Multiple sequence alignment - TraesCS1D01G119900

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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 TraesCS1D01G119900 chr1D 100.000 2258 0 0 1 2258 116944574 116946831 0 4170
1 TraesCS1D01G119900 chr1A 95.317 2050 69 19 216 2249 128633502 128635540 0 3229
2 TraesCS1D01G119900 chr1B 93.983 964 28 14 706 1659 179506877 179507820 0 1432
3 TraesCS1D01G119900 chr1B 96.198 605 18 4 112 715 179500442 179501042 0 985
4 TraesCS1D01G119900 chr1B 91.737 593 39 8 1658 2249 179507899 179508482 0 815


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 TraesCS1D01G119900 chr1D 116944574 116946831 2257 False 4170.0 4170 100.000 1 2258 1 chr1D.!!$F1 2257
1 TraesCS1D01G119900 chr1A 128633502 128635540 2038 False 3229.0 3229 95.317 216 2249 1 chr1A.!!$F1 2033
2 TraesCS1D01G119900 chr1B 179506877 179508482 1605 False 1123.5 1432 92.860 706 2249 2 chr1B.!!$F2 1543
3 TraesCS1D01G119900 chr1B 179500442 179501042 600 False 985.0 985 96.198 112 715 1 chr1B.!!$F1 603

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
81 82 0.033366 CCTCCGCCCCAAAAAGTTTG 59.967 55.0 0.0 0.0 0.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 2112 0.687354 ACGGTCAGGAATGCAGAGTT 59.313 50.0 0.0 0.0 0.0 3.01 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
23 24 6.795144 ATGATCTGGCCATTCAATACAAAA 57.205 33.333 19.19 0.00 0.00 2.44
24 25 6.602410 TGATCTGGCCATTCAATACAAAAA 57.398 33.333 5.51 0.00 0.00 1.94
25 26 6.397272 TGATCTGGCCATTCAATACAAAAAC 58.603 36.000 5.51 0.00 0.00 2.43
26 27 6.211184 TGATCTGGCCATTCAATACAAAAACT 59.789 34.615 5.51 0.00 0.00 2.66
27 28 6.024552 TCTGGCCATTCAATACAAAAACTC 57.975 37.500 5.51 0.00 0.00 3.01
28 29 5.538053 TCTGGCCATTCAATACAAAAACTCA 59.462 36.000 5.51 0.00 0.00 3.41
29 30 6.211184 TCTGGCCATTCAATACAAAAACTCAT 59.789 34.615 5.51 0.00 0.00 2.90
30 31 6.767456 TGGCCATTCAATACAAAAACTCATT 58.233 32.000 0.00 0.00 0.00 2.57
31 32 6.649973 TGGCCATTCAATACAAAAACTCATTG 59.350 34.615 0.00 0.00 0.00 2.82
32 33 6.650390 GGCCATTCAATACAAAAACTCATTGT 59.350 34.615 0.00 0.00 43.14 2.71
33 34 7.816995 GGCCATTCAATACAAAAACTCATTGTA 59.183 33.333 0.00 2.03 44.69 2.41
