Multiple sequence alignment - TraesCS6D01G037600

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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 TraesCS6D01G037600 chr6D 100.000 2351 0 0 1 2351 15587201 15584851 0.000000e+00 4342
1 TraesCS6D01G037600 chr6D 90.827 1548 102 18 819 2351 15551165 15549643 0.000000e+00 2036
2 TraesCS6D01G037600 chr6D 88.265 980 64 25 601 1552 15640282 15641238 0.000000e+00 1125
3 TraesCS6D01G037600 chr6D 86.550 171 9 4 601 759 15551349 15551181 2.400000e-40 176
4 TraesCS6D01G037600 chr6B 88.975 1297 101 21 819 2095 27485760 27484486 0.000000e+00 1565
5 TraesCS6D01G037600 chr6B 88.530 1299 105 25 819 2095 27419560 27418284 0.000000e+00 1533
6 TraesCS6D01G037600 chr6B 88.358 1297 109 20 819 2095 27455628 27454354 0.000000e+00 1520
7 TraesCS6D01G037600 chr6B 88.290 1298 109 20 819 2095 27532350 27531075 0.000000e+00 1515
8 TraesCS6D01G037600 chr6B 92.794 791 41 6 601 1378 27668971 27669758 0.000000e+00 1131
9 TraesCS6D01G037600 chr6B 88.797 607 62 5 1 602 241100042 241099437 0.000000e+00 739
10 TraesCS6D01G037600 chr6B 95.455 88 4 0 601 688 27455860 27455773 8.760000e-30 141
11 TraesCS6D01G037600 chr6B 94.318 88 5 0 601 688 27419792 27419705 4.080000e-28 135
12 TraesCS6D01G037600 chrUn 88.003 1367 85 38 601 1939 319197759 319196444 0.000000e+00 1543
13 TraesCS6D01G037600 chrUn 89.039 1186 92 20 1003 2171 348953558 348954722 0.000000e+00 1435
14 TraesCS6D01G037600 chrUn 92.834 628 38 5 819 1445 76409293 76409914 0.000000e+00 904
15 TraesCS6D01G037600 chrUn 89.427 681 61 8 1671 2351 76413671 76414340 0.000000e+00 848
16 TraesCS6D01G037600 chrUn 99.468 188 1 0 1801 1988 26385996 26386183 2.240000e-90 342
17 TraesCS6D01G037600 chrUn 92.973 185 13 0 2167 2351 322191405 322191221 1.070000e-68 270
18 TraesCS6D01G037600 chrUn 92.973 185 13 0 2167 2351 404648240 404648424 1.070000e-68 270
19 TraesCS6D01G037600 chrUn 91.892 185 15 0 2167 2351 355894118 355894302 2.320000e-65 259
20 TraesCS6D01G037600 chrUn 93.007 143 10 0 2029 2171 322192705 322192563 2.370000e-50 209
21 TraesCS6D01G037600 chrUn 93.007 143 10 0 2029 2171 425808717 425808575 2.370000e-50 209
22 TraesCS6D01G037600 chrUn 88.398 181 7 8 601 771 347746560 347746384 3.060000e-49 206
23 TraesCS6D01G037600 chrUn 94.318 88 5 0 601 688 441169252 441169165 4.080000e-28 135
24 TraesCS6D01G037600 chr6A 91.126 879 49 13 601 1456 16337936 16338808 0.000000e+00 1164
25 TraesCS6D01G037600 chr6A 91.033 368 33 0 1804 2171 16287969 16287602 4.510000e-137 497
