Multiple sequence alignment - TraesCS1B01G095600

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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 TraesCS1B01G095600 chr1B 100.000 4088 0 0 1 4088 99591482 99595569 0.000000e+00 7550.0
1 TraesCS1B01G095600 chr1B 87.640 89 8 2 2011 2096 411570500 411570412 2.600000e-17 100.0
2 TraesCS1B01G095600 chr1B 87.342 79 8 2 2016 2092 658497435 658497513 5.630000e-14 89.8
3 TraesCS1B01G095600 chr1D 91.609 2026 90 39 2122 4088 62413381 62415385 0.000000e+00 2726.0
4 TraesCS1B01G095600 chr1D 92.823 1045 29 8 621 1633 62411909 62412939 0.000000e+00 1472.0
5 TraesCS1B01G095600 chr1D 91.525 531 44 1 1 531 62407611 62408140 0.000000e+00 730.0
6 TraesCS1B01G095600 chr1D 93.496 369 23 1 1639 2006 62412995 62413363 7.730000e-152 547.0
7 TraesCS1B01G095600 chr1D 88.608 79 7 2 2016 2092 22976539 22976617 1.210000e-15 95.3
8 TraesCS1B01G095600 chr1A 92.030 1857 94 34 1489 3329 60351975 60353793 0.000000e+00 2560.0
9 TraesCS1B01G095600 chr1A 93.060 562 28 4 931 1489 60351394 60351947 0.000000e+00 811.0
10 TraesCS1B01G095600 chr1A 87.244 635 29 16 3487 4087 60353950 60354566 0.000000e+00 676.0
11 TraesCS1B01G095600 chr1A 95.327 214 8 2 585 797 60350693 60350905 5.060000e-89 339.0
12 TraesCS1B01G095600 chr1A 86.076 79 9 2 2016 2092 567969931 567970009 2.620000e-12 84.2
13 TraesCS1B01G095600 chr2D 91.549 71 4 2 2011 2079 470231791 470231721 3.360000e-16 97.1
14 TraesCS1B01G095600 chr5A 86.207 87 8 4 2009 2092 33929243 33929158 1.560000e-14 91.6
15 TraesCS1B01G095600 chr2A 94.737 57 3 0 2021 2077 102688052 102688108 5.630000e-14 89.8
16 TraesCS1B01G095600 chr6A 86.420 81 7 2 2016 2094 66388086 66388164 7.280000e-13 86.1
17 TraesCS1B01G095600 chr7B 84.884 86 10 2 2011 2093 533770822 533770907 2.620000e-12 84.2


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 TraesCS1B01G095600 chr1B 99591482 99595569 4087 False 7550.00 7550 100.00000 1 4088 1 chr1B.!!$F1 4087
1 TraesCS1B01G095600 chr1D 62407611 62415385 7774 False 1368.75 2726 92.36325 1 4088 4 chr1D.!!$F2 4087
2 TraesCS1B01G095600 chr1A 60350693 60354566 3873 False 1096.50 2560 91.91525 585 4087 4 chr1A.!!$F2 3502

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
554 555 0.106569 CCTGCCTGCCATATCACCAA 60.107 55.0 0.0 0.0 0.0 3.67 F
1955 6103 0.250901 ATCTTGGCTCGCTGTTGGTT 60.251 50.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 6504 0.313672 GAGGAGCGGCTGATGTCTAG 59.686 60.0 7.5 0.0 0.0 2.43 R
3450 7607 0.034896 CAACAGTCGCCCCAGTAAGT 59.965 55.0 0.0 0.0 0.0 2.24 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
34 35 6.172136 AGGAGAGATATGTGTCAAATGAGG 57.828 41.667 0.00 0.00 0.00 3.86
41 42 7.275920 AGATATGTGTCAAATGAGGGAGTTAC 58.724 38.462 0.00 0.00 0.00 2.50
43 44 6.620877 ATGTGTCAAATGAGGGAGTTACTA 57.379 37.500 0.00 0.00 0.00 1.82
69 70 6.425721 AGAATAAATGAACAAACGACCGAAGA 59.574 34.615 0.00 0.00 0.00 2.87
82 83 2.869192 GACCGAAGAGAATGGAAGATGC 59.131 50.000 0.00 0.00 0.00 3.91
92 93 1.377202 GGAAGATGCCGTGGAAGCA 60.377 57.895 0.00 0.00 45.94 3.91
107 108 4.702131 GTGGAAGCAAATGTAGGAAGACAT 59.298 41.667 0.00 0.00 41.92 3.06
113 114 9.294030 GAAGCAAATGTAGGAAGACATTATTTG 57.706 33.333 2.42 0.00 46.84 2.32
154 155 9.422196 GAATTCAACTTCGTGTAGTATTTATGC 57.578 33.333 0.00 0.00 0.00 3.14
202 203 8.932791 CACTCAACCTTACGTAGAATTTATGTT 58.067 33.333 0.00 0.00 0.00 2.71
