Multiple sequence alignment - TraesCS6B01G473200

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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 TraesCS6B01G473200 chr6B 100.000 2573 0 0 1 2573 720513756 720516328 0.000000e+00 4752.0
1 TraesCS6B01G473200 chr6B 85.714 91 13 0 458 548 123500598 123500508 2.110000e-16 97.1
2 TraesCS6B01G473200 chr6D 91.486 1656 101 13 789 2419 470618904 470617264 0.000000e+00 2241.0
3 TraesCS6B01G473200 chr6D 90.533 169 10 3 2408 2573 470617213 470617048 4.310000e-53 219.0
4 TraesCS6B01G473200 chr6A 89.805 1540 94 24 684 2198 615448158 615446657 0.000000e+00 1916.0
5 TraesCS6B01G473200 chr6A 90.308 454 25 7 1 445 615451154 615450711 6.170000e-161 577.0
6 TraesCS6B01G473200 chr6A 93.041 388 17 5 2189 2573 615443850 615443470 2.240000e-155 558.0
7 TraesCS6B01G473200 chr6A 97.143 35 1 0 647 681 615448210 615448176 2.760000e-05 60.2
8 TraesCS6B01G473200 chr3D 86.822 129 15 2 1823 1949 269465632 269465504 2.670000e-30 143.0
9 TraesCS6B01G473200 chr3D 87.356 87 11 0 458 544 422552605 422552691 1.630000e-17 100.0
10 TraesCS6B01G473200 chr7A 85.714 133 17 2 1823 1953 709821087 709821219 3.450000e-29 139.0
11 TraesCS6B01G473200 chr5D 84.962 133 17 3 1823 1952 190654381 190654513 5.780000e-27 132.0
12 TraesCS6B01G473200 chr5D 88.235 85 10 0 458 542 66292111 66292027 4.530000e-18 102.0
13 TraesCS6B01G473200 chr4D 85.271 129 17 2 1823 1949 489185727 489185599 5.780000e-27 132.0
14 TraesCS6B01G473200 chr4D 87.500 88 10 1 458 544 253767542 253767455 1.630000e-17 100.0
15 TraesCS6B01G473200 chr4B 85.271 129 17 2 1823 1949 413123518 413123390 5.780000e-27 132.0
16 TraesCS6B01G473200 chr5B 84.058 138 18 4 1814 1949 355692455 355692590 2.080000e-26 130.0
17 TraesCS6B01G473200 chr1A 82.517 143 23 2 1809 1949 521902184 521902042 9.670000e-25 124.0
18 TraesCS6B01G473200 chr1B 88.764 89 8 2 455 542 618126273 618126360 9.740000e-20 108.0
19 TraesCS6B01G473200 chr1B 85.149 101 14 1 457 557 121848650 121848551 4.530000e-18 102.0
20 TraesCS6B01G473200 chr3B 88.506 87 10 0 458 544 550666290 550666376 3.500000e-19 106.0
21 TraesCS6B01G473200 chr3B 86.957 92 11 1 458 549 341224307 341224397 4.530000e-18 102.0
22 TraesCS6B01G473200 chr7D 84.158 101 14 2 458 557 444474342 444474243 2.110000e-16 97.1


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 TraesCS6B01G473200 chr6B 720513756 720516328 2572 False 4752.0 4752 100.00000 1 2573 1 chr6B.!!$F1 2572
1 TraesCS6B01G473200 chr6D 470617048 470618904 1856 True 1230.0 2241 91.00950 789 2573 2 chr6D.!!$R1 1784
2 TraesCS6B01G473200 chr6A 615443470 615451154 7684 True 777.8 1916 92.57425 1 2573 4 chr6A.!!$R1 2572

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
740 3084 0.179073 CGGTTGCCTCACCTCTATGG 60.179 60.0 0.0 0.0 42.93 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2461 7737 0.696501 TTGAAGCTTCTACCCACCCC 59.303 55.0 26.09 0.0 0.0 4.95 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
24 25 3.119173 TGACTTCAAGTTTTGCCCTGTTG 60.119 43.478 0.00 0.00 0.00 3.33
46 47 4.756642 TGTCTGCCATGAAAGTTTAGTCAG 59.243 41.667 0.00 0.00 0.00 3.51
53 54 6.206829 GCCATGAAAGTTTAGTCAGTAGGTTT 59.793 38.462 0.00 0.00 0.00 3.27
79 80 6.514063 GGTCACAACCCTAGATTATGTAGTC 58.486 44.000 0.00 0.00 39.93 2.59
101 102 7.918076 AGTCCTTATATTTTGTCCTTGAGTGA 58.082 34.615 0.00 0.00 0.00 3.41
165 166 1.611491 CGTATGGTGCAAAAAGTGGGT 59.389 47.619 0.00 0.00 0.00 4.51
176 177 1.518056 AAAGTGGGTGCTGCACATCG 61.518 55.000 31.35 0.00 35.86 3.84
