Multiple sequence alignment - TraesCS7A01G022000

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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 TraesCS7A01G022000 chr7A 100.000 2907 0 0 1 2907 8822088 8824994 0.000000e+00 5369.0
1 TraesCS7A01G022000 chr7A 92.289 1232 72 13 967 2175 8884619 8885850 0.000000e+00 1727.0
2 TraesCS7A01G022000 chr7A 85.375 1012 75 24 967 1910 8688638 8689644 0.000000e+00 981.0
3 TraesCS7A01G022000 chr7A 88.672 256 20 4 6 256 8884286 8884537 1.310000e-78 303.0
4 TraesCS7A01G022000 chr7A 82.178 202 12 12 2730 2907 8886609 8886810 5.020000e-33 152.0
5 TraesCS7A01G022000 chr4A 88.571 2065 152 25 905 2907 731388863 731386821 0.000000e+00 2429.0
6 TraesCS7A01G022000 chr4A 92.816 1030 70 4 981 2007 731385374 731384346 0.000000e+00 1489.0
7 TraesCS7A01G022000 chr4A 91.963 535 43 0 1077 1611 731490504 731489970 0.000000e+00 750.0
8 TraesCS7A01G022000 chr4A 83.091 757 78 23 2176 2907 731383818 731383087 0.000000e+00 643.0
9 TraesCS7A01G022000 chr4A 85.096 208 17 4 60 257 731385642 731385439 1.770000e-47 200.0
10 TraesCS7A01G022000 chr4A 92.453 53 4 0 2123 2175 731383891 731383839 3.110000e-10 76.8
11 TraesCS7A01G022000 chr7D 92.636 1290 71 10 905 2175 8375836 8377120 0.000000e+00 1834.0
12 TraesCS7A01G022000 chr7D 92.944 992 57 7 1194 2175 8436055 8437043 0.000000e+00 1432.0
13 TraesCS7A01G022000 chr7D 87.161 849 68 21 1077 1907 8250451 8251276 0.000000e+00 926.0
14 TraesCS7A01G022000 chr7D 95.327 214 6 2 44 257 8375602 8375811 1.290000e-88 337.0
15 TraesCS7A01G022000 chr7D 84.211 266 34 5 1655 1915 7662977 7662715 4.810000e-63 252.0
16 TraesCS7A01G022000 chr7D 84.211 266 34 5 1655 1915 7681449 7681187 4.810000e-63 252.0
17 TraesCS7A01G022000 chr7D 82.673 202 10 7 2730 2907 8437849 8438049 3.880000e-34 156.0
18 TraesCS7A01G022000 chr7D 84.795 171 6 3 2756 2907 8377876 8378045 1.400000e-33 154.0
19 TraesCS7A01G022000 chr7D 85.047 107 16 0 778 884 448038492 448038598 3.060000e-20 110.0
20 TraesCS7A01G022000 chr7D 82.569 109 15 4 1908 2012 7545497 7545389 3.080000e-15 93.5
21 TraesCS7A01G022000 chr7D 88.571 70 8 0 1932 2001 8084521 8084452 5.160000e-13 86.1
22 TraesCS7A01G022000 chr5B 92.247 632 38 5 249 880 416532078 416532698 0.000000e+00 885.0
23 TraesCS7A01G022000 chr5B 82.938 844 109 21 1075 1904 707173703 707174525 0.000000e+00 728.0
24 TraesCS7A01G022000 chr3D 92.593 621 21 7 263 881 264149892 264149295 0.000000e+00 869.0
25 TraesCS7A01G022000 chr2B 88.584 219 25 0 257 475 732339165 732339383 1.720000e-67 267.0
26 TraesCS7A01G022000 chr2B 92.308 65 5 0 817 881 732341538 732341602 3.080000e-15 93.5
27 TraesCS7A01G022000 chr2B 90.769 65 6 0 817 881 732341466 732341530 1.440000e-13 87.9
