Multiple sequence alignment - TraesCS6A01G274500

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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 TraesCS6A01G274500 chr6A 100.000 4992 0 0 1 4992 501226131 501221140 0.000000e+00 9219.0
1 TraesCS6A01G274500 chr6A 87.923 207 15 7 4279 4476 501221659 501221454 8.350000e-58 235.0
2 TraesCS6A01G274500 chr6A 87.923 207 15 7 4473 4678 501221853 501221656 8.350000e-58 235.0
3 TraesCS6A01G274500 chr6A 97.727 44 1 0 4119 4162 501221638 501221595 5.360000e-10 76.8
4 TraesCS6A01G274500 chr6A 97.727 44 1 0 4494 4537 501222013 501221970 5.360000e-10 76.8
5 TraesCS6A01G274500 chr6A 95.455 44 2 0 4119 4162 501221832 501221789 2.490000e-08 71.3
6 TraesCS6A01G274500 chr6A 95.455 44 2 0 4300 4343 501222013 501221970 2.490000e-08 71.3
7 TraesCS6A01G274500 chr6D 96.211 4196 121 21 292 4475 359532877 359528708 0.000000e+00 6833.0
8 TraesCS6A01G274500 chr6D 87.250 549 37 17 4473 4992 359528911 359528367 3.330000e-166 595.0
9 TraesCS6A01G274500 chr6D 88.128 219 18 5 1 218 359533581 359533370 2.310000e-63 254.0
10 TraesCS6A01G274500 chr6D 97.727 44 1 0 4494 4537 359529067 359529024 5.360000e-10 76.8
11 TraesCS6A01G274500 chr6D 95.455 44 2 0 4300 4343 359529067 359529024 2.490000e-08 71.3
12 TraesCS6A01G274500 chr6B 97.089 2851 77 4 302 3148 541160978 541158130 0.000000e+00 4800.0
13 TraesCS6A01G274500 chr6B 94.432 1365 48 13 3135 4476 541158114 541156755 0.000000e+00 2074.0
14 TraesCS6A01G274500 chr6B 86.654 532 35 12 4486 4992 541156954 541156434 1.570000e-154 556.0
15 TraesCS6A01G274500 chr6B 89.450 218 21 1 2 217 541161355 541161138 1.770000e-69 274.0
16 TraesCS6A01G274500 chr6B 95.745 47 2 0 4491 4537 541157135 541157089 5.360000e-10 76.8
17 TraesCS6A01G274500 chr6B 93.617 47 3 0 4297 4343 541157135 541157089 2.490000e-08 71.3


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 TraesCS6A01G274500 chr6A 501221140 501226131 4991 True 9219.000000 9219 100.000000 1 4992 1 chr6A.!!$R1 4991
1 TraesCS6A01G274500 chr6D 359528367 359532877 4510 True 1894.025000 6833 94.160750 292 4992 4 chr6D.!!$R2 4700
2 TraesCS6A01G274500 chr6B 541156434 541161355 4921 True 1308.683333 4800 92.831167 2 4992 6 chr6B.!!$R1 4990

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
697 775 0.029567 GAGGTATGAGCTCGTGTCCG 59.970 60.0 18.98 0.0 32.69 4.79 F
1767 1848 0.393448 TGCATGTTGTGGCTGCAATT 59.607 45.0 0.50 0.0 42.53 2.32 F
2376 2457 0.744281 CCACCGTGGCTTCTGTTTTT 59.256 50.0 4.16 0.0 0.00 1.94 F
3458 3569 0.380378 TTGCTTGTCGTTGGCTGTTC 59.620 50.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 2457 0.755079 ATAGATCAGCAAGCCGCAGA 59.245 50.0 0.00 0.0 46.13 4.26 R
3045 3126 0.548031 TGCAGGGCTTAGAAGGATGG 59.452 55.0 0.00 0.0 0.00 3.51 R
3814 3926 0.585029 GCTTCTCTTCGCGCATTTCG 60.585 55.0 8.75 0.0 42.12 3.46 R
4535 4656 0.406361 AAAGGCATTCCCGGTGGTAA 59.594 50.0 0.00 0.0 39.21 2.85 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
27 28 6.294342 CGAGACAATACCTATCCGTCCAATTA 60.294 42.308 0.00 0.00 0.00 1.40
39 40 2.716398 GTCCAATTAAATTCTCGGCGC 58.284 47.619 0.00 0.00 0.00 6.53
45 46 4.946784 ATTAAATTCTCGGCGCATATCC 57.053 40.909 10.83 0.00 0.00 2.59
46 47 2.550830 AAATTCTCGGCGCATATCCT 57.449 45.000 10.83 0.00 0.00 3.24
49 50 2.941453 TTCTCGGCGCATATCCTATC 57.059 50.000 10.83 0.00 0.00 2.08
