Multiple sequence alignment - TraesCS5D01G536200

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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 TraesCS5D01G536200 chr5D 100.000 3586 0 0 1 3586 549645922 549649507 0.000000e+00 6623
1 TraesCS5D01G536200 chr5D 88.415 1148 114 10 1453 2594 549657077 549655943 0.000000e+00 1365
2 TraesCS5D01G536200 chr5D 79.487 585 73 25 819 1377 549657794 549657231 4.370000e-99 372
3 TraesCS5D01G536200 chr5B 89.163 3654 198 85 2 3586 701187132 701190656 0.000000e+00 4372
4 TraesCS5D01G536200 chr5B 88.847 1058 104 9 1544 2599 701196525 701195480 0.000000e+00 1288
5 TraesCS5D01G536200 chr5B 88.421 95 4 1 253 340 701197687 701197593 1.360000e-19 108
6 TraesCS5D01G536200 chr4A 90.286 2100 113 29 726 2747 621187744 621189830 0.000000e+00 2663
7 TraesCS5D01G536200 chr4A 91.731 907 75 0 1689 2595 621241381 621240475 0.000000e+00 1260
8 TraesCS5D01G536200 chr4A 87.935 489 28 10 7 484 621181499 621181967 6.770000e-152 547
9 TraesCS5D01G536200 chr4A 85.393 356 37 10 3017 3366 621190905 621191251 4.400000e-94 355
10 TraesCS5D01G536200 chr4A 94.372 231 12 1 3357 3586 621191270 621191500 1.580000e-93 353
11 TraesCS5D01G536200 chr4A 79.310 551 65 32 791 1315 621242336 621241809 1.230000e-89 340
12 TraesCS5D01G536200 chr4A 77.419 279 39 15 29 293 621242978 621242710 1.040000e-30 145
13 TraesCS5D01G536200 chr3A 80.465 215 38 2 2017 2229 671678266 671678054 1.030000e-35 161
14 TraesCS5D01G536200 chr3D 79.070 215 41 2 2017 2229 536143735 536143947 1.040000e-30 145


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 TraesCS5D01G536200 chr5D 549645922 549649507 3585 False 6623.000000 6623 100.000 1 3586 1 chr5D.!!$F1 3585
1 TraesCS5D01G536200 chr5D 549655943 549657794 1851 True 868.500000 1365 83.951 819 2594 2 chr5D.!!$R1 1775
2 TraesCS5D01G536200 chr5B 701187132 701190656 3524 False 4372.000000 4372 89.163 2 3586 1 chr5B.!!$F1 3584
3 TraesCS5D01G536200 chr5B 701195480 701197687 2207 True 698.000000 1288 88.634 253 2599 2 chr5B.!!$R1 2346
4 TraesCS5D01G536200 chr4A 621187744 621191500 3756 False 1123.666667 2663 90.017 726 3586 3 chr4A.!!$F2 2860
5 TraesCS5D01G536200 chr4A 621240475 621242978 2503 True 581.666667 1260 82.820 29 2595 3 chr4A.!!$R1 2566

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
462 523 0.032678 CACAGACTCTCGTGCACCTT 59.967 55.0 12.15 0.0 0.00 3.50 F
466 527 0.033504 GACTCTCGTGCACCTTCCAA 59.966 55.0 12.15 0.0 0.00 3.53 F
852 972 0.106149 CCGGAGCCGCCTATTTAAGT 59.894 55.0 0.00 0.0 38.24 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 1509 1.271597 GCTGGGAAGATGACTTGTGGT 60.272 52.381 0.0 0.0 36.39 4.16 R
