Multiple sequence alignment - TraesCS6B01G366400

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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 TraesCS6B01G366400 chr6B 100.000 4500 0 0 946 5445 639151538 639147039 0.000000e+00 8311
1 TraesCS6B01G366400 chr6B 100.000 686 0 0 1 686 639152483 639151798 0.000000e+00 1267
2 TraesCS6B01G366400 chr6B 87.795 508 47 6 4449 4950 639105520 639105022 1.020000e-161 580
3 TraesCS6B01G366400 chr6B 87.164 483 48 7 4453 4930 638958261 638957788 2.230000e-148 536
4 TraesCS6B01G366400 chr6B 83.333 510 53 20 4953 5445 638956780 638956286 5.010000e-120 442
5 TraesCS6B01G366400 chr6B 88.936 235 25 1 2243 2477 241057497 241057730 6.900000e-74 289
6 TraesCS6B01G366400 chr6D 95.477 3604 119 15 946 4516 423791360 423787768 0.000000e+00 5712
7 TraesCS6B01G366400 chr6D 87.482 711 54 17 6 686 423792131 423791426 0.000000e+00 787
8 TraesCS6B01G366400 chr6D 88.538 506 40 9 4453 4950 423652637 423653132 1.010000e-166 597
9 TraesCS6B01G366400 chr6D 85.941 505 50 16 4952 5445 423654134 423654628 2.250000e-143 520
10 TraesCS6B01G366400 chr6A 95.502 3557 122 10 946 4471 568497639 568494090 0.000000e+00 5648
11 TraesCS6B01G366400 chr6A 89.625 694 42 14 1 686 568498377 568497706 0.000000e+00 856
12 TraesCS6B01G366400 chr6A 88.889 513 36 13 4449 4950 553469274 553468772 3.610000e-171 612
13 TraesCS6B01G366400 chr6A 88.521 514 36 15 4449 4950 553428282 553427780 7.800000e-168 601
14 TraesCS6B01G366400 chr6A 88.178 516 37 15 4449 4950 568273388 568272883 1.310000e-165 593
15 TraesCS6B01G366400 chr6A 88.132 514 39 13 4449 4950 553455290 553454787 4.700000e-165 592
16 TraesCS6B01G366400 chr6A 88.109 513 40 14 4449 4950 553548200 553547698 1.690000e-164 590
17 TraesCS6B01G366400 chr6A 86.990 515 43 14 4449 4950 553390054 553389551 4.760000e-155 558
18 TraesCS6B01G366400 chr6A 82.365 499 61 14 4952 5445 553547213 553546737 5.080000e-110 409
19 TraesCS6B01G366400 chr6A 81.152 382 48 12 5023 5395 568140005 568140371 8.930000e-73 285
20 TraesCS6B01G366400 chr6A 81.437 334 53 8 4952 5280 279827373 279827702 1.160000e-66 265
21 TraesCS6B01G366400 chr7B 83.420 386 51 10 5069 5445 593129003 593129384 4.040000e-91 346
22 TraesCS6B01G366400 chr4A 83.904 292 41 5 4991 5280 513641161 513640874 1.930000e-69 274
23 TraesCS6B01G366400 chr3D 82.132 319 48 8 4965 5280 328714387 328714699 1.160000e-66 265
24 TraesCS6B01G366400 chr3D 82.019 317 47 9 4961 5273 334767042 334767352 1.500000e-65 261
25 TraesCS6B01G366400 chr4D 81.366 322 54 6 4961 5280 287798155 287797838 1.950000e-64 257
26 TraesCS6B01G366400 chr2A 91.892 74 5 1 1017 1089 731539581 731539654 9.650000e-18 102


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 TraesCS6B01G366400 chr6B 639147039 639152483 5444 True 4789.0 8311 100.0000 1 5445 2 chr6B.!!$R3 5444
