Multiple sequence alignment - TraesCS7D01G375800

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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 TraesCS7D01G375800 chr7D 100.000 3880 0 0 1 3880 486103001 486106880 0.000000e+00 7166.0
1 TraesCS7D01G375800 chr7D 77.083 624 118 19 3262 3880 486167239 486167842 1.730000e-88 337.0
2 TraesCS7D01G375800 chr7D 92.473 93 6 1 2622 2714 614538236 614538327 8.750000e-27 132.0
3 TraesCS7D01G375800 chr7D 85.714 98 12 2 953 1050 204256027 204256122 6.860000e-18 102.0
4 TraesCS7D01G375800 chr7D 90.909 55 2 3 76 129 486065780 486065832 1.930000e-08 71.3
5 TraesCS7D01G375800 chr7B 94.186 1376 51 11 1087 2448 513767564 513768924 0.000000e+00 2071.0
6 TraesCS7D01G375800 chr7B 91.083 1357 82 11 2442 3768 513768976 513770323 0.000000e+00 1799.0
7 TraesCS7D01G375800 chr7B 92.108 849 32 19 1 825 513766642 513767479 0.000000e+00 1164.0
8 TraesCS7D01G375800 chr7B 77.544 619 114 20 3262 3875 513956345 513956943 2.220000e-92 350.0
9 TraesCS7D01G375800 chr7B 89.076 119 9 2 3762 3880 513770404 513770518 1.120000e-30 145.0
10 TraesCS7D01G375800 chr7B 82.143 112 17 2 940 1050 168324436 168324545 4.130000e-15 93.5
11 TraesCS7D01G375800 chr7B 92.727 55 1 3 76 129 513764377 513764429 4.160000e-10 76.8
12 TraesCS7D01G375800 chr7A 95.032 946 32 6 1505 2448 554487981 554488913 0.000000e+00 1472.0
13 TraesCS7D01G375800 chr7A 88.861 1185 75 23 2593 3768 554489153 554490289 0.000000e+00 1404.0
14 TraesCS7D01G375800 chr7A 84.856 1281 74 50 1 1223 554486259 554487477 0.000000e+00 1181.0
15 TraesCS7D01G375800 chr7A 92.549 255 15 1 1263 1513 554487474 554487728 2.850000e-96 363.0
16 TraesCS7D01G375800 chr7A 89.412 170 13 1 2445 2609 554488970 554489139 3.930000e-50 209.0
17 TraesCS7D01G375800 chr7A 82.692 104 13 4 927 1026 36394241 36394343 1.920000e-13 87.9
18 TraesCS7D01G375800 chr7A 92.857 56 1 3 76 130 554484268 554484321 1.160000e-10 78.7
19 TraesCS7D01G375800 chr2A 78.153 563 102 15 3325 3880 137564034 137564582 4.800000e-89 339.0
20 TraesCS7D01G375800 chr5D 89.516 124 12 1 927 1050 443498161 443498283 5.190000e-34 156.0
21 TraesCS7D01G375800 chr5A 87.903 124 12 1 927 1050 559738910 559739030 4.040000e-30 143.0
22 TraesCS7D01G375800 chr5A 93.182 88 6 0 2627 2714 664803380 664803293 3.150000e-26 130.0
23 TraesCS7D01G375800 chr3A 94.382 89 4 1 2646 2733 685288882 685288970 6.760000e-28 135.0
24 TraesCS7D01G375800 chr3D 94.186 86 5 0 2636 2721 548393315 548393400 8.750000e-27 132.0
25 TraesCS7D01G375800 chr1A 93.258 89 5 1 2626 2714 47588475 47588388 3.150000e-26 130.0
26 TraesCS7D01G375800 chr1B 89.899 99 8 2 2628 2726 109738182 109738086 4.070000e-25 126.0
27 TraesCS7D01G375800 chr4D 91.304 92 7 1 2623 2714 484397358 484397268 1.460000e-24 124.0
28 TraesCS7D01G375800 chr3B 89.000 100 8 3 951 1050 71334408 71334312 1.890000e-23 121.0
