Multiple sequence alignment - TraesCS1D01G239500

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 TraesCS1D01G239500 chr1D 100.000 5466 0 0 1 5466 329492873 329487408 0.000000e+00 10094.0
1 TraesCS1D01G239500 chr1D 90.702 1581 93 19 3148 4715 475888399 475889938 0.000000e+00 2056.0
2 TraesCS1D01G239500 chr1D 84.026 457 36 21 712 1162 475886611 475887036 6.590000e-109 405.0
3 TraesCS1D01G239500 chr1B 92.952 2043 78 27 2708 4715 444059559 444057548 0.000000e+00 2915.0
4 TraesCS1D01G239500 chr1B 94.772 1779 59 14 2953 4715 442958287 442960047 0.000000e+00 2739.0
5 TraesCS1D01G239500 chr1B 92.365 1611 65 22 3148 4715 442963695 442965290 0.000000e+00 2241.0
6 TraesCS1D01G239500 chr1B 90.897 1560 87 16 3158 4715 661994820 661996326 0.000000e+00 2043.0
7 TraesCS1D01G239500 chr1B 84.955 1768 143 62 1 1719 442952549 442954242 0.000000e+00 1677.0
8 TraesCS1D01G239500 chr1B 85.488 1578 152 43 4 1570 444062441 444060930 0.000000e+00 1574.0
9 TraesCS1D01G239500 chr1B 86.828 949 76 13 1732 2673 442956952 442957858 0.000000e+00 1014.0
10 TraesCS1D01G239500 chr1B 86.726 904 74 24 1685 2573 444060831 444059959 0.000000e+00 963.0
11 TraesCS1D01G239500 chr1B 88.764 267 23 5 956 1219 661990228 661990490 2.460000e-83 320.0
12 TraesCS1D01G239500 chr1B 93.909 197 7 2 2953 3149 442963402 442963593 5.360000e-75 292.0
13 TraesCS1D01G239500 chr1B 83.264 239 9 9 2710 2936 442957845 442958064 2.010000e-44 191.0
14 TraesCS1D01G239500 chr1A 93.779 1752 59 17 2995 4715 426535154 426533422 0.000000e+00 2586.0
15 TraesCS1D01G239500 chr1A 88.319 1190 107 19 4 1183 426537978 426536811 0.000000e+00 1399.0
16 TraesCS1D01G239500 chr1A 81.878 607 71 14 1670 2268 426536320 426535745 4.950000e-130 475.0
17 TraesCS1D01G239500 chr3A 91.640 622 24 3 4872 5466 726392604 726393224 0.000000e+00 835.0
18 TraesCS1D01G239500 chr3A 89.691 97 9 1 4714 4809 726392515 726392611 7.440000e-24 122.0
19 TraesCS1D01G239500 chr3A 84.375 64 5 3 2286 2348 394479066 394479007 2.130000e-04 58.4
20 TraesCS1D01G239500 chr7B 87.605 597 47 16 4895 5466 625896319 625895725 0.000000e+00 667.0
21 TraesCS1D01G239500 chr7B 83.200 500 50 17 4995 5466 596616639 596616146 1.410000e-115 427.0
22 TraesCS1D01G239500 chr7B 89.545 220 14 6 5250 5463 377002157 377001941 2.510000e-68 270.0
23 TraesCS1D01G239500 chr7B 90.323 93 9 0 4717 4809 625896425 625896333 7.440000e-24 122.0
24 TraesCS1D01G239500 chr7B 78.238 193 31 7 4816 4998 596617174 596616983 4.470000e-21 113.0
25 TraesCS1D01G239500 chr6B 87.564 587 37 15 4906 5462 52560504 52561084 0.000000e+00 647.0
26 TraesCS1D01G239500 chr6B 80.556 684 91 27 4816 5461 713913918 713914597 6.360000e-134 488.0
27 TraesCS1D01G239500 chr5B 86.583 477 37 16 5011 5463 524362976 524363449 8.170000e-138 501.0
28 TraesCS1D01G239500 chr3B 81.959 582 72 14 4895 5445 68200865 68200286 3.860000e-126 462.0
29 TraesCS1D01G239500 chr3B 96.875 32 1 0 2317 2348 392762087 392762118 3.000000e-03 54.7
30 TraesCS1D01G239500 chr7D 80.915 634 70 23 4872 5463 5523317 5523941 2.320000e-123 453.0
31 TraesCS1D01G239500 chr7D 78.955 689 100 23 4817 5466 75170098 75169416 1.410000e-115 427.0
32 TraesCS1D01G239500 chr4B 80.973 452 71 11 4816 5254 613702397 613702846 1.460000e-90 344.0
33 TraesCS1D01G239500 chr4B 96.774 31 1 0 4838 4868 647293079 647293109 1.000000e-02 52.8
34 TraesCS1D01G239500 chr2B 81.395 387 62 8 4872 5254 172174483 172174103 1.910000e-79 307.0
35 TraesCS1D01G239500 chr2B 89.773 88 8 1 4721 4807 59633985 59633898 1.610000e-20 111.0
36 TraesCS1D01G239500 chr4A 94.186 86 5 0 4719 4804 729920318 729920233 1.240000e-26 132.0