28 TraesCS7A01G022000 chr2D 88.128 219 26 0 257 475 602077461 602077679 7.990000e-66 261.0
29 TraesCS7A01G022000 chr2D 90.278 72 7 0 810 881 602079980 602080051 8.580000e-16 95.3
30 TraesCS7A01G022000 chr7B 95.092 163 8 0 263 425 695893782 695893944 1.030000e-64 257.0
31 TraesCS7A01G022000 chr5A 84.783 184 14 12 257 432 367492605 367492782 3.850000e-39 172.0
32 TraesCS7A01G022000 chr6A 85.294 170 14 10 257 421 425307641 425307804 6.440000e-37 165.0
33 TraesCS7A01G022000 chr1B 82.778 180 27 3 256 432 370118706 370118528 1.080000e-34 158.0
34 TraesCS7A01G022000 chr1B 80.374 107 12 8 779 881 611576164 611576063 4.020000e-09 73.1
35 TraesCS7A01G022000 chr4B 83.140 172 24 4 257 425 406640742 406640911 5.020000e-33 152.0
36 TraesCS7A01G022000 chr3A 74.631 406 59 34 495 880 465879804 465880185 3.910000e-29 139.0
37 TraesCS7A01G022000 chr6B 83.495 103 17 0 777 879 610211505 610211607 2.380000e-16 97.1


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 TraesCS7A01G022000 chr7A 8822088 8824994 2906 False 5369.000000 5369 100.000000 1 2907 1 chr7A.!!$F2 2906
1 TraesCS7A01G022000 chr7A 8688638 8689644 1006 False 981.000000 981 85.375000 967 1910 1 chr7A.!!$F1 943
2 TraesCS7A01G022000 chr7A 8884286 8886810 2524 False 727.333333 1727 87.713000 6 2907 3 chr7A.!!$F3 2901
3 TraesCS7A01G022000 chr4A 731383087 731388863 5776 True 967.560000 2429 88.405400 60 2907 5 chr4A.!!$R2 2847
4 TraesCS7A01G022000 chr4A 731489970 731490504 534 True 750.000000 750 91.963000 1077 1611 1 chr4A.!!$R1 534
5 TraesCS7A01G022000 chr7D 8250451 8251276 825 False 926.000000 926 87.161000 1077 1907 1 chr7D.!!$F1 830
6 TraesCS7A01G022000 chr7D 8436055 8438049 1994 False 794.000000 1432 87.808500 1194 2907 2 chr7D.!!$F4 1713
7 TraesCS7A01G022000 chr7D 8375602 8378045 2443 False 775.000000 1834 90.919333 44 2907 3 chr7D.!!$F3 2863
8 TraesCS7A01G022000 chr5B 416532078 416532698 620 False 885.000000 885 92.247000 249 880 1 chr5B.!!$F1 631
9 TraesCS7A01G022000 chr5B 707173703 707174525 822 False 728.000000 728 82.938000 1075 1904 1 chr5B.!!$F2 829
10 TraesCS7A01G022000 chr3D 264149295 264149892 597 True 869.000000 869 92.593000 263 881 1 chr3D.!!$R1 618

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
890 898 0.247185 AACCGAATTTGCATGCCCAG 59.753 50.0 16.68 0.48 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2814 7158 0.536006 GCTTCCGATGCCTGGCTAAT 60.536 55.0 21.03 5.63 0.0 1.73 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
33 34 0.317854 GCAGTTTGTTTGTCCGGCTC 60.318 55.000 0.00 0.00 0.00 4.70
97 98 1.451207 TGCAGTGCAGTCCAACGTT 60.451 52.632 15.37 0.00 33.32 3.99
