Multiple sequence alignment - TraesCS6A01G319200

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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 TraesCS6A01G319200 chr6A 100.000 5525 0 0 977 6501 554818165 554823689 0.000000e+00 10203.0
1 TraesCS6A01G319200 chr6A 100.000 532 0 0 1 532 554817189 554817720 0.000000e+00 983.0
2 TraesCS6A01G319200 chr6B 94.769 5563 172 45 977 6501 614305649 614311130 0.000000e+00 8551.0
3 TraesCS6A01G319200 chr6B 87.415 294 13 10 242 522 614304850 614305132 3.780000e-82 316.0
4 TraesCS6A01G319200 chr6B 91.667 156 13 0 6346 6501 614436355 614436510 3.950000e-52 217.0
5 TraesCS6A01G319200 chr6B 87.368 190 14 7 6153 6341 614580779 614580959 6.610000e-50 209.0
6 TraesCS6A01G319200 chr6B 81.250 176 28 4 1 175 720556855 720557026 3.160000e-28 137.0
7 TraesCS6A01G319200 chr6D 95.642 4107 121 25 2431 6501 409342089 409346173 0.000000e+00 6540.0
8 TraesCS6A01G319200 chr6D 92.779 1274 59 12 977 2235 409340455 409341710 0.000000e+00 1812.0
9 TraesCS6A01G319200 chr6D 87.287 527 43 13 1 522 409339435 409339942 1.220000e-161 580.0
10 TraesCS6A01G319200 chr6D 98.077 156 2 1 2234 2389 409341748 409341902 2.990000e-68 270.0
11 TraesCS6A01G319200 chr3B 77.333 150 30 4 26 174 697908444 697908590 1.160000e-12 86.1
12 TraesCS6A01G319200 chr2A 91.837 49 2 2 7 55 33444691 33444737 4.210000e-07 67.6


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 TraesCS6A01G319200 chr6A 554817189 554823689 6500 False 5593.0 10203 100.00000 1 6501 2 chr6A.!!$F1 6500
1 TraesCS6A01G319200 chr6B 614304850 614311130 6280 False 4433.5 8551 91.09200 242 6501 2 chr6B.!!$F4 6259
2 TraesCS6A01G319200 chr6D 409339435 409346173 6738 False 2300.5 6540 93.44625 1 6501 4 chr6D.!!$F1 6500

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
467 489 0.253394 CTCCCTTCCTTCCCTTCCCT 60.253 60.000 0.00 0.0 0.00 4.20 F
1393 1501 0.033642 GGACGCCCTCAAGGTATAGC 59.966 60.000 0.00 0.0 38.26 2.97 F
1966 2084 1.395826 ATGGCAGGAGGCGAGTCTAC 61.396 60.000 0.00 0.0 46.16 2.59 F
2342 2504 1.404035 GTTGTGCCCTTGTTCGTCTTT 59.596 47.619 0.00 0.0 0.00 2.52 F
2395 2558 3.316029 TGCAATCACCTTGTCTGTTTCTG 59.684 43.478 0.00 0.0 37.18 3.02 F
4056 4395 0.321671 TCAAGGGTGGAGCTCTTTCG 59.678 55.000 14.64 0.0 35.26 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 1612 0.172352 GAAGACACTCCCTCTCTGCG 59.828 60.000 0.00 0.00 0.00 5.18 R
2661 3000 0.949397 CAGGATCCAATGTGATGGCG 59.051 55.000 15.82 0.00 40.46 5.69 R
3606 3945 1.064240 ACCCCAATACGGACAATTCCC 60.064 52.381 0.00 0.00 38.99 3.97 R
4056 4395 1.032014 TGGGCTTTGAAGTGTCAAGC 58.968 50.000 0.00 0.00 44.49 4.01 R
4509 4848 1.480954 TCAGGATACCTTCGAAGTGGC 59.519 52.381 23.03 9.69 37.17 5.01 R
5507 5849 0.172127 TCTCTGTCATGACGAGCTGC 59.828 55.000 28.03 6.57 34.42 5.25 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
39 40 3.005155 AGTCAGTGCTCCAAAATGCTTTC 59.995 43.478 0.00 0.00 0.00 2.62
43 44 3.068024 AGTGCTCCAAAATGCTTTCGAAA 59.932 39.130 10.71 10.71 0.00 3.46
44 45 3.801594 GTGCTCCAAAATGCTTTCGAAAA 59.198 39.130 12.41 0.00 0.00 2.29
58 59 5.513141 GCTTTCGAAAATAGCATCTTTGGAC 59.487 40.000 12.41 0.00 35.05 4.02
64 65 6.238842 CGAAAATAGCATCTTTGGACCATCAT 60.239 38.462 0.00 0.00 0.00 2.45
69 70 5.727434 AGCATCTTTGGACCATCATTTTTC 58.273 37.500 0.00 0.00 0.00 2.29
