Multiple sequence alignment - TraesCS2D01G373500

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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 TraesCS2D01G373500 chr2D 100.000 3609 0 0 1 3609 477106457 477102849 0.000000e+00 6665.0
1 TraesCS2D01G373500 chr2D 91.978 1072 80 5 1716 2784 477040760 477039692 0.000000e+00 1498.0
2 TraesCS2D01G373500 chr2D 89.424 1163 88 16 570 1725 477053581 477052447 0.000000e+00 1434.0
3 TraesCS2D01G373500 chr2D 94.521 73 3 1 406 477 10985529 10985457 1.060000e-20 111.0
4 TraesCS2D01G373500 chr2A 95.665 1730 64 5 1056 2782 619514084 619512363 0.000000e+00 2769.0
5 TraesCS2D01G373500 chr2A 90.051 1779 140 20 482 2246 619584459 619582704 0.000000e+00 2270.0
6 TraesCS2D01G373500 chr2A 92.703 603 42 2 2845 3447 619479322 619478722 0.000000e+00 869.0
7 TraesCS2D01G373500 chr2A 88.491 530 29 8 482 1010 619514577 619514079 2.380000e-171 612.0
8 TraesCS2D01G373500 chr2A 87.136 412 26 11 1 389 619515013 619514606 3.310000e-120 442.0
9 TraesCS2D01G373500 chr2A 84.767 407 43 5 1 389 619584889 619584484 1.210000e-104 390.0
10 TraesCS2D01G373500 chr2A 96.610 118 4 0 3443 3560 619478248 619478131 2.840000e-46 196.0
11 TraesCS2D01G373500 chr2A 94.118 119 5 1 2237 2353 619570448 619570330 2.860000e-41 180.0
12 TraesCS2D01G373500 chr2B 92.444 1469 103 6 1042 2503 559168811 559167344 0.000000e+00 2091.0
13 TraesCS2D01G373500 chr2B 90.854 164 15 0 2621 2784 559129036 559128873 1.690000e-53 220.0
14 TraesCS2D01G373500 chr2B 97.521 121 3 0 643 763 559169276 559169156 1.310000e-49 207.0
15 TraesCS2D01G373500 chr2B 88.235 136 8 2 2496 2624 559129425 559129291 4.820000e-34 156.0
16 TraesCS2D01G373500 chr5D 86.428 781 100 5 2782 3560 553765762 553764986 0.000000e+00 850.0
17 TraesCS2D01G373500 chr5B 86.061 782 103 5 2782 3560 697080501 697081279 0.000000e+00 835.0
18 TraesCS2D01G373500 chr5B 92.105 76 6 0 402 477 670524507 670524582 1.370000e-19 108.0
19 TraesCS2D01G373500 chr4A 77.932 1296 260 20 1059 2338 480557699 480556414 0.000000e+00 785.0
20 TraesCS2D01G373500 chr4A 77.063 1260 251 30 1059 2296 479903486 479902243 0.000000e+00 691.0
21 TraesCS2D01G373500 chr4D 77.149 1291 263 26 1067 2338 96712175 96713452 0.000000e+00 721.0
22 TraesCS2D01G373500 chr4D 97.959 49 1 0 3561 3609 123069804 123069852 6.420000e-13 86.1
23 TraesCS2D01G373500 chr4D 97.959 49 1 0 3561 3609 150455496 150455544 6.420000e-13 86.1
24 TraesCS2D01G373500 chr4D 97.959 49 1 0 3561 3609 206241457 206241409 6.420000e-13 86.1
25 TraesCS2D01G373500 chr4D 97.959 49 1 0 3561 3609 315482931 315482979 6.420000e-13 86.1
26 TraesCS2D01G373500 chr4D 97.959 49 1 0 3561 3609 360898210 360898162 6.420000e-13 86.1
