Multiple sequence alignment - TraesCS3A01G127400

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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 TraesCS3A01G127400 chr3A 100.000 6279 0 0 1 6279 102680407 102686685 0.000000e+00 11596.0
1 TraesCS3A01G127400 chr3A 84.770 348 29 14 5919 6257 102554683 102555015 1.690000e-85 327.0
2 TraesCS3A01G127400 chr3D 94.887 5907 171 68 419 6279 86352209 86358030 0.000000e+00 9114.0
3 TraesCS3A01G127400 chr3D 97.900 381 7 1 1 381 86351835 86352214 0.000000e+00 658.0
4 TraesCS3A01G127400 chr3D 84.012 344 30 14 5919 6257 85896454 85896777 2.200000e-79 307.0
5 TraesCS3A01G127400 chr3D 82.913 357 28 22 5919 6257 86236951 86237292 2.210000e-74 291.0
6 TraesCS3A01G127400 chr3B 95.638 5640 150 25 1 5602 136479270 136484851 0.000000e+00 8964.0
7 TraesCS3A01G127400 chr3B 88.580 683 34 15 5051 5706 130308065 130307400 0.000000e+00 789.0
8 TraesCS3A01G127400 chr3B 82.079 558 44 28 5736 6279 136491740 136492255 5.820000e-115 425.0
9 TraesCS3A01G127400 chr3B 83.944 355 27 15 5919 6258 136091380 136091719 4.730000e-81 313.0
10 TraesCS3A01G127400 chr3B 90.426 94 9 0 330 423 704578420 704578513 2.380000e-24 124.0
11 TraesCS3A01G127400 chr3B 83.838 99 12 4 327 423 23957930 23958026 2.410000e-14 91.6
12 TraesCS3A01G127400 chr1B 81.818 231 21 15 6027 6242 174784124 174783900 2.330000e-39 174.0
13 TraesCS3A01G127400 chr1D 81.333 225 28 13 6027 6241 114083491 114083271 3.010000e-38 171.0
14 TraesCS3A01G127400 chr1A 80.000 230 31 11 6027 6241 124190015 124189786 8.430000e-34 156.0
15 TraesCS3A01G127400 chr1A 87.755 98 11 1 327 423 2665715 2665812 5.140000e-21 113.0
16 TraesCS3A01G127400 chr6D 90.426 94 9 0 330 423 7414519 7414612 2.380000e-24 124.0
17 TraesCS3A01G127400 chr6B 89.796 98 9 1 327 423 717410452 717410549 2.380000e-24 124.0
18 TraesCS3A01G127400 chr6B 89.247 93 10 0 330 422 14312580 14312488 3.980000e-22 117.0
19 TraesCS3A01G127400 chr7A 91.954 87 7 0 337 423 573432791 573432705 8.550000e-24 122.0
20 TraesCS3A01G127400 chr7B 88.421 95 11 0 329 423 533775324 533775230 1.430000e-21 115.0


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 TraesCS3A01G127400 chr3A 102680407 102686685 6278 False 11596 11596 100.0000 1 6279 1 chr3A.!!$F2 6278
1 TraesCS3A01G127400 chr3D 86351835 86358030 6195 False 4886 9114 96.3935 1 6279 2 chr3D.!!$F3 6278
2 TraesCS3A01G127400 chr3B 136479270 136484851 5581 False 8964 8964 95.6380 1 5602 1 chr3B.!!$F3 5601
3 TraesCS3A01G127400 chr3B 130307400 130308065 665 True 789 789 88.5800 5051 5706 1 chr3B.!!$R1 655
4 TraesCS3A01G127400 chr3B 136491740 136492255 515 False 425 425 82.0790 5736 6279 1 chr3B.!!$F4 543

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
931 934 1.800805 CAGTGCCTTGTGTCGAAGAT 58.199 50.000 0.00 0.0 40.67 2.40 F