34 35 8.647226 GCCATTCAATACAAAAACTCATTGTAC 58.353 33.333 1.60 0.00 43.74 2.90
35 36 9.689976 CCATTCAATACAAAAACTCATTGTACA 57.310 29.630 0.00 0.00 43.74 2.90
41 42 9.840427 AATACAAAAACTCATTGTACATACAGC 57.160 29.630 0.00 0.00 43.74 4.40
42 43 7.270757 ACAAAAACTCATTGTACATACAGCA 57.729 32.000 0.00 0.00 39.14 4.41
43 44 7.711846 ACAAAAACTCATTGTACATACAGCAA 58.288 30.769 0.00 0.00 39.14 3.91
44 45 8.359642 ACAAAAACTCATTGTACATACAGCAAT 58.640 29.630 0.00 0.00 39.14 3.56
45 46 8.641155 CAAAAACTCATTGTACATACAGCAATG 58.359 33.333 0.00 9.43 46.25 2.82
53 54 7.686438 TTGTACATACAGCAATGATCAAACT 57.314 32.000 0.00 0.00 37.52 2.66
54 55 8.785329 TTGTACATACAGCAATGATCAAACTA 57.215 30.769 0.00 0.00 37.52 2.24
55 56 8.962884 TGTACATACAGCAATGATCAAACTAT 57.037 30.769 0.00 0.00 0.00 2.12
63 64 9.712305 ACAGCAATGATCAAACTATATACTACC 57.288 33.333 0.00 0.00 0.00 3.18
64 65 9.935241 CAGCAATGATCAAACTATATACTACCT 57.065 33.333 0.00 0.00 0.00 3.08
66 67 9.372369 GCAATGATCAAACTATATACTACCTCC 57.628 37.037 0.00 0.00 0.00 4.30
67 68 9.574458 CAATGATCAAACTATATACTACCTCCG 57.426 37.037 0.00 0.00 0.00 4.63
68 69 7.154435 TGATCAAACTATATACTACCTCCGC 57.846 40.000 0.00 0.00 0.00 5.54
69 70 5.972107 TCAAACTATATACTACCTCCGCC 57.028 43.478 0.00 0.00 0.00 6.13
70 71 4.768968 TCAAACTATATACTACCTCCGCCC 59.231 45.833 0.00 0.00 0.00 6.13
71 72 3.378861 ACTATATACTACCTCCGCCCC 57.621 52.381 0.00 0.00 0.00 5.80
72 73 2.651334 ACTATATACTACCTCCGCCCCA 59.349 50.000 0.00 0.00 0.00 4.96
73 74 2.708037 ATATACTACCTCCGCCCCAA 57.292 50.000 0.00 0.00 0.00 4.12
74 75 2.475339 TATACTACCTCCGCCCCAAA 57.525 50.000 0.00 0.00 0.00 3.28
75 76 1.587066 ATACTACCTCCGCCCCAAAA 58.413 50.000 0.00 0.00 0.00 2.44
76 77 1.360185 TACTACCTCCGCCCCAAAAA 58.640 50.000 0.00 0.00 0.00 1.94
77 78 0.037734 ACTACCTCCGCCCCAAAAAG 59.962 55.000 0.00 0.00 0.00 2.27
78 79 0.037734 CTACCTCCGCCCCAAAAAGT 59.962 55.000 0.00 0.00 0.00 2.66
79 80 0.479378 TACCTCCGCCCCAAAAAGTT 59.521 50.000 0.00 0.00 0.00 2.66
80 81 0.397957 ACCTCCGCCCCAAAAAGTTT 60.398 50.000 0.00 0.00 0.00 2.66
81 82 0.033366 CCTCCGCCCCAAAAAGTTTG 59.967 55.000 0.00 0.00 0.00 2.93
82 83 0.599991 CTCCGCCCCAAAAAGTTTGC 60.600 55.000 0.00 0.00 0.00 3.68
83 84 1.045911 TCCGCCCCAAAAAGTTTGCT 61.046 50.000 0.00 0.00 0.00 3.91