27 TraesCS2D01G373500 chr7A 76.769 1300 277 23 1029 2313 79335061 79333772 0.000000e+00 704.0
28 TraesCS2D01G373500 chr7A 82.908 784 127 7 2782 3560 539942864 539942083 0.000000e+00 699.0
29 TraesCS2D01G373500 chr7A 91.139 79 6 1 400 477 6948283 6948205 4.930000e-19 106.0
30 TraesCS2D01G373500 chr4B 76.828 1299 269 25 1059 2338 138276161 138277446 0.000000e+00 702.0
31 TraesCS2D01G373500 chr4B 75.697 251 53 7 2533 2782 441086050 441085807 6.330000e-23 119.0
32 TraesCS2D01G373500 chr5A 80.735 789 138 11 2778 3560 34390376 34389596 1.430000e-168 603.0
33 TraesCS2D01G373500 chr5A 94.521 73 4 0 405 477 678270042 678270114 2.950000e-21 113.0
34 TraesCS2D01G373500 chrUn 78.250 777 160 8 2786 3558 21949019 21948248 1.160000e-134 490.0
35 TraesCS2D01G373500 chrUn 84.232 241 29 7 2533 2765 28299953 28299714 3.630000e-55 226.0
36 TraesCS2D01G373500 chrUn 84.286 140 15 6 3425 3560 11964018 11964154 2.920000e-26 130.0
37 TraesCS2D01G373500 chrUn 92.105 76 6 0 402 477 35125967 35125892 1.370000e-19 108.0
38 TraesCS2D01G373500 chr3B 80.546 293 39 12 2506 2784 131061240 131061528 3.650000e-50 209.0
39 TraesCS2D01G373500 chr3B 82.126 207 31 5 2515 2721 619627090 619627290 4.790000e-39 172.0
40 TraesCS2D01G373500 chr3B 81.910 199 30 5 2515 2713 619866153 619866345 2.880000e-36 163.0
41 TraesCS2D01G373500 chr1D 81.203 266 38 8 2522 2781 349567381 349567640 1.700000e-48 204.0
42 TraesCS2D01G373500 chr1D 76.382 199 39 8 3366 3560 412165840 412165646 2.290000e-17 100.0
43 TraesCS2D01G373500 chr1D 97.959 49 1 0 3561 3609 60067006 60067054 6.420000e-13 86.1
44 TraesCS2D01G373500 chr7D 95.833 72 3 0 406 477 57777665 57777594 2.280000e-22 117.0
45 TraesCS2D01G373500 chr7D 93.056 72 5 0 406 477 176171800 176171729 4.930000e-19 106.0
46 TraesCS2D01G373500 chr7D 73.510 302 69 11 3239 3534 561636113 561636409 1.770000e-18 104.0
47 TraesCS2D01G373500 chr1A 83.206 131 18 2 2514 2644 449858153 449858279 2.280000e-22 117.0
48 TraesCS2D01G373500 chr1A 85.321 109 16 0 2676 2784 522460562 522460670 2.950000e-21 113.0
49 TraesCS2D01G373500 chr1A 93.056 72 5 0 402 473 397086827 397086898 4.930000e-19 106.0
50 TraesCS2D01G373500 chr6A 93.056 72 5 0 406 477 428778 428707 4.930000e-19 106.0
51 TraesCS2D01G373500 chr6A 96.970 33 1 0 2733 2765 602483978 602483946 5.030000e-04 56.5
52 TraesCS2D01G373500 chr6D 97.959 49 1 0 3561 3609 154771083 154771035 6.420000e-13 86.1
53 TraesCS2D01G373500 chr6D 97.959 49 1 0 3561 3609 237136258 237136306 6.420000e-13 86.1
54 TraesCS2D01G373500 chr6D 97.959 49 1 0 3561 3609 300796603 300796555 6.420000e-13 86.1


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 TraesCS2D01G373500 chr2D 477102849 477106457 3608 True 6665.000000 6665 100.000000 1 3609 1 chr2D.!!$R4 3608