37 TraesCS1D01G239500 chr4A 82.857 105 8 8 445 542 36071206 36071307 9.760000e-13 86.1
38 TraesCS1D01G239500 chr4A 83.562 73 12 0 4129 4201 641292198 641292126 9.820000e-08 69.4
39 TraesCS1D01G239500 chr5D 92.000 50 4 0 4157 4206 40979569 40979618 2.730000e-08 71.3
40 TraesCS1D01G239500 chr5D 86.441 59 4 1 4816 4870 4264682 4264740 1.640000e-05 62.1
41 TraesCS1D01G239500 chr5D 89.796 49 1 1 2300 2348 74366379 74366423 5.910000e-05 60.2
42 TraesCS1D01G239500 chrUn 83.562 73 12 0 4129 4201 474648602 474648530 9.820000e-08 69.4
43 TraesCS1D01G239500 chrUn 100.000 30 0 0 4816 4845 339362811 339362782 7.650000e-04 56.5
44 TraesCS1D01G239500 chr2D 86.667 60 4 2 4816 4871 618123432 618123373 4.570000e-06 63.9
45 TraesCS1D01G239500 chr2A 100.000 30 0 0 4816 4845 761016011 761016040 7.650000e-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 TraesCS1D01G239500 chr1D 329487408 329492873 5465 True 10094.000000 10094 100.000000 1 5466 1 chr1D.!!$R1 5465
1 TraesCS1D01G239500 chr1D 475886611 475889938 3327 False 1230.500000 2056 87.364000 712 4715 2 chr1D.!!$F1 4003
2 TraesCS1D01G239500 chr1B 661994820 661996326 1506 False 2043.000000 2043 90.897000 3158 4715 1 chr1B.!!$F2 1557
3 TraesCS1D01G239500 chr1B 444057548 444062441 4893 True 1817.333333 2915 88.388667 4 4715 3 chr1B.!!$R1 4711
4 TraesCS1D01G239500 chr1B 442952549 442965290 12741 False 1359.000000 2739 89.348833 1 4715 6 chr1B.!!$F3 4714
5 TraesCS1D01G239500 chr1A 426533422 426537978 4556 True 1486.666667 2586 87.992000 4 4715 3 chr1A.!!$R1 4711
6 TraesCS1D01G239500 chr3A 726392515 726393224 709 False 478.500000 835 90.665500 4714 5466 2 chr3A.!!$F1 752
7 TraesCS1D01G239500 chr7B 625895725 625896425 700 True 394.500000 667 88.964000 4717 5466 2 chr7B.!!$R3 749
8 TraesCS1D01G239500 chr7B 596616146 596617174 1028 True 270.000000 427 80.719000 4816 5466 2 chr7B.!!$R2 650
9 TraesCS1D01G239500 chr6B 52560504 52561084 580 False 647.000000 647 87.564000 4906 5462 1 chr6B.!!$F1 556
10 TraesCS1D01G239500 chr6B 713913918 713914597 679 False 488.000000 488 80.556000 4816 5461 1 chr6B.!!$F2 645
11 TraesCS1D01G239500 chr3B 68200286 68200865 579 True 462.000000 462 81.959000 4895 5445 1 chr3B.!!$R1 550
12 TraesCS1D01G239500 chr7D 5523317 5523941 624 False 453.000000 453 80.915000 4872 5463 1 chr7D.!!$F1 591
13 TraesCS1D01G239500 chr7D 75169416 75170098 682 True 427.000000 427 78.955000 4817 5466 1 chr7D.!!$R1 649

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
864 899 0.036577 AGTGCCTGCTGCTTCAGTAG 60.037 55.000 0.00 5.17 42.41 2.57 F
867 902 1.072173 TGCCTGCTGCTTCAGTAGAAA 59.928 47.619 12.43 0.00 44.84 2.52 F
915 954 1.163420 ACACACAAAGGCGCATCGAA 61.163 50.000 10.83 0.00 0.00 3.71 F
1877 4711 1.879380 CGTGGTGAGCAATCTCCAAAA 59.121 47.619 0.91 0.00 38.58 2.44 F
2347 5199 0.034756 TGGTGCGTGCAGTTCTACAT 59.965 50.000 0.00 0.00 0.00 2.29 F
2832 6032 0.179020 TGGCCTGGACTGTGTGAAAG 60.179 55.000 3.32 0.00 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1813 4647 0.170339 CGTGGATGTCGTCACTGCTA 59.830 55.000 0.00 0.0 0.00 3.49 R
1816 4650 0.241213 ACTCGTGGATGTCGTCACTG 59.759 55.000 0.00 0.0 0.00 3.66 R
2021 4865 0.249155 GGGTTGAGAACGTCACGTCA 60.249 55.000 1.67 0.0 39.99 4.35 R
2827 6027 3.243359 ACAGGCCAGGATTTTCTTTCA 57.757 42.857 5.01 0.0 0.00 2.69 R
4266 8139 1.073722 TGAGTCCCCGTACGTCAGT 59.926 57.895 15.21 0.0 0.00 3.41 R
4509 8399 0.610174 AGGTGCAGATTTCGCAGAGA 59.390 50.000 0.00 0.0 40.78 3.10 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
21 22 4.004196 GTGCAACTTTGTAGGGAGTAGT 57.996 45.455 0.00 0.00 0.00 2.73
