Multiple sequence alignment - TraesCS5A01G447400

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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 TraesCS5A01G447400 chr5A 100.000 6041 0 0 1 6041 626998166 626992126 0.000000e+00 11156.0
1 TraesCS5A01G447400 chr5A 85.889 574 71 3 23 595 625002015 625002579 2.410000e-168 603.0
2 TraesCS5A01G447400 chr5A 82.237 152 25 2 3982 4132 161916384 161916534 4.910000e-26 130.0
3 TraesCS5A01G447400 chr5D 94.657 4735 184 28 682 5380 500496894 500492193 0.000000e+00 7278.0
4 TraesCS5A01G447400 chr5D 93.164 512 30 4 5534 6041 500492136 500491626 0.000000e+00 747.0
5 TraesCS5A01G447400 chr5D 83.019 159 24 3 3976 4133 176094373 176094217 2.270000e-29 141.0
6 TraesCS5A01G447400 chr5D 83.784 74 7 3 358 427 259443704 259443632 1.410000e-06 65.8
7 TraesCS5A01G447400 chr5B 93.989 3344 150 28 2720 6041 622043672 622040358 0.000000e+00 5014.0
8 TraesCS5A01G447400 chr5B 91.298 1965 138 15 23 1961 622054806 622052849 0.000000e+00 2651.0
9 TraesCS5A01G447400 chr5B 94.995 1079 39 6 1667 2732 622052842 622051766 0.000000e+00 1679.0
10 TraesCS5A01G447400 chr2A 85.714 98 12 2 356 452 41652947 41653043 1.070000e-17 102.0
11 TraesCS5A01G447400 chr2D 84.694 98 15 0 355 452 37044462 37044559 1.390000e-16 99.0
12 TraesCS5A01G447400 chr2D 100.000 30 0 0 1 30 386195790 386195761 8.460000e-04 56.5
13 TraesCS5A01G447400 chr2B 84.375 96 15 0 355 450 63837420 63837325 1.790000e-15 95.3
14 TraesCS5A01G447400 chr2B 97.059 34 0 1 1 34 75752363 75752395 8.460000e-04 56.5
15 TraesCS5A01G447400 chr7B 84.286 70 10 1 358 427 589104771 589104703 3.910000e-07 67.6
16 TraesCS5A01G447400 chr7D 100.000 32 0 0 1 32 109161923 109161954 6.540000e-05 60.2
17 TraesCS5A01G447400 chr7D 94.595 37 2 0 1 37 173731387 173731351 2.350000e-04 58.4
18 TraesCS5A01G447400 chr1A 97.059 34 1 0 1 34 45710253 45710286 2.350000e-04 58.4
19 TraesCS5A01G447400 chr7A 96.970 33 1 0 1 33 265511779 265511747 8.460000e-04 56.5
20 TraesCS5A01G447400 chr7A 100.000 30 0 0 1 30 536132561 536132590 8.460000e-04 56.5
21 TraesCS5A01G447400 chr4D 100.000 30 0 0 1 30 504644550 504644521 8.460000e-04 56.5
22 TraesCS5A01G447400 chr1D 100.000 30 0 0 1 30 294052878 294052849 8.460000e-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 TraesCS5A01G447400 chr5A 626992126 626998166 6040 True 11156.0 11156 100.0000 1 6041 1 chr5A.!!$R1 6040
1 TraesCS5A01G447400 chr5A 625002015 625002579 564 False 603.0 603 85.8890 23 595 1 chr5A.!!$F2 572
2 TraesCS5A01G447400 chr5D 500491626 500496894 5268 True 4012.5 7278 93.9105 682 6041 2 chr5D.!!$R3 5359
3 TraesCS5A01G447400 chr5B 622040358 622043672 3314 True 5014.0 5014 93.9890 2720 6041 1 chr5B.!!$R1 3321
4 TraesCS5A01G447400 chr5B 622051766 622054806 3040 True 2165.0 2651 93.1465 23 2732 2 chr5B.!!$R2 2709

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
649 652 0.096976 CGGCTATGAAAGTGGTTGCG 59.903 55.000 0.00 0.00 0.00 4.85 F
650 653 0.179163 GGCTATGAAAGTGGTTGCGC 60.179 55.000 0.00 0.00 0.00 6.09 F
651 654 0.521291 GCTATGAAAGTGGTTGCGCA 59.479 50.000 5.66 5.66 0.00 6.09 F
914 938 0.787787 TCGTTGATCGCTTTGTTCCG 59.212 50.000 0.00 0.00 39.67 4.30 F
