Multiple sequence alignment - TraesCS3B01G351500

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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 TraesCS3B01G351500 chr3B 100.000 2336 0 0 1 2336 561542236 561539901 0 4314
1 TraesCS3B01G351500 chr3D 91.927 2304 108 36 58 2336 429600015 429597765 0 3153
2 TraesCS3B01G351500 chr3A 91.853 2234 127 21 127 2336 556458087 556460289 0 3066


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 TraesCS3B01G351500 chr3B 561539901 561542236 2335 True 4314 4314 100.000 1 2336 1 chr3B.!!$R1 2335
1 TraesCS3B01G351500 chr3D 429597765 429600015 2250 True 3153 3153 91.927 58 2336 1 chr3D.!!$R1 2278
2 TraesCS3B01G351500 chr3A 556458087 556460289 2202 False 3066 3066 91.853 127 2336 1 chr3A.!!$F1 2209

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
150 151 0.029035 CGGCTCGTCGCTTACAGTAT 59.971 55.0 0.0 0.0 39.13 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 1733 1.128692 GACAACATTTCTCGGCGAAGG 59.871 52.381 12.13 0.0 32.21 3.46 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
18 19 4.399180 TCGTTCCTCGAGAGTGCT 57.601 55.556 15.71 0.00 44.01 4.40
19 20 2.642425 TCGTTCCTCGAGAGTGCTT 58.358 52.632 15.71 0.00 44.01 3.91
20 21 0.959553 TCGTTCCTCGAGAGTGCTTT 59.040 50.000 15.71 0.00 44.01 3.51
21 22 1.063806 CGTTCCTCGAGAGTGCTTTG 58.936 55.000 15.71 0.00 42.86 2.77
22 23 1.603172 CGTTCCTCGAGAGTGCTTTGT 60.603 52.381 15.71 0.00 42.86 2.83
23 24 1.795286 GTTCCTCGAGAGTGCTTTGTG 59.205 52.381 15.71 0.00 0.00 3.33
24 25 1.040646 TCCTCGAGAGTGCTTTGTGT 58.959 50.000 15.71 0.00 0.00 3.72
25 26 1.143305 CCTCGAGAGTGCTTTGTGTG 58.857 55.000 15.71 0.00 0.00 3.82
26 27 1.539065 CCTCGAGAGTGCTTTGTGTGT 60.539 52.381 15.71 0.00 0.00 3.72
27 28 1.789464 CTCGAGAGTGCTTTGTGTGTC 59.211 52.381 6.58 0.00 0.00 3.67
28 29 1.409064 TCGAGAGTGCTTTGTGTGTCT 59.591 47.619 0.00 0.00 0.00 3.41
29 30 1.789464 CGAGAGTGCTTTGTGTGTCTC 59.211 52.381 0.00 0.00 0.00 3.36
30 31 2.544694 CGAGAGTGCTTTGTGTGTCTCT 60.545 50.000 0.00 0.00 35.41 3.10
31 32 2.799412 GAGAGTGCTTTGTGTGTCTCTG 59.201 50.000 0.00 0.00 33.31 3.35
32 33 2.169352 AGAGTGCTTTGTGTGTCTCTGT 59.831 45.455 0.00 0.00 32.19 3.41
33 34 3.384789 AGAGTGCTTTGTGTGTCTCTGTA 59.615 43.478 0.00 0.00 32.19 2.74
34 35 3.458189 AGTGCTTTGTGTGTCTCTGTAC 58.542 45.455 0.00 0.00 0.00 2.90
35 36 3.133003 AGTGCTTTGTGTGTCTCTGTACT 59.867 43.478 0.00 0.00 0.00 2.73
36 37 4.341235 AGTGCTTTGTGTGTCTCTGTACTA 59.659 41.667 0.00 0.00 0.00 1.82
37 38 5.011125 AGTGCTTTGTGTGTCTCTGTACTAT 59.989 40.000 0.00 0.00 0.00 2.12
38 39 5.696724 GTGCTTTGTGTGTCTCTGTACTATT 59.303 40.000 0.00 0.00 0.00 1.73
39 40 5.926542 TGCTTTGTGTGTCTCTGTACTATTC 59.073 40.000 0.00 0.00 0.00 1.75
