 0.00 3.16
2829 5832 3.701040 TGCACTTTTGAAAGCTCTCCTTT 59.299 39.130 3.48 0.00 46.19 3.11
2887 6072 0.808755 CACCAAATAGGCCCGAACAC 59.191 55.000 0.00 0.00 43.14 3.32
2923 6108 2.753966 GCACCGTGTAGCATGCCAG 61.754 63.158 15.66 1.14 31.71 4.85
2975 6160 1.522806 GATACCGCGCCATGTTGGA 60.523 57.895 0.00 0.00 40.96 3.53
2986 6171 6.480981 TGCCTATTTACTTAACAAGATACCGC 59.519 38.462 0.00 0.00 0.00 5.68
3078 8193 5.618056 ATGTGCTAGTTTGACTGAATGTG 57.382 39.130 0.00 0.00 0.00 3.21
3080 8195 6.974932 AGTATGTGCTAGTTTGACTGAATG 57.025 37.500 0.00 0.00 0.00 2.67
3133 8541 3.348647 TCTGTTTTAGCCATGCTAGCA 57.651 42.857 21.85 21.85 42.34 3.49
3169 8978 6.803366 ACTGGAGGGTATAACTCGTTTATT 57.197 37.500 0.00 0.00 35.82 1.40
3287 10206 0.464373 ATCATCACCATGTCCACCGC 60.464 55.000 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.