Multiple sequence alignment - TraesCS1A01G105700

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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 TraesCS1A01G105700 chr1A 100.000 7515 0 0 1 7515 102163806 102171320 0.000000e+00 13878.0
1 TraesCS1A01G105700 chr1A 94.686 207 9 2 4841 5046 102166933 102166728 3.380000e-83 320.0
2 TraesCS1A01G105700 chr1A 94.660 206 11 0 2923 3128 102168851 102168646 3.380000e-83 320.0
3 TraesCS1A01G105700 chr1A 80.909 220 19 14 607 812 102164068 102164278 1.310000e-32 152.0
4 TraesCS1A01G105700 chr1A 80.909 220 19 14 263 473 102164412 102164617 1.310000e-32 152.0
5 TraesCS1A01G105700 chr1A 74.274 241 46 15 4027 4259 381097174 381096942 3.740000e-13 87.9
6 TraesCS1A01G105700 chr1B 96.016 2937 92 19 1 2924 158314087 158311163 0.000000e+00 4752.0
7 TraesCS1A01G105700 chr1B 92.033 2548 108 28 5047 7515 158311172 158308641 0.000000e+00 3493.0
8 TraesCS1A01G105700 chr1B 82.488 217 13 8 607 807 158313825 158313618 4.660000e-37 167.0
9 TraesCS1A01G105700 chr1D 96.441 2501 62 12 442 2920 102777900 102775405 0.000000e+00 4100.0
10 TraesCS1A01G105700 chr1D 91.709 2545 101 31 5047 7515 102775411 102772901 0.000000e+00 3430.0
11 TraesCS1A01G105700 chr1D 92.736 413 26 3 1 409 102778314 102777902 1.810000e-165 593.0
12 TraesCS1A01G105700 chr1D 74.689 241 45 15 4027 4259 303516997 303516765 8.030000e-15 93.5
13 TraesCS1A01G105700 chr5B 97.794 2131 32 5 2919 5049 319887707 319885592 0.000000e+00 3661.0
14 TraesCS1A01G105700 chr5B 95.631 206 9 0 2923 3128 319885595 319885800 1.560000e-86 331.0
15 TraesCS1A01G105700 chr5B 94.737 209 8 3 4841 5048 319887500 319887706 9.410000e-84 322.0
16 TraesCS1A01G105700 chr5B 81.776 214 23 10 5331 5541 278011328 278011528 1.680000e-36 165.0
17 TraesCS1A01G105700 chr7B 99.012 1720 15 2 2923 4642 747590815 747592532 0.000000e+00 3081.0
18 TraesCS1A01G105700 chr7B 94.686 207 11 0 4841 5047 747591020 747590814 9.410000e-84 322.0
19 TraesCS1A01G105700 chr7B 93.868 212 13 0 2925 3136 4605281 4605070 3.380000e-83 320.0
20 TraesCS1A01G105700 chr2B 94.139 1109 46 8 3219 4322 108230046 108231140 0.000000e+00 1670.0
21 TraesCS1A01G105700 chr2B 92.803 528 16 6 4333 4842 108231263 108231786 0.000000e+00 745.0
22 TraesCS1A01G105700 chr2B 79.263 217 35 8 5331 5541 66667772 66667984 7.860000e-30 143.0
23 TraesCS1A01G105700 chr2A 93.207 1104 48 11 3221 4322 70869360 70870438 0.000000e+00 1598.0
24 TraesCS1A01G105700 chr2A 89.111 551 18 8 4333 4842 70870561 70871110 0.000000e+00 647.0
25 TraesCS1A01G105700 chr2D 93.122 1105 49 14 3228 4322 71758291 71759378 0.000000e+00 1594.0
26 TraesCS1A01G105700 chr2D 93.006 529 14 9 4333 4842 71759501 71760025 0.000000e+00 750.0
27 TraesCS1A01G105700 chr2D 93.720 207 12 1 4841 5047 274922632 274922427 7.320000e-80 309.0
28 TraesCS1A01G105700 chr2D 93.237 207 13 1 4840 5046 81514993 81514788 3.410000e-78 303.0
29 TraesCS1A01G105700 chr4D 94.444 216 11 1 2921 3136 455257794 455258008 1.560000e-86 331.0
30 TraesCS1A01G105700 chr4D 94.175 206 11 1 4841 5046 455258000 455257796 5.660000e-81 313.0
31 TraesCS1A01G105700 chr4D 100.000 32 0 0 5331 5362 49939305 49939274 8.140000e-05 60.2
32 TraesCS1A01G105700 chr6D 94.419 215 11 1 2922 3136 97559891 97559678 5.620000e-86 329.0
33 TraesCS1A01G105700 chr6D 81.443 194 30 4 5387 5577 466224851 466224661 3.630000e-33 154.0
34 TraesCS1A01G105700 chr6B 93.578 218 13 1 2923 3140 507371678 507371894 2.620000e-84 324.0
35 TraesCS1A01G105700 chr6B 93.720 207 13 0 4840 5046 507371884 507371678 2.040000e-80 311.0