126 127 2.472695 TACAGCTCATTTGACGCCTT 57.527 45.000 0.00 0.00 0.00 4.35
139 140 1.865340 GACGCCTTTTTCGAGTGAAGT 59.135 47.619 0.00 0.00 35.06 3.01
140 141 1.597663 ACGCCTTTTTCGAGTGAAGTG 59.402 47.619 0.00 0.00 35.06 3.16
141 142 1.660333 CGCCTTTTTCGAGTGAAGTGC 60.660 52.381 0.00 0.00 35.06 4.40
142 143 1.660333 GCCTTTTTCGAGTGAAGTGCG 60.660 52.381 0.00 0.00 35.06 5.34
143 144 1.597663 CCTTTTTCGAGTGAAGTGCGT 59.402 47.619 0.00 0.00 35.06 5.24
207 209 3.387699 CCCTCCCACACAAGAAAACAAAT 59.612 43.478 0.00 0.00 0.00 2.32
223 229 4.989279 ACAAATGCCATAGTGGATTGAC 57.011 40.909 13.09 0.00 40.96 3.18
261 267 0.689745 TCCACTCCCAACGATAGGGG 60.690 60.000 10.77 5.62 46.77 4.79
279 285 1.249407 GGTGGGCATAAAAACCGACA 58.751 50.000 0.00 0.00 36.47 4.35
295 301 1.574134 GACAAACCGAAGACCGAACA 58.426 50.000 0.00 0.00 41.76 3.18
378 384 6.456988 GGTTTCTACATCTGCTAACCGAATTG 60.457 42.308 0.00 0.00 0.00 2.32
436 442 5.107989 CCGAAGAAACCGATAATATGTCACG 60.108 44.000 0.00 0.00 0.00 4.35
560 566 1.762708 GTGCAAGGCCCAAGCTATTA 58.237 50.000 12.22 0.00 39.73 0.98
732 738 0.737804 GAGAGAGAGAGCGTGCATGA 59.262 55.000 10.93 0.00 0.00 3.07
746 752 3.436704 CGTGCATGAGTAGAAAACCACAT 59.563 43.478 0.00 0.00 0.00 3.21
811 819 4.186159 CCATACACCGAACCGAATAACTT 58.814 43.478 0.00 0.00 0.00 2.66
882 890 9.523730 GTTTTCATATTTGTTAACCGAATTTGC 57.476 29.630 2.48 0.00 30.23 3.68
883 891 8.818141 TTTCATATTTGTTAACCGAATTTGCA 57.182 26.923 2.48 0.00 30.23 4.08
884 892 8.994429 TTCATATTTGTTAACCGAATTTGCAT 57.006 26.923 2.48 0.00 30.23 3.96
885 893 8.404889 TCATATTTGTTAACCGAATTTGCATG 57.595 30.769 2.48 5.00 30.23 4.06
886 894 4.981389 TTTGTTAACCGAATTTGCATGC 57.019 36.364 11.82 11.82 0.00 4.06
887 895 2.953020 TGTTAACCGAATTTGCATGCC 58.047 42.857 16.68 0.00 0.00 4.40
888 896 2.267426 GTTAACCGAATTTGCATGCCC 58.733 47.619 16.68 0.00 0.00 5.36
889 897 1.550327 TAACCGAATTTGCATGCCCA 58.450 45.000 16.68 1.02 0.00 5.36
890 898 0.247185 AACCGAATTTGCATGCCCAG 59.753 50.000 16.68 0.48 0.00 4.45
891 899 1.142314 CCGAATTTGCATGCCCAGG 59.858 57.895 16.68 6.29 0.00 4.45
892 900 1.519898 CGAATTTGCATGCCCAGGC 60.520 57.895 16.68 0.38 42.35 4.85
893 901 1.153309 GAATTTGCATGCCCAGGCC 60.153 57.895 16.68 0.00 41.09 5.19
894 902 1.614226 AATTTGCATGCCCAGGCCT 60.614 52.632 16.68 0.00 41.09 5.19
895 903 0.325484 AATTTGCATGCCCAGGCCTA 60.325 50.000 16.68 0.00 41.09 3.93
896 904 1.044790 ATTTGCATGCCCAGGCCTAC 61.045 55.000 16.68 0.00 41.09 3.18
897 905 3.660422 TTGCATGCCCAGGCCTACC 62.660 63.158 16.68 0.00 41.09 3.18
898 906 4.902645 GCATGCCCAGGCCTACCC 62.903 72.222 3.98 0.00 41.09 3.69
899 907 3.419580 CATGCCCAGGCCTACCCA 61.420 66.667 3.98 2.36 41.09 4.51