73 74 7.360607 GCATCTTTGGACCATCATTTTTCTTTG 60.361 37.037 0.00 0.00 0.00 2.77
74 75 6.523840 TCTTTGGACCATCATTTTTCTTTGG 58.476 36.000 0.00 0.00 0.00 3.28
75 76 6.326064 TCTTTGGACCATCATTTTTCTTTGGA 59.674 34.615 0.00 0.00 0.00 3.53
77 78 4.022416 TGGACCATCATTTTTCTTTGGACG 60.022 41.667 0.00 0.00 0.00 4.79
78 79 4.217550 GGACCATCATTTTTCTTTGGACGA 59.782 41.667 0.00 0.00 0.00 4.20
79 80 5.376854 ACCATCATTTTTCTTTGGACGAG 57.623 39.130 0.00 0.00 0.00 4.18
82 87 5.858581 CCATCATTTTTCTTTGGACGAGTTC 59.141 40.000 0.00 0.00 0.00 3.01
120 125 6.483974 TGAATGATGAAAAATTGCAAGCACTT 59.516 30.769 4.94 0.00 0.00 3.16
151 156 5.850557 TCTCAATGTTTGCCAGAGAAAAA 57.149 34.783 0.00 0.00 32.83 1.94
153 158 4.692228 TCAATGTTTGCCAGAGAAAAACC 58.308 39.130 0.00 0.00 33.76 3.27
157 162 2.693074 GTTTGCCAGAGAAAAACCCAGA 59.307 45.455 0.00 0.00 0.00 3.86
196 201 3.332706 TTTTTCGTTCATCCGGGCT 57.667 47.368 0.00 0.00 0.00 5.19
197 202 2.476126 TTTTTCGTTCATCCGGGCTA 57.524 45.000 0.00 0.00 0.00 3.93
198 203 2.476126 TTTTCGTTCATCCGGGCTAA 57.524 45.000 0.00 0.00 0.00 3.09
210 215 2.014857 CCGGGCTAAAGCTAAGAAACC 58.985 52.381 0.00 0.00 41.70 3.27
216 221 3.181486 GCTAAAGCTAAGAAACCCCATGC 60.181 47.826 0.25 0.00 38.21 4.06
219 224 1.043116 GCTAAGAAACCCCATGCCCC 61.043 60.000 0.00 0.00 0.00 5.80
282 287 5.389520 AGGGAGGAAAGAAAGAAAGAAAGG 58.610 41.667 0.00 0.00 0.00 3.11
414 419 2.233431 GCAAGCCAACACAATATCCCAA 59.767 45.455 0.00 0.00 0.00 4.12
415 420 3.306641 GCAAGCCAACACAATATCCCAAA 60.307 43.478 0.00 0.00 0.00 3.28
416 421 4.497300 CAAGCCAACACAATATCCCAAAG 58.503 43.478 0.00 0.00 0.00 2.77
417 422 3.099141 AGCCAACACAATATCCCAAAGG 58.901 45.455 0.00 0.00 0.00 3.11
418 423 2.418609 GCCAACACAATATCCCAAAGGC 60.419 50.000 0.00 0.00 0.00 4.35
419 424 2.168313 CCAACACAATATCCCAAAGGCC 59.832 50.000 0.00 0.00 0.00 5.19
420 425 2.830923 CAACACAATATCCCAAAGGCCA 59.169 45.455 5.01 0.00 0.00 5.36
461 466 2.696504 CCCCCTCCCTTCCTTCCC 60.697 72.222 0.00 0.00 0.00 3.97
463 468 1.230314 CCCCTCCCTTCCTTCCCTT 60.230 63.158 0.00 0.00 0.00 3.95
467 489 0.253394 CTCCCTTCCTTCCCTTCCCT 60.253 60.000 0.00 0.00 0.00 4.20
469 491 1.627297 CCCTTCCTTCCCTTCCCTCG 61.627 65.000 0.00 0.00 0.00 4.63
522 544 4.821589 CTCGAAGCCACCGCCTCC 62.822 72.222 0.00 0.00 34.57 4.30
1390 1498 4.809513 AGGACGCCCTCAAGGTAT 57.190 55.556 0.00 0.00 38.86 2.73
1391 1499 3.939710 AGGACGCCCTCAAGGTATA 57.060 52.632 0.00 0.00 38.86 1.47
1392 1500 1.705873 AGGACGCCCTCAAGGTATAG 58.294 55.000 0.00 0.00 38.86 1.31
1393 1501 0.033642 GGACGCCCTCAAGGTATAGC 59.966 60.000 0.00 0.00 38.26 2.97
1402 1510 2.293677 CTCAAGGTATAGCGGATCGTGT 59.706 50.000 0.00 0.00 0.00 4.49
1413 1521 2.047844 ATCGTGTCGCTTGCAGCT 60.048 55.556 0.00 0.00 39.60 4.24
1426 1537 3.084579 CAGCTTTGCCGTAGCTCG 58.915 61.111 0.00 0.00 45.52 5.03
1446 1557 3.805422 TCGAACTTTGCGTGAACTAATGT 59.195 39.130 0.00 0.00 0.00 2.71
1447 1558 4.983538 TCGAACTTTGCGTGAACTAATGTA 59.016 37.500 0.00 0.00 0.00 2.29
1501 1612 4.072131 TGATTTGTTGTTGCCTCCTCTAC 58.928 43.478 0.00 0.00 0.00 2.59
1576 1687 1.482593 CGAGGTAAGCATGGAGTCCTT 59.517 52.381 11.33 0.19 0.00 3.36
1577 1688 2.482142 CGAGGTAAGCATGGAGTCCTTC 60.482 54.545 11.33 0.00 0.00 3.46
1578 1689 2.769095 GAGGTAAGCATGGAGTCCTTCT 59.231 50.000 11.33 1.67 0.00 2.85
1583 1694 1.558756 AGCATGGAGTCCTTCTTCCTG 59.441 52.381 11.33 0.00 0.00 3.86