36 TraesCS1A01G105700 chr6B 79.897 194 33 4 5387 5577 710663785 710663595 3.660000e-28 137.0
37 TraesCS1A01G105700 chr6B 79.381 194 34 4 5387 5577 711317295 711317105 1.700000e-26 132.0
38 TraesCS1A01G105700 chr3A 92.891 211 14 1 4840 5050 697692869 697692660 9.470000e-79 305.0
39 TraesCS1A01G105700 chr6A 88.934 244 27 0 2917 3160 566431157 566431400 1.230000e-77 302.0
40 TraesCS1A01G105700 chr5D 91.339 127 7 2 7246 7369 477298169 477298294 3.610000e-38 171.0
41 TraesCS1A01G105700 chr3D 79.447 253 40 10 5331 5575 443422352 443422600 1.300000e-37 169.0
42 TraesCS1A01G105700 chr7D 82.069 145 26 0 5443 5587 3188584 3188728 2.850000e-24 124.0


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 TraesCS1A01G105700 chr1A 102163806 102171320 7514 False 13878.000000 13878 100.000000 1 7515 1 chr1A.!!$F1 7514
1 TraesCS1A01G105700 chr1A 102166728 102168851 2123 True 320.000000 320 94.673000 2923 5046 2 chr1A.!!$R2 2123
2 TraesCS1A01G105700 chr1B 158308641 158314087 5446 True 2804.000000 4752 90.179000 1 7515 3 chr1B.!!$R1 7514
3 TraesCS1A01G105700 chr1D 102772901 102778314 5413 True 2707.666667 4100 93.628667 1 7515 3 chr1D.!!$R2 7514
4 TraesCS1A01G105700 chr5B 319885592 319887707 2115 True 3661.000000 3661 97.794000 2919 5049 1 chr5B.!!$R1 2130
5 TraesCS1A01G105700 chr5B 319885595 319887706 2111 False 326.500000 331 95.184000 2923 5048 2 chr5B.!!$F2 2125
6 TraesCS1A01G105700 chr7B 747590815 747592532 1717 False 3081.000000 3081 99.012000 2923 4642 1 chr7B.!!$F1 1719
7 TraesCS1A01G105700 chr2B 108230046 108231786 1740 False 1207.500000 1670 93.471000 3219 4842 2 chr2B.!!$F2 1623
8 TraesCS1A01G105700 chr2A 70869360 70871110 1750 False 1122.500000 1598 91.159000 3221 4842 2 chr2A.!!$F1 1621
9 TraesCS1A01G105700 chr2D 71758291 71760025 1734 False 1172.000000 1594 93.064000 3228 4842 2 chr2D.!!$F1 1614

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
573 578 0.465287 CTTTGCTGGTTGGCTGGTTT 59.535 50.000 0.00 0.00 0.00 3.27 F
1655 1667 0.033920 CAAGGCCAAAGTTTCCCTGC 59.966 55.000 5.01 0.00 0.00 4.85 F
2354 2382 0.469917 ACCTCCGTAAGATGGCCATG 59.530 55.000 26.56 8.15 43.02 3.66 F
2391 2419 0.964700 AAGCTCAAAGCCAAGAAGCC 59.035 50.000 0.00 0.00 43.77 4.35 F
2470 2498 2.568623 AAACAGCCAAGAGGTTCGAT 57.431 45.000 0.00 0.00 37.19 3.59 F
2666 2694 3.513912 TCAAATATGGTGTCTGGTCGAGT 59.486 43.478 0.00 0.00 0.00 4.18 F
4419 4866 0.599991 TGCAGATCAAGAACGCGTGT 60.600 50.000 14.98 2.40 0.00 4.49 F
5033 6220 1.343465 GACAAGTTTCAGGACTCCCGA 59.657 52.381 0.00 0.00 37.58 5.14 F
5779 6986 0.471780 TCTCACTCTGCAACCTCCCA 60.472 55.000 0.00 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2233 2261 0.037232 AGAGTGCCGTGAAGCCTAAC 60.037 55.000 0.00 0.0 0.00 2.34 R
2920 2948 0.263765 TCCCGGTGCTATTACCTCCT 59.736 55.000 0.00 0.0 38.62 3.69 R
3521 3668 1.371558 GGCCCACGAGAACTTGTCT 59.628 57.895 0.00 0.0 40.25 3.41 R
4314 4514 1.425031 CCGATGAACGTGTGCATGG 59.575 57.895 0.00 0.0 40.78 3.66 R
4365 4701 3.622826 CTGGACCCCGTGTTCCGT 61.623 66.667 0.00 0.0 33.66 4.69 R
4874 6061 4.704833 AGCCGGTCAGCGCAACAT 62.705 61.111 11.47 0.0 38.01 2.71 R
5571 6770 0.179065 GAAATACCCCCTCCGTTCCG 60.179 60.000 0.00 0.0 0.00 4.30 R
6252 7471 0.318699 GCGGTCTTTTTCAACTGGCC 60.319 55.000 0.00 0.0 0.00 5.36 R
7457 8785 0.313043 CGCCCGGATACAATACGACT 59.687 55.000 0.73 0.0 39.52 4.18 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
41 42 3.456280 GCTCAATGTTTGGTTTTGCTCA 58.544 40.909 0.00 0.00 0.00 4.26
42 43 3.870419 GCTCAATGTTTGGTTTTGCTCAA 59.130 39.130 0.00 0.00 0.00 3.02