26 TraesCS6D01G037600 chr6A 92.973 185 13 0 2167 2351 16286333 16286149 1.070000e-68 270
27 TraesCS6D01G037600 chr4D 93.590 546 32 2 58 600 430827537 430826992 0.000000e+00 811
28 TraesCS6D01G037600 chr5B 89.439 606 58 6 1 601 671363555 671362951 0.000000e+00 760
29 TraesCS6D01G037600 chr5B 89.180 573 55 6 33 601 331504738 331505307 0.000000e+00 708
30 TraesCS6D01G037600 chr3B 89.456 607 51 9 1 601 366144123 366143524 0.000000e+00 754
31 TraesCS6D01G037600 chr3B 87.007 608 68 9 1 602 145413264 145412662 0.000000e+00 675
32 TraesCS6D01G037600 chr7B 87.377 610 65 11 1 602 498139052 498139657 0.000000e+00 689
33 TraesCS6D01G037600 chr7B 87.070 611 65 12 1 601 220160591 220159985 0.000000e+00 678
34 TraesCS6D01G037600 chr5D 87.479 591 65 8 14 599 554083637 554083051 0.000000e+00 673


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 TraesCS6D01G037600 chr6D 15584851 15587201 2350 True 4342.0 4342 100.0000 1 2351 1 chr6D.!!$R1 2350
1 TraesCS6D01G037600 chr6D 15640282 15641238 956 False 1125.0 1125 88.2650 601 1552 1 chr6D.!!$F1 951
2 TraesCS6D01G037600 chr6D 15549643 15551349 1706 True 1106.0 2036 88.6885 601 2351 2 chr6D.!!$R2 1750
3 TraesCS6D01G037600 chr6B 27484486 27485760 1274 True 1565.0 1565 88.9750 819 2095 1 chr6B.!!$R1 1276
4 TraesCS6D01G037600 chr6B 27531075 27532350 1275 True 1515.0 1515 88.2900 819 2095 1 chr6B.!!$R2 1276
5 TraesCS6D01G037600 chr6B 27668971 27669758 787 False 1131.0 1131 92.7940 601 1378 1 chr6B.!!$F1 777
6 TraesCS6D01G037600 chr6B 27418284 27419792 1508 True 834.0 1533 91.4240 601 2095 2 chr6B.!!$R4 1494
7 TraesCS6D01G037600 chr6B 27454354 27455860 1506 True 830.5 1520 91.9065 601 2095 2 chr6B.!!$R5 1494
8 TraesCS6D01G037600 chr6B 241099437 241100042 605 True 739.0 739 88.7970 1 602 1 chr6B.!!$R3 601
9 TraesCS6D01G037600 chrUn 319196444 319197759 1315 True 1543.0 1543 88.0030 601 1939 1 chrUn.!!$R1 1338
10 TraesCS6D01G037600 chrUn 348953558 348954722 1164 False 1435.0 1435 89.0390 1003 2171 1 chrUn.!!$F2 1168
11 TraesCS6D01G037600 chrUn 76409293 76414340 5047 False 876.0 904 91.1305 819 2351 2 chrUn.!!$F5 1532
12 TraesCS6D01G037600 chrUn 322191221 322192705 1484 True 239.5 270 92.9900 2029 2351 2 chrUn.!!$R5 322
13 TraesCS6D01G037600 chr6A 16337936 16338808 872 False 1164.0 1164 91.1260 601 1456 1 chr6A.!!$F1 855
14 TraesCS6D01G037600 chr6A 16286149 16287969 1820 True 383.5 497 92.0030 1804 2351 2 chr6A.!!$R1 547
15 TraesCS6D01G037600 chr4D 430826992 430827537 545 True 811.0 811 93.5900 58 600 1 chr4D.!!$R1 542
