Multiple sequence alignment - TraesCS4B01G244800

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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 TraesCS4B01G244800 chr4B 100.000 3575 0 0 1 3575 506332041 506328467 0.000000e+00 6602
1 TraesCS4B01G244800 chr4D 96.967 2440 58 7 724 3152 409441217 409443651 0.000000e+00 4082
2 TraesCS4B01G244800 chr4D 95.913 367 15 0 3209 3575 409443652 409444018 2.380000e-166 595
3 TraesCS4B01G244800 chr4A 95.700 2256 64 11 554 2802 64576447 64574218 0.000000e+00 3598
4 TraesCS4B01G244800 chr4A 92.276 479 27 7 2819 3289 64574004 64573528 0.000000e+00 671
5 TraesCS4B01G244800 chr4A 87.213 305 24 3 3286 3575 64573436 64573132 2.060000e-87 333
6 TraesCS4B01G244800 chr2D 85.362 567 59 18 1 554 87390761 87390206 1.860000e-157 566
7 TraesCS4B01G244800 chr2D 89.749 439 40 5 1 437 508080182 508079747 1.120000e-154 556
8 TraesCS4B01G244800 chr2D 88.182 440 47 4 1 438 635510113 635509677 1.470000e-143 520
9 TraesCS4B01G244800 chr2D 87.955 440 48 4 1 438 635476131 635475695 6.840000e-142 514
10 TraesCS4B01G244800 chr7A 88.736 435 46 2 6 438 16922863 16922430 2.440000e-146 529
11 TraesCS4B01G244800 chr6D 88.584 438 47 3 1 437 177830778 177830343 2.440000e-146 529
12 TraesCS4B01G244800 chr5D 88.453 433 46 4 8 438 387295048 387294618 1.470000e-143 520
13 TraesCS4B01G244800 chrUn 87.955 440 48 4 1 438 31854742 31855178 6.840000e-142 514
14 TraesCS4B01G244800 chrUn 87.955 440 48 4 1 438 342854587 342854151 6.840000e-142 514


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 TraesCS4B01G244800 chr4B 506328467 506332041 3574 True 6602.0 6602 100.000000 1 3575 1 chr4B.!!$R1 3574
1 TraesCS4B01G244800 chr4D 409441217 409444018 2801 False 2338.5 4082 96.440000 724 3575 2 chr4D.!!$F1 2851
2 TraesCS4B01G244800 chr4A 64573132 64576447 3315 True 1534.0 3598 91.729667 554 3575 3 chr4A.!!$R1 3021
3 TraesCS4B01G244800 chr2D 87390206 87390761 555 True 566.0 566 85.362000 1 554 1 chr2D.!!$R1 553

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
858 894 0.107165 AAGCCGAAACCCAGCTATCC 60.107 55.0 0.0 0.0 35.3 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2646 2685 0.390472 GGAAGAGAGAACCAGCACCG 60.39 60.0 0.0 0.0 0.0 4.94 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
64 65 8.689251 TGATAGAGCGCAATTTAGTATATGTC 57.311 34.615 11.47 0.00 0.00 3.06
68 69 5.054477 AGCGCAATTTAGTATATGTCCGTT 58.946 37.500 11.47 0.00 0.00 4.44
98 99 9.594936 TTTAAGCTAGAATAGAGGCTAGAGATT 57.405 33.333 0.00 0.00 42.77 2.40
152 153 4.350368 AGAGATGAGACTAGATGCGAGA 57.650 45.455 0.00 0.00 0.00 4.04
180 181 6.544622 CAACGTCTACTTCTTTAGACTCGAT 58.455 40.000 8.30 0.00 44.05 3.59
195 196 2.989840 ACTCGATGAAGAAAGAAGCACG 59.010 45.455 0.00 0.00 0.00 5.34
202 203 3.187227 TGAAGAAAGAAGCACGCAAGATC 59.813 43.478 0.00 0.00 43.62 2.75
