Multiple sequence alignment - TraesCS6A01G039200

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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 TraesCS6A01G039200 chr6A 100.000 3227 0 0 1 3227 20249677 20252903 0.000000e+00 5960
1 TraesCS6A01G039200 chr6D 94.779 2011 83 8 564 2554 20253454 20255462 0.000000e+00 3112
2 TraesCS6A01G039200 chr6D 94.249 313 16 2 1 312 20253141 20253452 8.100000e-131 477
3 TraesCS6A01G039200 chr6B 91.958 2114 97 25 483 2559 34218921 34220998 0.000000e+00 2894
4 TraesCS6A01G039200 chr6B 93.316 374 25 0 1 374 34218476 34218849 1.310000e-153 553
5 TraesCS6A01G039200 chr6B 88.011 367 32 5 2863 3227 34221943 34222299 1.070000e-114 424
6 TraesCS6A01G039200 chr6B 78.754 626 95 25 2556 3166 34221121 34221723 5.050000e-103 385
7 TraesCS6A01G039200 chr6B 90.741 162 13 2 2672 2833 34221790 34221949 7.010000e-52 215
8 TraesCS6A01G039200 chr5B 95.556 90 4 0 396 485 411034866 411034777 9.330000e-31 145
9 TraesCS6A01G039200 chr5B 95.455 88 4 0 400 487 440023747 440023834 1.210000e-29 141
10 TraesCS6A01G039200 chrUn 94.444 90 5 0 397 486 101630887 101630798 4.340000e-29 139
11 TraesCS6A01G039200 chr2B 96.386 83 3 0 399 481 790112941 790113023 1.560000e-28 137
12 TraesCS6A01G039200 chr5A 93.407 91 6 0 394 484 393474472 393474382 5.620000e-28 135
13 TraesCS6A01G039200 chr7B 93.333 90 6 0 395 484 107127488 107127399 2.020000e-27 134
14 TraesCS6A01G039200 chr1D 92.473 93 5 2 398 489 275947621 275947712 7.260000e-27 132
15 TraesCS6A01G039200 chr4D 90.526 95 9 0 393 487 478670931 478670837 3.380000e-25 126
16 TraesCS6A01G039200 chr3A 89.796 98 10 0 384 481 52348280 52348377 3.380000e-25 126


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 TraesCS6A01G039200 chr6A 20249677 20252903 3226 False 5960.0 5960 100.000 1 3227 1 chr6A.!!$F1 3226
1 TraesCS6A01G039200 chr6D 20253141 20255462 2321 False 1794.5 3112 94.514 1 2554 2 chr6D.!!$F1 2553
2 TraesCS6A01G039200 chr6B 34218476 34222299 3823 False 894.2 2894 88.556 1 3227 5 chr6B.!!$F1 3226

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
966 1038 0.106335 TACTAGTAGCTCGGCTCGCT 59.894 55.0 0.0 3.01 40.44 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2931 3715 0.540923 GCCATCCACTCTCTCTGCTT 59.459 55.0 0.0 0.0 0.0 3.91 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
178 180 7.220108 GGTCATAACAAAGACACACTTGAAAAC 59.780 37.037 0.00 0.00 38.98 2.43
194 196 6.884836 ACTTGAAAACAGGTTAAAGTCACTCT 59.115 34.615 0.00 0.00 0.00 3.24
235 237 5.013287 GGGAGGGAAAGAAGAGTCTAAACTT 59.987 44.000 0.00 0.00 35.28 2.66
238 240 5.063880 GGGAAAGAAGAGTCTAAACTTGCA 58.936 41.667 11.96 0.00 35.28 4.08
242 244 7.805542 GGAAAGAAGAGTCTAAACTTGCAAATC 59.194 37.037 0.00 0.00 35.28 2.17
337 339 0.482446 AGGTGCAATCAACCCAGGAA 59.518 50.000 0.00 0.00 0.00 3.36
350 352 1.490574 CCAGGAACACCCAAAAACCA 58.509 50.000 0.00 0.00 37.41 3.67
353 355 3.494223 CCAGGAACACCCAAAAACCATTC 60.494 47.826 0.00 0.00 37.41 2.67
