Multiple sequence alignment - TraesCS1D01G286600

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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 TraesCS1D01G286600 chr1D 100.000 2621 0 0 1 2621 384846144 384843524 0.000000e+00 4841
1 TraesCS1D01G286600 chr1D 91.304 437 27 9 991 1424 63682189 63681761 1.050000e-163 586
2 TraesCS1D01G286600 chr1D 90.868 438 28 11 991 1424 388024499 388024928 6.290000e-161 577
3 TraesCS1D01G286600 chr1D 90.639 438 33 7 991 1424 388026983 388027416 2.260000e-160 575
4 TraesCS1D01G286600 chr1B 88.766 1175 95 23 624 1780 516962041 516960886 0.000000e+00 1404
5 TraesCS1D01G286600 chr1B 89.640 666 39 11 1799 2454 516960834 516960189 0.000000e+00 821
6 TraesCS1D01G286600 chr1B 86.678 593 44 12 1 587 516970719 516970156 2.210000e-175 625
7 TraesCS1D01G286600 chr1B 90.402 448 29 11 977 1424 104481614 104481181 6.290000e-161 577
8 TraesCS1D01G286600 chr1A 89.194 1166 67 30 633 1780 485011565 485010441 0.000000e+00 1400
9 TraesCS1D01G286600 chr1A 87.919 836 74 14 1799 2618 485010451 485009627 0.000000e+00 959
10 TraesCS1D01G286600 chr1A 92.037 427 25 8 1006 1431 62794580 62794162 2.250000e-165 592
11 TraesCS1D01G286600 chr1A 91.324 438 28 8 991 1424 490418202 490418633 8.080000e-165 590
12 TraesCS1D01G286600 chr1A 91.469 422 24 8 1006 1424 490759971 490760383 1.050000e-158 569
13 TraesCS1D01G286600 chr2D 95.050 101 5 0 347 447 593274339 593274239 2.700000e-35 159
14 TraesCS1D01G286600 chr2B 95.050 101 5 0 344 444 440223866 440223766 2.700000e-35 159
15 TraesCS1D01G286600 chr7A 93.333 105 7 0 344 448 629780018 629780122 3.490000e-34 156
16 TraesCS1D01G286600 chr6D 93.333 105 7 0 336 440 425085950 425086054 3.490000e-34 156
17 TraesCS1D01G286600 chr5A 92.661 109 7 1 336 443 339737764 339737872 3.490000e-34 156
18 TraesCS1D01G286600 chr2A 92.661 109 6 1 339 445 186408266 186408158 3.490000e-34 156
19 TraesCS1D01G286600 chr2A 90.435 115 10 1 330 444 672771899 672771786 1.620000e-32 150
20 TraesCS1D01G286600 chr7B 91.892 111 8 1 347 456 642496140 642496250 1.260000e-33 154
21 TraesCS1D01G286600 chr3B 93.269 104 7 0 338 441 714106395 714106498 1.260000e-33 154


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 TraesCS1D01G286600 chr1D 384843524 384846144 2620 True 4841.0 4841 100.0000 1 2621 1 chr1D.!!$R2 2620
1 TraesCS1D01G286600 chr1D 388024499 388027416 2917 False 576.0 577 90.7535 991 1424 2 chr1D.!!$F1 433
2 TraesCS1D01G286600 chr1B 516960189 516962041 1852 True 1112.5 1404 89.2030 624 2454 2 chr1B.!!$R3 1830
3 TraesCS1D01G286600 chr1B 516970156 516970719 563 True 625.0 625 86.6780 1 587 1 chr1B.!!$R2 586
4 TraesCS1D01G286600 chr1A 485009627 485011565 1938 True 1179.5 1400 88.5565 633 2618 2 chr1A.!!$R2 1985

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
505 511 0.184451 AAGTATGGGCAGCAGGATGG 59.816 55.0 0.0 0.0 35.86 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 4439 0.042448 GAATGAATAACCGCGACGCC 60.042 55.0 15.34 0.0 0.0 5.68 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
60 61 3.490348 CTCAAGGGTCCTGTGAATTGTT 58.510 45.455 0.00 0.00 0.00 2.83
