Multiple sequence alignment - TraesCS5D01G167000

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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 TraesCS5D01G167000 chr5D 100.000 6380 0 0 1 6380 260487660 260494039 0.000000e+00 11782
1 TraesCS5D01G167000 chr5A 96.034 3303 92 17 2345 5630 345232042 345235322 0.000000e+00 5337
2 TraesCS5D01G167000 chr5A 92.803 2376 109 22 1 2358 345229694 345232025 0.000000e+00 3384
3 TraesCS5D01G167000 chr5A 87.915 331 34 3 5891 6218 345239941 345240268 1.000000e-102 385
4 TraesCS5D01G167000 chr5A 88.235 153 18 0 6228 6380 345240333 345240485 3.930000e-42 183
5 TraesCS5D01G167000 chr5A 88.889 144 11 2 5643 5781 345237998 345238141 8.500000e-39 172
6 TraesCS5D01G167000 chr5B 93.717 2499 114 22 1865 4336 294002721 294000239 0.000000e+00 3705
7 TraesCS5D01G167000 chr5B 95.608 1275 46 7 4361 5630 294000160 293998891 0.000000e+00 2036
8 TraesCS5D01G167000 chr5B 93.362 1175 63 9 627 1791 294003892 294002723 0.000000e+00 1724
9 TraesCS5D01G167000 chr5B 92.989 542 26 6 1 542 294004455 294003926 0.000000e+00 780
10 TraesCS5D01G167000 chr5B 87.987 308 34 1 5914 6218 293960685 293960378 1.690000e-95 361
11 TraesCS5D01G167000 chr7D 77.105 1057 204 29 2443 3485 316405588 316404556 1.540000e-160 577
12 TraesCS5D01G167000 chr7A 76.460 1062 211 30 2443 3490 348207379 348208415 2.020000e-149 540
13 TraesCS5D01G167000 chr7A 80.345 290 46 5 5950 6229 149318046 149317758 6.480000e-50 209
14 TraesCS5D01G167000 chr7B 91.379 348 25 3 5876 6218 17213155 17213502 7.490000e-129 472
15 TraesCS5D01G167000 chr7B 89.972 359 31 3 5876 6229 17354779 17355137 5.830000e-125 459
16 TraesCS5D01G167000 chr7B 89.744 156 13 1 6228 6380 17355191 17355346 5.050000e-46 196
17 TraesCS5D01G167000 chr2D 84.302 172 27 0 5132 5303 459850263 459850092 1.100000e-37 169
18 TraesCS5D01G167000 chr2A 84.302 172 27 0 5132 5303 602807733 602807562 1.100000e-37 169


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 TraesCS5D01G167000 chr5D 260487660 260494039 6379 False 11782.00 11782 100.0000 1 6380 1 chr5D.!!$F1 6379
1 TraesCS5D01G167000 chr5A 345229694 345240485 10791 False 1892.20 5337 90.7752 1 6380 5 chr5A.!!$F1 6379
2 TraesCS5D01G167000 chr5B 293998891 294004455 5564 True 2061.25 3705 93.9190 1 5630 4 chr5B.!!$R2 5629
3 TraesCS5D01G167000 chr7D 316404556 316405588 1032 True 577.00 577 77.1050 2443 3485 1 chr7D.!!$R1 1042
4 TraesCS5D01G167000 chr7A 348207379 348208415 1036 False 540.00 540 76.4600 2443 3490 1 chr7A.!!$F1 1047
5 TraesCS5D01G167000 chr7B 17354779 17355346 567 False 327.50 459 89.8580 5876 6380 2 chr7B.!!$F2 504

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
516 519 1.066787 AGCAAGAGAAGTTACTCCGCC 60.067 52.381 0.00 0.00 36.87 6.13 F
1508 1538 1.070134 TGGAAGTTTGGACTCTGGTCG 59.930 52.381 0.00 0.00 42.97 4.79 F
1838 1871 1.001181 GGAGAGCTGCAGGATGAGATC 59.999 57.143 17.12 0.00 39.69 2.75 F
2154 2187 1.628846 GTGTCTACAATCCTGGGGTGT 59.371 52.381 8.03 8.03 0.00 4.16 F
2227 2262 3.636300 TGAATGCTTGTGTTTGGTAGCTT 59.364 39.130 0.00 0.00 34.77 3.74 F
4061 4145 1.071305 GCACAGTTTTCACAAATGCGC 60.071 47.619 0.00 0.00 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1852 1.001181 GGATCTCATCCTGCAGCTCTC 59.999 57.143 8.66 0.0 46.19 3.20 R
