Multiple sequence alignment - TraesCS2A01G277300

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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 TraesCS2A01G277300 chr2A 100.000 3013 0 0 1 3013 458971343 458968331 0.000000e+00 5565
1 TraesCS2A01G277300 chr2A 92.274 2084 118 23 538 2612 764066993 764069042 0.000000e+00 2916
2 TraesCS2A01G277300 chr2A 94.588 388 15 6 2606 2988 514766995 514767381 2.000000e-166 595
3 TraesCS2A01G277300 chr2A 92.963 270 17 2 2608 2875 14802194 14802463 2.820000e-105 392
4 TraesCS2A01G277300 chr4D 95.125 2072 99 2 542 2612 440465454 440463384 0.000000e+00 3265
5 TraesCS2A01G277300 chr4D 93.919 148 4 5 2871 3013 440461761 440461614 5.060000e-53 219
6 TraesCS2A01G277300 chr7D 94.699 2075 94 7 541 2612 530867457 530865396 0.000000e+00 3208
7 TraesCS2A01G277300 chr7D 94.169 2075 97 7 542 2612 596123081 596121027 0.000000e+00 3140
8 TraesCS2A01G277300 chr7D 94.477 1702 86 7 542 2240 592400973 592402669 0.000000e+00 2615
9 TraesCS2A01G277300 chr7D 95.086 1343 60 3 1272 2612 70680368 70679030 0.000000e+00 2109
10 TraesCS2A01G277300 chr7D 95.926 270 11 0 2606 2875 498408770 498409039 3.570000e-119 438
11 TraesCS2A01G277300 chr7D 93.704 270 16 1 2606 2875 530864155 530863887 1.300000e-108 403
12 TraesCS2A01G277300 chr7D 93.919 148 4 5 2871 3013 530863781 530863634 5.060000e-53 219
13 TraesCS2A01G277300 chr7D 93.919 148 4 5 2871 3013 592403819 592403966 5.060000e-53 219
14 TraesCS2A01G277300 chr7D 94.118 119 7 0 424 542 180853273 180853155 6.640000e-42 182
15 TraesCS2A01G277300 chr6A 94.602 2075 89 9 542 2612 508298181 508300236 0.000000e+00 3190
16 TraesCS2A01G277300 chr6A 92.857 1176 77 5 542 1711 134201700 134202874 0.000000e+00 1700
17 TraesCS2A01G277300 chr6A 96.585 410 12 2 2606 3013 508326783 508327192 0.000000e+00 678
18 TraesCS2A01G277300 chr5A 93.684 2074 107 6 542 2612 562130734 562132786 0.000000e+00 3083
19 TraesCS2A01G277300 chr5A 92.792 2081 113 21 539 2612 243925607 243927657 0.000000e+00 2977
20 TraesCS2A01G277300 chr5A 92.548 2080 117 19 542 2612 402974416 402976466 0.000000e+00 2948
21 TraesCS2A01G277300 chr5A 95.941 271 10 1 2606 2875 562142247 562142517 3.570000e-119 438
22 TraesCS2A01G277300 chr7A 92.582 2076 119 19 543 2612 47492055 47490009 0.000000e+00 2948
23 TraesCS2A01G277300 chr7A 95.866 387 12 4 2606 2988 134465022 134465408 9.170000e-175 623
24 TraesCS2A01G277300 chr1B 91.145 2078 149 17 542 2612 591152712 591154761 0.000000e+00 2785
25 TraesCS2A01G277300 chr1B 90.822 2081 143 22 542 2612 591203926 591205968 0.000000e+00 2741