1 TraesCS2D01G373500 chr2D 477039692 477040760 1068 True 1498.000000 1498 91.978000 1716 2784 1 chr2D.!!$R2 1068
2 TraesCS2D01G373500 chr2D 477052447 477053581 1134 True 1434.000000 1434 89.424000 570 1725 1 chr2D.!!$R3 1155
3 TraesCS2D01G373500 chr2A 619582704 619584889 2185 True 1330.000000 2270 87.409000 1 2246 2 chr2A.!!$R4 2245
4 TraesCS2D01G373500 chr2A 619512363 619515013 2650 True 1274.333333 2769 90.430667 1 2782 3 chr2A.!!$R3 2781
5 TraesCS2D01G373500 chr2A 619478131 619479322 1191 True 532.500000 869 94.656500 2845 3560 2 chr2A.!!$R2 715
6 TraesCS2D01G373500 chr2B 559167344 559169276 1932 True 1149.000000 2091 94.982500 643 2503 2 chr2B.!!$R2 1860
7 TraesCS2D01G373500 chr5D 553764986 553765762 776 True 850.000000 850 86.428000 2782 3560 1 chr5D.!!$R1 778
8 TraesCS2D01G373500 chr5B 697080501 697081279 778 False 835.000000 835 86.061000 2782 3560 1 chr5B.!!$F2 778
9 TraesCS2D01G373500 chr4A 480556414 480557699 1285 True 785.000000 785 77.932000 1059 2338 1 chr4A.!!$R2 1279
10 TraesCS2D01G373500 chr4A 479902243 479903486 1243 True 691.000000 691 77.063000 1059 2296 1 chr4A.!!$R1 1237
11 TraesCS2D01G373500 chr4D 96712175 96713452 1277 False 721.000000 721 77.149000 1067 2338 1 chr4D.!!$F1 1271
12 TraesCS2D01G373500 chr7A 79333772 79335061 1289 True 704.000000 704 76.769000 1029 2313 1 chr7A.!!$R2 1284
13 TraesCS2D01G373500 chr7A 539942083 539942864 781 True 699.000000 699 82.908000 2782 3560 1 chr7A.!!$R3 778
14 TraesCS2D01G373500 chr4B 138276161 138277446 1285 False 702.000000 702 76.828000 1059 2338 1 chr4B.!!$F1 1279
15 TraesCS2D01G373500 chr5A 34389596 34390376 780 True 603.000000 603 80.735000 2778 3560 1 chr5A.!!$R1 782
16 TraesCS2D01G373500 chrUn 21948248 21949019 771 True 490.000000 490 78.250000 2786 3558 1 chrUn.!!$R1 772

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
835 1013 0.523757 GTCTCAAGTAGGTCTCGCGC 60.524 60.0 0.00 0.0 0.00 6.86 F
1348 1527 0.031111 TCTTCCGGATCCACCCATCT 60.031 55.0 13.41 0.0 34.64 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2419 2622 1.676006 CCAGATAAACGGAACATGCCC 59.324 52.381 0.0 0.0 0.00 5.36 R
3143 3351 0.678395 TAACCTAACCGTCGTTGCCA 59.322 50.000 0.0 0.0 33.17 4.92 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
27 28 8.985315 TCTATTTGGGAGTTATAAGACTACGA 57.015 34.615 0.00 0.00 30.84 3.43
42 43 3.703052 GACTACGATGAAAGGGTTAGGGA 59.297 47.826 0.00 0.00 0.00 4.20
46 47 0.927029 ATGAAAGGGTTAGGGAGGGC 59.073 55.000 0.00 0.00 0.00 5.19
48 49 0.547075 GAAAGGGTTAGGGAGGGCTC 59.453 60.000 0.00 0.00 0.00 4.70
309 333 4.741676 GGCACTTTTGAGAATTTGTCACTG 59.258 41.667 0.00 0.00 0.00 3.66