84 85 0.179059 CCGCCCCAAAAAGTTTGCTT 60.179 50.000 0.00 0.00 36.30 3.91
85 86 1.662517 CGCCCCAAAAAGTTTGCTTT 58.337 45.000 0.00 0.00 46.01 3.51
86 87 2.483889 CCGCCCCAAAAAGTTTGCTTTA 60.484 45.455 0.00 0.00 43.52 1.85
87 88 3.198872 CGCCCCAAAAAGTTTGCTTTAA 58.801 40.909 0.00 0.00 43.52 1.52
88 89 3.623510 CGCCCCAAAAAGTTTGCTTTAAA 59.376 39.130 0.00 0.00 43.52 1.52
89 90 4.274705 CGCCCCAAAAAGTTTGCTTTAAAT 59.725 37.500 0.00 0.00 43.52 1.40
90 91 5.220951 CGCCCCAAAAAGTTTGCTTTAAATT 60.221 36.000 0.00 0.00 43.52 1.82
91 92 6.568869 GCCCCAAAAAGTTTGCTTTAAATTT 58.431 32.000 0.00 0.00 43.52 1.82
92 93 7.467403 CGCCCCAAAAAGTTTGCTTTAAATTTA 60.467 33.333 0.00 0.00 43.52 1.40
93 94 8.356657 GCCCCAAAAAGTTTGCTTTAAATTTAT 58.643 29.630 0.00 0.00 43.52 1.40
94 95 9.891828 CCCCAAAAAGTTTGCTTTAAATTTATC 57.108 29.630 0.00 0.00 43.52 1.75
125 126 9.219603 TGGATGTATCTCTAAGACAAGTTTTTG 57.780 33.333 0.00 0.00 40.24 2.44
127 128 7.979444 TGTATCTCTAAGACAAGTTTTTGGG 57.021 36.000 0.00 0.00 38.66 4.12
135 136 1.533033 AAGTTTTTGGGGGCGGAGG 60.533 57.895 0.00 0.00 0.00 4.30
145 146 2.201708 GGGCGGAGGAGTAGTAGCC 61.202 68.421 0.00 0.00 43.47 3.93
213 214 2.413112 CCTACGACACATGCAAGAGTTG 59.587 50.000 5.36 5.36 0.00 3.16
325 327 3.487544 GCGCCTATGTGTTCCAAATCTTC 60.488 47.826 0.00 0.00 0.00 2.87
517 519 2.802057 GCCGAACGTCACCATTAGCTAT 60.802 50.000 0.00 0.00 0.00 2.97
518 520 3.551454 GCCGAACGTCACCATTAGCTATA 60.551 47.826 0.00 0.00 0.00 1.31
598 601 6.112734 ACGTCTCCAAATCATTGCAGTAATA 58.887 36.000 0.00 0.00 35.10 0.98
599 602 6.037172 ACGTCTCCAAATCATTGCAGTAATAC 59.963 38.462 0.00 0.00 35.10 1.89
634 637 3.777106 TTCCAACTGACAGAAGCATCT 57.223 42.857 10.08 0.00 35.88 2.90
957 962 3.181491 CCTCTGCTCTACTGCTACAGTTC 60.181 52.174 5.44 0.00 42.59 3.01
1086 1095 2.964925 GCCAACGACGACAGCACA 60.965 61.111 0.00 0.00 0.00 4.57
1361 1372 5.487433 TGGTAGAGTGTTTGGTGTATCATG 58.513 41.667 0.00 0.00 0.00 3.07
1498 1509 3.077359 CAACTTCTGGTCTTGGATCACC 58.923 50.000 0.00 0.00 0.00 4.02
1550 1566 8.003784 GTCTTCTTTTGTTCGCATAAATTTTGG 58.996 33.333 0.00 0.00 0.00 3.28
1650 1671 7.664082 AGTAATCATTCGCATATCAAAGGAG 57.336 36.000 0.00 0.00 0.00 3.69
1703 1802 9.623000 AAAATTGATATCACATGACTCAGATGA 57.377 29.630 4.48 0.00 0.00 2.92
