Multiple sequence alignment - TraesCS2D01G329200

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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 TraesCS2D01G329200 chr2D 100.000 2464 0 0 1 2464 422323276 422325739 0.000000e+00 4551.0
1 TraesCS2D01G329200 chr2A 93.847 1284 54 13 1196 2464 568578317 568579590 0.000000e+00 1910.0
2 TraesCS2D01G329200 chr2A 90.746 389 33 3 3 390 568575734 568576120 1.310000e-142 516.0
3 TraesCS2D01G329200 chr2A 82.922 486 42 15 659 1123 568483352 568483817 1.370000e-107 399.0
4 TraesCS2D01G329200 chr2A 89.492 295 17 7 817 1111 568577904 568578184 6.480000e-96 361.0
5 TraesCS2D01G329200 chr2A 89.381 113 9 2 408 517 28248157 28248045 3.300000e-29 139.0
6 TraesCS2D01G329200 chr2A 87.500 128 5 1 651 778 568577786 568577902 1.190000e-28 137.0
7 TraesCS2D01G329200 chr2B 88.547 1266 77 33 716 1944 494876863 494878097 0.000000e+00 1472.0
8 TraesCS2D01G329200 chr2B 94.877 488 17 5 1980 2464 494878279 494878761 0.000000e+00 756.0
9 TraesCS2D01G329200 chr2B 90.127 395 21 6 2 390 494876151 494876533 4.730000e-137 497.0
10 TraesCS2D01G329200 chr2B 78.843 605 72 23 1196 1784 494860412 494860976 8.380000e-95 357.0
11 TraesCS2D01G329200 chr2B 90.964 166 6 3 571 728 494876522 494876686 5.340000e-52 215.0
12 TraesCS2D01G329200 chr2B 82.727 110 14 4 408 516 641081638 641081533 2.610000e-15 93.5
13 TraesCS2D01G329200 chr7D 90.361 166 10 4 408 571 46955684 46955845 1.920000e-51 213.0
14 TraesCS2D01G329200 chr7D 84.800 125 11 5 410 532 517149252 517149370 4.300000e-23 119.0
15 TraesCS2D01G329200 chr1B 91.837 147 8 4 408 553 591353631 591353488 4.150000e-48 202.0
16 TraesCS2D01G329200 chr1B 88.690 168 13 6 408 572 470551241 470551405 1.490000e-47 200.0
17 TraesCS2D01G329200 chr6D 87.879 165 15 3 408 571 357843976 357843816 3.230000e-44 189.0
18 TraesCS2D01G329200 chr3A 81.081 111 13 8 408 514 44235790 44235896 5.650000e-12 82.4
19 TraesCS2D01G329200 chr3A 80.909 110 12 9 409 514 43050263 43050367 7.310000e-11 78.7
20 TraesCS2D01G329200 chr3D 100.000 31 0 0 206 236 542739778 542739808 9.520000e-05 58.4


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 TraesCS2D01G329200 chr2D 422323276 422325739 2463 False 4551 4551 100.00000 1 2464 1 chr2D.!!$F1 2463
1 TraesCS2D01G329200 chr2A 568575734 568579590 3856 False 731 1910 90.39625 3 2464 4 chr2A.!!$F2 2461
2 TraesCS2D01G329200 chr2B 494876151 494878761 2610 False 735 1472 91.12875 2 2464 4 chr2B.!!$F2 2462
3 TraesCS2D01G329200 chr2B 494860412 494860976 564 False 357 357 78.84300 1196 1784 1 chr2B.!!$F1 588

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
387 394 0.17907 GAACCGAGATCCTTGAGGGC 60.179 60.0 0.0 0.0 35.41 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2081 4137 0.475906 ATAGCAGGAGGTTGATGGCC 59.524 55.0 0.0 0.0 0.0 5.36 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
