Multiple sequence alignment - TraesCS6B01G109400

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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 TraesCS6B01G109400 chr6B 100.000 5414 0 0 1 5414 90276740 90282153 0.000000e+00 9998.0
1 TraesCS6B01G109400 chr6B 85.789 760 66 22 987 1742 418139595 418140316 0.000000e+00 767.0
2 TraesCS6B01G109400 chr6D 91.754 4778 247 53 148 4856 38883744 38888443 0.000000e+00 6505.0
3 TraesCS6B01G109400 chr6D 90.045 221 18 4 5042 5259 38894590 38894809 3.190000e-72 283.0
4 TraesCS6B01G109400 chr6D 92.188 128 9 1 4918 5044 38888880 38889007 4.310000e-41 180.0
5 TraesCS6B01G109400 chr6D 88.889 90 9 1 22 110 38882962 38883051 5.730000e-20 110.0
6 TraesCS6B01G109400 chr6A 88.531 3418 249 68 1 3355 51405270 51408607 0.000000e+00 4008.0
7 TraesCS6B01G109400 chr6A 90.148 1350 90 12 3570 4895 51408759 51410089 0.000000e+00 1716.0
8 TraesCS6B01G109400 chr6A 94.567 497 26 1 4918 5414 51410154 51410649 0.000000e+00 767.0
9 TraesCS6B01G109400 chr5B 86.579 760 60 18 987 1742 711517458 711516737 0.000000e+00 800.0
10 TraesCS6B01G109400 chr7B 86.053 760 64 17 987 1742 20987924 20987203 0.000000e+00 778.0
11 TraesCS6B01G109400 chr7B 97.436 39 1 0 5251 5289 139609481 139609519 3.500000e-07 67.6
12 TraesCS6B01G109400 chr4B 83.548 620 50 26 987 1602 233161512 233160941 2.870000e-147 532.0
13 TraesCS6B01G109400 chr1B 85.033 461 44 11 987 1445 128661515 128661952 3.850000e-121 446.0
14 TraesCS6B01G109400 chr1B 83.077 260 34 6 1491 1742 128661963 128662220 1.520000e-55 228.0
15 TraesCS6B01G109400 chr4D 97.436 39 1 0 5251 5289 27578933 27578895 3.500000e-07 67.6
16 TraesCS6B01G109400 chr4D 95.000 40 1 1 5251 5289 123351241 123351280 1.630000e-05 62.1
17 TraesCS6B01G109400 chr4D 95.000 40 1 1 5251 5289 123562179 123562218 1.630000e-05 62.1
18 TraesCS6B01G109400 chr4D 95.000 40 1 1 5251 5289 134980542 134980581 1.630000e-05 62.1
19 TraesCS6B01G109400 chr4D 95.000 40 1 1 5251 5289 240993661 240993622 1.630000e-05 62.1
20 TraesCS6B01G109400 chr4D 95.000 40 1 1 5251 5289 450897073 450897034 1.630000e-05 62.1
21 TraesCS6B01G109400 chrUn 95.000 40 1 1 5251 5289 417899727 417899766 1.630000e-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 TraesCS6B01G109400 chr6B 90276740 90282153 5413 False 9998.000000 9998 100.000000 1 5414 1 chr6B.!!$F1 5413
1 TraesCS6B01G109400 chr6B 418139595 418140316 721 False 767.000000 767 85.789000 987 1742 1 chr6B.!!$F2 755
2 TraesCS6B01G109400 chr6D 38882962 38889007 6045 False 2265.000000 6505 90.943667 22 5044 3 chr6D.!!$F2 5022
3 TraesCS6B01G109400 chr6A 51405270 51410649 5379 False 2163.666667 4008 91.082000 1 5414 3 chr6A.!!$F1 5413
4 TraesCS6B01G109400 chr5B 711516737 711517458 721 True 800.000000 800 86.579000 987 1742 1 chr5B.!!$R1 755
5 TraesCS6B01G109400 chr7B 20987203 20987924 721 True 778.000000 778 86.053000 987 1742 1 chr7B.!!$R1 755
6 TraesCS6B01G109400 chr4B 233160941 233161512 571 True 532.000000 532 83.548000 987 1602 1 chr4B.!!$R1 615
7 TraesCS6B01G109400 chr1B 128661515 128662220 705 False 337.000000 446 84.055000 987 1742 2 chr1B.!!$F1 755

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
20 21 0.826062 GTATTTCCGGACGGAGGGAA 59.174 55.0 13.64 6.2 46.06 3.97 F
1365 2073 0.882484 TCGTTGAAATGCGTGCCTGA 60.882 50.0 0.00 0.0 0.00 3.86 F
