Multiple sequence alignment - TraesCS2D01G208400

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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 TraesCS2D01G208400 chr2D 100.000 3082 0 0 1 3082 162508131 162505050 0.000000e+00 5692.0
1 TraesCS2D01G208400 chr2D 84.100 239 34 2 115 352 577822898 577823133 8.600000e-56 228.0
2 TraesCS2D01G208400 chr2A 95.481 1195 39 2 1888 3082 173507141 173505962 0.000000e+00 1893.0
3 TraesCS2D01G208400 chr2A 91.281 1101 58 22 718 1801 173508739 173507660 0.000000e+00 1467.0
4 TraesCS2D01G208400 chr2A 93.865 163 9 1 541 702 173508887 173508725 8.540000e-61 244.0
5 TraesCS2D01G208400 chr2A 90.698 43 4 0 1542 1584 27327145 27327103 1.190000e-04 58.4
6 TraesCS2D01G208400 chr2B 95.028 1066 41 6 1885 2944 221925931 221924872 0.000000e+00 1664.0
7 TraesCS2D01G208400 chr2B 94.419 645 20 8 756 1391 221926560 221925923 0.000000e+00 977.0
8 TraesCS2D01G208400 chr2B 88.889 684 52 11 1 671 221931117 221930445 0.000000e+00 821.0
9 TraesCS2D01G208400 chr2B 98.592 142 2 0 2941 3082 221924792 221924651 5.100000e-63 252.0
10 TraesCS2D01G208400 chr2B 92.381 105 6 2 665 768 221926679 221926576 6.890000e-32 148.0
11 TraesCS2D01G208400 chr2B 90.698 43 3 1 1539 1581 597252920 597252961 4.290000e-04 56.5
12 TraesCS2D01G208400 chr6A 85.774 239 33 1 115 352 109796717 109796955 5.100000e-63 252.0
13 TraesCS2D01G208400 chr1D 85.185 243 33 3 115 355 439108966 439108725 2.370000e-61 246.0
14 TraesCS2D01G208400 chr6D 85.124 242 33 3 115 355 341998175 341997936 8.540000e-61 244.0
15 TraesCS2D01G208400 chr6D 90.244 41 4 0 1542 1582 156761490 156761450 2.000000e-03 54.7
16 TraesCS2D01G208400 chr5B 85.124 242 33 3 114 352 530653382 530653623 8.540000e-61 244.0
17 TraesCS2D01G208400 chr3A 84.615 247 35 3 111 355 1296266 1296021 3.070000e-60 243.0
18 TraesCS2D01G208400 chr6B 84.274 248 34 5 110 355 615643995 615643751 1.430000e-58 237.0
19 TraesCS2D01G208400 chr4A 83.884 242 39 0 114 355 563238650 563238409 6.650000e-57 231.0
20 TraesCS2D01G208400 chr5D 86.577 149 19 1 356 503 332433298 332433446 2.460000e-36 163.0
21 TraesCS2D01G208400 chr5A 81.250 160 26 3 354 510 670610549 670610391 3.230000e-25 126.0
22 TraesCS2D01G208400 chr7B 79.605 152 25 4 354 504 200717439 200717585 1.510000e-18 104.0
23 TraesCS2D01G208400 chr7B 96.875 32 1 0 1538 1569 20033014 20032983 2.000000e-03 54.7
24 TraesCS2D01G208400 chr7B 96.875 32 1 0 1539 1570 419032193 419032224 2.000000e-03 54.7
25 TraesCS2D01G208400 chr7A 97.059 34 1 0 1537 1570 686783296 686783263 1.190000e-04 58.4
26 TraesCS2D01G208400 chr7A 96.875 32 1 0 1539 1570 42306340 42306371 2.000000e-03 54.7