43 49 6.465948 TGATGAATTGGGGATTTTTGACTTG 58.534 36.000 0.00 0.00 0.00 3.16
53 59 6.256975 GGGGATTTTTGACTTGTTACACAAAC 59.743 38.462 0.15 0.00 37.69 2.93
54 60 6.814146 GGGATTTTTGACTTGTTACACAAACA 59.186 34.615 0.15 0.00 46.41 2.83
63 69 2.621055 TGTTACACAAACACCTCCATGC 59.379 45.455 0.00 0.00 43.22 4.06
64 70 2.621055 GTTACACAAACACCTCCATGCA 59.379 45.455 0.00 0.00 38.05 3.96
86 92 5.126061 GCAAAGATTGGCCTAATCAGAGAAA 59.874 40.000 22.09 0.00 46.20 2.52
91 97 7.051000 AGATTGGCCTAATCAGAGAAAAGTAC 58.949 38.462 22.09 0.00 46.20 2.73
131 137 0.995024 AAACCAGGCCTCTATGCACT 59.005 50.000 0.00 0.00 0.00 4.40
183 189 5.628193 CACGTCAAATCGTATATAGTGACCC 59.372 44.000 0.00 0.00 42.27 4.46
283 289 3.849951 CGCGTGGGTAGCCAGGAT 61.850 66.667 32.00 0.00 0.00 3.24
316 322 4.555709 GTGTGGGCCGTGGTGACA 62.556 66.667 0.00 0.00 38.70 3.58
323 329 0.872388 GGCCGTGGTGACAGTTTTAG 59.128 55.000 0.00 0.00 44.46 1.85
342 348 3.655615 AGCCCGGTTTTCCATGTATTA 57.344 42.857 0.00 0.00 40.70 0.98
382 389 6.985188 TTCTTTAATGAACCGAGATCCTTG 57.015 37.500 0.00 0.00 0.00 3.61
383 390 6.294361 TCTTTAATGAACCGAGATCCTTGA 57.706 37.500 0.00 0.00 0.00 3.02
384 391 6.341316 TCTTTAATGAACCGAGATCCTTGAG 58.659 40.000 0.00 0.00 0.00 3.02
385 392 3.550437 AATGAACCGAGATCCTTGAGG 57.450 47.619 0.00 0.00 0.00 3.86
386 393 1.195115 TGAACCGAGATCCTTGAGGG 58.805 55.000 0.00 0.00 35.41 4.30
387 394 0.179070 GAACCGAGATCCTTGAGGGC 60.179 60.000 0.00 0.00 35.41 5.19
388 395 1.627297 AACCGAGATCCTTGAGGGCC 61.627 60.000 0.00 0.00 35.41 5.80
389 396 2.419198 CGAGATCCTTGAGGGCCG 59.581 66.667 0.00 0.00 35.41 6.13
390 397 2.825264 GAGATCCTTGAGGGCCGG 59.175 66.667 0.00 0.00 35.41 6.13
391 398 2.770048 AGATCCTTGAGGGCCGGG 60.770 66.667 2.18 0.00 35.41 5.73
392 399 2.768344 GATCCTTGAGGGCCGGGA 60.768 66.667 2.18 11.59 35.41 5.14
393 400 2.286121 ATCCTTGAGGGCCGGGAA 60.286 61.111 2.18 0.64 35.41 3.97
394 401 1.921869 GATCCTTGAGGGCCGGGAAA 61.922 60.000 2.18 0.04 35.41 3.13
395 402 1.506028 ATCCTTGAGGGCCGGGAAAA 61.506 55.000 2.18 0.00 35.41 2.29
396 403 1.000359 CCTTGAGGGCCGGGAAAAT 60.000 57.895 2.18 0.00 0.00 1.82
397 404 0.257616 CCTTGAGGGCCGGGAAAATA 59.742 55.000 2.18 0.00 0.00 1.40
398 405 1.133482 CCTTGAGGGCCGGGAAAATAT 60.133 52.381 2.18 0.00 0.00 1.28
399 406 2.230660 CTTGAGGGCCGGGAAAATATC 58.769 52.381 2.18 0.00 0.00 1.63
400 407 1.217916 TGAGGGCCGGGAAAATATCA 58.782 50.000 2.18 0.00 0.00 2.15
401 408 1.133915 TGAGGGCCGGGAAAATATCAC 60.134 52.381 2.18 0.00 0.00 3.06
402 409 0.923358 AGGGCCGGGAAAATATCACA 59.077 50.000 2.18 0.00 0.00 3.58
403 410 1.499007 AGGGCCGGGAAAATATCACAT 59.501 47.619 2.18 0.00 0.00 3.21
404 411 1.613437 GGGCCGGGAAAATATCACATG 59.387 52.381 2.18 0.00 0.00 3.21
405 412 2.582052 GGCCGGGAAAATATCACATGA 58.418 47.619 2.18 0.00 0.00 3.07