29 TraesCS7D01G375800 chr4B 84.426 122 15 4 928 1049 663103638 663103521 2.450000e-22 117.0
30 TraesCS7D01G375800 chr5B 87.952 83 7 3 963 1044 9620991 9621071 1.150000e-15 95.3
31 TraesCS7D01G375800 chr5B 81.356 118 13 6 937 1052 525619942 525620052 1.920000e-13 87.9
32 TraesCS7D01G375800 chr6B 90.164 61 6 0 3820 3880 707255143 707255203 3.210000e-11 80.5


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 TraesCS7D01G375800 chr7D 486103001 486106880 3879 False 7166.000000 7166 100.0000 1 3880 1 chr7D.!!$F3 3879
1 TraesCS7D01G375800 chr7D 486167239 486167842 603 False 337.000000 337 77.0830 3262 3880 1 chr7D.!!$F4 618
2 TraesCS7D01G375800 chr7B 513764377 513770518 6141 False 1051.160000 2071 91.8360 1 3880 5 chr7B.!!$F3 3879
3 TraesCS7D01G375800 chr7B 513956345 513956943 598 False 350.000000 350 77.5440 3262 3875 1 chr7B.!!$F2 613
4 TraesCS7D01G375800 chr7A 554484268 554490289 6021 False 784.616667 1472 90.5945 1 3768 6 chr7A.!!$F2 3767
5 TraesCS7D01G375800 chr2A 137564034 137564582 548 False 339.000000 339 78.1530 3325 3880 1 chr2A.!!$F1 555

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
779 3565 0.109689 AGCGTCGGTCTCTTTCTTCG 60.110 55.0 0.00 0.0 0.00 3.79 F
829 3620 0.178975 TTCTTTTGGTGGCCATCCGT 60.179 50.0 15.03 0.0 31.53 4.69 F
1192 4005 0.247814 GACGCATCCGAGCAATTGTG 60.248 55.0 7.40 0.0 38.29 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2507 5660 0.463833 GGCCGGTTTCCATCAGGTAG 60.464 60.000 1.90 0.0 35.89 3.18 R
2723 5912 1.203994 CTGCAGGAGGATTTTTGCCAG 59.796 52.381 5.57 0.0 35.75 4.85 R
2884 6074 1.269309 TGCGCCATGTTGGTTTTACAC 60.269 47.619 4.18 0.0 40.46 2.90 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
403 3171 5.239306 AGAAATCATCAACGTGAATGTGTGT 59.761 36.000 9.50 0.00 0.00 3.72
412 3180 4.318332 ACGTGAATGTGTGTTCATCTGAT 58.682 39.130 0.00 0.00 39.99 2.90
413 3181 4.152938 ACGTGAATGTGTGTTCATCTGATG 59.847 41.667 11.42 11.42 39.99 3.07
415 3183 4.696877 GTGAATGTGTGTTCATCTGATGGA 59.303 41.667 17.06 6.14 39.99 3.41
416 3184 5.356190 GTGAATGTGTGTTCATCTGATGGAT 59.644 40.000 17.06 0.00 39.99 3.41
454 3223 3.425659 TCCGAATCCGAGATGATGATCT 58.574 45.455 0.00 0.00 42.02 2.75
553 3322 2.248835 CCGTTTCGTCCGTTGGCTT 61.249 57.895 0.00 0.00 0.00 4.35
561 3337 3.121030 CCGTTGGCTTCTGCTCCG 61.121 66.667 0.00 0.00 39.59 4.63
626 3405 6.498304 ACTGGAAATTGATGAAACATATCGC 58.502 36.000 0.00 0.00 0.00 4.58
644 3426 9.251792 ACATATCGCGTACATTTTTCAATACTA 57.748 29.630 5.77 0.00 0.00 1.82
711 3497 2.224621 CCACCCAGCATATTTCGGAGAT 60.225 50.000 0.00 0.00 35.04 2.75
779 3565 0.109689 AGCGTCGGTCTCTTTCTTCG 60.110 55.000 0.00 0.00 0.00 3.79
825 3616 2.397044 TCCTTTCTTTTGGTGGCCAT 57.603 45.000 9.72 0.00 31.53 4.40
827 3618 1.276138 CCTTTCTTTTGGTGGCCATCC 59.724 52.381 15.03 15.16 31.53 3.51