900 908 2.616893 ATGCCCAGGCCTACCCAA 60.617 61.111 3.98 0.00 41.09 4.12
901 909 2.996330 ATGCCCAGGCCTACCCAAC 61.996 63.158 3.98 0.00 41.09 3.77
902 910 4.796495 GCCCAGGCCTACCCAACG 62.796 72.222 3.98 0.00 36.11 4.10
903 911 3.006728 CCCAGGCCTACCCAACGA 61.007 66.667 3.98 0.00 36.11 3.85
933 941 1.187567 TCAGTAGCAGCCAGTGAGCA 61.188 55.000 0.00 0.00 34.23 4.26
935 943 2.105466 GTAGCAGCCAGTGAGCAGC 61.105 63.158 11.32 11.32 44.85 5.25
1921 5424 4.459685 ACGCTCTGATGACTAGTAGTGTTT 59.540 41.667 7.76 0.00 0.00 2.83
1938 5445 6.866179 AGTGTTTGTTCGAATACTATCGTC 57.134 37.500 0.00 0.00 43.19 4.20
1968 5475 6.406177 CCATGGAAGAGTTAATTTGGTGATGG 60.406 42.308 5.56 0.00 0.00 3.51
2052 5839 3.327464 CGCCTTGTTATGCGCATTT 57.673 47.368 30.42 8.81 44.64 2.32
2054 5841 1.991965 CGCCTTGTTATGCGCATTTTT 59.008 42.857 30.42 7.46 44.64 1.94
2082 5869 7.414222 AATGAAACAATCTCATTGCCAGTAT 57.586 32.000 0.00 0.00 43.98 2.12
2161 6012 5.502079 TGGAAAGAAGACTTGTTGTTACCA 58.498 37.500 0.00 4.42 36.39 3.25
2175 6026 4.148128 TGTTACCAAAACACTTCCCGTA 57.852 40.909 0.00 0.00 0.00 4.02
2209 6119 1.802636 CCACGTGCCCATGATTGAC 59.197 57.895 10.91 0.00 0.00 3.18
2213 6123 2.440065 TGCCCATGATTGACCCGC 60.440 61.111 0.00 0.00 0.00 6.13
2263 6173 1.008538 GGCGCAACAGAAACCACAG 60.009 57.895 10.83 0.00 0.00 3.66
2266 6176 1.727467 GCAACAGAAACCACAGCGT 59.273 52.632 0.00 0.00 0.00 5.07
2290 6202 7.974501 CGTAGATGGTGTATAGAGAAAACTGTT 59.025 37.037 0.00 0.00 0.00 3.16
2293 6205 7.607991 AGATGGTGTATAGAGAAAACTGTTTGG 59.392 37.037 6.53 0.00 0.00 3.28
2298 6210 8.496751 GTGTATAGAGAAAACTGTTTGGAGAAC 58.503 37.037 6.53 1.45 0.00 3.01
2301 6213 4.884164 AGAGAAAACTGTTTGGAGAACTGG 59.116 41.667 6.53 0.00 0.00 4.00
2304 6216 5.893824 AGAAAACTGTTTGGAGAACTGGAAT 59.106 36.000 6.53 0.00 0.00 3.01
2307 6219 6.884280 AACTGTTTGGAGAACTGGAATAAG 57.116 37.500 0.00 0.00 0.00 1.73
2318 6230 4.650972 ACTGGAATAAGGGCTTGTGTTA 57.349 40.909 0.00 0.00 0.00 2.41
2339 6289 0.239347 AAAGCACTGAACGCAGCATC 59.761 50.000 0.00 0.00 46.26 3.91
2343 6293 0.952497 CACTGAACGCAGCATCAGGT 60.952 55.000 22.73 10.50 45.36 4.00
2358 6308 1.408702 TCAGGTTTGTTGCAAAGGCTC 59.591 47.619 0.00 0.00 41.91 4.70
2362 6312 2.224018 GGTTTGTTGCAAAGGCTCATCA 60.224 45.455 0.00 0.00 41.91 3.07
2377 6327 3.114809 CTCATCAAGCAGATCAGACGAC 58.885 50.000 0.00 0.00 33.72 4.34
2378 6328 2.757314 TCATCAAGCAGATCAGACGACT 59.243 45.455 0.00 0.00 33.72 4.18
2379 6329 3.194329 TCATCAAGCAGATCAGACGACTT 59.806 43.478 0.00 0.00 33.72 3.01
2380 6330 3.667497 TCAAGCAGATCAGACGACTTT 57.333 42.857 0.00 0.00 0.00 2.66
2382 6332 5.330455 TCAAGCAGATCAGACGACTTTAT 57.670 39.130 0.00 0.00 0.00 1.40
2384 6334 7.043961 TCAAGCAGATCAGACGACTTTATAT 57.956 36.000 0.00 0.00 0.00 0.86
