Multiple sequence alignment - TraesCS1B01G458900

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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 TraesCS1B01G458900 chr1B 100.000 6639 0 0 1 6639 672686127 672679489 0.000000e+00 12224.0
1 TraesCS1B01G458900 chr1B 99.519 6444 4 2 1 6436 672332525 672338949 0.000000e+00 11703.0
2 TraesCS1B01G458900 chr1B 93.624 1929 120 2 2355 4282 180834316 180832390 0.000000e+00 2878.0
3 TraesCS1B01G458900 chr1B 90.712 646 44 4 4280 4913 180832352 180831711 0.000000e+00 846.0
4 TraesCS1B01G458900 chr1B 81.239 581 33 24 1718 2243 180834880 180834321 3.730000e-107 399.0
5 TraesCS1B01G458900 chr1B 99.074 108 1 0 2246 2353 619184393 619184500 1.890000e-45 195.0
6 TraesCS1B01G458900 chr1B 87.069 116 11 1 1718 1833 40819398 40819287 1.940000e-25 128.0
7 TraesCS1B01G458900 chr1B 72.105 380 106 0 3005 3384 464119073 464119452 1.510000e-21 115.0
8 TraesCS1B01G458900 chr1B 83.516 91 3 5 1873 1954 40819217 40819130 2.570000e-09 75.0
9 TraesCS1B01G458900 chr5B 88.793 696 62 8 4280 4963 647340497 647341188 0.000000e+00 839.0
10 TraesCS1B01G458900 chr5B 89.635 521 51 2 3419 3939 647339694 647340211 0.000000e+00 660.0
11 TraesCS1B01G458900 chr5B 92.531 241 18 0 4042 4282 647340219 647340459 4.930000e-91 346.0
12 TraesCS1B01G458900 chrUn 100.000 371 0 0 1 371 479027210 479027580 0.000000e+00 686.0
13 TraesCS1B01G458900 chrUn 78.947 418 26 26 1718 2080 70386322 70385912 1.860000e-55 228.0
14 TraesCS1B01G458900 chrUn 99.074 108 1 0 2246 2353 182426533 182426426 1.890000e-45 195.0
15 TraesCS1B01G458900 chrUn 99.065 107 1 0 2247 2353 231559222 231559328 6.790000e-45 193.0
16 TraesCS1B01G458900 chrUn 99.065 107 1 0 2247 2353 273328905 273328799 6.790000e-45 193.0
17 TraesCS1B01G458900 chr3D 89.783 460 44 2 1 460 462785013 462784557 2.670000e-163 586.0
18 TraesCS1B01G458900 chr3D 82.919 322 30 16 461 758 248813003 248812683 3.950000e-67 267.0
19 TraesCS1B01G458900 chr3D 85.714 63 9 0 4402 4464 590247073 590247135 4.300000e-07 67.6
20 TraesCS1B01G458900 chr4A 89.588 461 44 4 1 460 440132674 440132217 3.450000e-162 582.0
21 TraesCS1B01G458900 chr3A 89.056 466 47 4 1 466 605515846 605515385 5.770000e-160 575.0
22 TraesCS1B01G458900 chr3A 81.677 322 34 16 461 758 307917664 307917344 1.850000e-60 244.0
23 TraesCS1B01G458900 chr2D 88.913 460 48 1 1 460 310987515 310987059 1.250000e-156 564.0
24 TraesCS1B01G458900 chr2A 88.745 462 48 2 1 461 305416551 305416093 4.500000e-156 562.0
25 TraesCS1B01G458900 chr2A 88.720 461 46 5 1 460 487971629 487972084 5.810000e-155 558.0
26 TraesCS1B01G458900 chr6D 88.720 461 44 5 1 460 405276694 405276241 2.090000e-154 556.0
27 TraesCS1B01G458900 chr6D 85.714 63 9 0 4402 4464 364110157 364110219 4.300000e-07 67.6
28 TraesCS1B01G458900 chr6D 93.182 44 3 0 4402 4445 14483316 14483359 1.550000e-06 65.8
29 TraesCS1B01G458900 chr1D 90.464 388 20 7 916 1296 180807364 180806987 4.620000e-136 496.0
30 TraesCS1B01G458900 chr1D 78.261 276 14 23 1718 1954 25388120 25387852 1.160000e-27 135.0
31 TraesCS1B01G458900 chr1D 89.524 105 7 1 1729 1833 25445598 25445498 5.400000e-26 130.0
32 TraesCS1B01G458900 chr1D 85.714 63 9 0 4402 4464 50920508 50920570 4.300000e-07 67.6
33 TraesCS1B01G458900 chr7D 99.074 108 1 0 2246 2353 6943012 6942905 1.890000e-45 195.0
34 TraesCS1B01G458900 chr7A 99.074 108 1 0 2246 2353 60219827 60219934 1.890000e-45 195.0
