Multiple sequence alignment - TraesCS1B01G457600

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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 TraesCS1B01G457600 chr1B 100.000 6639 0 0 1 6639 672332533 672339171 0.000000e+00 12261.0
1 TraesCS1B01G457600 chr1B 99.518 6436 4 2 1 6417 672686119 672679692 0.000000e+00 11688.0
2 TraesCS1B01G457600 chr1B 93.624 1929 120 2 2355 4282 180834316 180832390 0.000000e+00 2878.0
3 TraesCS1B01G457600 chr1B 90.712 646 44 4 4280 4913 180832352 180831711 0.000000e+00 846.0
4 TraesCS1B01G457600 chr1B 81.239 581 33 24 1718 2243 180834880 180834321 3.730000e-107 399.0
5 TraesCS1B01G457600 chr1B 99.074 108 1 0 2246 2353 619184393 619184500 1.890000e-45 195.0
6 TraesCS1B01G457600 chr1B 87.069 116 11 1 1718 1833 40819398 40819287 1.940000e-25 128.0
7 TraesCS1B01G457600 chr1B 72.368 380 105 0 3005 3384 464119073 464119452 3.250000e-23 121.0
8 TraesCS1B01G457600 chr1B 83.516 91 3 5 1873 1954 40819217 40819130 2.570000e-09 75.0
9 TraesCS1B01G457600 chr5B 88.793 696 62 8 4280 4963 647340497 647341188 0.000000e+00 839.0
10 TraesCS1B01G457600 chr5B 89.635 521 51 2 3419 3939 647339694 647340211 0.000000e+00 660.0
11 TraesCS1B01G457600 chr5B 92.531 241 18 0 4042 4282 647340219 647340459 4.930000e-91 346.0
12 TraesCS1B01G457600 chrUn 100.000 363 0 0 1 363 479027218 479027580 0.000000e+00 671.0
13 TraesCS1B01G457600 chrUn 78.947 418 26 26 1718 2080 70386322 70385912 1.860000e-55 228.0
14 TraesCS1B01G457600 chrUn 99.074 108 1 0 2246 2353 182426533 182426426 1.890000e-45 195.0
15 TraesCS1B01G457600 chrUn 99.065 107 1 0 2247 2353 231559222 231559328 6.790000e-45 193.0
16 TraesCS1B01G457600 chrUn 99.065 107 1 0 2247 2353 273328905 273328799 6.790000e-45 193.0
17 TraesCS1B01G457600 chr4A 90.066 453 41 4 1 452 440132666 440132217 9.590000e-163 584.0
18 TraesCS1B01G457600 chr3D 90.044 452 42 2 1 452 462785005 462784557 3.450000e-162 582.0
19 TraesCS1B01G457600 chr3D 83.230 322 29 16 453 750 248813003 248812683 8.480000e-69 272.0
20 TraesCS1B01G457600 chr3D 85.714 63 9 0 4402 4464 590247073 590247135 4.300000e-07 67.6
21 TraesCS1B01G457600 chr3A 89.301 458 45 4 1 458 605515838 605515385 7.470000e-159 571.0
22 TraesCS1B01G457600 chr3A 81.988 322 33 16 453 750 307917664 307917344 3.970000e-62 250.0
23 TraesCS1B01G457600 chr2D 89.159 452 46 1 1 452 310987507 310987059 1.620000e-155 560.0
24 TraesCS1B01G457600 chr2A 89.438 445 43 2 10 453 305416534 305416093 5.810000e-155 558.0
25 TraesCS1B01G457600 chr2A 88.962 453 44 5 1 452 487971637 487972084 7.520000e-154 555.0
26 TraesCS1B01G457600 chr6D 88.962 453 42 5 1 452 405276686 405276241 2.710000e-153 553.0
27 TraesCS1B01G457600 chr6D 85.714 63 9 0 4402 4464 364110157 364110219 4.300000e-07 67.6
28 TraesCS1B01G457600 chr6D 93.182 44 3 0 4402 4445 14483316 14483359 1.550000e-06 65.8
29 TraesCS1B01G457600 chr1D 90.464 388 20 7 916 1296 180807364 180806987 4.620000e-136 496.0
30 TraesCS1B01G457600 chr1D 78.261 276 14 23 1718 1954 25388120 25387852 1.160000e-27 135.0
31 TraesCS1B01G457600 chr1D 89.524 105 7 1 1729 1833 25445598 25445498 5.400000e-26 130.0
32 TraesCS1B01G457600 chr1D 85.714 63 9 0 4402 4464 50920508 50920570 4.300000e-07 67.6
