Multiple sequence alignment - TraesCS7A01G254800

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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 TraesCS7A01G254800 chr7A 100.000 2775 0 0 1 2775 241659654 241662428 0.000000e+00 5125
1 TraesCS7A01G254800 chr7D 92.442 1892 85 29 567 2444 229785304 229787151 0.000000e+00 2649
2 TraesCS7A01G254800 chr7D 86.463 229 12 10 2475 2691 229787223 229787444 1.660000e-57 233
3 TraesCS7A01G254800 chr7D 93.204 103 7 0 1 103 229784653 229784755 4.790000e-33 152
4 TraesCS7A01G254800 chr7B 90.404 1907 84 35 580 2448 200349546 200351391 0.000000e+00 2416
5 TraesCS7A01G254800 chr7B 81.690 497 58 19 1918 2397 607319619 607320099 1.560000e-102 383
6 TraesCS7A01G254800 chr7B 88.852 305 13 13 2475 2771 200351460 200351751 3.400000e-94 355
7 TraesCS7A01G254800 chr7B 88.848 269 25 4 1 268 200348884 200349148 2.670000e-85 326
8 TraesCS7A01G254800 chr6B 80.488 533 66 18 1918 2429 614733240 614733755 9.380000e-100 374
9 TraesCS7A01G254800 chr6B 79.496 556 67 26 1918 2448 431500369 431499836 4.400000e-93 351


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 TraesCS7A01G254800 chr7A 241659654 241662428 2774 False 5125.000000 5125 100.000 1 2775 1 chr7A.!!$F1 2774
1 TraesCS7A01G254800 chr7D 229784653 229787444 2791 False 1011.333333 2649 90.703 1 2691 3 chr7D.!!$F1 2690
2 TraesCS7A01G254800 chr7B 200348884 200351751 2867 False 1032.333333 2416 89.368 1 2771 3 chr7B.!!$F2 2770
3 TraesCS7A01G254800 chr6B 614733240 614733755 515 False 374.000000 374 80.488 1918 2429 1 chr6B.!!$F1 511
4 TraesCS7A01G254800 chr6B 431499836 431500369 533 True 351.000000 351 79.496 1918 2448 1 chr6B.!!$R1 530


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
873 1112 0.32016 GCAGGAAAAAGGCAAGCCAG 60.32 55.0 14.4 0.0 38.92 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2477 2812 0.037605 CTAACCGACGCCCTGAAACT 60.038 55.0 0.0 0.0 0.0 2.66 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
30 31 7.542477 GGAGTGCACATGTATCTGTATATGTAC 59.458 40.741 21.04 0.00 39.67 2.90
51 52 4.708177 ACCAATCGATTGTCAGGGATTAG 58.292 43.478 30.71 16.72 36.06 1.73
54 55 5.453903 CCAATCGATTGTCAGGGATTAGAGT 60.454 44.000 30.71 0.00 36.06 3.24
59 60 6.371548 TCGATTGTCAGGGATTAGAGTTTTTG 59.628 38.462 0.00 0.00 0.00 2.44
71 72 6.628919 TTAGAGTTTTTGTTTAGTGGAGGC 57.371 37.500 0.00 0.00 0.00 4.70
72 73 3.889538 AGAGTTTTTGTTTAGTGGAGGCC 59.110 43.478 0.00 0.00 0.00 5.19