1594 1705 4.764308 GTCCTTCTTCCTGATTTGCTTCTT 59.236 41.667 0.00 0.00 0.00 2.52
1600 1711 5.702670 TCTTCCTGATTTGCTTCTTACTGTG 59.297 40.000 0.00 0.00 0.00 3.66
1611 1722 4.626042 CTTCTTACTGTGCTGTCTCTGTT 58.374 43.478 0.00 0.00 0.00 3.16
1636 1747 5.263872 ACTGGTGGGTAATGTTTGGAATA 57.736 39.130 0.00 0.00 0.00 1.75
1640 1751 5.654650 TGGTGGGTAATGTTTGGAATATGTC 59.345 40.000 0.00 0.00 0.00 3.06
1703 1814 1.558167 TTCTCATTACTGGGCCGGCA 61.558 55.000 30.85 7.71 0.00 5.69
1761 1872 5.963140 CACTGCAACATGAGTGTATCTAG 57.037 43.478 0.00 0.00 37.67 2.43
1781 1892 6.097129 ATCTAGTAAGAAGTGAGGTGCTAACC 59.903 42.308 0.00 0.00 40.19 2.85
1812 1923 7.389607 ACGGTAATTTATAGCAATCCCATACAC 59.610 37.037 0.00 0.00 0.00 2.90
1814 1925 9.953565 GGTAATTTATAGCAATCCCATACACTA 57.046 33.333 0.00 0.00 0.00 2.74
1878 1989 3.248266 GTCATTCTGCCTTGAATTGCAC 58.752 45.455 0.00 0.00 34.77 4.57
1928 2039 3.340814 AATGTGCTAGGAACTCAGGTG 57.659 47.619 0.00 0.00 41.75 4.00
1966 2084 1.395826 ATGGCAGGAGGCGAGTCTAC 61.396 60.000 0.00 0.00 46.16 2.59
1978 2096 4.514066 AGGCGAGTCTACGAACAAAAATTT 59.486 37.500 0.00 0.00 35.09 1.82
1992 2110 7.108173 CGAACAAAAATTTTGTACGATGTTTGC 59.892 33.333 22.39 5.66 35.04 3.68
2087 2206 3.551082 CGATTGCTTGTGACTTTGCAAAA 59.449 39.130 13.84 0.00 46.31 2.44
2147 2270 2.307496 TTGGTCAAGCACATTGGGAT 57.693 45.000 0.00 0.00 39.54 3.85
2342 2504 1.404035 GTTGTGCCCTTGTTCGTCTTT 59.596 47.619 0.00 0.00 0.00 2.52
2393 2556 3.988379 TGCAATCACCTTGTCTGTTTC 57.012 42.857 0.00 0.00 37.18 2.78
2395 2558 3.316029 TGCAATCACCTTGTCTGTTTCTG 59.684 43.478 0.00 0.00 37.18 3.02
2396 2559 3.565482 GCAATCACCTTGTCTGTTTCTGA 59.435 43.478 0.00 0.00 37.18 3.27
2398 2561 4.696479 ATCACCTTGTCTGTTTCTGACT 57.304 40.909 7.91 0.00 34.25 3.41
2399 2562 4.487714 TCACCTTGTCTGTTTCTGACTT 57.512 40.909 7.91 0.00 34.25 3.01
2400 2563 4.843728 TCACCTTGTCTGTTTCTGACTTT 58.156 39.130 7.91 0.00 34.25 2.66
2401 2564 4.876107 TCACCTTGTCTGTTTCTGACTTTC 59.124 41.667 7.91 0.00 34.25 2.62
2402 2565 4.878397 CACCTTGTCTGTTTCTGACTTTCT 59.122 41.667 7.91 0.00 34.25 2.52
2403 2566 4.878397 ACCTTGTCTGTTTCTGACTTTCTG 59.122 41.667 7.91 0.00 34.25 3.02
2404 2567 4.878397 CCTTGTCTGTTTCTGACTTTCTGT 59.122 41.667 7.91 0.00 34.25 3.41
2405 2568 5.007136 CCTTGTCTGTTTCTGACTTTCTGTC 59.993 44.000 7.91 0.00 45.54 3.51
2406 2569 5.344743 TGTCTGTTTCTGACTTTCTGTCT 57.655 39.130 7.91 0.00 45.54 3.41
2407 2570 5.352284 TGTCTGTTTCTGACTTTCTGTCTC 58.648 41.667 7.91 0.00 45.54 3.36
2408 2571 5.127845 TGTCTGTTTCTGACTTTCTGTCTCT 59.872 40.000 7.91 0.00 45.54 3.10
2470 2808 8.615878 TTAGTAGTACAAACAATTCATGCAGT 57.384 30.769 2.52 0.00 0.00 4.40
2627 2966 6.654582 TCTTACTTGCAATGACATGCTCTTTA 59.345 34.615 0.00 0.00 46.54 1.85
2661 3000 3.503363 TGCAGATTGAAGGTGATGTTGTC 59.497 43.478 0.00 0.00 0.00 3.18
3084 3423 4.309933 GCCGTAGTACTGTTGTAGGTTTT 58.690 43.478 5.39 0.00 0.00 2.43
3255 3594 7.884816 TGTTAGTATTAGCACTTTGTCAGAC 57.115 36.000 0.00 0.00 0.00 3.51
3598 3937 9.563748 TTGATGATGCAATATCTATTGAGACAA 57.436 29.630 12.92 7.35 44.40 3.18
3606 3945 8.295288 GCAATATCTATTGAGACAATTTCTGGG 58.705 37.037 12.92 0.00 44.40 4.45
3765 4104 8.258007 TCAAGACTTTCAGAAGAACTAGTTTCA 58.742 33.333 10.02 0.00 36.57 2.69
4056 4395 0.321671 TCAAGGGTGGAGCTCTTTCG 59.678 55.000 14.64 0.00 35.26 3.46
