Multiple sequence alignment - TraesCS6B01G283300

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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 TraesCS6B01G283300 chr6B 100.000 3849 0 0 1 3849 511566508 511570356 0.000000e+00 7108
1 TraesCS6B01G283300 chr6A 95.090 3096 88 24 1 3087 452777668 452774628 0.000000e+00 4817
2 TraesCS6B01G283300 chr6D 95.527 2571 61 17 1 2554 315626706 315624173 0.000000e+00 4061
3 TraesCS6B01G283300 chr6D 96.594 411 13 1 2551 2961 315624013 315623604 0.000000e+00 680
4 TraesCS6B01G283300 chr6D 96.269 134 4 1 2954 3087 315622548 315622416 6.470000e-53 219
5 TraesCS6B01G283300 chr7A 91.529 425 27 8 3431 3849 229178355 229178776 9.270000e-161 577
6 TraesCS6B01G283300 chr7A 89.030 237 16 2 3196 3422 229178139 229178375 6.290000e-73 285
7 TraesCS6B01G283300 chr2A 91.529 425 27 8 3431 3849 695270342 695270763 9.270000e-161 577
8 TraesCS6B01G283300 chr2A 92.825 223 16 0 3200 3422 695270140 695270362 1.330000e-84 324
9 TraesCS6B01G283300 chr4A 82.938 211 26 5 3202 3411 704156654 704156855 8.490000e-42 182


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 TraesCS6B01G283300 chr6B 511566508 511570356 3848 False 7108.000000 7108 100.0000 1 3849 1 chr6B.!!$F1 3848
1 TraesCS6B01G283300 chr6A 452774628 452777668 3040 True 4817.000000 4817 95.0900 1 3087 1 chr6A.!!$R1 3086
2 TraesCS6B01G283300 chr6D 315622416 315626706 4290 True 1653.333333 4061 96.1300 1 3087 3 chr6D.!!$R1 3086
3 TraesCS6B01G283300 chr7A 229178139 229178776 637 False 431.000000 577 90.2795 3196 3849 2 chr7A.!!$F1 653
4 TraesCS6B01G283300 chr2A 695270140 695270763 623 False 450.500000 577 92.1770 3200 3849 2 chr2A.!!$F1 649

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
877 882 1.034356 TGACAGAGAAACGGGTTCGA 58.966 50.0 0.0 0.00 41.52 3.71 F
1482 1490 0.796312 ATAAGCGACCTTGCAACACG 59.204 50.0 0.0 2.86 37.31 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2432 2456 0.792640 GTTGTGACATCAGCCGTGAG 59.207 55.0 0.0 0.00 35.66 3.51 R
3112 4363 0.031994 ATGCAAACAAGTGTTCCCGC 59.968 50.0 0.0 2.27 37.25 6.13 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
141 143 1.880027 GTGAGTTGGCTAACAAGTGGG 59.120 52.381 15.86 0.00 42.69 4.61
223 225 9.928236 GAAAAGTATCTGTCTTCAAATCTATGC 57.072 33.333 0.00 0.00 0.00 3.14
261 263 7.271511 TGAAAAGTTCCATTTTTATGCACACT 58.728 30.769 0.00 0.00 32.62 3.55
267 269 6.343716 TCCATTTTTATGCACACTTGATGT 57.656 33.333 0.00 0.00 44.81 3.06
272 274 9.786105 CATTTTTATGCACACTTGATGTATACA 57.214 29.630 8.27 8.27 40.64 2.29
312 314 8.314143 AGTTCAGTTTGAAATGCATTTATTGG 57.686 30.769 24.15 11.98 38.22 3.16
500 502 5.518848 TTTCTTGTCATTGTCATTGTGCT 57.481 34.783 0.00 0.00 0.00 4.40
877 882 1.034356 TGACAGAGAAACGGGTTCGA 58.966 50.000 0.00 0.00 41.52 3.71
973 978 9.453325 GAAATTGTGTTTCTAATAACCGAACAA 57.547 29.630 0.00 0.00 30.81 2.83
979 984 9.417284 GTGTTTCTAATAACCGAACAATTATCG 57.583 33.333 5.98 5.98 39.92 2.92
1217 1222 8.181308 GTGATTGCTCACGTTTTGGAACAATG 62.181 42.308 6.89 0.00 42.87 2.82
1414 1419 1.524165 CTCCAGATGCTGCTGCTCC 60.524 63.158 17.00 8.22 40.48 4.70
1482 1490 0.796312 ATAAGCGACCTTGCAACACG 59.204 50.000 0.00 2.86 37.31 4.49
1492 1500 2.549754 CCTTGCAACACGAAACTGAGAT 59.450 45.455 0.00 0.00 0.00 2.75
1519 1527 5.664294 TTCTCATTGTTAGGCATGCAAAT 57.336 34.783 21.36 7.30 0.00 2.32
1521 1529 5.653507 TCTCATTGTTAGGCATGCAAATTC 58.346 37.500 21.36 0.72 0.00 2.17
