Multiple sequence alignment - TraesCS4B01G108000

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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 TraesCS4B01G108000 chr4B 100.000 5506 0 0 1 5506 118289384 118294889 0.000000e+00 10168.0
1 TraesCS4B01G108000 chr4B 95.588 68 2 1 4132 4198 156532964 156533031 2.100000e-19 108.0
2 TraesCS4B01G108000 chr4A 94.108 3734 147 34 1814 5506 495797131 495800832 0.000000e+00 5609.0
3 TraesCS4B01G108000 chr4A 95.254 1791 65 11 56 1841 495795354 495797129 0.000000e+00 2819.0
4 TraesCS4B01G108000 chr4D 94.454 2290 70 30 3250 5506 83278910 83281175 0.000000e+00 3472.0
5 TraesCS4B01G108000 chr4D 95.711 1842 65 7 1 1841 83275169 83276997 0.000000e+00 2952.0
6 TraesCS4B01G108000 chr4D 93.073 895 34 8 2373 3253 83277628 83278508 0.000000e+00 1284.0
7 TraesCS4B01G108000 chr4D 95.226 398 18 1 1975 2371 83277123 83277520 3.620000e-176 628.0
8 TraesCS4B01G108000 chr4D 93.701 127 8 0 1814 1940 83276999 83277125 2.020000e-44 191.0
9 TraesCS4B01G108000 chr4D 95.652 69 2 1 4131 4198 139042974 139042906 5.830000e-20 110.0
10 TraesCS4B01G108000 chr4D 90.698 43 2 2 4078 4120 453314915 453314955 7.710000e-04 56.5
11 TraesCS4B01G108000 chr1A 97.101 69 1 1 4131 4198 432985396 432985328 1.250000e-21 115.0
12 TraesCS4B01G108000 chr1A 95.455 66 2 1 4131 4195 57303717 57303782 2.710000e-18 104.0
13 TraesCS4B01G108000 chr1A 100.000 28 0 0 4078 4105 432985483 432985456 1.000000e-02 52.8
14 TraesCS4B01G108000 chr7D 95.652 69 2 1 4131 4198 536135312 536135244 5.830000e-20 110.0
15 TraesCS4B01G108000 chr6A 95.238 63 2 1 4133 4194 603354552 603354490 1.260000e-16 99.0
16 TraesCS4B01G108000 chr6B 91.304 69 4 2 4131 4198 431701146 431701213 5.870000e-15 93.5
17 TraesCS4B01G108000 chr2B 100.000 29 0 0 4077 4105 132404561 132404533 3.000000e-03 54.7


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 TraesCS4B01G108000 chr4B 118289384 118294889 5505 False 10168.0 10168 100.000 1 5506 1 chr4B.!!$F1 5505
1 TraesCS4B01G108000 chr4A 495795354 495800832 5478 False 4214.0 5609 94.681 56 5506 2 chr4A.!!$F1 5450
2 TraesCS4B01G108000 chr4D 83275169 83281175 6006 False 1705.4 3472 94.433 1 5506 5 chr4D.!!$F2 5505

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
696 700 0.041312 GTGCTGTTTCGATGCGTGTT 60.041 50.0 0.00 0.00 0.00 3.32 F
924 928 1.224069 CCGCCTCGATTCGATGCAAT 61.224 55.0 27.74 0.00 45.03 3.56 F