26 TraesCS2A01G277300 chr1B 93.652 1087 62 3 1528 2612 637633989 637632908 0.000000e+00 1618
27 TraesCS2A01G277300 chr1B 86.979 192 15 9 2832 3013 148164807 148164998 1.090000e-49 207
28 TraesCS2A01G277300 chr5D 95.035 1289 58 6 538 1824 443521251 443522535 0.000000e+00 2021
29 TraesCS2A01G277300 chr5D 95.279 1165 53 2 1449 2612 351321021 351322184 0.000000e+00 1845
30 TraesCS2A01G277300 chr5D 94.595 148 3 5 2871 3013 443525012 443525159 1.090000e-54 224
31 TraesCS2A01G277300 chr3B 92.620 813 48 7 1808 2612 85165159 85164351 0.000000e+00 1158
32 TraesCS2A01G277300 chr3B 84.444 540 62 15 5 541 55457776 55458296 2.070000e-141 512
33 TraesCS2A01G277300 chr6B 95.756 542 23 0 1 542 715308587 715309128 0.000000e+00 874
34 TraesCS2A01G277300 chr3A 93.282 387 21 5 2606 2988 23140188 23139803 1.570000e-157 566
35 TraesCS2A01G277300 chr3A 85.714 546 61 12 5 541 45571088 45571625 7.290000e-156 560
36 TraesCS2A01G277300 chr3D 85.370 540 58 14 5 541 33160547 33161068 9.500000e-150 540
37 TraesCS2A01G277300 chr2B 94.030 268 15 1 2606 2872 62338094 62338361 3.620000e-109 405


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 TraesCS2A01G277300 chr2A 458968331 458971343 3012 True 5565.000000 5565 100.000000 1 3013 1 chr2A.!!$R1 3012
1 TraesCS2A01G277300 chr2A 764066993 764069042 2049 False 2916.000000 2916 92.274000 538 2612 1 chr2A.!!$F3 2074
2 TraesCS2A01G277300 chr4D 440461614 440465454 3840 True 1742.000000 3265 94.522000 542 3013 2 chr4D.!!$R1 2471
3 TraesCS2A01G277300 chr7D 596121027 596123081 2054 True 3140.000000 3140 94.169000 542 2612 1 chr7D.!!$R3 2070
4 TraesCS2A01G277300 chr7D 70679030 70680368 1338 True 2109.000000 2109 95.086000 1272 2612 1 chr7D.!!$R1 1340
5 TraesCS2A01G277300 chr7D 592400973 592403966 2993 False 1417.000000 2615 94.198000 542 3013 2 chr7D.!!$F2 2471
6 TraesCS2A01G277300 chr7D 530863634 530867457 3823 True 1276.666667 3208 94.107333 541 3013 3 chr7D.!!$R4 2472
7 TraesCS2A01G277300 chr6A 508298181 508300236 2055 False 3190.000000 3190 94.602000 542 2612 1 chr6A.!!$F2 2070
8 TraesCS2A01G277300 chr6A 134201700 134202874 1174 False 1700.000000 1700 92.857000 542 1711 1 chr6A.!!$F1 1169
9 TraesCS2A01G277300 chr5A 562130734 562132786 2052 False 3083.000000 3083 93.684000 542 2612 1 chr5A.!!$F3 2070
10 TraesCS2A01G277300 chr5A 243925607 243927657 2050 False 2977.000000 2977 92.792000 539 2612 1 chr5A.!!$F1 2073
11 TraesCS2A01G277300 chr5A 402974416 402976466 2050 False 2948.000000 2948 92.548000 542 2612 1 chr5A.!!$F2 2070
