Multiple sequence alignment - TraesCS2A01G392900

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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 TraesCS2A01G392900 chr2A 100.000 4684 0 0 1 4684 642907526 642912209 0.000000e+00 8650.0
1 TraesCS2A01G392900 chr2B 94.793 4014 157 28 1 3994 584691412 584695393 0.000000e+00 6207.0
2 TraesCS2A01G392900 chr2B 88.641 449 34 8 4245 4684 584719556 584719996 8.920000e-147 531.0
3 TraesCS2A01G392900 chr2D 93.936 3793 175 28 205 3979 498225181 498228936 0.000000e+00 5679.0
4 TraesCS2A01G392900 chr2D 89.183 453 28 8 4245 4684 498229393 498229837 3.190000e-151 545.0
5 TraesCS2A01G392900 chr2D 92.453 106 3 2 1 101 498224781 498224886 3.780000e-31 147.0
6 TraesCS2A01G392900 chr6D 77.191 890 172 18 2807 3685 317006125 317006994 1.510000e-134 490.0
7 TraesCS2A01G392900 chr6D 87.324 71 8 1 4329 4398 317076304 317076374 3.890000e-11 80.5
8 TraesCS2A01G392900 chr6B 83.845 489 74 4 3198 3685 507593083 507592599 1.190000e-125 460.0
9 TraesCS2A01G392900 chr6B 86.486 74 9 1 4329 4401 507477466 507477393 3.890000e-11 80.5
10 TraesCS2A01G392900 chr1A 82.984 382 60 5 3196 3573 387029171 387028791 1.610000e-89 340.0
11 TraesCS2A01G392900 chr1B 82.850 379 60 5 3199 3573 416822537 416822160 7.510000e-88 335.0
12 TraesCS2A01G392900 chr1D 82.322 379 62 5 3199 3573 307832742 307832365 1.630000e-84 324.0
13 TraesCS2A01G392900 chr5B 79.854 412 75 8 3163 3570 435158192 435158599 1.270000e-75 294.0
14 TraesCS2A01G392900 chr5A 79.901 403 71 10 3173 3570 469610198 469610595 2.130000e-73 287.0
15 TraesCS2A01G392900 chr6A 87.324 71 8 1 4329 4398 454675484 454675554 3.890000e-11 80.5


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 TraesCS2A01G392900 chr2A 642907526 642912209 4683 False 8650.000000 8650 100.000000 1 4684 1 chr2A.!!$F1 4683
1 TraesCS2A01G392900 chr2B 584691412 584695393 3981 False 6207.000000 6207 94.793000 1 3994 1 chr2B.!!$F1 3993
2 TraesCS2A01G392900 chr2D 498224781 498229837 5056 False 2123.666667 5679 91.857333 1 4684 3 chr2D.!!$F1 4683
3 TraesCS2A01G392900 chr6D 317006125 317006994 869 False 490.000000 490 77.191000 2807 3685 1 chr6D.!!$F1 878

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
670 902 0.104120 CATGCGTCTAATCCGGTGGA 59.896 55.0 0.00 0.0 35.55 4.02 F
1338 1572 0.178068 GACTATCAGCGAAAGGGCCA 59.822 55.0 6.18 0.0 0.00 5.36 F
2151 2385 0.186386 TGGAATTTTGTCCGGGTGGT 59.814 50.0 0.00 0.0 40.96 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1782 2016 0.605083 TATGGCTCCAGCTGCTATCG 59.395 55.0 8.66 0.0 41.70 2.92 R
3140 3401 0.036732 GGTTGATGGCACTCTGTCCA 59.963 55.0 0.00 0.0 36.70 4.02 R
4150 4471 0.038159 AAACGGGTTCTCGAGCTGAG 60.038 55.0 7.81 0.0 46.72 3.35 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
73 74 0.653636 CGCCGCTTTCCGCTTTATTA 59.346 50.000 0.00 0.00 36.13 0.98
74 75 1.263217 CGCCGCTTTCCGCTTTATTAT 59.737 47.619 0.00 0.00 36.13 1.28
75 76 2.286772 CGCCGCTTTCCGCTTTATTATT 60.287 45.455 0.00 0.00 36.13 1.40
139 148 1.912371 CTCCCACGCCTTTCGCTTTC 61.912 60.000 0.00 0.00 43.23 2.62
191 405 2.029844 GTCCTCCTCACAAGCGCAC 61.030 63.158 11.47 0.00 0.00 5.34
218 432 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
219 433 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
220 434 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
