Multiple sequence alignment - TraesCS7A01G439300

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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 TraesCS7A01G439300 chr7A 100.000 2831 0 0 1 2831 634440025 634437195 0.000000e+00 5228.0
1 TraesCS7A01G439300 chr7D 92.278 2603 124 37 1 2577 549124027 549121476 0.000000e+00 3622.0
2 TraesCS7A01G439300 chr7D 89.437 142 7 5 2692 2831 549121321 549121186 3.750000e-39 172.0
3 TraesCS7A01G439300 chr7D 86.301 73 7 3 2624 2693 8240779 8240707 3.020000e-10 76.8
4 TraesCS7A01G439300 chr7B 85.631 1545 98 47 1084 2557 592625468 592623977 0.000000e+00 1509.0
5 TraesCS7A01G439300 chr7B 92.570 498 16 7 536 1018 592625980 592625489 0.000000e+00 695.0
6 TraesCS7A01G439300 chr7B 87.719 285 31 3 2045 2327 592676548 592676266 2.100000e-86 329.0
7 TraesCS7A01G439300 chr7B 89.437 142 10 3 2692 2831 592623820 592623682 1.040000e-39 174.0
8 TraesCS7A01G439300 chr7B 93.814 97 6 0 460 556 592626099 592626003 2.270000e-31 147.0
9 TraesCS7A01G439300 chr7B 97.059 34 0 1 2602 2635 592675987 592675955 3.940000e-04 56.5
10 TraesCS7A01G439300 chr5D 93.439 442 26 3 1 440 399326926 399327366 0.000000e+00 652.0
11 TraesCS7A01G439300 chr1A 93.197 441 29 1 1 440 493004961 493004521 0.000000e+00 647.0
12 TraesCS7A01G439300 chr1A 92.744 441 31 1 1 440 564311813 564311373 1.110000e-178 636.0
13 TraesCS7A01G439300 chr5A 92.971 441 30 1 1 440 671959601 671960041 2.380000e-180 641.0
14 TraesCS7A01G439300 chr3D 92.971 441 30 1 1 440 69661714 69661274 2.380000e-180 641.0
15 TraesCS7A01G439300 chr3D 95.122 41 1 1 2660 2699 605068186 605068146 2.350000e-06 63.9
16 TraesCS7A01G439300 chr2B 92.938 439 30 1 3 440 717930017 717930455 3.080000e-179 638.0
17 TraesCS7A01G439300 chr4B 92.744 441 31 1 1 440 27479528 27479968 1.110000e-178 636.0
18 TraesCS7A01G439300 chr4B 97.500 40 0 1 2661 2699 487501491 487501530 1.820000e-07 67.6
19 TraesCS7A01G439300 chr5B 92.517 441 32 1 1 440 633278211 633277771 5.150000e-177 630.0
20 TraesCS7A01G439300 chr6B 97.500 40 0 1 2660 2698 271002426 271002387 1.820000e-07 67.6
21 TraesCS7A01G439300 chr2A 95.349 43 0 2 2660 2701 762890637 762890596 1.820000e-07 67.6
22 TraesCS7A01G439300 chr1B 97.500 40 0 1 2659 2697 659518191 659518230 1.820000e-07 67.6
23 TraesCS7A01G439300 chr6A 93.333 45 0 3 2661 2702 389379906 389379862 2.350000e-06 63.9
24 TraesCS7A01G439300 chr4D 97.368 38 0 1 2660 2696 505950861 505950898 2.350000e-06 63.9
25 TraesCS7A01G439300 chr3B 95.122 41 1 1 2660 2699 812816290 812816250 2.350000e-06 63.9


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 TraesCS7A01G439300 chr7A 634437195 634440025 2830 True 5228.00 5228 100.0000 1 2831 1 chr7A.!!$R1 2830
1 TraesCS7A01G439300 chr7D 549121186 549124027 2841 True 1897.00 3622 90.8575 1 2831 2 chr7D.!!$R2 2830
2 TraesCS7A01G439300 chr7B 592623682 592626099 2417 True 631.25 1509 90.3630 460 2831 4 chr7B.!!$R1 2371

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
990 1053 0.035881 CCTCTTGACTCCTGCTGCAA 59.964 55.0 3.02 0.0 0.0 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2449 2608 0.249657 CGAGTAATGCTCCCAGCCTC 60.25 60.0 0.0 0.0 41.51 4.7 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