313 337 6.020121 CACTTTTGAGAATTTGTCACTGCTTG 60.020 38.462 0.00 0.00 0.00 4.01
340 364 5.486526 TGAAATTGATTATTTGCCACACCC 58.513 37.500 0.00 0.00 36.59 4.61
361 385 7.671398 ACACCCTACTTTCAAATCTTGATGATT 59.329 33.333 0.00 0.00 46.49 2.57
415 453 8.904099 AGGATAAAATGTAAATACTCCTTCCG 57.096 34.615 0.00 0.00 0.00 4.30
416 454 8.491958 AGGATAAAATGTAAATACTCCTTCCGT 58.508 33.333 0.00 0.00 0.00 4.69
417 455 9.768662 GGATAAAATGTAAATACTCCTTCCGTA 57.231 33.333 0.00 0.00 0.00 4.02
421 459 9.729281 AAAATGTAAATACTCCTTCCGTAAAGA 57.271 29.630 0.00 0.00 37.12 2.52
422 460 9.729281 AAATGTAAATACTCCTTCCGTAAAGAA 57.271 29.630 0.00 0.00 37.12 2.52
423 461 9.729281 AATGTAAATACTCCTTCCGTAAAGAAA 57.271 29.630 0.00 0.00 37.12 2.52
424 462 9.901172 ATGTAAATACTCCTTCCGTAAAGAAAT 57.099 29.630 0.00 0.00 37.12 2.17
432 470 7.927092 ACTCCTTCCGTAAAGAAATATAAGAGC 59.073 37.037 0.00 0.00 37.12 4.09
433 471 7.788026 TCCTTCCGTAAAGAAATATAAGAGCA 58.212 34.615 0.00 0.00 37.12 4.26
434 472 8.429641 TCCTTCCGTAAAGAAATATAAGAGCAT 58.570 33.333 0.00 0.00 37.12 3.79
435 473 9.057089 CCTTCCGTAAAGAAATATAAGAGCATT 57.943 33.333 0.00 0.00 37.12 3.56
535 573 1.133216 GAAGAAATGAAAGAGGCGGCC 59.867 52.381 12.11 12.11 0.00 6.13
536 574 1.026718 AGAAATGAAAGAGGCGGCCG 61.027 55.000 24.05 24.05 0.00 6.13
537 575 1.993369 GAAATGAAAGAGGCGGCCGG 61.993 60.000 29.38 8.95 0.00 6.13
549 592 3.435186 GGCCGGCAAGTGCTTCTC 61.435 66.667 30.85 1.84 41.70 2.87
598 641 3.594775 CGCCCAGTGTTGCTGCAA 61.595 61.111 11.69 11.69 43.71 4.08
625 668 4.988598 CCCGCGTCTTGGTGCTGT 62.989 66.667 4.92 0.00 0.00 4.40
626 669 2.972505 CCGCGTCTTGGTGCTGTT 60.973 61.111 4.92 0.00 0.00 3.16
799 845 1.005630 GAGTGCAGCGACCAGAGTT 60.006 57.895 0.00 0.00 0.00 3.01
825 1003 2.035449 CGACCACCAACTGTCTCAAGTA 59.965 50.000 0.00 0.00 0.00 2.24
835 1013 0.523757 GTCTCAAGTAGGTCTCGCGC 60.524 60.000 0.00 0.00 0.00 6.86
861 1039 2.356780 CGGCCTCCGGTTCCTACTT 61.357 63.158 0.00 0.00 44.15 2.24
865 1043 0.908180 CCTCCGGTTCCTACTTGGGT 60.908 60.000 0.00 0.00 36.20 4.51
866 1044 0.981943 CTCCGGTTCCTACTTGGGTT 59.018 55.000 0.00 0.00 36.20 4.11
867 1045 2.181975 CTCCGGTTCCTACTTGGGTTA 58.818 52.381 0.00 0.00 36.20 2.85
868 1046 2.770232 CTCCGGTTCCTACTTGGGTTAT 59.230 50.000 0.00 0.00 36.20 1.89
970 1148 4.668118 TTCCGTCGGGGTGCGTTC 62.668 66.667 12.29 0.00 37.00 3.95
1001 1180 4.265073 ACCAGATCAGATTACAAGCCAAC 58.735 43.478 0.00 0.00 0.00 3.77
1011 1190 4.699925 TTACAAGCCAACAGACCTACTT 57.300 40.909 0.00 0.00 0.00 2.24
1016 1195 2.028020 AGCCAACAGACCTACTTGTAGC 60.028 50.000 2.46 0.00 0.00 3.58
1054 1233 7.148623 CCCGTTCACTACTGAAATTTAGAGAAC 60.149 40.741 14.21 14.21 40.06 3.01
1104 1283 2.356135 GTCAGAAATTTGCCGGAGCTA 58.644 47.619 5.05 0.00 40.80 3.32
