Multiple sequence alignment - TraesCS3D01G273000

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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 TraesCS3D01G273000 chr3D 100.000 5417 0 0 1 5417 378577301 378571885 0.000000e+00 10004.0
1 TraesCS3D01G273000 chr3D 98.824 85 1 0 4502 4586 6411275 6411359 9.400000e-33 152.0
2 TraesCS3D01G273000 chr3B 95.325 4535 153 24 1 4505 493654087 493649582 0.000000e+00 7145.0
3 TraesCS3D01G273000 chr3B 89.109 505 28 12 4588 5065 493649586 493649082 2.160000e-168 603.0
4 TraesCS3D01G273000 chr3B 89.644 309 21 7 5114 5417 493648659 493648357 3.060000e-102 383.0
5 TraesCS3D01G273000 chr3A 96.831 1483 32 5 3030 4505 502507111 502505637 0.000000e+00 2464.0
6 TraesCS3D01G273000 chr3A 96.375 1407 43 6 1584 2984 502508512 502507108 0.000000e+00 2309.0
7 TraesCS3D01G273000 chr3A 91.978 1608 76 19 1 1591 502509896 502508325 0.000000e+00 2206.0
8 TraesCS3D01G273000 chr3A 95.753 730 26 3 4585 5313 502505644 502504919 0.000000e+00 1171.0
9 TraesCS3D01G273000 chr3A 95.652 115 5 0 5303 5417 502499872 502499758 9.270000e-43 185.0
10 TraesCS3D01G273000 chr3A 94.792 96 5 0 4501 4596 308684887 308684792 3.380000e-32 150.0
11 TraesCS3D01G273000 chr1A 79.675 246 41 7 2773 3016 157084280 157084042 9.330000e-38 169.0
12 TraesCS3D01G273000 chr7B 77.397 292 53 13 2799 3084 501557645 501557929 1.560000e-35 161.0
13 TraesCS3D01G273000 chr7B 98.824 85 1 0 4502 4586 511301993 511302077 9.400000e-33 152.0
14 TraesCS3D01G273000 chr7B 82.524 103 16 2 2799 2901 501559146 501559246 7.470000e-14 89.8
15 TraesCS3D01G273000 chr5D 98.824 85 1 0 4501 4585 535711531 535711615 9.400000e-33 152.0
16 TraesCS3D01G273000 chr5D 98.810 84 1 0 4502 4585 126570262 126570179 3.380000e-32 150.0
17 TraesCS3D01G273000 chr7D 98.810 84 1 0 4502 4585 334858160 334858077 3.380000e-32 150.0
18 TraesCS3D01G273000 chr5B 98.810 84 1 0 4502 4585 139342379 139342296 3.380000e-32 150.0
19 TraesCS3D01G273000 chr1D 98.810 84 1 0 4502 4585 225405309 225405226 3.380000e-32 150.0
20 TraesCS3D01G273000 chr1B 98.810 84 1 0 4502 4585 254467468 254467551 3.380000e-32 150.0


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 TraesCS3D01G273000 chr3D 378571885 378577301 5416 True 10004.000000 10004 100.000000 1 5417 1 chr3D.!!$R1 5416
1 TraesCS3D01G273000 chr3B 493648357 493654087 5730 True 2710.333333 7145 91.359333 1 5417 3 chr3B.!!$R1 5416
2 TraesCS3D01G273000 chr3A 502504919 502509896 4977 True 2037.500000 2464 95.234250 1 5313 4 chr3A.!!$R3 5312

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
864 868 2.278596 CGGGGATACTGCGACACG 60.279 66.667 0.00 0.0 0.00 4.49 F
1432 1446 0.527817 CGGATAGTCGGCTTGTGGAC 60.528 60.000 0.00 0.0 0.00 4.02 F
2486 2508 2.202479 GCGGTGCCGAATTTCAGC 60.202 61.111 15.45 0.0 42.83 4.26 F
2765 2790 3.113322 GGCGTGTCCAGTTTTTCTTTTC 58.887 45.455 0.00 0.0 34.01 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 2238 0.251742 AGCCCTTTGTGCCTGCATAA 60.252 50.0 0.00 0.0 0.00 1.90 R
