Multiple sequence alignment - TraesCS5D01G379500

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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 TraesCS5D01G379500 chr5D 100.000 6335 0 0 1 6335 450519974 450526308 0.000000e+00 11699.0
1 TraesCS5D01G379500 chr5B 94.416 2561 103 26 666 3199 550374315 550376862 0.000000e+00 3901.0
2 TraesCS5D01G379500 chr5B 91.545 1372 59 20 4999 6335 550377264 550378613 0.000000e+00 1838.0
3 TraesCS5D01G379500 chr5B 95.396 391 11 2 3192 3576 550376890 550377279 3.250000e-172 616.0
4 TraesCS5D01G379500 chr5B 85.137 619 58 25 1 599 550349981 550350585 2.530000e-168 603.0
5 TraesCS5D01G379500 chr6D 97.405 1426 36 1 3572 4997 471620256 471618832 0.000000e+00 2427.0
6 TraesCS5D01G379500 chr6D 97.067 1398 36 1 3577 4974 262275986 262277378 0.000000e+00 2350.0
7 TraesCS5D01G379500 chr5A 89.271 1948 133 41 16 1900 569697698 569699632 0.000000e+00 2370.0
8 TraesCS5D01G379500 chr5A 93.351 1143 60 12 2067 3198 569699692 569700829 0.000000e+00 1676.0
9 TraesCS5D01G379500 chr5A 91.870 738 41 11 5010 5731 569701225 569701959 0.000000e+00 1013.0
10 TraesCS5D01G379500 chr5A 95.664 369 15 1 3192 3560 569700858 569701225 5.470000e-165 592.0
11 TraesCS5D01G379500 chr5A 80.392 408 35 24 5957 6335 569702579 569702970 1.050000e-67 268.0
12 TraesCS5D01G379500 chr1D 96.797 1405 43 1 3577 4979 435762367 435760963 0.000000e+00 2344.0
13 TraesCS5D01G379500 chr1D 92.982 57 4 0 105 161 299873594 299873650 4.070000e-12 84.2
14 TraesCS5D01G379500 chr4D 96.987 1394 41 1 3578 4971 1616627 1615235 0.000000e+00 2340.0
15 TraesCS5D01G379500 chr4D 81.500 200 29 6 279 474 424461289 424461484 2.360000e-34 158.0
16 TraesCS5D01G379500 chr4D 78.986 138 24 3 277 412 424055144 424055278 8.750000e-14 89.8
17 TraesCS5D01G379500 chr7A 96.574 1401 44 4 3580 4978 276420 275022 0.000000e+00 2318.0
18 TraesCS5D01G379500 chr7A 86.992 123 15 1 323 445 663762055 663761934 3.080000e-28 137.0
19 TraesCS5D01G379500 chr4B 96.233 1407 51 2 3573 4977 655094131 655092725 0.000000e+00 2303.0
20 TraesCS5D01G379500 chr7D 96.294 1403 45 4 3577 4977 634755014 634756411 0.000000e+00 2296.0
21 TraesCS5D01G379500 chr7D 75.105 478 81 28 29 474 550837784 550837313 8.380000e-44 189.0
22 TraesCS5D01G379500 chr6B 95.966 1413 51 5 3576 4984 204169084 204167674 0.000000e+00 2289.0
23 TraesCS5D01G379500 chr6B 79.710 414 53 19 38 435 188139514 188139912 2.910000e-68 270.0
24 TraesCS5D01G379500 chr2B 96.085 1405 53 1 3575 4977 68250983 68252387 0.000000e+00 2289.0
25 TraesCS5D01G379500 chr7B 77.197 478 73 24 29 474 595313083 595312610 4.910000e-61 246.0
26 TraesCS5D01G379500 chr2A 83.832 167 18 6 270 430 748449885 748450048 3.960000e-32 150.0
27 TraesCS5D01G379500 chr4A 80.838 167 27 5 28 192 110130204 110130041 6.670000e-25 126.0
28 TraesCS5D01G379500 chr3A 100.000 37 0 0 398 434 721241969 721241933 1.140000e-07 69.4


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 TraesCS5D01G379500 chr5D 450519974 450526308 6334 False 11699.000000 11699 100.000000 1 6335 1 chr5D.!!$F1 6334
1 TraesCS5D01G379500 chr5B 550374315 550378613 4298 False 2118.333333 3901 93.785667 666 6335 3 chr5B.!!$F2 5669
