Multiple sequence alignment - TraesCS3B01G354400

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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 TraesCS3B01G354400 chr3B 100.000 4970 0 0 1 4970 564780720 564775751 0.000000e+00 9178
1 TraesCS3B01G354400 chr3B 89.691 194 19 1 169 362 528661286 528661094 3.840000e-61 246
2 TraesCS3B01G354400 chr3B 89.172 157 13 4 207 360 143598536 143598691 5.080000e-45 193
3 TraesCS3B01G354400 chr3D 93.625 4361 157 56 443 4727 432551029 432546714 0.000000e+00 6401
4 TraesCS3B01G354400 chr3D 95.669 254 10 1 4718 4970 432546638 432546385 1.670000e-109 407
5 TraesCS3B01G354400 chr3A 93.764 3672 123 43 440 4044 570798842 570795210 0.000000e+00 5415
6 TraesCS3B01G354400 chr3A 95.635 252 10 1 4720 4970 570794256 570794005 2.150000e-108 403
7 TraesCS3B01G354400 chr3A 85.714 287 19 10 4275 4544 570794797 570794516 2.930000e-72 283
8 TraesCS3B01G354400 chr3A 92.118 203 10 3 4531 4733 570794499 570794303 1.050000e-71 281
9 TraesCS3B01G354400 chr4A 97.122 278 5 1 86 360 705243015 705242738 2.710000e-127 466
10 TraesCS3B01G354400 chr4A 96.591 88 1 1 1 86 705243651 705243564 1.440000e-30 145
11 TraesCS3B01G354400 chr6B 96.364 275 10 0 86 360 643248441 643248715 2.110000e-123 453
12 TraesCS3B01G354400 chr6B 96.591 88 1 1 1 86 643247664 643247751 1.440000e-30 145
13 TraesCS3B01G354400 chr7B 94.792 288 14 1 86 373 727134091 727133805 9.810000e-122 448
14 TraesCS3B01G354400 chr7B 97.854 233 5 0 129 361 421068343 421068111 2.150000e-108 403
15 TraesCS3B01G354400 chr7B 96.386 83 2 1 357 439 232264599 232264680 8.680000e-28 135
16 TraesCS3B01G354400 chr7B 93.258 89 3 2 1 86 727134320 727134232 1.450000e-25 128
17 TraesCS3B01G354400 chr2B 90.975 277 4 2 86 362 769546337 769546592 2.200000e-93 353
18 TraesCS3B01G354400 chr2B 96.591 88 1 1 1 86 769545559 769545646 1.440000e-30 145
19 TraesCS3B01G354400 chr5D 88.235 204 19 2 159 362 360900443 360900245 6.430000e-59 239
20 TraesCS3B01G354400 chr4B 97.674 129 3 0 232 360 621812085 621811957 6.480000e-54 222


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 TraesCS3B01G354400 chr3B 564775751 564780720 4969 True 9178.0 9178 100.00000 1 4970 1 chr3B.!!$R2 4969
1 TraesCS3B01G354400 chr3D 432546385 432551029 4644 True 3404.0 6401 94.64700 443 4970 2 chr3D.!!$R1 4527
2 TraesCS3B01G354400 chr3A 570794005 570798842 4837 True 1595.5 5415 91.80775 440 4970 4 chr3A.!!$R1 4530
3 TraesCS3B01G354400 chr4A 705242738 705243651 913 True 305.5 466 96.85650 1 360 2 chr4A.!!$R1 359
4 TraesCS3B01G354400 chr6B 643247664 643248715 1051 False 299.0 453 96.47750 1 360 2 chr6B.!!$F1 359
5 TraesCS3B01G354400 chr7B 727133805 727134320 515 True 288.0 448 94.02500 1 373 2 chr7B.!!$R2 372
6 TraesCS3B01G354400 chr2B 769545559 769546592 1033 False 249.0 353 93.78300 1 362 2 chr2B.!!$F1 361

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
208 914 0.111253 CAAGAACCTGGGCTTCACCT 59.889 55.000 0.00 0.0 39.10 4.00 F
423 1129 0.250640 ACACAGCAGCCAGAAGAAGG 60.251 55.000 0.00 0.0 0.00 3.46 F
1898 2673 0.689623 CTGGGAGCCACTCAACTTCT 59.310 55.000 0.00 0.0 31.08 2.85 F
2018 2793 1.220206 CTCAAGATGGAGCGCCTGT 59.780 57.895 8.34 0.0 34.31 4.00 F