12 TraesCS2A01G277300 chr7A 47490009 47492055 2046 True 2948.000000 2948 92.582000 543 2612 1 chr7A.!!$R1 2069
13 TraesCS2A01G277300 chr1B 591152712 591154761 2049 False 2785.000000 2785 91.145000 542 2612 1 chr1B.!!$F2 2070
14 TraesCS2A01G277300 chr1B 591203926 591205968 2042 False 2741.000000 2741 90.822000 542 2612 1 chr1B.!!$F3 2070
15 TraesCS2A01G277300 chr1B 637632908 637633989 1081 True 1618.000000 1618 93.652000 1528 2612 1 chr1B.!!$R1 1084
16 TraesCS2A01G277300 chr5D 351321021 351322184 1163 False 1845.000000 1845 95.279000 1449 2612 1 chr5D.!!$F1 1163
17 TraesCS2A01G277300 chr5D 443521251 443525159 3908 False 1122.500000 2021 94.815000 538 3013 2 chr5D.!!$F2 2475
18 TraesCS2A01G277300 chr3B 85164351 85165159 808 True 1158.000000 1158 92.620000 1808 2612 1 chr3B.!!$R1 804
19 TraesCS2A01G277300 chr3B 55457776 55458296 520 False 512.000000 512 84.444000 5 541 1 chr3B.!!$F1 536
20 TraesCS2A01G277300 chr6B 715308587 715309128 541 False 874.000000 874 95.756000 1 542 1 chr6B.!!$F1 541
21 TraesCS2A01G277300 chr3A 45571088 45571625 537 False 560.000000 560 85.714000 5 541 1 chr3A.!!$F1 536
22 TraesCS2A01G277300 chr3D 33160547 33161068 521 False 540.000000 540 85.370000 5 541 1 chr3D.!!$F1 536

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
174 182 0.517316 GCTTTTGTCTGTTCGGCGAT 59.483 50.0 11.76 0.0 0.00 4.58 F
1137 1160 0.178947 TTTTGCAGGAAACCCCCGAT 60.179 50.0 0.00 0.0 34.66 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 1365 0.327259 ATGCTGCACCACACATCTCT 59.673 50.0 3.57 0.00 0.00 3.10 R
2687 4877 0.739462 TGTTTGACTAGCATCGGCCG 60.739 55.0 22.12 22.12 42.56 6.13 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
66 68 6.456988 CCAAAACCATCAAGATCTACGCTAAC 60.457 42.308 0.00 0.00 0.00 2.34
169 177 3.758521 GCAATTGCTTTTGTCTGTTCG 57.241 42.857 23.21 0.00 38.21 3.95
174 182 0.517316 GCTTTTGTCTGTTCGGCGAT 59.483 50.000 11.76 0.00 0.00 4.58
228 236 2.223829 CGAGAGTCTCACCAACACTTGT 60.224 50.000 19.99 0.00 0.00 3.16
302 310 2.732289 GCCAGTCAAGAAAGGGCAA 58.268 52.632 0.00 0.00 44.01 4.52
304 312 1.620323 GCCAGTCAAGAAAGGGCAAAT 59.380 47.619 0.00 0.00 44.01 2.32
482 491 7.775053 ATTTTAGGTTTGTCTTCCAATAGCA 57.225 32.000 0.00 0.00 31.81 3.49
483 492 6.817765 TTTAGGTTTGTCTTCCAATAGCAG 57.182 37.500 0.00 0.00 31.81 4.24
484 493 4.373156 AGGTTTGTCTTCCAATAGCAGT 57.627 40.909 0.00 0.00 31.81 4.40
485 494 5.499004 AGGTTTGTCTTCCAATAGCAGTA 57.501 39.130 0.00 0.00 31.81 2.74
486 495 6.067217 AGGTTTGTCTTCCAATAGCAGTAT 57.933 37.500 0.00 0.00 31.81 2.12
487 496 6.485171 AGGTTTGTCTTCCAATAGCAGTATT 58.515 36.000 0.00 0.00 31.81 1.89