1704 1803 8.604640 AATTGATATCACATGACTCAGATGAC 57.395 34.615 4.48 0.00 0.00 3.06
1707 1806 7.376615 TGATATCACATGACTCAGATGACATC 58.623 38.462 7.39 7.39 0.00 3.06
1710 1809 5.658468 TCACATGACTCAGATGACATCTTC 58.342 41.667 15.50 11.31 37.58 2.87
1718 1817 7.601886 TGACTCAGATGACATCTTCTTCTTTTC 59.398 37.037 15.50 4.85 36.76 2.29
1720 1819 8.156165 ACTCAGATGACATCTTCTTCTTTTCTT 58.844 33.333 15.50 0.00 36.76 2.52
1785 1884 7.199048 ACTCCCATGGTATTCCTATCATATGA 58.801 38.462 11.73 8.10 27.31 2.15
1790 1889 7.772292 CCATGGTATTCCTATCATATGAACCAG 59.228 40.741 21.60 14.06 27.31 4.00
1825 1924 5.528600 TTCTGTTTCATCTCCCCCATTAA 57.471 39.130 0.00 0.00 0.00 1.40
1827 1926 3.954258 CTGTTTCATCTCCCCCATTAACC 59.046 47.826 0.00 0.00 0.00 2.85
1890 1989 6.718522 AAGAAAACCCTCGGTTAAAATTCA 57.281 33.333 0.00 0.00 46.20 2.57
1940 2041 0.914644 CATCCTCTCCCTTTCCTGCA 59.085 55.000 0.00 0.00 0.00 4.41
1945 2046 1.208293 CTCTCCCTTTCCTGCACTACC 59.792 57.143 0.00 0.00 0.00 3.18
1988 2089 1.471119 CCAGTAGCAGGAGACGGTTA 58.529 55.000 0.00 0.00 0.00 2.85
2004 2105 3.517901 ACGGTTATGAAGGTGGAGAATCA 59.482 43.478 0.00 0.00 36.25 2.57
2011 2112 3.769300 TGAAGGTGGAGAATCAGAATCGA 59.231 43.478 0.00 0.00 36.25 3.59
2085 2186 5.054477 CAGGACTTGAACTTAAAACTCGGA 58.946 41.667 0.00 0.00 0.00 4.55
2102 2205 7.404671 AACTCGGATTTATAACAATTTGGCT 57.595 32.000 0.78 0.00 0.00 4.75
2103 2206 7.027778 ACTCGGATTTATAACAATTTGGCTC 57.972 36.000 0.78 0.00 0.00 4.70
2104 2207 6.601613 ACTCGGATTTATAACAATTTGGCTCA 59.398 34.615 0.78 0.00 0.00 4.26
2128 2231 0.423544 AGAGGAAGGAGGGGTGGATT 59.576 55.000 0.00 0.00 0.00 3.01
2139 2243 2.511600 GTGGATTCCGTGGAGGCG 60.512 66.667 0.00 0.00 40.77 5.52
2155 2259 1.647629 GCGAAGGAGCGATAGACGA 59.352 57.895 0.00 0.00 45.77 4.20
2210 2314 2.703416 TCCAGCATCATCCGATTATGC 58.297 47.619 16.61 16.61 45.02 3.14
2211 2315 2.038820 TCCAGCATCATCCGATTATGCA 59.961 45.455 23.29 6.24 46.66 3.96
2230 2334 0.694771 ATGCTCTGGCTTTGTCCTCA 59.305 50.000 0.00 0.00 39.59 3.86
2232 2336 1.339438 TGCTCTGGCTTTGTCCTCATC 60.339 52.381 0.00 0.00 39.59 2.92
2245 2349 3.987868 TGTCCTCATCGAGTTTTCTTTCG 59.012 43.478 0.00 0.00 38.13 3.46
