Multiple sequence alignment - TraesCS1D01G228600

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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 TraesCS1D01G228600 chr1D 100.000 5750 0 0 846 6595 316623108 316617359 0.000000e+00 10619.0
1 TraesCS1D01G228600 chr1D 100.000 519 0 0 1 519 316623953 316623435 0.000000e+00 959.0
2 TraesCS1D01G228600 chr1D 80.556 396 57 13 2639 3021 442682854 442682466 3.010000e-73 287.0
3 TraesCS1D01G228600 chr1D 84.967 153 19 2 6434 6583 464256290 464256139 1.150000e-32 152.0
4 TraesCS1D01G228600 chr1D 93.333 90 6 0 5033 5122 381308672 381308583 4.150000e-27 134.0
5 TraesCS1D01G228600 chr1D 88.785 107 8 1 5021 5123 128529211 128529105 1.930000e-25 128.0
6 TraesCS1D01G228600 chr1B 92.097 5871 227 72 847 6595 428726679 428720924 0.000000e+00 8052.0
7 TraesCS1D01G228600 chr1B 98.844 173 2 0 347 519 428726924 428726752 6.420000e-80 309.0
8 TraesCS1D01G228600 chr1B 95.906 171 1 4 151 321 428731897 428731733 8.430000e-69 272.0
9 TraesCS1D01G228600 chr1B 90.588 85 8 0 7 91 428731980 428731896 5.410000e-21 113.0
10 TraesCS1D01G228600 chr1A 92.742 1915 93 18 3057 4932 397739986 397738079 0.000000e+00 2724.0
11 TraesCS1D01G228600 chr1A 92.149 1745 53 23 4929 6595 397738038 397736300 0.000000e+00 2386.0
12 TraesCS1D01G228600 chr1A 92.201 1295 72 6 1781 3066 397742702 397741428 0.000000e+00 1805.0
13 TraesCS1D01G228600 chr1A 93.843 877 22 11 846 1703 397743568 397742705 0.000000e+00 1291.0
14 TraesCS1D01G228600 chr1A 89.299 271 25 3 1 268 397747196 397746927 2.950000e-88 337.0
15 TraesCS1D01G228600 chr1A 81.048 248 27 13 2666 2908 535892373 535892605 5.250000e-41 180.0
16 TraesCS1D01G228600 chr1A 88.000 150 16 2 6434 6582 507075704 507075556 6.800000e-40 176.0
17 TraesCS1D01G228600 chr1A 95.098 102 3 2 418 519 397743744 397743645 6.840000e-35 159.0
18 TraesCS1D01G228600 chr1A 85.065 154 18 2 6434 6583 508209707 508209859 1.150000e-32 152.0
19 TraesCS1D01G228600 chr1A 87.850 107 9 1 5021 5123 352174093 352174199 8.980000e-24 122.0
20 TraesCS1D01G228600 chr1A 93.023 43 2 1 291 332 397743820 397743778 1.990000e-05 62.1
21 TraesCS1D01G228600 chr6A 86.624 157 15 5 6434 6586 53063719 53063565 1.140000e-37 169.0
22 TraesCS1D01G228600 chr7A 89.394 132 12 1 6434 6565 222779413 222779542 1.470000e-36 165.0
23 TraesCS1D01G228600 chr7A 87.850 107 9 1 5022 5124 692371845 692371739 8.980000e-24 122.0
24 TraesCS1D01G228600 chr7A 87.850 107 9 1 5022 5124 692395691 692395585 8.980000e-24 122.0
25 TraesCS1D01G228600 chr5B 84.524 168 18 4 6434 6595 586912707 586912872 6.840000e-35 159.0
26 TraesCS1D01G228600 chr5B 84.768 151 21 2 6434 6583 588793333 588793184 4.120000e-32 150.0
27 TraesCS1D01G228600 chr5A 83.929 168 18 3 6434 6594 546802731 546802566 1.150000e-32 152.0
28 TraesCS1D01G228600 chr2B 87.156 109 10 1 5021 5125 216462808 216462916 3.230000e-23 121.0
29 TraesCS1D01G228600 chr2B 96.296 54 2 0 4233 4286 113263474 113263421 9.110000e-14 89.8
30 TraesCS1D01G228600 chr2B 94.737 57 2 1 4233 4289 225571331 225571276 3.280000e-13 87.9
31 TraesCS1D01G228600 chr5D 85.965 114 12 1 5016 5125 59945727 59945840 1.160000e-22 119.0
32 TraesCS1D01G228600 chr2D 96.491 57 1 1 4233 4289 172409696 172409751 7.040000e-15 93.5
33 TraesCS1D01G228600 chr2D 94.444 54 2 1 4233 4286 74129616 74129564 1.520000e-11 82.4
34 TraesCS1D01G228600 chr2D 92.857 56 2 2 4233 4288 27924507 27924454 5.480000e-11 80.5
