Multiple sequence alignment - TraesCS3A01G389900

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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 TraesCS3A01G389900 chr3A 100.000 3657 0 0 935 4591 638206287 638209943 0.000000e+00 6754
1 TraesCS3A01G389900 chr3A 100.000 671 0 0 1 671 638205353 638206023 0.000000e+00 1240
2 TraesCS3A01G389900 chr3A 97.260 73 2 0 4518 4590 620470039 620469967 1.730000e-24 124
3 TraesCS3A01G389900 chr3D 94.850 3534 118 30 950 4447 496677267 496673762 0.000000e+00 5459
4 TraesCS3A01G389900 chr3D 87.351 419 24 8 266 671 496678074 496677672 1.950000e-123 453
5 TraesCS3A01G389900 chr3D 96.104 77 3 0 3 79 496678351 496678275 4.820000e-25 126
6 TraesCS3A01G389900 chr3B 95.706 2608 88 8 1861 4447 655629199 655626595 0.000000e+00 4174
7 TraesCS3A01G389900 chr3B 91.388 987 61 11 965 1950 655630019 655629056 0.000000e+00 1330
8 TraesCS3A01G389900 chr3B 89.501 381 24 8 299 667 655630864 655630488 6.950000e-128 468
9 TraesCS3A01G389900 chr3B 82.295 305 30 5 9 296 655634038 655633741 4.590000e-60 243
10 TraesCS3A01G389900 chr3B 96.154 78 3 0 4449 4526 655626536 655626459 1.340000e-25 128
11 TraesCS3A01G389900 chr7A 98.551 69 1 0 4523 4591 439804432 439804364 6.240000e-24 122
12 TraesCS3A01G389900 chr5D 97.222 72 2 0 4520 4591 491692859 491692788 6.240000e-24 122
13 TraesCS3A01G389900 chr5A 97.260 73 1 1 4520 4591 495320837 495320909 6.240000e-24 122
14 TraesCS3A01G389900 chr2A 96.000 75 3 0 4517 4591 209894280 209894206 6.240000e-24 122
15 TraesCS3A01G389900 chr1A 97.183 71 2 0 4521 4591 431676758 431676688 2.240000e-23 121
16 TraesCS3A01G389900 chr1D 90.217 92 7 2 4500 4591 386156698 386156787 8.070000e-23 119
17 TraesCS3A01G389900 chr5B 93.590 78 5 0 4514 4591 601395322 601395399 2.900000e-22 117
18 TraesCS3A01G389900 chr5B 95.652 69 3 0 4523 4591 515669567 515669499 1.350000e-20 111


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 TraesCS3A01G389900 chr3A 638205353 638209943 4590 False 3997.000000 6754 100.000000 1 4591 2 chr3A.!!$F1 4590
1 TraesCS3A01G389900 chr3D 496673762 496678351 4589 True 2012.666667 5459 92.768333 3 4447 3 chr3D.!!$R1 4444
2 TraesCS3A01G389900 chr3B 655626459 655634038 7579 True 1268.600000 4174 91.008800 9 4526 5 chr3B.!!$R1 4517

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
336 3266 0.969917 TTCCCCACATTTCCCGCATG 60.970 55.000 0.00 0.0 0.0 4.06 F
1422 4560 0.174389 TTGCGCTCTCTCTGATCACC 59.826 55.000 9.73 0.0 0.0 4.02 F
1482 4621 1.003851 ACGTTTGTGTTCTGTGTCCG 58.996 50.000 0.00 0.0 0.0 4.79 F
1541 4680 1.208535 ACTTGGTTCCGTGTTGACTGA 59.791 47.619 0.00 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 5176 0.250234 CACCTTCTCCGCTGGATGAA 59.750 55.000 0.00 4.34 0.00 2.57 R
2253 5392 1.852633 GCCTTTGGCCTCCTTGTTAT 58.147 50.000 3.32 0.00 44.06 1.89 R
3378 6522 1.972588 AGGTCAACCTGCTTATCCCT 58.027 50.000 0.00 0.00 46.55 4.20 R
3627 6771 8.663167 TGAATCAGATACCTCATGGAATTACAT 58.337 33.333 0.00 0.00 37.04 2.29 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
58 59 3.557577 TGTCGCAATGGACAATGAAAG 57.442 42.857 2.80 0.00 43.55 2.62
