Multiple sequence alignment - TraesCS2D01G515900

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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 TraesCS2D01G515900 chr2D 100.000 2720 0 0 1 2720 607282710 607285429 0.000000e+00 5024
1 TraesCS2D01G515900 chr2D 90.023 441 23 5 990 1421 603142118 603141690 3.960000e-153 551
2 TraesCS2D01G515900 chr2D 94.215 121 7 0 1453 1573 603141691 603141571 4.630000e-43 185
3 TraesCS2D01G515900 chr2D 87.037 108 11 1 1466 1573 603141327 603141223 4.760000e-23 119
4 TraesCS2D01G515900 chr2B 86.159 2637 143 113 9 2532 739370592 739368065 0.000000e+00 2643
5 TraesCS2D01G515900 chr2A 87.761 2206 109 57 601 2688 738921372 738923534 0.000000e+00 2429
6 TraesCS2D01G515900 chr2A 87.006 354 30 11 1 346 738920780 738921125 4.250000e-103 385
7 TraesCS2D01G515900 chr6A 81.020 490 28 22 2192 2650 184817907 184817452 2.020000e-86 329
8 TraesCS2D01G515900 chr7D 91.011 178 16 0 1201 1378 79964221 79964398 9.730000e-60 241
9 TraesCS2D01G515900 chr7B 91.011 178 16 0 1201 1378 27067544 27067721 9.730000e-60 241
10 TraesCS2D01G515900 chr7A 90.449 178 17 0 1201 1378 82942459 82942636 4.530000e-58 235
11 TraesCS2D01G515900 chr1D 80.000 185 33 4 1197 1379 475981249 475981067 1.700000e-27 134
12 TraesCS2D01G515900 chr1B 80.000 185 33 4 1197 1379 662193839 662193657 1.700000e-27 134
13 TraesCS2D01G515900 chr1A 80.000 185 33 4 1197 1379 571895377 571895195 1.700000e-27 134


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 TraesCS2D01G515900 chr2D 607282710 607285429 2719 False 5024 5024 100.0000 1 2720 1 chr2D.!!$F1 2719
1 TraesCS2D01G515900 chr2D 603141223 603142118 895 True 285 551 90.4250 990 1573 3 chr2D.!!$R1 583
2 TraesCS2D01G515900 chr2B 739368065 739370592 2527 True 2643 2643 86.1590 9 2532 1 chr2B.!!$R1 2523
3 TraesCS2D01G515900 chr2A 738920780 738923534 2754 False 1407 2429 87.3835 1 2688 2 chr2A.!!$F1 2687

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
427 500 0.035152 AATCGGCCATGTCAGCTTCA 60.035 50.0 2.24 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 2101 0.036164 CGGGTTGTGGATGACTGGAA 59.964 55.0 0.0 0.0 0.0 3.53 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
41 42 3.146847 GCGGGGGTAAGGATAATCTTTG 58.853 50.000 0.00 0.00 0.00 2.77
57 58 3.942829 TCTTTGTCATTGCCTAGTCAGG 58.057 45.455 0.00 0.00 45.77 3.86
70 71 5.221843 TGCCTAGTCAGGTCTGTTTTGTAAT 60.222 40.000 0.00 0.00 44.68 1.89
71 72 6.014070 TGCCTAGTCAGGTCTGTTTTGTAATA 60.014 38.462 0.00 0.00 44.68 0.98
72 73 6.877322 GCCTAGTCAGGTCTGTTTTGTAATAA 59.123 38.462 0.00 0.00 44.68 1.40
135 141 0.250597 AGCGGTTACTTGTTGACCCC 60.251 55.000 0.00 0.00 0.00 4.95
139 145 2.688958 CGGTTACTTGTTGACCCCAAAA 59.311 45.455 0.00 0.00 33.49 2.44
140 146 3.130693 CGGTTACTTGTTGACCCCAAAAA 59.869 43.478 0.00 0.00 33.49 1.94
161 167 1.948104 TGTGAACGGAACTTGGACAG 58.052 50.000 0.00 0.00 0.00 3.51
262 272 5.191426 CAACAGAGAAGGATGGATTGTGAT 58.809 41.667 0.00 0.00 0.00 3.06
264 274 3.564644 CAGAGAAGGATGGATTGTGATGC 59.435 47.826 0.00 0.00 0.00 3.91
269 279 1.302366 GATGGATTGTGATGCTGCGA 58.698 50.000 0.00 0.00 0.00 5.10
275 285 1.302366 TTGTGATGCTGCGATCATCC 58.698 50.000 14.63 6.80 39.54 3.51
