Multiple sequence alignment - TraesCS5D01G443300

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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 TraesCS5D01G443300 chr5D 100.000 5853 0 0 1 5853 494808504 494802652 0.000000e+00 10809
1 TraesCS5D01G443300 chr5B 91.308 2186 124 27 2290 4459 611377085 611374950 0.000000e+00 2924
2 TraesCS5D01G443300 chr5B 87.603 726 46 20 925 1640 611378484 611377793 0.000000e+00 802
3 TraesCS5D01G443300 chr5B 94.839 465 21 3 474 937 611379023 611378561 0.000000e+00 723
4 TraesCS5D01G443300 chr5B 93.697 476 24 4 1 474 611379606 611379135 0.000000e+00 708
5 TraesCS5D01G443300 chr5B 84.422 597 74 13 1684 2277 611377788 611377208 2.370000e-158 569
6 TraesCS5D01G443300 chr5B 89.647 425 40 3 4520 4943 611374927 611374506 6.670000e-149 538
7 TraesCS5D01G443300 chr5B 84.659 352 37 8 4933 5272 611374573 611374227 9.400000e-88 335
8 TraesCS5D01G443300 chr5B 83.981 206 18 7 5417 5621 611373956 611373765 3.600000e-42 183
9 TraesCS5D01G443300 chr5A 95.089 1466 59 8 2973 4434 618868098 618866642 0.000000e+00 2296
10 TraesCS5D01G443300 chr5A 93.173 1494 71 15 2964 4448 618952158 618950687 0.000000e+00 2165
11 TraesCS5D01G443300 chr5A 93.049 1338 74 7 4520 5853 618950653 618949331 0.000000e+00 1938
12 TraesCS5D01G443300 chr5A 91.447 1099 61 17 1683 2757 618953487 618952398 0.000000e+00 1478
13 TraesCS5D01G443300 chr5A 84.741 734 80 13 925 1640 618954210 618953491 0.000000e+00 706
14 TraesCS5D01G443300 chr5A 91.329 519 25 9 4423 4923 618866615 618866099 0.000000e+00 691
15 TraesCS5D01G443300 chr5A 96.181 419 11 4 2561 2979 618869392 618868979 0.000000e+00 680
16 TraesCS5D01G443300 chr5A 81.425 463 48 22 4933 5384 618866146 618865711 1.560000e-90 344
17 TraesCS5D01G443300 chr5A 88.929 280 25 1 2290 2563 618869993 618869714 2.020000e-89 340
18 TraesCS5D01G443300 chr5A 90.991 222 20 0 2056 2277 618870339 618870118 3.430000e-77 300
19 TraesCS5D01G443300 chr5A 90.769 195 18 0 2742 2936 618952352 618952158 1.620000e-65 261
20 TraesCS5D01G443300 chr5A 82.857 245 34 5 231 469 618959770 618959528 4.590000e-51 213
21 TraesCS5D01G443300 chr2A 80.039 511 91 10 3295 3801 319023911 319023408 9.270000e-98 368
22 TraesCS5D01G443300 chr2A 78.608 388 62 17 4045 4423 319023008 319022633 2.730000e-58 237
23 TraesCS5D01G443300 chr2D 79.843 511 92 10 3295 3801 273010521 273011024 4.310000e-96 363
24 TraesCS5D01G443300 chr2B 79.843 511 92 10 3295 3801 317240720 317241223 4.310000e-96 363


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 TraesCS5D01G443300 chr5D 494802652 494808504 5852 True 10809.000000 10809 100.000000 1 5853 1 chr5D.!!$R1 5852
1 TraesCS5D01G443300 chr5B 611373765 611379606 5841 True 847.750000 2924 88.769500 1 5621 8 chr5B.!!$R1 5620
2 TraesCS5D01G443300 chr5A 618949331 618954210 4879 True 1309.600000 2165 90.635800 925 5853 5 chr5A.!!$R3 4928
3 TraesCS5D01G443300 chr5A 618865711 618870339 4628 True 775.166667 2296 90.657333 2056 5384 6 chr5A.!!$R2 3328
4 TraesCS5D01G443300 chr2A 319022633 319023911 1278 True 302.500000 368 79.323500 3295 4423 2 chr2A.!!$R1 1128
5 TraesCS5D01G443300 chr2D 273010521 273011024 503 False 363.000000 363 79.843000 3295 3801 1 chr2D.!!$F1 506
6 TraesCS5D01G443300 chr2B 317240720 317241223 503 False 363.000000 363 79.843000 3295 3801 1 chr2B.!!$F1 506