35 TraesCS1B01G458900 chr2B 99.074 108 1 0 2246 2353 234530222 234530329 1.890000e-45 195.0
36 TraesCS1B01G458900 chr2B 99.074 108 1 0 2246 2353 449208391 449208498 1.890000e-45 195.0
37 TraesCS1B01G458900 chr6B 87.838 148 11 3 1093 1240 285560354 285560494 4.120000e-37 167.0
38 TraesCS1B01G458900 chr7B 76.647 167 27 10 4057 4217 746871959 746871799 1.530000e-11 82.4
39 TraesCS1B01G458900 chr3B 91.667 48 4 0 3393 3440 766171429 766171476 4.300000e-07 67.6
40 TraesCS1B01G458900 chr5A 76.423 123 26 3 3329 3449 71139372 71139251 5.560000e-06 63.9
41 TraesCS1B01G458900 chr5A 94.737 38 2 0 4414 4451 544404517 544404480 7.190000e-05 60.2


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 TraesCS1B01G458900 chr1B 672679489 672686127 6638 True 12224.000000 12224 100.000000 1 6639 1 chr1B.!!$R1 6638
1 TraesCS1B01G458900 chr1B 672332525 672338949 6424 False 11703.000000 11703 99.519000 1 6436 1 chr1B.!!$F3 6435
2 TraesCS1B01G458900 chr1B 180831711 180834880 3169 True 1374.333333 2878 88.525000 1718 4913 3 chr1B.!!$R3 3195
3 TraesCS1B01G458900 chr5B 647339694 647341188 1494 False 615.000000 839 90.319667 3419 4963 3 chr5B.!!$F1 1544

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
617 618 2.511373 CACCGGCAGCTAATCGCA 60.511 61.111 0.0 0.0 42.61 5.10 F
3157 3221 4.451629 TCAATCAGGTTTCCTCGTCTAC 57.548 45.455 0.0 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3157 3221 8.103948 ACAAGATTGATGAAGGAAAAGTACTG 57.896 34.615 0.0 0.0 0.0 2.74 R
5992 6109 1.879380 CCCATCAGTCGAGCAAAACAA 59.121 47.619 0.0 0.0 0.0 2.83 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
371 372 3.024547 CGTCCTCATAGTCCTTCTTGGA 58.975 50.000 0.00 0.00 43.86 3.53
617 618 2.511373 CACCGGCAGCTAATCGCA 60.511 61.111 0.00 0.00 42.61 5.10
3157 3221 4.451629 TCAATCAGGTTTCCTCGTCTAC 57.548 45.455 0.00 0.00 0.00 2.59
6440 6557 2.729378 GTGTACTTACACGGCCGAC 58.271 57.895 35.90 18.48 45.87 4.79
6441 6558 1.067199 GTGTACTTACACGGCCGACG 61.067 60.000 35.90 24.50 45.87 5.12
6442 6559 3.384738 GTGTACTTACACGGCCGACGA 62.385 57.143 35.90 13.30 45.87 4.20
6453 6570 3.103911 CCGACGACACGCTTGGTC 61.104 66.667 0.00 0.00 0.00 4.02
6454 6571 3.103911 CGACGACACGCTTGGTCC 61.104 66.667 0.00 0.00 31.55 4.46
6455 6572 2.028484 GACGACACGCTTGGTCCA 59.972 61.111 0.00 0.00 31.55 4.02
6456 6573 1.593209 GACGACACGCTTGGTCCAA 60.593 57.895 3.76 3.76 31.55 3.53
6457 6574 0.949105 GACGACACGCTTGGTCCAAT 60.949 55.000 4.34 0.00 31.55 3.16
6458 6575 1.227999 ACGACACGCTTGGTCCAATG 61.228 55.000 4.34 3.37 31.55 2.82
6459 6576 0.948623 CGACACGCTTGGTCCAATGA 60.949 55.000 4.34 0.00 31.55 2.57
6460 6577 0.798776 GACACGCTTGGTCCAATGAG 59.201 55.000 4.34 4.24 0.00 2.90
6461 6578 1.237285 ACACGCTTGGTCCAATGAGC 61.237 55.000 4.34 4.25 39.48 4.26
6462 6579 1.073025 ACGCTTGGTCCAATGAGCA 59.927 52.632 13.29 0.00 46.71 4.26
6467 6584 3.675995 TGGTCCAATGAGCAGCAAT 57.324 47.368 0.00 0.00 43.72 3.56
6468 6585 1.927487 TGGTCCAATGAGCAGCAATT 58.073 45.000 0.00 0.00 43.72 2.32
6469 6586 2.250031 TGGTCCAATGAGCAGCAATTT 58.750 42.857 0.00 0.00 43.72 1.82
6470 6587 2.028839 TGGTCCAATGAGCAGCAATTTG 60.029 45.455 0.00 0.00 43.72 2.32
6471 6588 1.997606 GTCCAATGAGCAGCAATTTGC 59.002 47.619 13.55 13.55 45.46 3.68
6482 6599 2.237393 GCAATTTGCAACCAAGGTGA 57.763 45.000 16.35 0.00 44.26 4.02
6483 6600 2.559440 GCAATTTGCAACCAAGGTGAA 58.441 42.857 16.35 0.00 44.26 3.18
6484 6601 2.545106 GCAATTTGCAACCAAGGTGAAG 59.455 45.455 16.35 0.00 44.26 3.02