2249 2353 3.985008 TCATCGAGTTTTCTTTCGTGGA 58.015 40.909 0.00 0.00 37.99 4.02
2250 2354 3.987868 TCATCGAGTTTTCTTTCGTGGAG 59.012 43.478 0.00 0.00 37.99 3.86
2251 2355 2.132762 TCGAGTTTTCTTTCGTGGAGC 58.867 47.619 0.00 0.00 37.99 4.70
2252 2356 1.194772 CGAGTTTTCTTTCGTGGAGCC 59.805 52.381 0.00 0.00 32.44 4.70
2253 2357 2.218603 GAGTTTTCTTTCGTGGAGCCA 58.781 47.619 0.00 0.00 0.00 4.75
2254 2358 2.222027 AGTTTTCTTTCGTGGAGCCAG 58.778 47.619 0.00 0.00 0.00 4.85
2255 2359 0.951558 TTTTCTTTCGTGGAGCCAGC 59.048 50.000 0.00 0.00 0.00 4.85
2256 2360 0.179032 TTTCTTTCGTGGAGCCAGCA 60.179 50.000 0.00 0.00 0.00 4.41
2257 2361 0.603707 TTCTTTCGTGGAGCCAGCAG 60.604 55.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.795144 TTTTGTATTGAATGGCCAGATCAT 57.205 33.333 21.07 14.51 0.00 2.45
1 2 6.211184 AGTTTTTGTATTGAATGGCCAGATCA 59.789 34.615 17.64 17.64 0.00 2.92
2 3 6.633856 AGTTTTTGTATTGAATGGCCAGATC 58.366 36.000 13.05 13.12 0.00 2.75
3 4 6.211184 TGAGTTTTTGTATTGAATGGCCAGAT 59.789 34.615 13.05 1.55 0.00 2.90
4 5 5.538053 TGAGTTTTTGTATTGAATGGCCAGA 59.462 36.000 13.05 0.00 0.00 3.86
5 6 5.782047 TGAGTTTTTGTATTGAATGGCCAG 58.218 37.500 13.05 0.00 0.00 4.85
6 7 5.798125 TGAGTTTTTGTATTGAATGGCCA 57.202 34.783 8.56 8.56 0.00 5.36
7 8 6.650390 ACAATGAGTTTTTGTATTGAATGGCC 59.350 34.615 0.00 0.00 35.61 5.36
8 9 7.656707 ACAATGAGTTTTTGTATTGAATGGC 57.343 32.000 0.00 0.00 35.61 4.40
9 10 9.689976 TGTACAATGAGTTTTTGTATTGAATGG 57.310 29.630 0.00 0.00 40.55 3.16
15 16 9.840427 GCTGTATGTACAATGAGTTTTTGTATT 57.160 29.630 0.00 0.00 40.55 1.89
16 17 9.008965 TGCTGTATGTACAATGAGTTTTTGTAT 57.991 29.630 0.00 0.00 40.55 2.29
17 18 8.384607 TGCTGTATGTACAATGAGTTTTTGTA 57.615 30.769 0.00 0.00 38.26 2.41
18 19 7.270757 TGCTGTATGTACAATGAGTTTTTGT 57.729 32.000 0.00 0.00 40.30 2.83
19 20 8.746922 ATTGCTGTATGTACAATGAGTTTTTG 57.253 30.769 0.00 0.00 35.50 2.44
28 29 8.284945 AGTTTGATCATTGCTGTATGTACAAT 57.715 30.769 0.00 0.00 35.50 2.71
29 30 7.686438 AGTTTGATCATTGCTGTATGTACAA 57.314 32.000 0.00 0.00 35.50 2.41
30 31 8.962884 ATAGTTTGATCATTGCTGTATGTACA 57.037 30.769 0.00 0.00 34.56 2.90
37 38 9.712305 GGTAGTATATAGTTTGATCATTGCTGT 57.288 33.333 0.00 0.00 0.00 4.40
38 39 9.935241 AGGTAGTATATAGTTTGATCATTGCTG 57.065 33.333 0.00 0.00 0.00 4.41