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
975 1188 0.324460 GAACGGGAGGAGGGAGAGAA 60.324 60.0 0.0 0.0 0.00 2.87 F
977 1190 0.615261 ACGGGAGGAGGGAGAGAAAC 60.615 60.0 0.0 0.0 0.00 2.78 F
1327 1555 0.647410 CGAGCTTAACTGACGGCATG 59.353 55.0 0.0 0.0 0.00 4.06 F
1709 1940 0.756442 TGTTGCTCTTTGCCTTGCCT 60.756 50.0 0.0 0.0 42.00 4.75 F
3144 4787 0.537188 ACTCAACTCAGTATGGGCCG 59.463 55.0 0.0 0.0 43.96 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2936 3692 0.032615 TGTCCAAACCTTGCCCAGTT 60.033 50.000 0.0 0.0 0.00 3.16 R
3001 4643 6.832384 AGAGCATCATGAATTACACAATCCTT 59.168 34.615 0.0 0.0 37.82 3.36 R
3144 4787 5.640732 TCTTTCTGAACTTTTGACAAGTGC 58.359 37.500 0.0 0.0 0.00 4.40 R
3649 5306 5.047519 AGCTTTCAATCAATCCTGAACTTGG 60.048 40.000 0.0 0.0 34.49 3.61 R
4976 6890 0.033503 TCATCTCGTCTGCCCTGGTA 60.034 55.000 0.0 0.0 0.00 3.25 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
24 25 2.688666 TAGGGGAGTGGCTGGCAG 60.689 66.667 10.94 10.94 0.00 4.85
127 128 4.360951 TTGGTAGGTTTCGATCCTTGTT 57.639 40.909 13.56 0.00 36.60 2.83
329 330 8.755696 TTTTCTCCATTTGTATTCCAAAATCG 57.244 30.769 0.00 0.00 45.72 3.34
349 350 7.410120 AATCGATTTGAAATTTCTAGGGCTT 57.590 32.000 18.64 2.93 0.00 4.35
414 415 7.064609 TGTTCATTTTTCATTTTTGCAACGGTA 59.935 29.630 0.00 0.00 0.00 4.02
458 461 3.433740 CCCCTTGCAAGATAGTAGGAACC 60.434 52.174 28.05 0.00 0.00 3.62
469 472 5.597182 AGATAGTAGGAACCGTTGCTTCATA 59.403 40.000 10.83 2.77 31.99 2.15
470 473 4.755266 AGTAGGAACCGTTGCTTCATAT 57.245 40.909 10.83 0.00 31.99 1.78
471 474 4.442706 AGTAGGAACCGTTGCTTCATATG 58.557 43.478 10.83 0.00 31.99 1.78
503 617 4.637534 GTCAGATGCCTATGTGTTGTCAAT 59.362 41.667 0.00 0.00 0.00 2.57
523 637 7.990314 TGTCAATCGAATTATTTATGACCTCCA 59.010 33.333 0.00 0.00 35.91 3.86
593 707 8.415192 TGTCGTATCATTGTTGATAAGTTACC 57.585 34.615 8.19 0.00 44.42 2.85
606 720 7.230849 TGATAAGTTACCGTAGAAGGACAAA 57.769 36.000 0.00 0.00 34.73 2.83
649 763 8.812329 CAATCAAAACGTTACTCCAAATTTTGA 58.188 29.630 10.72 11.16 42.20 2.69
661 775 3.181470 CCAAATTTTGACCCGTGGTTTCT 60.181 43.478 10.72 0.00 35.25 2.52
668 782 2.032071 CCGTGGTTTCTTCCGCCT 59.968 61.111 0.00 0.00 34.83 5.52
671 785 1.005394 GTGGTTTCTTCCGCCTCGA 60.005 57.895 0.00 0.00 32.43 4.04
682 796 3.322211 TCCGCCTCGAAAAGTCAAATA 57.678 42.857 0.00 0.00 0.00 1.40
753 867 2.275318 GGCTTTCTCCATTCGTCTCTG 58.725 52.381 0.00 0.00 0.00 3.35
758 872 2.185350 CCATTCGTCTCTGCGCCT 59.815 61.111 4.18 0.00 0.00 5.52
788 902 6.318913 TGTGATCTAAATTTCCTTTTCCCCA 58.681 36.000 0.00 0.00 0.00 4.96
791 905 6.784969 TGATCTAAATTTCCTTTTCCCCACAA 59.215 34.615 0.00 0.00 0.00 3.33
888 1003 0.897863 TGGCCCAGTGGAAAATTCGG 60.898 55.000 11.95 0.00 0.00 4.30
975 1188 0.324460 GAACGGGAGGAGGGAGAGAA 60.324 60.000 0.00 0.00 0.00 2.87
977 1190 0.615261 ACGGGAGGAGGGAGAGAAAC 60.615 60.000 0.00 0.00 0.00 2.78
1087 1300 4.787280 CCTCCGCCTCCACCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
1088 1301 3.151022 CTCCGCCTCCACCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
1108 1336 3.000819 CCTCGTACCCAGTGGCCA 61.001 66.667 0.00 0.00 33.59 5.36
1323 1551 1.443872 ACGCGAGCTTAACTGACGG 60.444 57.895 15.93 0.00 0.00 4.79
1326 1554 1.084370 GCGAGCTTAACTGACGGCAT 61.084 55.000 0.00 0.00 0.00 4.40