188 189 0.527565 GCACATCGCCTTCATTTGGT 59.472 50.000 0.00 0.00 32.94 3.67
189 190 1.067635 GCACATCGCCTTCATTTGGTT 60.068 47.619 0.00 0.00 32.94 3.67
190 191 2.610232 GCACATCGCCTTCATTTGGTTT 60.610 45.455 0.00 0.00 32.94 3.27
191 192 3.244976 CACATCGCCTTCATTTGGTTTC 58.755 45.455 0.00 0.00 0.00 2.78
192 193 2.890311 ACATCGCCTTCATTTGGTTTCA 59.110 40.909 0.00 0.00 0.00 2.69
214 215 7.905604 TCAGTTATTCCATTGTTGAGTAGTG 57.094 36.000 0.00 0.00 0.00 2.74
216 217 6.149308 CAGTTATTCCATTGTTGAGTAGTGCA 59.851 38.462 0.00 0.00 0.00 4.57
217 218 6.886459 AGTTATTCCATTGTTGAGTAGTGCAT 59.114 34.615 0.00 0.00 0.00 3.96
218 219 7.394359 AGTTATTCCATTGTTGAGTAGTGCATT 59.606 33.333 0.00 0.00 0.00 3.56
255 257 0.969149 TGCGCGATATCTCCCTTCAT 59.031 50.000 12.10 0.00 0.00 2.57
280 283 8.463930 TGGACATATCATTTCAATTTAGGGTC 57.536 34.615 0.00 0.00 0.00 4.46
300 303 3.512516 GGCACGATGGCTTGCTCC 61.513 66.667 0.00 0.00 40.14 4.70
318 321 1.200716 TCCCTGTTGTTACGTAGCTCG 59.799 52.381 10.88 0.00 46.00 5.03
334 337 3.930336 AGCTCGTCAGTCAATGATTTGA 58.070 40.909 0.00 0.00 40.92 2.69
343 346 8.727733 CGTCAGTCAATGATTTGATAATTTTCG 58.272 33.333 4.23 0.00 43.49 3.46
371 381 5.192927 CCATGTTCCTAGGAGTTTTATGCA 58.807 41.667 12.26 0.00 0.00 3.96
389 399 8.741101 TTTATGCAATGTCAATGAAACACTAC 57.259 30.769 0.00 0.00 0.00 2.73
390 400 6.579666 ATGCAATGTCAATGAAACACTACT 57.420 33.333 0.00 0.00 0.00 2.57
391 401 7.686438 ATGCAATGTCAATGAAACACTACTA 57.314 32.000 0.00 0.00 0.00 1.82
392 402 6.898041 TGCAATGTCAATGAAACACTACTAC 58.102 36.000 0.00 0.00 0.00 2.73
407 417 9.452287 AAACACTACTACAACTTTTCCAACTAA 57.548 29.630 0.00 0.00 0.00 2.24
462 472 2.025589 GCCAACTAGCCAACTACTCC 57.974 55.000 0.00 0.00 0.00 3.85
463 473 1.407025 GCCAACTAGCCAACTACTCCC 60.407 57.143 0.00 0.00 0.00 4.30
465 475 2.168728 CCAACTAGCCAACTACTCCCTC 59.831 54.545 0.00 0.00 0.00 4.30
466 476 2.162264 ACTAGCCAACTACTCCCTCC 57.838 55.000 0.00 0.00 0.00 4.30
467 477 1.033574 CTAGCCAACTACTCCCTCCG 58.966 60.000 0.00 0.00 0.00 4.63
469 479 0.971447 AGCCAACTACTCCCTCCGTC 60.971 60.000 0.00 0.00 0.00 4.79
470 480 1.957765 GCCAACTACTCCCTCCGTCC 61.958 65.000 0.00 0.00 0.00 4.79
471 481 1.328430 CCAACTACTCCCTCCGTCCC 61.328 65.000 0.00 0.00 0.00 4.46
472 482 0.613853 CAACTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
473 483 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
478 488 1.261480 CTCCCTCCGTCCCATGATAG 58.739 60.000 0.00 0.00 0.00 2.08
479 489 0.857675 TCCCTCCGTCCCATGATAGA 59.142 55.000 0.00 0.00 0.00 1.98
480 490 1.203063 TCCCTCCGTCCCATGATAGAG 60.203 57.143 0.00 0.00 0.00 2.43
481 491 1.261480 CCTCCGTCCCATGATAGAGG 58.739 60.000 0.00 0.00 36.74 3.69
482 492 1.261480 CTCCGTCCCATGATAGAGGG 58.739 60.000 10.91 10.91 46.90 4.30
483 493 0.561184 TCCGTCCCATGATAGAGGGT 59.439 55.000 14.64 0.00 45.64 4.34
484 494 0.681733 CCGTCCCATGATAGAGGGTG 59.318 60.000 0.00 0.00 45.64 4.61
489 499 4.600062 GTCCCATGATAGAGGGTGTTTTT 58.400 43.478 0.00 0.00 45.64 1.94
514 682 6.452244 GACACTGCAATAATGTCAAAAACC 57.548 37.500 12.68 0.00 41.94 3.27
515 683 4.981674 ACACTGCAATAATGTCAAAAACCG 59.018 37.500 0.00 0.00 0.00 4.44
516 684 4.981674 CACTGCAATAATGTCAAAAACCGT 59.018 37.500 0.00 0.00 0.00 4.83
517 685 5.116983 CACTGCAATAATGTCAAAAACCGTC 59.883 40.000 0.00 0.00 0.00 4.79
518 686 5.009610 ACTGCAATAATGTCAAAAACCGTCT 59.990 36.000 0.00 0.00 0.00 4.18
519 687 5.837437 TGCAATAATGTCAAAAACCGTCTT 58.163 33.333 0.00 0.00 0.00 3.01