283 293 5.070047 TGATGCTGCGATCATCCTATCATAT 59.930 40.000 9.63 0.00 39.54 1.78
305 315 3.022607 ACTTACCACGAGAAAGAACCG 57.977 47.619 0.00 0.00 0.00 4.44
306 316 2.363359 ACTTACCACGAGAAAGAACCGT 59.637 45.455 0.00 0.00 36.95 4.83
317 327 5.395486 CGAGAAAGAACCGTTCATGTTTTTC 59.605 40.000 13.69 12.68 0.00 2.29
319 329 6.863275 AGAAAGAACCGTTCATGTTTTTCTT 58.137 32.000 13.69 0.00 33.91 2.52
320 330 6.751888 AGAAAGAACCGTTCATGTTTTTCTTG 59.248 34.615 13.69 0.00 33.91 3.02
321 331 4.932146 AGAACCGTTCATGTTTTTCTTGG 58.068 39.130 13.69 0.00 0.00 3.61
322 332 4.642885 AGAACCGTTCATGTTTTTCTTGGA 59.357 37.500 13.69 0.00 0.00 3.53
364 428 1.518903 GGTGTTTCCACAGCCAGAGC 61.519 60.000 0.00 0.00 44.37 4.09
367 431 0.595095 GTTTCCACAGCCAGAGCAAG 59.405 55.000 0.00 0.00 43.56 4.01
368 432 1.174712 TTTCCACAGCCAGAGCAAGC 61.175 55.000 0.00 0.00 43.56 4.01
375 443 0.886563 AGCCAGAGCAAGCAATTGTC 59.113 50.000 7.40 0.00 43.56 3.18
381 449 1.340889 GAGCAAGCAATTGTCCACCAA 59.659 47.619 7.40 0.00 37.49 3.67
384 457 3.577848 AGCAAGCAATTGTCCACCAAATA 59.422 39.130 7.40 0.00 36.44 1.40
394 467 6.485830 TTGTCCACCAAATACAAATTCCAA 57.514 33.333 0.00 0.00 30.54 3.53
396 469 6.696411 TGTCCACCAAATACAAATTCCAATC 58.304 36.000 0.00 0.00 0.00 2.67
398 471 6.022315 TCCACCAAATACAAATTCCAATCCT 58.978 36.000 0.00 0.00 0.00 3.24
403 476 6.155049 CCAAATACAAATTCCAATCCTGAGGT 59.845 38.462 0.00 0.00 0.00 3.85
426 499 1.869767 CTAATCGGCCATGTCAGCTTC 59.130 52.381 2.24 0.00 0.00 3.86
427 500 0.035152 AATCGGCCATGTCAGCTTCA 60.035 50.000 2.24 0.00 0.00 3.02
428 501 0.463295 ATCGGCCATGTCAGCTTCAG 60.463 55.000 2.24 0.00 0.00 3.02
429 502 1.078918 CGGCCATGTCAGCTTCAGA 60.079 57.895 2.24 0.00 0.00 3.27
432 516 2.097825 GGCCATGTCAGCTTCAGAATT 58.902 47.619 0.00 0.00 0.00 2.17
436 520 4.397417 GCCATGTCAGCTTCAGAATTAAGT 59.603 41.667 0.00 0.00 0.00 2.24
464 548 2.926420 TTGACGCTAGCTGTGCCGA 61.926 57.895 13.93 0.00 0.00 5.54
466 550 1.519455 GACGCTAGCTGTGCCGAAT 60.519 57.895 13.93 0.00 0.00 3.34
470 554 1.212616 GCTAGCTGTGCCGAATGTAG 58.787 55.000 7.70 0.00 0.00 2.74
476 565 2.540515 CTGTGCCGAATGTAGTACAGG 58.459 52.381 9.25 5.96 33.69 4.00
486 575 7.259882 CCGAATGTAGTACAGGTACAAATACA 58.740 38.462 9.25 11.11 38.48 2.29
487 576 7.434307 CCGAATGTAGTACAGGTACAAATACAG 59.566 40.741 9.25 2.02 38.48 2.74
488 577 7.043590 CGAATGTAGTACAGGTACAAATACAGC 60.044 40.741 9.25 7.35 38.48 4.40
490 579 4.119442 AGTACAGGTACAAATACAGCCG 57.881 45.455 11.78 0.00 38.48 5.52
498 589 2.706890 ACAAATACAGCCGAACCGATT 58.293 42.857 0.00 0.00 0.00 3.34
507 598 0.098728 CCGAACCGATTGATGTTGCC 59.901 55.000 0.00 0.00 0.00 4.52
509 600 1.202065 CGAACCGATTGATGTTGCCTG 60.202 52.381 0.00 0.00 0.00 4.85
510 601 0.527565 AACCGATTGATGTTGCCTGC 59.472 50.000 0.00 0.00 0.00 4.85
532 625 4.320164 GCGAGAATTGTACGTATACGGATG 59.680 45.833 27.62 2.11 44.95 3.51
534 627 5.334337 CGAGAATTGTACGTATACGGATGGA 60.334 44.000 27.62 10.96 44.95 3.41
553 646 3.863142 GACTACTGGTCCAATACGTGT 57.137 47.619 0.00 0.00 38.93 4.49
554 647 4.970662 GACTACTGGTCCAATACGTGTA 57.029 45.455 0.00 0.00 38.93 2.90
555 648 5.511234 GACTACTGGTCCAATACGTGTAT 57.489 43.478 0.00 0.00 38.93 2.29