2 TraesCS5D01G379500 chr5B 550349981 550350585 604 False 603.000000 603 85.137000 1 599 1 chr5B.!!$F1 598
3 TraesCS5D01G379500 chr6D 471618832 471620256 1424 True 2427.000000 2427 97.405000 3572 4997 1 chr6D.!!$R1 1425
4 TraesCS5D01G379500 chr6D 262275986 262277378 1392 False 2350.000000 2350 97.067000 3577 4974 1 chr6D.!!$F1 1397
5 TraesCS5D01G379500 chr5A 569697698 569702970 5272 False 1183.800000 2370 90.109600 16 6335 5 chr5A.!!$F1 6319
6 TraesCS5D01G379500 chr1D 435760963 435762367 1404 True 2344.000000 2344 96.797000 3577 4979 1 chr1D.!!$R1 1402
7 TraesCS5D01G379500 chr4D 1615235 1616627 1392 True 2340.000000 2340 96.987000 3578 4971 1 chr4D.!!$R1 1393
8 TraesCS5D01G379500 chr7A 275022 276420 1398 True 2318.000000 2318 96.574000 3580 4978 1 chr7A.!!$R1 1398
9 TraesCS5D01G379500 chr4B 655092725 655094131 1406 True 2303.000000 2303 96.233000 3573 4977 1 chr4B.!!$R1 1404
10 TraesCS5D01G379500 chr7D 634755014 634756411 1397 False 2296.000000 2296 96.294000 3577 4977 1 chr7D.!!$F1 1400
11 TraesCS5D01G379500 chr6B 204167674 204169084 1410 True 2289.000000 2289 95.966000 3576 4984 1 chr6B.!!$R1 1408
12 TraesCS5D01G379500 chr2B 68250983 68252387 1404 False 2289.000000 2289 96.085000 3575 4977 1 chr2B.!!$F1 1402

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
596 615 0.673956 GTTCTTCACCCCTCGCCTTC 60.674 60.0 0.0 0.0 0.00 3.46 F
1391 1440 0.546747 CCCAACCCCTCTACCTCACA 60.547 60.0 0.0 0.0 0.00 3.58 F
1654 1715 0.029681 AGGCTGATCATAGTGGGGGT 60.030 55.0 0.0 0.0 0.00 4.95 F
3160 3252 0.102120 TGGCACCTTCAAGCAAAACG 59.898 50.0 0.0 0.0 0.00 3.60 F
4315 4447 1.372087 GCCATCAGGAACGCCAAGAG 61.372 60.0 0.0 0.0 36.89 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1477 1533 0.391228 TTGGTTCTGCAGCGTCACTA 59.609 50.000 9.47 0.0 0.00 2.74 R
3143 3235 1.921243 AACGTTTTGCTTGAAGGTGC 58.079 45.000 0.00 0.0 0.00 5.01 R
3600 3732 3.473647 CAGATGCAGAGGCCGGGA 61.474 66.667 2.18 0.0 40.13 5.14 R
4588 4720 0.961358 CTTCCTCCTCGTCAGTCCGT 60.961 60.000 0.00 0.0 0.00 4.69 R
6095 6694 0.532862 AGAACAGTCAACGGGCACAG 60.533 55.000 0.00 0.0 0.00 3.66 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
194 198 6.645790 TTTTTATGGCATGGCAATTTTGTT 57.354 29.167 27.04 10.30 0.00 2.83
195 199 6.645790 TTTTATGGCATGGCAATTTTGTTT 57.354 29.167 27.04 9.52 0.00 2.83
197 201 3.984508 TGGCATGGCAATTTTGTTTTG 57.015 38.095 21.13 0.00 0.00 2.44
367 383 8.034058 ACCTTCTTTTCTTTTGATCATACTCG 57.966 34.615 0.00 0.00 0.00 4.18
435 451 8.746530 AGCATGACATTTTTCATAATTCAGACT 58.253 29.630 0.00 0.00 34.29 3.24
498 516 8.903570 TCAAAATATAAATGTTAACTGGCACG 57.096 30.769 7.22 0.00 0.00 5.34
513 531 2.036475 TGGCACGCACCAAAATGTTAAT 59.964 40.909 0.00 0.00 36.55 1.40
584 603 9.810545 AAAGAAAAACATATTTTCCGTTCTTCA 57.189 25.926 9.39 0.00 37.01 3.02
585 604 8.797266 AGAAAAACATATTTTCCGTTCTTCAC 57.203 30.769 9.39 0.00 37.01 3.18
592 611 2.434359 CCGTTCTTCACCCCTCGC 60.434 66.667 0.00 0.00 0.00 5.03
594 613 2.943978 CGTTCTTCACCCCTCGCCT 61.944 63.158 0.00 0.00 0.00 5.52
595 614 1.375326 GTTCTTCACCCCTCGCCTT 59.625 57.895 0.00 0.00 0.00 4.35
596 615 0.673956 GTTCTTCACCCCTCGCCTTC 60.674 60.000 0.00 0.00 0.00 3.46