531 918 2.467566 ACCGTCTTACATTGTGGGAC 57.532 50.000 0.00 6.72 0.00 4.46
532 919 1.337447 ACCGTCTTACATTGTGGGACG 60.337 52.381 25.36 25.36 45.92 4.79
533 920 1.355971 CGTCTTACATTGTGGGACGG 58.644 55.000 24.96 14.26 43.69 4.79
534 921 1.067425 CGTCTTACATTGTGGGACGGA 60.067 52.381 24.96 5.37 43.69 4.69
536 923 1.553248 TCTTACATTGTGGGACGGAGG 59.447 52.381 0.00 0.00 0.00 4.30
538 925 0.252330 TACATTGTGGGACGGAGGGA 60.252 55.000 0.00 0.00 0.00 4.20
539 926 1.221840 CATTGTGGGACGGAGGGAG 59.778 63.158 0.00 0.00 0.00 4.30
540 927 1.229529 ATTGTGGGACGGAGGGAGT 60.230 57.895 0.00 0.00 0.00 3.85
546 2792 1.572415 TGGGACGGAGGGAGTAGTTAT 59.428 52.381 0.00 0.00 0.00 1.89
555 2801 6.774170 ACGGAGGGAGTAGTTATTTTTGTTTT 59.226 34.615 0.00 0.00 0.00 2.43
556 2802 7.286087 ACGGAGGGAGTAGTTATTTTTGTTTTT 59.714 33.333 0.00 0.00 0.00 1.94
574 2820 7.500720 TGTTTTTAGTTTCCAACCTACTAGC 57.499 36.000 0.00 0.00 0.00 3.42
576 2822 5.829062 TTTAGTTTCCAACCTACTAGCCA 57.171 39.130 0.00 0.00 0.00 4.75
577 2823 5.829062 TTAGTTTCCAACCTACTAGCCAA 57.171 39.130 0.00 0.00 0.00 4.52
578 2824 4.017177 AGTTTCCAACCTACTAGCCAAC 57.983 45.455 0.00 0.00 0.00 3.77
579 2825 3.651423 AGTTTCCAACCTACTAGCCAACT 59.349 43.478 0.00 0.00 0.00 3.16
621 2941 7.095060 CGAATATGCATCTTAGCTAATTGTGGT 60.095 37.037 0.19 0.00 34.99 4.16
625 2945 6.283694 TGCATCTTAGCTAATTGTGGTCTAG 58.716 40.000 6.64 0.00 34.99 2.43
626 2946 6.098266 TGCATCTTAGCTAATTGTGGTCTAGA 59.902 38.462 6.64 0.00 34.99 2.43
627 2947 6.986817 GCATCTTAGCTAATTGTGGTCTAGAA 59.013 38.462 6.64 0.00 0.00 2.10
628 2948 7.042389 GCATCTTAGCTAATTGTGGTCTAGAAC 60.042 40.741 6.64 0.00 0.00 3.01
651 2971 2.473984 CGTAAGTTCGAGTTTGACCACC 59.526 50.000 0.00 0.00 0.00 4.61
719 3054 0.527600 CATGCATGCATCTGTGTGGC 60.528 55.000 30.07 0.00 33.90 5.01
724 3068 2.046892 GCATCTGTGTGGCTCGGT 60.047 61.111 0.00 0.00 0.00 4.69
725 3069 1.672356 GCATCTGTGTGGCTCGGTT 60.672 57.895 0.00 0.00 0.00 4.44
738 3082 1.115467 CTCGGTTGCCTCACCTCTAT 58.885 55.000 0.00 0.00 34.22 1.98
739 3083 0.824109 TCGGTTGCCTCACCTCTATG 59.176 55.000 0.00 0.00 34.22 2.23
740 3084 0.179073 CGGTTGCCTCACCTCTATGG 60.179 60.000 0.00 0.00 42.93 2.74
741 3085 1.204146 GGTTGCCTCACCTCTATGGA 58.796 55.000 0.00 0.00 39.71 3.41
742 3086 1.771255 GGTTGCCTCACCTCTATGGAT 59.229 52.381 0.00 0.00 39.71 3.41
798 3142 6.451393 CCTATTTTCCTTACGATCTCAGGAG 58.549 44.000 0.00 0.00 38.00 3.69
857 3202 3.110178 CGTTGCTTCGTCGTCCCC 61.110 66.667 0.00 0.00 0.00 4.81
900 3245 7.067421 GTCTATCTATATATAGCACCACCCCA 58.933 42.308 14.03 0.00 30.79 4.96
933 3278 6.558775 GGCTATATATCCATGGAGATGGGTAA 59.441 42.308 28.39 11.25 46.54 2.85
934 3279 7.072454 GGCTATATATCCATGGAGATGGGTAAA 59.928 40.741 28.39 10.54 46.54 2.01
935 3280 7.934120 GCTATATATCCATGGAGATGGGTAAAC 59.066 40.741 28.39 10.05 46.54 2.01
936 3281 9.218525 CTATATATCCATGGAGATGGGTAAACT 57.781 37.037 28.39 6.71 46.54 2.66
938 3283 7.888514 ATATCCATGGAGATGGGTAAACTAA 57.111 36.000 21.04 0.00 46.54 2.24
939 3284 8.468547 ATATCCATGGAGATGGGTAAACTAAT 57.531 34.615 21.04 0.00 46.54 1.73
940 3285 8.904963 ATATCCATGGAGATGGGTAAACTAATT 58.095 33.333 21.04 0.00 46.54 1.40
943 3288 8.396272 CCATGGAGATGGGTAAACTAATTAAG 57.604 38.462 5.56 0.00 45.11 1.85
944 3289 8.217799 CCATGGAGATGGGTAAACTAATTAAGA 58.782 37.037 5.56 0.00 45.11 2.10
945 3290 9.627123 CATGGAGATGGGTAAACTAATTAAGAA 57.373 33.333 0.00 0.00 0.00 2.52
946 3291 9.853177 ATGGAGATGGGTAAACTAATTAAGAAG 57.147 33.333 0.00 0.00 0.00 2.85