211 212 5.411361 ACGTAGAATTTATGTTGCAGCTCAA 59.589 36.000 1.17 0.00 0.00 3.02
213 214 5.320549 AGAATTTATGTTGCAGCTCAAGG 57.679 39.130 1.17 0.00 34.91 3.61
228 229 2.484264 CTCAAGGAAACGACAATCCCAC 59.516 50.000 0.00 0.00 36.31 4.61
348 349 5.703592 ACATAAAACAAGACTATCGTGCCAA 59.296 36.000 0.00 0.00 28.70 4.52
364 365 1.600023 CCAAACGTGACCTTAAGCCA 58.400 50.000 0.00 0.00 0.00 4.75
395 396 3.123050 TCTTCCACGCACATAATCGATG 58.877 45.455 0.00 0.00 41.79 3.84
402 403 4.900182 CACGCACATAATCGATGTCAAATC 59.100 41.667 0.00 0.00 46.33 2.17
405 406 5.277011 CGCACATAATCGATGTCAAATCTGT 60.277 40.000 0.00 0.00 46.33 3.41
436 437 8.237811 ACAATCTTTCCTAACACAAAGTCATT 57.762 30.769 0.00 0.00 32.37 2.57
443 444 6.815089 TCCTAACACAAAGTCATTGCAAATT 58.185 32.000 1.71 0.00 43.13 1.82
444 445 7.271511 TCCTAACACAAAGTCATTGCAAATTT 58.728 30.769 1.71 0.00 43.13 1.82
462 463 6.307318 GCAAATTTCATGTTGCTTCTCTACAG 59.693 38.462 10.59 0.00 45.34 2.74
475 476 5.626578 GCTTCTCTACAGCAGAATCTTTCCT 60.627 44.000 0.00 0.00 37.22 3.36
501 502 6.858993 ACACAAAATCATTGCAAATTTCATGC 59.141 30.769 1.71 0.00 44.08 4.06
509 510 3.581755 TGCAAATTTCATGCTGCTTCTC 58.418 40.909 0.00 0.00 44.14 2.87
510 511 3.257375 TGCAAATTTCATGCTGCTTCTCT 59.743 39.130 0.00 0.00 44.14 3.10
533 534 9.462174 CTCTACATCAGAGTCAAATATGAAGAC 57.538 37.037 0.00 0.00 45.10 3.01
534 535 8.971073 TCTACATCAGAGTCAAATATGAAGACA 58.029 33.333 0.00 0.00 37.30 3.41
536 537 6.820656 ACATCAGAGTCAAATATGAAGACACC 59.179 38.462 0.00 0.00 37.30 4.16
540 541 4.265073 AGTCAAATATGAAGACACCTGCC 58.735 43.478 0.00 0.00 37.30 4.85
543 544 2.338577 ATATGAAGACACCTGCCTGC 57.661 50.000 0.00 0.00 0.00 4.85
544 545 0.253044 TATGAAGACACCTGCCTGCC 59.747 55.000 0.00 0.00 0.00 4.85
550 551 0.181114 GACACCTGCCTGCCATATCA 59.819 55.000 0.00 0.00 0.00 2.15
551 552 0.107017 ACACCTGCCTGCCATATCAC 60.107 55.000 0.00 0.00 0.00 3.06
552 553 0.820891 CACCTGCCTGCCATATCACC 60.821 60.000 0.00 0.00 0.00 4.02
553 554 1.281199 ACCTGCCTGCCATATCACCA 61.281 55.000 0.00 0.00 0.00 4.17
554 555 0.106569 CCTGCCTGCCATATCACCAA 60.107 55.000 0.00 0.00 0.00 3.67
555 556 1.685803 CCTGCCTGCCATATCACCAAA 60.686 52.381 0.00 0.00 0.00 3.28
558 559 3.106054 TGCCTGCCATATCACCAAATTT 58.894 40.909 0.00 0.00 0.00 1.82
560 561 3.132646 GCCTGCCATATCACCAAATTTCA 59.867 43.478 0.00 0.00 0.00 2.69
561 562 4.202284 GCCTGCCATATCACCAAATTTCAT 60.202 41.667 0.00 0.00 0.00 2.57
563 564 5.163385 CCTGCCATATCACCAAATTTCATGT 60.163 40.000 0.00 0.00 0.00 3.21
565 566 6.107343 TGCCATATCACCAAATTTCATGTTG 58.893 36.000 0.00 0.00 0.00 3.33
566 567 5.006941 GCCATATCACCAAATTTCATGTTGC 59.993 40.000 0.00 0.00 0.00 4.17
567 568 6.342906 CCATATCACCAAATTTCATGTTGCT 58.657 36.000 0.00 0.00 0.00 3.91
568 569 6.477688 CCATATCACCAAATTTCATGTTGCTC 59.522 38.462 0.00 0.00 0.00 4.26
569 570 5.733620 ATCACCAAATTTCATGTTGCTCT 57.266 34.783 0.00 0.00 0.00 4.09
570 571 6.839124 ATCACCAAATTTCATGTTGCTCTA 57.161 33.333 0.00 0.00 0.00 2.43
604 4302 3.593442 ACTCCAACACCCAAATCAGAA 57.407 42.857 0.00 0.00 0.00 3.02
609 4307 4.141274 TCCAACACCCAAATCAGAAAGAGA 60.141 41.667 0.00 0.00 0.00 3.10
610 4308 4.022849 CCAACACCCAAATCAGAAAGAGAC 60.023 45.833 0.00 0.00 0.00 3.36
611 4309 4.437682 ACACCCAAATCAGAAAGAGACA 57.562 40.909 0.00 0.00 0.00 3.41
613 4311 4.103153 ACACCCAAATCAGAAAGAGACAGA 59.897 41.667 0.00 0.00 0.00 3.41
614 4312 4.694509 CACCCAAATCAGAAAGAGACAGAG 59.305 45.833 0.00 0.00 0.00 3.35