3175 3207 0.108329 GGGAGATTCTTCGCGGACAA 60.108 55.0 6.13 0.0 0.00 3.18 R
3674 3707 0.537371 ACCAACAGGCTAACAGCACC 60.537 55.0 0.00 0.0 44.75 5.01 R
4538 4583 0.035056 AGCCCTTTCCATCAGTTCGG 60.035 55.0 0.00 0.0 0.00 4.30 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
493 494 2.804090 GGTGCGGTCGAACTCGTC 60.804 66.667 0.00 0.00 40.80 4.20
864 868 2.278596 CGGGGATACTGCGACACG 60.279 66.667 0.00 0.00 0.00 4.49
881 894 4.056050 GACACGAGTACAGTCCACAAAAT 58.944 43.478 0.00 0.00 0.00 1.82
1137 1151 2.728817 CGGTCGGCCTGATACTCC 59.271 66.667 3.66 0.00 0.00 3.85
1157 1171 4.832248 TCCGATTGAGCTGTTTGTCTAAT 58.168 39.130 0.00 0.00 0.00 1.73
1386 1400 6.417635 ACAGTTATGTTTGAATGTTTCGCTTG 59.582 34.615 0.00 0.00 35.63 4.01
1401 1415 1.530293 CGCTTGCTGAGATTAGATGGC 59.470 52.381 0.00 0.00 0.00 4.40
1432 1446 0.527817 CGGATAGTCGGCTTGTGGAC 60.528 60.000 0.00 0.00 0.00 4.02
1452 1466 2.812011 ACGAGGTGTTTGATTAACTGCC 59.188 45.455 0.00 0.00 37.64 4.85
1462 1476 6.211184 TGTTTGATTAACTGCCTCAATGGAAT 59.789 34.615 0.00 0.00 37.64 3.01
1478 1492 6.326064 TCAATGGAATTTGAGGTTTCTTTCCA 59.674 34.615 4.81 4.81 44.70 3.53
1527 1541 2.290323 GGTTGTGTTCCAGTAGGCTCAT 60.290 50.000 0.00 0.00 33.74 2.90
1544 1558 5.133660 AGGCTCATAGACTTCCTCTCTAAGA 59.866 44.000 0.00 0.00 17.74 2.10
1563 1577 9.667107 CTCTAAGAGGGTATGTTACATGAAAAA 57.333 33.333 8.26 0.00 0.00 1.94
1571 1585 7.562088 GGGTATGTTACATGAAAAATTAGGGGA 59.438 37.037 8.26 0.00 0.00 4.81
1684 1699 5.441718 TCTTCCCACTATTCATGAGCTTT 57.558 39.130 0.00 0.00 0.00 3.51
1725 1740 4.099266 GCTGATGCTTCCTCTCTAAGAGAA 59.901 45.833 7.53 0.67 39.29 2.87
1781 1796 3.287222 TGTGCTTCCTGTTAGCTGTTTT 58.713 40.909 0.00 0.00 39.38 2.43
1807 1822 7.716738 CTATTGAAGCATGAAGAAAAAGTCG 57.283 36.000 0.00 0.00 0.00 4.18
1858 1873 7.902920 ACATAACCTTTCAATCATATTGGCT 57.097 32.000 0.12 0.00 0.00 4.75
1859 1874 8.310122 ACATAACCTTTCAATCATATTGGCTT 57.690 30.769 0.12 0.00 0.00 4.35
1904 1919 9.088987 AGAATAAAATTGCTTCTTCCAAGGTAA 57.911 29.630 0.00 0.00 0.00 2.85
1923 1938 3.306472 AAACCAAGTGGCAGGAGTTAA 57.694 42.857 0.00 0.00 39.32 2.01
1985 2003 8.738645 AGGAAATACAAACTTGATCCTGATAC 57.261 34.615 0.00 0.00 33.17 2.24
2093 2114 8.887717 CATGGTTTTTCAGTAAATTTGTTCCAA 58.112 29.630 0.00 0.00 0.00 3.53
2124 2145 6.190587 AGTTATTCCATTTCCAAGAGAAGGG 58.809 40.000 0.00 0.00 35.40 3.95
2216 2238 6.656270 TCATGAATTTGTACTGACATCAAGCT 59.344 34.615 0.00 0.00 34.86 3.74
2486 2508 2.202479 GCGGTGCCGAATTTCAGC 60.202 61.111 15.45 0.00 42.83 4.26
2602 2626 8.584063 TGTAAACTGACTTTTAAACCTTTCCT 57.416 30.769 0.00 0.00 0.00 3.36
2744 2768 5.500234 TCCACAAATACTCATTTCCCTGAG 58.500 41.667 0.00 0.00 46.59 3.35
2765 2790 3.113322 GGCGTGTCCAGTTTTTCTTTTC 58.887 45.455 0.00 0.00 34.01 2.29
2917 2942 6.910536 TTATGTTGCCAATTTTTCGTTTGT 57.089 29.167 0.00 0.00 0.00 2.83
2990 3015 6.210984 TGGATCAGATCTGAGATATGGTTCAG 59.789 42.308 28.26 0.00 43.61 3.02
3046 3078 7.734924 AACCTGTATATTACATGCTGATGTG 57.265 36.000 0.08 0.00 43.03 3.21