62 63 5.055265 TCAAGGGTCCTGTGAATTGTTTA 57.945 39.130 0.00 0.00 0.00 2.01
145 146 8.959548 TGAGAACACATAATACAGATTGCAAAT 58.040 29.630 1.71 0.00 0.00 2.32
231 235 4.098914 ACTGGCATGTAAACTTCAGGAA 57.901 40.909 0.00 0.00 0.00 3.36
241 245 6.646267 TGTAAACTTCAGGAACGCCTATTAT 58.354 36.000 0.00 0.00 44.80 1.28
242 246 6.537301 TGTAAACTTCAGGAACGCCTATTATG 59.463 38.462 0.00 0.00 44.80 1.90
243 247 5.353394 AACTTCAGGAACGCCTATTATGA 57.647 39.130 0.00 0.00 44.80 2.15
244 248 5.353394 ACTTCAGGAACGCCTATTATGAA 57.647 39.130 0.00 0.00 44.80 2.57
245 249 5.741011 ACTTCAGGAACGCCTATTATGAAA 58.259 37.500 0.00 0.00 44.80 2.69
246 250 5.585047 ACTTCAGGAACGCCTATTATGAAAC 59.415 40.000 0.00 0.00 44.80 2.78
247 251 5.353394 TCAGGAACGCCTATTATGAAACT 57.647 39.130 0.00 0.00 44.80 2.66
248 252 5.116180 TCAGGAACGCCTATTATGAAACTG 58.884 41.667 0.00 0.00 44.80 3.16
249 253 5.105106 TCAGGAACGCCTATTATGAAACTGA 60.105 40.000 0.00 0.00 44.80 3.41
250 254 5.584649 CAGGAACGCCTATTATGAAACTGAA 59.415 40.000 0.00 0.00 44.80 3.02
251 255 6.260936 CAGGAACGCCTATTATGAAACTGAAT 59.739 38.462 0.00 0.00 44.80 2.57
252 256 7.441157 CAGGAACGCCTATTATGAAACTGAATA 59.559 37.037 0.00 0.00 44.80 1.75
253 257 7.990886 AGGAACGCCTATTATGAAACTGAATAA 59.009 33.333 0.00 0.00 44.74 1.40
254 258 8.784043 GGAACGCCTATTATGAAACTGAATAAT 58.216 33.333 0.00 0.00 34.27 1.28
295 299 2.288666 GTGGTGCAAACAGTCTGAAGA 58.711 47.619 6.91 0.00 0.00 2.87
311 315 7.812191 CAGTCTGAAGATAGGATACAAGCATAC 59.188 40.741 0.00 0.00 41.41 2.39
315 319 3.832490 AGATAGGATACAAGCATACGCCA 59.168 43.478 0.00 0.00 37.94 5.69
359 363 5.683681 TGTTAAAAACTACTCCCTCCGTTT 58.316 37.500 0.00 0.00 0.00 3.60
361 365 4.426736 AAAAACTACTCCCTCCGTTTCA 57.573 40.909 0.00 0.00 0.00 2.69
363 367 4.426736 AAACTACTCCCTCCGTTTCAAA 57.573 40.909 0.00 0.00 0.00 2.69
364 368 4.426736 AACTACTCCCTCCGTTTCAAAA 57.573 40.909 0.00 0.00 0.00 2.44
367 371 5.731591 ACTACTCCCTCCGTTTCAAAATAG 58.268 41.667 0.00 0.00 0.00 1.73
368 372 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
369 373 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
371 375 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
373 377 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
374 378 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
376 380 3.936453 CCGTTTCAAAATAGATGACCCGA 59.064 43.478 0.00 0.00 0.00 5.14
377 381 4.201783 CCGTTTCAAAATAGATGACCCGAC 60.202 45.833 0.00 0.00 0.00 4.79
382 386 8.674607 GTTTCAAAATAGATGACCCGACTTTAT 58.325 33.333 0.00 0.00 0.00 1.40
383 387 9.893634 TTTCAAAATAGATGACCCGACTTTATA 57.106 29.630 0.00 0.00 0.00 0.98
384 388 8.882415 TCAAAATAGATGACCCGACTTTATAC 57.118 34.615 0.00 0.00 0.00 1.47
385 389 8.701895 TCAAAATAGATGACCCGACTTTATACT 58.298 33.333 0.00 0.00 0.00 2.12
392 396 9.326413 AGATGACCCGACTTTATACTAAATTTG 57.674 33.333 0.00 0.00 0.00 2.32
393 397 9.106070 GATGACCCGACTTTATACTAAATTTGT 57.894 33.333 0.00 0.00 0.00 2.83
395 399 9.369904 TGACCCGACTTTATACTAAATTTGTAC 57.630 33.333 0.00 0.00 0.00 2.90
396 400 9.591792 GACCCGACTTTATACTAAATTTGTACT 57.408 33.333 0.00 0.00 0.00 2.73
441 445 2.093128 TCTATTTTGGAACGGAGGGAGC 60.093 50.000 0.00 0.00 0.00 4.70