221 435 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
225 439 2.703007 AGAGAGAGAGAGAGAGAGAGGC 59.297 54.545 0.00 0.00 0.00 4.70
226 440 1.414181 AGAGAGAGAGAGAGAGAGGCG 59.586 57.143 0.00 0.00 0.00 5.52
450 677 1.135333 TGTTTCCTTGTTTGGTTCGGC 59.865 47.619 0.00 0.00 0.00 5.54
521 748 0.811616 GGCGAAGATCTGAATGCGGT 60.812 55.000 0.00 0.00 0.00 5.68
526 753 3.173390 GATCTGAATGCGGTGCGGC 62.173 63.158 0.00 0.00 0.00 6.53
549 776 0.798776 GTTGGGTGCATTCTGAGTCG 59.201 55.000 0.00 0.00 0.00 4.18
587 816 2.043852 TGCGGTTTTGGTGGGTGT 60.044 55.556 0.00 0.00 0.00 4.16
603 832 1.075536 GGTGTCTTGGGGTTTGAGGAT 59.924 52.381 0.00 0.00 0.00 3.24
670 902 0.104120 CATGCGTCTAATCCGGTGGA 59.896 55.000 0.00 0.00 35.55 4.02
737 969 3.628646 CTCCCCGGGGTCTGCTTTG 62.629 68.421 38.73 10.59 36.47 2.77
829 1062 4.516365 TTGTTCTCCTCGTCTCCTTAAC 57.484 45.455 0.00 0.00 0.00 2.01
885 1118 3.057033 GTCTGTGCTGAAATTTGCCATCT 60.057 43.478 0.00 0.00 0.00 2.90
1011 1245 5.069648 TGCTAAGGTCTGAATGGAGATAGTG 59.930 44.000 0.00 0.00 0.00 2.74
1039 1273 3.393360 CGGAGCCTGAAGACCCTT 58.607 61.111 0.00 0.00 0.00 3.95
1266 1500 6.691508 TGATATGGATCTTATGAAGACGGTG 58.308 40.000 0.00 0.00 41.01 4.94
1309 1543 4.063967 CTGAGCCGCCGGTGTGTA 62.064 66.667 15.14 0.00 0.00 2.90
1338 1572 0.178068 GACTATCAGCGAAAGGGCCA 59.822 55.000 6.18 0.00 0.00 5.36
1417 1651 2.647297 GCAGTGGTGAAGGCTTGC 59.353 61.111 3.46 0.00 0.00 4.01
1419 1653 2.116125 AGTGGTGAAGGCTTGCCC 59.884 61.111 3.46 4.50 0.00 5.36
1422 1656 2.747855 GGTGAAGGCTTGCCCGAG 60.748 66.667 3.46 0.00 39.21 4.63
1506 1740 0.550914 AAACTGTGTCCTTGCCTCCA 59.449 50.000 0.00 0.00 0.00 3.86
1641 1875 4.331717 AGCAACCGCAGTAATAACACATAC 59.668 41.667 0.00 0.00 42.27 2.39
1782 2016 0.600255 ACAGCAGTGGTGTTAGCGAC 60.600 55.000 21.94 0.00 41.72 5.19
1941 2175 1.582968 CTGTGGTGACATTGGCAGC 59.417 57.895 14.82 14.82 46.14 5.25
2151 2385 0.186386 TGGAATTTTGTCCGGGTGGT 59.814 50.000 0.00 0.00 40.96 4.16
2231 2465 7.725397 AGCAAGGTATATTAAATCATGAGCCAA 59.275 33.333 0.09 0.00 0.00 4.52
2302 2538 9.296400 TCAGTATTTTTGTTTGTCAAGTTTAGC 57.704 29.630 0.00 0.00 37.35 3.09
2514 2761 3.136443 AGCAGCTAATATAGTGTTGCCCA 59.864 43.478 0.00 0.00 33.42 5.36
2528 2775 2.584608 CCCAGTTACTCGGGCAGG 59.415 66.667 6.88 0.00 35.09 4.85
2547 2794 5.067023 GGCAGGATTTCTGAATAAGGTCTTG 59.933 44.000 0.00 0.00 46.18 3.02
2577 2824 3.049708 TGAGATGGTGTGCAGAGAAAG 57.950 47.619 0.00 0.00 0.00 2.62
2731 2978 7.141758 AGCATCTTATCCTTCAATACCAGAA 57.858 36.000 0.00 0.00 0.00 3.02
3095 3356 4.036616 GCTTGTTTCATGCCCAAATTGTTT 59.963 37.500 0.00 0.00 0.00 2.83
3137 3398 4.553756 GACCAAAAAGACAAGGTCTGAC 57.446 45.455 0.00 0.00 42.59 3.51
3533 3794 2.285368 AACTGGGCCCTGATCCGA 60.285 61.111 33.43 5.51 0.00 4.55
3757 4021 2.290641 GGTCAGTGTGGTGTTGTGATTC 59.709 50.000 0.00 0.00 0.00 2.52
3828 4094 3.196901 TGAACTGGCCGAAATTAGCTAGA 59.803 43.478 13.15 0.00 39.75 2.43
3845 4111 5.366460 AGCTAGATGTGTTTGATCTCCATG 58.634 41.667 0.00 0.00 32.32 3.66
3940 4206 0.603569 GAAGAGTGGCTGTCTTCGGA 59.396 55.000 11.86 0.00 40.35 4.55
3944 4210 0.034059 AGTGGCTGTCTTCGGAGTTG 59.966 55.000 0.00 0.00 0.00 3.16
3959 4226 1.965930 GTTGTGCGCCATCACTGGA 60.966 57.895 4.18 0.00 46.37 3.86
3994 4261 0.763223 ACTGACCAGTTCCCCTCGTT 60.763 55.000 0.00 0.00 38.83 3.85