828 3619 0.965439 TTTCTTTTGGTGGCCATCCG 59.035 50.000 15.03 0.00 31.53 4.18
829 3620 0.178975 TTCTTTTGGTGGCCATCCGT 60.179 50.000 15.03 0.00 31.53 4.69
830 3621 0.608035 TCTTTTGGTGGCCATCCGTC 60.608 55.000 15.03 0.00 31.53 4.79
832 3623 2.398840 TTTTGGTGGCCATCCGTCGA 62.399 55.000 15.03 0.00 31.53 4.20
885 3698 0.322456 TTCTGCCTTCGGTTGATGGG 60.322 55.000 0.20 0.00 39.30 4.00
898 3711 0.453793 TGATGGGCGCAAATTAACCG 59.546 50.000 10.83 0.00 0.00 4.44
902 3715 0.806241 GGGCGCAAATTAACCGAAGA 59.194 50.000 10.83 0.00 0.00 2.87
910 3723 6.142639 GCGCAAATTAACCGAAGAAAAAGTTA 59.857 34.615 0.30 0.00 0.00 2.24
919 3732 5.180680 ACCGAAGAAAAAGTTATGCCTACAC 59.819 40.000 0.00 0.00 0.00 2.90
925 3738 4.382386 AAAGTTATGCCTACACCCAAGT 57.618 40.909 0.00 0.00 0.00 3.16
938 3751 1.913419 ACCCAAGTACCCATGACGAAT 59.087 47.619 0.00 0.00 0.00 3.34
945 3758 6.819649 CCAAGTACCCATGACGAATAGTAAAA 59.180 38.462 0.00 0.00 0.00 1.52
947 3760 8.548721 CAAGTACCCATGACGAATAGTAAAATC 58.451 37.037 0.00 0.00 0.00 2.17
1001 3814 6.778834 ACTTCATGGCATTGATTATGAACA 57.221 33.333 0.00 0.00 35.34 3.18
1005 3818 8.426881 TTCATGGCATTGATTATGAACAAATG 57.573 30.769 0.00 0.00 35.34 2.32
1007 3820 8.041919 TCATGGCATTGATTATGAACAAATGTT 58.958 29.630 0.00 0.00 41.64 2.71
1015 3828 6.529829 TGATTATGAACAAATGTTTTAGGCGC 59.470 34.615 0.00 0.00 38.56 6.53
1018 3831 5.440234 TGAACAAATGTTTTAGGCGCTTA 57.560 34.783 7.64 0.00 38.56 3.09
1019 3832 5.216648 TGAACAAATGTTTTAGGCGCTTAC 58.783 37.500 7.64 0.00 38.56 2.34
1031 3844 1.985684 GGCGCTTACAAAGTTTGATGC 59.014 47.619 22.23 18.56 0.00 3.91
1050 3863 9.955208 TTTGATGCTCAAATAACATCATATGAC 57.045 29.630 7.78 0.00 46.89 3.06
1052 3865 6.882610 TGCTCAAATAACATCATATGACCC 57.117 37.500 7.78 0.00 0.00 4.46
1054 3867 5.106555 GCTCAAATAACATCATATGACCCCG 60.107 44.000 7.78 0.00 0.00 5.73
1055 3868 4.759693 TCAAATAACATCATATGACCCCGC 59.240 41.667 7.78 0.00 0.00 6.13
1056 3869 4.365514 AATAACATCATATGACCCCGCA 57.634 40.909 7.78 0.00 0.00 5.69
1058 3871 2.727123 ACATCATATGACCCCGCAAA 57.273 45.000 7.78 0.00 0.00 3.68
1059 3872 3.011566 ACATCATATGACCCCGCAAAA 57.988 42.857 7.78 0.00 0.00 2.44
1060 3873 3.360867 ACATCATATGACCCCGCAAAAA 58.639 40.909 7.78 0.00 0.00 1.94
1098 3911 9.199982 TGAACTCCGTAGAAACTAAATACAAAG 57.800 33.333 0.00 0.00 0.00 2.77
1120 3933 5.114780 AGTCTGCTCAAACAGTGCATATAG 58.885 41.667 0.00 0.00 44.81 1.31
1190 4003 1.353103 GGACGCATCCGAGCAATTG 59.647 57.895 0.00 0.00 34.48 2.32
1191 4004 1.369091 GGACGCATCCGAGCAATTGT 61.369 55.000 7.40 0.00 34.48 2.71
1192 4005 0.247814 GACGCATCCGAGCAATTGTG 60.248 55.000 7.40 0.00 38.29 3.33
1193 4006 0.673333 ACGCATCCGAGCAATTGTGA 60.673 50.000 7.40 0.00 38.29 3.58
1194 4007 0.659427 CGCATCCGAGCAATTGTGAT 59.341 50.000 7.40 2.15 36.29 3.06
1195 4008 1.596220 CGCATCCGAGCAATTGTGATG 60.596 52.381 17.50 17.50 36.70 3.07
