Multiple sequence alignment - TraesCS2D01G340400

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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 TraesCS2D01G340400 chr2D 100.000 4677 0 0 1 4677 435039561 435044237 0.000000e+00 8637
1 TraesCS2D01G340400 chr2D 100.000 538 0 0 5038 5575 435044598 435045135 0.000000e+00 994
2 TraesCS2D01G340400 chr2B 97.098 2619 61 7 690 3303 513466125 513468733 0.000000e+00 4401
3 TraesCS2D01G340400 chr2B 95.438 1381 38 11 3302 4677 513468840 513470200 0.000000e+00 2178
4 TraesCS2D01G340400 chr2B 89.184 490 30 8 1 479 513465631 513466108 1.730000e-164 590
5 TraesCS2D01G340400 chr2B 87.061 541 47 15 5046 5575 513470239 513470767 1.730000e-164 590
6 TraesCS2D01G340400 chr2A 96.090 2711 85 10 599 3303 551820708 551818013 0.000000e+00 4399
7 TraesCS2D01G340400 chr2A 96.159 1380 48 3 3302 4677 551817931 551816553 0.000000e+00 2250
8 TraesCS2D01G340400 chr2A 91.921 557 32 7 1 555 551821262 551820717 0.000000e+00 767
9 TraesCS2D01G340400 chr2A 88.619 536 43 11 5046 5575 551816514 551815991 2.190000e-178 636


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 TraesCS2D01G340400 chr2D 435039561 435045135 5574 False 4815.50 8637 100.00000 1 5575 2 chr2D.!!$F1 5574
1 TraesCS2D01G340400 chr2B 513465631 513470767 5136 False 1939.75 4401 92.19525 1 5575 4 chr2B.!!$F1 5574
2 TraesCS2D01G340400 chr2A 551815991 551821262 5271 True 2013.00 4399 93.19725 1 5575 4 chr2A.!!$R1 5574

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
448 460 0.460311 ATAGAAGAAGTGACGGCCGG 59.540 55.000 31.76 11.88 0.00 6.13 F
1636 1648 1.140052 TCGGGTCAAGAAGAAGCACAA 59.860 47.619 0.00 0.00 0.00 3.33 F
3219 3235 0.536260 ACTTTTGCAGTTTGGCAGCA 59.464 45.000 0.00 0.00 45.88 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1761 1773 0.460987 GAGGTTGCTCTGGACCATCG 60.461 60.0 0.0 0.0 38.42 3.84 R
3305 3431 0.614979 TCTGAGCAGGGACCAGTACC 60.615 60.0 0.0 0.0 0.00 3.34 R
5038 5169 0.183492 ATGTGCAAGTCAGGGTGTGT 59.817 50.0 0.0 0.0 0.00 3.72 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
105 106 6.520272 AGGACTATGTGCTCTGTGATATTTC 58.480 40.000 0.00 0.00 24.24 2.17
112 113 2.156504 GCTCTGTGATATTTCCGCGATG 59.843 50.000 8.23 0.00 0.00 3.84
131 132 3.791973 TGCAAAACTAACCAGGTGTTG 57.208 42.857 0.00 0.00 37.83 3.33
167 168 7.899648 TTTACTTTTGGAAATGGAGGTGTTA 57.100 32.000 0.00 0.00 0.00 2.41
174 175 3.756963 GGAAATGGAGGTGTTAGTTGGAC 59.243 47.826 0.00 0.00 0.00 4.02
230 232 4.344104 CCATTTTTGTAGTCCCAGATGGT 58.656 43.478 0.00 0.00 34.77 3.55
231 233 4.399303 CCATTTTTGTAGTCCCAGATGGTC 59.601 45.833 0.00 0.00 34.77 4.02
294 297 5.199723 TGTACATACAGATACGGTTGGGTA 58.800 41.667 0.00 0.00 0.00 3.69
295 298 5.655974 TGTACATACAGATACGGTTGGGTAA 59.344 40.000 0.00 0.00 0.00 2.85
448 460 0.460311 ATAGAAGAAGTGACGGCCGG 59.540 55.000 31.76 11.88 0.00 6.13
479 491 4.638865 GTCCATTTTATTCCGCTTGGTAGT 59.361 41.667 0.00 0.00 0.00 2.73
480 492 5.818857 GTCCATTTTATTCCGCTTGGTAGTA 59.181 40.000 0.00 0.00 0.00 1.82