1327 1555 0.647410 CGAGCTTAACTGACGGCATG 59.353 55.000 0.00 0.00 0.00 4.06
1459 1688 2.423538 GAGTGCCACGGCTATGAATTTT 59.576 45.455 9.92 0.00 42.51 1.82
1485 1715 6.095377 ACTAATTAGCTTGCTGAATGTTTGC 58.905 36.000 12.54 0.00 0.00 3.68
1491 1721 3.422603 GCTTGCTGAATGTTTGCGATTTG 60.423 43.478 0.00 0.00 0.00 2.32
1497 1727 4.802999 TGAATGTTTGCGATTTGTGCATA 58.197 34.783 0.00 0.00 42.84 3.14
1501 1731 4.661125 TGTTTGCGATTTGTGCATAGATC 58.339 39.130 4.13 4.13 42.84 2.75
1502 1732 3.590720 TTGCGATTTGTGCATAGATCG 57.409 42.857 25.54 25.54 42.84 3.69
1637 1868 7.878547 TGAATTGTGTTATATTGAGCCATCA 57.121 32.000 0.00 0.00 0.00 3.07
1651 1882 5.869579 TGAGCCATCAAATAGGAGTAATCC 58.130 41.667 0.00 0.00 30.61 3.01
1652 1883 5.608437 TGAGCCATCAAATAGGAGTAATCCT 59.392 40.000 17.20 17.20 36.86 3.24
1653 1884 6.101734 TGAGCCATCAAATAGGAGTAATCCTT 59.898 38.462 18.34 2.57 35.41 3.36
1654 1885 6.915786 AGCCATCAAATAGGAGTAATCCTTT 58.084 36.000 18.34 6.71 41.12 3.11
1655 1886 7.357471 AGCCATCAAATAGGAGTAATCCTTTT 58.643 34.615 18.34 13.07 41.12 2.27
1656 1887 7.503902 AGCCATCAAATAGGAGTAATCCTTTTC 59.496 37.037 18.34 3.07 41.12 2.29
1657 1888 7.503902 GCCATCAAATAGGAGTAATCCTTTTCT 59.496 37.037 18.34 4.48 41.12 2.52
1709 1940 0.756442 TGTTGCTCTTTGCCTTGCCT 60.756 50.000 0.00 0.00 42.00 4.75
1728 1960 1.133790 CTGCTTAATGGTCCTTGCAGC 59.866 52.381 0.00 3.13 40.75 5.25
1747 1979 6.057533 TGCAGCTGTAGCATAAACTTATCAT 58.942 36.000 16.64 0.00 45.16 2.45
1781 2013 3.552384 TTTCCTCGTGGGTGGCGT 61.552 61.111 3.23 0.00 36.25 5.68
1782 2014 3.818121 TTTCCTCGTGGGTGGCGTG 62.818 63.158 3.23 0.00 36.25 5.34
1804 2038 3.610114 GCCGCCTAGCATAATGTTCATTG 60.610 47.826 8.11 0.00 0.00 2.82
1815 2049 6.019640 GCATAATGTTCATTGTAACATGGTGC 60.020 38.462 20.12 20.12 46.72 5.01
1816 2050 3.932545 TGTTCATTGTAACATGGTGCC 57.067 42.857 0.00 0.00 34.50 5.01
1833 2069 2.023673 TGCCCATGCTCTTAATTTCCG 58.976 47.619 0.00 0.00 38.71 4.30
1838 2074 4.580167 CCCATGCTCTTAATTTCCGAATCA 59.420 41.667 0.00 0.00 0.00 2.57
1848 2084 2.028420 TTCCGAATCATGTCTGCCTG 57.972 50.000 0.00 0.00 0.00 4.85
1861 2097 2.093764 GTCTGCCTGCTGAGTTAGTGAT 60.094 50.000 0.00 0.00 0.00 3.06
1863 2099 3.008375 TCTGCCTGCTGAGTTAGTGATTT 59.992 43.478 0.00 0.00 0.00 2.17
1868 2104 5.237815 CCTGCTGAGTTAGTGATTTGTGTA 58.762 41.667 0.00 0.00 0.00 2.90
1928 2179 7.376615 TGGTACTTCTTAGACAAAGCTACTTC 58.623 38.462 0.00 0.00 34.97 3.01
1954 2206 9.687717 CAATATTTTGTTTTCAACACTGTTGTC 57.312 29.630 19.21 10.43 41.97 3.18
1958 2210 5.295431 TGTTTTCAACACTGTTGTCAGAG 57.705 39.130 19.21 0.00 43.94 3.35
1971 2223 1.911357 TGTCAGAGGCACCATCATTCT 59.089 47.619 0.00 0.00 0.00 2.40
2002 2254 2.175530 CTACTGTAGGAAGTGCGACG 57.824 55.000 6.95 0.00 0.00 5.12
2251 2503 3.992643 AGATGATCTTCAGCTTGATCCG 58.007 45.455 10.90 0.00 40.71 4.18
2279 2531 3.888424 TGGCCATCACCATCTTGAG 57.112 52.632 0.00 0.00 33.75 3.02
2284 2536 2.942752 GCCATCACCATCTTGAGCAGAA 60.943 50.000 0.00 0.00 34.16 3.02
2302 2666 5.938438 CAGAAGCTCTTTTTCTGCTAACT 57.062 39.130 0.00 0.00 43.38 2.24
2307 2671 7.704047 AGAAGCTCTTTTTCTGCTAACTTTTTG 59.296 33.333 0.00 0.00 35.85 2.44
2505 2875 7.793927 TGACACTATGTTGTTGTGATTTACA 57.206 32.000 0.00 0.00 37.08 2.41
2572 3266 5.671463 ACCTCATTCTATCAGGACTCCTA 57.329 43.478 0.00 0.00 29.64 2.94