33 TraesCS1B01G457600 chr3B 86.341 205 25 3 548 750 348491174 348490971 3.120000e-53 220.0
34 TraesCS1B01G457600 chr3B 91.667 48 4 0 3393 3440 766171429 766171476 4.300000e-07 67.6
35 TraesCS1B01G457600 chr7D 99.074 108 1 0 2246 2353 6943012 6942905 1.890000e-45 195.0
36 TraesCS1B01G457600 chr7A 99.074 108 1 0 2246 2353 60219827 60219934 1.890000e-45 195.0
37 TraesCS1B01G457600 chr2B 99.074 108 1 0 2246 2353 234530222 234530329 1.890000e-45 195.0
38 TraesCS1B01G457600 chr2B 99.074 108 1 0 2246 2353 449208391 449208498 1.890000e-45 195.0
39 TraesCS1B01G457600 chr6B 87.838 148 11 3 1093 1240 285560354 285560494 4.120000e-37 167.0
40 TraesCS1B01G457600 chr7B 76.647 167 27 10 4057 4217 746871959 746871799 1.530000e-11 82.4
41 TraesCS1B01G457600 chr5A 76.423 123 26 3 3329 3449 71139372 71139251 5.560000e-06 63.9
42 TraesCS1B01G457600 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 TraesCS1B01G457600 chr1B 672332533 672339171 6638 False 12261.000000 12261 100.000000 1 6639 1 chr1B.!!$F3 6638
1 TraesCS1B01G457600 chr1B 672679692 672686119 6427 True 11688.000000 11688 99.518000 1 6417 1 chr1B.!!$R1 6416
2 TraesCS1B01G457600 chr1B 180831711 180834880 3169 True 1374.333333 2878 88.525000 1718 4913 3 chr1B.!!$R3 3195
3 TraesCS1B01G457600 chr5B 647339694 647341188 1494 False 615.000000 839 90.319667 3419 4963 3 chr5B.!!$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
363 364 2.101582 CGTCCTCATAGTCCTTCTTGGG 59.898 54.545 0.0 0.00 36.20 4.12 F
609 610 3.272334 CACCGGCAGCTAATCGCC 61.272 66.667 0.0 2.68 45.28 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2916 2972 5.824624 GCTTATCAATCAGGATGGAGTTTGA 59.175 40.000 0.0 0.0 36.16 2.69 R
6423 6551 3.703420 ACGGAGTATAAAGCTAACGCAG 58.297 45.455 0.0 0.0 41.94 5.18 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
363 364 2.101582 CGTCCTCATAGTCCTTCTTGGG 59.898 54.545 0.00 0.00 36.20 4.12
609 610 3.272334 CACCGGCAGCTAATCGCC 61.272 66.667 0.00 2.68 45.28 5.54
851 852 9.757227 TTTCTTTGTTTTTAGAGAGAGAGAGAG 57.243 33.333 0.00 0.00 0.00 3.20
2916 2972 0.540923 GGTTGAGCCTCTCAGCATCT 59.459 55.000 11.67 0.00 42.19 2.90
6424 6552 3.853475 GTGTACTTACACGGGTAATGCT 58.147 45.455 11.37 0.00 45.87 3.79
6425 6553 3.615496 GTGTACTTACACGGGTAATGCTG 59.385 47.826 11.37 1.64 45.87 4.41
6426 6554 1.734163 ACTTACACGGGTAATGCTGC 58.266 50.000 11.37 0.00 38.72 5.25
6427 6555 0.650512 CTTACACGGGTAATGCTGCG 59.349 55.000 11.37 0.00 38.72 5.18
6428 6556 0.037139 TTACACGGGTAATGCTGCGT 60.037 50.000 6.06 0.00 34.63 5.24
6429 6557 0.037139 TACACGGGTAATGCTGCGTT 60.037 50.000 12.30 12.30 0.00 4.84
6430 6558 0.037139 ACACGGGTAATGCTGCGTTA 60.037 50.000 10.13 10.13 0.00 3.18
6431 6559 0.650512 CACGGGTAATGCTGCGTTAG 59.349 55.000 14.25 6.24 0.00 2.34
6444 6572 3.703420 CTGCGTTAGCTTTATACTCCGT 58.297 45.455 0.00 0.00 45.42 4.69
6445 6573 4.852138 CTGCGTTAGCTTTATACTCCGTA 58.148 43.478 0.00 0.00 45.42 4.02
6446 6574 5.443185 TGCGTTAGCTTTATACTCCGTAT 57.557 39.130 0.00 0.00 45.42 3.06
6447 6575 5.835257 TGCGTTAGCTTTATACTCCGTATT 58.165 37.500 0.00 0.00 45.42 1.89
6448 6576 6.275335 TGCGTTAGCTTTATACTCCGTATTT 58.725 36.000 0.00 0.00 45.42 1.40