1041 1044 1.762522 CGCATGAGGAGGGTAGCCAT 61.763 60.000 14.62 0.0 0.00 4.40 F
1621 1624 1.945394 CTGGTATGCAAGGCACTGATC 59.055 52.381 0.00 0.0 43.04 2.92 F
2557 2560 0.681733 TGCAGGTCTCAAGGTCAGTC 59.318 55.000 0.00 0.0 0.00 3.51 F
3775 3793 1.000955 ACCACAAGACAGTAAGCCTCG 59.999 52.381 0.00 0.0 0.00 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 1811 0.035458 ACTACCACCTGCAAGCTGAC 59.965 55.000 0.16 0.0 0.00 3.51 R
2247 2250 1.340114 GCTTGACTACCTCCCTTTGGG 60.340 57.143 0.00 0.0 46.11 4.12 R
3539 3557 0.538057 CTGTTCCCCAAAGCTGAGCA 60.538 55.000 7.39 0.0 0.00 4.26 R
4494 4525 0.031857 CATGGGCGCTCAAAAACACA 59.968 50.000 17.15 0.0 0.00 3.72 R
5346 5394 0.038526 AGCAAAGCAGCAGCATTCAC 60.039 50.000 3.17 0.0 45.49 3.18 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
377 378 8.818141 AGATGTTATTACAACCATCATACGAG 57.182 34.615 0.00 0.00 37.91 4.18
378 379 8.421784 AGATGTTATTACAACCATCATACGAGT 58.578 33.333 0.00 0.00 37.91 4.18
379 380 9.687210 GATGTTATTACAACCATCATACGAGTA 57.313 33.333 0.00 0.00 37.91 2.59
380 381 8.861033 TGTTATTACAACCATCATACGAGTAC 57.139 34.615 0.00 0.00 0.00 2.73
381 382 8.468399 TGTTATTACAACCATCATACGAGTACA 58.532 33.333 0.00 0.00 0.00 2.90
382 383 9.472361 GTTATTACAACCATCATACGAGTACAT 57.528 33.333 0.00 0.00 0.00 2.29
384 385 7.764695 TTACAACCATCATACGAGTACATTG 57.235 36.000 0.00 0.00 0.00 2.82
385 386 5.972935 ACAACCATCATACGAGTACATTGA 58.027 37.500 0.00 0.00 0.00 2.57
386 387 6.582636 ACAACCATCATACGAGTACATTGAT 58.417 36.000 0.00 0.00 0.00 2.57
387 388 7.047891 ACAACCATCATACGAGTACATTGATT 58.952 34.615 0.00 0.00 0.00 2.57
388 389 7.011389 ACAACCATCATACGAGTACATTGATTG 59.989 37.037 0.00 0.00 0.00 2.67
389 390 6.582636 ACCATCATACGAGTACATTGATTGT 58.417 36.000 0.00 0.00 42.62 2.71
390 391 7.722363 ACCATCATACGAGTACATTGATTGTA 58.278 34.615 0.00 0.00 39.87 2.41
391 392 8.201464 ACCATCATACGAGTACATTGATTGTAA 58.799 33.333 0.00 0.00 42.37 2.41
392 393 9.208022 CCATCATACGAGTACATTGATTGTAAT 57.792 33.333 0.00 0.00 42.37 1.89
517 518 9.349713 TCACAAGTTTGTTACAAATATCTTCCT 57.650 29.630 13.84 1.77 39.91 3.36
675 678 9.406828 CGTAGCTTGCTGTATATTCATTAAGTA 57.593 33.333 5.26 0.00 0.00 2.24
931 934 1.800805 CAGTGCCTTGTGTCGAAGAT 58.199 50.000 0.00 0.00 40.67 2.40
968 971 6.866248 CCTTTTGTATTTGCGTTATTCTTGGT 59.134 34.615 0.00 0.00 0.00 3.67
1041 1044 1.762522 CGCATGAGGAGGGTAGCCAT 61.763 60.000 14.62 0.00 0.00 4.40
1063 1066 2.775032 TACACCTGCGAAACGGCCTC 62.775 60.000 0.00 0.00 0.00 4.70
1242 1245 3.419793 TGGCTCCTCCAACTTTGTG 57.580 52.632 0.00 0.00 43.21 3.33
1373 1376 7.094463 CCATAGTGATAGCAGGATTGAATTTCC 60.094 40.741 0.00 0.00 0.00 3.13
1621 1624 1.945394 CTGGTATGCAAGGCACTGATC 59.055 52.381 0.00 0.00 43.04 2.92
1808 1811 5.998454 AGAAATGATCGCAGAATTGGTAG 57.002 39.130 0.00 0.00 43.58 3.18
2382 2385 8.757164 TTCGAATAGCATAATAGTGTGTATGG 57.243 34.615 0.00 0.00 0.00 2.74