597 616 2.125512 CTTCACCCCTCGCCTTCG 60.126 66.667 0.00 0.00 0.00 3.79
604 645 2.721167 CCCTCGCCTTCGATGACCA 61.721 63.158 0.00 0.00 44.56 4.02
605 646 1.443407 CCTCGCCTTCGATGACCAT 59.557 57.895 0.00 0.00 44.56 3.55
615 656 4.142687 CCTTCGATGACCATTTTACACCAC 60.143 45.833 0.00 0.00 0.00 4.16
616 657 3.340034 TCGATGACCATTTTACACCACC 58.660 45.455 0.00 0.00 0.00 4.61
628 669 6.939132 TTTTACACCACCGAGTATTGAAAA 57.061 33.333 0.00 0.00 0.00 2.29
629 670 5.927954 TTACACCACCGAGTATTGAAAAC 57.072 39.130 0.00 0.00 0.00 2.43
635 676 4.944930 CCACCGAGTATTGAAAACCCATAA 59.055 41.667 0.00 0.00 0.00 1.90
768 811 8.332464 CAATTTTTCTTCAGTCGTAGTGTTGTA 58.668 33.333 0.00 0.00 0.00 2.41
773 816 4.761235 TCAGTCGTAGTGTTGTAGAAGG 57.239 45.455 0.00 0.00 0.00 3.46
775 818 4.454847 TCAGTCGTAGTGTTGTAGAAGGAG 59.545 45.833 0.00 0.00 0.00 3.69
786 829 5.163581 TGTTGTAGAAGGAGTACTATTCGCC 60.164 44.000 12.36 2.73 0.00 5.54
854 903 1.062587 CACCTTTCGAATTAGCCAGCG 59.937 52.381 0.00 0.00 0.00 5.18
1017 1066 4.853142 ATGGCCGCCGGTCTCCTA 62.853 66.667 10.05 0.00 0.00 2.94
1224 1273 3.141488 GAGAAGCGGCGGGAGAGA 61.141 66.667 9.78 0.00 0.00 3.10
1386 1435 1.999568 GGTCCCCAACCCCTCTACC 61.000 68.421 0.00 0.00 42.85 3.18
1391 1440 0.546747 CCCAACCCCTCTACCTCACA 60.547 60.000 0.00 0.00 0.00 3.58
1398 1447 0.976641 CCTCTACCTCACAGCCACAA 59.023 55.000 0.00 0.00 0.00 3.33
1407 1456 3.557898 CCTCACAGCCACAACTTCATACT 60.558 47.826 0.00 0.00 0.00 2.12
1408 1457 4.322725 CCTCACAGCCACAACTTCATACTA 60.323 45.833 0.00 0.00 0.00 1.82
1409 1458 4.566004 TCACAGCCACAACTTCATACTAC 58.434 43.478 0.00 0.00 0.00 2.73
1410 1459 3.684788 CACAGCCACAACTTCATACTACC 59.315 47.826 0.00 0.00 0.00 3.18
1411 1460 3.326588 ACAGCCACAACTTCATACTACCA 59.673 43.478 0.00 0.00 0.00 3.25
1412 1461 4.019321 ACAGCCACAACTTCATACTACCAT 60.019 41.667 0.00 0.00 0.00 3.55
1413 1462 5.188948 ACAGCCACAACTTCATACTACCATA 59.811 40.000 0.00 0.00 0.00 2.74
1444 1493 3.670359 GCGTTGTTGATTGCAGATTGCTA 60.670 43.478 2.48 0.00 45.31 3.49
1445 1494 3.848019 CGTTGTTGATTGCAGATTGCTAC 59.152 43.478 2.48 0.00 45.31 3.58
1446 1495 4.378770 CGTTGTTGATTGCAGATTGCTACT 60.379 41.667 2.48 0.00 45.31 2.57
1447 1496 4.690184 TGTTGATTGCAGATTGCTACTG 57.310 40.909 2.48 0.00 45.31 2.74
1504 1560 2.351641 CGCTGCAGAACCAAATTAGCAA 60.352 45.455 20.43 0.00 32.71 3.91
1514 1570 3.333680 ACCAAATTAGCAAGAAGAGGGGA 59.666 43.478 0.00 0.00 0.00 4.81
1525 1582 6.617371 AGCAAGAAGAGGGGAGATTAGAATTA 59.383 38.462 0.00 0.00 0.00 1.40
1567 1627 5.805994 CACCACTAGCTAGTTTACTGCTTAC 59.194 44.000 23.94 0.00 38.15 2.34
1589 1649 6.799926 ACAATTTGTTATCAACCCATTTGC 57.200 33.333 0.00 0.00 34.88 3.68
1604 1664 4.487948 CCATTTGCACCTACATTGTTCTG 58.512 43.478 0.00 0.00 0.00 3.02
1647 1707 1.627834 GGGGAAGGAGGCTGATCATAG 59.372 57.143 0.00 0.00 0.00 2.23
1653 1714 0.689623 GAGGCTGATCATAGTGGGGG 59.310 60.000 0.00 0.00 0.00 5.40
1654 1715 0.029681 AGGCTGATCATAGTGGGGGT 60.030 55.000 0.00 0.00 0.00 4.95
1655 1716 0.109342 GGCTGATCATAGTGGGGGTG 59.891 60.000 0.00 0.00 0.00 4.61
1656 1717 0.839946 GCTGATCATAGTGGGGGTGT 59.160 55.000 0.00 0.00 0.00 4.16
1657 1718 1.475751 GCTGATCATAGTGGGGGTGTG 60.476 57.143 0.00 0.00 0.00 3.82