1537 1545 5.477984 TGCAAATTCTACATCCAGAAGCTTT 59.522 36.000 0.00 0.00 37.93 3.51
1559 1569 7.428282 TTTTTCGCTCTTATGACATGTGTAA 57.572 32.000 1.15 1.44 0.00 2.41
1663 1673 4.413969 CAGATCTCTATGCTGTAGATGCG 58.586 47.826 0.00 0.00 30.19 4.73
1666 1676 2.554462 TCTCTATGCTGTAGATGCGGAC 59.446 50.000 0.82 0.00 0.00 4.79
1762 1772 5.249420 AGCTTAGGAAGAACTGTTGGAATC 58.751 41.667 0.00 0.00 0.00 2.52
1841 1851 1.668419 GCGGTTAGCCATCTGTCAAT 58.332 50.000 0.00 0.00 40.81 2.57
1962 1980 9.844790 CTTGTATGTGTCATGATTTGTAAATGT 57.155 29.630 0.00 0.00 0.00 2.71
1969 1987 8.268052 GTGTCATGATTTGTAAATGTGTTTGTG 58.732 33.333 0.00 0.00 0.00 3.33
2126 2144 5.291858 CACTTGTTGTCTATACGCATCACAT 59.708 40.000 0.00 0.00 0.00 3.21
2135 2153 5.922544 TCTATACGCATCACATGATTGTCAG 59.077 40.000 0.00 0.00 32.34 3.51
2140 2158 4.614306 CGCATCACATGATTGTCAGTTTGT 60.614 41.667 0.00 0.00 32.34 2.83
2284 2302 7.534723 TGAGGTCTATGTGTACTTTGTTAGT 57.465 36.000 0.00 0.00 41.04 2.24
2285 2303 7.959175 TGAGGTCTATGTGTACTTTGTTAGTT 58.041 34.615 0.00 0.00 38.33 2.24
2286 2304 9.081204 TGAGGTCTATGTGTACTTTGTTAGTTA 57.919 33.333 0.00 0.00 38.33 2.24
2287 2305 9.351570 GAGGTCTATGTGTACTTTGTTAGTTAC 57.648 37.037 0.00 0.00 38.33 2.50
2288 2306 9.086758 AGGTCTATGTGTACTTTGTTAGTTACT 57.913 33.333 0.00 0.00 38.33 2.24
2289 2307 9.702494 GGTCTATGTGTACTTTGTTAGTTACTT 57.298 33.333 0.00 0.00 38.33 2.24
2379 2397 6.594159 CCCTGAGTTTTACAAGGTACTATGTG 59.406 42.308 12.42 0.63 38.49 3.21
2383 2401 7.658575 TGAGTTTTACAAGGTACTATGTGGTTC 59.341 37.037 12.42 5.83 38.49 3.62
2393 2411 8.732746 AGGTACTATGTGGTTCAATTATGTTC 57.267 34.615 0.00 0.00 36.02 3.18
2394 2412 8.548877 AGGTACTATGTGGTTCAATTATGTTCT 58.451 33.333 0.00 0.00 36.02 3.01
2395 2413 8.612619 GGTACTATGTGGTTCAATTATGTTCTG 58.387 37.037 0.00 0.00 0.00 3.02
2396 2414 9.162764 GTACTATGTGGTTCAATTATGTTCTGT 57.837 33.333 0.00 0.00 0.00 3.41
2397 2415 8.635765 ACTATGTGGTTCAATTATGTTCTGTT 57.364 30.769 0.00 0.00 0.00 3.16
2398 2416 9.077885 ACTATGTGGTTCAATTATGTTCTGTTT 57.922 29.630 0.00 0.00 0.00 2.83
2432 2456 4.626042 CCAGATGGTATGACACTTCTAGC 58.374 47.826 0.00 0.00 0.00 3.42
2434 2458 5.508825 CCAGATGGTATGACACTTCTAGCTC 60.509 48.000 0.00 0.00 0.00 4.09
2479 2503 6.543831 GTCATGGATAACATAACTTTGCCTCT 59.456 38.462 0.00 0.00 37.84 3.69
2716 2904 4.771590 TGTTAGCTCCAAATTGAAGCAG 57.228 40.909 7.02 0.00 0.00 4.24
2779 2967 9.442047 AACTCATCTAAAAACTGTAATCTGAGG 57.558 33.333 0.00 0.00 32.66 3.86
2792 2980 5.769662 TGTAATCTGAGGTGCAATTTCAGTT 59.230 36.000 17.75 14.40 39.41 3.16
2878 3066 0.753867 TTGTACACCTGACTTGCGGA 59.246 50.000 0.00 0.00 0.00 5.54
2879 3067 0.973632 TGTACACCTGACTTGCGGAT 59.026 50.000 0.00 0.00 0.00 4.18
2880 3068 1.337728 TGTACACCTGACTTGCGGATG 60.338 52.381 0.00 0.00 0.00 3.51
2920 3108 7.231467 AGAGTCAATACCTTTGGTTGTAACAT 58.769 34.615 0.00 0.00 37.09 2.71
2945 3133 7.776107 TGGAACTAAAAATGTCATGTGTTTCA 58.224 30.769 0.00 0.00 0.00 2.69
2994 4245 5.179368 ACACGGTTGTTTGAATCACAGATAG 59.821 40.000 0.00 0.00 28.43 2.08
3091 4342 9.847224 ATTTGACCAAGTTTTAGAAGAACTAGA 57.153 29.630 0.00 0.00 36.38 2.43
3092 4343 9.847224 TTTGACCAAGTTTTAGAAGAACTAGAT 57.153 29.630 0.00 0.00 36.38 1.98
3093 4344 8.833231 TGACCAAGTTTTAGAAGAACTAGATG 57.167 34.615 0.00 0.00 36.38 2.90
3094 4345 8.647796 TGACCAAGTTTTAGAAGAACTAGATGA 58.352 33.333 0.00 0.00 36.38 2.92
3095 4346 9.660180 GACCAAGTTTTAGAAGAACTAGATGAT 57.340 33.333 0.00 0.00 36.38 2.45
3101 4352 9.032420 GTTTTAGAAGAACTAGATGATAACCCG 57.968 37.037 0.00 0.00 32.30 5.28