2270 2888 1.991167 CGGGTACTTGCCCCTACCA 60.991 63.158 0.0 0.0 45.91 3.25 R
2748 3369 3.802139 GTGGTAAAACAGGAAAAAGCAGC 59.198 43.478 0.0 0.0 0.00 5.25 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
52 53 6.403309 GGTTAATCACGGAGAAGGAATTGTTC 60.403 42.308 0.00 0.00 0.00 3.18
103 104 1.873591 GGGTGTATTAATGGAGCAGCG 59.126 52.381 0.00 0.00 0.00 5.18
105 106 3.202906 GGTGTATTAATGGAGCAGCGAA 58.797 45.455 0.00 0.00 0.00 4.70
108 109 4.332819 GTGTATTAATGGAGCAGCGAACTT 59.667 41.667 0.00 0.00 0.00 2.66
109 110 4.332543 TGTATTAATGGAGCAGCGAACTTG 59.667 41.667 0.00 0.00 0.00 3.16
118 125 3.491652 GCGAACTTGAGCGGAGGC 61.492 66.667 0.00 0.00 40.37 4.70
163 173 3.301274 AGGTAGAGGATAGAACAGTGCC 58.699 50.000 0.00 0.00 0.00 5.01
164 174 2.365941 GGTAGAGGATAGAACAGTGCCC 59.634 54.545 0.00 0.00 0.00 5.36
303 339 5.220557 CCAAAAGTTGGCTCAAAAAGTTG 57.779 39.130 0.00 0.00 45.17 3.16
316 352 4.283212 TCAAAAAGTTGGCCTCCCTAATTG 59.717 41.667 3.32 6.32 35.29 2.32
344 394 1.000827 CTCCATCGCATTAGTCTCGCT 60.001 52.381 0.00 0.00 0.00 4.93
345 395 1.001268 TCCATCGCATTAGTCTCGCTC 60.001 52.381 0.00 0.00 0.00 5.03
346 396 1.000827 CCATCGCATTAGTCTCGCTCT 60.001 52.381 0.00 0.00 0.00 4.09
347 397 2.315011 CATCGCATTAGTCTCGCTCTC 58.685 52.381 0.00 0.00 0.00 3.20
348 398 0.305009 TCGCATTAGTCTCGCTCTCG 59.695 55.000 0.00 0.00 0.00 4.04
349 399 1.265462 CGCATTAGTCTCGCTCTCGC 61.265 60.000 0.00 0.00 35.26 5.03
393 443 0.870307 CAATCGTCGATCCGTCACCC 60.870 60.000 8.45 0.00 0.00 4.61
394 444 1.317431 AATCGTCGATCCGTCACCCA 61.317 55.000 8.45 0.00 0.00 4.51
395 445 2.001361 ATCGTCGATCCGTCACCCAC 62.001 60.000 0.75 0.00 0.00 4.61
453 514 4.803426 CGGCCGGCACAGACTCTC 62.803 72.222 30.85 6.07 0.00 3.20
454 515 4.803426 GGCCGGCACAGACTCTCG 62.803 72.222 30.85 0.00 0.00 4.04
455 516 4.057428 GCCGGCACAGACTCTCGT 62.057 66.667 24.80 0.00 0.00 4.18
456 517 2.126307 CCGGCACAGACTCTCGTG 60.126 66.667 0.00 0.00 36.18 4.35
460 521 4.251760 CACAGACTCTCGTGCACC 57.748 61.111 12.15 0.00 0.00 5.01
461 522 1.662608 CACAGACTCTCGTGCACCT 59.337 57.895 12.15 0.00 0.00 4.00
462 523 0.032678 CACAGACTCTCGTGCACCTT 59.967 55.000 12.15 0.00 0.00 3.50
463 524 0.315568 ACAGACTCTCGTGCACCTTC 59.684 55.000 12.15 0.51 0.00 3.46
464 525 0.389166 CAGACTCTCGTGCACCTTCC 60.389 60.000 12.15 0.00 0.00 3.46
465 526 0.827925 AGACTCTCGTGCACCTTCCA 60.828 55.000 12.15 0.00 0.00 3.53
466 527 0.033504 GACTCTCGTGCACCTTCCAA 59.966 55.000 12.15 0.00 0.00 3.53
467 528 0.687354 ACTCTCGTGCACCTTCCAAT 59.313 50.000 12.15 0.00 0.00 3.16
