Multiple sequence alignment - TraesCS3B01G565400

Loading Multiple Alignment...

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 TraesCS3B01G565400 chr3B 100.000 2639 0 0 1 2639 798202910 798205548 0.000000e+00 4874
1 TraesCS3B01G565400 chr3B 83.268 1028 136 19 718 1717 798112341 798113360 0.000000e+00 913
2 TraesCS3B01G565400 chr3B 81.243 917 137 21 718 1627 798147744 798148632 0.000000e+00 708
3 TraesCS3B01G565400 chr3B 80.064 938 152 25 719 1653 792267196 792268101 0.000000e+00 664
4 TraesCS3B01G565400 chr3B 80.457 875 143 19 716 1588 792356080 792356928 0.000000e+00 643
5 TraesCS3B01G565400 chr3B 80.390 872 143 19 719 1588 793383546 793382701 2.860000e-179 638
6 TraesCS3B01G565400 chr3B 78.778 933 165 20 723 1649 793368974 793368069 1.750000e-166 595
7 TraesCS3B01G565400 chr3B 79.178 730 124 19 716 1443 792442827 792443530 5.110000e-132 481
8 TraesCS3B01G565400 chr3B 85.093 161 24 0 2152 2312 798204465 798204625 5.840000e-37 165
9 TraesCS3B01G565400 chr3B 85.093 161 24 0 1556 1716 798205061 798205221 5.840000e-37 165
10 TraesCS3B01G565400 chr3A 92.167 1698 66 17 56 1716 725422044 725423711 0.000000e+00 2337
11 TraesCS3B01G565400 chr3A 91.996 937 56 12 1716 2637 725423755 725424687 0.000000e+00 1297
12 TraesCS3B01G565400 chr3A 83.253 1033 130 24 718 1717 725090757 725091779 0.000000e+00 909
13 TraesCS3B01G565400 chr3A 82.705 1035 136 21 718 1717 725154446 725155472 0.000000e+00 880
14 TraesCS3B01G565400 chr3A 82.638 1031 138 18 719 1717 725103718 725104739 0.000000e+00 874
15 TraesCS3B01G565400 chr3A 79.211 938 160 23 720 1649 721565883 721566793 1.040000e-173 619
16 TraesCS3B01G565400 chr3A 84.270 267 33 5 2161 2424 725423560 725423820 4.360000e-63 252
17 TraesCS3B01G565400 chr3A 87.037 162 19 2 1556 1716 725424199 725424359 5.800000e-42 182
18 TraesCS3B01G565400 chr3A 77.328 247 19 22 275 514 724796285 724796069 7.720000e-21 111
19 TraesCS3B01G565400 chr3D 88.188 745 76 9 979 1716 594540459 594541198 0.000000e+00 878
20 TraesCS3B01G565400 chr3D 82.267 1032 144 22 725 1717 594693979 594695010 0.000000e+00 856
21 TraesCS3B01G565400 chr3D 80.769 884 122 22 716 1587 591124571 591125418 0.000000e+00 647
22 TraesCS3B01G565400 chr3D 79.302 831 133 24 720 1538 591177329 591178132 1.790000e-151 545
23 TraesCS3B01G565400 chr3D 89.939 328 28 4 2152 2477 594541038 594541362 4.060000e-113 418
24 TraesCS3B01G565400 chr3D 90.871 241 12 4 1899 2136 594541507 594541740 5.480000e-82 315
25 TraesCS3B01G565400 chr3D 91.071 112 7 1 1778 1886 594541342 594541453 5.890000e-32 148
26 TraesCS3B01G565400 chr3D 75.862 261 27 24 273 524 593965548 593965315 1.670000e-17 100
27 TraesCS3B01G565400 chrUn 80.734 872 140 19 719 1588 155024861 155024016 0.000000e+00 654


