Multiple sequence alignment - TraesCS6D01G301100

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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 TraesCS6D01G301100 chr6D 100.000 3769 0 0 1 3769 410830113 410826345 0.000000e+00 6961
1 TraesCS6D01G301100 chr6B 87.810 3954 166 130 2 3769 617647481 617643658 0.000000e+00 4340
2 TraesCS6D01G301100 chr6A 87.466 3295 170 95 491 3645 555754390 555751199 0.000000e+00 3572
3 TraesCS6D01G301100 chr6A 89.139 267 9 5 78 344 555754692 555754446 7.860000e-82 315
4 TraesCS6D01G301100 chr6A 91.489 141 8 1 3631 3767 555751178 555751038 1.380000e-44 191
5 TraesCS6D01G301100 chr2B 94.690 113 6 0 1532 1644 682194110 682194222 3.870000e-40 176


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 TraesCS6D01G301100 chr6D 410826345 410830113 3768 True 6961.000000 6961 100.000000 1 3769 1 chr6D.!!$R1 3768
1 TraesCS6D01G301100 chr6B 617643658 617647481 3823 True 4340.000000 4340 87.810000 2 3769 1 chr6B.!!$R1 3767
2 TraesCS6D01G301100 chr6A 555751038 555754692 3654 True 1359.333333 3572 89.364667 78 3767 3 chr6A.!!$R1 3689

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
487 532 0.107410 TGTCCCTTGCACACGTCTTT 60.107 50.0 0.00 0.0 0.0 2.52 F
1181 1285 0.106335 TTTCCAGAACGCCGTTACCA 59.894 50.0 0.79 0.0 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 1453 0.034574 TATGATGCCGCTGGGTTGTT 60.035 50.0 0.0 0.0 34.97 2.83 R
3005 3219 0.108138 AGCTACCCAACGATCTGCAC 60.108 55.0 0.0 0.0 0.00 4.57 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
71 72 4.379143 CGGTGTCGTCGTCGCTCA 62.379 66.667 0.00 0.00 36.96 4.26
125 140 1.153568 ATGCATCCACCAGTCGTCG 60.154 57.895 0.00 0.00 0.00 5.12
242 267 3.231736 ACCCACCGAACTCACGCT 61.232 61.111 0.00 0.00 0.00 5.07
263 288 4.028490 CGCCTGTGCCAAGGGGTA 62.028 66.667 9.88 0.00 43.52 3.69
277 305 1.912264 GGGTAGTAGATCCGGGGGC 60.912 68.421 0.00 0.00 0.00 5.80
326 354 2.994995 ACCTGCGATGTCGTCCCA 60.995 61.111 4.20 0.00 42.22 4.37
340 368 0.678048 GTCCCACGTACGGTACTCCT 60.678 60.000 21.06 0.00 0.00 3.69
341 369 0.677731 TCCCACGTACGGTACTCCTG 60.678 60.000 21.06 6.51 0.00 3.86
344 389 1.672356 ACGTACGGTACTCCTGCGT 60.672 57.895 21.06 5.23 32.41 5.24
346 391 0.109597 CGTACGGTACTCCTGCGTTT 60.110 55.000 15.69 0.00 0.00 3.60
347 392 1.343506 GTACGGTACTCCTGCGTTTG 58.656 55.000 10.99 0.00 0.00 2.93
349 394 0.606604 ACGGTACTCCTGCGTTTGAT 59.393 50.000 0.00 0.00 0.00 2.57
352 397 2.093783 CGGTACTCCTGCGTTTGATTTC 59.906 50.000 0.00 0.00 0.00 2.17
356 401 4.918810 ACTCCTGCGTTTGATTTCTTTT 57.081 36.364 0.00 0.00 0.00 2.27
357 402 5.262588 ACTCCTGCGTTTGATTTCTTTTT 57.737 34.783 0.00 0.00 0.00 1.94
378 423 4.710695 CGCTACACGGTCGGCACA 62.711 66.667 0.00 0.00 38.44 4.57
379 424 2.125673 GCTACACGGTCGGCACAT 60.126 61.111 0.00 0.00 0.00 3.21
380 425 2.452813 GCTACACGGTCGGCACATG 61.453 63.158 0.00 0.00 0.00 3.21
