Multiple sequence alignment - TraesCS7B01G096600

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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 TraesCS7B01G096600 chr7B 100.000 2829 0 0 1 2829 111341219 111338391 0.000000e+00 5225
1 TraesCS7B01G096600 chr7B 100.000 336 0 0 3220 3555 111338000 111337665 3.900000e-174 621
2 TraesCS7B01G096600 chr7D 92.908 1269 57 19 1586 2829 148267585 148266325 0.000000e+00 1814
3 TraesCS7B01G096600 chr7D 90.625 1280 55 22 57 1284 148269224 148267958 0.000000e+00 1639
4 TraesCS7B01G096600 chr7D 88.081 344 29 7 3220 3555 148266243 148265904 7.150000e-107 398
5 TraesCS7B01G096600 chr7D 91.985 262 13 1 1335 1588 148267874 148267613 9.380000e-96 361
6 TraesCS7B01G096600 chr7D 89.630 270 27 1 2090 2359 148263834 148263566 3.400000e-90 342
7 TraesCS7B01G096600 chr7D 77.465 568 101 15 2014 2555 148152657 148152091 7.410000e-82 315
8 TraesCS7B01G096600 chr7D 79.447 253 48 3 1449 1700 148153216 148152967 3.650000e-40 176
9 TraesCS7B01G096600 chr7D 79.279 222 28 11 1774 1980 148152874 148152656 4.790000e-29 139
10 TraesCS7B01G096600 chr7A 91.315 1278 63 23 1584 2829 149425795 149424534 0.000000e+00 1701
11 TraesCS7B01G096600 chr7A 88.133 1146 59 27 484 1588 149426930 149425821 0.000000e+00 1291
12 TraesCS7B01G096600 chr7A 80.425 659 110 14 1774 2416 149306948 149306293 5.340000e-133 484
13 TraesCS7B01G096600 chr7A 85.762 302 36 3 21 316 149467236 149466936 2.660000e-81 313
14 TraesCS7B01G096600 chr7A 93.056 144 10 0 1846 1989 149414731 149414588 1.000000e-50 211


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 TraesCS7B01G096600 chr7B 111337665 111341219 3554 True 2923.0 5225 100.000000 1 3555 2 chr7B.!!$R1 3554
1 TraesCS7B01G096600 chr7D 148263566 148269224 5658 True 910.8 1814 90.645800 57 3555 5 chr7D.!!$R2 3498
2 TraesCS7B01G096600 chr7D 148152091 148153216 1125 True 210.0 315 78.730333 1449 2555 3 chr7D.!!$R1 1106
3 TraesCS7B01G096600 chr7A 149424534 149426930 2396 True 1496.0 1701 89.724000 484 2829 2 chr7A.!!$R4 2345
4 TraesCS7B01G096600 chr7A 149306293 149306948 655 True 484.0 484 80.425000 1774 2416 1 chr7A.!!$R1 642

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
816 858 0.104090 ACCAAACCCTACCCCTGAGT 60.104 55.0 0.0 0.0 0.00 3.41 F
1332 1440 0.176449 CGAGCACAGATGATGGTCCA 59.824 55.0 0.0 0.0 40.68 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1902 0.109458 TACACGTAGGCGCTTGACAG 60.109 55.0 7.64 1.42 42.83 3.51 R
3319 3553 0.179094 AACTCCAAACGTGTGCTCGA 60.179 50.0 0.00 0.00 34.70 4.04 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
19 20 1.032014 ATGTGTGGAACTGTTGTGCC 58.968 50.000 0.00 0.00 42.46 5.01
20 21 1.034838 TGTGTGGAACTGTTGTGCCC 61.035 55.000 0.00 0.00 41.39 5.36
21 22 1.454847 TGTGGAACTGTTGTGCCCC 60.455 57.895 0.00 0.00 41.39 5.80
22 23 2.197324 TGGAACTGTTGTGCCCCC 59.803 61.111 0.00 0.00 41.39 5.40
23 24 2.983592 GGAACTGTTGTGCCCCCG 60.984 66.667 0.00 0.00 35.79 5.73
24 25 2.203294 GAACTGTTGTGCCCCCGT 60.203 61.111 0.00 0.00 0.00 5.28