4509 4848 4.260212 CCTTTGTACACACACTTCACTTCG 60.260 45.833 0.00 0.00 33.30 3.79
4761 5100 3.452627 TCCCTAACTCTGAAGATCTTGGC 59.547 47.826 14.00 0.00 0.00 4.52
4779 5118 2.675056 CGAGGCTGCTGAACACTGC 61.675 63.158 0.00 0.00 0.00 4.40
4848 5187 2.223923 GCTCTACATGTGGGCTCTACTG 60.224 54.545 9.11 0.00 0.00 2.74
4924 5263 8.539674 CAAAGTTTGTGTTGGTAAGCTTTATTC 58.460 33.333 3.20 0.00 35.89 1.75
4929 5268 7.124347 TGTGTTGGTAAGCTTTATTCTAACG 57.876 36.000 3.20 0.00 0.00 3.18
4949 5288 8.468399 TCTAACGGATTTGTGGTTTTACTTTTT 58.532 29.630 0.00 0.00 0.00 1.94
5086 5425 3.559655 TCCATTCTGTGTGTTTTGAGTCG 59.440 43.478 0.00 0.00 0.00 4.18
5140 5479 7.397892 ACGGAGGATATACTATGATGAAGTG 57.602 40.000 0.00 0.00 0.00 3.16
5173 5512 0.890683 CTGAATGGTTGGAAGCCACC 59.109 55.000 0.00 0.00 39.03 4.61
5203 5542 3.340727 GCTTGATGCATGCAGGAAC 57.659 52.632 26.69 16.48 42.31 3.62
5332 5674 1.277557 GGAGCAACTGAGACTGTGGAT 59.722 52.381 0.00 0.00 0.00 3.41
5440 5782 0.810648 TGGTTCTTCATGCAATCGGC 59.189 50.000 0.00 0.00 45.13 5.54
5507 5849 4.623167 CGTCATACTTCAAGTGACCAGAAG 59.377 45.833 0.00 11.56 43.27 2.85
5567 5909 2.483106 TCGTCCTAGTCGAACAAGACAG 59.517 50.000 5.08 0.00 43.24 3.51
5665 6007 7.228308 AGTGTTGTAGATACTCCTATCGTTACC 59.772 40.741 0.00 0.00 34.87 2.85
5673 6015 2.947652 CTCCTATCGTTACCGTTCTCCA 59.052 50.000 0.00 0.00 35.01 3.86
5726 6068 1.116536 TCGTGTGGTCAAGTGGCCTA 61.117 55.000 3.32 0.00 41.34 3.93
5727 6069 0.250124 CGTGTGGTCAAGTGGCCTAA 60.250 55.000 3.32 0.00 41.34 2.69
5768 6123 1.138859 TGACCAGGCGACTCATATTGG 59.861 52.381 0.00 0.00 40.21 3.16
5769 6124 0.179045 ACCAGGCGACTCATATTGGC 60.179 55.000 0.00 0.00 40.21 4.52
5770 6125 0.886490 CCAGGCGACTCATATTGGCC 60.886 60.000 0.00 0.00 44.07 5.36
5771 6126 3.642755 GGCGACTCATATTGGCCG 58.357 61.111 0.00 0.00 33.58 6.13
5773 6128 0.032952 GGCGACTCATATTGGCCGTA 59.967 55.000 0.00 0.00 33.58 4.02
5774 6129 1.419374 GCGACTCATATTGGCCGTAG 58.581 55.000 0.00 0.00 0.00 3.51
5775 6130 1.269621 GCGACTCATATTGGCCGTAGT 60.270 52.381 0.00 0.00 0.00 2.73
5776 6131 2.394708 CGACTCATATTGGCCGTAGTG 58.605 52.381 0.00 0.00 0.00 2.74
5777 6132 2.223735 CGACTCATATTGGCCGTAGTGT 60.224 50.000 0.00 0.00 0.00 3.55
5778 6133 3.737047 CGACTCATATTGGCCGTAGTGTT 60.737 47.826 0.00 0.00 0.00 3.32
5779 6134 3.531538 ACTCATATTGGCCGTAGTGTTG 58.468 45.455 0.00 0.00 0.00 3.33
5780 6135 3.055385 ACTCATATTGGCCGTAGTGTTGT 60.055 43.478 0.00 0.00 0.00 3.32
5781 6136 3.266636 TCATATTGGCCGTAGTGTTGTG 58.733 45.455 0.00 0.00 0.00 3.33
5782 6137 2.843401 TATTGGCCGTAGTGTTGTGT 57.157 45.000 0.00 0.00 0.00 3.72
5783 6138 2.843401 ATTGGCCGTAGTGTTGTGTA 57.157 45.000 0.00 0.00 0.00 2.90
5784 6139 2.843401 TTGGCCGTAGTGTTGTGTAT 57.157 45.000 0.00 0.00 0.00 2.29
5785 6140 2.087501 TGGCCGTAGTGTTGTGTATG 57.912 50.000 0.00 0.00 0.00 2.39
5786 6141 1.345089 TGGCCGTAGTGTTGTGTATGT 59.655 47.619 0.00 0.00 0.00 2.29
5787 6142 1.730064 GGCCGTAGTGTTGTGTATGTG 59.270 52.381 0.00 0.00 0.00 3.21
5976 6335 7.278424 CCAAATAAAATGTATTGGCACCTCTTG 59.722 37.037 0.00 0.00 36.25 3.02
5981 6340 7.480760 AAATGTATTGGCACCTCTTGTATTT 57.519 32.000 0.00 0.00 0.00 1.40
5982 6341 7.480760 AATGTATTGGCACCTCTTGTATTTT 57.519 32.000 0.00 0.00 0.00 1.82
5983 6342 6.266168 TGTATTGGCACCTCTTGTATTTTG 57.734 37.500 0.00 0.00 0.00 2.44
5989 6348 4.076394 GCACCTCTTGTATTTTGGTACCA 58.924 43.478 11.60 11.60 0.00 3.25