381 426 1.080093 CTACACGGTCGGCACATGT 60.080 57.895 0.00 0.00 0.00 3.21
382 427 1.351430 CTACACGGTCGGCACATGTG 61.351 60.000 21.83 21.83 36.80 3.21
397 442 5.327502 CACATGTGTGTTACAAAAATGCC 57.672 39.130 18.03 0.00 43.77 4.40
399 444 5.523188 CACATGTGTGTTACAAAAATGCCTT 59.477 36.000 18.03 0.00 43.77 4.35
400 445 5.523188 ACATGTGTGTTACAAAAATGCCTTG 59.477 36.000 5.63 0.00 43.77 3.61
403 448 6.631016 TGTGTGTTACAAAAATGCCTTGTTA 58.369 32.000 0.00 0.00 38.05 2.41
408 453 4.414337 ACAAAAATGCCTTGTTAGCCAA 57.586 36.364 0.00 0.00 33.16 4.52
411 456 2.309136 AATGCCTTGTTAGCCAACCT 57.691 45.000 0.00 0.00 33.41 3.50
415 460 0.251341 CCTTGTTAGCCAACCTGCCT 60.251 55.000 0.00 0.00 33.41 4.75
416 461 0.883833 CTTGTTAGCCAACCTGCCTG 59.116 55.000 0.00 0.00 33.41 4.85
417 462 1.178534 TTGTTAGCCAACCTGCCTGC 61.179 55.000 0.00 0.00 33.41 4.85
418 463 2.035626 TTAGCCAACCTGCCTGCC 59.964 61.111 0.00 0.00 0.00 4.85
419 464 3.918253 TTAGCCAACCTGCCTGCCG 62.918 63.158 0.00 0.00 0.00 5.69
425 470 1.149627 AACCTGCCTGCCGTTACAA 59.850 52.632 0.00 0.00 0.00 2.41
435 480 1.202952 TGCCGTTACAAATTCCCTGGT 60.203 47.619 0.00 0.00 0.00 4.00
437 482 1.201414 CCGTTACAAATTCCCTGGTGC 59.799 52.381 0.00 0.00 0.00 5.01
438 483 1.135803 CGTTACAAATTCCCTGGTGCG 60.136 52.381 0.00 0.00 0.00 5.34
439 484 0.885196 TTACAAATTCCCTGGTGCGC 59.115 50.000 0.00 0.00 0.00 6.09
440 485 1.302383 TACAAATTCCCTGGTGCGCG 61.302 55.000 0.00 0.00 0.00 6.86
441 486 2.033448 AAATTCCCTGGTGCGCGA 59.967 55.556 12.10 0.00 0.00 5.87
442 487 2.332654 AAATTCCCTGGTGCGCGAC 61.333 57.895 12.10 5.05 0.00 5.19
443 488 4.778143 ATTCCCTGGTGCGCGACC 62.778 66.667 12.10 15.62 46.37 4.79
447 492 4.680237 CCTGGTGCGCGACCTGAA 62.680 66.667 25.92 10.66 46.32 3.02
448 493 2.434884 CTGGTGCGCGACCTGAAT 60.435 61.111 23.38 0.00 46.32 2.57
476 521 2.448926 TGTCACGTACATGTCCCTTG 57.551 50.000 0.00 0.00 31.43 3.61
477 522 1.076332 GTCACGTACATGTCCCTTGC 58.924 55.000 0.00 0.00 0.00 4.01
478 523 0.682292 TCACGTACATGTCCCTTGCA 59.318 50.000 0.00 0.00 0.00 4.08
479 524 0.796312 CACGTACATGTCCCTTGCAC 59.204 55.000 0.00 0.00 0.00 4.57
480 525 0.394938 ACGTACATGTCCCTTGCACA 59.605 50.000 0.00 0.00 0.00 4.57
481 526 0.796312 CGTACATGTCCCTTGCACAC 59.204 55.000 0.00 0.00 0.00 3.82
482 527 0.796312 GTACATGTCCCTTGCACACG 59.204 55.000 0.00 0.00 0.00 4.49
483 528 0.394938 TACATGTCCCTTGCACACGT 59.605 50.000 0.00 0.00 0.00 4.49
484 529 0.884704 ACATGTCCCTTGCACACGTC 60.885 55.000 0.00 0.00 0.00 4.34
485 530 0.603707 CATGTCCCTTGCACACGTCT 60.604 55.000 0.00 0.00 0.00 4.18
486 531 0.108585 ATGTCCCTTGCACACGTCTT 59.891 50.000 0.00 0.00 0.00 3.01
487 532 0.107410 TGTCCCTTGCACACGTCTTT 60.107 50.000 0.00 0.00 0.00 2.52
488 533 1.021968 GTCCCTTGCACACGTCTTTT 58.978 50.000 0.00 0.00 0.00 2.27
489 534 1.002792 GTCCCTTGCACACGTCTTTTC 60.003 52.381 0.00 0.00 0.00 2.29