1 TraesCS6B01G366400 chr6B 638956286 638958261 1975 True 489.0 536 85.2485 4453 5445 2 chr6B.!!$R2 992
2 TraesCS6B01G366400 chr6D 423787768 423792131 4363 True 3249.5 5712 91.4795 6 4516 2 chr6D.!!$R1 4510
3 TraesCS6B01G366400 chr6D 423652637 423654628 1991 False 558.5 597 87.2395 4453 5445 2 chr6D.!!$F1 992
4 TraesCS6B01G366400 chr6A 568494090 568498377 4287 True 3252.0 5648 92.5635 1 4471 2 chr6A.!!$R7 4470
5 TraesCS6B01G366400 chr6A 553468772 553469274 502 True 612.0 612 88.8890 4449 4950 1 chr6A.!!$R4 501
6 TraesCS6B01G366400 chr6A 553427780 553428282 502 True 601.0 601 88.5210 4449 4950 1 chr6A.!!$R2 501
7 TraesCS6B01G366400 chr6A 568272883 568273388 505 True 593.0 593 88.1780 4449 4950 1 chr6A.!!$R5 501
8 TraesCS6B01G366400 chr6A 553454787 553455290 503 True 592.0 592 88.1320 4449 4950 1 chr6A.!!$R3 501
9 TraesCS6B01G366400 chr6A 553389551 553390054 503 True 558.0 558 86.9900 4449 4950 1 chr6A.!!$R1 501
10 TraesCS6B01G366400 chr6A 553546737 553548200 1463 True 499.5 590 85.2370 4449 5445 2 chr6A.!!$R6 996

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
684 720 2.603652 AACCGCCTCTTCCCCCTTC 61.604 63.158 0.0 0.0 0.00 3.46 F
1477 1524 0.252197 ATTGGTCCCTGCGAGTTACC 59.748 55.000 0.0 0.0 0.00 2.85 F
1676 1725 0.546122 TTGTTCCACTGACCTGCTGT 59.454 50.000 0.0 0.0 0.00 4.40 F
3426 3494 2.053627 CTGCAAGAAATGGTTGAACGC 58.946 47.619 0.0 0.0 34.07 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1840 1889 1.001293 CAGCGCCATAGCCAGATCTAA 59.999 52.381 2.29 0.0 38.01 2.10 R
2353 2421 1.778591 GCACATTTCGGTTCACAAACG 59.221 47.619 0.00 0.0 36.16 3.60 R
3600 3668 0.177604 CTGCAGGAGTGTGATCCCTC 59.822 60.000 5.57 0.0 40.53 4.30 R
4534 4603 0.035915 TCATGCCGGGATTCGAACAA 60.036 50.000 5.36 0.0 42.43 2.83 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
216 241 8.919145 TGTCAAATGGGTAGTTAAGTTTTTGAT 58.081 29.630 0.00 0.00 35.19 2.57
258 285 6.843676 GCATAAAATATGATGCACGCTTAG 57.156 37.500 10.95 0.00 46.29 2.18
271 298 4.693095 TGCACGCTTAGATTTATGTTCACA 59.307 37.500 0.00 0.00 0.00 3.58
293 320 9.050601 TCACACACAAGAAAAAGAAACAAAAAT 57.949 25.926 0.00 0.00 0.00 1.82
325 353 8.953990 CAGGAAGTGAAAAGTAAATAACAAACG 58.046 33.333 0.00 0.00 0.00 3.60
437 471 2.879103 AGAAGAAGAAATGGGCCGAA 57.121 45.000 0.00 0.00 0.00 4.30
502 538 3.185188 CCAGTGATTTGTTCTCACAGTCG 59.815 47.826 6.26 0.00 44.37 4.18
566 602 2.879462 CGCTCTCGTTACGTGGGC 60.879 66.667 19.84 19.84 42.34 5.36
682 718 3.330720 CAACCGCCTCTTCCCCCT 61.331 66.667 0.00 0.00 0.00 4.79
684 720 2.603652 AACCGCCTCTTCCCCCTTC 61.604 63.158 0.00 0.00 0.00 3.46
685 721 4.162690 CCGCCTCTTCCCCCTTCG 62.163 72.222 0.00 0.00 0.00 3.79
968 1004 3.646715 CAACCCCCTTCCTCCGCA 61.647 66.667 0.00 0.00 0.00 5.69
1090 1128 2.358737 CACGAACCTCAGGCCCAC 60.359 66.667 0.00 0.00 0.00 4.61
1372 1410 2.817470 CTTGCGATTGGGGCGGTTTG 62.817 60.000 0.00 0.00 0.00 2.93
