Multiple sequence alignment - TraesCS6B01G310300

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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 TraesCS6B01G310300 chr6B 100.000 2591 0 0 1 2591 555558295 555555705 0.000000e+00 4785.0
1 TraesCS6B01G310300 chr6A 90.714 1820 68 27 662 2479 511425566 511423846 0.000000e+00 2331.0
2 TraesCS6B01G310300 chr6A 79.959 484 59 17 8 490 511426096 511425650 3.220000e-84 322.0
3 TraesCS6B01G310300 chr6A 97.826 46 1 0 538 583 511425655 511425610 2.140000e-11 80.5
4 TraesCS6B01G310300 chr6A 95.349 43 1 1 2549 2591 511423409 511423368 1.660000e-07 67.6
5 TraesCS6B01G310300 chr6D 89.731 1860 109 30 9 1858 370369409 370367622 0.000000e+00 2302.0
6 TraesCS6B01G310300 chr6D 93.238 562 32 5 2032 2591 370367446 370366889 0.000000e+00 822.0
7 TraesCS6B01G310300 chr6D 97.345 113 3 0 1922 2034 370367620 370367508 2.630000e-45 193.0
8 TraesCS6B01G310300 chr1D 90.141 142 14 0 1383 1524 44620954 44620813 4.400000e-43 185.0
9 TraesCS6B01G310300 chr4D 98.485 66 1 0 1500 1565 472678178 472678243 1.630000e-22 117.0
10 TraesCS6B01G310300 chr4D 90.217 92 4 5 1382 1473 472678340 472678254 5.860000e-22 115.0
11 TraesCS6B01G310300 chr5B 95.238 42 2 0 446 487 375802270 375802229 1.660000e-07 67.6
12 TraesCS6B01G310300 chr1A 93.333 45 3 0 443 487 313908389 313908433 1.660000e-07 67.6
13 TraesCS6B01G310300 chr5A 89.796 49 5 0 442 490 601467971 601467923 2.150000e-06 63.9
14 TraesCS6B01G310300 chr2A 91.111 45 4 0 443 487 614574958 614574914 7.740000e-06 62.1
15 TraesCS6B01G310300 chr5D 100.000 30 0 0 457 486 397025667 397025696 3.600000e-04 56.5


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 TraesCS6B01G310300 chr6B 555555705 555558295 2590 True 4785.000000 4785 100.000 1 2591 1 chr6B.!!$R1 2590
1 TraesCS6B01G310300 chr6A 511423368 511426096 2728 True 700.275000 2331 90.962 8 2591 4 chr6A.!!$R1 2583
2 TraesCS6B01G310300 chr6D 370366889 370369409 2520 True 1105.666667 2302 93.438 9 2591 3 chr6D.!!$R1 2582

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
619 645 0.250081 GATTGGATGGCCGACTCTCC 60.25 60.0 0.0 0.0 36.79 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2398 2494 0.17668 TAGTAAGCAGCAGCAGCCTC 59.823 55.0 6.1 0.0 45.49 4.7 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
35 36 4.617530 CGACCTTCGTCAAGACCATCTTTA 60.618 45.833 0.00 0.00 39.11 1.85
46 47 5.825593 AGACCATCTTTAAGTCAGTTGGA 57.174 39.130 8.95 0.00 35.45 3.53
55 56 8.608844 TCTTTAAGTCAGTTGGAGAGAAAATC 57.391 34.615 0.00 0.00 0.00 2.17
93 94 3.593780 AGACAAAAGGGGCTAGAAAGGAT 59.406 43.478 0.00 0.00 0.00 3.24
94 95 3.696548 GACAAAAGGGGCTAGAAAGGATG 59.303 47.826 0.00 0.00 0.00 3.51
95 96 3.076032 ACAAAAGGGGCTAGAAAGGATGT 59.924 43.478 0.00 0.00 0.00 3.06
96 97 4.291249 ACAAAAGGGGCTAGAAAGGATGTA 59.709 41.667 0.00 0.00 0.00 2.29
97 98 5.222254 ACAAAAGGGGCTAGAAAGGATGTAA 60.222 40.000 0.00 0.00 0.00 2.41