62 64 7.169645 TGCTCAAACAAATAAAGCTGAATGTTC 59.830 33.333 0.00 0.00 34.11 3.18
97 99 1.648467 GCTGGTTGGCTGGTTCGATC 61.648 60.000 0.00 0.00 0.00 3.69
102 104 0.617935 TTGGCTGGTTCGATCCATGA 59.382 50.000 15.45 0.51 36.84 3.07
184 186 2.484651 CAGGCTCAGATTGATAGCATGC 59.515 50.000 10.51 10.51 40.58 4.06
201 203 1.447314 GCGGTTTAGCTAGCCACGT 60.447 57.895 12.13 0.00 0.00 4.49
276 278 4.484236 GCAATTGCTTGTGTAGTTGCATA 58.516 39.130 23.21 0.00 45.50 3.14
290 292 7.494625 GTGTAGTTGCATAGCTAACTAAATGGA 59.505 37.037 8.12 0.00 40.07 3.41
308 310 3.561143 TGGACTTGTTGCAAATACCACT 58.439 40.909 0.00 0.00 0.00 4.00
508 513 2.856231 TGTTAGGGATAGGCAAATGGGT 59.144 45.455 0.00 0.00 0.00 4.51
525 530 3.992643 TGGGTCTGTCAATTTTGCAATG 58.007 40.909 0.00 0.00 0.00 2.82
573 578 0.465287 CTTTGCTGGTTGGCTGGTTT 59.535 50.000 0.00 0.00 0.00 3.27
740 746 5.046304 TCACTTGTTTCCCAATGGTTTTGAA 60.046 36.000 0.00 0.00 31.20 2.69
741 747 5.645497 CACTTGTTTCCCAATGGTTTTGAAA 59.355 36.000 0.00 0.00 31.20 2.69
749 755 4.760715 CCCAATGGTTTTGAAATGATGCAA 59.239 37.500 0.00 0.00 0.00 4.08
912 918 3.423539 TGCCTTGTATGTTCAGAAGCT 57.576 42.857 0.00 0.00 0.00 3.74
914 920 4.905429 TGCCTTGTATGTTCAGAAGCTAA 58.095 39.130 0.00 0.00 0.00 3.09
918 924 6.969473 GCCTTGTATGTTCAGAAGCTAATTTC 59.031 38.462 0.00 0.00 0.00 2.17
999 1005 3.122613 GTCTTTCAGAGTGACTGCATTCG 59.877 47.826 0.00 0.00 45.38 3.34
1100 1106 6.043243 ACTCCATATGGTCCAACTGGTAATAG 59.957 42.308 21.28 8.48 36.34 1.73
1155 1161 5.476599 TGCTGGTTGAGTTGCATAGTTAATT 59.523 36.000 0.00 0.00 0.00 1.40
1261 1267 6.239543 GGAGATGTGGTGATCAAGATCTACAT 60.240 42.308 18.66 18.66 38.70 2.29
1456 1468 4.566907 GCCCTTACCCTTCAGAACATTGTA 60.567 45.833 0.00 0.00 0.00 2.41
1557 1569 6.390504 TCCTATACCCCACTATGATGTTCTT 58.609 40.000 0.00 0.00 0.00 2.52
1561 1573 3.054361 ACCCCACTATGATGTTCTTCCAC 60.054 47.826 0.00 0.00 0.00 4.02
1604 1616 1.137513 AGCACGTCGCAAACTCTTAC 58.862 50.000 11.58 0.00 46.13 2.34
1607 1619 1.519758 CACGTCGCAAACTCTTACGTT 59.480 47.619 0.00 0.00 43.63 3.99
1655 1667 0.033920 CAAGGCCAAAGTTTCCCTGC 59.966 55.000 5.01 0.00 0.00 4.85
1686 1698 6.709018 AAAAAGGGTATTACATGGAATCCG 57.291 37.500 6.39 0.00 0.00 4.18
1798 1810 3.181502 GCAAAATCTAGCAGCTGGAAGTC 60.182 47.826 17.12 0.00 35.30 3.01
1823 1835 6.368779 AACTATGGTACCTGCTAAACTTCA 57.631 37.500 14.36 0.00 0.00 3.02
2058 2083 7.491682 AGTTGCAAGTCAAGTGTTGATAATTT 58.508 30.769 0.00 0.00 42.47 1.82
2092 2117 3.100817 CGGTAAATGCAGAAGAAATGCG 58.899 45.455 0.00 0.00 46.87 4.73
2101 2126 3.242446 GCAGAAGAAATGCGCTTACTACC 60.242 47.826 9.73 2.55 33.31 3.18
2129 2157 1.841277 TGTATTACTCATGCCCCGGTT 59.159 47.619 0.00 0.00 0.00 4.44
2150 2178 1.952296 GGACATTCTGATGCCATGACC 59.048 52.381 0.00 0.00 36.72 4.02
2167 2195 4.503714 TGACCATATCTTCCAAACCTCC 57.496 45.455 0.00 0.00 0.00 4.30
2172 2200 4.335594 CCATATCTTCCAAACCTCCGTTTC 59.664 45.833 0.00 0.00 40.28 2.78
2177 2205 1.144093 TCCAAACCTCCGTTTCCATGT 59.856 47.619 0.00 0.00 40.28 3.21
2233 2261 6.976925 GCTTTGATGACAAAATCTCCTTATGG 59.023 38.462 0.00 0.00 43.92 2.74
2240 2268 6.079712 ACAAAATCTCCTTATGGTTAGGCT 57.920 37.500 0.00 0.00 32.59 4.58
2246 2274 2.169769 TCCTTATGGTTAGGCTTCACGG 59.830 50.000 0.00 0.00 32.59 4.94
2333 2361 7.056006 ACTATAATGCTTCACATGTTGGATCA 58.944 34.615 0.00 0.00 39.60 2.92
2354 2382 0.469917 ACCTCCGTAAGATGGCCATG 59.530 55.000 26.56 8.15 43.02 3.66
2391 2419 0.964700 AAGCTCAAAGCCAAGAAGCC 59.035 50.000 0.00 0.00 43.77 4.35
2430 2458 4.331968 TGGAAAGTTGAGTTCAGTGTGTT 58.668 39.130 0.00 0.00 0.00 3.32
2470 2498 2.568623 AAACAGCCAAGAGGTTCGAT 57.431 45.000 0.00 0.00 37.19 3.59