35 TraesCS1D01G228600 chr2A 96.491 57 1 1 4233 4289 177658379 177658324 7.040000e-15 93.5
36 TraesCS1D01G228600 chr7D 91.667 60 4 1 4233 4291 237415136 237415077 1.520000e-11 82.4


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 TraesCS1D01G228600 chr1D 316617359 316623953 6594 True 5789.000000 10619 100.000000 1 6595 2 chr1D.!!$R5 6594
1 TraesCS1D01G228600 chr1B 428720924 428726924 6000 True 4180.500000 8052 95.470500 347 6595 2 chr1B.!!$R1 6248
2 TraesCS1D01G228600 chr1A 397736300 397747196 10896 True 1252.014286 2724 92.622143 1 6595 7 chr1A.!!$R2 6594

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
495 3583 0.527565 GTCGTAGCTCCGGTAAACCA 59.472 55.000 0.00 0.0 35.14 3.67 F
887 3975 1.227102 CCGCCATCAATCCCTTCCA 59.773 57.895 0.00 0.0 0.00 3.53 F
2524 5632 1.202405 GGGCTTTGTTCCATAATGCGG 60.202 52.381 0.00 0.0 0.00 5.69 F
2525 5633 1.202405 GGCTTTGTTCCATAATGCGGG 60.202 52.381 0.00 0.0 0.00 6.13 F
2535 5643 1.476085 CATAATGCGGGCTTTGTTCCA 59.524 47.619 2.42 0.0 0.00 3.53 F
2541 5649 1.802508 GCGGGCTTTGTTCCATAATGC 60.803 52.381 0.00 0.0 0.00 3.56 F
4028 8624 2.100087 TCGTTTTCCTTTTTGCTGGGAC 59.900 45.455 0.00 0.0 0.00 4.46 F
4580 9202 0.178906 TGGATGGGGTGAGTGTCTCA 60.179 55.000 0.00 0.0 38.25 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 4887 0.250234 TGATCCAGTCCAAGGAAGCG 59.750 55.000 0.00 0.00 38.93 4.68 R
2682 5791 2.144482 GCAGTGGCATGCAATATTCC 57.856 50.000 21.36 0.00 45.77 3.01 R
4008 8604 2.100749 AGTCCCAGCAAAAAGGAAAACG 59.899 45.455 0.00 0.00 0.00 3.60 R
4139 8741 7.622672 TCTTTTTATAAAAGAAGCACGTAGCCG 60.623 37.037 10.40 0.00 36.22 5.52 R
4200 8802 9.250624 GAGGTAGTAGTAAAATAGATTGCACTG 57.749 37.037 0.00 0.00 0.00 3.66 R
4579 9201 1.542472 TGCAGATTGCCATTGACAGTG 59.458 47.619 0.00 0.00 44.23 3.66 R
5234 9908 0.383949 GGCGTGCCTGAAAGTTTCAA 59.616 50.000 18.55 2.19 39.58 2.69 R
6461 11216 1.202065 CGCCTTCCACGAATGTCATTG 60.202 52.381 1.88 0.00 0.00 2.82 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
39 40 4.686091 GCATCTAAAACAAGTGGAAAAGGC 59.314 41.667 0.00 0.00 0.00 4.35
58 59 0.807667 CTGAGAAGGATGTTCGGGCG 60.808 60.000 0.00 0.00 0.00 6.13
71 72 3.759618 TGTTCGGGCGAAAATAATCCTTT 59.240 39.130 0.00 0.00 35.75 3.11
81 82 5.220024 CGAAAATAATCCTTTTTGCGAGCAC 60.220 40.000 0.00 0.00 0.00 4.40
83 84 1.327303 AATCCTTTTTGCGAGCACCA 58.673 45.000 0.00 0.00 0.00 4.17
95 96 5.484173 TGCGAGCACCAAAATTATAGAAG 57.516 39.130 0.00 0.00 0.00 2.85
96 97 5.182487 TGCGAGCACCAAAATTATAGAAGA 58.818 37.500 0.00 0.00 0.00 2.87
138 139 8.979574 GTACTGATACTATATGCAAAGTGAACC 58.020 37.037 9.33 0.00 0.00 3.62
154 155 5.748402 AGTGAACCTGCATGATAAGATTCA 58.252 37.500 0.00 0.00 0.00 2.57
221 225 4.130118 CCTCCCAGTTTCCAGAATAATCG 58.870 47.826 0.00 0.00 0.00 3.34
225 229 4.757149 CCCAGTTTCCAGAATAATCGATCC 59.243 45.833 0.00 0.00 0.00 3.36
229 233 3.685139 TCCAGAATAATCGATCCAGCC 57.315 47.619 0.00 0.00 0.00 4.85
236 240 1.403814 AATCGATCCAGCCTTCGAGA 58.596 50.000 0.00 0.00 46.35 4.04
240 244 1.404181 CGATCCAGCCTTCGAGAAACA 60.404 52.381 0.00 0.00 37.55 2.83
260 264 5.722021 ACACCAGAACAATCCAATAAACC 57.278 39.130 0.00 0.00 0.00 3.27
265 269 5.048364 CCAGAACAATCCAATAAACCGTTCA 60.048 40.000 0.00 0.00 35.00 3.18
268 272 5.128992 ACAATCCAATAAACCGTTCAACC 57.871 39.130 0.00 0.00 0.00 3.77
269 273 4.830600 ACAATCCAATAAACCGTTCAACCT 59.169 37.500 0.00 0.00 0.00 3.50
270 274 5.303333 ACAATCCAATAAACCGTTCAACCTT 59.697 36.000 0.00 0.00 0.00 3.50