481 493 6.018180 GTCCATTTTATTCCGCTTGGTAGTAG 60.018 42.308 0.00 0.00 0.00 2.57
482 494 5.820947 CCATTTTATTCCGCTTGGTAGTAGT 59.179 40.000 0.00 0.00 0.00 2.73
483 495 6.987992 CCATTTTATTCCGCTTGGTAGTAGTA 59.012 38.462 0.00 0.00 0.00 1.82
484 496 7.660208 CCATTTTATTCCGCTTGGTAGTAGTAT 59.340 37.037 0.00 0.00 0.00 2.12
485 497 9.052759 CATTTTATTCCGCTTGGTAGTAGTATT 57.947 33.333 0.00 0.00 0.00 1.89
486 498 8.652810 TTTTATTCCGCTTGGTAGTAGTATTC 57.347 34.615 0.00 0.00 0.00 1.75
487 499 4.660789 TTCCGCTTGGTAGTAGTATTCC 57.339 45.455 0.00 0.00 0.00 3.01
488 500 3.634504 TCCGCTTGGTAGTAGTATTCCA 58.365 45.455 0.00 0.00 0.00 3.53
492 504 5.221461 CCGCTTGGTAGTAGTATTCCAGAAT 60.221 44.000 0.00 0.00 34.93 2.40
525 537 1.613925 GGTTGCCACCTTCTTTCCTTC 59.386 52.381 0.00 0.00 40.44 3.46
565 577 9.717942 ATGCTCATAATAAGATAGTCTTCAACC 57.282 33.333 0.00 0.00 37.89 3.77
566 578 8.150945 TGCTCATAATAAGATAGTCTTCAACCC 58.849 37.037 0.00 0.00 37.89 4.11
567 579 8.371699 GCTCATAATAAGATAGTCTTCAACCCT 58.628 37.037 0.00 0.00 37.89 4.34
568 580 9.921637 CTCATAATAAGATAGTCTTCAACCCTC 57.078 37.037 0.00 0.00 37.89 4.30
569 581 9.661954 TCATAATAAGATAGTCTTCAACCCTCT 57.338 33.333 0.00 0.00 37.89 3.69
572 584 8.616799 AATAAGATAGTCTTCAACCCTCTTCT 57.383 34.615 0.00 0.00 37.89 2.85
573 585 6.538945 AAGATAGTCTTCAACCCTCTTCTC 57.461 41.667 0.00 0.00 28.99 2.87
574 586 5.837829 AGATAGTCTTCAACCCTCTTCTCT 58.162 41.667 0.00 0.00 0.00 3.10
575 587 6.260663 AGATAGTCTTCAACCCTCTTCTCTT 58.739 40.000 0.00 0.00 0.00 2.85
576 588 6.728632 AGATAGTCTTCAACCCTCTTCTCTTT 59.271 38.462 0.00 0.00 0.00 2.52
577 589 5.222079 AGTCTTCAACCCTCTTCTCTTTC 57.778 43.478 0.00 0.00 0.00 2.62
578 590 4.656112 AGTCTTCAACCCTCTTCTCTTTCA 59.344 41.667 0.00 0.00 0.00 2.69
579 591 5.309282 AGTCTTCAACCCTCTTCTCTTTCAT 59.691 40.000 0.00 0.00 0.00 2.57
580 592 5.411053 GTCTTCAACCCTCTTCTCTTTCATG 59.589 44.000 0.00 0.00 0.00 3.07
581 593 3.679389 TCAACCCTCTTCTCTTTCATGC 58.321 45.455 0.00 0.00 0.00 4.06
582 594 3.328931 TCAACCCTCTTCTCTTTCATGCT 59.671 43.478 0.00 0.00 0.00 3.79
583 595 4.077822 CAACCCTCTTCTCTTTCATGCTT 58.922 43.478 0.00 0.00 0.00 3.91
584 596 5.013079 TCAACCCTCTTCTCTTTCATGCTTA 59.987 40.000 0.00 0.00 0.00 3.09
585 597 5.707066 ACCCTCTTCTCTTTCATGCTTAT 57.293 39.130 0.00 0.00 0.00 1.73
586 598 6.814954 ACCCTCTTCTCTTTCATGCTTATA 57.185 37.500 0.00 0.00 0.00 0.98
587 599 7.385894 ACCCTCTTCTCTTTCATGCTTATAT 57.614 36.000 0.00 0.00 0.00 0.86
588 600 7.449247 ACCCTCTTCTCTTTCATGCTTATATC 58.551 38.462 0.00 0.00 0.00 1.63
589 601 7.292120 ACCCTCTTCTCTTTCATGCTTATATCT 59.708 37.037 0.00 0.00 0.00 1.98
590 602 7.603404 CCCTCTTCTCTTTCATGCTTATATCTG 59.397 40.741 0.00 0.00 0.00 2.90
591 603 8.149647 CCTCTTCTCTTTCATGCTTATATCTGT 58.850 37.037 0.00 0.00 0.00 3.41
592 604 9.195411 CTCTTCTCTTTCATGCTTATATCTGTC 57.805 37.037 0.00 0.00 0.00 3.51
593 605 8.922237 TCTTCTCTTTCATGCTTATATCTGTCT 58.078 33.333 0.00 0.00 0.00 3.41
594 606 9.195411 CTTCTCTTTCATGCTTATATCTGTCTC 57.805 37.037 0.00 0.00 0.00 3.36