54 55 2.623416 TCGGCGCATATCCTATCCTATG 59.377 50.000 10.83 0.00 0.00 2.23
70 71 5.766702 TCCTATGTACGCGTAACAAAAAG 57.233 39.130 22.44 17.12 0.00 2.27
114 117 9.715121 GATTATGAATGCCAATGTAAAATCCAT 57.285 29.630 0.00 0.00 0.00 3.41
151 154 0.534877 TGAAAGGCATGCACGTGACT 60.535 50.000 22.23 2.68 39.79 3.41
156 159 2.774126 CATGCACGTGACTCGCAG 59.226 61.111 22.23 0.04 44.19 5.18
178 181 2.808202 GCCGCCTCAGATATCAACATGT 60.808 50.000 5.32 0.00 0.00 3.21
182 185 4.388165 CGCCTCAGATATCAACATGTCATC 59.612 45.833 5.32 0.29 0.00 2.92
195 198 7.552459 TCAACATGTCATCCTAGAATTTACGA 58.448 34.615 0.00 0.00 0.00 3.43
198 201 7.726216 ACATGTCATCCTAGAATTTACGATCA 58.274 34.615 0.00 0.00 0.00 2.92
202 205 5.839063 TCATCCTAGAATTTACGATCACCCT 59.161 40.000 0.00 0.00 0.00 4.34
209 212 2.953466 TTACGATCACCCTGTGCTAC 57.047 50.000 0.00 0.00 32.98 3.58
217 220 4.435436 CCTGTGCTACGAGCCGCA 62.435 66.667 0.00 0.00 41.51 5.69
236 267 1.265095 CATCGTAATGCATGGCTCCAC 59.735 52.381 0.00 0.00 0.00 4.02
429 507 0.391793 CCGTGCCTTTCCTCTTCCTC 60.392 60.000 0.00 0.00 0.00 3.71
481 559 0.486879 AAGCTCCAATCCCACCCAAA 59.513 50.000 0.00 0.00 0.00 3.28
677 755 0.446616 GATCTCGGGCGTTGGTTTTC 59.553 55.000 0.00 0.00 0.00 2.29
697 775 0.029567 GAGGTATGAGCTCGTGTCCG 59.970 60.000 18.98 0.00 32.69 4.79
756 834 3.686045 CTAGATCCGCCCCTCCGC 61.686 72.222 0.00 0.00 0.00 5.54
897 975 5.927689 TCTTGCTTTGCCTTAATTGATTGTG 59.072 36.000 0.00 0.00 0.00 3.33
985 1063 1.661112 GGTGAGAAGAATCTTTCGCCG 59.339 52.381 16.14 0.00 35.54 6.46
1029 1107 5.059833 GGAATCATAGTGGATGGAGTTGTC 58.940 45.833 0.00 0.00 36.08 3.18
1117 1195 1.654954 GCCAAGCATGCAGAGTGAGG 61.655 60.000 21.98 11.05 0.00 3.86
1170 1248 1.227497 GGAGCCCTCGATTGAGCAG 60.227 63.158 4.21 0.00 41.13 4.24
1212 1290 1.220477 GGAGAGCTCAAGTGAGGGC 59.780 63.158 17.77 0.00 42.29 5.19
1370 1451 3.497942 GGGAGTGGAAGTGTTACCAATGT 60.498 47.826 0.00 0.00 37.94 2.71
1428 1509 5.882557 GCCTCAGTCTTCTAATTCATCCAAA 59.117 40.000 0.00 0.00 0.00 3.28
1468 1549 4.874396 CACAGCTTGAATCTGATGCTTCTA 59.126 41.667 2.71 0.00 35.61 2.10
1590 1671 3.963733 TGGAACAGAAGATGCTGGG 57.036 52.632 0.00 0.00 40.20 4.45
1593 1674 1.377536 GAACAGAAGATGCTGGGCTC 58.622 55.000 0.00 0.00 40.20 4.70
1767 1848 0.393448 TGCATGTTGTGGCTGCAATT 59.607 45.000 0.50 0.00 42.53 2.32
1788 1869 4.032960 TCACTGCAACATGGGAAAGTAT 57.967 40.909 0.00 0.00 0.00 2.12
2059 2140 8.905702 CACTACAATTAGATGAAGCACAAAAAC 58.094 33.333 0.00 0.00 0.00 2.43
2178 2259 4.402851 GGTGACCATGAAGCTGCA 57.597 55.556 0.00 0.00 0.00 4.41
2376 2457 0.744281 CCACCGTGGCTTCTGTTTTT 59.256 50.000 4.16 0.00 0.00 1.94
2415 2496 7.011499 TCTATACAACAAAACAGGGAAGCTA 57.989 36.000 0.00 0.00 0.00 3.32
2829 2910 3.692690 ACTCTTCGAGGAAGCTAGAACT 58.307 45.455 0.00 0.00 39.29 3.01
2935 3016 5.353394 AAGGTAAGCTCCGTATTGATTCA 57.647 39.130 0.00 0.00 0.00 2.57
2940 3021 2.939103 AGCTCCGTATTGATTCACTTGC 59.061 45.455 0.00 0.00 0.00 4.01
3045 3126 7.928908 TGTTTGTTTGACTTCTCATTATTGC 57.071 32.000 0.00 0.00 0.00 3.56
3080 3161 3.627577 CCCTGCATAACCTACATGTGAAC 59.372 47.826 9.11 0.00 0.00 3.18
3084 3165 6.597672 CCTGCATAACCTACATGTGAACTTTA 59.402 38.462 9.11 0.00 0.00 1.85
3108 3190 1.985473 AAGTGAAGTGCTTCCATGCA 58.015 45.000 9.18 0.00 41.05 3.96
3121 3203 0.676466 CCATGCACACCTCGCCTTTA 60.676 55.000 0.00 0.00 0.00 1.85