454 460 1.449601 GGGAGCATGTGTACACCGG 60.450 63.158 22.91 15.40 0.00 5.28
457 463 1.635663 GAGCATGTGTACACCGGTGC 61.636 60.000 34.26 27.20 35.12 5.01
458 464 1.963855 GCATGTGTACACCGGTGCA 60.964 57.895 34.26 23.38 37.29 4.57
477 483 5.409520 GGTGCAGAAAAGAAATGGAAAATCC 59.590 40.000 0.00 0.00 36.96 3.01
500 506 3.482156 AGTATCAAGTATGGGCAGCAG 57.518 47.619 0.00 0.00 0.00 4.24
505 511 0.184451 AAGTATGGGCAGCAGGATGG 59.816 55.000 0.00 0.00 35.86 3.51
516 522 1.630369 AGCAGGATGGCTGAAGTAACA 59.370 47.619 0.00 0.00 43.89 2.41
527 533 8.663209 ATGGCTGAAGTAACATAGAGATAGAT 57.337 34.615 0.00 0.00 0.00 1.98
553 559 1.450360 AGTTCCTCCCCAAAGCTTCT 58.550 50.000 0.00 0.00 0.00 2.85
555 561 0.405585 TTCCTCCCCAAAGCTTCTGG 59.594 55.000 16.37 16.37 0.00 3.86
556 562 0.475632 TCCTCCCCAAAGCTTCTGGA 60.476 55.000 21.94 16.38 35.85 3.86
557 563 0.405585 CCTCCCCAAAGCTTCTGGAA 59.594 55.000 21.94 12.52 35.85 3.53
561 567 2.919602 TCCCCAAAGCTTCTGGAAGTAT 59.080 45.455 21.94 0.00 40.45 2.12
587 593 4.584325 AGTTCTTGGTGCTGCATTTAAAGA 59.416 37.500 5.27 9.97 0.00 2.52
588 594 4.771590 TCTTGGTGCTGCATTTAAAGAG 57.228 40.909 5.27 0.00 0.00 2.85
589 595 4.397420 TCTTGGTGCTGCATTTAAAGAGA 58.603 39.130 5.27 0.54 0.00 3.10
590 596 4.826733 TCTTGGTGCTGCATTTAAAGAGAA 59.173 37.500 5.27 0.00 0.00 2.87
591 597 5.301551 TCTTGGTGCTGCATTTAAAGAGAAA 59.698 36.000 5.27 0.00 0.00 2.52
592 598 5.125100 TGGTGCTGCATTTAAAGAGAAAG 57.875 39.130 5.27 0.00 0.00 2.62
593 599 4.826733 TGGTGCTGCATTTAAAGAGAAAGA 59.173 37.500 5.27 0.00 0.00 2.52
594 600 5.301551 TGGTGCTGCATTTAAAGAGAAAGAA 59.698 36.000 5.27 0.00 0.00 2.52
595 601 5.860716 GGTGCTGCATTTAAAGAGAAAGAAG 59.139 40.000 5.27 0.00 0.00 2.85
596 602 5.344396 GTGCTGCATTTAAAGAGAAAGAAGC 59.656 40.000 5.27 0.00 0.00 3.86
597 603 5.009911 TGCTGCATTTAAAGAGAAAGAAGCA 59.990 36.000 0.00 0.00 33.28 3.91
598 604 5.344396 GCTGCATTTAAAGAGAAAGAAGCAC 59.656 40.000 0.00 0.00 0.00 4.40
599 605 6.389830 TGCATTTAAAGAGAAAGAAGCACA 57.610 33.333 0.00 0.00 0.00 4.57
600 606 6.441274 TGCATTTAAAGAGAAAGAAGCACAG 58.559 36.000 0.00 0.00 0.00 3.66
601 607 5.860716 GCATTTAAAGAGAAAGAAGCACAGG 59.139 40.000 0.00 0.00 0.00 4.00
602 608 6.294176 GCATTTAAAGAGAAAGAAGCACAGGA 60.294 38.462 0.00 0.00 0.00 3.86
603 609 7.576477 GCATTTAAAGAGAAAGAAGCACAGGAT 60.576 37.037 0.00 0.00 0.00 3.24
604 610 7.823745 TTTAAAGAGAAAGAAGCACAGGATT 57.176 32.000 0.00 0.00 0.00 3.01
605 611 5.956068 AAAGAGAAAGAAGCACAGGATTC 57.044 39.130 0.00 0.00 39.70 2.52
606 612 4.630644 AGAGAAAGAAGCACAGGATTCA 57.369 40.909 0.00 0.00 41.82 2.57
607 613 4.577875 AGAGAAAGAAGCACAGGATTCAG 58.422 43.478 0.00 0.00 41.82 3.02
608 614 4.041444 AGAGAAAGAAGCACAGGATTCAGT 59.959 41.667 0.00 0.00 41.82 3.41
609 615 5.247110 AGAGAAAGAAGCACAGGATTCAGTA 59.753 40.000 0.00 0.00 41.82 2.74
610 616 6.059787 AGAAAGAAGCACAGGATTCAGTAT 57.940 37.500 0.00 0.00 41.82 2.12
611 617 6.112058 AGAAAGAAGCACAGGATTCAGTATC 58.888 40.000 0.00 0.00 41.82 2.24
623 629 6.926630 GGATTCAGTATCCCTCTAATCACT 57.073 41.667 0.00 0.00 46.20 3.41
624 630 6.696411 GGATTCAGTATCCCTCTAATCACTG 58.304 44.000 0.00 0.00 46.20 3.66