2506 2534 5.754782 AGTTGCCACATCCTATACATCAAA 58.245 37.500 0.00 0.00 0.00 2.69
2570 2598 8.402798 AGACTGATCAATATAACAGAGACGAT 57.597 34.615 0.00 0.00 34.88 3.73
2666 2694 3.513912 TCAAATATGGTGTCTGGTCGAGT 59.486 43.478 0.00 0.00 0.00 4.18
2920 2948 5.877564 GGTTGGTCCTGTTGATTTTCAAAAA 59.122 36.000 0.00 0.00 38.22 1.94
2921 2949 6.037062 GGTTGGTCCTGTTGATTTTCAAAAAG 59.963 38.462 0.00 0.00 38.22 2.27
3595 3755 4.200283 CCTCAGCCTCCGCGTCTC 62.200 72.222 4.92 0.00 41.18 3.36
4365 4701 0.745468 TGTGCATGAACAAGCAGCAA 59.255 45.000 3.25 0.00 42.14 3.91
4419 4866 0.599991 TGCAGATCAAGAACGCGTGT 60.600 50.000 14.98 2.40 0.00 4.49
5033 6220 1.343465 GACAAGTTTCAGGACTCCCGA 59.657 52.381 0.00 0.00 37.58 5.14
5049 6236 3.572642 TCCCGATGCTATTACCTCTTCA 58.427 45.455 0.00 0.00 0.00 3.02
5050 6237 3.964688 TCCCGATGCTATTACCTCTTCAA 59.035 43.478 0.00 0.00 0.00 2.69
5051 6238 4.407621 TCCCGATGCTATTACCTCTTCAAA 59.592 41.667 0.00 0.00 0.00 2.69
5052 6239 5.104693 TCCCGATGCTATTACCTCTTCAAAA 60.105 40.000 0.00 0.00 0.00 2.44
5053 6240 5.588648 CCCGATGCTATTACCTCTTCAAAAA 59.411 40.000 0.00 0.00 0.00 1.94
5253 6440 3.540617 TCTTGCACAGAAAACAGCTGTA 58.459 40.909 22.01 0.00 44.28 2.74
5301 6488 4.891627 TGTCTGTACATGTTTGTGTTGG 57.108 40.909 2.30 0.00 36.53 3.77
5302 6489 4.265893 TGTCTGTACATGTTTGTGTTGGT 58.734 39.130 2.30 0.00 36.53 3.67
5303 6490 4.334203 TGTCTGTACATGTTTGTGTTGGTC 59.666 41.667 2.30 0.00 36.53 4.02
5304 6491 4.574828 GTCTGTACATGTTTGTGTTGGTCT 59.425 41.667 2.30 0.00 36.53 3.85
5305 6492 5.756347 GTCTGTACATGTTTGTGTTGGTCTA 59.244 40.000 2.30 0.00 36.53 2.59
5306 6493 6.259167 GTCTGTACATGTTTGTGTTGGTCTAA 59.741 38.462 2.30 0.00 36.53 2.10
5307 6494 6.995686 TCTGTACATGTTTGTGTTGGTCTAAT 59.004 34.615 2.30 0.00 36.53 1.73
5308 6495 6.964908 TGTACATGTTTGTGTTGGTCTAATG 58.035 36.000 2.30 0.00 36.53 1.90
5309 6496 6.544197 TGTACATGTTTGTGTTGGTCTAATGT 59.456 34.615 2.30 0.00 36.53 2.71
5310 6497 7.715686 TGTACATGTTTGTGTTGGTCTAATGTA 59.284 33.333 2.30 0.00 36.53 2.29
5311 6498 7.202016 ACATGTTTGTGTTGGTCTAATGTAG 57.798 36.000 0.00 0.00 33.85 2.74
5312 6499 6.995686 ACATGTTTGTGTTGGTCTAATGTAGA 59.004 34.615 0.00 0.00 33.85 2.59
5558 6757 4.935352 TTGATTTGGGTCAAACTTGGAG 57.065 40.909 0.00 0.00 36.13 3.86
5559 6758 2.627699 TGATTTGGGTCAAACTTGGAGC 59.372 45.455 0.00 0.00 36.13 4.70
5571 6770 7.329471 GGTCAAACTTGGAGCTTCAATTATTTC 59.671 37.037 8.18 0.00 0.00 2.17
5598 6797 1.415289 GAGGGGGTATTTCGGTACTGG 59.585 57.143 0.85 0.00 0.00 4.00
5606 6805 2.058125 TTTCGGTACTGGCCCTGCAA 62.058 55.000 0.00 0.00 0.00 4.08
5663 6862 5.067954 TGATGCTGAATCAATATGACTGGG 58.932 41.667 0.00 0.00 42.49 4.45
5670 6869 6.291377 TGAATCAATATGACTGGGTAGCTTC 58.709 40.000 0.00 0.00 0.00 3.86
5684 6883 4.000988 GGTAGCTTCGTTTCTTTGGATGA 58.999 43.478 0.00 0.00 0.00 2.92
5688 6887 5.245531 AGCTTCGTTTCTTTGGATGATGTA 58.754 37.500 0.00 0.00 0.00 2.29
5689 6888 5.882557 AGCTTCGTTTCTTTGGATGATGTAT 59.117 36.000 0.00 0.00 0.00 2.29
5768 6975 3.371380 GCCATTTCCCTTGATCTCACTCT 60.371 47.826 0.00 0.00 0.00 3.24
5779 6986 0.471780 TCTCACTCTGCAACCTCCCA 60.472 55.000 0.00 0.00 0.00 4.37
5795 7002 2.554032 CTCCCACTGTTTTACTTGCAGG 59.446 50.000 0.00 0.00 34.79 4.85
5875 7082 2.574450 TGTCTGCTTGATTGCTTCACA 58.426 42.857 0.00 0.00 32.84 3.58
5876 7083 2.950975 TGTCTGCTTGATTGCTTCACAA 59.049 40.909 0.00 0.00 44.01 3.33
6049 7265 2.758089 GCACGATCTGGCAGGCAAG 61.758 63.158 15.73 6.65 0.00 4.01
6052 7268 3.001514 GATCTGGCAGGCAAGGGA 58.998 61.111 15.73 0.00 0.00 4.20
6077 7293 1.845143 AGCAGAGCTCATGGGAAGAAT 59.155 47.619 17.77 0.00 30.62 2.40