2862 3617 3.303351 AATGGGATGGTCTGATCCAAC 57.697 47.619 0.00 1.84 43.51 3.77
2936 3692 1.003442 ATCCCCTGGAGCAGCAGTA 59.997 57.895 0.00 0.00 34.05 2.74
2994 4636 1.134310 TGCTATCATGACACAGCCTGG 60.134 52.381 18.25 0.00 32.97 4.45
3001 4643 4.030216 TCATGACACAGCCTGGTAATAGA 58.970 43.478 0.00 0.00 0.00 1.98
3008 4650 4.818546 CACAGCCTGGTAATAGAAGGATTG 59.181 45.833 0.00 0.00 32.43 2.67
3144 4787 0.537188 ACTCAACTCAGTATGGGCCG 59.463 55.000 0.00 0.00 43.96 6.13
3427 5076 1.078709 TTGTGAGCGCATACTTCAGC 58.921 50.000 11.47 0.00 0.00 4.26
3552 5209 6.701400 GGTGTTTCACTAAATGCAGATTTGTT 59.299 34.615 0.00 0.00 33.63 2.83
3900 5587 7.545615 ACACACTTTTGGATTCTGAAGAAAAAC 59.454 33.333 0.00 0.00 37.61 2.43
3965 5760 6.043938 ACAGAAGGGAACAGGACTGTAAATTA 59.956 38.462 5.25 0.00 44.13 1.40
3974 5769 6.171213 ACAGGACTGTAAATTACTACTTGGC 58.829 40.000 2.58 0.00 42.90 4.52
4182 6037 7.069950 AGGCAGTTCCACTAAGAAAAATCTTTT 59.930 33.333 0.00 0.00 37.29 2.27
4207 6062 6.767524 TGTGACAACAATTTTAGGTTCTGT 57.232 33.333 0.00 0.00 31.82 3.41
4434 6290 4.522789 TGACACACTACTGCAATGACTAGA 59.477 41.667 0.00 0.00 0.00 2.43
4449 6344 3.442977 TGACTAGAAACTCGAGGGCTAAC 59.557 47.826 18.41 11.24 0.00 2.34
4499 6394 3.492102 ATATTATGCGCCTGGTCTTGT 57.508 42.857 4.18 0.00 0.00 3.16
4501 6396 2.309528 TTATGCGCCTGGTCTTGTAG 57.690 50.000 4.18 0.00 0.00 2.74
4506 6401 2.391389 GCCTGGTCTTGTAGCGTGC 61.391 63.158 0.00 0.00 0.00 5.34
4513 6408 1.129809 CTTGTAGCGTGCCGTTTCG 59.870 57.895 0.00 0.00 0.00 3.46
4524 6437 2.063266 TGCCGTTTCGCTACTTTACAG 58.937 47.619 0.00 0.00 0.00 2.74
4911 6825 0.036388 GGTCAGATCCTGGCGTGAAA 60.036 55.000 0.00 0.00 36.90 2.69
4916 6830 0.931005 GATCCTGGCGTGAAATCGAC 59.069 55.000 0.00 0.00 39.54 4.20
4917 6831 0.537188 ATCCTGGCGTGAAATCGACT 59.463 50.000 0.00 0.00 39.83 4.18
4925 6839 1.203994 CGTGAAATCGACTACCAGGGT 59.796 52.381 0.00 0.00 0.00 4.34
4932 6846 0.675837 CGACTACCAGGGTGAGACGA 60.676 60.000 0.06 0.00 0.00 4.20
4951 6865 4.203226 ACGAGATGAGAACTGCAGAGATA 58.797 43.478 23.35 2.70 0.00 1.98
4964 6878 3.230134 GCAGAGATAGTCAGATCCTGGT 58.770 50.000 0.00 0.00 30.73 4.00
4972 6886 2.975489 AGTCAGATCCTGGTGTGAACTT 59.025 45.455 0.00 0.00 31.51 2.66
4976 6890 4.042062 TCAGATCCTGGTGTGAACTTGATT 59.958 41.667 0.00 0.00 31.51 2.57
4996 6910 1.326213 ACCAGGGCAGACGAGATGAG 61.326 60.000 0.00 0.00 0.00 2.90
5074 6990 2.846532 CACCCCCAGCAGAAGGTT 59.153 61.111 0.00 0.00 0.00 3.50
5150 7076 1.372582 TCGCAGTCAAGATTCATGGC 58.627 50.000 0.00 0.00 0.00 4.40
5213 7143 2.346766 TGTGTTGTCTTGCATCACCT 57.653 45.000 0.00 0.00 43.56 4.00
5396 7333 3.376234 AGCGAGTTTCGTACTGCTACATA 59.624 43.478 11.95 0.00 42.81 2.29
5398 7335 4.738740 GCGAGTTTCGTACTGCTACATAAT 59.261 41.667 0.17 0.00 42.81 1.28
5400 7337 6.581542 GCGAGTTTCGTACTGCTACATAATAT 59.418 38.462 0.17 0.00 42.81 1.28
5401 7338 7.409449 GCGAGTTTCGTACTGCTACATAATATG 60.409 40.741 0.00 0.00 42.81 1.78
5403 7340 6.645415 AGTTTCGTACTGCTACATAATATGCC 59.355 38.462 0.00 0.00 35.19 4.40
5444 7545 2.159000 CCGACTGTGTAAGGGGTTATCC 60.159 54.545 0.00 0.00 0.00 2.59
5457 7558 1.985895 GGTTATCCCATCCCAGGTAGG 59.014 57.143 0.00 0.00 37.03 3.18
5572 7673 8.627403 TCTGAAGATTGAAATATTGATGAAGGC 58.373 33.333 0.00 0.00 0.00 4.35
5574 7675 8.920174 TGAAGATTGAAATATTGATGAAGGCAT 58.080 29.630 0.00 0.00 37.47 4.40