488 497 6.948309 AGGTTTGTCTTCCAATAGCAGTATTT 59.052 34.615 0.00 0.00 31.81 1.40
489 498 7.121315 AGGTTTGTCTTCCAATAGCAGTATTTC 59.879 37.037 0.00 0.00 31.81 2.17
490 499 7.094377 GGTTTGTCTTCCAATAGCAGTATTTCA 60.094 37.037 0.00 0.00 31.81 2.69
491 500 8.462016 GTTTGTCTTCCAATAGCAGTATTTCAT 58.538 33.333 0.00 0.00 31.81 2.57
492 501 9.679661 TTTGTCTTCCAATAGCAGTATTTCATA 57.320 29.630 0.00 0.00 31.81 2.15
493 502 8.893219 TGTCTTCCAATAGCAGTATTTCATAG 57.107 34.615 0.00 0.00 0.00 2.23
494 503 8.486210 TGTCTTCCAATAGCAGTATTTCATAGT 58.514 33.333 0.00 0.00 0.00 2.12
495 504 9.331282 GTCTTCCAATAGCAGTATTTCATAGTT 57.669 33.333 0.00 0.00 0.00 2.24
496 505 9.905713 TCTTCCAATAGCAGTATTTCATAGTTT 57.094 29.630 0.00 0.00 0.00 2.66
497 506 9.941664 CTTCCAATAGCAGTATTTCATAGTTTG 57.058 33.333 0.00 0.00 0.00 2.93
498 507 8.450578 TCCAATAGCAGTATTTCATAGTTTGG 57.549 34.615 0.00 0.00 0.00 3.28
499 508 8.052748 TCCAATAGCAGTATTTCATAGTTTGGT 58.947 33.333 0.00 0.00 30.07 3.67
500 509 8.686334 CCAATAGCAGTATTTCATAGTTTGGTT 58.314 33.333 0.00 0.00 0.00 3.67
501 510 9.507280 CAATAGCAGTATTTCATAGTTTGGTTG 57.493 33.333 0.00 0.00 0.00 3.77
502 511 8.807948 ATAGCAGTATTTCATAGTTTGGTTGT 57.192 30.769 0.00 0.00 0.00 3.32
503 512 7.524717 AGCAGTATTTCATAGTTTGGTTGTT 57.475 32.000 0.00 0.00 0.00 2.83
504 513 7.951591 AGCAGTATTTCATAGTTTGGTTGTTT 58.048 30.769 0.00 0.00 0.00 2.83
505 514 9.073475 AGCAGTATTTCATAGTTTGGTTGTTTA 57.927 29.630 0.00 0.00 0.00 2.01
506 515 9.124807 GCAGTATTTCATAGTTTGGTTGTTTAC 57.875 33.333 0.00 0.00 0.00 2.01
515 524 9.959749 CATAGTTTGGTTGTTTACTGTATTTGT 57.040 29.630 0.00 0.00 0.00 2.83
518 527 9.398538 AGTTTGGTTGTTTACTGTATTTGTAGA 57.601 29.630 0.00 0.00 0.00 2.59
521 530 8.330466 TGGTTGTTTACTGTATTTGTAGATGG 57.670 34.615 0.00 0.00 0.00 3.51
522 531 8.158132 TGGTTGTTTACTGTATTTGTAGATGGA 58.842 33.333 0.00 0.00 0.00 3.41
523 532 9.005777 GGTTGTTTACTGTATTTGTAGATGGAA 57.994 33.333 0.00 0.00 0.00 3.53
526 535 9.226606 TGTTTACTGTATTTGTAGATGGAAAGG 57.773 33.333 0.00 0.00 0.00 3.11
527 536 7.859325 TTACTGTATTTGTAGATGGAAAGGC 57.141 36.000 0.00 0.00 0.00 4.35
528 537 5.815581 ACTGTATTTGTAGATGGAAAGGCA 58.184 37.500 0.00 0.00 0.00 4.75
529 538 5.648092 ACTGTATTTGTAGATGGAAAGGCAC 59.352 40.000 0.00 0.00 0.00 5.01
530 539 4.947388 TGTATTTGTAGATGGAAAGGCACC 59.053 41.667 0.00 0.00 0.00 5.01
531 540 3.806949 TTTGTAGATGGAAAGGCACCT 57.193 42.857 0.00 0.00 0.00 4.00
532 541 4.919774 TTTGTAGATGGAAAGGCACCTA 57.080 40.909 0.00 0.00 0.00 3.08
533 542 4.919774 TTGTAGATGGAAAGGCACCTAA 57.080 40.909 0.00 0.00 0.00 2.69
534 543 5.450818 TTGTAGATGGAAAGGCACCTAAT 57.549 39.130 0.00 0.00 0.00 1.73