1690 1694 0.032912 ATCCATGCCATCACTGCCAA 60.033 50.0 0.00 0.00 0.00 4.52 F
1934 1967 0.109781 GTCGTGTGGCGCATTTGATT 60.110 50.0 10.83 0.00 41.07 2.57 F
2625 2767 0.181114 ACAGGTGAGCTCACTGCAAA 59.819 50.0 38.17 5.13 45.73 3.68 F
4399 5009 0.107945 CCACAGCCTCCTACTCTTGC 60.108 60.0 0.00 0.00 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1594 0.527565 CATACTTTGGCAGCACACCC 59.472 55.000 0.00 0.0 0.00 4.61 R
1941 1974 1.352622 TTCCTTGCTCCACCACTGGT 61.353 55.000 0.00 0.0 38.90 4.00 R
2997 3148 0.769247 AGTAGAACGCCCCAACCTTT 59.231 50.000 0.00 0.0 0.00 3.11 R
3865 4442 2.551270 AGCTCCTCAGGTTACCAATGA 58.449 47.619 3.51 0.0 0.00 2.57 R
4481 5091 0.039180 TACGAAGAGGCCCAGAGACA 59.961 55.000 0.00 0.0 0.00 3.41 R
5463 6073 0.390492 CCTGAGCATGTCGCCATCTA 59.610 55.000 0.00 0.0 44.04 1.98 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
36 37 2.347452 CCAACGACAACTATAAGCACCG 59.653 50.000 0.00 0.00 0.00 4.94
138 140 4.764823 GTGAAACTTGGGTCACATGGATAA 59.235 41.667 0.00 0.00 43.02 1.75
255 257 1.635817 GCCACCTGCTTCCCCTCATA 61.636 60.000 0.00 0.00 36.87 2.15
331 333 2.481185 GGCGGACGTTCATCAAAGTTTA 59.519 45.455 0.00 0.00 0.00 2.01
379 381 5.432157 CGCAATATTAAAACACTAGCGAGG 58.568 41.667 0.00 0.00 44.76 4.63
443 446 4.237976 TCTCCATTCGTCTCCTACTCTT 57.762 45.455 0.00 0.00 0.00 2.85
445 448 3.288964 TCCATTCGTCTCCTACTCTTCC 58.711 50.000 0.00 0.00 0.00 3.46
446 449 3.053544 TCCATTCGTCTCCTACTCTTCCT 60.054 47.826 0.00 0.00 0.00 3.36
447 450 3.316868 CCATTCGTCTCCTACTCTTCCTC 59.683 52.174 0.00 0.00 0.00 3.71
448 451 2.713863 TCGTCTCCTACTCTTCCTCC 57.286 55.000 0.00 0.00 0.00 4.30
539 543 0.537188 ACTGTGGATTAGTGCGAGGG 59.463 55.000 0.00 0.00 0.00 4.30
543 547 2.224670 TGTGGATTAGTGCGAGGGTTTT 60.225 45.455 0.00 0.00 0.00 2.43
605 609 4.173256 GGCCGAATTGGTGAGTATTTTTG 58.827 43.478 0.00 0.00 41.21 2.44
606 610 4.321675 GGCCGAATTGGTGAGTATTTTTGT 60.322 41.667 0.00 0.00 41.21 2.83
607 611 5.227152 GCCGAATTGGTGAGTATTTTTGTT 58.773 37.500 0.00 0.00 41.21 2.83
608 612 5.694458 GCCGAATTGGTGAGTATTTTTGTTT 59.306 36.000 0.00 0.00 41.21 2.83
609 613 6.201997 GCCGAATTGGTGAGTATTTTTGTTTT 59.798 34.615 0.00 0.00 41.21 2.43
670 674 1.338337 TCTTCTTGATCCGCCTCGATC 59.662 52.381 0.00 0.00 39.35 3.69
696 700 0.041312 GTGCTGTTTCGATGCGTGTT 60.041 50.000 0.00 0.00 0.00 3.32
752 756 2.236395 CCTCCAGTTCGGTCCTTTATGT 59.764 50.000 0.00 0.00 35.57 2.29
830 834 4.398549 TTCGAATCTTTGACGCGAATTT 57.601 36.364 15.93 0.00 36.24 1.82