5630 7731 5.416083 ACAATCTGATCAATGCACAAATGG 58.584 37.500 0.00 0.00 0.00 3.16
5654 7755 5.323371 TGAAATCGTCCAAAATCAATCCC 57.677 39.130 0.00 0.00 0.00 3.85
5696 7797 1.141019 CCCGTGTACGACATGAGGG 59.859 63.158 5.91 0.00 43.02 4.30
5700 7801 1.722011 GTGTACGACATGAGGGTTGG 58.278 55.000 0.00 0.00 0.00 3.77
5719 7820 2.114670 CCTACGGGCATGCACCTTG 61.115 63.158 21.36 5.83 0.00 3.61
5745 7846 9.290988 GACCTTAATTCTTCTTTCTTTCTTCCT 57.709 33.333 0.00 0.00 0.00 3.36
5753 7854 7.164803 TCTTCTTTCTTTCTTCCTTGATCTCC 58.835 38.462 0.00 0.00 0.00 3.71
5791 7892 1.134965 ACGCTTTTATCGCTGCTCTCT 60.135 47.619 0.00 0.00 0.00 3.10
5847 7948 1.099295 CATCAGGATGTGCATGCGGT 61.099 55.000 14.09 0.46 37.40 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.551856 ATCTGCCAGCCACTCCCCTA 62.552 60.000 0.00 0.00 0.00 3.53
24 25 0.179045 CCGTGGATTCACCTCCCATC 60.179 60.000 0.00 0.00 40.65 3.51
54 55 4.564613 GGCAAACTCTTCTCTCTAGGCTTT 60.565 45.833 0.00 0.00 0.00 3.51
100 101 2.793288 TCGAAACCTACCAAATCCCC 57.207 50.000 0.00 0.00 0.00 4.81
127 128 3.838565 TGCTTTCTCAAACCCATTACCA 58.161 40.909 0.00 0.00 0.00 3.25
276 277 9.985730 AACTCATATGTGAATTGTGTCATTTTT 57.014 25.926 11.60 0.00 33.05 1.94
329 330 7.826690 TGTACAAGCCCTAGAAATTTCAAATC 58.173 34.615 19.99 5.38 0.00 2.17
344 345 6.935741 TGTTCACAATATATGTACAAGCCC 57.064 37.500 0.00 0.00 41.46 5.19
389 390 6.254480 ACCGTTGCAAAAATGAAAAATGAAC 58.746 32.000 0.00 0.00 0.00 3.18
390 391 6.428385 ACCGTTGCAAAAATGAAAAATGAA 57.572 29.167 0.00 0.00 0.00 2.57
391 392 6.018669 GGTACCGTTGCAAAAATGAAAAATGA 60.019 34.615 0.00 0.00 0.00 2.57
393 394 6.052360 AGGTACCGTTGCAAAAATGAAAAAT 58.948 32.000 6.18 0.00 0.00 1.82
394 395 5.420409 AGGTACCGTTGCAAAAATGAAAAA 58.580 33.333 6.18 0.00 0.00 1.94
414 415 5.488341 GGTATGATACACACTTGACAAGGT 58.512 41.667 19.16 11.07 0.00 3.50
458 461 3.621794 GCTTTAGGCATATGAAGCAACG 58.378 45.455 17.51 2.06 42.94 4.10
469 472 1.303309 GCATCTGACGCTTTAGGCAT 58.697 50.000 0.00 0.00 41.91 4.40
470 473 0.744414 GGCATCTGACGCTTTAGGCA 60.744 55.000 0.00 0.00 41.91 4.75
471 474 0.462759 AGGCATCTGACGCTTTAGGC 60.463 55.000 0.00 0.00 37.64 3.93
481 595 3.979101 TGACAACACATAGGCATCTGA 57.021 42.857 0.00 0.00 0.00 3.27
503 617 4.748102 GCGTGGAGGTCATAAATAATTCGA 59.252 41.667 0.00 0.00 0.00 3.71
523 637 1.388547 TCAAACCTTTTGCTCAGCGT 58.611 45.000 0.00 0.00 0.00 5.07
633 747 4.542735 CACGGGTCAAAATTTGGAGTAAC 58.457 43.478 5.83 0.00 0.00 2.50
636 750 1.960689 CCACGGGTCAAAATTTGGAGT 59.039 47.619 5.83 0.00 0.00 3.85
649 763 2.281276 GCGGAAGAAACCACGGGT 60.281 61.111 0.00 0.00 37.65 5.28
661 775 1.956297 TTTGACTTTTCGAGGCGGAA 58.044 45.000 0.00 0.00 35.50 4.30
682 796 4.902448 GGTCTCCCTTGTATATGAAGGTCT 59.098 45.833 12.19 0.00 38.73 3.85
753 867 1.806461 TAGATCACATCGGGAGGCGC 61.806 60.000 0.00 0.00 0.00 6.53
758 872 5.630415 AGGAAATTTAGATCACATCGGGA 57.370 39.130 0.00 0.00 0.00 5.14
975 1188 1.004440 GCTTGCGGAGTCCTCTGTT 60.004 57.895 7.77 0.00 38.23 3.16
977 1190 1.088340 CATGCTTGCGGAGTCCTCTG 61.088 60.000 7.77 0.00 38.96 3.35
1081 1294 1.077858 GGTACGAGGACGAGGAGGT 60.078 63.158 0.00 0.00 42.66 3.85
1082 1295 1.823041 GGGTACGAGGACGAGGAGG 60.823 68.421 0.00 0.00 42.66 4.30
1083 1296 1.077930 TGGGTACGAGGACGAGGAG 60.078 63.158 0.00 0.00 42.66 3.69