493 538 0.380378 TTGCACACGTCTTTTCCTGC 59.620 50.000 0.00 0.00 0.00 4.85
512 557 1.799994 GCACACATTTGCCATTTCACC 59.200 47.619 0.00 0.00 36.42 4.02
517 562 3.919804 CACATTTGCCATTTCACCTAACG 59.080 43.478 0.00 0.00 0.00 3.18
519 564 1.540267 TTGCCATTTCACCTAACGGG 58.460 50.000 0.00 0.00 41.89 5.28
583 629 1.138036 CGGCGATCCTCGTACACAA 59.862 57.895 0.00 0.00 42.81 3.33
623 669 1.995484 CTCACATCATCACGTGTGGAC 59.005 52.381 16.51 0.00 44.41 4.02
624 670 1.078709 CACATCATCACGTGTGGACC 58.921 55.000 16.51 0.00 41.46 4.46
691 746 0.329596 GAAAGCAGATCAGGGGGTGT 59.670 55.000 0.00 0.00 0.00 4.16
784 849 0.875059 GGGAAGCCTTTCGACAGTTG 59.125 55.000 0.00 0.00 33.98 3.16
817 882 4.052229 GCAGTTGCAGGGCAGCAG 62.052 66.667 7.76 0.72 46.54 4.24
818 883 2.281970 CAGTTGCAGGGCAGCAGA 60.282 61.111 7.76 0.00 46.54 4.26
819 884 1.900016 CAGTTGCAGGGCAGCAGAA 60.900 57.895 7.76 0.00 46.54 3.02
834 899 0.764890 CAGAACAGAACCCACCCAGA 59.235 55.000 0.00 0.00 0.00 3.86
835 900 0.765510 AGAACAGAACCCACCCAGAC 59.234 55.000 0.00 0.00 0.00 3.51
838 903 2.153401 CAGAACCCACCCAGACCCA 61.153 63.158 0.00 0.00 0.00 4.51
839 904 1.847968 AGAACCCACCCAGACCCAG 60.848 63.158 0.00 0.00 0.00 4.45
955 1042 0.393808 GCAACGGCCCTCTCCAAATA 60.394 55.000 0.00 0.00 0.00 1.40
969 1056 3.181397 TCCAAATACGAACGTCGAATCC 58.819 45.455 13.06 0.00 43.74 3.01
970 1057 2.283351 CCAAATACGAACGTCGAATCCC 59.717 50.000 13.06 0.00 43.74 3.85
971 1058 2.924926 CAAATACGAACGTCGAATCCCA 59.075 45.455 13.06 0.00 43.74 4.37
972 1059 2.945447 ATACGAACGTCGAATCCCAA 57.055 45.000 13.06 0.00 43.74 4.12
973 1060 1.981254 TACGAACGTCGAATCCCAAC 58.019 50.000 13.06 0.00 43.74 3.77
1024 1123 3.448301 TGCCATCAGTTTCAAATCCATCC 59.552 43.478 0.00 0.00 0.00 3.51
1181 1285 0.106335 TTTCCAGAACGCCGTTACCA 59.894 50.000 0.79 0.00 0.00 3.25
1187 1291 1.202557 AGAACGCCGTTACCAACTCAA 60.203 47.619 0.79 0.00 0.00 3.02
1336 1449 1.946745 GAGAGAATCCAAAGGGCGAG 58.053 55.000 0.00 0.00 33.66 5.03
1337 1450 0.107459 AGAGAATCCAAAGGGCGAGC 60.107 55.000 0.00 0.00 33.66 5.03
1338 1451 1.077429 AGAATCCAAAGGGCGAGCC 60.077 57.895 5.37 5.37 0.00 4.70
1339 1452 2.438434 AATCCAAAGGGCGAGCCG 60.438 61.111 8.14 0.00 36.85 5.52
1340 1453 2.869503 GAATCCAAAGGGCGAGCCGA 62.870 60.000 8.14 0.00 36.85 5.54
1341 1454 2.478335 AATCCAAAGGGCGAGCCGAA 62.478 55.000 8.14 0.00 36.85 4.30
1874 2000 4.717778 TCCAAACCCTAGAATTCGGATACA 59.282 41.667 5.02 0.00 0.00 2.29
2022 2150 1.373570 CTGTCTCCGGCCAATTCTTC 58.626 55.000 2.24 0.00 0.00 2.87
2023 2151 0.035439 TGTCTCCGGCCAATTCTTCC 60.035 55.000 2.24 0.00 0.00 3.46
2033 2161 3.068024 GGCCAATTCTTCCGAATTATGCA 59.932 43.478 0.00 0.00 45.57 3.96
2038 2177 6.430925 CCAATTCTTCCGAATTATGCATCCTA 59.569 38.462 0.19 0.00 45.57 2.94
2062 2201 2.742372 TCCCGCTCGCTGCTTTTC 60.742 61.111 0.00 0.00 40.11 2.29
2291 2430 3.181529 GCTTCGCTTGCAAGTAAGTACTC 60.182 47.826 28.78 17.16 34.99 2.59