40 41 9.372369 GGAGGTAGTATATAGTTTGATCATTGC 57.628 37.037 0.00 0.00 0.00 3.56
41 42 9.574458 CGGAGGTAGTATATAGTTTGATCATTG 57.426 37.037 0.00 0.00 0.00 2.82
42 43 8.251721 GCGGAGGTAGTATATAGTTTGATCATT 58.748 37.037 0.00 0.00 0.00 2.57
43 44 7.147880 GGCGGAGGTAGTATATAGTTTGATCAT 60.148 40.741 0.00 0.00 0.00 2.45
44 45 6.152323 GGCGGAGGTAGTATATAGTTTGATCA 59.848 42.308 0.00 0.00 0.00 2.92
45 46 6.405619 GGGCGGAGGTAGTATATAGTTTGATC 60.406 46.154 0.00 0.00 0.00 2.92
46 47 5.421374 GGGCGGAGGTAGTATATAGTTTGAT 59.579 44.000 0.00 0.00 0.00 2.57
47 48 4.768968 GGGCGGAGGTAGTATATAGTTTGA 59.231 45.833 0.00 0.00 0.00 2.69
48 49 4.081807 GGGGCGGAGGTAGTATATAGTTTG 60.082 50.000 0.00 0.00 0.00 2.93
49 50 4.092279 GGGGCGGAGGTAGTATATAGTTT 58.908 47.826 0.00 0.00 0.00 2.66
50 51 3.076484 TGGGGCGGAGGTAGTATATAGTT 59.924 47.826 0.00 0.00 0.00 2.24
51 52 2.651334 TGGGGCGGAGGTAGTATATAGT 59.349 50.000 0.00 0.00 0.00 2.12
52 53 3.377253 TGGGGCGGAGGTAGTATATAG 57.623 52.381 0.00 0.00 0.00 1.31
53 54 3.831642 TTGGGGCGGAGGTAGTATATA 57.168 47.619 0.00 0.00 0.00 0.86
54 55 2.708037 TTGGGGCGGAGGTAGTATAT 57.292 50.000 0.00 0.00 0.00 0.86
55 56 2.475339 TTTGGGGCGGAGGTAGTATA 57.525 50.000 0.00 0.00 0.00 1.47
56 57 1.587066 TTTTGGGGCGGAGGTAGTAT 58.413 50.000 0.00 0.00 0.00 2.12
57 58 1.279846 CTTTTTGGGGCGGAGGTAGTA 59.720 52.381 0.00 0.00 0.00 1.82
58 59 0.037734 CTTTTTGGGGCGGAGGTAGT 59.962 55.000 0.00 0.00 0.00 2.73
59 60 0.037734 ACTTTTTGGGGCGGAGGTAG 59.962 55.000 0.00 0.00 0.00 3.18
60 61 0.479378 AACTTTTTGGGGCGGAGGTA 59.521 50.000 0.00 0.00 0.00 3.08
61 62 0.397957 AAACTTTTTGGGGCGGAGGT 60.398 50.000 0.00 0.00 0.00 3.85
62 63 0.033366 CAAACTTTTTGGGGCGGAGG 59.967 55.000 0.00 0.00 0.00 4.30
63 64 0.599991 GCAAACTTTTTGGGGCGGAG 60.600 55.000 1.07 0.00 0.00 4.63
64 65 1.045911 AGCAAACTTTTTGGGGCGGA 61.046 50.000 1.07 0.00 0.00 5.54
65 66 0.179059 AAGCAAACTTTTTGGGGCGG 60.179 50.000 1.07 0.00 29.41 6.13
66 67 1.662517 AAAGCAAACTTTTTGGGGCG 58.337 45.000 1.07 0.00 43.74 6.13
67 68 5.766150 ATTTAAAGCAAACTTTTTGGGGC 57.234 34.783 0.00 0.00 43.74 5.80
68 69 9.891828 GATAAATTTAAAGCAAACTTTTTGGGG 57.108 29.630 1.21 0.00 43.74 4.96
91 92 9.813826 TGTCTTAGAGATACATCCATTCTGATA 57.186 33.333 0.00 0.00 0.00 2.15
