Multiple sequence alignment - TraesCS4B01G112600

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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 TraesCS4B01G112600 chr4B 100.000 4981 0 0 1 4981 126601376 126596396 0.000000e+00 9199.0
1 TraesCS4B01G112600 chr4A 93.109 4745 225 47 296 4978 502031621 502026917 0.000000e+00 6857.0
2 TraesCS4B01G112600 chr4A 86.932 176 11 6 125 300 502031838 502031675 2.370000e-43 187.0
3 TraesCS4B01G112600 chr4D 92.792 2081 85 36 2924 4978 89538560 89536519 0.000000e+00 2952.0
4 TraesCS4B01G112600 chr4D 90.603 1990 125 21 4 1971 89541894 89539945 0.000000e+00 2582.0
5 TraesCS4B01G112600 chr4D 88.385 706 67 12 2226 2920 89539360 89538659 0.000000e+00 835.0
6 TraesCS4B01G112600 chr4D 89.720 214 21 1 1985 2198 89539564 89539352 6.350000e-69 272.0
7 TraesCS4B01G112600 chr1B 72.396 797 168 40 3226 3984 491983446 491982664 6.540000e-49 206.0
8 TraesCS4B01G112600 chr3B 77.647 340 61 12 3644 3980 647680708 647681035 5.090000e-45 193.0
9 TraesCS4B01G112600 chr3A 78.086 324 57 8 3661 3980 627864875 627865188 5.090000e-45 193.0
10 TraesCS4B01G112600 chr7D 88.281 128 15 0 3661 3788 412885765 412885638 2.400000e-33 154.0
11 TraesCS4B01G112600 chr7B 87.500 128 16 0 3661 3788 427302946 427302819 1.120000e-31 148.0
12 TraesCS4B01G112600 chr1A 72.183 568 130 21 3226 3776 466928147 466927591 1.120000e-31 148.0
13 TraesCS4B01G112600 chr7A 84.615 143 19 3 3646 3788 474296340 474296201 6.720000e-29 139.0
14 TraesCS4B01G112600 chr5A 94.872 39 2 0 4651 4689 588557354 588557392 1.500000e-05 62.1


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 TraesCS4B01G112600 chr4B 126596396 126601376 4980 True 9199.00 9199 100.0000 1 4981 1 chr4B.!!$R1 4980
1 TraesCS4B01G112600 chr4A 502026917 502031838 4921 True 3522.00 6857 90.0205 125 4978 2 chr4A.!!$R1 4853
2 TraesCS4B01G112600 chr4D 89536519 89541894 5375 True 1660.25 2952 90.3750 4 4978 4 chr4D.!!$R1 4974
3 TraesCS4B01G112600 chr1B 491982664 491983446 782 True 206.00 206 72.3960 3226 3984 1 chr1B.!!$R1 758

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
132 133 0.173481 GGAATTTTGGCTTCTCGGGC 59.827 55.000 0.00 0.00 0.00 6.13 F
247 250 0.320247 CCTGCATCATCCGGTAGAGC 60.320 60.000 0.00 7.26 0.00 4.09 F
387 453 0.322546 AGTGGGATTCCAGCGAAACC 60.323 55.000 4.80 0.00 45.05 3.27 F
538 604 0.965439 TTGGAAAATTGTGGCCCTCG 59.035 50.000 0.00 0.00 0.00 4.63 F
2042 2491 1.140312 AGAGGTGACTGAAAAGCCCA 58.860 50.000 0.00 0.00 44.43 5.36 F
2224 2673 1.476291 GGTCGGTTTCACCACCTTCTT 60.476 52.381 7.09 0.00 38.47 2.52 F
3287 3861 1.133790 CAGCCTCCTTACAATGCAAGC 59.866 52.381 0.00 0.00 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1071 1139 0.992970 TGCCATGGCCCAGAATCCTA 60.993 55.000 33.44 8.21 41.09 2.94 R
2224 2673 1.357137 TCCCACATGTAAGCACAGGA 58.643 50.000 0.00 0.00 38.76 3.86 R
2340 2789 2.034685 TGAGAACGTCTGTTGGAGTCTG 59.965 50.000 0.00 0.00 38.78 3.51 R
2555 3005 7.406553 TGACTTAGACTTGTCAAACGATTTTG 58.593 34.615 8.07 0.00 43.17 2.44 R