3102 4353 5.203060 AGAAGAACTAGATGATAACCCGC 57.797 43.478 0.00 0.00 0.00 6.13
3103 4354 4.039366 AGAAGAACTAGATGATAACCCGCC 59.961 45.833 0.00 0.00 0.00 6.13
3104 4355 2.296471 AGAACTAGATGATAACCCGCCG 59.704 50.000 0.00 0.00 0.00 6.46
3105 4356 1.700955 ACTAGATGATAACCCGCCGT 58.299 50.000 0.00 0.00 0.00 5.68
3106 4357 1.340248 ACTAGATGATAACCCGCCGTG 59.660 52.381 0.00 0.00 0.00 4.94
3107 4358 1.340248 CTAGATGATAACCCGCCGTGT 59.660 52.381 0.00 0.00 0.00 4.49
3108 4359 0.539986 AGATGATAACCCGCCGTGTT 59.460 50.000 0.00 0.00 0.00 3.32
3109 4360 0.655733 GATGATAACCCGCCGTGTTG 59.344 55.000 0.00 0.00 0.00 3.33
3110 4361 1.373590 ATGATAACCCGCCGTGTTGC 61.374 55.000 0.00 0.00 0.00 4.17
3111 4362 1.743995 GATAACCCGCCGTGTTGCT 60.744 57.895 0.00 0.00 0.00 3.91
3112 4363 1.977594 GATAACCCGCCGTGTTGCTG 61.978 60.000 0.00 0.00 0.00 4.41
3119 4370 4.025401 CCGTGTTGCTGCGGGAAC 62.025 66.667 21.88 21.88 43.85 3.62
3122 4373 2.191908 TGTTGCTGCGGGAACACT 59.808 55.556 26.64 0.00 46.11 3.55
3123 4374 1.453015 TGTTGCTGCGGGAACACTT 60.453 52.632 26.64 0.00 46.11 3.16
3124 4375 1.008538 GTTGCTGCGGGAACACTTG 60.009 57.895 23.46 0.00 42.21 3.16
3125 4376 1.453015 TTGCTGCGGGAACACTTGT 60.453 52.632 0.00 0.00 0.00 3.16
3126 4377 1.034838 TTGCTGCGGGAACACTTGTT 61.035 50.000 0.00 0.00 41.64 2.83
3127 4378 1.034838 TGCTGCGGGAACACTTGTTT 61.035 50.000 0.00 0.00 38.56 2.83
3128 4379 0.594796 GCTGCGGGAACACTTGTTTG 60.595 55.000 0.00 0.00 38.56 2.93
3129 4380 0.594796 CTGCGGGAACACTTGTTTGC 60.595 55.000 0.00 2.61 38.56 3.68
3130 4381 1.315981 TGCGGGAACACTTGTTTGCA 61.316 50.000 11.34 11.34 38.56 4.08
3131 4382 0.031994 GCGGGAACACTTGTTTGCAT 59.968 50.000 0.00 0.00 38.56 3.96
3132 4383 1.268352 GCGGGAACACTTGTTTGCATA 59.732 47.619 0.00 0.00 38.56 3.14
3133 4384 2.668279 GCGGGAACACTTGTTTGCATAG 60.668 50.000 0.00 0.00 38.56 2.23
3134 4385 2.552315 CGGGAACACTTGTTTGCATAGT 59.448 45.455 0.00 0.00 38.56 2.12
3135 4386 3.004315 CGGGAACACTTGTTTGCATAGTT 59.996 43.478 0.00 0.00 38.56 2.24
3136 4387 4.298332 GGGAACACTTGTTTGCATAGTTG 58.702 43.478 0.00 0.00 38.56 3.16
3137 4388 4.037446 GGGAACACTTGTTTGCATAGTTGA 59.963 41.667 0.00 0.00 38.56 3.18
3138 4389 5.278957 GGGAACACTTGTTTGCATAGTTGAT 60.279 40.000 0.00 0.00 38.56 2.57
3139 4390 5.630680 GGAACACTTGTTTGCATAGTTGATG 59.369 40.000 0.00 0.00 38.56 3.07
3154 4405 8.507470 CATAGTTGATGCATGATTTTGAGATG 57.493 34.615 2.46 0.00 0.00 2.90
3155 4406 6.769134 AGTTGATGCATGATTTTGAGATGA 57.231 33.333 2.46 0.00 0.00 2.92
3156 4407 7.165460 AGTTGATGCATGATTTTGAGATGAA 57.835 32.000 2.46 0.00 0.00 2.57
3157 4408 7.608153 AGTTGATGCATGATTTTGAGATGAAA 58.392 30.769 2.46 0.00 0.00 2.69
3158 4409 8.092068 AGTTGATGCATGATTTTGAGATGAAAA 58.908 29.630 2.46 0.00 0.00 2.29
3159 4410 8.714179 GTTGATGCATGATTTTGAGATGAAAAA 58.286 29.630 2.46 0.00 0.00 1.94
3160 4411 9.443323 TTGATGCATGATTTTGAGATGAAAAAT 57.557 25.926 2.46 0.00 39.36 1.82
3165 4416 9.646336 GCATGATTTTGAGATGAAAAATATTGC 57.354 29.630 0.00 10.13 37.35 3.56
3173 4424 9.545105 TTGAGATGAAAAATATTGCAAAACAGT 57.455 25.926 1.71 0.00 0.00 3.55
3185 4436 9.899661 ATATTGCAAAACAGTACTTAGGTATGA 57.100 29.630 1.71 0.00 0.00 2.15
3186 4437 8.807948 ATTGCAAAACAGTACTTAGGTATGAT 57.192 30.769 1.71 0.00 0.00 2.45
3187 4438 8.630054 TTGCAAAACAGTACTTAGGTATGATT 57.370 30.769 0.00 0.00 0.00 2.57
3188 4439 8.263940 TGCAAAACAGTACTTAGGTATGATTC 57.736 34.615 0.00 0.00 0.00 2.52