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 TraesCS3B01G565400 chr3B 798202910 798205548 2638 False 1734.666667 4874 90.06200 1 2639 3 chr3B.!!$F6 2638
1 TraesCS3B01G565400 chr3B 798112341 798113360 1019 False 913.000000 913 83.26800 718 1717 1 chr3B.!!$F4 999
2 TraesCS3B01G565400 chr3B 798147744 798148632 888 False 708.000000 708 81.24300 718 1627 1 chr3B.!!$F5 909
3 TraesCS3B01G565400 chr3B 792267196 792268101 905 False 664.000000 664 80.06400 719 1653 1 chr3B.!!$F1 934
4 TraesCS3B01G565400 chr3B 792356080 792356928 848 False 643.000000 643 80.45700 716 1588 1 chr3B.!!$F2 872
5 TraesCS3B01G565400 chr3B 793382701 793383546 845 True 638.000000 638 80.39000 719 1588 1 chr3B.!!$R2 869
6 TraesCS3B01G565400 chr3B 793368069 793368974 905 True 595.000000 595 78.77800 723 1649 1 chr3B.!!$R1 926
7 TraesCS3B01G565400 chr3B 792442827 792443530 703 False 481.000000 481 79.17800 716 1443 1 chr3B.!!$F3 727
8 TraesCS3B01G565400 chr3A 725422044 725424687 2643 False 1017.000000 2337 88.86750 56 2637 4 chr3A.!!$F5 2581
9 TraesCS3B01G565400 chr3A 725090757 725091779 1022 False 909.000000 909 83.25300 718 1717 1 chr3A.!!$F2 999
10 TraesCS3B01G565400 chr3A 725154446 725155472 1026 False 880.000000 880 82.70500 718 1717 1 chr3A.!!$F4 999
11 TraesCS3B01G565400 chr3A 725103718 725104739 1021 False 874.000000 874 82.63800 719 1717 1 chr3A.!!$F3 998
12 TraesCS3B01G565400 chr3A 721565883 721566793 910 False 619.000000 619 79.21100 720 1649 1 chr3A.!!$F1 929
13 TraesCS3B01G565400 chr3D 594693979 594695010 1031 False 856.000000 856 82.26700 725 1717 1 chr3D.!!$F3 992
14 TraesCS3B01G565400 chr3D 591124571 591125418 847 False 647.000000 647 80.76900 716 1587 1 chr3D.!!$F1 871
15 TraesCS3B01G565400 chr3D 591177329 591178132 803 False 545.000000 545 79.30200 720 1538 1 chr3D.!!$F2 818
16 TraesCS3B01G565400 chr3D 594540459 594541740 1281 False 439.750000 878 90.01725 979 2477 4 chr3D.!!$F4 1498
17 TraesCS3B01G565400 chrUn 155024016 155024861 845 True 654.000000 654 80.73400 719 1588 1 chrUn.!!$R1 869

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
200 201 0.035820 ATTGTTTTAGCCGGCGAGGA 60.036 50.0 23.2 5.62 45.00 3.71 F
201 202 0.250381 TTGTTTTAGCCGGCGAGGAA 60.250 50.0 23.2 11.95 45.00 3.36 F
1351 1453 0.103208 GTACTGCCATCCAGACCTCG 59.897 60.0 0.0 0.00 44.64 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1030 1066 0.246635 CTTCCGTCTCCGTCCAATGT 59.753 55.0 0.00 0.0 0.00 2.71 R
1354 1456 0.462759 GTGAGCCATGTAGGTCCTGC 60.463 60.0 0.00 0.0 40.61 4.85 R
2399 2587 0.035881 CCAAGCTGAGCAACCAGAGA 59.964 55.0 7.39 0.0 36.29 3.10 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