3656 3731 0.833287 CCTGCAGCCTAGCTTTCCTA 59.167 55.000 8.66 0.0 36.40 2.94 R
3981 4065 3.250744 CAGCAGAAAAGCACCATGAATG 58.749 45.455 0.00 0.0 36.85 2.67 R
4028 4112 1.029408 ACTGTGCCTGCAACGAACAA 61.029 50.000 0.00 0.0 0.00 2.83 R
4340 4437 0.038343 ACCGCACCATGTCAAAATGC 60.038 50.000 0.00 0.0 0.00 3.56 R
5644 5813 0.175989 CCCTCGGGTAGAGTTGCTTC 59.824 60.000 0.00 0.0 45.44 3.86 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
164 166 2.728690 TGAAATCACATGCTGGCAAC 57.271 45.000 0.00 0.00 0.00 4.17
281 283 6.859508 CGCAATATACCGTTAGTCAAGTCATA 59.140 38.462 0.00 0.00 0.00 2.15
283 285 9.204570 GCAATATACCGTTAGTCAAGTCATATT 57.795 33.333 0.00 0.00 0.00 1.28
331 333 2.637382 TCAAACCATACTCACAGGAGCA 59.363 45.455 0.00 0.00 45.42 4.26
354 357 7.283127 AGCAACGAGTCACCAAATATCATAAAT 59.717 33.333 0.00 0.00 0.00 1.40
409 412 8.607441 AAAAGAAATACTTCCAGGCATTTTTC 57.393 30.769 0.00 0.00 37.93 2.29
413 416 6.670695 AATACTTCCAGGCATTTTTCTGTT 57.329 33.333 0.00 0.00 0.00 3.16
414 417 4.326504 ACTTCCAGGCATTTTTCTGTTG 57.673 40.909 0.00 0.00 0.00 3.33
516 519 1.066787 AGCAAGAGAAGTTACTCCGCC 60.067 52.381 0.00 0.00 36.87 6.13
543 546 2.979813 CTGTAAACAAAAGCATCACGGC 59.020 45.455 0.00 0.00 0.00 5.68
547 550 2.989422 ACAAAAGCATCACGGCTAAC 57.011 45.000 0.00 0.00 45.07 2.34
548 551 1.539827 ACAAAAGCATCACGGCTAACC 59.460 47.619 0.00 0.00 45.07 2.85
581 590 1.985473 TTGCATTGCAGACCTTGTCT 58.015 45.000 11.76 0.00 44.44 3.41
587 596 4.318332 CATTGCAGACCTTGTCTCTGTAA 58.682 43.478 2.11 2.11 41.37 2.41
810 826 4.856801 CTCCCCATCCAACGGCCG 62.857 72.222 26.86 26.86 0.00 6.13
1410 1427 3.823281 TCGTTGGTGGTTTCTGTTAGA 57.177 42.857 0.00 0.00 0.00 2.10
1412 1429 4.710324 TCGTTGGTGGTTTCTGTTAGATT 58.290 39.130 0.00 0.00 0.00 2.40
1500 1530 5.163561 TGTCACTTGATTTGGAAGTTTGGAC 60.164 40.000 0.00 0.00 31.05 4.02
1501 1531 5.067805 GTCACTTGATTTGGAAGTTTGGACT 59.932 40.000 0.00 0.00 37.87 3.85
1502 1532 5.299279 TCACTTGATTTGGAAGTTTGGACTC 59.701 40.000 0.00 0.00 34.21 3.36
1503 1533 5.300286 CACTTGATTTGGAAGTTTGGACTCT 59.700 40.000 0.00 0.00 34.21 3.24
1504 1534 5.300286 ACTTGATTTGGAAGTTTGGACTCTG 59.700 40.000 0.00 0.00 34.21 3.35
1505 1535 4.144297 TGATTTGGAAGTTTGGACTCTGG 58.856 43.478 0.00 0.00 34.21 3.86
1506 1536 3.662759 TTTGGAAGTTTGGACTCTGGT 57.337 42.857 0.00 0.00 34.21 4.00
1507 1537 2.930826 TGGAAGTTTGGACTCTGGTC 57.069 50.000 0.00 0.00 41.43 4.02
1508 1538 1.070134 TGGAAGTTTGGACTCTGGTCG 59.930 52.381 0.00 0.00 42.97 4.79
1509 1539 1.343465 GGAAGTTTGGACTCTGGTCGA 59.657 52.381 0.00 0.00 42.97 4.20
1510 1540 2.405172 GAAGTTTGGACTCTGGTCGAC 58.595 52.381 7.13 7.13 42.97 4.20
1610 1641 3.781407 TCCACGATCCTGGGGTTATTTAA 59.219 43.478 10.43 0.00 31.41 1.52
1611 1642 4.414182 TCCACGATCCTGGGGTTATTTAAT 59.586 41.667 10.43 0.00 31.41 1.40
1631 1662 3.458779 TTAAATTTGTGGAGCGTACGC 57.541 42.857 32.17 32.17 42.33 4.42
1727 1760 1.601759 TGGAACAAGGCTCTGCAGC 60.602 57.895 9.47 0.00 39.80 5.25
1819 1852 3.865929 AAGTGTGTGAGCGAGCGGG 62.866 63.158 0.00 0.00 0.00 6.13
1820 1853 4.357947 GTGTGTGAGCGAGCGGGA 62.358 66.667 0.00 0.00 0.00 5.14
1838 1871 1.001181 GGAGAGCTGCAGGATGAGATC 59.999 57.143 17.12 0.00 39.69 2.75
1977 2010 4.399934 GTCTTCCTCTGAGGTAGTTACTGG 59.600 50.000 24.21 4.22 34.72 4.00