6105 7321 2.370189 ACCTGGCTAGATATTCTGCCAC 59.630 50.000 13.23 0.00 41.93 5.01
6135 7351 3.744426 GCACAGAAAGAAAACCGTAGCTA 59.256 43.478 0.00 0.00 0.00 3.32
6144 7360 4.698780 AGAAAACCGTAGCTATGGAAAACC 59.301 41.667 34.04 19.03 36.23 3.27
6210 7429 1.444895 CTTCAAACATGCCGGCTGC 60.445 57.895 29.70 0.50 41.77 5.25
6239 7458 2.537143 GAGGACAACTAACCTGGGAGA 58.463 52.381 0.00 0.00 36.57 3.71
6252 7471 0.685097 TGGGAGAAGGTTGAAGTCGG 59.315 55.000 0.00 0.00 0.00 4.79
6253 7472 0.036294 GGGAGAAGGTTGAAGTCGGG 60.036 60.000 0.00 0.00 0.00 5.14
6255 7474 0.673956 GAGAAGGTTGAAGTCGGGCC 60.674 60.000 0.00 0.00 0.00 5.80
6256 7475 1.072505 GAAGGTTGAAGTCGGGCCA 59.927 57.895 4.39 0.00 0.00 5.36
6279 7498 2.035632 TGAAAAAGACCGCCCACAAAT 58.964 42.857 0.00 0.00 0.00 2.32
6298 7517 2.203470 TTGCTGCCAACATCTCATCA 57.797 45.000 0.00 0.00 0.00 3.07
6331 7550 7.095017 CCTGAAGAGAATCCAACTGAAGTTAAC 60.095 40.741 0.00 0.00 35.83 2.01
6370 7589 3.560481 GTGCATCATCATCAACTCCAGAG 59.440 47.826 0.00 0.00 0.00 3.35
6392 7611 9.144747 CAGAGACGATTTATGAAGAAAAGAAGA 57.855 33.333 0.00 0.00 0.00 2.87
6415 7634 1.691195 TTGGGGAACACTGTGCTCGA 61.691 55.000 7.90 0.00 0.00 4.04
6522 7741 5.123820 TGAAGATGCCCAACTAAAAGATTCG 59.876 40.000 0.00 0.00 0.00 3.34
6537 7756 3.944087 AGATTCGAAAACCTTCCTCCTG 58.056 45.455 0.00 0.00 0.00 3.86
6575 7795 1.482593 CTTGCTCGTTGATAGGAGGGT 59.517 52.381 0.00 0.00 36.90 4.34
6601 7821 1.691196 TTGGGTTCTGACTTGCTTGG 58.309 50.000 0.00 0.00 0.00 3.61
6615 7835 0.609662 GCTTGGTAACCGTGGGAGTA 59.390 55.000 0.00 0.00 0.00 2.59
6632 7852 4.992951 GGGAGTAAACGTTCTTCAGCTTAA 59.007 41.667 0.00 0.00 0.00 1.85
6633 7853 5.642491 GGGAGTAAACGTTCTTCAGCTTAAT 59.358 40.000 0.00 0.00 0.00 1.40
6668 7904 2.422093 CCTGGATTTTAGGCTCAGGGAC 60.422 54.545 9.27 0.00 40.78 4.46
6717 7960 0.899720 TTTGGGCCTACAGTCTACCG 59.100 55.000 4.53 0.00 0.00 4.02
6784 8027 2.333926 CTCTTGGTAACGATGCACGAA 58.666 47.619 14.18 1.38 45.77 3.85
6864 8133 4.836125 TCTGTTGCTCATTGAGGTTTTC 57.164 40.909 15.28 0.00 0.00 2.29
6870 8139 2.819348 GCTCATTGAGGTTTTCCCCAGT 60.819 50.000 15.28 0.00 41.86 4.00
6888 8157 9.771534 TTCCCCAGTAAATTTATTTCAACTTTG 57.228 29.630 0.31 0.00 0.00 2.77
6892 8161 8.911662 CCAGTAAATTTATTTCAACTTTGTCCG 58.088 33.333 0.31 0.00 0.00 4.79
6940 8234 9.868277 CCATCAAATATCTAGTATCCTTGAGTC 57.132 37.037 0.00 0.00 28.30 3.36
6988 8282 1.821753 GGAGCTAGCTGTCAGTGAGAA 59.178 52.381 24.99 0.00 0.00 2.87
7032 8326 7.010091 GGTGGTGCATTTTGTACAATATTAAGC 59.990 37.037 9.56 10.33 34.53 3.09
7046 8340 2.627515 TTAAGCCTGCATGCTCTAGG 57.372 50.000 20.33 18.11 41.80 3.02
7104 8398 3.558931 TCTCTTTTCTTGTGCTGGTGA 57.441 42.857 0.00 0.00 0.00 4.02
7226 8520 5.451381 CGCATCTATCCAACCTTGTACTACA 60.451 44.000 0.00 0.00 0.00 2.74
7253 8547 2.291670 ACCTGGGTTAAACAACCACACA 60.292 45.455 8.69 0.00 44.60 3.72
7279 8573 2.165030 CTGAAACCATCCATCAAGTGCC 59.835 50.000 0.00 0.00 0.00 5.01
7457 8785 4.594970 TGGTCAGGTTCTCTTTGTTTTGA 58.405 39.130 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.405823 AAACCAAACATTGAGCCATGG 57.594 42.857 7.63 7.63 0.00 3.66
41 42 6.420604 CACCGAACATTCAGCTTTATTTGTTT 59.579 34.615 0.00 0.00 0.00 2.83
42 43 5.920273 CACCGAACATTCAGCTTTATTTGTT 59.080 36.000 0.00 0.00 0.00 2.83
44 45 5.343058 CACACCGAACATTCAGCTTTATTTG 59.657 40.000 0.00 0.00 0.00 2.32
48 50 2.225491 GCACACCGAACATTCAGCTTTA 59.775 45.455 0.00 0.00 0.00 1.85
62 64 2.353839 GCAAAGCACAGCACACCG 60.354 61.111 0.00 0.00 0.00 4.94
97 99 1.271379 ACCCCAAGAACGAACTCATGG 60.271 52.381 0.00 0.00 34.58 3.66