370 372 5.716094 ACCATTCGGTTTTGCCTTATAAAC 58.284 37.500 0.00 0.00 46.31 2.01
374 376 5.365403 TCGGTTTTGCCTTATAAACACAG 57.635 39.130 0.00 0.00 36.27 3.66
377 379 6.485984 TCGGTTTTGCCTTATAAACACAGTAA 59.514 34.615 0.00 0.00 36.27 2.24
378 380 6.579666 CGGTTTTGCCTTATAAACACAGTAAC 59.420 38.462 0.00 0.00 36.27 2.50
380 382 7.921745 GGTTTTGCCTTATAAACACAGTAACAA 59.078 33.333 0.00 0.00 36.27 2.83
381 383 9.303537 GTTTTGCCTTATAAACACAGTAACAAA 57.696 29.630 0.00 0.00 35.02 2.83
394 444 7.711846 ACACAGTAACAAATAACATCAGCAAA 58.288 30.769 0.00 0.00 0.00 3.68
396 446 9.195411 CACAGTAACAAATAACATCAGCAAAAT 57.805 29.630 0.00 0.00 0.00 1.82
404 454 9.722056 CAAATAACATCAGCAAAATACTACTCC 57.278 33.333 0.00 0.00 0.00 3.85
405 455 8.451908 AATAACATCAGCAAAATACTACTCCC 57.548 34.615 0.00 0.00 0.00 4.30
406 456 5.700402 ACATCAGCAAAATACTACTCCCT 57.300 39.130 0.00 0.00 0.00 4.20
407 457 5.675538 ACATCAGCAAAATACTACTCCCTC 58.324 41.667 0.00 0.00 0.00 4.30
408 458 5.426833 ACATCAGCAAAATACTACTCCCTCT 59.573 40.000 0.00 0.00 0.00 3.69
409 459 5.344743 TCAGCAAAATACTACTCCCTCTG 57.655 43.478 0.00 0.00 0.00 3.35
410 460 4.777896 TCAGCAAAATACTACTCCCTCTGT 59.222 41.667 0.00 0.00 0.00 3.41
411 461 5.955959 TCAGCAAAATACTACTCCCTCTGTA 59.044 40.000 0.00 0.00 0.00 2.74
412 462 6.439375 TCAGCAAAATACTACTCCCTCTGTAA 59.561 38.462 0.00 0.00 0.00 2.41
413 463 7.038587 TCAGCAAAATACTACTCCCTCTGTAAA 60.039 37.037 0.00 0.00 0.00 2.01
414 464 7.770897 CAGCAAAATACTACTCCCTCTGTAAAT 59.229 37.037 0.00 0.00 0.00 1.40
415 465 8.989131 AGCAAAATACTACTCCCTCTGTAAATA 58.011 33.333 0.00 0.00 0.00 1.40
416 466 9.609346 GCAAAATACTACTCCCTCTGTAAATAA 57.391 33.333 0.00 0.00 0.00 1.40
427 477 9.360093 CTCCCTCTGTAAATAAATATAAGAGCG 57.640 37.037 0.00 0.00 0.00 5.03
428 478 8.867097 TCCCTCTGTAAATAAATATAAGAGCGT 58.133 33.333 0.00 0.00 0.00 5.07
429 479 9.490379 CCCTCTGTAAATAAATATAAGAGCGTT 57.510 33.333 0.00 0.00 0.00 4.84
443 493 7.811117 ATAAGAGCGTTTAGATCACTACTCT 57.189 36.000 0.00 0.00 37.82 3.24
444 494 8.905660 ATAAGAGCGTTTAGATCACTACTCTA 57.094 34.615 0.00 0.00 37.82 2.43
445 495 6.854496 AGAGCGTTTAGATCACTACTCTAG 57.146 41.667 0.00 0.00 37.82 2.43
446 496 6.350906 AGAGCGTTTAGATCACTACTCTAGT 58.649 40.000 0.00 0.00 37.82 2.57
459 509 6.607735 ACTACTCTAGTGATCTAAACGCTC 57.392 41.667 0.00 0.00 37.69 5.03
460 510 6.350906 ACTACTCTAGTGATCTAAACGCTCT 58.649 40.000 0.00 0.00 37.69 4.09
461 511 6.824704 ACTACTCTAGTGATCTAAACGCTCTT 59.175 38.462 0.00 0.00 37.69 2.85
462 512 7.986320 ACTACTCTAGTGATCTAAACGCTCTTA 59.014 37.037 0.00 0.00 37.69 2.10
463 513 7.811117 ACTCTAGTGATCTAAACGCTCTTAT 57.189 36.000 0.00 0.00 0.00 1.73
464 514 8.905660 ACTCTAGTGATCTAAACGCTCTTATA 57.094 34.615 0.00 0.00 0.00 0.98
465 515 9.509956 ACTCTAGTGATCTAAACGCTCTTATAT 57.490 33.333 0.00 0.00 0.00 0.86
479 529 9.490379 AACGCTCTTATATTTATTTACAGAGGG 57.510 33.333 8.36 8.36 42.53 4.30
480 530 8.867097 ACGCTCTTATATTTATTTACAGAGGGA 58.133 33.333 14.96 0.00 40.49 4.20