6449 6577 6.199531 TGCGTTAGCTTTATACTCCGTATTTG 59.800 38.462 0.00 0.00 45.42 2.32
6450 6578 6.418819 GCGTTAGCTTTATACTCCGTATTTGA 59.581 38.462 0.00 0.00 41.01 2.69
6451 6579 7.043192 GCGTTAGCTTTATACTCCGTATTTGAA 60.043 37.037 0.00 0.00 41.01 2.69
6452 6580 8.264632 CGTTAGCTTTATACTCCGTATTTGAAC 58.735 37.037 0.00 0.00 30.79 3.18
6453 6581 9.090692 GTTAGCTTTATACTCCGTATTTGAACA 57.909 33.333 0.00 0.00 30.79 3.18
6454 6582 9.656040 TTAGCTTTATACTCCGTATTTGAACAA 57.344 29.630 0.00 0.00 30.79 2.83
6455 6583 8.197988 AGCTTTATACTCCGTATTTGAACAAG 57.802 34.615 0.00 0.00 30.79 3.16
6456 6584 7.822822 AGCTTTATACTCCGTATTTGAACAAGT 59.177 33.333 0.00 0.00 30.79 3.16
6457 6585 9.090692 GCTTTATACTCCGTATTTGAACAAGTA 57.909 33.333 0.00 0.00 30.79 2.24
6461 6589 6.342338 ACTCCGTATTTGAACAAGTAGAGT 57.658 37.500 0.00 0.00 0.00 3.24
6462 6590 6.756221 ACTCCGTATTTGAACAAGTAGAGTT 58.244 36.000 0.00 0.00 0.00 3.01
6463 6591 7.215085 ACTCCGTATTTGAACAAGTAGAGTTT 58.785 34.615 0.00 0.00 0.00 2.66
6464 6592 8.362639 ACTCCGTATTTGAACAAGTAGAGTTTA 58.637 33.333 0.00 0.00 0.00 2.01
6465 6593 9.367444 CTCCGTATTTGAACAAGTAGAGTTTAT 57.633 33.333 0.00 0.00 0.00 1.40
6466 6594 9.715121 TCCGTATTTGAACAAGTAGAGTTTATT 57.285 29.630 0.00 0.00 0.00 1.40
6491 6619 4.935885 TGTTTGGTTGTGAATTTGTTGC 57.064 36.364 0.00 0.00 0.00 4.17
6492 6620 4.318332 TGTTTGGTTGTGAATTTGTTGCA 58.682 34.783 0.00 0.00 0.00 4.08
6493 6621 4.391216 TGTTTGGTTGTGAATTTGTTGCAG 59.609 37.500 0.00 0.00 0.00 4.41
6494 6622 4.462508 TTGGTTGTGAATTTGTTGCAGA 57.537 36.364 0.00 0.00 0.00 4.26
6495 6623 4.669206 TGGTTGTGAATTTGTTGCAGAT 57.331 36.364 0.00 0.00 0.00 2.90
6496 6624 5.021033 TGGTTGTGAATTTGTTGCAGATT 57.979 34.783 0.00 0.00 0.00 2.40
6497 6625 5.049167 TGGTTGTGAATTTGTTGCAGATTC 58.951 37.500 5.71 5.71 36.10 2.52
6498 6626 5.049167 GGTTGTGAATTTGTTGCAGATTCA 58.951 37.500 9.92 9.92 40.81 2.57
6499 6627 5.176223 GGTTGTGAATTTGTTGCAGATTCAG 59.824 40.000 13.11 0.00 42.66 3.02
6500 6628 5.518848 TGTGAATTTGTTGCAGATTCAGT 57.481 34.783 13.11 0.00 42.66 3.41
6501 6629 6.631971 TGTGAATTTGTTGCAGATTCAGTA 57.368 33.333 13.11 5.66 42.66 2.74
6502 6630 6.671190 TGTGAATTTGTTGCAGATTCAGTAG 58.329 36.000 13.11 0.00 42.66 2.57
6503 6631 5.570589 GTGAATTTGTTGCAGATTCAGTAGC 59.429 40.000 13.11 1.92 42.66 3.58
6504 6632 5.474532 TGAATTTGTTGCAGATTCAGTAGCT 59.525 36.000 9.92 0.00 39.11 3.32
6505 6633 5.557891 ATTTGTTGCAGATTCAGTAGCTC 57.442 39.130 0.00 0.00 0.00 4.09
6506 6634 2.977914 TGTTGCAGATTCAGTAGCTCC 58.022 47.619 0.00 0.00 0.00 4.70
6507 6635 2.302733 TGTTGCAGATTCAGTAGCTCCA 59.697 45.455 0.00 0.00 0.00 3.86
6508 6636 3.054875 TGTTGCAGATTCAGTAGCTCCAT 60.055 43.478 0.00 0.00 0.00 3.41
6509 6637 3.189618 TGCAGATTCAGTAGCTCCATG 57.810 47.619 0.00 0.00 0.00 3.66
6510 6638 1.872313 GCAGATTCAGTAGCTCCATGC 59.128 52.381 0.00 0.00 43.29 4.06
6511 6639 2.744166 GCAGATTCAGTAGCTCCATGCA 60.744 50.000 0.00 0.00 45.94 3.96
6512 6640 3.741249 CAGATTCAGTAGCTCCATGCAT 58.259 45.455 0.00 0.00 45.94 3.96
6513 6641 3.747010 CAGATTCAGTAGCTCCATGCATC 59.253 47.826 0.00 0.00 45.94 3.91
6514 6642 2.229675 TTCAGTAGCTCCATGCATCG 57.770 50.000 0.00 0.00 45.94 3.84
6515 6643 1.402787 TCAGTAGCTCCATGCATCGA 58.597 50.000 0.00 0.00 45.94 3.59