1182 1361 4.200283 GGCTCCGTCTGCTCCTCG 62.200 72.222 0.00 0.00 0.00 4.63
1186 1365 3.374402 CCGTCTGCTCCTCGTGGT 61.374 66.667 2.99 0.00 34.23 4.16
1214 1393 0.608130 TATACCAGCCTATGCAGCCG 59.392 55.000 0.00 0.00 41.13 5.52
1348 1527 0.031111 TCTTCCGGATCCACCCATCT 60.031 55.000 13.41 0.00 34.64 2.90
1374 1553 3.312890 CAGGTATCTGATTGGGTCCTCT 58.687 50.000 0.00 0.00 43.49 3.69
1403 1582 2.024871 GATCACCGCCGACGAGAG 59.975 66.667 0.00 0.00 43.93 3.20
1461 1640 0.395311 AGATTGCTCTCCCGTCGGTA 60.395 55.000 11.06 0.00 0.00 4.02
1639 1818 5.564550 ACATCAGGGCATACATATTTCCTC 58.435 41.667 0.00 0.00 0.00 3.71
1651 1830 5.844004 ACATATTTCCTCATCCGTCTACAC 58.156 41.667 0.00 0.00 0.00 2.90
1682 1861 1.296392 TGGTTCTCATCCACAGCGG 59.704 57.895 0.00 0.00 0.00 5.52
2133 2330 2.694628 TCAGCTGAAGCCAAATTGTGTT 59.305 40.909 15.67 0.00 43.38 3.32
2419 2622 1.940613 GGCAGAAGCTACAATAACGGG 59.059 52.381 0.00 0.00 41.70 5.28
2433 2637 2.675075 CGGGGGCATGTTCCGTTT 60.675 61.111 12.94 0.00 39.04 3.60
2687 2891 1.993369 GCCGAGGGTGCTAAACATGC 61.993 60.000 0.00 0.00 0.00 4.06
2784 2988 4.359706 CAAGCCGGTCTTTTTATATTGGC 58.640 43.478 1.90 0.00 41.50 4.52
2800 3004 1.456705 GGCTCGAGTCCTCAGGGAT 60.457 63.158 15.13 0.00 44.33 3.85
2810 3014 1.974957 TCCTCAGGGATCGAACACAAA 59.025 47.619 0.00 0.00 36.57 2.83
2813 3017 1.974957 TCAGGGATCGAACACAAAGGA 59.025 47.619 0.00 0.00 0.00 3.36
2984 3190 2.520979 GATCTCCCGATAAAGCGATCG 58.479 52.381 11.69 11.69 46.62 3.69
3000 3206 3.635331 CGATCGAGCGGAAAATAGGTAA 58.365 45.455 16.65 0.00 0.00 2.85
3521 4216 2.694109 TGCAGATCTCAGACCATCTCAG 59.306 50.000 0.00 0.00 0.00 3.35
3560 4255 3.787001 GTCCTTCCCCGCCCAGAG 61.787 72.222 0.00 0.00 0.00 3.35
3561 4256 4.005978 TCCTTCCCCGCCCAGAGA 62.006 66.667 0.00 0.00 0.00 3.10
3562 4257 3.787001 CCTTCCCCGCCCAGAGAC 61.787 72.222 0.00 0.00 0.00 3.36
3563 4258 3.787001 CTTCCCCGCCCAGAGACC 61.787 72.222 0.00 0.00 0.00 3.85
3567 4262 3.646715 CCCGCCCAGAGACCCAAA 61.647 66.667 0.00 0.00 0.00 3.28
3568 4263 2.359975 CCGCCCAGAGACCCAAAC 60.360 66.667 0.00 0.00 0.00 2.93
3569 4264 2.750350 CGCCCAGAGACCCAAACT 59.250 61.111 0.00 0.00 0.00 2.66
3570 4265 1.376037 CGCCCAGAGACCCAAACTC 60.376 63.158 0.00 0.00 34.95 3.01
3571 4266 1.831652 CGCCCAGAGACCCAAACTCT 61.832 60.000 0.00 0.00 44.24 3.24
3572 4267 0.402121 GCCCAGAGACCCAAACTCTT 59.598 55.000 0.00 0.00 41.94 2.85
3573 4268 1.628846 GCCCAGAGACCCAAACTCTTA 59.371 52.381 0.00 0.00 41.94 2.10
3574 4269 2.039879 GCCCAGAGACCCAAACTCTTAA 59.960 50.000 0.00 0.00 41.94 1.85
3575 4270 3.870299 GCCCAGAGACCCAAACTCTTAAG 60.870 52.174 0.00 0.00 41.94 1.85
3576 4271 3.307762 CCCAGAGACCCAAACTCTTAAGG 60.308 52.174 1.85 0.00 41.94 2.69
3577 4272 3.583086 CCAGAGACCCAAACTCTTAAGGA 59.417 47.826 1.85 0.00 41.94 3.36