2999 3741 0.397564 TGGGTTTGAACTCCGTACCC 59.602 55.0 0.00 0.0 46.98 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 2236 0.035458 CCAGAGGTTCACCAGGTCAC 59.965 60.0 0.00 0.00 38.89 3.67 R
3001 3743 0.524414 TAGTCATGACACGTGGTCCG 59.476 55.0 27.02 5.73 46.38 4.79 R
4858 5932 0.179108 GTGTGTATCGCCTCTGACCC 60.179 60.0 0.00 0.00 0.00 4.46 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
20 21 0.826062 GTATTTCCGGACGGAGGGAA 59.174 55.000 13.64 6.20 46.06 3.97
87 90 1.413077 GGATAGGGTGAGAGGTTTCCG 59.587 57.143 0.00 0.00 0.00 4.30
94 97 2.224354 GGTGAGAGGTTTCCGTTTGGTA 60.224 50.000 0.00 0.00 36.30 3.25
95 98 3.558533 GGTGAGAGGTTTCCGTTTGGTAT 60.559 47.826 0.00 0.00 36.30 2.73
99 102 4.828829 AGAGGTTTCCGTTTGGTATAGTG 58.171 43.478 0.00 0.00 36.30 2.74
102 105 3.126343 GGTTTCCGTTTGGTATAGTGCAG 59.874 47.826 0.00 0.00 36.30 4.41
104 107 1.014352 CCGTTTGGTATAGTGCAGGC 58.986 55.000 0.00 0.00 0.00 4.85
105 108 1.014352 CGTTTGGTATAGTGCAGGCC 58.986 55.000 0.00 0.00 0.00 5.19
106 109 1.677518 CGTTTGGTATAGTGCAGGCCA 60.678 52.381 5.01 0.00 0.00 5.36
107 110 2.654863 GTTTGGTATAGTGCAGGCCAT 58.345 47.619 5.01 0.00 0.00 4.40
108 111 3.742954 CGTTTGGTATAGTGCAGGCCATA 60.743 47.826 5.01 0.00 0.00 2.74
109 112 3.485463 TTGGTATAGTGCAGGCCATAC 57.515 47.619 5.01 2.47 0.00 2.39
120 123 1.000955 CAGGCCATACCCATACTCGAC 59.999 57.143 5.01 0.00 40.58 4.20
126 129 4.870426 GCCATACCCATACTCGACATAATG 59.130 45.833 0.00 0.00 0.00 1.90
129 132 6.464222 CATACCCATACTCGACATAATGGTT 58.536 40.000 8.82 0.11 37.73 3.67
168 832 9.236006 GAGCATGGTATACTTTAAATCATGGAT 57.764 33.333 14.09 0.00 33.34 3.41
182 846 5.859205 ATCATGGATAAAGTGGAAAAGGC 57.141 39.130 0.00 0.00 0.00 4.35
188 852 1.170290 AAAGTGGAAAAGGCCGACGG 61.170 55.000 10.29 10.29 0.00 4.79
201 865 1.134907 GCCGACGGATGGACTTTTCTA 60.135 52.381 20.50 0.00 0.00 2.10
209 873 8.231837 CGACGGATGGACTTTTCTAATTTTTAA 58.768 33.333 0.00 0.00 0.00 1.52
250 914 6.496571 TGTTGGTAAAATCAACACGGTAAAG 58.503 36.000 1.68 0.00 46.29 1.85
261 925 4.081322 ACACGGTAAAGTCCACATTTCT 57.919 40.909 0.00 0.00 0.00 2.52
268 932 7.229907 ACGGTAAAGTCCACATTTCTACATTTT 59.770 33.333 0.00 0.00 0.00 1.82
269 933 7.749126 CGGTAAAGTCCACATTTCTACATTTTC 59.251 37.037 0.00 0.00 0.00 2.29
276 940 5.346822 CCACATTTCTACATTTTCTTGCAGC 59.653 40.000 0.00 0.00 0.00 5.25
293 957 1.862123 GCATATGTGCCGTGGATCG 59.138 57.895 2.47 0.00 45.76 3.69
312 976 3.185651 CGATCATCGCAATCGGACT 57.814 52.632 0.00 0.00 41.71 3.85
317 981 3.726291 TCATCGCAATCGGACTATTCA 57.274 42.857 0.00 0.00 36.13 2.57
327 991 7.195646 GCAATCGGACTATTCATTTCATCAAA 58.804 34.615 0.00 0.00 0.00 2.69
328 992 7.377928 GCAATCGGACTATTCATTTCATCAAAG 59.622 37.037 0.00 0.00 0.00 2.77
329 993 8.615211 CAATCGGACTATTCATTTCATCAAAGA 58.385 33.333 0.00 0.00 0.00 2.52
366 1039 6.919721 AGCGTGTTACACATTTTTATGGAAT 58.080 32.000 16.09 0.00 33.40 3.01
367 1040 7.375053 AGCGTGTTACACATTTTTATGGAATT 58.625 30.769 16.09 0.00 33.40 2.17
404 1077 7.957484 CACTTGATTGTTATAAAGACTGAACGG 59.043 37.037 0.00 0.00 0.00 4.44
421 1097 6.127310 ACTGAACGGCATTTCTTAGTCTCTAT 60.127 38.462 0.00 0.00 0.00 1.98
422 1098 6.042777 TGAACGGCATTTCTTAGTCTCTATG 58.957 40.000 0.00 0.00 0.00 2.23
429 1105 7.051000 GCATTTCTTAGTCTCTATGGAAAGGT 58.949 38.462 0.00 0.00 30.58 3.50
511 1187 4.202609 ACACCCATCTGAAAATGACTCCTT 60.203 41.667 0.00 0.00 0.00 3.36
535 1212 2.288395 CCAACACTGAATTGACCCAAGC 60.288 50.000 0.00 0.00 0.00 4.01