22 23 5.143376 GTGCAACTTTGTAGGGAGTAGTA 57.857 43.478 0.00 0.00 0.00 1.82
23 24 4.928020 GTGCAACTTTGTAGGGAGTAGTAC 59.072 45.833 0.00 0.00 0.00 2.73
91 97 2.785357 ACAATTTTCCAAGTCCCCCA 57.215 45.000 0.00 0.00 0.00 4.96
97 103 3.558608 TTTCCAAGTCCCCCATTTCAT 57.441 42.857 0.00 0.00 0.00 2.57
252 261 6.753107 ATAAAATGTACTGTTGGCCACTAC 57.247 37.500 3.88 1.66 0.00 2.73
271 280 6.255215 CACTACGTAATGGGTAGCAAAATTG 58.745 40.000 0.00 0.00 40.78 2.32
313 324 6.958255 TCTTGATATCGGTATGCACAATTTG 58.042 36.000 0.00 0.00 0.00 2.32
318 329 7.700234 TGATATCGGTATGCACAATTTGTTTTC 59.300 33.333 0.00 0.00 0.00 2.29
336 351 9.726438 TTTGTTTTCCAAGTTTCCAAATCTAAA 57.274 25.926 0.00 0.00 33.75 1.85
337 352 8.940768 TGTTTTCCAAGTTTCCAAATCTAAAG 57.059 30.769 0.00 0.00 0.00 1.85
338 353 8.754080 TGTTTTCCAAGTTTCCAAATCTAAAGA 58.246 29.630 0.00 0.00 0.00 2.52
339 354 9.594478 GTTTTCCAAGTTTCCAAATCTAAAGAA 57.406 29.630 0.00 0.00 0.00 2.52
396 411 0.689055 ACCCGGGTTCAAGTCCTAAC 59.311 55.000 24.16 0.00 0.00 2.34
401 416 2.812011 CGGGTTCAAGTCCTAACCTTTG 59.188 50.000 0.00 0.00 43.87 2.77
413 428 1.494960 AACCTTTGGCACATGTGGTT 58.505 45.000 26.55 17.56 39.40 3.67
448 464 9.820229 CTGAATTTATTTCAAACGTTAGCTACA 57.180 29.630 0.00 0.00 43.64 2.74
459 475 3.262420 CGTTAGCTACAAGGCATCTGTT 58.738 45.455 0.00 0.00 34.17 3.16
499 515 5.404466 AAGATATGCCAGCTCATCTCTAC 57.596 43.478 4.39 0.00 32.01 2.59
519 535 2.292918 ACAAGGTGCTCATAGGGGTAGA 60.293 50.000 0.00 0.00 0.00 2.59
529 545 2.547640 TAGGGGTAGAGCGTGCGTCT 62.548 60.000 0.00 0.00 0.00 4.18
544 560 2.007049 GCGTCTGTGTGTTCATAGGGG 61.007 57.143 0.00 0.00 34.31 4.79
546 562 2.494471 CGTCTGTGTGTTCATAGGGGTA 59.506 50.000 0.00 0.00 34.31 3.69
554 570 4.839550 TGTGTTCATAGGGGTAAGTGTGTA 59.160 41.667 0.00 0.00 0.00 2.90
555 571 5.486063 TGTGTTCATAGGGGTAAGTGTGTAT 59.514 40.000 0.00 0.00 0.00 2.29
557 573 4.682778 TCATAGGGGTAAGTGTGTATGC 57.317 45.455 0.00 0.00 0.00 3.14
558 574 3.069016 TCATAGGGGTAAGTGTGTATGCG 59.931 47.826 0.00 0.00 0.00 4.73
559 575 1.272807 AGGGGTAAGTGTGTATGCGT 58.727 50.000 0.00 0.00 0.00 5.24
560 576 1.066430 AGGGGTAAGTGTGTATGCGTG 60.066 52.381 0.00 0.00 0.00 5.34
561 577 1.338389 GGGGTAAGTGTGTATGCGTGT 60.338 52.381 0.00 0.00 0.00 4.49
562 578 2.094078 GGGGTAAGTGTGTATGCGTGTA 60.094 50.000 0.00 0.00 0.00 2.90
563 579 3.431207 GGGGTAAGTGTGTATGCGTGTAT 60.431 47.826 0.00 0.00 0.00 2.29
564 580 3.554324 GGGTAAGTGTGTATGCGTGTATG 59.446 47.826 0.00 0.00 0.00 2.39
565 581 4.178540 GGTAAGTGTGTATGCGTGTATGT 58.821 43.478 0.00 0.00 0.00 2.29
566 582 4.032445 GGTAAGTGTGTATGCGTGTATGTG 59.968 45.833 0.00 0.00 0.00 3.21
567 583 3.586100 AGTGTGTATGCGTGTATGTGA 57.414 42.857 0.00 0.00 0.00 3.58
568 584 4.123497 AGTGTGTATGCGTGTATGTGAT 57.877 40.909 0.00 0.00 0.00 3.06
569 585 5.257082 AGTGTGTATGCGTGTATGTGATA 57.743 39.130 0.00 0.00 0.00 2.15
570 586 5.656480 AGTGTGTATGCGTGTATGTGATAA 58.344 37.500 0.00 0.00 0.00 1.75
571 587 5.748630 AGTGTGTATGCGTGTATGTGATAAG 59.251 40.000 0.00 0.00 0.00 1.73
572 588 5.518847 GTGTGTATGCGTGTATGTGATAAGT 59.481 40.000 0.00 0.00 0.00 2.24
581 597 4.690748 GTGTATGTGATAAGTGTGTGTGCT 59.309 41.667 0.00 0.00 0.00 4.40
602 618 3.097877 TGTATGTGATCATCTGCGTCC 57.902 47.619 0.00 0.00 35.70 4.79
724 755 1.773856 TTGAGCATTCCCCACGTCCA 61.774 55.000 0.00 0.00 0.00 4.02
742 775 1.006519 CCATCCAAATGTACACCCCCA 59.993 52.381 0.00 0.00 0.00 4.96
750 783 0.178858 TGTACACCCCCATTCTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
751 784 0.255033 GTACACCCCCATTCTCCCAC 59.745 60.000 0.00 0.00 0.00 4.61
850 885 1.880027 CGCCTATAAATTGGGAGTGCC 59.120 52.381 0.00 0.00 0.00 5.01
856 891 1.538687 AAATTGGGAGTGCCTGCTGC 61.539 55.000 1.06 0.00 41.77 5.25