2385 6335 7.142021 TCAAGCAGATCAGACGACTTTATATC 58.858 38.462 0.00 0.00 0.00 1.63
2387 6337 7.225784 AGCAGATCAGACGACTTTATATCAT 57.774 36.000 0.00 0.00 0.00 2.45
2388 6338 7.089538 AGCAGATCAGACGACTTTATATCATG 58.910 38.462 0.00 0.00 0.00 3.07
2389 6339 6.865726 GCAGATCAGACGACTTTATATCATGT 59.134 38.462 0.00 0.00 0.00 3.21
2500 6653 2.558795 GAGCTAATCGGATGGCTGTAGA 59.441 50.000 18.88 0.00 35.01 2.59
2501 6654 2.965831 AGCTAATCGGATGGCTGTAGAA 59.034 45.455 14.93 0.00 33.50 2.10
2504 6657 4.574828 GCTAATCGGATGGCTGTAGAAAAA 59.425 41.667 8.37 0.00 0.00 1.94
2603 6794 1.071605 CTTAGTGGCTCACGTGAAGC 58.928 55.000 20.49 22.26 39.64 3.86
2604 6795 0.391228 TTAGTGGCTCACGTGAAGCA 59.609 50.000 28.66 18.01 39.64 3.91
2605 6796 0.391228 TAGTGGCTCACGTGAAGCAA 59.609 50.000 28.66 21.06 39.64 3.91
2607 6799 0.593128 GTGGCTCACGTGAAGCAATT 59.407 50.000 28.66 0.00 0.00 2.32
2609 6801 2.420022 GTGGCTCACGTGAAGCAATTAT 59.580 45.455 28.66 0.00 0.00 1.28
2618 6810 4.453136 ACGTGAAGCAATTATACGGTTGTT 59.547 37.500 0.00 0.00 38.92 2.83
2646 6838 3.030168 ATCGAACGGCAGCCCATGA 62.030 57.895 5.63 0.00 0.00 3.07
2659 6851 1.672881 GCCCATGAGGTCGATCTTTTG 59.327 52.381 0.00 0.41 38.26 2.44
2669 6861 5.615289 AGGTCGATCTTTTGGGATTATCAG 58.385 41.667 0.00 0.00 0.00 2.90
2670 6862 5.131142 AGGTCGATCTTTTGGGATTATCAGT 59.869 40.000 0.00 0.00 0.00 3.41
2671 6863 5.823045 GGTCGATCTTTTGGGATTATCAGTT 59.177 40.000 0.00 0.00 0.00 3.16
2672 6864 6.318900 GGTCGATCTTTTGGGATTATCAGTTT 59.681 38.462 0.00 0.00 0.00 2.66
2673 6865 7.497909 GGTCGATCTTTTGGGATTATCAGTTTA 59.502 37.037 0.00 0.00 0.00 2.01
2674 6866 9.057089 GTCGATCTTTTGGGATTATCAGTTTAT 57.943 33.333 0.00 0.00 0.00 1.40
2675 6867 9.273016 TCGATCTTTTGGGATTATCAGTTTATC 57.727 33.333 0.00 0.00 0.00 1.75
2676 6868 9.056005 CGATCTTTTGGGATTATCAGTTTATCA 57.944 33.333 0.00 0.00 0.00 2.15
2688 6880 1.345415 AGTTTATCACCCGGTCAACGT 59.655 47.619 0.00 0.00 42.24 3.99
2693 6885 0.822944 TCACCCGGTCAACGTGTAGA 60.823 55.000 0.00 0.00 42.24 2.59
2695 6887 0.752054 ACCCGGTCAACGTGTAGAAA 59.248 50.000 0.00 0.00 42.24 2.52
2696 6888 1.138661 ACCCGGTCAACGTGTAGAAAA 59.861 47.619 0.00 0.00 42.24 2.29
2813 7157 5.987347 AGCACTGGCATTATTTTATTCATGC 59.013 36.000 0.00 0.00 44.61 4.06
2814 7158 5.754406 GCACTGGCATTATTTTATTCATGCA 59.246 36.000 5.42 0.00 43.27 3.96
2818 7162 9.701098 ACTGGCATTATTTTATTCATGCATTAG 57.299 29.630 0.00 3.38 43.27 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.686355 AACTGCGGACAAAATCACCA 58.314 45.000 0.00 0.00 0.00 4.17
4 5 3.862845 ACAAACAAACTGCGGACAAAATC 59.137 39.130 0.00 0.00 0.00 2.17
6 7 3.246619 GACAAACAAACTGCGGACAAAA 58.753 40.909 0.00 0.00 0.00 2.44