25 26 2.518349 AACTGTTGTGCCCCCGTG 60.518 61.111 0.00 0.00 0.00 4.94
35 36 4.722700 CCCCCGTGCACCTCCTTG 62.723 72.222 12.15 0.00 0.00 3.61
36 37 4.722700 CCCCGTGCACCTCCTTGG 62.723 72.222 12.15 5.17 42.93 3.61
66 67 3.024547 TGGACAAGGACGATCTTCTAGG 58.975 50.000 0.00 0.00 0.00 3.02
69 70 1.069358 CAAGGACGATCTTCTAGGGCC 59.931 57.143 0.00 0.00 0.00 5.80
80 81 0.685131 TCTAGGGCCCGAATTCGACA 60.685 55.000 28.76 6.19 43.02 4.35
82 83 0.834612 TAGGGCCCGAATTCGACAAT 59.165 50.000 28.76 13.87 43.02 2.71
96 97 0.743345 GACAATGGCCGGAGTACACC 60.743 60.000 5.05 0.00 0.00 4.16
122 123 2.221299 CCGGGGTGTTCCTTCTCCA 61.221 63.158 0.00 0.00 35.33 3.86
168 169 8.932945 TGTACACATGCAATTTCAAAGTTTTA 57.067 26.923 0.00 0.00 0.00 1.52
176 177 6.980978 TGCAATTTCAAAGTTTTATCGTCCAA 59.019 30.769 0.00 0.00 0.00 3.53
272 274 6.310224 CGTATTTAGCCCCATTTCAAGTTTTG 59.690 38.462 0.00 0.00 0.00 2.44
305 307 0.823356 GCCCAATGCATACCGACCAT 60.823 55.000 0.00 0.00 40.77 3.55
334 336 0.183014 TACACCCAAACAAAGCCCGA 59.817 50.000 0.00 0.00 0.00 5.14
355 360 4.558697 CGAGAAAAATCCTTTCCGCCTTTT 60.559 41.667 0.00 0.00 0.00 2.27
357 362 4.100963 AGAAAAATCCTTTCCGCCTTTTGT 59.899 37.500 0.00 0.00 0.00 2.83
362 367 1.532078 TTTCCGCCTTTTGTCCCCC 60.532 57.895 0.00 0.00 0.00 5.40
363 368 3.853698 TTCCGCCTTTTGTCCCCCG 62.854 63.158 0.00 0.00 0.00 5.73
364 369 4.338710 CCGCCTTTTGTCCCCCGA 62.339 66.667 0.00 0.00 0.00 5.14
366 371 2.675423 GCCTTTTGTCCCCCGACC 60.675 66.667 0.00 0.00 38.32 4.79
367 372 2.840576 CCTTTTGTCCCCCGACCA 59.159 61.111 0.00 0.00 38.32 4.02
368 373 1.382629 CCTTTTGTCCCCCGACCAT 59.617 57.895 0.00 0.00 38.32 3.55
369 374 0.965363 CCTTTTGTCCCCCGACCATG 60.965 60.000 0.00 0.00 38.32 3.66
370 375 0.251165 CTTTTGTCCCCCGACCATGT 60.251 55.000 0.00 0.00 38.32 3.21
371 376 0.538516 TTTTGTCCCCCGACCATGTG 60.539 55.000 0.00 0.00 38.32 3.21
372 377 1.710996 TTTGTCCCCCGACCATGTGT 61.711 55.000 0.00 0.00 38.32 3.72
373 378 2.119484 TTGTCCCCCGACCATGTGTC 62.119 60.000 4.71 4.71 38.32 3.67
384 404 1.780309 ACCATGTGTCTTCCCCAAGAA 59.220 47.619 0.00 0.00 40.49 2.52
458 478 1.135460 GTAGAGGTCCTTTGTCCGACG 60.135 57.143 0.00 0.00 0.00 5.12
470 490 4.873129 CCGACGTCCCGAGGCATG 62.873 72.222 10.58 0.00 0.00 4.06
471 491 3.822192 CGACGTCCCGAGGCATGA 61.822 66.667 10.58 0.00 0.00 3.07
472 492 2.105128 GACGTCCCGAGGCATGAG 59.895 66.667 3.51 0.00 0.00 2.90
506 526 1.462791 GTGAAGTCAAAACAACCGCG 58.537 50.000 0.00 0.00 0.00 6.46
582 602 3.374220 TTCACTCGTACATCAACCGTT 57.626 42.857 0.00 0.00 0.00 4.44
587 607 1.135603 TCGTACATCAACCGTTCGGAG 60.136 52.381 18.28 9.73 0.00 4.63
588 608 1.135603 CGTACATCAACCGTTCGGAGA 60.136 52.381 18.28 14.38 0.00 3.71
589 609 2.257034 GTACATCAACCGTTCGGAGAC 58.743 52.381 18.28 1.38 34.32 3.36
722 755 3.067106 CACGTAACTGCTCACTCCAAAT 58.933 45.455 0.00 0.00 0.00 2.32
738 771 5.124936 ACTCCAAATTATTAACGGACCAAGC 59.875 40.000 0.00 0.00 0.00 4.01
739 772 5.258051 TCCAAATTATTAACGGACCAAGCT 58.742 37.500 0.00 0.00 0.00 3.74
740 773 6.416415 TCCAAATTATTAACGGACCAAGCTA 58.584 36.000 0.00 0.00 0.00 3.32
