Multiple sequence alignment - TraesCS6D01G246600

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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 TraesCS6D01G246600 chr6D 100.000 2731 0 0 1 2731 349916457 349913727 0 5044
1 TraesCS6D01G246600 chr6B 89.469 2279 148 40 467 2673 530572166 530574424 0 2795
2 TraesCS6D01G246600 chr6A 92.468 1872 106 17 820 2672 494477711 494479566 0 2643
3 TraesCS6D01G246600 chr6A 89.643 840 56 11 5 818 494476202 494477036 0 1040
4 TraesCS6D01G246600 chr2B 91.767 498 41 0 1072 1569 658210793 658210296 0 693
5 TraesCS6D01G246600 chr2D 91.365 498 43 0 1072 1569 552607712 552607215 0 682
6 TraesCS6D01G246600 chr2A 90.763 498 46 0 1072 1569 693243651 693243154 0 665


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 TraesCS6D01G246600 chr6D 349913727 349916457 2730 True 5044.0 5044 100.0000 1 2731 1 chr6D.!!$R1 2730
1 TraesCS6D01G246600 chr6B 530572166 530574424 2258 False 2795.0 2795 89.4690 467 2673 1 chr6B.!!$F1 2206
2 TraesCS6D01G246600 chr6A 494476202 494479566 3364 False 1841.5 2643 91.0555 5 2672 2 chr6A.!!$F1 2667

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
921 1683 0.322098 CCTTCACGGCCCAATACACA 60.322 55.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2605 3389 0.249073 GATGGCGTCGCTGTCATACT 60.249 55.0 18.11 0.0 0.0 2.12 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
19 20 2.165301 GGCCGAACCGAATCGACTG 61.165 63.158 3.36 0.00 45.48 3.51
23 24 1.464429 CGAACCGAATCGACTGAGCG 61.464 60.000 3.36 0.00 45.48 5.03
36 37 3.213402 GAGCGAGGGACCGGAGAG 61.213 72.222 9.46 0.00 0.00 3.20
89 90 0.913205 ACGCTAGAGAGGAGGTCTGA 59.087 55.000 0.00 0.00 34.71 3.27
94 95 1.779221 AGAGAGGAGGTCTGATGCAG 58.221 55.000 0.00 0.00 34.71 4.41
226 227 0.611200 TGCGCACTAGGTGTACCATT 59.389 50.000 5.66 0.00 38.89 3.16
241 244 5.010617 GTGTACCATTGGGATTGTTTTCTGT 59.989 40.000 7.78 0.00 38.05 3.41
291 294 2.170397 CAACCTTTGCTTGGTTTCCCTT 59.830 45.455 5.98 0.00 44.54 3.95
349 352 5.020071 TTCGCGAGAAGCAAAAGTTGTGT 62.020 43.478 9.59 0.00 46.92 3.72
393 417 2.254546 TGTGCTTCCACGAGAAACAT 57.745 45.000 0.00 0.00 45.04 2.71
415 439 1.834188 ATGTGCTTACCGAAAAGGGG 58.166 50.000 0.00 0.00 46.96 4.79
430 455 7.033185 CCGAAAAGGGGAAAAATACAGTTATG 58.967 38.462 0.00 0.00 35.97 1.90
435 460 5.656859 AGGGGAAAAATACAGTTATGCTTCC 59.343 40.000 0.00 0.00 32.78 3.46