3189 4440 7.880713 TGCAAAACAGTACTTAGGTATGATTCA 59.119 33.333 0.00 0.00 0.00 2.57
3190 4441 8.175716 GCAAAACAGTACTTAGGTATGATTCAC 58.824 37.037 0.00 0.00 0.00 3.18
3191 4442 9.436957 CAAAACAGTACTTAGGTATGATTCACT 57.563 33.333 0.00 0.00 0.00 3.41
3192 4443 9.654663 AAAACAGTACTTAGGTATGATTCACTC 57.345 33.333 0.00 0.00 0.00 3.51
3193 4444 8.596781 AACAGTACTTAGGTATGATTCACTCT 57.403 34.615 0.00 0.00 0.00 3.24
3194 4445 8.001881 ACAGTACTTAGGTATGATTCACTCTG 57.998 38.462 0.00 0.00 0.00 3.35
3195 4446 7.616150 ACAGTACTTAGGTATGATTCACTCTGT 59.384 37.037 0.00 0.00 0.00 3.41
3196 4447 9.121658 CAGTACTTAGGTATGATTCACTCTGTA 57.878 37.037 0.00 0.00 0.00 2.74
3197 4448 9.122779 AGTACTTAGGTATGATTCACTCTGTAC 57.877 37.037 0.00 0.00 0.00 2.90
3198 4449 7.028926 ACTTAGGTATGATTCACTCTGTACG 57.971 40.000 0.00 0.00 0.00 3.67
3222 4473 5.574443 GCAAAGAAGAATACATTGTCCAAGC 59.426 40.000 0.00 0.00 0.00 4.01
3270 4531 1.028868 GCACCTTGCACCAGAGATCC 61.029 60.000 0.00 0.00 44.26 3.36
3335 4596 8.012241 GTGCAAATAGTAGCAATATAAGTCTGC 58.988 37.037 0.00 0.00 43.20 4.26
3349 4610 0.315251 GTCTGCCTTTTTCCCACAGC 59.685 55.000 0.00 0.00 0.00 4.40
3413 4674 8.986477 ATTATGGAAAACTGAATTGCTACAAC 57.014 30.769 0.00 0.00 0.00 3.32
3414 4675 5.843673 TGGAAAACTGAATTGCTACAACA 57.156 34.783 0.00 0.00 0.00 3.33
3415 4676 5.830912 TGGAAAACTGAATTGCTACAACAG 58.169 37.500 0.00 0.00 35.14 3.16
3416 4677 5.221224 TGGAAAACTGAATTGCTACAACAGG 60.221 40.000 0.00 0.00 33.57 4.00
3417 4678 3.923017 AACTGAATTGCTACAACAGGC 57.077 42.857 0.00 0.00 33.57 4.85
3418 4679 3.146104 ACTGAATTGCTACAACAGGCT 57.854 42.857 0.00 0.00 33.57 4.58
3419 4680 3.490348 ACTGAATTGCTACAACAGGCTT 58.510 40.909 0.00 0.00 33.57 4.35
3420 4681 3.503748 ACTGAATTGCTACAACAGGCTTC 59.496 43.478 0.00 0.00 33.57 3.86
3421 4682 3.754965 TGAATTGCTACAACAGGCTTCT 58.245 40.909 0.00 0.00 0.00 2.85
3422 4683 4.144297 TGAATTGCTACAACAGGCTTCTT 58.856 39.130 0.00 0.00 0.00 2.52
3423 4684 4.584325 TGAATTGCTACAACAGGCTTCTTT 59.416 37.500 0.00 0.00 0.00 2.52
3424 4685 5.068987 TGAATTGCTACAACAGGCTTCTTTT 59.931 36.000 0.00 0.00 0.00 2.27
3425 4686 5.535753 ATTGCTACAACAGGCTTCTTTTT 57.464 34.783 0.00 0.00 0.00 1.94
3464 4725 5.700846 ACAGGCTTCTCGTTATATATCACG 58.299 41.667 12.26 12.26 37.77 4.35
3500 4762 3.622166 TGCTAAGTACCCTTTGTAGCC 57.378 47.619 0.00 0.00 31.54 3.93
3507 4769 4.168883 AGTACCCTTTGTAGCCTCTCTTT 58.831 43.478 0.00 0.00 0.00 2.52
3508 4770 3.704800 ACCCTTTGTAGCCTCTCTTTC 57.295 47.619 0.00 0.00 0.00 2.62
3510 4772 3.653352 ACCCTTTGTAGCCTCTCTTTCTT 59.347 43.478 0.00 0.00 0.00 2.52
3511 4773 4.844655 ACCCTTTGTAGCCTCTCTTTCTTA 59.155 41.667 0.00 0.00 0.00 2.10
3522 4784 8.964533 AGCCTCTCTTTCTTATATAGATCCAA 57.035 34.615 0.00 0.00 31.54 3.53
3560 4822 9.638176 AAATTAAGAGAGGCTTATGATCATGTT 57.362 29.630 18.72 0.00 38.79 2.71
3569 4831 8.332996 AGGCTTATGATCATGTTGAATGTATC 57.667 34.615 18.72 0.00 0.00 2.24
3576 4838 3.622612 TCATGTTGAATGTATCACAGCGG 59.377 43.478 0.00 0.00 37.92 5.52
3583 4845 4.391830 TGAATGTATCACAGCGGAAAGTTC 59.608 41.667 0.00 0.00 31.50 3.01
3632 4894 5.495640 CTTCTCCCTATTTCTTCTTGCACT 58.504 41.667 0.00 0.00 0.00 4.40
3658 4923 5.912149 AAGAAGATAATGCTGATACCCCA 57.088 39.130 0.00 0.00 0.00 4.96
3661 4926 2.076863 GATAATGCTGATACCCCACGC 58.923 52.381 0.00 0.00 0.00 5.34
3667 4932 2.435234 GATACCCCACGCGTTGCA 60.435 61.111 10.22 0.00 0.00 4.08
3668 4933 2.032834 ATACCCCACGCGTTGCAA 59.967 55.556 10.22 0.00 0.00 4.08