6485 6602 2.531522 ATTTGCAACCAAGGTGAAGC 57.468 45.000 0.00 0.00 31.52 3.86
6486 6603 1.484038 TTTGCAACCAAGGTGAAGCT 58.516 45.000 0.00 0.00 31.52 3.74
6487 6604 0.746063 TTGCAACCAAGGTGAAGCTG 59.254 50.000 0.00 0.00 0.00 4.24
6488 6605 1.108727 TGCAACCAAGGTGAAGCTGG 61.109 55.000 11.25 0.00 36.24 4.85
6489 6606 0.823356 GCAACCAAGGTGAAGCTGGA 60.823 55.000 0.00 0.00 34.16 3.86
6490 6607 0.954452 CAACCAAGGTGAAGCTGGAC 59.046 55.000 0.00 0.00 34.16 4.02
6491 6608 0.535102 AACCAAGGTGAAGCTGGACG 60.535 55.000 0.00 0.00 34.16 4.79
6492 6609 1.672356 CCAAGGTGAAGCTGGACGG 60.672 63.158 0.00 0.00 31.38 4.79
6493 6610 1.371183 CAAGGTGAAGCTGGACGGA 59.629 57.895 0.00 0.00 0.00 4.69
6494 6611 0.250295 CAAGGTGAAGCTGGACGGAA 60.250 55.000 0.00 0.00 0.00 4.30
6495 6612 0.693049 AAGGTGAAGCTGGACGGAAT 59.307 50.000 0.00 0.00 0.00 3.01
6496 6613 0.036010 AGGTGAAGCTGGACGGAATG 60.036 55.000 0.00 0.00 0.00 2.67
6497 6614 0.321653 GGTGAAGCTGGACGGAATGT 60.322 55.000 0.00 0.00 0.00 2.71
6498 6615 1.523758 GTGAAGCTGGACGGAATGTT 58.476 50.000 0.00 0.00 0.00 2.71
6499 6616 1.197721 GTGAAGCTGGACGGAATGTTG 59.802 52.381 0.00 0.00 0.00 3.33
6500 6617 1.202758 TGAAGCTGGACGGAATGTTGT 60.203 47.619 0.00 0.00 0.00 3.32
6501 6618 1.880027 GAAGCTGGACGGAATGTTGTT 59.120 47.619 0.00 0.00 0.00 2.83
6502 6619 1.523758 AGCTGGACGGAATGTTGTTC 58.476 50.000 0.00 0.00 0.00 3.18
6503 6620 1.202758 AGCTGGACGGAATGTTGTTCA 60.203 47.619 0.00 0.00 0.00 3.18
6504 6621 1.606668 GCTGGACGGAATGTTGTTCAA 59.393 47.619 0.00 0.00 0.00 2.69
6505 6622 2.228822 GCTGGACGGAATGTTGTTCAAT 59.771 45.455 0.00 0.00 0.00 2.57
6506 6623 3.825308 CTGGACGGAATGTTGTTCAATG 58.175 45.455 0.00 0.00 0.00 2.82
6507 6624 3.481453 TGGACGGAATGTTGTTCAATGA 58.519 40.909 0.00 0.00 0.00 2.57
6508 6625 3.501828 TGGACGGAATGTTGTTCAATGAG 59.498 43.478 0.00 0.00 0.00 2.90
6509 6626 3.119849 GGACGGAATGTTGTTCAATGAGG 60.120 47.826 0.00 0.00 0.00 3.86
6510 6627 3.750371 ACGGAATGTTGTTCAATGAGGA 58.250 40.909 0.00 0.00 0.00 3.71
6511 6628 4.335416 ACGGAATGTTGTTCAATGAGGAT 58.665 39.130 0.00 0.00 0.00 3.24
6512 6629 4.766891 ACGGAATGTTGTTCAATGAGGATT 59.233 37.500 0.00 0.00 0.00 3.01
6513 6630 5.097529 CGGAATGTTGTTCAATGAGGATTG 58.902 41.667 0.00 0.00 40.47 2.67
6514 6631 5.413499 GGAATGTTGTTCAATGAGGATTGG 58.587 41.667 0.00 0.00 39.68 3.16
6515 6632 5.185635 GGAATGTTGTTCAATGAGGATTGGA 59.814 40.000 0.00 0.00 39.68 3.53
6516 6633 6.127253 GGAATGTTGTTCAATGAGGATTGGAT 60.127 38.462 0.00 0.00 39.68 3.41
6517 6634 5.902613 TGTTGTTCAATGAGGATTGGATC 57.097 39.130 0.00 0.00 39.68 3.36
6518 6635 4.395854 TGTTGTTCAATGAGGATTGGATCG 59.604 41.667 0.00 0.00 39.68 3.69
6519 6636 2.945008 TGTTCAATGAGGATTGGATCGC 59.055 45.455 0.00 0.00 39.68 4.58
6520 6637 3.209410 GTTCAATGAGGATTGGATCGCT 58.791 45.455 0.00 0.00 39.68 4.93
6521 6638 2.842457 TCAATGAGGATTGGATCGCTG 58.158 47.619 0.00 0.00 39.68 5.18
6522 6639 2.435437 TCAATGAGGATTGGATCGCTGA 59.565 45.455 0.00 0.00 39.68 4.26
6523 6640 2.806818 CAATGAGGATTGGATCGCTGAG 59.193 50.000 0.00 0.00 36.12 3.35
6524 6641 0.105593 TGAGGATTGGATCGCTGAGC 59.894 55.000 0.00 0.00 0.00 4.26
6535 6652 4.503314 GCTGAGCGCCCCAATTGC 62.503 66.667 2.29 0.00 0.00 3.56
6536 6653 2.753043 CTGAGCGCCCCAATTGCT 60.753 61.111 2.29 0.00 42.73 3.91
6537 6654 2.283101 TGAGCGCCCCAATTGCTT 60.283 55.556 2.29 0.00 39.49 3.91
6538 6655 2.275547 CTGAGCGCCCCAATTGCTTC 62.276 60.000 2.29 0.00 39.49 3.86