3995 4262 0.396811 CTGACCAGTTCCCCTCGTTT 59.603 55.000 0.00 0.00 0.00 3.60
3996 4263 0.395312 TGACCAGTTCCCCTCGTTTC 59.605 55.000 0.00 0.00 0.00 2.78
3997 4264 0.321387 GACCAGTTCCCCTCGTTTCC 60.321 60.000 0.00 0.00 0.00 3.13
3998 4265 0.767060 ACCAGTTCCCCTCGTTTCCT 60.767 55.000 0.00 0.00 0.00 3.36
3999 4266 0.400594 CCAGTTCCCCTCGTTTCCTT 59.599 55.000 0.00 0.00 0.00 3.36
4000 4267 1.523758 CAGTTCCCCTCGTTTCCTTG 58.476 55.000 0.00 0.00 0.00 3.61
4001 4268 0.250770 AGTTCCCCTCGTTTCCTTGC 60.251 55.000 0.00 0.00 0.00 4.01
4002 4269 0.250770 GTTCCCCTCGTTTCCTTGCT 60.251 55.000 0.00 0.00 0.00 3.91
4003 4270 0.250727 TTCCCCTCGTTTCCTTGCTG 60.251 55.000 0.00 0.00 0.00 4.41
4004 4271 1.675641 CCCCTCGTTTCCTTGCTGG 60.676 63.158 0.00 0.00 37.10 4.85
4005 4272 1.073199 CCCTCGTTTCCTTGCTGGT 59.927 57.895 0.00 0.00 37.07 4.00
4006 4273 0.537371 CCCTCGTTTCCTTGCTGGTT 60.537 55.000 0.00 0.00 37.07 3.67
4007 4274 0.593128 CCTCGTTTCCTTGCTGGTTG 59.407 55.000 0.00 0.00 37.07 3.77
4008 4275 1.308998 CTCGTTTCCTTGCTGGTTGT 58.691 50.000 0.00 0.00 37.07 3.32
4009 4276 1.676006 CTCGTTTCCTTGCTGGTTGTT 59.324 47.619 0.00 0.00 37.07 2.83
4010 4277 1.403679 TCGTTTCCTTGCTGGTTGTTG 59.596 47.619 0.00 0.00 37.07 3.33
4011 4278 1.403679 CGTTTCCTTGCTGGTTGTTGA 59.596 47.619 0.00 0.00 37.07 3.18
4016 4283 4.057406 TCCTTGCTGGTTGTTGAATTTG 57.943 40.909 0.00 0.00 37.07 2.32
4018 4285 4.053295 CCTTGCTGGTTGTTGAATTTGAG 58.947 43.478 0.00 0.00 0.00 3.02
4060 4331 1.808411 ATTTCAGCGTGATTGGTCGT 58.192 45.000 0.00 0.00 0.00 4.34
4063 4334 1.006825 TCAGCGTGATTGGTCGTTCG 61.007 55.000 0.00 0.00 0.00 3.95
4069 4340 2.981805 CGTGATTGGTCGTTCGTTTAGA 59.018 45.455 0.00 0.00 0.00 2.10
4070 4341 3.611113 CGTGATTGGTCGTTCGTTTAGAT 59.389 43.478 0.00 0.00 0.00 1.98
4071 4342 4.490319 CGTGATTGGTCGTTCGTTTAGATG 60.490 45.833 0.00 0.00 0.00 2.90
4072 4343 3.369756 TGATTGGTCGTTCGTTTAGATGC 59.630 43.478 0.00 0.00 0.00 3.91
4073 4344 2.442212 TGGTCGTTCGTTTAGATGCA 57.558 45.000 0.00 0.00 0.00 3.96
4074 4345 2.333926 TGGTCGTTCGTTTAGATGCAG 58.666 47.619 0.00 0.00 0.00 4.41
4076 4347 2.092211 GGTCGTTCGTTTAGATGCAGTG 59.908 50.000 0.00 0.00 0.00 3.66
4077 4348 2.984471 GTCGTTCGTTTAGATGCAGTGA 59.016 45.455 0.00 0.00 0.00 3.41
4078 4349 3.427528 GTCGTTCGTTTAGATGCAGTGAA 59.572 43.478 0.00 0.00 0.00 3.18
4082 4353 6.533723 TCGTTCGTTTAGATGCAGTGAATTAT 59.466 34.615 0.00 0.00 0.00 1.28
4083 4354 6.841286 CGTTCGTTTAGATGCAGTGAATTATC 59.159 38.462 0.00 0.00 0.00 1.75
4084 4355 7.464045 CGTTCGTTTAGATGCAGTGAATTATCA 60.464 37.037 0.00 0.00 0.00 2.15
4131 4420 4.519350 TCTGTATACCGTGGAATAGCTGAG 59.481 45.833 0.00 0.00 0.00 3.35
4136 4425 2.224066 ACCGTGGAATAGCTGAGTATGC 60.224 50.000 0.00 0.00 0.00 3.14
4137 4426 2.408050 CGTGGAATAGCTGAGTATGCC 58.592 52.381 0.00 0.00 0.00 4.40
4139 4428 3.397482 GTGGAATAGCTGAGTATGCCTG 58.603 50.000 0.00 0.00 29.91 4.85
4143 4432 5.174395 GGAATAGCTGAGTATGCCTGTATG 58.826 45.833 0.00 0.00 0.00 2.39
4148 4469 5.688807 AGCTGAGTATGCCTGTATGAATTT 58.311 37.500 0.00 0.00 0.00 1.82
4149 4470 5.762218 AGCTGAGTATGCCTGTATGAATTTC 59.238 40.000 0.00 0.00 0.00 2.17
4150 4471 5.049129 GCTGAGTATGCCTGTATGAATTTCC 60.049 44.000 0.00 0.00 0.00 3.13
4152 4473 6.291377 TGAGTATGCCTGTATGAATTTCCTC 58.709 40.000 0.00 0.00 0.00 3.71
4165 4486 0.608640 TTTCCTCAGCTCGAGAACCC 59.391 55.000 18.75 0.00 45.45 4.11