98 99 5.530176 AAAGGGGCTAGAAAGGATGTAAA 57.470 39.130 0.00 0.00 0.00 2.01
99 100 4.779993 AGGGGCTAGAAAGGATGTAAAG 57.220 45.455 0.00 0.00 0.00 1.85
100 101 4.371681 AGGGGCTAGAAAGGATGTAAAGA 58.628 43.478 0.00 0.00 0.00 2.52
101 102 4.410555 AGGGGCTAGAAAGGATGTAAAGAG 59.589 45.833 0.00 0.00 0.00 2.85
102 103 4.409247 GGGGCTAGAAAGGATGTAAAGAGA 59.591 45.833 0.00 0.00 0.00 3.10
103 104 5.454045 GGGGCTAGAAAGGATGTAAAGAGAG 60.454 48.000 0.00 0.00 0.00 3.20
104 105 5.053811 GGCTAGAAAGGATGTAAAGAGAGC 58.946 45.833 0.00 0.00 0.00 4.09
105 106 5.395768 GGCTAGAAAGGATGTAAAGAGAGCA 60.396 44.000 0.00 0.00 0.00 4.26
106 107 6.287525 GCTAGAAAGGATGTAAAGAGAGCAT 58.712 40.000 0.00 0.00 0.00 3.79
107 108 6.765512 GCTAGAAAGGATGTAAAGAGAGCATT 59.234 38.462 0.00 0.00 0.00 3.56
108 109 7.281999 GCTAGAAAGGATGTAAAGAGAGCATTT 59.718 37.037 0.00 0.00 0.00 2.32
109 110 7.388460 AGAAAGGATGTAAAGAGAGCATTTG 57.612 36.000 0.00 0.00 0.00 2.32
132 133 0.532573 TGCTTCAACCCGTTTTGCAA 59.467 45.000 0.00 0.00 0.00 4.08
150 151 5.431420 TGCAATTGTTCGAGAAGCTAAAA 57.569 34.783 7.40 0.00 0.00 1.52
191 192 3.005554 CTCATGTGAGGTGATGACAACC 58.994 50.000 2.03 0.00 38.48 3.77
226 227 1.741706 CAACATGACTGTGGAGGATGC 59.258 52.381 0.00 0.00 35.22 3.91
227 228 1.283347 ACATGACTGTGGAGGATGCT 58.717 50.000 0.00 0.00 33.22 3.79
237 238 2.111384 TGGAGGATGCTAGTGAAGGAC 58.889 52.381 0.00 0.00 0.00 3.85
245 246 0.818296 CTAGTGAAGGACCTGACGGG 59.182 60.000 0.00 0.00 41.89 5.28
252 253 0.561184 AGGACCTGACGGGGATATGA 59.439 55.000 5.03 0.00 40.03 2.15
256 257 3.557264 GGACCTGACGGGGATATGAAATC 60.557 52.174 5.03 0.00 40.03 2.17
264 265 4.656112 ACGGGGATATGAAATCTGAGAACT 59.344 41.667 0.00 0.00 0.00 3.01
273 274 6.166984 TGAAATCTGAGAACTTGAGTGACT 57.833 37.500 0.00 0.00 0.00 3.41
284 285 3.007398 ACTTGAGTGACTCCATCCAACTC 59.993 47.826 10.52 0.00 0.00 3.01
291 292 2.769095 GACTCCATCCAACTCCTAGCTT 59.231 50.000 0.00 0.00 0.00 3.74
299 300 6.495181 CCATCCAACTCCTAGCTTAGAATCTA 59.505 42.308 0.00 0.00 0.00 1.98
300 301 7.015682 CCATCCAACTCCTAGCTTAGAATCTAA 59.984 40.741 2.44 2.44 0.00 2.10
307 308 7.014808 ACTCCTAGCTTAGAATCTAACCATGTC 59.985 40.741 0.00 0.00 0.00 3.06
312 313 6.609212 AGCTTAGAATCTAACCATGTCTGAGA 59.391 38.462 0.00 0.00 0.00 3.27
327 328 5.192927 TGTCTGAGAAGTTTGTCCAAATGT 58.807 37.500 0.00 0.00 32.36 2.71
328 329 5.066375 TGTCTGAGAAGTTTGTCCAAATGTG 59.934 40.000 0.00 0.00 32.36 3.21
330 331 5.066375 TCTGAGAAGTTTGTCCAAATGTGTG 59.934 40.000 0.00 0.00 32.36 3.82
333 334 6.071672 TGAGAAGTTTGTCCAAATGTGTGAAA 60.072 34.615 0.00 0.00 32.36 2.69
335 336 7.158021 AGAAGTTTGTCCAAATGTGTGAAAAA 58.842 30.769 0.00 0.00 32.36 1.94
365 366 6.366630 GCATTGAGCGACTTAAGAATAATCC 58.633 40.000 10.09 0.00 0.00 3.01
367 368 4.617959 TGAGCGACTTAAGAATAATCCGG 58.382 43.478 10.09 0.00 0.00 5.14
381 387 5.745312 ATAATCCGGTTGAGCATCTATGA 57.255 39.130 0.00 0.00 34.92 2.15