3537 4312 0.176680 GGAGATCAAGAAGCAGCGGA 59.823 55.000 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1047 1822 0.322456 CCTGGATTCGGTCTGCCAAA 60.322 55.0 0.00 0.00 34.09 3.28 R
1915 2690 0.550914 TGGAGTTGTGCTTGGGAACT 59.449 50.0 0.00 0.00 32.57 3.01 R
3212 3987 0.398318 GTCTTCCAGAGGTGGCTTGT 59.602 55.0 0.00 0.00 44.60 3.16 R
3566 4341 0.537143 AAGGGCGTGATCACTTTGCA 60.537 50.0 22.95 0.00 0.00 4.08 R
4457 5470 0.259938 ACCTCCCAGATGGCCAAATC 59.740 55.0 10.96 3.14 0.00 2.17 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
208 914 0.111253 CAAGAACCTGGGCTTCACCT 59.889 55.000 0.00 0.00 39.10 4.00
353 1059 1.370609 CTAGCGAGTCTCCGAACAGA 58.629 55.000 0.00 0.00 0.00 3.41
361 1067 2.826725 AGTCTCCGAACAGACCCTTAAG 59.173 50.000 0.00 0.00 43.53 1.85
363 1069 1.275291 CTCCGAACAGACCCTTAAGCA 59.725 52.381 0.00 0.00 0.00 3.91
366 1072 2.489971 CGAACAGACCCTTAAGCACAA 58.510 47.619 0.00 0.00 0.00 3.33
369 1075 4.327680 GAACAGACCCTTAAGCACAAGAT 58.672 43.478 0.00 0.00 0.00 2.40
373 1079 5.221843 ACAGACCCTTAAGCACAAGATACAA 60.222 40.000 0.00 0.00 0.00 2.41
374 1080 5.352569 CAGACCCTTAAGCACAAGATACAAG 59.647 44.000 0.00 0.00 0.00 3.16
375 1081 5.013183 AGACCCTTAAGCACAAGATACAAGT 59.987 40.000 0.00 0.00 0.00 3.16
376 1082 5.003804 ACCCTTAAGCACAAGATACAAGTG 58.996 41.667 0.00 0.00 36.39 3.16
377 1083 5.221843 ACCCTTAAGCACAAGATACAAGTGA 60.222 40.000 0.00 0.00 35.33 3.41
378 1084 5.352569 CCCTTAAGCACAAGATACAAGTGAG 59.647 44.000 0.00 0.00 35.33 3.51
379 1085 6.166279 CCTTAAGCACAAGATACAAGTGAGA 58.834 40.000 0.00 0.00 35.33 3.27
380 1086 6.650807 CCTTAAGCACAAGATACAAGTGAGAA 59.349 38.462 0.00 0.00 35.33 2.87
381 1087 7.148507 CCTTAAGCACAAGATACAAGTGAGAAG 60.149 40.741 0.00 0.00 35.33 2.85
382 1088 5.474578 AGCACAAGATACAAGTGAGAAGA 57.525 39.130 0.00 0.00 35.33 2.87
383 1089 5.858381 AGCACAAGATACAAGTGAGAAGAA 58.142 37.500 0.00 0.00 35.33 2.52
384 1090 6.471146 AGCACAAGATACAAGTGAGAAGAAT 58.529 36.000 0.00 0.00 35.33 2.40
385 1091 6.370994 AGCACAAGATACAAGTGAGAAGAATG 59.629 38.462 0.00 0.00 35.33 2.67
386 1092 6.402983 GCACAAGATACAAGTGAGAAGAATGG 60.403 42.308 0.00 0.00 35.33 3.16
387 1093 6.875726 CACAAGATACAAGTGAGAAGAATGGA 59.124 38.462 0.00 0.00 35.33 3.41
388 1094 7.064371 CACAAGATACAAGTGAGAAGAATGGAG 59.936 40.741 0.00 0.00 35.33 3.86
389 1095 5.669477 AGATACAAGTGAGAAGAATGGAGC 58.331 41.667 0.00 0.00 0.00 4.70
390 1096 5.424895 AGATACAAGTGAGAAGAATGGAGCT 59.575 40.000 0.00 0.00 0.00 4.09
391 1097 4.363991 ACAAGTGAGAAGAATGGAGCTT 57.636 40.909 0.00 0.00 0.00 3.74
392 1098 4.723309 ACAAGTGAGAAGAATGGAGCTTT 58.277 39.130 0.00 0.00 0.00 3.51
393 1099 4.518211 ACAAGTGAGAAGAATGGAGCTTTG 59.482 41.667 0.00 0.00 0.00 2.77
394 1100 3.683802 AGTGAGAAGAATGGAGCTTTGG 58.316 45.455 0.00 0.00 0.00 3.28
395 1101 2.163211 GTGAGAAGAATGGAGCTTTGGC 59.837 50.000 0.00 0.00 39.06 4.52
406 1112 3.339547 GCTTTGGCTAACCTCCACA 57.660 52.632 0.00 0.00 36.63 4.17
407 1113 0.881796 GCTTTGGCTAACCTCCACAC 59.118 55.000 0.00 0.00 36.63 3.82
408 1114 1.817740 GCTTTGGCTAACCTCCACACA 60.818 52.381 0.00 0.00 36.63 3.72
409 1115 2.154462 CTTTGGCTAACCTCCACACAG 58.846 52.381 0.00 0.00 36.63 3.66
410 1116 0.250727 TTGGCTAACCTCCACACAGC 60.251 55.000 0.00 0.00 36.63 4.40