1784 1849 1.123861 TCTTGGAGGCTGCACTCACT 61.124 55.000 8.71 0.00 39.27 3.41
1870 1947 8.101589 CATTGCTATGAGATCCATGCGTATGG 62.102 46.154 25.03 25.03 43.36 2.74
1900 1977 0.539051 AGTCTGCTCACTGGTATGCC 59.461 55.000 0.00 0.00 0.00 4.40
1903 1980 0.529337 CTGCTCACTGGTATGCCGAG 60.529 60.000 0.00 0.00 37.67 4.63
1909 1986 1.330655 ACTGGTATGCCGAGGGACTG 61.331 60.000 0.00 0.00 41.55 3.51
1951 2028 6.874288 AGAAAGAATATTGATGCTAGTGCC 57.126 37.500 0.00 0.00 38.71 5.01
1966 2043 2.320781 AGTGCCAAGTGACTCACTACT 58.679 47.619 12.22 9.00 44.62 2.57
1986 2063 3.244112 ACTTATTAGCTATGCCGGTGTCC 60.244 47.826 1.90 0.00 0.00 4.02
1992 2069 0.460284 CTATGCCGGTGTCCTGTGTC 60.460 60.000 1.90 0.00 0.00 3.67
1993 2070 1.188871 TATGCCGGTGTCCTGTGTCA 61.189 55.000 1.90 0.00 0.00 3.58
2003 2080 5.086104 GTGTCCTGTGTCACCTATGTTAT 57.914 43.478 0.00 0.00 0.00 1.89
2004 2081 6.216801 GTGTCCTGTGTCACCTATGTTATA 57.783 41.667 0.00 0.00 0.00 0.98
2006 2083 5.955959 TGTCCTGTGTCACCTATGTTATAGT 59.044 40.000 0.00 0.00 0.00 2.12
2008 2085 7.284716 TGTCCTGTGTCACCTATGTTATAGTAG 59.715 40.741 0.00 0.00 0.00 2.57
2040 2117 3.801698 AGTGACATCAGATGTATGTGGC 58.198 45.455 16.40 3.53 45.03 5.01
2049 2126 2.159184 AGATGTATGTGGCGTCAGTCAG 60.159 50.000 0.00 0.00 29.49 3.51
2083 2160 4.901868 TCCTGCTAAATGGTCGTTTAAGT 58.098 39.130 0.00 0.00 0.00 2.24
2130 2207 4.012374 ACCACATATGCAGAACAAGAAGG 58.988 43.478 1.58 0.00 0.00 3.46
2136 2213 2.991250 TGCAGAACAAGAAGGATAGCC 58.009 47.619 0.00 0.00 0.00 3.93
2180 2259 2.922503 TTCCAGAGCACTCGCCCA 60.923 61.111 0.00 0.00 39.83 5.36
2181 2260 2.849120 CTTCCAGAGCACTCGCCCAG 62.849 65.000 0.00 0.00 39.83 4.45
2218 2297 9.798994 CTCCCTCATTGATTCTTAGAAATTTTG 57.201 33.333 0.00 0.00 0.00 2.44
2237 2316 6.677781 TTTTGACAAGCCACTACATATAGC 57.322 37.500 0.00 0.00 30.75 2.97
2238 2317 5.614324 TTGACAAGCCACTACATATAGCT 57.386 39.130 0.00 0.00 34.64 3.32
2305 2393 7.683704 GCATGATCTGATTGCTAACTTTTCCAT 60.684 37.037 0.00 0.00 33.61 3.41
2443 2531 7.444299 AGCTTCACACAATTGGAATTATGTTT 58.556 30.769 10.83 0.00 34.05 2.83
2590 2681 4.383649 GCACATGTCATTGTTAGCTTGTTG 59.616 41.667 0.00 0.00 0.00 3.33
2655 2746 8.157159 GCATTTTGCATTGAGAATTGAAATTG 57.843 30.769 0.00 0.00 44.26 2.32
2662 2753 7.927092 TGCATTGAGAATTGAAATTGTTCTTCA 59.073 29.630 0.00 0.00 32.67 3.02
3143 3235 3.311322 TGAGCGTTGTTTGAGTTAAGTGG 59.689 43.478 0.00 0.00 0.00 4.00
3160 3252 0.102120 TGGCACCTTCAAGCAAAACG 59.898 50.000 0.00 0.00 0.00 3.60
3403 3535 5.050644 TGAGCATAAGCAAATGACTGTTG 57.949 39.130 2.72 0.00 45.49 3.33
3487 3619 6.657541 ACTCTTGGTTTGAACACTTTAACTGA 59.342 34.615 0.00 0.00 0.00 3.41
3561 3693 5.633830 TCTGCAAGAGATTTTCCATGTTC 57.366 39.130 0.00 0.00 38.67 3.18
3562 3694 5.072055 TCTGCAAGAGATTTTCCATGTTCA 58.928 37.500 0.00 0.00 38.67 3.18
3563 3695 5.713389 TCTGCAAGAGATTTTCCATGTTCAT 59.287 36.000 0.00 0.00 38.67 2.57
3564 3696 6.885918 TCTGCAAGAGATTTTCCATGTTCATA 59.114 34.615 0.00 0.00 38.67 2.15
3565 3697 7.558807 TCTGCAAGAGATTTTCCATGTTCATAT 59.441 33.333 0.00 0.00 38.67 1.78
3566 3698 8.750515 TGCAAGAGATTTTCCATGTTCATATA 57.249 30.769 0.00 0.00 0.00 0.86
3567 3699 8.623903 TGCAAGAGATTTTCCATGTTCATATAC 58.376 33.333 0.00 0.00 0.00 1.47