48 49 4.142071 CCTTGCTAGTTCATGAGCTACTCA 60.142 45.833 14.61 12.33 44.99 3.41
58 59 6.208988 TCATGAGCTACTCAATTACGTTCT 57.791 37.500 0.74 0.00 44.04 3.01
93 94 8.365060 TGATCATAAATGACATGGGAAAAACT 57.635 30.769 0.00 0.00 40.03 2.66
136 138 7.703058 TCATCTATAATGGATGAAGCGACTA 57.297 36.000 8.68 0.00 44.17 2.59
176 178 1.732259 CAACGCATTCACCACCTCTAC 59.268 52.381 0.00 0.00 0.00 2.59
184 186 1.064240 TCACCACCTCTACGCTATCCA 60.064 52.381 0.00 0.00 0.00 3.41
212 214 6.182627 TCACTTCAATCTTACTGCATCCAAT 58.817 36.000 0.00 0.00 0.00 3.16
246 248 1.398692 TCAAACCAAACCTCACTGCC 58.601 50.000 0.00 0.00 0.00 4.85
256 258 1.630369 ACCTCACTGCCATTGCTTCTA 59.370 47.619 0.00 0.00 38.71 2.10
276 278 1.056103 CTGTGAACGAGTCGAAGCAG 58.944 55.000 21.50 16.20 0.00 4.24
277 279 0.318699 TGTGAACGAGTCGAAGCAGG 60.319 55.000 21.50 0.00 0.00 4.85
285 287 1.201429 AGTCGAAGCAGGGGTCCATT 61.201 55.000 0.00 0.00 0.00 3.16
375 377 5.178061 AGTGTGTCATTATCAAATCTCGCA 58.822 37.500 0.00 0.00 0.00 5.10
376 378 5.819379 AGTGTGTCATTATCAAATCTCGCAT 59.181 36.000 0.00 0.00 0.00 4.73
733 793 1.201429 ATGCCCATCCCTACCGATCC 61.201 60.000 0.00 0.00 0.00 3.36
810 870 2.269241 CTCACCGCCCCTTCCTTC 59.731 66.667 0.00 0.00 0.00 3.46
811 871 3.327404 TCACCGCCCCTTCCTTCC 61.327 66.667 0.00 0.00 0.00 3.46
812 872 3.330720 CACCGCCCCTTCCTTCCT 61.331 66.667 0.00 0.00 0.00 3.36
813 873 2.531942 ACCGCCCCTTCCTTCCTT 60.532 61.111 0.00 0.00 0.00 3.36
884 947 0.883370 CGTCTATTTAAGCCGGCCCC 60.883 60.000 26.15 0.00 0.00 5.80
906 969 1.477553 ACCGCAATCATTGAAGCCAT 58.522 45.000 0.00 0.00 0.00 4.40
956 1019 2.726180 GACGACATCGATCGCCGG 60.726 66.667 11.09 0.00 46.22 6.13
957 1020 4.266070 ACGACATCGATCGCCGGG 62.266 66.667 11.09 1.90 46.22 5.73
975 1038 0.105913 GGGTCCCGATCTTCTCCTCT 60.106 60.000 0.00 0.00 0.00 3.69
990 1053 0.035881 CCTCTTGACTCCTGCTGCAA 59.964 55.000 3.02 0.00 0.00 4.08
1022 1091 0.468400 GCCTCCGAGGTACCATCTCT 60.468 60.000 15.94 0.00 37.80 3.10
1098 1167 5.923733 TGGTTCCTCTCTTCTCAGTTATC 57.076 43.478 0.00 0.00 0.00 1.75
1109 1178 6.878317 TCTTCTCAGTTATCGGTTGATGAAT 58.122 36.000 0.00 0.00 35.99 2.57
1240 1328 9.565213 AAAAGAAAGATTGCTTGATCGAAATAG 57.435 29.630 0.00 0.00 33.79 1.73
1294 1382 9.119418 TCTAACAGAAACAAAATGTTCTCATCA 57.881 29.630 0.00 0.00 40.14 3.07
1408 1497 4.098196 GGTTATTTCCTCTCTGCGTCTACT 59.902 45.833 0.00 0.00 0.00 2.57
1422 1511 3.437049 GCGTCTACTTGCTTCCTTTCAAT 59.563 43.478 0.00 0.00 0.00 2.57
1423 1512 4.436183 GCGTCTACTTGCTTCCTTTCAATC 60.436 45.833 0.00 0.00 0.00 2.67
1424 1513 4.690748 CGTCTACTTGCTTCCTTTCAATCA 59.309 41.667 0.00 0.00 0.00 2.57
1425 1514 5.179368 CGTCTACTTGCTTCCTTTCAATCAA 59.821 40.000 0.00 0.00 0.00 2.57
1426 1515 6.293407 CGTCTACTTGCTTCCTTTCAATCAAA 60.293 38.462 0.00 0.00 0.00 2.69
1427 1516 7.080724 GTCTACTTGCTTCCTTTCAATCAAAG 58.919 38.462 0.00 0.00 41.30 2.77
1428 1517 4.625028 ACTTGCTTCCTTTCAATCAAAGC 58.375 39.130 0.00 0.00 40.40 3.51
1429 1518 4.343239 ACTTGCTTCCTTTCAATCAAAGCT 59.657 37.500 6.91 0.00 42.15 3.74
1430 1519 5.536161 ACTTGCTTCCTTTCAATCAAAGCTA 59.464 36.000 6.91 0.00 42.15 3.32
1431 1520 5.376854 TGCTTCCTTTCAATCAAAGCTAC 57.623 39.130 6.91 0.00 42.15 3.58