75 76 8.416329 ACAATGAAAGACATTATCATTTAGGCC 58.584 33.333 0.00 0.00 46.01 5.19
82 83 6.006275 ACATTATCATTTAGGCCTGACACT 57.994 37.500 17.99 0.00 0.00 3.55
83 84 7.071196 AGACATTATCATTTAGGCCTGACACTA 59.929 37.037 17.99 0.00 0.00 2.74
85 86 7.716998 ACATTATCATTTAGGCCTGACACTAAG 59.283 37.037 17.99 0.00 31.48 2.18
91 92 1.153549 GCCTGACACTAAGCCCTCG 60.154 63.158 0.00 0.00 0.00 4.63
96 97 1.112113 GACACTAAGCCCTCGGATGA 58.888 55.000 0.00 0.00 0.00 2.92
108 109 4.799917 GCCCTCGGATGATTAGGTACTTTC 60.800 50.000 0.00 0.00 41.75 2.62
109 110 4.262506 CCCTCGGATGATTAGGTACTTTCC 60.263 50.000 0.00 0.00 41.75 3.13
132 133 3.893720 GTGAAACCAGCTCACAAGAATG 58.106 45.455 0.00 0.00 42.32 2.67
146 159 5.532032 TCACAAGAATGCAAGTTCTCATTGA 59.468 36.000 3.10 4.24 37.46 2.57
197 240 7.065324 TCAGACTTTTAACGATGTTTGTTCAGT 59.935 33.333 0.00 0.00 0.00 3.41
205 248 3.062099 CGATGTTTGTTCAGTATGGTCGG 59.938 47.826 0.00 0.00 36.16 4.79
212 255 3.006940 GTTCAGTATGGTCGGCATGAAA 58.993 45.455 0.00 0.00 36.16 2.69
213 256 3.342377 TCAGTATGGTCGGCATGAAAA 57.658 42.857 0.00 0.00 36.16 2.29
214 257 3.680490 TCAGTATGGTCGGCATGAAAAA 58.320 40.909 0.00 0.00 36.16 1.94
261 308 2.176148 TCCTATAGGGTGGTCGACATGA 59.824 50.000 18.97 0.00 36.25 3.07
296 352 9.888878 CAATGGACACTACAAATCATTATCATC 57.111 33.333 0.00 0.00 0.00 2.92
303 3233 4.703897 ACAAATCATTATCATCGACCCGT 58.296 39.130 0.00 0.00 0.00 5.28
304 3234 5.849510 ACAAATCATTATCATCGACCCGTA 58.150 37.500 0.00 0.00 0.00 4.02
336 3266 0.969917 TTCCCCACATTTCCCGCATG 60.970 55.000 0.00 0.00 0.00 4.06
400 3335 2.748461 TTCGCAGTTTGAAACCGAAG 57.252 45.000 14.89 2.23 32.70 3.79
405 3340 3.186909 GCAGTTTGAAACCGAAGCTTTT 58.813 40.909 0.00 0.00 0.00 2.27
411 3346 4.287238 TGAAACCGAAGCTTTTGAGTTC 57.713 40.909 0.00 2.40 0.00 3.01
416 3351 2.096713 CCGAAGCTTTTGAGTTCTGACG 60.097 50.000 0.00 0.00 0.00 4.35
505 3454 4.681978 GGCGAACAGGCTGGACGT 62.682 66.667 26.48 9.11 42.90 4.34
598 3547 4.748798 CCTCCCTGGCCTCCACCT 62.749 72.222 3.32 0.00 0.00 4.00
599 3548 3.086600 CTCCCTGGCCTCCACCTC 61.087 72.222 3.32 0.00 0.00 3.85
600 3549 4.741239 TCCCTGGCCTCCACCTCC 62.741 72.222 3.32 0.00 0.00 4.30
601 3550 4.748798 CCCTGGCCTCCACCTCCT 62.749 72.222 3.32 0.00 0.00 3.69
602 3551 3.086600 CCTGGCCTCCACCTCCTC 61.087 72.222 3.32 0.00 0.00 3.71
603 3552 3.086600 CTGGCCTCCACCTCCTCC 61.087 72.222 3.32 0.00 0.00 4.30
604 3553 3.615811 TGGCCTCCACCTCCTCCT 61.616 66.667 3.32 0.00 0.00 3.69
607 3556 3.114390 CCTCCACCTCCTCCTCCT 58.886 66.667 0.00 0.00 0.00 3.69
610 3559 2.041405 CCACCTCCTCCTCCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
616 3565 4.179599 CCTCCTCCTCCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1215 4348 1.686110 TCCGGGCCTTCTTCTCTCC 60.686 63.158 0.84 0.00 0.00 3.71
1228 4364 0.408309 TCTCTCCTCCGTCCCTGAAA 59.592 55.000 0.00 0.00 0.00 2.69
1239 4375 3.060602 CGTCCCTGAAACTCTGAAGTTC 58.939 50.000 0.00 0.00 45.07 3.01
1243 4379 2.548920 CCTGAAACTCTGAAGTTCCGCT 60.549 50.000 0.00 0.00 45.07 5.52
1244 4380 2.734079 CTGAAACTCTGAAGTTCCGCTC 59.266 50.000 0.00 0.00 45.07 5.03