2384 2387 7.039293 TCGAATAGCATAATAGTGTGTATGGGT 60.039 37.037 0.00 0.00 0.00 4.51
2481 2484 4.242475 TGACGTCTGTTTACTAGGCAATG 58.758 43.478 17.92 0.00 0.00 2.82
2557 2560 0.681733 TGCAGGTCTCAAGGTCAGTC 59.318 55.000 0.00 0.00 0.00 3.51
2567 2570 5.974751 GTCTCAAGGTCAGTCGATTATCTTC 59.025 44.000 0.00 0.00 0.00 2.87
2578 2581 7.665974 TCAGTCGATTATCTTCATTCCTAGCTA 59.334 37.037 0.00 0.00 0.00 3.32
2689 2692 9.739276 TCTCATAAGGTTTTAGTTCACATTGAT 57.261 29.630 0.00 0.00 0.00 2.57
2703 2706 8.742777 AGTTCACATTGATATTTTACTGCACAT 58.257 29.630 0.00 0.00 0.00 3.21
2751 2755 5.471116 TCTGACATCCACTTCAATGTTCAAG 59.529 40.000 0.00 0.00 36.28 3.02
2811 2824 8.772705 GCATGTTTTTGTTTTCCTATCATTTGA 58.227 29.630 0.00 0.00 0.00 2.69
2822 2835 6.078456 TCCTATCATTTGACCAAATCCAGT 57.922 37.500 5.10 0.00 38.84 4.00
2922 2935 5.351189 GGTTTCAAGCCGCATAAAATGATTT 59.649 36.000 0.00 0.00 0.00 2.17
3049 3063 3.681855 CATGCAAGAGCTTCTGAAATCG 58.318 45.455 0.00 0.00 42.74 3.34
3250 3264 5.567423 GCCTGTGTTGCTGGATTATTTTTCT 60.567 40.000 0.00 0.00 38.33 2.52
3310 3328 8.791675 TGATGAACATTTGAAAGTGCATTACTA 58.208 29.630 0.00 0.00 39.18 1.82
3431 3449 2.094700 TGACATCACGTAGGCTGAAGAC 60.095 50.000 0.00 0.00 0.00 3.01
3441 3459 1.703438 GGCTGAAGACTGCATCGCTG 61.703 60.000 0.00 0.00 41.61 5.18
3539 3557 5.103813 ACCCTCTGTTTTGTAGGTAAAAGGT 60.104 40.000 0.00 0.00 30.79 3.50
3695 3713 1.141053 CATACTGGTTACTGCTCCCCC 59.859 57.143 0.00 0.00 0.00 5.40
3774 3792 2.417719 CACCACAAGACAGTAAGCCTC 58.582 52.381 0.00 0.00 0.00 4.70
3775 3793 1.000955 ACCACAAGACAGTAAGCCTCG 59.999 52.381 0.00 0.00 0.00 4.63
3783 3801 5.251601 AGACAGTAAGCCTCGACTAATTC 57.748 43.478 0.00 0.00 0.00 2.17
4001 4019 9.899661 TGTACAGAATATTACAATACTTGCCTT 57.100 29.630 0.00 0.00 0.00 4.35
4192 4218 2.096417 GTGGAGCGTACAATGACAACAC 60.096 50.000 0.00 0.00 0.00 3.32
4241 4267 6.951198 TGATACTCTTTGTTCCTCTCTCTCTT 59.049 38.462 0.00 0.00 0.00 2.85
4242 4268 8.110271 TGATACTCTTTGTTCCTCTCTCTCTTA 58.890 37.037 0.00 0.00 0.00 2.10
4243 4269 8.887264 ATACTCTTTGTTCCTCTCTCTCTTAA 57.113 34.615 0.00 0.00 0.00 1.85
4244 4270 6.988522 ACTCTTTGTTCCTCTCTCTCTTAAC 58.011 40.000 0.00 0.00 0.00 2.01
4245 4271 6.551601 ACTCTTTGTTCCTCTCTCTCTTAACA 59.448 38.462 0.00 0.00 0.00 2.41
4248 4274 8.265055 TCTTTGTTCCTCTCTCTCTTAACAAAA 58.735 33.333 11.06 2.69 42.72 2.44
4298 4329 7.712204 TTTTTCTTCTTGTAACCAGACCTTT 57.288 32.000 0.00 0.00 0.00 3.11
4442 4473 3.519913 GACTTACCTCCTGACCCTTCATT 59.480 47.826 0.00 0.00 0.00 2.57
4465 4496 9.612620 CATTTTTCTGTTCATCAAAGTACCTAC 57.387 33.333 0.00 0.00 0.00 3.18
4494 4525 5.413833 CCATTTCTGTGTCATAGCAGTTCTT 59.586 40.000 0.00 0.00 34.57 2.52
4509 4540 1.852280 GTTCTTGTGTTTTTGAGCGCC 59.148 47.619 2.29 0.00 0.00 6.53
4523 4554 3.044059 GCGCCCATGTCTTCTGCAC 62.044 63.158 0.00 0.00 0.00 4.57