212 213 2.964389 GCAAGATCGAGCCTCCGC 60.964 66.667 0.00 0.00 0.00 5.54
222 223 0.179062 GAGCCTCCGCAGATCAACAT 60.179 55.000 0.00 0.00 37.52 2.71
251 252 4.384056 CATCGAGAAGGCACTAATCCAAT 58.616 43.478 0.00 0.00 38.49 3.16
257 258 5.741011 AGAAGGCACTAATCCAATTTACGA 58.259 37.500 0.00 0.00 38.49 3.43
258 259 6.177610 AGAAGGCACTAATCCAATTTACGAA 58.822 36.000 0.00 0.00 38.49 3.85
292 293 8.575649 TGGAAGTTGGTTATCTTCTAAAATCC 57.424 34.615 0.00 0.00 39.67 3.01
301 302 8.678199 GGTTATCTTCTAAAATCCCTTCTTGTG 58.322 37.037 0.00 0.00 0.00 3.33
313 314 4.775253 TCCCTTCTTGTGGTTCTTGTTTTT 59.225 37.500 0.00 0.00 0.00 1.94
398 399 9.214957 TGACGAAAATAGAAGATATGTGTTTGT 57.785 29.630 0.00 0.00 0.00 2.83
419 420 9.520204 GTTTGTGAAAAATATGTATGGAGATGG 57.480 33.333 0.00 0.00 0.00 3.51
428 429 1.126948 TATGGAGATGGGATGCGGCA 61.127 55.000 4.58 4.58 0.00 5.69
438 439 2.751436 ATGCGGCAGAAATGCGGT 60.751 55.556 9.25 0.00 37.44 5.68
439 440 1.436195 GATGCGGCAGAAATGCGGTA 61.436 55.000 9.25 5.51 37.44 4.02
440 441 1.714899 ATGCGGCAGAAATGCGGTAC 61.715 55.000 9.25 0.00 37.44 3.34
459 460 3.876198 GCCGGCGAATGCACGAAT 61.876 61.111 12.58 0.00 45.35 3.34
460 461 2.530497 GCCGGCGAATGCACGAATA 61.530 57.895 12.58 0.00 45.35 1.75
461 462 1.275657 CCGGCGAATGCACGAATAC 59.724 57.895 9.30 0.00 45.35 1.89
462 463 1.084290 CGGCGAATGCACGAATACG 60.084 57.895 0.00 0.00 45.35 3.06
464 465 0.648441 GGCGAATGCACGAATACGAA 59.352 50.000 0.24 0.00 45.35 3.85
466 467 1.905832 GCGAATGCACGAATACGAACG 60.906 52.381 0.24 0.00 43.06 3.95
467 468 1.330818 CGAATGCACGAATACGAACGG 60.331 52.381 0.00 0.00 42.66 4.44
468 469 1.921887 GAATGCACGAATACGAACGGA 59.078 47.619 0.00 0.00 42.66 4.69
469 470 1.274596 ATGCACGAATACGAACGGAC 58.725 50.000 0.00 0.00 42.66 4.79
471 472 1.274596 GCACGAATACGAACGGACAT 58.725 50.000 0.00 0.00 42.66 3.06
472 473 1.006391 GCACGAATACGAACGGACATG 60.006 52.381 0.00 0.00 42.66 3.21
473 474 2.521996 CACGAATACGAACGGACATGA 58.478 47.619 0.00 0.00 42.66 3.07
474 475 2.278094 CACGAATACGAACGGACATGAC 59.722 50.000 0.00 0.00 42.66 3.06
475 476 1.850441 CGAATACGAACGGACATGACC 59.150 52.381 0.00 0.58 42.66 4.02
476 477 2.199236 GAATACGAACGGACATGACCC 58.801 52.381 8.69 3.90 0.00 4.46
477 478 1.187974 ATACGAACGGACATGACCCA 58.812 50.000 8.69 0.00 0.00 4.51
478 479 1.187974 TACGAACGGACATGACCCAT 58.812 50.000 8.69 0.00 0.00 4.00
479 480 0.323629 ACGAACGGACATGACCCATT 59.676 50.000 8.69 3.52 0.00 3.16
493 498 1.616091 CCCATTGACCCATTGCCACC 61.616 60.000 0.00 0.00 0.00 4.61
528 533 2.049433 CGGACGAAACAGACGCCT 60.049 61.111 0.00 0.00 0.00 5.52
529 534 1.210931 CGGACGAAACAGACGCCTA 59.789 57.895 0.00 0.00 0.00 3.93
530 535 0.387622 CGGACGAAACAGACGCCTAA 60.388 55.000 0.00 0.00 0.00 2.69
533 538 3.514645 GGACGAAACAGACGCCTAATTA 58.485 45.455 0.00 0.00 0.00 1.40