27 TraesCS2D01G208400 chr3D 90.476 42 4 0 1542 1583 105182933 105182974 4.290000e-04 56.5


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 TraesCS2D01G208400 chr2D 162505050 162508131 3081 True 5692.000000 5692 100.000000 1 3082 1 chr2D.!!$R1 3081
1 TraesCS2D01G208400 chr2A 173505962 173508887 2925 True 1201.333333 1893 93.542333 541 3082 3 chr2A.!!$R2 2541
2 TraesCS2D01G208400 chr2B 221924651 221931117 6466 True 772.400000 1664 93.861800 1 3082 5 chr2B.!!$R1 3081

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
381 384 0.106519 CTTGGGCCGGGAATGATCTT 60.107 55.0 2.18 0.0 0.0 2.4 F
962 4785 0.478507 CCCTCCAAGTTCCAACACCT 59.521 55.0 0.00 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 5322 0.390124 TTTCTTCGGGCACGTACACT 59.610 50.000 8.89 0.0 41.85 3.55 R
2161 6433 1.208293 GGCTCTCCCTTACAACTCCAG 59.792 57.143 0.00 0.0 0.00 3.86 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
26 27 2.821969 TCCTTTTAGAACTACCGCGAGT 59.178 45.455 8.23 6.57 0.00 4.18
31 32 5.627499 TTTAGAACTACCGCGAGTTTCTA 57.373 39.130 8.23 11.88 39.79 2.10
37 38 6.750963 AGAACTACCGCGAGTTTCTATTTTAG 59.249 38.462 8.23 0.00 39.79 1.85
38 39 5.346522 ACTACCGCGAGTTTCTATTTTAGG 58.653 41.667 8.23 0.00 0.00 2.69
41 42 4.081807 ACCGCGAGTTTCTATTTTAGGACT 60.082 41.667 8.23 0.00 0.00 3.85
56 57 7.515957 TTTTAGGACTATCGCTTAGTTTTCG 57.484 36.000 0.30 0.00 41.35 3.46
78 80 6.304126 TCGTTTTTGAGAAATGAACTATCGC 58.696 36.000 0.00 0.00 0.00 4.58
81 83 7.006564 CGTTTTTGAGAAATGAACTATCGCTTC 59.993 37.037 0.00 0.00 0.00 3.86
82 84 5.702622 TTGAGAAATGAACTATCGCTTCG 57.297 39.130 0.00 0.00 0.00 3.79
83 85 4.112634 TGAGAAATGAACTATCGCTTCGG 58.887 43.478 0.00 0.00 0.00 4.30
168 171 9.909644 CATACTCATAACAGTTACAGGTATACC 57.090 37.037 14.54 14.54 0.00 2.73
175 178 5.667466 ACAGTTACAGGTATACCGATTTGG 58.333 41.667 16.31 7.43 46.41 3.28
178 181 6.423905 CAGTTACAGGTATACCGATTTGGATG 59.576 42.308 16.31 8.88 42.00 3.51
183 186 6.099269 ACAGGTATACCGATTTGGATGTAAGT 59.901 38.462 16.31 0.00 42.00 2.24
186 189 7.713942 AGGTATACCGATTTGGATGTAAGTTTC 59.286 37.037 16.31 0.00 42.00 2.78
288 291 7.397476 TCTCTGCTAGAGGAAATACTTCAAAGA 59.603 37.037 11.63 0.00 42.54 2.52
303 306 5.639931 ACTTCAAAGACTTCGATAAAGAGGC 59.360 40.000 0.00 0.00 38.44 4.70
305 308 6.525578 TCAAAGACTTCGATAAAGAGGCTA 57.474 37.500 0.00 0.00 38.44 3.93
380 383 1.533711 CTTGGGCCGGGAATGATCT 59.466 57.895 2.18 0.00 0.00 2.75
381 384 0.106519 CTTGGGCCGGGAATGATCTT 60.107 55.000 2.18 0.00 0.00 2.40
408 411 1.293498 GCAGGCCGTCGGATCATAT 59.707 57.895 17.49 0.00 0.00 1.78
439 442 8.681486 TCATCATGGTATCGATGAAAGATTTT 57.319 30.769 8.54 0.00 43.78 1.82