1084 1297 1.077930 CTGGGTACGAGGACGAGGA 60.078 63.158 0.00 0.00 42.66 3.71
1085 1298 1.378250 ACTGGGTACGAGGACGAGG 60.378 63.158 0.00 0.00 38.96 4.63
1086 1299 1.654954 CCACTGGGTACGAGGACGAG 61.655 65.000 0.00 0.00 38.96 4.18
1087 1300 1.676635 CCACTGGGTACGAGGACGA 60.677 63.158 0.00 0.00 38.96 4.20
1088 1301 2.882876 CCACTGGGTACGAGGACG 59.117 66.667 0.00 0.00 38.96 4.79
1089 1302 2.577593 GCCACTGGGTACGAGGAC 59.422 66.667 0.00 0.00 38.96 3.85
1090 1303 2.682494 GGCCACTGGGTACGAGGA 60.682 66.667 0.00 0.00 38.96 3.71
1165 1393 3.735097 GGTGGTGGCGGGGGTTAT 61.735 66.667 0.00 0.00 0.00 1.89
1210 1438 2.182030 GTCCTCCTCTTCGCACGG 59.818 66.667 0.00 0.00 0.00 4.94
1276 1504 2.355986 TTAGGCTGTCCGCGGATGT 61.356 57.895 33.58 16.24 40.44 3.06
1323 1551 0.305922 GTGCTGGAGATAACGCATGC 59.694 55.000 7.91 7.91 34.60 4.06
1326 1554 2.401583 AATGTGCTGGAGATAACGCA 57.598 45.000 0.00 0.00 0.00 5.24
1327 1555 2.285834 CGAAATGTGCTGGAGATAACGC 60.286 50.000 0.00 0.00 0.00 4.84
1459 1688 7.307694 CAAACATTCAGCAAGCTAATTAGTCA 58.692 34.615 13.91 0.00 0.00 3.41
1485 1715 6.198029 GGATCTATCGATCTATGCACAAATCG 59.802 42.308 16.24 16.24 44.42 3.34
1491 1721 3.957497 AGGGGATCTATCGATCTATGCAC 59.043 47.826 0.00 3.20 44.42 4.57
1497 1727 2.652348 ACCAGAGGGGATCTATCGATCT 59.348 50.000 0.00 0.00 44.42 2.75
1501 1731 3.643792 AGAAAACCAGAGGGGATCTATCG 59.356 47.826 0.00 0.00 41.15 2.92
1502 1732 5.638530 AAGAAAACCAGAGGGGATCTATC 57.361 43.478 0.00 0.00 41.15 2.08
1589 1820 5.357257 AGGCACCTACGTAGATAACAATTG 58.643 41.667 24.15 3.24 0.00 2.32
1603 1834 5.897377 ATAACACAATTCAAGGCACCTAC 57.103 39.130 0.00 0.00 0.00 3.18
1604 1835 7.831690 TCAATATAACACAATTCAAGGCACCTA 59.168 33.333 0.00 0.00 0.00 3.08
1605 1836 6.663093 TCAATATAACACAATTCAAGGCACCT 59.337 34.615 0.00 0.00 0.00 4.00
1606 1837 6.862209 TCAATATAACACAATTCAAGGCACC 58.138 36.000 0.00 0.00 0.00 5.01
1663 1894 8.909423 TCCCCAATTACTCCTATTTGATTTTT 57.091 30.769 0.00 0.00 0.00 1.94
1664 1895 9.506042 AATCCCCAATTACTCCTATTTGATTTT 57.494 29.630 0.00 0.00 0.00 1.82
1665 1896 8.927411 CAATCCCCAATTACTCCTATTTGATTT 58.073 33.333 0.00 0.00 0.00 2.17
1666 1897 8.067488 ACAATCCCCAATTACTCCTATTTGATT 58.933 33.333 0.00 0.00 0.00 2.57
1667 1898 7.595488 ACAATCCCCAATTACTCCTATTTGAT 58.405 34.615 0.00 0.00 0.00 2.57
1668 1899 6.980577 ACAATCCCCAATTACTCCTATTTGA 58.019 36.000 0.00 0.00 0.00 2.69
1669 1900 7.491682 CAACAATCCCCAATTACTCCTATTTG 58.508 38.462 0.00 0.00 0.00 2.32
1670 1901 6.098266 GCAACAATCCCCAATTACTCCTATTT 59.902 38.462 0.00 0.00 0.00 1.40
1671 1902 5.598417 GCAACAATCCCCAATTACTCCTATT 59.402 40.000 0.00 0.00 0.00 1.73
1672 1903 5.103515 AGCAACAATCCCCAATTACTCCTAT 60.104 40.000 0.00 0.00 0.00 2.57
1673 1904 4.229582 AGCAACAATCCCCAATTACTCCTA 59.770 41.667 0.00 0.00 0.00 2.94
1674 1905 3.011708 AGCAACAATCCCCAATTACTCCT 59.988 43.478 0.00 0.00 0.00 3.69
1675 1906 3.365472 AGCAACAATCCCCAATTACTCC 58.635 45.455 0.00 0.00 0.00 3.85
1676 1907 4.273318 AGAGCAACAATCCCCAATTACTC 58.727 43.478 0.00 0.00 0.00 2.59
1677 1908 4.322057 AGAGCAACAATCCCCAATTACT 57.678 40.909 0.00 0.00 0.00 2.24
1678 1909 5.170748 CAAAGAGCAACAATCCCCAATTAC 58.829 41.667 0.00 0.00 0.00 1.89
1679 1910 4.322650 GCAAAGAGCAACAATCCCCAATTA 60.323 41.667 0.00 0.00 44.79 1.40