3568 3700 8.844244 GCAAGAGATTTTCCATGTTCATATACT 58.156 33.333 0.00 0.00 0.00 2.12
3570 3702 8.388484 AGAGATTTTCCATGTTCATATACTGC 57.612 34.615 0.00 0.00 0.00 4.40
4315 4447 1.372087 GCCATCAGGAACGCCAAGAG 61.372 60.000 0.00 0.00 36.89 2.85
4922 5056 3.157949 GAAGGGGAGGAGGCGGAG 61.158 72.222 0.00 0.00 0.00 4.63
4993 5127 1.202891 CGGGGAGGGAACAAAAAGTCT 60.203 52.381 0.00 0.00 0.00 3.24
4994 5128 2.039348 CGGGGAGGGAACAAAAAGTCTA 59.961 50.000 0.00 0.00 0.00 2.59
4996 5130 3.418995 GGGAGGGAACAAAAAGTCTACC 58.581 50.000 0.00 0.00 0.00 3.18
4997 5131 3.418995 GGAGGGAACAAAAAGTCTACCC 58.581 50.000 0.00 0.00 37.88 3.69
5022 5156 8.744652 CCTCATATACTGCTAGTTACAGCTTAT 58.255 37.037 7.91 7.20 42.30 1.73
5114 5248 1.440353 CTAACTTGCCGCGTGTTGC 60.440 57.895 4.92 0.82 41.47 4.17
5156 5290 2.420687 GGACATGGAGTGACAAGATCCC 60.421 54.545 0.00 0.00 31.73 3.85
5235 5369 0.387622 CGAACGTCTTCGGCAACCTA 60.388 55.000 1.67 0.00 44.73 3.08
5512 5649 5.762218 CAGGGAAGCTATACATTTCCTTCAG 59.238 44.000 0.00 0.00 40.17 3.02
5796 6074 3.664107 TCTATTGTGACACAGTGAAGCC 58.336 45.455 13.41 0.00 0.00 4.35
5820 6098 1.937546 GCCACTTGTATGCCACCAGC 61.938 60.000 0.00 0.00 44.14 4.85
5830 6108 0.036732 TGCCACCAGCTCTTCGATTT 59.963 50.000 0.00 0.00 44.23 2.17
5843 6121 0.179111 TCGATTTTCGCGATGGAGCT 60.179 50.000 10.88 0.00 40.21 4.09
5852 6130 1.068264 CGCGATGGAGCTGAGCTATAA 60.068 52.381 7.08 0.00 39.88 0.98
5853 6131 2.416566 CGCGATGGAGCTGAGCTATAAT 60.417 50.000 7.08 0.69 39.88 1.28
5858 6136 5.468072 CGATGGAGCTGAGCTATAATTTGTT 59.532 40.000 7.08 0.00 39.88 2.83
5862 6140 5.825151 GGAGCTGAGCTATAATTTGTTTCCT 59.175 40.000 7.08 0.00 39.88 3.36
5885 6166 6.697892 CCTCACTCTCGATAACAAAGTTATCC 59.302 42.308 18.89 6.74 0.00 2.59
6049 6645 3.084039 ACCATGCATGTCTTGTAACAGG 58.916 45.455 24.58 7.77 34.19 4.00
6051 6647 3.127548 CCATGCATGTCTTGTAACAGGTC 59.872 47.826 24.58 0.00 33.62 3.85
6069 6665 6.365520 ACAGGTCCTGTATTTTCTTTCTTGT 58.634 36.000 23.57 0.00 43.46 3.16
6087 6686 1.550524 TGTGAGGACGAAGGATGGAAG 59.449 52.381 0.00 0.00 0.00 3.46
6089 6688 0.179070 GAGGACGAAGGATGGAAGGC 60.179 60.000 0.00 0.00 0.00 4.35
6095 6694 4.496336 AGGATGGAAGGCGGCTGC 62.496 66.667 14.21 11.45 41.71 5.25
6156 6766 8.727100 AAATGGAAATAGAAAAAGGAGAAGGT 57.273 30.769 0.00 0.00 0.00 3.50
6159 6769 9.822727 ATGGAAATAGAAAAAGGAGAAGGTAAA 57.177 29.630 0.00 0.00 0.00 2.01
6193 6811 2.427095 GAGAGAGAGAGAAGAAGCCCAC 59.573 54.545 0.00 0.00 0.00 4.61
6198 6816 2.039613 AGAGAGAAGAAGCCCACTTTGG 59.960 50.000 0.00 0.00 35.82 3.28
6207 6825 4.002797 CCACTTTGGGCAGTAGGC 57.997 61.111 0.00 0.00 43.74 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 9.252962 CATCCTCTTAACAATAAAAATGGCATC 57.747 33.333 0.00 0.00 0.00 3.91
92 93 7.555087 TGCCATCCTCTTAACAATAAAAATGG 58.445 34.615 0.00 0.00 0.00 3.16
192 196 5.497635 AATTGCCATGGTCAAAACAAAAC 57.502 34.783 20.56 0.00 0.00 2.43
194 198 4.133078 GGAATTGCCATGGTCAAAACAAA 58.867 39.130 20.56 3.00 36.34 2.83
195 199 3.390639 AGGAATTGCCATGGTCAAAACAA 59.609 39.130 20.56 12.66 40.02 2.83
197 201 3.244181 ACAGGAATTGCCATGGTCAAAAC 60.244 43.478 20.56 16.89 40.02 2.43
326 337 5.723672 AGAAGGTCGTGTGATCTAGAAAA 57.276 39.130 0.00 0.00 33.25 2.29