543 548 2.308039 GCCTAATTAGGGTCGCGCG 61.308 63.158 28.81 26.76 43.82 6.86
544 549 1.663702 CCTAATTAGGGTCGCGCGG 60.664 63.158 31.69 11.75 39.86 6.46
545 550 1.361271 CTAATTAGGGTCGCGCGGA 59.639 57.895 31.69 14.21 0.00 5.54
546 551 0.663568 CTAATTAGGGTCGCGCGGAG 60.664 60.000 31.69 1.17 0.00 4.63
547 552 1.386525 TAATTAGGGTCGCGCGGAGT 61.387 55.000 31.69 14.72 0.00 3.85
548 553 2.234913 AATTAGGGTCGCGCGGAGTT 62.235 55.000 31.69 15.89 0.00 3.01
549 554 1.386525 ATTAGGGTCGCGCGGAGTTA 61.387 55.000 31.69 14.83 0.00 2.24
550 555 1.996786 TTAGGGTCGCGCGGAGTTAG 61.997 60.000 31.69 0.00 0.00 2.34
553 558 4.493747 GTCGCGCGGAGTTAGCCT 62.494 66.667 31.69 0.00 0.00 4.58
554 559 2.825387 TCGCGCGGAGTTAGCCTA 60.825 61.111 31.69 2.53 0.00 3.93
555 560 2.103538 CGCGCGGAGTTAGCCTAA 59.896 61.111 24.84 0.00 0.00 2.69
556 561 2.228914 CGCGCGGAGTTAGCCTAAC 61.229 63.158 24.84 6.50 38.94 2.34
557 562 1.881709 GCGCGGAGTTAGCCTAACC 60.882 63.158 8.83 3.20 39.47 2.85
558 563 1.814527 CGCGGAGTTAGCCTAACCT 59.185 57.895 10.94 0.00 39.47 3.50
559 564 1.027357 CGCGGAGTTAGCCTAACCTA 58.973 55.000 10.94 0.00 39.47 3.08
560 565 1.268948 CGCGGAGTTAGCCTAACCTAC 60.269 57.143 10.94 3.73 39.47 3.18
561 566 1.068281 GCGGAGTTAGCCTAACCTACC 59.932 57.143 10.94 10.91 39.47 3.18
562 567 2.664015 CGGAGTTAGCCTAACCTACCT 58.336 52.381 10.94 0.00 39.47 3.08
563 568 3.029570 CGGAGTTAGCCTAACCTACCTT 58.970 50.000 10.94 0.00 39.47 3.50
564 569 3.067883 CGGAGTTAGCCTAACCTACCTTC 59.932 52.174 10.94 1.40 39.47 3.46
565 570 3.387374 GGAGTTAGCCTAACCTACCTTCC 59.613 52.174 10.94 6.76 39.47 3.46
566 571 3.382278 AGTTAGCCTAACCTACCTTCCC 58.618 50.000 10.94 0.00 39.47 3.97
578 583 3.777522 CCTACCTTCCCAATCTGAGAACT 59.222 47.826 0.00 0.00 0.00 3.01
604 609 5.008613 AGTGTTGTCGTGTTCTGCATTAAAT 59.991 36.000 0.00 0.00 0.00 1.40
617 622 3.181488 TGCATTAAATCCCATGCTTGTCG 60.181 43.478 5.77 0.00 45.21 4.35
648 653 8.877864 ACAAATCAAGGTTGAATAGTTCCATA 57.122 30.769 0.00 0.00 41.13 2.74
663 668 5.279384 AGTTCCATACTTTACTCATACGCG 58.721 41.667 3.53 3.53 31.29 6.01
700 708 8.445275 TCACTCTAGTAAGAAAAACAAATGCA 57.555 30.769 0.00 0.00 0.00 3.96
736 744 1.002624 GTTCCGCCCATGAGTCCAA 60.003 57.895 0.00 0.00 0.00 3.53
761 769 1.079543 GCGAGCAGGCTTTCTCAGA 60.080 57.895 12.38 0.00 0.00 3.27
809 826 7.519032 TTGAAGTATTTCCCGACAGAAAAAT 57.481 32.000 0.00 0.00 39.11 1.82
810 827 6.908825 TGAAGTATTTCCCGACAGAAAAATG 58.091 36.000 0.00 0.00 39.11 2.32
811 828 5.897377 AGTATTTCCCGACAGAAAAATGG 57.103 39.130 0.00 0.00 39.11 3.16
812 829 3.592898 ATTTCCCGACAGAAAAATGGC 57.407 42.857 0.00 0.00 39.11 4.40
834 851 5.006941 GGCTACACTACGAAAAACAAACTCA 59.993 40.000 0.00 0.00 0.00 3.41
836 853 7.130269 GCTACACTACGAAAAACAAACTCAAT 58.870 34.615 0.00 0.00 0.00 2.57
853 889 0.603065 AATTCAAGCCGAAACCCAGC 59.397 50.000 0.00 0.00 37.12 4.85