2998 3572 0.040514 TGCCATTTTCGACAAGCACG 60.041 50.000 0.00 0.00 0.00 5.34 R
3340 3914 0.884704 GCTGCAAGGAACCTTCGTCA 60.885 55.000 2.84 2.20 33.42 4.35 R
4436 5069 0.039165 GGCTTTGCACTGGTAAGCAC 60.039 55.000 18.92 7.36 44.60 4.40 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
40 41 1.293924 TCGGTAGAGACGACGGATTC 58.706 55.000 0.00 0.00 35.12 2.52
45 46 0.736053 AGAGACGACGGATTCTCAGC 59.264 55.000 14.24 0.00 40.76 4.26
50 51 0.590230 CGACGGATTCTCAGCTCGTC 60.590 60.000 10.79 10.79 44.35 4.20
74 75 2.006415 TCGGGATTTGGGCTGGGAT 61.006 57.895 0.00 0.00 0.00 3.85
86 87 3.764160 CTGGGATTGAGGCGCCTCC 62.764 68.421 44.85 33.38 42.09 4.30
109 110 3.942115 GAGTTGCCTCTTGACCTAATTCC 59.058 47.826 0.00 0.00 34.69 3.01
132 133 0.173481 GGAATTTTGGCTTCTCGGGC 59.827 55.000 0.00 0.00 0.00 6.13
210 211 2.676839 CCAAAGTAGAGCTGATGTGCTG 59.323 50.000 0.00 0.00 44.17 4.41
211 212 2.021355 AAGTAGAGCTGATGTGCTGC 57.979 50.000 0.00 0.00 44.17 5.25
236 239 7.443575 GCTATTTTCTTAGATCTTCCTGCATCA 59.556 37.037 0.00 0.00 0.00 3.07
247 250 0.320247 CCTGCATCATCCGGTAGAGC 60.320 60.000 0.00 7.26 0.00 4.09
263 266 5.415221 GGTAGAGCCAGTTATCATCTATGC 58.585 45.833 0.00 0.00 37.17 3.14
285 288 3.057315 CGTTGATTTATGCATCATCCCCC 60.057 47.826 0.19 0.00 33.07 5.40
289 292 5.218179 TGATTTATGCATCATCCCCCTTTT 58.782 37.500 0.19 0.00 0.00 2.27
327 387 5.185454 TCTGCTTGGTATTGTTGTAGATGG 58.815 41.667 0.00 0.00 0.00 3.51
332 392 7.120579 TGCTTGGTATTGTTGTAGATGGTTTAG 59.879 37.037 0.00 0.00 0.00 1.85
335 395 8.556213 TGGTATTGTTGTAGATGGTTTAGTTC 57.444 34.615 0.00 0.00 0.00 3.01
387 453 0.322546 AGTGGGATTCCAGCGAAACC 60.323 55.000 4.80 0.00 45.05 3.27
393 459 2.159379 GGATTCCAGCGAAACCATGTTC 60.159 50.000 0.00 0.00 39.98 3.18
442 508 4.442706 AGTAAGGTACCGAAATGCTCATG 58.557 43.478 6.18 0.00 0.00 3.07
462 528 3.011818 TGCTGCTGGAAATGTACATCTG 58.988 45.455 9.23 2.42 0.00 2.90
510 576 3.416156 CTGGGGAATTTAGCCAGATAGC 58.584 50.000 0.00 0.00 0.00 2.97
516 582 2.596904 TTTAGCCAGATAGCGTGGAC 57.403 50.000 1.30 0.00 37.23 4.02
534 600 2.547855 GGACTGTTGGAAAATTGTGGCC 60.548 50.000 0.00 0.00 0.00 5.36
535 601 1.416030 ACTGTTGGAAAATTGTGGCCC 59.584 47.619 0.00 0.00 0.00 5.80
536 602 1.693606 CTGTTGGAAAATTGTGGCCCT 59.306 47.619 0.00 0.00 0.00 5.19
537 603 1.691434 TGTTGGAAAATTGTGGCCCTC 59.309 47.619 0.00 0.00 0.00 4.30
538 604 0.965439 TTGGAAAATTGTGGCCCTCG 59.035 50.000 0.00 0.00 0.00 4.63
539 605 1.215382 GGAAAATTGTGGCCCTCGC 59.785 57.895 0.00 0.00 0.00 5.03
558 624 2.094649 CGCCCCTCGAGTTATCTATTCC 60.095 54.545 12.31 0.00 41.67 3.01
591 657 2.936498 GCGAGTAAGCTTTGGATGCTAA 59.064 45.455 3.20 0.00 40.22 3.09
595 661 5.107298 CGAGTAAGCTTTGGATGCTAATAGC 60.107 44.000 3.20 5.12 40.22 2.97
622 688 1.336755 TCTGTTTTGAAAGAAGCGGCC 59.663 47.619 0.00 0.00 0.00 6.13
663 729 6.098409 TCCTGAAGAGTGTTCCCTAACATATC 59.902 42.308 0.00 0.00 46.84 1.63
1360 1428 2.019249 TCAAGCAGGTAATGATGCAGC 58.981 47.619 0.00 0.00 45.01 5.25
1367 1435 4.756642 GCAGGTAATGATGCAGCTATGTTA 59.243 41.667 2.53 0.00 42.11 2.41
1415 1483 2.821546 TCTGGCAATATCGGTTCTTCG 58.178 47.619 0.00 0.00 0.00 3.79