625 631 6.295575 GGATTCAGTATCCCTCTAATCACTGG 60.296 46.154 0.00 0.00 46.20 4.00
626 632 5.144159 TCAGTATCCCTCTAATCACTGGT 57.856 43.478 0.00 0.00 35.29 4.00
627 633 4.895889 TCAGTATCCCTCTAATCACTGGTG 59.104 45.833 0.00 0.00 35.29 4.17
628 634 4.651503 CAGTATCCCTCTAATCACTGGTGT 59.348 45.833 0.53 0.00 31.83 4.16
629 635 4.896482 AGTATCCCTCTAATCACTGGTGTC 59.104 45.833 0.53 0.00 0.00 3.67
630 636 2.100197 TCCCTCTAATCACTGGTGTCG 58.900 52.381 0.53 0.00 0.00 4.35
664 671 6.487689 ACGATTTCTGAAAATCCTTCACTC 57.512 37.500 6.95 0.00 45.31 3.51
666 673 6.073003 ACGATTTCTGAAAATCCTTCACTCAC 60.073 38.462 6.95 0.00 45.31 3.51
678 685 5.895928 TCCTTCACTCACTCAATCTAATCG 58.104 41.667 0.00 0.00 0.00 3.34
698 705 2.222267 CGCCGTGATTTTTCGAAAATGC 60.222 45.455 23.05 17.47 0.00 3.56
716 723 2.020131 CCATCGACAATCTGCTGCC 58.980 57.895 0.00 0.00 0.00 4.85
735 742 2.693069 CCAAGAGCCACTGTTAGACTG 58.307 52.381 0.00 0.00 0.00 3.51
736 743 2.300152 CCAAGAGCCACTGTTAGACTGA 59.700 50.000 0.00 0.00 0.00 3.41
743 751 3.384668 CCACTGTTAGACTGACACACTG 58.615 50.000 0.00 0.00 0.00 3.66
769 777 1.410711 GTTTCATTTTTCGCGCCGC 59.589 52.632 0.00 0.00 0.00 6.53
770 778 1.001745 GTTTCATTTTTCGCGCCGCT 61.002 50.000 7.78 0.00 0.00 5.52
794 803 0.321919 ACATGCACCACAGAGCGAAT 60.322 50.000 0.00 0.00 31.34 3.34
820 842 1.442520 CGCACCAATGAAACGCAGG 60.443 57.895 0.00 0.00 0.00 4.85
1029 1053 3.645268 CTTCCCCGCTTCCCCCAAG 62.645 68.421 0.00 0.00 34.85 3.61
1115 3625 3.060000 TCGTCGGCGACCATGTCT 61.060 61.111 31.86 0.00 42.81 3.41
1139 3649 3.984732 GGCAAGGGAGGCAAGGGT 61.985 66.667 0.00 0.00 0.00 4.34
1441 3951 2.432628 GTCCACCTTCGTCCGCAG 60.433 66.667 0.00 0.00 0.00 5.18
1443 3953 4.379243 CCACCTTCGTCCGCAGCT 62.379 66.667 0.00 0.00 0.00 4.24
1560 4078 1.084018 ATGTCACCTGTTCCCCCATT 58.916 50.000 0.00 0.00 0.00 3.16
1648 4168 2.596046 TTCCCGTGCAAATGCCGT 60.596 55.556 2.46 0.00 41.18 5.68
1652 4172 2.502510 CGTGCAAATGCCGTGAGC 60.503 61.111 2.46 0.00 41.18 4.26
1667 4187 2.710760 GTGAGCTCGTCGAGATGTTAG 58.289 52.381 26.11 0.00 0.00 2.34
1668 4188 2.096174 GTGAGCTCGTCGAGATGTTAGT 59.904 50.000 26.11 0.41 0.00 2.24
1671 4191 4.024809 TGAGCTCGTCGAGATGTTAGTATG 60.025 45.833 26.11 0.00 0.00 2.39
1672 4192 4.127907 AGCTCGTCGAGATGTTAGTATGA 58.872 43.478 26.11 0.00 0.00 2.15
1678 4199 7.922837 TCGTCGAGATGTTAGTATGATTTACA 58.077 34.615 0.00 0.00 0.00 2.41
1701 4222 4.697352 AGTCCGTTCTTGATTGAATTCCTG 59.303 41.667 2.27 0.00 0.00 3.86
1753 4275 6.495181 TCTGTTAACTGAATCTCTGGAGAGTT 59.505 38.462 12.28 7.17 41.33 3.01
1855 4411 3.821636 CTGCAGGCCCATCTAGCGG 62.822 68.421 5.57 0.00 0.00 5.52
1956 4516 1.694639 GAACTCGTTACGACACCCAG 58.305 55.000 2.33 0.00 0.00 4.45
2019 4579 2.507110 TTCGCTGCTCCTTTCTCCCG 62.507 60.000 0.00 0.00 0.00 5.14
2086 4647 2.438434 CGCTTCCGCCCCAGAAAT 60.438 61.111 0.00 0.00 0.00 2.17
2088 4649 0.746563 CGCTTCCGCCCCAGAAATTA 60.747 55.000 0.00 0.00 0.00 1.40
2095 4656 1.819305 CGCCCCAGAAATTATCCCCTG 60.819 57.143 0.00 0.00 0.00 4.45
2334 4915 3.147595 CCGCTGGATCCGACTCCA 61.148 66.667 7.39 5.88 43.09 3.86
2350 4931 2.325511 CACGCGCGTCGAGGTATA 59.674 61.111 35.61 0.00 41.67 1.47