3050 3082 8.071967 CCTGTATATTACATGCTGATGTGTTTG 58.928 37.037 0.08 0.00 43.03 2.93
3169 3201 8.519526 AGTCTTTTGTATTTGTGAGTTTTGACA 58.480 29.630 0.00 0.00 0.00 3.58
3674 3707 8.208718 TGGACATTCTTATCTTATTTTGGACG 57.791 34.615 0.00 0.00 0.00 4.79
3707 3740 5.836358 AGCCTGTTGGTTTTTCTAATTACCA 59.164 36.000 0.00 0.00 38.82 3.25
3988 4021 4.692228 TGGAACAATTTTTCTGGTGCTTC 58.308 39.130 4.44 0.00 31.92 3.86
4249 4290 9.123902 GCATTATATGATATGCAGAAATACCCA 57.876 33.333 11.94 0.00 44.99 4.51
4393 4434 6.170506 ACTACGAAGAAAGGCAAATATGTCA 58.829 36.000 0.00 0.00 31.99 3.58
4457 4498 6.030548 TGTTCTCTGAAGAATACCTGACTG 57.969 41.667 0.00 0.00 43.26 3.51
4473 4514 3.495331 TGACTGGTGGTATGCATTTTGT 58.505 40.909 3.54 0.00 0.00 2.83
4511 4556 9.736023 TGAAGAAAATTCTCTTTGTTAAGCTTC 57.264 29.630 0.00 0.00 35.76 3.86
4512 4557 9.736023 GAAGAAAATTCTCTTTGTTAAGCTTCA 57.264 29.630 0.00 0.00 35.76 3.02
4514 4559 9.688592 AGAAAATTCTCTTTGTTAAGCTTCATG 57.311 29.630 0.00 0.00 29.94 3.07
4515 4560 7.880059 AAATTCTCTTTGTTAAGCTTCATGC 57.120 32.000 0.00 0.00 43.29 4.06
4516 4561 6.579666 ATTCTCTTTGTTAAGCTTCATGCA 57.420 33.333 0.00 0.00 45.94 3.96
4517 4562 5.362556 TCTCTTTGTTAAGCTTCATGCAC 57.637 39.130 0.00 0.00 45.94 4.57
4518 4563 5.065914 TCTCTTTGTTAAGCTTCATGCACT 58.934 37.500 0.00 0.00 45.94 4.40
4519 4564 6.230472 TCTCTTTGTTAAGCTTCATGCACTA 58.770 36.000 0.00 0.00 45.94 2.74
4520 4565 6.369890 TCTCTTTGTTAAGCTTCATGCACTAG 59.630 38.462 0.00 0.00 45.94 2.57
4521 4566 4.685169 TTGTTAAGCTTCATGCACTAGC 57.315 40.909 0.00 8.13 45.94 3.42
4522 4567 3.009723 TGTTAAGCTTCATGCACTAGCC 58.990 45.455 0.00 0.11 45.94 3.93
4523 4568 3.009723 GTTAAGCTTCATGCACTAGCCA 58.990 45.455 0.00 0.00 45.94 4.75
4524 4569 2.205022 AAGCTTCATGCACTAGCCAA 57.795 45.000 11.63 0.00 45.94 4.52
4525 4570 1.457346 AGCTTCATGCACTAGCCAAC 58.543 50.000 11.63 0.00 45.94 3.77
4526 4571 0.097674 GCTTCATGCACTAGCCAACG 59.902 55.000 5.46 0.00 42.31 4.10
4527 4572 0.097674 CTTCATGCACTAGCCAACGC 59.902 55.000 0.00 0.00 41.13 4.84
4528 4573 0.605050 TTCATGCACTAGCCAACGCA 60.605 50.000 0.00 0.00 41.13 5.24
4529 4574 0.605050 TCATGCACTAGCCAACGCAA 60.605 50.000 0.00 0.00 41.13 4.85
4530 4575 0.454957 CATGCACTAGCCAACGCAAC 60.455 55.000 0.00 0.00 41.13 4.17
4531 4576 1.586154 ATGCACTAGCCAACGCAACC 61.586 55.000 0.00 0.00 41.13 3.77
4532 4577 2.258013 GCACTAGCCAACGCAACCA 61.258 57.895 0.00 0.00 37.52 3.67
4533 4578 1.791103 GCACTAGCCAACGCAACCAA 61.791 55.000 0.00 0.00 37.52 3.67
4534 4579 0.665835 CACTAGCCAACGCAACCAAA 59.334 50.000 0.00 0.00 37.52 3.28
4535 4580 1.066303 CACTAGCCAACGCAACCAAAA 59.934 47.619 0.00 0.00 37.52 2.44
4536 4581 1.336755 ACTAGCCAACGCAACCAAAAG 59.663 47.619 0.00 0.00 37.52 2.27
4537 4582 1.336755 CTAGCCAACGCAACCAAAAGT 59.663 47.619 0.00 0.00 37.52 2.66
4538 4583 0.102300 AGCCAACGCAACCAAAAGTC 59.898 50.000 0.00 0.00 37.52 3.01
4539 4584 0.874175 GCCAACGCAACCAAAAGTCC 60.874 55.000 0.00 0.00 34.03 3.85