1432 1521 5.072741 TGCTTCCTTTCAATCAAAGCTACT 58.927 37.500 6.91 0.00 42.15 2.57
1433 1522 5.182001 TGCTTCCTTTCAATCAAAGCTACTC 59.818 40.000 6.91 0.00 42.15 2.59
1434 1523 5.392487 GCTTCCTTTCAATCAAAGCTACTCC 60.392 44.000 0.00 0.00 40.40 3.85
1491 1601 2.296190 AGTTTCAACCGCAAAGGGAATC 59.704 45.455 0.00 0.00 46.96 2.52
1503 1613 5.751028 CGCAAAGGGAATCACTAAAACAAAA 59.249 36.000 0.00 0.00 0.00 2.44
1506 1616 7.042725 GCAAAGGGAATCACTAAAACAAAACTC 60.043 37.037 0.00 0.00 0.00 3.01
1542 1652 8.779354 ACATTGGAACTGAACTAGAATTCTAC 57.221 34.615 11.24 3.10 0.00 2.59
1567 1682 1.133790 GCCTCACTGCTAATGCTTTGG 59.866 52.381 0.00 0.00 40.48 3.28
1570 1685 3.256631 CCTCACTGCTAATGCTTTGGTTT 59.743 43.478 0.00 0.00 40.48 3.27
1578 1693 3.769739 AATGCTTTGGTTTTTCTCCCC 57.230 42.857 0.00 0.00 0.00 4.81
1580 1695 1.037493 GCTTTGGTTTTTCTCCCCGT 58.963 50.000 0.00 0.00 0.00 5.28
1841 1989 3.511595 CGCTTGATGGGCACGCAT 61.512 61.111 0.00 0.00 41.48 4.73
1899 2056 7.619050 AGATATTGTTGTTGAGAGAGTCATGT 58.381 34.615 0.00 0.00 34.17 3.21
1900 2057 5.936686 ATTGTTGTTGAGAGAGTCATGTG 57.063 39.130 0.00 0.00 34.17 3.21
1901 2058 4.406648 TGTTGTTGAGAGAGTCATGTGT 57.593 40.909 0.00 0.00 34.17 3.72
1902 2059 4.122046 TGTTGTTGAGAGAGTCATGTGTG 58.878 43.478 0.00 0.00 34.17 3.82
1903 2060 3.391506 TGTTGAGAGAGTCATGTGTGG 57.608 47.619 0.00 0.00 34.17 4.17
1984 2141 9.382244 GTGTGTATGACTTAGAAAAATGAACAC 57.618 33.333 0.00 0.00 34.44 3.32
1985 2142 8.279800 TGTGTATGACTTAGAAAAATGAACACG 58.720 33.333 0.00 0.00 36.12 4.49
1986 2143 8.280497 GTGTATGACTTAGAAAAATGAACACGT 58.720 33.333 0.00 0.00 0.00 4.49
2016 2173 8.070171 CGACCACATGATTTACAATAGATTTCC 58.930 37.037 0.00 0.00 0.00 3.13
2093 2251 9.627395 CCGTCCATGTTAAATTTACACAAAATA 57.373 29.630 13.50 0.00 36.76 1.40
2174 2332 4.013728 GGGACATGTTATGTTTGGCACTA 58.986 43.478 0.00 0.00 45.03 2.74
2189 2347 4.300703 GGCACTAGCTTGAGACTGCTCA 62.301 54.545 1.04 0.00 44.04 4.26
2206 2365 2.005451 CTCAGGTTGGAGAAATCGCAG 58.995 52.381 0.00 0.00 37.05 5.18
2245 2404 0.595053 CCTGCTACCGTGTATCTGCG 60.595 60.000 0.00 0.00 0.00 5.18
2257 2416 3.552294 GTGTATCTGCGGCTTTCTTCTAC 59.448 47.826 0.00 0.00 0.00 2.59
2279 2438 2.094649 GGGGTATGTATACGCAGCTCTC 60.095 54.545 17.34 0.22 44.98 3.20
2297 2456 4.272018 GCTCTCTCGCACATGACAATTTAT 59.728 41.667 0.00 0.00 0.00 1.40
2442 2601 1.965643 ACGGCACTACCAAGTACAAGA 59.034 47.619 0.00 0.00 39.03 3.02
2449 2608 2.879103 ACCAAGTACAAGATGGTGGG 57.121 50.000 10.64 0.00 45.47 4.61
2450 2609 2.344592 ACCAAGTACAAGATGGTGGGA 58.655 47.619 10.64 0.00 45.47 4.37
2451 2610 2.305927 ACCAAGTACAAGATGGTGGGAG 59.694 50.000 10.64 0.00 45.47 4.30
2454 2613 0.912486 GTACAAGATGGTGGGAGGCT 59.088 55.000 0.00 0.00 0.00 4.58
2455 2614 0.911769 TACAAGATGGTGGGAGGCTG 59.088 55.000 0.00 0.00 0.00 4.85
2456 2615 1.077212 CAAGATGGTGGGAGGCTGG 60.077 63.158 0.00 0.00 0.00 4.85
2457 2616 2.311854 AAGATGGTGGGAGGCTGGG 61.312 63.158 0.00 0.00 0.00 4.45
2458 2617 2.692368 GATGGTGGGAGGCTGGGA 60.692 66.667 0.00 0.00 0.00 4.37
2459 2618 2.693864 ATGGTGGGAGGCTGGGAG 60.694 66.667 0.00 0.00 0.00 4.30
2462 2621 3.415087 GTGGGAGGCTGGGAGCAT 61.415 66.667 0.00 0.00 44.75 3.79
2463 2622 2.614969 TGGGAGGCTGGGAGCATT 60.615 61.111 0.00 0.00 44.75 3.56