861 865 8.098220 AGAAGAACACAAGCAAAATTGTTTTT 57.902 26.923 0.00 0.00 41.41 1.94
924 928 1.224069 CCGCCTCGATTCGATGCAAT 61.224 55.000 27.74 0.00 45.03 3.56
974 978 4.903054 TCAAATCTCACAGATGTGCTCTT 58.097 39.130 8.11 0.00 45.25 2.85
982 986 2.033801 ACAGATGTGCTCTTTGTTGTGC 59.966 45.455 0.00 0.00 29.16 4.57
1590 1594 0.911525 TTGGGGCAGAGAGGAAGGAG 60.912 60.000 0.00 0.00 0.00 3.69
1655 1659 4.863131 GCGTGCTAAACAGTGAGTATACTT 59.137 41.667 6.88 0.00 0.00 2.24
1688 1692 2.038690 CATCCATGCCATCACTGCC 58.961 57.895 0.00 0.00 0.00 4.85
1689 1693 0.753848 CATCCATGCCATCACTGCCA 60.754 55.000 0.00 0.00 0.00 4.92
1690 1694 0.032912 ATCCATGCCATCACTGCCAA 60.033 50.000 0.00 0.00 0.00 4.52
1691 1695 0.681887 TCCATGCCATCACTGCCAAG 60.682 55.000 0.00 0.00 0.00 3.61
1692 1696 0.968901 CCATGCCATCACTGCCAAGT 60.969 55.000 0.00 0.00 36.98 3.16
1753 1757 4.848562 ATCATTAACGACGATAGCCAGA 57.151 40.909 0.00 0.00 42.67 3.86
1902 1935 6.648879 AAAGCAAGCAATGTAGTCCTTTAA 57.351 33.333 0.00 0.00 0.00 1.52
1925 1958 2.554806 TTCTGTATAGTCGTGTGGCG 57.445 50.000 0.00 0.00 43.01 5.69
1934 1967 0.109781 GTCGTGTGGCGCATTTGATT 60.110 50.000 10.83 0.00 41.07 2.57
1941 1974 2.022934 TGGCGCATTTGATTATGCTCA 58.977 42.857 10.83 3.13 46.81 4.26
2068 2101 5.129155 TGGATTTTAAGGATTGCCAAGATGG 59.871 40.000 0.00 0.00 41.55 3.51
2069 2102 5.129320 GGATTTTAAGGATTGCCAAGATGGT 59.871 40.000 0.00 0.00 40.46 3.55
2072 2105 9.077885 GATTTTAAGGATTGCCAAGATGGTATA 57.922 33.333 0.00 0.00 40.46 1.47
2212 2245 5.127194 GTCACACCTGACAGAATGGATAGTA 59.873 44.000 3.32 0.00 45.57 1.82
2546 2688 1.135527 GCTTGCAGGCAATATGCTCAA 59.864 47.619 16.98 4.25 44.28 3.02
2619 2761 3.624861 CCAATCATTACAGGTGAGCTCAC 59.375 47.826 34.25 34.25 45.72 3.51
2620 2762 4.511527 CAATCATTACAGGTGAGCTCACT 58.488 43.478 38.17 25.19 45.73 3.41
2625 2767 0.181114 ACAGGTGAGCTCACTGCAAA 59.819 50.000 38.17 5.13 45.73 3.68
2627 2769 1.677576 CAGGTGAGCTCACTGCAAAAA 59.322 47.619 38.17 3.56 45.73 1.94
2663 2805 2.358582 CTGTTCCACAATGCAGTGTTGA 59.641 45.455 18.60 17.21 37.82 3.18
2844 2986 0.251073 ACGTGGTAAGTATGCCCACC 59.749 55.000 0.00 0.00 44.66 4.61
2972 3123 9.965902 AGTGAACTTTAGAGATACCATTTTGAT 57.034 29.630 0.00 0.00 0.00 2.57
3070 3221 6.947464 TGAGTTTCTTAGGTAAGATTGAGGG 58.053 40.000 0.29 0.00 41.52 4.30
3099 3250 6.363577 CAAGTAGTTGGGTACATGCATAAG 57.636 41.667 0.00 0.00 0.00 1.73
3231 3391 8.234136 TGTCTTCTCAGTGAAAAGTCTAAGTA 57.766 34.615 6.11 0.00 33.79 2.24