2039 2072 4.095185 CGTGTTTGGAAAGTTTGGACTGTA 59.905 41.667 0.00 0.00 35.91 2.74
2040 2073 5.578776 GTGTTTGGAAAGTTTGGACTGTAG 58.421 41.667 0.00 0.00 35.91 2.74
2041 2074 5.124936 GTGTTTGGAAAGTTTGGACTGTAGT 59.875 40.000 0.00 0.00 35.91 2.73
2042 2075 5.712917 TGTTTGGAAAGTTTGGACTGTAGTT 59.287 36.000 0.00 0.00 35.91 2.24
2043 2076 6.209788 TGTTTGGAAAGTTTGGACTGTAGTTT 59.790 34.615 0.00 0.00 35.91 2.66
2044 2077 7.393796 TGTTTGGAAAGTTTGGACTGTAGTTTA 59.606 33.333 0.00 0.00 35.91 2.01
2045 2078 8.410912 GTTTGGAAAGTTTGGACTGTAGTTTAT 58.589 33.333 0.00 0.00 35.91 1.40
2046 2079 7.504924 TGGAAAGTTTGGACTGTAGTTTATG 57.495 36.000 0.00 0.00 35.91 1.90
2047 2080 7.284074 TGGAAAGTTTGGACTGTAGTTTATGA 58.716 34.615 0.00 0.00 35.91 2.15
2048 2081 7.776030 TGGAAAGTTTGGACTGTAGTTTATGAA 59.224 33.333 0.00 0.00 35.91 2.57
2049 2082 8.793592 GGAAAGTTTGGACTGTAGTTTATGAAT 58.206 33.333 0.00 0.00 35.91 2.57
2050 2083 9.612620 GAAAGTTTGGACTGTAGTTTATGAATG 57.387 33.333 0.00 0.00 35.91 2.67
2087 2120 8.421784 TGTGACCAATAGGACTATAGTTGATTC 58.578 37.037 6.88 2.36 38.69 2.52
2107 2140 6.312918 TGATTCTGATCCTACTGTTTTTACGC 59.687 38.462 0.00 0.00 0.00 4.42
2154 2187 1.628846 GTGTCTACAATCCTGGGGTGT 59.371 52.381 8.03 8.03 0.00 4.16
2171 2206 5.821995 TGGGGTGTGTTTACTAAAGTAACAC 59.178 40.000 18.48 18.48 39.92 3.32
2172 2207 5.821995 GGGGTGTGTTTACTAAAGTAACACA 59.178 40.000 21.29 21.29 42.67 3.72
2227 2262 3.636300 TGAATGCTTGTGTTTGGTAGCTT 59.364 39.130 0.00 0.00 34.77 3.74
2283 2318 6.515272 AACTGTTTGTGGAATAATAGCTGG 57.485 37.500 0.00 0.00 0.00 4.85
2286 2321 5.321102 TGTTTGTGGAATAATAGCTGGTGT 58.679 37.500 0.00 0.00 0.00 4.16
2582 2648 9.840427 ATATTTATTAAGGTGCGTGCAATATTC 57.160 29.630 0.00 0.00 0.00 1.75
3811 3888 6.204301 CCTAGACAATCTGATGGCACTTATTG 59.796 42.308 10.41 10.41 0.00 1.90
3848 3925 6.951971 ACCTAGTGCTTTCTCATGATACTTT 58.048 36.000 0.00 0.00 0.00 2.66
3981 4065 5.994668 TGGTTTCCAAGCAATTTATTTGGTC 59.005 36.000 10.54 5.21 45.06 4.02
4028 4112 7.865706 AGTTCAATTTTCTGTCACTAACTGT 57.134 32.000 0.00 0.00 0.00 3.55
4061 4145 1.071305 GCACAGTTTTCACAAATGCGC 60.071 47.619 0.00 0.00 0.00 6.09
4237 4330 5.880054 TGTTAGCTTGCTAGATTTGAACC 57.120 39.130 0.00 0.00 0.00 3.62
4243 4336 4.938226 GCTTGCTAGATTTGAACCTACACT 59.062 41.667 0.00 0.00 0.00 3.55
4288 4385 6.757947 GGCATATAAATTTTCTCAAGCAAGCA 59.242 34.615 0.00 0.00 0.00 3.91
4341 4438 8.819974 CATTACCAATATTTTCTCATTGTTGGC 58.180 33.333 0.00 0.00 38.48 4.52
4342 4439 6.357579 ACCAATATTTTCTCATTGTTGGCA 57.642 33.333 0.00 0.00 38.48 4.92
4343 4440 6.949715 ACCAATATTTTCTCATTGTTGGCAT 58.050 32.000 0.00 0.00 38.48 4.40
4357 4501 0.038435 TGGCATTTTGACATGGTGCG 60.038 50.000 0.00 0.00 36.70 5.34
4412 4563 5.236478 CGTGGCCATAAATACTTCTGTTAGG 59.764 44.000 9.72 0.00 0.00 2.69
4439 4590 4.881850 ACGAAGTTTTCATCAGGAAACAGT 59.118 37.500 2.58 0.00 44.89 3.55
4446 4597 5.534207 TTCATCAGGAAACAGTGCAATTT 57.466 34.783 0.00 0.00 30.98 1.82
4483 4634 9.784531 TTTCCATCATGTAGATCTAGAATTTCC 57.215 33.333 1.64 0.00 33.72 3.13
4486 4637 9.217278 CCATCATGTAGATCTAGAATTTCCTTG 57.783 37.037 1.64 0.00 33.72 3.61
4582 4733 0.112995 TCCAGCAACCTTTCATGCCT 59.887 50.000 0.00 0.00 43.57 4.75
4773 4926 7.890127 TCTTCAATATGCCATATTTTCCTAGGG 59.110 37.037 9.46 0.00 33.34 3.53