6516 6644 1.966354 TCAGTAGCTCCATGCATCGAT 59.034 47.619 0.00 0.00 45.94 3.59
6517 6645 2.029560 TCAGTAGCTCCATGCATCGATC 60.030 50.000 0.00 0.00 45.94 3.69
6518 6646 2.029200 CAGTAGCTCCATGCATCGATCT 60.029 50.000 0.00 0.00 45.94 2.75
6519 6647 3.192212 CAGTAGCTCCATGCATCGATCTA 59.808 47.826 0.00 0.00 45.94 1.98
6520 6648 3.829026 AGTAGCTCCATGCATCGATCTAA 59.171 43.478 6.47 0.00 45.94 2.10
6521 6649 3.037431 AGCTCCATGCATCGATCTAAC 57.963 47.619 0.00 0.00 45.94 2.34
6522 6650 2.366590 AGCTCCATGCATCGATCTAACA 59.633 45.455 0.00 0.00 45.94 2.41
6523 6651 3.133691 GCTCCATGCATCGATCTAACAA 58.866 45.455 0.00 0.00 42.31 2.83
6524 6652 3.561310 GCTCCATGCATCGATCTAACAAA 59.439 43.478 0.00 0.00 42.31 2.83
6525 6653 4.035558 GCTCCATGCATCGATCTAACAAAA 59.964 41.667 0.00 0.00 42.31 2.44
6526 6654 5.449041 GCTCCATGCATCGATCTAACAAAAA 60.449 40.000 0.00 0.00 42.31 1.94
6561 6689 5.861222 TGCTGTACAACATGTTATCAGTG 57.139 39.130 24.26 12.63 30.86 3.66
6562 6690 5.304778 TGCTGTACAACATGTTATCAGTGT 58.695 37.500 24.26 16.49 30.86 3.55
6563 6691 6.459923 TGCTGTACAACATGTTATCAGTGTA 58.540 36.000 24.26 15.73 30.86 2.90
6564 6692 6.589907 TGCTGTACAACATGTTATCAGTGTAG 59.410 38.462 24.26 16.14 30.86 2.74
6565 6693 6.811665 GCTGTACAACATGTTATCAGTGTAGA 59.188 38.462 24.26 15.59 30.86 2.59
6566 6694 7.330946 GCTGTACAACATGTTATCAGTGTAGAA 59.669 37.037 24.26 10.82 30.86 2.10
6567 6695 8.757164 TGTACAACATGTTATCAGTGTAGAAG 57.243 34.615 11.53 0.00 0.00 2.85
6568 6696 8.364894 TGTACAACATGTTATCAGTGTAGAAGT 58.635 33.333 11.53 2.82 0.00 3.01
6569 6697 9.204570 GTACAACATGTTATCAGTGTAGAAGTT 57.795 33.333 11.53 0.00 0.00 2.66
6570 6698 8.311650 ACAACATGTTATCAGTGTAGAAGTTC 57.688 34.615 11.53 0.00 0.00 3.01
6571 6699 7.387948 ACAACATGTTATCAGTGTAGAAGTTCC 59.612 37.037 11.53 0.00 0.00 3.62
6572 6700 6.100004 ACATGTTATCAGTGTAGAAGTTCCG 58.900 40.000 0.00 0.00 0.00 4.30
6573 6701 5.717078 TGTTATCAGTGTAGAAGTTCCGT 57.283 39.130 0.00 0.00 0.00 4.69
6574 6702 5.706916 TGTTATCAGTGTAGAAGTTCCGTC 58.293 41.667 0.00 0.00 0.00 4.79
6575 6703 5.475909 TGTTATCAGTGTAGAAGTTCCGTCT 59.524 40.000 0.00 0.00 0.00 4.18
6576 6704 6.015688 TGTTATCAGTGTAGAAGTTCCGTCTT 60.016 38.462 0.00 0.00 0.00 3.01
6577 6705 4.238761 TCAGTGTAGAAGTTCCGTCTTG 57.761 45.455 0.00 0.00 0.00 3.02
6578 6706 3.887110 TCAGTGTAGAAGTTCCGTCTTGA 59.113 43.478 0.00 0.00 0.00 3.02
6579 6707 3.982058 CAGTGTAGAAGTTCCGTCTTGAC 59.018 47.826 0.00 0.00 0.00 3.18
6580 6708 3.890147 AGTGTAGAAGTTCCGTCTTGACT 59.110 43.478 0.00 0.00 0.00 3.41
6581 6709 4.341520 AGTGTAGAAGTTCCGTCTTGACTT 59.658 41.667 0.00 0.00 36.40 3.01
6582 6710 4.444720 GTGTAGAAGTTCCGTCTTGACTTG 59.555 45.833 0.00 0.00 34.02 3.16
6583 6711 3.821421 AGAAGTTCCGTCTTGACTTGT 57.179 42.857 0.00 0.00 34.02 3.16
6584 6712 3.458189 AGAAGTTCCGTCTTGACTTGTG 58.542 45.455 0.00 0.00 34.02 3.33
6585 6713 3.132289 AGAAGTTCCGTCTTGACTTGTGA 59.868 43.478 0.00 0.00 34.02 3.58
6586 6714 3.753294 AGTTCCGTCTTGACTTGTGAT 57.247 42.857 0.00 0.00 0.00 3.06
6587 6715 4.073293 AGTTCCGTCTTGACTTGTGATT 57.927 40.909 0.00 0.00 0.00 2.57
6588 6716 4.451900 AGTTCCGTCTTGACTTGTGATTT 58.548 39.130 0.00 0.00 0.00 2.17