3125 3207 3.275617 TGCACACCTCGCCTTTATTAT 57.724 42.857 0.00 0.00 0.00 1.28
3148 3230 9.554395 TTATTTGTCCATGATTTATCGCTAAGA 57.446 29.630 0.00 0.00 0.00 2.10
3150 3232 9.725019 ATTTGTCCATGATTTATCGCTAAGATA 57.275 29.630 0.00 0.00 40.66 1.98
3151 3233 9.554395 TTTGTCCATGATTTATCGCTAAGATAA 57.446 29.630 0.00 0.00 46.78 1.75
3232 3343 0.399091 TAGCCCTCAGATGTCCTGGG 60.399 60.000 0.00 0.00 43.15 4.45
3238 3349 2.564947 CCTCAGATGTCCTGGGTATAGC 59.435 54.545 0.00 0.00 41.93 2.97
3458 3569 0.380378 TTGCTTGTCGTTGGCTGTTC 59.620 50.000 0.00 0.00 0.00 3.18
3618 3730 6.625362 TGATGCTAGTTCTGAACTAAGAGTG 58.375 40.000 25.52 16.75 42.99 3.51
3641 3753 2.166664 CCAGTTGTACTCTGGTCTAGCC 59.833 54.545 21.32 0.00 45.09 3.93
3653 3765 1.109920 GTCTAGCCGGCCAGATCAGA 61.110 60.000 27.37 14.88 0.00 3.27
3811 3923 4.212214 GCCATTGAGATCTTGGAATACGTC 59.788 45.833 14.94 0.00 31.94 4.34
3814 3926 4.288670 TGAGATCTTGGAATACGTCGTC 57.711 45.455 0.00 0.00 0.00 4.20
4012 4124 5.965918 GTGAGTGAACTACAGCTTTTGAAAC 59.034 40.000 0.00 0.00 0.00 2.78
4216 4328 4.219033 CAATTAACTGTGCTCGTTGAACC 58.781 43.478 0.00 0.00 0.00 3.62
4241 4356 4.928020 GTGTGTTTTGCCTAGTCCTACTAC 59.072 45.833 0.00 0.00 0.00 2.73
4242 4357 4.836736 TGTGTTTTGCCTAGTCCTACTACT 59.163 41.667 0.00 0.00 0.00 2.57
4243 4358 6.012113 TGTGTTTTGCCTAGTCCTACTACTA 58.988 40.000 0.00 0.00 0.00 1.82
4244 4359 6.152323 TGTGTTTTGCCTAGTCCTACTACTAG 59.848 42.308 4.41 4.41 45.71 2.57
4245 4360 6.152492 GTGTTTTGCCTAGTCCTACTACTAGT 59.848 42.308 0.00 0.00 45.00 2.57
4340 4461 3.779759 TGTTGTAAAGTTGCAAAGGCTG 58.220 40.909 0.00 0.00 41.91 4.85
4363 4484 2.807676 ACCACCAGGAATGCCTTTTAG 58.192 47.619 0.00 0.00 43.90 1.85
4369 4490 2.096496 CAGGAATGCCTTTTAGTGCTCG 59.904 50.000 0.00 0.00 43.90 5.03
4383 4504 2.885861 CTCGGGCGCTAGTGAGTT 59.114 61.111 7.64 0.00 0.00 3.01
4397 4518 2.737252 AGTGAGTTCGATCTTTTTCGCC 59.263 45.455 0.00 0.00 38.97 5.54
4398 4519 2.478894 GTGAGTTCGATCTTTTTCGCCA 59.521 45.455 0.00 0.00 38.97 5.69
4399 4520 3.059188 GTGAGTTCGATCTTTTTCGCCAA 60.059 43.478 0.00 0.00 38.97 4.52
4400 4521 3.562141 TGAGTTCGATCTTTTTCGCCAAA 59.438 39.130 0.00 0.00 38.97 3.28
4401 4522 4.035792 TGAGTTCGATCTTTTTCGCCAAAA 59.964 37.500 0.00 0.00 38.97 2.44
4402 4523 4.927422 AGTTCGATCTTTTTCGCCAAAAA 58.073 34.783 1.97 1.97 38.84 1.94
4460 4581 7.407393 TTTTCCAGATTGTCATATGAATGCA 57.593 32.000 7.07 0.00 32.76 3.96
4461 4582 7.591421 TTTCCAGATTGTCATATGAATGCAT 57.409 32.000 7.07 0.00 38.54 3.96
4462 4583 8.694581 TTTCCAGATTGTCATATGAATGCATA 57.305 30.769 7.07 0.00 41.00 3.14
4463 4584 8.873186 TTCCAGATTGTCATATGAATGCATAT 57.127 30.769 7.07 0.00 46.12 1.78
4464 4585 8.873186 TCCAGATTGTCATATGAATGCATATT 57.127 30.769 7.07 0.00 43.46 1.28
4465 4586 9.962809 TCCAGATTGTCATATGAATGCATATTA 57.037 29.630 7.07 0.00 43.46 0.98
4466 4587 9.999009 CCAGATTGTCATATGAATGCATATTAC 57.001 33.333 7.07 10.13 43.46 1.89
4478 4599 8.938801 TGAATGCATATTACATGATTAACCCT 57.061 30.769 0.00 0.00 0.00 4.34
4482 4603 8.846943 TGCATATTACATGATTAACCCTACTG 57.153 34.615 0.00 0.00 0.00 2.74
4483 4604 8.436778 TGCATATTACATGATTAACCCTACTGT 58.563 33.333 0.00 0.00 0.00 3.55
4484 4605 9.284968 GCATATTACATGATTAACCCTACTGTT 57.715 33.333 0.00 0.00 0.00 3.16
4490 4611 8.964476 ACATGATTAACCCTACTGTTTAGATG 57.036 34.615 0.00 0.00 0.00 2.90