4882 5035 2.848858 TTACCGCTATCCGACCGGC 61.849 63.158 0.00 0.00 45.58 6.13
5105 5259 5.064198 TGTTAGGAAAGACGTGTTTGTTGAG 59.936 40.000 16.18 0.00 0.00 3.02
5226 5381 2.224257 GCTTCTGGAGATGGATCAGACC 60.224 54.545 0.00 0.00 37.28 3.85
5274 5429 1.743252 CGCTCTCAAGGCCAAGGTC 60.743 63.158 5.01 0.00 0.00 3.85
5384 5539 2.037121 GCCTCATCTCTTCCTAAGCTCC 59.963 54.545 0.00 0.00 0.00 4.70
5538 5697 9.319143 CATGGATTGGTTGTTTTGTTTAAGTTA 57.681 29.630 0.00 0.00 0.00 2.24
5544 5703 7.987649 TGGTTGTTTTGTTTAAGTTATCGTCT 58.012 30.769 0.00 0.00 0.00 4.18
5584 5753 0.934496 TGCTTTCTCGTTCGTGGTTG 59.066 50.000 0.00 0.00 0.00 3.77
5585 5754 0.935196 GCTTTCTCGTTCGTGGTTGT 59.065 50.000 0.00 0.00 0.00 3.32
5586 5755 1.329599 GCTTTCTCGTTCGTGGTTGTT 59.670 47.619 0.00 0.00 0.00 2.83
5587 5756 2.223180 GCTTTCTCGTTCGTGGTTGTTT 60.223 45.455 0.00 0.00 0.00 2.83
5588 5757 3.604392 CTTTCTCGTTCGTGGTTGTTTC 58.396 45.455 0.00 0.00 0.00 2.78
5589 5758 2.589798 TCTCGTTCGTGGTTGTTTCT 57.410 45.000 0.00 0.00 0.00 2.52
5590 5759 3.713858 TCTCGTTCGTGGTTGTTTCTA 57.286 42.857 0.00 0.00 0.00 2.10
5591 5760 4.247267 TCTCGTTCGTGGTTGTTTCTAT 57.753 40.909 0.00 0.00 0.00 1.98
5626 5795 4.517952 TTGGTTTGTGCCTATGATGTTG 57.482 40.909 0.00 0.00 0.00 3.33
5630 5799 4.941263 GGTTTGTGCCTATGATGTTGTCTA 59.059 41.667 0.00 0.00 0.00 2.59
5633 5802 5.876651 TGTGCCTATGATGTTGTCTATCT 57.123 39.130 0.00 0.00 0.00 1.98
5636 5805 3.923461 GCCTATGATGTTGTCTATCTCGC 59.077 47.826 0.00 0.00 0.00 5.03
5637 5806 4.321601 GCCTATGATGTTGTCTATCTCGCT 60.322 45.833 0.00 0.00 0.00 4.93
5638 5807 5.106118 GCCTATGATGTTGTCTATCTCGCTA 60.106 44.000 0.00 0.00 0.00 4.26
5639 5808 6.550843 CCTATGATGTTGTCTATCTCGCTAG 58.449 44.000 0.00 0.00 0.00 3.42
5640 5809 4.230314 TGATGTTGTCTATCTCGCTAGC 57.770 45.455 4.06 4.06 0.00 3.42
5641 5810 3.632145 TGATGTTGTCTATCTCGCTAGCA 59.368 43.478 16.45 0.92 0.00 3.49
5643 5812 4.450082 TGTTGTCTATCTCGCTAGCAAA 57.550 40.909 16.45 0.58 0.00 3.68
5644 5813 4.424626 TGTTGTCTATCTCGCTAGCAAAG 58.575 43.478 16.45 11.51 0.00 2.77
5656 8489 3.061429 CGCTAGCAAAGAAGCAACTCTAC 59.939 47.826 16.45 0.00 38.70 2.59
5663 8496 0.175989 GAAGCAACTCTACCCGAGGG 59.824 60.000 6.63 6.63 44.33 4.30
5673 8506 4.335647 CCCGAGGGTTGCTGCAGT 62.336 66.667 16.64 0.00 0.00 4.40
5692 8529 5.521010 TGCAGTACAAAACGTATATGTAGGC 59.479 40.000 16.56 16.56 34.31 3.93
5703 8540 7.572523 ACGTATATGTAGGCCGCTAAATATA 57.427 36.000 0.00 0.00 0.00 0.86
5723 8560 2.479566 TTTAGAGGCTGAGGCAACAG 57.520 50.000 9.23 7.23 40.87 3.16
5749 8586 8.882736 GGCAAATTTAGTGAAAATTCCTTATGG 58.117 33.333 0.00 0.00 45.12 2.74
5813 10319 4.600062 TGTTCTGGCTAGTATCTCTCACA 58.400 43.478 0.00 0.00 0.00 3.58
5823 10329 8.983724 GGCTAGTATCTCTCACAAAATCAATAC 58.016 37.037 0.00 0.00 0.00 1.89
5824 10330 8.695284 GCTAGTATCTCTCACAAAATCAATACG 58.305 37.037 0.00 0.00 0.00 3.06
5825 10331 9.737427 CTAGTATCTCTCACAAAATCAATACGT 57.263 33.333 0.00 0.00 0.00 3.57
5854 10386 4.415332 GCCGACTCGCCTCGTCAA 62.415 66.667 0.00 0.00 31.35 3.18
5855 10387 2.490217 CCGACTCGCCTCGTCAAT 59.510 61.111 0.00 0.00 31.35 2.57
5857 10389 0.099968 CCGACTCGCCTCGTCAATAA 59.900 55.000 0.00 0.00 31.35 1.40
5858 10390 1.468565 CCGACTCGCCTCGTCAATAAA 60.469 52.381 0.00 0.00 31.35 1.40