947 3292 7.773690 TGGAGATGGGTAAACTAATTAAGAAGC 59.226 37.037 0.00 0.00 0.00 3.86
948 3293 7.773690 GGAGATGGGTAAACTAATTAAGAAGCA 59.226 37.037 0.00 0.00 0.00 3.91
949 3294 9.174166 GAGATGGGTAAACTAATTAAGAAGCAA 57.826 33.333 0.00 0.00 0.00 3.91
950 3295 9.528489 AGATGGGTAAACTAATTAAGAAGCAAA 57.472 29.630 0.00 0.00 0.00 3.68
1031 3399 0.898789 TTCACCACCGTCTCCTCCTC 60.899 60.000 0.00 0.00 0.00 3.71
1033 3401 2.360980 CCACCGTCTCCTCCTCCT 59.639 66.667 0.00 0.00 0.00 3.69
1034 3402 1.305381 CCACCGTCTCCTCCTCCTT 60.305 63.158 0.00 0.00 0.00 3.36
1035 3403 1.324005 CCACCGTCTCCTCCTCCTTC 61.324 65.000 0.00 0.00 0.00 3.46
1036 3404 0.323908 CACCGTCTCCTCCTCCTTCT 60.324 60.000 0.00 0.00 0.00 2.85
1129 3512 0.042188 CAAGGTCAAGACGTTGTGCG 60.042 55.000 21.23 2.95 46.28 5.34
1174 3557 3.333189 CCTCCATGATCACGCGCG 61.333 66.667 30.96 30.96 0.00 6.86
1177 3560 2.885164 CCATGATCACGCGCGACA 60.885 61.111 39.36 27.44 0.00 4.35
1184 3567 3.391631 CACGCGCGACAACGAGAA 61.392 61.111 39.36 0.00 41.48 2.87
1186 3569 4.449161 CGCGCGACAACGAGAACG 62.449 66.667 28.94 0.00 41.48 3.95
1200 3583 0.505655 AGAACGTAAGCGCAAACGAC 59.494 50.000 32.20 24.79 41.55 4.34
1203 3586 1.055235 CGTAAGCGCAAACGACGAG 59.945 57.895 24.71 0.03 43.93 4.18
1251 3634 1.087501 CCGCCAAGCTCCTTCTTAAC 58.912 55.000 0.00 0.00 0.00 2.01
1329 3712 0.316607 CCGACGAGATCTGCTTCGAG 60.317 60.000 15.47 6.93 30.29 4.04
1335 3718 1.748493 GAGATCTGCTTCGAGACCTGT 59.252 52.381 0.00 0.00 0.00 4.00
1382 3765 1.154205 ACACTCGACAAGCTGTGCAC 61.154 55.000 10.75 10.75 34.14 4.57
1383 3766 1.951130 ACTCGACAAGCTGTGCACG 60.951 57.895 13.13 8.32 33.50 5.34
1488 3871 1.821136 CAAGGGGAAGCCAAGAACATC 59.179 52.381 0.00 0.00 0.00 3.06
1639 4024 6.937436 TGGTTAGTTTCCTTTTCTGTCTTC 57.063 37.500 0.00 0.00 0.00 2.87
1710 4101 1.972872 ATGCACACTGCTATTAGGGC 58.027 50.000 0.00 0.00 45.31 5.19
1853 4247 1.059835 GCTAAACTTCTTGAGCGCTCG 59.940 52.381 30.75 18.54 0.00 5.03
1875 4269 4.154737 CGGCATTGGAGTAATATGGTCATG 59.845 45.833 0.00 0.00 0.00 3.07
1882 4276 4.702131 GGAGTAATATGGTCATGGGATTGC 59.298 45.833 0.00 0.00 0.00 3.56
1894 4288 4.656575 TCATGGGATTGCCATGATTTGATT 59.343 37.500 29.68 0.00 45.88 2.57
1904 4298 8.481974 TTGCCATGATTTGATTGTTAAGATTG 57.518 30.769 0.00 0.00 0.00 2.67
1931 4326 2.777459 TTGCCCCTTGGGTCTTTTTA 57.223 45.000 4.84 0.00 46.51 1.52
1973 4368 9.313118 AGTTGTATCATTTGGTTTTGTTTTCTC 57.687 29.630 0.00 0.00 0.00 2.87
2055 4453 8.617290 AGACATTTTAACTCAATCCTACGTTT 57.383 30.769 0.00 0.00 0.00 3.60
2067 4465 8.246430 TCAATCCTACGTTTAGTGAATATCCT 57.754 34.615 0.00 0.00 0.00 3.24
2108 4506 7.749126 AGATGCATAGCTAACACGTTTAAAAAC 59.251 33.333 0.00 0.00 35.59 2.43
2125 4523 9.627657 GTTTAAAAACGGAAAGTAAAAAGCATC 57.372 29.630 0.00 0.00 0.00 3.91
2140 4538 6.385649 AAAAGCATCGACTTACAGGAAAAA 57.614 33.333 0.00 0.00 0.00 1.94
2173 4571 7.757242 AAACTAAGATGGAGGAGGTTCTATT 57.243 36.000 0.00 0.00 0.00 1.73
2174 4572 7.757242 AACTAAGATGGAGGAGGTTCTATTT 57.243 36.000 0.00 0.00 0.00 1.40
2183 4581 5.187967 GGAGGAGGTTCTATTTGAAGAGTCA 59.812 44.000 0.00 0.00 35.01 3.41
2288 7502 0.821517 TGGAGCCGGTGTGTACATAG 59.178 55.000 1.90 0.00 0.00 2.23
2289 7503 0.822164 GGAGCCGGTGTGTACATAGT 59.178 55.000 1.90 0.00 0.00 2.12
2290 7504 2.026641 GGAGCCGGTGTGTACATAGTA 58.973 52.381 1.90 0.00 0.00 1.82
2291 7505 2.223665 GGAGCCGGTGTGTACATAGTAC 60.224 54.545 1.90 0.51 0.00 2.73
2292 7506 2.424601 GAGCCGGTGTGTACATAGTACA 59.575 50.000 1.90 5.94 0.00 2.90
2293 7507 2.165030 AGCCGGTGTGTACATAGTACAC 59.835 50.000 25.57 25.57 45.77 2.90