595 607 8.242729 TCTCTTTCATGCTTATATCTGTCTCA 57.757 34.615 0.00 0.00 0.00 3.27
596 608 8.699130 TCTCTTTCATGCTTATATCTGTCTCAA 58.301 33.333 0.00 0.00 0.00 3.02
597 609 8.883954 TCTTTCATGCTTATATCTGTCTCAAG 57.116 34.615 0.00 0.00 0.00 3.02
607 619 2.067932 CTGTCTCAAGTTGGGGCCCA 62.068 60.000 24.76 24.76 0.00 5.36
620 632 1.339631 GGGGCCCAGGTTTAATTTTGC 60.340 52.381 26.86 0.00 0.00 3.68
622 634 2.615240 GGGCCCAGGTTTAATTTTGCAG 60.615 50.000 19.95 0.00 0.00 4.41
623 635 2.038426 GGCCCAGGTTTAATTTTGCAGT 59.962 45.455 0.00 0.00 0.00 4.40
624 636 3.066380 GCCCAGGTTTAATTTTGCAGTG 58.934 45.455 0.00 0.00 0.00 3.66
625 637 3.494223 GCCCAGGTTTAATTTTGCAGTGT 60.494 43.478 0.00 0.00 0.00 3.55
661 673 7.071950 TGTGTATATAAATGCTCCAGGGTTACT 59.928 37.037 0.00 0.00 0.00 2.24
662 674 8.591072 GTGTATATAAATGCTCCAGGGTTACTA 58.409 37.037 0.00 0.00 0.00 1.82
710 722 2.681344 CGGATTTAACTGTTGTAGGGCC 59.319 50.000 2.69 0.00 0.00 5.80
1109 1121 5.128919 GGATCCAGCAACAAACTCTATGAT 58.871 41.667 6.95 0.00 0.00 2.45
1233 1245 1.672881 GATGTGGATTTGGAAGCCGAG 59.327 52.381 0.00 0.00 40.70 4.63
1497 1509 1.837439 TCCTATGAACGGGCACATCTT 59.163 47.619 0.00 0.00 0.00 2.40
1506 1518 2.502510 GCACATCTTGCGTTGCCG 60.503 61.111 0.00 0.00 42.79 5.69
1578 1590 4.527157 GCTGCAATGAGCCGCGTC 62.527 66.667 4.92 0.00 43.52 5.19
1608 1620 1.347378 TGTATGTCTGCCAGTGAAGCA 59.653 47.619 0.00 0.00 38.82 3.91
1617 1629 1.287730 CCAGTGAAGCACGCTCAGTC 61.288 60.000 0.00 0.00 39.64 3.51
1623 1635 4.357947 GCACGCTCAGTCGGGTCA 62.358 66.667 0.00 0.00 34.89 4.02
1636 1648 1.140052 TCGGGTCAAGAAGAAGCACAA 59.860 47.619 0.00 0.00 0.00 3.33
1743 1755 1.899814 TCAGGAGCATCAAAGTACCGT 59.100 47.619 0.00 0.00 36.25 4.83
1755 1767 7.201609 GCATCAAAGTACCGTGATCTTTATTCA 60.202 37.037 6.02 0.00 32.06 2.57
1761 1773 7.371936 AGTACCGTGATCTTTATTCAGATAGC 58.628 38.462 0.00 0.00 33.36 2.97
1860 1872 4.119136 CACCAAGGTGTTTAAGCCAAAAG 58.881 43.478 11.08 0.00 40.91 2.27
2016 2028 1.665599 ACGCATTTTTGCTGCTGCC 60.666 52.632 13.47 0.00 37.48 4.85
2061 2073 1.187567 AAAGGCCATGTGGGTTCTGC 61.188 55.000 5.01 0.00 39.65 4.26
2154 2166 2.098831 GGGTCGCGTAAAGGCACTC 61.099 63.158 5.77 0.00 38.49 3.51
2178 2190 3.056628 GAGTGCATCTCTTGTCCCG 57.943 57.895 8.50 0.00 39.86 5.14
2869 2881 7.201609 GCGTGTATGTATTCTTTCCTTGAATGA 60.202 37.037 0.00 0.00 35.90 2.57
2870 2882 8.830580 CGTGTATGTATTCTTTCCTTGAATGAT 58.169 33.333 0.00 0.00 35.90 2.45
2934 2947 8.248253 GCTCAATGCATCAATGATAATATGGAA 58.752 33.333 0.00 0.00 42.31 3.53
3012 3027 6.392354 CATGTTCTGATAACCAGTGCATTTT 58.608 36.000 0.00 0.00 43.38 1.82
3032 3047 7.795272 GCATTTTGAACTATGAAAAGTTTGCTG 59.205 33.333 0.00 0.00 39.78 4.41
3035 3050 6.942532 TGAACTATGAAAAGTTTGCTGTCT 57.057 33.333 0.00 0.00 39.78 3.41
3158 3174 9.921637 AAAATACTGTCAGAAACTGAAAAACAA 57.078 25.926 6.91 0.00 42.46 2.83
3219 3235 0.536260 ACTTTTGCAGTTTGGCAGCA 59.464 45.000 0.00 0.00 45.88 4.41
3263 3279 1.270274 ACAAATGACATGCATGCACGT 59.730 42.857 25.37 23.09 37.28 4.49