1246 4061 4.767409 AGAAATGGAAAGTTAGGGTTGCTC 59.233 41.667 0.00 0.00 0.00 4.26
1291 4112 1.613925 GGAGAAAGTTGTGGAAAGGCC 59.386 52.381 0.00 0.00 37.10 5.19
1303 4124 2.827322 TGGAAAGGCCATCAGTTTCATG 59.173 45.455 5.01 0.00 43.33 3.07
1319 4140 8.673711 TCAGTTTCATGTATAATTTGCCACTAC 58.326 33.333 0.00 0.00 0.00 2.73
1395 4218 6.394025 AAACTTAAGGCATCGTTAAAACCA 57.606 33.333 7.53 0.00 0.00 3.67
1421 4244 5.642063 TGCAACAAAGGTGCTTCTAGTATAC 59.358 40.000 8.62 0.00 0.00 1.47
1429 4252 5.710567 AGGTGCTTCTAGTATACGCATATGA 59.289 40.000 6.97 0.00 32.75 2.15
1608 4696 5.316167 ACTGTGCTCTGTCCATTTTGAATA 58.684 37.500 0.00 0.00 0.00 1.75
1680 4768 3.751698 GGGATAGGCGGTAAAAATAGCTG 59.248 47.826 0.00 0.00 0.00 4.24
1820 4911 5.132648 AGGCTGATACAAGGATCCACAATTA 59.867 40.000 15.82 0.00 0.00 1.40
1878 4969 3.562557 TCGCATGATTCATTCTCCATGTG 59.437 43.478 0.00 0.00 44.38 3.21
1989 5082 1.008329 TGTTCGTTGTTTCACCGGTC 58.992 50.000 2.59 0.00 0.00 4.79
2007 5100 2.820197 GGTCCTTGGTTCTGATCAAACC 59.180 50.000 22.60 22.60 45.30 3.27
2091 5184 2.125188 GGAGGAGCAGCTGCAGAC 60.125 66.667 38.24 26.59 45.16 3.51
2421 5514 1.063469 CCGCACGTTCTTGTTTCTGTT 59.937 47.619 0.00 0.00 0.00 3.16
2422 5515 2.477189 CCGCACGTTCTTGTTTCTGTTT 60.477 45.455 0.00 0.00 0.00 2.83
2423 5516 3.168193 CGCACGTTCTTGTTTCTGTTTT 58.832 40.909 0.00 0.00 0.00 2.43
2424 5517 3.002149 CGCACGTTCTTGTTTCTGTTTTG 60.002 43.478 0.00 0.00 0.00 2.44
2425 5518 3.241646 GCACGTTCTTGTTTCTGTTTTGC 60.242 43.478 0.00 0.00 0.00 3.68
2459 5612 1.669760 GTGTGCATCGACGGGGAAA 60.670 57.895 0.00 0.00 0.00 3.13
2490 5643 4.802039 GGTTTTCTGCAGTCGACGATTATA 59.198 41.667 14.67 0.00 0.00 0.98
2507 5660 9.944941 GACGATTATAAATGTTGATCGATTCTC 57.055 33.333 10.53 0.00 41.37 2.87
2541 5694 5.416271 AACCGGCCACCTGTATATATAAG 57.584 43.478 0.00 0.00 0.00 1.73
2591 5744 1.403323 GGGCAATTGCAGAGTTCTAGC 59.597 52.381 30.32 9.80 44.36 3.42
2673 5862 3.733960 GAACCCACGCCCTTTCGC 61.734 66.667 0.00 0.00 0.00 4.70
2723 5912 1.668419 ACTCGGCCATATCAACTTGC 58.332 50.000 2.24 0.00 0.00 4.01
2750 5940 3.842007 AAATCCTCCTGCAGAGATCAG 57.158 47.619 17.39 2.55 46.50 2.90
2751 5941 2.771562 ATCCTCCTGCAGAGATCAGA 57.228 50.000 17.39 8.40 46.50 3.27
2778 5968 5.694006 CGCTTTCTACCATCATCCTTCTTAG 59.306 44.000 0.00 0.00 0.00 2.18
2779 5969 6.587273 GCTTTCTACCATCATCCTTCTTAGT 58.413 40.000 0.00 0.00 0.00 2.24
2787 5977 7.746703 ACCATCATCCTTCTTAGTTAATACCC 58.253 38.462 0.00 0.00 0.00 3.69
2865 6055 8.867097 TCCCACTAGGTATTTACTAGCTAATTG 58.133 37.037 0.00 0.00 41.22 2.32
3014 6208 3.427233 CCAGAGCATAGCAAAGAAAGTGC 60.427 47.826 0.00 0.00 42.55 4.40
3075 6269 1.448985 TTTCGGAGCCACATAGTTGC 58.551 50.000 0.00 0.00 0.00 4.17
3146 6340 7.730364 AATAACACTGGTCTTTTCAGTACTG 57.270 36.000 17.17 17.17 42.87 2.74