2464 2623 1.307778 TGGGAGGCTGGGAGCATTA 60.308 57.895 0.00 0.00 44.75 1.90
2465 2624 1.149401 GGGAGGCTGGGAGCATTAC 59.851 63.158 0.00 0.00 44.75 1.89
2466 2625 1.348775 GGGAGGCTGGGAGCATTACT 61.349 60.000 0.00 0.00 44.75 2.24
2467 2626 0.107643 GGAGGCTGGGAGCATTACTC 59.892 60.000 0.00 0.00 44.75 2.59
2492 2651 3.483587 GAGCACCACTCCTCCCAA 58.516 61.111 0.00 0.00 39.75 4.12
2566 2725 4.192429 GCATAGTGCAAAAATGTTCCCT 57.808 40.909 0.00 0.00 44.26 4.20
2568 2727 4.747810 CATAGTGCAAAAATGTTCCCTCC 58.252 43.478 0.00 0.00 0.00 4.30
2569 2728 1.970640 AGTGCAAAAATGTTCCCTCCC 59.029 47.619 0.00 0.00 0.00 4.30
2571 2730 1.691434 TGCAAAAATGTTCCCTCCCAC 59.309 47.619 0.00 0.00 0.00 4.61
2572 2731 1.691434 GCAAAAATGTTCCCTCCCACA 59.309 47.619 0.00 0.00 0.00 4.17
2573 2732 2.289010 GCAAAAATGTTCCCTCCCACAG 60.289 50.000 0.00 0.00 0.00 3.66
2578 2837 1.809133 TGTTCCCTCCCACAGTACAA 58.191 50.000 0.00 0.00 0.00 2.41
2584 2843 4.810345 TCCCTCCCACAGTACAAAATTTT 58.190 39.130 0.00 0.00 0.00 1.82
2590 2849 7.309990 CCTCCCACAGTACAAAATTTTCATCAT 60.310 37.037 0.00 0.00 0.00 2.45
2641 2900 9.005777 TCACCATTAAAAATATATTACCTCCGC 57.994 33.333 0.00 0.00 0.00 5.54
2642 2901 8.241367 CACCATTAAAAATATATTACCTCCGCC 58.759 37.037 0.00 0.00 0.00 6.13
2643 2902 7.395206 ACCATTAAAAATATATTACCTCCGCCC 59.605 37.037 0.00 0.00 0.00 6.13
2644 2903 7.147966 CCATTAAAAATATATTACCTCCGCCCC 60.148 40.741 0.00 0.00 0.00 5.80
2645 2904 5.327737 AAAAATATATTACCTCCGCCCCA 57.672 39.130 0.00 0.00 0.00 4.96
2646 2905 5.327737 AAAATATATTACCTCCGCCCCAA 57.672 39.130 0.00 0.00 0.00 4.12
2647 2906 5.327737 AAATATATTACCTCCGCCCCAAA 57.672 39.130 0.00 0.00 0.00 3.28
2648 2907 5.327737 AATATATTACCTCCGCCCCAAAA 57.672 39.130 0.00 0.00 0.00 2.44
2649 2908 3.895704 ATATTACCTCCGCCCCAAAAT 57.104 42.857 0.00 0.00 0.00 1.82
2650 2909 2.543037 ATTACCTCCGCCCCAAAATT 57.457 45.000 0.00 0.00 0.00 1.82
2651 2910 3.673543 ATTACCTCCGCCCCAAAATTA 57.326 42.857 0.00 0.00 0.00 1.40
2652 2911 3.673543 TTACCTCCGCCCCAAAATTAT 57.326 42.857 0.00 0.00 0.00 1.28
2653 2912 2.543037 ACCTCCGCCCCAAAATTATT 57.457 45.000 0.00 0.00 0.00 1.40
2654 2913 2.107366 ACCTCCGCCCCAAAATTATTG 58.893 47.619 0.00 0.00 0.00 1.90
2655 2914 2.107366 CCTCCGCCCCAAAATTATTGT 58.893 47.619 0.00 0.00 0.00 2.71
2656 2915 2.100749 CCTCCGCCCCAAAATTATTGTC 59.899 50.000 0.00 0.00 0.00 3.18
2657 2916 3.023832 CTCCGCCCCAAAATTATTGTCT 58.976 45.455 0.00 0.00 0.00 3.41
2658 2917 3.436243 TCCGCCCCAAAATTATTGTCTT 58.564 40.909 0.00 0.00 0.00 3.01
2659 2918 4.601084 TCCGCCCCAAAATTATTGTCTTA 58.399 39.130 0.00 0.00 0.00 2.10
2660 2919 5.017490 TCCGCCCCAAAATTATTGTCTTAA 58.983 37.500 0.00 0.00 0.00 1.85
2661 2920 5.480772 TCCGCCCCAAAATTATTGTCTTAAA 59.519 36.000 0.00 0.00 0.00 1.52
2662 2921 6.155393 TCCGCCCCAAAATTATTGTCTTAAAT 59.845 34.615 0.00 0.00 0.00 1.40
2663 2922 6.821160 CCGCCCCAAAATTATTGTCTTAAATT 59.179 34.615 0.00 0.00 0.00 1.82
2664 2923 7.982354 CCGCCCCAAAATTATTGTCTTAAATTA 59.018 33.333 0.00 0.00 0.00 1.40
2665 2924 9.372369 CGCCCCAAAATTATTGTCTTAAATTAA 57.628 29.630 0.00 0.00 0.00 1.40
2684 2943 8.996024 AAATTAAGACAATAATTTTGGGACGG 57.004 30.769 0.00 0.00 40.71 4.79
2685 2944 7.948034 ATTAAGACAATAATTTTGGGACGGA 57.052 32.000 0.00 0.00 0.00 4.69