3241 3401 8.095169 AGTGAAAAGTCTAAGTAATGGGTACAG 58.905 37.037 0.00 0.00 34.88 2.74
3335 3900 3.507162 TGGTGCTCAAATTCTGGAGAA 57.493 42.857 6.06 0.00 38.56 2.87
3343 3908 6.091437 GCTCAAATTCTGGAGAAATGTCTTG 58.909 40.000 6.06 0.00 37.61 3.02
3344 3909 6.294397 GCTCAAATTCTGGAGAAATGTCTTGT 60.294 38.462 6.06 0.00 37.61 3.16
3346 3911 6.772233 TCAAATTCTGGAGAAATGTCTTGTCA 59.228 34.615 0.00 0.00 37.61 3.58
3352 3927 5.624159 TGGAGAAATGTCTTGTCATTGTCT 58.376 37.500 0.00 0.00 37.96 3.41
3409 3984 8.401490 AGCATCCTCATAAAAGTTTGATATCC 57.599 34.615 0.00 0.00 0.00 2.59
3645 4221 6.658391 TGAACATATCATGTGTCATGGACAAA 59.342 34.615 9.39 0.00 44.07 2.83
3769 4346 4.971830 CGCATGTGTCCATTCAAATCATAC 59.028 41.667 0.00 0.00 0.00 2.39
3787 4364 5.419542 TCATACTCAACATGCTAGTGGTTC 58.580 41.667 0.00 0.00 0.00 3.62
3847 4424 6.051717 GCTTTCATGCCTAAGATAGTGAGAA 58.948 40.000 6.32 0.00 0.00 2.87
3865 4442 7.164803 AGTGAGAAATTGCTAGCTAAGAAACT 58.835 34.615 17.23 7.39 0.00 2.66
4015 4592 1.298859 CCTCAGTGCCAAACGTAGCC 61.299 60.000 0.00 0.00 0.00 3.93
4063 4640 4.152938 CGAACATCTTCTGCACAAGATTCA 59.847 41.667 13.85 0.00 40.52 2.57
4092 4669 3.691575 TGGGTTCACTGTTTTTGAGTCA 58.308 40.909 0.00 0.00 0.00 3.41
4113 4698 3.899836 CGACTAGTCGCATCGAGTT 57.100 52.632 30.44 0.00 46.50 3.01
4120 4705 4.633126 ACTAGTCGCATCGAGTTGTAACTA 59.367 41.667 8.81 0.00 41.58 2.24
4127 4712 4.689345 GCATCGAGTTGTAACTACAAGGTT 59.311 41.667 2.53 0.00 45.82 3.50
4128 4713 5.389516 GCATCGAGTTGTAACTACAAGGTTG 60.390 44.000 2.53 3.42 45.82 3.77
4180 4789 1.313812 CGCTACCCCAGAACGACTCT 61.314 60.000 0.00 0.00 33.23 3.24
4292 4902 8.463930 AGAAAAATGAAATGGTCTGACTGTTA 57.536 30.769 7.85 0.00 0.00 2.41
4293 4903 9.082313 AGAAAAATGAAATGGTCTGACTGTTAT 57.918 29.630 7.85 0.00 0.00 1.89
4294 4904 9.696917 GAAAAATGAAATGGTCTGACTGTTATT 57.303 29.630 7.85 1.82 0.00 1.40
4302 4912 6.726490 TGGTCTGACTGTTATTATACTCCC 57.274 41.667 7.85 0.00 0.00 4.30
4340 4950 2.356069 GGAGATGTTTGAGCGGGAAATC 59.644 50.000 0.00 0.00 0.00 2.17
4349 4959 1.877165 GCGGGAAATCGGTCGTCTC 60.877 63.158 0.00 0.00 0.00 3.36
4399 5009 0.107945 CCACAGCCTCCTACTCTTGC 60.108 60.000 0.00 0.00 0.00 4.01
4427 5037 1.709578 ACAGCAGAGACCTTGACTCA 58.290 50.000 0.00 0.00 36.91 3.41
4454 5064 3.446799 TGCAAGCATGTCTTTGAAACAC 58.553 40.909 9.83 0.00 31.27 3.32
4521 5131 6.202188 TCGTACTTAGTTCTTTCAGCCTTTTG 59.798 38.462 0.00 0.00 0.00 2.44