1245 4381 1.721926 GAAACTCTGAAGTTCCGCTCG 59.278 52.381 0.00 0.00 45.07 5.03
1246 4382 0.667792 AACTCTGAAGTTCCGCTCGC 60.668 55.000 0.00 0.00 42.10 5.03
1247 4383 1.807573 CTCTGAAGTTCCGCTCGCC 60.808 63.158 0.00 0.00 0.00 5.54
1309 4447 4.944372 GGTGCGGCGATCGGTAGG 62.944 72.222 18.30 0.00 39.69 3.18
1383 4521 1.038280 CCCGTTAGGCTTAGATCCGT 58.962 55.000 0.00 0.00 35.76 4.69
1384 4522 2.233271 CCCGTTAGGCTTAGATCCGTA 58.767 52.381 0.00 0.00 35.76 4.02
1385 4523 2.624838 CCCGTTAGGCTTAGATCCGTAA 59.375 50.000 0.00 0.00 35.76 3.18
1416 4554 1.621301 CGGTTGTTGCGCTCTCTCTG 61.621 60.000 9.73 0.00 0.00 3.35
1417 4555 0.319900 GGTTGTTGCGCTCTCTCTGA 60.320 55.000 9.73 0.00 0.00 3.27
1418 4556 1.674221 GGTTGTTGCGCTCTCTCTGAT 60.674 52.381 9.73 0.00 0.00 2.90
1419 4557 1.658095 GTTGTTGCGCTCTCTCTGATC 59.342 52.381 9.73 0.00 0.00 2.92
1420 4558 0.890683 TGTTGCGCTCTCTCTGATCA 59.109 50.000 9.73 0.00 0.00 2.92
1421 4559 1.276415 GTTGCGCTCTCTCTGATCAC 58.724 55.000 9.73 0.00 0.00 3.06
1422 4560 0.174389 TTGCGCTCTCTCTGATCACC 59.826 55.000 9.73 0.00 0.00 4.02
1423 4561 1.299014 GCGCTCTCTCTGATCACCG 60.299 63.158 0.00 0.00 0.00 4.94
1424 4562 1.719725 GCGCTCTCTCTGATCACCGA 61.720 60.000 0.00 0.00 0.00 4.69
1468 4607 2.465855 GTTGCCGAAATTTCCACGTTT 58.534 42.857 12.54 0.00 0.00 3.60
1482 4621 1.003851 ACGTTTGTGTTCTGTGTCCG 58.996 50.000 0.00 0.00 0.00 4.79
1522 4661 9.129209 GCTCCTGTCATCAGTTTTTAAATAAAC 57.871 33.333 0.00 0.00 39.82 2.01
1541 4680 1.208535 ACTTGGTTCCGTGTTGACTGA 59.791 47.619 0.00 0.00 0.00 3.41
1640 4779 6.615088 CCTACAATGAATGAAGGTTCTGTTG 58.385 40.000 0.00 0.00 34.08 3.33
1666 4805 2.076863 GATGTTGTACACCAGGAGCAC 58.923 52.381 0.00 0.00 0.00 4.40
1741 4880 4.813697 GTCTTGCTTTCAGAAGAGACAGTT 59.186 41.667 10.69 0.00 37.01 3.16
1834 4973 5.831702 ATCAAATTGATCTGTCAGAAGGC 57.168 39.130 6.64 0.41 29.59 4.35
2026 5165 5.083533 AGAGTCCTCATCTGACAAACATC 57.916 43.478 0.00 0.00 35.15 3.06
2028 5167 2.349886 GTCCTCATCTGACAAACATCGC 59.650 50.000 0.00 0.00 32.91 4.58
2037 5176 2.299013 TGACAAACATCGCCTCTGTAGT 59.701 45.455 0.00 0.00 0.00 2.73
2061 5200 1.599047 CAGCGGAGAAGGTGGATGT 59.401 57.895 0.00 0.00 36.11 3.06
2086 5225 1.273327 GATGTTCCCAAACCAGCAAGG 59.727 52.381 0.00 0.00 45.67 3.61
2095 5234 2.594303 CCAGCAAGGTTGGCACGA 60.594 61.111 0.00 0.00 0.00 4.35
2107 5246 2.027625 GGCACGAGTTGTTCCTCCG 61.028 63.158 0.00 0.00 30.27 4.63
2122 5261 2.576191 TCCTCCGGGTCTTGATGAATTT 59.424 45.455 0.00 0.00 0.00 1.82
2182 5321 2.880443 AGTCAAACTGGCCATGTGATT 58.120 42.857 5.51 4.17 0.00 2.57
2253 5392 2.000048 AGGGGCAAAGGTTCTGGATTA 59.000 47.619 0.00 0.00 0.00 1.75
2323 5462 3.914426 AAGTATCTCCGCAATCCTTGT 57.086 42.857 0.00 0.00 0.00 3.16
2645 5784 2.275134 TGCTGTGGAAAAGATGCTCA 57.725 45.000 0.00 0.00 0.00 4.26
2890 6029 6.279882 CAGAATTCCTGGAGATACAGTTCTC 58.720 44.000 0.65 4.86 41.21 2.87
2911 6050 6.336566 TCTCAAGATACTGATGCAGAAAGTC 58.663 40.000 0.82 0.00 35.18 3.01
3294 6435 3.965379 AGTTTCATGGATTTGCATGCA 57.035 38.095 18.46 18.46 34.82 3.96
3333 6474 8.534333 TGATATTGCTTGATACGATTCTAACC 57.466 34.615 0.00 0.00 0.00 2.85