2686 2945 5.897377 AAGACAATAATTTTGGGACGGAG 57.103 39.130 0.00 0.00 0.00 4.63
2687 2946 4.270008 AGACAATAATTTTGGGACGGAGG 58.730 43.478 0.00 0.00 0.00 4.30
2688 2947 3.361786 ACAATAATTTTGGGACGGAGGG 58.638 45.455 0.00 0.00 0.00 4.30
2689 2948 3.010808 ACAATAATTTTGGGACGGAGGGA 59.989 43.478 0.00 0.00 0.00 4.20
2690 2949 3.577805 ATAATTTTGGGACGGAGGGAG 57.422 47.619 0.00 0.00 0.00 4.30
2691 2950 1.073098 AATTTTGGGACGGAGGGAGT 58.927 50.000 0.00 0.00 0.00 3.85
2692 2951 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2693 2952 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
2704 2963 5.608449 ACGGAGGGAGTATAAAATTAGCAC 58.392 41.667 0.00 0.00 0.00 4.40
2709 2968 7.878644 GGAGGGAGTATAAAATTAGCACCTTAG 59.121 40.741 0.00 0.00 0.00 2.18
2719 2978 5.959618 ATTAGCACCTTAGGTTGTTGAAC 57.040 39.130 0.00 0.00 31.02 3.18
2820 3079 6.411376 TCCGGTTATCATGTTGAACTACAAT 58.589 36.000 0.00 0.00 40.76 2.71
2824 3083 8.661257 CGGTTATCATGTTGAACTACAATTGTA 58.339 33.333 17.16 17.16 40.76 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.831736 GCAAGGTTAGCTAGGTCCTCA 59.168 52.381 12.43 0.00 0.00 3.86
11 12 2.112190 AGCAAGGTTAGCTAGGTCCTC 58.888 52.381 12.43 4.44 41.32 3.71
77 78 7.396907 TCATGTCATTAGTTTTTCCCATGTCAT 59.603 33.333 0.00 0.00 32.40 3.06
176 178 6.369059 AGATTGAAGTGAATTTGGATAGCG 57.631 37.500 0.00 0.00 0.00 4.26
184 186 7.177216 TGGATGCAGTAAGATTGAAGTGAATTT 59.823 33.333 0.00 0.00 0.00 1.82
212 214 7.375053 GTTTGGTTTGAATCTTGCTAATACCA 58.625 34.615 0.00 0.00 0.00 3.25
246 248 3.990469 ACTCGTTCACAGTAGAAGCAATG 59.010 43.478 0.00 0.00 0.00 2.82
256 258 0.384309 TGCTTCGACTCGTTCACAGT 59.616 50.000 0.00 0.00 0.00 3.55
327 329 4.813027 CAGCAACATTTGGAGCAGTTATT 58.187 39.130 0.00 0.00 0.00 1.40
328 330 3.367703 GCAGCAACATTTGGAGCAGTTAT 60.368 43.478 0.00 0.00 0.00 1.89
733 793 2.737180 CATCCCCCTCGACCGATG 59.263 66.667 0.00 0.00 0.00 3.84
810 870 0.610232 CAGGGAAGGGAAGCACAAGG 60.610 60.000 0.00 0.00 0.00 3.61
811 871 1.246737 GCAGGGAAGGGAAGCACAAG 61.247 60.000 0.00 0.00 0.00 3.16
812 872 1.228552 GCAGGGAAGGGAAGCACAA 60.229 57.895 0.00 0.00 0.00 3.33
813 873 0.840288 TAGCAGGGAAGGGAAGCACA 60.840 55.000 0.00 0.00 0.00 4.57
880 943 2.358372 AATGATTGCGGTTGGGGGC 61.358 57.895 0.00 0.00 0.00 5.80
884 947 1.632422 GCTTCAATGATTGCGGTTGG 58.368 50.000 0.00 0.00 0.00 3.77
906 969 1.281577 TGATGATGCCTGCACCTGTTA 59.718 47.619 0.00 0.00 0.00 2.41
956 1019 0.105913 AGAGGAGAAGATCGGGACCC 60.106 60.000 0.00 0.00 0.00 4.46
957 1020 1.410882 CAAGAGGAGAAGATCGGGACC 59.589 57.143 0.00 0.00 0.00 4.46
958 1021 2.100087 GTCAAGAGGAGAAGATCGGGAC 59.900 54.545 0.00 0.00 0.00 4.46
975 1038 1.168407 GCAGTTGCAGCAGGAGTCAA 61.168 55.000 2.55 0.00 41.59 3.18
1022 1091 4.044825 TGGGTAAATAAGAAGGCAGGGAAA 59.955 41.667 0.00 0.00 0.00 3.13
1058 1127 5.106317 GGAACCATGCTACGAAAAATCAGAA 60.106 40.000 0.00 0.00 0.00 3.02
1059 1128 4.394920 GGAACCATGCTACGAAAAATCAGA 59.605 41.667 0.00 0.00 0.00 3.27
1060 1129 4.396166 AGGAACCATGCTACGAAAAATCAG 59.604 41.667 0.00 0.00 0.00 2.90
1068 1137 2.145397 AGAGAGGAACCATGCTACGA 57.855 50.000 0.00 0.00 0.00 3.43
1070 1139 3.449018 TGAGAAGAGAGGAACCATGCTAC 59.551 47.826 0.00 0.00 0.00 3.58