535 544 5.450818 TGTAGATGGAAAGGCACCTAATT 57.549 39.130 0.00 0.00 0.00 1.40
536 545 5.826643 TGTAGATGGAAAGGCACCTAATTT 58.173 37.500 0.00 0.00 0.00 1.82
620 631 6.946165 TCTACGATTTTGTGCGAAAAACTAA 58.054 32.000 0.00 0.00 32.12 2.24
796 812 2.665185 GTCTGAACGGCGGCTGTT 60.665 61.111 26.13 26.13 35.46 3.16
916 938 2.041976 GCTAGGTCAGCCTATCGCA 58.958 57.895 0.00 0.00 45.61 5.10
1015 1038 6.363167 ACATCAACATGGTTTCAATGGATT 57.637 33.333 0.00 0.00 33.82 3.01
1023 1046 5.178096 TGGTTTCAATGGATTCTCAGCTA 57.822 39.130 0.00 0.00 0.00 3.32
1047 1070 6.849085 TTTGTAAGTGCATAATGGTGGAAT 57.151 33.333 0.00 0.00 0.00 3.01
1137 1160 0.178947 TTTTGCAGGAAACCCCCGAT 60.179 50.000 0.00 0.00 34.66 4.18
1311 1336 2.159310 TGCACGCTAACTTGTTTTGCTT 60.159 40.909 0.00 0.00 34.15 3.91
1312 1337 3.065510 TGCACGCTAACTTGTTTTGCTTA 59.934 39.130 0.00 0.00 34.15 3.09
1340 1365 2.948315 TGTGTGATGTGTTTTGCTGCTA 59.052 40.909 0.00 0.00 0.00 3.49
1569 1628 9.032420 GTTAGGTGTTAACTGAATATAGCTGTC 57.968 37.037 7.22 0.00 38.87 3.51
1572 1631 8.267894 AGGTGTTAACTGAATATAGCTGTCAAT 58.732 33.333 7.22 0.00 0.00 2.57
1651 1712 9.678260 AACTGAATTTATCTCTGATGCTAAGTT 57.322 29.630 0.00 0.00 0.00 2.66
1885 2037 3.330701 TGGCCAGAGATTCTACAAAGGTT 59.669 43.478 0.00 0.00 0.00 3.50
2064 2217 5.999044 ACTATCAAGATGGCAAGATGTCTT 58.001 37.500 0.00 0.00 36.45 3.01
2301 3218 4.898265 AGAAGCTGGAGTATCTGATTGCTA 59.102 41.667 0.00 0.00 33.73 3.49
2336 3253 2.566279 TGGGCATGCAAGCAAAGATAAA 59.434 40.909 21.36 0.00 35.83 1.40
2467 3387 8.749354 AGGTGTATATTTTGGGAAAGTTTCATC 58.251 33.333 17.16 9.15 0.00 2.92
2602 3530 8.705048 ACTCATGCTAAGTTAAGTAAGTAAGC 57.295 34.615 0.00 0.00 0.00 3.09
2687 4877 8.823818 ACGTGGCTAACAACATATAATAAGTTC 58.176 33.333 0.00 0.00 0.00 3.01
2838 5030 6.321181 TGAATTTGGCAGTAACTTCTGAACTT 59.679 34.615 0.00 0.00 37.61 2.66
2855 5047 7.816640 TCTGAACTTTAGAAATGGCAATGTAC 58.183 34.615 0.00 0.00 0.00 2.90
2863 5055 8.755696 TTAGAAATGGCAATGTACAACAAATC 57.244 30.769 0.00 1.07 0.00 2.17
2881 5073 9.649024 CAACAAATCAAACAAATTAACATGTCC 57.351 29.630 0.00 0.00 0.00 4.02
2883 5075 8.825745 ACAAATCAAACAAATTAACATGTCCAC 58.174 29.630 0.00 0.00 0.00 4.02
2888 5080 7.276658 TCAAACAAATTAACATGTCCACAACAC 59.723 33.333 0.00 0.00 41.75 3.32
2889 5081 6.214191 ACAAATTAACATGTCCACAACACA 57.786 33.333 0.00 0.00 41.75 3.72
2892 5084 6.403866 AATTAACATGTCCACAACACACAT 57.596 33.333 0.00 0.00 41.75 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 96 7.925483 CACAGATTTCCTTCAAATTGTTGGTAA 59.075 33.333 0.00 0.00 34.60 2.85