3378 6522 5.010012 TGCAGATCTGAGTATGAGCGATTTA 59.990 40.000 27.04 0.00 0.00 1.40
3627 6771 2.935849 CCATATAATCGCGGCTGCATAA 59.064 45.455 19.50 2.10 42.97 1.90
3648 6792 8.671921 GCATAATGTAATTCCATGAGGTATCTG 58.328 37.037 0.00 0.00 37.87 2.90
3680 6824 9.767228 AAAAAGATCACATCTCTGAGATCATAG 57.233 33.333 17.03 8.89 46.14 2.23
3725 6870 9.712250 AGATTATCTAGCCTCATCATTGATCTA 57.288 33.333 0.00 0.00 0.00 1.98
3750 6895 3.525800 TTGGAGGGAAAAGGAAAGGAG 57.474 47.619 0.00 0.00 0.00 3.69
3925 7071 2.842256 GCTGGAGCCGGCAATCATG 61.842 63.158 31.54 14.94 46.81 3.07
4035 7195 1.100510 CATGAATCCTGTGCAGTGGG 58.899 55.000 5.22 0.00 0.00 4.61
4059 7219 2.599677 TCTTTATTTTTGGGTGGGCGT 58.400 42.857 0.00 0.00 0.00 5.68
4295 7475 5.928264 GCAAGTTTTTCTATTGCTTCCATGT 59.072 36.000 2.07 0.00 44.57 3.21
4306 7486 1.649664 CTTCCATGTCCAGCTTCTCG 58.350 55.000 0.00 0.00 0.00 4.04
4313 7493 0.034896 GTCCAGCTTCTCGGTTGGAA 59.965 55.000 1.90 0.00 45.51 3.53
4314 7494 0.984230 TCCAGCTTCTCGGTTGGAAT 59.016 50.000 0.00 0.00 42.18 3.01
4315 7495 1.351017 TCCAGCTTCTCGGTTGGAATT 59.649 47.619 0.00 0.00 42.18 2.17
4316 7496 2.162681 CCAGCTTCTCGGTTGGAATTT 58.837 47.619 0.00 0.00 39.46 1.82
4317 7497 2.162408 CCAGCTTCTCGGTTGGAATTTC 59.838 50.000 0.00 0.00 39.46 2.17
4318 7498 3.077359 CAGCTTCTCGGTTGGAATTTCT 58.923 45.455 0.00 0.00 0.00 2.52
4319 7499 3.077359 AGCTTCTCGGTTGGAATTTCTG 58.923 45.455 0.00 0.00 0.00 3.02
4320 7500 2.814336 GCTTCTCGGTTGGAATTTCTGT 59.186 45.455 0.00 0.00 0.00 3.41
4321 7501 3.365364 GCTTCTCGGTTGGAATTTCTGTG 60.365 47.826 0.00 0.00 0.00 3.66
4322 7502 3.485463 TCTCGGTTGGAATTTCTGTGT 57.515 42.857 0.00 0.00 0.00 3.72
4346 7536 8.845227 TGTATTTCTGTTTGAACAAGCTATTCA 58.155 29.630 8.83 8.83 38.66 2.57
4432 7622 1.409064 TGCGACATCTGGTTAGCTAGG 59.591 52.381 0.00 0.00 35.39 3.02
4447 7637 1.202417 GCTAGGCAATGACAGCTCGTA 60.202 52.381 3.79 0.00 0.00 3.43
4452 7699 2.484264 GGCAATGACAGCTCGTAGTTTT 59.516 45.455 0.00 0.00 0.00 2.43
4504 7751 3.181456 GGCATTCTCCTATGTCAGCTTCT 60.181 47.826 0.00 0.00 30.53 2.85
4522 7769 9.017509 TCAGCTTCTTCATTACTTTGATCATTT 57.982 29.630 0.00 0.00 0.00 2.32
4530 7777 8.964476 TCATTACTTTGATCATTTCTACTCCC 57.036 34.615 0.00 0.00 0.00 4.30
4531 7778 8.772250 TCATTACTTTGATCATTTCTACTCCCT 58.228 33.333 0.00 0.00 0.00 4.20
4532 7779 9.050601 CATTACTTTGATCATTTCTACTCCCTC 57.949 37.037 0.00 0.00 0.00 4.30
4533 7780 5.995446 ACTTTGATCATTTCTACTCCCTCC 58.005 41.667 0.00 0.00 0.00 4.30
4534 7781 4.672587 TTGATCATTTCTACTCCCTCCG 57.327 45.455 0.00 0.00 0.00 4.63
4535 7782 3.643237 TGATCATTTCTACTCCCTCCGT 58.357 45.455 0.00 0.00 0.00 4.69
4536 7783 4.030913 TGATCATTTCTACTCCCTCCGTT 58.969 43.478 0.00 0.00 0.00 4.44
4537 7784 4.099573 TGATCATTTCTACTCCCTCCGTTC 59.900 45.833 0.00 0.00 0.00 3.95
4538 7785 2.764572 TCATTTCTACTCCCTCCGTTCC 59.235 50.000 0.00 0.00 0.00 3.62
4539 7786 2.314071 TTTCTACTCCCTCCGTTCCA 57.686 50.000 0.00 0.00 0.00 3.53
4540 7787 2.314071 TTCTACTCCCTCCGTTCCAA 57.686 50.000 0.00 0.00 0.00 3.53
4541 7788 2.314071 TCTACTCCCTCCGTTCCAAA 57.686 50.000 0.00 0.00 0.00 3.28