406 413 3.157087 GGCCGGGAAAATATCACATGAT 58.843 45.455 2.18 0.00 38.51 2.45
407 414 4.331968 GGCCGGGAAAATATCACATGATA 58.668 43.478 2.18 4.11 40.85 2.15
408 415 4.764823 GGCCGGGAAAATATCACATGATAA 59.235 41.667 2.18 0.00 40.09 1.75
409 416 5.418840 GGCCGGGAAAATATCACATGATAAT 59.581 40.000 2.18 0.00 40.09 1.28
410 417 6.324819 GCCGGGAAAATATCACATGATAATG 58.675 40.000 2.18 0.00 40.09 1.90
411 418 6.071952 GCCGGGAAAATATCACATGATAATGT 60.072 38.462 2.18 0.00 40.09 2.71
429 436 8.912988 TGATAATGTGGATTTAGAATTTGGACC 58.087 33.333 0.00 0.00 0.00 4.46
430 437 9.136323 GATAATGTGGATTTAGAATTTGGACCT 57.864 33.333 0.00 0.00 0.00 3.85
431 438 6.780457 ATGTGGATTTAGAATTTGGACCTG 57.220 37.500 0.00 0.00 0.00 4.00
432 439 5.886609 TGTGGATTTAGAATTTGGACCTGA 58.113 37.500 0.00 0.00 0.00 3.86
433 440 6.310941 TGTGGATTTAGAATTTGGACCTGAA 58.689 36.000 0.00 0.00 0.00 3.02
434 441 6.780031 TGTGGATTTAGAATTTGGACCTGAAA 59.220 34.615 0.00 0.00 0.00 2.69
435 442 7.454380 TGTGGATTTAGAATTTGGACCTGAAAT 59.546 33.333 0.00 0.00 0.00 2.17
436 443 8.314021 GTGGATTTAGAATTTGGACCTGAAATT 58.686 33.333 2.89 2.89 36.04 1.82
437 444 8.879227 TGGATTTAGAATTTGGACCTGAAATTT 58.121 29.630 4.50 0.00 34.00 1.82
438 445 9.725019 GGATTTAGAATTTGGACCTGAAATTTT 57.275 29.630 4.50 2.44 34.00 1.82
444 451 8.923270 AGAATTTGGACCTGAAATTTTTAGTGA 58.077 29.630 4.50 0.00 34.00 3.41
445 452 9.710900 GAATTTGGACCTGAAATTTTTAGTGAT 57.289 29.630 4.50 0.00 34.00 3.06
447 454 8.885494 TTTGGACCTGAAATTTTTAGTGATTG 57.115 30.769 0.00 0.00 0.00 2.67
448 455 7.595819 TGGACCTGAAATTTTTAGTGATTGT 57.404 32.000 0.00 0.00 0.00 2.71
449 456 8.698973 TGGACCTGAAATTTTTAGTGATTGTA 57.301 30.769 0.00 0.00 0.00 2.41
450 457 8.573035 TGGACCTGAAATTTTTAGTGATTGTAC 58.427 33.333 0.00 0.00 0.00 2.90
451 458 8.573035 GGACCTGAAATTTTTAGTGATTGTACA 58.427 33.333 0.00 0.00 0.00 2.90
463 470 8.791327 TTAGTGATTGTACATTCATGTGATGT 57.209 30.769 20.14 17.26 41.89 3.06
464 471 7.312657 AGTGATTGTACATTCATGTGATGTC 57.687 36.000 20.14 7.79 41.89 3.06
465 472 6.880529 AGTGATTGTACATTCATGTGATGTCA 59.119 34.615 20.14 12.97 41.89 3.58
466 473 7.391275 AGTGATTGTACATTCATGTGATGTCAA 59.609 33.333 20.14 18.03 41.89 3.18
467 474 7.482743 GTGATTGTACATTCATGTGATGTCAAC 59.517 37.037 20.14 12.63 41.89 3.18
468 475 6.874288 TTGTACATTCATGTGATGTCAACA 57.126 33.333 16.81 14.38 41.89 3.33
469 476 7.451501 TTGTACATTCATGTGATGTCAACAT 57.548 32.000 16.81 0.00 41.89 2.71
470 477 8.558973 TTGTACATTCATGTGATGTCAACATA 57.441 30.769 16.81 8.43 41.89 2.29
471 478 7.973601 TGTACATTCATGTGATGTCAACATAC 58.026 34.615 16.81 11.11 41.89 2.39
472 479 7.605691 TGTACATTCATGTGATGTCAACATACA 59.394 33.333 16.81 12.86 41.89 2.29
473 480 7.634671 ACATTCATGTGATGTCAACATACAT 57.365 32.000 10.36 4.54 40.03 2.29
474 481 8.735692 ACATTCATGTGATGTCAACATACATA 57.264 30.769 10.36 6.35 40.03 2.29
475 482 9.176460 ACATTCATGTGATGTCAACATACATAA 57.824 29.630 10.36 10.35 40.03 1.90