556 649 5.258456 ACTACTGGTCCAATACGTGTATG 57.742 43.478 0.00 0.00 0.00 2.39
559 652 5.864418 ACTGGTCCAATACGTGTATGTAT 57.136 39.130 0.00 0.00 36.62 2.29
563 656 6.741109 TGGTCCAATACGTGTATGTATGTAG 58.259 40.000 0.00 0.00 35.30 2.74
576 669 6.671779 TGTATGTATGTAGGGATATGCATGGA 59.328 38.462 10.16 0.00 32.92 3.41
583 676 1.004044 GGGATATGCATGGACCTCTGG 59.996 57.143 10.16 0.00 0.00 3.86
584 677 1.004044 GGATATGCATGGACCTCTGGG 59.996 57.143 10.16 0.00 38.88 4.45
585 678 1.004044 GATATGCATGGACCTCTGGGG 59.996 57.143 10.16 0.00 41.89 4.96
594 687 3.760035 CCTCTGGGGTGTCGTCCG 61.760 72.222 0.00 0.00 0.00 4.79
595 688 3.760035 CTCTGGGGTGTCGTCCGG 61.760 72.222 0.00 0.00 0.00 5.14
596 689 4.289101 TCTGGGGTGTCGTCCGGA 62.289 66.667 0.00 0.00 36.18 5.14
597 690 4.065281 CTGGGGTGTCGTCCGGAC 62.065 72.222 25.28 25.28 46.27 4.79
607 700 2.183555 GTCCGGACGCAGGTTAGG 59.816 66.667 20.85 0.00 0.00 2.69
625 718 1.737816 GCGGTGGACCTAGCGATTA 59.262 57.895 16.29 0.00 43.66 1.75
639 732 3.774599 GATTAGGGGTGGCGCTGGG 62.775 68.421 7.64 0.00 0.00 4.45
770 874 7.881775 ATGATTATCCCAACCAAACTCTAAC 57.118 36.000 0.00 0.00 0.00 2.34
837 946 4.680975 GCAAATAGATAGATAGCCCGGACC 60.681 50.000 0.73 0.00 0.00 4.46
859 968 1.569072 GAGGGAGGGAAGAGAGAGAGT 59.431 57.143 0.00 0.00 0.00 3.24
870 979 1.752694 GAGAGAGTCCAGCTCCGCT 60.753 63.158 0.00 0.00 45.21 5.52
976 1091 3.169099 CCAGCATAGGAGCATAGGTAGT 58.831 50.000 0.00 0.00 36.85 2.73
1734 2082 3.359523 TGAAGCAGCCAAGCAGCG 61.360 61.111 0.00 0.00 45.54 5.18
1801 2155 1.525077 AGCTAGTCTCCGGAGAGCG 60.525 63.158 34.41 23.93 40.22 5.03
1848 2202 1.872952 TCAGCACAACCAACTCAATCG 59.127 47.619 0.00 0.00 0.00 3.34
1849 2203 1.603802 CAGCACAACCAACTCAATCGT 59.396 47.619 0.00 0.00 0.00 3.73
1861 2235 0.320374 TCAATCGTGTCCACCTGTCC 59.680 55.000 0.00 0.00 0.00 4.02
1869 2243 3.470888 CCACCTGTCCCCCTAGCG 61.471 72.222 0.00 0.00 0.00 4.26
1973 2359 0.845102 GAACAAGGGAGGGAGGGGAA 60.845 60.000 0.00 0.00 0.00 3.97
2062 2448 4.168760 CAATCGCCACCATCTTCTTTTTC 58.831 43.478 0.00 0.00 0.00 2.29
2202 2608 2.332063 TCGCCTCTGGATTTTGATCC 57.668 50.000 0.00 0.00 41.10 3.36
2245 2659 0.933097 TCGTACGTATCCAGTCGCTC 59.067 55.000 16.05 0.00 0.00 5.03
2246 2660 0.382758 CGTACGTATCCAGTCGCTCG 60.383 60.000 7.22 0.00 0.00 5.03
2247 2661 0.041488 GTACGTATCCAGTCGCTCGG 60.041 60.000 0.00 0.00 0.00 4.63
2248 2662 1.779025 TACGTATCCAGTCGCTCGGC 61.779 60.000 0.00 0.00 0.00 5.54
2249 2663 2.835705 CGTATCCAGTCGCTCGGCT 61.836 63.158 0.00 0.00 0.00 5.52
2250 2664 1.008309 GTATCCAGTCGCTCGGCTC 60.008 63.158 0.00 0.00 0.00 4.70
2383 2806 0.532573 TTCTCCGTCCATGTCTCTGC 59.467 55.000 0.00 0.00 0.00 4.26
2384 2807 1.142748 CTCCGTCCATGTCTCTGCC 59.857 63.158 0.00 0.00 0.00 4.85
2385 2808 1.305297 TCCGTCCATGTCTCTGCCT 60.305 57.895 0.00 0.00 0.00 4.75
2419 2842 3.861263 GAATCCGAACGTGCCGGC 61.861 66.667 22.73 22.73 46.10 6.13
2438 2872 1.808945 GCGCAATTATGGATCAGGGAG 59.191 52.381 0.30 0.00 0.00 4.30
2439 2873 1.808945 CGCAATTATGGATCAGGGAGC 59.191 52.381 0.00 0.00 0.00 4.70
2442 2876 0.326264 ATTATGGATCAGGGAGCGGC 59.674 55.000 0.00 0.00 0.00 6.53
2457 2891 4.171103 GGCGGGCCGATTGGTACT 62.171 66.667 33.44 0.00 37.67 2.73