3682 4947 1.851021 TTGCAACGGAACAGGATGCG 61.851 55.000 0.00 0.00 42.53 4.73
3695 4960 6.038271 GGAACAGGATGCGTAGATACAAATTT 59.962 38.462 0.00 0.00 42.53 1.82
3696 4961 7.225931 GGAACAGGATGCGTAGATACAAATTTA 59.774 37.037 0.00 0.00 42.53 1.40
3697 4962 7.478520 ACAGGATGCGTAGATACAAATTTAC 57.521 36.000 0.00 0.00 42.53 2.01
3767 5033 9.846248 AAATCTAAAGAAAAGCATCATGTACAC 57.154 29.630 0.00 0.00 0.00 2.90
3810 5076 5.880332 TGGAAATGACACTAAGCATCCTAAC 59.120 40.000 0.00 0.00 0.00 2.34
3819 5085 8.534954 ACACTAAGCATCCTAACATAGAAGTA 57.465 34.615 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 143 7.912250 CCAAGATCACAAAATGCTTATACAGTC 59.088 37.037 0.00 0.00 0.00 3.51
223 225 7.812690 TGGAACTTTTCATCCATCATATGAG 57.187 36.000 11.78 3.67 40.74 2.90
500 502 5.717178 ACAGCTATAACAAGGTCTCTCTGAA 59.283 40.000 0.00 0.00 0.00 3.02
588 591 5.294060 GCCGGCATTCATATTCAAAACAAAT 59.706 36.000 24.80 0.00 0.00 2.32
592 595 4.045636 AGCCGGCATTCATATTCAAAAC 57.954 40.909 31.54 0.00 0.00 2.43
877 882 4.965532 ACTATTCCTACAGAGCAACCTGAT 59.034 41.667 7.61 0.00 37.59 2.90
973 978 2.945668 GGAGGCTGCAAAGTTCGATAAT 59.054 45.455 0.00 0.00 0.00 1.28
979 984 0.813821 GATGGGAGGCTGCAAAGTTC 59.186 55.000 8.68 0.00 0.00 3.01
1217 1222 3.329386 TGTTGAGTAATCTGCAGCAGAC 58.671 45.455 27.73 15.50 43.63 3.51
1492 1500 4.379394 GCATGCCTAACAATGAGAAACGAA 60.379 41.667 6.36 0.00 0.00 3.85
1503 1511 5.973899 TGTAGAATTTGCATGCCTAACAA 57.026 34.783 16.68 0.00 0.00 2.83
1519 1527 4.154195 GCGAAAAAGCTTCTGGATGTAGAA 59.846 41.667 0.00 0.00 35.51 2.10
1521 1529 3.686726 AGCGAAAAAGCTTCTGGATGTAG 59.313 43.478 0.00 0.00 46.80 2.74
1537 1545 6.163476 AGTTACACATGTCATAAGAGCGAAA 58.837 36.000 0.00 0.00 0.00 3.46
1559 1569 6.933521 GGAATGACAACTGCATATGAGATAGT 59.066 38.462 6.97 1.92 0.00 2.12
1663 1673 3.689649 ACAATTCCGAAAGTGCATAGTCC 59.310 43.478 0.00 0.00 33.83 3.85
1762 1772 2.165030 GGAGTCAATTTGATGCACCTGG 59.835 50.000 1.78 0.00 0.00 4.45
1813 1823 0.882927 TGGCTAACCGCTGTTGTGAC 60.883 55.000 3.49 0.00 39.70 3.67
1841 1851 6.112734 ACATTGTCGGCTCATCAATAAAGTA 58.887 36.000 0.00 0.00 31.76 2.24
1851 1861 1.888512 AGCAAAACATTGTCGGCTCAT 59.111 42.857 4.54 0.00 0.00 2.90
1857 1867 2.095567 CAGAGGGAGCAAAACATTGTCG 60.096 50.000 0.00 0.00 0.00 4.35
2093 2111 6.861572 CGTATAGACAACAAGTGAAGACAGAA 59.138 38.462 0.00 0.00 0.00 3.02
2140 2158 7.400339 TGGCCATAGGACCAAAATAAACAAATA 59.600 33.333 0.00 0.00 31.46 1.40
2219 2237 4.217754 TCGGTGAACTGCAATTACAAAC 57.782 40.909 0.00 0.00 0.00 2.93
2220 2238 4.759693 AGATCGGTGAACTGCAATTACAAA 59.240 37.500 0.00 0.00 0.00 2.83
2221 2239 4.154015 CAGATCGGTGAACTGCAATTACAA 59.846 41.667 0.00 0.00 0.00 2.41
2222 2240 3.684305 CAGATCGGTGAACTGCAATTACA 59.316 43.478 0.00 0.00 0.00 2.41
2223 2241 3.932710 TCAGATCGGTGAACTGCAATTAC 59.067 43.478 0.00 0.00 33.43 1.89
2224 2242 4.200838 TCAGATCGGTGAACTGCAATTA 57.799 40.909 0.00 0.00 33.43 1.40
2225 2243 3.057969 TCAGATCGGTGAACTGCAATT 57.942 42.857 0.00 0.00 33.43 2.32
2226 2244 2.768253 TCAGATCGGTGAACTGCAAT 57.232 45.000 0.00 0.00 33.43 3.56
2227 2245 2.224281 ACTTCAGATCGGTGAACTGCAA 60.224 45.455 0.00 0.00 33.43 4.08
2276 2294 9.424319 TGCAAAACAAATGAAGTAACTAACAAA 57.576 25.926 0.00 0.00 0.00 2.83
2277 2295 8.988064 TGCAAAACAAATGAAGTAACTAACAA 57.012 26.923 0.00 0.00 0.00 2.83
2278 2296 8.462811 TCTGCAAAACAAATGAAGTAACTAACA 58.537 29.630 0.00 0.00 0.00 2.41
2279 2297 8.850454 TCTGCAAAACAAATGAAGTAACTAAC 57.150 30.769 0.00 0.00 0.00 2.34