4542 7789 2.829023 TCTACTCCCTCCGTTCCAAAT 58.171 47.619 0.00 0.00 0.00 2.32
4543 7790 3.178865 TCTACTCCCTCCGTTCCAAATT 58.821 45.455 0.00 0.00 0.00 1.82
4544 7791 4.355549 TCTACTCCCTCCGTTCCAAATTA 58.644 43.478 0.00 0.00 0.00 1.40
4545 7792 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
4546 7793 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4547 7794 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
4548 7795 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
4549 7796 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
4550 7797 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
4551 7798 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
4552 7799 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
4553 7800 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
4554 7801 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
4555 7802 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
4556 7803 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
4557 7804 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
4558 7805 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
4559 7806 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
4560 7807 4.092821 CCAAATTACTCGTCGCAGAAATGA 59.907 41.667 0.00 0.00 39.69 2.57
4561 7808 5.390461 CCAAATTACTCGTCGCAGAAATGAA 60.390 40.000 0.00 0.00 39.69 2.57
4562 7809 6.250819 CAAATTACTCGTCGCAGAAATGAAT 58.749 36.000 0.00 0.00 39.69 2.57
4563 7810 4.840401 TTACTCGTCGCAGAAATGAATG 57.160 40.909 0.00 0.00 39.69 2.67
4564 7811 2.688507 ACTCGTCGCAGAAATGAATGT 58.311 42.857 0.00 0.00 39.69 2.71
4565 7812 3.845178 ACTCGTCGCAGAAATGAATGTA 58.155 40.909 0.00 0.00 39.69 2.29
4566 7813 4.433615 ACTCGTCGCAGAAATGAATGTAT 58.566 39.130 0.00 0.00 39.69 2.29
4567 7814 4.504461 ACTCGTCGCAGAAATGAATGTATC 59.496 41.667 0.00 0.00 39.69 2.24
4568 7815 4.682787 TCGTCGCAGAAATGAATGTATCT 58.317 39.130 0.00 0.00 39.69 1.98
4569 7816 4.504097 TCGTCGCAGAAATGAATGTATCTG 59.496 41.667 0.00 0.00 39.69 2.90
4570 7817 4.318333 CGTCGCAGAAATGAATGTATCTGG 60.318 45.833 4.06 0.00 39.69 3.86
4571 7818 4.811024 GTCGCAGAAATGAATGTATCTGGA 59.189 41.667 4.06 0.00 39.69 3.86
4572 7819 5.294306 GTCGCAGAAATGAATGTATCTGGAA 59.706 40.000 4.06 0.00 39.69 3.53
4573 7820 5.294306 TCGCAGAAATGAATGTATCTGGAAC 59.706 40.000 4.06 0.00 39.69 3.62
4574 7821 5.295292 CGCAGAAATGAATGTATCTGGAACT 59.705 40.000 4.06 0.00 39.69 3.01
4575 7822 6.479990 CGCAGAAATGAATGTATCTGGAACTA 59.520 38.462 4.06 0.00 39.69 2.24
4576 7823 7.011389 CGCAGAAATGAATGTATCTGGAACTAA 59.989 37.037 4.06 0.00 39.69 2.24
4577 7824 8.677300 GCAGAAATGAATGTATCTGGAACTAAA 58.323 33.333 4.06 0.00 39.69 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 6.058183 AGTGTCAGGCCTAAATGATAATGTC 58.942 40.000 3.98 0.00 0.00 3.06
75 76 1.115467 ATCCGAGGGCTTAGTGTCAG 58.885 55.000 0.00 0.00 0.00 3.51
82 83 2.972348 ACCTAATCATCCGAGGGCTTA 58.028 47.619 0.00 0.00 34.41 3.09
83 84 1.807814 ACCTAATCATCCGAGGGCTT 58.192 50.000 0.00 0.00 34.41 4.35
85 86 2.249139 AGTACCTAATCATCCGAGGGC 58.751 52.381 0.00 0.00 34.41 5.19