130 248 3.332034 GGCATGCAATTTCTTTTCTGCT 58.668 40.909 21.36 0.00 35.78 4.24
133 251 6.275335 GGCATGCAATTTCTTTTCTGCTATA 58.725 36.000 21.36 0.00 35.78 1.31
134 252 6.199719 GGCATGCAATTTCTTTTCTGCTATAC 59.800 38.462 21.36 0.00 35.78 1.47
135 253 6.976925 GCATGCAATTTCTTTTCTGCTATACT 59.023 34.615 14.21 0.00 35.78 2.12
136 254 8.131100 GCATGCAATTTCTTTTCTGCTATACTA 58.869 33.333 14.21 0.00 35.78 1.82
261 379 7.189693 GACATGTTGTCACAGAAGTTAATGA 57.810 36.000 0.00 0.00 46.22 2.57
268 386 7.397892 TGTCACAGAAGTTAATGACCAAAAA 57.602 32.000 9.83 0.00 40.63 1.94
275 402 2.663826 TAATGACCAAAAATGCGGCC 57.336 45.000 0.00 0.00 0.00 6.13
296 423 3.292460 CCGCCAATACCCAAATAGGAAA 58.708 45.455 0.00 0.00 41.22 3.13
298 425 4.160626 CCGCCAATACCCAAATAGGAAAAA 59.839 41.667 0.00 0.00 41.22 1.94
345 581 9.520515 AATGTGTGTGTAATCTTAATTCCTCTT 57.479 29.630 0.00 0.00 0.00 2.85
397 634 1.030457 GCTCTGCCCATCCATCAAAG 58.970 55.000 0.00 0.00 0.00 2.77
426 663 3.566322 TGGTTTTATTTGGACACACCTCG 59.434 43.478 0.00 0.00 39.86 4.63
442 679 3.310774 CACCTCGCTCCATTCATAAACTG 59.689 47.826 0.00 0.00 0.00 3.16
447 684 3.374988 CGCTCCATTCATAAACTGCAAGA 59.625 43.478 0.00 0.00 37.43 3.02
483 720 6.462073 TGCGAGTACAAAAGTTACATTCTC 57.538 37.500 0.00 0.00 0.00 2.87
511 748 8.937634 ATTTATATCTTTGGTCGAAGTAACGT 57.062 30.769 0.00 0.00 34.70 3.99
513 750 9.507280 TTTATATCTTTGGTCGAAGTAACGTAG 57.493 33.333 0.00 0.00 34.70 3.51
600 837 8.169977 ACCAAGTTGCATGTATATTATCCTTG 57.830 34.615 0.00 0.00 0.00 3.61
601 838 7.231317 ACCAAGTTGCATGTATATTATCCTTGG 59.769 37.037 0.00 0.00 46.63 3.61
618 855 4.278669 TCCTTGGTCTGATAATCTACGAGC 59.721 45.833 0.00 0.00 0.00 5.03
633 870 5.885881 TCTACGAGCTTGAGAAAGAGATTC 58.114 41.667 8.31 0.00 38.39 2.52
644 881 4.260170 AGAAAGAGATTCGCAAGCAATCT 58.740 39.130 14.92 14.92 42.64 2.40
823 1062 3.249986 TCCGACGGTGGGTAATTAAAG 57.750 47.619 14.79 0.00 0.00 1.85
836 1075 7.936584 TGGGTAATTAAAGCCAATTAATCTCG 58.063 34.615 0.00 0.00 43.83 4.04
868 1107 2.287769 GCTTTTGCAGGAAAAAGGCAA 58.712 42.857 13.07 0.00 44.05 4.52
873 1112 0.320160 GCAGGAAAAAGGCAAGCCAG 60.320 55.000 14.40 0.00 38.92 4.85
924 1163 2.137528 CCCCACCCAAAGCCGTTTT 61.138 57.895 0.00 0.00 0.00 2.43
1002 1242 2.593026 CTATTCGCTCTCCCTCTCCTT 58.407 52.381 0.00 0.00 0.00 3.36
1003 1243 1.408969 ATTCGCTCTCCCTCTCCTTC 58.591 55.000 0.00 0.00 0.00 3.46
1027 1267 0.856982 TGATCTCTCCTCCTCCCCTC 59.143 60.000 0.00 0.00 0.00 4.30
1028 1268 0.114364 GATCTCTCCTCCTCCCCTCC 59.886 65.000 0.00 0.00 0.00 4.30