1432 1500 6.093495 GGTTCTTCGATGTTGGATGATTAACA 59.907 38.462 0.00 0.00 40.65 2.41
1485 1553 8.882736 TGTGAGATATCATGAACACAACATAAC 58.117 33.333 5.32 0.00 35.77 1.89
1601 1669 7.190501 GGGATAGATCTACCCAAACCTACTAT 58.809 42.308 24.43 1.17 42.81 2.12
1604 1672 9.536510 GATAGATCTACCCAAACCTACTATCTT 57.463 37.037 4.10 0.00 34.25 2.40
1675 1743 4.584638 TGTTGTATGGGCTATGGACTTT 57.415 40.909 0.00 0.00 0.00 2.66
1682 1750 6.998074 TGTATGGGCTATGGACTTTCATTTAG 59.002 38.462 0.00 0.00 0.00 1.85
1683 1751 5.708736 TGGGCTATGGACTTTCATTTAGA 57.291 39.130 0.00 0.00 0.00 2.10
1734 1802 8.044908 TGTACTTCAAACTTCTGGTTTCTAAGT 58.955 33.333 15.93 15.93 45.26 2.24
1776 1844 4.572389 GTCCTGATGTTATGCTTGTGTAGG 59.428 45.833 0.00 0.00 0.00 3.18
1781 1849 5.423931 TGATGTTATGCTTGTGTAGGGTAGA 59.576 40.000 0.00 0.00 0.00 2.59
1798 1866 9.591792 GTAGGGTAGAAAATTAACAACGATACT 57.408 33.333 0.00 0.00 0.00 2.12
1826 1896 2.112190 TCCATGCGTGTATTGGAGGTA 58.888 47.619 4.96 0.00 34.65 3.08
1930 2012 1.176527 GCCTGCCTCAAACTTGCATA 58.823 50.000 0.00 0.00 33.97 3.14
1962 2044 4.335400 TGTGCAGAACTACAGATTCACA 57.665 40.909 0.00 0.00 0.00 3.58
2042 2491 1.140312 AGAGGTGACTGAAAAGCCCA 58.860 50.000 0.00 0.00 44.43 5.36
2114 2563 7.778382 GTGATATAAATGTTTGGTAGGGGTCTT 59.222 37.037 0.00 0.00 0.00 3.01
2119 2568 2.158726 TGTTTGGTAGGGGTCTTGACAC 60.159 50.000 3.08 0.00 0.00 3.67
2224 2673 1.476291 GGTCGGTTTCACCACCTTCTT 60.476 52.381 7.09 0.00 38.47 2.52
2340 2789 3.837213 AAAGCATACATGTCAGTGCAC 57.163 42.857 24.02 9.40 39.94 4.57
2357 2806 1.806623 GCACAGACTCCAACAGACGTT 60.807 52.381 0.00 0.00 35.01 3.99
2555 3005 2.046892 ATGACACGGAGCACAGCC 60.047 61.111 0.00 0.00 0.00 4.85
2571 3021 3.486841 CACAGCCAAAATCGTTTGACAAG 59.513 43.478 0.81 0.00 45.99 3.16
2602 3052 7.379797 AGTCAACACAATATTATCTGTCGATCG 59.620 37.037 9.36 9.36 0.00 3.69
2622 3072 2.348666 CGGTAGCAATACACTGTTCTGC 59.651 50.000 6.95 6.95 0.00 4.26
2678 3133 1.819632 GCTGGGATGGTTACTGCCG 60.820 63.158 0.00 0.00 0.00 5.69
2685 3140 2.545322 GGATGGTTACTGCCGTACTAGC 60.545 54.545 0.00 0.00 0.00 3.42
3106 3680 4.451774 GCGAACAGTATATCGAGGTCTACT 59.548 45.833 0.00 0.00 41.43 2.57
3287 3861 1.133790 CAGCCTCCTTACAATGCAAGC 59.866 52.381 0.00 0.00 0.00 4.01
3340 3914 6.455690 AAGATTCTACTCCAAGAAAGGGTT 57.544 37.500 0.00 0.00 38.90 4.11
3362 3936 1.165907 CGAAGGTTCCTTGCAGCACA 61.166 55.000 8.95 0.00 0.00 4.57
3461 4035 1.597302 CATCCCTGCCTCATCGCTG 60.597 63.158 0.00 0.00 0.00 5.18
3500 4074 2.586425 CCTTGCCAACCGGATATCATT 58.414 47.619 9.46 0.00 0.00 2.57
3647 4224 2.586792 GGACAGGCCTTGAGCGAT 59.413 61.111 0.00 0.00 45.17 4.58
4042 4643 2.114411 GCTGACCGTCCCCCAAAA 59.886 61.111 0.00 0.00 0.00 2.44
4057 4658 3.449746 CCAAAATTAGGTGGGGACTCA 57.550 47.619 0.00 0.00 0.00 3.41
4066 4667 2.040412 AGGTGGGGACTCAATTCTGTTC 59.960 50.000 0.00 0.00 0.00 3.18
4097 4698 0.251634 TGATGCCATTGCGACTACCA 59.748 50.000 0.00 0.00 41.78 3.25
4131 4732 7.406151 AGGAATTAGAAGGGTTCCTCAGATTTA 59.594 37.037 0.23 0.00 46.63 1.40