1680 1911 3.557686 GCAAAGAGCAACAATCCCCAATT 60.558 43.478 0.00 0.00 44.79 2.32
1681 1912 2.027837 GCAAAGAGCAACAATCCCCAAT 60.028 45.455 0.00 0.00 44.79 3.16
1709 1940 1.176527 GCTGCAAGGACCATTAAGCA 58.823 50.000 0.00 0.00 0.00 3.91
1728 1960 9.988815 ACTCCTTATGATAAGTTTATGCTACAG 57.011 33.333 10.98 0.00 0.00 2.74
1747 1979 2.215196 GAAACACGGCAACACTCCTTA 58.785 47.619 0.00 0.00 0.00 2.69
1781 2013 1.134250 TGAACATTATGCTAGGCGGCA 60.134 47.619 13.08 10.22 46.63 5.69
1782 2014 1.593196 TGAACATTATGCTAGGCGGC 58.407 50.000 0.00 0.00 0.00 6.53
1815 2049 4.580167 TGATTCGGAAATTAAGAGCATGGG 59.420 41.667 0.00 0.00 0.00 4.00
1816 2050 5.756195 TGATTCGGAAATTAAGAGCATGG 57.244 39.130 0.00 0.00 0.00 3.66
1833 2069 1.941294 CTCAGCAGGCAGACATGATTC 59.059 52.381 0.00 0.00 0.00 2.52
1838 2074 1.905215 ACTAACTCAGCAGGCAGACAT 59.095 47.619 0.00 0.00 0.00 3.06
1861 2097 7.967854 CCAGCTTCGATGATAAATTTACACAAA 59.032 33.333 0.00 0.00 0.00 2.83
1863 2099 6.597672 ACCAGCTTCGATGATAAATTTACACA 59.402 34.615 0.00 4.88 0.00 3.72
1868 2104 6.515272 AACACCAGCTTCGATGATAAATTT 57.485 33.333 1.89 0.00 0.00 1.82
1881 2117 5.278218 CCAAACAAAACAAAAACACCAGCTT 60.278 36.000 0.00 0.00 0.00 3.74
1942 2194 1.331756 GTGCCTCTGACAACAGTGTTG 59.668 52.381 30.00 30.00 43.81 3.33
1943 2195 1.668419 GTGCCTCTGACAACAGTGTT 58.332 50.000 1.64 1.64 43.81 3.32
1954 2206 9.458727 AATATAATAAGAATGATGGTGCCTCTG 57.541 33.333 0.00 0.00 0.00 3.35
1958 2210 9.686683 AGGTAATATAATAAGAATGATGGTGCC 57.313 33.333 0.00 0.00 0.00 5.01
2002 2254 2.289002 CGAAGTTGCCTGATATCTTGGC 59.711 50.000 24.06 24.06 46.26 4.52
2251 2503 0.536006 GTGATGGCCATACCTCTGCC 60.536 60.000 20.84 3.78 45.56 4.85
2284 2536 7.100458 TCAAAAAGTTAGCAGAAAAAGAGCT 57.900 32.000 0.00 0.00 42.14 4.09
2323 2687 7.581213 ACCAAATTAATCTCTGTGTCAACAA 57.419 32.000 0.00 0.00 35.37 2.83
2329 2693 6.306987 ACAGGAACCAAATTAATCTCTGTGT 58.693 36.000 0.00 0.00 32.59 3.72
2505 2875 0.394352 GGGGACGGAATCACTGCATT 60.394 55.000 0.00 0.00 0.00 3.56
2572 3266 2.758979 CAAGCTCCATGAAATTGCTCCT 59.241 45.455 0.00 0.00 33.10 3.69
2603 3297 4.935205 TGCACTGTACTTATCATCCACAAC 59.065 41.667 0.00 0.00 0.00 3.32
2715 3409 8.991243 TCATTGATGATCAATTCAAAGGAAAC 57.009 30.769 17.45 0.00 44.03 2.78
2770 3525 7.823745 ATGTGAACTTGTCAAGGATTAAACT 57.176 32.000 16.85 0.00 38.23 2.66
2936 3692 0.032615 TGTCCAAACCTTGCCCAGTT 60.033 50.000 0.00 0.00 0.00 3.16
3001 4643 6.832384 AGAGCATCATGAATTACACAATCCTT 59.168 34.615 0.00 0.00 37.82 3.36
3144 4787 5.640732 TCTTTCTGAACTTTTGACAAGTGC 58.359 37.500 0.00 0.00 0.00 4.40
3427 5076 5.535406 ACCATAAGTATCCACTAGAGAACCG 59.465 44.000 0.00 0.00 33.48 4.44
3552 5209 5.048507 GGTAAAAATGCCGTAACACCAAAA 58.951 37.500 0.00 0.00 0.00 2.44
3649 5306 5.047519 AGCTTTCAATCAATCCTGAACTTGG 60.048 40.000 0.00 0.00 34.49 3.61
3900 5587 6.344500 ACACTAGCATCTTAGAAACTCCATG 58.656 40.000 0.00 0.00 0.00 3.66
4182 6037 7.607250 ACAGAACCTAAAATTGTTGTCACAAA 58.393 30.769 0.00 0.00 46.17 2.83
4207 6062 1.351017 GGACCTGTGTCATTCCAAGGA 59.649 52.381 0.00 0.00 43.65 3.36
4264 6119 2.769893 AGCATGATTGGCCAACAAAAC 58.230 42.857 23.27 10.95 43.46 2.43
4414 6270 5.928839 AGTTTCTAGTCATTGCAGTAGTGTG 59.071 40.000 0.00 0.00 0.00 3.82
4434 6290 3.139077 CAAACAGTTAGCCCTCGAGTTT 58.861 45.455 12.31 0.00 0.00 2.66
4449 6344 5.580691 TCAAGTACCGAGATTATGCAAACAG 59.419 40.000 0.00 0.00 0.00 3.16