411 1117 1.374947 GGCTAACCTCCACACAGCA 59.625 57.895 0.00 0.00 33.86 4.41
412 1118 0.674895 GGCTAACCTCCACACAGCAG 60.675 60.000 0.00 0.00 33.86 4.24
413 1119 1.301677 GCTAACCTCCACACAGCAGC 61.302 60.000 0.00 0.00 32.46 5.25
414 1120 0.674895 CTAACCTCCACACAGCAGCC 60.675 60.000 0.00 0.00 0.00 4.85
415 1121 1.414866 TAACCTCCACACAGCAGCCA 61.415 55.000 0.00 0.00 0.00 4.75
416 1122 2.359602 CCTCCACACAGCAGCCAG 60.360 66.667 0.00 0.00 0.00 4.85
417 1123 2.745698 CTCCACACAGCAGCCAGA 59.254 61.111 0.00 0.00 0.00 3.86
418 1124 1.071987 CTCCACACAGCAGCCAGAA 59.928 57.895 0.00 0.00 0.00 3.02
419 1125 0.954449 CTCCACACAGCAGCCAGAAG 60.954 60.000 0.00 0.00 0.00 2.85
420 1126 1.071987 CCACACAGCAGCCAGAAGA 59.928 57.895 0.00 0.00 0.00 2.87
421 1127 0.535780 CCACACAGCAGCCAGAAGAA 60.536 55.000 0.00 0.00 0.00 2.52
422 1128 0.873054 CACACAGCAGCCAGAAGAAG 59.127 55.000 0.00 0.00 0.00 2.85
423 1129 0.250640 ACACAGCAGCCAGAAGAAGG 60.251 55.000 0.00 0.00 0.00 3.46
436 1142 4.820716 CCAGAAGAAGGCTCTCATTAATGG 59.179 45.833 15.36 6.60 0.00 3.16
437 1143 4.275443 CAGAAGAAGGCTCTCATTAATGGC 59.725 45.833 15.36 10.59 0.00 4.40
438 1144 3.220674 AGAAGGCTCTCATTAATGGCC 57.779 47.619 20.51 20.51 42.74 5.36
439 1145 2.511218 AGAAGGCTCTCATTAATGGCCA 59.489 45.455 26.30 8.56 44.60 5.36
440 1146 2.355010 AGGCTCTCATTAATGGCCAC 57.645 50.000 26.30 11.84 44.60 5.01
441 1147 0.947244 GGCTCTCATTAATGGCCACG 59.053 55.000 22.20 0.00 42.08 4.94
442 1148 1.475034 GGCTCTCATTAATGGCCACGA 60.475 52.381 22.20 0.00 42.08 4.35
443 1149 2.288666 GCTCTCATTAATGGCCACGAA 58.711 47.619 8.16 5.39 0.00 3.85
444 1150 2.682856 GCTCTCATTAATGGCCACGAAA 59.317 45.455 8.16 2.52 0.00 3.46
445 1151 3.128589 GCTCTCATTAATGGCCACGAAAA 59.871 43.478 8.16 0.00 0.00 2.29
446 1152 4.662145 CTCTCATTAATGGCCACGAAAAC 58.338 43.478 8.16 0.00 0.00 2.43
447 1153 3.442273 TCTCATTAATGGCCACGAAAACC 59.558 43.478 8.16 0.00 0.00 3.27
496 1204 1.517242 GTTCCCTTGCAGACAGACAG 58.483 55.000 0.00 0.00 0.00 3.51
580 1305 3.364621 GCACGCATATTTGTCTTGTTTGG 59.635 43.478 0.00 0.00 0.00 3.28
595 1320 2.544686 TGTTTGGACATTCAACCGTACG 59.455 45.455 8.69 8.69 0.00 3.67
787 1533 0.880278 TGTGCGCAGTCCAAGTCTTC 60.880 55.000 12.22 0.00 0.00 2.87
788 1534 1.664649 TGCGCAGTCCAAGTCTTCG 60.665 57.895 5.66 0.00 0.00 3.79
789 1535 3.016474 GCGCAGTCCAAGTCTTCGC 62.016 63.158 0.30 0.00 39.72 4.70
790 1536 2.720758 CGCAGTCCAAGTCTTCGCG 61.721 63.158 0.00 0.00 34.89 5.87
898 1659 1.274712 TTTGTCCATTTCCCATGGCC 58.725 50.000 6.09 0.00 39.01 5.36
1045 1820 1.698506 TTCGTGCCCAAATCAGGTTT 58.301 45.000 0.00 0.00 0.00 3.27
1046 1821 1.243902 TCGTGCCCAAATCAGGTTTC 58.756 50.000 0.00 0.00 0.00 2.78
1047 1822 1.202879 TCGTGCCCAAATCAGGTTTCT 60.203 47.619 0.00 0.00 0.00 2.52
1053 1828 2.368221 CCCAAATCAGGTTTCTTTGGCA 59.632 45.455 7.59 0.00 44.87 4.92
1135 1910 2.431771 TTCGTGGCGTCCATCGTG 60.432 61.111 14.77 3.90 42.13 4.35
1276 2051 2.324330 CGTCAAGCGCATGGTGGAA 61.324 57.895 13.33 0.00 0.00 3.53
1898 2673 0.689623 CTGGGAGCCACTCAACTTCT 59.310 55.000 0.00 0.00 31.08 2.85
2018 2793 1.220206 CTCAAGATGGAGCGCCTGT 59.780 57.895 8.34 0.00 34.31 4.00
2667 3442 3.935828 TGTTTCATGCGGAATAACATCGA 59.064 39.130 0.00 0.00 34.91 3.59