559 1236 7.015098 AGCTCATACTATAGCAGTCAATGTTCT 59.985 37.037 0.00 0.00 41.32 3.01
560 1237 7.655328 GCTCATACTATAGCAGTCAATGTTCTT 59.345 37.037 0.00 0.00 38.80 2.52
566 1243 3.604582 AGCAGTCAATGTTCTTCTAGCC 58.395 45.455 0.00 0.00 0.00 3.93
567 1244 2.349886 GCAGTCAATGTTCTTCTAGCCG 59.650 50.000 0.00 0.00 0.00 5.52
582 1259 6.876789 TCTTCTAGCCGTTTTTATGTCATTCA 59.123 34.615 0.00 0.00 0.00 2.57
588 1265 5.627172 CCGTTTTTATGTCATTCACATCGT 58.373 37.500 0.00 0.00 42.62 3.73
589 1266 6.083630 CCGTTTTTATGTCATTCACATCGTT 58.916 36.000 0.00 0.00 42.62 3.85
590 1267 6.248420 CCGTTTTTATGTCATTCACATCGTTC 59.752 38.462 0.00 0.00 42.62 3.95
591 1268 7.015289 CGTTTTTATGTCATTCACATCGTTCT 58.985 34.615 0.00 0.00 42.62 3.01
595 1272 7.665561 TTATGTCATTCACATCGTTCTGAAA 57.334 32.000 0.00 0.00 42.62 2.69
596 1273 5.596268 TGTCATTCACATCGTTCTGAAAG 57.404 39.130 0.00 0.00 30.32 2.62
601 1280 5.907197 TTCACATCGTTCTGAAAGTCTTC 57.093 39.130 3.36 0.00 33.76 2.87
603 1282 4.039245 TCACATCGTTCTGAAAGTCTTCCT 59.961 41.667 3.36 0.00 33.76 3.36
913 1608 1.065102 CGAGTCTTTAATCCTCGCCGA 59.935 52.381 6.16 0.00 41.21 5.54
938 1635 2.418083 GCAAAGCCTCCCCCATTCG 61.418 63.158 0.00 0.00 0.00 3.34
970 1667 3.869272 GCAATCCACAGCTCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
1296 2003 3.847602 CGGCAGGAGCAGGAGGAG 61.848 72.222 0.00 0.00 44.61 3.69
1299 2006 2.433994 GCAGGAGCAGGAGGAGGAG 61.434 68.421 0.00 0.00 41.58 3.69
1365 2073 0.882484 TCGTTGAAATGCGTGCCTGA 60.882 50.000 0.00 0.00 0.00 3.86
1380 2088 2.158623 TGCCTGATTCTTCTTGGTGTGT 60.159 45.455 0.00 0.00 0.00 3.72
1395 2103 2.039348 GGTGTGTGGGGAGTAGCTTTTA 59.961 50.000 0.00 0.00 0.00 1.52
1458 2166 2.979649 GGTCTTCGACCCCTGACC 59.020 66.667 1.55 0.00 46.19 4.02
1459 2167 1.609794 GGTCTTCGACCCCTGACCT 60.610 63.158 1.55 0.00 46.19 3.85
1460 2168 1.592223 GTCTTCGACCCCTGACCTG 59.408 63.158 0.00 0.00 0.00 4.00
1528 2236 4.785453 GCTGGCGGTGGGGAAGAG 62.785 72.222 0.00 0.00 0.00 2.85
1643 2358 2.444895 GCGTGGAGGAGGGATCCT 60.445 66.667 12.58 0.00 44.06 3.24
1696 2411 7.390440 TGATTGGGTTCTCTTATACTTGTTGTG 59.610 37.037 0.00 0.00 0.00 3.33
1700 2415 6.708949 GGGTTCTCTTATACTTGTTGTGTGAA 59.291 38.462 0.00 0.00 0.00 3.18
1703 2418 9.472361 GTTCTCTTATACTTGTTGTGTGAAGTA 57.528 33.333 0.00 0.00 38.65 2.24
1704 2419 9.472361 TTCTCTTATACTTGTTGTGTGAAGTAC 57.528 33.333 0.00 0.00 37.46 2.73
1705 2420 8.857098 TCTCTTATACTTGTTGTGTGAAGTACT 58.143 33.333 0.00 0.00 37.46 2.73
1706 2421 8.812147 TCTTATACTTGTTGTGTGAAGTACTG 57.188 34.615 0.00 0.00 37.46 2.74
1707 2422 8.635328 TCTTATACTTGTTGTGTGAAGTACTGA 58.365 33.333 0.00 0.00 37.46 3.41
1708 2423 9.424319 CTTATACTTGTTGTGTGAAGTACTGAT 57.576 33.333 0.00 0.00 37.46 2.90
1919 2634 1.967066 CTGGAGGAGTGTCAGACAACT 59.033 52.381 4.32 5.11 0.00 3.16
1981 2696 5.453903 GCCTTGAGATGGTGAATTAGCTCTA 60.454 44.000 0.00 0.00 31.00 2.43
1985 2700 7.187824 TGAGATGGTGAATTAGCTCTAAGTT 57.812 36.000 0.00 0.00 31.00 2.66
2013 2728 5.171339 AGGTTGTCACTTCATGCTTATCT 57.829 39.130 0.00 0.00 0.00 1.98
2017 2732 7.665559 AGGTTGTCACTTCATGCTTATCTTTTA 59.334 33.333 0.00 0.00 0.00 1.52
2018 2733 8.462016 GGTTGTCACTTCATGCTTATCTTTTAT 58.538 33.333 0.00 0.00 0.00 1.40
2030 2745 8.798859 TGCTTATCTTTTATTCTCTCTTGCTT 57.201 30.769 0.00 0.00 0.00 3.91
2162 2877 8.565896 TTACTAGTGTTCATCAATGATGCTTT 57.434 30.769 17.81 4.93 39.63 3.51