444 447 9.869844 CATGGTATCGATGAAAGATTTTAACTC 57.130 33.333 8.54 0.00 0.00 3.01
468 472 6.371825 TCCACAATAACCAAACCAACAAAAAC 59.628 34.615 0.00 0.00 0.00 2.43
470 474 7.308589 CCACAATAACCAAACCAACAAAAACAA 60.309 33.333 0.00 0.00 0.00 2.83
471 475 8.239998 CACAATAACCAAACCAACAAAAACAAT 58.760 29.630 0.00 0.00 0.00 2.71
483 487 7.118535 ACCAACAAAAACAATTAACAGACCAAC 59.881 33.333 0.00 0.00 0.00 3.77
491 495 6.951643 ACAATTAACAGACCAACGTAAACTC 58.048 36.000 0.00 0.00 0.00 3.01
515 519 6.832384 TCATTAGGTCCGAACTATCACTTAGT 59.168 38.462 0.00 0.00 43.19 2.24
603 617 2.086869 ACAGAAAATGACTGCATCGGG 58.913 47.619 0.00 0.00 38.74 5.14
606 620 1.656818 AAAATGACTGCATCGGGCCG 61.657 55.000 22.51 22.51 43.89 6.13
696 4482 3.804325 CGGTAGACCTTGCACATATTCAG 59.196 47.826 0.00 0.00 0.00 3.02
703 4489 3.935203 CCTTGCACATATTCAGTCGAGTT 59.065 43.478 0.00 0.00 0.00 3.01
704 4490 4.201753 CCTTGCACATATTCAGTCGAGTTG 60.202 45.833 0.00 0.00 0.00 3.16
705 4491 3.925379 TGCACATATTCAGTCGAGTTGT 58.075 40.909 0.00 0.00 0.00 3.32
706 4492 3.926527 TGCACATATTCAGTCGAGTTGTC 59.073 43.478 0.00 0.00 0.00 3.18
707 4493 4.177026 GCACATATTCAGTCGAGTTGTCT 58.823 43.478 0.00 0.00 0.00 3.41
708 4494 4.266502 GCACATATTCAGTCGAGTTGTCTC 59.733 45.833 0.00 0.00 37.35 3.36
713 4499 7.441157 ACATATTCAGTCGAGTTGTCTCAAAAA 59.559 33.333 0.00 0.00 40.44 1.94
765 4551 4.321156 CCGAGATCCTGTCTGAATCTGATC 60.321 50.000 0.00 0.00 37.29 2.92
862 4679 3.112709 GGCTCGTGCAACCTCGAC 61.113 66.667 12.07 0.00 41.91 4.20
865 4682 1.444553 CTCGTGCAACCTCGACTCC 60.445 63.158 0.00 0.00 33.87 3.85
950 4770 2.606519 CCCGTCAGGTCCCTCCAA 60.607 66.667 0.00 0.00 39.02 3.53
951 4771 2.660064 CCCGTCAGGTCCCTCCAAG 61.660 68.421 0.00 0.00 39.02 3.61
953 4773 1.481056 CCGTCAGGTCCCTCCAAGTT 61.481 60.000 0.00 0.00 39.02 2.66
962 4785 0.478507 CCCTCCAAGTTCCAACACCT 59.521 55.000 0.00 0.00 0.00 4.00
1120 4944 1.270550 GTGAACTGATGGTTTGGCCTG 59.729 52.381 3.32 0.00 38.41 4.85
1393 5221 2.363795 CCCGCCTCACCTCACCTA 60.364 66.667 0.00 0.00 0.00 3.08
1432 5260 6.304356 CAGTTGTGCAGTTCTGAGATAAAA 57.696 37.500 3.84 0.00 0.00 1.52
1492 5322 5.508872 GCAAATGTTTGTGCAAAAATAGCA 58.491 33.333 5.11 0.00 40.58 3.49
1504 5334 1.734163 AAATAGCAGTGTACGTGCCC 58.266 50.000 14.64 0.00 42.24 5.36
1508 5338 2.380410 GCAGTGTACGTGCCCGAAG 61.380 63.158 8.50 0.00 37.88 3.79
1514 5344 1.868498 TGTACGTGCCCGAAGAAAAAG 59.132 47.619 0.00 0.00 37.88 2.27
1515 5345 2.137523 GTACGTGCCCGAAGAAAAAGA 58.862 47.619 0.00 0.00 37.88 2.52
1516 5346 1.226746 ACGTGCCCGAAGAAAAAGAG 58.773 50.000 0.00 0.00 37.88 2.85
1517 5347 0.110192 CGTGCCCGAAGAAAAAGAGC 60.110 55.000 0.00 0.00 35.63 4.09