2671 3446 2.218953 TGCGGAATAACATCGAGGAC 57.781 50.000 3.06 0.00 0.00 3.85
2725 3500 6.265196 TGAAGACCTTGATGCTACAAAACAAT 59.735 34.615 0.00 0.00 0.00 2.71
2741 3516 4.751767 AACAATGCTGGGTTGAAAAAGA 57.248 36.364 0.00 0.00 0.00 2.52
2743 3518 6.418057 AACAATGCTGGGTTGAAAAAGATA 57.582 33.333 0.00 0.00 0.00 1.98
3185 3960 7.342769 AGAAATCTGATGATAAAAGCATGCA 57.657 32.000 21.98 0.00 31.70 3.96
3212 3987 4.219115 CCTGACAAAGATAGAGCTCCCTA 58.781 47.826 10.93 0.00 0.00 3.53
3264 4039 2.266554 GAAGAGAGTGTGGATCGCAAG 58.733 52.381 0.00 0.00 0.00 4.01
3317 4092 1.198637 GCAGCGAAGAAACTGATTGCT 59.801 47.619 0.00 0.00 35.90 3.91
3326 4101 6.524586 CGAAGAAACTGATTGCTCCATTTTAC 59.475 38.462 0.00 0.00 0.00 2.01
3332 4107 4.608269 TGATTGCTCCATTTTACATCCCA 58.392 39.130 0.00 0.00 0.00 4.37
3333 4108 5.210430 TGATTGCTCCATTTTACATCCCAT 58.790 37.500 0.00 0.00 0.00 4.00
3361 4136 9.136323 GATTTTATGAGGATGGGTGAAGTTATT 57.864 33.333 0.00 0.00 0.00 1.40
3387 4162 0.393808 GAACAGCCCGCCCTTGATAA 60.394 55.000 0.00 0.00 0.00 1.75
3416 4191 2.634940 GGTATCATCCTGCAGAGCCTTA 59.365 50.000 17.39 0.00 0.00 2.69
3486 4261 3.008923 TCATTGTTCATCTGGTACTGCCA 59.991 43.478 0.00 0.00 46.95 4.92
3514 4289 1.824230 GAGGAGCTGATCACACTCAGT 59.176 52.381 18.27 8.37 43.75 3.41
3537 4312 0.176680 GGAGATCAAGAAGCAGCGGA 59.823 55.000 0.00 0.00 0.00 5.54
3566 4341 0.886490 CGAACAAGCTGCAGGGACTT 60.886 55.000 17.12 7.57 34.60 3.01
3628 4406 3.253220 TCTCCAAGGCCTACCAAAGTTA 58.747 45.455 5.16 0.00 39.06 2.24
3699 4477 3.692101 AGACTCAAGATCGTCGATTGTCT 59.308 43.478 9.52 13.77 35.38 3.41
3796 4574 2.224475 GGAGTGGGATGATGATGAGGTG 60.224 54.545 0.00 0.00 0.00 4.00
3835 4614 8.388183 GAGCCACTGTTGGATGAAAGATATGAT 61.388 40.741 0.00 0.00 43.53 2.45
3890 4669 8.313292 CCCAAAATTTCAGAGATACATTTTCCA 58.687 33.333 0.00 0.00 0.00 3.53
3935 4715 0.667792 GCATTCGACGGGCCTATCTC 60.668 60.000 0.84 0.00 0.00 2.75
3936 4716 0.962489 CATTCGACGGGCCTATCTCT 59.038 55.000 0.84 0.00 0.00 3.10
3944 4724 0.178068 GGGCCTATCTCTGCGTTTCA 59.822 55.000 0.84 0.00 0.00 2.69
3961 4741 8.245701 TGCGTTTCAAAGAAAATAAAAACAGT 57.754 26.923 0.00 0.00 0.00 3.55
3982 4767 5.595133 CAGTGTTTACTCCACCCCTTTTTAA 59.405 40.000 0.00 0.00 34.07 1.52
3984 4769 6.842280 AGTGTTTACTCCACCCCTTTTTAAAT 59.158 34.615 0.00 0.00 33.20 1.40
4057 4846 1.293924 GCCCTTCAGATGTGTCATCG 58.706 55.000 4.44 1.25 0.00 3.84
4109 4969 1.888512 GTGGACTGGACAATGCACATT 59.111 47.619 0.59 0.00 37.15 2.71
4129 4989 6.375945 CATTTGATGAATGGACCGTATGAA 57.624 37.500 0.00 0.00 41.19 2.57
4132 4992 5.034852 TGATGAATGGACCGTATGAATGT 57.965 39.130 0.00 0.00 0.00 2.71
4133 4993 5.056480 TGATGAATGGACCGTATGAATGTC 58.944 41.667 0.00 0.00 0.00 3.06
4165 5049 3.703001 ACCGAGTGTTGATCCAAATCT 57.297 42.857 0.00 0.00 32.75 2.40
4166 5050 3.338249 ACCGAGTGTTGATCCAAATCTG 58.662 45.455 0.00 0.00 32.75 2.90
4181 5069 5.066893 TCCAAATCTGAAATCTGTATGCAGC 59.933 40.000 5.85 0.00 42.29 5.25
4222 5110 4.582240 CAGCTAATCCATTCCTTCTTTCCC 59.418 45.833 0.00 0.00 0.00 3.97
4353 5349 3.981071 ACCTAGTTGCAAGCTGTGATA 57.019 42.857 0.00 0.00 0.00 2.15
4356 5357 4.002982 CCTAGTTGCAAGCTGTGATAACA 58.997 43.478 0.00 0.00 31.72 2.41