2292 2431 2.955614 TCGCTTGCAAGTAAGTACTCC 58.044 47.619 26.55 6.59 34.99 3.85
2293 2432 2.561419 TCGCTTGCAAGTAAGTACTCCT 59.439 45.455 26.55 0.00 34.99 3.69
2294 2433 3.760151 TCGCTTGCAAGTAAGTACTCCTA 59.240 43.478 26.55 0.00 34.99 2.94
2360 2499 0.458889 TCGCCGGAATTCTAACGTGG 60.459 55.000 5.05 0.00 0.00 4.94
2370 2509 3.361281 TTCTAACGTGGGAGCTCTCTA 57.639 47.619 16.21 0.00 0.00 2.43
2371 2510 2.641305 TCTAACGTGGGAGCTCTCTAC 58.359 52.381 16.21 11.37 0.00 2.59
2612 2768 5.445964 CATTATAGCCTAACCAACCAACCT 58.554 41.667 0.00 0.00 0.00 3.50
2676 2835 6.514012 TCACATATTCCCACCATTATCACT 57.486 37.500 0.00 0.00 0.00 3.41
2683 2842 3.016736 CCCACCATTATCACTTCACACC 58.983 50.000 0.00 0.00 0.00 4.16
2716 2889 2.091102 TTTTTCCCAGCAGCAGCAGC 62.091 55.000 3.17 0.46 45.49 5.25
2745 2919 7.901029 AGTTTTACTTCCCTACTGGTACTTAC 58.099 38.462 0.00 0.00 34.77 2.34
2746 2920 7.732140 AGTTTTACTTCCCTACTGGTACTTACT 59.268 37.037 0.00 0.00 34.77 2.24
2748 2922 5.997384 ACTTCCCTACTGGTACTTACTTG 57.003 43.478 0.00 0.00 34.77 3.16
2749 2923 5.400870 ACTTCCCTACTGGTACTTACTTGT 58.599 41.667 0.00 0.00 34.77 3.16
2750 2924 5.842874 ACTTCCCTACTGGTACTTACTTGTT 59.157 40.000 0.00 0.00 34.77 2.83
2751 2925 5.990120 TCCCTACTGGTACTTACTTGTTC 57.010 43.478 0.00 0.00 34.77 3.18
2752 2926 5.396485 TCCCTACTGGTACTTACTTGTTCA 58.604 41.667 0.00 0.00 34.77 3.18
2753 2927 6.021030 TCCCTACTGGTACTTACTTGTTCAT 58.979 40.000 0.00 0.00 34.77 2.57
2754 2928 6.154021 TCCCTACTGGTACTTACTTGTTCATC 59.846 42.308 0.00 0.00 34.77 2.92
2755 2929 6.070995 CCCTACTGGTACTTACTTGTTCATCA 60.071 42.308 0.00 0.00 0.00 3.07
2756 2930 7.036220 CCTACTGGTACTTACTTGTTCATCAG 58.964 42.308 0.00 0.00 0.00 2.90
2757 2931 6.665992 ACTGGTACTTACTTGTTCATCAGA 57.334 37.500 0.00 0.00 0.00 3.27
2758 2932 6.692486 ACTGGTACTTACTTGTTCATCAGAG 58.308 40.000 0.00 0.00 0.00 3.35
2761 2935 5.800941 GGTACTTACTTGTTCATCAGAGTCG 59.199 44.000 0.00 0.00 0.00 4.18
2764 2938 3.735237 ACTTGTTCATCAGAGTCGTGT 57.265 42.857 0.00 0.00 0.00 4.49
2774 2948 2.628178 TCAGAGTCGTGTTTGACAGGAT 59.372 45.455 6.73 0.00 43.65 3.24
2775 2949 3.824443 TCAGAGTCGTGTTTGACAGGATA 59.176 43.478 6.73 0.00 43.65 2.59
2780 2954 4.707448 AGTCGTGTTTGACAGGATAGATCT 59.293 41.667 0.00 0.00 43.65 2.75
2812 2990 6.932947 AGTCCCTTACTGTAATTGTCACTAC 58.067 40.000 0.00 0.00 36.93 2.73
2813 2991 6.070938 AGTCCCTTACTGTAATTGTCACTACC 60.071 42.308 0.00 0.00 36.93 3.18
2997 3203 2.490903 CTGGTCCTGCAAGAAGAAATGG 59.509 50.000 0.00 0.00 34.07 3.16
2999 3205 3.245371 TGGTCCTGCAAGAAGAAATGGAT 60.245 43.478 0.00 0.00 34.07 3.41
3005 3219 5.327091 CTGCAAGAAGAAATGGATACGTTG 58.673 41.667 0.00 0.00 40.70 4.10
3088 3308 1.961277 ACGGAAACAGCTTCGGCAG 60.961 57.895 0.00 0.00 44.74 4.85
3195 3422 3.650298 GAGGCTTCCATGGCAGGCA 62.650 63.158 33.38 3.17 38.05 4.75
3197 3424 3.145551 GCTTCCATGGCAGGCAGG 61.146 66.667 13.60 1.28 0.00 4.85