481 531 9.877178 CGCTCTTATATTTATTTACAGAGGGAT 57.123 33.333 4.76 0.00 40.49 3.85
494 544 3.197983 ACAGAGGGATTACTACACTTGGC 59.802 47.826 0.00 0.00 0.00 4.52
525 578 0.888619 AAGGAGAGCGTCGACATCAA 59.111 50.000 17.16 0.00 0.00 2.57
537 590 5.460419 GCGTCGACATCAAGAGAAAGATAAT 59.540 40.000 17.16 0.00 0.00 1.28
541 594 6.818142 TCGACATCAAGAGAAAGATAATGCAA 59.182 34.615 0.00 0.00 0.00 4.08
557 610 4.654091 ATGCAACACAAAGTAAAGCACT 57.346 36.364 0.00 0.00 40.05 4.40
566 619 6.546034 ACACAAAGTAAAGCACTGGTCTTAAT 59.454 34.615 0.00 0.00 37.63 1.40
580 633 4.035558 TGGTCTTAATGAGATGCGAATTGC 59.964 41.667 0.00 0.00 46.70 3.56
669 725 0.972983 AGCTAGCCACGACATGACCT 60.973 55.000 12.13 0.00 0.00 3.85
752 808 3.995048 GCAAAGGGAAGTGTGTAGTAGTC 59.005 47.826 0.00 0.00 0.00 2.59
776 832 3.754850 TGTCCATGCATGTTTCTCTCTTG 59.245 43.478 24.58 5.98 0.00 3.02
853 909 3.891366 CCCAAAATGAACAAGAGACACCT 59.109 43.478 0.00 0.00 0.00 4.00
918 990 1.270274 TCATCACCACATGCACAAAGC 59.730 47.619 0.00 0.00 45.96 3.51
966 1038 0.106335 TACTAGTAGCTCGGCTCGCT 59.894 55.000 0.00 3.01 40.44 4.93
989 1061 1.073964 CGATCGATCCATGTCCATGC 58.926 55.000 19.51 0.00 37.49 4.06
1029 1101 1.000486 CTCCTCCCCGTCTTCTCCA 60.000 63.158 0.00 0.00 0.00 3.86
1050 1125 3.068691 TCTTCTCCCACCTCCGCG 61.069 66.667 0.00 0.00 0.00 6.46
1136 1214 1.301874 ACGGCATTTCGTTTCCGGA 60.302 52.632 0.00 0.00 45.58 5.14
2210 2288 3.480133 CCGGGGAGATGACCACCC 61.480 72.222 0.00 0.00 42.58 4.61
2242 2320 0.684479 ATAGCGAGCCACACTCTCCA 60.684 55.000 0.00 0.00 43.85 3.86
2253 2331 0.393537 CACTCTCCACTGCCCATTCC 60.394 60.000 0.00 0.00 0.00 3.01
2256 2334 0.982852 TCTCCACTGCCCATTCCGAT 60.983 55.000 0.00 0.00 0.00 4.18
2297 2384 6.549952 AGAGATTCATTCTTGCGTTTCAATC 58.450 36.000 0.00 0.00 33.74 2.67
2507 2611 7.914871 CACAATGAAGTGTGTTTTGTAGATGAA 59.085 33.333 2.82 0.00 43.26 2.57
2519 2623 6.912203 TTTGTAGATGAACTCACGTTGAAA 57.088 33.333 0.00 0.00 32.39 2.69
2580 2810 1.001378 GCACGAAGGCAGATTTTGTGT 60.001 47.619 6.49 0.00 40.49 3.72
2584 2814 4.024048 CACGAAGGCAGATTTTGTGTAACT 60.024 41.667 0.00 0.00 35.92 2.24
2588 2818 6.401153 CGAAGGCAGATTTTGTGTAACTAGTC 60.401 42.308 0.00 0.00 38.04 2.59
2589 2819 5.246307 AGGCAGATTTTGTGTAACTAGTCC 58.754 41.667 0.00 0.00 38.04 3.85
2590 2820 5.001232 GGCAGATTTTGTGTAACTAGTCCA 58.999 41.667 0.00 0.00 38.04 4.02
2591 2821 5.648092 GGCAGATTTTGTGTAACTAGTCCAT 59.352 40.000 0.00 0.00 38.04 3.41
2592 2822 6.821665 GGCAGATTTTGTGTAACTAGTCCATA 59.178 38.462 0.00 0.00 38.04 2.74
2593 2823 7.499232 GGCAGATTTTGTGTAACTAGTCCATAT 59.501 37.037 0.00 0.00 38.04 1.78
2594 2824 8.893727 GCAGATTTTGTGTAACTAGTCCATATT 58.106 33.333 0.00 0.00 38.04 1.28
2635 2867 8.956533 TTTCTTTTTATTGTTTTCCCCAGAAG 57.043 30.769 0.00 0.00 32.35 2.85
2649 2881 6.658555 TCCCCAGAAGAAGAAATAATTCCT 57.341 37.500 0.00 0.00 36.12 3.36
2651 2883 7.119387 TCCCCAGAAGAAGAAATAATTCCTTC 58.881 38.462 0.00 0.00 36.12 3.46