468 529 1.899814 ACTCTCGTGCACCTTCCAATA 59.100 47.619 12.15 0.00 0.00 1.90
469 530 2.501723 ACTCTCGTGCACCTTCCAATAT 59.498 45.455 12.15 0.00 0.00 1.28
470 531 3.126831 CTCTCGTGCACCTTCCAATATC 58.873 50.000 12.15 0.00 0.00 1.63
471 532 2.158957 TCTCGTGCACCTTCCAATATCC 60.159 50.000 12.15 0.00 0.00 2.59
472 533 1.557371 TCGTGCACCTTCCAATATCCA 59.443 47.619 12.15 0.00 0.00 3.41
473 534 2.172505 TCGTGCACCTTCCAATATCCAT 59.827 45.455 12.15 0.00 0.00 3.41
474 535 2.549754 CGTGCACCTTCCAATATCCATC 59.450 50.000 12.15 0.00 0.00 3.51
475 536 2.887152 GTGCACCTTCCAATATCCATCC 59.113 50.000 5.22 0.00 0.00 3.51
476 537 2.513317 TGCACCTTCCAATATCCATCCA 59.487 45.455 0.00 0.00 0.00 3.41
477 538 3.140707 TGCACCTTCCAATATCCATCCAT 59.859 43.478 0.00 0.00 0.00 3.41
478 539 3.508793 GCACCTTCCAATATCCATCCATG 59.491 47.826 0.00 0.00 0.00 3.66
479 540 3.508793 CACCTTCCAATATCCATCCATGC 59.491 47.826 0.00 0.00 0.00 4.06
480 541 3.094572 CCTTCCAATATCCATCCATGCC 58.905 50.000 0.00 0.00 0.00 4.40
481 542 3.500836 CCTTCCAATATCCATCCATGCCA 60.501 47.826 0.00 0.00 0.00 4.92
482 543 3.159213 TCCAATATCCATCCATGCCAC 57.841 47.619 0.00 0.00 0.00 5.01
483 544 1.814394 CCAATATCCATCCATGCCACG 59.186 52.381 0.00 0.00 0.00 4.94
484 545 2.552809 CCAATATCCATCCATGCCACGA 60.553 50.000 0.00 0.00 0.00 4.35
485 546 2.745821 CAATATCCATCCATGCCACGAG 59.254 50.000 0.00 0.00 0.00 4.18
486 547 1.423584 TATCCATCCATGCCACGAGT 58.576 50.000 0.00 0.00 0.00 4.18
487 548 0.107456 ATCCATCCATGCCACGAGTC 59.893 55.000 0.00 0.00 0.00 3.36
488 549 0.977627 TCCATCCATGCCACGAGTCT 60.978 55.000 0.00 0.00 0.00 3.24
501 562 3.979495 CCACGAGTCTAGTACACACAAAC 59.021 47.826 0.00 0.00 0.00 2.93
502 563 4.498513 CCACGAGTCTAGTACACACAAACA 60.499 45.833 0.00 0.00 0.00 2.83
513 574 1.102978 ACACAAACAGCCAACCTGAC 58.897 50.000 0.00 0.00 44.64 3.51
522 583 0.033504 GCCAACCTGACGAACTCTGA 59.966 55.000 0.00 0.00 0.00 3.27
536 603 5.244851 ACGAACTCTGATATATGTCAGGCAT 59.755 40.000 24.29 13.26 44.51 4.40
568 635 8.565896 TTACATTATGATGATCCCATTGCTAC 57.434 34.615 4.20 0.00 36.73 3.58
599 695 9.729281 TTTTTCCTCATTTCTAATACTAACCGT 57.271 29.630 0.00 0.00 0.00 4.83
663 783 4.202080 GCCGTCCGATATATATAGTGCCAA 60.202 45.833 0.00 0.00 0.00 4.52
666 786 6.641314 CCGTCCGATATATATAGTGCCAAATC 59.359 42.308 0.00 0.00 0.00 2.17
685 805 6.531240 CCAAATCAAGGTGCATGTTATGTTAC 59.469 38.462 0.00 0.00 0.00 2.50
686 806 7.315142 CAAATCAAGGTGCATGTTATGTTACT 58.685 34.615 0.00 0.00 0.00 2.24
687 807 5.878332 TCAAGGTGCATGTTATGTTACTG 57.122 39.130 0.00 0.00 0.00 2.74
775 895 1.935933 CCGATTTTACGGTGCTAGCT 58.064 50.000 17.23 0.00 46.70 3.32