1475 1522 3.101437 TCTAATTGGTCCCTGCGAGTTA 58.899 45.455 0.00 0.00 0.00 2.24
1477 1524 0.252197 ATTGGTCCCTGCGAGTTACC 59.748 55.000 0.00 0.00 0.00 2.85
1481 1528 1.303888 TCCCTGCGAGTTACCGTCT 60.304 57.895 0.00 0.00 0.00 4.18
1519 1566 5.243283 GGGGTCTCGCTTTAGATTGATACTA 59.757 44.000 0.00 0.00 0.00 1.82
1520 1567 6.239232 GGGGTCTCGCTTTAGATTGATACTAA 60.239 42.308 0.00 0.00 0.00 2.24
1521 1568 7.379750 GGGTCTCGCTTTAGATTGATACTAAT 58.620 38.462 0.00 0.00 31.34 1.73
1576 1625 6.461640 TGATCCTGATACTCATGTTATGCTG 58.538 40.000 0.00 0.00 0.00 4.41
1644 1693 3.933332 GGATAACAGTACTCAACCAGTGC 59.067 47.826 0.00 0.00 37.99 4.40
1647 1696 0.670546 CAGTACTCAACCAGTGCGGG 60.671 60.000 0.00 0.00 42.38 6.13
1676 1725 0.546122 TTGTTCCACTGACCTGCTGT 59.454 50.000 0.00 0.00 0.00 4.40
1712 1761 7.614192 TGGATTCTGTAATTCCTTTTTAGGACC 59.386 37.037 0.00 0.00 37.76 4.46
1721 1770 8.809468 AATTCCTTTTTAGGACCAGAAGATAC 57.191 34.615 0.00 0.00 37.76 2.24
1726 1775 6.697641 TTTTAGGACCAGAAGATACCTGTT 57.302 37.500 0.00 0.00 32.90 3.16
1729 1778 7.801893 TTAGGACCAGAAGATACCTGTTTAA 57.198 36.000 0.00 0.00 32.90 1.52
1735 1784 7.287810 ACCAGAAGATACCTGTTTAACAACTT 58.712 34.615 0.00 0.99 33.58 2.66
1737 1786 7.308589 CCAGAAGATACCTGTTTAACAACTTGG 60.309 40.741 0.00 0.00 35.02 3.61
1738 1787 6.715264 AGAAGATACCTGTTTAACAACTTGGG 59.285 38.462 0.00 0.00 33.93 4.12
1765 1814 6.910433 GTGTAATTAAGTTGTGTTGTGAGGTG 59.090 38.462 0.00 0.00 0.00 4.00
1796 1845 8.308207 ACAGTTTGGTGTTTGTGTAAAAGTTAT 58.692 29.630 0.00 0.00 0.00 1.89
1798 1847 9.361315 AGTTTGGTGTTTGTGTAAAAGTTATTC 57.639 29.630 0.00 0.00 0.00 1.75
1840 1889 5.237344 GCTACTCATAATGGTCGCAAAATCT 59.763 40.000 0.00 0.00 0.00 2.40
1886 1935 4.176271 GTTTCTGGCTGGTTAAATGATGC 58.824 43.478 0.00 0.00 0.00 3.91
2010 2059 5.411781 AGAGAACTGACATTATGGTCGTTC 58.588 41.667 16.01 16.01 43.44 3.95
2200 2249 3.592898 ACGTCATGCTCACAGATGTAA 57.407 42.857 0.00 0.00 30.24 2.41
2297 2365 7.896383 TTACCTATTTTAGCTGCCAATTGAT 57.104 32.000 7.12 0.00 0.00 2.57
2318 2386 9.991388 ATTGATTTTGTTTCATTGTGTCTTTTG 57.009 25.926 0.00 0.00 0.00 2.44
2328 2396 5.300034 TCATTGTGTCTTTTGTGATCTGCTT 59.700 36.000 0.00 0.00 0.00 3.91
2335 2403 6.486320 TGTCTTTTGTGATCTGCTTGTCAATA 59.514 34.615 0.00 0.00 0.00 1.90
2353 2421 5.517770 GTCAATAAAATGCTGCTGGAACATC 59.482 40.000 0.00 0.00 38.20 3.06
2364 2432 2.604614 GCTGGAACATCGTTTGTGAACC 60.605 50.000 0.00 0.00 38.99 3.62
2381 2449 4.013050 TGAACCGAAATGTGCCATGATTA 58.987 39.130 0.00 0.00 0.00 1.75
2387 2455 5.516339 CCGAAATGTGCCATGATTAAAGTTC 59.484 40.000 0.00 0.00 0.00 3.01
2444 2512 6.638610 TGCAAATTTGTCCTTTTCTCTTGAA 58.361 32.000 19.03 0.00 0.00 2.69
2445 2513 7.274447 TGCAAATTTGTCCTTTTCTCTTGAAT 58.726 30.769 19.03 0.00 31.56 2.57
2446 2514 7.769970 TGCAAATTTGTCCTTTTCTCTTGAATT 59.230 29.630 19.03 0.00 31.56 2.17
2493 2561 4.577693 TGAGCTGATTGGTTGAATATCTGC 59.422 41.667 0.00 0.00 41.04 4.26