2720 3504 4.687483 GGAAAGCTCATCCAACAAACATTG 59.313 41.667 12.46 0.00 36.92 2.82
2727 3511 3.663995 TCCAACAAACATTGCCATCTG 57.336 42.857 0.00 0.00 0.00 2.90
2732 3516 2.957680 ACAAACATTGCCATCTGTGACA 59.042 40.909 0.00 0.00 0.00 3.58
2734 3518 4.766373 ACAAACATTGCCATCTGTGACATA 59.234 37.500 0.00 0.00 0.00 2.29
2765 3549 9.950496 ACAGATACAAGATTCAAATGAGTACTT 57.050 29.630 0.00 0.00 0.00 2.24
2825 3609 5.411669 GTGTTGTCTTAGGTCACAATAAGGG 59.588 44.000 0.52 0.00 35.05 3.95
2833 3617 4.785301 AGGTCACAATAAGGGATGTCATG 58.215 43.478 0.00 0.00 0.00 3.07
2834 3618 4.228210 AGGTCACAATAAGGGATGTCATGT 59.772 41.667 0.00 0.00 0.00 3.21
2835 3619 4.949856 GGTCACAATAAGGGATGTCATGTT 59.050 41.667 0.00 0.00 0.00 2.71
2836 3620 6.069673 AGGTCACAATAAGGGATGTCATGTTA 60.070 38.462 0.00 0.00 0.00 2.41
2837 3621 6.772716 GGTCACAATAAGGGATGTCATGTTAT 59.227 38.462 0.00 0.00 0.00 1.89
2838 3622 7.255242 GGTCACAATAAGGGATGTCATGTTATG 60.255 40.741 0.00 0.00 0.00 1.90
2839 3623 7.498900 GTCACAATAAGGGATGTCATGTTATGA 59.501 37.037 0.00 0.00 36.84 2.15
2840 3624 7.716560 TCACAATAAGGGATGTCATGTTATGAG 59.283 37.037 0.00 0.00 40.53 2.90
2841 3625 7.500227 CACAATAAGGGATGTCATGTTATGAGT 59.500 37.037 0.00 0.00 40.53 3.41
2842 3626 8.055181 ACAATAAGGGATGTCATGTTATGAGTT 58.945 33.333 0.00 0.00 40.53 3.01
2843 3627 8.906867 CAATAAGGGATGTCATGTTATGAGTTT 58.093 33.333 0.00 0.00 40.53 2.66
2844 3628 8.682936 ATAAGGGATGTCATGTTATGAGTTTC 57.317 34.615 0.00 0.00 40.53 2.78
2845 3629 6.319048 AGGGATGTCATGTTATGAGTTTCT 57.681 37.500 0.00 0.00 40.53 2.52
2846 3630 6.118170 AGGGATGTCATGTTATGAGTTTCTG 58.882 40.000 0.00 0.00 40.53 3.02
2847 3631 5.297776 GGGATGTCATGTTATGAGTTTCTGG 59.702 44.000 0.00 0.00 40.53 3.86
2848 3632 5.882557 GGATGTCATGTTATGAGTTTCTGGT 59.117 40.000 0.00 0.00 40.53 4.00
2849 3633 6.183360 GGATGTCATGTTATGAGTTTCTGGTG 60.183 42.308 0.00 0.00 40.53 4.17
2850 3634 5.863965 TGTCATGTTATGAGTTTCTGGTGA 58.136 37.500 0.00 0.00 40.53 4.02
2851 3635 6.475504 TGTCATGTTATGAGTTTCTGGTGAT 58.524 36.000 0.00 0.00 40.53 3.06
2852 3636 6.942005 TGTCATGTTATGAGTTTCTGGTGATT 59.058 34.615 0.00 0.00 40.53 2.57
2853 3637 7.094677 TGTCATGTTATGAGTTTCTGGTGATTG 60.095 37.037 0.00 0.00 40.53 2.67
2854 3638 7.119699 GTCATGTTATGAGTTTCTGGTGATTGA 59.880 37.037 0.00 0.00 40.53 2.57
2855 3639 6.801539 TGTTATGAGTTTCTGGTGATTGAC 57.198 37.500 0.00 0.00 0.00 3.18
2856 3640 6.295249 TGTTATGAGTTTCTGGTGATTGACA 58.705 36.000 0.00 0.00 0.00 3.58
2857 3641 6.942005 TGTTATGAGTTTCTGGTGATTGACAT 59.058 34.615 0.00 0.00 0.00 3.06
2858 3642 7.448161 TGTTATGAGTTTCTGGTGATTGACATT 59.552 33.333 0.00 0.00 0.00 2.71
2859 3643 8.946085 GTTATGAGTTTCTGGTGATTGACATTA 58.054 33.333 0.00 0.00 0.00 1.90
2860 3644 7.621428 ATGAGTTTCTGGTGATTGACATTAG 57.379 36.000 0.00 0.00 0.00 1.73
2861 3645 6.533730 TGAGTTTCTGGTGATTGACATTAGT 58.466 36.000 0.00 0.00 0.00 2.24
2862 3646 7.676004 TGAGTTTCTGGTGATTGACATTAGTA 58.324 34.615 0.00 0.00 0.00 1.82