2167 2882 6.208007 AGTGTTCATCAATGATGCTTTCTTCA 59.792 34.615 17.81 6.54 39.63 3.02
2171 2886 9.577110 GTTCATCAATGATGCTTTCTTCAATTA 57.423 29.630 17.81 0.00 39.63 1.40
2174 2889 8.978539 CATCAATGATGCTTTCTTCAATTATGG 58.021 33.333 10.55 0.00 33.17 2.74
2231 2946 1.366679 AGCATCTGATGTTGCTGACG 58.633 50.000 18.19 0.00 44.68 4.35
2273 2988 4.397103 AGTTACATCACTGCAATGTCCATG 59.603 41.667 5.79 0.06 38.31 3.66
2280 2995 4.157105 TCACTGCAATGTCCATGATTCAAG 59.843 41.667 0.00 0.00 0.00 3.02
2284 2999 5.231702 TGCAATGTCCATGATTCAAGTTTG 58.768 37.500 0.00 0.00 0.00 2.93
2289 3004 5.953183 TGTCCATGATTCAAGTTTGTATGC 58.047 37.500 0.00 0.00 0.00 3.14
2378 3093 5.308497 TCCAAAATACAAGGGACTAGTGTGA 59.692 40.000 0.00 0.00 38.49 3.58
2379 3094 6.001460 CCAAAATACAAGGGACTAGTGTGAA 58.999 40.000 0.00 0.00 38.49 3.18
2380 3095 6.149474 CCAAAATACAAGGGACTAGTGTGAAG 59.851 42.308 0.00 0.00 38.49 3.02
2499 3215 3.618690 ACTCAGTTCAGAATAGGCACC 57.381 47.619 0.00 0.00 0.00 5.01
2504 3220 2.500098 AGTTCAGAATAGGCACCGCTAA 59.500 45.455 0.00 0.00 0.00 3.09
2519 3235 7.068226 AGGCACCGCTAAGTAAATTTAATGATT 59.932 33.333 0.00 0.00 0.00 2.57
2581 3320 6.379133 ACGTATGGTAACTTGGTAAGATCAGA 59.621 38.462 0.00 0.00 37.61 3.27
2693 3432 6.176183 CCAGGACAGACTTCTAACATCATTT 58.824 40.000 0.00 0.00 0.00 2.32
2845 3585 4.757019 TGGTAACCACACAGTACAAAGA 57.243 40.909 0.00 0.00 0.00 2.52
2846 3586 4.699637 TGGTAACCACACAGTACAAAGAG 58.300 43.478 0.00 0.00 0.00 2.85
2873 3614 6.583050 CGAAGAAACTAGGAAGAGTTGTACAG 59.417 42.308 0.00 0.00 39.62 2.74
2945 3686 3.646534 TCCATGCTGTCTTCCTCATCTA 58.353 45.455 0.00 0.00 0.00 1.98
2993 3735 2.105993 AGTACCTGTGGGTTTGAACTCC 59.894 50.000 0.00 0.00 44.73 3.85
2999 3741 0.397564 TGGGTTTGAACTCCGTACCC 59.602 55.000 0.00 0.00 46.98 3.69
3000 3742 0.671472 GGGTTTGAACTCCGTACCCG 60.671 60.000 0.00 0.00 39.11 5.28
3001 3743 1.293963 GGTTTGAACTCCGTACCCGC 61.294 60.000 0.00 0.00 0.00 6.13
3108 3850 8.472413 ACTTATCACGTGCCTTATAGAAAGTTA 58.528 33.333 11.67 0.00 0.00 2.24
3137 3879 6.974622 GCATACTATTGTTTCCTTTGACATGG 59.025 38.462 0.00 0.00 0.00 3.66
3211 3953 4.855298 TTCCTATCTTTAACCACCCCTG 57.145 45.455 0.00 0.00 0.00 4.45
3231 3973 3.088532 TGTGCACCCAGTTATTCATTCC 58.911 45.455 15.69 0.00 0.00 3.01
3380 4124 9.927081 ATCAGTTATGTAATTCTGATTTCCCTT 57.073 29.630 0.00 0.00 40.90 3.95
3404 4148 8.713708 TTAAAGGAATGGTTTAGATTTGGTGA 57.286 30.769 0.00 0.00 0.00 4.02
3415 4159 8.793592 GGTTTAGATTTGGTGAATAACAAGTCT 58.206 33.333 7.95 7.95 43.28 3.24
3416 4160 9.612620 GTTTAGATTTGGTGAATAACAAGTCTG 57.387 33.333 11.75 0.00 41.68 3.51
3533 4279 6.633500 AGCATGACTTTAAAACTAGTGCAA 57.367 33.333 0.00 0.00 0.00 4.08
3552 4298 7.639945 AGTGCAAAACAGTAGAGTGAAATAAC 58.360 34.615 0.00 0.00 0.00 1.89
3557 4303 9.651718 CAAAACAGTAGAGTGAAATAACTTGTC 57.348 33.333 0.00 0.00 0.00 3.18
3558 4304 7.964604 AACAGTAGAGTGAAATAACTTGTCC 57.035 36.000 0.00 0.00 0.00 4.02
3613 4380 1.800586 AGAACATGTCGATGTGCACAC 59.199 47.619 24.37 14.98 42.30 3.82
3620 4389 3.175929 TGTCGATGTGCACACGTATTAG 58.824 45.455 28.29 13.95 0.00 1.73
3622 4391 2.164827 TCGATGTGCACACGTATTAGGT 59.835 45.455 28.29 11.51 0.00 3.08
3623 4392 3.377798 TCGATGTGCACACGTATTAGGTA 59.622 43.478 28.29 13.20 0.00 3.08
3629 4398 5.806502 TGTGCACACGTATTAGGTATACAAC 59.193 40.000 17.42 0.00 39.29 3.32
3647 4421 4.973168 ACAACTTACATCCTCTTGCTCAA 58.027 39.130 0.00 0.00 0.00 3.02