2706 2774 2.429930 CAACCTTCGGTGGCAGGA 59.570 61.111 0.00 0.00 35.34 3.86
3128 3196 2.766263 TGAACAGCGAGTGGGAGATTAT 59.234 45.455 0.00 0.00 0.00 1.28
3207 3275 5.016831 TCTCAGCAGTATAACTTCAGACCA 58.983 41.667 0.00 0.00 0.00 4.02
3276 3344 3.169099 AGGTGTTGCTATCTCTGTCAGT 58.831 45.455 0.00 0.00 0.00 3.41
3285 3353 2.381752 TCTCTGTCAGTCCTTCCACA 57.618 50.000 0.00 0.00 0.00 4.17
3289 3357 2.503765 TCTGTCAGTCCTTCCACAACAA 59.496 45.455 0.00 0.00 0.00 2.83
3318 3386 4.394729 AGAAAAATGGCACGGAAACTCTA 58.605 39.130 0.00 0.00 0.00 2.43
3426 3494 2.053627 CTGCAAGAAATGGTTGAACGC 58.946 47.619 0.00 0.00 34.07 4.84
3600 3668 4.837896 TGCTTCTACTCAGTCCATATCG 57.162 45.455 0.00 0.00 0.00 2.92
3663 3731 5.689383 TGACAGTTGCTAAAATCAAGGAC 57.311 39.130 0.00 0.00 0.00 3.85
3963 4031 4.940593 GGCTGCTCGGCGCTAGAG 62.941 72.222 22.71 22.71 40.11 2.43
3969 4037 3.515286 CTCGGCGCTAGAGCTCGTC 62.515 68.421 18.28 0.00 39.32 4.20
3984 4052 5.078411 AGCTCGTCACATACAAAGAGAAT 57.922 39.130 0.00 0.00 0.00 2.40
4035 4103 5.689383 TCAGCTGTTTGTTCAAGGATTAC 57.311 39.130 14.67 0.00 0.00 1.89
4190 4258 3.606384 GCATCATATTGAGCAGCGAGTTG 60.606 47.826 0.00 0.00 0.00 3.16
4311 4379 6.784176 TCATACCGATGTTTTTGATGTGATG 58.216 36.000 0.00 0.00 34.41 3.07
4334 4402 4.638421 GGTAACAGTAAGCATGCCAATGTA 59.362 41.667 19.42 8.61 36.08 2.29
4410 4478 9.138062 CAGATGTAGCTACTGAATCATATTGAC 57.862 37.037 23.84 0.00 34.07 3.18
4417 4485 6.143118 GCTACTGAATCATATTGACGTCTGTC 59.857 42.308 17.92 2.07 45.71 3.51
4484 4553 0.603569 ACTGAGAGACGACGGCAAAT 59.396 50.000 2.19 0.00 0.00 2.32
4495 4564 1.516169 CGGCAAATAACGGCTTGGC 60.516 57.895 0.61 0.61 42.86 4.52
4528 4597 2.805671 TCTATGTTCAACACCGTTGCAG 59.194 45.455 0.00 0.00 0.00 4.41
4529 4598 1.388547 ATGTTCAACACCGTTGCAGT 58.611 45.000 0.00 0.00 0.00 4.40
4530 4599 1.169577 TGTTCAACACCGTTGCAGTT 58.830 45.000 1.94 0.00 0.00 3.16
4531 4600 1.131504 TGTTCAACACCGTTGCAGTTC 59.868 47.619 1.94 0.00 0.00 3.01
4532 4601 0.375454 TTCAACACCGTTGCAGTTCG 59.625 50.000 1.94 0.00 0.00 3.95
4533 4602 0.460459 TCAACACCGTTGCAGTTCGA 60.460 50.000 9.03 0.00 0.00 3.71
4534 4603 0.586319 CAACACCGTTGCAGTTCGAT 59.414 50.000 9.03 0.00 0.00 3.59
4535 4604 1.002900 CAACACCGTTGCAGTTCGATT 60.003 47.619 9.03 0.26 0.00 3.34
4576 4645 4.451150 TGCACTTCCCGGCGCTAG 62.451 66.667 7.64 1.17 0.00 3.42
4654 4723 0.108585 AGTCACATCCAAGGCGTGTT 59.891 50.000 0.00 0.00 32.42 3.32
4683 4752 6.895782 AGGACCGGATTGTAATCTTGATTAA 58.104 36.000 9.46 0.00 35.73 1.40
4708 4777 8.601845 ATTTGTTTTAGGTCCATTTTTACAGC 57.398 30.769 0.00 0.00 0.00 4.40
4750 4821 5.467705 AGAAGCATTGCAGTTCATTTTCTC 58.532 37.500 11.91 0.00 0.00 2.87
4754 4825 4.082354 GCATTGCAGTTCATTTTCTCCTCT 60.082 41.667 3.15 0.00 0.00 3.69
4755 4826 5.124457 GCATTGCAGTTCATTTTCTCCTCTA 59.876 40.000 3.15 0.00 0.00 2.43