615 4313 4.594920 ACCCAAATCAGAAAGAGACAGAGA 59.405 41.667 0.00 0.00 0.00 3.10
616 4314 5.177326 CCCAAATCAGAAAGAGACAGAGAG 58.823 45.833 0.00 0.00 0.00 3.20
617 4315 5.177326 CCAAATCAGAAAGAGACAGAGAGG 58.823 45.833 0.00 0.00 0.00 3.69
929 4631 0.515564 CGGATCGAGCGGTTGTTTTT 59.484 50.000 1.01 0.00 0.00 1.94
1082 5138 4.265056 GTGTGTCGCCAAGGGGGT 62.265 66.667 3.15 0.00 39.65 4.95
1123 5185 3.077556 CGGAGGTGGAGGTGGAGG 61.078 72.222 0.00 0.00 0.00 4.30
1124 5186 2.122954 GGAGGTGGAGGTGGAGGT 59.877 66.667 0.00 0.00 0.00 3.85
1125 5187 1.990614 GGAGGTGGAGGTGGAGGTC 60.991 68.421 0.00 0.00 0.00 3.85
1126 5188 2.283966 AGGTGGAGGTGGAGGTCG 60.284 66.667 0.00 0.00 0.00 4.79
1127 5189 2.283676 GGTGGAGGTGGAGGTCGA 60.284 66.667 0.00 0.00 0.00 4.20
1128 5190 2.352032 GGTGGAGGTGGAGGTCGAG 61.352 68.421 0.00 0.00 0.00 4.04
1159 5221 1.376424 CTGCCTCGCATGGTGAGTT 60.376 57.895 6.11 0.00 38.37 3.01
1201 5263 4.100808 CCTCTCTTTGCTCCTATGCTAGTT 59.899 45.833 0.00 0.00 0.00 2.24
1280 5342 3.743521 TGCTGTATGCTTTCTTGTCTGT 58.256 40.909 0.00 0.00 43.37 3.41
1282 5344 4.214119 TGCTGTATGCTTTCTTGTCTGTTC 59.786 41.667 0.00 0.00 43.37 3.18
1369 5431 6.949352 ATGGCCATACTATTCTTGAAGTTG 57.051 37.500 19.18 0.00 0.00 3.16
1375 5437 7.229506 GCCATACTATTCTTGAAGTTGGCTTAT 59.770 37.037 15.30 0.00 41.51 1.73
1376 5438 9.778741 CCATACTATTCTTGAAGTTGGCTTATA 57.221 33.333 0.00 0.00 34.61 0.98
1379 5441 8.723942 ACTATTCTTGAAGTTGGCTTATACAG 57.276 34.615 0.00 0.00 34.61 2.74
1380 5442 8.322091 ACTATTCTTGAAGTTGGCTTATACAGT 58.678 33.333 0.00 0.00 34.61 3.55
1381 5443 9.817809 CTATTCTTGAAGTTGGCTTATACAGTA 57.182 33.333 0.00 0.00 34.61 2.74
1382 5444 8.723942 ATTCTTGAAGTTGGCTTATACAGTAG 57.276 34.615 0.00 0.00 34.61 2.57
1417 5479 6.066054 GAAGTTTGGTTTCTCTTCCTCTTG 57.934 41.667 0.00 0.00 32.73 3.02
1437 5502 3.282021 TGCAAGGAATGGTTATCTGCTC 58.718 45.455 0.00 0.00 0.00 4.26
1643 5739 5.925397 CAGGTTTTTGCTGCAAATATGTGTA 59.075 36.000 26.48 8.81 33.19 2.90
1644 5740 6.089820 CAGGTTTTTGCTGCAAATATGTGTAG 59.910 38.462 26.48 6.62 33.19 2.74
1708 5856 6.864165 GTCGGGCTTTTAATCATGTTGTTTAA 59.136 34.615 0.00 0.00 0.00 1.52
1726 5874 6.607019 TGTTTAACAGACTATGGGGAAAAGT 58.393 36.000 0.00 0.00 0.00 2.66
1732 5880 6.424032 ACAGACTATGGGGAAAAGTTTATCC 58.576 40.000 7.79 7.79 34.85 2.59
1753 5901 9.619316 TTATCCTGTTTGTATTTGTTTCGAATG 57.381 29.630 0.00 0.00 0.00 2.67
1934 6082 3.259374 TCCGGATAGATGATCTTTCAGCC 59.741 47.826 13.55 2.09 39.11 4.85
1955 6103 0.250901 ATCTTGGCTCGCTGTTGGTT 60.251 50.000 0.00 0.00 0.00 3.67
1989 6137 3.190439 AGTGCCTTCTATGGGGTAAGTT 58.810 45.455 0.00 0.00 0.00 2.66
1995 6143 6.444493 TGCCTTCTATGGGGTAAGTTAGTAAA 59.556 38.462 0.00 0.00 0.00 2.01
2100 6248 8.519799 TTTTTATAGAGGGAGTATTTGCTTGG 57.480 34.615 0.00 0.00 0.00 3.61
2115 6263 2.867429 GCTTGGTGCATTATGTCACAC 58.133 47.619 16.82 7.28 42.31 3.82
2116 6264 2.728846 GCTTGGTGCATTATGTCACACG 60.729 50.000 16.82 8.69 42.31 4.49
2117 6265 1.447945 TGGTGCATTATGTCACACGG 58.552 50.000 16.82 0.00 35.04 4.94
2118 6266 1.271108 TGGTGCATTATGTCACACGGT 60.271 47.619 16.82 0.00 35.04 4.83
2119 6267 1.396996 GGTGCATTATGTCACACGGTC 59.603 52.381 16.82 1.81 35.04 4.79
2120 6268 2.073056 GTGCATTATGTCACACGGTCA 58.927 47.619 12.42 0.00 33.63 4.02
2126 6274 5.541845 CATTATGTCACACGGTCATATCCT 58.458 41.667 0.00 0.00 0.00 3.24
2178 6326 4.471904 TTCCTCTGCTTGTATGTAGGTG 57.528 45.455 0.00 0.00 0.00 4.00
2199 6347 3.105928 GATGGCCATGGGGGTCCT 61.106 66.667 26.56 0.00 42.20 3.85