2863 3647 8.321353 TGAGTTTCTGGTGATTGACATTAGTAT 58.679 33.333 0.00 0.00 0.00 2.12
2864 3648 9.167311 GAGTTTCTGGTGATTGACATTAGTATT 57.833 33.333 0.00 0.00 0.00 1.89
2865 3649 9.520515 AGTTTCTGGTGATTGACATTAGTATTT 57.479 29.630 0.00 0.00 0.00 1.40
2866 3650 9.774742 GTTTCTGGTGATTGACATTAGTATTTC 57.225 33.333 0.00 0.00 0.00 2.17
2867 3651 9.513906 TTTCTGGTGATTGACATTAGTATTTCA 57.486 29.630 0.00 0.00 0.00 2.69
2868 3652 9.685276 TTCTGGTGATTGACATTAGTATTTCAT 57.315 29.630 0.00 0.00 0.00 2.57
2950 3734 0.540923 AAGCAGAGAGAGTGGATGGC 59.459 55.000 0.00 0.00 0.00 4.40
3001 3787 1.671379 GGTCGAAACCTCCAGGCAC 60.671 63.158 0.00 0.00 42.80 5.01
3019 3805 1.620323 CACATGGATCCTAGGATGCGA 59.380 52.381 31.09 22.48 44.35 5.10
3035 3821 7.639113 AGGATGCGACCATAATTTTCTTTAA 57.361 32.000 2.00 0.00 0.00 1.52
3050 3836 9.573133 AATTTTCTTTAAATAGATGTGAAGCGG 57.427 29.630 0.00 0.00 35.39 5.52
3059 3845 2.820197 AGATGTGAAGCGGCGATATAGA 59.180 45.455 12.98 0.00 0.00 1.98
3064 3850 4.814234 TGTGAAGCGGCGATATAGAAAAAT 59.186 37.500 12.98 0.00 0.00 1.82
3112 3898 4.157246 ACAGTACAGTGGACAACTATGGA 58.843 43.478 8.55 0.00 36.83 3.41
3113 3899 4.220821 ACAGTACAGTGGACAACTATGGAG 59.779 45.833 8.55 0.00 36.83 3.86
3114 3900 3.769844 AGTACAGTGGACAACTATGGAGG 59.230 47.826 8.55 0.00 36.83 4.30
3166 3952 5.491078 ACACCTAAAGTTGATATTCCTCCCA 59.509 40.000 0.00 0.00 0.00 4.37
3182 3968 1.490490 TCCCATGAAGTATGCCCTCAC 59.510 52.381 0.00 0.00 35.37 3.51
3195 3981 2.801162 CTCACGCCGATATCGCCG 60.801 66.667 24.85 24.85 45.98 6.46
3209 3995 4.101448 GCCGGGTCCAGCTCATGT 62.101 66.667 2.18 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.008118 GGATAAAGTTGAGCTAGATGTTGGC 59.992 44.000 0.00 0.00 0.00 4.52
146 148 3.810941 GTGTCTTTGTTATGACCGTTCCA 59.189 43.478 0.00 0.00 32.67 3.53
178 180 3.126001 TGGCAGAGTGACTTTAACCTG 57.874 47.619 0.00 0.00 0.00 4.00
194 196 2.437651 CTCCCTTTTTCCCTTTTTGGCA 59.562 45.455 0.00 0.00 0.00 4.92
235 237 4.927425 GGTTAGTGAGTTAGACGATTTGCA 59.073 41.667 0.00 0.00 0.00 4.08
238 240 9.148104 GTTATTGGTTAGTGAGTTAGACGATTT 57.852 33.333 0.00 0.00 0.00 2.17
242 244 6.392354 TGGTTATTGGTTAGTGAGTTAGACG 58.608 40.000 0.00 0.00 0.00 4.18
350 352 6.015772 ACTGTGTTTATAAGGCAAAACCGAAT 60.016 34.615 0.00 0.00 46.52 3.34
353 355 5.116069 ACTGTGTTTATAAGGCAAAACCG 57.884 39.130 0.00 0.00 46.52 4.44
365 367 9.840427 GCTGATGTTATTTGTTACTGTGTTTAT 57.160 29.630 0.00 0.00 0.00 1.40
370 372 8.572828 TTTTGCTGATGTTATTTGTTACTGTG 57.427 30.769 0.00 0.00 0.00 3.66
378 380 9.722056 GGAGTAGTATTTTGCTGATGTTATTTG 57.278 33.333 0.00 0.00 0.00 2.32
380 382 8.275040 AGGGAGTAGTATTTTGCTGATGTTATT 58.725 33.333 0.00 0.00 0.00 1.40
381 383 7.806180 AGGGAGTAGTATTTTGCTGATGTTAT 58.194 34.615 0.00 0.00 0.00 1.89
382 384 7.125811 AGAGGGAGTAGTATTTTGCTGATGTTA 59.874 37.037 0.00 0.00 0.00 2.41
401 451 9.360093 CGCTCTTATATTTATTTACAGAGGGAG 57.640 37.037 4.76 0.00 40.49 4.30
402 452 8.867097 ACGCTCTTATATTTATTTACAGAGGGA 58.133 33.333 14.96 0.00 40.49 4.20