4839 5449 5.446260 TCCTAGGGTTCTAATTTGTTCCC 57.554 43.478 9.46 11.53 35.56 3.97
4937 5547 5.114785 AGCACTAGTTAGCATCTGATACG 57.885 43.478 7.83 0.00 0.00 3.06
5085 5695 8.958119 ACTTCACTGTGAAATTCTGTAAGTTA 57.042 30.769 22.25 0.00 35.73 2.24
5185 5795 1.003355 AGTATGGCTGTGCTTGCGT 60.003 52.632 0.00 0.00 0.00 5.24
5207 5817 6.738649 GCGTTTTAAACTTTGCAAAATGTGAA 59.261 30.769 13.84 0.00 32.98 3.18
5208 5818 7.269297 GCGTTTTAAACTTTGCAAAATGTGAAA 59.731 29.630 13.84 4.99 32.98 2.69
5209 5819 8.774967 CGTTTTAAACTTTGCAAAATGTGAAAG 58.225 29.630 13.84 0.95 33.83 2.62
5210 5820 9.060547 GTTTTAAACTTTGCAAAATGTGAAAGG 57.939 29.630 13.84 0.54 32.82 3.11
5211 5821 5.816449 AAACTTTGCAAAATGTGAAAGGG 57.184 34.783 13.84 0.00 32.82 3.95
5212 5822 4.486125 ACTTTGCAAAATGTGAAAGGGT 57.514 36.364 13.84 0.45 32.82 4.34
5213 5823 4.842574 ACTTTGCAAAATGTGAAAGGGTT 58.157 34.783 13.84 0.00 32.82 4.11
5214 5824 5.983540 ACTTTGCAAAATGTGAAAGGGTTA 58.016 33.333 13.84 0.00 32.82 2.85
5215 5825 6.591001 ACTTTGCAAAATGTGAAAGGGTTAT 58.409 32.000 13.84 0.00 32.82 1.89
5216 5826 7.731054 ACTTTGCAAAATGTGAAAGGGTTATA 58.269 30.769 13.84 0.00 32.82 0.98
5228 5838 9.594478 TGTGAAAGGGTTATATACATATATGCG 57.406 33.333 12.79 0.00 31.69 4.73
5250 5860 4.069232 CGGAGCTTCACGAGGGCA 62.069 66.667 0.00 0.00 0.00 5.36
5309 5919 6.228258 AGCAAGATACAACGTAGGAAGAAAA 58.772 36.000 0.00 0.00 0.00 2.29
5310 5920 6.708949 AGCAAGATACAACGTAGGAAGAAAAA 59.291 34.615 0.00 0.00 0.00 1.94
5358 5968 2.298158 ATCGCCGCTACCACCTTGAG 62.298 60.000 0.00 0.00 0.00 3.02
5408 6018 6.764308 AAATGTGAAAGATGACCCACATAG 57.236 37.500 0.00 0.00 46.00 2.23
5463 6073 2.071778 TTTGGTCTGGAAAGCAAGCT 57.928 45.000 0.00 0.00 37.86 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.000938 AGTTGTCGTTGGACGGTCTAC 60.001 52.381 8.23 6.05 46.49 2.59
12 13 3.060363 GTGCTTATAGTTGTCGTTGGACG 59.940 47.826 0.00 0.00 46.49 4.79
16 17 2.347452 CCGGTGCTTATAGTTGTCGTTG 59.653 50.000 0.00 0.00 0.00 4.10
18 19 1.820519 TCCGGTGCTTATAGTTGTCGT 59.179 47.619 0.00 0.00 0.00 4.34
36 37 8.708742 GGCTTTACAATAGTTTTGATTTGTTCC 58.291 33.333 0.00 0.00 34.39 3.62
200 202 2.829720 AGAGATGTAAACGCTGTGGGTA 59.170 45.455 0.00 0.00 0.00 3.69
203 205 1.920574 CGAGAGATGTAAACGCTGTGG 59.079 52.381 0.00 0.00 0.00 4.17
255 257 9.171877 GAAATCTGGTGAGAATTATTGTCTTCT 57.828 33.333 3.81 0.00 34.48 2.85
331 333 3.059166 GCGACAAGAAATTGGTTTGCAT 58.941 40.909 0.00 0.00 0.00 3.96