2353 4934 2.426425 GCGCGTCGAGGTATACCG 60.426 66.667 16.31 5.75 42.08 4.02
2443 5028 1.103398 ATAAGCTCCGTGCATTGGCC 61.103 55.000 0.00 0.00 45.94 5.36
2455 5040 3.018856 TGCATTGGCCTGTTCTTATCTG 58.981 45.455 3.32 0.00 40.13 2.90
2460 5045 4.098914 TGGCCTGTTCTTATCTGTTTGT 57.901 40.909 3.32 0.00 0.00 2.83
2461 5046 4.072131 TGGCCTGTTCTTATCTGTTTGTC 58.928 43.478 3.32 0.00 0.00 3.18
2464 5049 4.154918 GCCTGTTCTTATCTGTTTGTCCTG 59.845 45.833 0.00 0.00 0.00 3.86
2494 5079 4.124238 TGTAACCAATTCGTAGCTATGGC 58.876 43.478 13.02 0.00 39.06 4.40
2501 5086 2.134201 TCGTAGCTATGGCAATCACG 57.866 50.000 13.02 7.44 41.70 4.35
2504 5089 0.467804 TAGCTATGGCAATCACGGCA 59.532 50.000 3.10 0.00 46.50 5.69
2519 5104 0.608640 CGGCAGTTGTAGAGGGTTCT 59.391 55.000 0.00 0.00 37.46 3.01
2530 5115 2.551270 AGAGGGTTCTGCCTTGTGATA 58.449 47.619 0.00 0.00 37.43 2.15
2531 5116 3.118531 AGAGGGTTCTGCCTTGTGATAT 58.881 45.455 0.00 0.00 37.43 1.63
2532 5117 3.118112 AGAGGGTTCTGCCTTGTGATATG 60.118 47.826 0.00 0.00 37.43 1.78
2533 5118 1.678101 GGGTTCTGCCTTGTGATATGC 59.322 52.381 0.00 0.00 37.43 3.14
2576 5162 4.878397 GCATAAGATGTGCTCCAACTAAGT 59.122 41.667 0.00 0.00 39.45 2.24
2580 5166 5.171339 AGATGTGCTCCAACTAAGTTGAT 57.829 39.130 0.00 0.00 45.28 2.57
2585 5171 5.412594 TGTGCTCCAACTAAGTTGATGATTC 59.587 40.000 0.00 0.00 45.28 2.52
2603 5189 8.542080 TGATGATTCTGGCTTGGAAAATAAAAT 58.458 29.630 0.00 0.00 0.00 1.82
2611 5197 9.305925 CTGGCTTGGAAAATAAAATGATTCTAC 57.694 33.333 0.00 0.00 0.00 2.59
2614 5200 9.521503 GCTTGGAAAATAAAATGATTCTACCTC 57.478 33.333 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 5.067023 CCTTGAGCCAAAAGATCAGTAATCC 59.933 44.000 0.00 0.00 43.01 3.01
60 61 4.724399 TGAGCTGTTCTGGAAATTGGTAA 58.276 39.130 0.00 0.00 0.00 2.85
62 63 3.228188 TGAGCTGTTCTGGAAATTGGT 57.772 42.857 0.00 0.00 0.00 3.67
124 125 9.740239 GATGAATTTGCAATCTGTATTATGTGT 57.260 29.630 0.00 0.00 0.00 3.72
145 146 4.271696 ACTGTTCTGACGGAATGATGAA 57.728 40.909 0.00 0.00 36.24 2.57
231 235 9.337396 TCAATTATTCAGTTTCATAATAGGCGT 57.663 29.630 0.00 0.00 0.00 5.68
241 245 6.704050 TCAGTCGTGTCAATTATTCAGTTTCA 59.296 34.615 0.00 0.00 0.00 2.69
242 246 7.117241 TCAGTCGTGTCAATTATTCAGTTTC 57.883 36.000 0.00 0.00 0.00 2.78
243 247 7.011950 TGTTCAGTCGTGTCAATTATTCAGTTT 59.988 33.333 0.00 0.00 0.00 2.66
244 248 6.481976 TGTTCAGTCGTGTCAATTATTCAGTT 59.518 34.615 0.00 0.00 0.00 3.16
245 249 5.989168 TGTTCAGTCGTGTCAATTATTCAGT 59.011 36.000 0.00 0.00 0.00 3.41
246 250 6.366061 TCTGTTCAGTCGTGTCAATTATTCAG 59.634 38.462 0.00 0.00 0.00 3.02
247 251 6.220201 TCTGTTCAGTCGTGTCAATTATTCA 58.780 36.000 0.00 0.00 0.00 2.57
248 252 6.706055 TCTGTTCAGTCGTGTCAATTATTC 57.294 37.500 0.00 0.00 0.00 1.75
249 253 7.352739 GTTTCTGTTCAGTCGTGTCAATTATT 58.647 34.615 0.00 0.00 0.00 1.40
250 254 6.346598 CGTTTCTGTTCAGTCGTGTCAATTAT 60.347 38.462 0.00 0.00 0.00 1.28
251 255 5.051307 CGTTTCTGTTCAGTCGTGTCAATTA 60.051 40.000 0.00 0.00 0.00 1.40
252 256 4.260212 CGTTTCTGTTCAGTCGTGTCAATT 60.260 41.667 0.00 0.00 0.00 2.32
253 257 3.245284 CGTTTCTGTTCAGTCGTGTCAAT 59.755 43.478 0.00 0.00 0.00 2.57
254 258 2.601314 CGTTTCTGTTCAGTCGTGTCAA 59.399 45.455 0.00 0.00 0.00 3.18