5859 10391 2.460918 CGACTCGCCTCGTCAATAAAT 58.539 47.619 0.00 0.00 0.00 1.40
5861 10393 4.039703 CGACTCGCCTCGTCAATAAATAA 58.960 43.478 0.00 0.00 0.00 1.40
5863 10395 5.331607 CGACTCGCCTCGTCAATAAATAAAG 60.332 44.000 0.00 0.00 0.00 1.85
5864 10396 5.657474 ACTCGCCTCGTCAATAAATAAAGA 58.343 37.500 0.00 0.00 0.00 2.52
5865 10397 5.519206 ACTCGCCTCGTCAATAAATAAAGAC 59.481 40.000 0.00 0.00 0.00 3.01
5866 10398 4.807304 TCGCCTCGTCAATAAATAAAGACC 59.193 41.667 0.00 0.00 0.00 3.85
5868 10400 5.501897 CGCCTCGTCAATAAATAAAGACCAC 60.502 44.000 0.00 0.00 0.00 4.16
5869 10401 5.501897 GCCTCGTCAATAAATAAAGACCACG 60.502 44.000 0.00 0.00 0.00 4.94
5870 10402 5.579511 CCTCGTCAATAAATAAAGACCACGT 59.420 40.000 0.00 0.00 0.00 4.49
5871 10403 6.091713 CCTCGTCAATAAATAAAGACCACGTT 59.908 38.462 0.00 0.00 0.00 3.99
5872 10404 7.360607 CCTCGTCAATAAATAAAGACCACGTTT 60.361 37.037 0.00 0.00 0.00 3.60
5873 10405 7.292292 TCGTCAATAAATAAAGACCACGTTTG 58.708 34.615 0.00 0.00 0.00 2.93
5892 10424 1.201647 TGAGACGCTTTAGAGGAACGG 59.798 52.381 0.00 0.00 0.00 4.44
5899 10431 2.290134 GCTTTAGAGGAACGGAAACCCT 60.290 50.000 0.00 0.00 0.00 4.34
5912 10444 1.755393 AAACCCTGACTCGCTCGGTT 61.755 55.000 0.00 0.00 0.00 4.44
5913 10445 2.125912 CCCTGACTCGCTCGGTTG 60.126 66.667 0.00 0.00 0.00 3.77
5914 10446 2.651361 CCTGACTCGCTCGGTTGT 59.349 61.111 0.00 0.00 0.00 3.32
5931 10468 1.106351 TGTCGGTTGTTGCAATGGCT 61.106 50.000 0.59 0.00 41.91 4.75
5998 10535 5.939457 CGGAGCTTATACATGAAGTATCGA 58.061 41.667 0.00 0.00 42.38 3.59
6009 10546 1.918609 GAAGTATCGAACCGTCTGCAC 59.081 52.381 0.00 0.00 0.00 4.57
6047 10584 1.768275 CCACATCCACCAGGTATGCTA 59.232 52.381 2.57 0.00 35.89 3.49
6143 10680 1.374252 CTGTCAGCGCCGTTAACCT 60.374 57.895 2.29 0.00 0.00 3.50
6149 10686 0.669625 AGCGCCGTTAACCTTGTCTC 60.670 55.000 2.29 0.00 0.00 3.36
6150 10687 0.669625 GCGCCGTTAACCTTGTCTCT 60.670 55.000 0.00 0.00 0.00 3.10
6151 10688 1.403249 GCGCCGTTAACCTTGTCTCTA 60.403 52.381 0.00 0.00 0.00 2.43
6257 10852 3.803162 GAGCCCCTCTCCCAAGCC 61.803 72.222 0.00 0.00 35.77 4.35
6263 10858 1.745264 CCTCTCCCAAGCCGAGATC 59.255 63.158 0.00 0.00 35.85 2.75
6279 10877 2.543067 GATCCCTCTGCCGCCTTTGT 62.543 60.000 0.00 0.00 0.00 2.83
6282 10880 2.037136 CCTCTGCCGCCTTTGTCAG 61.037 63.158 0.00 0.00 0.00 3.51
6306 10904 0.830648 CGCCCAACTATTCCTCTCCA 59.169 55.000 0.00 0.00 0.00 3.86
6315 10913 2.856039 ATTCCTCTCCAGCGACCCGA 62.856 60.000 0.00 0.00 0.00 5.14
6318 10916 2.044352 TCTCCAGCGACCCGATCA 60.044 61.111 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.040958 GTGAGCACAACGAAAGCCAG 60.041 55.000 0.00 0.00 0.00 4.85
157 159 1.165907 TGTTCCGAGCAAGTTGCCAG 61.166 55.000 24.02 17.27 46.52 4.85
164 166 4.393062 ACATGATAACTTGTTCCGAGCAAG 59.607 41.667 19.99 19.99 46.23 4.01
200 202 8.533569 TGGAGTTATTTCCTTTCTCAGTTTTT 57.466 30.769 0.00 0.00 38.12 1.94
331 333 9.832445 AGTATTTATGATATTTGGTGACTCGTT 57.168 29.630 0.00 0.00 0.00 3.85
354 357 9.767228 TGCTTTAATTGTTGTACTCTTACAGTA 57.233 29.630 0.00 0.00 39.44 2.74
409 412 3.989167 TCGGTTACGACCATTAACAACAG 59.011 43.478 0.00 0.00 46.91 3.16
543 546 3.853671 GCAATCATTTGTTGCGAGGTTAG 59.146 43.478 0.00 0.00 42.01 2.34
565 568 2.775890 ACAGAGACAAGGTCTGCAATG 58.224 47.619 3.21 0.74 43.53 2.82