609 613 3.692101 TCGCAGAGAGAAACAACCAAAAA 59.308 39.130 0.00 0.00 0.00 1.94
624 628 1.699656 CCGCACCAAGAATCGCAGAG 61.700 60.000 0.00 0.00 43.63 3.35
670 674 1.568612 ATCGAAACAGCACGGCACAG 61.569 55.000 0.00 0.00 0.00 3.66
696 700 3.434637 GAAGAAAACGCAGCAGAAACAA 58.565 40.909 0.00 0.00 0.00 2.83
752 756 0.252057 TGGTCAAGATCCGAGGTCCA 60.252 55.000 0.00 0.00 0.00 4.02
830 834 1.202592 TGCTTGTGTTCTTCTACGGCA 60.203 47.619 0.00 0.00 0.00 5.69
861 865 3.681417 CAGATCTCAGCAAACGACATGAA 59.319 43.478 0.00 0.00 0.00 2.57
867 871 1.338105 CCCACAGATCTCAGCAAACGA 60.338 52.381 0.00 0.00 0.00 3.85
974 978 0.179150 GACCAAACTGCGCACAACAA 60.179 50.000 5.66 0.00 0.00 2.83
982 986 1.016130 ATCTGCTCGACCAAACTGCG 61.016 55.000 0.00 0.00 0.00 5.18
1257 1261 4.039357 CTCGACGACCTGCGGTGT 62.039 66.667 4.94 4.26 46.49 4.16
1428 1432 2.053865 CGGCATGCCTTGTTCCCAT 61.054 57.895 33.07 0.00 0.00 4.00
1590 1594 0.527565 CATACTTTGGCAGCACACCC 59.472 55.000 0.00 0.00 0.00 4.61
1721 1725 8.642908 ATCGTCGTTAATGATTCTCAATTGTA 57.357 30.769 5.13 0.00 28.68 2.41
1919 1952 2.206815 GCATAATCAAATGCGCCACA 57.793 45.000 4.18 0.00 42.57 4.17
1925 1958 7.123218 ACCACTGGTGAGCATAATCAAATGC 62.123 44.000 0.00 0.58 42.89 3.56
1941 1974 1.352622 TTCCTTGCTCCACCACTGGT 61.353 55.000 0.00 0.00 38.90 4.00
2068 2101 7.041780 CCTCATGTTTCCTAAGTGCATGTATAC 60.042 40.741 0.00 0.00 38.35 1.47
2069 2102 6.992123 CCTCATGTTTCCTAAGTGCATGTATA 59.008 38.462 0.00 0.00 38.35 1.47
2072 2105 4.012374 CCTCATGTTTCCTAAGTGCATGT 58.988 43.478 0.00 0.00 38.35 3.21
2212 2245 7.178274 TGTTTTACATTTATGTTGCCAGAGGAT 59.822 33.333 0.02 0.00 41.97 3.24
2466 2607 7.476667 TGGAAATGTTTAACCATGCTATTACG 58.523 34.615 0.00 0.00 0.00 3.18
2515 2656 1.403249 GCCTGCAAGCAATGTTGGTAG 60.403 52.381 1.41 0.00 38.04 3.18
2546 2688 3.121544 GAGTTTTCGAACACGAGACCTT 58.878 45.455 8.70 0.00 37.35 3.50
2997 3148 0.769247 AGTAGAACGCCCCAACCTTT 59.231 50.000 0.00 0.00 0.00 3.11
3012 3163 6.308282 GTCCTCATTAACGTCACAGAAAGTAG 59.692 42.308 0.00 0.00 0.00 2.57
3070 3221 4.075963 TGTACCCAACTACTTGGTTGAC 57.924 45.455 7.01 0.00 46.55 3.18
3124 3275 9.612879 TCATATTTCTCCTCTCCAGAAGATATT 57.387 33.333 0.00 0.00 32.19 1.28
3125 3276 9.612879 TTCATATTTCTCCTCTCCAGAAGATAT 57.387 33.333 0.00 0.00 32.19 1.63
3126 3277 9.439461 TTTCATATTTCTCCTCTCCAGAAGATA 57.561 33.333 0.00 0.00 32.19 1.98
3127 3278 7.927683 TTCATATTTCTCCTCTCCAGAAGAT 57.072 36.000 0.00 0.00 32.19 2.40