6539 6656 3.068729 GAGCGCCCCAATTGCTTCC 62.069 63.158 2.29 0.00 39.49 3.46
6540 6657 3.070576 GCGCCCCAATTGCTTCCT 61.071 61.111 0.00 0.00 0.00 3.36
6541 6658 2.887360 CGCCCCAATTGCTTCCTG 59.113 61.111 0.00 0.00 0.00 3.86
6542 6659 2.580815 GCCCCAATTGCTTCCTGC 59.419 61.111 0.00 0.00 43.25 4.85
6551 6668 2.749441 GCTTCCTGCAGGCACTCC 60.749 66.667 28.91 10.15 42.31 3.85
6552 6669 2.045536 CTTCCTGCAGGCACTCCC 60.046 66.667 28.91 0.00 34.60 4.30
6553 6670 3.635268 CTTCCTGCAGGCACTCCCC 62.635 68.421 28.91 0.00 34.60 4.81
6554 6671 4.980592 TCCTGCAGGCACTCCCCA 62.981 66.667 28.91 4.97 34.60 4.96
6555 6672 4.729918 CCTGCAGGCACTCCCCAC 62.730 72.222 22.33 0.00 34.60 4.61
6556 6673 4.729918 CTGCAGGCACTCCCCACC 62.730 72.222 5.57 0.00 34.60 4.61
6559 6676 4.394712 CAGGCACTCCCCACCGAC 62.395 72.222 0.00 0.00 34.60 4.79
6562 6679 4.394712 GCACTCCCCACCGACCTG 62.395 72.222 0.00 0.00 0.00 4.00
6563 6680 2.923035 CACTCCCCACCGACCTGT 60.923 66.667 0.00 0.00 0.00 4.00
6564 6681 2.603776 ACTCCCCACCGACCTGTC 60.604 66.667 0.00 0.00 0.00 3.51
6565 6682 2.283966 CTCCCCACCGACCTGTCT 60.284 66.667 0.00 0.00 0.00 3.41
6566 6683 1.000019 CTCCCCACCGACCTGTCTA 60.000 63.158 0.00 0.00 0.00 2.59
6567 6684 0.613853 CTCCCCACCGACCTGTCTAA 60.614 60.000 0.00 0.00 0.00 2.10
6568 6685 0.042131 TCCCCACCGACCTGTCTAAT 59.958 55.000 0.00 0.00 0.00 1.73
6569 6686 0.464452 CCCCACCGACCTGTCTAATC 59.536 60.000 0.00 0.00 0.00 1.75
6570 6687 1.191535 CCCACCGACCTGTCTAATCA 58.808 55.000 0.00 0.00 0.00 2.57
6571 6688 1.134788 CCCACCGACCTGTCTAATCAC 60.135 57.143 0.00 0.00 0.00 3.06
6572 6689 1.825474 CCACCGACCTGTCTAATCACT 59.175 52.381 0.00 0.00 0.00 3.41
6573 6690 2.417379 CCACCGACCTGTCTAATCACTG 60.417 54.545 0.00 0.00 0.00 3.66
6574 6691 1.204941 ACCGACCTGTCTAATCACTGC 59.795 52.381 0.00 0.00 0.00 4.40
6575 6692 1.471676 CCGACCTGTCTAATCACTGCC 60.472 57.143 0.00 0.00 0.00 4.85
6576 6693 1.471676 CGACCTGTCTAATCACTGCCC 60.472 57.143 0.00 0.00 0.00 5.36
6577 6694 0.912486 ACCTGTCTAATCACTGCCCC 59.088 55.000 0.00 0.00 0.00 5.80
6578 6695 1.207791 CCTGTCTAATCACTGCCCCT 58.792 55.000 0.00 0.00 0.00 4.79
6579 6696 1.561542 CCTGTCTAATCACTGCCCCTT 59.438 52.381 0.00 0.00 0.00 3.95
6580 6697 2.636830 CTGTCTAATCACTGCCCCTTG 58.363 52.381 0.00 0.00 0.00 3.61
6581 6698 1.340017 TGTCTAATCACTGCCCCTTGC 60.340 52.381 0.00 0.00 41.77 4.01
6582 6699 1.065126 GTCTAATCACTGCCCCTTGCT 60.065 52.381 0.00 0.00 42.00 3.91
6583 6700 1.065199 TCTAATCACTGCCCCTTGCTG 60.065 52.381 0.00 0.00 43.93 4.41
6584 6701 0.680921 TAATCACTGCCCCTTGCTGC 60.681 55.000 0.00 0.00 42.24 5.25
6585 6702 2.436596 AATCACTGCCCCTTGCTGCT 62.437 55.000 0.00 0.00 42.24 4.24
6586 6703 2.833604 ATCACTGCCCCTTGCTGCTC 62.834 60.000 0.00 0.00 42.24 4.26
6587 6704 3.573229 ACTGCCCCTTGCTGCTCA 61.573 61.111 0.00 0.00 42.24 4.26
6588 6705 3.060615 CTGCCCCTTGCTGCTCAC 61.061 66.667 0.00 0.00 42.00 3.51
6589 6706 4.666253 TGCCCCTTGCTGCTCACC 62.666 66.667 0.00 0.00 42.00 4.02
6590 6707 4.666253 GCCCCTTGCTGCTCACCA 62.666 66.667 0.00 0.00 36.87 4.17
6591 6708 2.674380 CCCCTTGCTGCTCACCAC 60.674 66.667 0.00 0.00 0.00 4.16
6592 6709 3.052082 CCCTTGCTGCTCACCACG 61.052 66.667 0.00 0.00 0.00 4.94
6593 6710 3.052082 CCTTGCTGCTCACCACGG 61.052 66.667 0.00 0.00 0.00 4.94
6594 6711 2.031012 CTTGCTGCTCACCACGGA 59.969 61.111 0.00 0.00 0.00 4.69
6595 6712 2.280797 TTGCTGCTCACCACGGAC 60.281 61.111 0.00 0.00 0.00 4.79
6596 6713 4.662961 TGCTGCTCACCACGGACG 62.663 66.667 0.00 0.00 0.00 4.79