4540 4585 0.593773 CCAACGCAACCAAAAGTCCG 60.594 55.000 0.00 0.00 0.00 4.79
4541 4586 0.378962 CAACGCAACCAAAAGTCCGA 59.621 50.000 0.00 0.00 0.00 4.55
4542 4587 1.096416 AACGCAACCAAAAGTCCGAA 58.904 45.000 0.00 0.00 0.00 4.30
4543 4588 0.379316 ACGCAACCAAAAGTCCGAAC 59.621 50.000 0.00 0.00 0.00 3.95
4544 4589 0.661020 CGCAACCAAAAGTCCGAACT 59.339 50.000 0.00 0.00 37.32 3.01
4545 4590 1.596954 CGCAACCAAAAGTCCGAACTG 60.597 52.381 0.00 0.00 35.36 3.16
4546 4591 1.673920 GCAACCAAAAGTCCGAACTGA 59.326 47.619 0.00 0.00 35.36 3.41
4547 4592 2.293399 GCAACCAAAAGTCCGAACTGAT 59.707 45.455 0.00 0.00 35.36 2.90
4548 4593 3.853307 GCAACCAAAAGTCCGAACTGATG 60.853 47.826 0.00 0.00 35.36 3.07
4549 4594 2.504367 ACCAAAAGTCCGAACTGATGG 58.496 47.619 4.80 4.80 43.11 3.51
4550 4595 2.105821 ACCAAAAGTCCGAACTGATGGA 59.894 45.455 12.23 0.00 41.39 3.41
4551 4596 3.146066 CCAAAAGTCCGAACTGATGGAA 58.854 45.455 0.36 0.00 41.39 3.53
4552 4597 3.568007 CCAAAAGTCCGAACTGATGGAAA 59.432 43.478 0.36 0.00 41.39 3.13
4553 4598 4.320494 CCAAAAGTCCGAACTGATGGAAAG 60.320 45.833 0.36 0.00 41.39 2.62
4554 4599 2.770164 AGTCCGAACTGATGGAAAGG 57.230 50.000 0.00 0.00 35.67 3.11
4555 4600 1.279271 AGTCCGAACTGATGGAAAGGG 59.721 52.381 0.00 0.00 35.67 3.95
4556 4601 0.035439 TCCGAACTGATGGAAAGGGC 60.035 55.000 0.00 0.00 0.00 5.19
4557 4602 0.035056 CCGAACTGATGGAAAGGGCT 60.035 55.000 0.00 0.00 0.00 5.19
4558 4603 1.209504 CCGAACTGATGGAAAGGGCTA 59.790 52.381 0.00 0.00 0.00 3.93
4559 4604 2.280628 CGAACTGATGGAAAGGGCTAC 58.719 52.381 0.00 0.00 0.00 3.58
4560 4605 2.280628 GAACTGATGGAAAGGGCTACG 58.719 52.381 0.00 0.00 0.00 3.51
4561 4606 0.107654 ACTGATGGAAAGGGCTACGC 60.108 55.000 0.00 0.00 0.00 4.42
4562 4607 0.107703 CTGATGGAAAGGGCTACGCA 60.108 55.000 0.00 0.00 0.00 5.24
4563 4608 0.326595 TGATGGAAAGGGCTACGCAA 59.673 50.000 0.00 0.00 0.00 4.85
4564 4609 1.064758 TGATGGAAAGGGCTACGCAAT 60.065 47.619 0.00 0.00 0.00 3.56
4565 4610 1.604278 GATGGAAAGGGCTACGCAATC 59.396 52.381 0.00 0.00 0.00 2.67
4566 4611 0.393808 TGGAAAGGGCTACGCAATCC 60.394 55.000 0.00 0.00 0.00 3.01
4567 4612 0.393808 GGAAAGGGCTACGCAATCCA 60.394 55.000 0.00 0.00 0.00 3.41
4568 4613 0.733150 GAAAGGGCTACGCAATCCAC 59.267 55.000 0.00 0.00 0.00 4.02
4569 4614 0.037590 AAAGGGCTACGCAATCCACA 59.962 50.000 0.00 0.00 0.00 4.17
4570 4615 0.255890 AAGGGCTACGCAATCCACAT 59.744 50.000 0.00 0.00 0.00 3.21
4571 4616 1.128200 AGGGCTACGCAATCCACATA 58.872 50.000 0.00 0.00 0.00 2.29
4572 4617 1.699634 AGGGCTACGCAATCCACATAT 59.300 47.619 0.00 0.00 0.00 1.78
4573 4618 2.903784 AGGGCTACGCAATCCACATATA 59.096 45.455 0.00 0.00 0.00 0.86
4574 4619 3.000727 GGGCTACGCAATCCACATATAC 58.999 50.000 0.00 0.00 0.00 1.47
4575 4620 3.556213 GGGCTACGCAATCCACATATACA 60.556 47.826 0.00 0.00 0.00 2.29
4576 4621 3.432252 GGCTACGCAATCCACATATACAC 59.568 47.826 0.00 0.00 0.00 2.90
4577 4622 4.307432 GCTACGCAATCCACATATACACT 58.693 43.478 0.00 0.00 0.00 3.55
4578 4623 4.750098 GCTACGCAATCCACATATACACTT 59.250 41.667 0.00 0.00 0.00 3.16