4170 4491 0.038526 TCAGCTCGAGAACCCGTTTC 60.039 55.000 18.75 0.00 33.95 2.78
4174 4495 1.068055 GCTCGAGAACCCGTTTCAGTA 60.068 52.381 18.75 0.00 36.57 2.74
4175 4496 2.593257 CTCGAGAACCCGTTTCAGTAC 58.407 52.381 6.58 0.00 36.57 2.73
4177 4498 2.361757 TCGAGAACCCGTTTCAGTACAA 59.638 45.455 0.00 0.00 36.57 2.41
4178 4499 3.125316 CGAGAACCCGTTTCAGTACAAA 58.875 45.455 0.00 0.00 36.57 2.83
4179 4500 3.183775 CGAGAACCCGTTTCAGTACAAAG 59.816 47.826 0.00 0.00 36.57 2.77
4182 4503 3.832615 ACCCGTTTCAGTACAAAGTCT 57.167 42.857 0.00 0.00 0.00 3.24
4184 4505 3.118519 ACCCGTTTCAGTACAAAGTCTGT 60.119 43.478 0.00 0.00 42.47 3.41
4187 4508 4.684703 CCGTTTCAGTACAAAGTCTGTAGG 59.315 45.833 0.00 0.00 41.28 3.18
4188 4509 4.684703 CGTTTCAGTACAAAGTCTGTAGGG 59.315 45.833 0.00 0.00 41.28 3.53
4189 4510 5.608449 GTTTCAGTACAAAGTCTGTAGGGT 58.392 41.667 0.00 0.00 41.28 4.34
4190 4511 4.866508 TCAGTACAAAGTCTGTAGGGTG 57.133 45.455 0.00 0.00 41.28 4.61
4191 4512 3.006537 TCAGTACAAAGTCTGTAGGGTGC 59.993 47.826 0.00 0.00 41.28 5.01
4192 4513 2.969950 AGTACAAAGTCTGTAGGGTGCA 59.030 45.455 0.00 0.00 41.28 4.57
4193 4514 2.550830 ACAAAGTCTGTAGGGTGCAG 57.449 50.000 0.00 0.00 36.10 4.41
4194 4515 2.047061 ACAAAGTCTGTAGGGTGCAGA 58.953 47.619 0.00 0.00 40.28 4.26
4196 4517 2.808543 CAAAGTCTGTAGGGTGCAGAAC 59.191 50.000 0.00 0.00 43.57 3.01
4198 4519 1.620819 AGTCTGTAGGGTGCAGAACTG 59.379 52.381 0.00 0.00 43.57 3.16
4199 4520 1.344763 GTCTGTAGGGTGCAGAACTGT 59.655 52.381 3.77 0.00 43.57 3.55
4200 4521 2.047061 TCTGTAGGGTGCAGAACTGTT 58.953 47.619 0.00 0.00 39.70 3.16
4201 4522 3.006537 GTCTGTAGGGTGCAGAACTGTTA 59.993 47.826 3.77 0.00 43.57 2.41
4203 4524 3.236047 TGTAGGGTGCAGAACTGTTAGA 58.764 45.455 3.77 0.00 0.00 2.10
4204 4525 3.644265 TGTAGGGTGCAGAACTGTTAGAA 59.356 43.478 3.77 0.00 0.00 2.10
4205 4526 3.409026 AGGGTGCAGAACTGTTAGAAG 57.591 47.619 3.77 0.00 0.00 2.85
4206 4527 2.706190 AGGGTGCAGAACTGTTAGAAGT 59.294 45.455 3.77 0.00 0.00 3.01
4207 4528 3.136626 AGGGTGCAGAACTGTTAGAAGTT 59.863 43.478 3.77 0.00 43.08 2.66
4209 4530 5.061179 GGGTGCAGAACTGTTAGAAGTTTA 58.939 41.667 3.77 0.00 40.48 2.01
4210 4531 5.179555 GGGTGCAGAACTGTTAGAAGTTTAG 59.820 44.000 3.77 0.00 40.48 1.85
4211 4532 5.989777 GGTGCAGAACTGTTAGAAGTTTAGA 59.010 40.000 3.77 0.00 40.48 2.10
4212 4533 6.073711 GGTGCAGAACTGTTAGAAGTTTAGAC 60.074 42.308 3.77 0.00 40.48 2.59
4215 4536 6.444633 CAGAACTGTTAGAAGTTTAGACGGA 58.555 40.000 0.00 0.00 40.48 4.69
4216 4537 7.091443 CAGAACTGTTAGAAGTTTAGACGGAT 58.909 38.462 0.00 0.00 40.48 4.18
4217 4538 7.062371 CAGAACTGTTAGAAGTTTAGACGGATG 59.938 40.741 0.00 0.00 40.48 3.51
4218 4539 5.169295 ACTGTTAGAAGTTTAGACGGATGC 58.831 41.667 0.00 0.00 0.00 3.91
4220 4541 4.927425 TGTTAGAAGTTTAGACGGATGCAC 59.073 41.667 0.00 0.00 0.00 4.57
4222 4543 4.002906 AGAAGTTTAGACGGATGCACAA 57.997 40.909 0.00 0.00 0.00 3.33
4223 4544 4.385825 AGAAGTTTAGACGGATGCACAAA 58.614 39.130 0.00 0.00 0.00 2.83
4224 4545 5.003804 AGAAGTTTAGACGGATGCACAAAT 58.996 37.500 0.00 0.00 0.00 2.32
4225 4546 5.473504 AGAAGTTTAGACGGATGCACAAATT 59.526 36.000 0.00 0.00 0.00 1.82
4227 4548 5.003804 AGTTTAGACGGATGCACAAATTCT 58.996 37.500 0.00 0.00 0.00 2.40
4231 4552 3.189287 AGACGGATGCACAAATTCTGTTC 59.811 43.478 0.46 0.00 35.47 3.18
4235 4556 4.325204 CGGATGCACAAATTCTGTTCATTG 59.675 41.667 0.00 0.00 41.30 2.82