854 890 0.251341 ATTCAAGCCGAAACCCAGCT 60.251 50.000 0.00 0.00 37.12 4.24
855 891 0.398696 TTCAAGCCGAAACCCAGCTA 59.601 50.000 0.00 0.00 35.30 3.32
856 892 0.618458 TCAAGCCGAAACCCAGCTAT 59.382 50.000 0.00 0.00 35.30 2.97
857 893 1.017387 CAAGCCGAAACCCAGCTATC 58.983 55.000 0.00 0.00 35.30 2.08
858 894 0.107165 AAGCCGAAACCCAGCTATCC 60.107 55.000 0.00 0.00 35.30 2.59
859 895 1.223487 GCCGAAACCCAGCTATCCA 59.777 57.895 0.00 0.00 0.00 3.41
860 896 1.095807 GCCGAAACCCAGCTATCCAC 61.096 60.000 0.00 0.00 0.00 4.02
861 897 0.541863 CCGAAACCCAGCTATCCACT 59.458 55.000 0.00 0.00 0.00 4.00
862 898 1.760613 CCGAAACCCAGCTATCCACTA 59.239 52.381 0.00 0.00 0.00 2.74
863 899 2.224066 CCGAAACCCAGCTATCCACTAG 60.224 54.545 0.00 0.00 0.00 2.57
864 900 2.224066 CGAAACCCAGCTATCCACTAGG 60.224 54.545 0.00 0.00 0.00 3.02
1268 1307 2.219325 CTCATATCCTCCCTCGCCGC 62.219 65.000 0.00 0.00 0.00 6.53
1389 1428 2.077627 GATGGCTCGCTCGACTCTATA 58.922 52.381 0.00 0.00 0.00 1.31
1565 1604 1.674441 CTCCTACACCGCGATTCTACA 59.326 52.381 8.23 0.00 0.00 2.74
1835 1874 6.132056 GTCATCAAGTAGATAAAATGCGCAG 58.868 40.000 18.32 0.00 34.43 5.18
1933 1972 0.471617 AGTCTGCTTGCTGGAACACT 59.528 50.000 0.00 0.00 0.00 3.55
1995 2034 2.026822 CACTTTGATGGGTAGGCTCTGT 60.027 50.000 0.00 0.00 0.00 3.41
2118 2157 1.173913 GTGGAGTTGGGAAATTCCGG 58.826 55.000 5.87 0.00 37.43 5.14
2484 2523 4.000331 AGATACTTGCATCTTCATCCCG 58.000 45.455 0.00 0.00 30.93 5.14
2687 2726 1.973515 TCACACACCAGCAATCTCTCT 59.026 47.619 0.00 0.00 0.00 3.10
2706 2745 6.320926 TCTCTCTATCTTTCATCAGGTCAGTG 59.679 42.308 0.00 0.00 0.00 3.66
2707 2746 5.016051 TCTATCTTTCATCAGGTCAGTGC 57.984 43.478 0.00 0.00 0.00 4.40
2748 2787 8.040727 GCCATGGTTTAATTTCACCTTCTTTAT 58.959 33.333 14.67 0.00 33.76 1.40
2750 2789 8.872845 CATGGTTTAATTTCACCTTCTTTATGC 58.127 33.333 7.15 0.00 33.76 3.14
2815 3051 0.613853 ACGAGCACCCCAGCTAGTTA 60.614 55.000 0.00 0.00 46.17 2.24
2817 3053 1.486211 GAGCACCCCAGCTAGTTAGA 58.514 55.000 0.00 0.00 46.75 2.10
2876 3112 8.465273 AGAGAAAATATTGGGCATAAAGGTAC 57.535 34.615 0.00 0.00 0.00 3.34
3001 3237 9.638239 GCATTTTGGTGAAAGAGATTGTTTATA 57.362 29.630 0.00 0.00 0.00 0.98
3006 3242 9.739276 TTGGTGAAAGAGATTGTTTATAGATGT 57.261 29.630 0.00 0.00 0.00 3.06
3038 3274 8.369218 AGATTGCACTTCTTATTTTGTTTTGG 57.631 30.769 0.00 0.00 0.00 3.28
3092 3331 3.583806 TGTTGAAGTTGTGCCAAAAGTG 58.416 40.909 0.00 0.00 0.00 3.16
3159 3402 2.439507 TCCACTGCCTCTTCAAACTCTT 59.560 45.455 0.00 0.00 0.00 2.85
3161 3404 4.102524 TCCACTGCCTCTTCAAACTCTTAA 59.897 41.667 0.00 0.00 0.00 1.85
3162 3405 4.453819 CCACTGCCTCTTCAAACTCTTAAG 59.546 45.833 0.00 0.00 0.00 1.85
3165 3408 5.529060 ACTGCCTCTTCAAACTCTTAAGTTG 59.471 40.000 1.63 0.21 45.07 3.16
3166 3409 5.680619 TGCCTCTTCAAACTCTTAAGTTGA 58.319 37.500 1.63 2.75 45.07 3.18
3167 3410 6.299141 TGCCTCTTCAAACTCTTAAGTTGAT 58.701 36.000 1.63 0.00 45.07 2.57