1518 5348 0.951558 GTGCCCGAAGAAAAAGAGCA 59.048 50.000 0.00 0.00 0.00 4.26
1572 5404 7.040201 ACGTCCCATAATATAAGAGCGTTTCTA 60.040 37.037 0.00 0.00 34.14 2.10
1601 5433 5.778542 AGTGTATAATCCCTGTCTAGTGGT 58.221 41.667 0.00 0.00 0.00 4.16
1602 5434 5.598830 AGTGTATAATCCCTGTCTAGTGGTG 59.401 44.000 0.00 0.00 0.00 4.17
1605 5437 1.330655 ATCCCTGTCTAGTGGTGGCG 61.331 60.000 0.00 0.00 0.00 5.69
1606 5438 2.125512 CCTGTCTAGTGGTGGCGC 60.126 66.667 0.00 0.00 0.00 6.53
1623 5455 1.470098 GCGCATTGTCAGGAGTTGATT 59.530 47.619 0.30 0.00 38.29 2.57
1625 5457 3.242543 GCGCATTGTCAGGAGTTGATTAG 60.243 47.826 0.30 0.00 38.29 1.73
1650 5490 1.300481 GGAATTCTCGCCCTGTTAGC 58.700 55.000 5.23 0.00 0.00 3.09
1657 5497 3.127533 GCCCTGTTAGCTGTGGCG 61.128 66.667 0.00 0.00 44.37 5.69
1659 5499 3.127533 CCTGTTAGCTGTGGCGCC 61.128 66.667 22.73 22.73 44.37 6.53
1660 5500 3.490759 CTGTTAGCTGTGGCGCCG 61.491 66.667 23.90 8.96 44.37 6.46
1661 5501 3.932580 CTGTTAGCTGTGGCGCCGA 62.933 63.158 23.90 10.19 44.37 5.54
1662 5502 2.740826 GTTAGCTGTGGCGCCGAA 60.741 61.111 23.90 11.71 44.37 4.30
1663 5503 2.106683 GTTAGCTGTGGCGCCGAAT 61.107 57.895 23.90 8.35 44.37 3.34
1664 5504 1.813753 TTAGCTGTGGCGCCGAATC 60.814 57.895 23.90 12.62 44.37 2.52
1686 5526 3.606687 GCCGATCCTTTTAGAAGTTGGA 58.393 45.455 0.00 0.00 0.00 3.53
1687 5527 3.623510 GCCGATCCTTTTAGAAGTTGGAG 59.376 47.826 0.00 0.00 0.00 3.86
1688 5528 4.623171 GCCGATCCTTTTAGAAGTTGGAGA 60.623 45.833 0.00 0.00 0.00 3.71
1717 5557 2.094417 GCCTCATCGTTTTCCTCTTTCG 59.906 50.000 0.00 0.00 0.00 3.46
1718 5558 2.094417 CCTCATCGTTTTCCTCTTTCGC 59.906 50.000 0.00 0.00 0.00 4.70
1720 5560 2.736721 TCATCGTTTTCCTCTTTCGCAG 59.263 45.455 0.00 0.00 0.00 5.18
1724 5564 2.286833 CGTTTTCCTCTTTCGCAGTTCA 59.713 45.455 0.00 0.00 0.00 3.18
1727 5567 2.613026 TCCTCTTTCGCAGTTCAACA 57.387 45.000 0.00 0.00 0.00 3.33
1739 5579 4.260579 CGCAGTTCAACATGTTTACAGTCA 60.261 41.667 8.77 0.00 0.00 3.41
1746 5586 7.106439 TCAACATGTTTACAGTCAACCAATT 57.894 32.000 8.77 0.00 0.00 2.32
1801 5641 2.285220 CGCTGATGGTAATCGGAAGTTG 59.715 50.000 0.00 0.00 41.12 3.16
1802 5642 2.614057 GCTGATGGTAATCGGAAGTTGG 59.386 50.000 0.00 0.00 41.12 3.77
1804 5644 3.869065 TGATGGTAATCGGAAGTTGGTC 58.131 45.455 0.00 0.00 35.37 4.02
1805 5645 2.373540 TGGTAATCGGAAGTTGGTCG 57.626 50.000 0.00 0.00 0.00 4.79
1806 5646 1.894466 TGGTAATCGGAAGTTGGTCGA 59.106 47.619 0.00 0.00 37.33 4.20
1808 5648 2.669924 GGTAATCGGAAGTTGGTCGAAC 59.330 50.000 0.00 0.00 36.49 3.95
1810 5650 2.365408 ATCGGAAGTTGGTCGAACTC 57.635 50.000 0.33 0.00 44.68 3.01
1811 5651 0.039798 TCGGAAGTTGGTCGAACTCG 60.040 55.000 0.33 2.08 44.68 4.18
1836 5676 3.971468 CCCCCTTCCTTGATGGATAAA 57.029 47.619 0.00 0.00 45.68 1.40