3198 3425 3.145551 CTTCCATGGCAGGCAGGC 61.146 66.667 6.96 0.00 44.50 4.85
3229 3456 3.243128 GCCGTGGAAAGAAGGCTTA 57.757 52.632 0.00 0.00 45.67 3.09
3236 3463 1.683319 GGAAAGAAGGCTTAGCTGGGG 60.683 57.143 3.59 0.00 32.98 4.96
3325 3553 0.108281 GAGGGAAGTTACCGCTGTCC 60.108 60.000 0.00 0.00 0.00 4.02
3440 3685 3.262142 TAAACAAAGCGCCGCTGGC 62.262 57.895 14.52 9.20 46.75 4.85
3493 3738 2.677524 CACGGTGGGAGACGGGTA 60.678 66.667 0.00 0.00 0.00 3.69
3494 3739 2.362120 ACGGTGGGAGACGGGTAG 60.362 66.667 0.00 0.00 0.00 3.18
3495 3740 3.145551 CGGTGGGAGACGGGTAGG 61.146 72.222 0.00 0.00 0.00 3.18
3565 3818 5.936372 GTCAGTAGGTTGGTAAAAACTAGGG 59.064 44.000 0.00 0.00 0.00 3.53
3581 3834 1.074471 GGGGTAGGATGGGAGCAGA 60.074 63.158 0.00 0.00 0.00 4.26
3691 3987 3.465742 TGCTGGCTTTAATTTTGCACA 57.534 38.095 0.00 0.00 0.00 4.57
3752 4048 0.252197 ACCTCGCCTCATTGGTAACC 59.748 55.000 0.00 0.00 38.35 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.550606 GTGTTACACCGCAAAGATCCAA 59.449 45.455 3.79 0.00 0.00 3.53
13 14 4.506288 GGTTTTGGATGCTTTGTGTTACAC 59.494 41.667 8.76 8.76 34.56 2.90
14 15 4.160439 TGGTTTTGGATGCTTTGTGTTACA 59.840 37.500 0.00 0.00 0.00 2.41
56 57 2.152699 CCATGAGCGACGACGACAC 61.153 63.158 12.29 2.11 42.66 3.67
71 72 1.221840 GCCTGGTCGTGTGATCCAT 59.778 57.895 0.00 0.00 0.00 3.41
109 114 1.940883 TACCGACGACTGGTGGATGC 61.941 60.000 0.00 0.00 40.73 3.91
125 140 4.499019 CCACGGTGATATTTTTGGCATACC 60.499 45.833 10.28 0.00 0.00 2.73
219 242 1.292541 GAGTTCGGTGGGTGGAGTC 59.707 63.158 0.00 0.00 0.00 3.36
252 277 1.802553 GGATCTACTACCCCTTGGCA 58.197 55.000 0.00 0.00 33.59 4.92
253 278 0.680061 CGGATCTACTACCCCTTGGC 59.320 60.000 0.00 0.00 33.59 4.52
262 287 1.463824 GAGGCCCCCGGATCTACTA 59.536 63.158 0.73 0.00 0.00 1.82
263 288 2.201771 GAGGCCCCCGGATCTACT 59.798 66.667 0.73 0.00 0.00 2.57
326 354 1.237285 AACGCAGGAGTACCGTACGT 61.237 55.000 15.21 5.08 42.24 3.57
356 401 2.311701 CCGACCGTGTAGCGCAAAA 61.312 57.895 11.47 0.00 39.71 2.44
357 402 2.735478 CCGACCGTGTAGCGCAAA 60.735 61.111 11.47 0.00 39.71 3.68
363 408 1.080093 ACATGTGCCGACCGTGTAG 60.080 57.895 0.00 0.00 0.00 2.74
376 421 5.275067 AGGCATTTTTGTAACACACATGT 57.725 34.783 0.00 0.00 42.46 3.21
377 422 5.523188 ACAAGGCATTTTTGTAACACACATG 59.477 36.000 0.00 0.00 37.02 3.21
378 423 5.669477 ACAAGGCATTTTTGTAACACACAT 58.331 33.333 0.00 0.00 37.02 3.21
379 424 5.078411 ACAAGGCATTTTTGTAACACACA 57.922 34.783 0.00 0.00 37.02 3.72
380 425 6.292114 GCTAACAAGGCATTTTTGTAACACAC 60.292 38.462 0.00 0.00 37.77 3.82
381 426 5.751028 GCTAACAAGGCATTTTTGTAACACA 59.249 36.000 0.00 0.00 37.77 3.72
382 427 5.176774 GGCTAACAAGGCATTTTTGTAACAC 59.823 40.000 0.00 0.00 37.77 3.32
384 429 5.293560 TGGCTAACAAGGCATTTTTGTAAC 58.706 37.500 0.00 0.00 37.77 2.50
386 431 5.293560 GTTGGCTAACAAGGCATTTTTGTA 58.706 37.500 8.23 0.00 43.87 2.41