6589 6717 4.273480 AGTTCCGTCTTGACTTGTGATTTG 59.727 41.667 0.00 0.00 0.00 2.32
6590 6718 3.804036 TCCGTCTTGACTTGTGATTTGT 58.196 40.909 0.00 0.00 0.00 2.83
6591 6719 3.559655 TCCGTCTTGACTTGTGATTTGTG 59.440 43.478 0.00 0.00 0.00 3.33
6592 6720 3.559655 CCGTCTTGACTTGTGATTTGTGA 59.440 43.478 0.00 0.00 0.00 3.58
6593 6721 4.035091 CCGTCTTGACTTGTGATTTGTGAA 59.965 41.667 0.00 0.00 0.00 3.18
6594 6722 5.277974 CCGTCTTGACTTGTGATTTGTGAAT 60.278 40.000 0.00 0.00 0.00 2.57
6595 6723 5.848036 CGTCTTGACTTGTGATTTGTGAATC 59.152 40.000 0.00 0.00 41.67 2.52
6603 6731 1.539388 TGATTTGTGAATCACCGTGGC 59.461 47.619 11.24 0.00 45.03 5.01
6604 6732 0.521291 ATTTGTGAATCACCGTGGCG 59.479 50.000 11.24 0.00 32.73 5.69
6605 6733 0.816018 TTTGTGAATCACCGTGGCGT 60.816 50.000 11.24 0.00 32.73 5.68
6606 6734 1.502990 TTGTGAATCACCGTGGCGTG 61.503 55.000 11.24 0.00 32.73 5.34
6607 6735 2.358125 TGAATCACCGTGGCGTGG 60.358 61.111 0.00 0.00 34.36 4.94
6608 6736 3.799755 GAATCACCGTGGCGTGGC 61.800 66.667 0.00 0.00 34.36 5.01
6609 6737 4.329545 AATCACCGTGGCGTGGCT 62.330 61.111 0.00 0.00 34.36 4.75
6610 6738 4.760047 ATCACCGTGGCGTGGCTC 62.760 66.667 0.00 0.00 34.36 4.70
6612 6740 4.988598 CACCGTGGCGTGGCTCTT 62.989 66.667 0.00 0.00 0.00 2.85
6613 6741 4.988598 ACCGTGGCGTGGCTCTTG 62.989 66.667 0.00 0.00 0.00 3.02
6616 6744 3.730761 GTGGCGTGGCTCTTGCTG 61.731 66.667 0.00 0.00 39.59 4.41
6617 6745 4.254709 TGGCGTGGCTCTTGCTGT 62.255 61.111 0.00 0.00 39.59 4.40
6618 6746 3.426568 GGCGTGGCTCTTGCTGTC 61.427 66.667 0.00 0.00 39.59 3.51
6619 6747 2.358003 GCGTGGCTCTTGCTGTCT 60.358 61.111 0.00 0.00 39.59 3.41
6620 6748 2.386660 GCGTGGCTCTTGCTGTCTC 61.387 63.158 0.00 0.00 39.59 3.36
6621 6749 1.005748 CGTGGCTCTTGCTGTCTCA 60.006 57.895 0.00 0.00 39.59 3.27
6622 6750 1.013005 CGTGGCTCTTGCTGTCTCAG 61.013 60.000 0.00 0.00 39.59 3.35
6623 6751 0.673022 GTGGCTCTTGCTGTCTCAGG 60.673 60.000 0.00 0.00 39.59 3.86
6624 6752 1.744741 GGCTCTTGCTGTCTCAGGC 60.745 63.158 0.00 0.00 39.59 4.85
6625 6753 1.296068 GCTCTTGCTGTCTCAGGCT 59.704 57.895 0.00 0.00 36.03 4.58
6626 6754 0.321475 GCTCTTGCTGTCTCAGGCTT 60.321 55.000 0.00 0.00 36.03 4.35
6627 6755 1.440708 CTCTTGCTGTCTCAGGCTTG 58.559 55.000 0.00 0.00 31.21 4.01
6628 6756 0.761187 TCTTGCTGTCTCAGGCTTGT 59.239 50.000 0.00 0.00 31.21 3.16
6629 6757 1.141657 TCTTGCTGTCTCAGGCTTGTT 59.858 47.619 0.00 0.00 31.21 2.83
6630 6758 1.266175 CTTGCTGTCTCAGGCTTGTTG 59.734 52.381 0.00 0.00 31.21 3.33
6631 6759 0.469494 TGCTGTCTCAGGCTTGTTGA 59.531 50.000 0.00 0.00 31.21 3.18
6632 6760 1.155042 GCTGTCTCAGGCTTGTTGAG 58.845 55.000 0.00 0.00 42.68 3.02
6633 6761 1.805869 CTGTCTCAGGCTTGTTGAGG 58.194 55.000 0.00 0.00 41.83 3.86
6634 6762 1.071385 CTGTCTCAGGCTTGTTGAGGT 59.929 52.381 0.00 0.00 41.83 3.85
6635 6763 1.070758 TGTCTCAGGCTTGTTGAGGTC 59.929 52.381 0.00 0.00 41.83 3.85
6636 6764 0.318441 TCTCAGGCTTGTTGAGGTCG 59.682 55.000 0.00 0.00 41.83 4.79
6637 6765 0.318441 CTCAGGCTTGTTGAGGTCGA 59.682 55.000 0.00 0.00 38.68 4.20
6638 6766 0.033504 TCAGGCTTGTTGAGGTCGAC 59.966 55.000 7.13 7.13 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
363 364 2.294449 AAAAGAAGGTCCAAGGAGGC 57.706 50.000 0.00 0.00 37.29 4.70
844 845 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