776 896 3.088194 CCGATTTTACGGTGCTAGCTA 57.912 47.619 17.23 0.00 46.70 3.32
777 897 3.050619 CCGATTTTACGGTGCTAGCTAG 58.949 50.000 16.84 16.84 46.70 3.42
778 898 4.640304 CCGATTTTACGGTGCTAGCTAGC 61.640 52.174 34.20 34.20 46.70 3.42
852 972 0.106149 CCGGAGCCGCCTATTTAAGT 59.894 55.000 0.00 0.00 38.24 2.24
882 1004 3.365364 GCAACTCACACACTCCATTTAGC 60.365 47.826 0.00 0.00 0.00 3.09
893 1019 1.451936 CATTTAGCCCCTCCCTCCG 59.548 63.158 0.00 0.00 0.00 4.63
906 1034 1.592669 CCTCCGTGCTGGCTAATCG 60.593 63.158 0.00 0.00 37.80 3.34
913 1041 0.107752 TGCTGGCTAATCGCATCACA 60.108 50.000 0.00 0.00 41.67 3.58
922 1050 7.049754 TGGCTAATCGCATCACAATATCATAT 58.950 34.615 0.00 0.00 41.67 1.78
923 1051 8.203485 TGGCTAATCGCATCACAATATCATATA 58.797 33.333 0.00 0.00 41.67 0.86
924 1052 8.491152 GGCTAATCGCATCACAATATCATATAC 58.509 37.037 0.00 0.00 41.67 1.47
927 1055 7.920908 ATCGCATCACAATATCATATACTCG 57.079 36.000 0.00 0.00 0.00 4.18
986 1165 6.945938 AGTACATACTCGATCAGTTAGCTT 57.054 37.500 0.00 0.00 36.43 3.74
989 1168 4.098654 ACATACTCGATCAGTTAGCTTGCT 59.901 41.667 0.00 0.00 36.43 3.91
1201 1386 4.560856 GCCGCAACGCCACAACAA 62.561 61.111 0.00 0.00 0.00 2.83
1210 1395 2.052237 CCACAACAACAGCGCGTC 60.052 61.111 8.43 0.00 0.00 5.19
1226 1411 1.720805 CGTCCCGTTGTTCATCATCA 58.279 50.000 0.00 0.00 0.00 3.07
1315 1509 3.517296 TCACAAAGCCCAATTCTACCA 57.483 42.857 0.00 0.00 0.00 3.25
1340 1555 2.125552 TCATCTTCCCAGCACGCG 60.126 61.111 3.53 3.53 0.00 6.01
1378 1593 1.719246 TCAGTTTGCGATCGAGTTTCG 59.281 47.619 21.57 2.59 42.10 3.46
1385 1600 1.582502 GCGATCGAGTTTCGTACAAGG 59.417 52.381 21.57 0.00 41.35 3.61
1386 1601 2.730090 GCGATCGAGTTTCGTACAAGGA 60.730 50.000 21.57 0.00 41.35 3.36
1826 2444 2.046314 GCGGCACAAGGCTCCTTA 60.046 61.111 0.11 0.00 44.01 2.69
1907 2525 2.591753 CTGGTCGTGGCCATGGAT 59.408 61.111 24.78 0.00 37.96 3.41
1991 2609 3.179265 AACATCGACTTCGCCGCG 61.179 61.111 6.39 6.39 39.60 6.46
2270 2888 4.235762 ACGAAGCTGTGGCACGGT 62.236 61.111 26.18 16.70 41.65 4.83
2456 3074 2.497792 ATTGCTGCGTGGGGATTGGA 62.498 55.000 0.00 0.00 0.00 3.53
2519 3137 1.079819 CTATACCAGGATGCCGCCG 60.080 63.158 0.00 0.00 31.97 6.46
2680 3300 2.252714 GTGGGGATGGAGAGATAGACC 58.747 57.143 0.00 0.00 0.00 3.85
2697 3317 8.256356 AGATAGACCATAGAGTATTTGTTGCT 57.744 34.615 0.00 0.00 0.00 3.91
2698 3318 9.368416 AGATAGACCATAGAGTATTTGTTGCTA 57.632 33.333 0.00 0.00 0.00 3.49
2703 3323 8.263854 ACCATAGAGTATTTGTTGCTATACCT 57.736 34.615 0.00 0.00 0.00 3.08
2704 3324 8.368668 ACCATAGAGTATTTGTTGCTATACCTC 58.631 37.037 0.00 0.00 0.00 3.85