271 275 6.490721 ACAATCCAATAAACCGTTCAACCTTA 59.509 34.615 0.00 0.00 0.00 2.69
272 276 7.014422 ACAATCCAATAAACCGTTCAACCTTAA 59.986 33.333 0.00 0.00 0.00 1.85
273 277 6.956202 TCCAATAAACCGTTCAACCTTAAA 57.044 33.333 0.00 0.00 0.00 1.52
274 278 7.344095 TCCAATAAACCGTTCAACCTTAAAA 57.656 32.000 0.00 0.00 0.00 1.52
275 279 7.779073 TCCAATAAACCGTTCAACCTTAAAAA 58.221 30.769 0.00 0.00 0.00 1.94
276 280 7.921745 TCCAATAAACCGTTCAACCTTAAAAAG 59.078 33.333 0.00 0.00 0.00 2.27
277 281 7.921745 CCAATAAACCGTTCAACCTTAAAAAGA 59.078 33.333 0.00 0.00 0.00 2.52
329 3417 3.117434 CGTCACGGATTGGATTGAAAC 57.883 47.619 0.00 0.00 0.00 2.78
330 3418 2.473868 CGTCACGGATTGGATTGAAACG 60.474 50.000 0.00 0.00 0.00 3.60
331 3419 2.482721 GTCACGGATTGGATTGAAACGT 59.517 45.455 0.00 0.00 0.00 3.99
332 3420 2.739913 TCACGGATTGGATTGAAACGTC 59.260 45.455 0.00 0.00 0.00 4.34
333 3421 2.081462 ACGGATTGGATTGAAACGTCC 58.919 47.619 0.00 0.00 35.02 4.79
334 3422 1.400494 CGGATTGGATTGAAACGTCCC 59.600 52.381 0.00 0.00 33.45 4.46
335 3423 1.749063 GGATTGGATTGAAACGTCCCC 59.251 52.381 0.00 0.00 33.45 4.81
336 3424 2.620627 GGATTGGATTGAAACGTCCCCT 60.621 50.000 0.00 0.00 33.45 4.79
337 3425 2.194201 TTGGATTGAAACGTCCCCTC 57.806 50.000 0.00 0.00 33.45 4.30
338 3426 1.060729 TGGATTGAAACGTCCCCTCA 58.939 50.000 0.00 0.00 33.45 3.86
339 3427 1.003118 TGGATTGAAACGTCCCCTCAG 59.997 52.381 0.00 0.00 33.45 3.35
340 3428 1.278127 GGATTGAAACGTCCCCTCAGA 59.722 52.381 0.00 0.00 0.00 3.27
341 3429 2.290071 GGATTGAAACGTCCCCTCAGAA 60.290 50.000 0.00 0.00 0.00 3.02
342 3430 3.408634 GATTGAAACGTCCCCTCAGAAA 58.591 45.455 0.00 0.00 0.00 2.52
343 3431 3.284793 TTGAAACGTCCCCTCAGAAAA 57.715 42.857 0.00 0.00 0.00 2.29
344 3432 3.284793 TGAAACGTCCCCTCAGAAAAA 57.715 42.857 0.00 0.00 0.00 1.94
345 3433 3.211045 TGAAACGTCCCCTCAGAAAAAG 58.789 45.455 0.00 0.00 0.00 2.27
495 3583 0.527565 GTCGTAGCTCCGGTAAACCA 59.472 55.000 0.00 0.00 35.14 3.67
887 3975 1.227102 CCGCCATCAATCCCTTCCA 59.773 57.895 0.00 0.00 0.00 3.53
1130 4226 2.363018 CCTCGAGGAGCTGGACCA 60.363 66.667 28.21 0.00 37.39 4.02
1143 4239 2.424733 GGACCAGAGGTACGCTCCC 61.425 68.421 7.50 0.29 35.27 4.30
1519 4620 8.693625 AGTATTTTCTACTTCTGTATAAGGCGT 58.306 33.333 0.00 0.00 0.00 5.68
1520 4621 9.956720 GTATTTTCTACTTCTGTATAAGGCGTA 57.043 33.333 0.00 0.00 0.00 4.42
1598 4699 2.028112 GGTAGAACTGGATGCTGTGACA 60.028 50.000 0.00 0.00 0.00 3.58
1732 4838 4.008330 AGAATGAGAGCATGTCTTGTTGG 58.992 43.478 0.00 0.00 34.71 3.77
1741 4847 1.429930 TGTCTTGTTGGGTCCTAGCA 58.570 50.000 0.00 0.00 0.00 3.49
1957 5063 2.231964 TCATTCCTTCTGGTGCAAATGC 59.768 45.455 0.00 0.00 42.50 3.56
2075 5183 8.613060 TCTGAATTAGTATTCATTCATGGCTC 57.387 34.615 1.44 0.00 46.69 4.70
2084 5192 4.025040 TCATTCATGGCTCTGTTCAAGT 57.975 40.909 0.00 0.00 0.00 3.16
2108 5216 3.450457 CCTCTGTCATCTTCCAGTAAGCT 59.550 47.826 0.00 0.00 34.97 3.74
2147 5255 6.540914 TCAAGATAAAGTGACACGTTTTCCTT 59.459 34.615 12.02 9.84 0.00 3.36
2165 5273 6.392625 TTCCTTTATCTCACTGTATCTCCG 57.607 41.667 0.00 0.00 0.00 4.63
2351 5459 8.383619 CACCTTCTTGATGTTTCTTCTAATACG 58.616 37.037 0.00 0.00 0.00 3.06
2357 5465 9.708222 CTTGATGTTTCTTCTAATACGAAATGG 57.292 33.333 0.00 0.00 0.00 3.16
2366 5474 6.358118 TCTAATACGAAATGGTGCATGTTC 57.642 37.500 0.00 0.00 0.00 3.18
2403 5511 7.679659 GTGACACATTTTCCTTTTTAGTCAC 57.320 36.000 0.00 0.00 44.05 3.67
2455 5563 7.507304 AGTGTTCGTTTTGAATTACGTATGAG 58.493 34.615 0.00 0.00 39.21 2.90