3176 6376 7.617041 AAATGTACTCAAGGTAGATGAAAGC 57.383 36.000 0.00 0.00 35.07 3.51
3185 6385 6.716628 TCAAGGTAGATGAAAGCTGAAACATT 59.283 34.615 0.00 0.00 30.71 2.71
3273 6473 2.151502 TGTGTTTCCCAAAAGGCTCA 57.848 45.000 0.00 0.00 34.51 4.26
3331 6531 3.963383 GTTCAGCAACGAAGAAAAGGA 57.037 42.857 0.00 0.00 0.00 3.36
3389 6589 1.003718 GCACCGTCCACTTTAGGCT 60.004 57.895 0.00 0.00 0.00 4.58
3437 6637 1.738099 CGAAACTGAGGACAGCCGG 60.738 63.158 0.00 0.00 46.95 6.13
3463 6663 6.131961 TCTGTCTATCATCTCATTCACCTCA 58.868 40.000 0.00 0.00 0.00 3.86
3478 6678 2.875933 CACCTCAACCGCTGAAGTAAAA 59.124 45.455 0.00 0.00 32.17 1.52
3484 6684 6.137794 TCAACCGCTGAAGTAAAATTTTCA 57.862 33.333 6.72 0.00 32.75 2.69
3528 6728 4.496336 AAGCTCCTGCGCATCCCC 62.496 66.667 12.24 0.00 45.42 4.81
3570 6770 9.716531 GAATTCAAATTCTTTTTGATTCCCTCT 57.283 29.630 0.00 0.00 41.18 3.69
3586 6786 2.290641 CCCTCTGAACTTGTGGAAAACG 59.709 50.000 0.00 0.00 0.00 3.60
3623 6823 4.860907 GTGATTTCCAGCATTTAACTGCAG 59.139 41.667 18.69 13.48 44.77 4.41
3674 6874 2.214376 CCAAGTGGGTTGATAGGCAA 57.786 50.000 0.00 0.00 38.60 4.52
3683 6883 3.823304 GGGTTGATAGGCAATTGAGGATC 59.177 47.826 10.34 8.12 39.03 3.36
3719 6919 5.363101 CAGACTGCATATTCATACCAGTGT 58.637 41.667 6.67 1.87 36.93 3.55
3744 6944 9.811995 GTGGTGAACAGTTCAGTTACATATATA 57.188 33.333 16.68 0.00 41.01 0.86
3797 7083 5.764686 ACATTGCAAAATGACTGACTGACTA 59.235 36.000 1.71 0.00 34.39 2.59
3805 7092 7.913674 AAATGACTGACTGACTAAAGGAATC 57.086 36.000 0.00 0.00 0.00 2.52
3809 7096 2.093658 TGACTGACTAAAGGAATCGGGC 60.094 50.000 0.00 0.00 0.00 6.13
3812 7099 1.760613 TGACTAAAGGAATCGGGCGAT 59.239 47.619 0.00 0.00 36.23 4.58
3813 7100 2.960384 TGACTAAAGGAATCGGGCGATA 59.040 45.455 0.00 0.00 33.97 2.92
3833 7120 7.203218 GCGATATATATACCTCAATGTGCAGA 58.797 38.462 0.00 0.00 0.00 4.26
3834 7121 7.380870 GCGATATATATACCTCAATGTGCAGAG 59.619 40.741 0.00 0.00 0.00 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
305 3059 4.778415 CGAGAGGGACACGCCACG 62.778 72.222 0.00 0.00 38.95 4.94
412 3180 1.447838 GTTCGGCGCTTCTCATCCA 60.448 57.895 7.64 0.00 0.00 3.41
413 3181 0.102481 TAGTTCGGCGCTTCTCATCC 59.898 55.000 7.64 0.00 0.00 3.51
415 3183 1.269831 GGATAGTTCGGCGCTTCTCAT 60.270 52.381 7.64 0.00 0.00 2.90
416 3184 0.102481 GGATAGTTCGGCGCTTCTCA 59.898 55.000 7.64 0.00 0.00 3.27
454 3223 3.491964 CCTCATCTTAAACGTGGCGGATA 60.492 47.826 0.00 0.00 0.00 2.59
553 3322 0.900182 AGTCACATCCACGGAGCAGA 60.900 55.000 0.00 0.00 0.00 4.26
561 3337 1.001293 TGAGCTCACAGTCACATCCAC 59.999 52.381 13.74 0.00 0.00 4.02
644 3426 3.615155 GAAGAGCCAAGCCTACAATTCT 58.385 45.455 0.00 0.00 0.00 2.40
692 3474 4.974645 TTATCTCCGAAATATGCTGGGT 57.025 40.909 0.00 0.00 0.00 4.51
720 3506 1.890876 CCAACGGTTGGTCAGAATGA 58.109 50.000 27.87 0.00 45.93 2.57
742 3528 1.600413 GCTTTGGTCGCTTTGGTTGAG 60.600 52.381 0.00 0.00 0.00 3.02