388 433 3.498018 GGTTGGCTAACAAGGCATTTTTG 59.502 43.478 15.34 0.00 43.87 2.44
390 435 2.972021 AGGTTGGCTAACAAGGCATTTT 59.028 40.909 15.34 0.00 43.87 1.82
391 436 2.299867 CAGGTTGGCTAACAAGGCATTT 59.700 45.455 15.34 0.00 43.87 2.32
392 437 1.895131 CAGGTTGGCTAACAAGGCATT 59.105 47.619 15.34 0.00 43.87 3.56
394 439 1.178534 GCAGGTTGGCTAACAAGGCA 61.179 55.000 15.34 0.00 40.38 4.75
395 440 1.586541 GCAGGTTGGCTAACAAGGC 59.413 57.895 15.34 10.62 40.38 4.35
408 453 0.251165 ATTTGTAACGGCAGGCAGGT 60.251 50.000 0.00 0.00 0.00 4.00
411 456 0.885196 GGAATTTGTAACGGCAGGCA 59.115 50.000 0.00 0.00 0.00 4.75
415 460 1.202952 ACCAGGGAATTTGTAACGGCA 60.203 47.619 0.00 0.00 0.00 5.69
416 461 1.201414 CACCAGGGAATTTGTAACGGC 59.799 52.381 0.00 0.00 0.00 5.68
417 462 1.201414 GCACCAGGGAATTTGTAACGG 59.799 52.381 0.00 0.00 0.00 4.44
418 463 1.135803 CGCACCAGGGAATTTGTAACG 60.136 52.381 0.00 0.00 0.00 3.18
419 464 1.402325 GCGCACCAGGGAATTTGTAAC 60.402 52.381 0.30 0.00 0.00 2.50
420 465 0.885196 GCGCACCAGGGAATTTGTAA 59.115 50.000 0.30 0.00 0.00 2.41
421 466 1.302383 CGCGCACCAGGGAATTTGTA 61.302 55.000 8.75 0.00 0.00 2.41
425 470 2.746277 GTCGCGCACCAGGGAATT 60.746 61.111 8.75 0.00 34.84 2.17
435 480 2.557059 ATCACGATTCAGGTCGCGCA 62.557 55.000 8.75 0.00 45.12 6.09
437 482 0.525455 TGATCACGATTCAGGTCGCG 60.525 55.000 0.00 0.00 45.12 5.87
438 483 1.524355 CATGATCACGATTCAGGTCGC 59.476 52.381 0.00 0.00 45.12 5.19
439 484 2.791560 GACATGATCACGATTCAGGTCG 59.208 50.000 0.00 0.00 46.56 4.79
440 485 3.785486 TGACATGATCACGATTCAGGTC 58.215 45.455 17.97 17.97 43.00 3.85
441 486 3.893326 TGACATGATCACGATTCAGGT 57.107 42.857 0.00 0.00 29.99 4.00
476 521 0.317020 GTGCAGGAAAAGACGTGTGC 60.317 55.000 0.00 0.00 0.00 4.57
477 522 1.013596 TGTGCAGGAAAAGACGTGTG 58.986 50.000 0.00 0.00 0.00 3.82
478 523 1.014352 GTGTGCAGGAAAAGACGTGT 58.986 50.000 0.00 0.00 0.00 4.49
479 524 1.013596 TGTGTGCAGGAAAAGACGTG 58.986 50.000 0.00 0.00 0.00 4.49
480 525 1.967319 ATGTGTGCAGGAAAAGACGT 58.033 45.000 0.00 0.00 0.00 4.34
481 526 3.044986 CAAATGTGTGCAGGAAAAGACG 58.955 45.455 0.00 0.00 0.00 4.18
482 527 2.796593 GCAAATGTGTGCAGGAAAAGAC 59.203 45.455 0.00 0.00 44.29 3.01
483 528 2.224018 GGCAAATGTGTGCAGGAAAAGA 60.224 45.455 0.00 0.00 46.81 2.52
484 529 2.137523 GGCAAATGTGTGCAGGAAAAG 58.862 47.619 0.00 0.00 46.81 2.27
485 530 1.483827 TGGCAAATGTGTGCAGGAAAA 59.516 42.857 0.00 0.00 46.81 2.29
486 531 1.117994 TGGCAAATGTGTGCAGGAAA 58.882 45.000 0.00 0.00 46.81 3.13
487 532 1.340088 ATGGCAAATGTGTGCAGGAA 58.660 45.000 0.00 0.00 46.81 3.36
488 533 1.340088 AATGGCAAATGTGTGCAGGA 58.660 45.000 0.00 0.00 46.81 3.86
489 534 2.070783 GAAATGGCAAATGTGTGCAGG 58.929 47.619 0.00 0.00 46.81 4.85
493 538 3.389925 AGGTGAAATGGCAAATGTGTG 57.610 42.857 0.00 0.00 0.00 3.82
519 564 0.179243 CTTTACGCGCGGTGGTTAAC 60.179 55.000 35.22 0.00 0.00 2.01