4147 4748 7.201758 CCTCAGATTTATGCTGCTGATTTGTTA 60.202 37.037 0.00 0.00 36.85 2.41
4159 4760 7.573843 GCTGCTGATTTGTTATCACTGTACTTT 60.574 37.037 0.00 0.00 0.00 2.66
4175 4776 5.192927 TGTACTTTATCTCCATTGCTTGGG 58.807 41.667 6.44 0.00 46.45 4.12
4188 4789 1.153756 CTTGGGTCCTTGGCTTGGT 59.846 57.895 0.00 0.00 0.00 3.67
4202 4803 0.949105 CTTGGTGACGGCTGTGTACC 60.949 60.000 17.81 17.81 34.22 3.34
4245 4848 2.093711 CCATGGGTGTTCACTGACGATA 60.094 50.000 2.85 0.00 0.00 2.92
4298 4901 6.099341 ACTTGGTGTGTTTGAAATTGAACTC 58.901 36.000 0.00 0.00 0.00 3.01
4384 4987 6.974622 ACTTTGTGTTTGATTGCTTCTAAGTG 59.025 34.615 0.00 0.00 0.00 3.16
4408 5011 1.078426 ACCACACATAAGCTCGGCC 60.078 57.895 0.00 0.00 0.00 6.13
4413 5016 1.097547 CACATAAGCTCGGCCCTTGG 61.098 60.000 0.00 0.00 0.00 3.61
4435 5068 1.856265 CTTGCACTGAACCGGCCTTC 61.856 60.000 0.00 0.00 0.00 3.46
4436 5069 3.423154 GCACTGAACCGGCCTTCG 61.423 66.667 0.00 0.00 38.88 3.79
4437 5070 2.030562 CACTGAACCGGCCTTCGT 59.969 61.111 0.00 0.00 37.11 3.85
4438 5071 2.030562 ACTGAACCGGCCTTCGTG 59.969 61.111 0.00 0.00 37.11 4.35
4439 5072 3.423154 CTGAACCGGCCTTCGTGC 61.423 66.667 0.00 0.00 37.11 5.34
4440 5073 3.883744 CTGAACCGGCCTTCGTGCT 62.884 63.158 0.00 0.00 37.11 4.40
4441 5074 2.668550 GAACCGGCCTTCGTGCTT 60.669 61.111 0.00 0.00 37.11 3.91
4442 5075 1.375013 GAACCGGCCTTCGTGCTTA 60.375 57.895 0.00 0.00 37.11 3.09
4443 5076 1.632948 GAACCGGCCTTCGTGCTTAC 61.633 60.000 0.00 0.00 37.11 2.34
4444 5077 2.818274 CCGGCCTTCGTGCTTACC 60.818 66.667 0.00 0.00 37.11 2.85
4445 5078 2.047655 CGGCCTTCGTGCTTACCA 60.048 61.111 0.00 0.00 0.00 3.25
4446 5079 2.100631 CGGCCTTCGTGCTTACCAG 61.101 63.158 0.00 0.00 0.00 4.00
4447 5080 1.003718 GGCCTTCGTGCTTACCAGT 60.004 57.895 0.00 0.00 0.00 4.00
4448 5081 1.298859 GGCCTTCGTGCTTACCAGTG 61.299 60.000 0.00 0.00 0.00 3.66
4449 5082 1.912371 GCCTTCGTGCTTACCAGTGC 61.912 60.000 0.00 0.00 0.00 4.40
4450 5083 0.602638 CCTTCGTGCTTACCAGTGCA 60.603 55.000 0.00 0.00 36.79 4.57
4451 5084 1.225855 CTTCGTGCTTACCAGTGCAA 58.774 50.000 0.00 0.00 41.10 4.08
4452 5085 1.601903 CTTCGTGCTTACCAGTGCAAA 59.398 47.619 0.00 0.00 41.10 3.68
4491 5124 4.383679 GAAGAAAGATTCGAAAACGACGG 58.616 43.478 0.00 0.00 34.02 4.79
4499 5132 3.220507 TCGAAAACGACGGTGTCATAT 57.779 42.857 3.56 0.00 32.09 1.78
4521 5154 6.808008 ATTATTGTATGTATGTGCAGAGCC 57.192 37.500 0.00 0.00 0.00 4.70
4570 5203 3.044235 AGAGACATTGTCGATGCAACA 57.956 42.857 11.01 0.00 39.47 3.33
4601 5234 2.356665 TGTGGCAAGCAGAAAAGGTA 57.643 45.000 0.00 0.00 0.00 3.08
4609 5242 5.009710 GGCAAGCAGAAAAGGTAGTAAAAGT 59.990 40.000 0.00 0.00 0.00 2.66
4622 5255 7.370383 AGGTAGTAAAAGTGAAATGCATGTTG 58.630 34.615 0.00 0.00 0.00 3.33
4624 5257 7.114811 GGTAGTAAAAGTGAAATGCATGTTGTG 59.885 37.037 0.00 0.00 0.00 3.33
4628 5261 3.719924 AGTGAAATGCATGTTGTGGTTG 58.280 40.909 0.00 0.00 0.00 3.77
4630 5263 3.870419 GTGAAATGCATGTTGTGGTTGTT 59.130 39.130 0.00 0.00 0.00 2.83
4631 5264 4.332268 GTGAAATGCATGTTGTGGTTGTTT 59.668 37.500 0.00 0.00 0.00 2.83
4634 5267 4.879104 ATGCATGTTGTGGTTGTTTTTG 57.121 36.364 0.00 0.00 0.00 2.44