3788 4564 3.865571 ACCACTTCCCTTCACTACCTTA 58.134 45.455 0.00 0.00 0.00 2.69
3794 4570 3.869065 TCCCTTCACTACCTTATTTGCG 58.131 45.455 0.00 0.00 0.00 4.85
3810 4586 2.579207 TGCGTATGAGTGGTAAGAGC 57.421 50.000 0.00 0.00 0.00 4.09
3884 4662 7.869429 ACATGACATGAGAAAGGAACAAAAATC 59.131 33.333 22.19 0.00 0.00 2.17
4002 4783 0.976641 TGGAGTCAAGACGAGGCAAT 59.023 50.000 0.00 0.00 36.20 3.56
4146 4927 0.980754 TCCGGGCCTATCAGAAAGCA 60.981 55.000 0.84 0.00 0.00 3.91
4170 4951 3.650950 GCTGGGGAGCCACCTTCA 61.651 66.667 0.00 0.00 38.98 3.02
4172 4953 2.121963 TGGGGAGCCACCTTCACT 60.122 61.111 0.00 0.00 38.98 3.41
4554 5338 0.179936 GGCAGTTGATGAGAGAGGGG 59.820 60.000 0.00 0.00 0.00 4.79
4839 5630 7.354025 CACGTAGATGTGGTACAAAACATTA 57.646 36.000 8.83 3.20 44.16 1.90
4876 5952 0.613572 TGGGTCAGAGGCGATACACA 60.614 55.000 0.00 0.00 0.00 3.72
4877 5953 0.179108 GGGTCAGAGGCGATACACAC 60.179 60.000 0.00 0.00 0.00 3.82
4901 6010 9.853555 CACTGATAATTTTGTTTGCTATGGTTA 57.146 29.630 0.00 0.00 0.00 2.85
4956 6124 5.404946 TGTTCTTTACGGAGTATGTAGTGC 58.595 41.667 0.00 0.00 45.21 4.40
5082 6251 0.036732 TGGAACATCAGTGTCTGGCC 59.963 55.000 0.00 0.00 37.67 5.36
5148 6317 2.496470 CCTGGGAAGTAGGAGTACACAC 59.504 54.545 0.00 0.00 37.52 3.82
5233 6402 5.070001 TGGTTCTTCAGTTGGACTAATTGG 58.930 41.667 0.00 0.00 0.00 3.16
5236 6405 6.040504 GGTTCTTCAGTTGGACTAATTGGTTT 59.959 38.462 0.00 0.00 0.00 3.27
5237 6406 6.633500 TCTTCAGTTGGACTAATTGGTTTG 57.367 37.500 0.00 0.00 0.00 2.93
5297 6466 4.237724 GCCATTTTAGGTTTCAGCTTGAC 58.762 43.478 0.00 0.00 0.00 3.18
5312 6481 8.994429 TTCAGCTTGACATTTTGTTTTCTTAA 57.006 26.923 0.00 0.00 0.00 1.85
5336 6505 7.598189 AAAGGAAAGTAAAATAGAGACGAGC 57.402 36.000 0.00 0.00 0.00 5.03
5363 6532 2.727103 TTTTTCCCTCACAAGGCGG 58.273 52.632 0.00 0.00 41.85 6.13
5391 6560 2.757894 AAGCCTTCCTCCTCTCGATA 57.242 50.000 0.00 0.00 0.00 2.92
5395 6564 2.819726 GCCTTCCTCCTCTCGATATCCA 60.820 54.545 0.00 0.00 0.00 3.41
5396 6565 2.823154 CCTTCCTCCTCTCGATATCCAC 59.177 54.545 0.00 0.00 0.00 4.02
5407 6576 0.946221 GATATCCACCGGCGAGCTTG 60.946 60.000 9.30 0.00 0.00 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.826062 GTATTCCCTCCGTCCGGAAA 59.174 55.000 5.23 1.92 44.66 3.13
8 9 1.242076 ATACGTATTCCCTCCGTCCG 58.758 55.000 1.14 0.00 36.12 4.79
10 11 3.800506 CACAAATACGTATTCCCTCCGTC 59.199 47.826 20.57 0.00 36.12 4.79
20 21 7.284716 TCACTCTATCCACTCACAAATACGTAT 59.715 37.037 1.14 1.14 0.00 3.06
87 90 2.122783 TGGCCTGCACTATACCAAAC 57.877 50.000 3.32 0.00 0.00 2.93
94 97 1.449271 ATGGGTATGGCCTGCACTAT 58.551 50.000 3.32 0.00 37.43 2.12
95 98 1.697432 GTATGGGTATGGCCTGCACTA 59.303 52.381 3.32 0.00 37.43 2.74
99 102 0.320771 CGAGTATGGGTATGGCCTGC 60.321 60.000 3.32 0.00 37.43 4.85
102 105 1.045407 TGTCGAGTATGGGTATGGCC 58.955 55.000 0.00 0.00 0.00 5.36
104 107 5.046591 ACCATTATGTCGAGTATGGGTATGG 60.047 44.000 15.43 10.08 41.45 2.74
105 108 6.037786 ACCATTATGTCGAGTATGGGTATG 57.962 41.667 15.43 1.75 41.45 2.39
106 109 6.497259 AGAACCATTATGTCGAGTATGGGTAT 59.503 38.462 15.43 7.02 38.18 2.73
107 110 5.836898 AGAACCATTATGTCGAGTATGGGTA 59.163 40.000 15.43 0.00 38.18 3.69
108 111 4.654262 AGAACCATTATGTCGAGTATGGGT 59.346 41.667 15.43 10.99 40.69 4.51
109 112 5.011125 AGAGAACCATTATGTCGAGTATGGG 59.989 44.000 15.43 4.34 41.45 4.00
168 832 1.515081 CGTCGGCCTTTTCCACTTTA 58.485 50.000 0.00 0.00 0.00 1.85
180 844 1.366854 GAAAAGTCCATCCGTCGGCC 61.367 60.000 6.34 0.00 0.00 6.13