845 846 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
846 847 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
847 848 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
848 849 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
849 850 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
850 851 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
851 852 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2916 2972 5.824624 GCTTATCAATCAGGATGGAGTTTGA 59.175 40.000 0.00 0.00 36.16 2.69
6422 6550 4.039347 ACGGAGTATAAAGCTAACGCAGC 61.039 47.826 1.44 1.44 46.99 5.25
6423 6551 3.703420 ACGGAGTATAAAGCTAACGCAG 58.297 45.455 0.00 0.00 41.94 5.18
6424 6552 3.788333 ACGGAGTATAAAGCTAACGCA 57.212 42.857 0.00 0.00 41.94 5.24
6439 6567 7.653767 AAACTCTACTTGTTCAAATACGGAG 57.346 36.000 0.00 0.00 0.00 4.63
6440 6568 9.715121 AATAAACTCTACTTGTTCAAATACGGA 57.285 29.630 0.00 0.00 0.00 4.69
6465 6593 8.768955 GCAACAAATTCACAACCAAACATATAA 58.231 29.630 0.00 0.00 0.00 0.98
6466 6594 7.928167 TGCAACAAATTCACAACCAAACATATA 59.072 29.630 0.00 0.00 0.00 0.86
6467 6595 6.765036 TGCAACAAATTCACAACCAAACATAT 59.235 30.769 0.00 0.00 0.00 1.78
6468 6596 6.108687 TGCAACAAATTCACAACCAAACATA 58.891 32.000 0.00 0.00 0.00 2.29
6469 6597 4.940046 TGCAACAAATTCACAACCAAACAT 59.060 33.333 0.00 0.00 0.00 2.71
6470 6598 4.318332 TGCAACAAATTCACAACCAAACA 58.682 34.783 0.00 0.00 0.00 2.83
6471 6599 4.629200 TCTGCAACAAATTCACAACCAAAC 59.371 37.500 0.00 0.00 0.00 2.93
6472 6600 4.825422 TCTGCAACAAATTCACAACCAAA 58.175 34.783 0.00 0.00 0.00 3.28
6473 6601 4.462508 TCTGCAACAAATTCACAACCAA 57.537 36.364 0.00 0.00 0.00 3.67
6474 6602 4.669206 ATCTGCAACAAATTCACAACCA 57.331 36.364 0.00 0.00 0.00 3.67
6475 6603 5.049167 TGAATCTGCAACAAATTCACAACC 58.951 37.500 8.56 0.00 35.17 3.77
6476 6604 5.750067 ACTGAATCTGCAACAAATTCACAAC 59.250 36.000 8.56 0.00 35.17 3.32
6477 6605 5.904941 ACTGAATCTGCAACAAATTCACAA 58.095 33.333 8.56 0.00 35.17 3.33
6478 6606 5.518848 ACTGAATCTGCAACAAATTCACA 57.481 34.783 8.56 0.00 35.17 3.58
6479 6607 5.570589 GCTACTGAATCTGCAACAAATTCAC 59.429 40.000 8.56 0.00 35.17 3.18
6480 6608 5.474532 AGCTACTGAATCTGCAACAAATTCA 59.525 36.000 10.98 10.98 37.14 2.57
6481 6609 5.947443 AGCTACTGAATCTGCAACAAATTC 58.053 37.500 0.00 0.00 0.00 2.17
6482 6610 5.105997 GGAGCTACTGAATCTGCAACAAATT 60.106 40.000 0.00 0.00 0.00 1.82
6483 6611 4.397417 GGAGCTACTGAATCTGCAACAAAT 59.603 41.667 0.00 0.00 0.00 2.32
6484 6612 3.753272 GGAGCTACTGAATCTGCAACAAA 59.247 43.478 0.00 0.00 0.00 2.83
6485 6613 3.244526 TGGAGCTACTGAATCTGCAACAA 60.245 43.478 0.00 0.00 0.00 2.83
6486 6614 2.302733 TGGAGCTACTGAATCTGCAACA 59.697 45.455 0.00 0.00 0.00 3.33
6487 6615 2.977914 TGGAGCTACTGAATCTGCAAC 58.022 47.619 0.00 0.00 0.00 4.17
6488 6616 3.538591 CATGGAGCTACTGAATCTGCAA 58.461 45.455 0.00 0.00 32.16 4.08
6489 6617 2.744166 GCATGGAGCTACTGAATCTGCA 60.744 50.000 0.00 0.00 41.15 4.41
6490 6618 1.872313 GCATGGAGCTACTGAATCTGC 59.128 52.381 0.00 0.00 41.15 4.26
6491 6619 3.189618 TGCATGGAGCTACTGAATCTG 57.810 47.619 0.00 0.00 45.94 2.90
6492 6620 3.554544 CGATGCATGGAGCTACTGAATCT 60.555 47.826 2.46 0.00 45.94 2.40