4770 4801 8.200792 ACTGTTTTATGTTTGTTGGCATTCTTA 58.799 29.630 0.00 0.00 0.00 2.10
4777 4808 6.446318 TGTTTGTTGGCATTCTTATTGACTC 58.554 36.000 0.00 0.00 0.00 3.36
4853 4884 1.012841 GCAGGTATGAGCTGTGCTTC 58.987 55.000 7.44 0.00 44.96 3.86
4949 4980 1.420891 AGCCACCACCATTTGCAAAAT 59.579 42.857 17.19 1.85 0.00 1.82
5146 5188 2.738314 GGGCATCATTCAACTTTGTTGC 59.262 45.455 5.65 0.00 37.67 4.17
5365 5413 0.038526 GTGAATGCTGCTGCTTTGCT 60.039 50.000 19.18 0.00 40.48 3.91
5366 5414 0.038618 TGAATGCTGCTGCTTTGCTG 60.039 50.000 19.18 0.00 40.48 4.41
5403 5451 7.651704 CCAACTTGTTTGTGTATAAAAGAAGGG 59.348 37.037 9.64 3.22 40.41 3.95
5452 5510 4.290155 GTGTTGTGCCTGTAATCTTTGTG 58.710 43.478 0.00 0.00 0.00 3.33
5539 5598 5.862924 ACCGGATTATTATTCGCTGATTG 57.137 39.130 9.46 0.00 31.06 2.67
5554 5613 3.444916 CTGATTGTTGAATGCTGGATGC 58.555 45.455 0.00 0.00 43.25 3.91
5576 5635 5.758296 TGCGAGTTGGAACTATTTATCATCC 59.242 40.000 0.00 0.00 39.88 3.51
5596 5655 4.469657 TCCAATGTTTCTTGGTTGTAGCT 58.530 39.130 0.00 0.00 44.99 3.32
5602 5661 2.113860 TCTTGGTTGTAGCTCATGGC 57.886 50.000 0.00 0.00 42.19 4.40
5603 5662 1.098050 CTTGGTTGTAGCTCATGGCC 58.902 55.000 0.00 0.00 43.05 5.36
5604 5663 0.403655 TTGGTTGTAGCTCATGGCCA 59.596 50.000 8.56 8.56 43.05 5.36
5605 5664 0.625316 TGGTTGTAGCTCATGGCCAT 59.375 50.000 14.09 14.09 43.05 4.40
5608 5667 1.406539 GTTGTAGCTCATGGCCATTGG 59.593 52.381 17.92 12.88 43.05 3.16
5609 5668 0.625316 TGTAGCTCATGGCCATTGGT 59.375 50.000 17.92 19.17 43.05 3.67
5610 5669 1.312815 GTAGCTCATGGCCATTGGTC 58.687 55.000 17.92 5.70 43.05 4.02
5611 5670 0.179048 TAGCTCATGGCCATTGGTCG 60.179 55.000 17.92 4.30 43.05 4.79
5612 5671 1.750399 GCTCATGGCCATTGGTCGT 60.750 57.895 17.92 0.00 34.27 4.34
5613 5672 1.996786 GCTCATGGCCATTGGTCGTG 61.997 60.000 21.25 21.25 44.86 4.35
5614 5673 1.996786 CTCATGGCCATTGGTCGTGC 61.997 60.000 22.24 0.00 43.35 5.34
5615 5674 2.755469 ATGGCCATTGGTCGTGCC 60.755 61.111 14.09 0.00 44.27 5.01
5616 5675 3.286694 ATGGCCATTGGTCGTGCCT 62.287 57.895 14.09 0.00 44.32 4.75
5617 5676 2.676471 GGCCATTGGTCGTGCCTT 60.676 61.111 4.26 0.00 40.77 4.35
5630 5689 4.464112 GTCGTGCCTTCTTTGTTCATAAC 58.536 43.478 0.00 0.00 0.00 1.89
5650 5709 8.150296 TCATAACGATGATGATATGTGGACTTT 58.850 33.333 0.00 0.00 37.15 2.66
5651 5710 8.777413 CATAACGATGATGATATGTGGACTTTT 58.223 33.333 0.00 0.00 34.73 2.27
5652 5711 9.996554 ATAACGATGATGATATGTGGACTTTTA 57.003 29.630 0.00 0.00 0.00 1.52
5653 5712 7.715265 ACGATGATGATATGTGGACTTTTAC 57.285 36.000 0.00 0.00 0.00 2.01
5655 5714 7.987458 ACGATGATGATATGTGGACTTTTACTT 59.013 33.333 0.00 0.00 0.00 2.24
5656 5715 8.278408 CGATGATGATATGTGGACTTTTACTTG 58.722 37.037 0.00 0.00 0.00 3.16
5657 5716 7.864108 TGATGATATGTGGACTTTTACTTGG 57.136 36.000 0.00 0.00 0.00 3.61
5658 5717 7.629157 TGATGATATGTGGACTTTTACTTGGA 58.371 34.615 0.00 0.00 0.00 3.53