16 TraesCS6D01G037600 chr5B 671362951 671363555 604 True 760.0 760 89.4390 1 601 1 chr5B.!!$R1 600
17 TraesCS6D01G037600 chr5B 331504738 331505307 569 False 708.0 708 89.1800 33 601 1 chr5B.!!$F1 568
18 TraesCS6D01G037600 chr3B 366143524 366144123 599 True 754.0 754 89.4560 1 601 1 chr3B.!!$R2 600
19 TraesCS6D01G037600 chr3B 145412662 145413264 602 True 675.0 675 87.0070 1 602 1 chr3B.!!$R1 601
20 TraesCS6D01G037600 chr7B 498139052 498139657 605 False 689.0 689 87.3770 1 602 1 chr7B.!!$F1 601
21 TraesCS6D01G037600 chr7B 220159985 220160591 606 True 678.0 678 87.0700 1 601 1 chr7B.!!$R1 600
22 TraesCS6D01G037600 chr5D 554083051 554083637 586 True 673.0 673 87.4790 14 599 1 chr5D.!!$R1 585

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
816 897 0.818445 TTTGCTCGGCCGGTGTTTTA 60.818 50.0 27.83 2.05 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 7158 0.324943 GTCCTGCTTGGCTTGGACTA 59.675 55.0 19.29 0.0 43.5 2.59 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
427 431 2.125024 GCGGCGGCTAGGGTTTAA 60.125 61.111 9.78 0.00 35.83 1.52
464 469 4.338795 ACCATGTTAGAAGGGAGAGAGA 57.661 45.455 0.00 0.00 0.00 3.10
465 470 4.689062 ACCATGTTAGAAGGGAGAGAGAA 58.311 43.478 0.00 0.00 0.00 2.87
466 471 5.284582 ACCATGTTAGAAGGGAGAGAGAAT 58.715 41.667 0.00 0.00 0.00 2.40
468 473 6.054295 CCATGTTAGAAGGGAGAGAGAATTG 58.946 44.000 0.00 0.00 0.00 2.32
469 474 6.126940 CCATGTTAGAAGGGAGAGAGAATTGA 60.127 42.308 0.00 0.00 0.00 2.57
470 475 7.419981 CCATGTTAGAAGGGAGAGAGAATTGAT 60.420 40.741 0.00 0.00 0.00 2.57
471 476 6.882656 TGTTAGAAGGGAGAGAGAATTGATG 58.117 40.000 0.00 0.00 0.00 3.07
472 477 6.669591 TGTTAGAAGGGAGAGAGAATTGATGA 59.330 38.462 0.00 0.00 0.00 2.92
473 478 7.180946 TGTTAGAAGGGAGAGAGAATTGATGAA 59.819 37.037 0.00 0.00 0.00 2.57
474 479 6.633325 AGAAGGGAGAGAGAATTGATGAAA 57.367 37.500 0.00 0.00 0.00 2.69
475 480 7.210618 AGAAGGGAGAGAGAATTGATGAAAT 57.789 36.000 0.00 0.00 0.00 2.17
476 481 7.641249 AGAAGGGAGAGAGAATTGATGAAATT 58.359 34.615 0.00 0.00 41.33 1.82
477 482 8.776119 AGAAGGGAGAGAGAATTGATGAAATTA 58.224 33.333 0.00 0.00 38.64 1.40
478 483 9.571816 GAAGGGAGAGAGAATTGATGAAATTAT 57.428 33.333 0.00 0.00 38.64 1.28
479 484 9.933240 AAGGGAGAGAGAATTGATGAAATTATT 57.067 29.630 0.00 0.00 38.64 1.40
502 507 8.771920 ATTATTGTATTGTTTGAGTCTCGTGA 57.228 30.769 0.00 0.00 0.00 4.35
503 508 8.771920 TTATTGTATTGTTTGAGTCTCGTGAT 57.228 30.769 0.00 0.00 0.00 3.06
504 509 6.706055 TTGTATTGTTTGAGTCTCGTGATC 57.294 37.500 0.00 0.00 0.00 2.92