741 774 6.540914 TCCAAATTATTAACGGACCAAGCTAG 59.459 38.462 0.00 0.00 0.00 3.42
742 775 6.199393 CAAATTATTAACGGACCAAGCTAGC 58.801 40.000 6.62 6.62 0.00 3.42
744 777 0.738412 TTAACGGACCAAGCTAGCGC 60.738 55.000 9.55 0.00 0.00 5.92
767 800 0.109597 GCAAGCAGTTTGGTGATCCG 60.110 55.000 0.00 0.00 37.26 4.18
816 858 0.104090 ACCAAACCCTACCCCTGAGT 60.104 55.000 0.00 0.00 0.00 3.41
894 936 2.819595 CTGACCAATCACCGGCCG 60.820 66.667 21.04 21.04 0.00 6.13
925 969 1.006102 CAGAAACACTCTCGCGGGT 60.006 57.895 5.57 0.00 29.07 5.28
968 1018 2.082231 GTACTGTGACTAGAGCGTGGA 58.918 52.381 0.00 0.00 0.00 4.02
970 1020 1.271434 ACTGTGACTAGAGCGTGGAGA 60.271 52.381 0.00 0.00 0.00 3.71
971 1021 1.813178 CTGTGACTAGAGCGTGGAGAA 59.187 52.381 0.00 0.00 0.00 2.87
972 1022 2.229062 CTGTGACTAGAGCGTGGAGAAA 59.771 50.000 0.00 0.00 0.00 2.52
974 1024 2.229302 GTGACTAGAGCGTGGAGAAAGT 59.771 50.000 0.00 0.00 0.00 2.66
987 1050 3.439476 TGGAGAAAGTAGTAGTCTGCGAC 59.561 47.826 0.00 1.15 32.84 5.19
988 1051 3.181498 GGAGAAAGTAGTAGTCTGCGACC 60.181 52.174 5.29 0.00 32.18 4.79
991 1054 3.851976 AAGTAGTAGTCTGCGACCAAG 57.148 47.619 5.29 0.00 32.18 3.61
993 1056 2.488545 AGTAGTAGTCTGCGACCAAGTG 59.511 50.000 5.29 0.00 32.18 3.16
1275 1338 1.253034 GATGACGACGATCAAAGCGAC 59.747 52.381 0.00 0.00 30.82 5.19
1296 1404 2.487428 CCTGCAGAGGTCGTCTCG 59.513 66.667 17.39 0.00 46.82 4.04
1300 1408 1.170290 TGCAGAGGTCGTCTCGTTGA 61.170 55.000 0.00 0.00 46.82 3.18
1328 1436 0.935898 GCTTCGAGCACAGATGATGG 59.064 55.000 2.53 0.00 41.89 3.51
1329 1437 1.741732 GCTTCGAGCACAGATGATGGT 60.742 52.381 2.53 0.00 41.89 3.55
1330 1438 2.200067 CTTCGAGCACAGATGATGGTC 58.800 52.381 0.00 0.00 40.43 4.02
1331 1439 0.461548 TCGAGCACAGATGATGGTCC 59.538 55.000 0.00 0.00 40.68 4.46
1332 1440 0.176449 CGAGCACAGATGATGGTCCA 59.824 55.000 0.00 0.00 40.68 4.02
1333 1441 1.405933 CGAGCACAGATGATGGTCCAA 60.406 52.381 0.00 0.00 40.68 3.53
1357 1465 0.645868 GCGCATTTGAGAGTACGGTC 59.354 55.000 0.30 0.00 0.00 4.79
1377 1493 1.337071 CCTGTCGATATACGTGCACCT 59.663 52.381 12.15 1.77 43.13 4.00
1382 1498 3.615496 GTCGATATACGTGCACCTGTTTT 59.385 43.478 12.15 0.00 43.13 2.43
1386 1502 5.972973 CGATATACGTGCACCTGTTTTAGTA 59.027 40.000 12.15 5.35 37.22 1.82
1393 1509 5.504994 CGTGCACCTGTTTTAGTATGTTTGT 60.505 40.000 12.15 0.00 0.00 2.83
1407 1523 6.765403 AGTATGTTTGTTAACTCTGGCTACA 58.235 36.000 7.22 1.68 35.24 2.74
1411 1527 5.238432 TGTTTGTTAACTCTGGCTACATGTG 59.762 40.000 9.11 0.00 35.24 3.21
1702 1848 4.891566 CCTGTCTCAGGTACGTGC 57.108 61.111 10.71 0.00 45.82 5.34
1722 1870 2.584791 CACCGTGTACTTACGTGTACC 58.415 52.381 12.20 4.83 42.24 3.34
1728 1876 3.983344 GTGTACTTACGTGTACCCAAGTG 59.017 47.826 12.20 0.00 41.34 3.16
1740 1888 0.306533 CCCAAGTGGTTTTGTCGACG 59.693 55.000 11.62 0.00 0.00 5.12
1742 1890 1.666700 CCAAGTGGTTTTGTCGACGAA 59.333 47.619 14.37 14.37 0.00 3.85
1758 1906 3.240838 CGACGAACGAACGATTAACTGTC 60.241 47.826 11.97 0.00 45.77 3.51
1760 1908 4.043750 ACGAACGAACGATTAACTGTCAA 58.956 39.130 11.97 0.00 37.03 3.18