864 899 0.036577 AGTGCCTGCTGCTTCAGTAG 60.037 55.000 0.00 5.17 42.41 2.57
867 902 1.072173 TGCCTGCTGCTTCAGTAGAAA 59.928 47.619 12.43 0.00 44.84 2.52
875 910 2.224378 TGCTTCAGTAGAAAGCACAGCT 60.224 45.455 6.45 0.00 42.56 4.24
913 952 1.440850 CACACACAAAGGCGCATCG 60.441 57.895 10.83 0.00 0.00 3.84
915 954 1.163420 ACACACAAAGGCGCATCGAA 61.163 50.000 10.83 0.00 0.00 3.71
1089 1129 2.511600 GCGGTGCAGATAGCCGTT 60.512 61.111 13.47 0.00 46.41 4.44
1309 1353 5.045432 ACAACATCTATTTTAAGACGGGGGA 60.045 40.000 0.00 0.00 0.00 4.81
1314 1358 7.072076 ACATCTATTTTAAGACGGGGGAAGTAT 59.928 37.037 0.00 0.00 0.00 2.12
1347 1391 2.297880 TCGGTTGCAGCGGTATATATGT 59.702 45.455 7.94 0.00 39.89 2.29
1390 1434 2.534349 CGCCAACTAGCAATAGTGTACG 59.466 50.000 0.00 0.00 0.00 3.67
1651 1783 7.544804 AGGTTCCAGCTAAAATTCTGATTTT 57.455 32.000 0.00 3.05 45.09 1.82
1721 1853 7.476667 TGGTACAGTAATTATTTTGAATGGCG 58.523 34.615 0.00 0.00 0.00 5.69
1723 1855 7.855904 GGTACAGTAATTATTTTGAATGGCGAG 59.144 37.037 0.00 0.00 0.00 5.03
1729 4559 3.806625 ATTTTGAATGGCGAGGATTGG 57.193 42.857 0.00 0.00 0.00 3.16
1730 4560 2.214376 TTTGAATGGCGAGGATTGGT 57.786 45.000 0.00 0.00 0.00 3.67
1758 4588 5.073311 TGGATCAAGCACTAACTCAGTAC 57.927 43.478 0.00 0.00 34.98 2.73
1759 4589 4.081642 TGGATCAAGCACTAACTCAGTACC 60.082 45.833 0.00 0.00 34.98 3.34
1769 4599 8.591072 AGCACTAACTCAGTACCTTTTTATACA 58.409 33.333 0.00 0.00 34.98 2.29
1877 4711 1.879380 CGTGGTGAGCAATCTCCAAAA 59.121 47.619 0.91 0.00 38.58 2.44
1883 4717 4.687483 GGTGAGCAATCTCCAAAACATTTG 59.313 41.667 0.00 0.00 38.58 2.32
2021 4865 2.185004 CAAGAATTGTGGACTCCCGT 57.815 50.000 0.00 0.00 42.34 5.28
2048 4892 1.860078 GTTCTCAACCCGTTCTGCG 59.140 57.895 0.00 0.00 40.95 5.18
2119 4963 9.945904 AAAGAGAACCACTAAGAATTTACTAGG 57.054 33.333 0.00 0.00 0.00 3.02
2171 5015 4.141914 GGTCATATATCGTGGAAGGATCCC 60.142 50.000 8.55 0.00 45.95 3.85
2173 5017 0.608640 ATATCGTGGAAGGATCCCGC 59.391 55.000 8.55 0.00 45.95 6.13
2257 5109 5.694910 CACTCGACCTTTTCTTGTAGCTTTA 59.305 40.000 0.00 0.00 0.00 1.85
2287 5139 4.401202 TGAGTGCTGGAGTATAATGTTCGA 59.599 41.667 0.00 0.00 0.00 3.71
2288 5140 5.069119 TGAGTGCTGGAGTATAATGTTCGAT 59.931 40.000 0.00 0.00 0.00 3.59
2316 5168 3.056607 CCCATAGTTTGAGCTTTTGGGTG 60.057 47.826 3.39 0.00 36.63 4.61
2317 5169 3.826157 CCATAGTTTGAGCTTTTGGGTGA 59.174 43.478 0.00 0.00 0.00 4.02
2318 5170 4.082571 CCATAGTTTGAGCTTTTGGGTGAG 60.083 45.833 0.00 0.00 0.00 3.51
2319 5171 3.297134 AGTTTGAGCTTTTGGGTGAGA 57.703 42.857 0.00 0.00 0.00 3.27
2333 5185 1.230324 GTGAGAGAACTGGTTGGTGC 58.770 55.000 0.00 0.00 0.00 5.01
2347 5199 0.034756 TGGTGCGTGCAGTTCTACAT 59.965 50.000 0.00 0.00 0.00 2.29
2355 5207 2.668457 GTGCAGTTCTACATTGAGGTCG 59.332 50.000 0.00 0.00 0.00 4.79
2549 5420 0.320247 CGGCTGCACAGAGAGAAACT 60.320 55.000 0.50 0.00 0.00 2.66
2607 5791 1.202211 CCGGCCGTTGGTTATTTTAGC 60.202 52.381 26.12 0.00 0.00 3.09
2633 5822 5.799542 TTTTTGCGAGCGAGTTATTTTTC 57.200 34.783 0.00 0.00 0.00 2.29
2832 6032 0.179020 TGGCCTGGACTGTGTGAAAG 60.179 55.000 3.32 0.00 0.00 2.62
2841 6041 4.580167 TGGACTGTGTGAAAGAAAATCCTG 59.420 41.667 0.00 0.00 0.00 3.86
2955 6401 6.463995 AATTCGGTGGTTGTATATTTGCAT 57.536 33.333 0.00 0.00 0.00 3.96
3064 6514 3.633065 AGGCTTGATACTCGGTAGAAGTC 59.367 47.826 0.00 0.00 0.00 3.01
3079 6529 6.309737 CGGTAGAAGTCACAAATACTGGTAAC 59.690 42.308 0.00 0.00 0.00 2.50
3080 6530 6.309737 GGTAGAAGTCACAAATACTGGTAACG 59.690 42.308 0.00 0.00 42.51 3.18
3107 6568 5.298276 ACTCCTAGATGCTTAGAAGTTCGAG 59.702 44.000 0.00 1.31 0.00 4.04
3408 7268 4.827087 ATCGTGCCTCCGCTGCTG 62.827 66.667 0.00 0.00 35.36 4.41