505 510 5.778862 TGTATTGTTTGAGTCTCGTGATCA 58.221 37.500 0.00 0.00 0.00 2.92
506 511 6.398095 TGTATTGTTTGAGTCTCGTGATCAT 58.602 36.000 0.00 0.00 0.00 2.45
507 512 7.543756 TGTATTGTTTGAGTCTCGTGATCATA 58.456 34.615 0.00 0.00 0.00 2.15
508 513 8.197439 TGTATTGTTTGAGTCTCGTGATCATAT 58.803 33.333 0.00 0.00 0.00 1.78
509 514 9.678941 GTATTGTTTGAGTCTCGTGATCATATA 57.321 33.333 0.00 0.00 0.00 0.86
555 560 9.391006 ACTTAAAATACAAGACAAGTCAGAACA 57.609 29.630 2.72 0.00 0.00 3.18
559 564 9.736023 AAAATACAAGACAAGTCAGAACAAATC 57.264 29.630 2.72 0.00 0.00 2.17
560 565 5.757850 ACAAGACAAGTCAGAACAAATCC 57.242 39.130 2.72 0.00 0.00 3.01
561 566 5.440610 ACAAGACAAGTCAGAACAAATCCT 58.559 37.500 2.72 0.00 0.00 3.24
562 567 6.591935 ACAAGACAAGTCAGAACAAATCCTA 58.408 36.000 2.72 0.00 0.00 2.94
563 568 6.708054 ACAAGACAAGTCAGAACAAATCCTAG 59.292 38.462 2.72 0.00 0.00 3.02
564 569 6.426646 AGACAAGTCAGAACAAATCCTAGT 57.573 37.500 2.72 0.00 0.00 2.57
565 570 6.459923 AGACAAGTCAGAACAAATCCTAGTC 58.540 40.000 2.72 0.00 0.00 2.59
566 571 6.268847 AGACAAGTCAGAACAAATCCTAGTCT 59.731 38.462 2.72 0.00 0.00 3.24
567 572 7.451877 AGACAAGTCAGAACAAATCCTAGTCTA 59.548 37.037 2.72 0.00 0.00 2.59
568 573 8.140112 ACAAGTCAGAACAAATCCTAGTCTAT 57.860 34.615 0.00 0.00 0.00 1.98
569 574 8.254508 ACAAGTCAGAACAAATCCTAGTCTATC 58.745 37.037 0.00 0.00 0.00 2.08
570 575 8.474025 CAAGTCAGAACAAATCCTAGTCTATCT 58.526 37.037 0.00 0.00 0.00 1.98
571 576 8.232913 AGTCAGAACAAATCCTAGTCTATCTC 57.767 38.462 0.00 0.00 0.00 2.75
572 577 7.836685 AGTCAGAACAAATCCTAGTCTATCTCA 59.163 37.037 0.00 0.00 0.00 3.27
573 578 8.637986 GTCAGAACAAATCCTAGTCTATCTCAT 58.362 37.037 0.00 0.00 0.00 2.90
574 579 8.855110 TCAGAACAAATCCTAGTCTATCTCATC 58.145 37.037 0.00 0.00 0.00 2.92
575 580 8.859090 CAGAACAAATCCTAGTCTATCTCATCT 58.141 37.037 0.00 0.00 0.00 2.90
576 581 9.432982 AGAACAAATCCTAGTCTATCTCATCTT 57.567 33.333 0.00 0.00 0.00 2.40
579 584 8.646900 ACAAATCCTAGTCTATCTCATCTTTCC 58.353 37.037 0.00 0.00 0.00 3.13
580 585 8.869109 CAAATCCTAGTCTATCTCATCTTTCCT 58.131 37.037 0.00 0.00 0.00 3.36
609 614 7.591006 AACAATATACTCAACAACCAGTACG 57.409 36.000 0.00 0.00 0.00 3.67
695 754 4.456222 AGCTGCTATGAGGTACGTACTATG 59.544 45.833 24.07 10.45 0.00 2.23
787 866 2.753319 TCCATCAGGACGTTGACCA 58.247 52.632 0.00 0.00 39.61 4.02
813 894 2.978010 CTTTGCTCGGCCGGTGTT 60.978 61.111 27.83 0.00 0.00 3.32
815 896 2.070654 CTTTGCTCGGCCGGTGTTTT 62.071 55.000 27.83 0.00 0.00 2.43
816 897 0.818445 TTTGCTCGGCCGGTGTTTTA 60.818 50.000 27.83 2.05 0.00 1.52