534 541 9.217278 TGATTTTTGTTTCAAATGGTATCATGG 57.783 29.630 0.00 0.00 33.18 3.66
535 542 7.976135 TTTTTGTTTCAAATGGTATCATGGG 57.024 32.000 0.00 0.00 33.18 4.00
536 543 6.924913 TTTGTTTCAAATGGTATCATGGGA 57.075 33.333 0.00 0.00 33.18 4.37
537 544 6.528537 TTGTTTCAAATGGTATCATGGGAG 57.471 37.500 0.00 0.00 33.18 4.30
538 545 4.402155 TGTTTCAAATGGTATCATGGGAGC 59.598 41.667 0.00 0.00 33.18 4.70
539 546 3.949586 TCAAATGGTATCATGGGAGCA 57.050 42.857 0.00 0.00 33.18 4.26
540 547 4.458256 TCAAATGGTATCATGGGAGCAT 57.542 40.909 6.63 6.63 35.35 3.79
541 548 4.806892 TCAAATGGTATCATGGGAGCATT 58.193 39.130 15.26 15.26 43.65 3.56
542 549 4.585581 TCAAATGGTATCATGGGAGCATTG 59.414 41.667 19.30 14.86 41.60 2.82
543 550 2.662535 TGGTATCATGGGAGCATTGG 57.337 50.000 0.00 0.00 0.00 3.16
544 551 1.145531 TGGTATCATGGGAGCATTGGG 59.854 52.381 0.00 0.00 0.00 4.12
545 552 1.548582 GGTATCATGGGAGCATTGGGG 60.549 57.143 0.00 0.00 0.00 4.96
546 553 1.425066 GTATCATGGGAGCATTGGGGA 59.575 52.381 0.00 0.00 0.00 4.81
547 554 0.481567 ATCATGGGAGCATTGGGGAG 59.518 55.000 0.00 0.00 0.00 4.30
548 555 0.624206 TCATGGGAGCATTGGGGAGA 60.624 55.000 0.00 0.00 0.00 3.71
549 556 0.481567 CATGGGAGCATTGGGGAGAT 59.518 55.000 0.00 0.00 0.00 2.75
550 557 0.481567 ATGGGAGCATTGGGGAGATG 59.518 55.000 0.00 0.00 0.00 2.90
551 558 1.152368 GGGAGCATTGGGGAGATGG 59.848 63.158 0.00 0.00 0.00 3.51
552 559 1.649271 GGGAGCATTGGGGAGATGGT 61.649 60.000 0.00 0.00 37.89 3.55
553 560 1.140312 GGAGCATTGGGGAGATGGTA 58.860 55.000 0.00 0.00 35.54 3.25
554 561 1.707427 GGAGCATTGGGGAGATGGTAT 59.293 52.381 0.00 0.00 35.54 2.73
555 562 2.290577 GGAGCATTGGGGAGATGGTATC 60.291 54.545 0.00 0.00 35.54 2.24
556 563 2.373169 GAGCATTGGGGAGATGGTATCA 59.627 50.000 0.00 0.00 35.54 2.15
557 564 2.107204 AGCATTGGGGAGATGGTATCAC 59.893 50.000 0.00 0.00 33.80 3.06
558 565 2.815589 GCATTGGGGAGATGGTATCACC 60.816 54.545 0.00 0.00 39.04 4.02
559 566 2.587060 TTGGGGAGATGGTATCACCT 57.413 50.000 5.48 0.00 39.58 4.00
560 567 1.806496 TGGGGAGATGGTATCACCTG 58.194 55.000 5.48 0.00 39.58 4.00
561 568 1.293763 TGGGGAGATGGTATCACCTGA 59.706 52.381 5.48 0.00 39.58 3.86
562 569 2.089982 TGGGGAGATGGTATCACCTGAT 60.090 50.000 5.48 0.00 39.58 2.90
563 570 3.143933 TGGGGAGATGGTATCACCTGATA 59.856 47.826 5.48 0.00 39.58 2.15
573 580 3.715648 ATCACCTGATACTCTCCCCTT 57.284 47.619 0.00 0.00 32.01 3.95
574 581 4.834406 ATCACCTGATACTCTCCCCTTA 57.166 45.455 0.00 0.00 32.01 2.69
661 2265 7.509546 AGGTATAACATTACAAGGACCATCAG 58.490 38.462 0.00 0.00 0.00 2.90
666 2270 5.930135 ACATTACAAGGACCATCAGATACC 58.070 41.667 0.00 0.00 0.00 2.73
866 2666 2.220470 TCCCTAGACCCCTTACTAGCA 58.780 52.381 0.00 0.00 35.96 3.49
920 2724 6.543831 CCACTGATTTCCCTATAAAACCTCAG 59.456 42.308 0.00 0.00 32.67 3.35
1124 2941 4.080695 TGAGTTTCCTCTCCAATCTCCATG 60.081 45.833 0.00 0.00 38.61 3.66