4488 6383 2.391389 GCACGCTACAAGACCAGGC 61.391 63.158 0.00 0.00 0.00 4.85
4506 6401 3.572584 AGACTGTAAAGTAGCGAAACGG 58.427 45.455 0.00 0.00 0.00 4.44
4513 6408 4.796369 ACGTCAGAAGACTGTAAAGTAGC 58.204 43.478 0.00 0.00 42.73 3.58
4514 6409 7.859377 TGTTTACGTCAGAAGACTGTAAAGTAG 59.141 37.037 17.41 0.00 44.38 2.57
4515 6410 7.645340 GTGTTTACGTCAGAAGACTGTAAAGTA 59.355 37.037 17.41 11.55 44.38 2.24
4516 6411 6.474751 GTGTTTACGTCAGAAGACTGTAAAGT 59.525 38.462 17.41 0.00 44.38 2.66
4524 6437 7.328737 ACATCATAAGTGTTTACGTCAGAAGAC 59.671 37.037 0.00 0.00 41.46 3.01
4560 6473 2.284190 GCATGAAGGAAGCCTACAGAC 58.716 52.381 0.00 0.00 31.13 3.51
4582 6495 3.522731 GCGGCCAACACCAACACA 61.523 61.111 2.24 0.00 0.00 3.72
4642 6555 1.999735 GCGTTCGAAATGGACATCAGA 59.000 47.619 0.00 0.00 0.00 3.27
4911 6825 1.765230 GTCTCACCCTGGTAGTCGAT 58.235 55.000 0.00 0.00 0.00 3.59
4916 6830 1.678627 CATCTCGTCTCACCCTGGTAG 59.321 57.143 0.00 0.00 0.00 3.18
4917 6831 1.283905 TCATCTCGTCTCACCCTGGTA 59.716 52.381 0.00 0.00 0.00 3.25
4925 6839 2.162681 TGCAGTTCTCATCTCGTCTCA 58.837 47.619 0.00 0.00 0.00 3.27
4932 6846 5.199723 TGACTATCTCTGCAGTTCTCATCT 58.800 41.667 14.67 0.00 0.00 2.90
4951 6865 2.614259 AGTTCACACCAGGATCTGACT 58.386 47.619 0.00 0.00 32.44 3.41
4964 6878 2.107378 TGCCCTGGTAATCAAGTTCACA 59.893 45.455 0.00 0.00 0.00 3.58
4972 6886 0.824109 CTCGTCTGCCCTGGTAATCA 59.176 55.000 0.00 0.00 0.00 2.57
4976 6890 0.033503 TCATCTCGTCTGCCCTGGTA 60.034 55.000 0.00 0.00 0.00 3.25
4996 6910 1.068264 GCCCAAAGTTAGCTGCAGTTC 60.068 52.381 16.64 0.00 0.00 3.01
5036 6950 1.789506 GCTCTTCTCAACGCTCAACT 58.210 50.000 0.00 0.00 0.00 3.16
5058 6974 0.698818 CTTAACCTTCTGCTGGGGGT 59.301 55.000 7.98 5.79 0.00 4.95
5059 6975 0.698818 ACTTAACCTTCTGCTGGGGG 59.301 55.000 7.98 5.27 0.00 5.40
5074 6990 1.621317 TGTGCGGTCATCTGGAACTTA 59.379 47.619 0.00 0.00 0.00 2.24
5150 7076 9.394477 CTAACATCATCAAATGCATGTAGATTG 57.606 33.333 0.00 0.11 33.66 2.67
5213 7143 2.376518 AGAAAGAGGTCAGGGCATCAAA 59.623 45.455 0.00 0.00 0.00 2.69
5221 7151 9.734984 TTTAATTTACCTAAGAAAGAGGTCAGG 57.265 33.333 0.00 0.00 44.33 3.86
5444 7545 2.825532 CAACAAAACCTACCTGGGATGG 59.174 50.000 0.00 0.00 41.11 3.51
5445 7546 2.825532 CCAACAAAACCTACCTGGGATG 59.174 50.000 0.00 0.00 41.11 3.51
5446 7547 2.225267 CCCAACAAAACCTACCTGGGAT 60.225 50.000 0.00 0.00 45.43 3.85
5447 7548 1.146152 CCCAACAAAACCTACCTGGGA 59.854 52.381 0.00 0.00 45.43 4.37
5448 7549 1.146152 TCCCAACAAAACCTACCTGGG 59.854 52.381 0.00 0.00 44.19 4.45
5457 7558 1.096967 ACGGTCCGTCCCAACAAAAC 61.097 55.000 12.23 0.00 33.69 2.43
5567 7668 9.213799 CCTATCATTACTAAAAGAGATGCCTTC 57.786 37.037 0.00 0.00 0.00 3.46
5568 7669 8.938883 TCCTATCATTACTAAAAGAGATGCCTT 58.061 33.333 0.00 0.00 0.00 4.35
5601 7702 6.962686 TGTGCATTGATCAGATTGTAATAGC 58.037 36.000 0.00 0.00 0.00 2.97
5630 7731 5.979517 GGGATTGATTTTGGACGATTTCATC 59.020 40.000 0.00 0.00 0.00 2.92
5654 7755 0.030908 GGTAGATTGCCGAGACTCCG 59.969 60.000 0.00 0.00 0.00 4.63
5719 7820 9.290988 AGGAAGAAAGAAAGAAGAATTAAGGTC 57.709 33.333 0.00 0.00 0.00 3.85
5753 7854 2.268298 CGTTACAAAGGTGGAGATCCG 58.732 52.381 0.00 0.00 39.43 4.18


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

AutoCloner maintained by Alex Coulton.