92 93 8.718158 TGTCTTAGAGATACATCCATTCTGAT 57.282 34.615 0.00 0.00 0.00 2.90
93 94 8.539117 TTGTCTTAGAGATACATCCATTCTGA 57.461 34.615 0.00 0.00 0.00 3.27
94 95 8.420222 ACTTGTCTTAGAGATACATCCATTCTG 58.580 37.037 0.00 0.00 0.00 3.02
95 96 8.546083 ACTTGTCTTAGAGATACATCCATTCT 57.454 34.615 0.00 0.00 0.00 2.40
96 97 9.606631 AAACTTGTCTTAGAGATACATCCATTC 57.393 33.333 0.00 0.00 0.00 2.67
97 98 9.965902 AAAACTTGTCTTAGAGATACATCCATT 57.034 29.630 0.00 0.00 0.00 3.16
98 99 9.965902 AAAAACTTGTCTTAGAGATACATCCAT 57.034 29.630 0.00 0.00 0.00 3.41
99 100 9.219603 CAAAAACTTGTCTTAGAGATACATCCA 57.780 33.333 0.00 0.00 0.00 3.41
100 101 8.669243 CCAAAAACTTGTCTTAGAGATACATCC 58.331 37.037 0.00 0.00 0.00 3.51
101 102 8.669243 CCCAAAAACTTGTCTTAGAGATACATC 58.331 37.037 0.00 0.00 0.00 3.06
102 103 7.611855 CCCCAAAAACTTGTCTTAGAGATACAT 59.388 37.037 0.00 0.00 0.00 2.29
103 104 6.940298 CCCCAAAAACTTGTCTTAGAGATACA 59.060 38.462 0.00 0.00 0.00 2.29
104 105 6.374613 CCCCCAAAAACTTGTCTTAGAGATAC 59.625 42.308 0.00 0.00 0.00 2.24
105 106 6.481643 CCCCCAAAAACTTGTCTTAGAGATA 58.518 40.000 0.00 0.00 0.00 1.98
106 107 5.325239 CCCCCAAAAACTTGTCTTAGAGAT 58.675 41.667 0.00 0.00 0.00 2.75
107 108 4.725490 CCCCCAAAAACTTGTCTTAGAGA 58.275 43.478 0.00 0.00 0.00 3.10
108 109 3.255888 GCCCCCAAAAACTTGTCTTAGAG 59.744 47.826 0.00 0.00 0.00 2.43
109 110 3.227614 GCCCCCAAAAACTTGTCTTAGA 58.772 45.455 0.00 0.00 0.00 2.10
110 111 2.030274 CGCCCCCAAAAACTTGTCTTAG 60.030 50.000 0.00 0.00 0.00 2.18
125 126 1.531128 CTACTACTCCTCCGCCCCC 60.531 68.421 0.00 0.00 0.00 5.40
127 128 2.201708 GGCTACTACTCCTCCGCCC 61.202 68.421 0.00 0.00 0.00 6.13
135 136 4.184629 CTGATTTGTGGTGGCTACTACTC 58.815 47.826 17.26 7.72 38.90 2.59
145 146 1.081892 CTCGCTCCTGATTTGTGGTG 58.918 55.000 0.00 0.00 0.00 4.17
233 235 7.509546 AGTAAGCAATGGTACTATTACATGCT 58.490 34.615 9.58 9.58 41.85 3.79
234 236 7.730364 AGTAAGCAATGGTACTATTACATGC 57.270 36.000 3.92 4.92 35.58 4.06
325 327 6.830838 AGCCTGGAGGTGATTAAAATAGAAAG 59.169 38.462 0.00 0.00 37.57 2.62
517 519 6.691508 ACAGATGATATTGATTAGTGCGCTA 58.308 36.000 9.73 1.99 0.00 4.26
518 520 5.545588 ACAGATGATATTGATTAGTGCGCT 58.454 37.500 9.73 4.58 0.00 5.92