403 453 9.490379 AACGCTCTTATATTTATTTACAGAGGG 57.510 33.333 8.36 8.36 42.53 4.30
417 467 9.509956 AGAGTAGTGATCTAAACGCTCTTATAT 57.490 33.333 0.00 0.00 33.87 0.86
418 468 8.905660 AGAGTAGTGATCTAAACGCTCTTATA 57.094 34.615 0.00 0.00 33.87 0.98
419 469 7.811117 AGAGTAGTGATCTAAACGCTCTTAT 57.189 36.000 0.00 0.00 33.87 1.73
420 470 7.986320 ACTAGAGTAGTGATCTAAACGCTCTTA 59.014 37.037 13.02 4.45 37.69 2.10
421 471 6.824704 ACTAGAGTAGTGATCTAAACGCTCTT 59.175 38.462 13.02 0.80 37.69 2.85
422 472 6.350906 ACTAGAGTAGTGATCTAAACGCTCT 58.649 40.000 0.00 12.65 37.69 4.09
423 473 6.607735 ACTAGAGTAGTGATCTAAACGCTC 57.392 41.667 0.00 0.00 37.69 5.03
436 486 6.350906 AGAGCGTTTAGATCACTAGAGTAGT 58.649 40.000 0.00 0.00 37.82 2.73
437 487 6.854496 AGAGCGTTTAGATCACTAGAGTAG 57.146 41.667 0.00 0.00 37.82 2.57
438 488 8.905660 ATAAGAGCGTTTAGATCACTAGAGTA 57.094 34.615 0.00 0.00 37.82 2.59
439 489 7.811117 ATAAGAGCGTTTAGATCACTAGAGT 57.189 36.000 0.00 0.00 37.82 3.24
453 503 9.490379 CCCTCTGTAAATAAATATAAGAGCGTT 57.510 33.333 0.00 0.00 0.00 4.84
454 504 8.867097 TCCCTCTGTAAATAAATATAAGAGCGT 58.133 33.333 0.00 0.00 0.00 5.07
455 505 9.877178 ATCCCTCTGTAAATAAATATAAGAGCG 57.123 33.333 0.00 0.00 0.00 5.03
467 517 8.701895 CCAAGTGTAGTAATCCCTCTGTAAATA 58.298 37.037 0.00 0.00 0.00 1.40
468 518 7.565680 CCAAGTGTAGTAATCCCTCTGTAAAT 58.434 38.462 0.00 0.00 0.00 1.40
469 519 6.575649 GCCAAGTGTAGTAATCCCTCTGTAAA 60.576 42.308 0.00 0.00 0.00 2.01
470 520 5.105064 GCCAAGTGTAGTAATCCCTCTGTAA 60.105 44.000 0.00 0.00 0.00 2.41
471 521 4.404715 GCCAAGTGTAGTAATCCCTCTGTA 59.595 45.833 0.00 0.00 0.00 2.74
472 522 3.197983 GCCAAGTGTAGTAATCCCTCTGT 59.802 47.826 0.00 0.00 0.00 3.41
473 523 3.197766 TGCCAAGTGTAGTAATCCCTCTG 59.802 47.826 0.00 0.00 0.00 3.35
474 524 3.450904 TGCCAAGTGTAGTAATCCCTCT 58.549 45.455 0.00 0.00 0.00 3.69
475 525 3.906720 TGCCAAGTGTAGTAATCCCTC 57.093 47.619 0.00 0.00 0.00 4.30
476 526 4.650972 TTTGCCAAGTGTAGTAATCCCT 57.349 40.909 0.00 0.00 0.00 4.20
477 527 5.715434 TTTTTGCCAAGTGTAGTAATCCC 57.285 39.130 0.00 0.00 0.00 3.85
501 551 0.455295 GTCGACGCTCTCCTTCTGTG 60.455 60.000 0.00 0.00 0.00 3.66
511 561 2.264109 TTCTCTTGATGTCGACGCTC 57.736 50.000 11.62 10.79 0.00 5.03
525 578 7.516198 ACTTTGTGTTGCATTATCTTTCTCT 57.484 32.000 0.00 0.00 0.00 3.10
537 590 3.428725 CCAGTGCTTTACTTTGTGTTGCA 60.429 43.478 0.00 0.00 37.60 4.08
541 594 3.886123 AGACCAGTGCTTTACTTTGTGT 58.114 40.909 0.00 0.00 37.60 3.72
557 610 4.035558 GCAATTCGCATCTCATTAAGACCA 59.964 41.667 0.00 0.00 41.79 4.02
580 633 1.875963 GGGCGGTTGTGTTGATGAG 59.124 57.895 0.00 0.00 0.00 2.90
669 725 1.351017 GGGATCTGTGGTTGGAGTTGA 59.649 52.381 0.00 0.00 0.00 3.18
752 808 2.681848 GAGAGAAACATGCATGGACAGG 59.318 50.000 29.41 4.72 0.00 4.00
776 832 1.202428 CGGGAAACACTAGCCTAGCTC 60.202 57.143 0.00 0.00 40.44 4.09
853 909 5.313280 TGGTCTTTTCTTGGTTTAGGCTA 57.687 39.130 0.00 0.00 0.00 3.93