1199 1226 0.896019 CTCATCGGTATCGCCTCCCT 60.896 60.000 0.00 0.00 36.13 4.20 F
1233 1260 1.079750 GCCGTCTCCGCTTCTTTCT 60.080 57.895 0.00 0.00 0.00 2.52 F
1889 2218 1.904287 TTGCATTTCAGTTACCGGCT 58.096 45.000 0.00 0.00 0.00 5.52 F
2962 3303 1.480137 CTCGAGCCTGGAGATTCTTGT 59.520 52.381 0.00 0.00 33.27 3.16 F
3878 4223 1.134818 GCTGACATATGGGTCGTGACA 60.135 52.381 7.80 0.00 40.72 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2544 2880 1.255882 TGGGCGCAATTGTTCTGATT 58.744 45.000 10.83 0.00 0.00 2.57 R
2603 2943 5.106908 GCTCTTTAAAGTACCTGCTCAACAG 60.107 44.000 14.74 1.84 46.77 3.16 R
2656 2996 5.277154 CGTGCCCATTAAAGTTACCTTATCG 60.277 44.000 0.00 0.00 0.00 2.92 R
2830 3171 2.200067 GTTGATGAGATCAGCACTCCG 58.800 52.381 0.00 0.00 42.45 4.63 R
2922 3263 7.042187 GCTCGAGATATGATCACATCAACTTTT 60.042 37.037 18.75 0.00 43.50 2.27 R
2962 3303 9.317936 CAAGCTATCATACATTGTGACTCTTAA 57.682 33.333 0.00 0.00 0.00 1.85 R
3863 4208 0.177836 TGGCTGTCACGACCCATATG 59.822 55.000 0.00 0.00 0.00 1.78 R
4747 5106 0.234625 GCTGTTCGCAACGTGAATCA 59.765 50.000 0.00 0.00 38.92 2.57 R
5092 5453 0.107066 TCATGGAATGTGCCTGCGAT 60.107 50.000 0.00 0.00 46.80 4.58 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 4.437682 CCTCTAGGGCATATTTCCAACA 57.562 45.455 0.00 0.00 0.00 3.33
28 29 4.531732 AGGGCATATTTCCAACACAAACAT 59.468 37.500 0.00 0.00 0.00 2.71
59 60 4.353777 TGTAGTAGGAGAGGACATTGCTT 58.646 43.478 0.00 0.00 0.00 3.91
67 68 4.762251 GGAGAGGACATTGCTTTTAACAGT 59.238 41.667 0.00 0.00 0.00 3.55
84 85 1.593209 GTGAGGCGAACGTGGTGAA 60.593 57.895 0.00 0.00 0.00 3.18
88 89 2.396157 GGCGAACGTGGTGAATCCC 61.396 63.158 0.00 0.00 34.77 3.85
152 153 7.658179 ATGTTAGTGAGTGAGTGTGTTTATG 57.342 36.000 0.00 0.00 0.00 1.90
279 280 1.280421 GTGAAGTTCTCCAGATGGCCT 59.720 52.381 3.32 0.00 34.44 5.19
290 291 0.617413 AGATGGCCTCAACAGACCAG 59.383 55.000 3.32 0.00 35.20 4.00
341 342 3.432378 TCTCTCTTTCTCTAACGCCCTT 58.568 45.455 0.00 0.00 0.00 3.95
349 350 0.963962 TCTAACGCCCTTGACGTCTT 59.036 50.000 17.92 3.09 44.30 3.01
363 364 2.996621 GACGTCTTTGATCTTCCCACAG 59.003 50.000 8.70 0.00 0.00 3.66
371 372 5.378230 TTGATCTTCCCACAGCATATCTT 57.622 39.130 0.00 0.00 0.00 2.40
378 379 6.556495 TCTTCCCACAGCATATCTTAATCTCT 59.444 38.462 0.00 0.00 0.00 3.10
432 434 2.501316 AGAATAAAGTTGCCCCATTGCC 59.499 45.455 0.00 0.00 0.00 4.52
435 437 1.053264 AAAGTTGCCCCATTGCCACA 61.053 50.000 0.00 0.00 29.75 4.17
483 486 8.956426 AGTAGTAATTGGTGATTATTGTTGGTG 58.044 33.333 0.00 0.00 33.03 4.17
591 594 8.730680 GGTTGTCTATGTTGTGAGTAATTTGAT 58.269 33.333 0.00 0.00 0.00 2.57
619 622 5.359756 CCTAATGTCGTGAATTCATCTCCA 58.640 41.667 12.12 6.93 0.00 3.86
622 625 2.567169 TGTCGTGAATTCATCTCCAGGT 59.433 45.455 12.12 0.00 0.00 4.00
623 626 2.932614 GTCGTGAATTCATCTCCAGGTG 59.067 50.000 12.12 0.00 0.00 4.00
629 632 1.971149 TTCATCTCCAGGTGGGTCAT 58.029 50.000 0.00 0.00 38.11 3.06
646 649 3.270877 GTCATCGGCTATGAAAGTGGTT 58.729 45.455 2.96 0.00 46.17 3.67
647 650 3.063997 GTCATCGGCTATGAAAGTGGTTG 59.936 47.826 2.96 0.00 46.17 3.77
649 652 0.096976 CGGCTATGAAAGTGGTTGCG 59.903 55.000 0.00 0.00 0.00 4.85
650 653 0.179163 GGCTATGAAAGTGGTTGCGC 60.179 55.000 0.00 0.00 0.00 6.09
651 654 0.521291 GCTATGAAAGTGGTTGCGCA 59.479 50.000 5.66 5.66 0.00 6.09