1029 1269 1.376249 ATCTCTCCTCCTCCCCTCCC 61.376 65.000 0.00 0.00 0.00 4.30
1030 1270 3.036959 TCTCCTCCTCCCCTCCCC 61.037 72.222 0.00 0.00 0.00 4.81
1047 1287 1.431633 CCCCTCCCCAACCTAAGTTTT 59.568 52.381 0.00 0.00 32.45 2.43
1048 1288 2.158219 CCCCTCCCCAACCTAAGTTTTT 60.158 50.000 0.00 0.00 32.45 1.94
1049 1289 3.162666 CCCTCCCCAACCTAAGTTTTTC 58.837 50.000 0.00 0.00 32.45 2.29
1076 1316 1.380515 CGGCCTCTTCTCCTCTCCA 60.381 63.158 0.00 0.00 0.00 3.86
1100 1349 0.740737 CCAACCATCTCCCGCAATTC 59.259 55.000 0.00 0.00 0.00 2.17
1169 1419 3.209812 CCGCCGATCAGGACGAGA 61.210 66.667 15.78 0.00 45.00 4.04
1316 1566 3.827898 GTGGCGGACGAGGAGGAG 61.828 72.222 0.00 0.00 0.00 3.69
1346 1608 3.151022 GAGGAGGAGCCCAGGACG 61.151 72.222 0.00 0.00 37.37 4.79
1496 1758 1.874019 CTCCGCCGTCTTCATGTCG 60.874 63.158 0.00 0.00 0.00 4.35
1677 1939 3.491652 GCGCTGCGTTCCTCTTCC 61.492 66.667 24.04 0.00 0.00 3.46
1733 1995 0.110486 GGTTCCCACGGCCATGATAT 59.890 55.000 0.00 0.00 0.00 1.63
1734 1996 1.349688 GGTTCCCACGGCCATGATATA 59.650 52.381 0.00 0.00 0.00 0.86
1735 1997 2.615493 GGTTCCCACGGCCATGATATAG 60.615 54.545 0.00 0.00 0.00 1.31
1851 2113 9.476202 AAATTGTACTAGAATTGAAAAGGTTGC 57.524 29.630 0.00 0.00 0.00 4.17
1855 2119 9.515226 TGTACTAGAATTGAAAAGGTTGCTATT 57.485 29.630 0.00 0.00 0.00 1.73
1913 2177 7.971183 AAGAACAGGAGTTGTAAGAGAATTC 57.029 36.000 0.00 0.00 39.73 2.17
2037 2314 3.720818 CGCATCTCGAATTTTACACATGC 59.279 43.478 0.00 0.00 41.67 4.06
2085 2363 1.349688 TCGGTGGTGCCAATTAACTCT 59.650 47.619 0.00 0.00 36.97 3.24
2103 2381 1.349026 TCTTCTGGGCCTGAAGAACAG 59.651 52.381 38.28 22.57 42.45 3.16
2301 2602 3.813724 CAGGTGGAGGGGATGGGC 61.814 72.222 0.00 0.00 0.00 5.36
2315 2616 2.576615 GATGGGCTGGGATGTACTTTC 58.423 52.381 0.00 0.00 0.00 2.62
2336 2637 1.202405 GGTTGTTTTGTCCCAGCACAG 60.202 52.381 0.00 0.00 0.00 3.66
2337 2638 1.110442 TTGTTTTGTCCCAGCACAGG 58.890 50.000 0.00 0.00 0.00 4.00
2338 2639 1.363807 GTTTTGTCCCAGCACAGGC 59.636 57.895 0.00 0.00 41.61 4.85
2339 2640 1.076412 TTTTGTCCCAGCACAGGCA 60.076 52.632 0.00 0.00 44.61 4.75
2340 2641 1.391157 TTTTGTCCCAGCACAGGCAC 61.391 55.000 0.00 0.00 44.61 5.01
2341 2642 2.564561 TTTGTCCCAGCACAGGCACA 62.565 55.000 0.00 0.00 44.61 4.57
2346 2647 3.667282 CAGCACAGGCACAGCACC 61.667 66.667 0.00 0.00 44.61 5.01
2448 2759 0.627451 AAATCCCCAGCTGCATCTGA 59.373 50.000 18.94 0.00 36.19 3.27
2449 2760 0.183014 AATCCCCAGCTGCATCTGAG 59.817 55.000 18.94 5.55 36.19 3.35