443 468 1.667724 CAGTTATGCTTCCAAGAGCCG 59.332 52.381 0.00 0.00 42.01 5.52
448 473 1.079127 GCTTCCAAGAGCCGTGCTA 60.079 57.895 0.00 0.00 39.88 3.49
452 477 1.517257 CCAAGAGCCGTGCTACTCG 60.517 63.158 0.00 0.00 39.88 4.18
459 484 1.359459 GCCGTGCTACTCGAAAAGGG 61.359 60.000 0.00 0.00 0.00 3.95
539 576 4.782252 CACAATTGTGCTTTCAGGTTTG 57.218 40.909 24.69 0.00 39.39 2.93
557 596 4.743151 GGTTTGGTTTTCGATTTTCCTGAC 59.257 41.667 0.00 0.00 0.00 3.51
638 687 6.642707 TTTTGGTATCTCACGGTGAAAATT 57.357 33.333 12.54 0.28 0.00 1.82
639 688 5.621197 TTGGTATCTCACGGTGAAAATTG 57.379 39.130 12.54 0.09 0.00 2.32
653 702 6.591062 CGGTGAAAATTGTTCATGATTTGGAT 59.409 34.615 0.00 0.00 0.00 3.41
682 731 5.625311 GGTGCAAGAGATAAAACGTTTTGAG 59.375 40.000 31.26 15.59 0.00 3.02
696 745 8.488979 AAACGTTTTGAGAAAATGAATCTACG 57.511 30.769 7.96 0.00 39.23 3.51
719 776 4.557205 GAAAAGGACTCTCAAGTAGCGAA 58.443 43.478 0.00 0.00 35.28 4.70
728 785 2.548057 CTCAAGTAGCGAAAAGTTGGCA 59.452 45.455 0.00 0.00 36.79 4.92
861 1620 4.424566 CAGCCCAACATGTGCGGC 62.425 66.667 22.97 22.97 41.45 6.53
884 1646 3.430790 GCAGCCCATTTAATCTCCCAAAC 60.431 47.826 0.00 0.00 0.00 2.93
906 1668 2.478831 GCCTGATTCTGACGATCCTTC 58.521 52.381 0.00 0.00 0.00 3.46
921 1683 0.322098 CCTTCACGGCCCAATACACA 60.322 55.000 0.00 0.00 0.00 3.72
935 1697 2.623878 TACACACACACCACCGAATT 57.376 45.000 0.00 0.00 0.00 2.17
937 1699 2.489971 ACACACACACCACCGAATTAG 58.510 47.619 0.00 0.00 0.00 1.73
1175 1942 4.883354 CTGGCCCCCAAGATCGGC 62.883 72.222 0.00 0.25 42.23 5.54
1271 2038 2.029073 ACCGTCAAGCTCACCGTG 59.971 61.111 0.00 0.00 0.00 4.94
1665 2432 2.312390 GGTTTGCCAACTTGTTAGGGA 58.688 47.619 0.17 0.00 32.90 4.20
1669 2436 2.054799 TGCCAACTTGTTAGGGAGAGT 58.945 47.619 0.00 0.00 0.00 3.24
1675 2442 1.347707 CTTGTTAGGGAGAGTGTGGCA 59.652 52.381 0.00 0.00 0.00 4.92
1679 2446 0.904649 TAGGGAGAGTGTGGCATGTG 59.095 55.000 0.00 0.00 0.00 3.21
1683 2450 2.092968 GGGAGAGTGTGGCATGTGATAA 60.093 50.000 0.00 0.00 0.00 1.75
1687 2454 4.194640 AGAGTGTGGCATGTGATAACATC 58.805 43.478 0.00 0.00 0.00 3.06
1733 2500 6.944234 AATTAAAGCTAGGTAGAATGTGGC 57.056 37.500 0.00 0.00 0.00 5.01
1742 2509 6.712547 GCTAGGTAGAATGTGGCAAGATTATT 59.287 38.462 0.00 0.00 0.00 1.40
1750 2517 7.977853 AGAATGTGGCAAGATTATTTGTTGATC 59.022 33.333 0.00 0.00 0.00 2.92