2458 2892 2.895372 GCGGGCCGATTGGTACTG 60.895 66.667 33.44 0.00 37.67 2.74
2459 2893 2.895372 CGGGCCGATTGGTACTGC 60.895 66.667 24.41 0.00 37.67 4.40
2460 2894 2.590092 GGGCCGATTGGTACTGCT 59.410 61.111 0.00 0.00 37.67 4.24
2461 2895 1.827394 GGGCCGATTGGTACTGCTA 59.173 57.895 0.00 0.00 37.67 3.49
2462 2896 0.532196 GGGCCGATTGGTACTGCTAC 60.532 60.000 0.00 0.00 37.67 3.58
2463 2897 0.464452 GGCCGATTGGTACTGCTACT 59.536 55.000 0.00 0.00 37.67 2.57
2464 2898 1.538419 GGCCGATTGGTACTGCTACTC 60.538 57.143 0.00 0.00 37.67 2.59
2491 2925 1.299541 ATCTAATCGCCAACGCCAAG 58.700 50.000 0.00 0.00 39.84 3.61
2496 2930 4.383602 CGCCAACGCCAAGGAACG 62.384 66.667 0.00 0.00 0.00 3.95
2497 2931 4.038080 GCCAACGCCAAGGAACGG 62.038 66.667 0.00 0.00 0.00 4.44
2504 2938 1.299976 GCCAAGGAACGGAGTGGAT 59.700 57.895 0.00 0.00 45.00 3.41
2528 2962 2.306341 CTACATGAGCACAGAGGTGG 57.694 55.000 0.00 0.00 45.38 4.61
2529 2963 0.250234 TACATGAGCACAGAGGTGGC 59.750 55.000 0.00 0.00 45.38 5.01
2530 2964 1.002990 CATGAGCACAGAGGTGGCA 60.003 57.895 0.00 0.00 45.38 4.92
2531 2965 1.025113 CATGAGCACAGAGGTGGCAG 61.025 60.000 0.00 0.00 45.38 4.85
2535 2969 2.912624 GCACAGAGGTGGCAGCAAC 61.913 63.158 20.04 12.19 45.38 4.17
2544 2978 2.362120 GGCAGCAACTGGGCAGAT 60.362 61.111 0.00 0.00 35.83 2.90
2556 2990 0.757935 GGGCAGATGGGTCGTAGGTA 60.758 60.000 0.00 0.00 0.00 3.08
2564 2998 5.048643 CAGATGGGTCGTAGGTAGATTACTG 60.049 48.000 0.00 0.00 0.00 2.74
2567 3001 4.165950 TGGGTCGTAGGTAGATTACTGGTA 59.834 45.833 0.00 0.00 0.00 3.25
2568 3002 5.163055 TGGGTCGTAGGTAGATTACTGGTAT 60.163 44.000 0.00 0.00 0.00 2.73
2569 3003 5.182760 GGGTCGTAGGTAGATTACTGGTATG 59.817 48.000 0.00 0.00 0.00 2.39
2570 3004 6.000219 GGTCGTAGGTAGATTACTGGTATGA 59.000 44.000 0.00 0.00 0.00 2.15
2571 3005 6.658391 GGTCGTAGGTAGATTACTGGTATGAT 59.342 42.308 0.00 0.00 0.00 2.45
2572 3006 7.361885 GGTCGTAGGTAGATTACTGGTATGATG 60.362 44.444 0.00 0.00 0.00 3.07
2640 3096 3.716195 CCAGGCCACCACATCGGA 61.716 66.667 5.01 0.00 38.63 4.55
2641 3097 2.436646 CAGGCCACCACATCGGAC 60.437 66.667 5.01 0.00 38.63 4.79
2654 3110 0.605319 ATCGGACGGAAAGCAAAGCA 60.605 50.000 0.00 0.00 0.00 3.91
2662 3118 1.215014 GAAAGCAAAGCAACGCCCAC 61.215 55.000 0.00 0.00 0.00 4.61
2688 3144 1.447317 GGCCCGATGATGATTGCGTT 61.447 55.000 0.00 0.00 0.00 4.84
2689 3145 0.040958 GCCCGATGATGATTGCGTTC 60.041 55.000 0.00 0.00 0.00 3.95
2690 3146 1.586422 CCCGATGATGATTGCGTTCT 58.414 50.000 0.00 0.00 0.00 3.01
2691 3147 1.528586 CCCGATGATGATTGCGTTCTC 59.471 52.381 0.00 0.00 0.00 2.87
2692 3148 1.528586 CCGATGATGATTGCGTTCTCC 59.471 52.381 0.00 0.00 0.00 3.71
2693 3149 1.528586 CGATGATGATTGCGTTCTCCC 59.471 52.381 0.00 0.00 0.00 4.30
2694 3150 2.804572 CGATGATGATTGCGTTCTCCCT 60.805 50.000 0.00 0.00 0.00 4.20
2695 3151 2.315925 TGATGATTGCGTTCTCCCTC 57.684 50.000 0.00 0.00 0.00 4.30
2696 3152 1.833630 TGATGATTGCGTTCTCCCTCT 59.166 47.619 0.00 0.00 0.00 3.69
2697 3153 2.159043 TGATGATTGCGTTCTCCCTCTC 60.159 50.000 0.00 0.00 0.00 3.20
2698 3154 0.537188 TGATTGCGTTCTCCCTCTCC 59.463 55.000 0.00 0.00 0.00 3.71
2699 3155 0.528684 GATTGCGTTCTCCCTCTCCG 60.529 60.000 0.00 0.00 0.00 4.63