2503 5611 2.686405 TGGATGCAGATTGTGAATGCTC 59.314 45.455 0.00 0.00 40.62 4.26
2523 5631 1.533756 CGGGCTTTGTTCCATAATGCG 60.534 52.381 0.00 0.00 0.00 4.73
2524 5632 1.202405 GGGCTTTGTTCCATAATGCGG 60.202 52.381 0.00 0.00 0.00 5.69
2525 5633 1.202405 GGCTTTGTTCCATAATGCGGG 60.202 52.381 0.00 0.00 0.00 6.13
2526 5634 1.802508 GCTTTGTTCCATAATGCGGGC 60.803 52.381 0.00 0.00 0.00 6.13
2527 5635 1.750778 CTTTGTTCCATAATGCGGGCT 59.249 47.619 0.00 0.00 0.00 5.19
2528 5636 1.846007 TTGTTCCATAATGCGGGCTT 58.154 45.000 0.00 0.00 0.00 4.35
2529 5637 1.846007 TGTTCCATAATGCGGGCTTT 58.154 45.000 0.00 0.00 0.00 3.51
2530 5638 1.476085 TGTTCCATAATGCGGGCTTTG 59.524 47.619 2.42 0.00 0.00 2.77
2531 5639 1.476488 GTTCCATAATGCGGGCTTTGT 59.524 47.619 2.42 0.00 0.00 2.83
2532 5640 1.846007 TCCATAATGCGGGCTTTGTT 58.154 45.000 2.42 0.00 0.00 2.83
2533 5641 1.748493 TCCATAATGCGGGCTTTGTTC 59.252 47.619 2.42 0.00 0.00 3.18
2534 5642 1.202405 CCATAATGCGGGCTTTGTTCC 60.202 52.381 2.42 0.00 0.00 3.62
2535 5643 1.476085 CATAATGCGGGCTTTGTTCCA 59.524 47.619 2.42 0.00 0.00 3.53
2536 5644 1.846007 TAATGCGGGCTTTGTTCCAT 58.154 45.000 2.42 0.00 0.00 3.41
2537 5645 1.846007 AATGCGGGCTTTGTTCCATA 58.154 45.000 0.00 0.00 0.00 2.74
2538 5646 1.846007 ATGCGGGCTTTGTTCCATAA 58.154 45.000 0.00 0.00 0.00 1.90
2539 5647 1.846007 TGCGGGCTTTGTTCCATAAT 58.154 45.000 0.00 0.00 0.00 1.28
2540 5648 1.476085 TGCGGGCTTTGTTCCATAATG 59.524 47.619 0.00 0.00 0.00 1.90
2541 5649 1.802508 GCGGGCTTTGTTCCATAATGC 60.803 52.381 0.00 0.00 0.00 3.56
2633 5741 5.123227 GGCTAAGCATGGAGTATTTGTACA 58.877 41.667 0.00 0.00 0.00 2.90
2842 5951 8.725148 GTGGATATTCTTTATCACATGTCATCC 58.275 37.037 0.00 0.00 0.00 3.51
2898 6014 9.244799 TCAGTTATGTATGTTCGATGTATTCAC 57.755 33.333 0.00 0.00 0.00 3.18
2924 6040 6.306397 TGATTTCTTGAAAATCATGTCGTCG 58.694 36.000 8.67 0.00 40.53 5.12
2947 6063 7.538678 GTCGGAATATATTGATTTTGACATGCC 59.461 37.037 1.78 0.00 0.00 4.40
2969 6085 5.575957 CCTGTTTTGCACATGACTATCATC 58.424 41.667 0.00 0.00 34.28 2.92
3313 7881 2.734276 TTCATCGTCGTGGTTCATGA 57.266 45.000 0.00 0.00 0.00 3.07
3332 7900 8.954350 GTTCATGATTAGATTATGGCTTATGCT 58.046 33.333 0.00 0.00 39.59 3.79
3333 7901 9.524496 TTCATGATTAGATTATGGCTTATGCTT 57.476 29.630 0.00 0.00 39.59 3.91
3337 7905 8.506437 TGATTAGATTATGGCTTATGCTTTTCG 58.494 33.333 0.13 0.00 39.59 3.46
3407 7975 2.338500 GTGCCTGCACTCTACAAGTAC 58.662 52.381 14.77 0.00 43.12 2.73
3417 7985 6.972901 TGCACTCTACAAGTACATCTTATTCG 59.027 38.462 0.00 0.00 36.07 3.34
3440 8008 2.672961 TCATCATCGTGGTGACCTTC 57.327 50.000 2.11 0.00 31.53 3.46
3571 8167 9.559732 TGAAACAACATACCCTATATCATTCTG 57.440 33.333 0.00 0.00 0.00 3.02
3702 8298 6.826893 TTTGCTTGTTGTTGCTTTCTAATC 57.173 33.333 0.00 0.00 0.00 1.75
3773 8369 7.201522 CGACAAAAGAATTCTCCGATGATGTTA 60.202 37.037 8.78 0.00 0.00 2.41
3803 8399 6.061441 TCCTGGTTGGTGTATAATAATGCTG 58.939 40.000 0.00 0.00 37.07 4.41
3845 8441 6.791867 TCTGCATATGGACAGTAACTAAGT 57.208 37.500 4.56 0.00 35.37 2.24
3905 8501 5.542251 TGCATTGCTAGTGACCTGGTATATA 59.458 40.000 10.49 0.00 0.00 0.86
3918 8514 9.120538 TGACCTGGTATATATTTCTTTTCTTGC 57.879 33.333 0.00 0.00 0.00 4.01
4028 8624 2.100087 TCGTTTTCCTTTTTGCTGGGAC 59.900 45.455 0.00 0.00 0.00 4.46
4139 8741 6.202188 ACTGCATTGGCTTTACGTATGTATAC 59.798 38.462 0.00 0.00 41.91 1.47
4166 8768 7.480855 GGCTACGTGCTTCTTTTATAAAAAGAC 59.519 37.037 13.00 2.03 42.39 3.01
4236 8854 5.567138 TTACTACTACCTCCGTACTTTGC 57.433 43.478 0.00 0.00 0.00 3.68