382 388 3.674528 ATCCGGTTGAGCATCTATGAG 57.325 47.619 0.00 0.00 34.92 2.90
383 389 1.069204 TCCGGTTGAGCATCTATGAGC 59.931 52.381 0.00 0.00 34.92 4.26
384 390 1.069823 CCGGTTGAGCATCTATGAGCT 59.930 52.381 0.00 0.00 45.25 4.09
385 391 2.133553 CGGTTGAGCATCTATGAGCTG 58.866 52.381 0.00 0.00 42.04 4.24
391 397 6.094048 GGTTGAGCATCTATGAGCTGTTAAAA 59.906 38.462 0.00 0.00 42.04 1.52
396 402 6.317391 AGCATCTATGAGCTGTTAAAAAGGAC 59.683 38.462 0.00 0.00 40.13 3.85
413 419 7.833285 AAAAGGACTCAAGTTTGGCTATTTA 57.167 32.000 0.00 0.00 0.00 1.40
490 496 8.555166 TGTCGTTTTAGCAGTTCAATTTAAAG 57.445 30.769 0.00 0.00 0.00 1.85
491 497 7.166804 TGTCGTTTTAGCAGTTCAATTTAAAGC 59.833 33.333 0.00 0.00 0.00 3.51
492 498 7.166804 GTCGTTTTAGCAGTTCAATTTAAAGCA 59.833 33.333 0.00 0.00 0.00 3.91
493 499 7.378461 TCGTTTTAGCAGTTCAATTTAAAGCAG 59.622 33.333 0.00 0.00 0.00 4.24
494 500 7.167468 CGTTTTAGCAGTTCAATTTAAAGCAGT 59.833 33.333 0.00 0.00 0.00 4.40
495 501 8.817100 GTTTTAGCAGTTCAATTTAAAGCAGTT 58.183 29.630 0.00 0.00 0.00 3.16
496 502 8.574196 TTTAGCAGTTCAATTTAAAGCAGTTC 57.426 30.769 0.00 0.00 0.00 3.01
497 503 6.147864 AGCAGTTCAATTTAAAGCAGTTCA 57.852 33.333 0.00 0.00 0.00 3.18
498 504 6.572519 AGCAGTTCAATTTAAAGCAGTTCAA 58.427 32.000 0.00 0.00 0.00 2.69
499 505 7.212274 AGCAGTTCAATTTAAAGCAGTTCAAT 58.788 30.769 0.00 0.00 0.00 2.57
500 506 7.170320 AGCAGTTCAATTTAAAGCAGTTCAATG 59.830 33.333 0.00 0.00 0.00 2.82
501 507 7.042523 GCAGTTCAATTTAAAGCAGTTCAATGT 60.043 33.333 0.00 0.00 0.00 2.71
502 508 8.270799 CAGTTCAATTTAAAGCAGTTCAATGTG 58.729 33.333 0.00 0.00 0.00 3.21
503 509 8.196771 AGTTCAATTTAAAGCAGTTCAATGTGA 58.803 29.630 0.00 0.00 0.00 3.58
504 510 8.816144 GTTCAATTTAAAGCAGTTCAATGTGAA 58.184 29.630 0.00 0.00 33.32 3.18
526 532 9.297586 GTGAACTACTGAAACGACATATATGAA 57.702 33.333 19.63 0.00 0.00 2.57
528 534 8.873215 AACTACTGAAACGACATATATGAAGG 57.127 34.615 19.63 9.72 0.00 3.46
529 535 7.434492 ACTACTGAAACGACATATATGAAGGG 58.566 38.462 19.63 7.46 0.00 3.95
531 537 6.516718 ACTGAAACGACATATATGAAGGGAG 58.483 40.000 19.63 8.14 0.00 4.30
587 604 7.653647 TGAAGTATTGCGGACTTAAAACAAAT 58.346 30.769 0.00 0.00 37.27 2.32
589 606 5.861787 AGTATTGCGGACTTAAAACAAATGC 59.138 36.000 0.00 0.00 0.00 3.56
592 609 4.688021 TGCGGACTTAAAACAAATGCTTT 58.312 34.783 0.00 0.00 0.00 3.51
593 610 4.505922 TGCGGACTTAAAACAAATGCTTTG 59.494 37.500 6.98 6.98 45.95 2.77
608 634 8.072238 CAAATGCTTTGTGATATGATTGGATG 57.928 34.615 0.00 0.00 35.94 3.51
613 639 2.371510 TGTGATATGATTGGATGGCCGA 59.628 45.455 0.00 0.00 36.79 5.54
614 640 2.744202 GTGATATGATTGGATGGCCGAC 59.256 50.000 0.00 0.00 36.79 4.79
617 643 1.135094 ATGATTGGATGGCCGACTCT 58.865 50.000 0.00 0.00 36.79 3.24
618 644 0.465705 TGATTGGATGGCCGACTCTC 59.534 55.000 0.00 0.00 36.79 3.20
619 645 0.250081 GATTGGATGGCCGACTCTCC 60.250 60.000 0.00 0.00 36.79 3.71