598 601 9.113838 GTCAGTTGGAATGTATGATTCTATTGT 57.886 33.333 0.00 0.00 0.00 2.71
599 602 9.112725 TGTCAGTTGGAATGTATGATTCTATTG 57.887 33.333 0.00 0.00 0.00 1.90
612 615 4.008330 AGATGCTTCTGTCAGTTGGAATG 58.992 43.478 0.48 0.00 0.00 2.67
957 962 1.344942 CGAACTTGTCGCGGGAGAAG 61.345 60.000 29.97 29.97 46.16 2.85
1550 1566 7.878127 TCCTACAAAATTCATATCGAATCCCTC 59.122 37.037 0.00 0.00 43.83 4.30
1628 1649 8.675705 TTTCTCCTTTGATATGCGAATGATTA 57.324 30.769 0.00 0.00 0.00 1.75
1684 1783 7.541916 AGATGTCATCTGAGTCATGTGATAT 57.458 36.000 14.73 13.41 38.44 1.63
1723 1822 8.977412 TGTGATAACATACATCTCACTTTCCTA 58.023 33.333 0.00 0.00 37.65 2.94
1724 1823 7.766278 GTGTGATAACATACATCTCACTTTCCT 59.234 37.037 9.21 0.00 40.88 3.36
1725 1824 7.766278 AGTGTGATAACATACATCTCACTTTCC 59.234 37.037 12.03 0.00 46.92 3.13
1726 1825 8.709386 AGTGTGATAACATACATCTCACTTTC 57.291 34.615 12.03 0.00 46.92 2.62
1971 2072 3.014304 TCATAACCGTCTCCTGCTACT 57.986 47.619 0.00 0.00 0.00 2.57
1988 2089 4.406972 TCGATTCTGATTCTCCACCTTCAT 59.593 41.667 0.00 0.00 0.00 2.57
2004 2105 3.196469 TCAGGAATGCAGAGTTCGATTCT 59.804 43.478 0.00 0.00 0.00 2.40
2011 2112 0.687354 ACGGTCAGGAATGCAGAGTT 59.313 50.000 0.00 0.00 0.00 3.01
2085 2186 9.466497 TCTCTCTTGAGCCAAATTGTTATAAAT 57.534 29.630 0.00 0.00 40.03 1.40
2092 2193 3.328931 TCCTCTCTCTTGAGCCAAATTGT 59.671 43.478 0.00 0.00 40.03 2.71
2102 2205 1.007721 CCCCTCCTTCCTCTCTCTTGA 59.992 57.143 0.00 0.00 0.00 3.02
2103 2206 1.273552 ACCCCTCCTTCCTCTCTCTTG 60.274 57.143 0.00 0.00 0.00 3.02
2104 2207 1.097722 ACCCCTCCTTCCTCTCTCTT 58.902 55.000 0.00 0.00 0.00 2.85
2128 2231 3.068691 CTCCTTCGCCTCCACGGA 61.069 66.667 0.00 0.00 33.16 4.69
2139 2243 1.600912 GGCTTCGTCTATCGCTCCTTC 60.601 57.143 0.00 0.00 39.67 3.46
2180 2284 1.895707 GATGCTGGATTGGCCTCGG 60.896 63.158 3.32 0.00 37.63 4.63
2210 2314 1.093159 GAGGACAAAGCCAGAGCATG 58.907 55.000 0.00 0.00 43.56 4.06
2211 2315 0.694771 TGAGGACAAAGCCAGAGCAT 59.305 50.000 0.00 0.00 43.56 3.79
2230 2334 2.737252 GCTCCACGAAAGAAAACTCGAT 59.263 45.455 0.00 0.00 38.43 3.59
2232 2336 1.194772 GGCTCCACGAAAGAAAACTCG 59.805 52.381 0.00 0.00 40.87 4.18


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

AutoCloner maintained by Alex Coulton.