4757 4828 5.227569 TGCAGTTCATTTTCTCCTCTACA 57.772 39.130 0.00 0.00 0.00 2.74
4758 4829 5.809001 TGCAGTTCATTTTCTCCTCTACAT 58.191 37.500 0.00 0.00 0.00 2.29
4816 4895 9.663904 CCCATAATACGTAATCATGAAAAACAG 57.336 33.333 0.00 0.00 0.00 3.16
4848 4927 4.152402 CACTAAGTTTGACCATGAAGTCCG 59.848 45.833 0.00 0.00 35.83 4.79
4860 4939 5.584649 ACCATGAAGTCCGTATATGTTTGTG 59.415 40.000 0.00 0.00 0.00 3.33
4865 4944 8.604640 TGAAGTCCGTATATGTTTGTGTTTTA 57.395 30.769 0.00 0.00 0.00 1.52
4866 4945 8.714179 TGAAGTCCGTATATGTTTGTGTTTTAG 58.286 33.333 0.00 0.00 0.00 1.85
4908 4995 6.829811 TGATGCTGTTCATTTAGATTCCATGA 59.170 34.615 0.00 0.00 35.05 3.07
4938 5025 9.262472 CTAATAGAAAACACAATTGTAGTTCGC 57.738 33.333 11.53 12.23 36.02 4.70
4950 5037 1.602377 GTAGTTCGCTTGCCACAACTT 59.398 47.619 5.10 0.00 31.52 2.66
5023 6176 6.930667 AACTGCTCTTAAACCGTAAAGAAA 57.069 33.333 0.00 0.00 31.61 2.52
5024 6177 6.930667 ACTGCTCTTAAACCGTAAAGAAAA 57.069 33.333 0.00 0.00 31.61 2.29
5025 6178 7.506328 ACTGCTCTTAAACCGTAAAGAAAAT 57.494 32.000 0.00 0.00 31.61 1.82
5026 6179 7.937649 ACTGCTCTTAAACCGTAAAGAAAATT 58.062 30.769 0.00 0.00 31.61 1.82
5062 6215 1.196808 TGAAAAAGTTGCGCCTCGATC 59.803 47.619 4.18 0.00 0.00 3.69
5078 6231 5.479306 CCTCGATCATATATTTCCAACGGT 58.521 41.667 0.00 0.00 0.00 4.83
5079 6232 5.932303 CCTCGATCATATATTTCCAACGGTT 59.068 40.000 0.00 0.00 0.00 4.44
5085 6238 7.737972 TCATATATTTCCAACGGTTGTATGG 57.262 36.000 18.73 5.22 35.49 2.74
5090 6243 2.933573 TCCAACGGTTGTATGGTTTGT 58.066 42.857 18.73 0.00 35.66 2.83
5093 6246 5.071370 TCCAACGGTTGTATGGTTTGTATT 58.929 37.500 18.73 0.00 35.66 1.89
5142 6295 3.814005 AGAAAATACGCTCGGTACCAT 57.186 42.857 13.54 0.00 32.95 3.55
5143 6296 3.454375 AGAAAATACGCTCGGTACCATG 58.546 45.455 13.54 4.68 32.95 3.66
5188 6341 4.664188 GAAACTGCTTTTAAACCGTGACA 58.336 39.130 0.00 0.00 0.00 3.58
5245 6398 5.530915 CGCCTAATCCATAACTTTCCAATGA 59.469 40.000 0.00 0.00 0.00 2.57
5266 6419 2.814280 ATATTACACGCCTCCTTCCG 57.186 50.000 0.00 0.00 0.00 4.30
5272 6425 2.260434 CGCCTCCTTCCGACGAAA 59.740 61.111 0.00 0.00 0.00 3.46
5273 6426 1.153628 CGCCTCCTTCCGACGAAAT 60.154 57.895 0.00 0.00 0.00 2.17
5280 6433 4.142966 CCTCCTTCCGACGAAATGTTTAAC 60.143 45.833 0.00 0.00 0.00 2.01
5309 6469 0.887933 AGTACCAAAAAGGGCATGCG 59.112 50.000 12.44 0.00 43.89 4.73
5389 6549 5.397142 TCGGAGGAGGTTTAGAAGTTTAC 57.603 43.478 0.00 0.00 0.00 2.01
5395 6555 6.228995 AGGAGGTTTAGAAGTTTACGGAAAG 58.771 40.000 0.00 0.00 0.00 2.62
5397 6557 6.368243 GGAGGTTTAGAAGTTTACGGAAAGAG 59.632 42.308 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 88 5.689068 CCAAGCTAGCAGTTTCTTCTTTTTG 59.311 40.000 18.83 7.45 0.00 2.44
242 267 7.912056 ACATAAATCTAAGCGTGCATCATAT 57.088 32.000 0.00 0.00 0.00 1.78
243 268 7.440856 TGAACATAAATCTAAGCGTGCATCATA 59.559 33.333 0.00 0.00 0.00 2.15
245 270 5.584251 TGAACATAAATCTAAGCGTGCATCA 59.416 36.000 0.00 0.00 0.00 3.07