620 646 0.692419 ATTGGATGGCCGACTCTCCT 60.692 55.000 0.00 0.00 36.79 3.69
621 647 1.617018 TTGGATGGCCGACTCTCCTG 61.617 60.000 0.00 0.00 36.79 3.86
622 648 2.060980 GGATGGCCGACTCTCCTGT 61.061 63.158 0.00 0.00 0.00 4.00
623 649 1.439644 GATGGCCGACTCTCCTGTC 59.560 63.158 0.00 0.00 0.00 3.51
624 650 1.000993 ATGGCCGACTCTCCTGTCT 59.999 57.895 0.00 0.00 35.00 3.41
625 651 1.040339 ATGGCCGACTCTCCTGTCTC 61.040 60.000 0.00 0.00 35.00 3.36
626 652 2.766400 GGCCGACTCTCCTGTCTCG 61.766 68.421 0.00 0.00 35.00 4.04
627 653 2.041686 GCCGACTCTCCTGTCTCGT 61.042 63.158 0.00 0.00 35.00 4.18
628 654 1.984321 GCCGACTCTCCTGTCTCGTC 61.984 65.000 0.00 0.00 35.00 4.20
629 655 1.370587 CCGACTCTCCTGTCTCGTCC 61.371 65.000 0.00 0.00 35.00 4.79
630 656 1.370587 CGACTCTCCTGTCTCGTCCC 61.371 65.000 0.00 0.00 35.00 4.46
631 657 1.370587 GACTCTCCTGTCTCGTCCCG 61.371 65.000 0.00 0.00 34.39 5.14
632 658 1.377463 CTCTCCTGTCTCGTCCCGT 60.377 63.158 0.00 0.00 0.00 5.28
637 663 1.658114 CTGTCTCGTCCCGTGAACA 59.342 57.895 0.00 0.00 31.44 3.18
684 710 2.154462 CTTGTGTTCAAGGAAGCGGAT 58.846 47.619 0.64 0.00 45.02 4.18
688 714 1.804151 TGTTCAAGGAAGCGGATTTCG 59.196 47.619 0.00 0.00 42.76 3.46
721 747 3.533105 ACGACACGTGGCAGGACA 61.533 61.111 23.63 0.00 39.18 4.02
860 887 1.214217 CTTCCCCTTTCCTACCTCCC 58.786 60.000 0.00 0.00 0.00 4.30
861 888 0.253488 TTCCCCTTTCCTACCTCCCC 60.253 60.000 0.00 0.00 0.00 4.81
862 889 1.166973 TCCCCTTTCCTACCTCCCCT 61.167 60.000 0.00 0.00 0.00 4.79
863 890 0.694783 CCCCTTTCCTACCTCCCCTC 60.695 65.000 0.00 0.00 0.00 4.30
864 891 1.049289 CCCTTTCCTACCTCCCCTCG 61.049 65.000 0.00 0.00 0.00 4.63
865 892 1.687297 CCTTTCCTACCTCCCCTCGC 61.687 65.000 0.00 0.00 0.00 5.03
866 893 1.687297 CTTTCCTACCTCCCCTCGCC 61.687 65.000 0.00 0.00 0.00 5.54
867 894 4.517934 TCCTACCTCCCCTCGCCG 62.518 72.222 0.00 0.00 0.00 6.46
884 911 4.360101 GCACCGCGCTAATCAAAC 57.640 55.556 5.56 0.00 37.77 2.93
935 962 2.888594 CCGCAAGTAAGAAATCGAGGA 58.111 47.619 0.00 0.00 0.00 3.71
1374 1405 4.821589 GAGCGCTCCACCTTCCGG 62.822 72.222 27.22 0.00 0.00 5.14
1828 1860 5.455056 TTTTAACCCTCTTTTGCGCATAA 57.545 34.783 12.75 12.74 0.00 1.90
1884 1916 1.369689 CGCTGCATCTTATTGCGCC 60.370 57.895 4.18 0.00 45.77 6.53
1973 2005 8.492673 TTCTATTCTGTGACATGTTGGTTATC 57.507 34.615 0.00 0.00 0.00 1.75
1985 2017 6.486657 ACATGTTGGTTATCGAATATGGAAGG 59.513 38.462 0.00 0.00 36.07 3.46
2014 2046 8.926710 AGTAACTATGCGATTTAACATAGATGC 58.073 33.333 15.00 8.18 45.65 3.91
2034 2066 4.174009 TGCGTCTGTTTAGCTGATTAGTC 58.826 43.478 0.00 0.00 0.00 2.59
2105 2201 7.796054 AGAACTTGTAATATGCTAGTGTGGAT 58.204 34.615 0.00 0.00 0.00 3.41
2116 2212 4.571984 TGCTAGTGTGGATTTCATGATTCG 59.428 41.667 0.00 0.00 0.00 3.34
2137 2233 3.865745 CGTCTGAATCATGTCCCTAACAC 59.134 47.826 0.00 0.00 41.75 3.32
2167 2263 2.119655 GCAGCTCCTTGGATGCCTG 61.120 63.158 4.38 6.06 41.99 4.85