4491 4612 8.768397 ACATGATTAACCCTACTGTTTAGATGA 58.232 33.333 0.00 0.00 0.00 2.92
4492 4613 9.046296 CATGATTAACCCTACTGTTTAGATGAC 57.954 37.037 0.00 0.00 0.00 3.06
4493 4614 8.141298 TGATTAACCCTACTGTTTAGATGACA 57.859 34.615 0.00 0.00 0.00 3.58
4494 4615 8.038944 TGATTAACCCTACTGTTTAGATGACAC 58.961 37.037 0.00 0.00 0.00 3.67
4495 4616 5.818678 AACCCTACTGTTTAGATGACACA 57.181 39.130 0.00 0.00 0.00 3.72
4496 4617 5.818678 ACCCTACTGTTTAGATGACACAA 57.181 39.130 0.00 0.00 0.00 3.33
4497 4618 6.182507 ACCCTACTGTTTAGATGACACAAA 57.817 37.500 0.00 0.00 0.00 2.83
4498 4619 6.597562 ACCCTACTGTTTAGATGACACAAAA 58.402 36.000 0.00 0.00 0.00 2.44
4499 4620 7.057894 ACCCTACTGTTTAGATGACACAAAAA 58.942 34.615 0.00 0.00 0.00 1.94
4500 4621 7.724061 ACCCTACTGTTTAGATGACACAAAAAT 59.276 33.333 0.00 0.00 0.00 1.82
4501 4622 8.023128 CCCTACTGTTTAGATGACACAAAAATG 58.977 37.037 0.00 0.00 0.00 2.32
4502 4623 8.783093 CCTACTGTTTAGATGACACAAAAATGA 58.217 33.333 0.00 0.00 0.00 2.57
4505 4626 9.071276 ACTGTTTAGATGACACAAAAATGATCT 57.929 29.630 0.00 0.00 0.00 2.75
4506 4627 9.338291 CTGTTTAGATGACACAAAAATGATCTG 57.662 33.333 0.00 0.00 0.00 2.90
4507 4628 9.065798 TGTTTAGATGACACAAAAATGATCTGA 57.934 29.630 0.00 0.00 0.00 3.27
4511 4632 8.344446 AGATGACACAAAAATGATCTGATTGA 57.656 30.769 0.00 0.00 0.00 2.57
4512 4633 8.967918 AGATGACACAAAAATGATCTGATTGAT 58.032 29.630 0.00 0.00 38.27 2.57
4513 4634 9.582431 GATGACACAAAAATGATCTGATTGATT 57.418 29.630 0.00 0.00 35.14 2.57
4514 4635 8.751302 TGACACAAAAATGATCTGATTGATTG 57.249 30.769 0.00 0.00 35.14 2.67
4515 4636 8.361889 TGACACAAAAATGATCTGATTGATTGT 58.638 29.630 0.00 0.30 35.14 2.71
4516 4637 9.199982 GACACAAAAATGATCTGATTGATTGTT 57.800 29.630 0.00 0.00 35.14 2.83
4517 4638 8.984764 ACACAAAAATGATCTGATTGATTGTTG 58.015 29.630 16.86 16.86 35.14 3.33
4518 4639 8.984764 CACAAAAATGATCTGATTGATTGTTGT 58.015 29.630 17.69 17.69 35.14 3.32
4525 4646 9.850628 ATGATCTGATTGATTGTTGTAAAGTTG 57.149 29.630 0.00 0.00 35.14 3.16
4526 4647 7.809331 TGATCTGATTGATTGTTGTAAAGTTGC 59.191 33.333 0.00 0.00 35.14 4.17
4527 4648 7.036996 TCTGATTGATTGTTGTAAAGTTGCA 57.963 32.000 0.00 0.00 0.00 4.08
4528 4649 7.487484 TCTGATTGATTGTTGTAAAGTTGCAA 58.513 30.769 0.00 0.00 0.00 4.08
4529 4650 7.978414 TCTGATTGATTGTTGTAAAGTTGCAAA 59.022 29.630 0.00 0.00 34.63 3.68
4530 4651 8.129161 TGATTGATTGTTGTAAAGTTGCAAAG 57.871 30.769 0.00 0.00 34.63 2.77
4531 4652 6.900568 TTGATTGTTGTAAAGTTGCAAAGG 57.099 33.333 0.00 0.00 34.63 3.11
4532 4653 4.808364 TGATTGTTGTAAAGTTGCAAAGGC 59.192 37.500 0.00 0.00 34.63 4.35
4533 4654 4.464069 TTGTTGTAAAGTTGCAAAGGCT 57.536 36.364 0.00 0.00 41.91 4.58
4534 4655 5.584253 TTGTTGTAAAGTTGCAAAGGCTA 57.416 34.783 0.00 0.00 41.91 3.93
4535 4656 5.782893 TGTTGTAAAGTTGCAAAGGCTAT 57.217 34.783 0.00 0.00 41.91 2.97
4536 4657 6.155475 TGTTGTAAAGTTGCAAAGGCTATT 57.845 33.333 0.00 0.00 41.91 1.73
4537 4658 7.278461 TGTTGTAAAGTTGCAAAGGCTATTA 57.722 32.000 0.00 0.00 41.91 0.98
4538 4659 7.142680 TGTTGTAAAGTTGCAAAGGCTATTAC 58.857 34.615 0.00 5.66 41.91 1.89
4539 4660 6.262193 TGTAAAGTTGCAAAGGCTATTACC 57.738 37.500 0.00 0.00 41.91 2.85
4540 4661 5.770663 TGTAAAGTTGCAAAGGCTATTACCA 59.229 36.000 0.00 0.00 41.91 3.25
4541 4662 4.783764 AAGTTGCAAAGGCTATTACCAC 57.216 40.909 0.00 0.00 41.91 4.16
4542 4663 3.089284 AGTTGCAAAGGCTATTACCACC 58.911 45.455 0.00 0.00 41.91 4.61