6493 6621 2.735663 CGATGCATGGAGCTACTGAATC 59.264 50.000 2.46 1.99 45.94 2.52
6494 6622 2.366590 TCGATGCATGGAGCTACTGAAT 59.633 45.455 2.46 0.00 45.94 2.57
6495 6623 1.756538 TCGATGCATGGAGCTACTGAA 59.243 47.619 2.46 0.00 45.94 3.02
6496 6624 1.402787 TCGATGCATGGAGCTACTGA 58.597 50.000 2.46 0.00 45.94 3.41
6497 6625 2.029200 AGATCGATGCATGGAGCTACTG 60.029 50.000 25.36 0.00 45.94 2.74
6498 6626 2.246469 AGATCGATGCATGGAGCTACT 58.754 47.619 25.36 14.01 45.94 2.57
6499 6627 2.739885 AGATCGATGCATGGAGCTAC 57.260 50.000 25.36 12.24 45.94 3.58
6500 6628 3.573967 TGTTAGATCGATGCATGGAGCTA 59.426 43.478 26.54 26.54 45.94 3.32
6501 6629 2.366590 TGTTAGATCGATGCATGGAGCT 59.633 45.455 28.45 28.45 45.94 4.09
6502 6630 2.759191 TGTTAGATCGATGCATGGAGC 58.241 47.619 17.98 17.98 45.96 4.70
6503 6631 5.739752 TTTTGTTAGATCGATGCATGGAG 57.260 39.130 16.78 2.52 0.00 3.86
6538 6666 5.762711 ACACTGATAACATGTTGTACAGCAA 59.237 36.000 26.12 0.14 33.13 3.91
6539 6667 5.304778 ACACTGATAACATGTTGTACAGCA 58.695 37.500 26.12 15.12 33.13 4.41
6540 6668 5.862924 ACACTGATAACATGTTGTACAGC 57.137 39.130 26.12 12.24 33.13 4.40
6541 6669 8.757164 TTCTACACTGATAACATGTTGTACAG 57.243 34.615 21.42 23.91 34.69 2.74
6542 6670 8.364894 ACTTCTACACTGATAACATGTTGTACA 58.635 33.333 21.42 15.46 0.00 2.90
6543 6671 8.758633 ACTTCTACACTGATAACATGTTGTAC 57.241 34.615 21.42 11.96 0.00 2.90
6544 6672 9.419297 GAACTTCTACACTGATAACATGTTGTA 57.581 33.333 21.42 12.67 0.00 2.41
6545 6673 7.387948 GGAACTTCTACACTGATAACATGTTGT 59.612 37.037 21.42 14.88 0.00 3.32
6546 6674 7.411912 CGGAACTTCTACACTGATAACATGTTG 60.412 40.741 21.42 6.38 0.00 3.33
6547 6675 6.590292 CGGAACTTCTACACTGATAACATGTT 59.410 38.462 16.68 16.68 0.00 2.71
6548 6676 6.100004 CGGAACTTCTACACTGATAACATGT 58.900 40.000 0.00 0.00 0.00 3.21
6549 6677 6.100004 ACGGAACTTCTACACTGATAACATG 58.900 40.000 0.00 0.00 0.00 3.21
6550 6678 6.153000 AGACGGAACTTCTACACTGATAACAT 59.847 38.462 0.00 0.00 34.26 2.71
6551 6679 5.475909 AGACGGAACTTCTACACTGATAACA 59.524 40.000 0.00 0.00 34.26 2.41
6552 6680 5.952033 AGACGGAACTTCTACACTGATAAC 58.048 41.667 0.00 0.00 34.26 1.89
6553 6681 6.208007 TCAAGACGGAACTTCTACACTGATAA 59.792 38.462 0.00 0.00 35.25 1.75
6554 6682 5.708697 TCAAGACGGAACTTCTACACTGATA 59.291 40.000 0.00 0.00 35.25 2.15
6555 6683 4.523173 TCAAGACGGAACTTCTACACTGAT 59.477 41.667 0.00 0.00 35.25 2.90
6556 6684 3.887110 TCAAGACGGAACTTCTACACTGA 59.113 43.478 0.00 0.00 35.25 3.41
6557 6685 3.982058 GTCAAGACGGAACTTCTACACTG 59.018 47.826 0.00 0.00 35.25 3.66
6558 6686 3.890147 AGTCAAGACGGAACTTCTACACT 59.110 43.478 0.00 0.00 35.25 3.55
6559 6687 4.240175 AGTCAAGACGGAACTTCTACAC 57.760 45.455 0.00 0.00 35.25 2.90
6560 6688 4.098960 ACAAGTCAAGACGGAACTTCTACA 59.901 41.667 0.00 0.00 35.25 2.74
6561 6689 4.444720 CACAAGTCAAGACGGAACTTCTAC 59.555 45.833 0.00 0.00 35.25 2.59
6562 6690 4.340097 TCACAAGTCAAGACGGAACTTCTA 59.660 41.667 0.00 0.00 35.25 2.10
6563 6691 3.132289 TCACAAGTCAAGACGGAACTTCT 59.868 43.478 0.00 0.00 39.16 2.85
6564 6692 3.454375 TCACAAGTCAAGACGGAACTTC 58.546 45.455 0.00 0.00 36.20 3.01
6565 6693 3.536956 TCACAAGTCAAGACGGAACTT 57.463 42.857 0.00 0.00 36.20 2.66
6566 6694 3.753294 ATCACAAGTCAAGACGGAACT 57.247 42.857 0.00 0.00 36.20 3.01