1098 1167 8.615211 TGATTTTCTTGATCTATTCATCAACCG 58.385 33.333 0.00 0.00 37.77 4.44
1217 1305 6.238593 GCCTATTTCGATCAAGCAATCTTTCT 60.239 38.462 0.00 0.00 0.00 2.52
1240 1328 9.547753 TCTAACAGATCAAACATTATCTTAGCC 57.452 33.333 0.00 0.00 29.93 3.93
1294 1382 4.141711 ACAACAGTCTGCCGACCATAATAT 60.142 41.667 4.47 0.00 41.16 1.28
1408 1497 4.942761 AGCTTTGATTGAAAGGAAGCAA 57.057 36.364 8.81 0.00 43.78 3.91
1422 1511 2.224744 TGCATTGGTGGAGTAGCTTTGA 60.225 45.455 0.00 0.00 0.00 2.69
1423 1512 2.161855 TGCATTGGTGGAGTAGCTTTG 58.838 47.619 0.00 0.00 0.00 2.77
1424 1513 2.584835 TGCATTGGTGGAGTAGCTTT 57.415 45.000 0.00 0.00 0.00 3.51
1425 1514 2.814805 ATGCATTGGTGGAGTAGCTT 57.185 45.000 0.00 0.00 0.00 3.74
1426 1515 2.814805 AATGCATTGGTGGAGTAGCT 57.185 45.000 12.09 0.00 0.00 3.32
1427 1516 6.656693 AGATATAAATGCATTGGTGGAGTAGC 59.343 38.462 13.82 2.10 0.00 3.58
1428 1517 9.155975 GTAGATATAAATGCATTGGTGGAGTAG 57.844 37.037 13.82 0.00 0.00 2.57
1429 1518 8.100791 GGTAGATATAAATGCATTGGTGGAGTA 58.899 37.037 13.82 0.00 0.00 2.59
1430 1519 6.942576 GGTAGATATAAATGCATTGGTGGAGT 59.057 38.462 13.82 0.00 0.00 3.85
1431 1520 7.120285 CAGGTAGATATAAATGCATTGGTGGAG 59.880 40.741 13.82 0.00 0.00 3.86
1432 1521 6.942005 CAGGTAGATATAAATGCATTGGTGGA 59.058 38.462 13.82 0.00 0.00 4.02
1433 1522 6.349611 GCAGGTAGATATAAATGCATTGGTGG 60.350 42.308 13.82 0.00 33.92 4.61
1434 1523 6.432162 AGCAGGTAGATATAAATGCATTGGTG 59.568 38.462 13.82 0.43 36.15 4.17
1491 1601 4.035017 CGCTGTGGAGTTTTGTTTTAGTG 58.965 43.478 0.00 0.00 0.00 2.74
1503 1613 2.236146 TCCAATGTATTCGCTGTGGAGT 59.764 45.455 0.00 0.00 31.61 3.85
1506 1616 3.009723 AGTTCCAATGTATTCGCTGTGG 58.990 45.455 0.00 0.00 0.00 4.17
1542 1652 1.091771 CATTAGCAGTGAGGCCACCG 61.092 60.000 5.01 0.00 44.22 4.94
1567 1682 1.524008 CCTGCCACGGGGAGAAAAAC 61.524 60.000 8.67 0.00 44.17 2.43
1570 1685 4.344865 GCCTGCCACGGGGAGAAA 62.345 66.667 8.67 0.00 44.17 2.52
1841 1989 1.067416 GTCACGGCGGCATCATCTA 59.933 57.895 13.24 0.00 0.00 1.98
1899 2056 4.858680 TCGTGCAAACCGCCCACA 62.859 61.111 0.00 0.00 41.33 4.17
1900 2057 3.361977 ATCGTGCAAACCGCCCAC 61.362 61.111 0.00 0.00 41.33 4.61
1901 2058 3.361158 CATCGTGCAAACCGCCCA 61.361 61.111 0.00 0.00 41.33 5.36
1902 2059 1.579084 TAACATCGTGCAAACCGCCC 61.579 55.000 0.00 0.00 41.33 6.13
1903 2060 0.453782 GTAACATCGTGCAAACCGCC 60.454 55.000 0.00 0.00 41.33 6.13
1968 2125 5.064367 CGACGACGTGTTCATTTTTCTAAG 58.936 41.667 4.58 0.00 34.56 2.18
1984 2141 1.346365 AAATCATGTGGTCGACGACG 58.654 50.000 23.09 11.82 41.26 5.12
1985 2142 3.247442 TGTAAATCATGTGGTCGACGAC 58.753 45.455 22.17 22.17 0.00 4.34
1986 2143 3.579335 TGTAAATCATGTGGTCGACGA 57.421 42.857 9.92 1.86 0.00 4.20
2016 2173 8.635877 AAGAGCTGTAGAACATTAATAGAACG 57.364 34.615 0.00 0.00 0.00 3.95
2063 2220 2.939460 AATTTAACATGGACGGCTGC 57.061 45.000 0.00 0.00 0.00 5.25
2125 2283 1.703411 TTTGCAGCAAGTAGGCCTTT 58.297 45.000 12.58 0.00 0.00 3.11
2189 2347 1.902508 TCTCTGCGATTTCTCCAACCT 59.097 47.619 0.00 0.00 0.00 3.50
2245 2404 2.169978 ACATACCCCGTAGAAGAAAGCC 59.830 50.000 0.00 0.00 0.00 4.35
2248 2407 5.278463 GCGTATACATACCCCGTAGAAGAAA 60.278 44.000 3.32 0.00 0.00 2.52
2257 2416 0.601558 AGCTGCGTATACATACCCCG 59.398 55.000 3.32 0.00 0.00 5.73