4543 4664 1.745232 TGCAAAGGCTATTACCACCG 58.255 50.000 0.00 0.00 41.91 4.94
4544 4665 1.021968 GCAAAGGCTATTACCACCGG 58.978 55.000 0.00 0.00 36.96 5.28
4566 4687 0.328258 ATGCCTTTTAGTGCTCGGGT 59.672 50.000 0.00 0.00 0.00 5.28
4578 4699 1.071471 CTCGGGTGCCAGTGAGTTT 59.929 57.895 0.00 0.00 0.00 2.66
4579 4700 1.227823 TCGGGTGCCAGTGAGTTTG 60.228 57.895 0.00 0.00 0.00 2.93
4587 4708 4.202151 GGTGCCAGTGAGTTTGATCTTTTT 60.202 41.667 0.00 0.00 0.00 1.94
4726 4859 8.650143 AATCAATAATTTTCACCCTGTGTAGT 57.350 30.769 0.00 0.00 34.79 2.73
4730 4863 1.873698 TTTCACCCTGTGTAGTTCGC 58.126 50.000 0.00 0.00 34.79 4.70
4740 4873 2.156117 TGTGTAGTTCGCGTGTTAATGC 59.844 45.455 5.77 0.00 34.77 3.56
4838 4990 1.003866 GAGTTCGAGCACACAAACACC 60.004 52.381 1.01 0.00 0.00 4.16
4905 5057 2.011222 GGTCGTTGAACAGGTGTTTCA 58.989 47.619 0.00 0.00 38.56 2.69
4964 5116 6.042638 TGTTAGAGCAACTCTAGCAGAATT 57.957 37.500 14.73 0.00 44.88 2.17
4981 5133 8.712285 AGCAGAATTGACATAATTTGAATTGG 57.288 30.769 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.228343 GACGGATAGGTATTGTCTCGGG 59.772 54.545 0.00 0.00 0.00 5.14
27 28 2.550830 AGGATATGCGCCGAGAATTT 57.449 45.000 4.18 0.00 0.00 1.82
39 40 5.752892 ACGCGTACATAGGATAGGATATG 57.247 43.478 11.67 0.00 35.84 1.78
45 46 7.433131 TCTTTTTGTTACGCGTACATAGGATAG 59.567 37.037 20.44 9.82 0.00 2.08
46 47 7.257003 TCTTTTTGTTACGCGTACATAGGATA 58.743 34.615 20.44 0.00 0.00 2.59
49 50 5.766702 TCTTTTTGTTACGCGTACATAGG 57.233 39.130 20.44 11.33 0.00 2.57
54 55 5.199726 ACATGTTCTTTTTGTTACGCGTAC 58.800 37.500 20.44 14.48 0.00 3.67
99 102 8.641541 AGTAATTGCCTATGGATTTTACATTGG 58.358 33.333 0.00 0.00 41.94 3.16
114 117 7.996066 TGCCTTTCATATTGTAGTAATTGCCTA 59.004 33.333 0.00 0.00 0.00 3.93
156 159 0.106708 TGTTGATATCTGAGGCGGCC 59.893 55.000 12.11 12.11 0.00 6.13
158 161 3.062763 GACATGTTGATATCTGAGGCGG 58.937 50.000 0.00 0.00 0.00 6.13
164 167 9.722184 AATTCTAGGATGACATGTTGATATCTG 57.278 33.333 0.00 0.00 0.00 2.90
178 181 5.839063 AGGGTGATCGTAAATTCTAGGATGA 59.161 40.000 0.00 0.00 0.00 2.92
182 185 5.050490 CACAGGGTGATCGTAAATTCTAGG 58.950 45.833 0.00 0.00 35.23 3.02
192 195 0.963856 TCGTAGCACAGGGTGATCGT 60.964 55.000 0.00 0.00 35.23 3.73
195 198 1.517832 GCTCGTAGCACAGGGTGAT 59.482 57.895 0.00 0.00 41.89 3.06
198 201 3.760035 CGGCTCGTAGCACAGGGT 61.760 66.667 8.71 0.00 44.75 4.34
202 205 2.202743 GATGCGGCTCGTAGCACA 60.203 61.111 0.00 6.70 46.83 4.57
217 220 1.134128 TGTGGAGCCATGCATTACGAT 60.134 47.619 0.00 0.00 0.00 3.73
282 314 9.434275 TCCATGGAAGAAGAAATATAGAGTACA 57.566 33.333 13.46 0.00 0.00 2.90
284 316 8.871125 GGTCCATGGAAGAAGAAATATAGAGTA 58.129 37.037 18.20 0.00 0.00 2.59
285 317 7.570607 AGGTCCATGGAAGAAGAAATATAGAGT 59.429 37.037 18.20 0.00 0.00 3.24
292 324 4.934797 TGAGGTCCATGGAAGAAGAAAT 57.065 40.909 18.20 0.00 0.00 2.17
481 559 4.163839 ACAGGAGAGATTTTAGAGCTGCAT 59.836 41.667 1.02 0.00 0.00 3.96
697 775 1.504900 GTTTTGGGAATCGCCGGAC 59.495 57.895 5.05 0.00 37.63 4.79
756 834 2.253403 GAGTTAAGCGTGGGGAGGGG 62.253 65.000 0.00 0.00 0.00 4.79
812 890 0.393537 AGAGCTCCAATTTCGGCTGG 60.394 55.000 10.93 0.00 35.01 4.85
897 975 6.918022 CCACAATACCTTGAAAGAAACAGAAC 59.082 38.462 0.00 0.00 36.20 3.01
1029 1107 3.459145 CTCATGCTGAATCTCCTCTGTG 58.541 50.000 0.00 0.00 0.00 3.66
1117 1195 0.867746 TCAACGTGCATCTCAAGTGC 59.132 50.000 0.00 0.00 42.81 4.40