2474 2809 1.608590 CGGCATTGGTCAGTTTCAGTT 59.391 47.619 0.00 0.00 0.00 3.16
2475 2810 2.034558 CGGCATTGGTCAGTTTCAGTTT 59.965 45.455 0.00 0.00 0.00 2.66
2476 2811 3.642705 GGCATTGGTCAGTTTCAGTTTC 58.357 45.455 0.00 0.00 0.00 2.78
2477 2812 3.068024 GGCATTGGTCAGTTTCAGTTTCA 59.932 43.478 0.00 0.00 0.00 2.69
2478 2813 4.293415 GCATTGGTCAGTTTCAGTTTCAG 58.707 43.478 0.00 0.00 0.00 3.02
2479 2814 4.202050 GCATTGGTCAGTTTCAGTTTCAGT 60.202 41.667 0.00 0.00 0.00 3.41
2480 2815 5.679638 GCATTGGTCAGTTTCAGTTTCAGTT 60.680 40.000 0.00 0.00 0.00 3.16
2481 2816 5.975693 TTGGTCAGTTTCAGTTTCAGTTT 57.024 34.783 0.00 0.00 0.00 2.66
2482 2817 5.560966 TGGTCAGTTTCAGTTTCAGTTTC 57.439 39.130 0.00 0.00 0.00 2.78
2483 2818 5.007034 TGGTCAGTTTCAGTTTCAGTTTCA 58.993 37.500 0.00 0.00 0.00 2.69
2495 2849 0.320073 CAGTTTCAGGGCGTCGGTTA 60.320 55.000 0.00 0.00 0.00 2.85
2505 2859 1.435577 GCGTCGGTTAGGATTGTTGT 58.564 50.000 0.00 0.00 0.00 3.32
2506 2860 1.127951 GCGTCGGTTAGGATTGTTGTG 59.872 52.381 0.00 0.00 0.00 3.33
2507 2861 1.127951 CGTCGGTTAGGATTGTTGTGC 59.872 52.381 0.00 0.00 0.00 4.57
2508 2862 2.147958 GTCGGTTAGGATTGTTGTGCA 58.852 47.619 0.00 0.00 0.00 4.57
2531 2885 2.618816 GCATGGAGGTGTTGAGATCCAA 60.619 50.000 0.00 0.00 44.63 3.53
2532 2886 3.689347 CATGGAGGTGTTGAGATCCAAA 58.311 45.455 0.00 0.00 44.63 3.28
2534 2888 2.087646 GGAGGTGTTGAGATCCAAAGC 58.912 52.381 0.00 0.00 36.36 3.51
2535 2889 1.734465 GAGGTGTTGAGATCCAAAGCG 59.266 52.381 0.00 0.00 36.36 4.68
2536 2890 1.347707 AGGTGTTGAGATCCAAAGCGA 59.652 47.619 0.00 0.00 36.36 4.93
2537 2891 1.734465 GGTGTTGAGATCCAAAGCGAG 59.266 52.381 0.00 0.00 36.36 5.03
2542 2896 1.753649 TGAGATCCAAAGCGAGAGGAG 59.246 52.381 0.00 0.00 34.40 3.69
2543 2897 1.068434 GAGATCCAAAGCGAGAGGAGG 59.932 57.143 0.00 0.00 34.40 4.30
2545 2899 1.341156 ATCCAAAGCGAGAGGAGGGG 61.341 60.000 0.00 0.00 34.40 4.79
2547 2901 1.990060 CAAAGCGAGAGGAGGGGGA 60.990 63.158 0.00 0.00 0.00 4.81
2548 2902 1.687493 AAAGCGAGAGGAGGGGGAG 60.687 63.158 0.00 0.00 0.00 4.30
2549 2903 3.687828 AAGCGAGAGGAGGGGGAGG 62.688 68.421 0.00 0.00 0.00 4.30
2571 2931 1.226435 GGTGCGTTGCGTGTTTGAA 60.226 52.632 0.00 0.00 0.00 2.69
2593 2953 2.669794 AGCCATGGATGGATCCTGACC 61.670 57.143 18.40 13.50 44.64 4.02
2615 2975 1.751924 CGAGTAAGTGGGAGGGAGAAG 59.248 57.143 0.00 0.00 0.00 2.85
2645 3009 1.603931 GCTGAAAGTTTCCTGGCTTGC 60.604 52.381 13.01 3.04 35.30 4.01
2709 3073 2.428890 CAGAACGCAGGAATAGGTCTCT 59.571 50.000 0.00 0.00 27.96 3.10