1762 1910 4.383679 GAACGAACGATTAACTGTCAAGC 58.616 43.478 0.14 0.00 0.00 4.01
1764 1912 2.759038 GAACGATTAACTGTCAAGCGC 58.241 47.619 0.55 0.00 38.28 5.92
1765 1913 1.076332 ACGATTAACTGTCAAGCGCC 58.924 50.000 2.29 0.00 38.28 6.53
1767 1915 2.094390 ACGATTAACTGTCAAGCGCCTA 60.094 45.455 2.29 0.00 38.28 3.93
1768 1916 2.281762 CGATTAACTGTCAAGCGCCTAC 59.718 50.000 2.29 0.00 0.00 3.18
1783 1957 2.361483 TACGTGTAGGCCGAGGCA 60.361 61.111 16.65 0.00 44.11 4.75
1788 1962 4.162690 GTAGGCCGAGGCACCCAG 62.163 72.222 16.65 0.00 44.11 4.45
2616 2839 1.448922 GCTGTACGTTGTTGCCCCAA 61.449 55.000 0.00 0.00 0.00 4.12
2617 2840 1.025812 CTGTACGTTGTTGCCCCAAA 58.974 50.000 0.00 0.00 0.00 3.28
2618 2841 1.611491 CTGTACGTTGTTGCCCCAAAT 59.389 47.619 0.00 0.00 0.00 2.32
2619 2842 1.609555 TGTACGTTGTTGCCCCAAATC 59.390 47.619 0.00 0.00 0.00 2.17
2620 2843 1.068125 GTACGTTGTTGCCCCAAATCC 60.068 52.381 0.00 0.00 0.00 3.01
2731 2960 7.341445 AGAATTTTTGTACTTACAAGTGGCA 57.659 32.000 4.86 1.75 45.77 4.92
2766 2995 7.174946 TGAAACTTGACACTCTTTCTCAAAGTT 59.825 33.333 0.00 0.00 39.52 2.66
2814 3044 6.638873 CACTCTCATAAACTCGCCAACTATAG 59.361 42.308 0.00 0.00 0.00 1.31
2818 3049 7.705325 TCTCATAAACTCGCCAACTATAGTTTC 59.295 37.037 15.60 9.50 40.38 2.78
3251 3482 5.049405 CCTTTTCTGCGTACAATCTCACTTT 60.049 40.000 0.00 0.00 0.00 2.66
3252 3483 4.990543 TTCTGCGTACAATCTCACTTTG 57.009 40.909 0.00 0.00 0.00 2.77
3253 3484 2.736721 TCTGCGTACAATCTCACTTTGC 59.263 45.455 0.00 0.00 0.00 3.68
3254 3485 1.804151 TGCGTACAATCTCACTTTGCC 59.196 47.619 0.00 0.00 0.00 4.52
3255 3486 1.130561 GCGTACAATCTCACTTTGCCC 59.869 52.381 0.00 0.00 0.00 5.36
3256 3487 2.422597 CGTACAATCTCACTTTGCCCA 58.577 47.619 0.00 0.00 0.00 5.36
3310 3544 1.351017 TGTTCCCCTTTCGAGCTCAAT 59.649 47.619 15.40 0.00 0.00 2.57
3319 3553 4.872691 CCTTTCGAGCTCAATGTAGTTGAT 59.127 41.667 15.40 0.00 45.36 2.57
3321 3555 3.695816 TCGAGCTCAATGTAGTTGATCG 58.304 45.455 15.40 7.21 45.36 3.69
3322 3556 3.695816 CGAGCTCAATGTAGTTGATCGA 58.304 45.455 15.40 0.00 45.46 3.59
3323 3557 3.728221 CGAGCTCAATGTAGTTGATCGAG 59.272 47.826 15.40 0.00 45.46 4.04
3325 3559 3.118992 AGCTCAATGTAGTTGATCGAGCA 60.119 43.478 0.00 0.00 45.36 4.26
3326 3560 3.000724 GCTCAATGTAGTTGATCGAGCAC 59.999 47.826 1.08 0.00 45.36 4.40
3327 3561 4.176271 CTCAATGTAGTTGATCGAGCACA 58.824 43.478 1.08 0.00 45.36 4.57
3328 3562 3.926527 TCAATGTAGTTGATCGAGCACAC 59.073 43.478 1.08 5.36 41.79 3.82
3329 3563 1.977188 TGTAGTTGATCGAGCACACG 58.023 50.000 1.08 0.00 0.00 4.49
3349 3583 5.047847 CACGTTTGGAGTTCAGTTAGAGAA 58.952 41.667 0.00 0.00 0.00 2.87
3356 3590 8.603242 TTGGAGTTCAGTTAGAGAATAACAAC 57.397 34.615 1.07 0.00 0.00 3.32
3373 3607 8.761575 AATAACAACATGATTCAACAACCATC 57.238 30.769 0.00 0.00 0.00 3.51
3375 3609 6.159299 ACAACATGATTCAACAACCATCAA 57.841 33.333 0.00 0.00 30.79 2.57
3399 3633 3.819368 TCAAACTGATGAGCTTCCAACA 58.181 40.909 0.00 0.00 0.00 3.33
3410 3644 1.587946 GCTTCCAACAAACTTTGCACG 59.412 47.619 1.14 0.00 0.00 5.34