2182 2278 4.099881 GGATGCCTGAAAAGATTATGGCAA 59.900 41.667 8.57 0.00 44.61 4.52
2226 2322 4.792068 TGGATTGTTCTTCTGTTCTTGGT 58.208 39.130 0.00 0.00 0.00 3.67
2235 2331 8.328758 TGTTCTTCTGTTCTTGGTCCAATATAT 58.671 33.333 4.34 0.00 0.00 0.86
2265 2361 3.074390 TGGATGGACTGTGGACAGATTTT 59.926 43.478 13.74 0.00 46.59 1.82
2325 2421 7.764443 TGAATTAGTTTAGTCAAATCTCCTCGG 59.236 37.037 0.00 0.00 0.00 4.63
2390 2486 1.862827 GCAGCTTGCCTTGAACAAAAG 59.137 47.619 0.00 0.00 37.42 2.27
2396 2492 5.122239 AGCTTGCCTTGAACAAAAGAAAAAC 59.878 36.000 0.00 0.00 0.00 2.43
2397 2493 5.122239 GCTTGCCTTGAACAAAAGAAAAACT 59.878 36.000 0.00 0.00 0.00 2.66
2398 2494 6.479095 TTGCCTTGAACAAAAGAAAAACTG 57.521 33.333 0.00 0.00 0.00 3.16
2399 2495 5.788450 TGCCTTGAACAAAAGAAAAACTGA 58.212 33.333 0.00 0.00 0.00 3.41
2401 2497 5.291858 GCCTTGAACAAAAGAAAAACTGAGG 59.708 40.000 0.00 0.00 0.00 3.86
2402 2498 5.291858 CCTTGAACAAAAGAAAAACTGAGGC 59.708 40.000 0.00 0.00 0.00 4.70
2403 2499 5.659440 TGAACAAAAGAAAAACTGAGGCT 57.341 34.783 0.00 0.00 0.00 4.58
2404 2500 5.410067 TGAACAAAAGAAAAACTGAGGCTG 58.590 37.500 0.00 0.00 0.00 4.85
2405 2501 3.785486 ACAAAAGAAAAACTGAGGCTGC 58.215 40.909 0.00 0.00 0.00 5.25
2406 2502 3.448660 ACAAAAGAAAAACTGAGGCTGCT 59.551 39.130 0.00 0.00 0.00 4.24
2479 2575 3.793465 GCTGTGTTTCTTTGCTCCTGAAC 60.793 47.826 0.00 0.00 0.00 3.18
2481 2577 3.953612 TGTGTTTCTTTGCTCCTGAACAT 59.046 39.130 0.00 0.00 0.00 2.71
2505 2985 1.484038 TTTGTTGCTTGGTCTGCCTT 58.516 45.000 0.00 0.00 35.27 4.35
2518 2998 2.802247 GTCTGCCTTCAAATTTGTTGCC 59.198 45.455 17.47 6.43 0.00 4.52
2521 3001 2.433604 TGCCTTCAAATTTGTTGCCTGA 59.566 40.909 17.47 0.00 0.00 3.86
2526 3006 6.661669 CCTTCAAATTTGTTGCCTGATTTTC 58.338 36.000 17.47 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.038763 TGACGAAGGTCGCCTATCATAAAT 59.961 41.667 0.00 0.00 46.49 1.40
1 2 3.382227 TGACGAAGGTCGCCTATCATAAA 59.618 43.478 0.00 0.00 46.49 1.40
2 3 2.953648 TGACGAAGGTCGCCTATCATAA 59.046 45.455 0.00 0.00 46.49 1.90
3 4 2.578786 TGACGAAGGTCGCCTATCATA 58.421 47.619 0.00 0.00 46.49 2.15
4 5 1.399714 TGACGAAGGTCGCCTATCAT 58.600 50.000 0.00 0.00 46.49 2.45
5 6 1.134367 CTTGACGAAGGTCGCCTATCA 59.866 52.381 0.00 2.15 46.49 2.15
6 7 1.404391 TCTTGACGAAGGTCGCCTATC 59.596 52.381 0.00 0.00 46.49 2.08
35 36 5.066593 GGTGATTTTCTCTCCAACTGACTT 58.933 41.667 0.00 0.00 37.45 3.01
46 47 4.152647 GGGAAAAGTGGGTGATTTTCTCT 58.847 43.478 9.49 0.00 40.94 3.10
55 56 2.383855 TGTCTTTGGGAAAAGTGGGTG 58.616 47.619 0.00 0.00 0.00 4.61
93 94 5.362556 GCACTTCAAATGCTCTCTTTACA 57.637 39.130 0.00 0.00 40.08 2.41
108 109 1.757682 AAACGGGTTGAAGCACTTCA 58.242 45.000 8.99 8.99 46.72 3.02
109 110 2.459934 CAAAACGGGTTGAAGCACTTC 58.540 47.619 3.37 3.37 39.91 3.01
117 118 2.969628 ACAATTGCAAAACGGGTTGA 57.030 40.000 13.60 0.00 0.00 3.18
150 151 7.018349 ACATGAGATCTCTGGATCCCATATTTT 59.982 37.037 22.95 0.00 42.75 1.82