102 104 2.430248 ACAAACCCCAAGAACGAACT 57.570 45.000 0.00 0.00 0.00 3.01
161 163 1.146637 GCTATCAATCTGAGCCTGCG 58.853 55.000 0.00 0.00 0.00 5.18
163 165 2.484651 GCATGCTATCAATCTGAGCCTG 59.515 50.000 11.37 0.00 35.63 4.85
184 186 2.503920 ATACGTGGCTAGCTAAACCG 57.496 50.000 15.72 11.23 0.00 4.44
201 203 4.336153 TCGAACATGTGTAACTCGCCTATA 59.664 41.667 11.17 0.00 38.04 1.31
241 243 7.095271 ACACAAGCAATTGCAATAATTGTAACC 60.095 33.333 30.89 7.23 45.16 2.85
276 278 5.070001 TGCAACAAGTCCATTTAGTTAGCT 58.930 37.500 0.00 0.00 0.00 3.32
290 292 6.490040 ACAAGATAGTGGTATTTGCAACAAGT 59.510 34.615 0.00 0.00 0.00 3.16
308 310 4.627035 CAGTGCGATGACAGAAACAAGATA 59.373 41.667 0.00 0.00 0.00 1.98
363 368 3.427573 AGGCTATACCCCAAACAAACAC 58.572 45.455 0.00 0.00 40.58 3.32
508 513 4.933505 TGGTCATTGCAAAATTGACAGA 57.066 36.364 25.27 13.38 39.77 3.41
573 578 5.900425 ACAAAGTAACAAACACATGCATCA 58.100 33.333 0.00 0.00 0.00 3.07
671 676 3.222855 CAACCCCCAAACAGCGCA 61.223 61.111 11.47 0.00 0.00 6.09
740 746 5.410355 AAACCTGCTAATGTTGCATCATT 57.590 34.783 22.85 22.85 39.86 2.57
741 747 5.172934 CAAAACCTGCTAATGTTGCATCAT 58.827 37.500 4.37 4.37 39.86 2.45
749 755 6.719370 TCATTAACTCCAAAACCTGCTAATGT 59.281 34.615 0.00 0.00 0.00 2.71
914 920 9.872684 ATCAGTTCATCACCATAATTAGGAAAT 57.127 29.630 0.00 0.00 0.00 2.17
918 924 6.931281 ACGATCAGTTCATCACCATAATTAGG 59.069 38.462 0.00 0.00 0.00 2.69
999 1005 3.626670 CAGAGTTTGCCTCAAGATCCATC 59.373 47.826 0.00 0.00 43.12 3.51
1125 1131 2.158827 TGCAACTCAACCAGCAAGACTA 60.159 45.455 0.00 0.00 33.48 2.59
1165 1171 6.380079 ACCAAGAGAATAAAGTCAGGTGAT 57.620 37.500 0.00 0.00 0.00 3.06
1261 1267 6.220930 CACTTCTGCAGTACTAACCAAGTAA 58.779 40.000 14.67 0.00 42.37 2.24
1288 1294 7.202016 TGAATCAAGAACGAAACTAGCATTT 57.798 32.000 0.00 0.00 0.00 2.32
1296 1302 7.113544 GGAGAACAATTGAATCAAGAACGAAAC 59.886 37.037 13.59 0.00 0.00 2.78
1456 1468 3.813443 CAAACCTGCCATCAGCTATAGT 58.187 45.455 0.84 0.00 44.23 2.12
1604 1616 5.235186 GGGATGAACAGACTATCATTGAACG 59.765 44.000 4.83 0.00 36.45 3.95
1607 1619 4.721274 TGGGGATGAACAGACTATCATTGA 59.279 41.667 4.83 0.00 36.45 2.57
1686 1698 8.819643 AAGAAACACTAGTTGATTGTAGAGAC 57.180 34.615 0.00 0.00 38.17 3.36
1768 1780 3.379372 GCTGCTAGATTTTGCTTCCATGA 59.621 43.478 0.00 0.00 0.00 3.07
1798 1810 5.007385 AGTTTAGCAGGTACCATAGTTCG 57.993 43.478 15.94 0.00 0.00 3.95
1823 1835 0.460311 GCATACCTGTAGAGCACGGT 59.540 55.000 0.00 0.00 37.64 4.83
1887 1899 9.005777 CCTGGCTATTTAAGTTTAACACTAACA 57.994 33.333 0.00 0.00 32.94 2.41
1888 1900 9.006839 ACCTGGCTATTTAAGTTTAACACTAAC 57.993 33.333 0.00 0.00 32.94 2.34
1889 1901 9.223099 GACCTGGCTATTTAAGTTTAACACTAA 57.777 33.333 0.00 0.00 32.94 2.24
1897 1913 5.256806 ACAGGACCTGGCTATTTAAGTTT 57.743 39.130 25.34 0.00 35.51 2.66
2092 2117 2.240493 ACATGCATCCGGTAGTAAGC 57.760 50.000 0.00 0.00 0.00 3.09
2129 2157 2.646930 GTCATGGCATCAGAATGTCCA 58.353 47.619 0.00 4.73 40.75 4.02
2150 2178 4.335594 GGAAACGGAGGTTTGGAAGATATG 59.664 45.833 0.00 0.00 46.04 1.78
2221 2249 5.685075 CGTGAAGCCTAACCATAAGGAGATT 60.685 44.000 0.00 0.00 36.08 2.40
2233 2261 0.037232 AGAGTGCCGTGAAGCCTAAC 60.037 55.000 0.00 0.00 0.00 2.34
2240 2268 1.204704 CCATGTAGAGAGTGCCGTGAA 59.795 52.381 0.00 0.00 0.00 3.18
2246 2274 0.755686 CTCCCCCATGTAGAGAGTGC 59.244 60.000 0.00 0.00 0.00 4.40
2333 2361 0.325296 TGGCCATCTTACGGAGGTCT 60.325 55.000 0.00 0.00 0.00 3.85
2354 2382 2.353109 GCTTGGTTGGAATTTCTCAGCC 60.353 50.000 11.31 11.31 35.27 4.85
2391 2419 8.977505 CAACTTTCCAGTTAAACCATTTACATG 58.022 33.333 0.00 0.00 41.69 3.21