31 32 3.599584 GGCCTAGCCCGTTTTTCC 58.400 61.111 0.00 0.00 44.06 3.13
32 33 2.404186 GGCCTAGCCCGTTTTTCCG 61.404 63.158 0.00 0.00 44.06 4.30
34 35 2.404186 CCTAGCCCGTTTTTCCGGC 61.404 63.158 0.00 0.00 46.71 6.13
35 36 2.743149 TAGCCCGTTTTTCCGGCG 60.743 61.111 0.00 0.00 46.71 6.46
41 42 3.723348 GTTTTTCCGGCGCGCTCT 61.723 61.111 32.29 0.00 0.00 4.09
42 43 3.419759 TTTTTCCGGCGCGCTCTC 61.420 61.111 32.29 13.86 0.00 3.20
43 44 3.876589 TTTTTCCGGCGCGCTCTCT 62.877 57.895 32.29 0.00 0.00 3.10
54 55 3.476740 CGCTCTCTGGGCCATTTAA 57.523 52.632 6.72 0.00 0.00 1.52
69 70 4.153475 GCCATTTAACGAACACTCTTAGCA 59.847 41.667 0.00 0.00 0.00 3.49
103 104 1.719780 CGTTCTGCACGTAGTTTCCTC 59.280 52.381 0.00 0.00 41.61 3.71
109 110 6.519679 TCTGCACGTAGTTTCCTCTATTTA 57.480 37.500 0.00 0.00 41.61 1.40
112 113 8.133627 TCTGCACGTAGTTTCCTCTATTTATAC 58.866 37.037 0.00 0.00 41.61 1.47
144 145 6.904011 TGGTACGTAAATTGTTTTAACACGTG 59.096 34.615 15.48 15.48 37.80 4.49
148 149 6.683708 ACGTAAATTGTTTTAACACGTGACAG 59.316 34.615 25.01 5.13 36.62 3.51
158 159 4.012554 CGTGACAGACGTGCAAGT 57.987 55.556 4.50 4.50 43.50 3.16
200 201 0.035820 ATTGTTTTAGCCGGCGAGGA 60.036 50.000 23.20 5.62 45.00 3.71
201 202 0.250381 TTGTTTTAGCCGGCGAGGAA 60.250 50.000 23.20 11.95 45.00 3.36
202 203 0.250381 TGTTTTAGCCGGCGAGGAAA 60.250 50.000 23.20 16.87 45.00 3.13
222 251 1.890041 CCAGGAAAACGACGGCACA 60.890 57.895 0.00 0.00 0.00 4.57
237 266 1.086634 GCACAGCCGGACTCTTGATC 61.087 60.000 5.05 0.00 0.00 2.92
245 274 3.664107 CCGGACTCTTGATCAAACTTGA 58.336 45.455 9.88 2.37 42.14 3.02
283 312 1.005037 TACTCACCACGCAAGCCAG 60.005 57.895 0.00 0.00 45.62 4.85
309 338 8.299262 ACACGCTTGCAAACTCTATTATATAG 57.701 34.615 0.00 0.00 0.00 1.31
310 339 7.926555 ACACGCTTGCAAACTCTATTATATAGT 59.073 33.333 0.00 0.00 0.00 2.12
311 340 9.406828 CACGCTTGCAAACTCTATTATATAGTA 57.593 33.333 0.00 0.00 0.00 1.82
312 341 9.976511 ACGCTTGCAAACTCTATTATATAGTAA 57.023 29.630 0.00 0.00 0.00 2.24
337 366 1.675720 AAGGCTGCACACCAACCAAC 61.676 55.000 0.50 0.00 31.85 3.77
338 367 2.127232 GGCTGCACACCAACCAACT 61.127 57.895 0.50 0.00 29.78 3.16
346 375 3.687698 GCACACCAACCAACTAATACGAT 59.312 43.478 0.00 0.00 0.00 3.73
347 376 4.871557 GCACACCAACCAACTAATACGATA 59.128 41.667 0.00 0.00 0.00 2.92
348 377 5.220529 GCACACCAACCAACTAATACGATAC 60.221 44.000 0.00 0.00 0.00 2.24
349 378 5.005012 CACACCAACCAACTAATACGATACG 59.995 44.000 0.00 0.00 0.00 3.06
350 379 5.105797 ACACCAACCAACTAATACGATACGA 60.106 40.000 0.00 0.00 0.00 3.43
351 380 5.230726 CACCAACCAACTAATACGATACGAC 59.769 44.000 0.00 0.00 0.00 4.34
352 381 4.438797 CCAACCAACTAATACGATACGACG 59.561 45.833 0.00 0.00 39.31 5.12
353 382 5.265477 CAACCAACTAATACGATACGACGA 58.735 41.667 0.00 0.00 37.03 4.20