2282 2300 9.683069 CTTATCTGCAAAACAAATGAAGTAACT 57.317 29.630 0.00 0.00 0.00 2.24
2283 2301 9.463443 ACTTATCTGCAAAACAAATGAAGTAAC 57.537 29.630 0.00 0.00 0.00 2.50
2288 2306 9.809096 TGTTTACTTATCTGCAAAACAAATGAA 57.191 25.926 7.88 0.00 37.17 2.57
2289 2307 9.809096 TTGTTTACTTATCTGCAAAACAAATGA 57.191 25.926 16.82 0.00 43.32 2.57
2379 2397 7.214467 TCCAGAAACAGAACATAATTGAACC 57.786 36.000 0.00 0.00 0.00 3.62
2383 2401 8.680001 TCATCATCCAGAAACAGAACATAATTG 58.320 33.333 0.00 0.00 0.00 2.32
2432 2456 0.792640 GTTGTGACATCAGCCGTGAG 59.207 55.000 0.00 0.00 35.66 3.51
2434 2458 1.135888 CATGTTGTGACATCAGCCGTG 60.136 52.381 2.59 0.00 44.55 4.94
2479 2503 5.180271 AGGGCGTTTGATTTATTAGTTCGA 58.820 37.500 0.00 0.00 0.00 3.71
2525 2550 5.749596 TGTACCAATGTTGTCAACTGAAG 57.250 39.130 16.45 6.14 0.00 3.02
2625 2813 7.498225 CAAAATGACAATACCAGTTAAAACGC 58.502 34.615 0.00 0.00 0.00 4.84
2716 2904 7.872483 TCAAATTTTTCAATCTCCTTAGTTGCC 59.128 33.333 0.00 0.00 0.00 4.52
2779 2967 6.668323 ACACACTATACAACTGAAATTGCAC 58.332 36.000 0.00 0.00 32.47 4.57
2792 2980 7.470935 TCTTGCCTACTTTACACACTATACA 57.529 36.000 0.00 0.00 0.00 2.29
2878 3066 6.092955 TGACTCTACAAAACTCGGTAACAT 57.907 37.500 0.00 0.00 0.00 2.71
2879 3067 5.518848 TGACTCTACAAAACTCGGTAACA 57.481 39.130 0.00 0.00 0.00 2.41
2880 3068 7.062722 GGTATTGACTCTACAAAACTCGGTAAC 59.937 40.741 0.00 0.00 33.44 2.50
2920 3108 7.776107 TGAAACACATGACATTTTTAGTTCCA 58.224 30.769 0.00 0.00 0.00 3.53
2945 3133 7.107639 AGTTACCAAAACAACAAATGCTACT 57.892 32.000 0.00 0.00 0.00 2.57
2994 4245 4.204799 ACGGTGGGATTATTTTTCCTAGC 58.795 43.478 0.00 0.00 38.46 3.42
3087 4338 1.340248 ACACGGCGGGTTATCATCTAG 59.660 52.381 10.05 0.00 0.00 2.43
3088 4339 1.405872 ACACGGCGGGTTATCATCTA 58.594 50.000 10.05 0.00 0.00 1.98
3089 4340 0.539986 AACACGGCGGGTTATCATCT 59.460 50.000 28.21 0.00 0.00 2.90
3090 4341 0.655733 CAACACGGCGGGTTATCATC 59.344 55.000 28.78 0.00 0.00 2.92
3091 4342 1.373590 GCAACACGGCGGGTTATCAT 61.374 55.000 28.78 1.33 0.00 2.45
3092 4343 2.036006 GCAACACGGCGGGTTATCA 61.036 57.895 28.78 0.00 0.00 2.15
3093 4344 1.743995 AGCAACACGGCGGGTTATC 60.744 57.895 28.78 21.20 39.27 1.75
3094 4345 2.038269 CAGCAACACGGCGGGTTAT 61.038 57.895 28.78 16.61 39.27 1.89
3095 4346 2.666862 CAGCAACACGGCGGGTTA 60.667 61.111 28.78 0.00 39.27 2.85
3103 4354 3.276091 TGTTCCCGCAGCAACACG 61.276 61.111 0.00 0.00 0.00 4.49
3104 4355 2.331451 GTGTTCCCGCAGCAACAC 59.669 61.111 10.52 10.52 44.10 3.32
3105 4356 1.453015 AAGTGTTCCCGCAGCAACA 60.453 52.632 0.00 0.00 0.00 3.33
3106 4357 1.008538 CAAGTGTTCCCGCAGCAAC 60.009 57.895 0.00 0.00 0.00 4.17
3107 4358 1.034838 AACAAGTGTTCCCGCAGCAA 61.035 50.000 0.00 0.00 31.64 3.91
3108 4359 1.034838 AAACAAGTGTTCCCGCAGCA 61.035 50.000 0.00 0.00 37.25 4.41
3109 4360 0.594796 CAAACAAGTGTTCCCGCAGC 60.595 55.000 0.00 0.00 37.25 5.25
3110 4361 0.594796 GCAAACAAGTGTTCCCGCAG 60.595 55.000 0.00 0.00 37.25 5.18
3111 4362 1.315981 TGCAAACAAGTGTTCCCGCA 61.316 50.000 10.22 10.22 37.25 5.69
3112 4363 0.031994 ATGCAAACAAGTGTTCCCGC 59.968 50.000 0.00 2.27 37.25 6.13
3113 4364 2.552315 ACTATGCAAACAAGTGTTCCCG 59.448 45.455 0.00 0.00 37.25 5.14
3114 4365 4.037446 TCAACTATGCAAACAAGTGTTCCC 59.963 41.667 0.00 0.00 37.25 3.97
3115 4366 5.181690 TCAACTATGCAAACAAGTGTTCC 57.818 39.130 0.00 0.00 37.25 3.62
3116 4367 6.680055 CATCAACTATGCAAACAAGTGTTC 57.320 37.500 0.00 0.00 37.25 3.18
3129 4380 8.349983 TCATCTCAAAATCATGCATCAACTATG 58.650 33.333 0.00 0.00 38.74 2.23