182 846 2.953466 TAGAAAAGTCCATCCGTCGG 57.047 50.000 4.39 4.39 0.00 4.79
201 865 9.918630 CAGGTTGATCTTGACTCATTAAAAATT 57.081 29.630 0.00 0.00 0.00 1.82
209 873 4.202503 ACCAACAGGTTGATCTTGACTCAT 60.203 41.667 13.47 0.00 42.93 2.90
218 882 6.744112 TGTTGATTTTACCAACAGGTTGATC 58.256 36.000 13.47 8.38 46.03 2.92
234 898 4.200874 TGTGGACTTTACCGTGTTGATTT 58.799 39.130 0.00 0.00 0.00 2.17
250 914 6.446318 TGCAAGAAAATGTAGAAATGTGGAC 58.554 36.000 0.00 0.00 0.00 4.02
276 940 1.862123 GCGATCCACGGCACATATG 59.138 57.895 0.00 0.00 42.83 1.78
304 968 8.737168 TCTTTGATGAAATGAATAGTCCGATT 57.263 30.769 0.00 0.00 0.00 3.34
327 991 4.993029 ACACGCTCTAGCTAAATTCTCT 57.007 40.909 0.00 0.00 39.32 3.10
328 992 6.020520 GTGTAACACGCTCTAGCTAAATTCTC 60.021 42.308 0.00 0.00 36.17 2.87
329 993 5.805994 GTGTAACACGCTCTAGCTAAATTCT 59.194 40.000 0.00 0.00 36.17 2.40
378 1051 7.957484 CCGTTCAGTCTTTATAACAATCAAGTG 59.043 37.037 0.00 0.00 0.00 3.16
383 1056 6.417191 TGCCGTTCAGTCTTTATAACAATC 57.583 37.500 0.00 0.00 0.00 2.67
384 1057 7.391148 AATGCCGTTCAGTCTTTATAACAAT 57.609 32.000 0.00 0.00 0.00 2.71
387 1060 7.073342 AGAAATGCCGTTCAGTCTTTATAAC 57.927 36.000 0.00 0.00 0.00 1.89
388 1061 7.681939 AAGAAATGCCGTTCAGTCTTTATAA 57.318 32.000 0.00 0.00 32.24 0.98
390 1063 6.879458 ACTAAGAAATGCCGTTCAGTCTTTAT 59.121 34.615 8.12 0.00 35.68 1.40
391 1064 6.228258 ACTAAGAAATGCCGTTCAGTCTTTA 58.772 36.000 8.12 0.00 35.68 1.85
404 1077 7.051000 ACCTTTCCATAGAGACTAAGAAATGC 58.949 38.462 0.00 0.00 0.00 3.56
421 1097 5.189145 GTCCAGGAGTATCTAAACCTTTCCA 59.811 44.000 0.00 0.00 33.73 3.53
422 1098 5.396548 GGTCCAGGAGTATCTAAACCTTTCC 60.397 48.000 0.00 0.00 33.73 3.13
429 1105 7.037586 ACAAAAGATGGTCCAGGAGTATCTAAA 60.038 37.037 13.45 0.00 33.73 1.85
432 1108 4.785376 ACAAAAGATGGTCCAGGAGTATCT 59.215 41.667 8.90 8.90 33.73 1.98
438 1114 3.256704 AGGTACAAAAGATGGTCCAGGA 58.743 45.455 0.00 0.00 0.00 3.86
511 1187 4.171878 TGGGTCAATTCAGTGTTGGTTA 57.828 40.909 0.00 0.00 0.00 2.85
535 1212 9.190858 GAAGAACATTGACTGCTATAGTATGAG 57.809 37.037 0.84 0.00 40.53 2.90
559 1236 6.428465 TGTGAATGACATAAAAACGGCTAGAA 59.572 34.615 0.00 0.00 0.00 2.10
560 1237 5.935206 TGTGAATGACATAAAAACGGCTAGA 59.065 36.000 0.00 0.00 0.00 2.43
564 1241 4.495472 CGATGTGAATGACATAAAAACGGC 59.505 41.667 0.00 0.00 45.90 5.68
566 1243 7.006476 CAGAACGATGTGAATGACATAAAAACG 59.994 37.037 0.00 0.00 45.90 3.60
567 1244 8.015087 TCAGAACGATGTGAATGACATAAAAAC 58.985 33.333 0.00 0.00 45.90 2.43
582 1259 4.608948 AGGAAGACTTTCAGAACGATGT 57.391 40.909 0.00 0.00 34.90 3.06
743 1434 9.674068 GTTGGAACTCCTTTTCTATCTATTTCT 57.326 33.333 0.00 0.00 36.82 2.52
798 1489 1.138883 TAGCGATGTGACGACTGGC 59.861 57.895 0.00 0.00 35.09 4.85
1296 2003 2.549169 CTTGCAGGGAAGCCTCCTCC 62.549 65.000 0.32 0.00 42.05 4.30
1299 2006 2.044551 CCTTGCAGGGAAGCCTCC 60.045 66.667 9.80 0.00 41.59 4.30
1365 2073 1.780309 TCCCCACACACCAAGAAGAAT 59.220 47.619 0.00 0.00 0.00 2.40
1380 2088 4.906618 CTTTGACTAAAAGCTACTCCCCA 58.093 43.478 0.00 0.00 38.99 4.96
1395 2103 0.814010 AAGAACACGCGGCTTTGACT 60.814 50.000 12.47 2.33 0.00 3.41
1527 2235 1.051812 CAGAGGTTCACCAGGTCACT 58.948 55.000 0.00 0.00 38.89 3.41
1528 2236 0.035458 CCAGAGGTTCACCAGGTCAC 59.965 60.000 0.00 0.00 38.89 3.67
1643 2358 7.782168 ATCTACTGAGAAGTGATATTCACCTGA 59.218 37.037 4.10 0.00 39.80 3.86