1341 1431 0.682852 CCTACTGGTCCAACGTCCAA 59.317 55.000 0.00 0.00 33.06 3.53
1365 1457 9.736023 CAATTCTATTGATTTTGGCTTACCTAC 57.264 33.333 0.00 0.00 36.63 3.18
1379 1475 1.472188 ACCTACTACGTGCTTCTCCC 58.528 55.000 0.00 0.00 0.00 4.30
1387 1483 0.387202 CGTGCTTCTCCCATCGATCT 59.613 55.000 0.00 0.00 0.00 2.75
1388 1484 1.863267 GTGCTTCTCCCATCGATCTG 58.137 55.000 0.00 0.00 0.00 2.90
1393 1489 1.070445 CTCCCATCGATCTGTGCCC 59.930 63.158 0.00 0.00 0.00 5.36
1396 1492 0.887836 CCCATCGATCTGTGCCCATG 60.888 60.000 0.00 0.00 0.00 3.66
1408 1504 0.040058 TGCCCATGGAGTTGATGCTT 59.960 50.000 15.22 0.00 0.00 3.91
1415 1511 2.995283 TGGAGTTGATGCTTCTGGATG 58.005 47.619 0.88 0.00 0.00 3.51
1441 5050 4.159135 TCTTCTCACCAAACGGTACCTATC 59.841 45.833 10.90 0.00 33.92 2.08
1459 5068 9.971922 GTACCTATCGTTTATTGTAAGTGGTAT 57.028 33.333 0.00 0.00 0.00 2.73
1478 5087 6.001460 TGGTATATAAGGCCTTGTACAATGC 58.999 40.000 28.77 23.06 0.00 3.56
1502 5121 3.084039 TGCAATGCAAGGTCTTTAGAGG 58.916 45.455 5.01 0.00 34.76 3.69
1503 5122 3.084786 GCAATGCAAGGTCTTTAGAGGT 58.915 45.455 0.00 0.00 0.00 3.85
1506 5125 8.434092 TGCAATGCAAGGTCTTTAGAGGTACT 62.434 42.308 5.01 0.00 37.06 2.73
1543 5171 5.636543 AGAAACCGGTATTTTCTCAAGTACG 59.363 40.000 8.00 0.00 38.67 3.67
1555 5183 6.790285 TTCTCAAGTACGGGTGTTTATTTC 57.210 37.500 0.00 0.00 0.00 2.17
1642 5318 7.656707 AAAACCAGTTTATATTTGCAAGCTG 57.343 32.000 0.00 0.00 34.04 4.24
1705 5381 2.352821 TGGCTGGCCAATGCATGTC 61.353 57.895 17.88 2.11 44.12 3.06
1731 5407 2.352814 GGCTCTTTTCTCGCTCACTACA 60.353 50.000 0.00 0.00 0.00 2.74
1742 5418 2.416296 CGCTCACTACACCGTGGATTAA 60.416 50.000 3.03 0.00 35.63 1.40
1746 5422 2.676342 CACTACACCGTGGATTAAAGCC 59.324 50.000 3.03 0.00 0.00 4.35
1747 5423 2.303600 ACTACACCGTGGATTAAAGCCA 59.696 45.455 3.03 0.00 0.00 4.75
1777 5453 4.307834 CGAGTAATGTGTCGGTTTTCTG 57.692 45.455 0.00 0.00 32.40 3.02
1787 5463 3.695060 TGTCGGTTTTCTGCCTTTGTTTA 59.305 39.130 0.00 0.00 0.00 2.01
1789 5465 4.679654 GTCGGTTTTCTGCCTTTGTTTATG 59.320 41.667 0.00 0.00 0.00 1.90
1920 5627 7.332926 ACATGGCGAAAACAATTTAATTATGCA 59.667 29.630 0.00 0.00 0.00 3.96
1961 5668 5.939883 CAGGATATCACCAAACTTCACAAGA 59.060 40.000 4.83 0.00 0.00 3.02
1973 5680 5.854010 ACTTCACAAGAGAGTAGAACACA 57.146 39.130 0.00 0.00 0.00 3.72
1974 5681 6.222038 ACTTCACAAGAGAGTAGAACACAA 57.778 37.500 0.00 0.00 0.00 3.33
2092 5806 7.117454 CCGATGTATTTCGTTATGTTTCACTC 58.883 38.462 0.00 0.00 37.42 3.51
2154 5868 1.126488 TGCATTCCCCAACAAAGCAA 58.874 45.000 0.00 0.00 0.00 3.91