3232 3475 2.169561 TCTCCGTTGCATATTGCCTGTA 59.830 45.455 0.00 0.00 44.23 2.74
3280 3523 1.234821 TTCGGGTGATGCACTTGTTC 58.765 50.000 0.00 0.00 34.40 3.18
3336 3675 3.857052 TGCTTCCTGTGTTAATAGTCCG 58.143 45.455 0.00 0.00 0.00 4.79
3367 3720 6.818644 TCAGTAAGCTGTATGAATCTCCAAAC 59.181 38.462 0.00 0.00 43.05 2.93
3422 3775 7.435068 TCTTGTGCTAAAGTTTTATCTGGTC 57.565 36.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 4.684703 ACGGACATATACTAAATTGCGCTC 59.315 41.667 9.73 0.00 0.00 5.03
52 53 9.090692 GCTTAAAGTGAACGGACATATACTAAA 57.909 33.333 0.00 0.00 0.00 1.85
59 60 6.519679 TCTAGCTTAAAGTGAACGGACATA 57.480 37.500 0.00 0.00 0.00 2.29
64 65 6.697892 CCTCTATTCTAGCTTAAAGTGAACGG 59.302 42.308 0.00 0.00 0.00 4.44
68 69 7.999545 TCTAGCCTCTATTCTAGCTTAAAGTGA 59.000 37.037 0.00 0.00 36.79 3.41
75 76 8.611257 TCTAATCTCTAGCCTCTATTCTAGCTT 58.389 37.037 0.00 0.00 36.79 3.74
123 124 6.369890 GCATCTAGTCTCATCTCTAGTCTCTG 59.630 46.154 0.00 0.00 36.17 3.35
128 129 5.011635 TCTCGCATCTAGTCTCATCTCTAGT 59.988 44.000 0.00 0.00 36.17 2.57
152 153 6.766452 GTCTAAAGAAGTAGACGTTGCTTT 57.234 37.500 0.00 0.00 40.37 3.51
180 181 2.560504 TCTTGCGTGCTTCTTTCTTCA 58.439 42.857 0.00 0.00 0.00 3.02
195 196 2.964389 GCGGAGGCTCGATCTTGC 60.964 66.667 8.69 1.82 35.83 4.01
202 203 1.880340 GTTGATCTGCGGAGGCTCG 60.880 63.158 8.69 5.22 40.82 5.03
212 213 5.007332 TCTCGATGCATTCAATGTTGATCTG 59.993 40.000 0.00 0.00 37.00 2.90
222 223 1.739466 GTGCCTTCTCGATGCATTCAA 59.261 47.619 0.00 0.00 37.34 2.69
251 252 6.293735 CCAACTTCCATAACTGCTTTCGTAAA 60.294 38.462 0.00 0.00 0.00 2.01
257 258 6.948309 AGATAACCAACTTCCATAACTGCTTT 59.052 34.615 0.00 0.00 0.00 3.51
258 259 6.485171 AGATAACCAACTTCCATAACTGCTT 58.515 36.000 0.00 0.00 0.00 3.91
291 292 4.736126 AAAACAAGAACCACAAGAAGGG 57.264 40.909 0.00 0.00 0.00 3.95
351 352 9.905171 TCGTCATTGATTTTTGATACATGAAAA 57.095 25.926 0.00 0.00 0.00 2.29
354 355 9.905171 TTTTCGTCATTGATTTTTGATACATGA 57.095 25.926 0.00 0.00 0.00 3.07
368 369 9.599866 ACACATATCTTCTATTTTCGTCATTGA 57.400 29.630 0.00 0.00 0.00 2.57
398 399 7.177216 GCATCCCATCTCCATACATATTTTTCA 59.823 37.037 0.00 0.00 0.00 2.69
405 406 2.501316 CCGCATCCCATCTCCATACATA 59.499 50.000 0.00 0.00 0.00 2.29
413 414 0.464373 TTTCTGCCGCATCCCATCTC 60.464 55.000 0.00 0.00 0.00 2.75
414 415 0.184451 ATTTCTGCCGCATCCCATCT 59.816 50.000 0.00 0.00 0.00 2.90
417 418 2.417257 GCATTTCTGCCGCATCCCA 61.417 57.895 0.00 0.00 42.88 4.37
419 420 2.025156 CGCATTTCTGCCGCATCC 59.975 61.111 0.00 0.00 46.07 3.51
444 445 1.084290 CGTATTCGTGCATTCGCCG 60.084 57.895 0.00 0.00 37.32 6.46
445 446 0.648441 TTCGTATTCGTGCATTCGCC 59.352 50.000 0.00 0.00 38.33 5.54
446 447 1.715030 GTTCGTATTCGTGCATTCGC 58.285 50.000 0.00 0.00 38.33 4.70
447 448 1.330818 CCGTTCGTATTCGTGCATTCG 60.331 52.381 0.00 0.00 38.33 3.34