7 8 2.416162 GGACAAACAAACTGCGGACAAA 60.416 45.455 0.00 0.00 0.00 2.83
8 9 1.133407 GGACAAACAAACTGCGGACAA 59.867 47.619 0.00 0.00 0.00 3.18
9 10 0.736053 GGACAAACAAACTGCGGACA 59.264 50.000 0.00 0.00 0.00 4.02
50 51 2.254459 CAAGTCTAGTACAGTGCAGCG 58.746 52.381 0.00 0.00 0.00 5.18
52 53 4.505313 TCACAAGTCTAGTACAGTGCAG 57.495 45.455 0.00 0.00 36.72 4.41
97 98 4.162131 TCAAATGAGCTGTATGCCTGTCTA 59.838 41.667 0.00 0.00 44.23 2.59
126 127 0.303493 GCACGCACTTCACTCGAAAA 59.697 50.000 0.00 0.00 0.00 2.29
141 142 3.475774 GTCACGGGTAAGCGCACG 61.476 66.667 11.47 8.58 0.00 5.34
142 143 1.500512 TTTGTCACGGGTAAGCGCAC 61.501 55.000 11.47 0.00 0.00 5.34
143 144 1.227586 TTTGTCACGGGTAAGCGCA 60.228 52.632 11.47 0.00 0.00 6.09
207 209 0.908910 ACGGTCAATCCACTATGGCA 59.091 50.000 0.00 0.00 37.47 4.92
260 266 1.249407 TGTCGGTTTTTATGCCCACC 58.751 50.000 0.00 0.00 0.00 4.61
261 267 3.054166 GTTTGTCGGTTTTTATGCCCAC 58.946 45.455 0.00 0.00 0.00 4.61
279 285 2.480845 CTTCTGTTCGGTCTTCGGTTT 58.519 47.619 0.00 0.00 39.77 3.27
295 301 2.745821 GGTTTATTCGGTTTCGGCTTCT 59.254 45.455 0.00 0.00 36.95 2.85
378 384 7.420002 AGTAAAAACTGTAACCAACCGAATTC 58.580 34.615 0.00 0.00 0.00 2.17
425 431 2.803133 GCTGGCTGCTCGTGACATATTA 60.803 50.000 9.31 0.00 38.95 0.98
476 482 3.851128 GAGGACCTACTGGCGGGC 61.851 72.222 0.00 0.00 36.63 6.13
477 483 3.528370 CGAGGACCTACTGGCGGG 61.528 72.222 0.00 0.00 36.63 6.13
478 484 2.754658 ACGAGGACCTACTGGCGG 60.755 66.667 0.00 0.00 36.63 6.13
479 485 2.490217 CACGAGGACCTACTGGCG 59.510 66.667 0.00 0.00 36.63 5.69
480 486 2.184579 GCACGAGGACCTACTGGC 59.815 66.667 0.00 0.00 36.63 4.85
481 487 2.044555 TCGCACGAGGACCTACTGG 61.045 63.158 0.00 0.00 39.83 4.00
482 488 1.136984 GTCGCACGAGGACCTACTG 59.863 63.158 0.00 0.00 0.00 2.74
483 489 1.303074 TGTCGCACGAGGACCTACT 60.303 57.895 0.00 0.00 33.46 2.57
484 490 1.136984 CTGTCGCACGAGGACCTAC 59.863 63.158 0.00 0.00 33.46 3.18
485 491 2.697761 GCTGTCGCACGAGGACCTA 61.698 63.158 0.00 0.00 35.78 3.08
486 492 4.057428 GCTGTCGCACGAGGACCT 62.057 66.667 0.00 0.00 35.78 3.85
569 575 1.001393 GGCTCACATCGGGGGAAAA 60.001 57.895 0.00 0.00 0.00 2.29
732 738 6.655078 ATTTCTGCAATGTGGTTTTCTACT 57.345 33.333 0.00 0.00 32.36 2.57
746 752 4.305989 AGTCGCAAAAGAATTTCTGCAA 57.694 36.364 0.00 0.00 37.28 4.08
791 799 4.186159 CCAAGTTATTCGGTTCGGTGTAT 58.814 43.478 0.00 0.00 0.00 2.29
881 889 4.902645 GGGTAGGCCTGGGCATGC 62.903 72.222 23.25 9.90 44.11 4.06
882 890 2.995077 TTGGGTAGGCCTGGGCATG 61.995 63.158 23.25 0.00 44.11 4.06
883 891 2.616893 TTGGGTAGGCCTGGGCAT 60.617 61.111 23.25 10.44 44.11 4.40
884 892 3.657350 GTTGGGTAGGCCTGGGCA 61.657 66.667 23.25 5.66 44.11 5.36