3293 3309 4.714802 ACAGGATATACAGGTAAGCACACA 59.285 41.667 0.00 0.00 0.00 3.72
3294 3310 5.188948 ACAGGATATACAGGTAAGCACACAA 59.811 40.000 0.00 0.00 0.00 3.33
3296 3312 6.767902 CAGGATATACAGGTAAGCACACAAAT 59.232 38.462 0.00 0.00 0.00 2.32
3305 3431 9.066892 ACAGGTAAGCACACAAATATATTATGG 57.933 33.333 12.11 3.44 0.00 2.74
3311 3437 8.621532 AGCACACAAATATATTATGGGTACTG 57.378 34.615 12.30 2.85 0.00 2.74
3314 3440 8.999431 CACACAAATATATTATGGGTACTGGTC 58.001 37.037 12.30 0.00 0.00 4.02
3319 3445 1.209621 TTATGGGTACTGGTCCCTGC 58.790 55.000 10.00 0.00 44.84 4.85
3320 3446 0.341961 TATGGGTACTGGTCCCTGCT 59.658 55.000 10.00 0.34 44.84 4.24
3449 3578 1.131504 GAGAGACACTGTAGACGGCTG 59.868 57.143 0.00 0.00 0.00 4.85
3512 3641 5.771666 TCAATCAAGATCAGCCAGAAGTTTT 59.228 36.000 0.00 0.00 0.00 2.43
3583 3712 1.850377 TGCGTGCCATGTTTTTCTTG 58.150 45.000 0.00 0.00 0.00 3.02
3584 3713 1.406898 TGCGTGCCATGTTTTTCTTGA 59.593 42.857 0.00 0.00 0.00 3.02
3668 3799 4.883585 TGGCTATAGCTGAAGTTGGATTTG 59.116 41.667 23.53 0.00 41.70 2.32
3706 3837 2.165167 TCAAGGGCAGAGAAAATGCAG 58.835 47.619 0.00 0.00 45.68 4.41
3727 3858 5.133941 CAGAGCCTGATACAAGGAGTACTA 58.866 45.833 0.00 0.00 40.02 1.82
4111 4242 0.389948 GTGAGCAGGGTCGTTTCGAT 60.390 55.000 0.00 0.00 38.42 3.59
4385 4516 7.013369 AGTCCTTGACATTTCCTAACAGTTTTC 59.987 37.037 0.00 0.00 34.60 2.29
4478 4609 4.318332 TGTCTCCAGATTTTACAGTGCAG 58.682 43.478 0.00 0.00 0.00 4.41
4597 4728 4.269183 CAGGTACATTGCCCTGTATTTGA 58.731 43.478 12.62 0.00 42.72 2.69
4624 4755 0.464916 TGCATCAGTAGGCCATGCAG 60.465 55.000 20.48 6.66 46.22 4.41
4661 4792 3.619979 GCTCTGTTACTAGTGGCCATGTT 60.620 47.826 9.72 0.00 0.00 2.71
4666 4797 4.277174 TGTTACTAGTGGCCATGTTGTTTG 59.723 41.667 9.72 0.00 0.00 2.93
5054 5185 4.557554 CACACACCCTGACTTGCA 57.442 55.556 0.00 0.00 0.00 4.08
5127 5258 4.027437 AGCCTTTTGTGTCCTGGTAAAAA 58.973 39.130 0.00 0.00 0.00 1.94
5130 5261 6.325286 AGCCTTTTGTGTCCTGGTAAAAATAA 59.675 34.615 0.00 0.00 0.00 1.40
5131 5262 7.016170 AGCCTTTTGTGTCCTGGTAAAAATAAT 59.984 33.333 0.00 0.00 0.00 1.28
5132 5263 8.308207 GCCTTTTGTGTCCTGGTAAAAATAATA 58.692 33.333 0.00 0.00 0.00 0.98
5133 5264 9.855021 CCTTTTGTGTCCTGGTAAAAATAATAG 57.145 33.333 0.00 0.00 0.00 1.73
5159 5290 9.305925 GTAATCAAATTCCCATGCTCTAAAAAG 57.694 33.333 0.00 0.00 0.00 2.27
5171 5303 5.083136 GCTCTAAAAAGCAAAAAGGTTGC 57.917 39.130 2.85 2.85 45.22 4.17
5200 5332 6.751888 CCAAACTTATTTTCTTTCATAGGGCG 59.248 38.462 0.00 0.00 0.00 6.13
5233 5365 9.967346 TGATCGGTTTTACATGAAAATTTACAA 57.033 25.926 0.00 0.00 39.22 2.41
5235 5367 8.288217 TCGGTTTTACATGAAAATTTACAAGC 57.712 30.769 0.00 0.00 39.22 4.01
5245 5377 8.658609 CATGAAAATTTACAAGCACATAAAGGG 58.341 33.333 0.00 0.00 0.00 3.95
5263 5395 1.275856 GGGCTCAAACAATTGGCATGA 59.724 47.619 10.83 9.71 37.15 3.07
5264 5396 2.613691 GGCTCAAACAATTGGCATGAG 58.386 47.619 22.74 22.74 40.30 2.90
5266 5398 3.555586 GGCTCAAACAATTGGCATGAGTT 60.556 43.478 25.28 4.67 39.68 3.01
5267 5399 4.060205 GCTCAAACAATTGGCATGAGTTT 58.940 39.130 25.28 9.69 39.68 2.66