2779 3551 6.399639 TTCCTGTTTTACCACTTTCATTCC 57.600 37.500 0.00 0.00 0.00 3.01
2876 4463 8.617809 TGTAAACACAAAACATCCTTCTAGAAC 58.382 33.333 0.00 0.00 0.00 3.01
2950 4537 9.875675 TTTTCAAAATTTGTGAACACTTTTCAG 57.124 25.926 5.56 2.48 34.78 3.02
2951 4538 8.824159 TTCAAAATTTGTGAACACTTTTCAGA 57.176 26.923 5.56 4.21 30.08 3.27
2986 4573 9.322773 TGAATTGTTTTTAAATTGACATGAGCA 57.677 25.926 0.00 0.00 0.00 4.26
3062 4649 7.667043 AGTTATTTCTTTAGTTGCATGACGA 57.333 32.000 0.00 0.00 0.00 4.20
3063 4650 8.268850 AGTTATTTCTTTAGTTGCATGACGAT 57.731 30.769 0.00 0.00 0.00 3.73
3065 4652 9.341899 GTTATTTCTTTAGTTGCATGACGATTT 57.658 29.630 0.00 0.00 0.00 2.17
3147 4739 7.483375 TGAATAATTTTAAAACCGACATGAGCG 59.517 33.333 1.97 2.39 0.00 5.03
3299 4893 4.625607 AGGTTAGTTGCTAGCTTGTTCT 57.374 40.909 17.23 9.16 0.00 3.01
3306 4900 6.246420 AGTTGCTAGCTTGTTCTGTTATTG 57.754 37.500 17.23 0.00 0.00 1.90
3310 4904 1.812571 AGCTTGTTCTGTTATTGGCCG 59.187 47.619 0.00 0.00 0.00 6.13
3311 4905 1.732405 GCTTGTTCTGTTATTGGCCGC 60.732 52.381 0.00 0.00 0.00 6.53
3331 4925 2.097142 GCTCTGCATTCATTCACTGGTC 59.903 50.000 0.00 0.00 0.00 4.02
3367 4989 5.339008 AGAATCTTGCGAATGTACTACCA 57.661 39.130 0.00 0.00 0.00 3.25
3370 4992 2.829720 TCTTGCGAATGTACTACCACCT 59.170 45.455 0.00 0.00 0.00 4.00
3405 5027 3.446161 TGGTCCTAGAATCAAGTACCACG 59.554 47.826 0.00 0.00 30.84 4.94
3433 5055 9.811655 ATCGTTAGTTCATAATAATTGCATTCG 57.188 29.630 0.00 0.00 0.00 3.34
3446 5068 9.595823 AATAATTGCATTCGTGTACTTACTACT 57.404 29.630 0.00 0.00 0.00 2.57
3447 5069 6.887376 ATTGCATTCGTGTACTTACTACTG 57.113 37.500 0.00 0.00 0.00 2.74
3448 5070 5.381174 TGCATTCGTGTACTTACTACTGT 57.619 39.130 0.00 0.00 0.00 3.55
3463 5090 0.032615 ACTGTCCTAGCTAGCTGCCT 60.033 55.000 27.68 3.12 44.23 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.230864 GCACGCTAATTTCGTTGACAC 58.769 47.619 3.17 0.00 38.19 3.67
7 8 1.062525 GGCTGGCACGCTAATTTCG 59.937 57.895 8.45 0.00 0.00 3.46
66 67 2.161410 CACCCCACACGTATTGACATTG 59.839 50.000 0.00 0.00 0.00 2.82
67 68 2.224670 ACACCCCACACGTATTGACATT 60.225 45.455 0.00 0.00 0.00 2.71
68 69 1.349688 ACACCCCACACGTATTGACAT 59.650 47.619 0.00 0.00 0.00 3.06
103 104 1.743252 CTGGCCTCCGCTCAAGTTC 60.743 63.158 3.32 0.00 34.44 3.01
105 106 3.710722 CCTGGCCTCCGCTCAAGT 61.711 66.667 3.32 0.00 34.44 3.16
136 143 3.232662 GTTCTATCCTCTACCTCCCCAC 58.767 54.545 0.00 0.00 0.00 4.61
164 174 1.734477 CTGTGAGGTCTCCGTTGCG 60.734 63.158 0.00 0.00 0.00 4.85
303 339 1.387295 GCAGTGCAATTAGGGAGGCC 61.387 60.000 11.09 0.00 0.00 5.19
316 352 1.651240 AATGCGATGGAGTGCAGTGC 61.651 55.000 8.58 8.58 45.52 4.40