4578 9200 0.914644 CATGGATGGGGTGAGTGTCT 59.085 55.000 0.00 0.00 0.00 3.41
4579 9201 1.134280 CATGGATGGGGTGAGTGTCTC 60.134 57.143 0.00 0.00 0.00 3.36
4580 9202 0.178906 TGGATGGGGTGAGTGTCTCA 60.179 55.000 0.00 0.00 38.25 3.27
4593 9215 2.158769 AGTGTCTCACTGTCAATGGCAA 60.159 45.455 1.44 0.00 43.63 4.52
4594 9216 2.816087 GTGTCTCACTGTCAATGGCAAT 59.184 45.455 0.00 0.00 0.00 3.56
4595 9217 3.076621 TGTCTCACTGTCAATGGCAATC 58.923 45.455 0.00 0.00 0.00 2.67
4596 9218 3.244665 TGTCTCACTGTCAATGGCAATCT 60.245 43.478 0.00 0.00 0.00 2.40
4597 9219 3.126514 GTCTCACTGTCAATGGCAATCTG 59.873 47.826 0.00 0.00 0.00 2.90
4613 9235 4.984161 GCAATCTGCACACATTTGTAGTTT 59.016 37.500 0.00 0.00 44.26 2.66
4653 9275 8.777413 CCTATAATGACCACATGTATGAACAAG 58.223 37.037 0.00 0.00 39.58 3.16
4748 9370 9.407380 TGTTGGTTTCATTAGTGCATATATTCT 57.593 29.630 0.00 0.00 0.00 2.40
4810 9432 8.253113 CCATTTTGCCCATGTATCCTTTATATC 58.747 37.037 0.00 0.00 0.00 1.63
4952 9621 7.042797 AGTAAGACTTGTGCACAATTCATTT 57.957 32.000 36.47 28.26 37.81 2.32
5009 9678 5.754782 TGTAAGGTGCATCCATAATGAGTT 58.245 37.500 0.00 0.00 37.59 3.01
5030 9699 8.111545 TGAGTTTGTTCTATGGTACTACCTCTA 58.888 37.037 6.79 0.00 39.58 2.43
5112 9785 4.471904 TGAGCGTCAACTAATTCCAGAT 57.528 40.909 0.00 0.00 0.00 2.90
5117 9790 4.680708 GCGTCAACTAATTCCAGATGGAGA 60.681 45.833 1.13 0.00 46.36 3.71
5122 9795 7.068839 GTCAACTAATTCCAGATGGAGAGAGTA 59.931 40.741 1.13 0.00 46.36 2.59
5163 9836 5.183713 CCAACTGATTTTAGCAGTCATCCAA 59.816 40.000 0.00 0.00 45.27 3.53
5170 9843 6.524101 TTTTAGCAGTCATCCAAATAACCC 57.476 37.500 0.00 0.00 0.00 4.11
5214 9887 6.864151 AGAGCACTTCCATATATGAGCATA 57.136 37.500 14.54 0.00 0.00 3.14
5234 9908 9.587772 GAGCATATAGTATCCATTTAACATCGT 57.412 33.333 0.00 0.00 0.00 3.73
5286 9960 4.402155 TGCTCCTTTGTCAGTTTGTGAATT 59.598 37.500 0.00 0.00 36.74 2.17
5423 10099 9.985318 CATCTTTCTTGTTAATCAATCAGTCTC 57.015 33.333 0.00 0.00 35.35 3.36
5424 10100 9.730705 ATCTTTCTTGTTAATCAATCAGTCTCA 57.269 29.630 0.00 0.00 35.35 3.27
5431 10107 9.506018 TTGTTAATCAATCAGTCTCAGAAATCA 57.494 29.630 0.00 0.00 0.00 2.57
6121 10805 4.843147 TCGAGTGTAAAATTTGTGTGCTG 58.157 39.130 0.00 0.00 0.00 4.41
6126 10810 7.270757 AGTGTAAAATTTGTGTGCTGTATGA 57.729 32.000 0.00 0.00 0.00 2.15
6170 10854 1.824230 ACAACAGGCAGCAGACAAAAA 59.176 42.857 0.00 0.00 0.00 1.94
6178 10862 3.005791 GGCAGCAGACAAAAATTACACCT 59.994 43.478 0.00 0.00 0.00 4.00
6188 10872 7.393515 AGACAAAAATTACACCTAATCCAGACC 59.606 37.037 0.00 0.00 0.00 3.85
6217 10926 2.125106 GCGATTTGGCTCCCGAGT 60.125 61.111 0.00 0.00 0.00 4.18
6270 10979 7.172190 CGAGAATTACAATCAGCATGGTAGAAT 59.828 37.037 0.00 0.00 36.16 2.40
6363 11089 2.033372 TGACGTGGAGTTTCTACACCA 58.967 47.619 0.00 0.00 41.96 4.17
6393 11119 4.640771 ATGTCTGGGTGTGAACAGTAAT 57.359 40.909 0.00 0.00 36.17 1.89
6394 11120 5.755409 ATGTCTGGGTGTGAACAGTAATA 57.245 39.130 0.00 0.00 36.17 0.98
6395 11121 4.890088 TGTCTGGGTGTGAACAGTAATAC 58.110 43.478 0.00 0.00 36.17 1.89
6503 11258 6.201997 GGCGTGGTAAAGAAAACAAAATTGAT 59.798 34.615 0.00 0.00 0.00 2.57
6545 11305 0.755686 ACGCATTTTGGGGCTTTGAA 59.244 45.000 0.00 0.00 34.28 2.69
6579 11339 6.511767 GCCACGACTTCGATCAATATGATTTT 60.512 38.462 5.47 0.00 37.20 1.82
6583 11343 7.064609 ACGACTTCGATCAATATGATTTTGTGT 59.935 33.333 5.47 0.00 37.20 3.72
6584 11344 7.371615 CGACTTCGATCAATATGATTTTGTGTG 59.628 37.037 0.00 0.00 37.20 3.82