3137 3288 7.659390 CCATCCACTAGTTTCATATTTCTCCTC 59.341 40.741 0.00 0.00 0.00 3.71
3231 3391 7.971368 AAACTTATTTATGCCTGTACCCATT 57.029 32.000 0.00 0.00 0.00 3.16
3294 3859 7.567048 GCACCATCGATATTTAACAGTAGTTCG 60.567 40.741 0.00 0.00 39.15 3.95
3335 3900 7.716998 ACTTCTTACAGACAATGACAAGACATT 59.283 33.333 0.00 0.00 40.50 2.71
3343 3908 7.324178 ACCATAGACTTCTTACAGACAATGAC 58.676 38.462 0.00 0.00 0.00 3.06
3344 3909 7.482169 ACCATAGACTTCTTACAGACAATGA 57.518 36.000 0.00 0.00 0.00 2.57
3346 3911 7.907389 TCAACCATAGACTTCTTACAGACAAT 58.093 34.615 0.00 0.00 0.00 2.71
3352 3927 9.706691 CTAAAGTTCAACCATAGACTTCTTACA 57.293 33.333 0.00 0.00 0.00 2.41
3364 3939 3.507622 GCTTCAGCCTAAAGTTCAACCAT 59.492 43.478 0.00 0.00 34.31 3.55
3365 3940 2.884639 GCTTCAGCCTAAAGTTCAACCA 59.115 45.455 0.00 0.00 34.31 3.67
3409 3984 8.854979 TGAGTTCACTTAAAACATGATTGTTG 57.145 30.769 0.00 0.00 45.30 3.33
3712 4288 6.691508 TCGTATGCATGAATATACAGAAGCT 58.308 36.000 10.16 0.00 31.65 3.74
3746 4322 3.490800 TGATTTGAATGGACACATGCG 57.509 42.857 0.00 0.00 35.19 4.73
3769 4346 6.595326 TGAAATAGAACCACTAGCATGTTGAG 59.405 38.462 0.00 0.00 34.35 3.02
3787 4364 6.855836 AGCATACACAAACCACATGAAATAG 58.144 36.000 0.00 0.00 0.00 1.73
3847 4424 6.660949 ACCAATGAGTTTCTTAGCTAGCAATT 59.339 34.615 18.83 0.00 0.00 2.32
3865 4442 2.551270 AGCTCCTCAGGTTACCAATGA 58.449 47.619 3.51 0.00 0.00 2.57
3983 4560 4.598807 TGGCACTGAGGTGGATTATGATAT 59.401 41.667 0.00 0.00 43.18 1.63
4063 4640 7.616313 TCAAAAACAGTGAACCCAATTAAACT 58.384 30.769 0.00 0.00 0.00 2.66
4106 4683 6.092955 TCAACCTTGTAGTTACAACTCGAT 57.907 37.500 0.00 0.00 40.93 3.59
4107 4684 5.518848 TCAACCTTGTAGTTACAACTCGA 57.481 39.130 0.00 0.00 40.93 4.04
4113 4698 4.053295 GCGACTTCAACCTTGTAGTTACA 58.947 43.478 0.00 0.00 38.64 2.41
4120 4705 1.670811 CAGTTGCGACTTCAACCTTGT 59.329 47.619 3.02 0.00 45.47 3.16
4127 4712 1.597854 CCCTGCAGTTGCGACTTCA 60.598 57.895 13.81 4.87 45.83 3.02
4128 4713 1.569479 GACCCTGCAGTTGCGACTTC 61.569 60.000 13.81 0.00 45.83 3.01
4180 4789 3.496884 CCAATCAAGGTTTTCGAGTCGAA 59.503 43.478 23.54 23.54 44.28 3.71
4276 4886 8.211629 GGGAGTATAATAACAGTCAGACCATTT 58.788 37.037 0.00 0.00 0.00 2.32
4292 4902 7.998383 TGTTGAACTGCAATATGGGAGTATAAT 59.002 33.333 4.46 0.00 38.61 1.28
4293 4903 7.342581 TGTTGAACTGCAATATGGGAGTATAA 58.657 34.615 4.46 1.08 38.61 0.98
4294 4904 6.894682 TGTTGAACTGCAATATGGGAGTATA 58.105 36.000 4.46 0.00 38.61 1.47