4236 4557 5.472148 GGATGCACAAATTCTGTTCATTGA 58.528 37.500 0.00 0.00 41.30 2.57
4238 4559 4.300803 TGCACAAATTCTGTTCATTGAGC 58.699 39.130 0.00 0.00 39.02 4.26
4241 4562 4.682860 CACAAATTCTGTTCATTGAGCACC 59.317 41.667 0.00 0.00 35.47 5.01
4242 4563 4.240096 CAAATTCTGTTCATTGAGCACCC 58.760 43.478 0.00 0.00 0.00 4.61
4261 4751 1.646540 CGCCGCACAAGAGAAAACA 59.353 52.632 0.00 0.00 0.00 2.83
4268 4758 2.286418 GCACAAGAGAAAACACGACCTG 60.286 50.000 0.00 0.00 0.00 4.00
4272 4762 1.968493 AGAGAAAACACGACCTGGCTA 59.032 47.619 0.00 0.00 0.00 3.93
4274 4764 3.135994 GAGAAAACACGACCTGGCTAAA 58.864 45.455 0.00 0.00 0.00 1.85
4313 4804 4.172232 TCCATCCCCTCCTCCCCG 62.172 72.222 0.00 0.00 0.00 5.73
4343 4836 2.034066 CCATGGTGAAGCGGTGGT 59.966 61.111 2.57 0.00 0.00 4.16
4395 4889 3.468140 GGTACCCACGCCTCCTCC 61.468 72.222 0.00 0.00 0.00 4.30
4396 4890 3.468140 GTACCCACGCCTCCTCCC 61.468 72.222 0.00 0.00 0.00 4.30
4406 4900 2.284699 CTCCTCCCCACTTCCGGT 60.285 66.667 0.00 0.00 0.00 5.28
4411 4905 3.087906 CCCCACTTCCGGTAGGGG 61.088 72.222 22.06 22.06 42.15 4.79
4435 4929 2.042843 TCGGCCTCTCCTCTTCCC 60.043 66.667 0.00 0.00 0.00 3.97
4437 4931 2.041265 GGCCTCTCCTCTTCCCCA 59.959 66.667 0.00 0.00 0.00 4.96
4442 4936 1.484038 CTCTCCTCTTCCCCACTCAG 58.516 60.000 0.00 0.00 0.00 3.35
4443 4937 0.787084 TCTCCTCTTCCCCACTCAGT 59.213 55.000 0.00 0.00 0.00 3.41
4444 4938 1.190643 CTCCTCTTCCCCACTCAGTC 58.809 60.000 0.00 0.00 0.00 3.51
4449 4944 0.842467 CTTCCCCACTCAGTCCCCTT 60.842 60.000 0.00 0.00 0.00 3.95
4450 4945 0.494551 TTCCCCACTCAGTCCCCTTA 59.505 55.000 0.00 0.00 0.00 2.69
4459 4954 3.698820 GTCCCCTTACGCCACGGT 61.699 66.667 0.00 0.00 0.00 4.83
4549 5044 2.136649 CGATATGCTCGCCAAGTCG 58.863 57.895 0.00 0.00 41.14 4.18
4550 5045 1.856012 GATATGCTCGCCAAGTCGC 59.144 57.895 0.00 0.00 0.00 5.19
4551 5046 1.560860 GATATGCTCGCCAAGTCGCC 61.561 60.000 0.00 0.00 0.00 5.54
4552 5047 2.310327 ATATGCTCGCCAAGTCGCCA 62.310 55.000 0.00 0.00 0.00 5.69
4615 5117 1.522569 GTGAGTCCTGGCGCCTAAT 59.477 57.895 29.70 12.56 0.00 1.73
4646 5148 4.443598 GGGATTTTGTTTGGGTTGCTTGTA 60.444 41.667 0.00 0.00 0.00 2.41
4660 5162 0.611200 CTTGTACCGGTGGATGGTGA 59.389 55.000 19.93 0.00 40.73 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 405 4.892345 TCTCTCTCTCTCTCTCTCTCTCTG 59.108 50.000 0.00 0.00 0.00 3.35
219 433 4.803426 CACCCAGACGCGCCTCTC 62.803 72.222 5.73 0.00 0.00 3.20
226 440 3.291101 TAACTCCGCACCCAGACGC 62.291 63.158 0.00 0.00 0.00 5.19
497 724 1.156645 ATTCAGATCTTCGCCGCTGC 61.157 55.000 0.00 0.00 0.00 5.25
499 726 1.156645 GCATTCAGATCTTCGCCGCT 61.157 55.000 0.00 0.00 0.00 5.52
526 753 2.035626 AGAATGCACCCAACCCGG 59.964 61.111 0.00 0.00 0.00 5.73
527 754 1.303236 TCAGAATGCACCCAACCCG 60.303 57.895 0.00 0.00 34.76 5.28
528 755 0.251341 ACTCAGAATGCACCCAACCC 60.251 55.000 0.00 0.00 34.76 4.11
529 756 1.168714 GACTCAGAATGCACCCAACC 58.831 55.000 0.00 0.00 34.76 3.77
530 757 0.798776 CGACTCAGAATGCACCCAAC 59.201 55.000 0.00 0.00 34.76 3.77
531 758 0.684535 TCGACTCAGAATGCACCCAA 59.315 50.000 0.00 0.00 34.76 4.12
549 776 0.321122 CAGAATCCCCGCAGCCTATC 60.321 60.000 0.00 0.00 0.00 2.08
587 816 3.010138 CAGGTTATCCTCAAACCCCAAGA 59.990 47.826 1.47 0.00 46.33 3.02
603 832 2.489985 CCCACCAAATCACACCAGGTTA 60.490 50.000 0.00 0.00 0.00 2.85
611 840 2.461695 ACAACAACCCACCAAATCACA 58.538 42.857 0.00 0.00 0.00 3.58