5659 5718 8.274322 TGATGATATGTGGACTTTTACTTGGAT 58.726 33.333 0.00 0.00 0.00 3.41
5660 5719 7.864108 TGATATGTGGACTTTTACTTGGATG 57.136 36.000 0.00 0.00 0.00 3.51
5661 5720 7.402054 TGATATGTGGACTTTTACTTGGATGT 58.598 34.615 0.00 0.00 0.00 3.06
5662 5721 8.544622 TGATATGTGGACTTTTACTTGGATGTA 58.455 33.333 0.00 0.00 0.00 2.29
5663 5722 8.964476 ATATGTGGACTTTTACTTGGATGTAG 57.036 34.615 0.00 0.00 0.00 2.74
5664 5723 6.182507 TGTGGACTTTTACTTGGATGTAGT 57.817 37.500 0.00 0.00 0.00 2.73
5665 5724 6.597562 TGTGGACTTTTACTTGGATGTAGTT 58.402 36.000 0.00 0.00 0.00 2.24
5666 5725 6.485313 TGTGGACTTTTACTTGGATGTAGTTG 59.515 38.462 0.00 0.00 0.00 3.16
5667 5726 6.001460 TGGACTTTTACTTGGATGTAGTTGG 58.999 40.000 0.00 0.00 0.00 3.77
5677 5736 3.075283 TGGATGTAGTTGGATGTTTGGGT 59.925 43.478 0.00 0.00 0.00 4.51
5707 5766 1.534717 AAGACGAAACGGAGGGGGA 60.535 57.895 0.00 0.00 0.00 4.81
5709 5768 1.980772 GACGAAACGGAGGGGGAGA 60.981 63.158 0.00 0.00 0.00 3.71
5710 5769 1.946475 GACGAAACGGAGGGGGAGAG 61.946 65.000 0.00 0.00 0.00 3.20
5711 5770 2.585153 GAAACGGAGGGGGAGAGC 59.415 66.667 0.00 0.00 0.00 4.09
5712 5771 3.372554 GAAACGGAGGGGGAGAGCG 62.373 68.421 0.00 0.00 0.00 5.03
5752 5811 1.078848 CTCAACTGAAGGAGCCCGG 60.079 63.158 0.00 0.00 0.00 5.73
5784 5847 3.006677 GGGCCTGGCTTATCCACA 58.993 61.111 19.68 0.00 40.72 4.17
5797 5861 1.848886 ATCCACACGTTTCCCCTCCC 61.849 60.000 0.00 0.00 0.00 4.30
5830 5894 0.601841 CCACCTTTAGCAACGGACGT 60.602 55.000 0.00 0.00 0.00 4.34
5851 5916 1.752694 GAAGCCAGCCCGCCAATTA 60.753 57.895 0.00 0.00 0.00 1.40
5852 5917 1.304879 AAGCCAGCCCGCCAATTAA 60.305 52.632 0.00 0.00 0.00 1.40
5853 5918 0.902516 AAGCCAGCCCGCCAATTAAA 60.903 50.000 0.00 0.00 0.00 1.52
5854 5919 1.153647 GCCAGCCCGCCAATTAAAC 60.154 57.895 0.00 0.00 0.00 2.01
5855 5920 1.515487 CCAGCCCGCCAATTAAACC 59.485 57.895 0.00 0.00 0.00 3.27
5856 5921 1.515487 CAGCCCGCCAATTAAACCC 59.485 57.895 0.00 0.00 0.00 4.11
5859 5924 1.894512 CCCGCCAATTAAACCCACC 59.105 57.895 0.00 0.00 0.00 4.61
5865 5930 0.613572 CAATTAAACCCACCCGCCCT 60.614 55.000 0.00 0.00 0.00 5.19
5889 5960 0.469917 TCCATTCCATTCCTCTCGCC 59.530 55.000 0.00 0.00 0.00 5.54
5917 5988 4.814294 GCGTCAGGAATCGCCGGT 62.814 66.667 1.90 0.00 45.54 5.28
6112 6192 3.827898 CTGGAGGAGGACCGCGAC 61.828 72.222 8.23 0.17 41.83 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 6.830324 TGACCTGCTCTATTGCATAAGAAAAT 59.170 34.615 0.00 0.00 42.48 1.82
117 118 3.628008 TCGACAGGCCAGAAGATAGTAA 58.372 45.455 5.01 0.00 0.00 2.24
283 284 9.772973 TGTTTACATATAACACTGTCTGTTCTT 57.227 29.630 0.00 0.00 42.49 2.52
320 321 6.812998 TGGGACGGATGAAGTACTTAAATAG 58.187 40.000 8.42 3.41 0.00 1.73
373 374 9.817809 AGATGTTATTACAATCAATGTACTCGT 57.182 29.630 0.00 0.00 44.11 4.18
392 393 8.591072 CCCTCCGTCCTAAAATATAAGATGTTA 58.409 37.037 0.00 0.00 0.00 2.41