6601 6718 4.436998 CTCACCACGGACGCCCTC 62.437 72.222 0.00 0.00 0.00 4.30
6602 6719 4.988716 TCACCACGGACGCCCTCT 62.989 66.667 0.00 0.00 0.00 3.69
6603 6720 4.003788 CACCACGGACGCCCTCTT 62.004 66.667 0.00 0.00 0.00 2.85
6604 6721 3.239253 ACCACGGACGCCCTCTTT 61.239 61.111 0.00 0.00 0.00 2.52
6605 6722 2.434359 CCACGGACGCCCTCTTTC 60.434 66.667 0.00 0.00 0.00 2.62
6606 6723 2.342279 CACGGACGCCCTCTTTCA 59.658 61.111 0.00 0.00 0.00 2.69
6607 6724 1.738099 CACGGACGCCCTCTTTCAG 60.738 63.158 0.00 0.00 0.00 3.02
6608 6725 2.815647 CGGACGCCCTCTTTCAGC 60.816 66.667 0.00 0.00 0.00 4.26
6609 6726 2.436824 GGACGCCCTCTTTCAGCC 60.437 66.667 0.00 0.00 0.00 4.85
6610 6727 2.347490 GACGCCCTCTTTCAGCCA 59.653 61.111 0.00 0.00 0.00 4.75
6611 6728 2.032681 ACGCCCTCTTTCAGCCAC 59.967 61.111 0.00 0.00 0.00 5.01
6612 6729 2.032528 CGCCCTCTTTCAGCCACA 59.967 61.111 0.00 0.00 0.00 4.17
6613 6730 2.037136 CGCCCTCTTTCAGCCACAG 61.037 63.158 0.00 0.00 0.00 3.66
6614 6731 2.338785 GCCCTCTTTCAGCCACAGC 61.339 63.158 0.00 0.00 40.32 4.40
6615 6732 1.073722 CCCTCTTTCAGCCACAGCA 59.926 57.895 0.00 0.00 43.56 4.41
6616 6733 1.239968 CCCTCTTTCAGCCACAGCAC 61.240 60.000 0.00 0.00 43.56 4.40
6617 6734 1.239968 CCTCTTTCAGCCACAGCACC 61.240 60.000 0.00 0.00 43.56 5.01
6618 6735 0.535780 CTCTTTCAGCCACAGCACCA 60.536 55.000 0.00 0.00 43.56 4.17
6619 6736 0.111061 TCTTTCAGCCACAGCACCAT 59.889 50.000 0.00 0.00 43.56 3.55
6620 6737 0.963962 CTTTCAGCCACAGCACCATT 59.036 50.000 0.00 0.00 43.56 3.16
6621 6738 1.342174 CTTTCAGCCACAGCACCATTT 59.658 47.619 0.00 0.00 43.56 2.32
6622 6739 0.961019 TTCAGCCACAGCACCATTTC 59.039 50.000 0.00 0.00 43.56 2.17
6623 6740 0.111061 TCAGCCACAGCACCATTTCT 59.889 50.000 0.00 0.00 43.56 2.52
6624 6741 0.242825 CAGCCACAGCACCATTTCTG 59.757 55.000 0.00 0.00 43.56 3.02
6625 6742 0.178981 AGCCACAGCACCATTTCTGT 60.179 50.000 0.00 0.00 43.67 3.41
6626 6743 0.675633 GCCACAGCACCATTTCTGTT 59.324 50.000 0.00 0.00 41.19 3.16
6627 6744 1.069049 GCCACAGCACCATTTCTGTTT 59.931 47.619 0.00 0.00 41.19 2.83
6628 6745 2.483538 GCCACAGCACCATTTCTGTTTT 60.484 45.455 0.00 0.00 41.19 2.43
6629 6746 3.795877 CCACAGCACCATTTCTGTTTTT 58.204 40.909 0.00 0.00 41.19 1.94
6630 6747 4.739137 GCCACAGCACCATTTCTGTTTTTA 60.739 41.667 0.00 0.00 41.19 1.52
6631 6748 5.540911 CCACAGCACCATTTCTGTTTTTAT 58.459 37.500 0.00 0.00 41.19 1.40
6632 6749 6.686630 CCACAGCACCATTTCTGTTTTTATA 58.313 36.000 0.00 0.00 41.19 0.98
6633 6750 7.151308 CCACAGCACCATTTCTGTTTTTATAA 58.849 34.615 0.00 0.00 41.19 0.98
6634 6751 7.818930 CCACAGCACCATTTCTGTTTTTATAAT 59.181 33.333 0.00 0.00 41.19 1.28
6635 6752 9.206870 CACAGCACCATTTCTGTTTTTATAATT 57.793 29.630 0.00 0.00 41.19 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
371 372 3.052869 ACAAAAAGAAGGTCCAAGGAGGT 60.053 43.478 0.00 0.00 39.02 3.85
3157 3221 8.103948 ACAAGATTGATGAAGGAAAAGTACTG 57.896 34.615 0.00 0.00 0.00 2.74
5989 6106 4.358851 CCATCAGTCGAGCAAAACAAAAA 58.641 39.130 0.00 0.00 0.00 1.94
5990 6107 3.243367 CCCATCAGTCGAGCAAAACAAAA 60.243 43.478 0.00 0.00 0.00 2.44
5991 6108 2.293122 CCCATCAGTCGAGCAAAACAAA 59.707 45.455 0.00 0.00 0.00 2.83
5992 6109 1.879380 CCCATCAGTCGAGCAAAACAA 59.121 47.619 0.00 0.00 0.00 2.83
6436 6553 3.103911 GACCAAGCGTGTCGTCGG 61.104 66.667 0.00 0.00 0.00 4.79
6437 6554 3.103911 GGACCAAGCGTGTCGTCG 61.104 66.667 0.00 0.00 33.46 5.12
6438 6555 0.949105 ATTGGACCAAGCGTGTCGTC 60.949 55.000 13.43 0.00 33.46 4.20