747 3533 1.082104 GACGCTTTGGTCGCTTTGG 60.082 57.895 0.00 0.00 0.00 3.28
748 3534 4.515107 GACGCTTTGGTCGCTTTG 57.485 55.556 0.00 0.00 0.00 2.77
755 3541 0.106149 AAAGAGACCGACGCTTTGGT 59.894 50.000 0.73 0.73 44.42 3.67
756 3542 0.790814 GAAAGAGACCGACGCTTTGG 59.209 55.000 13.40 0.00 45.64 3.28
779 3565 0.902516 AGGAGCAGTGTCCAGAGGTC 60.903 60.000 12.45 0.00 39.34 3.85
885 3698 4.443063 ACTTTTTCTTCGGTTAATTTGCGC 59.557 37.500 0.00 0.00 0.00 6.09
898 3711 5.475564 TGGGTGTAGGCATAACTTTTTCTTC 59.524 40.000 0.00 0.00 0.00 2.87
902 3715 5.144832 ACTTGGGTGTAGGCATAACTTTTT 58.855 37.500 0.00 0.00 0.00 1.94
910 3723 0.916809 GGGTACTTGGGTGTAGGCAT 59.083 55.000 0.00 0.00 0.00 4.40
919 3732 2.710096 ATTCGTCATGGGTACTTGGG 57.290 50.000 0.00 0.00 0.00 4.12
967 3780 7.218614 TCAATGCCATGAAGTTTCTGATTTTT 58.781 30.769 0.00 0.00 0.00 1.94
968 3781 6.761312 TCAATGCCATGAAGTTTCTGATTTT 58.239 32.000 0.00 0.00 0.00 1.82
969 3782 6.349243 TCAATGCCATGAAGTTTCTGATTT 57.651 33.333 0.00 0.00 0.00 2.17
970 3783 5.988310 TCAATGCCATGAAGTTTCTGATT 57.012 34.783 0.00 0.00 0.00 2.57
971 3784 6.540438 AATCAATGCCATGAAGTTTCTGAT 57.460 33.333 0.00 0.00 32.06 2.90
972 3785 5.988310 AATCAATGCCATGAAGTTTCTGA 57.012 34.783 0.00 0.00 32.06 3.27
973 3786 7.485810 TCATAATCAATGCCATGAAGTTTCTG 58.514 34.615 0.00 0.00 35.38 3.02
974 3787 7.649533 TCATAATCAATGCCATGAAGTTTCT 57.350 32.000 0.00 0.00 35.38 2.52
1001 3814 5.838529 ACTTTGTAAGCGCCTAAAACATTT 58.161 33.333 2.29 0.00 0.00 2.32
1005 3818 5.275494 TCAAACTTTGTAAGCGCCTAAAAC 58.725 37.500 2.29 0.00 0.00 2.43
1007 3820 5.457140 CATCAAACTTTGTAAGCGCCTAAA 58.543 37.500 2.29 0.00 0.00 1.85
1031 3844 5.106555 GCGGGGTCATATGATGTTATTTGAG 60.107 44.000 9.02 0.00 0.00 3.02
1060 3873 8.786826 TTCTACGGAGTTCATATGATGTTTTT 57.213 30.769 6.17 0.00 37.78 1.94
1061 3874 8.665685 GTTTCTACGGAGTTCATATGATGTTTT 58.334 33.333 6.17 0.00 37.78 2.43
1062 3875 8.041323 AGTTTCTACGGAGTTCATATGATGTTT 58.959 33.333 6.17 0.00 37.78 2.83
1063 3876 7.556844 AGTTTCTACGGAGTTCATATGATGTT 58.443 34.615 6.17 0.00 37.78 2.71
1064 3877 7.113658 AGTTTCTACGGAGTTCATATGATGT 57.886 36.000 6.17 3.67 37.78 3.06
1065 3878 9.529325 TTTAGTTTCTACGGAGTTCATATGATG 57.471 33.333 6.17 0.00 37.78 3.07
1071 3884 9.715121 TTTGTATTTAGTTTCTACGGAGTTCAT 57.285 29.630 0.00 0.00 37.78 2.57
1072 3885 9.199982 CTTTGTATTTAGTTTCTACGGAGTTCA 57.800 33.333 0.00 0.00 37.78 3.18
1073 3886 9.201127 ACTTTGTATTTAGTTTCTACGGAGTTC 57.799 33.333 0.00 0.00 37.78 3.01
1074 3887 9.201127 GACTTTGTATTTAGTTTCTACGGAGTT 57.799 33.333 0.00 0.00 37.78 3.01
1076 3889 8.861101 CAGACTTTGTATTTAGTTTCTACGGAG 58.139 37.037 0.00 0.00 0.00 4.63
1077 3890 7.330208 GCAGACTTTGTATTTAGTTTCTACGGA 59.670 37.037 0.00 0.00 0.00 4.69
1078 3891 7.331193 AGCAGACTTTGTATTTAGTTTCTACGG 59.669 37.037 0.00 0.00 0.00 4.02