340 356 8.034058 AGTATGATCAAAAGAAAAGAAGGTCG 57.966 34.615 0.00 0.00 0.00 4.79
479 495 4.095185 GGTGCGTGCCAGTTAACATTTATA 59.905 41.667 8.61 0.00 0.00 0.98
481 497 2.226912 GGTGCGTGCCAGTTAACATTTA 59.773 45.455 8.61 0.00 0.00 1.40
498 516 4.000325 GGGTCCAATTAACATTTTGGTGC 59.000 43.478 5.65 1.69 42.47 5.01
562 581 6.926826 GGGTGAAGAACGGAAAATATGTTTTT 59.073 34.615 1.43 0.00 37.65 1.94
566 585 4.014406 GGGGTGAAGAACGGAAAATATGT 58.986 43.478 0.00 0.00 0.00 2.29
569 588 3.618019 CGAGGGGTGAAGAACGGAAAATA 60.618 47.826 0.00 0.00 0.00 1.40
577 596 0.673956 GAAGGCGAGGGGTGAAGAAC 60.674 60.000 0.00 0.00 0.00 3.01
580 599 2.125512 CGAAGGCGAGGGGTGAAG 60.126 66.667 0.00 0.00 40.82 3.02
592 611 4.006989 TGGTGTAAAATGGTCATCGAAGG 58.993 43.478 0.00 0.00 0.00 3.46
594 613 3.754323 GGTGGTGTAAAATGGTCATCGAA 59.246 43.478 0.00 0.00 0.00 3.71
595 614 3.340034 GGTGGTGTAAAATGGTCATCGA 58.660 45.455 0.00 0.00 0.00 3.59
596 615 2.095213 CGGTGGTGTAAAATGGTCATCG 59.905 50.000 0.00 0.00 0.00 3.84
597 616 3.340034 TCGGTGGTGTAAAATGGTCATC 58.660 45.455 0.00 0.00 0.00 2.92
604 645 7.364970 GTTTTCAATACTCGGTGGTGTAAAAT 58.635 34.615 0.00 0.00 0.00 1.82
605 646 6.238703 GGTTTTCAATACTCGGTGGTGTAAAA 60.239 38.462 0.00 0.00 0.00 1.52
615 656 6.503589 TTGTTATGGGTTTTCAATACTCGG 57.496 37.500 0.00 0.00 0.00 4.63
616 657 7.487829 CCATTTGTTATGGGTTTTCAATACTCG 59.512 37.037 0.00 0.00 35.58 4.18
628 669 6.126911 ACTGTTCAAAACCATTTGTTATGGGT 60.127 34.615 8.53 0.00 45.02 4.51
629 670 6.287525 ACTGTTCAAAACCATTTGTTATGGG 58.712 36.000 8.53 0.00 45.02 4.00
635 676 5.398603 TGTGACTGTTCAAAACCATTTGT 57.601 34.783 1.69 0.00 45.02 2.83
744 787 6.920569 ACAACACTACGACTGAAGAAAAAT 57.079 33.333 0.00 0.00 0.00 1.82
768 811 3.633418 ACAGGCGAATAGTACTCCTTCT 58.367 45.455 0.00 0.00 0.00 2.85
773 816 3.550678 CGGAAAACAGGCGAATAGTACTC 59.449 47.826 0.00 0.00 0.00 2.59
775 818 3.061697 CACGGAAAACAGGCGAATAGTAC 59.938 47.826 0.00 0.00 0.00 2.73
786 829 1.532868 CCAGAAGAGCACGGAAAACAG 59.467 52.381 0.00 0.00 0.00 3.16
854 903 0.332972 AGGAAGAAAGGATGGGTGGC 59.667 55.000 0.00 0.00 0.00 5.01
928 977 5.002464 TCTACACGTCAGTTAAATAGCCC 57.998 43.478 0.00 0.00 0.00 5.19
1386 1435 3.668447 AGTATGAAGTTGTGGCTGTGAG 58.332 45.455 0.00 0.00 0.00 3.51
1391 1440 4.844349 ATGGTAGTATGAAGTTGTGGCT 57.156 40.909 0.00 0.00 0.00 4.75
1398 1447 3.069158 GCGGTGGTATGGTAGTATGAAGT 59.931 47.826 0.00 0.00 0.00 3.01
1407 1456 4.210093 CGCGGCGGTGGTATGGTA 62.210 66.667 15.84 0.00 0.00 3.25
1410 1459 3.860125 CAACGCGGCGGTGGTATG 61.860 66.667 31.31 13.22 41.23 2.39
1411 1460 3.887335 AACAACGCGGCGGTGGTAT 62.887 57.895 39.07 24.29 45.03 2.73
1412 1461 4.605634 AACAACGCGGCGGTGGTA 62.606 61.111 39.07 0.00 45.03 3.25
1444 1493 1.301637 TGTACATGTGCTGCGCAGT 60.302 52.632 35.80 19.95 40.08 4.40
1445 1494 1.133253 GTGTACATGTGCTGCGCAG 59.867 57.895 32.83 32.83 40.08 5.18
1446 1495 1.567746 CTGTGTACATGTGCTGCGCA 61.568 55.000 19.11 19.11 35.60 6.09
1447 1496 1.133253 CTGTGTACATGTGCTGCGC 59.867 57.895 15.25 6.19 0.00 6.09
1448 1497 1.133253 GCTGTGTACATGTGCTGCG 59.867 57.895 15.25 4.35 0.00 5.18
1460 1514 1.694150 ACTATGTCAGTGTGGCTGTGT 59.306 47.619 0.00 0.00 45.23 3.72