449 450 1.657094 GTCCGTTCGTATTCGTGCATT 59.343 47.619 0.00 0.00 38.33 3.56
450 451 1.274596 GTCCGTTCGTATTCGTGCAT 58.725 50.000 0.00 0.00 38.33 3.96
451 452 0.039346 TGTCCGTTCGTATTCGTGCA 60.039 50.000 0.00 0.00 38.33 4.57
452 453 1.006391 CATGTCCGTTCGTATTCGTGC 60.006 52.381 0.00 0.00 38.33 5.34
453 454 2.278094 GTCATGTCCGTTCGTATTCGTG 59.722 50.000 0.00 0.00 38.33 4.35
454 455 2.523015 GTCATGTCCGTTCGTATTCGT 58.477 47.619 0.00 0.00 38.33 3.85
455 456 1.850441 GGTCATGTCCGTTCGTATTCG 59.150 52.381 0.00 0.00 38.55 3.34
457 458 1.551430 TGGGTCATGTCCGTTCGTATT 59.449 47.619 2.78 0.00 0.00 1.89
458 459 1.187974 TGGGTCATGTCCGTTCGTAT 58.812 50.000 2.78 0.00 0.00 3.06
459 460 1.187974 ATGGGTCATGTCCGTTCGTA 58.812 50.000 2.78 0.00 0.00 3.43
460 461 0.323629 AATGGGTCATGTCCGTTCGT 59.676 50.000 2.78 0.00 0.00 3.85
461 462 0.726827 CAATGGGTCATGTCCGTTCG 59.273 55.000 10.77 5.63 31.64 3.95
462 463 1.737793 GTCAATGGGTCATGTCCGTTC 59.262 52.381 10.77 0.00 31.64 3.95
464 465 0.035439 GGTCAATGGGTCATGTCCGT 60.035 55.000 2.78 0.26 0.00 4.69
466 467 0.331278 TGGGTCAATGGGTCATGTCC 59.669 55.000 0.00 0.00 0.00 4.02
467 468 2.428171 CAATGGGTCAATGGGTCATGTC 59.572 50.000 0.00 0.00 0.00 3.06
468 469 2.459644 CAATGGGTCAATGGGTCATGT 58.540 47.619 0.00 0.00 0.00 3.21
469 470 1.137479 GCAATGGGTCAATGGGTCATG 59.863 52.381 0.00 0.00 0.00 3.07
471 472 0.614415 GGCAATGGGTCAATGGGTCA 60.614 55.000 0.00 0.00 0.00 4.02
472 473 0.614415 TGGCAATGGGTCAATGGGTC 60.614 55.000 0.00 0.00 0.00 4.46
473 474 0.904394 GTGGCAATGGGTCAATGGGT 60.904 55.000 0.00 0.00 29.11 4.51
474 475 1.616091 GGTGGCAATGGGTCAATGGG 61.616 60.000 0.00 0.00 29.11 4.00
475 476 1.616091 GGGTGGCAATGGGTCAATGG 61.616 60.000 0.00 0.00 29.11 3.16
476 477 1.616091 GGGGTGGCAATGGGTCAATG 61.616 60.000 0.00 0.00 29.11 2.82
477 478 1.306056 GGGGTGGCAATGGGTCAAT 60.306 57.895 0.00 0.00 29.11 2.57
478 479 2.119391 GGGGTGGCAATGGGTCAA 59.881 61.111 0.00 0.00 29.11 3.18
479 480 3.991318 GGGGGTGGCAATGGGTCA 61.991 66.667 0.00 0.00 0.00 4.02
493 498 0.375803 CGCTTTTTATCCGTTCGGGG 59.624 55.000 11.37 0.00 36.01 5.73
497 502 1.994779 TCGTCCGCTTTTTATCCGTTC 59.005 47.619 0.00 0.00 0.00 3.95
504 509 2.219216 CGTCTGTTTCGTCCGCTTTTTA 59.781 45.455 0.00 0.00 0.00 1.52
526 531 1.663702 CCGCGCGACCCTAATTAGG 60.664 63.158 34.63 22.75 43.25 2.69
528 533 1.361271 CTCCGCGCGACCCTAATTA 59.639 57.895 34.63 3.57 0.00 1.40
529 534 2.106332 CTCCGCGCGACCCTAATT 59.894 61.111 34.63 0.00 0.00 1.40
530 535 1.386525 TAACTCCGCGCGACCCTAAT 61.387 55.000 34.63 12.72 0.00 1.73
533 538 3.823330 CTAACTCCGCGCGACCCT 61.823 66.667 34.63 15.40 0.00 4.34
543 548 3.387374 GGAAGGTAGGTTAGGCTAACTCC 59.613 52.174 30.40 27.00 38.68 3.85
544 549 3.387374 GGGAAGGTAGGTTAGGCTAACTC 59.613 52.174 30.40 21.94 38.68 3.01
545 550 3.246240 TGGGAAGGTAGGTTAGGCTAACT 60.246 47.826 30.40 20.60 38.68 2.24