4636 5269 3.006247 GCATGTTGTGGTTGTTTTTGGT 58.994 40.909 0.00 0.00 0.00 3.67
4640 5273 3.071023 TGTTGTGGTTGTTTTTGGTTCCA 59.929 39.130 0.00 0.00 0.00 3.53
4641 5274 4.257731 GTTGTGGTTGTTTTTGGTTCCAT 58.742 39.130 0.00 0.00 0.00 3.41
4642 5275 4.130286 TGTGGTTGTTTTTGGTTCCATC 57.870 40.909 0.00 0.00 0.00 3.51
4643 5276 3.118592 TGTGGTTGTTTTTGGTTCCATCC 60.119 43.478 0.00 0.00 0.00 3.51
4644 5277 3.107601 TGGTTGTTTTTGGTTCCATCCA 58.892 40.909 0.00 0.00 35.49 3.41
4693 5327 5.981174 TCAAGAGATAACGGAACAAAAACG 58.019 37.500 0.00 0.00 0.00 3.60
4697 5331 4.050553 AGATAACGGAACAAAAACGACGA 58.949 39.130 0.00 0.00 0.00 4.20
4699 5333 5.863397 AGATAACGGAACAAAAACGACGATA 59.137 36.000 0.00 0.00 0.00 2.92
4700 5334 4.379374 AACGGAACAAAAACGACGATAG 57.621 40.909 0.00 0.00 46.19 2.08
4702 5336 2.410730 CGGAACAAAAACGACGATAGCT 59.589 45.455 0.00 0.00 42.67 3.32
4703 5337 3.120786 CGGAACAAAAACGACGATAGCTT 60.121 43.478 0.00 0.00 42.67 3.74
4709 5343 5.867716 ACAAAAACGACGATAGCTTGAGTAT 59.132 36.000 0.00 0.00 42.67 2.12
4712 5346 9.177304 CAAAAACGACGATAGCTTGAGTATATA 57.823 33.333 0.00 0.00 42.67 0.86
4713 5347 8.951954 AAAACGACGATAGCTTGAGTATATAG 57.048 34.615 0.00 0.00 42.67 1.31
4714 5348 7.902387 AACGACGATAGCTTGAGTATATAGA 57.098 36.000 0.00 0.00 42.67 1.98
4715 5349 8.495361 AACGACGATAGCTTGAGTATATAGAT 57.505 34.615 0.00 0.00 42.67 1.98
4716 5350 9.597170 AACGACGATAGCTTGAGTATATAGATA 57.403 33.333 0.00 0.00 42.67 1.98
4717 5351 9.251792 ACGACGATAGCTTGAGTATATAGATAG 57.748 37.037 0.00 0.00 42.67 2.08
4718 5352 9.465985 CGACGATAGCTTGAGTATATAGATAGA 57.534 37.037 0.00 0.00 42.67 1.98
4747 5381 9.298774 GAAGAAAGAAAATTAAGCATGGATGAG 57.701 33.333 0.00 0.00 0.00 2.90
4754 5388 6.645790 AATTAAGCATGGATGAGATGAACC 57.354 37.500 0.00 0.00 0.00 3.62
4755 5389 3.657398 AAGCATGGATGAGATGAACCA 57.343 42.857 0.00 0.00 36.83 3.67
4776 5410 3.244814 CAGCTAGCTCATGACATCGAAAC 59.755 47.826 16.15 0.00 0.00 2.78
4781 5422 2.749621 GCTCATGACATCGAAACCCTTT 59.250 45.455 0.00 0.00 0.00 3.11
4802 5443 1.601171 CCTGGAGCAAGACAGAGGG 59.399 63.158 0.00 0.00 36.86 4.30
4907 5548 2.162208 TGCCATCTCGCATCAACTTTTC 59.838 45.455 0.00 0.00 32.62 2.29
4908 5549 2.421424 GCCATCTCGCATCAACTTTTCT 59.579 45.455 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.621991 GAGATCGGCTAAACATGCTAAGA 58.378 43.478 0.00 0.00 0.00 2.10
1 2 3.426859 CGAGATCGGCTAAACATGCTAAG 59.573 47.826 0.00 0.00 35.37 2.18
2 3 3.381045 CGAGATCGGCTAAACATGCTAA 58.619 45.455 0.00 0.00 35.37 3.09
26 27 0.736053 GCTGAGAATCCGTCGTCTCT 59.264 55.000 11.33 1.30 40.82 3.10
34 35 1.941734 GCGACGAGCTGAGAATCCG 60.942 63.158 0.00 0.00 44.04 4.18
45 46 0.736325 AAATCCCGACAAGCGACGAG 60.736 55.000 0.00 0.00 44.57 4.18
50 51 3.051392 GCCCAAATCCCGACAAGCG 62.051 63.158 0.00 0.00 40.47 4.68
56 57 1.580066 AATCCCAGCCCAAATCCCGA 61.580 55.000 0.00 0.00 0.00 5.14
58 59 0.032217 TCAATCCCAGCCCAAATCCC 60.032 55.000 0.00 0.00 0.00 3.85
95 96 2.542550 TCCACGGGAATTAGGTCAAGA 58.457 47.619 0.00 0.00 0.00 3.02