2711 3075 1.025812 ACGCAGGAATAGGTCTCTCG 58.974 55.000 0.00 0.00 0.00 4.04
2712 3076 0.318275 CGCAGGAATAGGTCTCTCGC 60.318 60.000 0.00 0.00 0.00 5.03
2713 3077 0.032815 GCAGGAATAGGTCTCTCGCC 59.967 60.000 0.00 0.00 0.00 5.54
2714 3078 0.676736 CAGGAATAGGTCTCTCGCCC 59.323 60.000 0.00 0.00 0.00 6.13
2715 3079 0.470268 AGGAATAGGTCTCTCGCCCC 60.470 60.000 0.00 0.00 0.00 5.80
2716 3080 1.473497 GGAATAGGTCTCTCGCCCCC 61.473 65.000 0.00 0.00 0.00 5.40
2717 3081 0.470268 GAATAGGTCTCTCGCCCCCT 60.470 60.000 0.00 0.00 0.00 4.79
2771 3135 1.101049 GCGTGAGAGGGAGAGAGAGG 61.101 65.000 0.00 0.00 0.00 3.69
2772 3136 0.465460 CGTGAGAGGGAGAGAGAGGG 60.465 65.000 0.00 0.00 0.00 4.30
2773 3137 0.106217 GTGAGAGGGAGAGAGAGGGG 60.106 65.000 0.00 0.00 0.00 4.79
2774 3138 1.152546 GAGAGGGAGAGAGAGGGGC 60.153 68.421 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.777865 ATTGGTACATATACAGATACATGTGC 57.222 34.615 9.11 0.00 39.30 4.57
30 31 4.960938 TCTAATCCCTGACAATCGATTGG 58.039 43.478 34.69 20.81 41.96 3.16
51 52 3.889538 AGGCCTCCACTAAACAAAAACTC 59.110 43.478 0.00 0.00 0.00 3.01
54 55 5.202004 TGTAAGGCCTCCACTAAACAAAAA 58.798 37.500 5.23 0.00 0.00 1.94
59 60 3.697619 ACTGTAAGGCCTCCACTAAAC 57.302 47.619 5.23 0.00 39.30 2.01
71 72 4.848562 GGAAAACTTCCCAACTGTAAGG 57.151 45.455 0.00 0.00 44.30 2.69
247 365 6.129115 CGCATTTTTGGTCATTAACTTCTGTG 60.129 38.462 0.00 0.00 0.00 3.66
249 367 5.345741 CCGCATTTTTGGTCATTAACTTCTG 59.654 40.000 0.00 0.00 0.00 3.02
251 369 4.091365 GCCGCATTTTTGGTCATTAACTTC 59.909 41.667 0.00 0.00 0.00 3.01
275 402 2.649531 TCCTATTTGGGTATTGGCGG 57.350 50.000 0.00 0.00 36.20 6.13
325 561 8.049117 AGATGCAAGAGGAATTAAGATTACACA 58.951 33.333 0.00 0.00 0.00 3.72
326 562 8.443953 AGATGCAAGAGGAATTAAGATTACAC 57.556 34.615 0.00 0.00 0.00 2.90
345 581 7.077605 CGAGTGAAATTTTGTCTTTAGATGCA 58.922 34.615 0.00 0.00 0.00 3.96
397 634 4.806775 GTGTCCAAATAAAACCAACACCAC 59.193 41.667 0.00 0.00 31.64 4.16
426 663 4.970662 TCTTGCAGTTTATGAATGGAGC 57.029 40.909 0.00 0.00 0.00 4.70
442 679 6.322491 ACTCGCAAAAGGTAAATAATCTTGC 58.678 36.000 0.00 0.00 35.49 4.01
505 742 8.435430 GTCCACCTAAATTTGTAACTACGTTAC 58.565 37.037 0.00 9.35 45.80 2.50
511 748 7.444299 ACTTCGTCCACCTAAATTTGTAACTA 58.556 34.615 0.00 0.00 0.00 2.24
512 749 6.293698 ACTTCGTCCACCTAAATTTGTAACT 58.706 36.000 0.00 0.00 0.00 2.24
513 750 6.549912 ACTTCGTCCACCTAAATTTGTAAC 57.450 37.500 0.00 0.00 0.00 2.50
514 751 7.571080 AAACTTCGTCCACCTAAATTTGTAA 57.429 32.000 0.00 0.00 0.00 2.41