191 192 5.090757 GTCATGTTGTGCATAATGACACAG 58.909 41.667 19.24 4.23 46.65 3.66
200 201 3.337358 CTCCACAGTCATGTTGTGCATA 58.663 45.455 20.43 11.30 43.50 3.14
226 227 0.818296 CCCGTCAGGTCCTTCACTAG 59.182 60.000 0.00 0.00 35.12 2.57
227 228 0.613853 CCCCGTCAGGTCCTTCACTA 60.614 60.000 0.00 0.00 35.12 2.74
237 238 3.324846 TCAGATTTCATATCCCCGTCAGG 59.675 47.826 0.00 0.00 37.24 3.86
245 246 7.984050 TCACTCAAGTTCTCAGATTTCATATCC 59.016 37.037 0.00 0.00 0.00 2.59
252 253 5.070981 TGGAGTCACTCAAGTTCTCAGATTT 59.929 40.000 7.24 0.00 32.06 2.17
256 257 4.493547 GATGGAGTCACTCAAGTTCTCAG 58.506 47.826 7.24 0.00 32.06 3.35
264 265 2.303022 GGAGTTGGATGGAGTCACTCAA 59.697 50.000 7.24 0.00 31.08 3.02
273 274 4.265856 TCTAAGCTAGGAGTTGGATGGA 57.734 45.455 0.00 0.00 0.00 3.41
284 285 7.014711 TCAGACATGGTTAGATTCTAAGCTAGG 59.985 40.741 27.09 20.27 0.00 3.02
291 292 7.962995 ACTTCTCAGACATGGTTAGATTCTA 57.037 36.000 0.00 0.00 0.00 2.10
299 300 4.137543 GGACAAACTTCTCAGACATGGTT 58.862 43.478 0.00 0.00 0.00 3.67
300 301 3.136443 TGGACAAACTTCTCAGACATGGT 59.864 43.478 0.00 0.00 0.00 3.55
307 308 5.066375 TCACACATTTGGACAAACTTCTCAG 59.934 40.000 0.00 0.00 32.51 3.35
333 334 6.374333 TCTTAAGTCGCTCAATGCCTAATTTT 59.626 34.615 1.63 0.00 38.78 1.82
335 336 5.428253 TCTTAAGTCGCTCAATGCCTAATT 58.572 37.500 1.63 0.00 38.78 1.40
339 340 3.334583 TTCTTAAGTCGCTCAATGCCT 57.665 42.857 1.63 0.00 38.78 4.75
341 342 6.366630 GGATTATTCTTAAGTCGCTCAATGC 58.633 40.000 1.63 0.00 38.57 3.56
365 366 2.133553 CAGCTCATAGATGCTCAACCG 58.866 52.381 0.00 0.00 37.44 4.44
367 368 6.668541 TTTAACAGCTCATAGATGCTCAAC 57.331 37.500 0.00 0.00 34.41 3.18
381 387 6.405842 CCAAACTTGAGTCCTTTTTAACAGCT 60.406 38.462 0.00 0.00 0.00 4.24
382 388 5.748630 CCAAACTTGAGTCCTTTTTAACAGC 59.251 40.000 0.00 0.00 0.00 4.40
383 389 5.748630 GCCAAACTTGAGTCCTTTTTAACAG 59.251 40.000 0.00 0.00 0.00 3.16
384 390 5.420739 AGCCAAACTTGAGTCCTTTTTAACA 59.579 36.000 0.00 0.00 0.00 2.41
385 391 5.902681 AGCCAAACTTGAGTCCTTTTTAAC 58.097 37.500 0.00 0.00 0.00 2.01
391 397 8.422577 AATTAAATAGCCAAACTTGAGTCCTT 57.577 30.769 0.00 0.00 0.00 3.36
494 500 5.813157 TGTCGTTTCAGTAGTTCACATTGAA 59.187 36.000 0.00 0.00 33.32 2.69
495 501 5.353111 TGTCGTTTCAGTAGTTCACATTGA 58.647 37.500 0.00 0.00 0.00 2.57
496 502 5.651172 TGTCGTTTCAGTAGTTCACATTG 57.349 39.130 0.00 0.00 0.00 2.82
497 503 9.817809 ATATATGTCGTTTCAGTAGTTCACATT 57.182 29.630 0.00 0.00 0.00 2.71
498 504 9.249457 CATATATGTCGTTTCAGTAGTTCACAT 57.751 33.333 4.43 0.00 0.00 3.21
499 505 8.463607 TCATATATGTCGTTTCAGTAGTTCACA 58.536 33.333 12.42 0.00 0.00 3.58
500 506 8.851960 TCATATATGTCGTTTCAGTAGTTCAC 57.148 34.615 12.42 0.00 0.00 3.18
501 507 9.516314 CTTCATATATGTCGTTTCAGTAGTTCA 57.484 33.333 12.42 0.00 0.00 3.18
502 508 8.969267 CCTTCATATATGTCGTTTCAGTAGTTC 58.031 37.037 12.42 0.00 0.00 3.01
503 509 7.926555 CCCTTCATATATGTCGTTTCAGTAGTT 59.073 37.037 12.42 0.00 0.00 2.24