4386 5390 0.806868 TACGTACCTCGAGTTGCTGG 59.193 55.000 12.31 0.00 42.86 4.85
4387 5391 1.153823 CGTACCTCGAGTTGCTGGG 60.154 63.158 12.31 0.00 42.86 4.45
4395 5408 2.293122 CTCGAGTTGCTGGGATCTAGAG 59.707 54.545 3.62 0.00 0.00 2.43
4404 5417 3.258123 GCTGGGATCTAGAGTTCCTGATC 59.742 52.174 11.37 0.00 34.96 2.92
4445 5458 2.159366 CGAATCTGTAGGACTTCACGCT 60.159 50.000 0.00 0.00 0.00 5.07
4452 5465 0.250338 AGGACTTCACGCTTTGGGAC 60.250 55.000 0.00 0.00 0.00 4.46
4455 5468 2.338500 GACTTCACGCTTTGGGACTAG 58.662 52.381 0.00 0.00 0.00 2.57
4456 5469 1.002087 ACTTCACGCTTTGGGACTAGG 59.998 52.381 0.00 0.00 0.00 3.02
4457 5470 0.323629 TTCACGCTTTGGGACTAGGG 59.676 55.000 0.00 0.00 0.00 3.53
4459 5472 0.541863 CACGCTTTGGGACTAGGGAT 59.458 55.000 0.00 0.00 0.00 3.85
4460 5473 1.065418 CACGCTTTGGGACTAGGGATT 60.065 52.381 0.00 0.00 0.00 3.01
4461 5474 1.633945 ACGCTTTGGGACTAGGGATTT 59.366 47.619 0.00 0.00 0.00 2.17
4462 5475 2.017049 CGCTTTGGGACTAGGGATTTG 58.983 52.381 0.00 0.00 0.00 2.32
4463 5476 2.379005 GCTTTGGGACTAGGGATTTGG 58.621 52.381 0.00 0.00 0.00 3.28
4464 5477 2.379005 CTTTGGGACTAGGGATTTGGC 58.621 52.381 0.00 0.00 0.00 4.52
4465 5478 0.629058 TTGGGACTAGGGATTTGGCC 59.371 55.000 0.00 0.00 0.00 5.36
4468 5481 1.202940 GGGACTAGGGATTTGGCCATC 60.203 57.143 6.09 0.75 30.17 3.51
4529 5542 1.609501 CAGGAACGGGGAGGACTGA 60.610 63.158 0.00 0.00 0.00 3.41
4535 5548 1.455959 CGGGGAGGACTGAGGGTAG 60.456 68.421 0.00 0.00 0.00 3.18
4558 5601 3.869473 TACCGCCAACTGGACGCAC 62.869 63.158 0.00 0.00 37.39 5.34
4559 5602 4.988598 CCGCCAACTGGACGCACT 62.989 66.667 0.00 0.00 37.39 4.40
4563 5606 1.071471 CCAACTGGACGCACTTCCT 59.929 57.895 0.00 0.00 36.51 3.36
4704 5748 6.926630 ATGGGCTTTTGAAATACTAAACCA 57.073 33.333 0.00 0.00 0.00 3.67
4750 5939 9.364989 CGAATTGATGTAAATTAACCAAACCAT 57.635 29.630 0.00 0.00 29.89 3.55
4789 5978 7.820044 TGTGGTAAACAATCTCAAAACAAAC 57.180 32.000 0.00 0.00 35.24 2.93
4875 6065 0.984230 TGGGATCTCAACCACCTCAC 59.016 55.000 0.00 0.00 0.00 3.51
4879 6069 2.224769 GGATCTCAACCACCTCACCAAA 60.225 50.000 0.00 0.00 0.00 3.28
4966 6156 8.461222 TCAATGCAGATGAAGTTATTAACAAGG 58.539 33.333 9.15 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 791 0.114364 GGTTTCCTGGGGTGAATGGT 59.886 55.000 0.00 0.00 0.00 3.55
353 1059 5.003804 CACTTGTATCTTGTGCTTAAGGGT 58.996 41.667 4.29 0.00 0.00 4.34
361 1067 6.402983 CCATTCTTCTCACTTGTATCTTGTGC 60.403 42.308 0.00 0.00 0.00 4.57
363 1069 7.009179 TCCATTCTTCTCACTTGTATCTTGT 57.991 36.000 0.00 0.00 0.00 3.16
366 1072 5.424895 AGCTCCATTCTTCTCACTTGTATCT 59.575 40.000 0.00 0.00 0.00 1.98
369 1075 5.489792 AAGCTCCATTCTTCTCACTTGTA 57.510 39.130 0.00 0.00 0.00 2.41
373 1079 3.683802 CCAAAGCTCCATTCTTCTCACT 58.316 45.455 0.00 0.00 0.00 3.41
374 1080 2.163211 GCCAAAGCTCCATTCTTCTCAC 59.837 50.000 0.00 0.00 35.50 3.51
375 1081 2.440409 GCCAAAGCTCCATTCTTCTCA 58.560 47.619 0.00 0.00 35.50 3.27
388 1094 0.881796 GTGTGGAGGTTAGCCAAAGC 59.118 55.000 0.00 0.00 37.12 3.51
389 1095 2.154462 CTGTGTGGAGGTTAGCCAAAG 58.846 52.381 0.00 0.00 37.12 2.77
390 1096 1.817740 GCTGTGTGGAGGTTAGCCAAA 60.818 52.381 0.00 0.00 37.12 3.28
391 1097 0.250727 GCTGTGTGGAGGTTAGCCAA 60.251 55.000 0.00 0.00 37.12 4.52