6439 6556 1.070786 ATTGGACCAAGCGTGTCGT 59.929 52.632 13.43 0.00 33.46 4.34
6440 6557 0.948623 TCATTGGACCAAGCGTGTCG 60.949 55.000 13.43 0.00 33.46 4.35
6441 6558 0.798776 CTCATTGGACCAAGCGTGTC 59.201 55.000 13.43 0.00 0.00 3.67
6442 6559 1.237285 GCTCATTGGACCAAGCGTGT 61.237 55.000 13.43 0.00 0.00 4.49
6443 6560 1.236616 TGCTCATTGGACCAAGCGTG 61.237 55.000 13.43 6.52 37.57 5.34
6444 6561 0.957395 CTGCTCATTGGACCAAGCGT 60.957 55.000 13.43 0.00 37.57 5.07
6445 6562 1.798735 CTGCTCATTGGACCAAGCG 59.201 57.895 13.43 6.58 37.57 4.68
6446 6563 1.246056 TGCTGCTCATTGGACCAAGC 61.246 55.000 13.43 11.23 35.31 4.01
6447 6564 1.250328 TTGCTGCTCATTGGACCAAG 58.750 50.000 13.43 5.31 0.00 3.61
6448 6565 1.927487 ATTGCTGCTCATTGGACCAA 58.073 45.000 9.92 9.92 0.00 3.67
6449 6566 1.927487 AATTGCTGCTCATTGGACCA 58.073 45.000 0.00 0.00 0.00 4.02
6450 6567 2.613691 CAAATTGCTGCTCATTGGACC 58.386 47.619 0.00 0.00 0.00 4.46
6451 6568 1.997606 GCAAATTGCTGCTCATTGGAC 59.002 47.619 11.19 0.00 40.96 4.02
6452 6569 1.619332 TGCAAATTGCTGCTCATTGGA 59.381 42.857 19.34 1.77 45.31 3.53
6453 6570 2.087501 TGCAAATTGCTGCTCATTGG 57.912 45.000 19.34 0.00 45.31 3.16
6454 6571 2.158841 GGTTGCAAATTGCTGCTCATTG 59.841 45.455 19.34 4.50 45.31 2.82
6455 6572 2.224329 TGGTTGCAAATTGCTGCTCATT 60.224 40.909 19.34 0.00 45.31 2.57
6456 6573 1.345089 TGGTTGCAAATTGCTGCTCAT 59.655 42.857 19.34 0.00 45.31 2.90
6457 6574 0.751452 TGGTTGCAAATTGCTGCTCA 59.249 45.000 19.34 9.20 45.31 4.26
6458 6575 1.796459 CTTGGTTGCAAATTGCTGCTC 59.204 47.619 19.34 6.84 45.31 4.26
6459 6576 1.541670 CCTTGGTTGCAAATTGCTGCT 60.542 47.619 19.34 0.00 45.31 4.24
6460 6577 0.869730 CCTTGGTTGCAAATTGCTGC 59.130 50.000 19.34 11.08 45.31 5.25
6461 6578 1.868498 CACCTTGGTTGCAAATTGCTG 59.132 47.619 19.34 2.43 45.31 4.41
6462 6579 1.761784 TCACCTTGGTTGCAAATTGCT 59.238 42.857 19.34 0.00 45.31 3.91
6463 6580 2.237393 TCACCTTGGTTGCAAATTGC 57.763 45.000 11.58 11.58 45.29 3.56
6464 6581 2.545106 GCTTCACCTTGGTTGCAAATTG 59.455 45.455 0.00 0.00 0.00 2.32
6465 6582 2.435437 AGCTTCACCTTGGTTGCAAATT 59.565 40.909 0.00 0.00 0.00 1.82
6466 6583 2.041701 AGCTTCACCTTGGTTGCAAAT 58.958 42.857 0.00 0.00 0.00 2.32
6467 6584 1.136695 CAGCTTCACCTTGGTTGCAAA 59.863 47.619 0.00 0.00 0.00 3.68
6468 6585 0.746063 CAGCTTCACCTTGGTTGCAA 59.254 50.000 0.00 0.00 0.00 4.08
6469 6586 1.108727 CCAGCTTCACCTTGGTTGCA 61.109 55.000 10.30 0.00 0.00 4.08
6470 6587 0.823356 TCCAGCTTCACCTTGGTTGC 60.823 55.000 0.00 0.00 33.65 4.17
6471 6588 0.954452 GTCCAGCTTCACCTTGGTTG 59.046 55.000 0.00 0.00 33.65 3.77
6472 6589 0.535102 CGTCCAGCTTCACCTTGGTT 60.535 55.000 0.00 0.00 33.65 3.67
6473 6590 1.071471 CGTCCAGCTTCACCTTGGT 59.929 57.895 0.00 0.00 33.65 3.67
6474 6591 1.672356 CCGTCCAGCTTCACCTTGG 60.672 63.158 0.00 0.00 0.00 3.61
6475 6592 0.250295 TTCCGTCCAGCTTCACCTTG 60.250 55.000 0.00 0.00 0.00 3.61
6476 6593 0.693049 ATTCCGTCCAGCTTCACCTT 59.307 50.000 0.00 0.00 0.00 3.50
6477 6594 0.036010 CATTCCGTCCAGCTTCACCT 60.036 55.000 0.00 0.00 0.00 4.00
6478 6595 0.321653 ACATTCCGTCCAGCTTCACC 60.322 55.000 0.00 0.00 0.00 4.02
6479 6596 1.197721 CAACATTCCGTCCAGCTTCAC 59.802 52.381 0.00 0.00 0.00 3.18
6480 6597 1.202758 ACAACATTCCGTCCAGCTTCA 60.203 47.619 0.00 0.00 0.00 3.02
6481 6598 1.523758 ACAACATTCCGTCCAGCTTC 58.476 50.000 0.00 0.00 0.00 3.86
6482 6599 1.880027 GAACAACATTCCGTCCAGCTT 59.120 47.619 0.00 0.00 0.00 3.74
6483 6600 1.202758 TGAACAACATTCCGTCCAGCT 60.203 47.619 0.00 0.00 0.00 4.24