2279 2438 8.619146 ACAAATTATAAATTGTCATGTGCGAG 57.381 30.769 12.23 0.00 34.84 5.03
2397 2556 3.901797 CTCCCGGCACAACTCCACC 62.902 68.421 0.00 0.00 0.00 4.61
2442 2601 2.693864 CTCCCAGCCTCCCACCAT 60.694 66.667 0.00 0.00 0.00 3.55
2449 2608 0.249657 CGAGTAATGCTCCCAGCCTC 60.250 60.000 0.00 0.00 41.51 4.70
2450 2609 0.978146 ACGAGTAATGCTCCCAGCCT 60.978 55.000 0.00 0.00 41.51 4.58
2451 2610 0.811616 CACGAGTAATGCTCCCAGCC 60.812 60.000 0.00 0.00 41.51 4.85
2454 2613 1.153647 CGCACGAGTAATGCTCCCA 60.154 57.895 0.00 0.00 41.10 4.37
2455 2614 1.883084 CCGCACGAGTAATGCTCCC 60.883 63.158 0.00 0.00 41.10 4.30
2456 2615 1.883084 CCCGCACGAGTAATGCTCC 60.883 63.158 0.00 0.00 41.10 4.70
2457 2616 1.883084 CCCCGCACGAGTAATGCTC 60.883 63.158 0.00 0.00 41.10 4.26
2458 2617 2.186903 CCCCGCACGAGTAATGCT 59.813 61.111 0.00 0.00 41.10 3.79
2459 2618 1.883084 CTCCCCGCACGAGTAATGC 60.883 63.158 0.00 0.00 39.81 3.56
2460 2619 1.883084 GCTCCCCGCACGAGTAATG 60.883 63.158 0.00 0.00 38.92 1.90
2461 2620 2.355986 TGCTCCCCGCACGAGTAAT 61.356 57.895 0.00 0.00 45.47 1.89
2462 2621 2.992689 TGCTCCCCGCACGAGTAA 60.993 61.111 0.00 0.00 45.47 2.24
2485 2644 1.561076 TGACAGTCCATGATTGGGAGG 59.439 52.381 0.00 0.00 43.81 4.30
2489 2648 1.012086 CGCTGACAGTCCATGATTGG 58.988 55.000 3.99 0.00 45.15 3.16
2492 2651 0.977627 TCCCGCTGACAGTCCATGAT 60.978 55.000 3.99 0.00 0.00 2.45
2508 2667 5.506317 CGAGTTGATATTTTGCCTTGATCCC 60.506 44.000 0.00 0.00 0.00 3.85
2540 2699 5.469760 GGAACATTTTTGCACTATGCCTTTT 59.530 36.000 0.00 0.00 44.23 2.27
2541 2700 4.996758 GGAACATTTTTGCACTATGCCTTT 59.003 37.500 0.00 0.00 44.23 3.11
2542 2701 4.563374 GGGAACATTTTTGCACTATGCCTT 60.563 41.667 0.00 0.00 44.23 4.35
2543 2702 3.055891 GGGAACATTTTTGCACTATGCCT 60.056 43.478 0.00 0.00 44.23 4.75
2546 2705 4.381932 GGGAGGGAACATTTTTGCACTATG 60.382 45.833 0.00 0.00 0.00 2.23
2557 2716 2.344592 TGTACTGTGGGAGGGAACATT 58.655 47.619 0.00 0.00 0.00 2.71
2558 2717 2.038863 TGTACTGTGGGAGGGAACAT 57.961 50.000 0.00 0.00 0.00 2.71
2560 2719 2.943036 TTTGTACTGTGGGAGGGAAC 57.057 50.000 0.00 0.00 0.00 3.62
2562 2721 4.463050 AAATTTTGTACTGTGGGAGGGA 57.537 40.909 0.00 0.00 0.00 4.20
2564 2723 5.782893 TGAAAATTTTGTACTGTGGGAGG 57.217 39.130 8.47 0.00 0.00 4.30
2565 2724 6.980593 TGATGAAAATTTTGTACTGTGGGAG 58.019 36.000 8.47 0.00 0.00 4.30
2566 2725 6.968263 TGATGAAAATTTTGTACTGTGGGA 57.032 33.333 8.47 0.00 0.00 4.37
2568 2727 8.991243 ATGATGATGAAAATTTTGTACTGTGG 57.009 30.769 8.47 0.00 0.00 4.17
2600 2859 4.877378 ATGGTGAATGTGCATCAAGTTT 57.123 36.364 0.00 0.00 31.75 2.66
2602 2861 5.981088 TTAATGGTGAATGTGCATCAAGT 57.019 34.783 0.00 0.00 31.75 3.16
2619 2878 7.394923 TGGGGCGGAGGTAATATATTTTTAATG 59.605 37.037 2.68 0.00 0.00 1.90
2633 2892 3.292460 CAATAATTTTGGGGCGGAGGTA 58.708 45.455 0.00 0.00 0.00 3.08
2634 2893 2.107366 CAATAATTTTGGGGCGGAGGT 58.893 47.619 0.00 0.00 0.00 3.85
2635 2894 2.100749 GACAATAATTTTGGGGCGGAGG 59.899 50.000 0.00 0.00 0.00 4.30
2636 2895 3.023832 AGACAATAATTTTGGGGCGGAG 58.976 45.455 0.00 0.00 0.00 4.63
2637 2896 3.094484 AGACAATAATTTTGGGGCGGA 57.906 42.857 0.00 0.00 0.00 5.54
2638 2897 3.885724 AAGACAATAATTTTGGGGCGG 57.114 42.857 0.00 0.00 0.00 6.13