885 893 4.796495 CGTTGGGTAGGCCTGGGC 62.796 72.222 17.99 13.15 41.06 5.36
886 894 2.536997 CTTCGTTGGGTAGGCCTGGG 62.537 65.000 17.99 0.00 34.45 4.45
887 895 1.078426 CTTCGTTGGGTAGGCCTGG 60.078 63.158 17.99 0.00 34.45 4.45
888 896 0.391263 GACTTCGTTGGGTAGGCCTG 60.391 60.000 17.99 0.00 34.45 4.85
889 897 0.544595 AGACTTCGTTGGGTAGGCCT 60.545 55.000 11.78 11.78 34.45 5.19
890 898 0.391263 CAGACTTCGTTGGGTAGGCC 60.391 60.000 0.00 0.00 0.00 5.19
891 899 1.019805 GCAGACTTCGTTGGGTAGGC 61.020 60.000 0.00 0.00 0.00 3.93
892 900 0.736325 CGCAGACTTCGTTGGGTAGG 60.736 60.000 0.00 0.00 0.00 3.18
893 901 0.242825 TCGCAGACTTCGTTGGGTAG 59.757 55.000 0.00 0.00 0.00 3.18
894 902 0.675083 TTCGCAGACTTCGTTGGGTA 59.325 50.000 0.00 0.00 34.32 3.69
895 903 0.034896 ATTCGCAGACTTCGTTGGGT 59.965 50.000 0.00 0.00 34.32 4.51
896 904 0.721718 GATTCGCAGACTTCGTTGGG 59.278 55.000 0.00 0.00 34.32 4.12
897 905 1.428448 TGATTCGCAGACTTCGTTGG 58.572 50.000 0.00 0.00 34.32 3.77
935 943 1.979693 CCGGCCCCTAGCTAGCTAG 60.980 68.421 35.39 35.39 44.07 3.42
936 944 2.117640 CCGGCCCCTAGCTAGCTA 59.882 66.667 22.85 22.85 43.05 3.32
985 1002 2.350895 CATGTCCCGGCAAGGTCA 59.649 61.111 0.00 0.00 38.74 4.02
1781 5284 0.606604 ACGTACTTGAGGTTCGGCAT 59.393 50.000 0.00 0.00 41.80 4.40
1938 5445 6.095440 ACCAAATTAACTCTTCCATGGAATCG 59.905 38.462 27.20 21.38 33.28 3.34
2013 5800 4.553429 GCGGTAATAATGCGCATGAAATAC 59.447 41.667 26.09 21.57 0.00 1.89
2016 5803 2.287308 GGCGGTAATAATGCGCATGAAA 60.287 45.455 26.09 13.27 0.00 2.69
2052 5839 6.427547 GGCAATGAGATTGTTTCATTTCCAAA 59.572 34.615 10.40 0.00 43.44 3.28
2054 5841 5.481105 GGCAATGAGATTGTTTCATTTCCA 58.519 37.500 10.40 0.00 43.44 3.53
2082 5869 3.497763 CCTTCCCCATAACGGCAATATCA 60.498 47.826 0.00 0.00 0.00 2.15
2132 5983 4.156455 ACAAGTCTTCTTTCCAAGCAGA 57.844 40.909 0.00 0.00 0.00 4.26
2161 6012 5.450826 GGACAACATTTACGGGAAGTGTTTT 60.451 40.000 10.76 5.49 43.33 2.43
2175 6026 2.190170 TGGCGTGCGGACAACATTT 61.190 52.632 8.11 0.00 0.00 2.32
2213 6123 2.172851 AACAAATGCCATGTTGCAGG 57.827 45.000 3.06 0.00 45.93 4.85
2251 6161 2.612972 CCATCTACGCTGTGGTTTCTGT 60.613 50.000 0.00 0.00 0.00 3.41
2252 6162 2.002586 CCATCTACGCTGTGGTTTCTG 58.997 52.381 0.00 0.00 0.00 3.02
2263 6173 6.418226 CAGTTTTCTCTATACACCATCTACGC 59.582 42.308 0.00 0.00 0.00 4.42
2266 6176 9.653287 CAAACAGTTTTCTCTATACACCATCTA 57.347 33.333 0.00 0.00 0.00 1.98
2273 6183 8.429641 AGTTCTCCAAACAGTTTTCTCTATACA 58.570 33.333 0.00 0.00 0.00 2.29
2281 6193 5.576447 TTCCAGTTCTCCAAACAGTTTTC 57.424 39.130 0.00 0.00 0.00 2.29
2290 6202 2.919602 AGCCCTTATTCCAGTTCTCCAA 59.080 45.455 0.00 0.00 0.00 3.53
2293 6205 3.691609 CACAAGCCCTTATTCCAGTTCTC 59.308 47.826 0.00 0.00 0.00 2.87