3130 4381 8.459911 TCATCTCAAAATCATGCATCAACTAT 57.540 30.769 0.00 0.00 0.00 2.12
3131 4382 7.868906 TCATCTCAAAATCATGCATCAACTA 57.131 32.000 0.00 0.00 0.00 2.24
3132 4383 6.769134 TCATCTCAAAATCATGCATCAACT 57.231 33.333 0.00 0.00 0.00 3.16
3133 4384 7.821595 TTTCATCTCAAAATCATGCATCAAC 57.178 32.000 0.00 0.00 0.00 3.18
3134 4385 8.834749 TTTTTCATCTCAAAATCATGCATCAA 57.165 26.923 0.00 0.00 0.00 2.57
3139 4390 9.646336 GCAATATTTTTCATCTCAAAATCATGC 57.354 29.630 10.04 10.04 37.72 4.06
3147 4398 9.545105 ACTGTTTTGCAATATTTTTCATCTCAA 57.455 25.926 0.00 0.00 0.00 3.02
3159 4410 9.899661 TCATACCTAAGTACTGTTTTGCAATAT 57.100 29.630 0.00 0.00 0.00 1.28
3160 4411 9.899661 ATCATACCTAAGTACTGTTTTGCAATA 57.100 29.630 0.00 0.00 0.00 1.90
3161 4412 8.807948 ATCATACCTAAGTACTGTTTTGCAAT 57.192 30.769 0.00 0.00 0.00 3.56
3162 4413 8.630054 AATCATACCTAAGTACTGTTTTGCAA 57.370 30.769 0.00 0.00 0.00 4.08
3163 4414 7.880713 TGAATCATACCTAAGTACTGTTTTGCA 59.119 33.333 0.00 0.00 0.00 4.08
3164 4415 8.175716 GTGAATCATACCTAAGTACTGTTTTGC 58.824 37.037 0.00 0.00 0.00 3.68
3165 4416 9.436957 AGTGAATCATACCTAAGTACTGTTTTG 57.563 33.333 0.00 0.00 0.00 2.44
3166 4417 9.654663 GAGTGAATCATACCTAAGTACTGTTTT 57.345 33.333 0.00 0.00 0.00 2.43
3167 4418 9.036980 AGAGTGAATCATACCTAAGTACTGTTT 57.963 33.333 0.00 0.00 0.00 2.83
3168 4419 8.470805 CAGAGTGAATCATACCTAAGTACTGTT 58.529 37.037 0.00 0.00 0.00 3.16
3169 4420 7.616150 ACAGAGTGAATCATACCTAAGTACTGT 59.384 37.037 0.00 0.00 0.00 3.55
3170 4421 8.001881 ACAGAGTGAATCATACCTAAGTACTG 57.998 38.462 0.00 0.00 0.00 2.74
3171 4422 9.122779 GTACAGAGTGAATCATACCTAAGTACT 57.877 37.037 0.00 0.00 0.00 2.73
3172 4423 8.068977 CGTACAGAGTGAATCATACCTAAGTAC 58.931 40.741 0.00 0.00 0.00 2.73
3173 4424 7.255035 GCGTACAGAGTGAATCATACCTAAGTA 60.255 40.741 0.00 0.00 0.00 2.24
3174 4425 6.459848 GCGTACAGAGTGAATCATACCTAAGT 60.460 42.308 0.00 0.00 0.00 2.24
3175 4426 5.915758 GCGTACAGAGTGAATCATACCTAAG 59.084 44.000 0.00 0.00 0.00 2.18
3176 4427 5.358725 TGCGTACAGAGTGAATCATACCTAA 59.641 40.000 0.00 0.00 0.00 2.69
3177 4428 4.885325 TGCGTACAGAGTGAATCATACCTA 59.115 41.667 0.00 0.00 0.00 3.08
3178 4429 3.699538 TGCGTACAGAGTGAATCATACCT 59.300 43.478 0.00 0.00 0.00 3.08
3179 4430 4.041740 TGCGTACAGAGTGAATCATACC 57.958 45.455 0.00 0.00 0.00 2.73
3180 4431 5.805486 TCTTTGCGTACAGAGTGAATCATAC 59.195 40.000 0.00 0.00 30.16 2.39
3181 4432 5.961272 TCTTTGCGTACAGAGTGAATCATA 58.039 37.500 0.00 0.00 30.16 2.15
3182 4433 4.820897 TCTTTGCGTACAGAGTGAATCAT 58.179 39.130 0.00 0.00 30.16 2.45
3183 4434 4.251543 TCTTTGCGTACAGAGTGAATCA 57.748 40.909 0.00 0.00 30.16 2.57
3184 4435 4.923871 TCTTCTTTGCGTACAGAGTGAATC 59.076 41.667 0.00 0.00 30.16 2.52
3185 4436 4.883083 TCTTCTTTGCGTACAGAGTGAAT 58.117 39.130 0.00 0.00 30.16 2.57
3186 4437 4.316205 TCTTCTTTGCGTACAGAGTGAA 57.684 40.909 0.00 0.00 30.16 3.18
3187 4438 4.316205 TTCTTCTTTGCGTACAGAGTGA 57.684 40.909 0.00 0.00 30.16 3.41
3188 4439 5.633601 TGTATTCTTCTTTGCGTACAGAGTG 59.366 40.000 0.00 0.00 30.16 3.51
3189 4440 5.779922 TGTATTCTTCTTTGCGTACAGAGT 58.220 37.500 0.00 0.00 30.16 3.24
3190 4441 6.893958 ATGTATTCTTCTTTGCGTACAGAG 57.106 37.500 0.00 0.00 0.00 3.35
3191 4442 6.649141 ACAATGTATTCTTCTTTGCGTACAGA 59.351 34.615 0.00 0.00 0.00 3.41
3192 4443 6.831769 ACAATGTATTCTTCTTTGCGTACAG 58.168 36.000 0.00 0.00 0.00 2.74
3193 4444 6.128391 GGACAATGTATTCTTCTTTGCGTACA 60.128 38.462 0.00 0.00 0.00 2.90