109 110 1.135689 CGAGAAGCCAAAATTCCACGG 60.136 52.381 0.00 0.00 0.00 4.94
123 124 5.723672 TGTAGAATAATAGGCCCGAGAAG 57.276 43.478 0.00 0.00 0.00 2.85
132 133 9.011095 TCACCGAGTTAGATGTAGAATAATAGG 57.989 37.037 0.00 0.00 0.00 2.57
182 183 2.041620 TCAGCTCTACTTTGGGGCAAAT 59.958 45.455 0.00 0.00 32.70 2.32
210 211 7.443575 TGATGCAGGAAGATCTAAGAAAATAGC 59.556 37.037 0.00 0.00 0.00 2.97
211 212 8.899427 TGATGCAGGAAGATCTAAGAAAATAG 57.101 34.615 0.00 0.00 0.00 1.73
217 220 4.021632 CGGATGATGCAGGAAGATCTAAGA 60.022 45.833 0.00 0.00 0.00 2.10
247 250 6.791887 AATCAACGCATAGATGATAACTGG 57.208 37.500 0.00 0.00 40.82 4.00
263 266 3.057315 GGGGGATGATGCATAAATCAACG 60.057 47.826 18.69 0.00 39.90 4.10
293 296 9.461312 AACAATACCAAGCAGAACAAATATAGA 57.539 29.630 0.00 0.00 0.00 1.98
294 297 9.507280 CAACAATACCAAGCAGAACAAATATAG 57.493 33.333 0.00 0.00 0.00 1.31
327 387 5.386729 CGCAAGTACACTACACGAACTAAAC 60.387 44.000 0.00 0.00 0.00 2.01
332 392 2.653890 TCGCAAGTACACTACACGAAC 58.346 47.619 0.00 0.00 39.48 3.95
335 395 3.047796 ACTTTCGCAAGTACACTACACG 58.952 45.455 0.00 0.00 41.81 4.49
387 453 5.061311 CAGCCTAAAAATTGAAGCGAACATG 59.939 40.000 0.00 0.00 0.00 3.21
393 459 3.221964 AGCAGCCTAAAAATTGAAGCG 57.778 42.857 0.00 0.00 0.00 4.68
394 460 8.137437 TCAATATAGCAGCCTAAAAATTGAAGC 58.863 33.333 0.00 0.00 33.29 3.86
442 508 3.012518 ACAGATGTACATTTCCAGCAGC 58.987 45.455 10.30 0.00 0.00 5.25
462 528 5.415077 TGAAGTAGCCACAACTAGAGAGTAC 59.585 44.000 0.00 0.00 33.58 2.73
510 576 3.371168 CACAATTTTCCAACAGTCCACG 58.629 45.455 0.00 0.00 0.00 4.94
516 582 1.693606 AGGGCCACAATTTTCCAACAG 59.306 47.619 6.18 0.00 0.00 3.16
537 603 2.094649 GGAATAGATAACTCGAGGGGCG 60.095 54.545 18.41 0.00 42.69 6.13
538 604 3.166679 AGGAATAGATAACTCGAGGGGC 58.833 50.000 18.41 3.06 0.00 5.80
539 605 4.833380 TCAAGGAATAGATAACTCGAGGGG 59.167 45.833 18.41 0.00 0.00 4.79
540 606 6.597832 ATCAAGGAATAGATAACTCGAGGG 57.402 41.667 18.41 0.00 0.00 4.30
558 624 4.615949 AGCTTACTCGCATGACTATCAAG 58.384 43.478 0.00 0.00 0.00 3.02
591 657 8.506168 TTCTTTCAAAACAGAATATCCGCTAT 57.494 30.769 0.00 0.00 0.00 2.97
595 661 5.734498 CGCTTCTTTCAAAACAGAATATCCG 59.266 40.000 0.00 0.00 0.00 4.18
622 688 6.878317 TCTTCAGGAACACTTATAGGACATG 58.122 40.000 0.00 0.00 0.00 3.21
663 729 9.353999 GGTGGCTTACAACTTTTGATTATAAAG 57.646 33.333 0.00 0.00 38.32 1.85
670 736 3.844640 AGGGTGGCTTACAACTTTTGAT 58.155 40.909 0.00 0.00 36.85 2.57
1071 1139 0.992970 TGCCATGGCCCAGAATCCTA 60.993 55.000 33.44 8.21 41.09 2.94
1173 1241 4.937015 TCAATCACATCTCGAAGCAATTCA 59.063 37.500 0.00 0.00 0.00 2.57
1305 1373 7.410120 AAAAGTGATCTTTCCACAAAACTCT 57.590 32.000 0.00 0.00 42.26 3.24
1367 1435 6.320672 CCAGCAAAGAAGGATAATCTGACATT 59.679 38.462 0.00 0.00 0.00 2.71
1387 1455 1.612676 GATATTGCCAGATGCCAGCA 58.387 50.000 0.00 0.00 40.16 4.41
1485 1553 5.824904 ATTAGAACACATGCTAAAGCTGG 57.175 39.130 3.26 0.00 42.66 4.85
1601 1669 3.769844 CTGAGGTAAGGCAGAGGTAAAGA 59.230 47.826 0.00 0.00 34.06 2.52
1604 1672 2.225547 ACCTGAGGTAAGGCAGAGGTAA 60.226 50.000 0.07 0.00 41.46 2.85