966 1038 1.367471 GACATGGATCGATCGGGCA 59.633 57.895 18.81 11.80 0.00 5.36
989 1061 1.375396 TTGGTCATGGAACGCTCCG 60.375 57.895 0.00 0.00 45.85 4.63
1029 1101 0.397816 CGGAGGTGGGAGAAGAGGAT 60.398 60.000 0.00 0.00 0.00 3.24
1050 1125 1.421410 CTTCGTACTGGCGATGGTGC 61.421 60.000 0.00 0.00 40.76 5.01
1113 1191 0.872388 GAAACGAAATGCCGTGGTCT 59.128 50.000 0.00 0.00 42.54 3.85
1136 1214 1.437772 CTCGACGTCGTCTATGGCCT 61.438 60.000 34.40 0.00 40.80 5.19
1141 1219 2.532256 CGCCCTCGACGTCGTCTAT 61.532 63.158 34.40 0.00 40.80 1.98
2242 2320 1.274703 ACTGGATCGGAATGGGCAGT 61.275 55.000 0.00 0.00 0.00 4.40
2253 2331 1.347097 CTCACACGCACACTGGATCG 61.347 60.000 0.00 0.00 0.00 3.69
2256 2334 1.106944 TCTCTCACACGCACACTGGA 61.107 55.000 0.00 0.00 0.00 3.86
2387 2491 9.505995 GGAACGAGTAACAAAATAAAAAGAACA 57.494 29.630 0.00 0.00 0.00 3.18
2388 2492 9.726232 AGGAACGAGTAACAAAATAAAAAGAAC 57.274 29.630 0.00 0.00 0.00 3.01
2389 2493 9.724839 CAGGAACGAGTAACAAAATAAAAAGAA 57.275 29.630 0.00 0.00 0.00 2.52
2390 2494 9.111613 TCAGGAACGAGTAACAAAATAAAAAGA 57.888 29.630 0.00 0.00 0.00 2.52
2391 2495 9.166126 GTCAGGAACGAGTAACAAAATAAAAAG 57.834 33.333 0.00 0.00 0.00 2.27
2392 2496 8.675504 TGTCAGGAACGAGTAACAAAATAAAAA 58.324 29.630 0.00 0.00 0.00 1.94
2393 2497 8.211116 TGTCAGGAACGAGTAACAAAATAAAA 57.789 30.769 0.00 0.00 0.00 1.52
2404 2508 7.972832 ACATAAAAATTGTCAGGAACGAGTA 57.027 32.000 0.00 0.00 0.00 2.59
2507 2611 8.498054 AATATGAGATTCATTTCAACGTGAGT 57.502 30.769 0.00 0.00 41.79 3.41
2535 2639 8.117988 GCACGATATCAAAATTACTTTCCGTTA 58.882 33.333 3.12 0.00 0.00 3.18
2536 2640 6.964934 GCACGATATCAAAATTACTTTCCGTT 59.035 34.615 3.12 0.00 0.00 4.44
2559 2663 1.001487 CACAAAATCTGCCTTCGTGCA 60.001 47.619 0.00 0.00 39.37 4.57
2567 2797 5.001232 TGGACTAGTTACACAAAATCTGCC 58.999 41.667 0.00 0.00 0.00 4.85
2613 2843 8.421002 TCTTCTTCTGGGGAAAACAATAAAAAG 58.579 33.333 0.00 0.00 0.00 2.27
2614 2844 8.312669 TCTTCTTCTGGGGAAAACAATAAAAA 57.687 30.769 0.00 0.00 0.00 1.94
2629 2861 6.094048 TGCGAAGGAATTATTTCTTCTTCTGG 59.906 38.462 20.03 8.37 32.41 3.86
2630 2862 7.076842 TGCGAAGGAATTATTTCTTCTTCTG 57.923 36.000 20.03 8.67 32.41 3.02
2632 2864 8.742554 TTTTGCGAAGGAATTATTTCTTCTTC 57.257 30.769 20.03 13.41 37.93 2.87
2690 3474 1.272092 TGGATGAGCTTTCCCCAAGTG 60.272 52.381 12.65 0.00 34.56 3.16
2748 3532 7.375106 CTTGAGCAAGTACTCATTTGAATCT 57.625 36.000 0.00 0.00 45.75 2.40
2791 3575 9.821662 GTGACCTAAGACAACACAATTTTATAC 57.178 33.333 0.00 0.00 0.00 1.47
2800 3584 5.995282 CCTTATTGTGACCTAAGACAACACA 59.005 40.000 0.00 0.00 39.22 3.72
2803 3587 5.801380 TCCCTTATTGTGACCTAAGACAAC 58.199 41.667 4.24 0.00 34.98 3.32
2806 3590 5.990668 ACATCCCTTATTGTGACCTAAGAC 58.009 41.667 4.24 0.00 0.00 3.01
2825 3609 6.595326 TCACCAGAAACTCATAACATGACATC 59.405 38.462 0.00 0.00 35.06 3.06
2833 3617 6.801539 TGTCAATCACCAGAAACTCATAAC 57.198 37.500 0.00 0.00 0.00 1.89
2834 3618 9.166173 CTAATGTCAATCACCAGAAACTCATAA 57.834 33.333 0.00 0.00 0.00 1.90