6585 11345 8.267620 ACTTCGATCAATATGATTTTGTGTGA 57.732 30.769 0.00 0.00 37.20 3.58
6586 11346 8.896744 ACTTCGATCAATATGATTTTGTGTGAT 58.103 29.630 0.00 0.00 37.20 3.06
6587 11347 9.166126 CTTCGATCAATATGATTTTGTGTGATG 57.834 33.333 0.00 0.00 37.20 3.07
6588 11348 8.436046 TCGATCAATATGATTTTGTGTGATGA 57.564 30.769 0.00 0.00 37.20 2.92
6589 11349 8.891720 TCGATCAATATGATTTTGTGTGATGAA 58.108 29.630 0.00 0.00 37.20 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.515414 ACTTGTTTTAGATGCTCTTGAATAACC 58.485 33.333 0.00 0.00 0.00 2.85
6 7 8.514594 CCACTTGTTTTAGATGCTCTTGAATAA 58.485 33.333 0.00 0.00 0.00 1.40
13 14 6.015940 CCTTTTCCACTTGTTTTAGATGCTCT 60.016 38.462 0.00 0.00 0.00 4.09
27 28 2.443255 TCCTTCTCAGCCTTTTCCACTT 59.557 45.455 0.00 0.00 0.00 3.16
28 29 2.057922 TCCTTCTCAGCCTTTTCCACT 58.942 47.619 0.00 0.00 0.00 4.00
39 40 0.807667 CGCCCGAACATCCTTCTCAG 60.808 60.000 0.00 0.00 0.00 3.35
58 59 5.062183 GGTGCTCGCAAAAAGGATTATTTTC 59.938 40.000 0.00 0.00 31.25 2.29
71 72 5.888691 TCTATAATTTTGGTGCTCGCAAA 57.111 34.783 0.00 0.00 0.00 3.68
128 129 5.885230 TCTTATCATGCAGGTTCACTTTG 57.115 39.130 0.00 0.00 0.00 2.77
193 197 4.620086 TCTGGAAACTGGGAGGAGTATA 57.380 45.455 0.00 0.00 0.00 1.47
221 225 2.003301 GTGTTTCTCGAAGGCTGGATC 58.997 52.381 0.00 0.00 0.00 3.36
225 229 1.151668 CTGGTGTTTCTCGAAGGCTG 58.848 55.000 0.00 0.00 0.00 4.85
229 233 4.083802 GGATTGTTCTGGTGTTTCTCGAAG 60.084 45.833 0.00 0.00 0.00 3.79
236 240 6.521162 GGTTTATTGGATTGTTCTGGTGTTT 58.479 36.000 0.00 0.00 0.00 2.83
240 244 4.403734 ACGGTTTATTGGATTGTTCTGGT 58.596 39.130 0.00 0.00 0.00 4.00
282 286 7.254863 GCGAACCAACTTATATTTTCCGGATTA 60.255 37.037 4.15 0.00 0.00 1.75
283 287 6.459161 GCGAACCAACTTATATTTTCCGGATT 60.459 38.462 4.15 0.00 0.00 3.01
284 288 5.008316 GCGAACCAACTTATATTTTCCGGAT 59.992 40.000 4.15 0.00 0.00 4.18
286 290 4.496840 GGCGAACCAACTTATATTTTCCGG 60.497 45.833 0.00 0.00 35.26 5.14
287 291 4.594136 GGCGAACCAACTTATATTTTCCG 58.406 43.478 0.00 0.00 35.26 4.30
288 292 4.095334 ACGGCGAACCAACTTATATTTTCC 59.905 41.667 16.62 0.00 34.57 3.13
289 293 5.163834 TGACGGCGAACCAACTTATATTTTC 60.164 40.000 16.62 0.00 34.57 2.29
296 3384 0.940519 CGTGACGGCGAACCAACTTA 60.941 55.000 16.62 0.00 34.57 2.24
325 3413 3.473625 TCTTTTTCTGAGGGGACGTTTC 58.526 45.455 0.00 0.00 0.00 2.78
326 3414 3.570912 TCTTTTTCTGAGGGGACGTTT 57.429 42.857 0.00 0.00 0.00 3.60
328 3416 3.570912 TTTCTTTTTCTGAGGGGACGT 57.429 42.857 0.00 0.00 0.00 4.34
329 3417 4.911514 TTTTTCTTTTTCTGAGGGGACG 57.088 40.909 0.00 0.00 0.00 4.79
495 3583 2.185350 CTCAGGGCGTGCGAGATT 59.815 61.111 1.51 0.00 0.00 2.40
887 3975 1.619669 GGGTGGGGAGGTGGAGATT 60.620 63.158 0.00 0.00 0.00 2.40
1130 4226 1.823041 GCGTAGGGAGCGTACCTCT 60.823 63.158 10.11 0.00 40.57 3.69
1518 4619 3.771577 ATAGGCACATTGGGCTACTAC 57.228 47.619 11.32 0.00 46.94 2.73
1519 4620 4.445735 GGAAATAGGCACATTGGGCTACTA 60.446 45.833 11.32 5.13 46.94 1.82
1520 4621 3.555966 GAAATAGGCACATTGGGCTACT 58.444 45.455 11.32 2.80 46.94 2.57
1598 4699 5.414360 CATCACATACTACAAGCTGTCACT 58.586 41.667 0.00 0.00 0.00 3.41
1732 4838 2.103263 CACCAATCTACCTGCTAGGACC 59.897 54.545 8.91 0.00 37.67 4.46
1741 4847 4.398319 CACAAGGAAACACCAATCTACCT 58.602 43.478 0.00 0.00 42.04 3.08
1781 4887 0.250234 TGATCCAGTCCAAGGAAGCG 59.750 55.000 0.00 0.00 38.93 4.68
1935 5041 3.841643 CATTTGCACCAGAAGGAATGAC 58.158 45.455 0.00 0.00 38.69 3.06
2075 5183 4.892433 AGATGACAGAGGAACTTGAACAG 58.108 43.478 0.00 0.00 41.55 3.16