1698 1766 4.051922 AGTTTGAAGTACAGAGAACTGCG 58.948 43.478 0.00 0.00 46.95 5.18
1798 1866 4.155099 CCAATACACGCATGGACTAAAACA 59.845 41.667 0.00 0.00 36.27 2.83
1962 2044 6.551385 CTTTCAAGCAAAGTACAGAGTCAT 57.449 37.500 0.00 0.00 37.33 3.06
2055 2504 5.960105 GTGAAAAAGAGCGATTAGTATGTGC 59.040 40.000 0.00 0.00 0.00 4.57
2114 2563 9.483916 TCTAATTAAAAATGAAGAGACGTGTCA 57.516 29.630 15.80 2.98 0.00 3.58
2224 2673 1.357137 TCCCACATGTAAGCACAGGA 58.643 50.000 0.00 0.00 38.76 3.86
2276 2725 7.275888 ACATCTTTTAAAATCACTGCACAGA 57.724 32.000 4.31 0.00 0.00 3.41
2278 2727 6.265196 AGGACATCTTTTAAAATCACTGCACA 59.735 34.615 0.09 0.00 0.00 4.57
2316 2765 4.759183 TGCACTGACATGTATGCTTTTACA 59.241 37.500 22.64 4.78 38.90 2.41
2323 2772 2.094894 GTCTGTGCACTGACATGTATGC 59.905 50.000 37.29 17.71 42.22 3.14
2325 2774 3.368843 GGAGTCTGTGCACTGACATGTAT 60.369 47.826 40.51 27.91 44.20 2.29
2340 2789 2.034685 TGAGAACGTCTGTTGGAGTCTG 59.965 50.000 0.00 0.00 38.78 3.51
2555 3005 7.406553 TGACTTAGACTTGTCAAACGATTTTG 58.593 34.615 8.07 0.00 43.17 2.44
2586 3036 6.510879 TTGCTACCGATCGACAGATAATAT 57.489 37.500 18.66 0.00 37.19 1.28
2602 3052 3.334691 TGCAGAACAGTGTATTGCTACC 58.665 45.455 24.06 5.05 35.85 3.18
2633 3083 7.270047 TGGGTATGTAAAGTAGTGCAGATAAC 58.730 38.462 0.00 0.00 0.00 1.89
2678 3133 6.844696 TGCAGCAGTAAATATTGCTAGTAC 57.155 37.500 9.70 2.60 45.76 2.73
2685 3140 6.151691 ACACAACTTGCAGCAGTAAATATTG 58.848 36.000 0.00 0.00 0.00 1.90
2998 3572 0.040514 TGCCATTTTCGACAAGCACG 60.041 50.000 0.00 0.00 0.00 5.34
3082 3656 3.211865 AGACCTCGATATACTGTTCGCA 58.788 45.455 0.00 0.00 35.39 5.10
3106 3680 6.493115 ACCTCATTTTTCCAATGTATGTGTCA 59.507 34.615 0.00 0.00 0.00 3.58
3175 3749 9.817809 AGTACGAACATATGTCAGATTAAATGT 57.182 29.630 9.23 0.00 0.00 2.71
3287 3861 1.197721 GTCCCAGAATGCGAAACACTG 59.802 52.381 0.00 0.00 31.97 3.66
3340 3914 0.884704 GCTGCAAGGAACCTTCGTCA 60.885 55.000 2.84 2.20 33.42 4.35
3362 3936 2.896685 GGAGACCTGAGCTATGCTGTAT 59.103 50.000 0.00 0.00 39.88 2.29
3461 4035 3.909086 GACACTGCCACCAGCCTCC 62.909 68.421 0.00 0.00 43.02 4.30
3500 4074 1.969923 TCGTCTAGGGAACGGGAAAAA 59.030 47.619 2.99 0.00 0.00 1.94
3881 4482 5.041191 AGTCCATGGTGAACATATCCTTC 57.959 43.478 12.58 0.00 37.84 3.46
4042 4643 3.852578 ACAGAATTGAGTCCCCACCTAAT 59.147 43.478 0.00 0.00 0.00 1.73
4057 4658 1.873591 GCGACACACAGGAACAGAATT 59.126 47.619 0.00 0.00 0.00 2.17
4066 4667 2.393768 GGCATCAGCGACACACAGG 61.394 63.158 0.00 0.00 43.41 4.00
4097 4698 6.493802 GGAACCCTTCTAATTCCTCAGTTTTT 59.506 38.462 0.00 0.00 39.11 1.94
4131 4732 4.703575 ACAGTGATAACAAATCAGCAGCAT 59.296 37.500 0.00 0.00 0.00 3.79
4147 4748 6.893583 AGCAATGGAGATAAAGTACAGTGAT 58.106 36.000 0.00 0.00 29.56 3.06
4175 4776 1.966451 CCGTCACCAAGCCAAGGAC 60.966 63.158 0.00 0.00 0.00 3.85
4188 4789 1.842052 TATCAGGTACACAGCCGTCA 58.158 50.000 0.00 0.00 0.00 4.35
4202 4803 7.558161 TGGAGTTTGCTCATAACATTATCAG 57.442 36.000 0.00 0.00 43.37 2.90
4245 4848 5.420725 TGTACAGGTCACTCAGCAAATAT 57.579 39.130 0.00 0.00 0.00 1.28