2223 6371 2.086869 GCTGCAGCCTACATGAAAAGA 58.913 47.619 28.76 0.00 34.31 2.52
2239 6387 3.446442 AAAGACATGCCATGAGGTTCT 57.554 42.857 12.53 0.36 37.19 3.01
2295 6443 7.289310 TGCAAGTGGATGATATATTCCTTCAA 58.711 34.615 5.28 0.00 32.95 2.69
2301 6449 7.607991 GTGGATGATATATTCCTTCAATCCGTT 59.392 37.037 5.28 0.00 32.95 4.44
2337 6485 4.090057 GCGTTCCTGCAAGCCGAC 62.090 66.667 0.00 0.00 34.15 4.79
2356 6504 0.590195 CCTTGCGCTGGCTGATAATC 59.410 55.000 9.73 0.00 40.82 1.75
2385 6533 3.599584 CGCTCCTCCGGAACTACA 58.400 61.111 5.23 0.00 0.00 2.74
2401 6549 2.270923 CTACAGCACTCGCAGCATTAA 58.729 47.619 0.00 0.00 42.27 1.40
2586 6734 1.674221 GGCATAGCGATGGAGATGTCC 60.674 57.143 8.97 0.83 44.24 4.02
2713 6861 1.596934 GGCGACTGGGACATGAAGA 59.403 57.895 0.00 0.00 38.20 2.87
2718 6866 1.211457 GACTGGGACATGAAGATGCCT 59.789 52.381 0.00 0.00 38.20 4.75
2952 7100 0.320421 CCGACAACCTCACCGTCATT 60.320 55.000 0.00 0.00 0.00 2.57
2964 7112 0.667993 CCGTCATTGTGGTGTGCTTT 59.332 50.000 0.00 0.00 0.00 3.51
3076 7224 2.686470 TGAGGAGCTGGCTGGAGG 60.686 66.667 0.00 0.00 0.00 4.30
3088 7236 3.438017 CTGGAGGCTGACCGCTAGC 62.438 68.421 4.06 4.06 37.52 3.42
3089 7237 3.151022 GGAGGCTGACCGCTAGCT 61.151 66.667 13.93 0.00 42.76 3.32
3094 7242 1.065600 GCTGACCGCTAGCTCTCTG 59.934 63.158 13.93 11.29 38.14 3.35
3116 7264 0.392595 TTGAGATGCCTGCTCTGCTG 60.393 55.000 0.00 0.00 33.57 4.41
3119 7267 2.124653 ATGCCTGCTCTGCTGCTC 60.125 61.111 0.00 0.00 0.00 4.26
3122 7270 2.125065 CCTGCTCTGCTGCTCCTG 60.125 66.667 0.00 0.00 0.00 3.86
3124 7272 3.318006 CTGCTCTGCTGCTCCTGCT 62.318 63.158 0.00 0.00 40.48 4.24
3196 7344 2.905075 TCGGTCGAGGAATCGTAACTA 58.095 47.619 0.00 0.00 0.00 2.24
3340 7494 6.334989 TGCTGTTGTACATAGTACATGGTAC 58.665 40.000 10.44 11.70 37.28 3.34
3354 7508 0.458889 TGGTACTACATCCGTTGCGC 60.459 55.000 0.00 0.00 0.00 6.09
3450 7607 5.240844 TCGATTCAGAGAAGTGTGAGTGTTA 59.759 40.000 0.00 0.00 0.00 2.41
3451 7608 5.343593 CGATTCAGAGAAGTGTGAGTGTTAC 59.656 44.000 0.00 0.00 0.00 2.50
3460 7617 3.323979 AGTGTGAGTGTTACTTACTGGGG 59.676 47.826 5.64 0.00 35.92 4.96
3463 7620 1.547372 GAGTGTTACTTACTGGGGCGA 59.453 52.381 0.00 0.00 0.00 5.54
3465 7622 1.274447 GTGTTACTTACTGGGGCGACT 59.726 52.381 0.00 0.00 0.00 4.18
3520 7724 6.787085 AACTCTTCATGAAAAACTAGGACG 57.213 37.500 9.88 0.00 0.00 4.79
3521 7725 6.097915 ACTCTTCATGAAAAACTAGGACGA 57.902 37.500 9.88 0.00 0.00 4.20
3522 7726 6.702329 ACTCTTCATGAAAAACTAGGACGAT 58.298 36.000 9.88 0.00 0.00 3.73
3523 7727 6.591834 ACTCTTCATGAAAAACTAGGACGATG 59.408 38.462 9.88 0.00 0.00 3.84
3524 7728 5.351465 TCTTCATGAAAAACTAGGACGATGC 59.649 40.000 9.88 0.00 0.00 3.91
3525 7729 4.832248 TCATGAAAAACTAGGACGATGCT 58.168 39.130 0.00 0.00 0.00 3.79
3527 7731 5.351465 TCATGAAAAACTAGGACGATGCTTC 59.649 40.000 0.00 0.00 0.00 3.86
3549 7775 3.181488 CGCCATCAGCTAGAGATCATAGG 60.181 52.174 0.00 0.00 40.39 2.57
3578 7808 1.523154 GCCGTGGTGAATGAAGCCAA 61.523 55.000 0.00 0.00 33.66 4.52
3593 7823 0.448197 GCCAAAGAAGACTTAGCGGC 59.552 55.000 0.00 0.00 38.19 6.53
3599 7829 1.362406 GAAGACTTAGCGGCAGTGGC 61.362 60.000 6.62 6.62 40.13 5.01
3610 7840 1.742831 CGGCAGTGGCAAATTTAGCTA 59.257 47.619 17.80 0.00 43.71 3.32
3622 7852 6.751888 GGCAAATTTAGCTAAACATACCACTG 59.248 38.462 20.85 8.94 0.00 3.66
3711 7949 0.250513 CTCACCTAACCCACAGCTCC 59.749 60.000 0.00 0.00 0.00 4.70