3194 4445 6.128391 TGGACAATGTATTCTTCTTTGCGTAC 60.128 38.462 0.00 0.00 0.00 3.67
3195 4446 5.935206 TGGACAATGTATTCTTCTTTGCGTA 59.065 36.000 0.00 0.00 0.00 4.42
3196 4447 4.759693 TGGACAATGTATTCTTCTTTGCGT 59.240 37.500 0.00 0.00 0.00 5.24
3197 4448 5.295431 TGGACAATGTATTCTTCTTTGCG 57.705 39.130 0.00 0.00 0.00 4.85
3198 4449 5.574443 GCTTGGACAATGTATTCTTCTTTGC 59.426 40.000 0.00 0.00 0.00 3.68
3222 4473 0.390866 AGAGCACACCTGCAGAATCG 60.391 55.000 17.39 0.00 46.97 3.34
3298 4559 5.178438 GCTACTATTTGCACTAGCTTCCATC 59.822 44.000 0.00 0.00 42.74 3.51
3335 4596 5.064441 CTCAATAAGCTGTGGGAAAAAGG 57.936 43.478 0.00 0.00 0.00 3.11
3349 4610 7.468922 TTCATGACTAACGATGCTCAATAAG 57.531 36.000 0.00 0.00 0.00 1.73
3361 4622 8.673626 ATTTACATTTGCTTTCATGACTAACG 57.326 30.769 0.00 0.00 0.00 3.18
3400 4661 3.754965 AGAAGCCTGTTGTAGCAATTCA 58.245 40.909 0.00 0.00 0.00 2.57
3424 4685 3.502211 GCCTGTTGTAGCAGCTCTAAAAA 59.498 43.478 0.00 0.00 35.28 1.94
3425 4686 3.074412 GCCTGTTGTAGCAGCTCTAAAA 58.926 45.455 0.00 0.00 35.28 1.52
3426 4687 2.303022 AGCCTGTTGTAGCAGCTCTAAA 59.697 45.455 0.00 0.00 35.28 1.85
3427 4688 1.902508 AGCCTGTTGTAGCAGCTCTAA 59.097 47.619 0.00 0.00 35.28 2.10
3428 4689 1.561643 AGCCTGTTGTAGCAGCTCTA 58.438 50.000 0.00 0.00 35.28 2.43
3429 4690 0.689623 AAGCCTGTTGTAGCAGCTCT 59.310 50.000 0.00 0.00 35.28 4.09
3430 4691 1.082690 GAAGCCTGTTGTAGCAGCTC 58.917 55.000 0.00 0.00 35.28 4.09
3431 4692 0.689623 AGAAGCCTGTTGTAGCAGCT 59.310 50.000 0.00 0.00 35.28 4.24
3432 4693 1.082690 GAGAAGCCTGTTGTAGCAGC 58.917 55.000 0.00 0.00 35.28 5.25
3433 4694 1.337260 ACGAGAAGCCTGTTGTAGCAG 60.337 52.381 0.00 0.00 36.31 4.24
3434 4695 0.679505 ACGAGAAGCCTGTTGTAGCA 59.320 50.000 0.00 0.00 0.00 3.49
3435 4696 1.797025 AACGAGAAGCCTGTTGTAGC 58.203 50.000 0.00 0.00 0.00 3.58
3436 4697 8.297426 TGATATATAACGAGAAGCCTGTTGTAG 58.703 37.037 0.00 0.00 0.00 2.74
3437 4698 8.080417 GTGATATATAACGAGAAGCCTGTTGTA 58.920 37.037 0.00 0.00 0.00 2.41
3438 4699 6.924060 GTGATATATAACGAGAAGCCTGTTGT 59.076 38.462 0.00 0.00 0.00 3.32
3439 4700 6.088217 CGTGATATATAACGAGAAGCCTGTTG 59.912 42.308 16.45 0.00 42.32 3.33
3440 4701 6.150318 CGTGATATATAACGAGAAGCCTGTT 58.850 40.000 16.45 0.00 42.32 3.16
3464 4725 8.141909 GGTACTTAGCATTTTCAAATATTCCCC 58.858 37.037 0.00 0.00 0.00 4.81
3522 4784 8.328014 AGCCTCTCTTAATTTCTGAGAAAATCT 58.672 33.333 12.10 2.60 36.56 2.40
3538 4800 7.365497 TCAACATGATCATAAGCCTCTCTTA 57.635 36.000 8.15 0.00 41.17 2.10
3560 4822 3.937814 ACTTTCCGCTGTGATACATTCA 58.062 40.909 0.00 0.00 0.00 2.57
3569 4831 0.234884 GTTCCGAACTTTCCGCTGTG 59.765 55.000 3.88 0.00 0.00 3.66
3576 4838 6.347969 GGGTACAAACATAGTTCCGAACTTTC 60.348 42.308 18.73 0.00 42.81 2.62
3583 4845 4.181578 CAGAGGGTACAAACATAGTTCCG 58.818 47.826 0.00 0.00 0.00 4.30
3632 4894 8.278639 TGGGGTATCAGCATTATCTTCTTTTTA 58.721 33.333 0.00 0.00 0.00 1.52
3643 4906 0.249699 CGCGTGGGGTATCAGCATTA 60.250 55.000 0.00 0.00 0.00 1.90
3667 4932 0.892755 TCTACGCATCCTGTTCCGTT 59.107 50.000 0.00 0.00 35.36 4.44
3668 4933 1.112113 ATCTACGCATCCTGTTCCGT 58.888 50.000 0.00 0.00 37.68 4.69
3676 4941 9.730420 ATTTTGTAAATTTGTATCTACGCATCC 57.270 29.630 0.00 0.00 0.00 3.51
3755 5021 4.931601 TGAGACTTCTTGTGTACATGATGC 59.068 41.667 0.00 0.00 32.23 3.91
3761 5027 8.773645 CATTGTATTTGAGACTTCTTGTGTACA 58.226 33.333 0.00 0.00 0.00 2.90
3767 5033 9.350357 CATTTCCATTGTATTTGAGACTTCTTG 57.650 33.333 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.