6018 6377 5.049198 TGTTCAGCTTATTCAAAGCAGACTG 60.049 40.000 11.90 0.00 45.30 3.51
6154 6530 1.267433 CGGTTCTACGTAGAGAGCACG 60.267 57.143 23.51 19.16 44.80 5.34
6170 6546 0.234884 CACGCTCTTCCGTTTGTTCC 59.765 55.000 0.00 0.00 39.83 3.62
6179 6555 1.134759 TCCGTTTGTTCCGTTGAGTCA 60.135 47.619 0.00 0.00 0.00 3.41
6192 6568 3.745975 CGTTGAGTCAGTTGGATTTGCTA 59.254 43.478 0.00 0.00 0.00 3.49
6199 6575 2.100252 CAGTTGGATTTGCTATGGCCTG 59.900 50.000 3.32 0.00 37.74 4.85
6272 6648 3.525268 AAGTTGGTTGAGCAAAAGGTG 57.475 42.857 0.00 0.00 0.00 4.00
6307 6683 1.473677 TGGTACGGAAATGACGTCGAT 59.526 47.619 11.62 2.87 44.37 3.59
6308 6684 2.682352 TGGTACGGAAATGACGTCGATA 59.318 45.455 11.62 0.00 44.37 2.92
6356 6752 4.631234 TGGGATGAACAATACTCCTACCT 58.369 43.478 0.00 0.00 0.00 3.08
6364 6760 5.934402 ACAATACTCCTACCTTCACGAAT 57.066 39.130 0.00 0.00 0.00 3.34
6383 6779 3.933155 ATTGAATGCTCATCGAACGAC 57.067 42.857 0.00 0.00 0.00 4.34
6390 6786 4.307443 TGCTCATCGAACGACTGAATAT 57.693 40.909 0.00 0.00 0.00 1.28
6402 6798 9.353999 CGAACGACTGAATATTTGGATATATGA 57.646 33.333 0.00 0.00 0.00 2.15
6417 6815 8.324191 TGGATATATGAAGAACTCTTTGGACT 57.676 34.615 0.00 0.00 36.11 3.85
6420 6818 9.474920 GATATATGAAGAACTCTTTGGACTGAG 57.525 37.037 0.00 0.00 36.11 3.35
6424 6822 6.414732 TGAAGAACTCTTTGGACTGAGAAAA 58.585 36.000 0.00 0.00 36.11 2.29
6444 6842 7.187480 AGAAAAGTTTGAAACTCGCTAGAAAC 58.813 34.615 11.44 0.00 41.91 2.78
6453 6851 6.706270 TGAAACTCGCTAGAAACTTTCTGAAT 59.294 34.615 13.44 0.00 40.94 2.57
6455 6853 5.784177 ACTCGCTAGAAACTTTCTGAATCA 58.216 37.500 13.44 0.00 40.94 2.57
6456 6854 5.635700 ACTCGCTAGAAACTTTCTGAATCAC 59.364 40.000 13.44 0.00 40.94 3.06
6458 6856 5.405571 TCGCTAGAAACTTTCTGAATCACAC 59.594 40.000 13.44 0.00 40.94 3.82
6472 6870 4.693566 TGAATCACACGTCCAGTTTTATCC 59.306 41.667 0.00 0.00 0.00 2.59
6484 6882 3.487574 CAGTTTTATCCGCATCGAGAGAC 59.512 47.826 0.00 0.00 46.97 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.959639 TTTTGGAGCACTGACTTTATCTTT 57.040 33.333 0.00 0.00 0.00 2.52
18 19 3.311966 GAAAGCATTTTGGAGCACTGAC 58.688 45.455 0.00 0.00 39.27 3.51
23 24 3.724508 TTTCGAAAGCATTTTGGAGCA 57.275 38.095 6.47 0.00 39.27 4.26
24 25 5.220284 GCTATTTTCGAAAGCATTTTGGAGC 60.220 40.000 14.02 6.90 39.27 4.70
39 40 4.963276 TGGTCCAAAGATGCTATTTTCG 57.037 40.909 0.00 0.00 0.00 3.46
43 44 7.427989 AAAATGATGGTCCAAAGATGCTATT 57.572 32.000 0.00 0.00 0.00 1.73
44 45 7.343833 AGAAAAATGATGGTCCAAAGATGCTAT 59.656 33.333 0.00 0.00 0.00 2.97
51 52 6.424812 GTCCAAAGAAAAATGATGGTCCAAAG 59.575 38.462 0.00 0.00 32.90 2.77
54 55 4.022416 CGTCCAAAGAAAAATGATGGTCCA 60.022 41.667 0.00 0.00 32.90 4.02
55 56 4.217550 TCGTCCAAAGAAAAATGATGGTCC 59.782 41.667 0.00 0.00 32.90 4.46
58 59 5.376854 ACTCGTCCAAAGAAAAATGATGG 57.623 39.130 0.00 0.00 0.00 3.51
73 74 1.068474 CACATTCGTGGAACTCGTCC 58.932 55.000 0.00 0.00 46.06 4.79
74 75 2.060326 TCACATTCGTGGAACTCGTC 57.940 50.000 0.00 0.00 46.06 4.20
75 76 2.736721 CAATCACATTCGTGGAACTCGT 59.263 45.455 0.00 0.00 46.06 4.18
77 78 5.122239 TCATTCAATCACATTCGTGGAACTC 59.878 40.000 0.00 0.00 43.79 3.01
78 79 5.003160 TCATTCAATCACATTCGTGGAACT 58.997 37.500 0.00 0.00 43.79 3.01
79 80 5.295431 TCATTCAATCACATTCGTGGAAC 57.705 39.130 0.00 0.00 43.79 3.62
82 87 5.488645 TCATCATTCAATCACATTCGTGG 57.511 39.130 0.00 0.00 43.79 4.94