3769 8027 3.914426 TCTGCCTTCCCTAAATCTGAC 57.086 47.619 0.00 0.00 0.00 3.51
3794 8052 1.739466 CGCCTAAAAATCAGCTGCAGA 59.261 47.619 20.43 0.00 0.00 4.26
3914 8173 1.557832 CCACGGAAGGGAAGGTGATAA 59.442 52.381 0.00 0.00 35.60 1.75
3916 8175 1.838077 ACGGAAGGGAAGGTGATAAGG 59.162 52.381 0.00 0.00 0.00 2.69
3917 8176 1.475213 CGGAAGGGAAGGTGATAAGGC 60.475 57.143 0.00 0.00 0.00 4.35
3918 8177 1.564348 GGAAGGGAAGGTGATAAGGCA 59.436 52.381 0.00 0.00 0.00 4.75
3990 8252 2.359602 CAGTCACTGGCCTGCAGG 60.360 66.667 29.34 29.34 38.53 4.85
3992 8254 2.149383 AGTCACTGGCCTGCAGGAA 61.149 57.895 37.21 21.71 37.39 3.36
3994 8256 2.674380 CACTGGCCTGCAGGAACC 60.674 66.667 37.21 27.54 37.39 3.62
3995 8257 3.971702 ACTGGCCTGCAGGAACCC 61.972 66.667 37.21 26.80 37.39 4.11
3996 8258 3.655211 CTGGCCTGCAGGAACCCT 61.655 66.667 37.21 0.00 37.39 4.34
4067 8337 2.958355 ACCCACAAGAGTCAAATGGTTG 59.042 45.455 0.00 0.00 35.95 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.034635 ACACATATCTCTCCTCACCACC 58.965 50.000 0.00 0.00 0.00 4.61
9 10 6.183360 CCTCATTTGACACATATCTCTCCTCA 60.183 42.308 0.00 0.00 0.00 3.86
10 11 6.222389 CCTCATTTGACACATATCTCTCCTC 58.778 44.000 0.00 0.00 0.00 3.71
41 42 7.735500 TCGGTCGTTTGTTCATTTATTCTTAG 58.264 34.615 0.00 0.00 0.00 2.18
43 44 6.548441 TCGGTCGTTTGTTCATTTATTCTT 57.452 33.333 0.00 0.00 0.00 2.52
53 54 3.120649 CCATTCTCTTCGGTCGTTTGTTC 60.121 47.826 0.00 0.00 0.00 3.18
63 64 2.216898 GGCATCTTCCATTCTCTTCGG 58.783 52.381 0.00 0.00 0.00 4.30
69 70 0.911769 TCCACGGCATCTTCCATTCT 59.088 50.000 0.00 0.00 0.00 2.40
82 83 2.107950 TCCTACATTTGCTTCCACGG 57.892 50.000 0.00 0.00 0.00 4.94
107 108 9.393249 GAATTCAGACATCAAAACGACAAATAA 57.607 29.630 0.00 0.00 0.00 1.40
113 114 6.430451 AGTTGAATTCAGACATCAAAACGAC 58.570 36.000 8.41 0.00 35.07 4.34
122 123 6.223852 ACTACACGAAGTTGAATTCAGACAT 58.776 36.000 8.41 3.59 41.61 3.06
154 155 2.323939 TTATTTGACAAGCAACGCGG 57.676 45.000 12.47 0.00 35.91 6.46
202 203 0.179059 TGTCGTTTCCTTGAGCTGCA 60.179 50.000 1.02 0.00 0.00 4.41
211 212 2.779506 GAAGTGGGATTGTCGTTTCCT 58.220 47.619 0.00 0.00 32.34 3.36
213 214 1.463444 CCGAAGTGGGATTGTCGTTTC 59.537 52.381 0.00 0.00 0.00 2.78
228 229 1.400242 GCAGCTGCAACTAAACCGAAG 60.400 52.381 33.36 0.00 41.59 3.79
342 343 1.334689 GCTTAAGGTCACGTTTGGCAC 60.335 52.381 4.29 0.00 0.00 5.01
345 346 1.265905 GTGGCTTAAGGTCACGTTTGG 59.734 52.381 4.29 0.00 40.88 3.28
364 365 0.598065 GCGTGGAAGATGCCTTTTGT 59.402 50.000 0.00 0.00 31.62 2.83
372 373 3.123050 TCGATTATGTGCGTGGAAGATG 58.877 45.455 0.00 0.00 0.00 2.90
395 396 3.187227 AGATTGTCGTGCACAGATTTGAC 59.813 43.478 18.64 14.69 35.97 3.18
402 403 2.146342 AGGAAAGATTGTCGTGCACAG 58.854 47.619 18.64 9.95 35.97 3.66
405 406 3.496884 GTGTTAGGAAAGATTGTCGTGCA 59.503 43.478 0.00 0.00 0.00 4.57
462 463 6.913170 TGATTTTGTGTAGGAAAGATTCTGC 58.087 36.000 0.00 0.00 0.00 4.26
465 466 7.814107 TGCAATGATTTTGTGTAGGAAAGATTC 59.186 33.333 0.00 0.00 0.00 2.52
475 476 8.016229 GCATGAAATTTGCAATGATTTTGTGTA 58.984 29.630 9.80 0.00 39.90 2.90
509 510 9.029243 GTGTCTTCATATTTGACTCTGATGTAG 57.971 37.037 0.00 0.00 0.00 2.74
510 511 7.981789 GGTGTCTTCATATTTGACTCTGATGTA 59.018 37.037 0.00 0.00 0.00 2.29
519 520 4.095483 CAGGCAGGTGTCTTCATATTTGAC 59.905 45.833 0.00 0.00 0.00 3.18
520 521 4.264253 CAGGCAGGTGTCTTCATATTTGA 58.736 43.478 0.00 0.00 0.00 2.69
524 525 1.133976 GGCAGGCAGGTGTCTTCATAT 60.134 52.381 0.00 0.00 0.00 1.78