295 299 4.617253 TTGGCGTATGCTTGTATCCTAT 57.383 40.909 6.92 0.00 42.25 2.57
311 315 4.264380 GTCTTTTTGTTGTGTACTTTGGCG 59.736 41.667 0.00 0.00 0.00 5.69
315 319 6.584185 ACAGGTCTTTTTGTTGTGTACTTT 57.416 33.333 0.00 0.00 0.00 2.66
359 363 8.701895 AGTATAAAGTCGGGTCATCTATTTTGA 58.298 33.333 0.00 0.00 0.00 2.69
367 371 9.106070 ACAAATTTAGTATAAAGTCGGGTCATC 57.894 33.333 0.00 0.00 0.00 2.92
369 373 9.369904 GTACAAATTTAGTATAAAGTCGGGTCA 57.630 33.333 0.00 0.00 0.00 4.02
403 407 9.003658 CCAAAATAGATGACTCAAGTTTGTACT 57.996 33.333 0.00 0.00 35.68 2.73
405 409 9.567776 TTCCAAAATAGATGACTCAAGTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
406 410 8.352942 GTTCCAAAATAGATGACTCAAGTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
407 411 7.535258 CGTTCCAAAATAGATGACTCAAGTTTG 59.465 37.037 0.00 0.00 0.00 2.93
409 413 6.149474 CCGTTCCAAAATAGATGACTCAAGTT 59.851 38.462 0.00 0.00 0.00 2.66
410 414 5.643777 CCGTTCCAAAATAGATGACTCAAGT 59.356 40.000 0.00 0.00 0.00 3.16
411 415 5.874810 TCCGTTCCAAAATAGATGACTCAAG 59.125 40.000 0.00 0.00 0.00 3.02
412 416 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
413 417 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
414 418 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
415 419 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
416 420 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
417 421 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
418 422 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
419 423 3.433740 GCTCCCTCCGTTCCAAAATAGAT 60.434 47.826 0.00 0.00 0.00 1.98
420 424 2.093128 GCTCCCTCCGTTCCAAAATAGA 60.093 50.000 0.00 0.00 0.00 1.98
421 425 2.289565 GCTCCCTCCGTTCCAAAATAG 58.710 52.381 0.00 0.00 0.00 1.73
422 426 1.631388 TGCTCCCTCCGTTCCAAAATA 59.369 47.619 0.00 0.00 0.00 1.40
423 427 0.404040 TGCTCCCTCCGTTCCAAAAT 59.596 50.000 0.00 0.00 0.00 1.82
424 428 0.404040 ATGCTCCCTCCGTTCCAAAA 59.596 50.000 0.00 0.00 0.00 2.44
425 429 0.322456 CATGCTCCCTCCGTTCCAAA 60.322 55.000 0.00 0.00 0.00 3.28
427 431 1.918293 ACATGCTCCCTCCGTTCCA 60.918 57.895 0.00 0.00 0.00 3.53
441 445 0.320334 TCTGCACCGGTGTACACATG 60.320 55.000 33.92 20.56 0.00 3.21
454 460 5.409520 GGGATTTTCCATTTCTTTTCTGCAC 59.590 40.000 0.00 0.00 38.64 4.57
457 463 8.127150 ACTAGGGATTTTCCATTTCTTTTCTG 57.873 34.615 0.00 0.00 38.64 3.02
458 464 9.997172 ATACTAGGGATTTTCCATTTCTTTTCT 57.003 29.630 0.00 0.00 38.64 2.52
477 483 3.324846 TGCTGCCCATACTTGATACTAGG 59.675 47.826 0.00 0.00 0.00 3.02
500 506 5.537300 TCTCTATGTTACTTCAGCCATCC 57.463 43.478 0.00 0.00 0.00 3.51
516 522 9.474313 GGAGGAACTTGTCATATCTATCTCTAT 57.526 37.037 0.00 0.00 41.55 1.98
527 533 3.561313 GCTTTGGGGAGGAACTTGTCATA 60.561 47.826 0.00 0.00 41.55 2.15
553 559 4.072131 GCACCAAGAACTTCATACTTCCA 58.928 43.478 0.00 0.00 0.00 3.53
555 561 4.378874 GCAGCACCAAGAACTTCATACTTC 60.379 45.833 0.00 0.00 0.00 3.01
556 562 3.503748 GCAGCACCAAGAACTTCATACTT 59.496 43.478 0.00 0.00 0.00 2.24
557 563 3.077359 GCAGCACCAAGAACTTCATACT 58.923 45.455 0.00 0.00 0.00 2.12
561 567 1.985473 ATGCAGCACCAAGAACTTCA 58.015 45.000 0.00 0.00 0.00 3.02