86 91 9.485591 GCAATTTTTCATCATTCAATCACATTC 57.514 29.630 0.00 0.00 0.00 2.67
87 92 9.004717 TGCAATTTTTCATCATTCAATCACATT 57.995 25.926 0.00 0.00 0.00 2.71
96 101 6.476243 AGTGCTTGCAATTTTTCATCATTC 57.524 33.333 0.00 0.00 0.00 2.67
97 102 6.870971 AAGTGCTTGCAATTTTTCATCATT 57.129 29.167 0.00 0.00 0.00 2.57
108 113 6.985645 TGAGAAATGTTTTAAGTGCTTGCAAT 59.014 30.769 0.00 0.00 0.00 3.56
181 186 2.010043 GCTTTAGCCCGGATGAACGAA 61.010 52.381 0.73 0.00 33.11 3.85
194 199 3.181486 GCATGGGGTTTCTTAGCTTTAGC 60.181 47.826 0.00 0.00 42.49 3.09
196 201 3.361786 GGCATGGGGTTTCTTAGCTTTA 58.638 45.455 0.00 0.00 0.00 1.85
197 202 2.179427 GGCATGGGGTTTCTTAGCTTT 58.821 47.619 0.00 0.00 0.00 3.51
198 203 1.619704 GGGCATGGGGTTTCTTAGCTT 60.620 52.381 0.00 0.00 0.00 3.74
216 221 0.764369 TATACCCTCTGCTGCTGGGG 60.764 60.000 17.73 17.73 44.97 4.96
219 224 2.149578 GCAATATACCCTCTGCTGCTG 58.850 52.381 0.00 0.00 0.00 4.41
227 232 2.325761 CTACGCACGCAATATACCCTC 58.674 52.381 0.00 0.00 0.00 4.30
228 233 1.000506 CCTACGCACGCAATATACCCT 59.999 52.381 0.00 0.00 0.00 4.34
229 234 1.425412 CCTACGCACGCAATATACCC 58.575 55.000 0.00 0.00 0.00 3.69
251 256 1.612442 CTTTCCTCCCTCCGGGTGA 60.612 63.158 0.00 0.00 44.74 4.02
262 267 6.299922 TCTCCCTTTCTTTCTTTCTTTCCTC 58.700 40.000 0.00 0.00 0.00 3.71
263 268 6.267492 TCTCCCTTTCTTTCTTTCTTTCCT 57.733 37.500 0.00 0.00 0.00 3.36
264 269 6.961360 TTCTCCCTTTCTTTCTTTCTTTCC 57.039 37.500 0.00 0.00 0.00 3.13
265 270 6.920758 GCTTTCTCCCTTTCTTTCTTTCTTTC 59.079 38.462 0.00 0.00 0.00 2.62
282 287 2.881352 CGCCTCGTCGCTTTCTCC 60.881 66.667 0.00 0.00 0.00 3.71
328 333 3.408851 GTTTGGTCGGTCGGCGAC 61.409 66.667 30.72 30.72 35.82 5.19
479 501 4.015541 GGGGACAGGATATAATAGAGGGGA 60.016 50.000 0.00 0.00 0.00 4.81
1393 1501 2.792290 CTGCAAGCGACACGATCCG 61.792 63.158 0.00 0.00 0.00 4.18
1413 1521 1.529438 CAAAGTTCGAGCTACGGCAAA 59.471 47.619 0.90 0.00 42.82 3.68
1426 1537 9.210426 CAATATACATTAGTTCACGCAAAGTTC 57.790 33.333 0.00 0.00 0.00 3.01
1470 1581 5.752955 AGGCAACAACAAATCAACACATTAC 59.247 36.000 0.00 0.00 41.41 1.89
1501 1612 0.172352 GAAGACACTCCCTCTCTGCG 59.828 60.000 0.00 0.00 0.00 5.18
1576 1687 5.702670 CACAGTAAGAAGCAAATCAGGAAGA 59.297 40.000 0.00 0.00 0.00 2.87
1577 1688 5.618640 GCACAGTAAGAAGCAAATCAGGAAG 60.619 44.000 0.00 0.00 0.00 3.46
1578 1689 4.216257 GCACAGTAAGAAGCAAATCAGGAA 59.784 41.667 0.00 0.00 0.00 3.36
1583 1694 4.453819 AGACAGCACAGTAAGAAGCAAATC 59.546 41.667 0.00 0.00 0.00 2.17
1594 1705 4.216472 CAGTAGAACAGAGACAGCACAGTA 59.784 45.833 0.00 0.00 0.00 2.74
1600 1711 2.353208 CCACCAGTAGAACAGAGACAGC 60.353 54.545 0.00 0.00 0.00 4.40
1611 1722 3.911260 TCCAAACATTACCCACCAGTAGA 59.089 43.478 0.00 0.00 0.00 2.59
1636 1747 1.086696 GTACGCCTGCAACATGACAT 58.913 50.000 0.00 0.00 0.00 3.06
1761 1872 3.251571 CGGTTAGCACCTCACTTCTTAC 58.748 50.000 0.00 0.00 41.64 2.34
1781 1892 6.128742 GGGATTGCTATAAATTACCGTACACG 60.129 42.308 0.00 0.00 39.44 4.49
1812 1923 6.647067 GCCTTTGCACTATCCACTAATAGTAG 59.353 42.308 0.00 0.00 39.82 2.57
1814 1925 5.131142 AGCCTTTGCACTATCCACTAATAGT 59.869 40.000 0.00 0.00 41.98 2.12
1966 2084 7.108173 GCAAACATCGTACAAAATTTTTGTTCG 59.892 33.333 31.29 31.29 42.07 3.95
1978 2096 3.738282 GCAAAATGGCAAACATCGTACAA 59.262 39.130 0.00 0.00 39.40 2.41