1079 3892 8.240883 AGCAGACTTTGTATTTAGTTTCTACG 57.759 34.615 0.00 0.00 0.00 3.51
1080 3893 9.204570 TGAGCAGACTTTGTATTTAGTTTCTAC 57.795 33.333 0.00 0.00 0.00 2.59
1081 3894 9.772973 TTGAGCAGACTTTGTATTTAGTTTCTA 57.227 29.630 0.00 0.00 0.00 2.10
1082 3895 8.677148 TTGAGCAGACTTTGTATTTAGTTTCT 57.323 30.769 0.00 0.00 0.00 2.52
1083 3896 9.170584 GTTTGAGCAGACTTTGTATTTAGTTTC 57.829 33.333 0.00 0.00 0.00 2.78
1098 3911 4.872691 ACTATATGCACTGTTTGAGCAGAC 59.127 41.667 1.73 0.00 44.80 3.51
1128 3941 7.654520 GTCACCGCCAGTTTTCAACTATATATA 59.345 37.037 0.00 0.00 40.46 0.86
1130 3943 5.813672 GTCACCGCCAGTTTTCAACTATATA 59.186 40.000 0.00 0.00 40.46 0.86
1135 3948 1.021968 GTCACCGCCAGTTTTCAACT 58.978 50.000 0.00 0.00 44.06 3.16
1145 3958 2.151202 GATTTTCTCAAGTCACCGCCA 58.849 47.619 0.00 0.00 0.00 5.69
1180 3993 4.376717 CGATACATCATCACAATTGCTCGG 60.377 45.833 5.05 0.00 32.71 4.63
1181 3994 4.209911 ACGATACATCATCACAATTGCTCG 59.790 41.667 5.05 0.00 32.71 5.03
1291 4112 8.192774 AGTGGCAAATTATACATGAAACTGATG 58.807 33.333 0.00 0.00 0.00 3.07
1379 4202 1.539827 GCACTGGTTTTAACGATGCCT 59.460 47.619 0.00 0.00 0.00 4.75
1393 4216 0.461135 AAGCACCTTTGTTGCACTGG 59.539 50.000 0.00 0.00 0.00 4.00
1395 4218 1.767759 AGAAGCACCTTTGTTGCACT 58.232 45.000 0.00 0.00 0.00 4.40
1680 4768 3.045492 CCACGTAACGGCCACACC 61.045 66.667 2.24 0.00 0.00 4.16
1820 4911 5.769662 TGAAATGGAAGACTAATGTGCAGTT 59.230 36.000 0.00 0.00 0.00 3.16
1878 4969 4.474226 AATCTGAACACAAGAAAGACGC 57.526 40.909 0.00 0.00 0.00 5.19
2007 5100 3.522553 GACCTCTACCATTCCAACGAAG 58.477 50.000 0.00 0.00 0.00 3.79
2339 5432 4.899239 CATCTCGTGGAGGCCGGC 62.899 72.222 21.18 21.18 0.00 6.13
2421 5514 0.680618 CACCCATCCAGCAAAGCAAA 59.319 50.000 0.00 0.00 0.00 3.68
2422 5515 1.186917 CCACCCATCCAGCAAAGCAA 61.187 55.000 0.00 0.00 0.00 3.91
2423 5516 1.607178 CCACCCATCCAGCAAAGCA 60.607 57.895 0.00 0.00 0.00 3.91
2424 5517 1.607467 ACCACCCATCCAGCAAAGC 60.607 57.895 0.00 0.00 0.00 3.51
2425 5518 0.540365 ACACCACCCATCCAGCAAAG 60.540 55.000 0.00 0.00 0.00 2.77
2459 5612 3.438087 CGACTGCAGAAAACCAGATGAAT 59.562 43.478 23.35 0.00 33.40 2.57
2490 5643 6.878317 TCAGGTAGAGAATCGATCAACATTT 58.122 36.000 0.00 0.00 42.67 2.32
2507 5660 0.463833 GGCCGGTTTCCATCAGGTAG 60.464 60.000 1.90 0.00 35.89 3.18
2541 5694 3.332034 ACCGGCAGTTATGTACACTTTC 58.668 45.455 0.00 0.00 0.00 2.62
2567 5720 3.700538 AGAACTCTGCAATTGCCCATTA 58.299 40.909 26.94 7.59 41.18 1.90
2632 5820 6.322456 TCAAATCCCACTGTGAACAATTTACA 59.678 34.615 9.86 0.00 0.00 2.41
2633 5821 6.744112 TCAAATCCCACTGTGAACAATTTAC 58.256 36.000 9.86 0.00 0.00 2.01
2638 5827 4.647424 GTTCAAATCCCACTGTGAACAA 57.353 40.909 9.86 0.00 45.87 2.83
2723 5912 1.203994 CTGCAGGAGGATTTTTGCCAG 59.796 52.381 5.57 0.00 35.75 4.85
2750 5940 4.192317 AGGATGATGGTAGAAAGCGTTTC 58.808 43.478 3.26 3.26 39.96 2.78