665 668 1.212751 GCGCAAGTGTGGGGAATTC 59.787 57.895 0.30 0.00 38.13 2.17
666 669 1.523154 GCGCAAGTGTGGGGAATTCA 61.523 55.000 0.30 0.00 38.13 2.57
672 675 2.795329 AGTGTGGGGAATTCACATGTC 58.205 47.619 10.48 0.00 45.32 3.06
675 678 2.374839 TGTGGGGAATTCACATGTCAGA 59.625 45.455 10.48 0.00 39.83 3.27
690 694 4.281898 TGTCAGATGGGCATGATGATAG 57.718 45.455 0.00 0.00 0.00 2.08
715 719 2.752030 TGAAGGAGACTATGAGGTGGG 58.248 52.381 0.00 0.00 42.68 4.61
775 792 1.068474 CGTTGTCGAGGGTCATGAAC 58.932 55.000 0.73 0.73 39.71 3.18
783 800 4.455877 GTCGAGGGTCATGAACTCAATTTT 59.544 41.667 21.74 0.00 0.00 1.82
800 817 7.611855 ACTCAATTTTCGTTCTATCCAAGGATT 59.388 33.333 6.95 0.00 36.17 3.01
802 819 9.627123 TCAATTTTCGTTCTATCCAAGGATTAT 57.373 29.630 6.95 0.00 36.17 1.28
811 828 5.932303 TCTATCCAAGGATTATAGCGCAAAC 59.068 40.000 11.47 0.00 36.17 2.93
827 844 1.129058 AAACTGTGAGGTTCTCGGGT 58.871 50.000 0.00 0.00 32.35 5.28
878 898 1.377333 GGTCGGAAAAGGCCCTCTG 60.377 63.158 0.00 0.00 0.00 3.35
880 900 0.955919 GTCGGAAAAGGCCCTCTGTG 60.956 60.000 0.00 0.00 0.00 3.66
881 901 2.335712 CGGAAAAGGCCCTCTGTGC 61.336 63.158 0.00 0.00 0.00 4.57
898 922 4.695231 CAACGCCCTCGACGTCGT 62.695 66.667 34.40 14.75 44.30 4.34
914 938 0.787787 TCGTTGATCGCTTTGTTCCG 59.212 50.000 0.00 0.00 39.67 4.30
961 985 1.227380 CCTCGATCCCAAGCTTCGG 60.227 63.158 3.29 3.29 33.82 4.30
1199 1226 0.896019 CTCATCGGTATCGCCTCCCT 60.896 60.000 0.00 0.00 36.13 4.20
1214 1241 4.891727 CCTCGCCCCGTTGATCCG 62.892 72.222 0.00 0.00 0.00 4.18
1233 1260 1.079750 GCCGTCTCCGCTTCTTTCT 60.080 57.895 0.00 0.00 0.00 2.52
1251 1278 6.196571 TCTTTCTTTTCGGTTTCATTTCGTC 58.803 36.000 0.00 0.00 0.00 4.20
1288 1315 2.271800 CTAGAGGCGTCGCATTTCTTT 58.728 47.619 20.50 4.59 0.00 2.52
1408 1436 2.672651 TGCATGGTGGCTGGTTCG 60.673 61.111 0.00 0.00 34.04 3.95
1538 1566 2.669300 ATTTGTGTGTGCACTGCAAA 57.331 40.000 24.49 24.49 45.44 3.68
1701 1730 9.899226 CCTATCTTTTCCTTTTTACTGTTCTTG 57.101 33.333 0.00 0.00 0.00 3.02
1724 1753 5.163457 TGGGAGTTTTGATTGTTTTCAGGTC 60.163 40.000 0.00 0.00 0.00 3.85
1809 2136 7.807977 TCTCTTTTGCAATCTAATATGACCC 57.192 36.000 0.00 0.00 0.00 4.46
1833 2162 5.048504 CACTGAGTGCCACTTACAATCATTT 60.049 40.000 0.00 0.00 40.86 2.32
1867 2196 2.915463 GACTCGTACGTTCATGAGTTGG 59.085 50.000 16.05 0.00 43.30 3.77
1889 2218 1.904287 TTGCATTTCAGTTACCGGCT 58.096 45.000 0.00 0.00 0.00 5.52
1921 2250 7.362234 AGAGGCCATAAACATTACCCTAAAAT 58.638 34.615 5.01 0.00 0.00 1.82
1963 2292 6.780706 AAACAGTTCTACATTCCAGTAACG 57.219 37.500 0.00 0.00 0.00 3.18
2105 2434 5.827797 GGATCTAATGGTAGGCATGTTCAAA 59.172 40.000 0.00 0.00 0.00 2.69
2116 2445 6.715347 AGGCATGTTCAAATATTACCTTCC 57.285 37.500 0.00 0.00 0.00 3.46
2121 2450 9.516314 GCATGTTCAAATATTACCTTCCTTTAC 57.484 33.333 0.00 0.00 0.00 2.01
2267 2596 3.311322 TGACACGTGATGAAACTGAAACC 59.689 43.478 25.01 0.00 0.00 3.27
2396 2725 6.426646 AACTCCCTCTGTTCCATATATGTC 57.573 41.667 11.73 3.05 0.00 3.06
2397 2726 4.841246 ACTCCCTCTGTTCCATATATGTCC 59.159 45.833 11.73 0.08 0.00 4.02
2408 2737 6.092955 TCCATATATGTCCGTGGTCTTAAC 57.907 41.667 11.73 0.00 33.47 2.01
2544 2880 5.721960 AGAAGCTACTTAGTCCCAAATCAGA 59.278 40.000 0.00 0.00 0.00 3.27