1477 1533 0.391228 TTGGTTCTGCAGCGTCACTA 59.609 50.000 9.47 0.00 0.00 2.74
1478 1534 0.463654 TTTGGTTCTGCAGCGTCACT 60.464 50.000 9.47 0.00 0.00 3.41
1479 1535 0.593128 ATTTGGTTCTGCAGCGTCAC 59.407 50.000 9.47 2.73 0.00 3.67
1504 1560 8.879227 CAATCTAATTCTAATCTCCCCTCTTCT 58.121 37.037 0.00 0.00 0.00 2.85
1525 1582 3.181445 TGGTGTGTAGCTTGGTTCAATCT 60.181 43.478 0.00 0.00 0.00 2.40
1567 1627 6.348376 GGTGCAAATGGGTTGATAACAAATTG 60.348 38.462 0.00 0.00 39.87 2.32
1580 1640 2.888212 ACAATGTAGGTGCAAATGGGT 58.112 42.857 0.00 0.00 0.00 4.51
1589 1649 5.009631 TCCAATTCCAGAACAATGTAGGTG 58.990 41.667 0.00 0.00 0.00 4.00
1604 1664 5.450965 CCATGTTCTGCAAGTATCCAATTCC 60.451 44.000 0.00 0.00 33.76 3.01
1647 1707 2.498056 CCTGCAAACACACCCCCAC 61.498 63.158 0.00 0.00 0.00 4.61
1653 1714 1.954362 TTGGCCACCTGCAAACACAC 61.954 55.000 3.88 0.00 43.89 3.82
1654 1715 1.674764 CTTGGCCACCTGCAAACACA 61.675 55.000 3.88 0.00 43.89 3.72
1655 1716 1.067916 CTTGGCCACCTGCAAACAC 59.932 57.895 3.88 0.00 43.89 3.32
1656 1717 2.132996 CCTTGGCCACCTGCAAACA 61.133 57.895 3.88 0.00 43.89 2.83
1657 1718 1.809567 CTCCTTGGCCACCTGCAAAC 61.810 60.000 3.88 0.00 43.89 2.93
1703 1768 1.162800 GCCCCAGATCGAACATCTGC 61.163 60.000 8.69 0.00 43.03 4.26
1784 1849 1.248785 GCGAGGAGGGGCGTATGATA 61.249 60.000 0.00 0.00 0.00 2.15
1870 1947 3.702045 AGTGAGCAGACTACAGGTAATCC 59.298 47.826 0.00 0.00 0.00 3.01
1872 1949 3.449018 CCAGTGAGCAGACTACAGGTAAT 59.551 47.826 0.00 0.00 0.00 1.89
1900 1977 2.408050 GCTTATATGCACAGTCCCTCG 58.592 52.381 5.76 0.00 0.00 4.63
1903 1980 1.878102 CGGGCTTATATGCACAGTCCC 60.878 57.143 12.83 3.16 35.83 4.46
1951 2028 9.457110 CATAGCTAATAAGTAGTGAGTCACTTG 57.543 37.037 29.84 13.69 42.59 3.16
1966 2043 2.969950 AGGACACCGGCATAGCTAATAA 59.030 45.455 0.00 0.00 0.00 1.40
1986 2063 9.117183 TGTACTACTATAACATAGGTGACACAG 57.883 37.037 8.08 0.00 0.00 3.66
2003 2080 7.571025 TGATGTCACTCCACTATGTACTACTA 58.429 38.462 0.00 0.00 0.00 1.82
2004 2081 6.424032 TGATGTCACTCCACTATGTACTACT 58.576 40.000 0.00 0.00 0.00 2.57
2006 2083 6.659824 TCTGATGTCACTCCACTATGTACTA 58.340 40.000 0.00 0.00 0.00 1.82
2008 2085 5.836821 TCTGATGTCACTCCACTATGTAC 57.163 43.478 0.00 0.00 0.00 2.90
2049 2126 2.918712 TAGCAGGATTCAGCTAAGGC 57.081 50.000 0.00 0.00 40.15 4.35
2055 2132 2.289002 CGACCATTTAGCAGGATTCAGC 59.711 50.000 0.00 0.00 0.00 4.26
2058 2135 4.965119 AAACGACCATTTAGCAGGATTC 57.035 40.909 0.00 0.00 0.00 2.52
2059 2136 5.944007 ACTTAAACGACCATTTAGCAGGATT 59.056 36.000 0.00 0.00 0.00 3.01
2060 2137 5.354234 CACTTAAACGACCATTTAGCAGGAT 59.646 40.000 0.00 0.00 0.00 3.24
2065 2142 5.857822 ACTCACTTAAACGACCATTTAGC 57.142 39.130 0.00 0.00 0.00 3.09
2083 2160 6.775142 TGTTGGTTTCATCCTTCATTAACTCA 59.225 34.615 0.00 0.00 0.00 3.41
2130 2207 0.470833 TCTCCCTGGCTCTGGCTATC 60.471 60.000 0.00 0.00 38.73 2.08
2136 2213 0.401738 TTTGGTTCTCCCTGGCTCTG 59.598 55.000 0.00 0.00 0.00 3.35
2180 2259 2.614001 GAGGGAGCCATGAACCTCT 58.386 57.895 14.01 0.38 44.74 3.69
2218 2297 6.334202 GGATAGCTATATGTAGTGGCTTGTC 58.666 44.000 6.13 0.00 34.88 3.18
2590 2681 2.675348 GAGATGCAGCTAAGGTTGTGAC 59.325 50.000 3.45 0.00 0.00 3.67