4298 4901 5.255596 CAATGAAGCGTCATAGTTTAACCG 58.744 41.667 15.69 0.00 44.02 4.44
4384 4987 2.622436 GAGCTTATGTGTGGTGACCTC 58.378 52.381 2.11 0.00 0.00 3.85
4408 5011 0.595095 GTTCAGTGCAAGAGCCAAGG 59.405 55.000 0.00 0.00 41.13 3.61
4413 5016 2.970974 GCCGGTTCAGTGCAAGAGC 61.971 63.158 1.90 0.00 42.57 4.09
4414 5017 2.328099 GGCCGGTTCAGTGCAAGAG 61.328 63.158 1.90 0.00 0.00 2.85
4418 5051 2.281484 GAAGGCCGGTTCAGTGCA 60.281 61.111 1.90 0.00 0.00 4.57
4435 5068 0.385974 GCTTTGCACTGGTAAGCACG 60.386 55.000 13.82 0.00 42.84 5.34
4436 5069 0.039165 GGCTTTGCACTGGTAAGCAC 60.039 55.000 18.92 7.36 44.60 4.40
4437 5070 0.178992 AGGCTTTGCACTGGTAAGCA 60.179 50.000 18.92 0.00 44.60 3.91
4438 5071 0.242017 CAGGCTTTGCACTGGTAAGC 59.758 55.000 10.91 10.91 42.65 3.09
4449 5082 0.458669 GGATGTGGATGCAGGCTTTG 59.541 55.000 0.00 0.00 0.00 2.77
4450 5083 1.033746 CGGATGTGGATGCAGGCTTT 61.034 55.000 0.00 0.00 0.00 3.51
4451 5084 1.452651 CGGATGTGGATGCAGGCTT 60.453 57.895 0.00 0.00 0.00 4.35
4452 5085 1.913951 TTCGGATGTGGATGCAGGCT 61.914 55.000 0.00 0.00 0.00 4.58
4462 5095 5.530519 TTTCGAATCTTTCTTCGGATGTG 57.469 39.130 0.00 0.00 46.12 3.21
4499 5132 5.679601 TGGCTCTGCACATACATACAATAA 58.320 37.500 0.00 0.00 0.00 1.40
4552 5185 1.806542 GGTGTTGCATCGACAATGTCT 59.193 47.619 11.92 0.00 37.71 3.41
4558 5191 2.139917 GTAACAGGTGTTGCATCGACA 58.860 47.619 5.59 0.00 39.84 4.35
4570 5203 2.100749 GCTTGCCACAAAAGTAACAGGT 59.899 45.455 0.00 0.00 0.00 4.00
4601 5234 5.984926 CCACAACATGCATTTCACTTTTACT 59.015 36.000 0.00 0.00 0.00 2.24
4609 5242 3.815856 ACAACCACAACATGCATTTCA 57.184 38.095 0.00 0.00 0.00 2.69
4622 5255 3.118592 TGGATGGAACCAAAAACAACCAC 60.119 43.478 0.00 0.00 36.96 4.16
4624 5257 3.828875 TGGATGGAACCAAAAACAACC 57.171 42.857 0.00 0.00 36.96 3.77
4652 5285 2.759355 TGATAGTGGAACCGGATCCTT 58.241 47.619 28.84 19.69 40.35 3.36
4653 5286 2.471815 TGATAGTGGAACCGGATCCT 57.528 50.000 28.84 14.25 40.35 3.24
4659 5292 4.976731 CGTTATCTCTTGATAGTGGAACCG 59.023 45.833 0.00 0.00 36.62 4.44
4669 5302 6.425721 TCGTTTTTGTTCCGTTATCTCTTGAT 59.574 34.615 0.00 0.00 36.74 2.57
4720 5354 9.028284 TCATCCATGCTTAATTTTCTTTCTTCT 57.972 29.630 0.00 0.00 0.00 2.85
4721 5355 9.298774 CTCATCCATGCTTAATTTTCTTTCTTC 57.701 33.333 0.00 0.00 0.00 2.87
4722 5356 9.028284 TCTCATCCATGCTTAATTTTCTTTCTT 57.972 29.630 0.00 0.00 0.00 2.52
4743 5377 3.036819 TGAGCTAGCTGGTTCATCTCAT 58.963 45.455 24.99 0.00 0.00 2.90
4747 5381 3.129871 GTCATGAGCTAGCTGGTTCATC 58.870 50.000 24.99 11.99 35.53 2.92
4754 5388 2.789491 TCGATGTCATGAGCTAGCTG 57.211 50.000 24.99 9.28 0.00 4.24
4755 5389 3.452474 GTTTCGATGTCATGAGCTAGCT 58.548 45.455 19.45 19.45 0.00 3.32
4776 5410 1.000396 CTTGCTCCAGGGGAAAGGG 60.000 63.158 0.00 0.00 0.00 3.95
4781 5422 0.906756 CTCTGTCTTGCTCCAGGGGA 60.907 60.000 0.00 0.00 0.00 4.81
4907 5548 2.449137 AATTCCTTGATGCTCCCCAG 57.551 50.000 0.00 0.00 0.00 4.45
4908 5549 2.312741 AGAAATTCCTTGATGCTCCCCA 59.687 45.455 0.00 0.00 0.00 4.96


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

AutoCloner maintained by Alex Coulton.