670 902 4.341806 TGCAGAACAGAATCACAAACCAAT 59.658 37.500 0.00 0.00 0.00 3.16
737 969 2.481276 GCAAATTATCGGAAACCCAGCC 60.481 50.000 0.00 0.00 0.00 4.85
829 1062 2.287188 GCAACAGTCACACACAGATTGG 60.287 50.000 0.00 0.00 0.00 3.16
896 1129 0.962489 AGACACAAGGACGACAGGAG 59.038 55.000 0.00 0.00 0.00 3.69
1011 1245 1.070758 TCAGGCTCCGCAATCTTATCC 59.929 52.381 0.00 0.00 0.00 2.59
1039 1273 1.691195 TTCCGAGCAGTGACCACCAA 61.691 55.000 0.00 0.00 0.00 3.67
1233 1467 6.820152 TCATAAGATCCATATCAATTGGCTCG 59.180 38.462 5.42 0.00 35.13 5.03
1266 1500 4.371786 TCTCCTCATCAATTGCGACATAC 58.628 43.478 0.00 0.00 0.00 2.39
1309 1543 0.390860 GCTGATAGTCCTCGCACCAT 59.609 55.000 0.00 0.00 0.00 3.55
1338 1572 2.045524 AGCGAGAGGTCATCCATGAAT 58.954 47.619 0.00 0.00 38.75 2.57
1389 1623 2.429058 CCACTGCCTGCACAGACT 59.571 61.111 11.03 0.00 40.25 3.24
1417 1651 1.305381 ACACCTTCCTCTCCTCGGG 60.305 63.158 0.00 0.00 0.00 5.14
1419 1653 0.814457 CAGACACCTTCCTCTCCTCG 59.186 60.000 0.00 0.00 0.00 4.63
1422 1656 0.610687 CACCAGACACCTTCCTCTCC 59.389 60.000 0.00 0.00 0.00 3.71
1506 1740 3.194542 CACAGTCTTTCTCCTCCGAATCT 59.805 47.826 0.00 0.00 0.00 2.40
1521 1755 1.209019 GATGCATCCCAGACACAGTCT 59.791 52.381 16.23 0.00 44.44 3.24
1629 1863 8.397575 TGGCTTCACTTTTGTATGTGTTATTA 57.602 30.769 0.00 0.00 35.82 0.98
1630 1864 7.283625 TGGCTTCACTTTTGTATGTGTTATT 57.716 32.000 0.00 0.00 35.82 1.40
1631 1865 6.892658 TGGCTTCACTTTTGTATGTGTTAT 57.107 33.333 0.00 0.00 35.82 1.89
1661 1895 4.160439 TCTCTACAGTAAGCATGGTTCCAG 59.840 45.833 14.50 1.89 0.00 3.86
1662 1896 4.093743 TCTCTACAGTAAGCATGGTTCCA 58.906 43.478 14.50 0.00 0.00 3.53
1782 2016 0.605083 TATGGCTCCAGCTGCTATCG 59.395 55.000 8.66 0.00 41.70 2.92
1818 2052 4.289672 GGATCATTCCCCTTATGAGGCTTA 59.710 45.833 0.00 0.00 42.09 3.09
1842 2076 1.332997 GCATGAATCGCCTTTCCTCTG 59.667 52.381 0.00 0.00 0.00 3.35
2058 2292 3.794737 TGGATGATCCAGAAGCTGC 57.205 52.632 10.75 0.00 42.67 5.25
2283 2517 6.096695 GGAGTGCTAAACTTGACAAACAAAA 58.903 36.000 0.00 0.00 40.07 2.44
2502 2749 2.093658 CCGAGTAACTGGGCAACACTAT 60.094 50.000 0.00 0.00 39.74 2.12
2514 2761 2.093447 CAGAAATCCTGCCCGAGTAACT 60.093 50.000 0.00 0.00 35.89 2.24
2528 2775 7.389053 ACAGTCACAAGACCTTATTCAGAAATC 59.611 37.037 0.00 0.00 46.15 2.17
2547 2794 3.372206 GCACACCATCTCATAACAGTCAC 59.628 47.826 0.00 0.00 0.00 3.67
2577 2824 7.367285 TGCAGACTACATTTGAACAAATAACC 58.633 34.615 11.58 2.43 38.84 2.85
2684 2931 4.813750 AAGCAAAAGCTAATTGGAGCAT 57.186 36.364 12.56 0.00 45.43 3.79
3095 3356 4.576463 GTCTTTTTCTTGCTCTTCTGACCA 59.424 41.667 0.00 0.00 0.00 4.02
3137 3398 0.325933 TGATGGCACTCTGTCCAAGG 59.674 55.000 0.00 0.00 35.75 3.61
3140 3401 0.036732 GGTTGATGGCACTCTGTCCA 59.963 55.000 0.00 0.00 36.70 4.02
3757 4021 3.994392 ACTGACATAAACAGCACCGTAAG 59.006 43.478 0.00 0.00 38.74 2.34
3828 4094 4.019051 TCAGGACATGGAGATCAAACACAT 60.019 41.667 0.00 0.00 0.00 3.21
3931 4197 1.954146 GCGCACAACTCCGAAGACA 60.954 57.895 0.30 0.00 0.00 3.41
3940 4206 1.968017 CCAGTGATGGCGCACAACT 60.968 57.895 10.83 3.87 41.19 3.16
3944 4210 0.955428 TTTCTCCAGTGATGGCGCAC 60.955 55.000 10.83 0.00 39.05 5.34
3959 4226 1.347707 TCAGTCAGAATGCCCGTTTCT 59.652 47.619 0.00 0.00 34.76 2.52
3994 4261 4.161189 TCAAATTCAACAACCAGCAAGGAA 59.839 37.500 1.83 0.00 41.22 3.36