5268 5400 4.084223 GCTCAAACAATTGGCATGAGTTTG 60.084 41.667 25.28 22.44 46.20 2.93
5305 5438 7.483691 GCGTCGGAAAAATAGTTTGATATGTTT 59.516 33.333 0.00 0.00 0.00 2.83
5364 5506 2.678769 GCCTTTGGAATGCAGAAATGGG 60.679 50.000 0.00 0.00 0.00 4.00
5403 5545 4.985413 ACCACAATCACATAAATTCTGCG 58.015 39.130 0.00 0.00 0.00 5.18
5441 5584 2.360475 GCTGGAGAGTTGGCACCC 60.360 66.667 0.00 0.00 0.00 4.61
5476 5619 0.543410 TTTAGGGGAGTCTGCGGACA 60.543 55.000 27.02 2.54 44.36 4.02
5500 5643 5.045872 GGATTCAGTCTAAATGCATTTGCC 58.954 41.667 30.43 18.59 41.18 4.52
5502 5645 3.700538 TCAGTCTAAATGCATTTGCCCT 58.299 40.909 30.43 19.93 41.18 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.952030 TCATATACACACAAGATGTAAAAGGAA 57.048 29.630 0.00 0.00 40.64 3.36
71 72 4.487804 AGCACATAGTCCTCCTGTCATAT 58.512 43.478 0.00 0.00 0.00 1.78
105 106 0.519519 TGGTTAGTTTTGCATCGCGG 59.480 50.000 6.13 0.00 0.00 6.46
112 113 3.092334 CCAACACCTGGTTAGTTTTGC 57.908 47.619 0.00 0.00 40.78 3.68
167 168 1.848886 GACCCATTCCCCGTCCAACT 61.849 60.000 0.00 0.00 0.00 3.16
174 175 1.525995 CATTCGGACCCATTCCCCG 60.526 63.158 0.00 0.00 42.27 5.73
230 232 1.982430 TCCAGAGCAATGGAAGCGA 59.018 52.632 7.41 0.00 46.45 4.93
231 233 4.623814 TCCAGAGCAATGGAAGCG 57.376 55.556 7.41 0.00 46.45 4.68
448 460 4.729746 GCGGAATAAAATGGACCGAAGAAC 60.730 45.833 0.00 0.00 45.31 3.01
482 494 5.598005 CCCCAAAATGCTGTATTCTGGAATA 59.402 40.000 11.79 0.00 32.50 1.75
483 495 4.406649 CCCCAAAATGCTGTATTCTGGAAT 59.593 41.667 11.79 1.40 34.93 3.01
484 496 3.768757 CCCCAAAATGCTGTATTCTGGAA 59.231 43.478 11.79 0.00 0.00 3.53
485 497 3.245586 ACCCCAAAATGCTGTATTCTGGA 60.246 43.478 11.79 0.00 0.00 3.86
486 498 3.099141 ACCCCAAAATGCTGTATTCTGG 58.901 45.455 4.07 4.07 0.00 3.86
487 499 4.497300 CAACCCCAAAATGCTGTATTCTG 58.503 43.478 0.00 0.00 0.00 3.02
488 500 3.055891 GCAACCCCAAAATGCTGTATTCT 60.056 43.478 0.00 0.00 37.12 2.40
492 504 0.972883 GGCAACCCCAAAATGCTGTA 59.027 50.000 0.00 0.00 39.94 2.74
494 506 1.753470 TGGCAACCCCAAAATGCTG 59.247 52.632 0.00 0.00 41.82 4.41
555 567 4.656112 TGAAAGAGAAGAGGGTTGAAGACT 59.344 41.667 0.00 0.00 0.00 3.24
557 569 5.555017 CATGAAAGAGAAGAGGGTTGAAGA 58.445 41.667 0.00 0.00 0.00 2.87
558 570 4.155644 GCATGAAAGAGAAGAGGGTTGAAG 59.844 45.833 0.00 0.00 0.00 3.02
559 571 4.074970 GCATGAAAGAGAAGAGGGTTGAA 58.925 43.478 0.00 0.00 0.00 2.69
560 572 3.328931 AGCATGAAAGAGAAGAGGGTTGA 59.671 43.478 0.00 0.00 0.00 3.18
561 573 3.683802 AGCATGAAAGAGAAGAGGGTTG 58.316 45.455 0.00 0.00 0.00 3.77
562 574 4.379302 AAGCATGAAAGAGAAGAGGGTT 57.621 40.909 0.00 0.00 0.00 4.11
563 575 5.707066 ATAAGCATGAAAGAGAAGAGGGT 57.293 39.130 0.00 0.00 0.00 4.34
564 576 7.603404 CAGATATAAGCATGAAAGAGAAGAGGG 59.397 40.741 0.00 0.00 0.00 4.30
565 577 8.149647 ACAGATATAAGCATGAAAGAGAAGAGG 58.850 37.037 0.00 0.00 0.00 3.69
566 578 9.195411 GACAGATATAAGCATGAAAGAGAAGAG 57.805 37.037 0.00 0.00 0.00 2.85
567 579 8.922237 AGACAGATATAAGCATGAAAGAGAAGA 58.078 33.333 0.00 0.00 0.00 2.87