517 518 3.638160 GGAAGCATGGGATTGAATAAGCA 59.362 43.478 0.00 0.00 0.00 3.91
610 613 7.854557 TCCAGAGAATCAACACATGAATTAG 57.145 36.000 0.00 0.00 42.54 1.73
619 622 7.094205 ACCAATAACAATCCAGAGAATCAACAC 60.094 37.037 0.00 0.00 37.82 3.32
621 624 7.396540 ACCAATAACAATCCAGAGAATCAAC 57.603 36.000 0.00 0.00 37.82 3.18
713 716 9.465199 TCATGTCCAAAAAGATCAGATCATTTA 57.535 29.630 12.85 0.00 30.82 1.40
908 911 1.159713 TCGACACAAGGCACTGCAAG 61.160 55.000 2.82 0.00 40.86 4.01
931 934 6.861055 GCAAATACAAAAGGACGATCTTGAAA 59.139 34.615 0.00 0.00 0.00 2.69
968 971 7.724287 TCAAAATGTGAATCCTTCAATGTGAA 58.276 30.769 0.00 0.00 42.15 3.18
1041 1044 0.947180 GCCGTTTCGCAGGTGTAGAA 60.947 55.000 0.00 0.00 0.00 2.10
1050 1053 3.621805 TCCAGAGGCCGTTTCGCA 61.622 61.111 0.00 0.00 0.00 5.10
1063 1066 2.099921 AGTACAAGCTGCTATCGTCCAG 59.900 50.000 0.90 0.00 0.00 3.86
1242 1245 1.686110 AGATGAGGTCGGGTGGTCC 60.686 63.158 0.00 0.00 0.00 4.46
1373 1376 3.603532 TCAGTCTCAGCTTTATTGCCTG 58.396 45.455 0.00 0.00 0.00 4.85
1621 1624 7.645340 CACAATAGTTTGAACCTTGAGAGTTTG 59.355 37.037 11.47 0.00 36.64 2.93
1808 1811 0.035458 ACTACCACCTGCAAGCTGAC 59.965 55.000 0.16 0.00 0.00 3.51
2247 2250 1.340114 GCTTGACTACCTCCCTTTGGG 60.340 57.143 0.00 0.00 46.11 4.12
2382 2385 6.531948 GGAATGTGATTCGTGATAGCTATACC 59.468 42.308 6.13 0.00 40.17 2.73
2384 2387 7.227049 TGGAATGTGATTCGTGATAGCTATA 57.773 36.000 6.13 0.00 40.17 1.31
2689 2692 9.838975 CACAGTATGAAAATGTGCAGTAAAATA 57.161 29.630 0.00 0.00 39.69 1.40
2703 2706 6.245408 AGCACTAAATCCCACAGTATGAAAA 58.755 36.000 0.00 0.00 39.69 2.29
2751 2755 2.102578 CACCCCAAATGTGAAGGGATC 58.897 52.381 4.31 0.00 45.80 3.36
2800 2812 6.406177 CCAACTGGATTTGGTCAAATGATAGG 60.406 42.308 12.94 4.85 40.77 2.57
2811 2824 2.380064 TTGCTCCAACTGGATTTGGT 57.620 45.000 0.00 0.00 45.60 3.67
2898 2911 3.843999 TCATTTTATGCGGCTTGAAACC 58.156 40.909 7.76 0.00 0.00 3.27
2922 2935 4.402155 GTGATAATGGACCATGGCAAAAGA 59.598 41.667 13.04 0.00 0.00 2.52
3049 3063 3.502595 GGGTAGCTTCAAACTCTTTCCAC 59.497 47.826 0.00 0.00 0.00 4.02
3221 3235 1.604308 CCAGCAACACAGGCATGGA 60.604 57.895 2.31 0.00 33.91 3.41
3310 3328 3.181483 GCATTTCAAATGGAAGGCGAGAT 60.181 43.478 12.14 0.00 36.72 2.75
3363 3381 2.293122 CGTCCATGCCTCAGAAAAACAA 59.707 45.455 0.00 0.00 0.00 2.83
3470 3488 9.601217 GATAAAGTAGCTAATGGAAGAAGTTCA 57.399 33.333 5.50 0.00 33.93 3.18
3516 3534 5.240844 CACCTTTTACCTACAAAACAGAGGG 59.759 44.000 0.00 0.00 34.41 4.30
3539 3557 0.538057 CTGTTCCCCAAAGCTGAGCA 60.538 55.000 7.39 0.00 0.00 4.26
3629 3647 0.759346 AGAACACCGGCTTTCTGAGT 59.241 50.000 15.63 0.00 30.65 3.41
3695 3713 2.172082 AGATGGTGGAGGTGATGATGTG 59.828 50.000 0.00 0.00 0.00 3.21
3774 3792 6.712241 ACTGAATTGACACAGAATTAGTCG 57.288 37.500 0.00 0.00 37.54 4.18
3775 3793 7.173218 TCCAACTGAATTGACACAGAATTAGTC 59.827 37.037 0.00 0.00 41.23 2.59