2566 2906 2.016318 TCAGAACAATTGCGCCCATAG 58.984 47.619 4.18 0.00 0.00 2.23
2603 2943 3.223157 CAATTACAGGTCGACAAAACGC 58.777 45.455 18.91 0.00 0.00 4.84
2656 2996 3.287222 TGATAACCTACCAGCATTTGCC 58.713 45.455 0.00 0.00 43.38 4.52
2737 3077 7.014422 ACCATTTTATTCTGGTGGTTTCGTTAA 59.986 33.333 0.00 0.00 44.06 2.01
2744 3084 2.944349 TGGTGGTTTCGTTAACAGTTCC 59.056 45.455 6.39 3.51 38.55 3.62
2774 3114 2.691526 TCCATACCTCACCGACATGTAC 59.308 50.000 0.00 0.00 0.00 2.90
2782 3122 4.055360 CTCACCGACATGTACAAGTTTGA 58.945 43.478 5.05 7.80 0.00 2.69
2922 3263 9.158233 CAAACTACCGATTACTTCTTTATGGAA 57.842 33.333 0.00 0.00 0.00 3.53
2962 3303 1.480137 CTCGAGCCTGGAGATTCTTGT 59.520 52.381 0.00 0.00 33.27 3.16
3249 3590 9.760077 AAATTTAGACTAAAGTTGAACTCTCGA 57.240 29.630 17.37 0.00 35.02 4.04
3381 3722 6.551601 TCTCTCTGAACATCCTTCCCTTATAC 59.448 42.308 0.00 0.00 0.00 1.47
3445 3786 6.607735 ATTTATGCAATTGCTTATTGTGCC 57.392 33.333 29.37 0.00 44.52 5.01
3863 4208 8.272190 GTTCTCTAGAAATGCCAAAGGCTGAC 62.272 46.154 9.71 0.00 41.83 3.51
3872 4217 2.301346 CCAAAGGCTGACATATGGGTC 58.699 52.381 7.80 0.00 38.29 4.46
3878 4223 1.134818 GCTGACATATGGGTCGTGACA 60.135 52.381 7.80 0.00 40.72 3.58
3923 4268 5.127194 TGGATACTGTGCGAAGATCTACTTT 59.873 40.000 0.00 0.00 36.75 2.66
3935 4280 7.531534 GCGAAGATCTACTTTACGTAAGAGATC 59.468 40.741 28.39 28.39 41.59 2.75
3988 4333 4.883585 TGAATTTCTGGGCTGATATGTGAC 59.116 41.667 0.00 0.00 0.00 3.67
4107 4452 6.128254 GGAAAGGAACACTTCTACACTTATGC 60.128 42.308 0.00 0.00 38.85 3.14
4180 4526 8.085296 TCTTTGTTGTGTGTAAAATGTCTTGTT 58.915 29.630 0.00 0.00 0.00 2.83
4183 4529 7.148641 TGTTGTGTGTAAAATGTCTTGTTTGT 58.851 30.769 0.00 0.00 0.00 2.83
4186 4532 5.005299 GTGTGTAAAATGTCTTGTTTGTGGC 59.995 40.000 0.00 0.00 0.00 5.01
4307 4653 8.432013 TGTCTACATGATGCTAATTCCTATGTT 58.568 33.333 0.00 0.00 0.00 2.71
4415 4766 2.027192 TCCTGACGCAGCCTAATTTTCT 60.027 45.455 1.84 0.00 0.00 2.52
4447 4798 7.982224 TGCATTCTCTGTTTCATCTGATTTAG 58.018 34.615 0.00 0.00 0.00 1.85
4549 4900 5.130809 TCATCAATATGGGAGACATCACACA 59.869 40.000 0.00 0.00 43.11 3.72
4647 5006 3.321111 CACCTTGTAGGACCACGCTATAT 59.679 47.826 0.00 0.00 37.67 0.86
4657 5016 2.227194 CCACGCTATATGGTTTTCCCC 58.773 52.381 0.00 0.00 39.73 4.81
4712 5071 1.547372 GATGACATGCCCTTTGTGCTT 59.453 47.619 0.00 0.00 0.00 3.91
4730 5089 6.563422 TGTGCTTTTGACATATGAATTAGCC 58.437 36.000 10.38 6.47 0.00 3.93
4744 5103 3.498774 ATTAGCCGATCTTTGCAGGAT 57.501 42.857 4.29 4.29 0.00 3.24
4747 5106 1.211457 AGCCGATCTTTGCAGGATCTT 59.789 47.619 21.26 10.16 37.88 2.40
4807 5166 1.263217 GTGGAGTGCAATTTCGACGTT 59.737 47.619 0.00 0.00 0.00 3.99
4828 5187 3.216800 TGTTGATGCTGTGAAGAAGCTT 58.783 40.909 0.00 0.00 41.42 3.74
4878 5239 5.165961 AGATTGCCAAAAGCTACTCTACA 57.834 39.130 0.00 0.00 44.23 2.74
4948 5309 0.315568 GGACTCAATCGGGAGGATCG 59.684 60.000 0.00 0.00 39.27 3.69
4960 5321 2.431942 GGATCGTGTGCGTTCCGT 60.432 61.111 2.06 0.00 44.04 4.69
4968 5329 2.586635 TGCGTTCCGTTGAAGCGT 60.587 55.556 0.00 0.00 31.42 5.07
5092 5453 5.888724 AGAGTGACATCTTCTCCGAAGAATA 59.111 40.000 10.02 0.00 40.68 1.75
5097 5458 4.038042 ACATCTTCTCCGAAGAATATCGCA 59.962 41.667 10.02 0.00 40.68 5.10