129 137 7.683437 ATTGCTGGTACTTACCTTTAGTTTC 57.317 36.000 6.97 0.00 46.58 2.78
169 177 5.767816 AATTAACCATGGAAGTTATCGCC 57.232 39.130 21.47 0.00 30.17 5.54
174 182 9.528489 AAGAAGCTTAATTAACCATGGAAGTTA 57.472 29.630 21.47 10.38 0.00 2.24
228 236 3.681594 CGCTTAGGGCTTGAAGGTCATTA 60.682 47.826 0.00 0.00 39.13 1.90
302 310 5.036117 AGTTATCACCGCTAACCATCATT 57.964 39.130 0.00 0.00 30.89 2.57
304 312 3.704566 AGAGTTATCACCGCTAACCATCA 59.295 43.478 0.00 0.00 30.89 3.07
399 408 1.663911 TCTGAAGGGGATTTCCGGAA 58.336 50.000 14.35 14.35 36.71 4.30
400 409 1.559682 CTTCTGAAGGGGATTTCCGGA 59.440 52.381 0.00 0.00 36.71 5.14
402 411 3.274288 CTTCTTCTGAAGGGGATTTCCG 58.726 50.000 16.83 0.00 44.33 4.30
461 470 5.876357 ACTGCTATTGGAAGACAAACCTAA 58.124 37.500 0.00 0.00 43.46 2.69
462 471 5.499004 ACTGCTATTGGAAGACAAACCTA 57.501 39.130 0.00 0.00 43.46 3.08
463 472 4.373156 ACTGCTATTGGAAGACAAACCT 57.627 40.909 0.00 0.00 43.46 3.50
464 473 6.759497 AATACTGCTATTGGAAGACAAACC 57.241 37.500 0.00 0.00 43.46 3.27
465 474 7.816640 TGAAATACTGCTATTGGAAGACAAAC 58.183 34.615 0.00 0.00 43.46 2.93
466 475 7.994425 TGAAATACTGCTATTGGAAGACAAA 57.006 32.000 0.00 0.00 43.46 2.83
467 476 9.330063 CTATGAAATACTGCTATTGGAAGACAA 57.670 33.333 0.00 0.00 44.54 3.18
468 477 8.486210 ACTATGAAATACTGCTATTGGAAGACA 58.514 33.333 0.00 0.00 0.00 3.41
469 478 8.894768 ACTATGAAATACTGCTATTGGAAGAC 57.105 34.615 0.00 0.00 0.00 3.01
470 479 9.905713 AAACTATGAAATACTGCTATTGGAAGA 57.094 29.630 0.00 0.00 0.00 2.87
471 480 9.941664 CAAACTATGAAATACTGCTATTGGAAG 57.058 33.333 0.00 0.00 0.00 3.46
472 481 8.902806 CCAAACTATGAAATACTGCTATTGGAA 58.097 33.333 0.00 0.00 35.58 3.53
473 482 8.052748 ACCAAACTATGAAATACTGCTATTGGA 58.947 33.333 0.00 0.00 36.72 3.53
474 483 8.225603 ACCAAACTATGAAATACTGCTATTGG 57.774 34.615 0.00 0.00 38.63 3.16
475 484 9.507280 CAACCAAACTATGAAATACTGCTATTG 57.493 33.333 0.00 0.00 0.00 1.90
476 485 9.243105 ACAACCAAACTATGAAATACTGCTATT 57.757 29.630 0.00 0.00 0.00 1.73
477 486 8.807948 ACAACCAAACTATGAAATACTGCTAT 57.192 30.769 0.00 0.00 0.00 2.97
478 487 8.630054 AACAACCAAACTATGAAATACTGCTA 57.370 30.769 0.00 0.00 0.00 3.49
479 488 7.524717 AACAACCAAACTATGAAATACTGCT 57.475 32.000 0.00 0.00 0.00 4.24
480 489 9.124807 GTAAACAACCAAACTATGAAATACTGC 57.875 33.333 0.00 0.00 0.00 4.40
489 498 9.959749 ACAAATACAGTAAACAACCAAACTATG 57.040 29.630 0.00 0.00 0.00 2.23
492 501 9.398538 TCTACAAATACAGTAAACAACCAAACT 57.601 29.630 0.00 0.00 0.00 2.66
495 504 8.788806 CCATCTACAAATACAGTAAACAACCAA 58.211 33.333 0.00 0.00 0.00 3.67
496 505 8.158132 TCCATCTACAAATACAGTAAACAACCA 58.842 33.333 0.00 0.00 0.00 3.67