393 443 3.345011 TGGTGACATGCGTGCGTG 61.345 61.111 12.31 12.31 38.78 5.34
453 514 2.036958 TGGATATTGGAAGGTGCACG 57.963 50.000 11.45 0.00 0.00 5.34
454 515 2.887152 GGATGGATATTGGAAGGTGCAC 59.113 50.000 8.80 8.80 0.00 4.57
455 516 2.513317 TGGATGGATATTGGAAGGTGCA 59.487 45.455 0.00 0.00 0.00 4.57
456 517 3.228188 TGGATGGATATTGGAAGGTGC 57.772 47.619 0.00 0.00 0.00 5.01
457 518 3.508793 GCATGGATGGATATTGGAAGGTG 59.491 47.826 0.00 0.00 0.00 4.00
458 519 3.501019 GGCATGGATGGATATTGGAAGGT 60.501 47.826 0.00 0.00 0.00 3.50
459 520 3.094572 GGCATGGATGGATATTGGAAGG 58.905 50.000 0.00 0.00 0.00 3.46
460 521 3.508793 GTGGCATGGATGGATATTGGAAG 59.491 47.826 0.00 0.00 0.00 3.46
461 522 3.499338 GTGGCATGGATGGATATTGGAA 58.501 45.455 0.00 0.00 0.00 3.53
462 523 2.552809 CGTGGCATGGATGGATATTGGA 60.553 50.000 0.00 0.00 0.00 3.53
463 524 1.814394 CGTGGCATGGATGGATATTGG 59.186 52.381 0.00 0.00 0.00 3.16
464 525 2.745821 CTCGTGGCATGGATGGATATTG 59.254 50.000 6.90 0.00 0.00 1.90
465 526 2.373169 ACTCGTGGCATGGATGGATATT 59.627 45.455 6.90 0.00 0.00 1.28
466 527 1.980765 ACTCGTGGCATGGATGGATAT 59.019 47.619 6.90 0.00 0.00 1.63
467 528 1.344438 GACTCGTGGCATGGATGGATA 59.656 52.381 6.90 0.00 0.00 2.59
468 529 0.107456 GACTCGTGGCATGGATGGAT 59.893 55.000 6.90 0.00 0.00 3.41
469 530 0.977627 AGACTCGTGGCATGGATGGA 60.978 55.000 6.90 0.00 0.00 3.41
470 531 0.752658 TAGACTCGTGGCATGGATGG 59.247 55.000 6.90 0.00 0.00 3.51
471 532 1.410517 ACTAGACTCGTGGCATGGATG 59.589 52.381 6.90 0.61 0.00 3.51
472 533 1.781786 ACTAGACTCGTGGCATGGAT 58.218 50.000 6.90 0.00 0.00 3.41
473 534 2.022195 GTACTAGACTCGTGGCATGGA 58.978 52.381 6.90 0.00 0.00 3.41
474 535 1.749063 TGTACTAGACTCGTGGCATGG 59.251 52.381 6.90 0.22 0.00 3.66
475 536 2.163613 TGTGTACTAGACTCGTGGCATG 59.836 50.000 0.00 0.00 0.00 4.06
476 537 2.163815 GTGTGTACTAGACTCGTGGCAT 59.836 50.000 0.00 0.00 0.00 4.40
477 538 1.538512 GTGTGTACTAGACTCGTGGCA 59.461 52.381 0.00 0.00 0.00 4.92
478 539 1.538512 TGTGTGTACTAGACTCGTGGC 59.461 52.381 0.00 0.00 0.00 5.01
479 540 3.909776 TTGTGTGTACTAGACTCGTGG 57.090 47.619 0.00 0.00 0.00 4.94
480 541 4.603985 TGTTTGTGTGTACTAGACTCGTG 58.396 43.478 0.00 0.00 0.00 4.35
481 542 4.792057 GCTGTTTGTGTGTACTAGACTCGT 60.792 45.833 0.00 0.00 0.00 4.18
482 543 3.669122 GCTGTTTGTGTGTACTAGACTCG 59.331 47.826 0.00 0.00 0.00 4.18
483 544 3.988517 GGCTGTTTGTGTGTACTAGACTC 59.011 47.826 0.00 0.00 0.00 3.36
484 545 3.386726 TGGCTGTTTGTGTGTACTAGACT 59.613 43.478 0.00 0.00 0.00 3.24
485 546 3.724374 TGGCTGTTTGTGTGTACTAGAC 58.276 45.455 0.00 0.00 0.00 2.59