600 609 9.932207 TCTTACTCCGTCTGTGAATTTAAAATA 57.068 29.630 0.00 0.00 0.00 1.40
617 626 8.792831 ATTACATGTAAATACGTCTTACTCCG 57.207 34.615 21.57 10.22 31.73 4.63
710 725 1.603172 GGTATTCAGGGTCGATGAGCG 60.603 57.143 0.00 0.00 42.69 5.03
767 783 2.511600 CTTGGACGGCCGTGATCC 60.512 66.667 39.65 30.49 36.79 3.36
988 1005 1.951130 CCGCCATCACCGATCGAAG 60.951 63.158 18.66 8.62 0.00 3.79
1410 1427 1.973281 CAGCCACCGCCTGAACAAT 60.973 57.895 0.00 0.00 34.57 2.71
1412 1429 3.535629 CTCAGCCACCGCCTGAACA 62.536 63.158 0.00 0.00 34.57 3.18
1610 1641 3.437395 TGCGTACGCTCCACAAATTTAAT 59.563 39.130 36.99 0.00 42.51 1.40
1611 1642 2.806818 TGCGTACGCTCCACAAATTTAA 59.193 40.909 36.99 12.64 42.51 1.52
1727 1760 3.726517 CACAACCAGCCCTTCGCG 61.727 66.667 0.00 0.00 44.76 5.87
1819 1852 1.001181 GGATCTCATCCTGCAGCTCTC 59.999 57.143 8.66 0.00 46.19 3.20
1820 1853 1.050204 GGATCTCATCCTGCAGCTCT 58.950 55.000 8.66 0.00 46.19 4.09
1838 1871 1.750399 GGCACCACTACATGCAGGG 60.750 63.158 2.31 0.00 43.93 4.45
1839 1872 2.108514 CGGCACCACTACATGCAGG 61.109 63.158 0.00 0.00 43.93 4.85
2042 2075 9.460019 TGGTCACATTCATAAACTCATTCATAA 57.540 29.630 0.00 0.00 0.00 1.90
2043 2076 9.460019 TTGGTCACATTCATAAACTCATTCATA 57.540 29.630 0.00 0.00 0.00 2.15
2044 2077 7.943079 TGGTCACATTCATAAACTCATTCAT 57.057 32.000 0.00 0.00 0.00 2.57
2045 2078 7.757941 TTGGTCACATTCATAAACTCATTCA 57.242 32.000 0.00 0.00 0.00 2.57
2046 2079 9.941664 CTATTGGTCACATTCATAAACTCATTC 57.058 33.333 0.00 0.00 0.00 2.67
2047 2080 8.906867 CCTATTGGTCACATTCATAAACTCATT 58.093 33.333 0.00 0.00 0.00 2.57
2048 2081 8.274322 TCCTATTGGTCACATTCATAAACTCAT 58.726 33.333 0.00 0.00 34.23 2.90
2049 2082 7.552687 GTCCTATTGGTCACATTCATAAACTCA 59.447 37.037 0.00 0.00 34.23 3.41
2050 2083 7.770897 AGTCCTATTGGTCACATTCATAAACTC 59.229 37.037 0.00 0.00 34.23 3.01
2087 2120 6.481954 AAAGCGTAAAAACAGTAGGATCAG 57.518 37.500 0.00 0.00 0.00 2.90
2104 2137 2.625790 TGGGATAAAACAGCAAAAGCGT 59.374 40.909 0.00 0.00 0.00 5.07
2107 2140 3.006752 TGCCTGGGATAAAACAGCAAAAG 59.993 43.478 0.00 0.00 33.43 2.27
2227 2262 3.758755 ATATCATCTTCGCAGGAGCAA 57.241 42.857 0.00 0.00 42.27 3.91
2283 2318 3.288092 AGAAACTTCCCAAGGACAACAC 58.712 45.455 0.00 0.00 0.00 3.32
2286 2321 4.781775 TGTAGAAACTTCCCAAGGACAA 57.218 40.909 0.00 0.00 0.00 3.18
3650 3725 3.070878 GCAGCCTAGCTTTCCTATCTTCT 59.929 47.826 0.00 0.00 36.40 2.85
3656 3731 0.833287 CCTGCAGCCTAGCTTTCCTA 59.167 55.000 8.66 0.00 36.40 2.94
3811 3888 3.821033 AGCACTAGGTCCACAAATTGAAC 59.179 43.478 0.00 0.00 0.00 3.18
3848 3925 9.595823 GAACATTTAGCTGGTAATACTGAACTA 57.404 33.333 0.00 0.00 0.00 2.24
3913 3997 7.970384 TCATAAAACACCACAATTCTATCGAC 58.030 34.615 0.00 0.00 0.00 4.20
3981 4065 3.250744 CAGCAGAAAAGCACCATGAATG 58.749 45.455 0.00 0.00 36.85 2.67
4028 4112 1.029408 ACTGTGCCTGCAACGAACAA 61.029 50.000 0.00 0.00 0.00 2.83
4061 4145 1.273327 GTTTGAGCCATTGGAACAGGG 59.727 52.381 6.95 0.00 42.39 4.45
4199 4283 9.520204 GCAAGCTAACAACATAATATTGACAAT 57.480 29.630 5.87 5.87 0.00 2.71
4200 4284 8.739039 AGCAAGCTAACAACATAATATTGACAA 58.261 29.630 0.00 0.00 0.00 3.18
4202 4286 9.869844 CTAGCAAGCTAACAACATAATATTGAC 57.130 33.333 3.11 0.00 0.00 3.18
4340 4437 0.038343 ACCGCACCATGTCAAAATGC 60.038 50.000 0.00 0.00 0.00 3.56