568 580 9.195411 GAGACAGATATAAGCATGAAAGAGAAG 57.805 37.037 0.00 0.00 0.00 2.85
569 581 8.699130 TGAGACAGATATAAGCATGAAAGAGAA 58.301 33.333 0.00 0.00 0.00 2.87
570 582 8.242729 TGAGACAGATATAAGCATGAAAGAGA 57.757 34.615 0.00 0.00 0.00 3.10
571 583 8.883954 TTGAGACAGATATAAGCATGAAAGAG 57.116 34.615 0.00 0.00 0.00 2.85
572 584 8.481314 ACTTGAGACAGATATAAGCATGAAAGA 58.519 33.333 0.00 0.00 0.00 2.52
573 585 8.659925 ACTTGAGACAGATATAAGCATGAAAG 57.340 34.615 0.00 0.00 0.00 2.62
574 586 8.886719 CAACTTGAGACAGATATAAGCATGAAA 58.113 33.333 0.00 0.00 0.00 2.69
575 587 7.496920 CCAACTTGAGACAGATATAAGCATGAA 59.503 37.037 0.00 0.00 0.00 2.57
576 588 6.988580 CCAACTTGAGACAGATATAAGCATGA 59.011 38.462 0.00 0.00 0.00 3.07
577 589 6.204301 CCCAACTTGAGACAGATATAAGCATG 59.796 42.308 0.00 0.00 0.00 4.06
578 590 6.294473 CCCAACTTGAGACAGATATAAGCAT 58.706 40.000 0.00 0.00 0.00 3.79
579 591 5.396772 CCCCAACTTGAGACAGATATAAGCA 60.397 44.000 0.00 0.00 0.00 3.91
580 592 5.059833 CCCCAACTTGAGACAGATATAAGC 58.940 45.833 0.00 0.00 0.00 3.09
581 593 5.059833 GCCCCAACTTGAGACAGATATAAG 58.940 45.833 0.00 0.00 0.00 1.73
582 594 4.141482 GGCCCCAACTTGAGACAGATATAA 60.141 45.833 0.00 0.00 0.00 0.98
583 595 3.391296 GGCCCCAACTTGAGACAGATATA 59.609 47.826 0.00 0.00 0.00 0.86
584 596 2.173569 GGCCCCAACTTGAGACAGATAT 59.826 50.000 0.00 0.00 0.00 1.63
585 597 1.559682 GGCCCCAACTTGAGACAGATA 59.440 52.381 0.00 0.00 0.00 1.98
586 598 0.329596 GGCCCCAACTTGAGACAGAT 59.670 55.000 0.00 0.00 0.00 2.90
587 599 1.761174 GGCCCCAACTTGAGACAGA 59.239 57.895 0.00 0.00 0.00 3.41
588 600 1.303643 GGGCCCCAACTTGAGACAG 60.304 63.158 12.23 0.00 0.00 3.51
589 601 2.067932 CTGGGCCCCAACTTGAGACA 62.068 60.000 22.27 0.00 30.80 3.41
590 602 1.303643 CTGGGCCCCAACTTGAGAC 60.304 63.158 22.27 0.00 30.80 3.36
591 603 2.538141 CCTGGGCCCCAACTTGAGA 61.538 63.158 22.27 0.00 30.80 3.27
592 604 2.036256 CCTGGGCCCCAACTTGAG 59.964 66.667 22.27 7.82 30.80 3.02
593 605 1.955458 AAACCTGGGCCCCAACTTGA 61.955 55.000 22.27 0.00 30.80 3.02
594 606 0.178947 TAAACCTGGGCCCCAACTTG 60.179 55.000 22.27 3.37 30.80 3.16
595 607 0.563672 TTAAACCTGGGCCCCAACTT 59.436 50.000 22.27 10.44 30.80 2.66
596 608 0.790339 ATTAAACCTGGGCCCCAACT 59.210 50.000 22.27 2.08 30.80 3.16
597 609 1.651737 AATTAAACCTGGGCCCCAAC 58.348 50.000 22.27 0.00 30.80 3.77
607 619 7.112452 AGAAGAACACTGCAAAATTAAACCT 57.888 32.000 0.00 0.00 0.00 3.50
661 673 8.287904 ACCCCAAAGATAGGATGATTGTAATA 57.712 34.615 0.00 0.00 0.00 0.98
662 674 7.166758 ACCCCAAAGATAGGATGATTGTAAT 57.833 36.000 0.00 0.00 0.00 1.89
710 722 6.893759 AGATAAATCGAGAGACATGTACGAG 58.106 40.000 17.04 7.86 46.97 4.18
1038 1050 0.764890 CCAGGGTTCTTGACAGTGGA 59.235 55.000 0.00 0.00 35.60 4.02
1109 1121 4.467438 TGTCAGAAGGAGATGCATACTTGA 59.533 41.667 13.55 5.90 0.00 3.02
1506 1518 1.822371 ACTTCTTCCTCGCTCTTCTCC 59.178 52.381 0.00 0.00 0.00 3.71
1578 1590 1.091771 CAGACATACAAGGGCTGCCG 61.092 60.000 13.40 1.04 0.00 5.69
1608 1620 1.461091 TTCTTGACCCGACTGAGCGT 61.461 55.000 0.00 0.00 0.00 5.07