3430 3664 5.516996 CACGACGCTCCACTAGAAATATAA 58.483 41.667 0.00 0.00 0.00 0.98
3434 3668 7.222224 ACGACGCTCCACTAGAAATATAAAAAG 59.778 37.037 0.00 0.00 0.00 2.27
3473 3707 5.695851 AAGGTTCTACATGCTTTCAACTG 57.304 39.130 0.00 0.00 0.00 3.16
3479 3713 7.653311 GGTTCTACATGCTTTCAACTGAAAAAT 59.347 33.333 6.36 1.44 42.72 1.82
3506 3740 9.719355 AAAAACTTTCAACTTACCTGTGAAATT 57.281 25.926 0.00 0.00 0.00 1.82
3507 3741 9.719355 AAAACTTTCAACTTACCTGTGAAATTT 57.281 25.926 0.00 0.00 0.00 1.82
3508 3742 8.926715 AACTTTCAACTTACCTGTGAAATTTC 57.073 30.769 11.41 11.41 0.00 2.17
3509 3743 8.062065 ACTTTCAACTTACCTGTGAAATTTCA 57.938 30.769 16.91 16.91 34.20 2.69
3510 3744 8.527810 ACTTTCAACTTACCTGTGAAATTTCAA 58.472 29.630 22.07 11.61 39.21 2.69
3511 3745 9.364989 CTTTCAACTTACCTGTGAAATTTCAAA 57.635 29.630 22.07 16.26 39.21 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.032014 GGCACAACAGTTCCACACAT 58.968 50.000 0.00 0.00 0.00 3.21
1 2 1.034838 GGGCACAACAGTTCCACACA 61.035 55.000 0.00 0.00 0.00 3.72
2 3 1.733526 GGGCACAACAGTTCCACAC 59.266 57.895 0.00 0.00 0.00 3.82
3 4 1.454847 GGGGCACAACAGTTCCACA 60.455 57.895 0.00 0.00 0.00 4.17
4 5 2.200337 GGGGGCACAACAGTTCCAC 61.200 63.158 0.00 0.00 0.00 4.02
5 6 2.197324 GGGGGCACAACAGTTCCA 59.803 61.111 0.00 0.00 0.00 3.53
6 7 2.983592 CGGGGGCACAACAGTTCC 60.984 66.667 0.00 0.00 0.00 3.62
7 8 2.203294 ACGGGGGCACAACAGTTC 60.203 61.111 0.00 0.00 0.00 3.01
8 9 2.518349 CACGGGGGCACAACAGTT 60.518 61.111 0.00 0.00 0.00 3.16
18 19 4.722700 CAAGGAGGTGCACGGGGG 62.723 72.222 11.45 0.00 0.00 5.40
19 20 4.722700 CCAAGGAGGTGCACGGGG 62.723 72.222 11.45 1.81 0.00 5.73
43 44 3.601443 AGAAGATCGTCCTTGTCCAAG 57.399 47.619 4.93 0.00 38.14 3.61
44 45 3.447586 CCTAGAAGATCGTCCTTGTCCAA 59.552 47.826 4.93 0.00 0.00 3.53
45 46 3.024547 CCTAGAAGATCGTCCTTGTCCA 58.975 50.000 4.93 0.00 0.00 4.02
46 47 2.362717 CCCTAGAAGATCGTCCTTGTCC 59.637 54.545 4.93 0.00 0.00 4.02
47 48 2.223852 GCCCTAGAAGATCGTCCTTGTC 60.224 54.545 4.93 0.00 0.00 3.18
48 49 1.757699 GCCCTAGAAGATCGTCCTTGT 59.242 52.381 4.93 0.00 0.00 3.16
49 50 1.069358 GGCCCTAGAAGATCGTCCTTG 59.931 57.143 4.93 0.00 0.00 3.61
50 51 1.415200 GGCCCTAGAAGATCGTCCTT 58.585 55.000 4.93 0.00 0.00 3.36
51 52 0.470268 GGGCCCTAGAAGATCGTCCT 60.470 60.000 17.04 0.00 0.00 3.85
52 53 1.807495 CGGGCCCTAGAAGATCGTCC 61.807 65.000 22.43 0.00 0.00 4.79
53 54 0.822532 TCGGGCCCTAGAAGATCGTC 60.823 60.000 22.43 0.00 0.00 4.20
54 55 0.396695 TTCGGGCCCTAGAAGATCGT 60.397 55.000 22.43 0.00 0.00 3.73
55 56 0.969894 ATTCGGGCCCTAGAAGATCG 59.030 55.000 22.43 2.59 0.00 3.69
61 62 0.685131 TGTCGAATTCGGGCCCTAGA 60.685 55.000 26.47 7.94 40.29 2.43
66 67 1.727467 CCATTGTCGAATTCGGGCC 59.273 57.895 26.47 15.31 40.29 5.80
69 70 1.351707 CGGCCATTGTCGAATTCGG 59.648 57.895 26.47 11.16 43.95 4.30
80 81 2.582436 CGGTGTACTCCGGCCATT 59.418 61.111 25.11 0.00 45.88 3.16
108 109 0.390472 CTCGCTGGAGAAGGAACACC 60.390 60.000 0.00 0.00 43.27 4.16
149 150 7.116090 TGGACGATAAAACTTTGAAATTGCATG 59.884 33.333 0.00 0.00 0.00 4.06