246 271 5.904080 GTGAACATAAATCTAAGCGTGCATC 59.096 40.000 0.00 0.00 0.00 3.91
247 272 5.353956 TGTGAACATAAATCTAAGCGTGCAT 59.646 36.000 0.00 0.00 0.00 3.96
249 274 5.022021 GTGTGAACATAAATCTAAGCGTGC 58.978 41.667 0.00 0.00 0.00 5.34
250 275 6.015504 GTGTGTGAACATAAATCTAAGCGTG 58.984 40.000 0.00 0.00 0.00 5.34
251 276 5.699001 TGTGTGTGAACATAAATCTAAGCGT 59.301 36.000 0.00 0.00 0.00 5.07
258 285 9.515020 TCTTTTTCTTGTGTGTGAACATAAATC 57.485 29.630 0.00 0.00 0.00 2.17
404 437 6.515272 TTCTTCTTCTTTTTCTGCTGTTGT 57.485 33.333 0.00 0.00 0.00 3.32
407 440 6.462067 CCCATTTCTTCTTCTTTTTCTGCTGT 60.462 38.462 0.00 0.00 0.00 4.40
408 441 5.924825 CCCATTTCTTCTTCTTTTTCTGCTG 59.075 40.000 0.00 0.00 0.00 4.41
437 471 3.678056 TCTACACTCTTTGCGAATGGT 57.322 42.857 0.00 0.00 0.00 3.55
448 482 5.844601 AGGGTTTCTCCTATTCTACACTCT 58.155 41.667 0.00 0.00 34.92 3.24
502 538 2.586792 CTACTGGTGGAGCCCTGC 59.413 66.667 0.00 0.00 36.04 4.85
580 616 1.248486 GGTCCGGATGAGATGATCGA 58.752 55.000 7.81 0.00 0.00 3.59
615 651 3.186119 GGAAGACTGAGCTTCGATGAAG 58.814 50.000 1.89 2.22 44.04 3.02
949 985 2.609610 CGGAGGAAGGGGGTTGGA 60.610 66.667 0.00 0.00 0.00 3.53
1090 1128 3.041940 GGTTGACGACCTGCACGG 61.042 66.667 4.42 0.65 45.55 4.94
1399 1437 2.104859 CACACATGCCCAGCGAGAG 61.105 63.158 0.00 0.00 0.00 3.20
1475 1522 3.347216 CCCAATCAATTTGAGAGACGGT 58.653 45.455 5.21 0.00 37.53 4.83
1477 1524 2.684881 CCCCCAATCAATTTGAGAGACG 59.315 50.000 5.21 0.00 37.53 4.18
1481 1528 3.622206 CGAGACCCCCAATCAATTTGAGA 60.622 47.826 5.21 0.00 37.53 3.27
1644 1693 1.609555 TGGAACAAAATTTCGACCCCG 59.390 47.619 0.00 0.00 31.92 5.73
1647 1696 4.287720 GTCAGTGGAACAAAATTTCGACC 58.712 43.478 0.00 0.00 44.16 4.79
1676 1725 9.258629 AGGAATTACAGAATCCAATTCAATCAA 57.741 29.630 11.88 0.00 41.71 2.57
1712 1761 7.308589 CCCAAGTTGTTAAACAGGTATCTTCTG 60.309 40.741 1.45 0.00 38.88 3.02
1721 1770 3.445805 ACACACCCAAGTTGTTAAACAGG 59.554 43.478 1.45 0.00 38.88 4.00
1726 1775 8.522542 ACTTAATTACACACCCAAGTTGTTAA 57.477 30.769 1.45 0.00 0.00 2.01
1729 1778 6.801575 CAACTTAATTACACACCCAAGTTGT 58.198 36.000 14.08 0.00 43.74 3.32
1735 1784 5.652891 ACAACACAACTTAATTACACACCCA 59.347 36.000 0.00 0.00 0.00 4.51
1737 1786 6.787225 TCACAACACAACTTAATTACACACC 58.213 36.000 0.00 0.00 0.00 4.16
1738 1787 6.910433 CCTCACAACACAACTTAATTACACAC 59.090 38.462 0.00 0.00 0.00 3.82
1765 1814 5.243426 ACACAAACACCAAACTGTATCAC 57.757 39.130 0.00 0.00 0.00 3.06
1796 1845 9.507329 GAGTAGCAGAAATATAATCCAATGGAA 57.493 33.333 5.89 0.00 34.34 3.53
1798 1847 8.853077 TGAGTAGCAGAAATATAATCCAATGG 57.147 34.615 0.00 0.00 0.00 3.16
1840 1889 1.001293 CAGCGCCATAGCCAGATCTAA 59.999 52.381 2.29 0.00 38.01 2.10
1886 1935 5.525378 CCTCTCCCGTTCATTCAGAAAATAG 59.475 44.000 0.00 0.00 38.13 1.73
2010 2059 8.562892 ACACAACAAACTTCTTCTAATCATCAG 58.437 33.333 0.00 0.00 0.00 2.90