1617 1629 1.593196 TTGTGCTTCTTCTTGACCCG 58.407 50.000 0.00 0.00 0.00 5.28
1623 1635 3.439857 TGCCCTATTGTGCTTCTTCTT 57.560 42.857 0.00 0.00 0.00 2.52
1636 1648 1.771255 GTCCTCAGTTCCATGCCCTAT 59.229 52.381 0.00 0.00 0.00 2.57
1743 1755 6.997655 ACCATCGCTATCTGAATAAAGATCA 58.002 36.000 0.00 0.00 37.98 2.92
1755 1767 0.965439 GCTCTGGACCATCGCTATCT 59.035 55.000 0.00 0.00 0.00 1.98
1761 1773 0.460987 GAGGTTGCTCTGGACCATCG 60.461 60.000 0.00 0.00 38.42 3.84
1800 1812 2.443887 TTTCTTGGAACGGTACCTCG 57.556 50.000 10.90 0.00 0.00 4.63
2016 2028 4.098654 TCTTCGAGAGAGAGGCAATTTAGG 59.901 45.833 0.00 0.00 43.69 2.69
2061 2073 6.145858 CAGAGAAGAGAATGACACACTCTTTG 59.854 42.308 19.89 13.75 46.49 2.77
2178 2190 1.335689 ACCTTGAAGCGTGACGAGTAC 60.336 52.381 10.10 0.00 0.00 2.73
2974 2989 4.019771 TCAGAACATGCCACACCATTACTA 60.020 41.667 0.00 0.00 0.00 1.82
2984 2999 3.127548 CACTGGTTATCAGAACATGCCAC 59.872 47.826 0.00 0.00 46.18 5.01
3012 3027 6.942532 AGACAGCAAACTTTTCATAGTTCA 57.057 33.333 0.00 0.00 37.37 3.18
3032 3047 5.662674 AGTGGAACAGAAGGTATGTAGAC 57.337 43.478 0.00 0.00 41.80 2.59
3035 3050 7.549147 AACTTAGTGGAACAGAAGGTATGTA 57.451 36.000 0.00 0.00 41.80 2.29
3158 3174 8.470002 GTTGCCTTATTTCTTGATGTCCTTAAT 58.530 33.333 0.00 0.00 0.00 1.40
3161 3177 6.012745 AGTTGCCTTATTTCTTGATGTCCTT 58.987 36.000 0.00 0.00 0.00 3.36
3219 3235 6.782082 TTCTGCTACTATGTCAGATTCAGT 57.218 37.500 0.00 0.00 36.81 3.41
3263 3279 6.553953 TTACCTGTATATCCTGTTGCTGAA 57.446 37.500 0.00 0.00 0.00 3.02
3305 3431 0.614979 TCTGAGCAGGGACCAGTACC 60.615 60.000 0.00 0.00 0.00 3.34
3311 3437 5.489792 TTATATCATTCTGAGCAGGGACC 57.510 43.478 0.00 0.00 0.00 4.46
3314 3440 9.902684 AGAAATATTATATCATTCTGAGCAGGG 57.097 33.333 0.00 0.00 0.00 4.45
3344 3473 1.562942 ACCCAGTCATCTGCACATGAT 59.437 47.619 7.96 0.00 40.09 2.45
3346 3475 2.696989 TACCCAGTCATCTGCACATG 57.303 50.000 0.00 0.00 40.09 3.21
3449 3578 4.074970 TCCTCCAGATGTTTTCAAGCTTC 58.925 43.478 0.00 0.00 0.00 3.86
3512 3641 7.739995 TGATAGGATTCCTTCTTTCTTGAGA 57.260 36.000 11.25 0.00 34.61 3.27
3564 3693 1.406898 TCAAGAAAAACATGGCACGCA 59.593 42.857 0.00 0.00 0.00 5.24
3583 3712 4.706962 ACAAACCTATGAGAAGGCCAATTC 59.293 41.667 5.01 0.00 40.62 2.17
3584 3713 4.463891 CACAAACCTATGAGAAGGCCAATT 59.536 41.667 5.01 0.00 40.62 2.32
3638 3769 2.461300 TCAGCTATAGCCACCTCTGT 57.539 50.000 21.17 0.00 43.38 3.41
3668 3799 2.032680 TGATAGGTGATCCGGGTGACC 61.033 57.143 16.68 16.68 38.82 4.02
3706 3837 4.888239 TGTAGTACTCCTTGTATCAGGCTC 59.112 45.833 0.00 0.00 33.35 4.70
3727 3858 1.300697 GAACCCGAGAACGTGCTGT 60.301 57.895 0.00 0.00 37.88 4.40
3862 3993 4.564406 GGTTCATCCTCATCTGTCACTGTT 60.564 45.833 0.00 0.00 0.00 3.16
3976 4107 0.606401 CGGAGCCATGAACTGTTGGT 60.606 55.000 0.00 0.00 35.34 3.67
4111 4242 1.050988 GGTCAGGCTCCTGGATGCTA 61.051 60.000 15.32 0.00 43.75 3.49
4404 4535 0.591170 AACGTTTCCTGCCGAACATG 59.409 50.000 0.00 0.00 0.00 3.21
4478 4609 4.095483 CAGGAGAAACAATGAGTATGGTGC 59.905 45.833 0.00 0.00 0.00 5.01