2700 3156 2.579684 ATTGCGTTCTCCCTCTCCGC 62.580 60.000 0.00 0.00 44.27 5.54
2701 3157 3.760035 GCGTTCTCCCTCTCCGCA 61.760 66.667 0.00 0.00 43.53 5.69
2702 3158 2.492090 CGTTCTCCCTCTCCGCAG 59.508 66.667 0.00 0.00 0.00 5.18
2703 3159 2.344203 CGTTCTCCCTCTCCGCAGT 61.344 63.158 0.00 0.00 0.00 4.40
2704 3160 1.216710 GTTCTCCCTCTCCGCAGTG 59.783 63.158 0.00 0.00 0.00 3.66
2705 3161 2.650116 TTCTCCCTCTCCGCAGTGC 61.650 63.158 4.58 4.58 0.00 4.40
2706 3162 3.385384 CTCCCTCTCCGCAGTGCA 61.385 66.667 16.83 0.00 0.00 4.57
2707 3163 2.685017 TCCCTCTCCGCAGTGCAT 60.685 61.111 16.83 0.00 0.00 3.96
2708 3164 2.513204 CCCTCTCCGCAGTGCATG 60.513 66.667 16.83 5.56 0.00 4.06
2716 3172 2.406401 GCAGTGCATGCGTGGATC 59.594 61.111 18.59 0.06 46.99 3.36
2717 3173 2.705220 CAGTGCATGCGTGGATCG 59.295 61.111 14.09 0.00 43.12 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.000274 CCCGCAGAAAGGAAAAAGGTG 60.000 52.381 0.00 0.00 0.00 4.00
15 16 1.882308 TATCCTTACCCCCGCAGAAA 58.118 50.000 0.00 0.00 0.00 2.52
18 19 1.978580 AGATTATCCTTACCCCCGCAG 59.021 52.381 0.00 0.00 0.00 5.18
139 145 3.283751 TGTCCAAGTTCCGTTCACATTT 58.716 40.909 0.00 0.00 0.00 2.32
140 146 2.878406 CTGTCCAAGTTCCGTTCACATT 59.122 45.455 0.00 0.00 0.00 2.71
161 167 0.889186 TTGCCGCTCTGGTTTCTTCC 60.889 55.000 0.00 0.00 41.21 3.46
222 228 3.050275 GCTCACCAACCCTCGTGC 61.050 66.667 0.00 0.00 0.00 5.34
262 272 6.097412 AGTTATATGATAGGATGATCGCAGCA 59.903 38.462 0.00 0.00 30.33 4.41
264 274 9.457110 GTAAGTTATATGATAGGATGATCGCAG 57.543 37.037 0.00 0.00 0.00 5.18
269 279 9.475620 TCGTGGTAAGTTATATGATAGGATGAT 57.524 33.333 0.00 0.00 0.00 2.45
283 293 4.037923 ACGGTTCTTTCTCGTGGTAAGTTA 59.962 41.667 0.00 0.00 35.70 2.24
305 315 5.696270 GGTCCAATCCAAGAAAAACATGAAC 59.304 40.000 0.00 0.00 0.00 3.18
306 316 5.365025 TGGTCCAATCCAAGAAAAACATGAA 59.635 36.000 0.00 0.00 34.24 2.57
317 327 0.321564 TGTCGCTGGTCCAATCCAAG 60.322 55.000 0.00 0.00 37.01 3.61
319 329 0.605319 GTTGTCGCTGGTCCAATCCA 60.605 55.000 0.00 0.00 36.00 3.41
320 330 0.605319 TGTTGTCGCTGGTCCAATCC 60.605 55.000 0.00 0.00 0.00 3.01
321 331 1.069227 GTTGTTGTCGCTGGTCCAATC 60.069 52.381 0.00 0.00 0.00 2.67
322 332 0.951558 GTTGTTGTCGCTGGTCCAAT 59.048 50.000 0.00 0.00 0.00 3.16
358 380 1.068055 GTGGACAATTGCTTGCTCTGG 60.068 52.381 5.05 0.00 35.69 3.86
359 423 1.068055 GGTGGACAATTGCTTGCTCTG 60.068 52.381 5.05 0.00 35.69 3.35
364 428 4.880759 TGTATTTGGTGGACAATTGCTTG 58.119 39.130 5.05 0.00 39.21 4.01
367 431 6.128309 GGAATTTGTATTTGGTGGACAATTGC 60.128 38.462 5.05 0.00 39.21 3.56
368 432 6.933521 TGGAATTTGTATTTGGTGGACAATTG 59.066 34.615 3.24 3.24 39.21 2.32
375 443 6.070881 TCAGGATTGGAATTTGTATTTGGTGG 60.071 38.462 0.00 0.00 0.00 4.61
381 449 8.116026 AGTTACCTCAGGATTGGAATTTGTATT 58.884 33.333 0.00 0.00 0.00 1.89
384 457 5.892348 AGTTACCTCAGGATTGGAATTTGT 58.108 37.500 0.00 0.00 0.00 2.83
394 467 2.633481 GGCCGATTAGTTACCTCAGGAT 59.367 50.000 0.00 0.00 0.00 3.24
396 469 1.760613 TGGCCGATTAGTTACCTCAGG 59.239 52.381 0.00 0.00 0.00 3.86
398 471 2.769663 ACATGGCCGATTAGTTACCTCA 59.230 45.455 0.00 0.00 0.00 3.86
403 476 2.434336 AGCTGACATGGCCGATTAGTTA 59.566 45.455 0.00 0.00 0.00 2.24