2835 3619 8.321353 ACTAATGTCAATCACCAGAAACTCATA 58.679 33.333 0.00 0.00 0.00 2.15
2836 3620 7.170965 ACTAATGTCAATCACCAGAAACTCAT 58.829 34.615 0.00 0.00 0.00 2.90
2837 3621 6.533730 ACTAATGTCAATCACCAGAAACTCA 58.466 36.000 0.00 0.00 0.00 3.41
2838 3622 8.723942 ATACTAATGTCAATCACCAGAAACTC 57.276 34.615 0.00 0.00 0.00 3.01
2839 3623 9.520515 AAATACTAATGTCAATCACCAGAAACT 57.479 29.630 0.00 0.00 0.00 2.66
2840 3624 9.774742 GAAATACTAATGTCAATCACCAGAAAC 57.225 33.333 0.00 0.00 0.00 2.78
2841 3625 9.513906 TGAAATACTAATGTCAATCACCAGAAA 57.486 29.630 0.00 0.00 0.00 2.52
2842 3626 9.685276 ATGAAATACTAATGTCAATCACCAGAA 57.315 29.630 0.00 0.00 32.96 3.02
2929 3713 2.617532 GCCATCCACTCTCTCTGCTTTT 60.618 50.000 0.00 0.00 0.00 2.27
2930 3714 1.065564 GCCATCCACTCTCTCTGCTTT 60.066 52.381 0.00 0.00 0.00 3.51
2931 3715 0.540923 GCCATCCACTCTCTCTGCTT 59.459 55.000 0.00 0.00 0.00 3.91
2932 3716 1.674764 CGCCATCCACTCTCTCTGCT 61.675 60.000 0.00 0.00 0.00 4.24
2938 3722 0.729690 GCTTTTCGCCATCCACTCTC 59.270 55.000 0.00 0.00 0.00 3.20
2940 3724 2.024176 TAGCTTTTCGCCATCCACTC 57.976 50.000 0.00 0.00 40.39 3.51
2944 3728 4.335594 AGTGTTTATAGCTTTTCGCCATCC 59.664 41.667 0.00 0.00 40.39 3.51
2945 3729 5.485662 AGTGTTTATAGCTTTTCGCCATC 57.514 39.130 0.00 0.00 40.39 3.51
2974 3758 2.424557 GAGGTTTCGACCTTCCCTTTC 58.575 52.381 0.00 0.00 40.86 2.62
2975 3759 1.073444 GGAGGTTTCGACCTTCCCTTT 59.927 52.381 0.00 0.00 40.86 3.11
2976 3760 0.691332 GGAGGTTTCGACCTTCCCTT 59.309 55.000 0.00 0.00 40.86 3.95
2978 3762 0.036294 CTGGAGGTTTCGACCTTCCC 60.036 60.000 9.23 2.91 40.86 3.97
2986 3772 1.308069 CCATGTGCCTGGAGGTTTCG 61.308 60.000 0.00 0.00 38.69 3.46
2996 3782 1.983691 CATCCTAGGATCCATGTGCCT 59.016 52.381 22.02 0.00 35.82 4.75
3001 3787 1.066573 GGTCGCATCCTAGGATCCATG 60.067 57.143 22.02 13.29 31.62 3.66
3035 3821 2.533266 ATCGCCGCTTCACATCTATT 57.467 45.000 0.00 0.00 0.00 1.73
3039 3825 3.217599 TCTATATCGCCGCTTCACATC 57.782 47.619 0.00 0.00 0.00 3.06
3045 3831 8.324163 AGATTTATTTTTCTATATCGCCGCTT 57.676 30.769 0.00 0.00 0.00 4.68
3095 3881 2.902608 TCCTCCATAGTTGTCCACTGT 58.097 47.619 0.00 0.00 35.97 3.55
3096 3882 3.600388 GTTCCTCCATAGTTGTCCACTG 58.400 50.000 0.00 0.00 35.97 3.66
3097 3883 2.572104 GGTTCCTCCATAGTTGTCCACT 59.428 50.000 0.00 0.00 36.43 4.00
3098 3884 2.304761 TGGTTCCTCCATAGTTGTCCAC 59.695 50.000 0.00 0.00 41.93 4.02
3099 3885 2.626785 TGGTTCCTCCATAGTTGTCCA 58.373 47.619 0.00 0.00 41.93 4.02
3112 3898 7.060421 TGTTCTTAATCTTTCTTGTGGTTCCT 58.940 34.615 0.00 0.00 0.00 3.36
3113 3899 7.272037 TGTTCTTAATCTTTCTTGTGGTTCC 57.728 36.000 0.00 0.00 0.00 3.62
3114 3900 9.581099 TTTTGTTCTTAATCTTTCTTGTGGTTC 57.419 29.630 0.00 0.00 0.00 3.62
3153 3939 5.280676 GGCATACTTCATGGGAGGAATATCA 60.281 44.000 0.00 0.00 34.97 2.15
3166 3952 0.179045 GGCGTGAGGGCATACTTCAT 60.179 55.000 0.00 0.00 41.77 2.57
3195 3981 0.912486 AACCTACATGAGCTGGACCC 59.088 55.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.