392 1098 1.374947 GCTGTGTGGAGGTTAGCCA 59.625 57.895 0.00 0.00 37.19 4.75
393 1099 0.674895 CTGCTGTGTGGAGGTTAGCC 60.675 60.000 0.00 0.00 33.60 3.93
394 1100 1.301677 GCTGCTGTGTGGAGGTTAGC 61.302 60.000 0.00 0.00 34.46 3.09
395 1101 0.674895 GGCTGCTGTGTGGAGGTTAG 60.675 60.000 0.00 0.00 34.46 2.34
396 1102 1.374947 GGCTGCTGTGTGGAGGTTA 59.625 57.895 0.00 0.00 34.46 2.85
397 1103 2.113986 GGCTGCTGTGTGGAGGTT 59.886 61.111 0.00 0.00 34.46 3.50
398 1104 3.170672 TGGCTGCTGTGTGGAGGT 61.171 61.111 0.00 0.00 34.46 3.85
399 1105 2.359602 CTGGCTGCTGTGTGGAGG 60.360 66.667 0.00 0.00 34.46 4.30
400 1106 0.954449 CTTCTGGCTGCTGTGTGGAG 60.954 60.000 0.00 0.00 37.17 3.86
401 1107 1.071987 CTTCTGGCTGCTGTGTGGA 59.928 57.895 0.00 0.00 0.00 4.02
402 1108 0.535780 TTCTTCTGGCTGCTGTGTGG 60.536 55.000 0.00 0.00 0.00 4.17
403 1109 0.873054 CTTCTTCTGGCTGCTGTGTG 59.127 55.000 0.00 0.00 0.00 3.82
404 1110 0.250640 CCTTCTTCTGGCTGCTGTGT 60.251 55.000 0.00 0.00 0.00 3.72
405 1111 1.584380 GCCTTCTTCTGGCTGCTGTG 61.584 60.000 0.00 0.00 46.38 3.66
406 1112 1.303155 GCCTTCTTCTGGCTGCTGT 60.303 57.895 0.00 0.00 46.38 4.40
407 1113 3.588336 GCCTTCTTCTGGCTGCTG 58.412 61.111 0.00 0.00 46.38 4.41
413 1119 4.820716 CCATTAATGAGAGCCTTCTTCTGG 59.179 45.833 17.23 0.00 32.53 3.86
414 1120 4.275443 GCCATTAATGAGAGCCTTCTTCTG 59.725 45.833 17.23 0.00 32.53 3.02
415 1121 4.459330 GCCATTAATGAGAGCCTTCTTCT 58.541 43.478 17.23 0.00 32.53 2.85
416 1122 3.567585 GGCCATTAATGAGAGCCTTCTTC 59.432 47.826 20.70 0.97 40.57 2.87
417 1123 3.053395 TGGCCATTAATGAGAGCCTTCTT 60.053 43.478 25.28 0.00 44.19 2.52
418 1124 2.511218 TGGCCATTAATGAGAGCCTTCT 59.489 45.455 25.28 0.00 44.19 2.85
419 1125 2.620585 GTGGCCATTAATGAGAGCCTTC 59.379 50.000 25.28 17.74 44.19 3.46
420 1126 2.659428 GTGGCCATTAATGAGAGCCTT 58.341 47.619 25.28 0.00 44.19 4.35
421 1127 1.475751 CGTGGCCATTAATGAGAGCCT 60.476 52.381 25.28 0.00 44.19 4.58
422 1128 0.947244 CGTGGCCATTAATGAGAGCC 59.053 55.000 21.01 21.01 44.13 4.70
423 1129 1.953559 TCGTGGCCATTAATGAGAGC 58.046 50.000 17.23 11.32 0.00 4.09
424 1130 4.438744 GGTTTTCGTGGCCATTAATGAGAG 60.439 45.833 17.23 1.50 0.00 3.20
425 1131 3.442273 GGTTTTCGTGGCCATTAATGAGA 59.558 43.478 17.23 5.44 0.00 3.27
426 1132 3.428862 GGGTTTTCGTGGCCATTAATGAG 60.429 47.826 17.23 8.12 0.00 2.90
427 1133 2.494073 GGGTTTTCGTGGCCATTAATGA 59.506 45.455 17.23 0.00 0.00 2.57
428 1134 2.232452 TGGGTTTTCGTGGCCATTAATG 59.768 45.455 9.72 8.58 0.00 1.90
429 1135 2.495669 CTGGGTTTTCGTGGCCATTAAT 59.504 45.455 9.72 0.00 0.00 1.40
430 1136 1.889829 CTGGGTTTTCGTGGCCATTAA 59.110 47.619 9.72 3.16 0.00 1.40
431 1137 1.202952 ACTGGGTTTTCGTGGCCATTA 60.203 47.619 9.72 0.00 0.00 1.90
432 1138 0.469144 ACTGGGTTTTCGTGGCCATT 60.469 50.000 9.72 0.00 0.00 3.16
433 1139 1.152830 ACTGGGTTTTCGTGGCCAT 59.847 52.632 9.72 0.00 0.00 4.40
434 1140 1.826054 CACTGGGTTTTCGTGGCCA 60.826 57.895 0.00 0.00 0.00 5.36
435 1141 1.826487 ACACTGGGTTTTCGTGGCC 60.826 57.895 0.00 0.00 33.13 5.36
436 1142 1.358759 CACACTGGGTTTTCGTGGC 59.641 57.895 0.00 0.00 33.13 5.01
437 1143 1.101049 AGCACACTGGGTTTTCGTGG 61.101 55.000 0.00 0.00 33.13 4.94
438 1144 1.263217 GTAGCACACTGGGTTTTCGTG 59.737 52.381 0.00 0.00 34.92 4.35