1134 2951 6.115446 TCTCCAATCTCCATGTATGTTTGTC 58.885 40.000 0.00 0.00 0.00 3.18
1154 3013 4.397103 TGTCAGTTTTGAGATGCATCCATC 59.603 41.667 23.06 15.21 46.61 3.51
1175 3034 2.071540 CACCCATGGATTGATCGATCG 58.928 52.381 20.03 9.36 0.00 3.69
1244 3103 0.032813 ATGGCCTGAACATTGGAGGG 60.033 55.000 3.32 0.00 0.00 4.30
1483 3345 2.264794 CCGTCAGACTTTCCCCGG 59.735 66.667 0.00 0.00 0.00 5.73
1631 3517 9.173021 CAAATATTATGGAATAACGATGCCCTA 57.827 33.333 0.00 0.00 42.43 3.53
1857 3757 4.123506 TCAGCGTTCTATGTGTGTCAAAA 58.876 39.130 0.00 0.00 0.00 2.44
1881 3787 7.698836 ACTTATTTTGTTGCTTGTTCACATC 57.301 32.000 0.00 0.00 0.00 3.06
1894 3800 2.114670 CACATCCGGGTCATGGCAC 61.115 63.158 0.00 0.00 0.00 5.01
1986 4039 6.981559 TCGCACTACATGTATGTATAAGCAAA 59.018 34.615 5.91 7.33 41.92 3.68
2002 4055 0.389426 CAAACAGGAATGCTGGCAGC 60.389 55.000 31.91 31.91 42.82 5.25
2081 4137 0.872021 GCCACTAGCGAATCCGACAG 60.872 60.000 0.00 0.00 38.22 3.51
2152 4208 0.254462 GGGGGAGAAGAGCAAGGAAG 59.746 60.000 0.00 0.00 0.00 3.46
2385 4441 1.203523 CTCTGTCTGTAGCCTGTGGAC 59.796 57.143 0.00 0.00 0.00 4.02
2416 4473 8.388103 ACATATGCGTTTATGTACTTGAGAAAC 58.612 33.333 1.58 0.00 40.22 2.78
2448 4505 6.412362 AGTGGTGATACTATTCAGATGTCC 57.588 41.667 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.170397 TCAAATCCCTAATCTGCAGCGA 59.830 45.455 9.47 0.00 0.00 4.93
4 5 6.041182 CCAATTCATCAAATCCCTAATCTGCA 59.959 38.462 0.00 0.00 0.00 4.41
43 49 2.621055 TGCATGGAGGTGTTTGTGTAAC 59.379 45.455 0.00 0.00 37.26 2.50
53 59 1.134907 GCCAATCTTTGCATGGAGGTG 60.135 52.381 7.48 2.63 36.27 4.00
54 60 1.188863 GCCAATCTTTGCATGGAGGT 58.811 50.000 7.48 0.00 36.27 3.85
55 61 0.462789 GGCCAATCTTTGCATGGAGG 59.537 55.000 7.48 0.00 36.27 4.30
57 63 2.824689 TAGGCCAATCTTTGCATGGA 57.175 45.000 5.01 0.00 36.27 3.41
58 64 3.385433 TGATTAGGCCAATCTTTGCATGG 59.615 43.478 21.12 0.00 43.10 3.66
59 65 4.340097 TCTGATTAGGCCAATCTTTGCATG 59.660 41.667 21.12 0.00 43.10 4.06
60 66 4.539726 TCTGATTAGGCCAATCTTTGCAT 58.460 39.130 21.12 0.00 43.10 3.96
61 67 3.949754 CTCTGATTAGGCCAATCTTTGCA 59.050 43.478 21.12 7.38 43.10 4.08
62 68 4.202441 TCTCTGATTAGGCCAATCTTTGC 58.798 43.478 21.12 4.12 43.10 3.68
63 69 6.764308 TTTCTCTGATTAGGCCAATCTTTG 57.236 37.500 21.12 14.26 43.10 2.77
64 70 6.950619 ACTTTTCTCTGATTAGGCCAATCTTT 59.049 34.615 21.12 0.00 43.10 2.52
86 92 0.179078 TTGTTGACCGCCACGTACTT 60.179 50.000 0.00 0.00 0.00 2.24
91 97 1.227999 ATCACTTGTTGACCGCCACG 61.228 55.000 0.00 0.00 36.92 4.94
131 137 4.316205 AGGTCATTATTCGACGTATGCA 57.684 40.909 0.00 0.00 34.04 3.96
183 189 5.289595 TGCACTTAGGAATACGCTCATTAG 58.710 41.667 0.00 0.00 0.00 1.73
235 241 0.324943 GCCACTGCCCACTAGAAAGA 59.675 55.000 0.00 0.00 0.00 2.52
241 247 4.697756 GCACGCCACTGCCCACTA 62.698 66.667 0.00 0.00 0.00 2.74