4341 4438 2.437200 AACCGCACCATGTCAAAATG 57.563 45.000 0.00 0.00 0.00 2.32
4342 4439 3.467374 AAAACCGCACCATGTCAAAAT 57.533 38.095 0.00 0.00 0.00 1.82
4343 4440 2.969628 AAAACCGCACCATGTCAAAA 57.030 40.000 0.00 0.00 0.00 2.44
4389 4540 6.354130 TCCTAACAGAAGTATTTATGGCCAC 58.646 40.000 8.16 0.00 29.82 5.01
4412 4563 7.581476 TGTTTCCTGATGAAAACTTCGTTATC 58.419 34.615 0.00 0.00 44.30 1.75
4439 4590 3.379688 GGAAAACCCAAAAGCAAATTGCA 59.620 39.130 20.82 0.00 39.54 4.08
4520 4671 4.104383 AGACCACACTTTGTCAATCCAT 57.896 40.909 0.00 0.00 33.89 3.41
4582 4733 1.852157 ACCACCTGGCCTCATTCCA 60.852 57.895 3.32 0.00 39.32 3.53
4606 4757 6.463331 CCATAGGCATCATAAAGTTTGGCATT 60.463 38.462 0.00 0.00 37.14 3.56
4882 5035 2.903855 GGATCAGGCATGCCACGG 60.904 66.667 37.18 25.21 38.92 4.94
5093 5247 1.670811 AGGTCAAGCTCAACAAACACG 59.329 47.619 0.00 0.00 0.00 4.49
5105 5259 4.668941 GCAACAAACAAAACAAGGTCAAGC 60.669 41.667 0.00 0.00 0.00 4.01
5274 5429 3.976701 AACCTCCATGGCTTCGGCG 62.977 63.158 6.96 0.00 42.91 6.46
5277 5432 3.071580 GAGAACCTCCATGGCTTCG 57.928 57.895 6.96 0.00 40.22 3.79
5384 5539 0.502275 GTGCAAAAATTGTCGCCGTG 59.498 50.000 0.00 0.00 0.00 4.94
5538 5697 2.820059 TTCAGTGACAAGCAGACGAT 57.180 45.000 0.00 0.00 0.00 3.73
5544 5703 5.474532 AGCAAGATAAATTCAGTGACAAGCA 59.525 36.000 0.00 0.00 0.00 3.91
5584 5753 5.121454 CCAAACAGTGCTCAGAGATAGAAAC 59.879 44.000 0.00 0.00 0.00 2.78
5585 5754 5.221722 ACCAAACAGTGCTCAGAGATAGAAA 60.222 40.000 0.00 0.00 0.00 2.52
5586 5755 4.284490 ACCAAACAGTGCTCAGAGATAGAA 59.716 41.667 0.00 0.00 0.00 2.10
5587 5756 3.834813 ACCAAACAGTGCTCAGAGATAGA 59.165 43.478 0.00 0.00 0.00 1.98
5588 5757 4.199432 ACCAAACAGTGCTCAGAGATAG 57.801 45.455 0.00 0.00 0.00 2.08
5589 5758 4.623932 AACCAAACAGTGCTCAGAGATA 57.376 40.909 0.00 0.00 0.00 1.98
5590 5759 3.498774 AACCAAACAGTGCTCAGAGAT 57.501 42.857 0.00 0.00 0.00 2.75
5591 5760 2.945008 CAAACCAAACAGTGCTCAGAGA 59.055 45.455 0.00 0.00 0.00 3.10
5626 5795 3.733727 GCTTCTTTGCTAGCGAGATAGAC 59.266 47.826 18.02 11.60 0.00 2.59
5630 5799 2.675348 GTTGCTTCTTTGCTAGCGAGAT 59.325 45.455 18.02 0.00 40.26 2.75
5633 5802 2.069273 GAGTTGCTTCTTTGCTAGCGA 58.931 47.619 10.77 5.12 40.26 4.93
5636 5805 3.935828 GGGTAGAGTTGCTTCTTTGCTAG 59.064 47.826 0.00 0.00 0.00 3.42
5637 5806 3.616560 CGGGTAGAGTTGCTTCTTTGCTA 60.617 47.826 0.00 0.00 0.00 3.49
5638 5807 2.784347 GGGTAGAGTTGCTTCTTTGCT 58.216 47.619 0.00 0.00 0.00 3.91
5639 5808 1.464997 CGGGTAGAGTTGCTTCTTTGC 59.535 52.381 0.00 0.00 0.00 3.68
5640 5809 2.996621 CTCGGGTAGAGTTGCTTCTTTG 59.003 50.000 0.00 0.00 41.99 2.77
5641 5810 2.028020 CCTCGGGTAGAGTTGCTTCTTT 60.028 50.000 0.00 0.00 45.44 2.52
5643 5812 1.187087 CCTCGGGTAGAGTTGCTTCT 58.813 55.000 0.00 0.00 45.44 2.85
5644 5813 0.175989 CCCTCGGGTAGAGTTGCTTC 59.824 60.000 0.00 0.00 45.44 3.86
5656 8489 2.954684 TACTGCAGCAACCCTCGGG 61.955 63.158 15.27 0.00 42.03 5.14
5663 8496 2.468532 ACGTTTTGTACTGCAGCAAC 57.531 45.000 15.27 13.23 0.00 4.17
5664 8497 5.410132 ACATATACGTTTTGTACTGCAGCAA 59.590 36.000 15.27 8.23 35.44 3.91
5665 8498 4.932799 ACATATACGTTTTGTACTGCAGCA 59.067 37.500 15.27 0.00 35.44 4.41
5666 8499 5.464965 ACATATACGTTTTGTACTGCAGC 57.535 39.130 15.27 0.00 35.44 5.25
5667 8500 6.292168 GCCTACATATACGTTTTGTACTGCAG 60.292 42.308 13.48 13.48 35.44 4.41