407 480 1.209261 TGAAGCTGACATGGCCGATTA 59.791 47.619 0.00 0.00 0.00 1.75
411 484 0.674581 TTCTGAAGCTGACATGGCCG 60.675 55.000 0.00 0.00 0.00 6.13
412 485 1.760192 ATTCTGAAGCTGACATGGCC 58.240 50.000 0.00 0.00 0.00 5.36
417 490 5.178797 GGCTACTTAATTCTGAAGCTGACA 58.821 41.667 0.00 0.00 0.00 3.58
419 492 5.420725 TGGCTACTTAATTCTGAAGCTGA 57.579 39.130 0.00 0.00 0.00 4.26
420 493 5.819379 TCATGGCTACTTAATTCTGAAGCTG 59.181 40.000 0.00 0.00 0.00 4.24
426 499 6.237942 CGTCAACTCATGGCTACTTAATTCTG 60.238 42.308 0.00 0.00 0.00 3.02
427 500 5.812642 CGTCAACTCATGGCTACTTAATTCT 59.187 40.000 0.00 0.00 0.00 2.40
428 501 5.502544 GCGTCAACTCATGGCTACTTAATTC 60.503 44.000 0.00 0.00 0.00 2.17
429 502 4.332819 GCGTCAACTCATGGCTACTTAATT 59.667 41.667 0.00 0.00 0.00 1.40
432 516 2.496070 AGCGTCAACTCATGGCTACTTA 59.504 45.455 0.00 0.00 31.03 2.24
436 520 1.202417 GCTAGCGTCAACTCATGGCTA 60.202 52.381 0.00 0.00 35.28 3.93
464 548 7.046033 GGCTGTATTTGTACCTGTACTACATT 58.954 38.462 8.75 0.00 37.00 2.71
466 550 5.393352 CGGCTGTATTTGTACCTGTACTACA 60.393 44.000 8.75 7.98 37.00 2.74
470 554 4.114058 TCGGCTGTATTTGTACCTGTAC 57.886 45.455 0.45 0.45 36.63 2.90
476 565 2.609350 TCGGTTCGGCTGTATTTGTAC 58.391 47.619 0.00 0.00 0.00 2.90
486 575 1.086696 CAACATCAATCGGTTCGGCT 58.913 50.000 0.00 0.00 0.00 5.52
487 576 0.523335 GCAACATCAATCGGTTCGGC 60.523 55.000 0.00 0.00 0.00 5.54
488 577 0.098728 GGCAACATCAATCGGTTCGG 59.901 55.000 0.00 0.00 0.00 4.30
490 579 1.468054 GCAGGCAACATCAATCGGTTC 60.468 52.381 0.00 0.00 41.41 3.62
498 589 1.469703 CAATTCTCGCAGGCAACATCA 59.530 47.619 0.00 0.00 41.41 3.07
507 598 3.662645 CCGTATACGTACAATTCTCGCAG 59.337 47.826 22.87 0.00 37.74 5.18
509 600 3.877064 TCCGTATACGTACAATTCTCGC 58.123 45.455 22.87 0.00 37.74 5.03
510 601 4.849926 CCATCCGTATACGTACAATTCTCG 59.150 45.833 22.87 4.71 37.74 4.04
534 627 4.708421 ACATACACGTATTGGACCAGTAGT 59.292 41.667 0.00 0.00 0.00 2.73
549 642 5.961272 TGCATATCCCTACATACATACACG 58.039 41.667 0.00 0.00 0.00 4.49
550 643 6.763135 CCATGCATATCCCTACATACATACAC 59.237 42.308 0.00 0.00 0.00 2.90
551 644 6.671779 TCCATGCATATCCCTACATACATACA 59.328 38.462 0.00 0.00 0.00 2.29
552 645 6.986817 GTCCATGCATATCCCTACATACATAC 59.013 42.308 0.00 0.00 0.00 2.39
553 646 6.099701 GGTCCATGCATATCCCTACATACATA 59.900 42.308 0.00 0.00 0.00 2.29
554 647 5.104360 GGTCCATGCATATCCCTACATACAT 60.104 44.000 0.00 0.00 0.00 2.29
555 648 4.225042 GGTCCATGCATATCCCTACATACA 59.775 45.833 0.00 0.00 0.00 2.29
556 649 4.471386 AGGTCCATGCATATCCCTACATAC 59.529 45.833 0.00 0.00 0.00 2.39
559 652 2.906389 GAGGTCCATGCATATCCCTACA 59.094 50.000 0.00 0.00 0.00 2.74
563 656 1.004044 CCAGAGGTCCATGCATATCCC 59.996 57.143 0.00 0.00 0.00 3.85
590 683 2.183555 CCTAACCTGCGTCCGGAC 59.816 66.667 25.28 25.28 0.00 4.79
591 684 3.766691 GCCTAACCTGCGTCCGGA 61.767 66.667 0.00 0.00 0.00 5.14
598 691 2.436115 GTCCACCGCCTAACCTGC 60.436 66.667 0.00 0.00 0.00 4.85
599 692 0.974010 TAGGTCCACCGCCTAACCTG 60.974 60.000 3.21 0.00 42.08 4.00
604 697 2.635787 ATCGCTAGGTCCACCGCCTA 62.636 60.000 0.00 0.00 42.08 3.93
607 700 0.318784 CTAATCGCTAGGTCCACCGC 60.319 60.000 0.00 0.00 42.08 5.68