2662 2753 8.262933 TGCTAGCTTGATCTAATATATGCACAT 58.737 33.333 17.23 0.00 0.00 3.21
3143 3235 1.921243 AACGTTTTGCTTGAAGGTGC 58.079 45.000 0.00 0.00 0.00 5.01
3391 3523 7.654520 AGGTCAATCAAAATCAACAGTCATTTG 59.345 33.333 0.00 0.00 33.43 2.32
3397 3529 6.906157 ATGAGGTCAATCAAAATCAACAGT 57.094 33.333 0.00 0.00 31.76 3.55
3403 3535 8.465201 AGCTAGAAAATGAGGTCAATCAAAATC 58.535 33.333 0.00 0.00 31.76 2.17
3487 3619 6.874134 GGTGTTGTATGTCATAGTTCTGACTT 59.126 38.462 5.87 2.55 44.73 3.01
3600 3732 3.473647 CAGATGCAGAGGCCGGGA 61.474 66.667 2.18 0.00 40.13 5.14
3857 3989 4.643387 GGAGCGGTGGCAGTTGGT 62.643 66.667 0.00 0.00 43.41 3.67
4588 4720 0.961358 CTTCCTCCTCGTCAGTCCGT 60.961 60.000 0.00 0.00 0.00 4.69
4993 5127 6.433404 GCTGTAACTAGCAGTATATGAGGGTA 59.567 42.308 0.00 0.00 43.17 3.69
4994 5128 5.244178 GCTGTAACTAGCAGTATATGAGGGT 59.756 44.000 0.00 0.00 43.17 4.34
4996 5130 6.582677 AGCTGTAACTAGCAGTATATGAGG 57.417 41.667 0.00 0.00 46.07 3.86
5114 5248 2.545526 CCAGCGTACCTGATTAATGCAG 59.454 50.000 11.58 0.50 44.64 4.41
5156 5290 4.384056 TCTTTTCTTGTCCTCTTGCTCTG 58.616 43.478 0.00 0.00 0.00 3.35
5519 5660 7.856145 ATGTATAGCTTTCCTCTTGTCTTTG 57.144 36.000 0.00 0.00 0.00 2.77
5525 5666 6.881602 GGGGAATATGTATAGCTTTCCTCTTG 59.118 42.308 10.19 0.00 34.69 3.02
5772 6050 5.874810 GGCTTCACTGTGTCACAATAGATTA 59.125 40.000 7.18 0.00 0.00 1.75
5796 6074 2.690326 GGCATACAAGTGGCCGTAG 58.310 57.895 0.00 0.00 38.04 3.51
5820 6098 2.193447 TCCATCGCGAAAATCGAAGAG 58.807 47.619 15.24 0.00 43.74 2.85
5830 6108 1.384222 TAGCTCAGCTCCATCGCGAA 61.384 55.000 15.24 0.00 40.44 4.70
5843 6121 7.624549 AGAGTGAGGAAACAAATTATAGCTCA 58.375 34.615 0.00 0.00 0.00 4.26
5852 6130 6.464222 TGTTATCGAGAGTGAGGAAACAAAT 58.536 36.000 0.00 0.00 0.00 2.32
5853 6131 5.849510 TGTTATCGAGAGTGAGGAAACAAA 58.150 37.500 0.00 0.00 0.00 2.83
5858 6136 5.723672 ACTTTGTTATCGAGAGTGAGGAA 57.276 39.130 0.00 0.00 0.00 3.36
5862 6140 6.380274 AGGGATAACTTTGTTATCGAGAGTGA 59.620 38.462 18.36 0.00 33.38 3.41
5885 6166 3.571401 GCATCTTCATGAAATACCCCAGG 59.429 47.826 9.88 0.00 30.57 4.45
6049 6645 6.710744 TCCTCACAAGAAAGAAAATACAGGAC 59.289 38.462 0.00 0.00 0.00 3.85
6051 6647 6.347725 CGTCCTCACAAGAAAGAAAATACAGG 60.348 42.308 0.00 0.00 0.00 4.00
6069 6665 1.195115 CCTTCCATCCTTCGTCCTCA 58.805 55.000 0.00 0.00 0.00 3.86
6095 6694 0.532862 AGAACAGTCAACGGGCACAG 60.533 55.000 0.00 0.00 0.00 3.66
6102 6701 3.978687 AGAACAGGTAGAACAGTCAACG 58.021 45.455 0.00 0.00 0.00 4.10
6159 6769 9.401058 CTTCTCTCTCTCTCTCTCTCTTTTATT 57.599 37.037 0.00 0.00 0.00 1.40
6161 6771 8.146053 TCTTCTCTCTCTCTCTCTCTCTTTTA 57.854 38.462 0.00 0.00 0.00 1.52
6163 6773 6.627087 TCTTCTCTCTCTCTCTCTCTCTTT 57.373 41.667 0.00 0.00 0.00 2.52
6164 6774 6.627087 TTCTTCTCTCTCTCTCTCTCTCTT 57.373 41.667 0.00 0.00 0.00 2.85
6206 6824 2.594365 ATTCCATTCCAGGGCCAGGC 62.594 60.000 10.69 1.26 0.00 4.85
6207 6825 0.757935 CATTCCATTCCAGGGCCAGG 60.758 60.000 9.04 9.04 0.00 4.45
6208 6826 0.757935 CCATTCCATTCCAGGGCCAG 60.758 60.000 6.18 0.00 0.00 4.85
6209 6827 1.310715 CCATTCCATTCCAGGGCCA 59.689 57.895 6.18 0.00 0.00 5.36
6243 6877 4.517703 GTCTCGGTCGCCTCGTCG 62.518 72.222 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.