1751 2518 6.839124 TGTGGCAAGATTATTTGTTGATCT 57.161 33.333 0.00 0.00 32.30 2.75
1830 2597 8.055279 ACTTGTATTGTTAGGATGAATGTTGG 57.945 34.615 0.00 0.00 0.00 3.77
1842 2609 4.558226 TGAATGTTGGTCATGCTAGTCT 57.442 40.909 0.00 0.00 36.81 3.24
1877 2644 7.581213 TTTGTCTGGTCACATTGTATTCTTT 57.419 32.000 0.00 0.00 0.00 2.52
1914 2681 5.756347 ACATTCTGTTCTTAAACTGCGTACA 59.244 36.000 0.00 0.00 36.30 2.90
2112 2879 5.505181 AGTGGTTCCATTGTGAGACTATT 57.495 39.130 0.00 0.00 0.00 1.73
2216 2984 7.911727 TCATTGATGTTTTGAGCGATTCTTATG 59.088 33.333 0.00 0.00 0.00 1.90
2461 3240 5.599999 ATGACTGGACTGTAGATTGTACC 57.400 43.478 0.00 0.00 0.00 3.34
2464 3243 5.483937 TGACTGGACTGTAGATTGTACCATT 59.516 40.000 0.00 0.00 0.00 3.16
2471 3250 8.451748 GGACTGTAGATTGTACCATTTTTCTTC 58.548 37.037 0.00 0.00 0.00 2.87
2472 3251 8.918202 ACTGTAGATTGTACCATTTTTCTTCA 57.082 30.769 0.00 0.00 0.00 3.02
2473 3252 9.520515 ACTGTAGATTGTACCATTTTTCTTCAT 57.479 29.630 0.00 0.00 0.00 2.57
2475 3254 8.956426 TGTAGATTGTACCATTTTTCTTCATCC 58.044 33.333 0.00 0.00 0.00 3.51
2477 3256 8.655935 AGATTGTACCATTTTTCTTCATCCTT 57.344 30.769 0.00 0.00 0.00 3.36
2497 3280 3.747854 TGACAGCCATTTTGCATTTGA 57.252 38.095 0.00 0.00 0.00 2.69
2499 3282 4.059511 TGACAGCCATTTTGCATTTGAAG 58.940 39.130 0.00 0.00 0.00 3.02
2572 3355 7.500141 ACCTGCTATTGTTTGAAAATTTGTCT 58.500 30.769 0.00 0.00 0.00 3.41
2596 3379 7.015877 TCTGTCTGGGCTATTTATATTACCGTT 59.984 37.037 0.00 0.00 0.00 4.44
2598 3381 7.015877 TGTCTGGGCTATTTATATTACCGTTCT 59.984 37.037 0.00 0.00 0.00 3.01
2639 3423 4.855531 ACGCCATCAGTGAAAAGTTAAAC 58.144 39.130 0.00 0.00 0.00 2.01
2650 3435 6.884836 AGTGAAAAGTTAAACCTGTCAGAAGT 59.115 34.615 0.00 0.00 0.00 3.01
2676 3462 2.106844 CGAAAAGCAGGCCATACCC 58.893 57.895 5.01 0.00 40.58 3.69
2677 3463 0.679640 CGAAAAGCAGGCCATACCCA 60.680 55.000 5.01 0.00 40.58 4.51
2678 3464 1.555967 GAAAAGCAGGCCATACCCAA 58.444 50.000 5.01 0.00 40.58 4.12
2679 3465 1.899142 GAAAAGCAGGCCATACCCAAA 59.101 47.619 5.01 0.00 40.58 3.28
2680 3466 1.560505 AAAGCAGGCCATACCCAAAG 58.439 50.000 5.01 0.00 40.58 2.77
2681 3467 0.972471 AAGCAGGCCATACCCAAAGC 60.972 55.000 5.01 0.00 40.58 3.51
2682 3468 1.380380 GCAGGCCATACCCAAAGCT 60.380 57.895 5.01 0.00 40.58 3.74
2683 3469 0.972471 GCAGGCCATACCCAAAGCTT 60.972 55.000 5.01 0.00 40.58 3.74