3783 3801 4.790878 CATGTCCAACTGAATTGACACAG 58.209 43.478 0.00 0.00 41.23 3.66
3994 4012 8.598075 GCATCAACAGAATAAATAAAAGGCAAG 58.402 33.333 0.00 0.00 0.00 4.01
4004 4022 8.177663 CGAGTTTGTAGCATCAACAGAATAAAT 58.822 33.333 0.00 0.00 0.00 1.40
4005 4023 7.172532 ACGAGTTTGTAGCATCAACAGAATAAA 59.827 33.333 0.00 0.00 0.00 1.40
4006 4024 6.649141 ACGAGTTTGTAGCATCAACAGAATAA 59.351 34.615 0.00 0.00 0.00 1.40
4007 4025 6.090763 CACGAGTTTGTAGCATCAACAGAATA 59.909 38.462 0.00 0.00 0.00 1.75
4008 4026 4.997395 ACGAGTTTGTAGCATCAACAGAAT 59.003 37.500 0.00 0.00 0.00 2.40
4442 4473 8.918202 ATGTAGGTACTTTGATGAACAGAAAA 57.082 30.769 0.00 0.00 41.75 2.29
4465 4496 4.142337 TGCTATGACACAGAAATGGCAATG 60.142 41.667 0.00 0.00 42.20 2.82
4494 4525 0.031857 CATGGGCGCTCAAAAACACA 59.968 50.000 17.15 0.00 0.00 3.72
4509 4540 1.735386 CAGAGGTGCAGAAGACATGG 58.265 55.000 0.00 0.00 0.00 3.66
4597 4628 8.809066 TGCTTATACTGTACTTTAACCTGAAGA 58.191 33.333 0.00 0.00 0.00 2.87
4770 4801 5.555017 AGTAACATGCAAGTGAGAGTCAAT 58.445 37.500 0.00 0.00 0.00 2.57
4777 4808 4.060900 ACAGTGAGTAACATGCAAGTGAG 58.939 43.478 0.00 0.00 0.00 3.51
4853 4884 2.335712 GCGAGGCTTTTCCCCACTG 61.336 63.158 0.00 0.00 34.51 3.66
4949 4980 3.161450 GTGGCGCCCCTATCTCCA 61.161 66.667 26.77 0.00 0.00 3.86
4952 4983 4.853142 TCCGTGGCGCCCCTATCT 62.853 66.667 26.77 0.00 0.00 1.98
5117 5148 3.025978 GTTGAATGATGCCCAATGGAGA 58.974 45.455 0.00 0.00 0.00 3.71
5146 5188 2.940561 GTTGCCACGGGTAACACG 59.059 61.111 15.44 0.00 45.37 4.49
5346 5394 0.038526 AGCAAAGCAGCAGCATTCAC 60.039 50.000 3.17 0.00 45.49 3.18
5365 5413 4.972733 AGTTGGCATGGCACGGCA 62.973 61.111 23.26 5.46 37.12 5.69
5366 5414 3.683937 AAGTTGGCATGGCACGGC 61.684 61.111 23.26 14.76 0.00 5.68
5380 5428 8.528044 TTCCCTTCTTTTATACACAAACAAGT 57.472 30.769 0.00 0.00 0.00 3.16
5403 5451 5.637387 CCTACAACAGCTTCTCTTCTCTTTC 59.363 44.000 0.00 0.00 0.00 2.62
5452 5510 6.759827 AGACATATAACGGTTATTGGTGTGTC 59.240 38.462 17.74 19.50 33.27 3.67
5539 5598 1.089920 ACTCGCATCCAGCATTCAAC 58.910 50.000 0.00 0.00 46.13 3.18
5554 5613 7.786178 TTGGATGATAAATAGTTCCAACTCG 57.214 36.000 0.00 0.00 40.57 4.18
5576 5635 5.437289 TGAGCTACAACCAAGAAACATTG 57.563 39.130 0.00 0.00 0.00 2.82
5596 5655 2.045708 GCACGACCAATGGCCATGA 61.046 57.895 21.63 0.00 0.00 3.07
5602 5661 1.068333 CAAAGAAGGCACGACCAATGG 60.068 52.381 0.00 0.00 43.14 3.16
5603 5662 1.608590 ACAAAGAAGGCACGACCAATG 59.391 47.619 0.00 0.00 43.14 2.82
5604 5663 1.981256 ACAAAGAAGGCACGACCAAT 58.019 45.000 0.00 0.00 43.14 3.16
5605 5664 1.673920 GAACAAAGAAGGCACGACCAA 59.326 47.619 0.00 0.00 43.14 3.67
5608 5667 4.464112 GTTATGAACAAAGAAGGCACGAC 58.536 43.478 0.00 0.00 0.00 4.34
5609 5668 3.185594 CGTTATGAACAAAGAAGGCACGA 59.814 43.478 0.00 0.00 0.00 4.35
5610 5669 3.185594 TCGTTATGAACAAAGAAGGCACG 59.814 43.478 0.00 0.00 0.00 5.34