1696 2411 6.109359 AGGCATTCAGTAATCAGTACTTCAC 58.891 40.000 0.00 0.00 41.37 3.18
1700 2415 7.716998 CCAAATAGGCATTCAGTAATCAGTACT 59.283 37.037 0.00 0.00 44.33 2.73
1703 2418 5.829924 CCCAAATAGGCATTCAGTAATCAGT 59.170 40.000 0.00 0.00 35.39 3.41
1704 2419 6.064060 TCCCAAATAGGCATTCAGTAATCAG 58.936 40.000 0.00 0.00 35.39 2.90
1705 2420 6.012337 TCCCAAATAGGCATTCAGTAATCA 57.988 37.500 0.00 0.00 35.39 2.57
1706 2421 5.048434 GCTCCCAAATAGGCATTCAGTAATC 60.048 44.000 0.00 0.00 35.39 1.75
1707 2422 4.829492 GCTCCCAAATAGGCATTCAGTAAT 59.171 41.667 0.00 0.00 35.39 1.89
1708 2423 4.079787 AGCTCCCAAATAGGCATTCAGTAA 60.080 41.667 0.00 0.00 35.39 2.24
1919 2634 1.811965 CAATGCACTTTCATCGTCCCA 59.188 47.619 0.00 0.00 0.00 4.37
1981 2696 4.141711 TGAAGTGACAACCTAGCAGAACTT 60.142 41.667 0.00 0.00 0.00 2.66
1985 2700 3.866066 GCATGAAGTGACAACCTAGCAGA 60.866 47.826 0.00 0.00 0.00 4.26
2013 2728 6.294176 GGAACTGCAAGCAAGAGAGAATAAAA 60.294 38.462 0.00 0.00 37.60 1.52
2017 2732 3.080319 GGAACTGCAAGCAAGAGAGAAT 58.920 45.455 0.00 0.00 37.60 2.40
2018 2733 2.498167 GGAACTGCAAGCAAGAGAGAA 58.502 47.619 0.00 0.00 37.60 2.87
2030 2745 1.140312 ACAGAAGAAGGGGAACTGCA 58.860 50.000 0.00 0.00 32.67 4.41
2064 2779 2.418609 CCATATCCGGCGAGCAATGATA 60.419 50.000 9.30 6.08 0.00 2.15
2162 2877 5.528600 TCTCAAACCCCCATAATTGAAGA 57.471 39.130 0.00 0.00 31.94 2.87
2167 2882 8.742437 TCCTATAAATCTCAAACCCCCATAATT 58.258 33.333 0.00 0.00 0.00 1.40
2171 2886 5.917087 TCTCCTATAAATCTCAAACCCCCAT 59.083 40.000 0.00 0.00 0.00 4.00
2174 2889 6.062749 GGTTCTCCTATAAATCTCAAACCCC 58.937 44.000 0.00 0.00 0.00 4.95
2217 2932 3.058016 ACAATTTCCGTCAGCAACATCAG 60.058 43.478 0.00 0.00 0.00 2.90
2231 2946 8.359060 TGTAACTGCAATTTTACACAATTTCC 57.641 30.769 9.92 0.00 34.09 3.13
2273 2988 6.681777 ACAAGGAAGCATACAAACTTGAATC 58.318 36.000 8.96 0.00 38.80 2.52
2280 2995 4.367450 TGCAAACAAGGAAGCATACAAAC 58.633 39.130 0.00 0.00 31.05 2.93
2284 2999 3.928375 CCATTGCAAACAAGGAAGCATAC 59.072 43.478 1.71 0.00 39.96 2.39
2289 3004 3.749665 TTCCCATTGCAAACAAGGAAG 57.250 42.857 1.71 0.00 39.96 3.46
2536 3252 1.899814 TGAGGTATCCACAGAAGCGTT 59.100 47.619 0.00 0.00 0.00 4.84
2581 3320 5.581126 TCAGCACACTTGACAAAGAAAAT 57.419 34.783 0.00 0.00 36.84 1.82
2780 3520 1.614413 GAGGTTATCTAGCTGTCCCCG 59.386 57.143 0.00 0.00 33.94 5.73
2845 3585 5.302313 ACAACTCTTCCTAGTTTCTTCGTCT 59.698 40.000 0.00 0.00 37.61 4.18
2846 3586 5.530712 ACAACTCTTCCTAGTTTCTTCGTC 58.469 41.667 0.00 0.00 37.61 4.20
2873 3614 6.529829 TGACATGTTTTTAAGTTTGACACTGC 59.470 34.615 0.00 0.00 35.12 4.40
2945 3686 6.317088 CACGTGCTTTATTGAGATGATGTTT 58.683 36.000 0.82 0.00 0.00 2.83
2999 3741 3.478394 CATGACACGTGGTCCGCG 61.478 66.667 23.03 23.03 46.38 6.46
3000 3742 2.048597 TCATGACACGTGGTCCGC 60.049 61.111 21.57 4.19 46.38 5.54
3001 3743 0.524414 TAGTCATGACACGTGGTCCG 59.476 55.000 27.02 5.73 46.38 4.79
3108 3850 9.407380 TGTCAAAGGAAACAATAGTATGCATAT 57.593 29.630 10.16 2.05 0.00 1.78
3137 3879 6.506500 AAAAGGACAGATGACATGAACATC 57.493 37.500 20.92 20.92 42.81 3.06
3154 3896 6.707440 TGCAATAACAGAAGACAAAAAGGA 57.293 33.333 0.00 0.00 0.00 3.36
3211 3953 3.356290 AGGAATGAATAACTGGGTGCAC 58.644 45.455 8.80 8.80 0.00 4.57
3270 4012 9.734620 TTTCATCAAGATAAAATAGGCAATTCG 57.265 29.630 0.00 0.00 0.00 3.34
3380 4124 8.713708 TTCACCAAATCTAAACCATTCCTTTA 57.286 30.769 0.00 0.00 0.00 1.85
3404 4148 7.391148 AACAACTGTTGACAGACTTGTTATT 57.609 32.000 26.00 3.26 44.32 1.40