4579 4624 5.107453 GCTACGCAATCCACATATACACTTC 60.107 44.000 0.00 0.00 0.00 3.01
4580 4625 4.765273 ACGCAATCCACATATACACTTCA 58.235 39.130 0.00 0.00 0.00 3.02
4581 4626 5.182487 ACGCAATCCACATATACACTTCAA 58.818 37.500 0.00 0.00 0.00 2.69
4582 4627 5.064707 ACGCAATCCACATATACACTTCAAC 59.935 40.000 0.00 0.00 0.00 3.18
4583 4628 5.064579 CGCAATCCACATATACACTTCAACA 59.935 40.000 0.00 0.00 0.00 3.33
4584 4629 6.258160 GCAATCCACATATACACTTCAACAC 58.742 40.000 0.00 0.00 0.00 3.32
4585 4630 6.094048 GCAATCCACATATACACTTCAACACT 59.906 38.462 0.00 0.00 0.00 3.55
4603 4648 5.811399 ACACTCTTGTTCACGATTCAAAA 57.189 34.783 0.00 0.00 28.43 2.44
4612 4657 5.974751 TGTTCACGATTCAAAAAGTAAAGCC 59.025 36.000 0.00 0.00 0.00 4.35
4692 4738 7.449247 TCATTTTGCTTAAATTAGCTGGGTTT 58.551 30.769 0.00 0.00 41.76 3.27
4700 4746 8.655970 GCTTAAATTAGCTGGGTTTAACATTTG 58.344 33.333 0.00 0.00 38.15 2.32
4702 4748 7.961325 AAATTAGCTGGGTTTAACATTTGTG 57.039 32.000 0.00 0.00 0.00 3.33
4770 4816 6.893583 AGTCATCACTGAGGCAGTATAAAAT 58.106 36.000 0.00 0.00 43.43 1.82
5085 5413 9.507280 CTTATAGTTGCAAGTCCATATGTTTTG 57.493 33.333 10.78 4.62 0.00 2.44
5090 5418 5.170021 TGCAAGTCCATATGTTTTGAATGC 58.830 37.500 12.57 11.04 0.00 3.56
5147 5594 4.139786 CAAAGATGGGTAGCTGCACATAT 58.860 43.478 20.25 14.44 31.77 1.78
5148 5595 5.308014 CAAAGATGGGTAGCTGCACATATA 58.692 41.667 20.25 0.00 31.77 0.86
5176 5623 4.156556 TGGAAAATCTGCTTCCTTTCATCG 59.843 41.667 3.61 0.00 42.52 3.84
5239 5686 8.934023 TTTGGTATTTTGTAGGATCAAAGTCT 57.066 30.769 0.00 0.00 38.32 3.24
5292 5739 2.957474 TCTGCTTTAGGGCAAAAAGGT 58.043 42.857 11.34 0.00 41.94 3.50
5308 5755 8.495148 GGCAAAAAGGTGAACAAAAAGTATATG 58.505 33.333 0.00 0.00 0.00 1.78
5355 5806 9.302345 TGTTTCTTCTATTCATACTAAAGAGCG 57.698 33.333 0.00 0.00 0.00 5.03
5377 5828 0.874390 TCGCAAACAACATCCTCAGC 59.126 50.000 0.00 0.00 0.00 4.26
5380 5831 2.352030 CGCAAACAACATCCTCAGCAAT 60.352 45.455 0.00 0.00 0.00 3.56
5407 5858 3.814842 TGTCATCAGGAAACATGTGACAC 59.185 43.478 0.00 0.00 40.47 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.821589 GCCCGGGAGCTGTTCGAG 62.822 72.222 29.31 0.00 0.00 4.04
58 59 0.179134 CCTCACGTACAGCTACCTGC 60.179 60.000 0.00 0.00 43.02 4.85
230 231 0.892755 TGTACATGGACACCGTCTCC 59.107 55.000 6.68 0.00 32.47 3.71
443 444 4.144727 TCCCTCCTCCCCTCGCTC 62.145 72.222 0.00 0.00 0.00 5.03
446 447 1.456705 CTTCTCCCTCCTCCCCTCG 60.457 68.421 0.00 0.00 0.00 4.63
449 450 0.340208 TCTTCTTCTCCCTCCTCCCC 59.660 60.000 0.00 0.00 0.00 4.81
859 863 2.787601 TTGTGGACTGTACTCGTGTC 57.212 50.000 0.00 0.00 0.00 3.67
864 868 3.058224 GTGGCATTTTGTGGACTGTACTC 60.058 47.826 0.00 0.00 0.00 2.59
981 995 0.108585 TCCTTTCTGCAAGCCGACTT 59.891 50.000 0.00 0.00 36.19 3.01
1038 1052 1.377856 GCAAGGGAAGTGGAGGAGC 60.378 63.158 0.00 0.00 0.00 4.70
1075 1089 2.383527 CGAAGAAGCGGAGTGGTGC 61.384 63.158 0.00 0.00 0.00 5.01
1133 1147 2.037772 AGACAAACAGCTCAATCGGAGT 59.962 45.455 0.00 0.00 45.88 3.85