2326 7540 3.005050 CCAGCACATCAGTTGAAACACAT 59.995 43.478 0.00 0.00 0.00 3.21
2461 7737 3.302221 CCAAACATATTACGAACGCTCCG 60.302 47.826 0.00 0.00 0.00 4.63
2515 7791 9.277783 GAATATATAAGGATGACTTGCAGTGTT 57.722 33.333 0.00 0.00 40.37 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.119137 ACAACAGGGCAAAACTTGAAGTC 60.119 43.478 0.00 0.00 0.00 3.01
17 18 1.542915 CTTTCATGGCAGACAACAGGG 59.457 52.381 0.00 0.00 0.00 4.45
24 25 4.757149 ACTGACTAAACTTTCATGGCAGAC 59.243 41.667 10.24 0.00 0.00 3.51
77 78 8.561738 TTCACTCAAGGACAAAATATAAGGAC 57.438 34.615 0.00 0.00 0.00 3.85
101 102 9.349713 GGAAAAAGGGTCTTGGAAAATTAAATT 57.650 29.630 0.00 0.00 0.00 1.82
176 177 5.869344 GGAATAACTGAAACCAAATGAAGGC 59.131 40.000 0.00 0.00 0.00 4.35
188 189 8.783093 CACTACTCAACAATGGAATAACTGAAA 58.217 33.333 0.00 0.00 0.00 2.69
189 190 7.094805 GCACTACTCAACAATGGAATAACTGAA 60.095 37.037 0.00 0.00 0.00 3.02
190 191 6.371548 GCACTACTCAACAATGGAATAACTGA 59.628 38.462 0.00 0.00 0.00 3.41
191 192 6.149308 TGCACTACTCAACAATGGAATAACTG 59.851 38.462 0.00 0.00 0.00 3.16
192 193 6.237901 TGCACTACTCAACAATGGAATAACT 58.762 36.000 0.00 0.00 0.00 2.24
214 215 2.943033 AGTGTGGCGGAAGTAATAATGC 59.057 45.455 0.00 0.00 0.00 3.56
216 217 3.377172 GCAAGTGTGGCGGAAGTAATAAT 59.623 43.478 0.00 0.00 0.00 1.28
217 218 2.745281 GCAAGTGTGGCGGAAGTAATAA 59.255 45.455 0.00 0.00 0.00 1.40
218 219 2.352388 GCAAGTGTGGCGGAAGTAATA 58.648 47.619 0.00 0.00 0.00 0.98
255 257 8.058235 TGACCCTAAATTGAAATGATATGTCCA 58.942 33.333 0.00 0.00 0.00 4.02
280 283 2.180017 GCAAGCCATCGTGCCTTG 59.820 61.111 4.93 4.93 40.97 3.61
334 337 6.850752 AGGAACATGGGAAACGAAAATTAT 57.149 33.333 0.00 0.00 0.00 1.28
343 346 4.302559 AACTCCTAGGAACATGGGAAAC 57.697 45.455 13.77 0.00 0.00 2.78
371 381 8.677148 AGTTGTAGTAGTGTTTCATTGACATT 57.323 30.769 0.00 0.00 0.00 2.71
413 423 7.179269 TGGCTACTTGGTTGGAAACTAATAAT 58.821 34.615 0.00 0.00 46.35 1.28
416 426 4.993028 TGGCTACTTGGTTGGAAACTAAT 58.007 39.130 0.00 0.00 46.35 1.73
445 455 2.168728 GGAGGGAGTAGTTGGCTAGTTG 59.831 54.545 0.00 0.00 31.38 3.16
446 456 2.468915 GGAGGGAGTAGTTGGCTAGTT 58.531 52.381 0.00 0.00 31.38 2.24
447 457 1.685491 CGGAGGGAGTAGTTGGCTAGT 60.685 57.143 0.00 0.00 33.77 2.57
448 458 1.033574 CGGAGGGAGTAGTTGGCTAG 58.966 60.000 0.00 0.00 0.00 3.42
449 459 0.333993 ACGGAGGGAGTAGTTGGCTA 59.666 55.000 0.00 0.00 0.00 3.93
451 461 1.516423 GACGGAGGGAGTAGTTGGC 59.484 63.158 0.00 0.00 0.00 4.52
452 462 1.328430 GGGACGGAGGGAGTAGTTGG 61.328 65.000 0.00 0.00 0.00 3.77
453 463 0.613853 TGGGACGGAGGGAGTAGTTG 60.614 60.000 0.00 0.00 0.00 3.16
454 464 0.338814 ATGGGACGGAGGGAGTAGTT 59.661 55.000 0.00 0.00 0.00 2.24
455 465 0.397254 CATGGGACGGAGGGAGTAGT 60.397 60.000 0.00 0.00 0.00 2.73
456 466 0.106167 TCATGGGACGGAGGGAGTAG 60.106 60.000 0.00 0.00 0.00 2.57
457 467 0.561184 ATCATGGGACGGAGGGAGTA 59.439 55.000 0.00 0.00 0.00 2.59
458 468 0.561184 TATCATGGGACGGAGGGAGT 59.439 55.000 0.00 0.00 0.00 3.85
459 469 1.203063 TCTATCATGGGACGGAGGGAG 60.203 57.143 0.00 0.00 0.00 4.30
460 470 0.857675 TCTATCATGGGACGGAGGGA 59.142 55.000 0.00 0.00 0.00 4.20
462 472 1.261480 CCTCTATCATGGGACGGAGG 58.739 60.000 0.00 0.00 38.16 4.30
463 473 1.261480 CCCTCTATCATGGGACGGAG 58.739 60.000 0.00 0.00 46.15 4.63
465 475 0.681733 CACCCTCTATCATGGGACGG 59.318 60.000 4.93 0.00 46.15 4.79
466 476 1.414158 ACACCCTCTATCATGGGACG 58.586 55.000 4.93 0.00 46.15 4.79
467 477 3.933861 AAACACCCTCTATCATGGGAC 57.066 47.619 4.93 0.00 46.15 4.46