546 551 3.109928 TGGGAAGGTAGGTTAGGCTAAC 58.890 50.000 25.70 25.70 37.94 2.34
547 552 3.495186 TGGGAAGGTAGGTTAGGCTAA 57.505 47.619 2.04 2.04 0.00 3.09
548 553 3.495186 TTGGGAAGGTAGGTTAGGCTA 57.505 47.619 0.00 0.00 0.00 3.93
549 554 2.354261 TTGGGAAGGTAGGTTAGGCT 57.646 50.000 0.00 0.00 0.00 4.58
550 555 2.778270 AGATTGGGAAGGTAGGTTAGGC 59.222 50.000 0.00 0.00 0.00 3.93
551 556 4.037927 TCAGATTGGGAAGGTAGGTTAGG 58.962 47.826 0.00 0.00 0.00 2.69
552 557 4.962995 TCTCAGATTGGGAAGGTAGGTTAG 59.037 45.833 0.00 0.00 0.00 2.34
553 558 4.955335 TCTCAGATTGGGAAGGTAGGTTA 58.045 43.478 0.00 0.00 0.00 2.85
554 559 3.803340 TCTCAGATTGGGAAGGTAGGTT 58.197 45.455 0.00 0.00 0.00 3.50
555 560 3.491766 TCTCAGATTGGGAAGGTAGGT 57.508 47.619 0.00 0.00 0.00 3.08
556 561 3.777522 AGTTCTCAGATTGGGAAGGTAGG 59.222 47.826 0.00 0.00 37.56 3.18
557 562 4.467795 TCAGTTCTCAGATTGGGAAGGTAG 59.532 45.833 0.00 0.00 37.56 3.18
558 563 4.425772 TCAGTTCTCAGATTGGGAAGGTA 58.574 43.478 0.00 0.00 37.56 3.08
559 564 3.251484 TCAGTTCTCAGATTGGGAAGGT 58.749 45.455 0.00 0.00 37.56 3.50
560 565 3.262915 ACTCAGTTCTCAGATTGGGAAGG 59.737 47.826 0.00 0.00 37.56 3.46
561 566 4.252073 CACTCAGTTCTCAGATTGGGAAG 58.748 47.826 0.00 0.00 37.56 3.46
562 567 3.648067 ACACTCAGTTCTCAGATTGGGAA 59.352 43.478 0.00 0.00 33.81 3.97
563 568 3.242867 ACACTCAGTTCTCAGATTGGGA 58.757 45.455 0.00 0.00 0.00 4.37
564 569 3.692257 ACACTCAGTTCTCAGATTGGG 57.308 47.619 0.00 0.00 0.00 4.12
565 570 4.384056 ACAACACTCAGTTCTCAGATTGG 58.616 43.478 0.00 0.00 38.74 3.16
566 571 4.149571 CGACAACACTCAGTTCTCAGATTG 59.850 45.833 0.00 0.00 38.74 2.67
578 583 1.286501 GCAGAACACGACAACACTCA 58.713 50.000 0.00 0.00 0.00 3.41
604 609 1.558167 TTAGCCCGACAAGCATGGGA 61.558 55.000 0.00 0.00 46.41 4.37
617 622 4.864704 TTCAACCTTGATTTGTTAGCCC 57.135 40.909 0.00 0.00 37.00 5.19
648 653 7.766219 ATACATTTTCGCGTATGAGTAAAGT 57.234 32.000 19.73 3.73 0.00 2.66
708 716 1.747745 GGGCGGAACATAGGCGTTT 60.748 57.895 0.00 0.00 0.00 3.60
710 718 2.742116 ATGGGCGGAACATAGGCGT 61.742 57.895 0.00 0.00 0.00 5.68
711 719 2.111043 ATGGGCGGAACATAGGCG 59.889 61.111 0.00 0.00 0.00 5.52
712 720 0.886490 CTCATGGGCGGAACATAGGC 60.886 60.000 0.00 0.00 0.00 3.93
713 721 0.469917 ACTCATGGGCGGAACATAGG 59.530 55.000 0.00 0.00 0.00 2.57
714 722 1.541233 GGACTCATGGGCGGAACATAG 60.541 57.143 0.00 0.00 0.00 2.23
715 723 0.468226 GGACTCATGGGCGGAACATA 59.532 55.000 0.00 0.00 0.00 2.29
716 724 1.224592 GGACTCATGGGCGGAACAT 59.775 57.895 0.00 0.00 0.00 2.71
717 725 1.773856 TTGGACTCATGGGCGGAACA 61.774 55.000 0.00 0.00 0.00 3.18
718 726 1.002624 TTGGACTCATGGGCGGAAC 60.003 57.895 0.00 0.00 0.00 3.62
719 727 1.002624 GTTGGACTCATGGGCGGAA 60.003 57.895 0.00 0.00 0.00 4.30
720 728 1.561769 ATGTTGGACTCATGGGCGGA 61.562 55.000 0.00 0.00 0.00 5.54