2639 2898 7.841915 AATTTAAGACAATAATTTTGGGGCG 57.158 32.000 0.00 0.00 0.00 6.13
2659 2918 8.808092 TCCGTCCCAAAATTATTGTCTTAATTT 58.192 29.630 0.00 0.00 41.33 1.82
2660 2919 8.356000 TCCGTCCCAAAATTATTGTCTTAATT 57.644 30.769 0.00 0.00 34.11 1.40
2661 2920 7.068226 CCTCCGTCCCAAAATTATTGTCTTAAT 59.932 37.037 0.00 0.00 0.00 1.40
2662 2921 6.376018 CCTCCGTCCCAAAATTATTGTCTTAA 59.624 38.462 0.00 0.00 0.00 1.85
2663 2922 5.883673 CCTCCGTCCCAAAATTATTGTCTTA 59.116 40.000 0.00 0.00 0.00 2.10
2664 2923 4.705023 CCTCCGTCCCAAAATTATTGTCTT 59.295 41.667 0.00 0.00 0.00 3.01
2665 2924 4.270008 CCTCCGTCCCAAAATTATTGTCT 58.730 43.478 0.00 0.00 0.00 3.41
2666 2925 3.380320 CCCTCCGTCCCAAAATTATTGTC 59.620 47.826 0.00 0.00 0.00 3.18
2667 2926 3.010808 TCCCTCCGTCCCAAAATTATTGT 59.989 43.478 0.00 0.00 0.00 2.71
2668 2927 3.626930 TCCCTCCGTCCCAAAATTATTG 58.373 45.455 0.00 0.00 0.00 1.90
2669 2928 3.268595 ACTCCCTCCGTCCCAAAATTATT 59.731 43.478 0.00 0.00 0.00 1.40
2670 2929 2.850568 ACTCCCTCCGTCCCAAAATTAT 59.149 45.455 0.00 0.00 0.00 1.28
2671 2930 2.271777 ACTCCCTCCGTCCCAAAATTA 58.728 47.619 0.00 0.00 0.00 1.40
2672 2931 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2673 2932 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2674 2933 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2675 2934 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
2676 2935 2.852714 TTATACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
2677 2936 2.852714 TTTATACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
2678 2937 4.701651 AATTTTATACTCCCTCCGTCCC 57.298 45.455 0.00 0.00 0.00 4.46
2679 2938 5.221581 TGCTAATTTTATACTCCCTCCGTCC 60.222 44.000 0.00 0.00 0.00 4.79
2680 2939 5.695363 GTGCTAATTTTATACTCCCTCCGTC 59.305 44.000 0.00 0.00 0.00 4.79
2681 2940 5.454329 GGTGCTAATTTTATACTCCCTCCGT 60.454 44.000 0.00 0.00 0.00 4.69
2682 2941 4.995487 GGTGCTAATTTTATACTCCCTCCG 59.005 45.833 0.00 0.00 0.00 4.63
2683 2942 6.189036 AGGTGCTAATTTTATACTCCCTCC 57.811 41.667 0.00 0.00 0.00 4.30
2684 2943 7.878644 CCTAAGGTGCTAATTTTATACTCCCTC 59.121 40.741 0.00 0.00 0.00 4.30
2685 2944 7.350124 ACCTAAGGTGCTAATTTTATACTCCCT 59.650 37.037 0.00 0.00 32.98 4.20
2686 2945 7.515586 ACCTAAGGTGCTAATTTTATACTCCC 58.484 38.462 0.00 0.00 32.98 4.30
2687 2946 8.837389 CAACCTAAGGTGCTAATTTTATACTCC 58.163 37.037 0.00 0.00 35.34 3.85
2688 2947 9.392259 ACAACCTAAGGTGCTAATTTTATACTC 57.608 33.333 0.00 0.00 35.34 2.59
2689 2948 9.749340 AACAACCTAAGGTGCTAATTTTATACT 57.251 29.630 0.00 0.00 35.34 2.12
2690 2949 9.783256 CAACAACCTAAGGTGCTAATTTTATAC 57.217 33.333 0.00 0.00 35.34 1.47
2691 2950 9.742144 TCAACAACCTAAGGTGCTAATTTTATA 57.258 29.630 0.00 0.00 35.34 0.98
2692 2951 8.644374 TCAACAACCTAAGGTGCTAATTTTAT 57.356 30.769 0.00 0.00 35.34 1.40
2693 2952 8.354426 GTTCAACAACCTAAGGTGCTAATTTTA 58.646 33.333 0.00 0.00 35.34 1.52
2704 2963 6.202516 TGAACAAAGTTCAACAACCTAAGG 57.797 37.500 9.91 0.00 32.22 2.69
2709 2968 5.866633 TGAACATGAACAAAGTTCAACAACC 59.133 36.000 15.54 6.30 45.95 3.77
2790 3049 7.666623 AGTTCAACATGATAACCGGAATTTTT 58.333 30.769 9.46 0.00 0.00 1.94
2795 3054 5.795972 TGTAGTTCAACATGATAACCGGAA 58.204 37.500 9.46 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.