2084 5192 4.081420 GCTTACTGGAAGATGACAGAGGAA 60.081 45.833 3.18 0.00 37.33 3.36
2147 5255 4.788679 TGTCCGGAGATACAGTGAGATAA 58.211 43.478 3.06 0.00 0.00 1.75
2221 5329 3.311596 AGAGCTGTACAACGTCAAAAACC 59.688 43.478 0.00 0.00 0.00 3.27
2256 5364 7.360776 GCACAACAAATCAAAAGAAAACCAAGA 60.361 33.333 0.00 0.00 0.00 3.02
2266 5374 8.953507 AAAAGAAAAGCACAACAAATCAAAAG 57.046 26.923 0.00 0.00 0.00 2.27
2351 5459 3.058293 TGTTCTCGAACATGCACCATTTC 60.058 43.478 8.32 0.00 45.42 2.17
2530 5638 4.770795 AGACAGGTGTAGCATTATGGAAC 58.229 43.478 0.00 0.00 0.00 3.62
2531 5639 6.747414 ATAGACAGGTGTAGCATTATGGAA 57.253 37.500 0.00 0.00 0.00 3.53
2532 5640 8.435931 AATATAGACAGGTGTAGCATTATGGA 57.564 34.615 0.00 0.00 0.00 3.41
2533 5641 8.535335 AGAATATAGACAGGTGTAGCATTATGG 58.465 37.037 0.00 0.00 0.00 2.74
2534 5642 9.579768 GAGAATATAGACAGGTGTAGCATTATG 57.420 37.037 0.00 0.00 0.00 1.90
2535 5643 9.540538 AGAGAATATAGACAGGTGTAGCATTAT 57.459 33.333 0.00 0.00 0.00 1.28
2536 5644 8.941995 AGAGAATATAGACAGGTGTAGCATTA 57.058 34.615 0.00 0.00 0.00 1.90
2537 5645 7.847711 AGAGAATATAGACAGGTGTAGCATT 57.152 36.000 0.00 0.00 0.00 3.56
2538 5646 7.847711 AAGAGAATATAGACAGGTGTAGCAT 57.152 36.000 0.00 0.00 0.00 3.79
2539 5647 8.941995 ATAAGAGAATATAGACAGGTGTAGCA 57.058 34.615 0.00 0.00 0.00 3.49
2592 5700 8.815912 TGCTTAGCCATCTATTATTAGTCATCA 58.184 33.333 0.29 0.00 0.00 3.07
2600 5708 7.025520 ACTCCATGCTTAGCCATCTATTATT 57.974 36.000 0.29 0.00 0.00 1.40
2633 5741 8.594550 ACTGTTGACAGACTGTTAACCTTATAT 58.405 33.333 29.80 13.24 43.55 0.86
2682 5791 2.144482 GCAGTGGCATGCAATATTCC 57.856 50.000 21.36 0.00 45.77 3.01
2842 5951 4.907879 AGCAACAAAACTTGGAAGAGAG 57.092 40.909 0.00 0.00 34.12 3.20
2924 6040 8.362639 ACAGGCATGTCAAAATCAATATATTCC 58.637 33.333 0.00 0.00 32.99 3.01
2947 6063 5.356190 AGGATGATAGTCATGTGCAAAACAG 59.644 40.000 0.00 0.00 43.64 3.16
2969 6085 1.280133 TGGCCACTGATCTCTTCAAGG 59.720 52.381 0.00 0.00 32.78 3.61
3278 7846 8.889717 ACGACGATGAAAATAAATCCATAACTT 58.110 29.630 0.00 0.00 0.00 2.66
3291 7859 4.000325 TCATGAACCACGACGATGAAAAT 59.000 39.130 0.00 0.00 0.00 1.82
3313 7881 8.396272 ACGAAAAGCATAAGCCATAATCTAAT 57.604 30.769 0.00 0.00 43.56 1.73
3337 7905 9.649024 GTGTCAATATAGTAACTCTTCGAGTAC 57.351 37.037 0.00 0.00 42.59 2.73
3407 7975 7.329471 ACCACGATGATGATTACGAATAAGATG 59.671 37.037 0.00 0.00 0.00 2.90
3417 7985 4.060038 AGGTCACCACGATGATGATTAC 57.940 45.455 0.00 0.00 0.00 1.89
3440 8008 7.230108 AGTTCAAGAATGGCATGACTATATTGG 59.770 37.037 0.00 0.00 0.00 3.16
3482 8050 8.905660 TGCCTACAGTAACTGTATAAACAAAA 57.094 30.769 0.00 0.00 44.49 2.44
3659 8255 6.315393 AGCAAAATAGAATGGTGTAAGGTACG 59.685 38.462 0.00 0.00 0.00 3.67
3773 8369 5.836024 TTATACACCAACCAGGAAAGAGT 57.164 39.130 0.00 0.00 41.22 3.24
3803 8399 4.142966 GCAGATTGAATGGCAAAAGAAAGC 60.143 41.667 0.00 0.00 40.48 3.51
3905 8501 4.647424 TGTGTTCCGCAAGAAAAGAAAT 57.353 36.364 0.00 0.00 43.02 2.17
4008 8604 2.100749 AGTCCCAGCAAAAAGGAAAACG 59.899 45.455 0.00 0.00 0.00 3.60
4139 8741 7.622672 TCTTTTTATAAAAGAAGCACGTAGCCG 60.623 37.037 10.40 0.00 36.22 5.52
4200 8802 9.250624 GAGGTAGTAGTAAAATAGATTGCACTG 57.749 37.037 0.00 0.00 0.00 3.66
4578 9200 1.814394 GCAGATTGCCATTGACAGTGA 59.186 47.619 0.00 0.00 37.42 3.41
4579 9201 1.542472 TGCAGATTGCCATTGACAGTG 59.458 47.619 0.00 0.00 44.23 3.66
4580 9202 1.542915 GTGCAGATTGCCATTGACAGT 59.457 47.619 0.00 0.00 44.23 3.55