5108 5469 2.158769 AGAATATCGCAGGCACATTCCA 60.159 45.455 0.00 0.00 0.00 3.53
5196 5557 9.577110 TGTTGCATCATCTTATTCTTTCATTTC 57.423 29.630 0.00 0.00 0.00 2.17
5199 5560 9.744468 TGCATCATCTTATTCTTTCATTTCATG 57.256 29.630 0.00 0.00 0.00 3.07
5200 5561 9.193133 GCATCATCTTATTCTTTCATTTCATGG 57.807 33.333 0.00 0.00 0.00 3.66
5409 5770 2.402564 GATGTCAAGAGGATGGAGGGA 58.597 52.381 0.00 0.00 0.00 4.20
5424 5786 2.633481 GGAGGGATGTAGGCGACTAAAT 59.367 50.000 0.00 0.00 46.54 1.40
5489 5852 3.750639 TTTAGCAAATTTAGGGACGCG 57.249 42.857 3.53 3.53 0.00 6.01
5505 5868 4.210746 GGGACGCGGATAAATTAAGTTCTC 59.789 45.833 12.47 0.00 0.00 2.87
5527 5890 9.998106 TTCTCTAAATATACAACTAGGGATTGC 57.002 33.333 0.00 0.00 0.00 3.56
5564 5927 3.628942 TGAGCATACAAGCAAGCAATAGG 59.371 43.478 0.00 0.00 36.85 2.57
5594 5957 1.275573 ACCTTCGCTCTTGGGACTAAC 59.724 52.381 0.00 0.00 34.79 2.34
5613 5978 7.172019 GGACTAACCTGATTTCAAACTTAACGA 59.828 37.037 0.00 0.00 35.41 3.85
5661 6026 9.878667 TCGTCATCAATACCAAAATCTACTTAA 57.121 29.630 0.00 0.00 0.00 1.85
5676 6043 7.744678 ATCTACTTAAGGGCCTAAAAGTACA 57.255 36.000 26.04 20.43 34.23 2.90
5758 6126 8.623903 CCAGTGATTTGTGCATACATAGTTAAT 58.376 33.333 0.00 0.00 36.53 1.40
5780 6148 2.432146 TCCGATCTGGAACAAGGAGATG 59.568 50.000 4.13 0.00 46.38 2.90
5823 6192 1.002250 CAGACGACACGTTTCCCTCG 61.002 60.000 0.00 0.00 41.37 4.63
5847 6216 4.517832 ACGGGAACAAGTGAAACCTTATTC 59.482 41.667 0.00 0.00 37.80 1.75
5856 6225 5.491982 AGTGAAACCTTATTCCTAGCACAG 58.508 41.667 0.00 0.00 37.80 3.66
5884 6253 2.223226 TGACAATACAAATCATGGCGCG 60.223 45.455 0.00 0.00 0.00 6.86
5947 6317 1.134670 ACCGAGGATAACAAGCTGAGC 60.135 52.381 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.137543 GTGTTGGAAATATGCCCTAGAGG 58.862 47.826 0.00 0.00 39.47 3.69
1 2 4.780815 TGTGTTGGAAATATGCCCTAGAG 58.219 43.478 0.00 0.00 0.00 2.43
2 3 4.853468 TGTGTTGGAAATATGCCCTAGA 57.147 40.909 0.00 0.00 0.00 2.43
3 4 5.184864 TGTTTGTGTTGGAAATATGCCCTAG 59.815 40.000 0.00 0.00 0.00 3.02
4 5 5.080337 TGTTTGTGTTGGAAATATGCCCTA 58.920 37.500 0.00 0.00 0.00 3.53
5 6 3.900601 TGTTTGTGTTGGAAATATGCCCT 59.099 39.130 0.00 0.00 0.00 5.19
6 7 4.264460 TGTTTGTGTTGGAAATATGCCC 57.736 40.909 0.00 0.00 0.00 5.36
7 8 9.762933 ATAATATGTTTGTGTTGGAAATATGCC 57.237 29.630 0.00 0.00 0.00 4.40
59 60 1.862201 CACGTTCGCCTCACTGTTAAA 59.138 47.619 0.00 0.00 0.00 1.52
67 68 0.669318 GATTCACCACGTTCGCCTCA 60.669 55.000 0.00 0.00 0.00 3.86
279 280 3.627123 CACAAACATGACTGGTCTGTTGA 59.373 43.478 0.00 0.00 34.04 3.18
290 291 0.944386 ACTCGTGGCACAAACATGAC 59.056 50.000 19.09 0.00 44.16 3.06
341 342 2.367241 TGTGGGAAGATCAAAGACGTCA 59.633 45.455 19.50 0.00 0.00 4.35
349 350 5.378230 AAGATATGCTGTGGGAAGATCAA 57.622 39.130 0.00 0.00 0.00 2.57
363 364 9.507329 TTTGATTGGGTAGAGATTAAGATATGC 57.493 33.333 0.00 0.00 0.00 3.14
371 372 8.781951 AGGAAGATTTTGATTGGGTAGAGATTA 58.218 33.333 0.00 0.00 0.00 1.75
378 379 8.112822 TCAATGTAGGAAGATTTTGATTGGGTA 58.887 33.333 0.00 0.00 0.00 3.69
432 434 3.751518 AGTAGCTAAAACCCCTTGTGTG 58.248 45.455 0.00 0.00 0.00 3.82
435 437 5.546887 ACTCTTAGTAGCTAAAACCCCTTGT 59.453 40.000 0.00 0.00 0.00 3.16
465 468 6.471233 TTCAACACCAACAATAATCACCAA 57.529 33.333 0.00 0.00 0.00 3.67