3527 4273 7.499232 AGTTATTTCACTCTACTGTTTTGCACT 59.501 33.333 0.00 0.00 0.00 4.40
3533 4279 8.211629 AGGACAAGTTATTTCACTCTACTGTTT 58.788 33.333 0.00 0.00 0.00 2.83
3541 4287 8.603242 TTAGTTCAGGACAAGTTATTTCACTC 57.397 34.615 0.00 0.00 0.00 3.51
3552 4298 4.899502 AGGTGACATTAGTTCAGGACAAG 58.100 43.478 0.00 0.00 0.00 3.16
3557 4303 3.411446 TGCAAGGTGACATTAGTTCAGG 58.589 45.455 0.00 0.00 0.00 3.86
3558 4304 4.696877 TCATGCAAGGTGACATTAGTTCAG 59.303 41.667 0.00 0.00 0.00 3.02
3613 4380 9.837525 GAGGATGTAAGTTGTATACCTAATACG 57.162 37.037 0.00 0.00 43.03 3.06
3620 4389 6.583562 AGCAAGAGGATGTAAGTTGTATACC 58.416 40.000 0.00 0.00 0.00 2.73
3622 4391 7.418337 TGAGCAAGAGGATGTAAGTTGTATA 57.582 36.000 0.00 0.00 0.00 1.47
3623 4392 6.299805 TGAGCAAGAGGATGTAAGTTGTAT 57.700 37.500 0.00 0.00 0.00 2.29
3629 4398 5.971763 AGTAGTTGAGCAAGAGGATGTAAG 58.028 41.667 0.00 0.00 0.00 2.34
3647 4421 6.979238 GCATAAAACGGAGACAGATAAGTAGT 59.021 38.462 0.00 0.00 0.00 2.73
3788 4564 3.871594 GCTCTTACCACTCATACGCAAAT 59.128 43.478 0.00 0.00 0.00 2.32
3794 4570 5.479306 TGTTTCAGCTCTTACCACTCATAC 58.521 41.667 0.00 0.00 0.00 2.39
3810 4586 8.484641 TCACTATTCAAATAGCTCTGTTTCAG 57.515 34.615 9.22 0.00 41.62 3.02
3955 4736 8.137437 TGTTCCAAGATCAAAACAAAAGAGATC 58.863 33.333 0.00 0.00 36.29 2.75
3958 4739 7.221452 CACTGTTCCAAGATCAAAACAAAAGAG 59.779 37.037 0.00 0.00 31.75 2.85
4554 5338 0.885879 CTTTTTACCCCGTTGCCTCC 59.114 55.000 0.00 0.00 0.00 4.30
4588 5372 2.710096 TAGCTGGAATCCCTTTTCCG 57.290 50.000 0.00 0.00 46.85 4.30
4636 5420 3.447229 TCCAGTTCACATAGAAGATCGCA 59.553 43.478 0.00 0.00 36.78 5.10
4716 5500 3.126831 GAGCCACTCACTGCATACATAC 58.873 50.000 0.00 0.00 0.00 2.39
4815 5606 5.856126 ATGTTTTGTACCACATCTACGTG 57.144 39.130 0.00 0.00 36.61 4.49
4858 5932 0.179108 GTGTGTATCGCCTCTGACCC 60.179 60.000 0.00 0.00 0.00 4.46
4956 6124 1.555533 AGGGCCTTAGAACGAAAGAGG 59.444 52.381 0.00 0.00 0.00 3.69
5061 6230 2.092968 GGCCAGACACTGATGTTCCATA 60.093 50.000 0.00 0.00 39.95 2.74
5077 6246 2.403252 ATCAGTTTTAGACCGGCCAG 57.597 50.000 0.00 0.00 0.00 4.85
5082 6251 5.236478 ACTGTGAACAATCAGTTTTAGACCG 59.764 40.000 0.00 0.00 41.33 4.79
5148 6317 1.654137 GCTTTGGTGAACACGCACG 60.654 57.895 0.00 0.00 39.66 5.34
5233 6402 9.691362 TTTAGCCAATTGACTTATCTTTCAAAC 57.309 29.630 7.12 0.00 35.42 2.93
5236 6405 8.402798 TGTTTAGCCAATTGACTTATCTTTCA 57.597 30.769 7.12 0.00 0.00 2.69
5237 6406 9.860898 ATTGTTTAGCCAATTGACTTATCTTTC 57.139 29.630 7.12 0.00 31.01 2.62
5312 6481 6.310711 CGCTCGTCTCTATTTTACTTTCCTTT 59.689 38.462 0.00 0.00 0.00 3.11
5346 6515 1.901464 GCCGCCTTGTGAGGGAAAA 60.901 57.895 0.00 0.00 43.75 2.29
5347 6516 1.485294 TAGCCGCCTTGTGAGGGAAA 61.485 55.000 0.00 0.00 43.75 3.13
5348 6517 1.899437 CTAGCCGCCTTGTGAGGGAA 61.899 60.000 0.00 0.00 43.75 3.97
5349 6518 2.284331 TAGCCGCCTTGTGAGGGA 60.284 61.111 0.00 0.00 43.75 4.20
5350 6519 2.187946 CTAGCCGCCTTGTGAGGG 59.812 66.667 0.00 0.00 43.75 4.30
5351 6520 2.187946 CCTAGCCGCCTTGTGAGG 59.812 66.667 0.00 0.00 46.50 3.86
5363 6532 1.408961 GGAGGAAGGCTTTTCCCTAGC 60.409 57.143 16.65 3.07 39.39 3.42
5391 6560 3.706373 ACAAGCTCGCCGGTGGAT 61.706 61.111 16.49 1.27 0.00 3.41
5395 6564 3.254024 AATCCACAAGCTCGCCGGT 62.254 57.895 1.90 0.00 0.00 5.28
5396 6565 2.436646 AATCCACAAGCTCGCCGG 60.437 61.111 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.