376 405 7.798982 ACGATCGAATCAAAAAGAGAAGAAAAC 59.201 33.333 24.34 0.00 0.00 2.43
394 423 2.456073 ACCAATAGTACGCTCCTCCT 57.544 50.000 0.00 0.00 0.00 3.69
395 424 3.589951 ACCAATAGTACGCTCCTCCTA 57.410 47.619 0.00 0.00 0.00 2.94
396 425 3.220940 ACCAATAGTACGCTCCTCCTAC 58.779 50.000 0.00 0.00 0.00 3.18
397 426 3.220110 CCAATAGTACGCTCCTCCTACA 58.780 50.000 0.00 0.00 0.00 2.74
398 427 3.827302 CCAATAGTACGCTCCTCCTACAT 59.173 47.826 0.00 0.00 0.00 2.29
399 428 4.082679 CCAATAGTACGCTCCTCCTACATC 60.083 50.000 0.00 0.00 0.00 3.06
400 429 4.644163 ATAGTACGCTCCTCCTACATCT 57.356 45.455 0.00 0.00 0.00 2.90
409 438 2.090775 TCCTCCTACATCTACATGGGCA 60.091 50.000 0.00 0.00 33.82 5.36
424 453 3.849953 GCATGGCGTCGTCGGTTC 61.850 66.667 3.90 0.00 37.56 3.62
651 680 1.674057 CAACGACTGGCTCTCCCTT 59.326 57.895 0.00 0.00 0.00 3.95
687 716 2.071778 ACTGCACCACCAACAAAGAT 57.928 45.000 0.00 0.00 0.00 2.40
690 719 0.319813 GCACCACCAACAAAGATGGC 60.320 55.000 0.00 0.00 41.89 4.40
726 755 2.644418 CGGTCGGAACACCACGTA 59.356 61.111 0.00 0.00 36.01 3.57
1030 1066 0.621571 CCTCATCCCCCTTGACCTCA 60.622 60.000 0.00 0.00 0.00 3.86
1093 1129 0.443478 TGTCATCAAGCAATCGCACG 59.557 50.000 0.00 0.00 42.27 5.34
1122 1164 9.888878 CATGATTATGATGATACCACTTTTGAC 57.111 33.333 0.00 0.00 36.36 3.18
1164 1218 4.062293 ACGATGACCAAAATCAAGACGAA 58.938 39.130 0.00 0.00 32.32 3.85
1188 1278 2.022129 CGACAACGGTGCAGAGGAC 61.022 63.158 0.00 0.00 35.72 3.85
1315 1414 0.108756 GTCACGTGGGAAGCTACTCC 60.109 60.000 17.00 0.00 34.41 3.85
1337 1436 4.499865 CCTGGTAAGACATCATCGGTACTG 60.500 50.000 0.00 0.00 0.00 2.74
1351 1453 0.103208 GTACTGCCATCCAGACCTCG 59.897 60.000 0.00 0.00 44.64 4.63
1354 1456 0.249784 CTGCCATCCAGACCTCGATG 60.250 60.000 0.00 0.00 44.64 3.84
1358 1460 0.249784 CATCCAGACCTCGATGCAGG 60.250 60.000 0.00 0.00 39.80 4.85
1369 1498 0.882042 CGATGCAGGACCTACATGGC 60.882 60.000 12.20 2.76 40.22 4.40
1578 1707 2.915657 AGTCCGGTACTTCTAACCCT 57.084 50.000 0.00 0.00 33.35 4.34
1663 1792 8.761575 ATATGCAAAAAGGTTATGACACAAAG 57.238 30.769 0.00 0.00 0.00 2.77
1668 1797 5.529581 AAAGGTTATGACACAAAGTTGGG 57.470 39.130 0.00 0.00 37.67 4.12
1683 1812 8.265055 CACAAAGTTGGGACCTAAGATTAGATA 58.735 37.037 1.08 0.00 31.80 1.98
1685 1814 9.853177 CAAAGTTGGGACCTAAGATTAGATATT 57.147 33.333 1.08 0.00 32.47 1.28
1693 1822 9.847224 GGACCTAAGATTAGATATTGGAAACAA 57.153 33.333 1.08 0.00 43.22 2.83
1716 1845 9.417561 ACAATATGTCATCATGAATTTCCTCTT 57.582 29.630 0.00 0.00 35.70 2.85
1875 2052 6.036408 GGAATTGTTGGTGGTACGTAGATTAC 59.964 42.308 0.00 0.00 0.00 1.89
1889 2066 5.175859 CGTAGATTACTTTTGCCTTGAGGA 58.824 41.667 0.06 0.00 37.39 3.71
1891 2068 6.984474 CGTAGATTACTTTTGCCTTGAGGATA 59.016 38.462 0.06 0.00 37.39 2.59