486 547 4.124238 GTTGGCTGTTTGTGTGTACTAGA 58.876 43.478 0.00 0.00 0.00 2.43
487 548 3.250040 GGTTGGCTGTTTGTGTGTACTAG 59.750 47.826 0.00 0.00 0.00 2.57
488 549 3.118186 AGGTTGGCTGTTTGTGTGTACTA 60.118 43.478 0.00 0.00 0.00 1.82
501 562 0.034059 AGAGTTCGTCAGGTTGGCTG 59.966 55.000 0.00 0.00 0.00 4.85
502 563 0.034059 CAGAGTTCGTCAGGTTGGCT 59.966 55.000 0.00 0.00 0.00 4.75
596 692 7.159322 ACTAGAGCTTATCCATATGTAACGG 57.841 40.000 0.00 0.00 0.00 4.44
640 760 3.317149 TGGCACTATATATATCGGACGGC 59.683 47.826 0.00 0.35 0.00 5.68
656 776 1.274167 CATGCACCTTGATTTGGCACT 59.726 47.619 0.00 0.00 37.30 4.40
663 783 6.127647 CCAGTAACATAACATGCACCTTGATT 60.128 38.462 0.00 0.00 0.00 2.57
666 786 4.458989 ACCAGTAACATAACATGCACCTTG 59.541 41.667 0.00 0.00 0.00 3.61
703 823 9.160496 CTCAGCAAGATTTCTTCTACTGTATTT 57.840 33.333 11.39 0.00 38.77 1.40
707 827 4.934602 GCTCAGCAAGATTTCTTCTACTGT 59.065 41.667 0.00 0.00 38.77 3.55
708 828 4.934001 TGCTCAGCAAGATTTCTTCTACTG 59.066 41.667 0.00 7.64 38.91 2.74
710 830 5.467902 CTGCTCAGCAAGATTTCTTCTAC 57.532 43.478 0.00 0.00 38.41 2.59
868 990 1.408822 GGAGGGGCTAAATGGAGTGTG 60.409 57.143 0.00 0.00 0.00 3.82
906 1034 8.466086 TGAACGAGTATATGATATTGTGATGC 57.534 34.615 0.00 0.00 0.00 3.91
922 1050 4.700213 TGAGTGATGAGTGATGAACGAGTA 59.300 41.667 0.00 0.00 0.00 2.59
923 1051 3.507622 TGAGTGATGAGTGATGAACGAGT 59.492 43.478 0.00 0.00 0.00 4.18
924 1052 4.102035 TGAGTGATGAGTGATGAACGAG 57.898 45.455 0.00 0.00 0.00 4.18
927 1055 6.101997 TGTGTATGAGTGATGAGTGATGAAC 58.898 40.000 0.00 0.00 0.00 3.18
986 1165 1.293179 CCCATATCGATCGCCAGCA 59.707 57.895 11.09 0.00 0.00 4.41
989 1168 0.608130 CTTCCCCATATCGATCGCCA 59.392 55.000 11.09 0.00 0.00 5.69
1193 1378 2.052237 GACGCGCTGTTGTTGTGG 60.052 61.111 5.73 0.00 0.00 4.17
1194 1379 2.052237 GGACGCGCTGTTGTTGTG 60.052 61.111 5.73 0.00 0.00 3.33
1210 1395 0.734889 GCCTGATGATGAACAACGGG 59.265 55.000 0.00 0.00 46.42 5.28
1315 1509 1.271597 GCTGGGAAGATGACTTGTGGT 60.272 52.381 0.00 0.00 36.39 4.16
1340 1555 2.151202 TGACCTTTTCTTCATGCCGAC 58.849 47.619 0.00 0.00 0.00 4.79
1378 1593 5.829233 GCAAAAAGCAGATTTCCTTGTAC 57.171 39.130 0.00 0.00 44.79 2.90
1592 2182 8.745837 CAAATTTGCCGCTATTAATTCTACAAG 58.254 33.333 5.01 0.00 0.00 3.16
1693 2310 2.599645 CTTCCCTCCCTGACATGGCG 62.600 65.000 0.00 0.00 0.00 5.69
1991 2609 3.330267 CTTGGAGAGGAAGTACTTGTGC 58.670 50.000 14.14 0.00 0.00 4.57
2270 2888 1.991167 CGGGTACTTGCCCCTACCA 60.991 63.158 0.00 0.00 45.91 3.25
2306 2924 4.153986 GCTTCTTCATCATGTTGAACACG 58.846 43.478 13.94 6.53 32.39 4.49
2456 3074 5.187772 GCCCTTCAAATCCCTAATCTTGTTT 59.812 40.000 0.00 0.00 0.00 2.83