736 744 1.174712 AAAGCCTGCTCGCAACATGT 61.175 50.000 0.00 0.00 0.00 3.21
761 769 0.970427 GCCCGGTCCATTCCAAACAT 60.970 55.000 0.00 0.00 0.00 2.71
809 826 4.877251 AGTTTGTTTTTCGTAGTGTAGCCA 59.123 37.500 0.00 0.00 0.00 4.75
810 827 5.006941 TGAGTTTGTTTTTCGTAGTGTAGCC 59.993 40.000 0.00 0.00 0.00 3.93
811 828 6.039781 TGAGTTTGTTTTTCGTAGTGTAGC 57.960 37.500 0.00 0.00 0.00 3.58
812 829 9.155053 GAATTGAGTTTGTTTTTCGTAGTGTAG 57.845 33.333 0.00 0.00 0.00 2.74
834 851 0.603065 GCTGGGTTTCGGCTTGAATT 59.397 50.000 0.00 0.00 44.20 2.17
836 853 3.758172 GCTGGGTTTCGGCTTGAA 58.242 55.556 0.00 0.00 44.20 2.69
853 889 1.638529 CCTGGCCTCCTAGTGGATAG 58.361 60.000 3.32 0.00 42.29 2.08
854 890 0.471971 GCCTGGCCTCCTAGTGGATA 60.472 60.000 7.66 0.00 42.29 2.59
855 891 1.768077 GCCTGGCCTCCTAGTGGAT 60.768 63.158 7.66 0.00 42.29 3.41
856 892 2.365635 GCCTGGCCTCCTAGTGGA 60.366 66.667 7.66 0.00 40.69 4.02
857 893 3.483869 GGCCTGGCCTCCTAGTGG 61.484 72.222 30.42 0.00 46.69 4.00
996 1035 4.271016 GGGCGGAAGGGCATAGGG 62.271 72.222 0.00 0.00 44.56 3.53
1389 1428 1.686355 TCGCAAGGAAAATGTGGTGT 58.314 45.000 0.00 0.00 38.47 4.16
1565 1604 1.050988 ACCCTGCTCGCAGTATCCAT 61.051 55.000 16.82 0.00 42.15 3.41
1792 1831 1.637553 ACATGCCTCATCCAAGAACCT 59.362 47.619 0.00 0.00 0.00 3.50
1854 1893 8.585018 TCAAATAGAATACTCAGTGTCTCAACA 58.415 33.333 0.00 0.00 0.00 3.33
1933 1972 2.877097 TGCCAGCCTAATTCTTCACA 57.123 45.000 0.00 0.00 0.00 3.58
1995 2034 0.964700 TTGCAAAATCACCGGCATCA 59.035 45.000 0.00 0.00 35.98 3.07
2118 2157 7.442364 TCATTATCTATTAGACACTTTGCCAGC 59.558 37.037 0.00 0.00 0.00 4.85
2293 2332 9.554724 GACAAATTTTCGATCTTTACATAAGCA 57.445 29.630 0.00 0.00 0.00 3.91
2388 2427 2.038033 TCTTACTCCTTTGACCAACCGG 59.962 50.000 0.00 0.00 38.77 5.28
2484 2523 6.429521 TCCCAGCATAATACCCTAACTAAC 57.570 41.667 0.00 0.00 0.00 2.34
2646 2685 0.390472 GGAAGAGAGAACCAGCACCG 60.390 60.000 0.00 0.00 0.00 4.94
2687 2726 3.785486 CGCACTGACCTGATGAAAGATA 58.215 45.455 0.00 0.00 0.00 1.98
2706 2745 2.861462 TGGCATAATTTTAGGTGCGC 57.139 45.000 0.00 0.00 38.43 6.09
2707 2746 3.068024 ACCATGGCATAATTTTAGGTGCG 59.932 43.478 13.04 0.00 38.43 5.34
2750 2789 6.093495 TGAAAAACTAGCTGGGATTAACATCG 59.907 38.462 0.85 0.00 0.00 3.84
2815 3051 3.054802 GGTTGATCATCTTGTCCAGGTCT 60.055 47.826 0.00 0.00 0.00 3.85
2817 3053 2.915604 AGGTTGATCATCTTGTCCAGGT 59.084 45.455 0.00 0.00 0.00 4.00
2876 3112 4.142403 ACCATAACATGAAGCACAAATCCG 60.142 41.667 0.00 0.00 0.00 4.18
3206 3449 2.016318 CAATATGCAACGGAGAGGCAA 58.984 47.619 0.00 0.00 42.16 4.52
3232 3475 7.666623 ACTTTCCATTTCCGTGTTTAATCATT 58.333 30.769 0.00 0.00 0.00 2.57
3280 3523 6.422776 ACCAGCTTAATTTCATACTTGACG 57.577 37.500 0.00 0.00 0.00 4.35
3316 3654 4.113354 CTCGGACTATTAACACAGGAAGC 58.887 47.826 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.