91 92 4.100498 TCACCGGAAAGTACCTAATCATCC 59.900 45.833 9.46 0.00 0.00 3.51
96 97 4.041938 TGGTTTCACCGGAAAGTACCTAAT 59.958 41.667 9.46 0.00 43.35 1.73
109 110 0.588252 CTTGTGAGCTGGTTTCACCG 59.412 55.000 0.00 0.00 42.58 4.94
120 121 3.251729 TGAGAACTTGCATTCTTGTGAGC 59.748 43.478 4.13 0.00 39.08 4.26
126 127 6.585695 ACATCAATGAGAACTTGCATTCTT 57.414 33.333 4.13 0.00 39.08 2.52
181 195 4.151689 CGACCATACTGAACAAACATCGTT 59.848 41.667 0.00 0.00 0.00 3.85
190 233 1.552792 TCATGCCGACCATACTGAACA 59.447 47.619 0.00 0.00 31.47 3.18
216 259 9.780186 GGATTATTATTAGCAAGTACTGTCCTT 57.220 33.333 0.00 0.00 0.00 3.36
217 260 9.160412 AGGATTATTATTAGCAAGTACTGTCCT 57.840 33.333 0.00 0.00 0.00 3.85
239 282 3.165875 CATGTCGACCACCCTATAGGAT 58.834 50.000 21.07 0.00 39.89 3.24
261 308 3.951037 TGTAGTGTCCATTGCAACAGTTT 59.049 39.130 0.00 0.00 31.68 2.66
296 352 0.179184 CGGCCAAATTTTACGGGTCG 60.179 55.000 2.24 5.07 42.52 4.79
303 3233 2.037381 GTGGGGAAACGGCCAAATTTTA 59.963 45.455 2.24 0.00 0.00 1.52
304 3234 1.132500 TGGGGAAACGGCCAAATTTT 58.868 45.000 2.24 0.00 0.00 1.82
342 3272 1.213296 ATCACGGGGTAGAAAGCCAT 58.787 50.000 0.00 0.00 45.66 4.40
380 3315 2.793237 GCTTCGGTTTCAAACTGCGAAA 60.793 45.455 13.22 0.18 35.64 3.46
400 3335 2.032808 GTCACCGTCAGAACTCAAAAGC 60.033 50.000 0.00 0.00 0.00 3.51
405 3340 1.535226 CGTTGTCACCGTCAGAACTCA 60.535 52.381 0.00 0.00 0.00 3.41
411 3346 2.279851 TGCCGTTGTCACCGTCAG 60.280 61.111 0.00 0.00 0.00 3.51
416 3351 3.357079 CTGCCTGCCGTTGTCACC 61.357 66.667 0.00 0.00 0.00 4.02
485 3434 4.069232 TCCAGCCTGTTCGCCTCG 62.069 66.667 0.00 0.00 0.00 4.63
489 3438 3.414700 CACGTCCAGCCTGTTCGC 61.415 66.667 5.85 0.00 0.00 4.70
490 3439 2.022129 GACACGTCCAGCCTGTTCG 61.022 63.158 4.65 4.65 0.00 3.95
492 3441 2.029073 CGACACGTCCAGCCTGTT 59.971 61.111 0.00 0.00 0.00 3.16
504 3453 2.348140 GATTCATGCCGCGTCGACAC 62.348 60.000 17.16 4.66 0.00 3.67
505 3454 2.125713 ATTCATGCCGCGTCGACA 60.126 55.556 17.16 0.00 0.00 4.35
593 3542 2.041405 GGGAGGAGGAGGAGGTGG 60.041 72.222 0.00 0.00 0.00 4.61
594 3543 2.041405 GGGGAGGAGGAGGAGGTG 60.041 72.222 0.00 0.00 0.00 4.00
595 3544 3.369388 GGGGGAGGAGGAGGAGGT 61.369 72.222 0.00 0.00 0.00 3.85
596 3545 3.039526 AGGGGGAGGAGGAGGAGG 61.040 72.222 0.00 0.00 0.00 4.30
597 3546 2.612251 GAGGGGGAGGAGGAGGAG 59.388 72.222 0.00 0.00 0.00 3.69
598 3547 3.036959 GGAGGGGGAGGAGGAGGA 61.037 72.222 0.00 0.00 0.00 3.71
599 3548 4.179599 GGGAGGGGGAGGAGGAGG 62.180 77.778 0.00 0.00 0.00 4.30
600 3549 4.179599 GGGGAGGGGGAGGAGGAG 62.180 77.778 0.00 0.00 0.00 3.69
616 3565 2.612115 AAGGCAGGTGGAGAGGGG 60.612 66.667 0.00 0.00 0.00 4.79
620 3582 1.274703 GGATGGAAGGCAGGTGGAGA 61.275 60.000 0.00 0.00 0.00 3.71
1194 4327 2.203938 AGAAGAAGGCCCGGACCA 60.204 61.111 10.37 0.00 0.00 4.02
1215 4348 1.257743 TCAGAGTTTCAGGGACGGAG 58.742 55.000 0.00 0.00 31.97 4.63
1228 4364 1.080434 GCGAGCGGAACTTCAGAGT 60.080 57.895 0.00 0.00 37.87 3.24
1239 4375 0.811219 TTCATCATCAAGGCGAGCGG 60.811 55.000 0.00 0.00 0.00 5.52
1243 4379 3.817084 GGATTCATTCATCATCAAGGCGA 59.183 43.478 0.00 0.00 0.00 5.54