3578 4273 4.226168 CCAGAGACCCAAACTCTTAAGGAT 59.774 45.833 1.85 0.00 41.94 3.24
3579 4274 5.280727 CCAGAGACCCAAACTCTTAAGGATT 60.281 44.000 1.85 0.00 41.94 3.01
3580 4275 6.070194 CCAGAGACCCAAACTCTTAAGGATTA 60.070 42.308 1.85 0.00 41.94 1.75
3581 4276 7.366011 CCAGAGACCCAAACTCTTAAGGATTAT 60.366 40.741 1.85 0.00 41.94 1.28
3582 4277 7.497249 CAGAGACCCAAACTCTTAAGGATTATG 59.503 40.741 1.85 0.00 41.94 1.90
3583 4278 6.663734 AGACCCAAACTCTTAAGGATTATGG 58.336 40.000 1.85 5.60 0.00 2.74
3584 4279 5.766590 ACCCAAACTCTTAAGGATTATGGG 58.233 41.667 22.08 22.08 37.68 4.00
3585 4280 5.494706 ACCCAAACTCTTAAGGATTATGGGA 59.505 40.000 26.75 0.00 35.77 4.37
3586 4281 6.162241 ACCCAAACTCTTAAGGATTATGGGAT 59.838 38.462 26.75 15.61 35.77 3.85
3587 4282 6.717084 CCCAAACTCTTAAGGATTATGGGATC 59.283 42.308 20.45 0.00 31.24 3.36
3588 4283 7.421853 CCCAAACTCTTAAGGATTATGGGATCT 60.422 40.741 20.45 0.00 31.24 2.75
3589 4284 8.660435 CCAAACTCTTAAGGATTATGGGATCTA 58.340 37.037 1.85 0.00 31.24 1.98
3592 4287 8.980832 ACTCTTAAGGATTATGGGATCTATGT 57.019 34.615 1.85 0.00 31.24 2.29
3593 4288 8.820831 ACTCTTAAGGATTATGGGATCTATGTG 58.179 37.037 1.85 0.00 31.24 3.21
3594 4289 8.972662 TCTTAAGGATTATGGGATCTATGTGA 57.027 34.615 1.85 0.00 0.00 3.58
3595 4290 9.392506 TCTTAAGGATTATGGGATCTATGTGAA 57.607 33.333 1.85 0.00 0.00 3.18
3597 4292 9.793259 TTAAGGATTATGGGATCTATGTGAAAC 57.207 33.333 0.00 0.00 37.35 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.627395 CATCGTAGTCTTATAACTCCCAAATAG 57.373 37.037 0.00 0.00 0.00 1.73
27 28 0.927029 GCCCTCCCTAACCCTTTCAT 59.073 55.000 0.00 0.00 0.00 2.57
129 147 4.848357 CCATTTTGGTGTGTCTCTATCCT 58.152 43.478 0.00 0.00 31.35 3.24
143 161 4.449068 CAGCGCTACTAGATACCATTTTGG 59.551 45.833 10.99 0.00 45.02 3.28
212 236 1.133976 GGCAGTGCAAGATAGGGATGT 60.134 52.381 18.61 0.00 0.00 3.06
309 333 6.689669 GGCAAATAATCAATTTCAATGCAAGC 59.310 34.615 0.00 0.00 35.54 4.01
313 337 6.962678 GTGTGGCAAATAATCAATTTCAATGC 59.037 34.615 0.00 0.00 35.54 3.56
389 424 9.338622 CGGAAGGAGTATTTACATTTTATCCTT 57.661 33.333 2.93 2.93 46.01 3.36
406 444 7.927092 GCTCTTATATTTCTTTACGGAAGGAGT 59.073 37.037 0.00 0.00 35.98 3.85
407 445 7.926555 TGCTCTTATATTTCTTTACGGAAGGAG 59.073 37.037 0.00 0.00 35.98 3.69
408 446 7.788026 TGCTCTTATATTTCTTTACGGAAGGA 58.212 34.615 0.00 0.00 35.98 3.36
409 447 8.608844 ATGCTCTTATATTTCTTTACGGAAGG 57.391 34.615 1.66 0.00 35.98 3.46
465 503 9.998106 GCTCCTATGTACTCCAAGAAATATAAA 57.002 33.333 0.00 0.00 0.00 1.40
466 504 9.381038 AGCTCCTATGTACTCCAAGAAATATAA 57.619 33.333 0.00 0.00 0.00 0.98
467 505 8.807118 CAGCTCCTATGTACTCCAAGAAATATA 58.193 37.037 0.00 0.00 0.00 0.86
468 506 7.675062 CAGCTCCTATGTACTCCAAGAAATAT 58.325 38.462 0.00 0.00 0.00 1.28