6484 6601 1.234821 TGAACAACATTCCGTCCAGC 58.765 50.000 0.00 0.00 0.00 4.85
6485 6602 3.501828 TCATTGAACAACATTCCGTCCAG 59.498 43.478 0.00 0.00 0.00 3.86
6486 6603 3.481453 TCATTGAACAACATTCCGTCCA 58.519 40.909 0.00 0.00 0.00 4.02
6487 6604 3.119849 CCTCATTGAACAACATTCCGTCC 60.120 47.826 0.00 0.00 0.00 4.79
6488 6605 3.751175 TCCTCATTGAACAACATTCCGTC 59.249 43.478 0.00 0.00 0.00 4.79
6489 6606 3.750371 TCCTCATTGAACAACATTCCGT 58.250 40.909 0.00 0.00 0.00 4.69
6490 6607 4.970662 ATCCTCATTGAACAACATTCCG 57.029 40.909 0.00 0.00 0.00 4.30
6491 6608 5.185635 TCCAATCCTCATTGAACAACATTCC 59.814 40.000 0.00 0.00 41.97 3.01
6492 6609 6.271488 TCCAATCCTCATTGAACAACATTC 57.729 37.500 0.00 0.00 41.97 2.67
6493 6610 6.405065 CGATCCAATCCTCATTGAACAACATT 60.405 38.462 0.00 0.00 41.97 2.71
6494 6611 5.066893 CGATCCAATCCTCATTGAACAACAT 59.933 40.000 0.00 0.00 41.97 2.71
6495 6612 4.395854 CGATCCAATCCTCATTGAACAACA 59.604 41.667 0.00 0.00 41.97 3.33
6496 6613 4.731773 GCGATCCAATCCTCATTGAACAAC 60.732 45.833 0.00 0.00 41.97 3.32
6497 6614 3.378112 GCGATCCAATCCTCATTGAACAA 59.622 43.478 0.00 0.00 41.97 2.83
6498 6615 2.945008 GCGATCCAATCCTCATTGAACA 59.055 45.455 0.00 0.00 41.97 3.18
6499 6616 3.003068 CAGCGATCCAATCCTCATTGAAC 59.997 47.826 0.00 0.00 41.97 3.18
6500 6617 3.118298 TCAGCGATCCAATCCTCATTGAA 60.118 43.478 0.00 0.00 41.97 2.69
6501 6618 2.435437 TCAGCGATCCAATCCTCATTGA 59.565 45.455 0.00 0.00 41.97 2.57
6502 6619 2.806818 CTCAGCGATCCAATCCTCATTG 59.193 50.000 0.00 0.00 39.45 2.82
6503 6620 2.809665 GCTCAGCGATCCAATCCTCATT 60.810 50.000 0.00 0.00 0.00 2.57
6504 6621 1.270732 GCTCAGCGATCCAATCCTCAT 60.271 52.381 0.00 0.00 0.00 2.90
6505 6622 0.105593 GCTCAGCGATCCAATCCTCA 59.894 55.000 0.00 0.00 0.00 3.86
6506 6623 2.911594 GCTCAGCGATCCAATCCTC 58.088 57.895 0.00 0.00 0.00 3.71
6519 6636 2.275547 GAAGCAATTGGGGCGCTCAG 62.276 60.000 10.74 0.00 34.11 3.35
6520 6637 2.283101 AAGCAATTGGGGCGCTCA 60.283 55.556 10.74 4.50 34.11 4.26
6521 6638 2.491621 GAAGCAATTGGGGCGCTC 59.508 61.111 7.64 1.18 34.11 5.03
6522 6639 3.070576 GGAAGCAATTGGGGCGCT 61.071 61.111 7.64 0.00 37.68 5.92
6523 6640 3.070576 AGGAAGCAATTGGGGCGC 61.071 61.111 7.72 0.00 36.08 6.53
6524 6641 2.887360 CAGGAAGCAATTGGGGCG 59.113 61.111 7.72 0.00 36.08 6.13
6525 6642 2.580815 GCAGGAAGCAATTGGGGC 59.419 61.111 7.72 0.00 44.79 5.80
6534 6651 2.749441 GGAGTGCCTGCAGGAAGC 60.749 66.667 37.21 23.03 45.96 3.86
6535 6652 2.045536 GGGAGTGCCTGCAGGAAG 60.046 66.667 37.21 10.80 37.39 3.46
6536 6653 3.650950 GGGGAGTGCCTGCAGGAA 61.651 66.667 37.21 25.79 37.39 3.36
6537 6654 4.980592 TGGGGAGTGCCTGCAGGA 62.981 66.667 37.21 18.42 37.39 3.86
6538 6655 4.729918 GTGGGGAGTGCCTGCAGG 62.730 72.222 29.34 29.34 38.53 4.85
6539 6656 4.729918 GGTGGGGAGTGCCTGCAG 62.730 72.222 6.78 6.78 0.00 4.41
6542 6659 4.394712 GTCGGTGGGGAGTGCCTG 62.395 72.222 0.00 0.00 0.00 4.85
6545 6662 4.394712 CAGGTCGGTGGGGAGTGC 62.395 72.222 0.00 0.00 0.00 4.40
6546 6663 2.923035 ACAGGTCGGTGGGGAGTG 60.923 66.667 0.00 0.00 0.00 3.51
6547 6664 1.797018 TAGACAGGTCGGTGGGGAGT 61.797 60.000 0.00 0.00 34.09 3.85
6548 6665 0.613853 TTAGACAGGTCGGTGGGGAG 60.614 60.000 0.00 0.00 34.09 4.30
6549 6666 0.042131 ATTAGACAGGTCGGTGGGGA 59.958 55.000 0.00 0.00 34.09 4.81
6550 6667 0.464452 GATTAGACAGGTCGGTGGGG 59.536 60.000 0.00 0.00 34.09 4.96
6551 6668 1.134788 GTGATTAGACAGGTCGGTGGG 60.135 57.143 0.00 0.00 34.09 4.61