1837 5677 3.837355 CCCCCTTCCTTGATGGATAAAG 58.163 50.000 0.00 0.00 45.68 1.85
1839 5679 4.079212 CCCCCTTCCTTGATGGATAAAGAA 60.079 45.833 0.00 0.00 45.68 2.52
1840 5680 5.518865 CCCCTTCCTTGATGGATAAAGAAA 58.481 41.667 0.00 0.00 45.68 2.52
1841 5681 5.957774 CCCCTTCCTTGATGGATAAAGAAAA 59.042 40.000 0.00 0.00 45.68 2.29
1842 5682 6.097412 CCCCTTCCTTGATGGATAAAGAAAAG 59.903 42.308 0.00 0.00 45.68 2.27
1844 5684 7.562821 CCCTTCCTTGATGGATAAAGAAAAGAT 59.437 37.037 0.00 0.00 45.68 2.40
1847 5687 8.970859 TCCTTGATGGATAAAGAAAAGATCTC 57.029 34.615 0.00 0.00 40.56 2.75
1848 5688 8.776119 TCCTTGATGGATAAAGAAAAGATCTCT 58.224 33.333 0.00 0.00 40.56 3.10
1849 5689 8.838365 CCTTGATGGATAAAGAAAAGATCTCTG 58.162 37.037 0.00 0.00 35.94 3.35
1850 5690 9.610705 CTTGATGGATAAAGAAAAGATCTCTGA 57.389 33.333 0.00 0.00 37.42 3.27
1851 5691 9.964354 TTGATGGATAAAGAAAAGATCTCTGAA 57.036 29.630 0.00 0.00 37.42 3.02
1855 5695 9.401058 TGGATAAAGAAAAGATCTCTGAATTCC 57.599 33.333 2.27 0.00 37.42 3.01
1856 5696 8.845227 GGATAAAGAAAAGATCTCTGAATTCCC 58.155 37.037 2.27 0.00 37.42 3.97
1857 5697 9.625747 GATAAAGAAAAGATCTCTGAATTCCCT 57.374 33.333 2.27 0.00 37.42 4.20
1859 5699 8.800370 AAAGAAAAGATCTCTGAATTCCCTAC 57.200 34.615 2.27 0.00 37.42 3.18
1989 6261 8.695456 CCTGCAAAAACACTAGGGATATTAAAT 58.305 33.333 0.00 0.00 0.00 1.40
2093 6365 3.580731 GTGCTTCTAAGGACACAGAGAC 58.419 50.000 9.22 0.00 45.43 3.36
2161 6433 8.208718 TGCTTATACATCCATGTGTTTTAGTC 57.791 34.615 2.26 0.00 41.89 2.59
2182 6458 1.276622 GGAGTTGTAAGGGAGAGCCA 58.723 55.000 0.00 0.00 35.15 4.75
2225 6501 5.464722 GTGTGATGATCAATACCAGCTACAG 59.535 44.000 0.00 0.00 0.00 2.74
2257 6533 1.939934 GCTTATGCACCTTGTATGCGA 59.060 47.619 0.00 0.00 46.49 5.10
2303 6579 3.727970 GCTTAGGAAAAGCACCGATTTCG 60.728 47.826 4.91 0.00 42.56 3.46
2329 6605 6.198966 GGACAAACAAATAAACTTGACAGCTG 59.801 38.462 13.48 13.48 0.00 4.24
2344 6620 9.745018 ACTTGACAGCTGCCATAATAATAATAT 57.255 29.630 15.27 0.00 0.00 1.28
2416 6692 8.765219 GCTTGAAATATTTAGACTCGCATCTAA 58.235 33.333 0.00 4.60 39.01 2.10
2700 6976 6.789268 TGAAAATTTCAGAGGAGGGAACATA 58.211 36.000 4.03 0.00 34.08 2.29
2703 6979 9.408648 GAAAATTTCAGAGGAGGGAACATAATA 57.591 33.333 0.11 0.00 0.00 0.98
2919 7196 4.940046 TCAAGAATAAGCTGAAAGGAGCAG 59.060 41.667 0.00 0.00 41.83 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.922103 AGAAACTCGCGGTAGTTCTAAAAG 59.078 41.667 12.91 0.00 38.76 2.27
31 32 7.763071 ACGAAAACTAAGCGATAGTCCTAAAAT 59.237 33.333 5.81 0.00 44.22 1.82
37 38 5.774878 AAACGAAAACTAAGCGATAGTCC 57.225 39.130 5.81 0.00 44.22 3.85
38 39 7.285788 TCAAAAACGAAAACTAAGCGATAGTC 58.714 34.615 5.81 0.00 44.22 2.59