2684 3470 1.684869 GCAGGCCATACCCAAAGCTTA 60.685 52.381 5.01 0.00 40.58 3.09
2685 3471 2.733956 CAGGCCATACCCAAAGCTTAA 58.266 47.619 5.01 0.00 40.58 1.85
2686 3472 3.096092 CAGGCCATACCCAAAGCTTAAA 58.904 45.455 5.01 0.00 40.58 1.52
2687 3473 3.706086 CAGGCCATACCCAAAGCTTAAAT 59.294 43.478 5.01 0.00 40.58 1.40
2688 3474 4.892934 CAGGCCATACCCAAAGCTTAAATA 59.107 41.667 5.01 0.00 40.58 1.40
2689 3475 4.893524 AGGCCATACCCAAAGCTTAAATAC 59.106 41.667 5.01 0.00 40.58 1.89
2690 3476 4.647399 GGCCATACCCAAAGCTTAAATACA 59.353 41.667 0.00 0.00 0.00 2.29
2691 3477 5.451381 GGCCATACCCAAAGCTTAAATACAC 60.451 44.000 0.00 0.00 0.00 2.90
2692 3478 5.451381 GCCATACCCAAAGCTTAAATACACC 60.451 44.000 0.00 0.00 0.00 4.16
2693 3479 5.068591 CCATACCCAAAGCTTAAATACACCC 59.931 44.000 0.00 0.00 0.00 4.61
2694 3480 4.120946 ACCCAAAGCTTAAATACACCCA 57.879 40.909 0.00 0.00 0.00 4.51
2695 3481 4.086457 ACCCAAAGCTTAAATACACCCAG 58.914 43.478 0.00 0.00 0.00 4.45
2696 3482 3.119137 CCCAAAGCTTAAATACACCCAGC 60.119 47.826 0.00 0.00 0.00 4.85
2697 3483 3.119137 CCAAAGCTTAAATACACCCAGCC 60.119 47.826 0.00 0.00 0.00 4.85
2698 3484 2.437085 AGCTTAAATACACCCAGCCC 57.563 50.000 0.00 0.00 0.00 5.19
2699 3485 1.063942 AGCTTAAATACACCCAGCCCC 60.064 52.381 0.00 0.00 0.00 5.80
2700 3486 1.341581 GCTTAAATACACCCAGCCCCA 60.342 52.381 0.00 0.00 0.00 4.96
2701 3487 2.375146 CTTAAATACACCCAGCCCCAC 58.625 52.381 0.00 0.00 0.00 4.61
2702 3488 1.373536 TAAATACACCCAGCCCCACA 58.626 50.000 0.00 0.00 0.00 4.17
2703 3489 0.485099 AAATACACCCAGCCCCACAA 59.515 50.000 0.00 0.00 0.00 3.33
2704 3490 0.251608 AATACACCCAGCCCCACAAC 60.252 55.000 0.00 0.00 0.00 3.32
2705 3491 1.140134 ATACACCCAGCCCCACAACT 61.140 55.000 0.00 0.00 0.00 3.16
2706 3492 1.357272 TACACCCAGCCCCACAACTT 61.357 55.000 0.00 0.00 0.00 2.66
2707 3493 1.903404 CACCCAGCCCCACAACTTC 60.903 63.158 0.00 0.00 0.00 3.01
2708 3494 2.391130 ACCCAGCCCCACAACTTCA 61.391 57.895 0.00 0.00 0.00 3.02
2709 3495 1.152567 CCCAGCCCCACAACTTCAA 60.153 57.895 0.00 0.00 0.00 2.69
2710 3496 0.542702 CCCAGCCCCACAACTTCAAT 60.543 55.000 0.00 0.00 0.00 2.57
2711 3497 0.890683 CCAGCCCCACAACTTCAATC 59.109 55.000 0.00 0.00 0.00 2.67
2712 3498 0.890683 CAGCCCCACAACTTCAATCC 59.109 55.000 0.00 0.00 0.00 3.01
2713 3499 0.482446 AGCCCCACAACTTCAATCCA 59.518 50.000 0.00 0.00 0.00 3.41
2714 3500 1.133199 AGCCCCACAACTTCAATCCAA 60.133 47.619 0.00 0.00 0.00 3.53