316 322 2.368311 TGGAAAACCGGGCTAAAACT 57.632 45.000 6.32 0.00 0.00 2.66
323 329 3.181484 GGTTAATACATGGAAAACCGGGC 60.181 47.826 6.32 0.00 31.09 6.13
382 389 1.133915 TGTGATATTTTCCCGGCCCTC 60.134 52.381 0.00 0.00 0.00 4.30
383 390 0.923358 TGTGATATTTTCCCGGCCCT 59.077 50.000 0.00 0.00 0.00 5.19
384 391 1.613437 CATGTGATATTTTCCCGGCCC 59.387 52.381 0.00 0.00 0.00 5.80
385 392 2.582052 TCATGTGATATTTTCCCGGCC 58.418 47.619 0.00 0.00 0.00 6.13
386 393 5.957842 TTATCATGTGATATTTTCCCGGC 57.042 39.130 0.00 0.00 36.94 6.13
387 394 7.452880 ACATTATCATGTGATATTTTCCCGG 57.547 36.000 0.00 0.00 42.46 5.73
403 410 8.912988 GGTCCAAATTCTAAATCCACATTATCA 58.087 33.333 0.00 0.00 0.00 2.15
404 411 9.136323 AGGTCCAAATTCTAAATCCACATTATC 57.864 33.333 0.00 0.00 0.00 1.75
405 412 8.917088 CAGGTCCAAATTCTAAATCCACATTAT 58.083 33.333 0.00 0.00 0.00 1.28
406 413 8.112822 TCAGGTCCAAATTCTAAATCCACATTA 58.887 33.333 0.00 0.00 0.00 1.90
407 414 6.953520 TCAGGTCCAAATTCTAAATCCACATT 59.046 34.615 0.00 0.00 0.00 2.71
408 415 6.493166 TCAGGTCCAAATTCTAAATCCACAT 58.507 36.000 0.00 0.00 0.00 3.21
409 416 5.886609 TCAGGTCCAAATTCTAAATCCACA 58.113 37.500 0.00 0.00 0.00 4.17
410 417 6.834168 TTCAGGTCCAAATTCTAAATCCAC 57.166 37.500 0.00 0.00 0.00 4.02
411 418 8.434589 AATTTCAGGTCCAAATTCTAAATCCA 57.565 30.769 0.00 0.00 29.14 3.41
412 419 9.725019 AAAATTTCAGGTCCAAATTCTAAATCC 57.275 29.630 0.00 0.00 33.24 3.01
418 425 8.923270 TCACTAAAAATTTCAGGTCCAAATTCT 58.077 29.630 0.00 0.00 33.24 2.40
419 426 9.710900 ATCACTAAAAATTTCAGGTCCAAATTC 57.289 29.630 0.00 0.00 33.24 2.17
421 428 9.492973 CAATCACTAAAAATTTCAGGTCCAAAT 57.507 29.630 0.00 0.00 0.00 2.32
422 429 8.482128 ACAATCACTAAAAATTTCAGGTCCAAA 58.518 29.630 0.00 0.00 0.00 3.28
423 430 8.017418 ACAATCACTAAAAATTTCAGGTCCAA 57.983 30.769 0.00 0.00 0.00 3.53
424 431 7.595819 ACAATCACTAAAAATTTCAGGTCCA 57.404 32.000 0.00 0.00 0.00 4.02
425 432 8.573035 TGTACAATCACTAAAAATTTCAGGTCC 58.427 33.333 0.00 0.00 0.00 4.46
437 444 9.230122 ACATCACATGAATGTACAATCACTAAA 57.770 29.630 15.71 3.49 39.39 1.85
438 445 8.791327 ACATCACATGAATGTACAATCACTAA 57.209 30.769 15.71 3.15 39.39 2.24
439 446 8.040132 TGACATCACATGAATGTACAATCACTA 58.960 33.333 15.71 2.80 39.39 2.74
440 447 6.880529 TGACATCACATGAATGTACAATCACT 59.119 34.615 15.71 1.73 39.39 3.41
441 448 7.075674 TGACATCACATGAATGTACAATCAC 57.924 36.000 15.71 1.86 39.39 3.06
442 449 7.174599 TGTTGACATCACATGAATGTACAATCA 59.825 33.333 15.73 15.73 39.39 2.57
443 450 7.529158 TGTTGACATCACATGAATGTACAATC 58.471 34.615 15.27 0.73 39.39 2.67
444 451 7.451501 TGTTGACATCACATGAATGTACAAT 57.548 32.000 15.27 0.00 39.39 2.71
445 452 6.874288 TGTTGACATCACATGAATGTACAA 57.126 33.333 15.27 16.04 39.39 2.41
446 453 7.605691 TGTATGTTGACATCACATGAATGTACA 59.394 33.333 15.27 15.99 37.03 2.90
447 454 7.973601 TGTATGTTGACATCACATGAATGTAC 58.026 34.615 15.27 12.27 37.03 2.90