491 501 5.116983 CGGTTTTTGACATTATTGCAGTGTC 59.883 40.000 13.41 13.41 41.90 3.67
492 502 4.981674 CGGTTTTTGACATTATTGCAGTGT 59.018 37.500 0.00 0.00 0.00 3.55
494 504 5.009610 AGACGGTTTTTGACATTATTGCAGT 59.990 36.000 0.00 0.00 0.00 4.40
496 506 5.446143 AGACGGTTTTTGACATTATTGCA 57.554 34.783 0.00 0.00 0.00 4.08
501 669 7.858382 CACAATGTAAGACGGTTTTTGACATTA 59.142 33.333 10.44 0.00 35.02 1.90
515 683 2.618053 CTCCGTCCCACAATGTAAGAC 58.382 52.381 5.24 5.24 0.00 3.01
516 684 1.553248 CCTCCGTCCCACAATGTAAGA 59.447 52.381 0.00 0.00 0.00 2.10
517 685 1.406887 CCCTCCGTCCCACAATGTAAG 60.407 57.143 0.00 0.00 0.00 2.34
518 686 0.616371 CCCTCCGTCCCACAATGTAA 59.384 55.000 0.00 0.00 0.00 2.41
519 687 0.252330 TCCCTCCGTCCCACAATGTA 60.252 55.000 0.00 0.00 0.00 2.29
531 918 6.812879 AAACAAAAATAACTACTCCCTCCG 57.187 37.500 0.00 0.00 0.00 4.63
555 2801 7.310237 CTAGTTGGCTAGTAGGTTGGAAACTAA 60.310 40.741 0.00 0.00 42.03 2.24
556 2802 6.154021 CTAGTTGGCTAGTAGGTTGGAAACTA 59.846 42.308 0.00 0.00 42.03 2.24
558 2804 5.176592 CTAGTTGGCTAGTAGGTTGGAAAC 58.823 45.833 0.00 0.00 41.84 2.78
559 2805 5.416271 CTAGTTGGCTAGTAGGTTGGAAA 57.584 43.478 0.00 0.00 39.77 3.13
587 2833 8.662781 AGCTAAGATGCATATTCGTAGAAAAA 57.337 30.769 10.37 0.00 37.23 1.94
588 2834 9.758651 TTAGCTAAGATGCATATTCGTAGAAAA 57.241 29.630 10.37 1.92 37.23 2.29
589 2835 9.929180 ATTAGCTAAGATGCATATTCGTAGAAA 57.071 29.630 10.37 5.01 37.23 2.52
591 2837 9.358872 CAATTAGCTAAGATGCATATTCGTAGA 57.641 33.333 10.37 0.00 34.99 2.59
592 2838 9.144747 ACAATTAGCTAAGATGCATATTCGTAG 57.855 33.333 10.37 7.09 34.99 3.51
593 2839 8.925700 CACAATTAGCTAAGATGCATATTCGTA 58.074 33.333 10.37 0.00 34.99 3.43
595 2841 7.095060 ACCACAATTAGCTAAGATGCATATTCG 60.095 37.037 10.37 5.47 34.99 3.34
597 2843 7.941238 AGACCACAATTAGCTAAGATGCATATT 59.059 33.333 11.88 11.88 34.99 1.28
599 2845 6.830912 AGACCACAATTAGCTAAGATGCATA 58.169 36.000 12.54 0.00 34.99 3.14
607 2927 6.097356 CGTGTTCTAGACCACAATTAGCTAA 58.903 40.000 19.09 8.99 0.00 3.09
610 2930 4.243270 ACGTGTTCTAGACCACAATTAGC 58.757 43.478 19.09 0.00 0.00 3.09
621 2941 5.679734 AACTCGAACTTACGTGTTCTAGA 57.320 39.130 20.29 10.10 43.10 2.43
625 2945 4.317628 GGTCAAACTCGAACTTACGTGTTC 60.318 45.833 8.35 8.35 44.82 3.18
626 2946 3.553105 GGTCAAACTCGAACTTACGTGTT 59.447 43.478 0.00 0.00 46.53 3.32
627 2947 3.118542 GGTCAAACTCGAACTTACGTGT 58.881 45.455 0.00 0.00 40.70 4.49
628 2948 3.060740 GTGGTCAAACTCGAACTTACGTG 60.061 47.826 0.00 0.00 34.70 4.49
630 2950 2.473984 GGTGGTCAAACTCGAACTTACG 59.526 50.000 0.00 0.00 0.00 3.18
631 2951 2.804527 GGGTGGTCAAACTCGAACTTAC 59.195 50.000 0.00 0.00 0.00 2.34
632 2952 3.116079 GGGTGGTCAAACTCGAACTTA 57.884 47.619 0.00 0.00 0.00 2.24
633 2953 1.963172 GGGTGGTCAAACTCGAACTT 58.037 50.000 0.00 0.00 0.00 2.66
639 2959 2.140717 CACTAACGGGTGGTCAAACTC 58.859 52.381 0.00 0.00 33.95 3.01
640 2960 1.812708 GCACTAACGGGTGGTCAAACT 60.813 52.381 7.36 0.00 37.65 2.66
641 2961 0.589708 GCACTAACGGGTGGTCAAAC 59.410 55.000 7.36 0.00 37.65 2.93
642 2962 0.535553 GGCACTAACGGGTGGTCAAA 60.536 55.000 7.36 0.00 37.65 2.69
643 2963 1.071814 GGCACTAACGGGTGGTCAA 59.928 57.895 7.36 0.00 37.65 3.18
644 2964 1.839747 AGGCACTAACGGGTGGTCA 60.840 57.895 7.36 0.00 36.02 4.02
645 2965 1.375523 CAGGCACTAACGGGTGGTC 60.376 63.158 7.36 0.00 36.02 4.02
651 2971 3.118454 CGTGGCAGGCACTAACGG 61.118 66.667 23.66 5.12 36.02 4.44
681 3001 2.729194 TGCCACAAACTGTAAACCACT 58.271 42.857 0.00 0.00 0.00 4.00