2200 2249 8.641498 AAATGATTCAACCAGATAAAGACACT 57.359 30.769 0.00 0.00 0.00 3.55
2268 2336 7.896383 TTGGCAGCTAAAATAGGTAAATGAT 57.104 32.000 0.00 0.00 34.67 2.45
2297 2365 7.953158 TCACAAAAGACACAATGAAACAAAA 57.047 28.000 0.00 0.00 0.00 2.44
2318 2386 6.252869 CAGCATTTTATTGACAAGCAGATCAC 59.747 38.462 0.00 0.00 0.00 3.06
2328 2396 4.280425 TGTTCCAGCAGCATTTTATTGACA 59.720 37.500 0.00 0.00 0.00 3.58
2335 2403 1.888512 ACGATGTTCCAGCAGCATTTT 59.111 42.857 0.00 0.00 0.00 1.82
2353 2421 1.778591 GCACATTTCGGTTCACAAACG 59.221 47.619 0.00 0.00 36.16 3.60
2364 2432 6.625740 AGGAACTTTAATCATGGCACATTTCG 60.626 38.462 0.00 0.00 39.04 3.46
2381 2449 8.598041 ACTTAAGACATATGACAGAGGAACTTT 58.402 33.333 10.38 0.00 41.55 2.66
2468 2536 6.405065 GCAGATATTCAACCAATCAGCTCAAA 60.405 38.462 0.00 0.00 31.60 2.69
2493 2561 2.933495 TCAGAACGACGATAACCCTG 57.067 50.000 0.00 0.00 0.00 4.45
2706 2774 2.375146 GTGGGTGTGTTCAAGGAGTTT 58.625 47.619 0.00 0.00 0.00 2.66
3128 3196 4.081254 CCACTGATGAATCTCTCTCCAACA 60.081 45.833 0.00 0.00 0.00 3.33
3276 3344 5.560722 TCTTCTGTATTGTTGTGGAAGGA 57.439 39.130 0.00 0.00 33.33 3.36
3285 3353 5.920273 CGTGCCATTTTTCTTCTGTATTGTT 59.080 36.000 0.00 0.00 0.00 2.83
3289 3357 4.331968 TCCGTGCCATTTTTCTTCTGTAT 58.668 39.130 0.00 0.00 0.00 2.29
3318 3386 6.933514 TCCTTCAGGCCAATAATTCTTTTT 57.066 33.333 5.01 0.00 34.44 1.94
3442 3510 3.287222 CTCTTCCTGTTTTGACACCCAA 58.713 45.455 0.00 0.00 0.00 4.12
3600 3668 0.177604 CTGCAGGAGTGTGATCCCTC 59.822 60.000 5.57 0.00 40.53 4.30
3663 3731 1.486310 TCTCCCATTCCAAGACCATCG 59.514 52.381 0.00 0.00 0.00 3.84
3963 4031 4.033358 CCATTCTCTTTGTATGTGACGAGC 59.967 45.833 0.00 0.00 0.00 5.03
3969 4037 4.878397 GGGTCTCCATTCTCTTTGTATGTG 59.122 45.833 0.00 0.00 0.00 3.21
3984 4052 0.250295 CTGCAAAACGAGGGTCTCCA 60.250 55.000 0.00 0.00 34.83 3.86
4192 4260 4.003788 CGCCACACCTCTTCGGGT 62.004 66.667 0.00 0.00 40.73 5.28
4311 4379 3.443681 ACATTGGCATGCTTACTGTTACC 59.556 43.478 18.92 0.00 33.05 2.85
4334 4402 3.961408 ACAGAAAGTCTACATAGGCCGAT 59.039 43.478 0.00 0.00 0.00 4.18
4371 4439 6.161855 AGCTACATCTGAATTGATCCGTTA 57.838 37.500 0.00 0.00 0.00 3.18
4410 4478 1.414181 AGGGATGCCATAAGACAGACG 59.586 52.381 5.86 0.00 0.00 4.18
4447 4516 1.165270 GTGTGCCCACCAACTACATC 58.835 55.000 0.00 0.00 35.44 3.06
4451 4520 0.396435 CTCAGTGTGCCCACCAACTA 59.604 55.000 0.00 0.00 42.88 2.24
4484 4553 1.017177 CGCTACAAGCCAAGCCGTTA 61.017 55.000 0.00 0.00 38.18 3.18
4495 4564 4.033990 TGAACATAGAGCTCGCTACAAG 57.966 45.455 8.37 0.00 0.00 3.16
4532 4601 1.002468 CATGCCGGGATTCGAACAATC 60.002 52.381 5.36 0.00 42.43 2.67
4533 4602 1.024271 CATGCCGGGATTCGAACAAT 58.976 50.000 5.36 0.00 42.43 2.71
4534 4603 0.035915 TCATGCCGGGATTCGAACAA 60.036 50.000 5.36 0.00 42.43 2.83
4535 4604 0.742990 GTCATGCCGGGATTCGAACA 60.743 55.000 5.36 0.00 42.43 3.18
4548 4617 0.239347 GGAAGTGCACTGTGTCATGC 59.761 55.000 22.49 4.74 42.40 4.06