466 469 6.662865 ATTCAACACCAACAATAATCACCA 57.337 33.333 0.00 0.00 0.00 4.17
474 477 9.388506 TGAATTAACAAATTCAACACCAACAAT 57.611 25.926 10.30 0.00 43.77 2.71
535 538 3.210227 CAAACACACCACAGACCATACA 58.790 45.455 0.00 0.00 0.00 2.29
538 541 2.023673 CACAAACACACCACAGACCAT 58.976 47.619 0.00 0.00 0.00 3.55
585 588 6.479972 TCACGACATTAGGGTCTATCAAAT 57.520 37.500 0.00 0.00 35.63 2.32
591 594 5.925506 TGAATTCACGACATTAGGGTCTA 57.074 39.130 3.38 0.00 35.63 2.59
619 622 0.398522 TCATAGCCGATGACCCACCT 60.399 55.000 0.00 0.00 39.78 4.00
622 625 1.837439 ACTTTCATAGCCGATGACCCA 59.163 47.619 0.00 0.00 44.53 4.51
623 626 2.213499 CACTTTCATAGCCGATGACCC 58.787 52.381 0.00 0.00 44.53 4.46
629 632 1.448985 GCAACCACTTTCATAGCCGA 58.551 50.000 0.00 0.00 0.00 5.54
646 649 1.523154 GAATTCCCCACACTTGCGCA 61.523 55.000 5.66 5.66 0.00 6.09
647 650 1.212751 GAATTCCCCACACTTGCGC 59.787 57.895 0.00 0.00 0.00 6.09
649 652 1.327303 TGTGAATTCCCCACACTTGC 58.673 50.000 2.27 0.00 39.36 4.01
650 653 2.892852 ACATGTGAATTCCCCACACTTG 59.107 45.455 0.00 0.00 45.87 3.16
651 654 3.157087 GACATGTGAATTCCCCACACTT 58.843 45.455 1.15 0.00 45.87 3.16
665 668 2.047002 TCATGCCCATCTGACATGTG 57.953 50.000 1.15 0.00 41.51 3.21
666 669 2.173996 TCATCATGCCCATCTGACATGT 59.826 45.455 0.00 0.00 41.51 3.21
672 675 4.281898 TCACTATCATCATGCCCATCTG 57.718 45.455 0.00 0.00 0.00 2.90
675 678 5.251182 TCATTCACTATCATCATGCCCAT 57.749 39.130 0.00 0.00 0.00 4.00
690 694 5.355596 CACCTCATAGTCTCCTTCATTCAC 58.644 45.833 0.00 0.00 0.00 3.18
746 760 4.886579 ACCCTCGACAACGTTATACTTTT 58.113 39.130 0.00 0.00 40.69 2.27
775 792 6.985188 TCCTTGGATAGAACGAAAATTGAG 57.015 37.500 0.00 0.00 0.00 3.02
783 800 5.621555 GCGCTATAATCCTTGGATAGAACGA 60.622 44.000 0.00 0.00 0.00 3.85
800 817 3.056107 AGAACCTCACAGTTTGCGCTATA 60.056 43.478 9.73 0.00 0.00 1.31
802 819 1.070134 AGAACCTCACAGTTTGCGCTA 59.930 47.619 9.73 0.00 0.00 4.26
811 828 0.320771 CCAACCCGAGAACCTCACAG 60.321 60.000 0.00 0.00 0.00 3.66
827 844 2.969300 GAACGGTCTGTTGGGGCCAA 62.969 60.000 4.39 0.00 42.09 4.52
881 901 4.695231 ACGACGTCGAGGGCGTTG 62.695 66.667 41.52 20.76 46.02 4.10
898 922 2.163818 AGACGGAACAAAGCGATCAA 57.836 45.000 0.00 0.00 0.00 2.57
1233 1260 5.613795 CGATCAGACGAAATGAAACCGAAAA 60.614 40.000 0.00 0.00 35.09 2.29
1251 1278 1.672854 TAGGCCCAACGGACGATCAG 61.673 60.000 0.00 0.00 45.05 2.90
1288 1315 1.171308 CGGACTCGTCTCCCAGTTTA 58.829 55.000 0.00 0.00 0.00 2.01
1408 1436 5.571784 TGAATGAGTGAGATTGAATTGGC 57.428 39.130 0.00 0.00 0.00 4.52
1501 1529 7.231317 CACACAAATACCCCATATTAGCTGATT 59.769 37.037 0.00 0.00 32.86 2.57
1603 1631 7.873505 ACAGTCCACTTCTAAACTATCAGAAAC 59.126 37.037 0.00 0.00 30.68 2.78
1685 1714 6.465439 AAACTCCCAAGAACAGTAAAAAGG 57.535 37.500 0.00 0.00 0.00 3.11
1701 1730 5.069119 AGACCTGAAAACAATCAAAACTCCC 59.931 40.000 0.00 0.00 0.00 4.30
1724 1753 8.147058 AGCTTAGATGACCAACTGACATATAAG 58.853 37.037 17.02 17.02 43.00 1.73
1809 2136 3.402110 TGATTGTAAGTGGCACTCAGTG 58.598 45.455 22.31 0.00 36.51 3.66
1833 2162 1.308783 ACGAGTCAGAGATCTGCGCA 61.309 55.000 10.98 10.98 43.46 6.09
1867 2196 3.119495 AGCCGGTAACTGAAATGCAATTC 60.119 43.478 7.59 7.59 33.67 2.17