528 574 3.849953 GGACCTGCTTTACGCGCG 61.850 66.667 30.96 30.96 43.27 6.86
529 575 2.434359 AGGACCTGCTTTACGCGC 60.434 61.111 5.73 0.00 43.27 6.86
583 629 1.600916 GGCGGTTGAAGCTGAAGGT 60.601 57.895 0.00 0.00 34.52 3.50
623 669 1.450312 GGTCTGCAATCCACTCCGG 60.450 63.158 0.00 0.00 0.00 5.14
624 670 1.450312 GGGTCTGCAATCCACTCCG 60.450 63.158 8.73 0.00 0.00 4.63
667 722 0.807667 CCCTGATCTGCTTTCGTCCG 60.808 60.000 0.00 0.00 0.00 4.79
815 880 0.764890 TCTGGGTGGGTTCTGTTCTG 59.235 55.000 0.00 0.00 0.00 3.02
817 882 0.250770 GGTCTGGGTGGGTTCTGTTC 60.251 60.000 0.00 0.00 0.00 3.18
818 883 1.716028 GGGTCTGGGTGGGTTCTGTT 61.716 60.000 0.00 0.00 0.00 3.16
819 884 2.154074 GGGTCTGGGTGGGTTCTGT 61.154 63.158 0.00 0.00 0.00 3.41
955 1042 0.668401 GGTTGGGATTCGACGTTCGT 60.668 55.000 0.00 0.00 41.35 3.85
1088 1188 2.176273 CGAGATTGCCCCTGCTTCG 61.176 63.158 0.00 0.00 38.71 3.79
1092 1192 2.514824 GGACGAGATTGCCCCTGC 60.515 66.667 0.00 0.00 38.26 4.85
1301 1414 4.304413 TCCCCCGTCCGGAGTGAA 62.304 66.667 3.06 0.00 37.50 3.18
1333 1446 3.423154 GCTGGGTTGTTCGGCTCG 61.423 66.667 0.00 0.00 33.96 5.03
1334 1447 3.423154 CGCTGGGTTGTTCGGCTC 61.423 66.667 0.00 0.00 34.56 4.70
1338 1451 3.039202 GATGCCGCTGGGTTGTTCG 62.039 63.158 0.00 0.00 34.97 3.95
1339 1452 1.315257 ATGATGCCGCTGGGTTGTTC 61.315 55.000 0.00 0.00 34.97 3.18
1340 1453 0.034574 TATGATGCCGCTGGGTTGTT 60.035 50.000 0.00 0.00 34.97 2.83
1341 1454 0.183492 ATATGATGCCGCTGGGTTGT 59.817 50.000 0.00 0.00 34.97 3.32
1431 1548 2.770904 TACTTCCCCATCGCCCCC 60.771 66.667 0.00 0.00 0.00 5.40
1874 2000 5.248640 TCAGCAAAAAGGAGATCTCGAATT 58.751 37.500 16.46 8.42 0.00 2.17
1917 2045 4.537433 GGAGCGCCTGCCTGTAGG 62.537 72.222 2.29 0.00 44.31 3.18
2022 2150 3.081804 GGGGTTAGGATGCATAATTCGG 58.918 50.000 0.00 0.00 0.00 4.30
2023 2151 2.742053 CGGGGTTAGGATGCATAATTCG 59.258 50.000 0.00 0.00 0.00 3.34
2055 2194 3.317711 TCTCGCCTGAATTTTGAAAAGCA 59.682 39.130 0.00 0.00 0.00 3.91
2062 2201 2.092838 GTCGTCTCTCGCCTGAATTTTG 59.907 50.000 0.00 0.00 39.67 2.44
2291 2430 0.175760 TCCGCTGCTGCTAAAGTAGG 59.824 55.000 14.03 5.62 38.94 3.18
2292 2431 2.010145 TTCCGCTGCTGCTAAAGTAG 57.990 50.000 14.03 0.00 41.30 2.57
2293 2432 2.465860 TTTCCGCTGCTGCTAAAGTA 57.534 45.000 14.03 0.00 36.97 2.24
2294 2433 1.826385 ATTTCCGCTGCTGCTAAAGT 58.174 45.000 14.03 2.02 36.97 2.66
2360 2499 0.465824 TACCTGGCGTAGAGAGCTCC 60.466 60.000 10.93 1.70 34.52 4.70
2370 2509 0.319297 GTCGAAGTTGTACCTGGCGT 60.319 55.000 0.00 0.00 0.00 5.68
2371 2510 1.342082 CGTCGAAGTTGTACCTGGCG 61.342 60.000 0.00 0.00 0.00 5.69
2612 2768 4.280436 AGTTGTTGATGAATCGGTGGTA 57.720 40.909 0.00 0.00 0.00 3.25
2676 2835 2.638325 TCAGGATTAAGGGGGTGTGAA 58.362 47.619 0.00 0.00 0.00 3.18
2683 2842 4.619679 TGGGAAAAATCAGGATTAAGGGG 58.380 43.478 0.00 0.00 0.00 4.79
2719 2892 9.025041 GTAAGTACCAGTAGGGAAGTAAAACTA 57.975 37.037 0.00 0.00 41.15 2.24