571 808 9.816354 GGATAATATACATGCAACTTGGTTTTT 57.184 29.630 0.00 0.00 0.00 1.94
572 809 9.200817 AGGATAATATACATGCAACTTGGTTTT 57.799 29.630 0.00 0.00 0.00 2.43
573 810 8.766994 AGGATAATATACATGCAACTTGGTTT 57.233 30.769 0.00 0.00 0.00 3.27
574 811 8.632679 CAAGGATAATATACATGCAACTTGGTT 58.367 33.333 0.00 0.00 0.00 3.67
575 812 7.231317 CCAAGGATAATATACATGCAACTTGGT 59.769 37.037 0.00 0.00 43.67 3.67
576 813 7.596494 CCAAGGATAATATACATGCAACTTGG 58.404 38.462 0.00 0.00 43.34 3.61
577 814 8.169977 ACCAAGGATAATATACATGCAACTTG 57.830 34.615 0.00 0.00 33.37 3.16
578 815 8.220559 AGACCAAGGATAATATACATGCAACTT 58.779 33.333 0.00 0.00 0.00 2.66
579 816 7.663081 CAGACCAAGGATAATATACATGCAACT 59.337 37.037 0.00 0.00 0.00 3.16
580 817 7.661437 TCAGACCAAGGATAATATACATGCAAC 59.339 37.037 0.00 0.00 0.00 4.17
581 818 7.744733 TCAGACCAAGGATAATATACATGCAA 58.255 34.615 0.00 0.00 0.00 4.08
582 819 7.315066 TCAGACCAAGGATAATATACATGCA 57.685 36.000 0.00 0.00 0.00 3.96
600 837 5.239744 TCTCAAGCTCGTAGATTATCAGACC 59.760 44.000 0.00 0.00 33.89 3.85
601 838 6.307031 TCTCAAGCTCGTAGATTATCAGAC 57.693 41.667 0.00 0.00 33.89 3.51
633 870 1.089920 AGTTGCCTAGATTGCTTGCG 58.910 50.000 0.00 0.00 0.00 4.85
660 897 5.221048 GGGCATTTGCGTACTTTGAATAGAT 60.221 40.000 0.00 0.00 43.26 1.98
734 971 6.703607 GTGTTCCAGATATCACTTGGACATAG 59.296 42.308 10.85 0.00 0.00 2.23
735 972 6.408092 GGTGTTCCAGATATCACTTGGACATA 60.408 42.308 10.85 0.00 0.00 2.29
736 973 5.431765 GTGTTCCAGATATCACTTGGACAT 58.568 41.667 10.85 0.00 0.00 3.06
737 974 4.323485 GGTGTTCCAGATATCACTTGGACA 60.323 45.833 10.85 9.78 0.00 4.02
738 975 4.192317 GGTGTTCCAGATATCACTTGGAC 58.808 47.826 10.85 7.86 0.00 4.02
787 1026 1.156736 CGGATCAGGCGTTGTCTTTT 58.843 50.000 0.00 0.00 0.00 2.27
823 1062 6.035843 TGAAGAAAATGCGAGATTAATTGGC 58.964 36.000 0.00 0.00 0.00 4.52
836 1075 3.185797 CCTGCAAAAGCTGAAGAAAATGC 59.814 43.478 0.00 0.00 31.15 3.56
894 1133 3.621682 TGGGTGGGGTAAGTTGAATTT 57.378 42.857 0.00 0.00 0.00 1.82
924 1163 2.588620 GCCCGGAGAGAGAAAGAGATA 58.411 52.381 0.73 0.00 0.00 1.98
1002 1242 2.176798 GGAGGAGGAGAGATCAAGGAGA 59.823 54.545 0.00 0.00 0.00 3.71
1003 1243 2.597455 GGAGGAGGAGAGATCAAGGAG 58.403 57.143 0.00 0.00 0.00 3.69
1027 1267 1.081481 AAACTTAGGTTGGGGAGGGG 58.919 55.000 0.00 0.00 35.63 4.79
1028 1268 2.992847 AAAACTTAGGTTGGGGAGGG 57.007 50.000 0.00 0.00 35.63 4.30
1029 1269 3.162666 GGAAAAACTTAGGTTGGGGAGG 58.837 50.000 0.00 0.00 35.63 4.30
1030 1270 3.162666 GGGAAAAACTTAGGTTGGGGAG 58.837 50.000 0.00 0.00 35.63 4.30