176 177 4.218312 AGGCTTCAGTTCCAAATTCTGTT 58.782 39.130 0.00 0.00 0.00 3.16
254 256 3.008266 CCATCAAAACTTGAAATGGGGCT 59.992 43.478 2.38 0.00 43.95 5.19
256 258 4.040217 TCACCATCAAAACTTGAAATGGGG 59.960 41.667 11.73 8.70 42.15 4.96
272 274 3.005155 GCATTGGGCTAGAATTCACCATC 59.995 47.826 8.44 0.00 40.25 3.51
305 307 4.171878 TGTTTGGGTGTATGAACTGGAA 57.828 40.909 0.00 0.00 0.00 3.53
334 336 4.100963 ACAAAAGGCGGAAAGGATTTTTCT 59.899 37.500 0.36 0.00 39.27 2.52
355 360 2.528127 ACACATGGTCGGGGGACA 60.528 61.111 0.00 0.00 0.00 4.02
364 369 1.444933 TCTTGGGGAAGACACATGGT 58.555 50.000 0.00 0.00 0.00 3.55
366 371 1.806542 CGTTCTTGGGGAAGACACATG 59.193 52.381 0.00 0.00 34.23 3.21
367 372 1.697432 TCGTTCTTGGGGAAGACACAT 59.303 47.619 0.00 0.00 34.23 3.21
368 373 1.124780 TCGTTCTTGGGGAAGACACA 58.875 50.000 0.00 0.00 34.23 3.72
369 374 2.028020 AGATCGTTCTTGGGGAAGACAC 60.028 50.000 0.00 0.00 34.23 3.67
370 375 2.233922 GAGATCGTTCTTGGGGAAGACA 59.766 50.000 0.00 0.00 34.23 3.41
371 376 2.498078 AGAGATCGTTCTTGGGGAAGAC 59.502 50.000 0.00 0.00 34.23 3.01
372 377 2.761208 GAGAGATCGTTCTTGGGGAAGA 59.239 50.000 0.00 0.00 34.23 2.87
373 378 2.159028 GGAGAGATCGTTCTTGGGGAAG 60.159 54.545 0.00 0.00 34.23 3.46
384 404 0.180642 TGTAGAGGCGGAGAGATCGT 59.819 55.000 0.00 0.00 0.00 3.73
458 478 1.890979 CATGCTCATGCCTCGGGAC 60.891 63.158 0.00 0.00 38.71 4.46
468 488 1.022982 CGCCAGTGTGTCATGCTCAT 61.023 55.000 0.00 0.00 0.00 2.90
469 489 1.668793 CGCCAGTGTGTCATGCTCA 60.669 57.895 0.00 0.00 0.00 4.26
470 490 1.669115 ACGCCAGTGTGTCATGCTC 60.669 57.895 0.00 0.00 0.00 4.26
471 491 1.962822 CACGCCAGTGTGTCATGCT 60.963 57.895 3.16 0.00 43.15 3.79
472 492 2.557805 CACGCCAGTGTGTCATGC 59.442 61.111 3.16 0.00 43.15 4.06
482 502 2.450160 GTTGTTTTGACTTCACGCCAG 58.550 47.619 0.00 0.00 0.00 4.85
506 526 1.735920 CTCAGACGGCAGCTGTCAC 60.736 63.158 31.75 11.66 41.77 3.67
518 538 2.029844 GCCAACACTCGGCTCAGAC 61.030 63.158 0.00 0.00 46.56 3.51
722 755 3.450578 CGCTAGCTTGGTCCGTTAATAA 58.549 45.455 13.93 0.00 0.00 1.40
744 777 3.181493 GGATCACCAAACTGCTTGCATAG 60.181 47.826 0.00 0.00 33.27 2.23
745 778 2.754552 GGATCACCAAACTGCTTGCATA 59.245 45.455 0.00 0.00 33.27 3.14
746 779 1.547372 GGATCACCAAACTGCTTGCAT 59.453 47.619 0.00 0.00 33.27 3.96
747 780 0.961019 GGATCACCAAACTGCTTGCA 59.039 50.000 0.00 0.00 33.27 4.08
748 781 0.109597 CGGATCACCAAACTGCTTGC 60.110 55.000 0.00 0.00 33.27 4.01
749 782 0.109597 GCGGATCACCAAACTGCTTG 60.110 55.000 0.00 0.00 35.59 4.01
750 783 0.250901 AGCGGATCACCAAACTGCTT 60.251 50.000 0.00 0.00 42.53 3.91
751 784 0.613260 TAGCGGATCACCAAACTGCT 59.387 50.000 0.00 0.00 46.08 4.24
767 800 4.637873 GTAGCCACGCTAGCTAGC 57.362 61.111 31.88 31.88 43.26 3.42
816 858 1.888436 CTTCTGGTGAGCCTACCGCA 61.888 60.000 2.87 0.00 43.87 5.69
865 907 4.803426 GGTCAGCTGACGCGGGAG 62.803 72.222 34.28 6.67 45.65 4.30
894 936 1.405105 TGTTTCTGCTTTGGCTGACAC 59.595 47.619 7.05 7.05 44.06 3.67
925 969 1.039856 GTTGGCCAGCTTTTGAAGGA 58.960 50.000 13.08 0.00 0.00 3.36