1244 4380 3.819337 AGGATTCATTCATCATCAAGGCG 59.181 43.478 0.00 0.00 0.00 5.52
1245 4381 4.583489 ACAGGATTCATTCATCATCAAGGC 59.417 41.667 0.00 0.00 0.00 4.35
1246 4382 5.507482 GCACAGGATTCATTCATCATCAAGG 60.507 44.000 0.00 0.00 0.00 3.61
1247 4383 5.507482 GGCACAGGATTCATTCATCATCAAG 60.507 44.000 0.00 0.00 0.00 3.02
1309 4447 1.001815 CACGGACAATCCACCAAACAC 60.002 52.381 0.00 0.00 35.91 3.32
1421 4559 1.101049 ACAACCAGCAACCTGTTCGG 61.101 55.000 0.00 0.00 37.38 4.30
1422 4560 0.738389 AACAACCAGCAACCTGTTCG 59.262 50.000 0.00 0.00 37.38 3.95
1423 4561 3.211045 TCTAACAACCAGCAACCTGTTC 58.789 45.455 0.00 0.00 37.38 3.18
1424 4562 3.290948 TCTAACAACCAGCAACCTGTT 57.709 42.857 0.00 0.00 37.38 3.16
1468 4607 3.469008 AAATCTCGGACACAGAACACA 57.531 42.857 0.00 0.00 0.00 3.72
1482 4621 3.851098 ACAGGAGCGTTCAGTAAATCTC 58.149 45.455 0.53 0.00 0.00 2.75
1522 4661 1.867233 CTCAGTCAACACGGAACCAAG 59.133 52.381 0.00 0.00 0.00 3.61
1541 4680 7.605691 AGAAATCAGACGAAGAAAATGTGATCT 59.394 33.333 0.00 0.00 0.00 2.75
1640 4779 2.851263 TGGTGTACAACATCAGGACC 57.149 50.000 10.22 0.00 33.64 4.46
1666 4805 0.673644 ACACCGCCAAATTCTCCTCG 60.674 55.000 0.00 0.00 0.00 4.63
1741 4880 2.369860 ACACACTTCATCTTCCTGCAGA 59.630 45.455 17.39 0.00 0.00 4.26
1834 4973 0.593128 CAGTTTGTTCTTCGCCCTGG 59.407 55.000 0.00 0.00 0.00 4.45
2026 5165 1.804372 GCTGGATGAACTACAGAGGCG 60.804 57.143 0.00 0.00 34.21 5.52
2028 5167 1.202463 CCGCTGGATGAACTACAGAGG 60.202 57.143 0.00 0.00 43.79 3.69
2037 5176 0.250234 CACCTTCTCCGCTGGATGAA 59.750 55.000 0.00 4.34 0.00 2.57
2061 5200 2.627699 GCTGGTTTGGGAACATCTTCAA 59.372 45.455 0.00 0.00 42.32 2.69
2107 5246 6.106673 TCTCGTCTTAAATTCATCAAGACCC 58.893 40.000 7.82 0.00 43.33 4.46
2182 5321 1.263356 CACTAGGTTCCCTTCGGTGA 58.737 55.000 0.00 0.00 34.61 4.02
2253 5392 1.852633 GCCTTTGGCCTCCTTGTTAT 58.147 50.000 3.32 0.00 44.06 1.89
2323 5462 3.264706 TGACATATTTTCCCTCCACGGAA 59.735 43.478 0.00 0.00 40.23 4.30
2645 5784 8.378565 TCTATTCTCAACTGGAATCAAGTTCTT 58.621 33.333 0.00 0.00 37.01 2.52
2890 6029 5.181009 TGGACTTTCTGCATCAGTATCTTG 58.819 41.667 0.00 0.00 32.61 3.02
2911 6050 3.331478 AAGCTCACATCAAGAGACTGG 57.669 47.619 0.00 0.00 35.09 4.00
3022 6161 6.601217 ACTCCAATTTTATCTTCTCCAAGAGC 59.399 38.462 0.00 0.00 42.13 4.09
3333 6474 3.978855 CACACAACAGCATGATTCACAAG 59.021 43.478 0.00 0.00 39.69 3.16
3378 6522 1.972588 AGGTCAACCTGCTTATCCCT 58.027 50.000 0.00 0.00 46.55 4.20
3627 6771 8.663167 TGAATCAGATACCTCATGGAATTACAT 58.337 33.333 0.00 0.00 37.04 2.29
3725 6870 5.669904 TCCTTTCCTTTTCCCTCCAAATTTT 59.330 36.000 0.00 0.00 0.00 1.82
3774 6919 4.216257 TCTGCTGCACCTTTAAAATGACTC 59.784 41.667 0.00 0.00 0.00 3.36
3925 7071 0.808755 CATGCCACGGTTAACCTTCC 59.191 55.000 22.12 7.15 0.00 3.46
4035 7195 4.062293 GCCCACCCAAAAATAAAGAACAC 58.938 43.478 0.00 0.00 0.00 3.32
4059 7219 3.625897 CACCACCGCTGGACAGGA 61.626 66.667 3.11 0.00 40.55 3.86
4186 7361 3.508793 ACCTTTGATGAGCCATTGACTTG 59.491 43.478 0.00 0.00 0.00 3.16
4295 7475 0.984230 ATTCCAACCGAGAAGCTGGA 59.016 50.000 0.00 0.00 36.16 3.86
4306 7486 6.981722 ACAGAAATACACAGAAATTCCAACC 58.018 36.000 0.00 0.00 0.00 3.77