3705 7565 0.945813 CGGTCTACATCCTCTCGTCC 59.054 60.000 0.00 0.00 0.00 4.79
4224 8084 5.258216 AGGAGAAGAAGGTCAGTACTACA 57.742 43.478 0.00 0.00 0.00 2.74
4266 8139 9.389755 TGTAAATGTAATTATCAGTTGCTAGCA 57.610 29.630 14.93 14.93 33.67 3.49
4267 8140 9.651718 GTAAATGTAATTATCAGTTGCTAGCAC 57.348 33.333 19.17 12.82 33.67 4.40
4268 8141 8.511604 AAATGTAATTATCAGTTGCTAGCACT 57.488 30.769 19.17 14.98 33.67 4.40
4269 8142 6.908870 TGTAATTATCAGTTGCTAGCACTG 57.091 37.500 27.52 27.52 0.00 3.66
4448 8321 0.465278 GATGGAGCTCAAAGGAGGCC 60.465 60.000 17.19 0.00 41.67 5.19
4479 8357 3.261897 CCGGCATAACTCAGGGATTATCT 59.738 47.826 0.00 0.00 0.00 1.98
4482 8372 6.323996 CCGGCATAACTCAGGGATTATCTATA 59.676 42.308 0.00 0.00 0.00 1.31
4509 8399 3.704566 TCCATACTTCGGCAGTGATACTT 59.295 43.478 0.00 0.00 35.97 2.24
4510 8400 4.051922 CCATACTTCGGCAGTGATACTTC 58.948 47.826 0.00 0.00 35.97 3.01
4511 8401 4.202161 CCATACTTCGGCAGTGATACTTCT 60.202 45.833 0.00 0.00 35.97 2.85
4527 8417 1.396301 CTTCTCTGCGAAATCTGCACC 59.604 52.381 0.00 0.00 37.44 5.01
4528 8418 0.610174 TCTCTGCGAAATCTGCACCT 59.390 50.000 0.00 0.00 37.44 4.00
4529 8419 1.824852 TCTCTGCGAAATCTGCACCTA 59.175 47.619 0.00 0.00 37.44 3.08
4530 8420 2.432146 TCTCTGCGAAATCTGCACCTAT 59.568 45.455 0.00 0.00 37.44 2.57
4531 8421 2.543012 CTCTGCGAAATCTGCACCTATG 59.457 50.000 0.00 0.00 37.44 2.23
4532 8422 2.093500 TCTGCGAAATCTGCACCTATGT 60.093 45.455 0.00 0.00 37.44 2.29
4547 8437 5.223382 CACCTATGTCTATGTGAATCGTCC 58.777 45.833 0.00 0.00 0.00 4.79
4715 13855 5.788450 TCGCAATGTATCATTTTGGGTTTT 58.212 33.333 0.00 0.00 35.51 2.43
4734 13874 7.068470 TGGGTTTTACTTCTTTTTCGGTACAAT 59.932 33.333 0.00 0.00 0.00 2.71
4752 13893 4.086457 ACAATCCCCTAAACACATCAACC 58.914 43.478 0.00 0.00 0.00 3.77
4787 13928 6.216662 TCTTCATACCCCTTCATAACAAAGGA 59.783 38.462 3.49 0.00 45.15 3.36
4795 13936 5.474876 CCCTTCATAACAAAGGATAGGATGC 59.525 44.000 3.49 0.00 45.15 3.91
4868 14013 7.386299 CGAGATTTCTTCATACCCCTTCATAAG 59.614 40.741 0.00 0.00 0.00 1.73
4883 14028 7.435192 CCCCTTCATAAGAATTTTGAAATACGC 59.565 37.037 0.00 0.00 43.55 4.42
4891 14040 0.797542 TTTGAAATACGCCCCGAACG 59.202 50.000 0.00 0.00 0.00 3.95
4954 14116 1.306482 TGAAGGCTGGAGAGAGGGG 60.306 63.158 0.00 0.00 0.00 4.79
4993 14503 3.342377 TCACAAAATACATGCCTCCGA 57.658 42.857 0.00 0.00 0.00 4.55
5171 14683 6.155827 CGCACAGGAGAAATTGGAAATAAAA 58.844 36.000 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.402997 AGTACTACTCCCTACAAAGTTGC 57.597 43.478 0.00 0.00 0.00 4.17
44 45 8.768501 AACTTTTAGTTTCCTCCATTTTCTCT 57.231 30.769 0.00 0.00 34.11 3.10
221 229 7.147811 GGCCAACAGTACATTTTATAATTGGGA 60.148 37.037 0.00 0.00 0.00 4.37
239 248 2.006888 CCATTACGTAGTGGCCAACAG 58.993 52.381 22.32 1.45 45.73 3.16
240 249 1.339247 CCCATTACGTAGTGGCCAACA 60.339 52.381 27.00 0.00 45.73 3.33
252 261 5.303747 TCACAATTTTGCTACCCATTACG 57.696 39.130 0.00 0.00 0.00 3.18
286 295 7.750229 ATTGTGCATACCGATATCAAGATTT 57.250 32.000 3.12 0.00 0.00 2.17
288 297 7.229306 ACAAATTGTGCATACCGATATCAAGAT 59.771 33.333 0.00 0.00 0.00 2.40
290 299 6.728200 ACAAATTGTGCATACCGATATCAAG 58.272 36.000 0.00 0.00 0.00 3.02
291 300 6.691754 ACAAATTGTGCATACCGATATCAA 57.308 33.333 0.00 0.00 0.00 2.57
293 302 7.167468 GGAAAACAAATTGTGCATACCGATATC 59.833 37.037 0.00 0.00 0.00 1.63
313 324 9.594478 TTCTTTAGATTTGGAAACTTGGAAAAC 57.406 29.630 0.00 0.00 0.00 2.43
318 329 7.968405 CGGTATTCTTTAGATTTGGAAACTTGG 59.032 37.037 0.00 0.00 0.00 3.61
358 373 0.324738 TGGGCAGGTTTCACCACAAA 60.325 50.000 0.00 0.00 41.95 2.83
396 411 0.752054 ACAACCACATGTGCCAAAGG 59.248 50.000 20.81 8.22 30.82 3.11