4576 4645 1.623542 ATGCCCCCAACTAGACGTCC 61.624 60.000 13.01 0.00 0.00 4.79
4631 4700 1.623811 ACGCCTTGGATGTGACTACTT 59.376 47.619 0.00 0.00 0.00 2.24
4654 4723 5.174037 AGATTACAATCCGGTCCTTTTGA 57.826 39.130 0.00 0.00 36.04 2.69
4683 4752 8.207545 TGCTGTAAAAATGGACCTAAAACAAAT 58.792 29.630 0.00 0.00 0.00 2.32
4796 4873 6.740905 CGCAACTGTTTTTCATGATTACGTAT 59.259 34.615 0.00 0.00 0.00 3.06
4800 4877 5.219633 ACCGCAACTGTTTTTCATGATTAC 58.780 37.500 0.00 0.00 0.00 1.89
4816 4895 3.547413 GGTCAAACTTAGTGAACCGCAAC 60.547 47.826 0.00 0.00 0.00 4.17
4889 4976 6.406370 AGTCGTCATGGAATCTAAATGAACA 58.594 36.000 0.00 0.00 32.38 3.18
4908 4995 9.485206 ACTACAATTGTGTTTTCTATTAGTCGT 57.515 29.630 21.42 0.00 39.30 4.34
4938 5025 6.900568 TTGTGATTTTTAAGTTGTGGCAAG 57.099 33.333 0.00 0.00 0.00 4.01
4972 6124 9.796062 CAAATTTACCGAAACATGAAAATTCTG 57.204 29.630 0.00 0.00 0.00 3.02
4973 6125 9.757227 TCAAATTTACCGAAACATGAAAATTCT 57.243 25.926 0.00 0.00 0.00 2.40
4977 6129 9.372369 AGTTTCAAATTTACCGAAACATGAAAA 57.628 25.926 23.67 0.62 46.98 2.29
4981 6133 6.420604 AGCAGTTTCAAATTTACCGAAACATG 59.579 34.615 23.67 19.87 46.98 3.21
4982 6134 6.512297 AGCAGTTTCAAATTTACCGAAACAT 58.488 32.000 23.67 12.98 46.98 2.71
5030 6183 8.129211 GGCGCAACTTTTTCATATAGAATACTT 58.871 33.333 10.83 0.00 35.83 2.24
5062 6215 7.504924 ACCATACAACCGTTGGAAATATATG 57.495 36.000 15.60 11.72 34.52 1.78
5078 6231 8.563123 TTGTCGGAATAATACAAACCATACAA 57.437 30.769 0.00 0.00 30.54 2.41
5079 6232 7.201661 GCTTGTCGGAATAATACAAACCATACA 60.202 37.037 0.00 0.00 33.05 2.29
5119 6272 5.266733 TGGTACCGAGCGTATTTTCTTAT 57.733 39.130 7.57 0.00 0.00 1.73
5120 6273 4.717233 TGGTACCGAGCGTATTTTCTTA 57.283 40.909 7.57 0.00 0.00 2.10
5121 6274 3.598019 TGGTACCGAGCGTATTTTCTT 57.402 42.857 7.57 0.00 0.00 2.52
5122 6275 3.454375 CATGGTACCGAGCGTATTTTCT 58.546 45.455 7.57 0.00 0.00 2.52
5188 6341 5.334569 CCACGTTGAACACTTTCCGATATTT 60.335 40.000 0.00 0.00 0.00 1.40
5245 6398 4.082354 GTCGGAAGGAGGCGTGTAATATAT 60.082 45.833 0.00 0.00 0.00 0.86
5266 6419 5.396947 TGTTTGCGATGTTAAACATTTCGTC 59.603 36.000 2.59 0.00 39.27 4.20
5272 6425 5.239744 TGGTACTGTTTGCGATGTTAAACAT 59.760 36.000 0.00 0.00 43.44 2.71
5273 6426 4.575236 TGGTACTGTTTGCGATGTTAAACA 59.425 37.500 0.00 0.00 42.57 2.83
5280 6433 3.980775 CCTTTTTGGTACTGTTTGCGATG 59.019 43.478 0.00 0.00 0.00 3.84
5318 6478 5.766150 AAACTACACTGCAATGTTAGCAA 57.234 34.783 5.94 0.00 42.17 3.91
5333 6493 2.807967 CTGCACTGCTAGCAAAACTACA 59.192 45.455 19.86 10.09 42.17 2.74
5389 6549 0.173481 TCTGGTCGATGCTCTTTCCG 59.827 55.000 0.00 0.00 0.00 4.30
5395 6555 6.481644 AGAATATTTCTTTCTGGTCGATGCTC 59.518 38.462 0.00 0.00 36.36 4.26
5397 6557 6.610741 AGAATATTTCTTTCTGGTCGATGC 57.389 37.500 0.00 0.00 36.36 3.91


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

AutoCloner maintained by Alex Coulton.