987 1050 2.185867 GCCATGCATGCCACTTGG 59.814 61.111 21.69 16.98 35.87 3.61
988 1051 2.202690 CGCCATGCATGCCACTTG 60.203 61.111 21.69 7.57 0.00 3.16
1076 1139 2.439960 TTCCTCTGCACCACCACGT 61.440 57.895 0.00 0.00 0.00 4.49
1312 1420 0.461548 GGACCATCATCTGTGCTCGA 59.538 55.000 0.00 0.00 0.00 4.04
1320 1428 2.743183 GCGCTTACTTGGACCATCATCT 60.743 50.000 0.00 0.00 0.00 2.90
1322 1430 1.065491 TGCGCTTACTTGGACCATCAT 60.065 47.619 9.73 0.00 0.00 2.45
1323 1431 0.323302 TGCGCTTACTTGGACCATCA 59.677 50.000 9.73 0.00 0.00 3.07
1324 1432 1.668419 ATGCGCTTACTTGGACCATC 58.332 50.000 9.73 0.00 0.00 3.51
1325 1433 2.128771 AATGCGCTTACTTGGACCAT 57.871 45.000 9.73 0.00 0.00 3.55
1326 1434 1.539388 CAAATGCGCTTACTTGGACCA 59.461 47.619 9.73 0.00 0.00 4.02
1327 1435 1.810151 TCAAATGCGCTTACTTGGACC 59.190 47.619 9.73 0.00 0.00 4.46
1328 1436 2.742053 TCTCAAATGCGCTTACTTGGAC 59.258 45.455 9.73 0.00 0.00 4.02
1329 1437 3.002791 CTCTCAAATGCGCTTACTTGGA 58.997 45.455 9.73 4.28 0.00 3.53
1330 1438 2.744202 ACTCTCAAATGCGCTTACTTGG 59.256 45.455 9.73 0.14 0.00 3.61
1331 1439 4.490959 CGTACTCTCAAATGCGCTTACTTG 60.491 45.833 9.73 5.12 0.00 3.16
1332 1440 3.612860 CGTACTCTCAAATGCGCTTACTT 59.387 43.478 9.73 0.00 0.00 2.24
1333 1441 3.179830 CGTACTCTCAAATGCGCTTACT 58.820 45.455 9.73 0.00 0.00 2.24
1357 1465 1.337071 AGGTGCACGTATATCGACAGG 59.663 52.381 10.95 0.00 42.86 4.00
1377 1493 8.347035 GCCAGAGTTAACAAACATACTAAAACA 58.653 33.333 8.61 0.00 0.00 2.83
1382 1498 7.898918 TGTAGCCAGAGTTAACAAACATACTA 58.101 34.615 8.61 0.00 0.00 1.82
1386 1502 6.003950 ACATGTAGCCAGAGTTAACAAACAT 58.996 36.000 8.61 4.00 0.00 2.71
1393 1509 3.007940 AGCACACATGTAGCCAGAGTTAA 59.992 43.478 16.30 0.00 0.00 2.01
1407 1523 1.339055 ACCTACGCATGAAGCACACAT 60.339 47.619 0.00 0.00 46.13 3.21
1411 1527 1.002366 CTCACCTACGCATGAAGCAC 58.998 55.000 0.00 0.00 46.13 4.40
1598 1744 2.959357 GACGACGTCGAGGAACCGT 61.959 63.158 41.52 19.47 43.02 4.83
1722 1870 1.292061 TCGTCGACAAAACCACTTGG 58.708 50.000 17.16 0.00 42.17 3.61
1736 1884 2.653584 ACAGTTAATCGTTCGTTCGTCG 59.346 45.455 0.00 0.00 41.41 5.12
1737 1885 3.665409 TGACAGTTAATCGTTCGTTCGTC 59.335 43.478 2.67 0.00 0.00 4.20
1738 1886 3.631144 TGACAGTTAATCGTTCGTTCGT 58.369 40.909 2.67 0.00 0.00 3.85
1739 1887 4.615386 CTTGACAGTTAATCGTTCGTTCG 58.385 43.478 0.00 0.00 0.00 3.95
1740 1888 4.383679 GCTTGACAGTTAATCGTTCGTTC 58.616 43.478 0.00 0.00 0.00 3.95
1742 1890 2.407361 CGCTTGACAGTTAATCGTTCGT 59.593 45.455 0.00 0.00 0.00 3.85
1747 1895 1.359848 AGGCGCTTGACAGTTAATCG 58.640 50.000 7.64 0.00 0.00 3.34
1749 1897 2.268298 CGTAGGCGCTTGACAGTTAAT 58.732 47.619 7.64 0.00 0.00 1.40
1750 1898 1.000060 ACGTAGGCGCTTGACAGTTAA 60.000 47.619 7.64 0.00 42.83 2.01
1751 1899 0.599558 ACGTAGGCGCTTGACAGTTA 59.400 50.000 7.64 0.00 42.83 2.24
1753 1901 1.372997 CACGTAGGCGCTTGACAGT 60.373 57.895 7.64 3.33 42.83 3.55
1754 1902 0.109458 TACACGTAGGCGCTTGACAG 60.109 55.000 7.64 1.42 42.83 3.51
1755 1903 0.109458 CTACACGTAGGCGCTTGACA 60.109 55.000 7.64 0.00 42.83 3.58