2751 5941 4.222124 AGGATGATGGTAGAAAGCGTTT 57.778 40.909 0.00 0.00 0.00 3.60
2787 5977 8.197439 ACAGGTTCAGAAAATGTTTTAGAAAGG 58.803 33.333 6.98 4.27 30.92 3.11
2840 6030 8.095169 CCAATTAGCTAGTAAATACCTAGTGGG 58.905 40.741 0.00 0.00 41.89 4.61
2865 6055 3.190535 ACACGATGCTTTGTTCCAATACC 59.809 43.478 0.00 0.00 0.00 2.73
2873 6063 4.640789 TGGTTTTACACGATGCTTTGTT 57.359 36.364 0.00 0.00 0.00 2.83
2884 6074 1.269309 TGCGCCATGTTGGTTTTACAC 60.269 47.619 4.18 0.00 40.46 2.90
3014 6208 2.884012 TCTGTAGCATGTTGTTGGTTGG 59.116 45.455 0.00 0.00 0.00 3.77
3144 6338 7.097192 TCTACCTTGAGTACATTTTAGTGCAG 58.903 38.462 0.00 0.00 0.00 4.41
3145 6339 6.999950 TCTACCTTGAGTACATTTTAGTGCA 58.000 36.000 0.00 0.00 0.00 4.57
3146 6340 7.764443 TCATCTACCTTGAGTACATTTTAGTGC 59.236 37.037 0.00 0.00 0.00 4.40
3176 6376 7.709947 ACCATTAGCATACATGAATGTTTCAG 58.290 34.615 0.00 0.00 43.98 3.02
3185 6385 8.673711 GTTTTCAACTACCATTAGCATACATGA 58.326 33.333 0.00 0.00 0.00 3.07
3273 6473 7.381323 TCGCTATATGTTCACATGATTGATCT 58.619 34.615 0.00 0.00 37.15 2.75
3331 6531 2.838202 ACTGGACCTTACCATTGACGAT 59.162 45.455 0.00 0.00 39.34 3.73
3337 6537 3.074538 AGAAAGCACTGGACCTTACCATT 59.925 43.478 0.00 0.00 39.34 3.16
3389 6589 3.805807 GCCTCTAAAGTGTTGCTGGTGTA 60.806 47.826 0.00 0.00 0.00 2.90
3433 6633 2.822561 TGAGATGATAGACAGATCCGGC 59.177 50.000 0.00 0.00 0.00 6.13
3437 6637 7.039853 TGAGGTGAATGAGATGATAGACAGATC 60.040 40.741 0.00 0.00 0.00 2.75
3478 6678 1.131126 CTTGTGCCGCTCGATGAAAAT 59.869 47.619 0.00 0.00 0.00 1.82
3484 6684 2.816958 CTGCTTGTGCCGCTCGAT 60.817 61.111 0.00 0.00 38.71 3.59
3528 6728 1.656652 ATTCCTCAAGTTCATCGCCG 58.343 50.000 0.00 0.00 0.00 6.46
3570 6770 3.813166 GAGGATCGTTTTCCACAAGTTCA 59.187 43.478 4.98 0.00 38.32 3.18
3586 6786 1.927895 AATCACGCGTCAAGAGGATC 58.072 50.000 9.86 0.00 0.00 3.36
3623 6823 1.002544 CAAGTTCTGGGAGGAGGTCAC 59.997 57.143 0.00 0.00 0.00 3.67
3674 6874 2.301296 CCCTACATGCTCGATCCTCAAT 59.699 50.000 0.00 0.00 0.00 2.57
3683 6883 0.529337 CAGTCTGCCCTACATGCTCG 60.529 60.000 0.00 0.00 0.00 5.03
3768 6969 8.453320 TCAGTCAGTCATTTTGCAATGTTATAG 58.547 33.333 0.00 0.00 40.78 1.31
3780 7066 7.118390 CGATTCCTTTAGTCAGTCAGTCATTTT 59.882 37.037 0.00 0.00 0.00 1.82
3797 7083 6.553852 AGGTATATATATCGCCCGATTCCTTT 59.446 38.462 8.59 0.00 36.17 3.11
3805 7092 5.920840 CACATTGAGGTATATATATCGCCCG 59.079 44.000 0.00 0.00 0.00 6.13
3809 7096 8.409371 ACTCTGCACATTGAGGTATATATATCG 58.591 37.037 0.00 0.00 34.84 2.92
3812 7099 9.088987 TCAACTCTGCACATTGAGGTATATATA 57.911 33.333 5.76 0.00 34.84 0.86
3813 7100 7.966812 TCAACTCTGCACATTGAGGTATATAT 58.033 34.615 5.76 0.00 34.84 0.86
3833 7120 1.425066 TGCTTCCCCAACATCTCAACT 59.575 47.619 0.00 0.00 0.00 3.16
3834 7121 1.909700 TGCTTCCCCAACATCTCAAC 58.090 50.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.