4597 4728 1.474677 GCCTACTGATGCAGTGATGCT 60.475 52.381 10.15 0.00 45.01 3.79
4624 4755 2.028567 ACAGAGCAGCAAGACCTCTAAC 60.029 50.000 0.00 0.00 34.37 2.34
5037 5168 0.747644 TGTGCAAGTCAGGGTGTGTG 60.748 55.000 0.00 0.00 0.00 3.82
5038 5169 0.183492 ATGTGCAAGTCAGGGTGTGT 59.817 50.000 0.00 0.00 0.00 3.72
5039 5170 2.183478 TATGTGCAAGTCAGGGTGTG 57.817 50.000 0.00 0.00 0.00 3.82
5040 5171 3.519510 ACTATATGTGCAAGTCAGGGTGT 59.480 43.478 0.00 0.00 0.00 4.16
5041 5172 3.873361 CACTATATGTGCAAGTCAGGGTG 59.127 47.826 0.00 0.00 40.06 4.61
5042 5173 4.142609 CACTATATGTGCAAGTCAGGGT 57.857 45.455 0.00 0.00 40.06 4.34
5052 5183 6.749139 TGAGGATACAAGACACTATATGTGC 58.251 40.000 5.52 0.00 45.66 4.57
5065 5196 8.613060 ATGTACAAGCATATTGAGGATACAAG 57.387 34.615 0.00 0.00 41.41 3.16
5082 5213 8.925700 GGCTCCTTTTTCATTAAAATGTACAAG 58.074 33.333 0.00 2.82 35.29 3.16
5130 5261 9.866655 TTTAGAGCATGGGAATTTGATTACTAT 57.133 29.630 0.00 0.00 0.00 2.12
5131 5262 9.693739 TTTTAGAGCATGGGAATTTGATTACTA 57.306 29.630 0.00 0.00 0.00 1.82
5132 5263 8.593945 TTTTAGAGCATGGGAATTTGATTACT 57.406 30.769 0.00 0.00 0.00 2.24
5133 5264 9.305925 CTTTTTAGAGCATGGGAATTTGATTAC 57.694 33.333 0.00 0.00 0.00 1.89
5134 5265 7.981225 GCTTTTTAGAGCATGGGAATTTGATTA 59.019 33.333 0.00 0.00 42.25 1.75
5135 5266 6.820152 GCTTTTTAGAGCATGGGAATTTGATT 59.180 34.615 0.00 0.00 42.25 2.57
5136 5267 6.343703 GCTTTTTAGAGCATGGGAATTTGAT 58.656 36.000 0.00 0.00 42.25 2.57
5159 5290 3.318875 GGTGCGCAACCTTTTTGC 58.681 55.556 16.48 0.00 46.55 3.68
5170 5302 4.742659 TGAAAGAAAATAAGTTTGGTGCGC 59.257 37.500 0.00 0.00 0.00 6.09
5171 5303 7.273381 CCTATGAAAGAAAATAAGTTTGGTGCG 59.727 37.037 0.00 0.00 0.00 5.34
5183 5315 3.088532 TGTGCGCCCTATGAAAGAAAAT 58.911 40.909 4.18 0.00 0.00 1.82
5200 5332 3.889196 TGTAAAACCGATCAGTTGTGC 57.111 42.857 0.00 0.00 0.00 4.57
5233 5365 2.875296 TGTTTGAGCCCTTTATGTGCT 58.125 42.857 0.00 0.00 38.24 4.40
5235 5367 4.931002 CCAATTGTTTGAGCCCTTTATGTG 59.069 41.667 4.43 0.00 34.60 3.21
5245 5377 3.308438 ACTCATGCCAATTGTTTGAGC 57.692 42.857 20.67 11.37 37.84 4.26
5275 5408 6.483385 TCAAACTATTTTTCCGACGCATTA 57.517 33.333 0.00 0.00 0.00 1.90
5334 5472 1.815003 CATTCCAAAGGCCACACTCTC 59.185 52.381 5.01 0.00 0.00 3.20
5335 5473 1.915141 CATTCCAAAGGCCACACTCT 58.085 50.000 5.01 0.00 0.00 3.24
5336 5474 0.244721 GCATTCCAAAGGCCACACTC 59.755 55.000 5.01 0.00 0.00 3.51
5337 5475 0.469705 TGCATTCCAAAGGCCACACT 60.470 50.000 5.01 0.00 0.00 3.55
5338 5476 0.037975 CTGCATTCCAAAGGCCACAC 60.038 55.000 5.01 0.00 0.00 3.82
5364 5506 5.437289 TGTGGTTCATCTTGTTTGATCAC 57.563 39.130 0.00 0.00 32.76 3.06
5403 5545 3.184379 GCTTCGGGCAAAATTTTGAGTTC 59.816 43.478 30.40 14.68 40.55 3.01
5463 5606 0.179097 GAATCCTGTCCGCAGACTCC 60.179 60.000 1.05 0.00 45.28 3.85
5476 5619 5.163478 GGCAAATGCATTTAGACTGAATCCT 60.163 40.000 23.69 0.00 44.36 3.24
5500 5643 4.452455 ACAAATAACAAGAACTCGCTCAGG 59.548 41.667 0.00 0.00 0.00 3.86
5502 5645 7.485418 TTTACAAATAACAAGAACTCGCTCA 57.515 32.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.