1758 1906 4.088421 CCTACACGTAGGCGCTTG 57.912 61.111 7.64 0.00 45.36 4.01
1765 1913 2.412112 GCCTCGGCCTACACGTAG 59.588 66.667 0.00 0.00 34.56 3.51
1767 1915 4.065281 GTGCCTCGGCCTACACGT 62.065 66.667 0.00 0.00 41.09 4.49
1768 1916 4.814294 GGTGCCTCGGCCTACACG 62.814 72.222 0.00 0.00 41.09 4.49
1783 1957 1.975407 CGAGTACACGTCCCTGGGT 60.975 63.158 13.56 0.00 0.00 4.51
1788 1962 2.482374 CGTCCGAGTACACGTCCC 59.518 66.667 11.73 0.00 0.00 4.46
1994 2182 2.203070 GTTGCCGCCCGAGATGAT 60.203 61.111 0.00 0.00 0.00 2.45
2565 2788 2.127534 GCAAAACCACGTACGCGG 60.128 61.111 20.39 20.39 43.45 6.46
2616 2839 4.280174 GCATGCATGATTCCTAACTGGATT 59.720 41.667 30.64 0.00 45.68 3.01
2617 2840 3.825014 GCATGCATGATTCCTAACTGGAT 59.175 43.478 30.64 0.00 45.68 3.41
2618 2841 3.216800 GCATGCATGATTCCTAACTGGA 58.783 45.455 30.64 0.00 44.51 3.86
2619 2842 2.953648 TGCATGCATGATTCCTAACTGG 59.046 45.455 30.64 0.00 37.10 4.00
2620 2843 3.550233 GCTGCATGCATGATTCCTAACTG 60.550 47.826 30.64 13.71 42.31 3.16
2731 2960 6.294473 AGAGTGTCAAGTTTCAGAATCATGT 58.706 36.000 0.00 0.00 0.00 3.21
3225 3456 2.742053 GAGATTGTACGCAGAAAAGGCA 59.258 45.455 0.00 0.00 0.00 4.75
3227 3458 3.997021 AGTGAGATTGTACGCAGAAAAGG 59.003 43.478 0.00 0.00 0.00 3.11
3228 3459 5.597813 AAGTGAGATTGTACGCAGAAAAG 57.402 39.130 0.00 0.00 0.00 2.27
3251 3482 6.436847 TCTTCATTTAACTTGATGAATGGGCA 59.563 34.615 1.73 0.00 40.39 5.36
3252 3483 6.866480 TCTTCATTTAACTTGATGAATGGGC 58.134 36.000 1.73 0.00 40.39 5.36
3253 3484 9.956720 GTATCTTCATTTAACTTGATGAATGGG 57.043 33.333 1.73 0.00 40.39 4.00
3254 3485 9.655769 CGTATCTTCATTTAACTTGATGAATGG 57.344 33.333 1.73 0.00 40.39 3.16
3255 3486 9.655769 CCGTATCTTCATTTAACTTGATGAATG 57.344 33.333 1.73 0.00 40.39 2.67
3256 3487 9.613428 TCCGTATCTTCATTTAACTTGATGAAT 57.387 29.630 1.73 0.00 40.39 2.57
3310 3544 1.268625 ACGTGTGCTCGATCAACTACA 59.731 47.619 0.00 0.00 34.70 2.74
3319 3553 0.179094 AACTCCAAACGTGTGCTCGA 60.179 50.000 0.00 0.00 34.70 4.04
3321 3555 1.261619 CTGAACTCCAAACGTGTGCTC 59.738 52.381 0.00 0.00 0.00 4.26
3322 3556 1.299541 CTGAACTCCAAACGTGTGCT 58.700 50.000 0.00 0.00 0.00 4.40
3323 3557 1.014352 ACTGAACTCCAAACGTGTGC 58.986 50.000 0.00 0.00 0.00 4.57
3325 3559 4.098960 TCTCTAACTGAACTCCAAACGTGT 59.901 41.667 0.00 0.00 0.00 4.49
3326 3560 4.617959 TCTCTAACTGAACTCCAAACGTG 58.382 43.478 0.00 0.00 0.00 4.49
3327 3561 4.931661 TCTCTAACTGAACTCCAAACGT 57.068 40.909 0.00 0.00 0.00 3.99
3328 3562 7.384115 TGTTATTCTCTAACTGAACTCCAAACG 59.616 37.037 0.00 0.00 0.00 3.60
3329 3563 8.603242 TGTTATTCTCTAACTGAACTCCAAAC 57.397 34.615 0.00 0.00 0.00 2.93
3349 3583 7.894708 TGATGGTTGTTGAATCATGTTGTTAT 58.105 30.769 0.00 0.00 32.72 1.89
3356 3590 6.391537 TGATGTTGATGGTTGTTGAATCATG 58.608 36.000 0.00 0.00 32.72 3.07
3410 3644 7.224949 AGCTTTTTATATTTCTAGTGGAGCGTC 59.775 37.037 0.00 0.00 0.00 5.19
3430 3664 5.532779 CCTTAGTTCTTGAGTGGAAGCTTTT 59.467 40.000 0.00 0.00 0.00 2.27
3434 3668 4.009370 ACCTTAGTTCTTGAGTGGAAGC 57.991 45.455 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.