2745 2919 4.507756 TCAAACACGACTCTGATGAACAAG 59.492 41.667 0.00 0.00 0.00 3.16
2746 2920 4.270084 GTCAAACACGACTCTGATGAACAA 59.730 41.667 0.00 0.00 32.92 2.83
2748 2922 3.802139 TGTCAAACACGACTCTGATGAAC 59.198 43.478 0.00 0.00 36.82 3.18
2749 2923 4.051237 CTGTCAAACACGACTCTGATGAA 58.949 43.478 0.00 0.00 36.82 2.57
2750 2924 3.552890 CCTGTCAAACACGACTCTGATGA 60.553 47.826 0.00 0.00 36.82 2.92
2751 2925 2.733552 CCTGTCAAACACGACTCTGATG 59.266 50.000 0.00 0.00 36.82 3.07
2752 2926 2.628178 TCCTGTCAAACACGACTCTGAT 59.372 45.455 0.00 0.00 36.82 2.90
2753 2927 2.028876 TCCTGTCAAACACGACTCTGA 58.971 47.619 0.00 0.00 36.82 3.27
2754 2928 2.509052 TCCTGTCAAACACGACTCTG 57.491 50.000 0.00 0.00 36.82 3.35
2755 2929 4.079970 TCTATCCTGTCAAACACGACTCT 58.920 43.478 0.00 0.00 36.82 3.24
2756 2930 4.436242 TCTATCCTGTCAAACACGACTC 57.564 45.455 0.00 0.00 36.82 3.36
2757 2931 4.707448 AGATCTATCCTGTCAAACACGACT 59.293 41.667 0.00 0.00 36.82 4.18
2758 2932 5.000012 AGATCTATCCTGTCAAACACGAC 58.000 43.478 0.00 0.00 36.40 4.34
2761 2935 5.066634 TCGAGAGATCTATCCTGTCAAACAC 59.933 44.000 11.67 0.00 33.31 3.32
2997 3203 2.029244 CCAACGATCTGCACAACGTATC 59.971 50.000 0.00 0.00 38.00 2.24
2999 3205 1.424403 CCAACGATCTGCACAACGTA 58.576 50.000 0.00 0.00 38.00 3.57
3005 3219 0.108138 AGCTACCCAACGATCTGCAC 60.108 55.000 0.00 0.00 0.00 4.57
3207 3434 1.949257 CCTTCTTTCCACGGCACAC 59.051 57.895 0.00 0.00 0.00 3.82
3208 3435 1.896660 GCCTTCTTTCCACGGCACA 60.897 57.895 0.00 0.00 42.06 4.57
3252 3479 4.760047 CGTCGGCCCAGGAACCAG 62.760 72.222 0.00 0.00 0.00 4.00
3288 3515 1.852626 CCCCTTCTTCCCTGGGTGT 60.853 63.158 13.56 0.00 39.31 4.16
3289 3516 1.541368 TCCCCTTCTTCCCTGGGTG 60.541 63.158 13.56 7.37 39.31 4.61
3290 3517 1.229984 CTCCCCTTCTTCCCTGGGT 60.230 63.158 13.56 0.00 39.31 4.51
3325 3553 3.528370 CGACGGCAGAGGTAGGGG 61.528 72.222 0.00 0.00 0.00 4.79
3368 3596 0.392998 AGGGTAATCGCCACTTGCTG 60.393 55.000 0.00 0.00 38.05 4.41
3384 3612 2.352651 CACTAATCATTCACGCACAGGG 59.647 50.000 0.00 0.00 0.00 4.45
3440 3685 1.605753 CATGTGCCATGGATCCAGAG 58.394 55.000 21.33 14.59 0.00 3.35
3492 3737 0.402861 CTTAATGCCCCCTCCCCCTA 60.403 60.000 0.00 0.00 0.00 3.53
3493 3738 1.701390 CTTAATGCCCCCTCCCCCT 60.701 63.158 0.00 0.00 0.00 4.79
3494 3739 2.779072 CCTTAATGCCCCCTCCCCC 61.779 68.421 0.00 0.00 0.00 5.40
3495 3740 1.293683 TTCCTTAATGCCCCCTCCCC 61.294 60.000 0.00 0.00 0.00 4.81
3565 3818 1.337118 CTCTCTGCTCCCATCCTACC 58.663 60.000 0.00 0.00 0.00 3.18
3581 3834 2.132996 CAGCGGCATCTCTCCCTCT 61.133 63.158 1.45 0.00 0.00 3.69
3634 3891 3.041940 GTGGTGCAGTTCGTCCCG 61.042 66.667 0.00 0.00 0.00 5.14
3691 3987 1.684869 CCCCACACACCACAAGTTTCT 60.685 52.381 0.00 0.00 0.00 2.52
3722 4018 2.179517 GCGAGGTCACACGAGAGG 59.820 66.667 0.00 0.00 32.15 3.69


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

AutoCloner maintained by Alex Coulton.