5611 5670 4.742438 TCGTTATGAACAAAGAAGGCAC 57.258 40.909 0.00 0.00 0.00 5.01
5612 5671 5.000591 TCATCGTTATGAACAAAGAAGGCA 58.999 37.500 0.00 0.00 39.20 4.75
5613 5672 5.545658 TCATCGTTATGAACAAAGAAGGC 57.454 39.130 0.00 0.00 39.20 4.35
5614 5673 7.307493 TCATCATCGTTATGAACAAAGAAGG 57.693 36.000 0.00 0.00 45.12 3.46
5617 5676 9.546428 ACATATCATCATCGTTATGAACAAAGA 57.454 29.630 0.00 0.00 45.12 2.52
5630 5689 7.953158 AGTAAAAGTCCACATATCATCATCG 57.047 36.000 0.00 0.00 0.00 3.84
5650 5709 6.432783 CCAAACATCCAACTACATCCAAGTAA 59.567 38.462 0.00 0.00 0.00 2.24
5651 5710 5.943416 CCAAACATCCAACTACATCCAAGTA 59.057 40.000 0.00 0.00 0.00 2.24
5652 5711 4.766891 CCAAACATCCAACTACATCCAAGT 59.233 41.667 0.00 0.00 0.00 3.16
5653 5712 4.158394 CCCAAACATCCAACTACATCCAAG 59.842 45.833 0.00 0.00 0.00 3.61
5655 5714 3.075283 ACCCAAACATCCAACTACATCCA 59.925 43.478 0.00 0.00 0.00 3.41
5656 5715 3.697166 ACCCAAACATCCAACTACATCC 58.303 45.455 0.00 0.00 0.00 3.51
5657 5716 7.404671 AAATACCCAAACATCCAACTACATC 57.595 36.000 0.00 0.00 0.00 3.06
5658 5717 7.790782 AAAATACCCAAACATCCAACTACAT 57.209 32.000 0.00 0.00 0.00 2.29
5659 5718 7.604657 AAAAATACCCAAACATCCAACTACA 57.395 32.000 0.00 0.00 0.00 2.74
5677 5736 9.090692 CCTCCGTTTCGTCTTCTTATAAAAATA 57.909 33.333 0.00 0.00 0.00 1.40
5687 5746 1.542187 CCCCCTCCGTTTCGTCTTCT 61.542 60.000 0.00 0.00 0.00 2.85
5722 5781 1.005630 AGTTGAGAGCTGACGGCAC 60.006 57.895 9.39 1.64 44.79 5.01
5723 5782 1.005748 CAGTTGAGAGCTGACGGCA 60.006 57.895 9.39 0.00 44.79 5.69
5724 5783 0.319900 TTCAGTTGAGAGCTGACGGC 60.320 55.000 0.00 0.00 42.00 5.68
5725 5784 1.671261 CCTTCAGTTGAGAGCTGACGG 60.671 57.143 0.00 3.96 42.97 4.79
5726 5785 1.270826 TCCTTCAGTTGAGAGCTGACG 59.729 52.381 0.00 0.00 42.00 4.35
5727 5786 2.930455 GCTCCTTCAGTTGAGAGCTGAC 60.930 54.545 13.22 0.00 46.50 3.51
5728 5787 1.274728 GCTCCTTCAGTTGAGAGCTGA 59.725 52.381 13.22 0.00 46.50 4.26
5729 5788 1.724429 GCTCCTTCAGTTGAGAGCTG 58.276 55.000 13.22 0.00 46.50 4.24
5732 5791 0.108424 CGGGCTCCTTCAGTTGAGAG 60.108 60.000 0.00 0.00 0.00 3.20
5733 5792 1.544825 CCGGGCTCCTTCAGTTGAGA 61.545 60.000 0.00 0.00 0.00 3.27
5784 5847 4.932911 TTATAAAAGGGAGGGGAAACGT 57.067 40.909 0.00 0.00 0.00 3.99
5797 5861 5.278315 GCTAAAGGTGGCGGGATTATAAAAG 60.278 44.000 0.00 0.00 0.00 2.27
5840 5904 1.216977 GTGGGTTTAATTGGCGGGC 59.783 57.895 0.00 0.00 0.00 6.13
5865 5930 1.770658 AGAGGAATGGAATGGATCGCA 59.229 47.619 0.00 0.00 0.00 5.10
5869 5934 1.072965 GGCGAGAGGAATGGAATGGAT 59.927 52.381 0.00 0.00 0.00 3.41
5873 5938 2.579873 CATTGGCGAGAGGAATGGAAT 58.420 47.619 0.00 0.00 0.00 3.01
5889 5960 4.170062 CTGACGCGGCTGCCATTG 62.170 66.667 20.29 9.81 38.08 2.82
5910 5981 3.803082 CGGAGAACGTACCGGCGA 61.803 66.667 9.30 0.00 44.59 5.54
6120 6200 4.891727 CGAACCGCCTCATCCCCG 62.892 72.222 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.