587 593 4.363991 ACTGAATCCTGTGCTTCTTTCT 57.636 40.909 0.00 0.00 0.00 2.52
588 594 6.356757 GATACTGAATCCTGTGCTTCTTTC 57.643 41.667 0.00 0.00 0.00 2.62
601 607 6.268847 ACCAGTGATTAGAGGGATACTGAATC 59.731 42.308 0.00 0.00 38.16 2.52
602 608 6.042552 CACCAGTGATTAGAGGGATACTGAAT 59.957 42.308 0.00 0.00 38.16 2.57
603 609 5.363868 CACCAGTGATTAGAGGGATACTGAA 59.636 44.000 0.00 0.00 38.16 3.02
604 610 4.895889 CACCAGTGATTAGAGGGATACTGA 59.104 45.833 0.00 0.00 38.16 3.41
605 611 4.651503 ACACCAGTGATTAGAGGGATACTG 59.348 45.833 4.48 0.00 36.27 2.74
606 612 4.884961 ACACCAGTGATTAGAGGGATACT 58.115 43.478 4.48 0.00 0.00 2.12
607 613 4.261656 CGACACCAGTGATTAGAGGGATAC 60.262 50.000 4.48 0.00 0.00 2.24
608 614 3.889538 CGACACCAGTGATTAGAGGGATA 59.110 47.826 4.48 0.00 0.00 2.59
609 615 2.695666 CGACACCAGTGATTAGAGGGAT 59.304 50.000 4.48 0.00 0.00 3.85
610 616 2.100197 CGACACCAGTGATTAGAGGGA 58.900 52.381 4.48 0.00 0.00 4.20
611 617 1.137086 CCGACACCAGTGATTAGAGGG 59.863 57.143 4.48 0.00 0.00 4.30
612 618 1.825474 ACCGACACCAGTGATTAGAGG 59.175 52.381 4.48 1.46 0.00 3.69
613 619 3.056821 TCAACCGACACCAGTGATTAGAG 60.057 47.826 4.48 0.00 0.00 2.43
614 620 2.894765 TCAACCGACACCAGTGATTAGA 59.105 45.455 4.48 0.00 0.00 2.10
615 621 2.993899 GTCAACCGACACCAGTGATTAG 59.006 50.000 4.48 0.00 42.13 1.73
616 622 3.034721 GTCAACCGACACCAGTGATTA 57.965 47.619 4.48 0.00 42.13 1.75
617 623 1.878953 GTCAACCGACACCAGTGATT 58.121 50.000 4.48 0.00 42.13 2.57
618 624 3.606886 GTCAACCGACACCAGTGAT 57.393 52.632 4.48 0.00 42.13 3.06
630 636 8.671986 GATTTTCAGAAATCGTTGGTGTCAACC 61.672 40.741 0.00 0.00 42.25 3.77
648 654 6.654161 AGATTGAGTGAGTGAAGGATTTTCAG 59.346 38.462 0.00 0.00 0.00 3.02
664 671 2.809446 TCACGGCGATTAGATTGAGTG 58.191 47.619 16.62 0.00 0.00 3.51
666 673 5.409643 AAAATCACGGCGATTAGATTGAG 57.590 39.130 16.62 0.00 43.83 3.02
678 685 2.092055 GGCATTTTCGAAAAATCACGGC 59.908 45.455 25.77 19.70 0.00 5.68
698 705 0.745486 TGGCAGCAGATTGTCGATGG 60.745 55.000 0.00 0.00 0.00 3.51
716 723 3.243873 TGTCAGTCTAACAGTGGCTCTTG 60.244 47.826 0.00 0.00 30.46 3.02
777 785 0.251354 AGATTCGCTCTGTGGTGCAT 59.749 50.000 0.00 0.00 31.12 3.96
778 786 0.671472 CAGATTCGCTCTGTGGTGCA 60.671 55.000 6.65 0.00 45.42 4.57
794 803 3.364864 CGTTTCATTGGTGCGAATTCAGA 60.365 43.478 6.22 0.00 0.00 3.27
863 886 2.223595 TGCGCCTGAAAATTTTCGTTCA 60.224 40.909 22.51 13.93 40.01 3.18
954 977 1.527370 GGAATTGGGGAGGTCGAGG 59.473 63.158 0.00 0.00 0.00 4.63
1029 1053 2.331451 GGCTTGTGGTGTTGCGAC 59.669 61.111 0.00 0.00 0.00 5.19
1451 3961 0.596600 TTGTTGACTGACGACGAGGC 60.597 55.000 0.00 0.00 35.76 4.70
1457 3967 0.596600 GCGGAGTTGTTGACTGACGA 60.597 55.000 0.00 0.00 39.19 4.20
1459 3969 1.228657 GGGCGGAGTTGTTGACTGAC 61.229 60.000 0.00 0.00 39.19 3.51
1493 4003 3.127533 ATGGCAGTTTCCTCGCGC 61.128 61.111 0.00 0.00 0.00 6.86
1496 4006 1.813513 AAGACATGGCAGTTTCCTCG 58.186 50.000 0.00 0.00 0.00 4.63
1500 4010 5.182001 ACTGAACATAAGACATGGCAGTTTC 59.818 40.000 0.00 0.00 36.25 2.78
1554 4072 2.620251 TCTGCGATAGACAAATGGGG 57.380 50.000 0.00 0.00 39.76 4.96
1560 4078 6.058833 ACTAGAGAGATTCTGCGATAGACAA 58.941 40.000 0.00 0.00 36.61 3.18