504 510 7.287005 TCCCTTCATATATGTCGTTTCAGTAGT 59.713 37.037 12.42 0.00 0.00 2.73
505 511 7.658261 TCCCTTCATATATGTCGTTTCAGTAG 58.342 38.462 12.42 0.00 0.00 2.57
506 512 7.287005 ACTCCCTTCATATATGTCGTTTCAGTA 59.713 37.037 12.42 0.00 0.00 2.74
507 513 6.098409 ACTCCCTTCATATATGTCGTTTCAGT 59.902 38.462 12.42 5.06 0.00 3.41
508 514 6.516718 ACTCCCTTCATATATGTCGTTTCAG 58.483 40.000 12.42 4.53 0.00 3.02
509 515 6.479972 ACTCCCTTCATATATGTCGTTTCA 57.520 37.500 12.42 0.00 0.00 2.69
553 570 6.322491 AGTCCGCAATACTTCAAAATAAAGC 58.678 36.000 0.00 0.00 0.00 3.51
587 604 4.038282 GCCATCCAATCATATCACAAAGCA 59.962 41.667 0.00 0.00 0.00 3.91
589 606 4.320714 CGGCCATCCAATCATATCACAAAG 60.321 45.833 2.24 0.00 0.00 2.77
592 609 2.371510 TCGGCCATCCAATCATATCACA 59.628 45.455 2.24 0.00 0.00 3.58
593 610 2.744202 GTCGGCCATCCAATCATATCAC 59.256 50.000 2.24 0.00 0.00 3.06
598 624 1.071385 GAGAGTCGGCCATCCAATCAT 59.929 52.381 2.24 0.00 0.00 2.45
607 633 1.679305 GAGACAGGAGAGTCGGCCA 60.679 63.158 2.24 0.00 43.24 5.36
608 634 2.766400 CGAGACAGGAGAGTCGGCC 61.766 68.421 0.00 0.00 43.24 6.13
613 639 4.747218 GGGACGAGACAGGAGAGT 57.253 61.111 0.00 0.00 0.00 3.24
626 652 0.727122 CGTAGACGTGTTCACGGGAC 60.727 60.000 25.14 18.29 37.45 4.46
627 653 1.575922 CGTAGACGTGTTCACGGGA 59.424 57.895 25.14 10.21 37.45 5.14
628 654 4.141883 CGTAGACGTGTTCACGGG 57.858 61.111 25.14 8.61 37.45 5.28
629 655 4.141883 CCGTAGACGTGTTCACGG 57.858 61.111 25.14 12.01 46.85 4.94
630 656 2.704758 GTCCGTAGACGTGTTCACG 58.295 57.895 21.13 21.13 37.74 4.35
652 678 3.713288 TGAACACAAGACGGACTTACTG 58.287 45.455 0.00 0.00 37.03 2.74
653 679 4.369182 CTTGAACACAAGACGGACTTACT 58.631 43.478 4.23 0.00 42.26 2.24
656 682 2.169769 TCCTTGAACACAAGACGGACTT 59.830 45.455 10.89 0.00 42.26 3.01
676 702 1.593469 GGCTAGTTCGAAATCCGCTTC 59.407 52.381 15.98 1.69 38.37 3.86
684 710 1.273048 TGGTAAGCGGCTAGTTCGAAA 59.727 47.619 1.35 0.00 0.00 3.46
688 714 0.171903 TCGTGGTAAGCGGCTAGTTC 59.828 55.000 1.35 0.00 0.00 3.01
721 747 1.329599 GTGTCCGTTGCGTTTTCTCTT 59.670 47.619 0.00 0.00 0.00 2.85
867 894 1.226295 GGTTTGATTAGCGCGGTGC 60.226 57.895 23.02 10.80 46.98 5.01
868 895 1.024579 AGGGTTTGATTAGCGCGGTG 61.025 55.000 23.02 0.00 0.00 4.94
869 896 0.743345 GAGGGTTTGATTAGCGCGGT 60.743 55.000 17.70 17.70 0.00 5.68
870 897 1.762222 CGAGGGTTTGATTAGCGCGG 61.762 60.000 8.83 0.00 0.00 6.46
871 898 1.636340 CGAGGGTTTGATTAGCGCG 59.364 57.895 0.00 0.00 0.00 6.86
872 899 1.352056 GCGAGGGTTTGATTAGCGC 59.648 57.895 0.00 0.00 36.12 5.92
873 900 1.762222 CGGCGAGGGTTTGATTAGCG 61.762 60.000 0.00 0.00 0.00 4.26
874 901 2.014594 CGGCGAGGGTTTGATTAGC 58.985 57.895 0.00 0.00 0.00 3.09
875 902 0.742990 TGCGGCGAGGGTTTGATTAG 60.743 55.000 12.98 0.00 0.00 1.73
876 903 1.022451 GTGCGGCGAGGGTTTGATTA 61.022 55.000 12.98 0.00 0.00 1.75
877 904 2.033448 TGCGGCGAGGGTTTGATT 59.967 55.556 12.98 0.00 0.00 2.57