1893 2070 6.360618 AGATTACTTTTGCCTTGAGGATAGG 58.639 40.000 0.06 0.00 37.39 2.57
1904 2086 2.111384 TGAGGATAGGCCACTGACTTC 58.889 52.381 5.01 0.00 40.02 3.01
1926 2108 2.548904 CGACGGTGGTTTAATTGGTTGA 59.451 45.455 0.00 0.00 0.00 3.18
2004 2186 2.203139 CAGTTGGCGTCACACCCA 60.203 61.111 0.00 0.00 0.00 4.51
2009 2191 0.604243 TTGGCGTCACACCCATACAC 60.604 55.000 0.00 0.00 0.00 2.90
2042 2224 1.856802 TTGATCGACAGATGATGCCG 58.143 50.000 0.00 0.00 37.19 5.69
2062 2244 3.980775 CCGGTTTGTCATCATTGAAACAC 59.019 43.478 0.00 0.00 32.48 3.32
2068 2250 5.565592 TGTCATCATTGAAACACTATGCC 57.434 39.130 0.00 0.00 32.48 4.40
2141 2323 1.442769 ACATCATATTCATCGCGCCC 58.557 50.000 0.00 0.00 0.00 6.13
2179 2361 4.157246 TCTGGTACTTCTAGCCTGTCAAA 58.843 43.478 0.00 0.00 0.00 2.69
2194 2376 6.096846 AGCCTGTCAAAGTTTTGTGAGTATTT 59.903 34.615 4.67 0.00 39.18 1.40
2283 2465 4.287552 TGGAACCTAAGACTAGATGTCCC 58.712 47.826 0.00 0.00 46.46 4.46
2416 2604 3.517100 TCTTATCTCTGGTTGCTCAGCTT 59.483 43.478 0.00 0.00 34.91 3.74
2490 2678 7.652727 TGCATATGTAAGAGTAACTCTAGCAG 58.347 38.462 4.29 0.00 40.28 4.24
2506 2694 0.874390 GCAGATGCCACGAAAACTCA 59.126 50.000 0.00 0.00 34.31 3.41
2517 2705 4.023878 CCACGAAAACTCATCCCGTAAAAA 60.024 41.667 0.00 0.00 31.83 1.94
2542 2731 0.474273 ACAGTCCCCCTAAACCGGAA 60.474 55.000 9.46 0.00 0.00 4.30
2566 2755 2.435234 TACCGTGGCGCATTGGAC 60.435 61.111 10.83 0.00 0.00 4.02
2577 2766 2.208431 CGCATTGGACAGAAGAGATCC 58.792 52.381 0.00 0.00 0.00 3.36
2587 2813 6.180472 GGACAGAAGAGATCCCACAAAAATA 58.820 40.000 0.00 0.00 0.00 1.40
2588 2814 6.317391 GGACAGAAGAGATCCCACAAAAATAG 59.683 42.308 0.00 0.00 0.00 1.73
2592 2818 7.065563 CAGAAGAGATCCCACAAAAATAGTCAG 59.934 40.741 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 3.184206 CGGAAAAACGGGCTAGGC 58.816 61.111 8.00 8.00 0.00 3.93
24 25 3.646735 GAGAGCGCGCCGGAAAAAC 62.647 63.158 30.33 9.09 0.00 2.43
25 26 3.419759 GAGAGCGCGCCGGAAAAA 61.420 61.111 30.33 0.00 0.00 1.94
26 27 4.373116 AGAGAGCGCGCCGGAAAA 62.373 61.111 30.33 0.00 0.00 2.29
34 35 2.923426 TAAATGGCCCAGAGAGCGCG 62.923 60.000 0.00 0.00 0.00 6.86
35 36 0.748005 TTAAATGGCCCAGAGAGCGC 60.748 55.000 0.00 0.00 0.00 5.92
36 37 1.017387 GTTAAATGGCCCAGAGAGCG 58.983 55.000 0.00 0.00 0.00 5.03
37 38 1.017387 CGTTAAATGGCCCAGAGAGC 58.983 55.000 0.00 0.00 0.00 4.09
38 39 2.678336 GTTCGTTAAATGGCCCAGAGAG 59.322 50.000 0.00 0.00 0.00 3.20
39 40 2.039216 TGTTCGTTAAATGGCCCAGAGA 59.961 45.455 0.00 0.00 0.00 3.10
40 41 2.161609 GTGTTCGTTAAATGGCCCAGAG 59.838 50.000 0.00 0.00 0.00 3.35
41 42 2.156098 GTGTTCGTTAAATGGCCCAGA 58.844 47.619 0.00 0.00 0.00 3.86
42 43 2.159382 AGTGTTCGTTAAATGGCCCAG 58.841 47.619 0.00 0.00 0.00 4.45