719 3054 1.115467 ATAGAGGTGAGGCAACCGAG 58.885 55.000 3.99 0.00 45.53 4.63
724 3068 2.103094 CGAATCCATAGAGGTGAGGCAA 59.897 50.000 0.00 0.00 39.02 4.52
725 3069 1.688735 CGAATCCATAGAGGTGAGGCA 59.311 52.381 0.00 0.00 39.02 4.75
738 3082 1.679139 GCCATGGTCAATCGAATCCA 58.321 50.000 14.67 0.00 0.00 3.41
739 3083 0.954452 GGCCATGGTCAATCGAATCC 59.046 55.000 12.68 0.00 0.00 3.01
740 3084 1.334869 GTGGCCATGGTCAATCGAATC 59.665 52.381 23.33 2.31 0.00 2.52
741 3085 1.392589 GTGGCCATGGTCAATCGAAT 58.607 50.000 23.33 0.00 0.00 3.34
742 3086 0.679640 GGTGGCCATGGTCAATCGAA 60.680 55.000 23.33 0.00 0.00 3.71
769 3113 3.806625 TCGTAAGGAAAATAGGGGTCG 57.193 47.619 0.00 0.00 38.47 4.79
770 3114 5.070047 TGAGATCGTAAGGAAAATAGGGGTC 59.930 44.000 0.00 0.00 38.47 4.46
798 3142 6.647067 GGAGGTATATGTGTGAGCTATGTTTC 59.353 42.308 0.00 0.00 0.00 2.78
845 3190 1.379576 AGGGTAGGGGACGACGAAG 60.380 63.158 0.00 0.00 36.74 3.79
900 3245 7.031415 TCCATGGATATATAGCCAAATGTGT 57.969 36.000 22.90 3.31 45.93 3.72
934 3279 9.549078 GCCTAGACTATTTGCTTCTTAATTAGT 57.451 33.333 0.00 0.00 30.92 2.24
935 3280 8.994170 GGCCTAGACTATTTGCTTCTTAATTAG 58.006 37.037 0.00 0.00 0.00 1.73
936 3281 8.714906 AGGCCTAGACTATTTGCTTCTTAATTA 58.285 33.333 1.29 0.00 0.00 1.40
937 3282 7.578203 AGGCCTAGACTATTTGCTTCTTAATT 58.422 34.615 1.29 0.00 0.00 1.40
938 3283 7.142995 AGGCCTAGACTATTTGCTTCTTAAT 57.857 36.000 1.29 0.00 0.00 1.40
939 3284 6.408206 GGAGGCCTAGACTATTTGCTTCTTAA 60.408 42.308 4.42 0.00 0.00 1.85
940 3285 5.070580 GGAGGCCTAGACTATTTGCTTCTTA 59.929 44.000 4.42 0.00 0.00 2.10
941 3286 4.141597 GGAGGCCTAGACTATTTGCTTCTT 60.142 45.833 4.42 0.00 0.00 2.52
942 3287 3.389656 GGAGGCCTAGACTATTTGCTTCT 59.610 47.826 4.42 0.00 0.00 2.85
943 3288 3.134804 TGGAGGCCTAGACTATTTGCTTC 59.865 47.826 4.42 0.00 0.00 3.86
944 3289 3.115390 TGGAGGCCTAGACTATTTGCTT 58.885 45.455 4.42 0.00 0.00 3.91
945 3290 2.764269 TGGAGGCCTAGACTATTTGCT 58.236 47.619 4.42 0.00 0.00 3.91
946 3291 3.206964 GTTGGAGGCCTAGACTATTTGC 58.793 50.000 4.42 0.00 0.00 3.68
947 3292 3.118738 ACGTTGGAGGCCTAGACTATTTG 60.119 47.826 4.42 0.00 0.00 2.32
948 3293 3.105283 ACGTTGGAGGCCTAGACTATTT 58.895 45.455 4.42 0.00 0.00 1.40
949 3294 2.748388 ACGTTGGAGGCCTAGACTATT 58.252 47.619 4.42 0.00 0.00 1.73
950 3295 2.456073 ACGTTGGAGGCCTAGACTAT 57.544 50.000 4.42 0.00 0.00 2.12
951 3296 2.648059 GTACGTTGGAGGCCTAGACTA 58.352 52.381 4.42 0.00 0.00 2.59
952 3297 1.472188 GTACGTTGGAGGCCTAGACT 58.528 55.000 4.42 0.00 0.00 3.24
1031 3399 1.604396 GACGACGACGAAGAAGAAGG 58.396 55.000 15.32 0.00 42.66 3.46
1033 3401 0.583438 ACGACGACGACGAAGAAGAA 59.417 50.000 25.15 0.00 42.66 2.52
1034 3402 0.162507 GACGACGACGACGAAGAAGA 59.837 55.000 25.15 0.00 42.66 2.87
1035 3403 0.788645 GGACGACGACGACGAAGAAG 60.789 60.000 25.15 2.87 42.66 2.85
1036 3404 1.205064 GGACGACGACGACGAAGAA 59.795 57.895 25.15 0.00 42.66 2.52
1091 3462 4.404098 GGTTGTCCCCATCGGCGT 62.404 66.667 6.85 0.00 0.00 5.68
1111 3494 1.772063 GCGCACAACGTCTTGACCTT 61.772 55.000 0.30 0.00 46.11 3.50
1112 3495 2.244651 GCGCACAACGTCTTGACCT 61.245 57.895 0.30 0.00 46.11 3.85
1184 3567 1.602877 CTCGTCGTTTGCGCTTACGT 61.603 55.000 25.82 0.00 42.83 3.57
1186 3569 0.362512 CTCTCGTCGTTTGCGCTTAC 59.637 55.000 9.73 5.62 38.14 2.34
1187 3570 1.342082 GCTCTCGTCGTTTGCGCTTA 61.342 55.000 9.73 0.00 38.14 3.09
1189 3572 3.106407 GCTCTCGTCGTTTGCGCT 61.106 61.111 9.73 0.00 38.14 5.92
1200 3583 1.153289 CATCCCCACAAGGCTCTCG 60.153 63.158 0.00 0.00 0.00 4.04