41 42 7.410800 TCTCAAAAACGAAAACTAAGCGATA 57.589 32.000 0.00 0.00 0.00 2.92
56 57 7.006564 CGAAGCGATAGTTCATTTCTCAAAAAC 59.993 37.037 0.00 0.00 39.35 2.43
155 158 6.285990 ACATCCAAATCGGTATACCTGTAAC 58.714 40.000 19.68 0.00 35.57 2.50
161 164 7.496591 TGAAACTTACATCCAAATCGGTATACC 59.503 37.037 12.27 12.27 35.57 2.73
168 171 8.795786 TTTTCTTGAAACTTACATCCAAATCG 57.204 30.769 0.00 0.00 0.00 3.34
259 262 8.768501 TGAAGTATTTCCTCTAGCAGAGATTA 57.231 34.615 12.91 1.21 45.07 1.75
267 270 7.009723 CGAAGTCTTTGAAGTATTTCCTCTAGC 59.990 40.741 0.00 0.00 32.09 3.42
273 276 9.974750 CTTTATCGAAGTCTTTGAAGTATTTCC 57.025 33.333 6.61 0.00 32.09 3.13
282 285 5.407407 AGCCTCTTTATCGAAGTCTTTGA 57.593 39.130 4.95 4.95 36.70 2.69
283 286 6.100004 TGTAGCCTCTTTATCGAAGTCTTTG 58.900 40.000 0.00 0.00 36.70 2.77
288 291 5.817816 CCAATTGTAGCCTCTTTATCGAAGT 59.182 40.000 4.43 0.00 36.70 3.01
303 306 5.437289 TTGTTGCTTCAGTCCAATTGTAG 57.563 39.130 4.43 0.00 0.00 2.74
305 308 4.099881 ACATTGTTGCTTCAGTCCAATTGT 59.900 37.500 4.43 0.00 0.00 2.71
380 383 1.739035 CGACGGCCTGCATTTCTAGAA 60.739 52.381 0.00 0.00 0.00 2.10
381 384 0.179111 CGACGGCCTGCATTTCTAGA 60.179 55.000 0.00 0.00 0.00 2.43
439 442 5.892119 TGTTGGTTTGGTTATTGTGGAGTTA 59.108 36.000 0.00 0.00 0.00 2.24
444 447 6.149474 TGTTTTTGTTGGTTTGGTTATTGTGG 59.851 34.615 0.00 0.00 0.00 4.17
453 457 7.960195 GTCTGTTAATTGTTTTTGTTGGTTTGG 59.040 33.333 0.00 0.00 0.00 3.28
468 472 6.950545 TGAGTTTACGTTGGTCTGTTAATTG 58.049 36.000 0.00 0.00 0.00 2.32
470 474 7.739498 AATGAGTTTACGTTGGTCTGTTAAT 57.261 32.000 0.00 0.00 0.00 1.40
471 475 7.385752 CCTAATGAGTTTACGTTGGTCTGTTAA 59.614 37.037 0.00 0.00 0.00 2.01
483 487 4.741342 AGTTCGGACCTAATGAGTTTACG 58.259 43.478 0.00 0.00 0.00 3.18
491 495 7.040473 ACTAAGTGATAGTTCGGACCTAATG 57.960 40.000 0.00 0.00 42.31 1.90
532 536 8.397148 ACTACTACTAAGCGATAGTTTGTTCTC 58.603 37.037 9.97 0.00 42.31 2.87
619 633 0.953471 CAACGAGACGGCCCAAATCA 60.953 55.000 0.00 0.00 0.00 2.57
713 4499 5.003804 AGGCACTCGACTGAATATGTTTTT 58.996 37.500 0.00 0.00 0.00 1.94
765 4551 0.806868 ACATGCAGCGTGGAGAAATG 59.193 50.000 19.05 1.66 0.00 2.32
950 4770 1.071471 CCGCTCAGGTGTTGGAACT 59.929 57.895 0.00 0.00 34.51 3.01
951 4771 2.617274 GCCGCTCAGGTGTTGGAAC 61.617 63.158 0.00 0.00 43.70 3.62
953 4773 3.241530 AGCCGCTCAGGTGTTGGA 61.242 61.111 0.00 0.00 43.70 3.53
1393 5221 6.040729 TGCACAACTGCTTGGCATATATAATT 59.959 34.615 0.00 0.00 44.57 1.40
1432 5260 0.761187 AGCATATGAGCACCCGTGAT 59.239 50.000 6.97 0.00 36.85 3.06
1492 5322 0.390124 TTTCTTCGGGCACGTACACT 59.610 50.000 8.89 0.00 41.85 3.55