6567 6695 4.035208 ACAAATCACAAGTCAAGACGGAAC 59.965 41.667 0.00 0.00 36.20 3.62
6568 6696 4.035091 CACAAATCACAAGTCAAGACGGAA 59.965 41.667 0.00 0.00 36.20 4.30
6569 6697 3.559655 CACAAATCACAAGTCAAGACGGA 59.440 43.478 0.00 0.00 36.20 4.69
6570 6698 3.559655 TCACAAATCACAAGTCAAGACGG 59.440 43.478 0.00 0.00 36.20 4.79
6571 6699 4.794248 TCACAAATCACAAGTCAAGACG 57.206 40.909 0.00 0.00 36.20 4.18
6572 6700 6.728200 TGATTCACAAATCACAAGTCAAGAC 58.272 36.000 0.00 0.00 44.94 3.01
6573 6701 6.940831 TGATTCACAAATCACAAGTCAAGA 57.059 33.333 0.00 0.00 44.94 3.02
6584 6712 1.465689 CGCCACGGTGATTCACAAATC 60.466 52.381 18.09 0.37 41.48 2.17
6585 6713 0.521291 CGCCACGGTGATTCACAAAT 59.479 50.000 18.09 0.40 35.86 2.32
6586 6714 0.816018 ACGCCACGGTGATTCACAAA 60.816 50.000 18.09 0.00 35.86 2.83
6587 6715 1.227704 ACGCCACGGTGATTCACAA 60.228 52.632 18.09 0.00 35.86 3.33
6588 6716 1.958715 CACGCCACGGTGATTCACA 60.959 57.895 18.09 0.00 40.38 3.58
6589 6717 2.677003 CCACGCCACGGTGATTCAC 61.677 63.158 10.28 8.34 40.38 3.18
6590 6718 2.358125 CCACGCCACGGTGATTCA 60.358 61.111 10.28 0.00 40.38 2.57
6591 6719 3.799755 GCCACGCCACGGTGATTC 61.800 66.667 10.28 0.00 40.38 2.52
6592 6720 4.329545 AGCCACGCCACGGTGATT 62.330 61.111 10.28 0.00 40.38 2.57
6593 6721 4.760047 GAGCCACGCCACGGTGAT 62.760 66.667 10.28 0.00 40.38 3.06
6595 6723 4.988598 AAGAGCCACGCCACGGTG 62.989 66.667 0.00 0.00 37.66 4.94
6596 6724 4.988598 CAAGAGCCACGCCACGGT 62.989 66.667 0.00 0.00 0.00 4.83
6599 6727 3.730761 CAGCAAGAGCCACGCCAC 61.731 66.667 0.00 0.00 43.56 5.01
6600 6728 4.254709 ACAGCAAGAGCCACGCCA 62.255 61.111 0.00 0.00 43.56 5.69
6601 6729 3.426568 GACAGCAAGAGCCACGCC 61.427 66.667 0.00 0.00 43.56 5.68
6602 6730 2.358003 AGACAGCAAGAGCCACGC 60.358 61.111 0.00 0.00 43.56 5.34
6603 6731 1.005748 TGAGACAGCAAGAGCCACG 60.006 57.895 0.00 0.00 43.56 4.94
6604 6732 0.673022 CCTGAGACAGCAAGAGCCAC 60.673 60.000 0.00 0.00 43.56 5.01
6605 6733 1.675801 CCTGAGACAGCAAGAGCCA 59.324 57.895 0.00 0.00 43.56 4.75
6606 6734 1.744741 GCCTGAGACAGCAAGAGCC 60.745 63.158 0.00 0.00 43.56 4.70
6607 6735 0.321475 AAGCCTGAGACAGCAAGAGC 60.321 55.000 0.00 0.00 42.56 4.09
6608 6736 1.270732 ACAAGCCTGAGACAGCAAGAG 60.271 52.381 0.00 0.00 0.00 2.85
6609 6737 0.761187 ACAAGCCTGAGACAGCAAGA 59.239 50.000 0.00 0.00 0.00 3.02
6610 6738 1.266175 CAACAAGCCTGAGACAGCAAG 59.734 52.381 0.00 0.00 0.00 4.01
6611 6739 1.134128 TCAACAAGCCTGAGACAGCAA 60.134 47.619 0.00 0.00 0.00 3.91
6612 6740 0.469494 TCAACAAGCCTGAGACAGCA 59.531 50.000 0.00 0.00 0.00 4.41
6613 6741 1.155042 CTCAACAAGCCTGAGACAGC 58.845 55.000 0.00 0.00 42.51 4.40
6614 6742 1.071385 ACCTCAACAAGCCTGAGACAG 59.929 52.381 1.42 0.00 42.51 3.51
6615 6743 1.070758 GACCTCAACAAGCCTGAGACA 59.929 52.381 1.42 0.00 42.51 3.41
6616 6744 1.802069 GACCTCAACAAGCCTGAGAC 58.198 55.000 1.42 0.00 42.51 3.36
6617 6745 0.318441 CGACCTCAACAAGCCTGAGA 59.682 55.000 1.42 0.00 42.51 3.27
6618 6746 0.318441 TCGACCTCAACAAGCCTGAG 59.682 55.000 0.00 0.00 40.08 3.35
6619 6747 0.033504 GTCGACCTCAACAAGCCTGA 59.966 55.000 3.51 0.00 0.00 3.86
6620 6748 2.533318 GTCGACCTCAACAAGCCTG 58.467 57.895 3.51 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.