1203 3586 2.440980 GCCATCCCCACAAGGCTC 60.441 66.667 0.00 0.00 43.70 4.70
1300 3683 1.680522 ATCTCGTCGGCCTTGCTCAT 61.681 55.000 0.00 0.00 0.00 2.90
1329 3712 2.147150 GTCAGCTCCTTGAAACAGGTC 58.853 52.381 0.00 0.00 35.15 3.85
1335 3718 1.593196 CGTTGGTCAGCTCCTTGAAA 58.407 50.000 0.00 0.00 0.00 2.69
1392 3775 2.115291 GTCGATTTGGGGGAGCTGC 61.115 63.158 0.00 0.00 0.00 5.25
1488 3871 1.874019 CTTGGAGACATCGTCGGCG 60.874 63.158 1.15 1.15 42.32 6.46
1590 3973 5.443185 ACGTAACAACAGCTAGTACTCAA 57.557 39.130 0.00 0.00 0.00 3.02
1639 4024 5.300286 CCAAGGAAACTAATAAGATGCCCAG 59.700 44.000 0.00 0.00 42.68 4.45
1822 4216 6.908825 TCAAGAAGTTTAGCGTGCAATTAAT 58.091 32.000 0.00 0.00 0.00 1.40
1849 4243 2.744202 CCATATTACTCCAATGCCGAGC 59.256 50.000 0.00 0.00 0.00 5.03
1853 4247 4.460382 CCATGACCATATTACTCCAATGCC 59.540 45.833 0.00 0.00 0.00 4.40
1856 4250 6.725101 ATCCCATGACCATATTACTCCAAT 57.275 37.500 0.00 0.00 0.00 3.16
1875 4269 4.411256 ACAATCAAATCATGGCAATCCC 57.589 40.909 0.00 0.00 0.00 3.85
1894 4288 6.213195 AGGGGCAAATTCAATCAATCTTAACA 59.787 34.615 0.00 0.00 0.00 2.41
1904 4298 2.696989 CCCAAGGGGCAAATTCAATC 57.303 50.000 0.00 0.00 35.35 2.67
1949 4344 7.436673 CGGAGAAAACAAAACCAAATGATACAA 59.563 33.333 0.00 0.00 0.00 2.41
1955 4350 4.206200 CGACGGAGAAAACAAAACCAAATG 59.794 41.667 0.00 0.00 0.00 2.32
1958 4353 2.097791 CCGACGGAGAAAACAAAACCAA 59.902 45.455 8.64 0.00 0.00 3.67
2030 4428 8.617290 AAACGTAGGATTGAGTTAAAATGTCT 57.383 30.769 0.00 0.00 0.00 3.41
2055 4453 9.862149 TGTTATGTAGAGTCAGGATATTCACTA 57.138 33.333 0.00 0.00 0.00 2.74
2067 4465 6.925718 GCTATGCATCTTGTTATGTAGAGTCA 59.074 38.462 0.19 0.00 34.49 3.41
2108 4506 4.663636 AGTCGATGCTTTTTACTTTCCG 57.336 40.909 0.00 0.00 0.00 4.30
2110 4508 7.015877 CCTGTAAGTCGATGCTTTTTACTTTC 58.984 38.462 0.00 0.00 32.85 2.62
2114 4512 6.476243 TTCCTGTAAGTCGATGCTTTTTAC 57.524 37.500 0.00 0.00 0.00 2.01
2140 4538 7.667635 CCTCCTCCATCTTAGTTTTTCTTTCTT 59.332 37.037 0.00 0.00 0.00 2.52
2141 4539 7.171653 CCTCCTCCATCTTAGTTTTTCTTTCT 58.828 38.462 0.00 0.00 0.00 2.52
2142 4540 6.943146 ACCTCCTCCATCTTAGTTTTTCTTTC 59.057 38.462 0.00 0.00 0.00 2.62
2143 4541 6.853490 ACCTCCTCCATCTTAGTTTTTCTTT 58.147 36.000 0.00 0.00 0.00 2.52
2144 4542 6.455690 ACCTCCTCCATCTTAGTTTTTCTT 57.544 37.500 0.00 0.00 0.00 2.52
2145 4543 6.273495 AGAACCTCCTCCATCTTAGTTTTTCT 59.727 38.462 0.00 0.00 0.00 2.52
2146 4544 6.477253 AGAACCTCCTCCATCTTAGTTTTTC 58.523 40.000 0.00 0.00 0.00 2.29
2173 4571 4.558898 GCGGAGTAGTCTTTGACTCTTCAA 60.559 45.833 3.30 0.00 42.40 2.69
2174 4572 3.057456 GCGGAGTAGTCTTTGACTCTTCA 60.057 47.826 3.30 0.00 42.40 3.02
2183 4581 1.568504 TGGATGGCGGAGTAGTCTTT 58.431 50.000 0.00 0.00 0.00 2.52
2288 7502 3.374058 GTGCTGGGTATTCATGTGTGTAC 59.626 47.826 0.00 0.00 0.00 2.90
2289 7503 3.008485 TGTGCTGGGTATTCATGTGTGTA 59.992 43.478 0.00 0.00 0.00 2.90
2290 7504 2.224744 TGTGCTGGGTATTCATGTGTGT 60.225 45.455 0.00 0.00 0.00 3.72
2291 7505 2.435422 TGTGCTGGGTATTCATGTGTG 58.565 47.619 0.00 0.00 0.00 3.82
2292 7506 2.877097 TGTGCTGGGTATTCATGTGT 57.123 45.000 0.00 0.00 0.00 3.72
2293 7507 3.281158 TGATGTGCTGGGTATTCATGTG 58.719 45.455 0.00 0.00 0.00 3.21
2294 7508 3.054139 ACTGATGTGCTGGGTATTCATGT 60.054 43.478 0.00 0.00 0.00 3.21
2371 7585 2.571212 CTTTGGCGGCAATCCTATGTA 58.429 47.619 26.07 6.76 0.00 2.29
2426 7702 2.136298 TGTTTGGCAACTGGTTGAGA 57.864 45.000 16.41 0.07 42.93 3.27
2461 7737 0.696501 TTGAAGCTTCTACCCACCCC 59.303 55.000 26.09 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.