1137 1151 6.893958 AGTATTAGACAAACAGCTCAATCG 57.106 37.500 0.00 0.00 0.00 3.34
1386 1400 2.035193 TCGTCAGCCATCTAATCTCAGC 59.965 50.000 0.00 0.00 0.00 4.26
1401 1415 3.164358 CGACTATCCGCATTATCGTCAG 58.836 50.000 0.00 0.00 0.00 3.51
1432 1446 3.074412 AGGCAGTTAATCAAACACCTCG 58.926 45.455 0.00 0.00 40.88 4.63
1462 1476 8.754080 TCTTAAATTGTGGAAAGAAACCTCAAA 58.246 29.630 0.00 0.00 41.77 2.69
1544 1558 7.563556 CCCCTAATTTTTCATGTAACATACCCT 59.436 37.037 0.00 0.00 0.00 4.34
1563 1577 9.990868 AGTAAACACATCTAATTTTCCCCTAAT 57.009 29.630 0.00 0.00 0.00 1.73
1565 1579 8.607713 TCAGTAAACACATCTAATTTTCCCCTA 58.392 33.333 0.00 0.00 0.00 3.53
1566 1580 7.466804 TCAGTAAACACATCTAATTTTCCCCT 58.533 34.615 0.00 0.00 0.00 4.79
1684 1699 6.582636 CATCAGCCTATTAGAACACAACCTA 58.417 40.000 0.00 0.00 0.00 3.08
1807 1822 4.925054 CACACACCAAATGGACAATTCATC 59.075 41.667 6.42 0.00 38.94 2.92
1856 1871 3.317993 TCTTCTTACAAAGGCACCAAAGC 59.682 43.478 0.00 0.00 0.00 3.51
1858 1873 4.787551 TCTCTTCTTACAAAGGCACCAAA 58.212 39.130 0.00 0.00 0.00 3.28
1859 1874 4.431416 TCTCTTCTTACAAAGGCACCAA 57.569 40.909 0.00 0.00 0.00 3.67
1904 1919 3.117663 TCTTTAACTCCTGCCACTTGGTT 60.118 43.478 0.00 0.00 37.57 3.67
1923 1938 6.884832 TCCGTACATCTATTCACCAATTCTT 58.115 36.000 0.00 0.00 0.00 2.52
1985 2003 4.613925 AGCATCATGTGACACTATAGGG 57.386 45.455 7.20 0.00 0.00 3.53
2093 2114 9.838339 CTCTTGGAAATGGAATAACTACAGTAT 57.162 33.333 0.00 0.00 0.00 2.12
2105 2126 4.953781 ATCCCTTCTCTTGGAAATGGAA 57.046 40.909 0.00 0.00 37.99 3.53
2216 2238 0.251742 AGCCCTTTGTGCCTGCATAA 60.252 50.000 0.00 0.00 0.00 1.90
2602 2626 1.070134 CGGAAATTCCCGGAGATGCTA 59.930 52.381 0.73 0.00 45.43 3.49
2744 2768 2.863401 AAAGAAAAACTGGACACGCC 57.137 45.000 0.00 0.00 37.10 5.68
2917 2942 2.110352 CATGCACATCCAGCTCGCA 61.110 57.895 0.00 0.00 36.95 5.10
2969 2994 6.040278 GTCACTGAACCATATCTCAGATCTGA 59.960 42.308 23.75 23.75 41.38 3.27
3023 3055 6.830912 ACACATCAGCATGTAATATACAGGT 58.169 36.000 4.39 0.00 41.69 4.00
3092 3124 7.010023 GCGATCTAAGCGGACATAAAAATTAG 58.990 38.462 0.00 0.00 0.00 1.73
3169 3201 3.502211 AGATTCTTCGCGGACAAATTTGT 59.498 39.130 23.49 23.49 45.65 2.83
3175 3207 0.108329 GGGAGATTCTTCGCGGACAA 60.108 55.000 6.13 0.00 0.00 3.18
3638 3671 8.915057 AGATAAGAATGTCCAACTATTCATGG 57.085 34.615 0.00 0.00 36.11 3.66
3674 3707 0.537371 ACCAACAGGCTAACAGCACC 60.537 55.000 0.00 0.00 44.75 5.01
3735 3768 6.542370 TCTCCAGAACTTACCAAACAGAAAAG 59.458 38.462 0.00 0.00 0.00 2.27
3891 3924 6.005823 TCAAGAGAATTCAAGGCTCATCAAA 58.994 36.000 8.44 0.00 0.00 2.69
3988 4021 1.310933 GCACTGGTGGAATGCCTCTG 61.311 60.000 2.84 0.00 33.06 3.35
4165 4200 9.586435 CATATTATGAATATAAGTGGACAGCGA 57.414 33.333 0.00 0.00 32.91 4.93
4249 4290 9.557061 CATACATCTTCCATAGCATGCTATAAT 57.443 33.333 33.97 20.59 37.16 1.28
4393 4434 8.416329 GGCCTACAAATATTGAATCAACTGAAT 58.584 33.333 0.00 0.00 0.00 2.57
4457 4498 5.650703 AGTAGGTAACAAAATGCATACCACC 59.349 40.000 14.87 9.79 36.28 4.61
4498 4543 5.091431 GCTAGTGCATGAAGCTTAACAAAG 58.909 41.667 0.00 0.00 45.94 2.77