1534 5366 2.537633 TGGGACGTAGGGAATACAGT 57.462 50.000 0.00 0.00 33.65 3.55
1535 5367 5.740290 ATTATGGGACGTAGGGAATACAG 57.260 43.478 0.00 0.00 33.65 2.74
1540 5372 6.154021 GCTCTTATATTATGGGACGTAGGGAA 59.846 42.308 0.00 0.00 0.00 3.97
1546 5378 5.464030 AACGCTCTTATATTATGGGACGT 57.536 39.130 0.00 0.00 0.00 4.34
1547 5379 6.157211 AGAAACGCTCTTATATTATGGGACG 58.843 40.000 0.00 0.00 0.00 4.79
1572 5404 5.459505 AGACAGGGATTATACACTACTGCT 58.540 41.667 0.00 0.00 0.00 4.24
1601 5433 1.073025 AACTCCTGACAATGCGCCA 59.927 52.632 4.18 0.00 0.00 5.69
1602 5434 0.955428 TCAACTCCTGACAATGCGCC 60.955 55.000 4.18 0.00 0.00 6.53
1605 5437 4.937620 TGACTAATCAACTCCTGACAATGC 59.062 41.667 0.00 0.00 36.69 3.56
1623 5455 2.771943 AGGGCGAGAATTCCATTGACTA 59.228 45.455 0.65 0.00 0.00 2.59
1625 5457 1.672881 CAGGGCGAGAATTCCATTGAC 59.327 52.381 0.65 0.00 0.00 3.18
1659 5499 2.739292 TCTAAAAGGATCGGCGATTCG 58.261 47.619 24.81 8.74 0.00 3.34
1660 5500 4.120589 ACTTCTAAAAGGATCGGCGATTC 58.879 43.478 24.81 22.62 36.78 2.52
1661 5501 4.138487 ACTTCTAAAAGGATCGGCGATT 57.862 40.909 24.81 10.94 36.78 3.34
1662 5502 3.821421 ACTTCTAAAAGGATCGGCGAT 57.179 42.857 24.26 24.26 36.78 4.58
1663 5503 3.259064 CAACTTCTAAAAGGATCGGCGA 58.741 45.455 13.87 13.87 36.78 5.54
1664 5504 2.351726 CCAACTTCTAAAAGGATCGGCG 59.648 50.000 0.00 0.00 36.78 6.46
1665 5505 3.606687 TCCAACTTCTAAAAGGATCGGC 58.393 45.455 0.00 0.00 36.78 5.54
1666 5506 5.086104 TCTCCAACTTCTAAAAGGATCGG 57.914 43.478 0.00 0.00 36.78 4.18
1667 5507 6.398918 TCTTCTCCAACTTCTAAAAGGATCG 58.601 40.000 0.00 0.00 36.78 3.69
1672 5512 7.494298 GGCTATCTCTTCTCCAACTTCTAAAAG 59.506 40.741 0.00 0.00 38.54 2.27
1686 5526 5.452636 GGAAAACGATGAGGCTATCTCTTCT 60.453 44.000 0.00 0.00 41.71 2.85
1687 5527 4.747605 GGAAAACGATGAGGCTATCTCTTC 59.252 45.833 0.00 0.00 42.86 2.87
1688 5528 4.407296 AGGAAAACGATGAGGCTATCTCTT 59.593 41.667 0.00 0.00 42.86 2.85
1717 5557 5.168526 TGACTGTAAACATGTTGAACTGC 57.831 39.130 12.82 12.78 0.00 4.40
1718 5558 5.971202 GGTTGACTGTAAACATGTTGAACTG 59.029 40.000 12.82 17.86 0.00 3.16
1720 5560 5.885881 TGGTTGACTGTAAACATGTTGAAC 58.114 37.500 12.82 13.84 0.00 3.18
1724 5564 7.923878 GGTTAATTGGTTGACTGTAAACATGTT 59.076 33.333 4.92 4.92 0.00 2.71
1727 5567 6.294286 CCGGTTAATTGGTTGACTGTAAACAT 60.294 38.462 10.12 0.00 30.43 2.71
1739 5579 3.945640 AGATAGGCCGGTTAATTGGTT 57.054 42.857 1.90 0.00 0.00 3.67
1746 5586 0.812412 GCGCAAAGATAGGCCGGTTA 60.812 55.000 0.30 0.00 0.00 2.85
1822 5662 8.776119 AGAGATCTTTTCTTTATCCATCAAGGA 58.224 33.333 0.00 0.00 42.83 3.36
1823 5663 8.838365 CAGAGATCTTTTCTTTATCCATCAAGG 58.162 37.037 0.00 0.00 33.74 3.61
1830 5670 8.845227 GGGAATTCAGAGATCTTTTCTTTATCC 58.155 37.037 7.93 0.00 33.74 2.59