614 707 1.408453 GCCACCCCTAATCGCTAGGT 61.408 60.000 8.94 0.00 45.42 3.08
655 748 0.610232 CTGTTTGGAAGGGAGCCTGG 60.610 60.000 0.00 0.00 32.13 4.45
702 801 1.586564 GAAGAGGACATCGACGGCG 60.587 63.158 2.87 2.87 39.35 6.46
732 831 0.179029 AATCATAAACCGGGCGGGAG 60.179 55.000 18.95 2.46 39.97 4.30
733 832 1.129917 TAATCATAAACCGGGCGGGA 58.870 50.000 18.95 0.00 39.97 5.14
736 835 2.081462 GGGATAATCATAAACCGGGCG 58.919 52.381 6.32 0.00 0.00 6.13
737 836 3.149005 TGGGATAATCATAAACCGGGC 57.851 47.619 6.32 0.00 0.00 6.13
740 839 6.096282 AGTTTGGTTGGGATAATCATAAACCG 59.904 38.462 0.00 0.00 39.94 4.44
770 874 0.115349 TTTTGTGGGTGGGGGTATGG 59.885 55.000 0.00 0.00 0.00 2.74
837 946 0.467290 CTCTCTCTTCCCTCCCTCCG 60.467 65.000 0.00 0.00 0.00 4.63
870 979 1.527148 TAGCTTTTGGTGTGCGGCA 60.527 52.632 0.00 0.00 0.00 5.69
873 984 0.517316 GGAGTAGCTTTTGGTGTGCG 59.483 55.000 0.00 0.00 0.00 5.34
914 1029 3.039526 CTCCCCTCTCCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
968 1083 2.966516 GAGCTGCCTACCAACTACCTAT 59.033 50.000 0.00 0.00 0.00 2.57
976 1091 0.036010 GAAGCTGAGCTGCCTACCAA 60.036 55.000 8.16 0.00 39.62 3.67
1726 2074 0.443088 CTGCTTCTTCTCGCTGCTTG 59.557 55.000 0.00 0.00 0.00 4.01
1751 2099 1.168714 GGTTGTGGATGACTGGAAGC 58.831 55.000 0.00 0.00 37.60 3.86
1753 2101 0.036164 CGGGTTGTGGATGACTGGAA 59.964 55.000 0.00 0.00 0.00 3.53
1814 2168 5.067413 GGTTGTGCTGAATCTGATTGATCAT 59.933 40.000 7.78 0.00 36.02 2.45
1848 2202 1.229400 TAGGGGGACAGGTGGACAC 60.229 63.158 0.00 0.00 0.00 3.67
1849 2203 1.080354 CTAGGGGGACAGGTGGACA 59.920 63.158 0.00 0.00 0.00 4.02
2032 2418 4.269183 AGATGGTGGCGATTGTTTTATCA 58.731 39.130 0.00 0.00 0.00 2.15
2062 2448 6.049149 ACTCGATAACAGAGAGAGAGAGAAG 58.951 44.000 0.00 0.00 38.97 2.85
2113 2515 6.980051 ACTGGGACGATTAATTAACAGAAC 57.020 37.500 14.68 1.89 0.00 3.01
2202 2608 5.123227 ACCACTGGATCAAATTGTATACGG 58.877 41.667 0.71 0.00 0.00 4.02
2383 2806 0.803117 CAGACACAAGCATGCAGAGG 59.197 55.000 21.98 9.14 0.00 3.69
2384 2807 1.804601 TCAGACACAAGCATGCAGAG 58.195 50.000 21.98 12.85 0.00 3.35
2385 2808 2.259266 TTCAGACACAAGCATGCAGA 57.741 45.000 21.98 1.47 0.00 4.26
2394 2817 2.131972 CACGTTCGGATTCAGACACAA 58.868 47.619 0.00 0.00 0.00 3.33
2419 2842 1.808945 GCTCCCTGATCCATAATTGCG 59.191 52.381 0.00 0.00 0.00 4.85
2442 2876 2.023414 TAGCAGTACCAATCGGCCCG 62.023 60.000 0.00 0.00 34.57 6.13
2444 2878 0.464452 AGTAGCAGTACCAATCGGCC 59.536 55.000 0.00 0.00 34.57 6.13
2445 2879 1.854227 GAGTAGCAGTACCAATCGGC 58.146 55.000 0.00 0.00 34.57 5.54
2446 2880 1.404391 ACGAGTAGCAGTACCAATCGG 59.596 52.381 0.00 0.00 31.76 4.18
2447 2881 2.451132 CACGAGTAGCAGTACCAATCG 58.549 52.381 0.00 0.00 33.04 3.34
2448 2882 2.810650 CCACGAGTAGCAGTACCAATC 58.189 52.381 0.00 0.00 0.00 2.67
2449 2883 1.134788 GCCACGAGTAGCAGTACCAAT 60.135 52.381 0.00 0.00 0.00 3.16
2450 2884 0.245539 GCCACGAGTAGCAGTACCAA 59.754 55.000 0.00 0.00 0.00 3.67
2451 2885 0.611062 AGCCACGAGTAGCAGTACCA 60.611 55.000 0.00 0.00 0.00 3.25
2452 2886 1.386533 TAGCCACGAGTAGCAGTACC 58.613 55.000 0.00 0.00 0.00 3.34
2453 2887 3.315749 AGATTAGCCACGAGTAGCAGTAC 59.684 47.826 0.00 0.00 0.00 2.73
2454 2888 3.552875 AGATTAGCCACGAGTAGCAGTA 58.447 45.455 0.00 0.00 0.00 2.74