436 452 3.262420 CAGATGCCTTGTAGCTAACGTT 58.738 45.455 5.88 5.88 0.00 3.99
499 515 2.366916 CTCTACCCCTATGAGCACCTTG 59.633 54.545 0.00 0.00 0.00 3.61
519 535 2.202878 AACACACAGACGCACGCT 60.203 55.556 0.00 0.00 0.00 5.07
529 545 3.649023 ACACTTACCCCTATGAACACACA 59.351 43.478 0.00 0.00 0.00 3.72
544 560 4.860352 TCACATACACGCATACACACTTAC 59.140 41.667 0.00 0.00 0.00 2.34
546 562 3.920446 TCACATACACGCATACACACTT 58.080 40.909 0.00 0.00 0.00 3.16
554 570 4.329801 CACACACTTATCACATACACGCAT 59.670 41.667 0.00 0.00 0.00 4.73
555 571 3.677596 CACACACTTATCACATACACGCA 59.322 43.478 0.00 0.00 0.00 5.24
557 573 4.434198 GCACACACACTTATCACATACACG 60.434 45.833 0.00 0.00 0.00 4.49
558 574 4.690748 AGCACACACACTTATCACATACAC 59.309 41.667 0.00 0.00 0.00 2.90
559 575 4.893608 AGCACACACACTTATCACATACA 58.106 39.130 0.00 0.00 0.00 2.29
560 576 5.179368 ACAAGCACACACACTTATCACATAC 59.821 40.000 0.00 0.00 0.00 2.39
561 577 5.304778 ACAAGCACACACACTTATCACATA 58.695 37.500 0.00 0.00 0.00 2.29
562 578 4.136796 ACAAGCACACACACTTATCACAT 58.863 39.130 0.00 0.00 0.00 3.21
563 579 3.540617 ACAAGCACACACACTTATCACA 58.459 40.909 0.00 0.00 0.00 3.58
564 580 5.179368 ACATACAAGCACACACACTTATCAC 59.821 40.000 0.00 0.00 0.00 3.06
565 581 5.179182 CACATACAAGCACACACACTTATCA 59.821 40.000 0.00 0.00 0.00 2.15
566 582 5.408299 TCACATACAAGCACACACACTTATC 59.592 40.000 0.00 0.00 0.00 1.75
567 583 5.304778 TCACATACAAGCACACACACTTAT 58.695 37.500 0.00 0.00 0.00 1.73
568 584 4.698575 TCACATACAAGCACACACACTTA 58.301 39.130 0.00 0.00 0.00 2.24
569 585 3.540617 TCACATACAAGCACACACACTT 58.459 40.909 0.00 0.00 0.00 3.16
570 586 3.192541 TCACATACAAGCACACACACT 57.807 42.857 0.00 0.00 0.00 3.55
571 587 3.498018 TGATCACATACAAGCACACACAC 59.502 43.478 0.00 0.00 0.00 3.82
572 588 3.737850 TGATCACATACAAGCACACACA 58.262 40.909 0.00 0.00 0.00 3.72
581 597 3.457234 GGACGCAGATGATCACATACAA 58.543 45.455 0.00 0.00 36.82 2.41
724 755 3.272020 AGAATGGGGGTGTACATTTGGAT 59.728 43.478 0.00 0.00 37.43 3.41
742 775 8.733092 TTCTCTATCATTATCAGTGGGAGAAT 57.267 34.615 0.00 0.00 37.93 2.40
750 783 5.843421 AGTGGCCTTCTCTATCATTATCAGT 59.157 40.000 3.32 0.00 0.00 3.41
751 784 6.357579 AGTGGCCTTCTCTATCATTATCAG 57.642 41.667 3.32 0.00 0.00 2.90
850 885 2.159234 GTGCTTTCTACTGAAGCAGCAG 59.841 50.000 11.38 4.50 42.89 4.24
856 891 3.929610 GGTAGCTGTGCTTTCTACTGAAG 59.070 47.826 0.00 0.00 40.44 3.02
864 899 1.790387 CGCTGGTAGCTGTGCTTTC 59.210 57.895 0.00 0.00 39.60 2.62
867 902 3.320879 ATGCGCTGGTAGCTGTGCT 62.321 57.895 29.20 16.85 39.60 4.40
888 923 1.216941 GCCTTTGTGTGTGCATGCAC 61.217 55.000 38.00 38.00 46.33 4.57
913 952 0.668535 GCGGCTGGGATGGTAATTTC 59.331 55.000 0.00 0.00 0.00 2.17
915 954 0.179018 GAGCGGCTGGGATGGTAATT 60.179 55.000 7.50 0.00 0.00 1.40
1287 1331 5.703730 TCCCCCGTCTTAAAATAGATGTT 57.296 39.130 0.00 0.00 30.69 2.71
1291 1335 8.591072 CATATACTTCCCCCGTCTTAAAATAGA 58.409 37.037 0.00 0.00 0.00 1.98
1292 1336 7.822822 CCATATACTTCCCCCGTCTTAAAATAG 59.177 40.741 0.00 0.00 0.00 1.73
1309 1353 4.689612 ACCGACATCAAGCCATATACTT 57.310 40.909 0.00 0.00 0.00 2.24
1314 1358 1.339535 TGCAACCGACATCAAGCCATA 60.340 47.619 0.00 0.00 0.00 2.74
1347 1391 4.329392 GTTAATGACCCTCTTTTCGGGAA 58.671 43.478 1.44 0.00 44.90 3.97
1390 1434 5.302360 TGCCCGAAATGGACTATATTGTAC 58.698 41.667 0.00 0.00 42.00 2.90
1503 1598 9.567776 TCTGGTTTCACACTTTTTCTCATATAA 57.432 29.630 0.00 0.00 0.00 0.98
1598 1716 5.072872 CCTCAATCCCTCCTCTGATAATTGT 59.927 44.000 0.00 0.00 0.00 2.71
1610 1740 1.141185 CCTTACCCCTCAATCCCTCC 58.859 60.000 0.00 0.00 0.00 4.30
1656 1788 9.872684 ATCACAGATCCAAGGTTCATAATAATT 57.127 29.630 0.00 0.00 0.00 1.40