2748 3369 3.802139 GTGGTAAAACAGGAAAAAGCAGC 59.198 43.478 0.00 0.00 0.00 5.25
2752 3373 8.716646 AATGAAAGTGGTAAAACAGGAAAAAG 57.283 30.769 0.00 0.00 0.00 2.27
3037 4624 8.766000 TCGTCATGCAACTAAAGAAATAACTA 57.234 30.769 0.00 0.00 0.00 2.24
3038 4625 7.667043 TCGTCATGCAACTAAAGAAATAACT 57.333 32.000 0.00 0.00 0.00 2.24
3039 4626 8.895932 AATCGTCATGCAACTAAAGAAATAAC 57.104 30.769 0.00 0.00 0.00 1.89
3040 4627 9.906660 AAAATCGTCATGCAACTAAAGAAATAA 57.093 25.926 0.00 0.00 0.00 1.40
3041 4628 9.906660 AAAAATCGTCATGCAACTAAAGAAATA 57.093 25.926 0.00 0.00 0.00 1.40
3042 4629 8.816640 AAAAATCGTCATGCAACTAAAGAAAT 57.183 26.923 0.00 0.00 0.00 2.17
3120 4712 9.301153 GCTCATGTCGGTTTTAAAATTATTCAT 57.699 29.630 3.52 3.94 0.00 2.57
3136 4728 1.368641 TCCAAATTCGCTCATGTCGG 58.631 50.000 9.47 0.00 0.00 4.79
3137 4729 3.469899 TTTCCAAATTCGCTCATGTCG 57.530 42.857 0.00 0.00 0.00 4.35
3143 4735 3.670523 GTCAAGCTTTTCCAAATTCGCTC 59.329 43.478 0.00 0.00 0.00 5.03
3147 4739 4.625028 AGCAGTCAAGCTTTTCCAAATTC 58.375 39.130 0.00 0.00 43.70 2.17
3187 4780 6.885735 AAAGTGCTCACATGTTGTAAAAAC 57.114 33.333 0.00 0.00 0.00 2.43
3273 4867 8.319146 AGAACAAGCTAGCAACTAACCTATTTA 58.681 33.333 18.83 0.00 0.00 1.40
3276 4870 6.109359 CAGAACAAGCTAGCAACTAACCTAT 58.891 40.000 18.83 0.00 0.00 2.57
3279 4873 4.065789 ACAGAACAAGCTAGCAACTAACC 58.934 43.478 18.83 0.00 0.00 2.85
3284 4878 5.393962 CCAATAACAGAACAAGCTAGCAAC 58.606 41.667 18.83 3.15 0.00 4.17
3299 4893 0.394216 ATGCAGAGCGGCCAATAACA 60.394 50.000 2.24 0.00 0.00 2.41
3306 4900 1.358046 GAATGAATGCAGAGCGGCC 59.642 57.895 0.00 0.00 0.00 6.13
3310 4904 2.089980 ACCAGTGAATGAATGCAGAGC 58.910 47.619 0.00 0.00 0.00 4.09
3311 4905 3.340928 TGACCAGTGAATGAATGCAGAG 58.659 45.455 0.00 0.00 0.00 3.35
3331 4925 5.510674 CGCAAGATTCTCTGCAAATTAACTG 59.489 40.000 15.99 0.00 43.02 3.16
3367 4989 3.926671 AGGACCAGCTATATCCTAGAGGT 59.073 47.826 10.19 0.00 41.22 3.85
3405 5027 8.955061 ATGCAATTATTATGAACTAACGATGC 57.045 30.769 0.00 0.00 0.00 3.91
3433 5055 6.018016 GCTAGCTAGGACAGTAGTAAGTACAC 60.018 46.154 22.10 0.00 33.55 2.90
3445 5067 0.673437 GAGGCAGCTAGCTAGGACAG 59.327 60.000 18.86 4.90 44.79 3.51
3446 5068 0.033109 TGAGGCAGCTAGCTAGGACA 60.033 55.000 18.86 12.70 44.79 4.02
3447 5069 1.272212 GATGAGGCAGCTAGCTAGGAC 59.728 57.143 18.86 8.57 44.79 3.85
3448 5070 1.133356 TGATGAGGCAGCTAGCTAGGA 60.133 52.381 18.86 0.00 44.79 2.94
3463 5090 7.933577 GGTAGATGAACCTAACATGATTGATGA 59.066 37.037 0.00 0.00 36.53 2.92


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

AutoCloner maintained by Alex Coulton.