439 1145 1.589803 GTAGCACACTGGGTTTTCGT 58.410 50.000 0.00 0.00 0.00 3.85
440 1146 0.872388 GGTAGCACACTGGGTTTTCG 59.128 55.000 0.00 0.00 0.00 3.46
441 1147 0.872388 CGGTAGCACACTGGGTTTTC 59.128 55.000 0.00 0.00 0.00 2.29
442 1148 1.170290 GCGGTAGCACACTGGGTTTT 61.170 55.000 0.00 0.00 44.35 2.43
443 1149 1.599797 GCGGTAGCACACTGGGTTT 60.600 57.895 0.00 0.00 44.35 3.27
444 1150 2.032071 GCGGTAGCACACTGGGTT 59.968 61.111 0.00 0.00 44.35 4.11
496 1204 0.390340 TCGAGCCAGTCAATGACAGC 60.390 55.000 16.38 16.85 34.60 4.40
580 1305 0.986992 CGTCCGTACGGTTGAATGTC 59.013 55.000 32.16 12.89 45.50 3.06
662 1394 2.981350 ATGGCGTCGGGCGTTTTT 60.981 55.556 3.17 0.00 44.92 1.94
820 1566 3.496870 CCTTAGCCAAGAAGGAACACACT 60.497 47.826 0.00 0.00 45.52 3.55
898 1659 0.109342 AGTTGGAGCTTGTGGGTGAG 59.891 55.000 0.00 0.00 0.00 3.51
1045 1820 0.690192 TGGATTCGGTCTGCCAAAGA 59.310 50.000 0.00 0.00 34.09 2.52
1046 1821 1.089920 CTGGATTCGGTCTGCCAAAG 58.910 55.000 0.00 0.00 34.09 2.77
1047 1822 0.322456 CCTGGATTCGGTCTGCCAAA 60.322 55.000 0.00 0.00 34.09 3.28
1053 1828 2.427245 CGAGGCCTGGATTCGGTCT 61.427 63.158 12.00 0.00 39.69 3.85
1082 1857 2.587194 CGAGCCGAATGCCTCAGG 60.587 66.667 0.00 0.00 42.71 3.86
1561 2336 1.144716 GAGCATCTCGTCCATGCCA 59.855 57.895 10.88 0.00 46.76 4.92
1915 2690 0.550914 TGGAGTTGTGCTTGGGAACT 59.449 50.000 0.00 0.00 32.57 3.01
2667 3442 2.435693 GGCGCCTCATACAGGTCCT 61.436 63.158 22.15 0.00 45.61 3.85
2671 3446 2.146342 CAATTAGGCGCCTCATACAGG 58.854 52.381 36.73 14.06 46.82 4.00
2681 3456 1.032114 AACAGAGGGCAATTAGGCGC 61.032 55.000 0.00 0.00 45.36 6.53
2725 3500 3.119531 CGCATATCTTTTTCAACCCAGCA 60.120 43.478 0.00 0.00 0.00 4.41
2741 3516 0.464036 TGGAAGAAGCCGTCGCATAT 59.536 50.000 0.00 0.00 37.52 1.78
2743 3518 1.448540 CTGGAAGAAGCCGTCGCAT 60.449 57.895 0.00 0.00 33.77 4.73
3185 3960 4.285863 AGCTCTATCTTTGTCAGGCTACT 58.714 43.478 0.00 0.00 0.00 2.57
3212 3987 0.398318 GTCTTCCAGAGGTGGCTTGT 59.602 55.000 0.00 0.00 44.60 3.16
3264 4039 1.497223 CTCCGCTAGATTGCTGCAGC 61.497 60.000 31.89 31.89 42.50 5.25
3326 4101 6.931838 CCATCCTCATAAAATCAATGGGATG 58.068 40.000 17.60 17.60 43.27 3.51
3332 4107 7.128077 ACTTCACCCATCCTCATAAAATCAAT 58.872 34.615 0.00 0.00 0.00 2.57
3333 4108 6.493166 ACTTCACCCATCCTCATAAAATCAA 58.507 36.000 0.00 0.00 0.00 2.57
3361 4136 2.280797 GCGGGCTGTTCACACTCA 60.281 61.111 0.00 0.00 0.00 3.41
3416 4191 6.043706 CCCCTGTAGATGATCTTTACCTTCAT 59.956 42.308 0.00 0.00 32.93 2.57
3431 4206 2.367202 CGCACCCACCCCTGTAGAT 61.367 63.158 0.00 0.00 0.00 1.98
3486 4261 1.273495 TGATCAGCTCCTCCAGTCCTT 60.273 52.381 0.00 0.00 0.00 3.36
3514 4289 2.740904 CGCTGCTTCTTGATCTCCATCA 60.741 50.000 0.00 0.00 37.24 3.07
3537 4312 2.128035 CAGCTTGTTCGTCTTCGTTCT 58.872 47.619 0.00 0.00 38.33 3.01
3566 4341 0.537143 AAGGGCGTGATCACTTTGCA 60.537 50.000 22.95 0.00 0.00 4.08
3628 4406 2.581354 CTACTGCTCAGCGCCCTT 59.419 61.111 2.29 0.00 38.05 3.95
3661 4439 4.099633 TGAGTCTCTTCAGTGATGGGAAT 58.900 43.478 10.03 9.23 0.00 3.01
3667 4445 4.704540 ACGATCTTGAGTCTCTTCAGTGAT 59.295 41.667 0.65 0.00 0.00 3.06
3835 4614 8.659925 ACATAATGCACAAAAACTGAATTCAA 57.340 26.923 9.88 0.00 0.00 2.69