878 905 2.746277 GTGCGGCGAGGGTTTGAT 60.746 61.111 12.98 0.00 0.00 2.57
901 928 0.321741 TTGCGGCGAGGGTTTGATTA 60.322 50.000 12.98 0.00 0.00 1.75
935 962 1.873270 GCGGGGTTTTGGATTTCGCT 61.873 55.000 0.00 0.00 38.82 4.93
996 1027 1.809619 CGTGTAGACCACCATGGCG 60.810 63.158 13.04 0.90 42.67 5.69
1395 1426 0.955428 GCCTGAACTGCGTCCAATCA 60.955 55.000 0.00 0.00 0.00 2.57
1398 1429 1.597854 CTGCCTGAACTGCGTCCAA 60.598 57.895 0.00 0.00 0.00 3.53
1612 1643 3.681897 CAGATCCAGAACGACCAAGAAAG 59.318 47.826 0.00 0.00 0.00 2.62
1613 1644 3.323691 TCAGATCCAGAACGACCAAGAAA 59.676 43.478 0.00 0.00 0.00 2.52
1614 1645 2.897326 TCAGATCCAGAACGACCAAGAA 59.103 45.455 0.00 0.00 0.00 2.52
1781 1813 4.397420 TCTCCACATACAACACAGCAATT 58.603 39.130 0.00 0.00 0.00 2.32
1828 1860 6.762187 CAGATCAGAATGTAGCTCAACAAGAT 59.238 38.462 0.00 0.00 37.40 2.40
1905 1937 2.571212 TGACAACAGCAGGGTTAACAG 58.429 47.619 8.10 0.00 0.00 3.16
1973 2005 6.366332 GCATAGTTACTCACCTTCCATATTCG 59.634 42.308 0.00 0.00 0.00 3.34
1985 2017 9.459640 TCTATGTTAAATCGCATAGTTACTCAC 57.540 33.333 10.22 0.00 42.89 3.51
2014 2046 4.659088 TCGACTAATCAGCTAAACAGACG 58.341 43.478 0.00 0.00 0.00 4.18
2034 2066 5.106948 ACAATTGCGCCATAGATAGATTTCG 60.107 40.000 4.18 0.00 0.00 3.46
2116 2212 4.192317 GGTGTTAGGGACATGATTCAGAC 58.808 47.826 0.00 0.00 41.10 3.51
2167 2263 7.983484 AGAATCAACCATTGCCATAATCTTTTC 59.017 33.333 0.00 0.00 0.00 2.29
2182 2278 6.891361 TCCATGTCATAACAAGAATCAACCAT 59.109 34.615 0.00 0.00 39.30 3.55
2235 2331 3.330405 TCCACAGTCCATCCAAATCAAGA 59.670 43.478 0.00 0.00 0.00 3.02
2265 2361 7.001674 ACTTAACCACCATGAAAACAGACATA 58.998 34.615 0.00 0.00 0.00 2.29
2314 2410 1.351017 TGCAAGAACCCGAGGAGATTT 59.649 47.619 0.00 0.00 0.00 2.17
2315 2411 0.984230 TGCAAGAACCCGAGGAGATT 59.016 50.000 0.00 0.00 0.00 2.40
2323 2419 4.766404 AATTCTTACTTGCAAGAACCCG 57.234 40.909 32.50 14.82 44.92 5.28
2325 2421 7.871853 TGTCTTAATTCTTACTTGCAAGAACC 58.128 34.615 32.50 5.98 44.92 3.62
2390 2486 0.957362 AGCAGCAGCCTCAGTTTTTC 59.043 50.000 0.00 0.00 43.56 2.29
2396 2492 1.078637 TAAGCAGCAGCAGCCTCAG 60.079 57.895 6.10 0.00 45.49 3.35
2397 2493 1.376424 GTAAGCAGCAGCAGCCTCA 60.376 57.895 6.10 0.00 45.49 3.86
2398 2494 0.176680 TAGTAAGCAGCAGCAGCCTC 59.823 55.000 6.10 0.00 45.49 4.70
2399 2495 0.177604 CTAGTAAGCAGCAGCAGCCT 59.822 55.000 6.10 0.00 45.49 4.58
2479 2575 4.802039 GCAGACCAAGCAACAAATCATATG 59.198 41.667 0.00 0.00 0.00 1.78
2481 2577 3.193267 GGCAGACCAAGCAACAAATCATA 59.807 43.478 0.00 0.00 35.26 2.15
2505 2985 7.621428 TTTGAAAATCAGGCAACAAATTTGA 57.379 28.000 24.64 0.31 34.43 2.69
2518 2998 8.456471 TCATGTGCTAGAAGATTTGAAAATCAG 58.544 33.333 16.06 7.29 45.59 2.90
2521 3001 8.114331 TGTCATGTGCTAGAAGATTTGAAAAT 57.886 30.769 0.00 0.00 0.00 1.82
2526 3006 6.537660 TGAGATGTCATGTGCTAGAAGATTTG 59.462 38.462 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.