4313 7493 9.520204 CTTGTTCAAACAGAAATACACAGAAAT 57.480 29.630 0.00 0.00 40.50 2.17
4314 7494 7.487829 GCTTGTTCAAACAGAAATACACAGAAA 59.512 33.333 0.00 0.00 40.50 2.52
4315 7495 6.972328 GCTTGTTCAAACAGAAATACACAGAA 59.028 34.615 0.00 0.00 40.50 3.02
4316 7496 6.318648 AGCTTGTTCAAACAGAAATACACAGA 59.681 34.615 0.00 0.00 40.50 3.41
4317 7497 6.498304 AGCTTGTTCAAACAGAAATACACAG 58.502 36.000 0.00 0.00 40.50 3.66
4318 7498 6.449635 AGCTTGTTCAAACAGAAATACACA 57.550 33.333 0.00 0.00 40.50 3.72
4319 7499 9.118236 GAATAGCTTGTTCAAACAGAAATACAC 57.882 33.333 0.00 0.00 40.50 2.90
4320 7500 8.845227 TGAATAGCTTGTTCAAACAGAAATACA 58.155 29.630 10.70 0.00 40.50 2.29
4321 7501 9.846248 ATGAATAGCTTGTTCAAACAGAAATAC 57.154 29.630 15.45 0.00 40.50 1.89
4322 7502 9.844790 CATGAATAGCTTGTTCAAACAGAAATA 57.155 29.630 15.45 0.00 40.50 1.40
4432 7622 3.813529 AAAACTACGAGCTGTCATTGC 57.186 42.857 0.00 0.00 0.00 3.56
4504 7751 9.396022 GGGAGTAGAAATGATCAAAGTAATGAA 57.604 33.333 0.00 0.00 32.06 2.57
4522 7769 2.314071 TTTGGAACGGAGGGAGTAGA 57.686 50.000 0.00 0.00 0.00 2.59
4526 7773 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
4527 7774 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
4528 7775 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4529 7776 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4530 7777 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
4531 7778 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
4532 7779 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
4533 7780 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
4534 7781 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
4535 7782 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
4536 7783 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
4537 7784 4.092821 TCATTTCTGCGACGAGTAATTTGG 59.907 41.667 0.00 0.00 0.00 3.28
4538 7785 5.203358 TCATTTCTGCGACGAGTAATTTG 57.797 39.130 0.00 0.00 0.00 2.32
4539 7786 5.856126 TTCATTTCTGCGACGAGTAATTT 57.144 34.783 0.00 0.00 0.00 1.82
4540 7787 5.351465 ACATTCATTTCTGCGACGAGTAATT 59.649 36.000 0.00 0.00 0.00 1.40
4541 7788 4.870426 ACATTCATTTCTGCGACGAGTAAT 59.130 37.500 0.00 0.00 0.00 1.89
4542 7789 4.242475 ACATTCATTTCTGCGACGAGTAA 58.758 39.130 0.00 0.00 0.00 2.24
4543 7790 3.845178 ACATTCATTTCTGCGACGAGTA 58.155 40.909 0.00 0.00 0.00 2.59
4544 7791 2.688507 ACATTCATTTCTGCGACGAGT 58.311 42.857 0.00 0.00 0.00 4.18
4545 7792 4.742167 AGATACATTCATTTCTGCGACGAG 59.258 41.667 0.00 0.00 0.00 4.18
4546 7793 4.504097 CAGATACATTCATTTCTGCGACGA 59.496 41.667 0.00 0.00 30.23 4.20
4547 7794 4.318333 CCAGATACATTCATTTCTGCGACG 60.318 45.833 0.00 0.00 35.38 5.12
4548 7795 4.811024 TCCAGATACATTCATTTCTGCGAC 59.189 41.667 0.00 0.00 35.38 5.19
4549 7796 5.022282 TCCAGATACATTCATTTCTGCGA 57.978 39.130 0.00 0.00 35.38 5.10
4550 7797 5.295292 AGTTCCAGATACATTCATTTCTGCG 59.705 40.000 0.00 0.00 35.38 5.18
4551 7798 6.690194 AGTTCCAGATACATTCATTTCTGC 57.310 37.500 0.00 0.00 35.38 4.26


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

AutoCloner maintained by Alex Coulton.