1170 1248 2.198406 TCACACACGTTGTTGTAGAGC 58.802 47.619 0.00 0.00 35.67 4.09
1212 1290 4.969196 CGTGATGGGGATCCGCCG 62.969 72.222 24.83 16.94 39.47 6.46
1370 1451 1.837439 CATTCCCAGCAGTAGGTACCA 59.163 52.381 15.94 0.00 0.00 3.25
1428 1509 4.829492 AGCTGTGATTTTGTAGCCTTCTTT 59.171 37.500 0.00 0.00 36.86 2.52
1560 1641 7.148188 GCATCTTCTGTTCCATTCTGTGATTTA 60.148 37.037 0.00 0.00 0.00 1.40
1590 1671 1.473434 CCAAGGTCTGGGTTATCGAGC 60.473 57.143 0.00 0.00 42.17 5.03
1767 1848 2.363306 ACTTTCCCATGTTGCAGTGA 57.637 45.000 0.00 0.00 0.00 3.41
1788 1869 2.609747 AGGACAGGTACAGCTTCTTCA 58.390 47.619 0.00 0.00 0.00 3.02
2199 2280 3.142838 GCGACCATGGCCATGCTT 61.143 61.111 36.08 25.80 37.49 3.91
2292 2373 1.134818 TGGTAAGCACATACAGCCTCG 60.135 52.381 0.00 0.00 0.00 4.63
2376 2457 0.755079 ATAGATCAGCAAGCCGCAGA 59.245 50.000 0.00 0.00 46.13 4.26
2415 2496 7.405292 TCTCACAGTATGATTTTGATTCCCTT 58.595 34.615 0.00 0.00 39.69 3.95
2829 2910 2.354704 CCCGTATTCTTGCTCCAGAACA 60.355 50.000 0.00 0.00 35.57 3.18
2935 3016 6.998673 AGTATAGAAGAAACAACTTGGCAAGT 59.001 34.615 26.54 26.54 45.46 3.16
2940 3021 6.801539 TGCAGTATAGAAGAAACAACTTGG 57.198 37.500 0.00 0.00 0.00 3.61
3011 3092 9.677567 GAGAAGTCAAACAAACATATTAGCAAA 57.322 29.630 0.00 0.00 0.00 3.68
3045 3126 0.548031 TGCAGGGCTTAGAAGGATGG 59.452 55.000 0.00 0.00 0.00 3.51
3080 3161 9.132521 CATGGAAGCACTTCACTTTTATTAAAG 57.867 33.333 12.21 2.71 41.20 1.85
3084 3165 5.010922 TGCATGGAAGCACTTCACTTTTATT 59.989 36.000 12.21 0.00 40.11 1.40
3108 3190 4.638865 GGACAAATAATAAAGGCGAGGTGT 59.361 41.667 0.00 0.00 0.00 4.16
3125 3207 9.554395 TTATCTTAGCGATAAATCATGGACAAA 57.446 29.630 0.00 0.00 40.66 2.83
3157 3268 2.358957 TGAGAGCAACCAAATGGATCG 58.641 47.619 6.42 0.00 38.94 3.69
3232 3343 6.814146 GGCTTTACTCATATCCTGTGCTATAC 59.186 42.308 0.00 0.00 0.00 1.47
3238 3349 7.716998 ACTTTATGGCTTTACTCATATCCTGTG 59.283 37.037 0.00 0.00 0.00 3.66
3422 3533 7.271223 CGACAAGCAACTAAAGATGGTTTTATG 59.729 37.037 2.38 0.00 36.60 1.90
3683 3795 8.489990 TCTTAATCTCAGATTTGCTTTCAGAG 57.510 34.615 4.90 0.00 0.00 3.35
3718 3830 4.845225 ACATATTCTGAGAGGGAGATGCAT 59.155 41.667 0.00 0.00 0.00 3.96
3811 3923 1.014399 CTCTTCGCGCATTTCGACG 60.014 57.895 8.75 0.00 41.67 5.12
3814 3926 0.585029 GCTTCTCTTCGCGCATTTCG 60.585 55.000 8.75 0.00 42.12 3.46
3868 3980 3.626924 AACTCGGCAAGCCTCCGT 61.627 61.111 9.73 0.49 46.49 4.69
4012 4124 4.452455 AGCGTCATAGTGTTCCTTTTTCTG 59.548 41.667 0.00 0.00 0.00 3.02
4216 4328 0.872388 GGACTAGGCAAAACACACCG 59.128 55.000 0.00 0.00 0.00 4.94
4340 4461 2.215942 AAGGCATTCCTGGTGGTAAC 57.784 50.000 0.00 0.00 43.40 2.50
4363 4484 4.129737 TCACTAGCGCCCGAGCAC 62.130 66.667 2.29 0.00 39.83 4.40
4369 4490 0.595310 GATCGAACTCACTAGCGCCC 60.595 60.000 2.29 0.00 0.00 6.13
4375 4496 3.924686 GGCGAAAAAGATCGAACTCACTA 59.075 43.478 0.00 0.00 45.48 2.74
4435 4556 7.838884 TGCATTCATATGACAATCTGGAAAAA 58.161 30.769 4.48 0.00 33.37 1.94
4436 4557 7.407393 TGCATTCATATGACAATCTGGAAAA 57.593 32.000 4.48 0.00 33.37 2.29
4437 4558 7.591421 ATGCATTCATATGACAATCTGGAAA 57.409 32.000 4.48 0.00 33.37 3.13
4438 4559 8.873186 ATATGCATTCATATGACAATCTGGAA 57.127 30.769 3.54 0.00 42.61 3.53
4439 4560 8.873186 AATATGCATTCATATGACAATCTGGA 57.127 30.769 3.54 0.53 43.22 3.86
4440 4561 9.999009 GTAATATGCATTCATATGACAATCTGG 57.001 33.333 3.54 0.00 42.70 3.86