3995 4262 3.703556 TCAAATTCAACAACCAGCAAGGA 59.296 39.130 1.83 0.00 41.22 3.36
3996 4263 4.053295 CTCAAATTCAACAACCAGCAAGG 58.947 43.478 0.00 0.00 45.67 3.61
3997 4264 4.053295 CCTCAAATTCAACAACCAGCAAG 58.947 43.478 0.00 0.00 0.00 4.01
3998 4265 3.703556 TCCTCAAATTCAACAACCAGCAA 59.296 39.130 0.00 0.00 0.00 3.91
3999 4266 3.295093 TCCTCAAATTCAACAACCAGCA 58.705 40.909 0.00 0.00 0.00 4.41
4000 4267 4.320608 TTCCTCAAATTCAACAACCAGC 57.679 40.909 0.00 0.00 0.00 4.85
4045 4315 1.282248 ACGAACGACCAATCACGCTG 61.282 55.000 0.14 0.00 0.00 5.18
4048 4318 2.981805 TCTAAACGAACGACCAATCACG 59.018 45.455 0.14 0.00 0.00 4.35
4060 4331 7.841915 TGATAATTCACTGCATCTAAACGAA 57.158 32.000 0.00 0.00 0.00 3.85
4111 4400 4.850347 ACTCAGCTATTCCACGGTATAC 57.150 45.455 0.00 0.00 0.00 1.47
4114 4403 3.005472 GCATACTCAGCTATTCCACGGTA 59.995 47.826 0.00 0.00 0.00 4.02
4117 4406 2.036475 AGGCATACTCAGCTATTCCACG 59.964 50.000 0.00 0.00 0.00 4.94
4118 4407 3.181461 ACAGGCATACTCAGCTATTCCAC 60.181 47.826 0.00 0.00 0.00 4.02
4131 4420 5.049129 GCTGAGGAAATTCATACAGGCATAC 60.049 44.000 12.33 0.00 0.00 2.39
4136 4425 3.806521 CGAGCTGAGGAAATTCATACAGG 59.193 47.826 0.00 0.00 0.00 4.00
4137 4426 4.686972 TCGAGCTGAGGAAATTCATACAG 58.313 43.478 0.00 2.60 0.00 2.74
4139 4428 4.938080 TCTCGAGCTGAGGAAATTCATAC 58.062 43.478 7.81 0.00 45.32 2.39
4143 4432 2.933260 GGTTCTCGAGCTGAGGAAATTC 59.067 50.000 7.81 0.00 45.32 2.17
4148 4469 2.046864 CGGGTTCTCGAGCTGAGGA 61.047 63.158 7.81 2.51 45.32 3.71
4149 4470 1.878656 AACGGGTTCTCGAGCTGAGG 61.879 60.000 7.81 0.00 45.32 3.86
4150 4471 0.038159 AAACGGGTTCTCGAGCTGAG 60.038 55.000 7.81 0.00 46.72 3.35
4152 4473 0.319555 TGAAACGGGTTCTCGAGCTG 60.320 55.000 7.81 1.34 37.13 4.24
4165 4486 4.684703 CCCTACAGACTTTGTACTGAAACG 59.315 45.833 0.00 0.00 41.29 3.60
4170 4491 3.244078 TGCACCCTACAGACTTTGTACTG 60.244 47.826 0.00 0.00 41.29 2.74
4174 4495 2.047061 TCTGCACCCTACAGACTTTGT 58.953 47.619 0.00 0.00 39.21 2.83
4175 4496 2.808543 GTTCTGCACCCTACAGACTTTG 59.191 50.000 0.00 0.00 43.64 2.77
4177 4498 2.037772 CAGTTCTGCACCCTACAGACTT 59.962 50.000 0.00 0.00 43.64 3.01
4178 4499 1.620819 CAGTTCTGCACCCTACAGACT 59.379 52.381 0.00 0.00 43.64 3.24
4179 4500 1.344763 ACAGTTCTGCACCCTACAGAC 59.655 52.381 0.00 0.00 43.64 3.51
4182 4503 3.236047 TCTAACAGTTCTGCACCCTACA 58.764 45.455 0.00 0.00 0.00 2.74
4184 4505 3.901844 ACTTCTAACAGTTCTGCACCCTA 59.098 43.478 0.00 0.00 0.00 3.53
4187 4508 5.989777 TCTAAACTTCTAACAGTTCTGCACC 59.010 40.000 0.00 0.00 35.87 5.01
4188 4509 6.345882 CGTCTAAACTTCTAACAGTTCTGCAC 60.346 42.308 0.00 0.00 35.87 4.57
4189 4510 5.690409 CGTCTAAACTTCTAACAGTTCTGCA 59.310 40.000 0.00 0.00 35.87 4.41
4190 4511 5.118817 CCGTCTAAACTTCTAACAGTTCTGC 59.881 44.000 0.00 0.00 35.87 4.26
4191 4512 6.444633 TCCGTCTAAACTTCTAACAGTTCTG 58.555 40.000 0.00 0.00 35.87 3.02
4192 4513 6.645790 TCCGTCTAAACTTCTAACAGTTCT 57.354 37.500 0.00 0.00 35.87 3.01
4193 4514 6.183360 GCATCCGTCTAAACTTCTAACAGTTC 60.183 42.308 0.00 0.00 35.87 3.01
4194 4515 5.638234 GCATCCGTCTAAACTTCTAACAGTT 59.362 40.000 0.00 0.00 38.74 3.16
4196 4517 5.062308 GTGCATCCGTCTAAACTTCTAACAG 59.938 44.000 0.00 0.00 0.00 3.16
4198 4519 4.927425 TGTGCATCCGTCTAAACTTCTAAC 59.073 41.667 0.00 0.00 0.00 2.34
4199 4520 5.142061 TGTGCATCCGTCTAAACTTCTAA 57.858 39.130 0.00 0.00 0.00 2.10