531 532 0.181114 TGATATGGCAGGCAGGTGTC 59.819 55.000 1.89 0.00 0.00 3.67
533 534 0.820891 GGTGATATGGCAGGCAGGTG 60.821 60.000 1.89 0.00 0.00 4.00
534 535 1.281199 TGGTGATATGGCAGGCAGGT 61.281 55.000 1.89 0.00 0.00 4.00
536 537 1.766494 TTTGGTGATATGGCAGGCAG 58.234 50.000 1.89 0.00 0.00 4.85
540 541 5.909477 ACATGAAATTTGGTGATATGGCAG 58.091 37.500 0.00 0.00 0.00 4.85
543 544 6.342906 AGCAACATGAAATTTGGTGATATGG 58.657 36.000 0.00 0.00 33.51 2.74
544 545 7.262772 AGAGCAACATGAAATTTGGTGATATG 58.737 34.615 0.00 0.00 33.51 1.78
550 551 7.039504 AGTGAATAGAGCAACATGAAATTTGGT 60.040 33.333 0.00 0.00 36.17 3.67
551 552 7.318141 AGTGAATAGAGCAACATGAAATTTGG 58.682 34.615 0.00 0.00 0.00 3.28
552 553 8.752766 AAGTGAATAGAGCAACATGAAATTTG 57.247 30.769 0.00 0.00 0.00 2.32
553 554 9.768662 AAAAGTGAATAGAGCAACATGAAATTT 57.231 25.926 0.00 0.00 0.00 1.82
554 555 9.199982 CAAAAGTGAATAGAGCAACATGAAATT 57.800 29.630 0.00 0.00 0.00 1.82
555 556 8.362639 ACAAAAGTGAATAGAGCAACATGAAAT 58.637 29.630 0.00 0.00 0.00 2.17
558 559 6.882610 ACAAAAGTGAATAGAGCAACATGA 57.117 33.333 0.00 0.00 0.00 3.07
560 561 8.850156 AGTTAACAAAAGTGAATAGAGCAACAT 58.150 29.630 8.61 0.00 0.00 2.71
561 562 8.220755 AGTTAACAAAAGTGAATAGAGCAACA 57.779 30.769 8.61 0.00 0.00 3.33
563 564 7.500892 TGGAGTTAACAAAAGTGAATAGAGCAA 59.499 33.333 8.61 0.00 0.00 3.91
565 566 7.435068 TGGAGTTAACAAAAGTGAATAGAGC 57.565 36.000 8.61 0.00 0.00 4.09
566 567 8.836413 TGTTGGAGTTAACAAAAGTGAATAGAG 58.164 33.333 8.61 0.00 37.60 2.43
567 568 8.617809 GTGTTGGAGTTAACAAAAGTGAATAGA 58.382 33.333 8.61 0.00 41.75 1.98
568 569 7.860872 GGTGTTGGAGTTAACAAAAGTGAATAG 59.139 37.037 8.61 0.00 41.75 1.73
569 570 7.201839 GGGTGTTGGAGTTAACAAAAGTGAATA 60.202 37.037 8.61 0.00 41.75 1.75
570 571 6.406512 GGGTGTTGGAGTTAACAAAAGTGAAT 60.407 38.462 8.61 0.00 41.75 2.57
604 4302 1.287739 CTCTCCCCCTCTCTGTCTCTT 59.712 57.143 0.00 0.00 0.00 2.85
609 4307 2.641746 CCCCTCTCCCCCTCTCTGT 61.642 68.421 0.00 0.00 0.00 3.41
610 4308 1.891296 TTCCCCTCTCCCCCTCTCTG 61.891 65.000 0.00 0.00 0.00 3.35
611 4309 1.162951 TTTCCCCTCTCCCCCTCTCT 61.163 60.000 0.00 0.00 0.00 3.10
613 4311 0.327964 CATTTCCCCTCTCCCCCTCT 60.328 60.000 0.00 0.00 0.00 3.69
614 4312 0.327576 TCATTTCCCCTCTCCCCCTC 60.328 60.000 0.00 0.00 0.00 4.30
615 4313 0.123266 TTCATTTCCCCTCTCCCCCT 59.877 55.000 0.00 0.00 0.00 4.79
616 4314 1.145945 GATTCATTTCCCCTCTCCCCC 59.854 57.143 0.00 0.00 0.00 5.40
617 4315 1.852965 TGATTCATTTCCCCTCTCCCC 59.147 52.381 0.00 0.00 0.00 4.81
929 4631 7.201911 GGAAAAGAAAGGAGAAATCTTCCAACA 60.202 37.037 0.00 0.00 32.45 3.33
987 5043 4.457496 ACCATCTCCGCGCACCAG 62.457 66.667 8.75 0.00 0.00 4.00
988 5044 4.758251 CACCATCTCCGCGCACCA 62.758 66.667 8.75 0.00 0.00 4.17
1123 5185 4.517703 CTCGACGGCGACCTCGAC 62.518 72.222 10.67 0.00 42.51 4.20
1126 5188 4.838486 CAGCTCGACGGCGACCTC 62.838 72.222 10.67 1.14 42.51 3.85
1159 5221 2.044252 AGGAGTCTTAGCGGCGGA 60.044 61.111 9.78 0.00 0.00 5.54
1201 5263 6.044054 TCTCTTTAGGGATATACGGTCTCAGA 59.956 42.308 0.00 0.00 0.00 3.27
1280 5342 5.408604 GCGTCCTCAAATCTGTTCTAAAGAA 59.591 40.000 0.00 0.00 0.00 2.52
1282 5344 4.690748 TGCGTCCTCAAATCTGTTCTAAAG 59.309 41.667 0.00 0.00 0.00 1.85
1369 5431 6.015603 CCCTAACCAGTACTACTGTATAAGCC 60.016 46.154 14.00 0.00 44.50 4.35
1375 5437 6.144845 ACTTCCCTAACCAGTACTACTGTA 57.855 41.667 14.00 1.95 44.50 2.74
1376 5438 5.008165 ACTTCCCTAACCAGTACTACTGT 57.992 43.478 14.00 0.91 44.50 3.55