4499 4544 4.082787 GGCTAGTGCATGAAGCTTAACAAA 60.083 41.667 14.92 0.00 45.94 2.83
4500 4545 3.440173 GGCTAGTGCATGAAGCTTAACAA 59.560 43.478 14.92 0.00 45.94 2.83
4501 4546 3.009723 GGCTAGTGCATGAAGCTTAACA 58.990 45.455 14.92 0.00 45.94 2.41
4502 4547 3.009723 TGGCTAGTGCATGAAGCTTAAC 58.990 45.455 14.92 0.00 45.94 2.01
4503 4548 3.348647 TGGCTAGTGCATGAAGCTTAA 57.651 42.857 14.92 0.00 45.94 1.85
4504 4549 3.009723 GTTGGCTAGTGCATGAAGCTTA 58.990 45.455 14.92 5.14 45.94 3.09
4505 4550 1.815003 GTTGGCTAGTGCATGAAGCTT 59.185 47.619 14.92 0.00 45.94 3.74
4506 4551 1.457346 GTTGGCTAGTGCATGAAGCT 58.543 50.000 14.92 0.00 45.94 3.74
4507 4552 0.097674 CGTTGGCTAGTGCATGAAGC 59.902 55.000 0.00 8.84 45.96 3.86
4508 4553 0.097674 GCGTTGGCTAGTGCATGAAG 59.902 55.000 0.00 0.00 41.91 3.02
4509 4554 0.605050 TGCGTTGGCTAGTGCATGAA 60.605 50.000 0.00 0.00 41.91 2.57
4510 4555 0.605050 TTGCGTTGGCTAGTGCATGA 60.605 50.000 0.00 0.00 41.91 3.07
4511 4556 0.454957 GTTGCGTTGGCTAGTGCATG 60.455 55.000 0.00 0.00 41.91 4.06
4512 4557 1.586154 GGTTGCGTTGGCTAGTGCAT 61.586 55.000 0.00 0.00 41.91 3.96
4513 4558 2.258013 GGTTGCGTTGGCTAGTGCA 61.258 57.895 0.00 0.00 41.91 4.57
4514 4559 1.791103 TTGGTTGCGTTGGCTAGTGC 61.791 55.000 0.00 0.00 40.82 4.40
4515 4560 0.665835 TTTGGTTGCGTTGGCTAGTG 59.334 50.000 0.00 0.00 40.82 2.74
4516 4561 1.336755 CTTTTGGTTGCGTTGGCTAGT 59.663 47.619 0.00 0.00 40.82 2.57
4517 4562 1.336755 ACTTTTGGTTGCGTTGGCTAG 59.663 47.619 0.00 0.00 40.82 3.42
4518 4563 1.335496 GACTTTTGGTTGCGTTGGCTA 59.665 47.619 0.00 0.00 40.82 3.93
4519 4564 0.102300 GACTTTTGGTTGCGTTGGCT 59.898 50.000 0.00 0.00 40.82 4.75
4520 4565 0.874175 GGACTTTTGGTTGCGTTGGC 60.874 55.000 0.00 0.00 40.52 4.52
4521 4566 0.593773 CGGACTTTTGGTTGCGTTGG 60.594 55.000 0.00 0.00 0.00 3.77
4522 4567 0.378962 TCGGACTTTTGGTTGCGTTG 59.621 50.000 0.00 0.00 0.00 4.10
4523 4568 1.096416 TTCGGACTTTTGGTTGCGTT 58.904 45.000 0.00 0.00 0.00 4.84
4524 4569 0.379316 GTTCGGACTTTTGGTTGCGT 59.621 50.000 0.00 0.00 0.00 5.24
4525 4570 0.661020 AGTTCGGACTTTTGGTTGCG 59.339 50.000 0.00 0.00 29.87 4.85
4526 4571 1.673920 TCAGTTCGGACTTTTGGTTGC 59.326 47.619 0.00 0.00 32.54 4.17
4527 4572 3.304659 CCATCAGTTCGGACTTTTGGTTG 60.305 47.826 12.08 0.00 33.55 3.77
4528 4573 2.884639 CCATCAGTTCGGACTTTTGGTT 59.115 45.455 12.08 0.00 33.55 3.67
4529 4574 2.105821 TCCATCAGTTCGGACTTTTGGT 59.894 45.455 17.54 0.00 36.97 3.67
4530 4575 2.778299 TCCATCAGTTCGGACTTTTGG 58.222 47.619 13.60 13.60 36.98 3.28
4531 4576 4.320494 CCTTTCCATCAGTTCGGACTTTTG 60.320 45.833 0.00 0.00 32.54 2.44
4532 4577 3.821033 CCTTTCCATCAGTTCGGACTTTT 59.179 43.478 0.00 0.00 32.54 2.27
4533 4578 3.412386 CCTTTCCATCAGTTCGGACTTT 58.588 45.455 0.00 0.00 32.54 2.66
4534 4579 2.290323 CCCTTTCCATCAGTTCGGACTT 60.290 50.000 0.00 0.00 32.54 3.01
4535 4580 1.279271 CCCTTTCCATCAGTTCGGACT 59.721 52.381 0.00 0.00 36.25 3.85
4536 4581 1.739067 CCCTTTCCATCAGTTCGGAC 58.261 55.000 0.00 0.00 0.00 4.79