2715 3501 1.901833 GCCCCACAACTTCAATCCAAT 59.098 47.619 0.00 0.00 0.00 3.16
2716 3502 3.096092 GCCCCACAACTTCAATCCAATA 58.904 45.455 0.00 0.00 0.00 1.90
2717 3503 3.513515 GCCCCACAACTTCAATCCAATAA 59.486 43.478 0.00 0.00 0.00 1.40
2718 3504 4.162131 GCCCCACAACTTCAATCCAATAAT 59.838 41.667 0.00 0.00 0.00 1.28
2719 3505 5.338300 GCCCCACAACTTCAATCCAATAATT 60.338 40.000 0.00 0.00 0.00 1.40
2720 3506 6.710278 CCCCACAACTTCAATCCAATAATTT 58.290 36.000 0.00 0.00 0.00 1.82
2721 3507 7.580495 GCCCCACAACTTCAATCCAATAATTTA 60.580 37.037 0.00 0.00 0.00 1.40
2722 3508 7.763985 CCCCACAACTTCAATCCAATAATTTAC 59.236 37.037 0.00 0.00 0.00 2.01
2723 3509 7.763985 CCCACAACTTCAATCCAATAATTTACC 59.236 37.037 0.00 0.00 0.00 2.85
2724 3510 8.531146 CCACAACTTCAATCCAATAATTTACCT 58.469 33.333 0.00 0.00 0.00 3.08
2725 3511 9.927668 CACAACTTCAATCCAATAATTTACCTT 57.072 29.630 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.165301 CAGTCGATTCGGTTCGGCC 61.165 63.158 6.18 0.00 44.56 6.13
2 3 1.140407 CTCAGTCGATTCGGTTCGGC 61.140 60.000 6.18 4.66 43.84 5.54
3 4 1.140407 GCTCAGTCGATTCGGTTCGG 61.140 60.000 6.18 0.00 39.56 4.30
19 20 2.969300 ATCTCTCCGGTCCCTCGCTC 62.969 65.000 0.00 0.00 0.00 5.03
23 24 1.403687 CCCAATCTCTCCGGTCCCTC 61.404 65.000 0.00 0.00 0.00 4.30
66 67 2.025699 AGACCTCCTCTCTAGCGTCTTT 60.026 50.000 0.00 0.00 0.00 2.52
78 79 1.470632 CGAACTGCATCAGACCTCCTC 60.471 57.143 0.29 0.00 35.18 3.71
94 95 2.608090 GGTTGCTCCAAGTATAGCGAAC 59.392 50.000 0.00 0.00 41.77 3.95
166 167 2.743928 CCACTTGGTGCGCTCCTC 60.744 66.667 27.24 4.48 31.34 3.71
189 190 2.699768 AACACATGGCGGCGAATGG 61.700 57.895 21.74 14.81 0.00 3.16
219 220 5.722021 ACAGAAAACAATCCCAATGGTAC 57.278 39.130 0.00 0.00 0.00 3.34
226 227 3.885976 TGGGTACAGAAAACAATCCCA 57.114 42.857 0.00 0.00 40.70 4.37
291 294 1.196012 AAAAAGACCGGCCAAAACCA 58.804 45.000 0.00 0.00 0.00 3.67
393 417 3.759618 CCCCTTTTCGGTAAGCACATTTA 59.240 43.478 0.00 0.00 0.00 1.40
415 439 7.486232 GCTCTTGGAAGCATAACTGTATTTTTC 59.514 37.037 0.00 0.00 42.05 2.29
430 455 1.079127 TAGCACGGCTCTTGGAAGC 60.079 57.895 1.46 0.00 40.44 3.86
435 460 0.109272 TTCGAGTAGCACGGCTCTTG 60.109 55.000 1.46 4.62 40.44 3.02
443 468 4.933400 TGTATTTCCCTTTTCGAGTAGCAC 59.067 41.667 0.00 0.00 0.00 4.40
448 473 6.264518 ACAATTGTGTATTTCCCTTTTCGAGT 59.735 34.615 11.07 0.00 35.72 4.18