1076 1316 2.971598 CGGGAGATGGTTGGGTGCT 61.972 63.158 0.00 0.00 0.00 4.40
1109 1358 1.033574 CGGGTGTAGAGGTCATCTCC 58.966 60.000 0.00 0.00 43.44 3.71
1110 1359 0.386113 GCGGGTGTAGAGGTCATCTC 59.614 60.000 0.00 0.00 42.75 2.75
1111 1360 1.384989 CGCGGGTGTAGAGGTCATCT 61.385 60.000 0.00 0.00 42.47 2.90
1252 1502 4.148825 CCTCTTCCTCCGCCACCG 62.149 72.222 0.00 0.00 0.00 4.94
1255 1505 3.003173 CCACCTCTTCCTCCGCCA 61.003 66.667 0.00 0.00 0.00 5.69
1308 1558 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1309 1559 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1310 1560 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1311 1561 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1312 1562 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1313 1563 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1314 1564 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1315 1565 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1316 1566 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1570 1832 2.369257 CTACAGCGCCGATCCATGGT 62.369 60.000 12.58 0.00 0.00 3.55
1677 1939 7.375544 CGCAAGAAAGAGAAAGAAAGAAAGAAG 59.624 37.037 0.00 0.00 43.02 2.85
1913 2177 6.423001 GCTGTAATAGTCGGTAATTAACAGGG 59.577 42.308 0.64 0.00 0.00 4.45
1995 2272 1.474077 GGCAGGCACAAGAATCGAATT 59.526 47.619 0.00 0.00 0.00 2.17
1996 2273 1.098050 GGCAGGCACAAGAATCGAAT 58.902 50.000 0.00 0.00 0.00 3.34
2037 2314 1.845809 GCCGTTTGTCAGACTGCCAG 61.846 60.000 1.31 0.00 0.00 4.85
2085 2363 1.349026 CTCTGTTCTTCAGGCCCAGAA 59.651 52.381 0.00 3.15 43.76 3.02
2301 2602 3.053831 ACAACCGAAAGTACATCCCAG 57.946 47.619 0.00 0.00 0.00 4.45
2315 2616 0.248866 GTGCTGGGACAAAACAACCG 60.249 55.000 0.00 0.00 38.70 4.44
2336 2637 4.314440 TCTCACCGGTGCTGTGCC 62.314 66.667 30.25 0.00 33.71 5.01
2337 2638 2.740055 CTCTCACCGGTGCTGTGC 60.740 66.667 30.25 0.00 33.71 4.57
2338 2639 1.665916 CACTCTCACCGGTGCTGTG 60.666 63.158 30.25 28.23 35.01 3.66
2339 2640 1.399744 TTCACTCTCACCGGTGCTGT 61.400 55.000 30.25 22.56 33.91 4.40
2340 2641 0.668706 CTTCACTCTCACCGGTGCTG 60.669 60.000 30.25 23.01 33.91 4.41
2341 2642 0.827925 TCTTCACTCTCACCGGTGCT 60.828 55.000 30.25 8.85 33.91 4.40
2346 2647 2.163509 TCTTCCTCTTCACTCTCACCG 58.836 52.381 0.00 0.00 0.00 4.94
2444 2755 0.973632 ACCAATGCCGTACACTCAGA 59.026 50.000 0.00 0.00 0.00 3.27
2448 2759 0.685097 ACTGACCAATGCCGTACACT 59.315 50.000 0.00 0.00 0.00 3.55