2455 2889 2.379972 AGATTAGCCACGAGTAGCAGT 58.620 47.619 0.00 0.00 0.00 4.40
2456 2890 4.569761 TTAGATTAGCCACGAGTAGCAG 57.430 45.455 0.00 0.00 0.00 4.24
2457 2891 4.320275 CGATTAGATTAGCCACGAGTAGCA 60.320 45.833 0.00 0.00 0.00 3.49
2458 2892 4.159857 CGATTAGATTAGCCACGAGTAGC 58.840 47.826 0.00 0.00 0.00 3.58
2459 2893 4.159857 GCGATTAGATTAGCCACGAGTAG 58.840 47.826 0.00 0.00 0.00 2.57
2460 2894 4.156664 GCGATTAGATTAGCCACGAGTA 57.843 45.455 0.00 0.00 0.00 2.59
2461 2895 3.014604 GCGATTAGATTAGCCACGAGT 57.985 47.619 0.00 0.00 0.00 4.18
2491 2925 1.404843 AGCTAGATCCACTCCGTTCC 58.595 55.000 0.00 0.00 0.00 3.62
2496 2930 4.782019 CTCATGTAGCTAGATCCACTCC 57.218 50.000 0.00 0.00 0.00 3.85
2521 2955 2.433446 CCAGTTGCTGCCACCTCT 59.567 61.111 0.00 0.00 0.00 3.69
2522 2956 2.674380 CCCAGTTGCTGCCACCTC 60.674 66.667 0.00 0.00 0.00 3.85
2523 2957 4.982701 GCCCAGTTGCTGCCACCT 62.983 66.667 0.00 0.00 0.00 4.00
2525 2959 3.677648 CTGCCCAGTTGCTGCCAC 61.678 66.667 0.00 0.00 0.00 5.01
2526 2960 3.214190 ATCTGCCCAGTTGCTGCCA 62.214 57.895 0.00 0.00 0.00 4.92
2527 2961 2.362120 ATCTGCCCAGTTGCTGCC 60.362 61.111 0.00 0.00 0.00 4.85
2528 2962 2.707849 CCATCTGCCCAGTTGCTGC 61.708 63.158 0.00 0.00 0.00 5.25
2529 2963 2.050350 CCCATCTGCCCAGTTGCTG 61.050 63.158 1.69 0.00 0.00 4.41
2530 2964 2.357836 CCCATCTGCCCAGTTGCT 59.642 61.111 1.69 0.00 0.00 3.91
2531 2965 2.036256 ACCCATCTGCCCAGTTGC 59.964 61.111 1.69 0.00 0.00 4.17
2535 2969 1.443407 CTACGACCCATCTGCCCAG 59.557 63.158 0.00 0.00 0.00 4.45
2544 2978 3.053395 ACCAGTAATCTACCTACGACCCA 60.053 47.826 0.00 0.00 0.00 4.51
2556 2990 5.396772 CCACACACCATCATACCAGTAATCT 60.397 44.000 0.00 0.00 0.00 2.40
2564 2998 1.280710 TCACCCACACACCATCATACC 59.719 52.381 0.00 0.00 0.00 2.73
2567 3001 2.449464 CAATCACCCACACACCATCAT 58.551 47.619 0.00 0.00 0.00 2.45
2568 3002 1.547449 CCAATCACCCACACACCATCA 60.547 52.381 0.00 0.00 0.00 3.07
2569 3003 1.176527 CCAATCACCCACACACCATC 58.823 55.000 0.00 0.00 0.00 3.51
2570 3004 0.482446 ACCAATCACCCACACACCAT 59.518 50.000 0.00 0.00 0.00 3.55
2571 3005 0.260230 AACCAATCACCCACACACCA 59.740 50.000 0.00 0.00 0.00 4.17
2572 3006 1.408969 AAACCAATCACCCACACACC 58.591 50.000 0.00 0.00 0.00 4.16
2624 3080 2.436646 GTCCGATGTGGTGGCCTG 60.437 66.667 3.32 0.00 39.52 4.85
2640 3096 1.299089 GCGTTGCTTTGCTTTCCGT 60.299 52.632 0.00 0.00 0.00 4.69
2641 3097 2.016165 GGCGTTGCTTTGCTTTCCG 61.016 57.895 0.00 0.00 0.00 4.30
2662 3118 3.933722 ATCATCGGGCCGGAGCTG 61.934 66.667 27.98 17.81 39.73 4.24
2673 3129 1.528586 GGGAGAACGCAATCATCATCG 59.471 52.381 0.00 0.00 0.00 3.84
2688 3144 3.071206 GCACTGCGGAGAGGGAGA 61.071 66.667 12.26 0.00 0.00 3.71
2689 3145 2.729479 ATGCACTGCGGAGAGGGAG 61.729 63.158 12.26 0.00 0.00 4.30
2690 3146 2.685017 ATGCACTGCGGAGAGGGA 60.685 61.111 12.26 3.76 0.00 4.20
2691 3147 2.513204 CATGCACTGCGGAGAGGG 60.513 66.667 12.26 0.37 0.00 4.30
2692 3148 3.200593 GCATGCACTGCGGAGAGG 61.201 66.667 14.21 3.21 41.97 3.69
2700 3156 2.705220 CGATCCACGCATGCACTG 59.295 61.111 19.57 11.80 34.51 3.66


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

AutoCloner maintained by Alex Coulton.