534 571 4.743151 GTCAGGAAAATCGAAAACCAAACC 59.257 41.667 0.00 0.00 0.00 3.27
539 576 5.462068 CCAAAAGTCAGGAAAATCGAAAACC 59.538 40.000 0.00 0.00 0.00 3.27
609 658 9.451002 TTTCACCGTGAGATACCAAAAATATAA 57.549 29.630 0.64 0.00 0.00 0.98
610 659 9.451002 TTTTCACCGTGAGATACCAAAAATATA 57.549 29.630 0.64 0.00 0.00 0.86
611 660 7.931578 TTTCACCGTGAGATACCAAAAATAT 57.068 32.000 0.64 0.00 0.00 1.28
612 661 7.747155 TTTTCACCGTGAGATACCAAAAATA 57.253 32.000 0.64 0.00 0.00 1.40
617 666 5.067273 ACAATTTTCACCGTGAGATACCAA 58.933 37.500 0.64 0.00 0.00 3.67
625 674 5.703978 ATCATGAACAATTTTCACCGTGA 57.296 34.783 0.00 0.00 0.00 4.35
628 677 5.925397 TCCAAATCATGAACAATTTTCACCG 59.075 36.000 0.00 2.29 0.00 4.94
638 687 3.833650 ACCTTGCATCCAAATCATGAACA 59.166 39.130 0.00 0.00 0.00 3.18
639 688 4.178540 CACCTTGCATCCAAATCATGAAC 58.821 43.478 0.00 0.00 0.00 3.18
682 731 7.334671 AGAGTCCTTTTCCGTAGATTCATTTTC 59.665 37.037 0.00 0.00 0.00 2.29
696 745 3.056749 TCGCTACTTGAGAGTCCTTTTCC 60.057 47.826 0.00 0.00 37.33 3.13
827 913 2.956333 GGCTGAAGTAGTGGGTGTTTTT 59.044 45.455 0.00 0.00 0.00 1.94
828 914 2.583143 GGCTGAAGTAGTGGGTGTTTT 58.417 47.619 0.00 0.00 0.00 2.43
834 1593 0.400213 TGTTGGGCTGAAGTAGTGGG 59.600 55.000 0.00 0.00 0.00 4.61
861 1620 0.954452 GGGAGATTAAATGGGCTGCG 59.046 55.000 0.00 0.00 0.00 5.18
884 1646 0.598680 GGATCGTCAGAATCAGGCCG 60.599 60.000 0.00 0.00 0.00 6.13
906 1668 0.886938 TGTGTGTGTATTGGGCCGTG 60.887 55.000 0.00 0.00 0.00 4.94
921 1683 0.398696 TGGCTAATTCGGTGGTGTGT 59.601 50.000 0.00 0.00 0.00 3.72
935 1697 0.699981 GGGTTAGGGTTTGGTGGCTA 59.300 55.000 0.00 0.00 0.00 3.93
937 1699 1.608336 GGGGTTAGGGTTTGGTGGC 60.608 63.158 0.00 0.00 0.00 5.01
1036 1798 1.379044 GGATTGGCTGTGGGGAGTG 60.379 63.158 0.00 0.00 0.00 3.51
1037 1799 1.542375 AGGATTGGCTGTGGGGAGT 60.542 57.895 0.00 0.00 0.00 3.85
1038 1800 1.225704 GAGGATTGGCTGTGGGGAG 59.774 63.158 0.00 0.00 0.00 4.30
1039 1801 2.308722 GGAGGATTGGCTGTGGGGA 61.309 63.158 0.00 0.00 0.00 4.81
1040 1802 2.276740 GGAGGATTGGCTGTGGGG 59.723 66.667 0.00 0.00 0.00 4.96
1271 2038 2.751436 TTGGCCTGGCGATTCTGC 60.751 61.111 13.40 0.00 0.00 4.26
1648 2415 2.441750 ACTCTCCCTAACAAGTTGGCAA 59.558 45.455 7.96 0.00 0.00 4.52
1665 2432 3.701205 TGTTATCACATGCCACACTCT 57.299 42.857 0.00 0.00 0.00 3.24