2430 2458 6.095160 TGTTTTTCTTTACTTAAGTTCGGCCA 59.905 34.615 14.49 0.00 35.28 5.36
2470 2498 3.064207 GTGGCAACTATTTCTGACGACA 58.936 45.455 0.00 0.00 37.61 4.35
2506 2534 1.961394 CTGGATTGCCAATATGCAGCT 59.039 47.619 0.00 0.00 45.41 4.24
2570 2598 1.646912 TGGGATACACCACCTCGAAA 58.353 50.000 0.00 0.00 41.20 3.46
2666 2694 3.820557 CTTCTTGTTTCCCTGAAGACCA 58.179 45.455 0.00 0.00 38.42 4.02
2920 2948 0.263765 TCCCGGTGCTATTACCTCCT 59.736 55.000 0.00 0.00 38.62 3.69
2921 2949 0.680061 CTCCCGGTGCTATTACCTCC 59.320 60.000 0.00 0.00 38.62 4.30
3521 3668 1.371558 GGCCCACGAGAACTTGTCT 59.628 57.895 0.00 0.00 40.25 3.41
3590 3750 3.878519 GGAGACGCGGAGGAGACG 61.879 72.222 12.47 0.00 0.00 4.18
3591 3751 3.519930 GGGAGACGCGGAGGAGAC 61.520 72.222 12.47 0.00 0.00 3.36
3592 3752 3.700831 GAGGGAGACGCGGAGGAGA 62.701 68.421 12.47 0.00 0.00 3.71
3593 3753 3.213402 GAGGGAGACGCGGAGGAG 61.213 72.222 12.47 0.00 0.00 3.69
3594 3754 4.816984 GGAGGGAGACGCGGAGGA 62.817 72.222 12.47 0.00 0.00 3.71
4314 4514 1.425031 CCGATGAACGTGTGCATGG 59.575 57.895 0.00 0.00 40.78 3.66
4365 4701 3.622826 CTGGACCCCGTGTTCCGT 61.623 66.667 0.00 0.00 33.66 4.69
4874 6061 4.704833 AGCCGGTCAGCGCAACAT 62.705 61.111 11.47 0.00 38.01 2.71
5033 6220 8.680903 CATGTCTTTTTGAAGAGGTAATAGCAT 58.319 33.333 0.00 0.00 0.00 3.79
5049 6236 4.405358 TGCTCCAAAAGTCCATGTCTTTTT 59.595 37.500 17.42 7.47 41.30 1.94
5050 6237 3.960102 TGCTCCAAAAGTCCATGTCTTTT 59.040 39.130 15.46 15.46 43.14 2.27
5051 6238 3.565307 TGCTCCAAAAGTCCATGTCTTT 58.435 40.909 7.14 7.14 36.81 2.52
5052 6239 3.228188 TGCTCCAAAAGTCCATGTCTT 57.772 42.857 0.00 0.00 0.00 3.01
5053 6240 2.957402 TGCTCCAAAAGTCCATGTCT 57.043 45.000 0.00 0.00 0.00 3.41
5301 6488 7.639945 AGCAAACAACAAACTCTACATTAGAC 58.360 34.615 0.00 0.00 0.00 2.59
5302 6489 7.801716 AGCAAACAACAAACTCTACATTAGA 57.198 32.000 0.00 0.00 0.00 2.10
5303 6490 7.096477 GCAAGCAAACAACAAACTCTACATTAG 60.096 37.037 0.00 0.00 0.00 1.73
5304 6491 6.695278 GCAAGCAAACAACAAACTCTACATTA 59.305 34.615 0.00 0.00 0.00 1.90
5305 6492 5.519927 GCAAGCAAACAACAAACTCTACATT 59.480 36.000 0.00 0.00 0.00 2.71
5306 6493 5.043248 GCAAGCAAACAACAAACTCTACAT 58.957 37.500 0.00 0.00 0.00 2.29
5307 6494 4.157656 AGCAAGCAAACAACAAACTCTACA 59.842 37.500 0.00 0.00 0.00 2.74
5308 6495 4.672409 AGCAAGCAAACAACAAACTCTAC 58.328 39.130 0.00 0.00 0.00 2.59
5309 6496 4.981806 AGCAAGCAAACAACAAACTCTA 57.018 36.364 0.00 0.00 0.00 2.43
5310 6497 3.874392 AGCAAGCAAACAACAAACTCT 57.126 38.095 0.00 0.00 0.00 3.24
5311 6498 4.672409 AGTAGCAAGCAAACAACAAACTC 58.328 39.130 0.00 0.00 0.00 3.01
5312 6499 4.440112 GGAGTAGCAAGCAAACAACAAACT 60.440 41.667 0.00 0.00 0.00 2.66
5541 6740 2.452600 AGCTCCAAGTTTGACCCAAA 57.547 45.000 0.00 0.00 0.00 3.28
5555 6754 4.495844 CCGTTCCGAAATAATTGAAGCTCC 60.496 45.833 0.00 0.00 0.00 4.70
5558 6757 4.495844 CCTCCGTTCCGAAATAATTGAAGC 60.496 45.833 0.00 0.00 0.00 3.86
5559 6758 4.035208 CCCTCCGTTCCGAAATAATTGAAG 59.965 45.833 0.00 0.00 0.00 3.02
5571 6770 0.179065 GAAATACCCCCTCCGTTCCG 60.179 60.000 0.00 0.00 0.00 4.30
5606 6805 3.193267 TCTGTTTGTTTGTGAAAGCAGCT 59.807 39.130 0.00 0.00 0.00 4.24
5663 6862 5.122396 ACATCATCCAAAGAAACGAAGCTAC 59.878 40.000 0.00 0.00 0.00 3.58
5684 6883 9.582648 TCCATGAATTCTCATTGATGAATACAT 57.417 29.630 7.05 0.00 40.49 2.29
5688 6887 8.740906 GCTATCCATGAATTCTCATTGATGAAT 58.259 33.333 7.05 5.87 41.92 2.57
5689 6888 7.942894 AGCTATCCATGAATTCTCATTGATGAA 59.057 33.333 7.05 0.00 41.92 2.57
5768 6975 2.092103 AGTAAAACAGTGGGAGGTTGCA 60.092 45.455 0.00 0.00 0.00 4.08