43 44 2.156098 GAGTGTTCGTTAAATGGCCCA 58.844 47.619 0.00 0.00 0.00 5.36
44 45 2.433436 AGAGTGTTCGTTAAATGGCCC 58.567 47.619 0.00 0.00 0.00 5.80
45 46 4.436986 GCTAAGAGTGTTCGTTAAATGGCC 60.437 45.833 0.00 0.00 0.00 5.36
46 47 4.153475 TGCTAAGAGTGTTCGTTAAATGGC 59.847 41.667 0.00 0.00 0.00 4.40
47 48 5.856126 TGCTAAGAGTGTTCGTTAAATGG 57.144 39.130 0.00 0.00 0.00 3.16
48 49 7.149128 GCTTTTGCTAAGAGTGTTCGTTAAATG 60.149 37.037 3.72 0.00 43.35 2.32
49 50 6.856426 GCTTTTGCTAAGAGTGTTCGTTAAAT 59.144 34.615 3.72 0.00 43.35 1.40
50 51 6.196571 GCTTTTGCTAAGAGTGTTCGTTAAA 58.803 36.000 3.72 0.00 43.35 1.52
51 52 5.744490 GCTTTTGCTAAGAGTGTTCGTTAA 58.256 37.500 3.72 0.00 43.35 2.01
52 53 5.338614 GCTTTTGCTAAGAGTGTTCGTTA 57.661 39.130 3.72 0.00 43.35 3.18
53 54 4.210832 GCTTTTGCTAAGAGTGTTCGTT 57.789 40.909 3.72 0.00 43.35 3.85
54 55 3.879932 GCTTTTGCTAAGAGTGTTCGT 57.120 42.857 3.72 0.00 43.35 3.85
69 70 2.032808 GCAGAACGAAGACGAAGCTTTT 60.033 45.455 0.00 0.00 42.66 2.27
103 104 6.645790 ACGTACCACCCTCAGTATAAATAG 57.354 41.667 0.00 0.00 0.00 1.73
109 110 5.188359 ACAATTTACGTACCACCCTCAGTAT 59.812 40.000 0.00 0.00 0.00 2.12
112 113 3.934068 ACAATTTACGTACCACCCTCAG 58.066 45.455 0.00 0.00 0.00 3.35
144 145 5.233689 AGTTTAAGTAACTTGCACGTCTGTC 59.766 40.000 0.00 0.00 44.73 3.51
200 201 0.879090 GCCGTCGTTTTCCTGGATTT 59.121 50.000 0.00 0.00 0.00 2.17
201 202 0.250553 TGCCGTCGTTTTCCTGGATT 60.251 50.000 0.00 0.00 0.00 3.01
202 203 0.953960 GTGCCGTCGTTTTCCTGGAT 60.954 55.000 0.00 0.00 0.00 3.41
222 251 1.625818 AGTTTGATCAAGAGTCCGGCT 59.374 47.619 8.41 0.00 0.00 5.52
251 280 9.623000 TGCGTGGTGAGTAGTACATATATATAT 57.377 33.333 2.52 0.00 0.00 0.86
252 281 9.452287 TTGCGTGGTGAGTAGTACATATATATA 57.548 33.333 2.52 0.00 0.00 0.86
253 282 7.933215 TGCGTGGTGAGTAGTACATATATAT 57.067 36.000 2.52 0.00 0.00 0.86
254 283 7.574404 GCTTGCGTGGTGAGTAGTACATATATA 60.574 40.741 2.52 0.00 0.00 0.86
257 286 4.736759 GCTTGCGTGGTGAGTAGTACATAT 60.737 45.833 2.52 0.00 0.00 1.78
279 308 1.658409 GTTTGCAAGCGTGTCTGGC 60.658 57.895 0.00 0.00 42.29 4.85
283 312 3.813529 AATAGAGTTTGCAAGCGTGTC 57.186 42.857 7.70 0.40 0.00 3.67
309 338 2.098117 GGTGTGCAGCCTTGATGATTAC 59.902 50.000 0.00 0.00 0.00 1.89
310 339 2.290832 TGGTGTGCAGCCTTGATGATTA 60.291 45.455 8.50 0.00 0.00 1.75
311 340 1.180029 GGTGTGCAGCCTTGATGATT 58.820 50.000 0.00 0.00 0.00 2.57
312 341 0.038599 TGGTGTGCAGCCTTGATGAT 59.961 50.000 8.50 0.00 0.00 2.45
313 342 0.178995 TTGGTGTGCAGCCTTGATGA 60.179 50.000 8.50 0.00 0.00 2.92
314 343 0.038892 GTTGGTGTGCAGCCTTGATG 60.039 55.000 8.50 0.00 0.00 3.07
337 366 6.464311 TGATTCGATCGTCGTATCGTATTAG 58.536 40.000 15.94 0.66 45.55 1.73