448 455 8.735692 ATGTATGTTGACATCACATGAATGTA 57.264 30.769 15.27 4.37 35.76 2.29
449 456 7.634671 ATGTATGTTGACATCACATGAATGT 57.365 32.000 15.23 15.23 34.97 2.71
508 515 9.217278 CCATGATACCATTTGAAACAAAAATCA 57.783 29.630 0.00 0.00 0.00 2.57
509 516 8.667463 CCCATGATACCATTTGAAACAAAAATC 58.333 33.333 0.00 0.00 0.00 2.17
510 517 8.381636 TCCCATGATACCATTTGAAACAAAAAT 58.618 29.630 0.00 0.00 0.00 1.82
511 518 7.739825 TCCCATGATACCATTTGAAACAAAAA 58.260 30.769 0.00 0.00 0.00 1.94
512 519 7.308450 TCCCATGATACCATTTGAAACAAAA 57.692 32.000 0.00 0.00 0.00 2.44
513 520 6.574073 GCTCCCATGATACCATTTGAAACAAA 60.574 38.462 0.00 0.00 0.00 2.83
514 521 5.105392 GCTCCCATGATACCATTTGAAACAA 60.105 40.000 0.00 0.00 0.00 2.83
515 522 4.402155 GCTCCCATGATACCATTTGAAACA 59.598 41.667 0.00 0.00 0.00 2.83
516 523 4.402155 TGCTCCCATGATACCATTTGAAAC 59.598 41.667 0.00 0.00 0.00 2.78
517 524 4.608269 TGCTCCCATGATACCATTTGAAA 58.392 39.130 0.00 0.00 0.00 2.69
518 525 4.248174 TGCTCCCATGATACCATTTGAA 57.752 40.909 0.00 0.00 0.00 2.69
519 526 3.949586 TGCTCCCATGATACCATTTGA 57.050 42.857 0.00 0.00 0.00 2.69
520 527 4.262292 CCAATGCTCCCATGATACCATTTG 60.262 45.833 0.00 0.00 0.00 2.32
521 528 3.899360 CCAATGCTCCCATGATACCATTT 59.101 43.478 0.00 0.00 0.00 2.32
522 529 3.503365 CCAATGCTCCCATGATACCATT 58.497 45.455 0.00 0.00 0.00 3.16
523 530 2.225192 CCCAATGCTCCCATGATACCAT 60.225 50.000 0.00 0.00 0.00 3.55
524 531 1.145531 CCCAATGCTCCCATGATACCA 59.854 52.381 0.00 0.00 0.00 3.25
525 532 1.548582 CCCCAATGCTCCCATGATACC 60.549 57.143 0.00 0.00 0.00 2.73
526 533 1.425066 TCCCCAATGCTCCCATGATAC 59.575 52.381 0.00 0.00 0.00 2.24
527 534 1.706866 CTCCCCAATGCTCCCATGATA 59.293 52.381 0.00 0.00 0.00 2.15
528 535 0.481567 CTCCCCAATGCTCCCATGAT 59.518 55.000 0.00 0.00 0.00 2.45
529 536 0.624206 TCTCCCCAATGCTCCCATGA 60.624 55.000 0.00 0.00 0.00 3.07
530 537 0.481567 ATCTCCCCAATGCTCCCATG 59.518 55.000 0.00 0.00 0.00 3.66
531 538 0.481567 CATCTCCCCAATGCTCCCAT 59.518 55.000 0.00 0.00 0.00 4.00
532 539 1.648302 CCATCTCCCCAATGCTCCCA 61.648 60.000 0.00 0.00 0.00 4.37
533 540 1.152368 CCATCTCCCCAATGCTCCC 59.848 63.158 0.00 0.00 0.00 4.30
534 541 1.140312 TACCATCTCCCCAATGCTCC 58.860 55.000 0.00 0.00 0.00 4.70
535 542 2.373169 TGATACCATCTCCCCAATGCTC 59.627 50.000 0.00 0.00 0.00 4.26
536 543 2.107204 GTGATACCATCTCCCCAATGCT 59.893 50.000 0.00 0.00 0.00 3.79
537 544 2.508526 GTGATACCATCTCCCCAATGC 58.491 52.381 0.00 0.00 0.00 3.56
538 545 2.713167 AGGTGATACCATCTCCCCAATG 59.287 50.000 0.28 0.00 41.95 2.82
539 546 2.713167 CAGGTGATACCATCTCCCCAAT 59.287 50.000 0.28 0.00 41.95 3.16
540 547 2.126882 CAGGTGATACCATCTCCCCAA 58.873 52.381 0.28 0.00 41.95 4.12
541 548 1.293763 TCAGGTGATACCATCTCCCCA 59.706 52.381 0.28 0.00 41.95 4.96
542 549 2.103153 TCAGGTGATACCATCTCCCC 57.897 55.000 0.28 0.00 41.95 4.81