469 507 6.463049 GCAGCTCCTATGTACTCCAAGAAATA 60.463 42.308 0.00 0.00 0.00 1.40
470 508 5.686124 GCAGCTCCTATGTACTCCAAGAAAT 60.686 44.000 0.00 0.00 0.00 2.17
471 509 4.383118 GCAGCTCCTATGTACTCCAAGAAA 60.383 45.833 0.00 0.00 0.00 2.52
472 510 3.133003 GCAGCTCCTATGTACTCCAAGAA 59.867 47.826 0.00 0.00 0.00 2.52
473 511 2.695666 GCAGCTCCTATGTACTCCAAGA 59.304 50.000 0.00 0.00 0.00 3.02
474 512 2.432146 TGCAGCTCCTATGTACTCCAAG 59.568 50.000 0.00 0.00 0.00 3.61
475 513 2.168521 GTGCAGCTCCTATGTACTCCAA 59.831 50.000 0.00 0.00 31.44 3.53
476 514 1.757118 GTGCAGCTCCTATGTACTCCA 59.243 52.381 0.00 0.00 31.44 3.86
477 515 1.757118 TGTGCAGCTCCTATGTACTCC 59.243 52.381 0.00 0.00 34.74 3.85
478 516 3.742433 ATGTGCAGCTCCTATGTACTC 57.258 47.619 0.00 0.00 34.74 2.59
479 517 4.494091 AAATGTGCAGCTCCTATGTACT 57.506 40.909 0.00 0.00 34.74 2.73
480 518 5.334414 GCATAAATGTGCAGCTCCTATGTAC 60.334 44.000 0.00 0.00 44.43 2.90
559 602 1.585006 GGGAGAAGCGACAGAACGA 59.415 57.895 0.00 0.00 35.09 3.85
611 654 2.050985 GCAACAGCACCAAGACGC 60.051 61.111 0.00 0.00 0.00 5.19
799 845 2.377628 GACAGTTGGTGGTCGCTCCA 62.378 60.000 0.00 0.00 45.01 3.86
861 1039 5.310451 GTGACCTCACTTGTAAATAACCCA 58.690 41.667 0.00 0.00 43.25 4.51
970 1148 3.834489 ATCTGATCTGGTACAAGGCAG 57.166 47.619 12.33 12.33 38.70 4.85
1016 1195 1.153549 GAACGGGGCAGCTACAGAG 60.154 63.158 0.00 0.00 0.00 3.35
1054 1233 4.838152 CTCCATCGGCGGTGGGTG 62.838 72.222 36.44 25.40 37.34 4.61
1104 1283 1.227147 CATCAATACGTCCCGCGGT 60.227 57.895 26.12 7.98 46.52 5.68
1182 1361 2.482142 GCTGGTATAGACAGAGCACCAC 60.482 54.545 8.22 0.00 38.20 4.16
1186 1365 2.461300 AGGCTGGTATAGACAGAGCA 57.539 50.000 11.52 0.00 36.64 4.26
1214 1393 0.517316 CCGTTTGTACAGCTCAAGCC 59.483 55.000 0.00 0.00 43.38 4.35
1348 1527 1.134007 CCCAATCAGATACCTGCTGCA 60.134 52.381 0.88 0.88 40.20 4.41
1374 1553 1.225426 GGTGATCAGCCAGCCATGA 59.775 57.895 14.08 0.00 0.00 3.07
1403 1582 0.456628 GAGAAGGTGTAGCTCGGACC 59.543 60.000 0.00 0.00 0.00 4.46
1639 1818 2.096980 TGTAGCTTCGTGTAGACGGATG 59.903 50.000 12.92 4.45 46.11 3.51
1651 1830 3.325870 TGAGAACCACAATGTAGCTTCG 58.674 45.455 0.00 0.00 0.00 3.79
2133 2330 7.940688 ACATATGCCTCATCATCAGTGAAATAA 59.059 33.333 1.58 0.00 38.01 1.40
2419 2622 1.676006 CCAGATAAACGGAACATGCCC 59.324 52.381 0.00 0.00 0.00 5.36
2430 2634 4.859245 GCAACTTTAGCAAGCCAGATAAAC 59.141 41.667 0.00 0.00 32.57 2.01
2433 2637 3.955471 AGCAACTTTAGCAAGCCAGATA 58.045 40.909 0.00 0.00 32.57 1.98
2687 2891 2.656422 CGCTCCATTGTTTTGCGTTAAG 59.344 45.455 0.00 0.00 41.45 1.85
2800 3004 2.614481 GGGCTATGTCCTTTGTGTTCGA 60.614 50.000 0.00 0.00 0.00 3.71
2810 3014 1.828660 CTCCGACGGGCTATGTCCT 60.829 63.158 15.25 0.00 32.68 3.85