2171 7158 2.555199 GCAATTAGCAGGTCATCGAGT 58.445 47.619 0.00 0.00 44.79 4.18
2216 7205 6.710295 ACATGCTACTCTGACACAAATTACAA 59.290 34.615 0.00 0.00 0.00 2.41
2224 7216 3.249799 TGACACAAATTACAACAGAGCCG 59.750 43.478 0.00 0.00 0.00 5.52
2243 7235 1.444119 GCAAAGACCGACAAGGCACA 61.444 55.000 0.00 0.00 46.52 4.57
2246 7238 1.523758 AAGACCGACAAGGCACAATC 58.476 50.000 0.00 0.00 46.52 2.67
2336 7328 4.579384 CCGCCAACCACCCACACT 62.579 66.667 0.00 0.00 0.00 3.55
2341 7333 1.073199 CAACCACCCACACTCCTCC 59.927 63.158 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
427 431 3.245122 ACATGGTATCAGTTTCCGGGTTT 60.245 43.478 0.00 0.00 0.00 3.27
476 481 9.863845 TCACGAGACTCAAACAATACAATAATA 57.136 29.630 2.82 0.00 0.00 0.98
477 482 8.771920 TCACGAGACTCAAACAATACAATAAT 57.228 30.769 2.82 0.00 0.00 1.28
478 483 8.771920 ATCACGAGACTCAAACAATACAATAA 57.228 30.769 2.82 0.00 0.00 1.40
479 484 8.032451 TGATCACGAGACTCAAACAATACAATA 58.968 33.333 2.82 0.00 0.00 1.90
480 485 6.873605 TGATCACGAGACTCAAACAATACAAT 59.126 34.615 2.82 0.00 0.00 2.71
481 486 6.220201 TGATCACGAGACTCAAACAATACAA 58.780 36.000 2.82 0.00 0.00 2.41
482 487 5.778862 TGATCACGAGACTCAAACAATACA 58.221 37.500 2.82 0.00 0.00 2.29
483 488 6.893958 ATGATCACGAGACTCAAACAATAC 57.106 37.500 0.00 0.00 0.00 1.89
529 534 9.391006 TGTTCTGACTTGTCTTGTATTTTAAGT 57.609 29.630 2.35 0.00 0.00 2.24
533 538 9.736023 GATTTGTTCTGACTTGTCTTGTATTTT 57.264 29.630 2.35 0.00 0.00 1.82
534 539 8.352942 GGATTTGTTCTGACTTGTCTTGTATTT 58.647 33.333 2.35 0.00 0.00 1.40
535 540 7.721399 AGGATTTGTTCTGACTTGTCTTGTATT 59.279 33.333 2.35 0.00 0.00 1.89
536 541 7.227156 AGGATTTGTTCTGACTTGTCTTGTAT 58.773 34.615 2.35 0.00 0.00 2.29
537 542 6.591935 AGGATTTGTTCTGACTTGTCTTGTA 58.408 36.000 2.35 0.00 0.00 2.41
538 543 5.440610 AGGATTTGTTCTGACTTGTCTTGT 58.559 37.500 2.35 0.00 0.00 3.16
539 544 6.708054 ACTAGGATTTGTTCTGACTTGTCTTG 59.292 38.462 0.00 0.00 0.00 3.02
540 545 6.831976 ACTAGGATTTGTTCTGACTTGTCTT 58.168 36.000 0.00 0.00 0.00 3.01
541 546 6.268847 AGACTAGGATTTGTTCTGACTTGTCT 59.731 38.462 0.00 0.00 36.64 3.41
542 547 6.459923 AGACTAGGATTTGTTCTGACTTGTC 58.540 40.000 0.00 0.00 33.18 3.18
543 548 6.426646 AGACTAGGATTTGTTCTGACTTGT 57.573 37.500 0.00 0.00 0.00 3.16
544 549 8.474025 AGATAGACTAGGATTTGTTCTGACTTG 58.526 37.037 0.00 0.00 0.00 3.16
545 550 8.602472 AGATAGACTAGGATTTGTTCTGACTT 57.398 34.615 0.00 0.00 0.00 3.01
546 551 7.836685 TGAGATAGACTAGGATTTGTTCTGACT 59.163 37.037 0.00 0.00 0.00 3.41
547 552 8.001881 TGAGATAGACTAGGATTTGTTCTGAC 57.998 38.462 0.00 0.00 0.00 3.51