2298 6210 4.331968 TGTAACACAAGCCCTTATTCCAG 58.668 43.478 0.00 0.00 0.00 3.86
2301 6213 5.161358 GCTTTGTAACACAAGCCCTTATTC 58.839 41.667 4.99 0.00 39.53 1.75
2304 6216 3.316868 GTGCTTTGTAACACAAGCCCTTA 59.683 43.478 13.79 0.00 39.53 2.69
2307 6219 1.681264 AGTGCTTTGTAACACAAGCCC 59.319 47.619 13.79 6.82 39.53 5.19
2318 6230 1.356624 GCTGCGTTCAGTGCTTTGT 59.643 52.632 0.00 0.00 42.29 2.83
2339 6289 1.136695 TGAGCCTTTGCAACAAACCTG 59.863 47.619 0.00 0.00 41.13 4.00
2343 6293 3.719924 CTTGATGAGCCTTTGCAACAAA 58.280 40.909 0.00 0.00 41.13 2.83
2358 6308 3.162202 AGTCGTCTGATCTGCTTGATG 57.838 47.619 0.00 0.00 35.14 3.07
2362 6312 7.043961 TGATATAAAGTCGTCTGATCTGCTT 57.956 36.000 0.00 0.00 0.00 3.91
2407 6455 2.078392 GCCTTGTTGCAATCCCAAATG 58.922 47.619 0.59 0.00 0.00 2.32
2456 6510 3.260632 ACCCAGTCTTTGCAACAAGTTTT 59.739 39.130 0.00 0.00 0.00 2.43
2458 6611 2.166254 CACCCAGTCTTTGCAACAAGTT 59.834 45.455 0.00 0.00 0.00 2.66
2468 6621 2.093447 CCGATTAGCTCACCCAGTCTTT 60.093 50.000 0.00 0.00 0.00 2.52
2475 6628 0.603975 GCCATCCGATTAGCTCACCC 60.604 60.000 0.00 0.00 0.00 4.61
2589 6751 2.177394 TAATTGCTTCACGTGAGCCA 57.823 45.000 26.34 20.76 0.00 4.75
2603 6794 3.372822 AGCCGTGAACAACCGTATAATTG 59.627 43.478 0.00 0.00 0.00 2.32
2604 6795 3.602483 AGCCGTGAACAACCGTATAATT 58.398 40.909 0.00 0.00 0.00 1.40
2605 6796 3.192466 GAGCCGTGAACAACCGTATAAT 58.808 45.455 0.00 0.00 0.00 1.28
2607 6799 1.135024 GGAGCCGTGAACAACCGTATA 60.135 52.381 0.00 0.00 0.00 1.47
2609 6801 1.005867 GGAGCCGTGAACAACCGTA 60.006 57.895 0.00 0.00 0.00 4.02
2618 6810 2.180769 CGTTCGATGGAGCCGTGA 59.819 61.111 0.00 0.00 0.00 4.35
2646 6838 5.131142 ACTGATAATCCCAAAAGATCGACCT 59.869 40.000 0.00 0.00 0.00 3.85
2659 6851 4.202430 ACCGGGTGATAAACTGATAATCCC 60.202 45.833 6.32 0.00 0.00 3.85
2669 6861 1.461897 CACGTTGACCGGGTGATAAAC 59.538 52.381 3.30 3.06 42.24 2.01
2670 6862 1.798283 CACGTTGACCGGGTGATAAA 58.202 50.000 3.30 0.00 42.24 1.40
2671 6863 3.518381 CACGTTGACCGGGTGATAA 57.482 52.632 3.30 0.00 42.24 1.75
2688 6880 6.150474 GCTATAACAACAAGGGCTTTTCTACA 59.850 38.462 0.00 0.00 0.00 2.74
2693 6885 5.337491 CCATGCTATAACAACAAGGGCTTTT 60.337 40.000 0.00 0.00 0.00 2.27
2695 6887 3.701040 CCATGCTATAACAACAAGGGCTT 59.299 43.478 0.00 0.00 0.00 4.35
2696 6888 3.053693 TCCATGCTATAACAACAAGGGCT 60.054 43.478 0.00 0.00 0.00 5.19
2813 7157 1.233019 CTTCCGATGCCTGGCTAATG 58.767 55.000 21.03 7.00 0.00 1.90
2814 7158 0.536006 GCTTCCGATGCCTGGCTAAT 60.536 55.000 21.03 5.63 0.00 1.73
2818 7162 2.517875 ATGCTTCCGATGCCTGGC 60.518 61.111 12.87 12.87 0.00 4.85


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

AutoCloner maintained by Alex Coulton.