2147 2270 2.235155 TCACGCCAAGAGCAGGTAATTA 59.765 45.455 0.00 0.00 44.04 1.40
2342 2504 1.847737 AGGTTAATATTGCCCACGGGA 59.152 47.619 6.21 0.00 37.50 5.14
2396 2559 8.830915 TTCTCAGGATTATAGAGACAGAAAGT 57.169 34.615 0.00 0.00 38.07 2.66
2398 2561 9.877178 GTTTTCTCAGGATTATAGAGACAGAAA 57.123 33.333 0.00 0.00 38.07 2.52
2399 2562 9.035890 TGTTTTCTCAGGATTATAGAGACAGAA 57.964 33.333 0.00 0.00 38.07 3.02
2400 2563 8.595362 TGTTTTCTCAGGATTATAGAGACAGA 57.405 34.615 0.00 0.00 38.07 3.41
2401 2564 9.829507 AATGTTTTCTCAGGATTATAGAGACAG 57.170 33.333 0.00 0.00 38.07 3.51
2402 2565 9.823647 GAATGTTTTCTCAGGATTATAGAGACA 57.176 33.333 0.00 0.00 38.07 3.41
2627 2966 3.499338 TCAATCTGCAAAGTGGGTCAAT 58.501 40.909 0.00 0.00 0.00 2.57
2661 3000 0.949397 CAGGATCCAATGTGATGGCG 59.051 55.000 15.82 0.00 40.46 5.69
3084 3423 4.566488 GGGAAATCTGAGAAAGGAGCAAGA 60.566 45.833 0.00 0.00 0.00 3.02
3255 3594 2.672961 TCAGCCTCTGTTTGATACCG 57.327 50.000 0.00 0.00 32.61 4.02
3369 3708 1.144913 TGTCCACCCTTTCCCAAGAAG 59.855 52.381 0.00 0.00 32.35 2.85
3598 3937 1.357761 ACGGACAATTCCCCCAGAAAT 59.642 47.619 0.00 0.00 38.99 2.17
3606 3945 1.064240 ACCCCAATACGGACAATTCCC 60.064 52.381 0.00 0.00 38.99 3.97
3693 4032 4.324267 GCAAGGTGTAAACACTGGTAGAT 58.676 43.478 12.65 0.00 45.73 1.98
3765 4104 6.687744 AGCCTGTCTACCCCAGGATTAAGT 62.688 50.000 10.52 0.00 46.13 2.24
4056 4395 1.032014 TGGGCTTTGAAGTGTCAAGC 58.968 50.000 0.00 0.00 44.49 4.01
4509 4848 1.480954 TCAGGATACCTTCGAAGTGGC 59.519 52.381 23.03 9.69 37.17 5.01
4694 5033 1.359474 ACAGTGCCTCTCTCCCTTCTA 59.641 52.381 0.00 0.00 0.00 2.10
4761 5100 2.675056 GCAGTGTTCAGCAGCCTCG 61.675 63.158 0.00 0.00 0.00 4.63
4779 5118 1.547372 CTGGCCCACTTCCTTTCATTG 59.453 52.381 0.00 0.00 0.00 2.82
4848 5187 6.205658 GCACCATTATTACCTCATTCCTCTTC 59.794 42.308 0.00 0.00 0.00 2.87
4924 5263 8.536407 CAAAAAGTAAAACCACAAATCCGTTAG 58.464 33.333 0.00 0.00 0.00 2.34
4929 5268 6.536941 TCTGCAAAAAGTAAAACCACAAATCC 59.463 34.615 0.00 0.00 0.00 3.01
5086 5425 5.769484 ACATCAGAAAATCATGATCAGGC 57.231 39.130 9.06 0.00 33.91 4.85
5140 5479 6.234177 CAACCATTCAGTAGATAATCCCTCC 58.766 44.000 0.00 0.00 0.00 4.30
5173 5512 0.523072 CATCAAGCACCAAGGTTCCG 59.477 55.000 0.00 0.00 35.33 4.30
5350 5692 2.213499 ACTTCAACTTTCACTGCCTCG 58.787 47.619 0.00 0.00 0.00 4.63
5440 5782 4.143333 ACCGGACAATCCTCGCCG 62.143 66.667 9.46 0.00 43.20 6.46
5507 5849 0.172127 TCTCTGTCATGACGAGCTGC 59.828 55.000 28.03 6.57 34.42 5.25
5567 5909 7.803724 ACCTTTCTGTCACATTTTATTACGAC 58.196 34.615 0.00 0.00 0.00 4.34
5665 6007 5.294552 GGAGGTGAATAAGAAATGGAGAACG 59.705 44.000 0.00 0.00 0.00 3.95
5673 6015 4.860022 CCACAGGGAGGTGAATAAGAAAT 58.140 43.478 0.00 0.00 41.32 2.17
5726 6068 1.515521 CGGCCTCGGAGCAAAAAGTT 61.516 55.000 0.00 0.00 0.00 2.66
5727 6069 1.966451 CGGCCTCGGAGCAAAAAGT 60.966 57.895 0.00 0.00 0.00 2.66
5768 6123 1.127951 GCACATACACAACACTACGGC 59.872 52.381 0.00 0.00 0.00 5.68
5769 6124 2.409012 TGCACATACACAACACTACGG 58.591 47.619 0.00 0.00 0.00 4.02
5770 6125 3.057019 ACTGCACATACACAACACTACG 58.943 45.455 0.00 0.00 0.00 3.51
5771 6126 4.055360 TCACTGCACATACACAACACTAC 58.945 43.478 0.00 0.00 0.00 2.73
5773 6128 3.192541 TCACTGCACATACACAACACT 57.807 42.857 0.00 0.00 0.00 3.55
5774 6129 3.250762 ACATCACTGCACATACACAACAC 59.749 43.478 0.00 0.00 0.00 3.32