2813 3017 2.838225 CCCTCCGACGGGCTATGT 60.838 66.667 15.25 0.00 37.41 2.29
2832 3036 3.744426 ACGGATGTACTTAAGTGCAACAC 59.256 43.478 26.83 19.97 43.49 3.32
2984 3190 3.121544 CCGACTTACCTATTTTCCGCTC 58.878 50.000 0.00 0.00 0.00 5.03
3000 3206 4.361971 TGGGACCTCGAGCCGACT 62.362 66.667 6.99 0.00 0.00 4.18
3143 3351 0.678395 TAACCTAACCGTCGTTGCCA 59.322 50.000 0.00 0.00 33.17 4.92
3227 3441 5.335348 CCAACACCCTATTTTTGTTAGACCG 60.335 44.000 0.00 0.00 32.19 4.79
3228 3442 5.537295 ACCAACACCCTATTTTTGTTAGACC 59.463 40.000 0.00 0.00 32.19 3.85
3345 3560 2.366533 GTGGTTAGGGCCTAGCTTTTC 58.633 52.381 24.21 10.27 0.00 2.29
3521 4216 6.035975 GGACAACAAGCAAAAATACCATATGC 59.964 38.462 0.00 0.00 37.28 3.14
3534 4229 0.821711 CGGGGAAGGACAACAAGCAA 60.822 55.000 0.00 0.00 0.00 3.91
3560 4255 6.944234 CCATAATCCTTAAGAGTTTGGGTC 57.056 41.667 3.36 0.00 37.83 4.46
3563 4258 7.521669 AGATCCCATAATCCTTAAGAGTTTGG 58.478 38.462 3.36 4.50 40.22 3.28
3566 4261 9.398921 ACATAGATCCCATAATCCTTAAGAGTT 57.601 33.333 3.36 0.91 0.00 3.01
3567 4262 8.820831 CACATAGATCCCATAATCCTTAAGAGT 58.179 37.037 3.36 0.00 0.00 3.24
3568 4263 9.040259 TCACATAGATCCCATAATCCTTAAGAG 57.960 37.037 3.36 0.00 0.00 2.85
3569 4264 8.972662 TCACATAGATCCCATAATCCTTAAGA 57.027 34.615 3.36 0.00 0.00 2.10
3571 4266 9.793259 GTTTCACATAGATCCCATAATCCTTAA 57.207 33.333 0.00 0.00 0.00 1.85
3572 4267 8.944138 TGTTTCACATAGATCCCATAATCCTTA 58.056 33.333 0.00 0.00 0.00 2.69
3573 4268 7.815383 TGTTTCACATAGATCCCATAATCCTT 58.185 34.615 0.00 0.00 0.00 3.36
3574 4269 7.392766 TGTTTCACATAGATCCCATAATCCT 57.607 36.000 0.00 0.00 0.00 3.24
3575 4270 7.667219 ACATGTTTCACATAGATCCCATAATCC 59.333 37.037 0.00 0.00 36.53 3.01
3576 4271 8.627208 ACATGTTTCACATAGATCCCATAATC 57.373 34.615 0.00 0.00 36.53 1.75
3577 4272 9.071276 GAACATGTTTCACATAGATCCCATAAT 57.929 33.333 13.36 0.00 36.53 1.28
3578 4273 7.502226 GGAACATGTTTCACATAGATCCCATAA 59.498 37.037 13.36 0.00 36.53 1.90
3579 4274 6.998074 GGAACATGTTTCACATAGATCCCATA 59.002 38.462 13.36 0.00 36.53 2.74
3580 4275 5.829924 GGAACATGTTTCACATAGATCCCAT 59.170 40.000 13.36 0.00 36.53 4.00
3581 4276 5.192927 GGAACATGTTTCACATAGATCCCA 58.807 41.667 13.36 0.00 36.53 4.37
3582 4277 4.273480 CGGAACATGTTTCACATAGATCCC 59.727 45.833 17.08 6.13 36.53 3.85
3583 4278 4.876107 ACGGAACATGTTTCACATAGATCC 59.124 41.667 17.08 6.73 36.53 3.36
3584 4279 6.250819 CAACGGAACATGTTTCACATAGATC 58.749 40.000 17.08 0.00 36.53 2.75
3585 4280 6.182039 CAACGGAACATGTTTCACATAGAT 57.818 37.500 17.08 0.00 36.53 1.98
3586 4281 5.605564 CAACGGAACATGTTTCACATAGA 57.394 39.130 17.08 0.00 36.53 1.98


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

AutoCloner maintained by Alex Coulton.