1712 1844 2.214376 AACCAATCCTCGCCATTCAA 57.786 45.000 0.00 0.00 0.00 2.69
1721 1853 5.920193 TTGATCCAATCAAACCAATCCTC 57.080 39.130 0.00 0.00 45.57 3.71
1730 4560 8.175702 ACTGAGTTAGTGCTTGATCCAATCAAA 61.176 37.037 4.13 0.00 42.45 2.69
1758 4588 6.734137 ACACACACACACATGTATAAAAAGG 58.266 36.000 0.00 0.00 36.72 3.11
1808 4642 5.154932 GTGGATGTCGTCACTGCTATATAC 58.845 45.833 0.00 0.00 0.00 1.47
1809 4643 4.083484 CGTGGATGTCGTCACTGCTATATA 60.083 45.833 0.00 0.00 0.00 0.86
1810 4644 3.304726 CGTGGATGTCGTCACTGCTATAT 60.305 47.826 0.00 0.00 0.00 0.86
1811 4645 2.032924 CGTGGATGTCGTCACTGCTATA 59.967 50.000 0.00 0.00 0.00 1.31
1812 4646 1.202302 CGTGGATGTCGTCACTGCTAT 60.202 52.381 0.00 0.00 0.00 2.97
1813 4647 0.170339 CGTGGATGTCGTCACTGCTA 59.830 55.000 0.00 0.00 0.00 3.49
1815 4649 1.073216 CTCGTGGATGTCGTCACTGC 61.073 60.000 0.00 0.00 0.00 4.40
1816 4650 0.241213 ACTCGTGGATGTCGTCACTG 59.759 55.000 0.00 0.00 0.00 3.66
1817 4651 1.738350 CTACTCGTGGATGTCGTCACT 59.262 52.381 0.00 0.00 0.00 3.41
1856 4690 0.396435 TTGGAGATTGCTCACCACGT 59.604 50.000 0.00 0.00 41.21 4.49
1877 4711 5.645497 GCCAACATCTTCTACTCTCAAATGT 59.355 40.000 0.00 0.00 0.00 2.71
1883 4717 3.784701 TCGCCAACATCTTCTACTCTC 57.215 47.619 0.00 0.00 0.00 3.20
1951 4795 2.995258 CACCAATTGTGCAGCATTAACC 59.005 45.455 0.00 0.00 38.34 2.85
1974 4818 2.346803 AGCCAACGTGCAACAGTATAG 58.653 47.619 0.36 0.00 35.74 1.31
1987 4831 4.685169 ATTCTTGATGTGTTAGCCAACG 57.315 40.909 0.00 0.00 37.48 4.10
2021 4865 0.249155 GGGTTGAGAACGTCACGTCA 60.249 55.000 1.67 0.00 39.99 4.35
2048 4892 3.818787 CGCATGTCAAGCAGGGCC 61.819 66.667 0.00 0.00 0.00 5.80
2119 4963 2.556534 TCTAGGTCTAGAAAACGCGC 57.443 50.000 5.73 0.00 39.08 6.86
2148 4992 4.141914 GGGATCCTTCCACGATATATGACC 60.142 50.000 12.58 0.00 44.60 4.02
2171 5015 2.931969 TCTAGCATCTCAAATGTGTGCG 59.068 45.455 0.00 0.00 40.54 5.34
2173 5017 6.101997 TGTAGTCTAGCATCTCAAATGTGTG 58.898 40.000 0.00 0.00 0.00 3.82
2228 5077 5.638596 ACAAGAAAAGGTCGAGTGTTTTT 57.361 34.783 0.00 0.00 0.00 1.94
2248 5100 3.436704 GCACTCAGCATTGTAAAGCTACA 59.563 43.478 0.00 0.00 44.79 2.74
2287 5139 3.663198 AGCTCAAACTATGGGAGAGGAT 58.337 45.455 0.00 0.00 0.00 3.24
2288 5140 3.121929 AGCTCAAACTATGGGAGAGGA 57.878 47.619 0.00 0.00 0.00 3.71
2316 5168 0.249911 ACGCACCAACCAGTTCTCTC 60.250 55.000 0.00 0.00 0.00 3.20
2317 5169 0.532862 CACGCACCAACCAGTTCTCT 60.533 55.000 0.00 0.00 0.00 3.10
2318 5170 1.941812 CACGCACCAACCAGTTCTC 59.058 57.895 0.00 0.00 0.00 2.87
2319 5171 2.186826 GCACGCACCAACCAGTTCT 61.187 57.895 0.00 0.00 0.00 3.01
2333 5185 2.668457 GACCTCAATGTAGAACTGCACG 59.332 50.000 0.00 0.00 0.00 5.34
2347 5199 3.973206 TCTAATTCAAGCCGACCTCAA 57.027 42.857 0.00 0.00 0.00 3.02
2510 5381 4.932799 GCCGGCAAATAAACCTGTTTTTAT 59.067 37.500 24.80 0.00 33.84 1.40
2511 5382 4.039366 AGCCGGCAAATAAACCTGTTTTTA 59.961 37.500 31.54 0.00 34.23 1.52
2530 5401 0.320247 AGTTTCTCTCTGTGCAGCCG 60.320 55.000 0.00 0.00 0.00 5.52
2739 5929 8.840321 CACTATAAAGACGATGGATTGGAATTT 58.160 33.333 0.00 0.00 0.00 1.82
2741 5931 6.428159 GCACTATAAAGACGATGGATTGGAAT 59.572 38.462 0.00 0.00 0.00 3.01
2827 6027 3.243359 ACAGGCCAGGATTTTCTTTCA 57.757 42.857 5.01 0.00 0.00 2.69
2832 6032 6.039829 CCTCTAAAATACAGGCCAGGATTTTC 59.960 42.308 28.77 0.00 34.31 2.29
2841 6041 4.880120 GTGTTACCCTCTAAAATACAGGCC 59.120 45.833 0.00 0.00 0.00 5.19
2917 6147 7.498443 ACCACCGAATTAACCTCTAGATAAAG 58.502 38.462 0.00 0.00 0.00 1.85
2965 6411 9.959721 GGAAAATGCATATCTCTAACCCTTATA 57.040 33.333 0.00 0.00 0.00 0.98
2966 6412 8.448008 TGGAAAATGCATATCTCTAACCCTTAT 58.552 33.333 0.00 0.00 0.00 1.73