1648 4168 2.357075 ACTAACATCTCGACGAGCTCA 58.643 47.619 20.11 3.45 0.00 4.26
1652 4172 8.068380 TGTAAATCATACTAACATCTCGACGAG 58.932 37.037 18.91 18.91 0.00 4.18
1667 4187 7.772332 ATCAAGAACGGACTGTAAATCATAC 57.228 36.000 0.00 0.00 0.00 2.39
1668 4188 8.038351 TCAATCAAGAACGGACTGTAAATCATA 58.962 33.333 0.00 0.00 0.00 2.15
1671 4191 6.721571 TCAATCAAGAACGGACTGTAAATC 57.278 37.500 0.00 0.00 0.00 2.17
1672 4192 7.687941 ATTCAATCAAGAACGGACTGTAAAT 57.312 32.000 0.00 0.00 0.00 1.40
1678 4199 4.697352 CAGGAATTCAATCAAGAACGGACT 59.303 41.667 7.93 0.00 0.00 3.85
1701 4222 1.068921 GGGAGATTCAGAGAGCCGC 59.931 63.158 0.00 0.00 0.00 6.53
1753 4275 1.691976 TCTGCCTTCTTCGGAGAAACA 59.308 47.619 7.73 8.02 45.90 2.83
1784 4306 5.452078 CAACTCTGCATAACCCTCAAAAA 57.548 39.130 0.00 0.00 0.00 1.94
1838 4394 3.865383 CCGCTAGATGGGCCTGCA 61.865 66.667 4.53 0.00 0.00 4.41
1881 4439 0.042448 GAATGAATAACCGCGACGCC 60.042 55.000 15.34 0.00 0.00 5.68
2035 4595 0.978667 GAGGGTGGGAAGAGGAGGAC 60.979 65.000 0.00 0.00 0.00 3.85
2086 4647 1.423794 GGGCGGGATTCAGGGGATAA 61.424 60.000 0.00 0.00 0.00 1.75
2088 4649 3.178611 GGGCGGGATTCAGGGGAT 61.179 66.667 0.00 0.00 0.00 3.85
2095 4656 3.809374 AATCGAGCGGGCGGGATTC 62.809 63.158 0.00 0.00 0.00 2.52
2106 4667 1.598882 GATTCAGGGGGAAATCGAGC 58.401 55.000 0.00 0.00 39.39 5.03
2173 4735 7.463119 CGGACGAATTGAATTGAATTGAATTGG 60.463 37.037 17.71 17.82 36.45 3.16
2246 4823 1.792118 GACAAGGTCAACCAACCGCC 61.792 60.000 1.33 0.00 44.49 6.13
2247 4824 1.652563 GACAAGGTCAACCAACCGC 59.347 57.895 1.33 0.00 44.49 5.68
2248 4825 1.938861 CGACAAGGTCAACCAACCG 59.061 57.895 1.33 0.00 44.49 4.44
2249 4826 1.652563 GCGACAAGGTCAACCAACC 59.347 57.895 1.33 0.00 39.80 3.77
2250 4827 1.652563 GGCGACAAGGTCAACCAAC 59.347 57.895 1.33 0.00 38.89 3.77
2251 4828 1.890041 CGGCGACAAGGTCAACCAA 60.890 57.895 0.00 0.00 38.89 3.67
2252 4829 2.280524 CGGCGACAAGGTCAACCA 60.281 61.111 0.00 0.00 38.89 3.67
2334 4915 2.325857 GTATACCTCGACGCGCGT 59.674 61.111 38.52 38.52 41.80 6.01
2386 4967 7.339482 ACCATCCCTAATACTTTCTCTGAAAC 58.661 38.462 0.00 0.00 0.00 2.78
2443 5028 4.697352 CCCAGGACAAACAGATAAGAACAG 59.303 45.833 0.00 0.00 0.00 3.16
2455 5040 1.966451 CAGCGGACCCAGGACAAAC 60.966 63.158 0.00 0.00 0.00 2.93
2460 5045 2.288025 GGTTACAGCGGACCCAGGA 61.288 63.158 0.00 0.00 0.00 3.86
2461 5046 2.119484 TTGGTTACAGCGGACCCAGG 62.119 60.000 0.00 0.00 34.99 4.45
2464 5049 1.092348 GAATTGGTTACAGCGGACCC 58.908 55.000 0.00 0.00 34.99 4.46
2494 5079 2.002586 CCTCTACAACTGCCGTGATTG 58.997 52.381 0.00 0.00 0.00 2.67
2501 5086 1.946283 GCAGAACCCTCTACAACTGCC 60.946 57.143 0.00 0.00 42.91 4.85
2504 5089 2.031495 AGGCAGAACCCTCTACAACT 57.969 50.000 0.00 0.00 40.58 3.16
2519 5104 0.392863 ACAGCGCATATCACAAGGCA 60.393 50.000 11.47 0.00 0.00 4.75
2557 5143 4.973168 TCAACTTAGTTGGAGCACATCTT 58.027 39.130 22.82 0.00 42.99 2.40
2576 5162 7.479352 TTATTTTCCAAGCCAGAATCATCAA 57.521 32.000 0.00 0.00 0.00 2.57
2580 5166 7.905265 TCATTTTATTTTCCAAGCCAGAATCA 58.095 30.769 0.00 0.00 0.00 2.57
2585 5171 9.305925 GTAGAATCATTTTATTTTCCAAGCCAG 57.694 33.333 0.00 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.