1669 2436 4.219264 TGAGATGTTATCACATGCCACA 57.781 40.909 0.00 0.00 44.22 4.17
1709 2476 7.570132 TGCCACATTCTACCTAGCTTTAATTA 58.430 34.615 0.00 0.00 0.00 1.40
1733 2500 8.886719 TGAGCACTAGATCAACAAATAATCTTG 58.113 33.333 0.00 0.00 37.20 3.02
1742 2509 4.212143 AGCATGAGCACTAGATCAACAA 57.788 40.909 0.00 0.00 44.32 2.83
1750 2517 8.554835 TCTATAGTTACTAGCATGAGCACTAG 57.445 38.462 0.00 0.00 45.49 2.57
1751 2518 8.951243 CATCTATAGTTACTAGCATGAGCACTA 58.049 37.037 0.00 0.00 45.49 2.74
1794 2561 7.390440 TCCTAACAATACAAGTTCACAATCCAG 59.610 37.037 0.00 0.00 0.00 3.86
1856 2623 5.182001 AGCAAAGAATACAATGTGACCAGAC 59.818 40.000 0.00 0.00 0.00 3.51
1861 2628 9.793252 AATTCATAGCAAAGAATACAATGTGAC 57.207 29.630 0.00 0.00 33.58 3.67
1899 2666 6.205853 ACAATGGATTTGTACGCAGTTTAAGA 59.794 34.615 0.00 0.00 46.75 2.10
1900 2667 6.378582 ACAATGGATTTGTACGCAGTTTAAG 58.621 36.000 0.00 0.00 46.75 1.85
2060 2827 5.640732 TGACAAAAGTTTCTTCTTCAGCAC 58.359 37.500 0.00 0.00 0.00 4.40
2112 2879 8.354426 GCAAGGTACTCATTAAACCAGTAAAAA 58.646 33.333 0.00 0.00 38.49 1.94
2216 2984 3.786048 GCAAATGCAGCGACTAACAATAC 59.214 43.478 0.00 0.00 41.59 1.89
2318 3086 9.875691 GGTTAAGATCAAATAAGGCATTTTTCT 57.124 29.630 0.00 0.00 34.49 2.52
2324 3092 9.603921 CAATTTGGTTAAGATCAAATAAGGCAT 57.396 29.630 10.07 0.00 41.15 4.40
2406 3174 9.739276 TCCATGTCTGAATTCTTTTACATTACT 57.261 29.630 7.05 0.00 0.00 2.24
2413 3183 9.519191 TTCTGAATCCATGTCTGAATTCTTTTA 57.481 29.630 7.05 0.00 30.69 1.52
2461 3240 5.166398 GGCTGTCAAGGATGAAGAAAAATG 58.834 41.667 0.00 0.00 37.30 2.32
2464 3243 3.831323 TGGCTGTCAAGGATGAAGAAAA 58.169 40.909 0.00 0.00 37.30 2.29
2471 3250 2.028839 TGCAAAATGGCTGTCAAGGATG 60.029 45.455 0.00 0.00 34.04 3.51
2472 3251 2.250031 TGCAAAATGGCTGTCAAGGAT 58.750 42.857 0.00 0.00 34.04 3.24
2473 3252 1.702182 TGCAAAATGGCTGTCAAGGA 58.298 45.000 0.00 0.00 34.04 3.36
2475 3254 4.059511 TCAAATGCAAAATGGCTGTCAAG 58.940 39.130 0.00 0.00 34.04 3.02
2477 3256 3.747854 TCAAATGCAAAATGGCTGTCA 57.252 38.095 0.00 0.00 34.04 3.58
2497 3280 4.524328 CAGAAAATTGGGCAGACCTAACTT 59.476 41.667 0.00 0.00 39.54 2.66
2499 3282 4.079253 TCAGAAAATTGGGCAGACCTAAC 58.921 43.478 0.00 0.00 39.54 2.34
2572 3355 6.675413 ACGGTAATATAAATAGCCCAGACA 57.325 37.500 0.00 0.00 0.00 3.41
2596 3379 5.034797 CGTCGCTGTCATACTGAATAAAGA 58.965 41.667 0.00 0.00 0.00 2.52