5779 6986 4.777463 AGTGTACCTGCAAGTAAAACAGT 58.223 39.130 0.00 0.00 0.00 3.55
5795 7002 3.881937 AGTTCCGGGAACATAGTGTAC 57.118 47.619 34.54 11.53 44.11 2.90
5875 7082 2.092968 TGCTTCTTCCGCCTCATACATT 60.093 45.455 0.00 0.00 0.00 2.71
5876 7083 1.486310 TGCTTCTTCCGCCTCATACAT 59.514 47.619 0.00 0.00 0.00 2.29
5943 7159 1.404851 GCAGAGACAGCTTAGGGACAC 60.405 57.143 0.00 0.00 0.00 3.67
5950 7166 0.460811 CATGGCGCAGAGACAGCTTA 60.461 55.000 10.83 0.00 44.06 3.09
6049 7265 0.465824 ATGAGCTCTGCTGCATTCCC 60.466 55.000 16.19 0.00 39.88 3.97
6052 7268 0.752009 CCCATGAGCTCTGCTGCATT 60.752 55.000 16.19 0.00 39.88 3.56
6077 7293 3.637821 ATATCTAGCCAGGTTCCCAGA 57.362 47.619 0.00 0.00 0.00 3.86
6105 7321 1.159285 TTCTTTCTGTGCAGATGCCG 58.841 50.000 2.47 0.00 41.18 5.69
6135 7351 0.673644 CTCACGAGCCGGTTTTCCAT 60.674 55.000 1.90 0.00 40.70 3.41
6144 7360 2.202797 CCACATCCTCACGAGCCG 60.203 66.667 0.00 0.00 0.00 5.52
6239 7458 1.073199 CTGGCCCGACTTCAACCTT 59.927 57.895 0.00 0.00 0.00 3.50
6252 7471 0.318699 GCGGTCTTTTTCAACTGGCC 60.319 55.000 0.00 0.00 0.00 5.36
6253 7472 0.318699 GGCGGTCTTTTTCAACTGGC 60.319 55.000 0.00 0.00 39.70 4.85
6255 7474 1.028905 TGGGCGGTCTTTTTCAACTG 58.971 50.000 0.00 0.00 0.00 3.16
6256 7475 1.029681 GTGGGCGGTCTTTTTCAACT 58.970 50.000 0.00 0.00 0.00 3.16
6279 7498 2.203470 TGATGAGATGTTGGCAGCAA 57.797 45.000 8.44 0.00 32.61 3.91
6298 7517 4.104383 TGGATTCTCTTCAGGTGCTTTT 57.896 40.909 0.00 0.00 0.00 2.27
6331 7550 0.319211 CACTGTGCACCAAGGCATTG 60.319 55.000 15.69 3.60 46.92 2.82
6359 7578 5.914898 TCATAAATCGTCTCTGGAGTTGA 57.085 39.130 0.00 0.00 0.00 3.18
6360 7579 6.333416 TCTTCATAAATCGTCTCTGGAGTTG 58.667 40.000 0.00 0.00 0.00 3.16
6361 7580 6.531503 TCTTCATAAATCGTCTCTGGAGTT 57.468 37.500 0.00 0.00 0.00 3.01
6392 7611 1.076024 AGCACAGTGTTCCCCAATGAT 59.924 47.619 1.61 0.00 41.63 2.45
6415 7634 2.024464 ACTCATAGGAGGACTGACTGCT 60.024 50.000 9.55 0.00 45.81 4.24
6419 7638 3.181480 GCTTCACTCATAGGAGGACTGAC 60.181 52.174 9.55 0.00 45.81 3.51
6522 7741 2.155279 GCTGACAGGAGGAAGGTTTTC 58.845 52.381 4.26 0.00 0.00 2.29
6575 7795 3.632145 GCAAGTCAGAACCCAAAAGAGAA 59.368 43.478 0.00 0.00 0.00 2.87
6601 7821 2.438868 ACGTTTACTCCCACGGTTAC 57.561 50.000 0.00 0.00 40.84 2.50
6632 7852 3.275848 TCCAGGCTGCCCTACTTATAT 57.724 47.619 16.57 0.00 40.33 0.86
6633 7853 2.787339 TCCAGGCTGCCCTACTTATA 57.213 50.000 16.57 0.00 40.33 0.98
6668 7904 3.367087 CCTGAAAAGCATGAAAGCCTCTG 60.367 47.826 0.00 0.00 34.23 3.35
6717 7960 7.500559 ACTTGCATATTTCCTTTCCAGATAGTC 59.499 37.037 0.00 0.00 0.00 2.59
6721 7964 7.284034 CACTACTTGCATATTTCCTTTCCAGAT 59.716 37.037 0.00 0.00 0.00 2.90
6784 8027 5.163513 CACAACAAAAGAGCAACAGAAAGT 58.836 37.500 0.00 0.00 0.00 2.66
6864 8133 9.203421 GACAAAGTTGAAATAAATTTACTGGGG 57.797 33.333 0.00 0.00 0.00 4.96
6870 8139 8.083462 GGGTCGGACAAAGTTGAAATAAATTTA 58.917 33.333 10.76 0.00 0.00 1.40
6940 8234 1.318886 TGCACACACAACCCAACAGG 61.319 55.000 0.00 0.00 43.78 4.00
6988 8282 3.496331 CACCAACCAACCTAATCCAAGT 58.504 45.455 0.00 0.00 0.00 3.16
7032 8326 0.835941 ACCTTCCTAGAGCATGCAGG 59.164 55.000 21.98 18.00 0.00 4.85
7104 8398 4.421948 GTTCGACCAAAGACGATGATAGT 58.578 43.478 0.00 0.00 39.79 2.12
7253 8547 4.590222 ACTTGATGGATGGTTTCAGCTTTT 59.410 37.500 0.00 0.00 0.00 2.27
7279 8573 2.254546 TGGTGCTACAAGAGTGGTTG 57.745 50.000 0.00 0.00 0.00 3.77
7317 8613 1.267806 CTCTGTTCGTGCCTGCAAATT 59.732 47.619 0.00 0.00 0.00 1.82
7457 8785 0.313043 CGCCCGGATACAATACGACT 59.687 55.000 0.73 0.00 39.52 4.18


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

AutoCloner maintained by Alex Coulton.