4452 4573 9.537852 AGGGTTAATCATGTAATATGCATTCAT 57.462 29.630 3.54 2.64 36.73 2.57
4453 4574 8.938801 AGGGTTAATCATGTAATATGCATTCA 57.061 30.769 3.54 0.08 0.00 2.57
4456 4577 9.453572 CAGTAGGGTTAATCATGTAATATGCAT 57.546 33.333 3.79 3.79 0.00 3.96
4457 4578 8.436778 ACAGTAGGGTTAATCATGTAATATGCA 58.563 33.333 0.00 0.00 0.00 3.96
4458 4579 8.848474 ACAGTAGGGTTAATCATGTAATATGC 57.152 34.615 0.00 0.00 0.00 3.14
4465 4586 8.768397 TCATCTAAACAGTAGGGTTAATCATGT 58.232 33.333 0.00 0.00 0.00 3.21
4466 4587 9.046296 GTCATCTAAACAGTAGGGTTAATCATG 57.954 37.037 0.00 0.00 0.00 3.07
4467 4588 8.768397 TGTCATCTAAACAGTAGGGTTAATCAT 58.232 33.333 0.00 0.00 0.00 2.45
4468 4589 8.038944 GTGTCATCTAAACAGTAGGGTTAATCA 58.961 37.037 0.00 0.00 0.00 2.57
4469 4590 8.038944 TGTGTCATCTAAACAGTAGGGTTAATC 58.961 37.037 0.00 0.00 0.00 1.75
4470 4591 7.913789 TGTGTCATCTAAACAGTAGGGTTAAT 58.086 34.615 0.00 0.00 0.00 1.40
4471 4592 7.305813 TGTGTCATCTAAACAGTAGGGTTAA 57.694 36.000 0.00 0.00 0.00 2.01
4472 4593 6.921486 TGTGTCATCTAAACAGTAGGGTTA 57.079 37.500 0.00 0.00 0.00 2.85
4473 4594 5.818678 TGTGTCATCTAAACAGTAGGGTT 57.181 39.130 0.00 0.00 0.00 4.11
4474 4595 5.818678 TTGTGTCATCTAAACAGTAGGGT 57.181 39.130 0.00 0.00 0.00 4.34
4475 4596 7.504924 TTTTTGTGTCATCTAAACAGTAGGG 57.495 36.000 0.00 0.00 0.00 3.53
4476 4597 8.783093 TCATTTTTGTGTCATCTAAACAGTAGG 58.217 33.333 0.00 0.00 0.00 3.18
4479 4600 9.071276 AGATCATTTTTGTGTCATCTAAACAGT 57.929 29.630 0.00 0.00 0.00 3.55
4480 4601 9.338291 CAGATCATTTTTGTGTCATCTAAACAG 57.662 33.333 0.00 0.00 0.00 3.16
4481 4602 9.065798 TCAGATCATTTTTGTGTCATCTAAACA 57.934 29.630 0.00 0.00 0.00 2.83
4485 4606 9.452287 TCAATCAGATCATTTTTGTGTCATCTA 57.548 29.630 0.00 0.00 0.00 1.98
4486 4607 8.344446 TCAATCAGATCATTTTTGTGTCATCT 57.656 30.769 0.00 0.00 0.00 2.90
4487 4608 9.582431 AATCAATCAGATCATTTTTGTGTCATC 57.418 29.630 0.00 0.00 35.39 2.92
4488 4609 9.366216 CAATCAATCAGATCATTTTTGTGTCAT 57.634 29.630 0.00 0.00 35.39 3.06
4489 4610 8.361889 ACAATCAATCAGATCATTTTTGTGTCA 58.638 29.630 0.00 0.00 35.39 3.58
4490 4611 8.752766 ACAATCAATCAGATCATTTTTGTGTC 57.247 30.769 0.00 0.00 35.39 3.67
4491 4612 8.984764 CAACAATCAATCAGATCATTTTTGTGT 58.015 29.630 0.00 0.00 35.39 3.72
4492 4613 8.984764 ACAACAATCAATCAGATCATTTTTGTG 58.015 29.630 13.81 0.00 35.39 3.33
4499 4620 9.850628 CAACTTTACAACAATCAATCAGATCAT 57.149 29.630 0.00 0.00 35.39 2.45
4500 4621 7.809331 GCAACTTTACAACAATCAATCAGATCA 59.191 33.333 0.00 0.00 35.39 2.92
4501 4622 7.809331 TGCAACTTTACAACAATCAATCAGATC 59.191 33.333 0.00 0.00 35.39 2.75
4502 4623 7.660112 TGCAACTTTACAACAATCAATCAGAT 58.340 30.769 0.00 0.00 39.09 2.90
4503 4624 7.036996 TGCAACTTTACAACAATCAATCAGA 57.963 32.000 0.00 0.00 0.00 3.27
4504 4625 7.697352 TTGCAACTTTACAACAATCAATCAG 57.303 32.000 0.00 0.00 0.00 2.90
4505 4626 7.224362 CCTTTGCAACTTTACAACAATCAATCA 59.776 33.333 0.00 0.00 0.00 2.57
4506 4627 7.566709 CCTTTGCAACTTTACAACAATCAATC 58.433 34.615 0.00 0.00 0.00 2.67
4507 4628 6.018016 GCCTTTGCAACTTTACAACAATCAAT 60.018 34.615 0.00 0.00 37.47 2.57
4508 4629 5.293079 GCCTTTGCAACTTTACAACAATCAA 59.707 36.000 0.00 0.00 37.47 2.57
4509 4630 4.808364 GCCTTTGCAACTTTACAACAATCA 59.192 37.500 0.00 0.00 37.47 2.57
4510 4631 5.049828 AGCCTTTGCAACTTTACAACAATC 58.950 37.500 0.00 0.00 41.13 2.67