1377 5439 5.997384 AACTTCCCTAACCAGTACTACTG 57.003 43.478 9.02 9.02 45.53 2.74
1378 5440 5.247792 CCAAACTTCCCTAACCAGTACTACT 59.752 44.000 0.00 0.00 0.00 2.57
1379 5441 5.012458 ACCAAACTTCCCTAACCAGTACTAC 59.988 44.000 0.00 0.00 0.00 2.73
1380 5442 5.157395 ACCAAACTTCCCTAACCAGTACTA 58.843 41.667 0.00 0.00 0.00 1.82
1381 5443 3.978672 ACCAAACTTCCCTAACCAGTACT 59.021 43.478 0.00 0.00 0.00 2.73
1382 5444 4.362470 ACCAAACTTCCCTAACCAGTAC 57.638 45.455 0.00 0.00 0.00 2.73
1417 5479 2.289002 CGAGCAGATAACCATTCCTTGC 59.711 50.000 0.00 0.00 0.00 4.01
1437 5502 1.872952 TGTCAGACTTTTGCATCCACG 59.127 47.619 1.31 0.00 0.00 4.94
1518 5611 7.902920 ACACAAATGGCTCCAATAATTAGAT 57.097 32.000 0.00 0.00 0.00 1.98
1643 5739 3.566523 GTCTCAATCGTTTCGTCAGACT 58.433 45.455 0.00 0.00 0.00 3.24
1644 5740 2.662156 GGTCTCAATCGTTTCGTCAGAC 59.338 50.000 0.00 0.00 0.00 3.51
1708 5856 6.217693 AGGATAAACTTTTCCCCATAGTCTGT 59.782 38.462 0.00 0.00 32.05 3.41
1732 5880 6.746104 TGCATTCGAAACAAATACAAACAG 57.254 33.333 0.00 0.00 0.00 3.16
1753 5901 4.584327 ACATTACCACCTTGTTTCTTGC 57.416 40.909 0.00 0.00 0.00 4.01
1832 5980 4.734843 ATTGGGTACAAACTGTAGGGTT 57.265 40.909 0.00 0.00 40.55 4.11
1835 5983 5.526111 CCGAATATTGGGTACAAACTGTAGG 59.474 44.000 8.28 0.00 40.55 3.18
1934 6082 1.651240 CCAACAGCGAGCCAAGATGG 61.651 60.000 0.00 0.00 41.55 3.51
2074 6222 9.136323 CCAAGCAAATACTCCCTCTATAAAAAT 57.864 33.333 0.00 0.00 0.00 1.82
2076 6224 7.556275 CACCAAGCAAATACTCCCTCTATAAAA 59.444 37.037 0.00 0.00 0.00 1.52
2081 6229 3.370527 GCACCAAGCAAATACTCCCTCTA 60.371 47.826 0.00 0.00 44.79 2.43
2082 6230 2.619074 GCACCAAGCAAATACTCCCTCT 60.619 50.000 0.00 0.00 44.79 3.69
2100 6248 2.073056 TGACCGTGTGACATAATGCAC 58.927 47.619 0.00 0.00 35.63 4.57
2107 6255 3.031013 TGAGGATATGACCGTGTGACAT 58.969 45.455 0.00 0.00 34.73 3.06
2108 6256 2.427095 CTGAGGATATGACCGTGTGACA 59.573 50.000 0.00 0.00 34.73 3.58
2109 6257 2.799917 GCTGAGGATATGACCGTGTGAC 60.800 54.545 0.00 0.00 34.73 3.67
2110 6258 1.409064 GCTGAGGATATGACCGTGTGA 59.591 52.381 0.00 0.00 34.73 3.58
2111 6259 1.136891 TGCTGAGGATATGACCGTGTG 59.863 52.381 0.00 0.00 34.73 3.82
2112 6260 1.485124 TGCTGAGGATATGACCGTGT 58.515 50.000 0.00 0.00 34.73 4.49
2113 6261 2.159043 AGTTGCTGAGGATATGACCGTG 60.159 50.000 0.00 0.00 34.73 4.94
2114 6262 2.111384 AGTTGCTGAGGATATGACCGT 58.889 47.619 0.00 0.00 34.73 4.83
2115 6263 2.477825 CAGTTGCTGAGGATATGACCG 58.522 52.381 0.00 0.00 32.44 4.79
2116 6264 2.216898 GCAGTTGCTGAGGATATGACC 58.783 52.381 0.00 0.00 38.21 4.02
2117 6265 1.863454 CGCAGTTGCTGAGGATATGAC 59.137 52.381 2.29 0.00 39.32 3.06
2118 6266 1.807755 GCGCAGTTGCTGAGGATATGA 60.808 52.381 0.30 0.00 39.32 2.15
2119 6267 0.585357 GCGCAGTTGCTGAGGATATG 59.415 55.000 0.30 0.00 39.32 1.78
2120 6268 0.533755 GGCGCAGTTGCTGAGGATAT 60.534 55.000 10.83 0.00 39.32 1.63
2126 6274 0.804364 CATTAAGGCGCAGTTGCTGA 59.196 50.000 10.83 0.00 39.32 4.26
2141 6289 5.415701 GCAGAGGAAACAAGACAATCCATTA 59.584 40.000 0.00 0.00 34.30 1.90
2178 6326 1.306056 ACCCCCATGGCCATCAAAC 60.306 57.895 17.61 0.00 37.83 2.93
2199 6347 0.542805 TCATGTAGGCTGCAGCATCA 59.457 50.000 37.63 29.90 44.36 3.07
2223 6371 2.592102 ACAAGAACCTCATGGCATGT 57.408 45.000 25.62 7.71 36.63 3.21
2239 6387 4.844085 TGGGAACTCTCTATCCTCAAACAA 59.156 41.667 0.00 0.00 35.95 2.83
2295 6443 3.131396 GCGAATACATTCCTCAACGGAT 58.869 45.455 0.00 0.00 42.70 4.18
2301 6449 1.570813 CGCTGCGAATACATTCCTCA 58.429 50.000 18.66 0.00 33.28 3.86