1889 2218 2.181125 TGTTTATGGCCTCTACGTCCA 58.819 47.619 3.32 0.00 0.00 4.02
2105 2434 7.145474 ACGGAATGGTAAAGGAAGGTAATAT 57.855 36.000 0.00 0.00 0.00 1.28
2116 2445 4.868734 GGAGACAGTTACGGAATGGTAAAG 59.131 45.833 0.00 0.00 34.41 1.85
2121 2450 1.475280 TCGGAGACAGTTACGGAATGG 59.525 52.381 0.00 0.00 0.00 3.16
2267 2596 7.172703 AGGTACGTTAAGAAATTGAGTTCAAGG 59.827 37.037 0.00 0.00 39.47 3.61
2396 2725 6.183360 TGTCCATTATCTAGTTAAGACCACGG 60.183 42.308 9.04 0.00 36.93 4.94
2397 2726 6.802608 TGTCCATTATCTAGTTAAGACCACG 58.197 40.000 9.04 0.00 36.93 4.94
2408 2737 7.044181 TGAAGTTGCTCTTGTCCATTATCTAG 58.956 38.462 0.00 0.00 36.40 2.43
2544 2880 1.255882 TGGGCGCAATTGTTCTGATT 58.744 45.000 10.83 0.00 0.00 2.57
2566 2906 7.094634 ACCTGTAATTGTTCATGAATCAGTCAC 60.095 37.037 12.12 5.80 39.72 3.67
2603 2943 5.106908 GCTCTTTAAAGTACCTGCTCAACAG 60.107 44.000 14.74 1.84 46.77 3.16
2656 2996 5.277154 CGTGCCCATTAAAGTTACCTTATCG 60.277 44.000 0.00 0.00 0.00 2.92
2737 3077 7.133133 AGGTATGGATATTAAACGGAACTGT 57.867 36.000 0.00 0.00 0.00 3.55
2744 3084 5.632347 GTCGGTGAGGTATGGATATTAAACG 59.368 44.000 0.00 0.00 0.00 3.60
2782 3122 6.777782 TGGGGAAATGCTTTTAACATCAAAT 58.222 32.000 0.00 0.00 0.00 2.32
2830 3171 2.200067 GTTGATGAGATCAGCACTCCG 58.800 52.381 0.00 0.00 42.45 4.63
2922 3263 7.042187 GCTCGAGATATGATCACATCAACTTTT 60.042 37.037 18.75 0.00 43.50 2.27
2962 3303 9.317936 CAAGCTATCATACATTGTGACTCTTAA 57.682 33.333 0.00 0.00 0.00 1.85
3276 3617 5.602561 TCTTAGTAGATTCCTTATGCTGCCA 59.397 40.000 0.00 0.00 0.00 4.92
3358 3699 5.302059 CGTATAAGGGAAGGATGTTCAGAGA 59.698 44.000 0.00 0.00 0.00 3.10
3445 3786 3.550233 CCTCCTGTGATATTACGGTCACG 60.550 52.174 5.79 0.00 45.88 4.35
3612 3956 9.369672 AGAGGAAATAAGTATAGAACCTACCAG 57.630 37.037 0.00 0.00 0.00 4.00
3625 3969 9.083422 CCAGATATGTCAGAGAGGAAATAAGTA 57.917 37.037 0.00 0.00 0.00 2.24
3626 3970 7.472663 GCCAGATATGTCAGAGAGGAAATAAGT 60.473 40.741 0.00 0.00 0.00 2.24
3863 4208 0.177836 TGGCTGTCACGACCCATATG 59.822 55.000 0.00 0.00 0.00 1.78
3872 4217 2.002586 CCAGAAACTATGGCTGTCACG 58.997 52.381 0.00 0.00 0.00 4.35
3878 4223 3.525800 ACCAAACCAGAAACTATGGCT 57.474 42.857 0.00 0.00 41.87 4.75
4000 4345 5.471797 TGTTTGCCTGAAATCTATTTGACGA 59.528 36.000 0.00 0.00 0.00 4.20
4001 4346 5.698832 TGTTTGCCTGAAATCTATTTGACG 58.301 37.500 0.00 0.00 0.00 4.35
4107 4452 0.926155 CTTGCTGGATCACATCGTCG 59.074 55.000 0.00 0.00 0.00 5.12
4180 4526 2.676744 CGATATGTCAGCGCCACAA 58.323 52.632 13.34 4.61 0.00 3.33
4186 4532 1.258982 GGAGTTTGCGATATGTCAGCG 59.741 52.381 0.00 0.00 39.63 5.18
4334 4684 0.875059 GGCGTCAAAGGAGGAAACTG 59.125 55.000 0.00 0.00 44.43 3.16
4415 4766 9.269453 CAGATGAAACAGAGAATGCATCTATAA 57.731 33.333 0.00 0.00 40.11 0.98
4521 4872 7.614974 TGTGATGTCTCCCATATTGATGAAAAA 59.385 33.333 0.00 0.00 34.73 1.94
4549 4900 4.960938 TGTGAGACATTCAGTAGCTTGTT 58.039 39.130 0.00 0.00 36.21 2.83
4647 5006 9.127560 AGATGATATATAATCAGGGGAAAACCA 57.872 33.333 11.96 0.00 42.91 3.67
4654 5013 9.097946 TCTGCATAGATGATATATAATCAGGGG 57.902 37.037 11.96 1.21 0.00 4.79
4677 5036 5.685954 GCATGTCATCTATGTGCAAAATCTG 59.314 40.000 0.00 0.00 35.93 2.90
4690 5049 2.025981 AGCACAAAGGGCATGTCATCTA 60.026 45.455 0.00 0.00 0.00 1.98