5775 6130 3.475575 ACATCACTGCACATACACAACA 58.524 40.909 0.00 0.00 0.00 3.33
5776 6131 5.801350 ATACATCACTGCACATACACAAC 57.199 39.130 0.00 0.00 0.00 3.32
5777 6132 5.936956 TGAATACATCACTGCACATACACAA 59.063 36.000 0.00 0.00 31.50 3.33
5778 6133 5.486526 TGAATACATCACTGCACATACACA 58.513 37.500 0.00 0.00 31.50 3.72
5858 6214 0.382873 CATCATGCATGAACCCACCG 59.617 55.000 31.79 11.42 40.69 4.94
5976 6335 6.364976 GCTGAACACAAATGGTACCAAAATAC 59.635 38.462 20.76 6.69 0.00 1.89
5981 6340 3.561143 AGCTGAACACAAATGGTACCAA 58.439 40.909 20.76 2.16 0.00 3.67
5982 6341 3.222173 AGCTGAACACAAATGGTACCA 57.778 42.857 18.99 18.99 0.00 3.25
5983 6342 5.897377 ATAAGCTGAACACAAATGGTACC 57.103 39.130 4.43 4.43 0.00 3.34
5989 6348 6.514947 TGCTTTGAATAAGCTGAACACAAAT 58.485 32.000 10.46 0.00 43.38 2.32
6018 6377 7.713764 AACTAATCATGCACAAAAAGAAACC 57.286 32.000 0.00 0.00 0.00 3.27
6098 6474 1.909376 CGCACGCTATCTGTAACTGT 58.091 50.000 0.00 0.00 0.00 3.55
6099 6475 0.572590 GCGCACGCTATCTGTAACTG 59.427 55.000 7.96 0.00 38.26 3.16
6100 6476 0.527817 GGCGCACGCTATCTGTAACT 60.528 55.000 15.36 0.00 41.60 2.24
6101 6477 0.527817 AGGCGCACGCTATCTGTAAC 60.528 55.000 15.36 0.00 41.60 2.50
6102 6478 0.248907 GAGGCGCACGCTATCTGTAA 60.249 55.000 15.36 0.00 41.60 2.41
6103 6479 1.359117 GAGGCGCACGCTATCTGTA 59.641 57.895 15.36 0.00 41.60 2.74
6137 6513 1.664659 GAGCGTGCTCTCTACGTAGAA 59.335 52.381 24.66 14.86 43.09 2.10
6154 6530 0.942252 AACGGAACAAACGGAAGAGC 59.058 50.000 0.00 0.00 35.23 4.09
6170 6546 2.549754 AGCAAATCCAACTGACTCAACG 59.450 45.455 0.00 0.00 0.00 4.10
6179 6555 2.381911 CAGGCCATAGCAAATCCAACT 58.618 47.619 5.01 0.00 42.56 3.16
6192 6568 1.227556 GACGTTATCGCCAGGCCAT 60.228 57.895 5.01 0.00 41.18 4.40
6199 6575 1.591863 GGGCAGAGACGTTATCGCC 60.592 63.158 19.47 19.47 41.18 5.54
6272 6648 1.466558 GTACCAGAAAGAAGCTGCTGC 59.533 52.381 1.35 7.62 40.05 5.25
6273 6649 1.728971 CGTACCAGAAAGAAGCTGCTG 59.271 52.381 1.35 0.00 32.06 4.41
6274 6650 1.338200 CCGTACCAGAAAGAAGCTGCT 60.338 52.381 0.00 0.00 32.06 4.24
6307 6683 1.006043 TCCGAATGGGGGTTGCAATTA 59.994 47.619 0.59 0.00 36.01 1.40
6308 6684 0.252012 TCCGAATGGGGGTTGCAATT 60.252 50.000 0.59 0.00 36.01 2.32
6364 6760 2.667969 CAGTCGTTCGATGAGCATTCAA 59.332 45.455 0.00 0.00 36.78 2.69
6390 6786 9.396022 GTCCAAAGAGTTCTTCATATATCCAAA 57.604 33.333 0.00 0.00 34.61 3.28
6402 6798 6.418946 ACTTTTCTCAGTCCAAAGAGTTCTT 58.581 36.000 0.00 0.00 37.91 2.52
6403 6799 5.995446 ACTTTTCTCAGTCCAAAGAGTTCT 58.005 37.500 0.00 0.00 32.73 3.01
6404 6800 6.685527 AACTTTTCTCAGTCCAAAGAGTTC 57.314 37.500 0.00 0.00 32.73 3.01
6406 6802 6.180472 TCAAACTTTTCTCAGTCCAAAGAGT 58.820 36.000 0.00 0.00 32.73 3.24
6417 6815 6.046593 TCTAGCGAGTTTCAAACTTTTCTCA 58.953 36.000 3.76 0.00 43.03 3.27
6420 6818 7.187480 AGTTTCTAGCGAGTTTCAAACTTTTC 58.813 34.615 3.76 0.00 43.03 2.29
6424 6822 6.539103 AGAAAGTTTCTAGCGAGTTTCAAACT 59.461 34.615 16.60 1.21 40.78 2.66
6444 6842 3.393800 ACTGGACGTGTGATTCAGAAAG 58.606 45.455 0.00 0.00 0.00 2.62
6453 6851 2.679450 CGGATAAAACTGGACGTGTGA 58.321 47.619 0.00 0.00 0.00 3.58
6455 6853 1.270412 TGCGGATAAAACTGGACGTGT 60.270 47.619 0.00 0.00 0.00 4.49
6456 6854 1.434555 TGCGGATAAAACTGGACGTG 58.565 50.000 0.00 0.00 0.00 4.49
6458 6856 1.257936 CGATGCGGATAAAACTGGACG 59.742 52.381 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.