4295 4905 5.754782 TGTTGAACTGCAATATGGGAGTAT 58.245 37.500 4.46 0.00 38.61 2.12
4302 4912 5.356190 ACATCTCCTGTTGAACTGCAATATG 59.644 40.000 0.00 1.26 39.03 1.78
4340 4950 0.243907 ACAATGACCTGAGACGACCG 59.756 55.000 0.00 0.00 0.00 4.79
4349 4959 2.612672 CTGCTGCTGATACAATGACCTG 59.387 50.000 0.00 0.00 0.00 4.00
4399 5009 3.011119 AGGTCTCTGCTGTTACTACGAG 58.989 50.000 0.00 0.00 0.00 4.18
4427 5037 3.130869 TCAAAGACATGCTTGCAAACTGT 59.869 39.130 0.00 4.22 36.80 3.55
4481 5091 0.039180 TACGAAGAGGCCCAGAGACA 59.961 55.000 0.00 0.00 0.00 3.41
4521 5131 2.287103 GTGGTTTGGAACTCACGAGAAC 59.713 50.000 0.00 0.00 0.00 3.01
4602 5212 1.067354 CAAATGTGCTGCTCCTTTCCC 60.067 52.381 0.00 0.00 0.00 3.97
4839 5449 4.750098 ACAACATAGAGAAACAAGACCACG 59.250 41.667 0.00 0.00 0.00 4.94
4937 5547 3.924144 TGTGGCACATTTAAAAGCATCC 58.076 40.909 17.96 2.47 44.52 3.51
5037 5647 1.948834 CAGCATGTCAACACCAAGTCA 59.051 47.619 0.00 0.00 0.00 3.41
5085 5695 5.589855 TGTATCAAATGAAACGAGATGGCAT 59.410 36.000 0.00 0.00 0.00 4.40
5185 5795 8.239998 CCCTTTCACATTTTGCAAAGTTTAAAA 58.760 29.630 12.41 10.48 0.00 1.52
5207 5817 7.217200 CCAGCGCATATATGTATATAACCCTT 58.783 38.462 11.47 0.00 0.00 3.95
5208 5818 6.741521 GCCAGCGCATATATGTATATAACCCT 60.742 42.308 11.47 0.00 34.03 4.34
5209 5819 5.408604 GCCAGCGCATATATGTATATAACCC 59.591 44.000 11.47 0.00 34.03 4.11
5210 5820 5.118664 CGCCAGCGCATATATGTATATAACC 59.881 44.000 11.47 0.00 34.03 2.85
5211 5821 5.118664 CCGCCAGCGCATATATGTATATAAC 59.881 44.000 11.47 0.00 38.24 1.89
5212 5822 5.010213 TCCGCCAGCGCATATATGTATATAA 59.990 40.000 11.47 0.00 38.24 0.98
5213 5823 4.521256 TCCGCCAGCGCATATATGTATATA 59.479 41.667 11.47 0.00 38.24 0.86
5214 5824 3.320826 TCCGCCAGCGCATATATGTATAT 59.679 43.478 11.47 0.00 38.24 0.86
5215 5825 2.691011 TCCGCCAGCGCATATATGTATA 59.309 45.455 11.47 0.00 38.24 1.47
5216 5826 1.480545 TCCGCCAGCGCATATATGTAT 59.519 47.619 11.47 0.00 38.24 2.29
5279 5889 7.812690 TCCTACGTTGTATCTTGCTTATCTA 57.187 36.000 0.00 0.00 0.00 1.98
5309 5919 6.208599 TGCTGGAATAAGGTTTCTTCGATTTT 59.791 34.615 0.00 0.00 34.59 1.82
5310 5920 5.710099 TGCTGGAATAAGGTTTCTTCGATTT 59.290 36.000 0.00 0.00 34.59 2.17
5332 5942 4.017877 GTAGCGGCGATGGCATGC 62.018 66.667 12.98 9.90 42.47 4.06
5463 6073 0.390492 CCTGAGCATGTCGCCATCTA 59.610 55.000 0.00 0.00 44.04 1.98


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

AutoCloner maintained by Alex Coulton.