338 367 6.393720 TGATTCGATCGTCGTATCGTATTA 57.606 37.500 15.94 12.96 45.55 0.98
346 375 5.633927 TCTCTTTTTGATTCGATCGTCGTA 58.366 37.500 15.94 0.00 41.35 3.43
347 376 4.482386 TCTCTTTTTGATTCGATCGTCGT 58.518 39.130 15.94 2.03 41.35 4.34
348 377 5.286320 TCTTCTCTTTTTGATTCGATCGTCG 59.714 40.000 15.94 0.00 42.10 5.12
349 378 6.633668 TCTTCTCTTTTTGATTCGATCGTC 57.366 37.500 15.94 6.90 0.00 4.20
350 379 7.421530 TTTCTTCTCTTTTTGATTCGATCGT 57.578 32.000 15.94 0.00 0.00 3.73
351 380 7.269297 GGTTTTCTTCTCTTTTTGATTCGATCG 59.731 37.037 9.36 9.36 0.00 3.69
352 381 8.076178 TGGTTTTCTTCTCTTTTTGATTCGATC 58.924 33.333 0.00 0.00 0.00 3.69
353 382 7.940850 TGGTTTTCTTCTCTTTTTGATTCGAT 58.059 30.769 0.00 0.00 0.00 3.59
376 405 3.220110 TGTAGGAGGAGCGTACTATTGG 58.780 50.000 0.00 0.00 38.39 3.16
382 411 3.474600 TGTAGATGTAGGAGGAGCGTAC 58.525 50.000 0.00 0.00 38.13 3.67
394 423 1.270785 CGCCATGCCCATGTAGATGTA 60.271 52.381 7.42 0.00 37.11 2.29
395 424 0.535780 CGCCATGCCCATGTAGATGT 60.536 55.000 7.42 0.00 37.11 3.06
396 425 0.535780 ACGCCATGCCCATGTAGATG 60.536 55.000 7.42 0.00 37.11 2.90
397 426 0.250467 GACGCCATGCCCATGTAGAT 60.250 55.000 7.42 0.00 37.11 1.98
398 427 1.146041 GACGCCATGCCCATGTAGA 59.854 57.895 7.42 0.00 37.11 2.59
399 428 2.246739 CGACGCCATGCCCATGTAG 61.247 63.158 7.42 3.74 37.11 2.74
400 429 2.203001 CGACGCCATGCCCATGTA 60.203 61.111 7.42 0.00 37.11 2.29
409 438 2.126071 CAGAACCGACGACGCCAT 60.126 61.111 0.64 0.00 38.29 4.40
424 453 3.123620 GAGGCCGAAGCACTGCAG 61.124 66.667 13.48 13.48 42.56 4.41
557 586 3.257561 CGATGACGAAGCAGCCCG 61.258 66.667 3.50 3.50 42.66 6.13
599 628 1.152204 TTGGAGTTGTCGGGGAGGA 60.152 57.895 0.00 0.00 0.00 3.71
687 716 2.525629 TCCTCCTGGTTGTCGCCA 60.526 61.111 0.00 0.00 36.97 5.69
690 719 2.660064 CCCCTCCTCCTGGTTGTCG 61.660 68.421 0.00 0.00 34.23 4.35
726 755 2.549754 GTGCAAGACATAGTTGTGCACT 59.450 45.455 19.41 0.00 44.08 4.40
1030 1066 0.246635 CTTCCGTCTCCGTCCAATGT 59.753 55.000 0.00 0.00 0.00 2.71
1058 1094 2.761559 TGACACGTGTTCCCATTGTAG 58.238 47.619 24.26 0.00 0.00 2.74
1093 1129 5.503927 AGTGGTATCATCATAATCATGGCC 58.496 41.667 0.00 0.00 32.61 5.36
1122 1164 0.877649 CATCATCGTCGCCCTCCTTG 60.878 60.000 0.00 0.00 0.00 3.61
1164 1218 0.597637 CTGCACCGTTGTCGTCTTCT 60.598 55.000 0.00 0.00 35.01 2.85
1188 1278 6.534436 AGTCATTGTCTTCTTCTTCATCATCG 59.466 38.462 0.00 0.00 0.00 3.84
1315 1414 4.611943 CAGTACCGATGATGTCTTACCAG 58.388 47.826 0.00 0.00 0.00 4.00
1337 1436 1.596477 GCATCGAGGTCTGGATGGC 60.596 63.158 19.49 11.15 43.27 4.40
1351 1453 0.471617 AGCCATGTAGGTCCTGCATC 59.528 55.000 18.73 9.60 34.76 3.91
1354 1456 0.462759 GTGAGCCATGTAGGTCCTGC 60.463 60.000 0.00 0.00 40.61 4.85
1358 1460 1.134670 GGACAGTGAGCCATGTAGGTC 60.135 57.143 0.00 0.00 40.61 3.85