2337 6485 0.590195 GATTATCAGCCAGCGCAAGG 59.410 55.000 11.47 12.94 37.52 3.61
2343 6491 5.144692 TGATGTCTAGATTATCAGCCAGC 57.855 43.478 14.96 2.31 0.00 4.85
2356 6504 0.313672 GAGGAGCGGCTGATGTCTAG 59.686 60.000 7.50 0.00 0.00 2.43
2385 6533 2.322355 AGATTAATGCTGCGAGTGCT 57.678 45.000 0.00 0.00 43.34 4.40
2401 6549 3.525199 AGCACATCTTACCTCCCAAAGAT 59.475 43.478 0.00 0.00 41.92 2.40
2586 6734 1.966451 GTTTGCCCTGTGGTCTCGG 60.966 63.158 0.00 0.00 0.00 4.63
2713 6861 2.267006 CGTGGAGCAGTCAGGCAT 59.733 61.111 0.00 0.00 35.83 4.40
2718 6866 4.357947 GGCGACGTGGAGCAGTCA 62.358 66.667 0.11 0.00 37.23 3.41
2952 7100 1.821759 CGACCCAAAGCACACCACA 60.822 57.895 0.00 0.00 0.00 4.17
3116 7264 1.036707 CACTAGGTAGGAGCAGGAGC 58.963 60.000 0.00 0.00 42.56 4.70
3119 7267 0.749649 CAGCACTAGGTAGGAGCAGG 59.250 60.000 0.00 0.00 32.95 4.85
3122 7270 0.103937 CAGCAGCACTAGGTAGGAGC 59.896 60.000 0.00 0.00 0.00 4.70
3124 7272 0.041238 ACCAGCAGCACTAGGTAGGA 59.959 55.000 0.00 0.00 30.76 2.94
3196 7344 3.061369 AGGGAACTAAAAGGGAAGTGGT 58.939 45.455 0.00 0.00 40.61 4.16
3241 7391 4.677182 AGAATGCCCCTACAAAAACTGAT 58.323 39.130 0.00 0.00 0.00 2.90
3242 7392 4.079253 GAGAATGCCCCTACAAAAACTGA 58.921 43.478 0.00 0.00 0.00 3.41
3340 7494 2.125310 TGGGCGCAACGGATGTAG 60.125 61.111 10.83 0.00 0.00 2.74
3354 7508 2.484287 AAAGCAGGTCCATCCGTGGG 62.484 60.000 0.00 0.00 46.06 4.61
3393 7547 3.065648 GCCCCGCGAATATTTCTGTTAAA 59.934 43.478 8.23 0.00 0.00 1.52
3410 7567 2.818132 GAGATGACCAGAGCCCCG 59.182 66.667 0.00 0.00 0.00 5.73
3424 7581 4.075682 ACTCACACTTCTCTGAATCGAGA 58.924 43.478 0.00 1.76 38.23 4.04
3450 7607 0.034896 CAACAGTCGCCCCAGTAAGT 59.965 55.000 0.00 0.00 0.00 2.24
3451 7608 1.298859 GCAACAGTCGCCCCAGTAAG 61.299 60.000 0.00 0.00 0.00 2.34
3528 7732 3.132646 CCCTATGATCTCTAGCTGATGGC 59.867 52.174 0.00 0.00 42.19 4.40
3529 7733 4.352009 ACCCTATGATCTCTAGCTGATGG 58.648 47.826 0.00 0.00 0.00 3.51
3549 7775 4.016706 ACCACGGCACCTGCTACC 62.017 66.667 0.00 0.00 41.70 3.18
3578 7808 1.338200 CCACTGCCGCTAAGTCTTCTT 60.338 52.381 0.00 0.00 37.65 2.52
3593 7823 6.751888 GGTATGTTTAGCTAAATTTGCCACTG 59.248 38.462 21.28 0.00 0.00 3.66
3599 7829 8.730680 AGACAGTGGTATGTTTAGCTAAATTTG 58.269 33.333 21.28 12.58 32.25 2.32
3610 7840 3.428999 CGGATCGAGACAGTGGTATGTTT 60.429 47.826 0.00 0.00 32.25 2.83
3652 7882 1.683365 GTGCCAGCCATTCCACCAT 60.683 57.895 0.00 0.00 0.00 3.55
3680 7910 1.866483 TAGGTGAGGGGGCGTGTCTA 61.866 60.000 0.00 0.00 0.00 2.59
3711 7949 1.548719 GGGATTGGGTTCCGGAAAAAG 59.451 52.381 20.79 0.00 36.58 2.27
3752 7993 2.431057 TCTCGTCAGATTTAGGGAAGGC 59.569 50.000 0.00 0.00 0.00 4.35
3757 7998 1.536284 GGCGTCTCGTCAGATTTAGGG 60.536 57.143 0.00 0.00 0.00 3.53
3760 8001 4.707030 TTTAGGCGTCTCGTCAGATTTA 57.293 40.909 0.00 0.00 32.13 1.40
3769 8027 2.029728 CAGCTGATTTTTAGGCGTCTCG 59.970 50.000 8.42 0.00 0.00 4.04
3794 8052 2.684927 GCATTGAACCCACCTGCTATCT 60.685 50.000 0.00 0.00 31.81 1.98
3914 8173 5.149973 TCAATACATTTGTGCATTTGCCT 57.850 34.783 0.00 0.00 41.18 4.75
3916 8175 4.201744 GGCTCAATACATTTGTGCATTTGC 60.202 41.667 12.62 0.00 39.76 3.68
3917 8176 4.930405 TGGCTCAATACATTTGTGCATTTG 59.070 37.500 12.62 0.00 39.76 2.32
3918 8177 5.149973 TGGCTCAATACATTTGTGCATTT 57.850 34.783 12.62 0.00 39.76 2.32
4067 8337 3.040147 TCTGTAGCTGTTGTTACCTGC 57.960 47.619 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.