543 550 4.810191 GTATCAGGTGATACCATCTCCC 57.190 50.000 16.32 0.00 46.87 4.30
552 559 4.834406 AAGGGGAGAGTATCAGGTGATA 57.166 45.455 0.00 0.00 37.82 2.15
553 560 3.715648 AAGGGGAGAGTATCAGGTGAT 57.284 47.619 0.00 0.00 37.82 3.06
554 561 4.547671 CTTAAGGGGAGAGTATCAGGTGA 58.452 47.826 0.00 0.00 37.82 4.02
555 562 3.643792 CCTTAAGGGGAGAGTATCAGGTG 59.356 52.174 14.25 0.00 37.82 4.00
556 563 3.930035 CCTTAAGGGGAGAGTATCAGGT 58.070 50.000 14.25 0.00 37.82 4.00
648 655 2.695666 CTCGGTATCTGATGGTCCTTGT 59.304 50.000 0.00 0.00 0.00 3.16
649 656 2.695666 ACTCGGTATCTGATGGTCCTTG 59.304 50.000 0.00 0.01 0.00 3.61
764 2564 4.919754 ACCGTGCTAGTTTTACTTAACGAG 59.080 41.667 0.00 0.00 32.48 4.18
858 2658 1.003580 AGCTGGCTTGCTTGCTAGTAA 59.996 47.619 13.91 0.00 42.42 2.24
920 2724 0.677288 GGTACAGGTTTGGGGTTTGC 59.323 55.000 0.00 0.00 0.00 3.68
1124 2941 6.437928 TGCATCTCAAAACTGACAAACATAC 58.562 36.000 0.00 0.00 0.00 2.39
1134 2951 3.697542 TGGATGGATGCATCTCAAAACTG 59.302 43.478 25.28 0.00 0.00 3.16
1155 3014 2.071540 CGATCGATCAATCCATGGGTG 58.928 52.381 24.40 10.89 0.00 4.61
1156 3015 1.002430 CCGATCGATCAATCCATGGGT 59.998 52.381 24.40 0.00 0.00 4.51
1157 3016 1.730501 CCGATCGATCAATCCATGGG 58.269 55.000 24.40 11.19 0.00 4.00
1175 3034 1.200020 AGTGCAACGATTTAGCAAGCC 59.800 47.619 0.00 0.00 45.86 4.35
1483 3345 0.594110 CTACCTACCTAGCTGCGCTC 59.406 60.000 9.73 0.00 40.44 5.03
1496 3358 9.118300 GCTTCTTGTAACTATGTACTCTACCTA 57.882 37.037 0.00 0.00 0.00 3.08
1497 3359 7.835181 AGCTTCTTGTAACTATGTACTCTACCT 59.165 37.037 0.00 0.00 0.00 3.08
1498 3360 7.998580 AGCTTCTTGTAACTATGTACTCTACC 58.001 38.462 0.00 0.00 0.00 3.18
1501 3363 8.192110 GCTAAGCTTCTTGTAACTATGTACTCT 58.808 37.037 0.00 0.00 0.00 3.24
1502 3364 8.192110 AGCTAAGCTTCTTGTAACTATGTACTC 58.808 37.037 0.00 0.00 33.89 2.59
1503 3365 8.068892 AGCTAAGCTTCTTGTAACTATGTACT 57.931 34.615 0.00 0.00 33.89 2.73
1622 3508 1.480954 ACTGTACCAACTAGGGCATCG 59.519 52.381 0.00 0.00 43.89 3.84
1631 3517 7.290248 ACCAGCTAATGATATACTGTACCAACT 59.710 37.037 0.00 0.00 0.00 3.16
1747 3646 1.372872 GCACATCCGGCACAAAACC 60.373 57.895 0.00 0.00 0.00 3.27
1770 3669 5.663106 ACATGTAGATATAGCATACCCCCAG 59.337 44.000 0.00 0.00 0.00 4.45
1857 3757 6.701400 GGATGTGAACAAGCAACAAAATAAGT 59.299 34.615 0.00 0.00 0.00 2.24
1881 3787 2.746412 TTCAGTGTGCCATGACCCGG 62.746 60.000 0.00 0.00 0.00 5.73
1894 3800 2.223829 ACTCACCAGAACGAGTTCAGTG 60.224 50.000 22.29 22.29 39.45 3.66
2002 4055 8.200792 AGAGGTATAGCTTTCTTTCATGTACTG 58.799 37.037 5.80 0.00 0.00 2.74
2081 4137 0.475906 ATAGCAGGAGGTTGATGGCC 59.524 55.000 0.00 0.00 0.00 5.36
2385 4441 6.268797 AGTACATAAACGCATATGTGTTCG 57.731 37.500 29.48 22.84 46.75 3.95
2416 4473 9.254133 CTGAATAGTATCACCACTACATTCTTG 57.746 37.037 0.00 0.00 33.94 3.02


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

AutoCloner maintained by Alex Coulton.