4712 5071 8.344831 CAAAGATCGGCTAATTCATATGTCAAA 58.655 33.333 1.90 0.00 0.00 2.69
4730 5089 4.573607 TGAATCAAGATCCTGCAAAGATCG 59.426 41.667 16.66 7.49 44.02 3.69
4744 5103 2.205911 TGTTCGCAACGTGAATCAAGA 58.794 42.857 2.68 0.00 34.54 3.02
4747 5106 0.234625 GCTGTTCGCAACGTGAATCA 59.765 50.000 0.00 0.00 38.92 2.57
4807 5166 2.854963 AGCTTCTTCACAGCATCAACA 58.145 42.857 0.00 0.00 39.99 3.33
4828 5187 3.069443 GGGACACAATTCCAAGCTTTTCA 59.931 43.478 0.00 0.00 37.40 2.69
4960 5321 2.813172 TGATCTCATTTGCACGCTTCAA 59.187 40.909 0.00 0.00 0.00 2.69
4968 5329 5.985530 CGTAGTTCCTATGATCTCATTTGCA 59.014 40.000 0.00 0.00 37.76 4.08
5056 5417 3.712016 TGTCACTCTCTCTGCTACTCT 57.288 47.619 0.00 0.00 0.00 3.24
5061 5422 3.696051 GAGAAGATGTCACTCTCTCTGCT 59.304 47.826 0.00 0.00 0.00 4.24
5069 5430 4.442375 TTCTTCGGAGAAGATGTCACTC 57.558 45.455 12.53 0.00 45.90 3.51
5092 5453 0.107066 TCATGGAATGTGCCTGCGAT 60.107 50.000 0.00 0.00 46.80 4.58
5097 5458 2.242965 TCTGGATTCATGGAATGTGCCT 59.757 45.455 0.00 0.00 46.80 4.75
5166 5527 8.741841 TGAAAGAATAAGATGATGCAACATTCA 58.258 29.630 11.11 5.47 0.00 2.57
5170 5531 9.577110 GAAATGAAAGAATAAGATGATGCAACA 57.423 29.630 0.00 0.00 0.00 3.33
5378 5739 6.716934 TCCTCTTGACATCCTACTTACATC 57.283 41.667 0.00 0.00 0.00 3.06
5379 5740 6.042552 CCATCCTCTTGACATCCTACTTACAT 59.957 42.308 0.00 0.00 0.00 2.29
5380 5741 5.363868 CCATCCTCTTGACATCCTACTTACA 59.636 44.000 0.00 0.00 0.00 2.41
5381 5742 5.598830 TCCATCCTCTTGACATCCTACTTAC 59.401 44.000 0.00 0.00 0.00 2.34
5382 5743 5.777449 TCCATCCTCTTGACATCCTACTTA 58.223 41.667 0.00 0.00 0.00 2.24
5383 5744 4.624913 TCCATCCTCTTGACATCCTACTT 58.375 43.478 0.00 0.00 0.00 2.24
5384 5745 4.222336 CTCCATCCTCTTGACATCCTACT 58.778 47.826 0.00 0.00 0.00 2.57
5385 5746 3.323403 CCTCCATCCTCTTGACATCCTAC 59.677 52.174 0.00 0.00 0.00 3.18
5386 5747 3.581101 CCTCCATCCTCTTGACATCCTA 58.419 50.000 0.00 0.00 0.00 2.94
5387 5748 2.406559 CCTCCATCCTCTTGACATCCT 58.593 52.381 0.00 0.00 0.00 3.24
5388 5749 1.419387 CCCTCCATCCTCTTGACATCC 59.581 57.143 0.00 0.00 0.00 3.51
5435 5797 4.951715 TGAATTGCTTCCTTGTATGCTCAT 59.048 37.500 0.00 0.00 0.00 2.90
5505 5868 7.390718 GGTGGCAATCCCTAGTTGTATATTTAG 59.609 40.741 0.00 0.00 0.00 1.85
5525 5888 8.767436 TGTATGCTCATATATTATAAGGTGGCA 58.233 33.333 0.00 0.00 0.00 4.92
5564 5927 1.067495 AGAGCGAAGGTTGCAGAGTAC 60.067 52.381 0.00 0.00 39.88 2.73
5594 5957 6.898041 TGTGATCGTTAAGTTTGAAATCAGG 58.102 36.000 0.00 0.00 0.00 3.86
5613 5978 6.765036 ACGAGCAATCAAGAGATTAATGTGAT 59.235 34.615 0.00 0.00 42.46 3.06
5629 5994 5.484173 TTTGGTATTGATGACGAGCAATC 57.516 39.130 0.00 0.00 39.02 2.67
5661 6026 2.574824 ACCGAATGTACTTTTAGGCCCT 59.425 45.455 0.00 0.00 0.00 5.19
5719 6086 0.874390 TCACTGGCGCATTTTCACTC 59.126 50.000 10.83 0.00 0.00 3.51
5780 6148 0.109132 GGTACTGTGCAGCCAAATGC 60.109 55.000 0.00 0.00 46.68 3.56
5823 6192 1.963172 AGGTTTCACTTGTTCCCGTC 58.037 50.000 0.00 0.00 0.00 4.79
5847 6216 6.539826 TGTATTGTCATTTGATCTGTGCTAGG 59.460 38.462 0.00 0.00 0.00 3.02
5856 6225 7.096353 CGCCATGATTTGTATTGTCATTTGATC 60.096 37.037 0.00 0.00 30.57 2.92
5947 6317 7.072177 TGAAACCATTATCGCAGTCTTAAAG 57.928 36.000 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.