6552 6669 1.825474 AGTGATTAGACAGGTCGGTGG 59.175 52.381 0.00 0.00 34.09 4.61
6553 6670 2.881074 CAGTGATTAGACAGGTCGGTG 58.119 52.381 0.00 0.00 34.09 4.94
6554 6671 1.204941 GCAGTGATTAGACAGGTCGGT 59.795 52.381 0.00 0.00 34.09 4.69
6555 6672 1.471676 GGCAGTGATTAGACAGGTCGG 60.472 57.143 0.00 0.00 34.09 4.79
6556 6673 1.471676 GGGCAGTGATTAGACAGGTCG 60.472 57.143 0.00 0.00 34.09 4.79
6557 6674 1.134371 GGGGCAGTGATTAGACAGGTC 60.134 57.143 0.00 0.00 0.00 3.85
6558 6675 0.912486 GGGGCAGTGATTAGACAGGT 59.088 55.000 0.00 0.00 0.00 4.00
6559 6676 1.207791 AGGGGCAGTGATTAGACAGG 58.792 55.000 0.00 0.00 0.00 4.00
6560 6677 2.636830 CAAGGGGCAGTGATTAGACAG 58.363 52.381 0.00 0.00 0.00 3.51
6561 6678 1.340017 GCAAGGGGCAGTGATTAGACA 60.340 52.381 0.00 0.00 43.97 3.41
6562 6679 1.383523 GCAAGGGGCAGTGATTAGAC 58.616 55.000 0.00 0.00 43.97 2.59
6563 6680 3.882131 GCAAGGGGCAGTGATTAGA 57.118 52.632 0.00 0.00 43.97 2.10
6573 6690 4.666253 TGGTGAGCAGCAAGGGGC 62.666 66.667 0.00 0.00 45.30 5.80
6574 6691 2.674380 GTGGTGAGCAGCAAGGGG 60.674 66.667 3.70 0.00 40.82 4.79
6575 6692 3.052082 CGTGGTGAGCAGCAAGGG 61.052 66.667 3.70 0.00 40.82 3.95
6577 6694 2.031012 TCCGTGGTGAGCAGCAAG 59.969 61.111 3.70 6.30 40.82 4.01
6578 6695 2.280797 GTCCGTGGTGAGCAGCAA 60.281 61.111 3.70 0.00 40.82 3.91
6579 6696 4.662961 CGTCCGTGGTGAGCAGCA 62.663 66.667 0.00 0.00 36.34 4.41
6584 6701 4.436998 GAGGGCGTCCGTGGTGAG 62.437 72.222 0.00 0.00 38.33 3.51
6585 6702 4.988716 AGAGGGCGTCCGTGGTGA 62.989 66.667 0.00 0.00 38.33 4.02
6586 6703 3.530910 AAAGAGGGCGTCCGTGGTG 62.531 63.158 0.00 0.00 38.33 4.17
6587 6704 3.236003 GAAAGAGGGCGTCCGTGGT 62.236 63.158 0.00 0.00 38.33 4.16
6588 6705 2.434359 GAAAGAGGGCGTCCGTGG 60.434 66.667 0.00 0.00 38.33 4.94
6589 6706 1.738099 CTGAAAGAGGGCGTCCGTG 60.738 63.158 0.00 0.00 38.33 4.94
6590 6707 2.657237 CTGAAAGAGGGCGTCCGT 59.343 61.111 0.00 0.00 38.33 4.69
6591 6708 2.815647 GCTGAAAGAGGGCGTCCG 60.816 66.667 0.00 0.00 38.33 4.79
6592 6709 2.436824 GGCTGAAAGAGGGCGTCC 60.437 66.667 0.00 0.00 34.07 4.79
6593 6710 2.035442 GTGGCTGAAAGAGGGCGTC 61.035 63.158 0.00 0.00 34.07 5.19
6594 6711 2.032681 GTGGCTGAAAGAGGGCGT 59.967 61.111 0.00 0.00 34.07 5.68
6595 6712 2.032528 TGTGGCTGAAAGAGGGCG 59.967 61.111 0.00 0.00 34.07 6.13
6596 6713 2.338785 GCTGTGGCTGAAAGAGGGC 61.339 63.158 0.00 0.00 34.07 5.19
6597 6714 1.073722 TGCTGTGGCTGAAAGAGGG 59.926 57.895 0.00 0.00 39.59 4.30
6598 6715 1.239968 GGTGCTGTGGCTGAAAGAGG 61.240 60.000 0.00 0.00 39.59 3.69
6599 6716 0.535780 TGGTGCTGTGGCTGAAAGAG 60.536 55.000 0.00 0.00 39.59 2.85
6600 6717 0.111061 ATGGTGCTGTGGCTGAAAGA 59.889 50.000 0.00 0.00 39.59 2.52
6601 6718 0.963962 AATGGTGCTGTGGCTGAAAG 59.036 50.000 0.00 0.00 39.59 2.62
6602 6719 1.340889 GAAATGGTGCTGTGGCTGAAA 59.659 47.619 0.00 0.00 39.59 2.69
6603 6720 0.961019 GAAATGGTGCTGTGGCTGAA 59.039 50.000 0.00 0.00 39.59 3.02
6604 6721 0.111061 AGAAATGGTGCTGTGGCTGA 59.889 50.000 0.00 0.00 39.59 4.26
6605 6722 0.242825 CAGAAATGGTGCTGTGGCTG 59.757 55.000 0.00 0.00 39.59 4.85
6606 6723 0.178981 ACAGAAATGGTGCTGTGGCT 60.179 50.000 0.00 0.00 43.26 4.75
6607 6724 0.675633 AACAGAAATGGTGCTGTGGC 59.324 50.000 0.00 0.00 44.06 5.01
6608 6725 3.457610 AAAACAGAAATGGTGCTGTGG 57.542 42.857 0.00 0.00 44.06 4.17
6609 6726 8.761575 ATTATAAAAACAGAAATGGTGCTGTG 57.238 30.769 0.00 0.00 44.06 3.66


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

AutoCloner maintained by Alex Coulton.