5669 8502 5.050567 GGCCTACATATACGTTTTGTACTGC 60.051 44.000 0.00 3.85 35.44 4.40
5670 8503 5.174398 CGGCCTACATATACGTTTTGTACTG 59.826 44.000 0.00 0.00 35.44 2.74
5672 8505 4.084900 GCGGCCTACATATACGTTTTGTAC 60.085 45.833 0.00 0.00 35.44 2.90
5673 8506 4.050553 GCGGCCTACATATACGTTTTGTA 58.949 43.478 0.00 0.00 37.49 2.41
5703 8540 2.356535 CCTGTTGCCTCAGCCTCTAAAT 60.357 50.000 0.48 0.00 38.69 1.40
5710 8547 1.538687 ATTTGCCTGTTGCCTCAGCC 61.539 55.000 0.48 0.00 40.16 4.85
5723 8560 8.882736 CCATAAGGAATTTTCACTAAATTTGCC 58.117 33.333 0.00 0.00 44.46 4.52
5749 8586 4.403734 TCAATAAAGAACTTGGTCCCACC 58.596 43.478 0.00 0.00 39.22 4.61
5798 10304 8.695284 CGTATTGATTTTGTGAGAGATACTAGC 58.305 37.037 0.00 0.00 0.00 3.42
5813 10319 5.687166 TCCCTCCACTACGTATTGATTTT 57.313 39.130 13.97 0.00 0.00 1.82
5823 10329 2.050350 TCGGCTTCCCTCCACTACG 61.050 63.158 0.00 0.00 0.00 3.51
5824 10330 0.971447 AGTCGGCTTCCCTCCACTAC 60.971 60.000 0.00 0.00 0.00 2.73
5825 10331 0.683504 GAGTCGGCTTCCCTCCACTA 60.684 60.000 0.00 0.00 0.00 2.74
5826 10332 1.985116 GAGTCGGCTTCCCTCCACT 60.985 63.158 0.00 0.00 0.00 4.00
5854 10386 7.057149 CGTCTCAAACGTGGTCTTTATTTAT 57.943 36.000 0.00 0.00 46.42 1.40
5855 10387 6.456447 CGTCTCAAACGTGGTCTTTATTTA 57.544 37.500 0.00 0.00 46.42 1.40
5857 10389 4.985044 CGTCTCAAACGTGGTCTTTATT 57.015 40.909 0.00 0.00 46.42 1.40
5869 10401 3.121445 CGTTCCTCTAAAGCGTCTCAAAC 59.879 47.826 0.00 0.00 0.00 2.93
5870 10402 3.314553 CGTTCCTCTAAAGCGTCTCAAA 58.685 45.455 0.00 0.00 0.00 2.69
5871 10403 2.352421 CCGTTCCTCTAAAGCGTCTCAA 60.352 50.000 0.00 0.00 0.00 3.02
5872 10404 1.201647 CCGTTCCTCTAAAGCGTCTCA 59.798 52.381 0.00 0.00 0.00 3.27
5873 10405 1.471684 TCCGTTCCTCTAAAGCGTCTC 59.528 52.381 0.00 0.00 0.00 3.36
5892 10424 1.446272 CCGAGCGAGTCAGGGTTTC 60.446 63.158 0.00 0.00 0.00 2.78
5899 10431 2.254350 CGACAACCGAGCGAGTCA 59.746 61.111 0.00 0.00 41.76 3.41
5912 10444 1.106351 AGCCATTGCAACAACCGACA 61.106 50.000 0.00 0.00 41.13 4.35
5913 10445 0.664166 CAGCCATTGCAACAACCGAC 60.664 55.000 0.00 0.00 41.13 4.79
5914 10446 1.659233 CAGCCATTGCAACAACCGA 59.341 52.632 0.00 0.00 41.13 4.69
5985 10522 3.770666 CAGACGGTTCGATACTTCATGT 58.229 45.455 0.00 0.00 0.00 3.21
5988 10525 1.542472 TGCAGACGGTTCGATACTTCA 59.458 47.619 0.00 0.00 0.00 3.02
6009 10546 1.143969 GGATTTGGTCTACGTCGGCG 61.144 60.000 8.42 8.42 44.93 6.46
6129 10666 0.949105 AGACAAGGTTAACGGCGCTG 60.949 55.000 16.39 16.39 0.00 5.18
6143 10680 2.972713 AGCAAGGAGTGGTTAGAGACAA 59.027 45.455 0.00 0.00 32.77 3.18
6149 10686 0.678048 GGGCAGCAAGGAGTGGTTAG 60.678 60.000 0.00 0.00 35.13 2.34
6150 10687 1.378762 GGGCAGCAAGGAGTGGTTA 59.621 57.895 0.00 0.00 35.13 2.85
6151 10688 2.116125 GGGCAGCAAGGAGTGGTT 59.884 61.111 0.00 0.00 35.13 3.67
6221 10761 1.524165 CCAGAGGATCAGCAGCAGC 60.524 63.158 0.00 0.00 37.82 5.25
6257 10852 4.292178 GGCGGCAGAGGGATCTCG 62.292 72.222 3.07 0.00 44.47 4.04
6263 10858 2.747855 GACAAAGGCGGCAGAGGG 60.748 66.667 13.08 0.00 0.00 4.30
6279 10877 1.895020 AATAGTTGGGCGACGGCTGA 61.895 55.000 21.48 7.25 39.81 4.26
6282 10880 2.178235 GGAATAGTTGGGCGACGGC 61.178 63.158 13.84 13.84 38.90 5.68


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

AutoCloner maintained by Alex Coulton.