548 553 8.774546 ATGAGATAGACTAGGATTTGTTCTGA 57.225 34.615 0.00 0.00 0.00 3.27
549 554 8.859090 AGATGAGATAGACTAGGATTTGTTCTG 58.141 37.037 0.00 0.00 0.00 3.02
550 555 9.432982 AAGATGAGATAGACTAGGATTTGTTCT 57.567 33.333 0.00 0.00 0.00 3.01
553 558 8.646900 GGAAAGATGAGATAGACTAGGATTTGT 58.353 37.037 0.00 0.00 0.00 2.83
554 559 8.869109 AGGAAAGATGAGATAGACTAGGATTTG 58.131 37.037 0.00 0.00 0.00 2.32
583 588 9.142515 CGTACTGGTTGTTGAGTATATTGTTTA 57.857 33.333 0.00 0.00 0.00 2.01
584 589 7.360607 GCGTACTGGTTGTTGAGTATATTGTTT 60.361 37.037 0.00 0.00 0.00 2.83
585 590 6.091713 GCGTACTGGTTGTTGAGTATATTGTT 59.908 38.462 0.00 0.00 0.00 2.83
586 591 5.579511 GCGTACTGGTTGTTGAGTATATTGT 59.420 40.000 0.00 0.00 0.00 2.71
587 592 5.006358 GGCGTACTGGTTGTTGAGTATATTG 59.994 44.000 0.00 0.00 0.00 1.90
588 593 5.105064 AGGCGTACTGGTTGTTGAGTATATT 60.105 40.000 0.00 0.00 0.00 1.28
589 594 4.404715 AGGCGTACTGGTTGTTGAGTATAT 59.595 41.667 0.00 0.00 0.00 0.86
590 595 3.765511 AGGCGTACTGGTTGTTGAGTATA 59.234 43.478 0.00 0.00 0.00 1.47
591 596 2.565834 AGGCGTACTGGTTGTTGAGTAT 59.434 45.455 0.00 0.00 0.00 2.12
592 597 1.965643 AGGCGTACTGGTTGTTGAGTA 59.034 47.619 0.00 0.00 0.00 2.59
593 598 0.756903 AGGCGTACTGGTTGTTGAGT 59.243 50.000 0.00 0.00 0.00 3.41
594 599 1.798813 GAAGGCGTACTGGTTGTTGAG 59.201 52.381 0.00 0.00 0.00 3.02
595 600 1.414919 AGAAGGCGTACTGGTTGTTGA 59.585 47.619 0.00 0.00 0.00 3.18
596 601 1.798813 GAGAAGGCGTACTGGTTGTTG 59.201 52.381 0.00 0.00 0.00 3.33
597 602 1.270678 GGAGAAGGCGTACTGGTTGTT 60.271 52.381 0.00 0.00 0.00 2.83
598 603 0.320697 GGAGAAGGCGTACTGGTTGT 59.679 55.000 0.00 0.00 0.00 3.32
599 604 0.608640 AGGAGAAGGCGTACTGGTTG 59.391 55.000 0.00 0.00 0.00 3.77
609 614 0.179097 GACGTCATGGAGGAGAAGGC 60.179 60.000 11.55 0.00 0.00 4.35
695 754 4.036262 TGGTGTCGGATTTATTAATGCAGC 59.964 41.667 0.00 0.00 32.12 5.25
787 866 2.735126 CGGCCGAGCAAAGCAAATTAAT 60.735 45.455 24.07 0.00 0.00 1.40
811 892 5.156804 ACGCATCGGATCTGAAATAAAAC 57.843 39.130 8.65 0.00 0.00 2.43
812 893 4.026062 CGACGCATCGGATCTGAAATAAAA 60.026 41.667 8.65 0.00 44.99 1.52
813 894 3.489416 CGACGCATCGGATCTGAAATAAA 59.511 43.478 8.65 0.00 44.99 1.40
815 896 2.661594 CGACGCATCGGATCTGAAATA 58.338 47.619 8.65 0.00 44.99 1.40
816 897 1.491670 CGACGCATCGGATCTGAAAT 58.508 50.000 8.65 0.00 44.99 2.17
1365 1457 0.738975 TCGATGGGAGAAGCACGTAG 59.261 55.000 0.00 0.00 0.00 3.51
1379 1475 0.107268 TCCATGGGCACAGATCGATG 59.893 55.000 13.02 0.00 0.00 3.84