1831 5671 9.625747 AGGGAATTCAGAGATCTTTTCTTTATC 57.374 33.333 7.93 0.00 33.74 1.75
1834 5674 8.386264 TGTAGGGAATTCAGAGATCTTTTCTTT 58.614 33.333 7.93 0.00 33.74 2.52
1836 5676 7.502060 TGTAGGGAATTCAGAGATCTTTTCT 57.498 36.000 7.93 0.00 37.41 2.52
1837 5677 8.567285 TTTGTAGGGAATTCAGAGATCTTTTC 57.433 34.615 7.93 0.00 0.00 2.29
1839 5679 8.940397 TTTTTGTAGGGAATTCAGAGATCTTT 57.060 30.769 7.93 0.00 0.00 2.52
1865 5820 9.461312 TGAGTTGAATGCTATGTATAAAGGTTT 57.539 29.630 0.00 0.00 0.00 3.27
1872 5827 9.131791 TGAGTAGTGAGTTGAATGCTATGTATA 57.868 33.333 0.00 0.00 0.00 1.47
1873 5828 8.011844 TGAGTAGTGAGTTGAATGCTATGTAT 57.988 34.615 0.00 0.00 0.00 2.29
1874 5829 7.404671 TGAGTAGTGAGTTGAATGCTATGTA 57.595 36.000 0.00 0.00 0.00 2.29
1876 5831 6.238049 GCTTGAGTAGTGAGTTGAATGCTATG 60.238 42.308 0.00 0.00 0.00 2.23
1877 5832 5.814705 GCTTGAGTAGTGAGTTGAATGCTAT 59.185 40.000 0.00 0.00 0.00 2.97
1878 5833 5.047021 AGCTTGAGTAGTGAGTTGAATGCTA 60.047 40.000 0.00 0.00 0.00 3.49
1882 5837 4.993584 CACAGCTTGAGTAGTGAGTTGAAT 59.006 41.667 0.00 0.00 33.99 2.57
1883 5838 4.371786 CACAGCTTGAGTAGTGAGTTGAA 58.628 43.478 0.00 0.00 33.99 2.69
1885 5840 3.062763 CCACAGCTTGAGTAGTGAGTTG 58.937 50.000 1.41 0.00 33.99 3.16
1917 6189 7.221452 GCACATGAATAAATGGCTTGTAGAAAG 59.779 37.037 0.00 0.00 31.46 2.62
1954 6226 3.131046 AGTGTTTTTGCAGGTTTCAGAGG 59.869 43.478 0.00 0.00 0.00 3.69
1989 6261 9.086758 ACAGATGATGAATATCTCAGTGTATCA 57.913 33.333 0.00 0.00 37.52 2.15
2093 6365 5.088739 GCAAACGATTTCATACACTTCTGG 58.911 41.667 0.00 0.00 0.00 3.86
2161 6433 1.208293 GGCTCTCCCTTACAACTCCAG 59.792 57.143 0.00 0.00 0.00 3.86
2182 6458 3.580458 ACACAGTTCTCTAGGCACAAGAT 59.420 43.478 0.00 0.00 0.00 2.40
2257 6533 9.359653 AGCAAGGCATGATAATTCTTTATTAGT 57.640 29.630 0.00 0.00 32.40 2.24
2303 6579 5.462068 GCTGTCAAGTTTATTTGTTTGTCCC 59.538 40.000 0.00 0.00 0.00 4.46
2344 6620 9.914131 CTCGGAGATGTCATCAGTAATTATTAA 57.086 33.333 15.20 0.00 33.89 1.40
2416 6692 1.228154 GAGAGTTGGCCCCGTGTTT 60.228 57.895 0.00 0.00 0.00 2.83
2419 6695 1.218316 GTAGAGAGTTGGCCCCGTG 59.782 63.158 0.00 0.00 0.00 4.94
2700 6976 7.538575 GTGTTTGTCTATGGCTGAACATTATT 58.461 34.615 0.00 0.00 32.39 1.40
2703 6979 4.083324 CGTGTTTGTCTATGGCTGAACATT 60.083 41.667 0.00 0.00 32.39 2.71
2714 6990 2.157834 TCCGTTGCGTGTTTGTCTAT 57.842 45.000 0.00 0.00 0.00 1.98
2919 7196 5.391312 ACATGTTAAAGGTGCCAATCTTC 57.609 39.130 0.00 0.00 0.00 2.87
3007 7367 6.154363 CAGGTACCCCATATCAAATTTTGTGT 59.846 38.462 8.74 2.77 0.00 3.72
3011 7371 5.363580 CAGCAGGTACCCCATATCAAATTTT 59.636 40.000 8.74 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.