3064 6514 6.570692 AGGAGTATCGTTACCAGTATTTGTG 58.429 40.000 0.00 0.00 34.37 3.33
3079 6529 6.811253 ACTTCTAAGCATCTAGGAGTATCG 57.189 41.667 0.76 0.00 36.19 2.92
3080 6530 7.173562 TCGAACTTCTAAGCATCTAGGAGTATC 59.826 40.741 2.77 3.26 36.83 2.24
3239 7099 4.143333 CCGGGAAGATCGTGCGGT 62.143 66.667 0.00 0.00 0.00 5.68
3802 7662 4.527157 GACGGCGCATGAGCAAGC 62.527 66.667 23.18 7.28 42.27 4.01
3879 7739 4.595538 AGCCCGAACACGAACGCA 62.596 61.111 0.00 0.00 0.00 5.24
4170 8030 1.226802 CACGATGAGCTCCACGAGG 60.227 63.158 27.51 18.05 0.00 4.63
4224 8084 3.367992 TTACAACGTCCGTGTGTACAT 57.632 42.857 0.00 0.00 0.00 2.29
4263 8136 2.282674 TCCCCGTACGTCAGTGCT 60.283 61.111 15.21 0.00 0.00 4.40
4264 8137 2.126189 GTCCCCGTACGTCAGTGC 60.126 66.667 15.21 0.00 0.00 4.40
4265 8138 1.239296 TGAGTCCCCGTACGTCAGTG 61.239 60.000 15.21 0.00 0.00 3.66
4266 8139 1.073722 TGAGTCCCCGTACGTCAGT 59.926 57.895 15.21 0.00 0.00 3.41
4267 8140 1.505353 GTGAGTCCCCGTACGTCAG 59.495 63.158 15.21 2.20 0.00 3.51
4268 8141 2.327343 CGTGAGTCCCCGTACGTCA 61.327 63.158 15.21 7.97 0.00 4.35
4269 8142 2.482374 CGTGAGTCCCCGTACGTC 59.518 66.667 15.21 5.18 0.00 4.34
4372 8245 1.433879 GTAGAGCGCCGTCATGAGT 59.566 57.895 2.29 0.00 0.00 3.41
4448 8321 3.130819 TTATGCCGGGCAAGCGTG 61.131 61.111 27.70 0.00 43.62 5.34
4479 8357 6.717997 TCACTGCCGAAGTATGGAGTATTATA 59.282 38.462 0.00 0.00 36.83 0.98
4482 8372 3.704566 TCACTGCCGAAGTATGGAGTATT 59.295 43.478 0.00 0.00 36.83 1.89
4509 8399 0.610174 AGGTGCAGATTTCGCAGAGA 59.390 50.000 0.00 0.00 40.78 3.10
4510 8400 2.299993 TAGGTGCAGATTTCGCAGAG 57.700 50.000 0.00 0.00 40.78 3.35
4511 8401 2.093500 ACATAGGTGCAGATTTCGCAGA 60.093 45.455 0.00 0.00 40.78 4.26
4527 8417 4.023107 ACCGGACGATTCACATAGACATAG 60.023 45.833 9.46 0.00 0.00 2.23
4528 8418 3.887110 ACCGGACGATTCACATAGACATA 59.113 43.478 9.46 0.00 0.00 2.29
4529 8419 2.693591 ACCGGACGATTCACATAGACAT 59.306 45.455 9.46 0.00 0.00 3.06
4530 8420 2.097036 ACCGGACGATTCACATAGACA 58.903 47.619 9.46 0.00 0.00 3.41
4531 8421 2.865343 ACCGGACGATTCACATAGAC 57.135 50.000 9.46 0.00 0.00 2.59
4532 8422 3.056393 ACAAACCGGACGATTCACATAGA 60.056 43.478 9.46 0.00 0.00 1.98
4547 8437 2.911819 ACAGTTGAACACACAAACCG 57.088 45.000 0.00 0.00 0.00 4.44
4715 13855 5.013391 AGGGGATTGTACCGAAAAAGAAGTA 59.987 40.000 0.00 0.00 0.00 2.24
4723 13863 4.202440 TGTGTTTAGGGGATTGTACCGAAA 60.202 41.667 0.00 0.00 0.00 3.46
4734 13874 2.066592 TGGGTTGATGTGTTTAGGGGA 58.933 47.619 0.00 0.00 0.00 4.81
4752 13893 3.134804 AGGGGTATGAAGAAATCTCGTGG 59.865 47.826 0.00 0.00 0.00 4.94
4810 13951 6.494146 TGTTTAGGGGGTTGTATCGAATTTTT 59.506 34.615 0.00 0.00 0.00 1.94
4811 13952 6.011481 TGTTTAGGGGGTTGTATCGAATTTT 58.989 36.000 0.00 0.00 0.00 1.82
4812 13953 5.416639 GTGTTTAGGGGGTTGTATCGAATTT 59.583 40.000 0.00 0.00 0.00 1.82
4813 13954 4.945543 GTGTTTAGGGGGTTGTATCGAATT 59.054 41.667 0.00 0.00 0.00 2.17
4814 13955 4.019141 TGTGTTTAGGGGGTTGTATCGAAT 60.019 41.667 0.00 0.00 0.00 3.34
4819 13960 4.938575 TGATGTGTTTAGGGGGTTGTAT 57.061 40.909 0.00 0.00 0.00 2.29
4868 14013 3.768468 TCGGGGCGTATTTCAAAATTC 57.232 42.857 0.00 0.00 0.00 2.17
4883 14028 3.599412 CCCATATACACGTTCGGGG 57.401 57.895 0.00 0.00 0.00 5.73
4891 14040 2.104281 GTGTCTCCCACCCCATATACAC 59.896 54.545 0.00 0.00 38.18 2.90
4954 14116 4.698304 TGTGAATTTTTACATCTCGGGTCC 59.302 41.667 0.00 0.00 0.00 4.46
4993 14503 8.964476 ATAAATGTCTGTGGTTCGATTCTTAT 57.036 30.769 0.00 0.00 0.00 1.73
5129 14640 0.029700 CGTTTTTCGTGGTGTTCCCC 59.970 55.000 0.00 0.00 34.52 4.81


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

AutoCloner maintained by Alex Coulton.