1387 1483 0.966875 GCATCAACTCCATGGGCACA 60.967 55.000 13.02 0.00 0.00 4.57
1388 1484 0.682209 AGCATCAACTCCATGGGCAC 60.682 55.000 13.02 0.00 0.00 5.01
1393 1489 2.995283 TCCAGAAGCATCAACTCCATG 58.005 47.619 0.00 0.00 0.00 3.66
1396 1492 2.941720 GACATCCAGAAGCATCAACTCC 59.058 50.000 0.00 0.00 0.00 3.85
1408 1504 3.175438 TGGTGAGAAGAGACATCCAGA 57.825 47.619 0.00 0.00 0.00 3.86
1441 5050 8.715088 GGCCTTATATACCACTTACAATAAACG 58.285 37.037 0.00 0.00 0.00 3.60
1459 5068 5.221224 GCATTGCATTGTACAAGGCCTTATA 60.221 40.000 34.56 18.20 46.15 0.98
1460 5069 4.441913 GCATTGCATTGTACAAGGCCTTAT 60.442 41.667 34.56 23.92 46.15 1.73
1461 5070 3.119173 GCATTGCATTGTACAAGGCCTTA 60.119 43.478 34.56 22.97 46.15 2.69
1462 5071 2.354003 GCATTGCATTGTACAAGGCCTT 60.354 45.455 34.56 22.43 46.15 4.35
1478 5087 5.063180 TCTAAAGACCTTGCATTGCATTG 57.937 39.130 12.95 9.11 38.76 2.82
1502 5121 8.777413 ACCGGTTTCTTTTTACAAATAGAGTAC 58.223 33.333 0.00 0.00 29.82 2.73
1503 5122 8.907222 ACCGGTTTCTTTTTACAAATAGAGTA 57.093 30.769 0.00 0.00 29.82 2.59
1521 5149 4.692155 CCGTACTTGAGAAAATACCGGTTT 59.308 41.667 15.04 0.14 0.00 3.27
1543 5171 7.385778 TGTGCTACATTAGAAATAAACACCC 57.614 36.000 0.00 0.00 0.00 4.61
1555 5183 9.967346 TCTAAGTAAGCTTATGTGCTACATTAG 57.033 33.333 9.88 8.40 43.24 1.73
1642 5318 3.201290 CAACATCTGGACCATGTAGAGC 58.799 50.000 1.11 0.00 33.12 4.09
1705 5381 3.188786 CGAGAAAAGAGCCCGGCG 61.189 66.667 3.05 0.00 0.00 6.46
1742 5418 1.812686 TACTCGGTCTTGCGTGGCTT 61.813 55.000 0.00 0.00 0.00 4.35
1746 5422 1.390123 CACATTACTCGGTCTTGCGTG 59.610 52.381 0.00 0.00 0.00 5.34
1747 5423 1.000506 ACACATTACTCGGTCTTGCGT 59.999 47.619 0.00 0.00 0.00 5.24
1889 5596 9.871299 AATTAAATTGTTTTCGCCATGTTTAAC 57.129 25.926 0.00 0.00 0.00 2.01
1920 5627 4.112634 TCCTGGTGTTCTAGGCAAAAAT 57.887 40.909 0.00 0.00 41.33 1.82
2027 5737 7.825270 ACATACACCCGAATGAATAGTAAAACA 59.175 33.333 0.00 0.00 0.00 2.83
2033 5743 4.407621 TCCACATACACCCGAATGAATAGT 59.592 41.667 0.00 0.00 0.00 2.12
2092 5806 0.941542 TTTTTGAGAAGACCGGCGTG 59.058 50.000 6.01 0.00 0.00 5.34
2154 5868 3.570550 GGACTACTCGATGACCTGCTAAT 59.429 47.826 0.00 0.00 0.00 1.73
2171 7158 0.324943 GTCCTGCTTGGCTTGGACTA 59.675 55.000 19.29 0.00 43.50 2.59
2216 7205 2.357517 CGGTCTTTGCGGCTCTGT 60.358 61.111 0.00 0.00 0.00 3.41
2224 7216 1.282875 GTGCCTTGTCGGTCTTTGC 59.717 57.895 0.00 0.00 34.25 3.68
2243 7235 1.973281 CACGCCTGCCCTTGTGATT 60.973 57.895 0.00 0.00 34.29 2.57


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

AutoCloner maintained by Alex Coulton.