1663 1792 7.974504 TCCAATATCTAATCTTAGGTCCCAAC 58.025 38.462 0.00 0.00 0.00 3.77
1685 1814 9.806203 GAAATTCATGATGACATATTGTTTCCA 57.194 29.630 0.00 0.00 35.09 3.53
1760 1934 3.874873 TTGCCGAGATGAGCAACG 58.125 55.556 0.00 0.00 43.74 4.10
1794 1968 4.080919 TGCTGCTCCACACATCTATACTTT 60.081 41.667 0.00 0.00 0.00 2.66
1808 1982 3.286751 GGTTTGCGTGCTGCTCCA 61.287 61.111 0.00 0.00 46.63 3.86
1889 2066 0.824759 GTCGGAAGTCAGTGGCCTAT 59.175 55.000 3.32 0.00 0.00 2.57
1891 2068 2.932234 CGTCGGAAGTCAGTGGCCT 61.932 63.158 3.32 0.00 0.00 5.19
1893 2070 2.432628 CCGTCGGAAGTCAGTGGC 60.433 66.667 4.91 0.00 0.00 5.01
1904 2086 1.525941 ACCAATTAAACCACCGTCGG 58.474 50.000 10.48 10.48 0.00 4.79
1926 2108 1.623311 TCCGATCAGGTGTGACATTGT 59.377 47.619 0.00 0.00 41.99 2.71
2004 2186 6.238731 CGATCAAATGGCCTATTGTTGTGTAT 60.239 38.462 17.12 5.93 0.00 2.29
2009 2191 4.096231 TGTCGATCAAATGGCCTATTGTTG 59.904 41.667 17.12 8.82 0.00 3.33
2042 2224 6.308766 GCATAGTGTTTCAATGATGACAAACC 59.691 38.462 2.27 0.00 34.61 3.27
2062 2244 7.772166 TCTCATCTGGTAATATAACGGCATAG 58.228 38.462 0.00 0.00 0.00 2.23
2068 2250 7.600375 ACAAGCATCTCATCTGGTAATATAACG 59.400 37.037 0.00 0.00 0.00 3.18
2173 2355 7.831753 TCCAAAATACTCACAAAACTTTGACA 58.168 30.769 9.12 0.00 40.55 3.58
2179 2361 6.750039 CGTTGTTCCAAAATACTCACAAAACT 59.250 34.615 0.00 0.00 0.00 2.66
2194 2376 3.135167 AGGGAAGAGTAACGTTGTTCCAA 59.865 43.478 23.58 0.08 38.79 3.53
2399 2587 0.035881 CCAAGCTGAGCAACCAGAGA 59.964 55.000 7.39 0.00 36.29 3.10
2400 2588 1.584380 GCCAAGCTGAGCAACCAGAG 61.584 60.000 7.39 0.00 36.29 3.35
2416 2604 7.953005 TCACTGATAAGGATTTTTATTGCCA 57.047 32.000 0.00 0.00 0.00 4.92
2490 2678 1.401905 GGGATGAGTTTTCGTGGCATC 59.598 52.381 0.00 0.00 35.74 3.91
2517 2705 3.307904 CGGTTTAGGGGGACTGTAATGTT 60.308 47.826 0.00 0.00 0.00 2.71
2519 2707 2.420967 CCGGTTTAGGGGGACTGTAATG 60.421 54.545 0.00 0.00 0.00 1.90
2520 2708 1.841919 CCGGTTTAGGGGGACTGTAAT 59.158 52.381 0.00 0.00 0.00 1.89
2521 2709 1.203288 TCCGGTTTAGGGGGACTGTAA 60.203 52.381 0.00 0.00 0.00 2.41
2524 2712 0.916809 ATTCCGGTTTAGGGGGACTG 59.083 55.000 0.00 0.00 0.00 3.51
2527 2715 2.506644 CTGTAATTCCGGTTTAGGGGGA 59.493 50.000 0.00 0.00 0.00 4.81
2542 2731 0.177141 ATGCGCCACGGTACTGTAAT 59.823 50.000 7.11 0.00 0.00 1.89
2566 2755 6.881065 TGACTATTTTTGTGGGATCTCTTCTG 59.119 38.462 0.00 0.00 0.00 3.02
2577 2766 2.811431 TGACCGCTGACTATTTTTGTGG 59.189 45.455 0.00 0.00 0.00 4.17
2587 2813 0.900182 TCCACATCTGACCGCTGACT 60.900 55.000 0.00 0.00 0.00 3.41
2588 2814 0.459237 CTCCACATCTGACCGCTGAC 60.459 60.000 0.00 0.00 0.00 3.51
2592 2818 2.512515 GGCTCCACATCTGACCGC 60.513 66.667 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.