497 506 8.556213 TCCATCTACAAATACAGTAAACAACC 57.444 34.615 0.00 0.00 0.00 3.77
500 509 9.226606 CCTTTCCATCTACAAATACAGTAAACA 57.773 33.333 0.00 0.00 0.00 2.83
501 510 8.182227 GCCTTTCCATCTACAAATACAGTAAAC 58.818 37.037 0.00 0.00 0.00 2.01
502 511 7.885922 TGCCTTTCCATCTACAAATACAGTAAA 59.114 33.333 0.00 0.00 0.00 2.01
503 512 7.335924 GTGCCTTTCCATCTACAAATACAGTAA 59.664 37.037 0.00 0.00 0.00 2.24
504 513 6.821665 GTGCCTTTCCATCTACAAATACAGTA 59.178 38.462 0.00 0.00 0.00 2.74
505 514 5.648092 GTGCCTTTCCATCTACAAATACAGT 59.352 40.000 0.00 0.00 0.00 3.55
506 515 5.066505 GGTGCCTTTCCATCTACAAATACAG 59.933 44.000 0.00 0.00 0.00 2.74
507 516 4.947388 GGTGCCTTTCCATCTACAAATACA 59.053 41.667 0.00 0.00 0.00 2.29
508 517 5.193679 AGGTGCCTTTCCATCTACAAATAC 58.806 41.667 0.00 0.00 0.00 1.89
509 518 5.450818 AGGTGCCTTTCCATCTACAAATA 57.549 39.130 0.00 0.00 0.00 1.40
510 519 4.322057 AGGTGCCTTTCCATCTACAAAT 57.678 40.909 0.00 0.00 0.00 2.32
511 520 3.806949 AGGTGCCTTTCCATCTACAAA 57.193 42.857 0.00 0.00 0.00 2.83
512 521 4.919774 TTAGGTGCCTTTCCATCTACAA 57.080 40.909 0.00 0.00 28.57 2.41
513 522 5.450818 AATTAGGTGCCTTTCCATCTACA 57.549 39.130 0.00 0.00 28.57 2.74
514 523 7.719633 TCATAAATTAGGTGCCTTTCCATCTAC 59.280 37.037 0.00 0.00 28.57 2.59
515 524 7.811282 TCATAAATTAGGTGCCTTTCCATCTA 58.189 34.615 0.00 0.00 0.00 1.98
516 525 6.672593 TCATAAATTAGGTGCCTTTCCATCT 58.327 36.000 0.00 0.00 0.00 2.90
517 526 6.772716 TCTCATAAATTAGGTGCCTTTCCATC 59.227 38.462 0.00 0.00 0.00 3.51
518 527 6.672593 TCTCATAAATTAGGTGCCTTTCCAT 58.327 36.000 0.00 0.00 0.00 3.41
519 528 6.073447 TCTCATAAATTAGGTGCCTTTCCA 57.927 37.500 0.00 0.00 0.00 3.53
520 529 6.038714 CACTCTCATAAATTAGGTGCCTTTCC 59.961 42.308 0.00 0.00 0.00 3.13
521 530 6.599638 ACACTCTCATAAATTAGGTGCCTTTC 59.400 38.462 0.00 0.00 0.00 2.62
522 531 6.485171 ACACTCTCATAAATTAGGTGCCTTT 58.515 36.000 0.00 0.00 0.00 3.11
523 532 6.067217 ACACTCTCATAAATTAGGTGCCTT 57.933 37.500 0.00 0.00 0.00 4.35
524 533 5.700402 ACACTCTCATAAATTAGGTGCCT 57.300 39.130 0.00 0.00 0.00 4.75
525 534 6.759497 AAACACTCTCATAAATTAGGTGCC 57.241 37.500 0.00 0.00 0.00 5.01
526 535 8.182227 GGTTAAACACTCTCATAAATTAGGTGC 58.818 37.037 0.00 0.00 0.00 5.01
527 536 9.226606 TGGTTAAACACTCTCATAAATTAGGTG 57.773 33.333 0.00 0.00 0.00 4.00
528 537 9.802039 TTGGTTAAACACTCTCATAAATTAGGT 57.198 29.630 0.00 0.00 0.00 3.08
536 545 9.059260 GGTAGTTTTTGGTTAAACACTCTCATA 57.941 33.333 0.00 0.00 37.78 2.15
620 631 4.346418 TGCCATGGTTTAGGACAAATTTGT 59.654 37.500 23.49 23.49 45.65 2.83
690 705 1.002624 GGCCAACCGGTCAGATTCA 60.003 57.895 8.04 0.00 36.65 2.57