4200 4521 4.794278 TGTGCATCCGTCTAAACTTCTA 57.206 40.909 0.00 0.00 0.00 2.10
4201 4522 3.678056 TGTGCATCCGTCTAAACTTCT 57.322 42.857 0.00 0.00 0.00 2.85
4203 4524 5.473504 AGAATTTGTGCATCCGTCTAAACTT 59.526 36.000 0.00 0.00 0.00 2.66
4204 4525 5.003804 AGAATTTGTGCATCCGTCTAAACT 58.996 37.500 0.00 0.00 0.00 2.66
4205 4526 5.088739 CAGAATTTGTGCATCCGTCTAAAC 58.911 41.667 0.00 0.00 0.00 2.01
4206 4527 4.759693 ACAGAATTTGTGCATCCGTCTAAA 59.240 37.500 0.00 0.00 38.99 1.85
4207 4528 4.323417 ACAGAATTTGTGCATCCGTCTAA 58.677 39.130 0.00 0.00 38.99 2.10
4209 4530 2.783135 ACAGAATTTGTGCATCCGTCT 58.217 42.857 0.00 0.00 38.99 4.18
4210 4531 3.058293 TGAACAGAATTTGTGCATCCGTC 60.058 43.478 0.00 0.00 40.56 4.79
4211 4532 2.884012 TGAACAGAATTTGTGCATCCGT 59.116 40.909 0.00 0.00 40.56 4.69
4212 4533 3.557577 TGAACAGAATTTGTGCATCCG 57.442 42.857 0.00 0.00 40.56 4.18
4217 4538 4.149396 GTGCTCAATGAACAGAATTTGTGC 59.851 41.667 0.00 0.00 40.74 4.57
4218 4539 4.682860 GGTGCTCAATGAACAGAATTTGTG 59.317 41.667 0.00 0.00 40.74 3.33
4220 4541 4.240096 GGGTGCTCAATGAACAGAATTTG 58.760 43.478 0.00 0.00 0.00 2.32
4222 4543 2.827921 GGGGTGCTCAATGAACAGAATT 59.172 45.455 0.00 0.00 0.00 2.17
4223 4544 2.450476 GGGGTGCTCAATGAACAGAAT 58.550 47.619 0.00 0.00 0.00 2.40
4224 4545 1.881925 CGGGGTGCTCAATGAACAGAA 60.882 52.381 0.00 0.00 0.00 3.02
4225 4546 0.321564 CGGGGTGCTCAATGAACAGA 60.322 55.000 0.00 0.00 0.00 3.41
4227 4548 1.971167 GCGGGGTGCTCAATGAACA 60.971 57.895 0.00 0.00 41.73 3.18
4241 4562 2.258013 TTTTCTCTTGTGCGGCGGG 61.258 57.895 9.78 0.00 0.00 6.13
4242 4563 1.082104 GTTTTCTCTTGTGCGGCGG 60.082 57.895 9.78 0.00 0.00 6.13
4248 4738 2.287915 CCAGGTCGTGTTTTCTCTTGTG 59.712 50.000 0.00 0.00 0.00 3.33
4261 4751 2.047560 GCGGTTTAGCCAGGTCGT 60.048 61.111 0.00 0.00 36.97 4.34
4294 4785 2.851588 GGGAGGAGGGGATGGAGC 60.852 72.222 0.00 0.00 0.00 4.70
4296 4787 4.172232 CGGGGAGGAGGGGATGGA 62.172 72.222 0.00 0.00 0.00 3.41
4343 4836 3.264845 GTTGGCCTCCAGGGGGAA 61.265 66.667 10.80 0.00 44.38 3.97
4357 4850 1.296056 GGTTCATGACGTCGGGGTTG 61.296 60.000 11.62 3.72 0.00 3.77
4395 4889 1.907222 GAACCCCTACCGGAAGTGGG 61.907 65.000 9.46 14.97 46.57 4.61
4396 4890 1.600638 GAACCCCTACCGGAAGTGG 59.399 63.158 9.46 5.81 0.00 4.00
4400 4894 3.393106 GGCGAACCCCTACCGGAA 61.393 66.667 9.46 0.00 0.00 4.30
4411 4905 4.516195 GGAGAGGCCGAGGCGAAC 62.516 72.222 8.14 2.21 43.06 3.95
4426 4920 0.252284 GGACTGAGTGGGGAAGAGGA 60.252 60.000 0.00 0.00 0.00 3.71
4435 4929 1.218316 GCGTAAGGGGACTGAGTGG 59.782 63.158 0.00 0.00 42.68 4.00
4437 4931 1.229082 TGGCGTAAGGGGACTGAGT 60.229 57.895 0.00 0.00 42.68 3.41
4442 4936 3.654173 GACCGTGGCGTAAGGGGAC 62.654 68.421 3.77 0.00 38.28 4.46
4443 4937 3.384532 GACCGTGGCGTAAGGGGA 61.385 66.667 3.77 0.00 38.28 4.81
4444 4938 4.807039 CGACCGTGGCGTAAGGGG 62.807 72.222 3.77 0.00 38.28 4.79
4459 4954 1.672030 CCACATGAACTGCAGCCGA 60.672 57.895 15.27 0.00 0.00 5.54
4534 5029 2.202878 GGCGACTTGGCGAGCATA 60.203 61.111 0.37 0.00 0.00 3.14
4615 5117 2.158842 CCAAACAAAATCCCACAGCCAA 60.159 45.455 0.00 0.00 0.00 4.52
4619 5121 3.465871 CAACCCAAACAAAATCCCACAG 58.534 45.455 0.00 0.00 0.00 3.66
4646 5148 1.990060 CTCCTCACCATCCACCGGT 60.990 63.158 0.00 0.00 37.16 5.28
4660 5162 3.181429 TGGAAAACAAATCAGCTCCTCCT 60.181 43.478 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.