4537 4582 0.035439 GCCCTTTCCATCAGTTCGGA 60.035 55.000 0.00 0.00 0.00 4.55
4538 4583 0.035056 AGCCCTTTCCATCAGTTCGG 60.035 55.000 0.00 0.00 0.00 4.30
4539 4584 2.280628 GTAGCCCTTTCCATCAGTTCG 58.719 52.381 0.00 0.00 0.00 3.95
4540 4585 2.280628 CGTAGCCCTTTCCATCAGTTC 58.719 52.381 0.00 0.00 0.00 3.01
4541 4586 2.403252 CGTAGCCCTTTCCATCAGTT 57.597 50.000 0.00 0.00 0.00 3.16
4556 4601 5.983118 TGAAGTGTATATGTGGATTGCGTAG 59.017 40.000 0.00 0.00 0.00 3.51
4557 4602 5.908341 TGAAGTGTATATGTGGATTGCGTA 58.092 37.500 0.00 0.00 0.00 4.42
4558 4603 4.765273 TGAAGTGTATATGTGGATTGCGT 58.235 39.130 0.00 0.00 0.00 5.24
4559 4604 5.064579 TGTTGAAGTGTATATGTGGATTGCG 59.935 40.000 0.00 0.00 0.00 4.85
4560 4605 6.094048 AGTGTTGAAGTGTATATGTGGATTGC 59.906 38.462 0.00 0.00 0.00 3.56
4561 4606 7.550551 AGAGTGTTGAAGTGTATATGTGGATTG 59.449 37.037 0.00 0.00 0.00 2.67
4562 4607 7.624549 AGAGTGTTGAAGTGTATATGTGGATT 58.375 34.615 0.00 0.00 0.00 3.01
4563 4608 7.187824 AGAGTGTTGAAGTGTATATGTGGAT 57.812 36.000 0.00 0.00 0.00 3.41
4564 4609 6.605471 AGAGTGTTGAAGTGTATATGTGGA 57.395 37.500 0.00 0.00 0.00 4.02
4565 4610 6.650807 ACAAGAGTGTTGAAGTGTATATGTGG 59.349 38.462 7.07 0.00 32.58 4.17
4566 4611 7.658179 ACAAGAGTGTTGAAGTGTATATGTG 57.342 36.000 7.07 0.00 32.58 3.21
4581 4626 5.811399 TTTTGAATCGTGAACAAGAGTGT 57.189 34.783 0.00 0.00 40.75 3.55
4582 4627 6.258160 ACTTTTTGAATCGTGAACAAGAGTG 58.742 36.000 0.00 0.00 0.00 3.51
4583 4628 6.436843 ACTTTTTGAATCGTGAACAAGAGT 57.563 33.333 0.00 0.00 0.00 3.24
4584 4629 8.835467 TTTACTTTTTGAATCGTGAACAAGAG 57.165 30.769 0.00 0.00 0.00 2.85
4585 4630 7.431084 GCTTTACTTTTTGAATCGTGAACAAGA 59.569 33.333 0.00 0.00 0.00 3.02
4612 4657 6.936533 CTGTACTAAGCAGAGCGAAATTTTCG 60.937 42.308 23.64 23.64 44.57 3.46
4692 4738 6.537301 ACTCACGAGTTTCTTCACAAATGTTA 59.463 34.615 0.00 0.00 38.83 2.41
4700 4746 7.813852 ACAATATACTCACGAGTTTCTTCAC 57.186 36.000 4.79 0.00 42.54 3.18
4702 4748 9.021863 CCTAACAATATACTCACGAGTTTCTTC 57.978 37.037 4.79 0.00 42.54 2.87
5085 5413 9.630098 CCTACCATTTACATCATAAATGCATTC 57.370 33.333 13.38 0.00 41.24 2.67
5147 5594 3.010584 AGGAAGCAGATTTTCCAAGCCTA 59.989 43.478 6.77 0.00 45.28 3.93
5148 5595 2.174360 GGAAGCAGATTTTCCAAGCCT 58.826 47.619 0.00 0.00 42.93 4.58
5176 5623 0.807496 GCTGCCACATGAAGAACTCC 59.193 55.000 0.00 0.00 0.00 3.85
5239 5686 2.034685 CACGAGTTGGAGTTCACAGAGA 59.965 50.000 0.00 0.00 0.00 3.10
5308 5755 6.676237 ACACATTTCCATTGTTTCCAAAAC 57.324 33.333 0.00 0.00 33.44 2.43
5355 5806 3.751621 CTGAGGATGTTGTTTGCGAATC 58.248 45.455 0.00 0.00 0.00 2.52
5361 5812 5.987347 AGAAAATTGCTGAGGATGTTGTTTG 59.013 36.000 0.00 0.00 0.00 2.93
5372 5823 4.698780 TCCTGATGACAGAAAATTGCTGAG 59.301 41.667 8.18 0.00 46.03 3.35
5377 5828 7.115805 CACATGTTTCCTGATGACAGAAAATTG 59.884 37.037 0.00 0.00 46.03 2.32
5380 5831 5.827267 TCACATGTTTCCTGATGACAGAAAA 59.173 36.000 0.00 0.00 46.03 2.29


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

AutoCloner maintained by Alex Coulton.