2598 3381 3.550275 GCGTCGCTGTCATACTGAATAAA 59.450 43.478 10.68 0.00 0.00 1.40
2605 3389 0.249073 GATGGCGTCGCTGTCATACT 60.249 55.000 18.11 0.00 0.00 2.12
2616 3400 4.742438 TTAACTTTTCACTGATGGCGTC 57.258 40.909 0.00 0.00 0.00 5.19
2673 3459 4.086457 CTGGGTGTATTTAAGCTTTGGGT 58.914 43.478 3.20 0.00 0.00 4.51
2674 3460 3.119137 GCTGGGTGTATTTAAGCTTTGGG 60.119 47.826 3.20 0.00 0.00 4.12
2675 3461 3.119137 GGCTGGGTGTATTTAAGCTTTGG 60.119 47.826 3.20 0.00 34.29 3.28
2676 3462 3.119137 GGGCTGGGTGTATTTAAGCTTTG 60.119 47.826 3.20 0.00 34.29 2.77
2677 3463 3.096852 GGGCTGGGTGTATTTAAGCTTT 58.903 45.455 3.20 0.00 34.29 3.51
2678 3464 2.623239 GGGGCTGGGTGTATTTAAGCTT 60.623 50.000 3.48 3.48 34.29 3.74
2679 3465 1.063942 GGGGCTGGGTGTATTTAAGCT 60.064 52.381 0.00 0.00 34.29 3.74
2680 3466 1.341581 TGGGGCTGGGTGTATTTAAGC 60.342 52.381 0.00 0.00 0.00 3.09
2681 3467 2.291282 TGTGGGGCTGGGTGTATTTAAG 60.291 50.000 0.00 0.00 0.00 1.85
2682 3468 1.711375 TGTGGGGCTGGGTGTATTTAA 59.289 47.619 0.00 0.00 0.00 1.52
2683 3469 1.373536 TGTGGGGCTGGGTGTATTTA 58.626 50.000 0.00 0.00 0.00 1.40
2684 3470 0.485099 TTGTGGGGCTGGGTGTATTT 59.515 50.000 0.00 0.00 0.00 1.40
2685 3471 0.251608 GTTGTGGGGCTGGGTGTATT 60.252 55.000 0.00 0.00 0.00 1.89
2686 3472 1.140134 AGTTGTGGGGCTGGGTGTAT 61.140 55.000 0.00 0.00 0.00 2.29
2687 3473 1.357272 AAGTTGTGGGGCTGGGTGTA 61.357 55.000 0.00 0.00 0.00 2.90
2688 3474 2.640581 GAAGTTGTGGGGCTGGGTGT 62.641 60.000 0.00 0.00 0.00 4.16
2689 3475 1.903404 GAAGTTGTGGGGCTGGGTG 60.903 63.158 0.00 0.00 0.00 4.61
2690 3476 1.943730 TTGAAGTTGTGGGGCTGGGT 61.944 55.000 0.00 0.00 0.00 4.51
2691 3477 0.542702 ATTGAAGTTGTGGGGCTGGG 60.543 55.000 0.00 0.00 0.00 4.45
2692 3478 0.890683 GATTGAAGTTGTGGGGCTGG 59.109 55.000 0.00 0.00 0.00 4.85
2693 3479 0.890683 GGATTGAAGTTGTGGGGCTG 59.109 55.000 0.00 0.00 0.00 4.85
2694 3480 0.482446 TGGATTGAAGTTGTGGGGCT 59.518 50.000 0.00 0.00 0.00 5.19
2695 3481 1.337118 TTGGATTGAAGTTGTGGGGC 58.663 50.000 0.00 0.00 0.00 5.80
2696 3482 5.937975 ATTATTGGATTGAAGTTGTGGGG 57.062 39.130 0.00 0.00 0.00 4.96
2697 3483 7.763985 GGTAAATTATTGGATTGAAGTTGTGGG 59.236 37.037 0.00 0.00 0.00 4.61
2698 3484 8.531146 AGGTAAATTATTGGATTGAAGTTGTGG 58.469 33.333 0.00 0.00 0.00 4.17
2699 3485 9.927668 AAGGTAAATTATTGGATTGAAGTTGTG 57.072 29.630 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.