2449 2760 1.519408 AACTGACCAATGCCGTACAC 58.481 50.000 0.00 0.00 0.00 2.90
2474 2809 1.301401 CCGACGCCCTGAAACTGAA 60.301 57.895 0.00 0.00 0.00 3.02
2475 2810 2.035237 AACCGACGCCCTGAAACTGA 62.035 55.000 0.00 0.00 0.00 3.41
2476 2811 0.320073 TAACCGACGCCCTGAAACTG 60.320 55.000 0.00 0.00 0.00 3.16
2477 2812 0.037605 CTAACCGACGCCCTGAAACT 60.038 55.000 0.00 0.00 0.00 2.66
2478 2813 1.017701 CCTAACCGACGCCCTGAAAC 61.018 60.000 0.00 0.00 0.00 2.78
2479 2814 1.186917 TCCTAACCGACGCCCTGAAA 61.187 55.000 0.00 0.00 0.00 2.69
2480 2815 0.974010 ATCCTAACCGACGCCCTGAA 60.974 55.000 0.00 0.00 0.00 3.02
2481 2816 0.974010 AATCCTAACCGACGCCCTGA 60.974 55.000 0.00 0.00 0.00 3.86
2482 2817 0.810031 CAATCCTAACCGACGCCCTG 60.810 60.000 0.00 0.00 0.00 4.45
2483 2818 1.262640 ACAATCCTAACCGACGCCCT 61.263 55.000 0.00 0.00 0.00 5.19
2495 2849 1.206132 CCATGCATGCACAACAATCCT 59.794 47.619 25.37 0.00 0.00 3.24
2505 2859 0.251253 TCAACACCTCCATGCATGCA 60.251 50.000 25.04 25.04 0.00 3.96
2506 2860 0.454600 CTCAACACCTCCATGCATGC 59.545 55.000 21.69 11.82 0.00 4.06
2507 2861 2.118313 TCTCAACACCTCCATGCATG 57.882 50.000 20.19 20.19 0.00 4.06
2508 2862 2.422519 GGATCTCAACACCTCCATGCAT 60.423 50.000 0.00 0.00 0.00 3.96
2531 2885 2.042435 CTCCCCCTCCTCTCGCTT 60.042 66.667 0.00 0.00 0.00 4.68
2532 2886 4.150454 CCTCCCCCTCCTCTCGCT 62.150 72.222 0.00 0.00 0.00 4.93
2534 2888 4.548513 CCCCTCCCCCTCCTCTCG 62.549 77.778 0.00 0.00 0.00 4.04
2535 2889 3.036959 TCCCCTCCCCCTCCTCTC 61.037 72.222 0.00 0.00 0.00 3.20
2536 2890 3.039526 CTCCCCTCCCCCTCCTCT 61.040 72.222 0.00 0.00 0.00 3.69
2537 2891 4.179599 CCTCCCCTCCCCCTCCTC 62.180 77.778 0.00 0.00 0.00 3.71
2593 2953 2.005960 CTCCCTCCCACTTACTCGCG 62.006 65.000 0.00 0.00 0.00 5.87
2594 2954 0.683504 TCTCCCTCCCACTTACTCGC 60.684 60.000 0.00 0.00 0.00 5.03
2595 2955 1.751924 CTTCTCCCTCCCACTTACTCG 59.248 57.143 0.00 0.00 0.00 4.18
2615 2975 0.606673 AACTTTCAGCCTCCGCTTCC 60.607 55.000 0.00 0.00 45.55 3.46
2645 3009 2.015588 GCCCATGTGATGTGAGTGAGG 61.016 57.143 0.00 0.00 0.00 3.86
2713 3077 4.767892 AAGGCAGGGAGGGAGGGG 62.768 72.222 0.00 0.00 0.00 4.79
2714 3078 3.415087 CAAGGCAGGGAGGGAGGG 61.415 72.222 0.00 0.00 0.00 4.30
2715 3079 1.793820 AAACAAGGCAGGGAGGGAGG 61.794 60.000 0.00 0.00 0.00 4.30
2716 3080 0.113190 AAAACAAGGCAGGGAGGGAG 59.887 55.000 0.00 0.00 0.00 4.30
2717 3081 1.354368 CTAAAACAAGGCAGGGAGGGA 59.646 52.381 0.00 0.00 0.00 4.20



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

AutoCloner maintained by Alex Coulton.