4581 9203 1.542472 TGTGCAGATTGCCATTGACAG 59.458 47.619 0.00 0.00 44.23 3.51
4582 9204 1.270274 GTGTGCAGATTGCCATTGACA 59.730 47.619 0.00 0.00 44.23 3.58
4583 9205 1.270274 TGTGTGCAGATTGCCATTGAC 59.730 47.619 0.00 0.00 44.23 3.18
4584 9206 1.618487 TGTGTGCAGATTGCCATTGA 58.382 45.000 0.00 0.00 44.23 2.57
4585 9207 2.665649 ATGTGTGCAGATTGCCATTG 57.334 45.000 0.00 0.00 44.23 2.82
4586 9208 3.244284 ACAAATGTGTGCAGATTGCCATT 60.244 39.130 0.00 0.00 44.23 3.16
4587 9209 2.300723 ACAAATGTGTGCAGATTGCCAT 59.699 40.909 0.00 0.00 44.23 4.40
4588 9210 1.687660 ACAAATGTGTGCAGATTGCCA 59.312 42.857 0.00 0.00 44.23 4.92
4589 9211 2.443887 ACAAATGTGTGCAGATTGCC 57.556 45.000 0.00 0.00 44.23 4.52
4593 9215 6.039717 ACTGAAAACTACAAATGTGTGCAGAT 59.960 34.615 0.00 0.00 38.82 2.90
4594 9216 5.356751 ACTGAAAACTACAAATGTGTGCAGA 59.643 36.000 0.00 0.00 38.82 4.26
4595 9217 5.581605 ACTGAAAACTACAAATGTGTGCAG 58.418 37.500 0.00 0.00 38.82 4.41
4596 9218 5.574891 ACTGAAAACTACAAATGTGTGCA 57.425 34.783 0.00 0.00 38.82 4.57
4597 9219 5.458779 GGAACTGAAAACTACAAATGTGTGC 59.541 40.000 0.00 0.00 38.82 4.57
4613 9235 6.291377 GTCATTATAGGCATCTGGAACTGAA 58.709 40.000 0.00 0.00 40.32 3.02
4748 9370 4.693566 GGAAGTTCATCAATGTAACGTCCA 59.306 41.667 20.99 0.00 40.88 4.02
4810 9432 8.511604 ACCTCAGTATATTCCATTGTGAAAAG 57.488 34.615 0.00 0.00 0.00 2.27
4862 9485 5.866207 ACTGTTTTAGACTTTAGGGTGAGG 58.134 41.667 0.00 0.00 0.00 3.86
4899 9522 9.506018 TTTTCTCAGATCAACTGTCAATTATGA 57.494 29.630 0.00 0.00 45.86 2.15
4906 9531 7.055667 ACTAGTTTTCTCAGATCAACTGTCA 57.944 36.000 9.24 0.00 45.86 3.58
4916 9541 6.924060 GCACAAGTCTTACTAGTTTTCTCAGA 59.076 38.462 0.00 0.00 0.00 3.27
5009 9678 7.724506 CCAGATAGAGGTAGTACCATAGAACAA 59.275 40.741 21.49 0.00 41.95 2.83
5030 9699 4.471904 TGAGCGTCAACTAATTCCAGAT 57.528 40.909 0.00 0.00 0.00 2.90
5112 9785 6.732896 AACTTCAGAAAAGTACTCTCTCCA 57.267 37.500 0.00 0.00 0.00 3.86
5117 9790 5.605488 TGGGGTAACTTCAGAAAAGTACTCT 59.395 40.000 0.00 0.00 0.00 3.24
5227 9900 3.380004 TGCCTGAAAGTTTCAACGATGTT 59.620 39.130 18.55 0.00 39.58 2.71
5229 9902 3.300009 GTGCCTGAAAGTTTCAACGATG 58.700 45.455 18.55 7.20 39.58 3.84
5230 9903 2.032030 CGTGCCTGAAAGTTTCAACGAT 60.032 45.455 26.14 0.00 41.45 3.73
5234 9908 0.383949 GGCGTGCCTGAAAGTTTCAA 59.616 50.000 18.55 2.19 39.58 2.69
5286 9960 4.080356 AGGCAAATGCACAACCTCTAGATA 60.080 41.667 7.80 0.00 44.36 1.98
5431 10107 9.959721 AACTTGGTGTATACATCTAACAGAAAT 57.040 29.630 16.88 0.00 0.00 2.17
5955 10639 9.319223 GAAAGATTAGTGACAAAACTTCGATTC 57.681 33.333 0.00 0.00 0.00 2.52
6170 10854 2.704065 CCCGGTCTGGATTAGGTGTAAT 59.296 50.000 0.00 0.00 42.00 1.89
6178 10862 3.158648 CCGGCCCGGTCTGGATTA 61.159 66.667 15.86 0.00 42.73 1.75
6217 10926 5.213891 TGAGTGTAAAGTGAGCAGATGAA 57.786 39.130 0.00 0.00 0.00 2.57
6270 10979 4.971939 TGGTCATGAAGATGTTGACAGAA 58.028 39.130 0.00 0.00 41.17 3.02
6363 11089 2.433604 CACACCCAGACATATGAGCTCT 59.566 50.000 16.19 3.04 0.00 4.09
6428 11154 8.563289 AAATTTTGCATGCACAACAAATTTAG 57.437 26.923 32.36 0.00 34.05 1.85
6430 11156 7.033791 TGAAATTTTGCATGCACAACAAATTT 58.966 26.923 33.11 33.11 36.33 1.82
6431 11157 6.561614 TGAAATTTTGCATGCACAACAAATT 58.438 28.000 24.89 24.89 33.62 1.82
6461 11216 1.202065 CGCCTTCCACGAATGTCATTG 60.202 52.381 1.88 0.00 0.00 2.82
6503 11258 8.747666 GCGTTTGAAAGTAACATTTTCATAACA 58.252 29.630 16.40 0.00 42.31 2.41


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

AutoCloner maintained by Alex Coulton.