3890 4669 1.152963 AAAGCCCGGCATAAGCGAT 60.153 52.632 13.15 0.00 43.41 4.58
3931 4711 9.528018 TTTTTATTTTCTTTGAAACGCAGAGAT 57.472 25.926 0.00 0.00 37.55 2.75
3935 4715 8.379902 ACTGTTTTTATTTTCTTTGAAACGCAG 58.620 29.630 0.00 0.00 31.53 5.18
3936 4716 8.165428 CACTGTTTTTATTTTCTTTGAAACGCA 58.835 29.630 0.00 0.00 31.53 5.24
3961 4741 7.678207 AATTTAAAAAGGGGTGGAGTAAACA 57.322 32.000 0.00 0.00 0.00 2.83
4057 4846 8.038492 ACAAAAGCATAATCTCTCAGAAGAAC 57.962 34.615 0.00 0.00 0.00 3.01
4109 4969 5.436175 ACATTCATACGGTCCATTCATCAA 58.564 37.500 0.00 0.00 0.00 2.57
4121 4981 0.179084 ACCGGCAGACATTCATACGG 60.179 55.000 0.00 0.00 44.86 4.02
4126 4986 0.687920 TTGGTACCGGCAGACATTCA 59.312 50.000 7.57 0.00 0.00 2.57
4127 4987 1.084289 GTTGGTACCGGCAGACATTC 58.916 55.000 7.57 0.00 0.00 2.67
4129 4989 1.298667 GGTTGGTACCGGCAGACAT 59.701 57.895 7.57 0.00 34.01 3.06
4148 5032 7.094463 ACAGATTTCAGATTTGGATCAACACTC 60.094 37.037 0.00 0.00 34.60 3.51
4181 5069 2.831366 GCATCAGCCATCAGCCGTG 61.831 63.158 0.00 0.00 45.47 4.94
4206 5094 1.340017 CGCAGGGAAAGAAGGAATGGA 60.340 52.381 0.00 0.00 0.00 3.41
4208 5096 1.470098 CACGCAGGGAAAGAAGGAATG 59.530 52.381 0.00 0.00 0.00 2.67
4211 5099 1.302511 GCACGCAGGGAAAGAAGGA 60.303 57.895 0.00 0.00 0.00 3.36
4222 5110 3.117171 GACAGGCAGAGCACGCAG 61.117 66.667 0.00 0.00 0.00 5.18
4278 5271 6.435591 TCTGTGATGAGGATACATCTATCACC 59.564 42.308 19.70 7.08 44.61 4.02
4353 5349 1.936436 TACGTACATCGGCGCCTGTT 61.936 55.000 24.42 11.00 44.69 3.16
4356 5357 2.410469 GTACGTACATCGGCGCCT 59.590 61.111 26.68 8.22 44.69 5.52
4387 5391 3.258123 GCTGGGATCAGGAACTCTAGATC 59.742 52.174 0.00 0.00 41.19 2.75
4395 5408 1.648467 GCAACGCTGGGATCAGGAAC 61.648 60.000 0.00 0.00 41.19 3.62
4445 5458 1.006639 GGCCAAATCCCTAGTCCCAAA 59.993 52.381 0.00 0.00 0.00 3.28
4452 5465 1.202976 CCCAGATGGCCAAATCCCTAG 60.203 57.143 10.96 0.00 0.00 3.02
4455 5468 0.468771 CTCCCAGATGGCCAAATCCC 60.469 60.000 10.96 0.00 0.00 3.85
4456 5469 0.468771 CCTCCCAGATGGCCAAATCC 60.469 60.000 10.96 0.00 0.00 3.01
4457 5470 0.259938 ACCTCCCAGATGGCCAAATC 59.740 55.000 10.96 3.14 0.00 2.17
4459 5472 1.383799 CACCTCCCAGATGGCCAAA 59.616 57.895 10.96 0.00 0.00 3.28
4460 5473 2.615465 CCACCTCCCAGATGGCCAA 61.615 63.158 10.96 0.00 0.00 4.52
4461 5474 3.016971 CCACCTCCCAGATGGCCA 61.017 66.667 8.56 8.56 0.00 5.36
4464 5477 3.083349 TCGCCACCTCCCAGATGG 61.083 66.667 0.00 0.00 29.51 3.51
4465 5478 2.187946 GTCGCCACCTCCCAGATG 59.812 66.667 0.00 0.00 0.00 2.90
4544 5557 2.617274 GGAAGTGCGTCCAGTTGGC 61.617 63.158 0.00 0.00 37.65 4.52
4558 5601 2.352805 GTGTGGGCCCAGAGGAAG 59.647 66.667 29.55 0.00 33.47 3.46
4559 5602 3.636231 CGTGTGGGCCCAGAGGAA 61.636 66.667 32.32 11.07 33.47 3.36
4563 5606 3.625897 CTGACGTGTGGGCCCAGA 61.626 66.667 29.55 24.56 0.00 3.86
4662 5706 8.289182 AGCCCATAGTATAATTTTTACTCCCT 57.711 34.615 3.22 0.00 32.35 4.20
4696 5740 8.762645 TCAATTAGATCTGAGACATGGTTTAGT 58.237 33.333 5.18 0.00 0.00 2.24
4697 5741 9.775854 ATCAATTAGATCTGAGACATGGTTTAG 57.224 33.333 5.18 0.00 28.20 1.85
4761 5950 8.226819 TGTTTTGAGATTGTTTACCACATACA 57.773 30.769 0.00 0.00 34.43 2.29


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

AutoCloner maintained by Alex Coulton.