782 798 4.555709 ACCAACAGCCGCCGTTCA 62.556 61.111 0.00 0.00 0.00 3.18
1015 1038 7.227314 CCATTATGCACTTACAAATAGCTGAGA 59.773 37.037 0.00 0.00 0.00 3.27
1023 1046 6.849085 TTCCACCATTATGCACTTACAAAT 57.151 33.333 0.00 0.00 0.00 2.32
1047 1070 6.804083 TGAACTAACCCTAACCCTAACTCTA 58.196 40.000 0.00 0.00 0.00 2.43
1311 1336 5.106197 GCAAAACACATCACACATCTCCATA 60.106 40.000 0.00 0.00 0.00 2.74
1312 1337 4.321452 GCAAAACACATCACACATCTCCAT 60.321 41.667 0.00 0.00 0.00 3.41
1340 1365 0.327259 ATGCTGCACCACACATCTCT 59.673 50.000 3.57 0.00 0.00 3.10
1368 1410 6.378280 ACACATCTCTACACATCACACATCTA 59.622 38.462 0.00 0.00 0.00 1.98
1481 1540 2.683768 AGGTGTTCTCAGGTTCAGTCT 58.316 47.619 0.00 0.00 0.00 3.24
1651 1712 5.731957 TCATAGTAAGCACACAACACCTA 57.268 39.130 0.00 0.00 0.00 3.08
1814 1883 4.162320 CCACAGTTCACACCTACATCCTAT 59.838 45.833 0.00 0.00 0.00 2.57
2033 2186 6.716628 TCTTGCCATCTTGATAGTCAAAAAGT 59.283 34.615 0.00 0.00 35.73 2.66
2324 3241 5.505181 TCCTCTCCAGTTTATCTTTGCTT 57.495 39.130 0.00 0.00 0.00 3.91
2336 3253 1.661463 TTGCCTTGATCCTCTCCAGT 58.339 50.000 0.00 0.00 0.00 4.00
2467 3387 5.188434 TCCTTCATACCATTCTGAAAGCAG 58.812 41.667 0.00 0.00 43.67 4.24
2602 3530 3.233578 AGCGTGCGTTGAATAAAACATG 58.766 40.909 0.00 0.00 0.00 3.21
2639 4829 4.292208 TGTTCAGCGTGCGTTGCG 62.292 61.111 3.61 0.00 37.44 4.85
2687 4877 0.739462 TGTTTGACTAGCATCGGCCG 60.739 55.000 22.12 22.12 42.56 6.13
2838 5030 8.363390 TGATTTGTTGTACATTGCCATTTCTAA 58.637 29.630 0.00 0.00 0.00 2.10
2855 5047 9.649024 GGACATGTTAATTTGTTTGATTTGTTG 57.351 29.630 0.00 0.00 0.00 3.33
2863 5055 7.063898 TGTGTTGTGGACATGTTAATTTGTTTG 59.936 33.333 0.00 0.00 41.10 2.93
2875 5067 3.565063 TCAGAATGTGTGTTGTGGACATG 59.435 43.478 0.00 0.00 37.82 3.21
2877 5069 3.274095 TCAGAATGTGTGTTGTGGACA 57.726 42.857 0.00 0.00 37.40 4.02
2878 5070 4.836125 ATTCAGAATGTGTGTTGTGGAC 57.164 40.909 0.00 0.00 37.40 4.02
2879 5071 5.850557 AAATTCAGAATGTGTGTTGTGGA 57.149 34.783 0.00 0.00 37.40 4.02
2880 5072 6.144402 GCTTAAATTCAGAATGTGTGTTGTGG 59.856 38.462 0.00 0.00 37.40 4.17
2881 5073 6.696583 TGCTTAAATTCAGAATGTGTGTTGTG 59.303 34.615 0.00 0.00 37.40 3.33
2883 5075 6.364165 CCTGCTTAAATTCAGAATGTGTGTTG 59.636 38.462 0.00 0.00 37.40 3.33
2888 5080 5.320549 AGCCTGCTTAAATTCAGAATGTG 57.679 39.130 0.00 0.00 37.40 3.21
2889 5081 6.183347 ACTAGCCTGCTTAAATTCAGAATGT 58.817 36.000 0.00 0.00 37.40 2.71
2892 5084 5.817816 GCTACTAGCCTGCTTAAATTCAGAA 59.182 40.000 0.00 0.00 34.48 3.02


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

AutoCloner maintained by Alex Coulton.