4511 4632 5.022282 AGCCTTTGCAACTTTACAACAAT 57.978 34.783 0.00 0.00 41.13 2.71
4512 4633 4.464069 AGCCTTTGCAACTTTACAACAA 57.536 36.364 0.00 0.00 41.13 2.83
4513 4634 5.782893 ATAGCCTTTGCAACTTTACAACA 57.217 34.783 0.00 0.00 41.13 3.33
4514 4635 6.584942 GGTAATAGCCTTTGCAACTTTACAAC 59.415 38.462 0.00 0.00 41.13 3.32
4515 4636 6.265649 TGGTAATAGCCTTTGCAACTTTACAA 59.734 34.615 0.00 0.00 41.13 2.41
4516 4637 5.770663 TGGTAATAGCCTTTGCAACTTTACA 59.229 36.000 0.00 0.00 41.13 2.41
4517 4638 6.090783 GTGGTAATAGCCTTTGCAACTTTAC 58.909 40.000 0.00 5.61 41.13 2.01
4518 4639 5.184287 GGTGGTAATAGCCTTTGCAACTTTA 59.816 40.000 0.00 0.00 41.13 1.85
4519 4640 4.021456 GGTGGTAATAGCCTTTGCAACTTT 60.021 41.667 0.00 0.00 41.13 2.66
4520 4641 3.509967 GGTGGTAATAGCCTTTGCAACTT 59.490 43.478 0.00 0.00 41.13 2.66
4521 4642 3.089284 GGTGGTAATAGCCTTTGCAACT 58.911 45.455 0.00 0.00 41.13 3.16
4522 4643 2.159435 CGGTGGTAATAGCCTTTGCAAC 60.159 50.000 0.00 0.00 41.13 4.17
4523 4644 2.088423 CGGTGGTAATAGCCTTTGCAA 58.912 47.619 0.00 0.00 41.13 4.08
4524 4645 1.680555 CCGGTGGTAATAGCCTTTGCA 60.681 52.381 0.00 0.00 41.13 4.08
4525 4646 1.021968 CCGGTGGTAATAGCCTTTGC 58.978 55.000 0.00 0.00 37.95 3.68
4526 4647 1.210967 TCCCGGTGGTAATAGCCTTTG 59.789 52.381 0.00 0.00 0.00 2.77
4527 4648 1.587066 TCCCGGTGGTAATAGCCTTT 58.413 50.000 0.00 0.00 0.00 3.11
4528 4649 1.587066 TTCCCGGTGGTAATAGCCTT 58.413 50.000 0.00 0.00 0.00 4.35
4529 4650 1.420138 CATTCCCGGTGGTAATAGCCT 59.580 52.381 0.00 0.00 0.00 4.58
4530 4651 1.892209 CATTCCCGGTGGTAATAGCC 58.108 55.000 0.00 0.00 0.00 3.93
4531 4652 1.235724 GCATTCCCGGTGGTAATAGC 58.764 55.000 0.00 0.00 0.00 2.97
4532 4653 1.420138 AGGCATTCCCGGTGGTAATAG 59.580 52.381 0.00 0.00 39.21 1.73
4533 4654 1.513858 AGGCATTCCCGGTGGTAATA 58.486 50.000 0.00 0.00 39.21 0.98
4534 4655 0.629058 AAGGCATTCCCGGTGGTAAT 59.371 50.000 0.00 0.00 39.21 1.89
4535 4656 0.406361 AAAGGCATTCCCGGTGGTAA 59.594 50.000 0.00 0.00 39.21 2.85
4536 4657 0.406361 AAAAGGCATTCCCGGTGGTA 59.594 50.000 0.00 0.00 39.21 3.25
4537 4658 0.406361 TAAAAGGCATTCCCGGTGGT 59.594 50.000 0.00 0.00 39.21 4.16
4538 4659 1.102978 CTAAAAGGCATTCCCGGTGG 58.897 55.000 0.00 0.00 39.21 4.61
4539 4660 1.472480 CACTAAAAGGCATTCCCGGTG 59.528 52.381 0.00 0.00 39.21 4.94
4540 4661 1.834188 CACTAAAAGGCATTCCCGGT 58.166 50.000 0.00 0.00 39.21 5.28
4541 4662 0.455815 GCACTAAAAGGCATTCCCGG 59.544 55.000 0.00 0.00 39.21 5.73
4542 4663 1.401905 GAGCACTAAAAGGCATTCCCG 59.598 52.381 0.00 0.00 39.21 5.14
4543 4664 1.401905 CGAGCACTAAAAGGCATTCCC 59.598 52.381 0.00 0.00 0.00 3.97
4544 4665 1.401905 CCGAGCACTAAAAGGCATTCC 59.598 52.381 0.00 0.00 0.00 3.01
4566 4687 4.261155 CGAAAAAGATCAAACTCACTGGCA 60.261 41.667 0.00 0.00 0.00 4.92
4578 4699 9.689976 TTTTGATTCTTTATGCGAAAAAGATCA 57.310 25.926 8.27 10.28 41.34 2.92
4726 4859 2.409012 TGAGAAGCATTAACACGCGAA 58.591 42.857 15.93 0.00 0.00 4.70
4730 4863 7.700322 ATAGTACATGAGAAGCATTAACACG 57.300 36.000 0.00 0.00 34.15 4.49
4821 4973 0.730265 GTGGTGTTTGTGTGCTCGAA 59.270 50.000 0.00 0.00 0.00 3.71
4838 4990 5.470098 AGCAAGTAATAACAAGTGGAGTGTG 59.530 40.000 0.00 0.00 0.00 3.82
4905 5057 7.892241 TCATTAGTTGTTGTAGTAGGACTAGGT 59.108 37.037 0.00 0.00 30.12 3.08
4964 5116 5.126869 ACGGATGCCAATTCAAATTATGTCA 59.873 36.000 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.