40 41 6.159988 GCTTTGTGTGTCTCTGTACTATTCT 58.840 40.000 0.00 0.00 0.00 2.40
41 42 6.647067 GCTTTGTGTGTCTCTGTACTATTCTT 59.353 38.462 0.00 0.00 0.00 2.52
42 43 7.148722 GCTTTGTGTGTCTCTGTACTATTCTTC 60.149 40.741 0.00 0.00 0.00 2.87
43 44 6.268825 TGTGTGTCTCTGTACTATTCTTCC 57.731 41.667 0.00 0.00 0.00 3.46
44 45 5.773176 TGTGTGTCTCTGTACTATTCTTCCA 59.227 40.000 0.00 0.00 0.00 3.53
45 46 6.071896 TGTGTGTCTCTGTACTATTCTTCCAG 60.072 42.308 0.00 0.00 0.00 3.86
46 47 6.010850 TGTGTCTCTGTACTATTCTTCCAGT 58.989 40.000 0.00 0.00 0.00 4.00
47 48 7.120873 GTGTGTCTCTGTACTATTCTTCCAGTA 59.879 40.741 0.00 0.00 0.00 2.74
48 49 7.834681 TGTGTCTCTGTACTATTCTTCCAGTAT 59.165 37.037 0.00 0.00 30.37 2.12
49 50 8.132362 GTGTCTCTGTACTATTCTTCCAGTATG 58.868 40.741 0.00 0.00 30.37 2.39
50 51 7.834681 TGTCTCTGTACTATTCTTCCAGTATGT 59.165 37.037 0.00 0.00 30.37 2.29
51 52 8.132362 GTCTCTGTACTATTCTTCCAGTATGTG 58.868 40.741 0.00 0.00 30.37 3.21
52 53 6.806751 TCTGTACTATTCTTCCAGTATGTGC 58.193 40.000 0.00 0.00 30.37 4.57
53 54 6.607600 TCTGTACTATTCTTCCAGTATGTGCT 59.392 38.462 0.00 0.00 30.37 4.40
54 55 7.124298 TCTGTACTATTCTTCCAGTATGTGCTT 59.876 37.037 0.00 0.00 30.37 3.91
55 56 7.265673 TGTACTATTCTTCCAGTATGTGCTTC 58.734 38.462 0.00 0.00 30.37 3.86
56 57 6.299805 ACTATTCTTCCAGTATGTGCTTCA 57.700 37.500 0.00 0.00 0.00 3.02
62 63 2.299013 TCCAGTATGTGCTTCAGTCGTT 59.701 45.455 0.00 0.00 0.00 3.85
65 66 2.987149 AGTATGTGCTTCAGTCGTTTCG 59.013 45.455 0.00 0.00 0.00 3.46
73 74 0.596577 TCAGTCGTTTCGGGACTCTG 59.403 55.000 0.00 0.00 42.63 3.35
75 76 1.538512 CAGTCGTTTCGGGACTCTGTA 59.461 52.381 0.00 0.00 42.63 2.74
76 77 2.163815 CAGTCGTTTCGGGACTCTGTAT 59.836 50.000 0.00 0.00 42.63 2.29
77 78 2.163815 AGTCGTTTCGGGACTCTGTATG 59.836 50.000 0.00 0.00 40.63 2.39
78 79 2.094854 GTCGTTTCGGGACTCTGTATGT 60.095 50.000 0.00 0.00 0.00 2.29
110 111 7.454260 AACCCATTTTCTTCTGTCTATTGAC 57.546 36.000 0.00 0.00 43.20 3.18
111 112 5.643777 ACCCATTTTCTTCTGTCTATTGACG 59.356 40.000 2.86 0.00 45.70 4.35
122 123 6.630071 TCTGTCTATTGACGAATTCACATGA 58.370 36.000 6.22 2.46 45.70 3.07
125 126 6.183360 TGTCTATTGACGAATTCACATGAAGC 60.183 38.462 6.22 0.00 45.70 3.86
150 151 0.029035 CGGCTCGTCGCTTACAGTAT 59.971 55.000 0.00 0.00 39.13 2.12
151 152 1.262417 CGGCTCGTCGCTTACAGTATA 59.738 52.381 0.00 0.00 39.13 1.47
158 159 3.181503 CGTCGCTTACAGTATAGTGTGGT 60.182 47.826 21.21 0.00 31.46 4.16
189 193 1.508088 GGAGGACGCAGGCAAATTG 59.492 57.895 0.00 0.00 0.00 2.32
205 210 4.327087 GCAAATTGCAAGTTATTCTTCCCG 59.673 41.667 12.36 0.00 44.26 5.14
207 212 4.965119 ATTGCAAGTTATTCTTCCCGAC 57.035 40.909 4.94 0.00 33.63 4.79
265 270 3.961408 CACCTACTATAGCTCCACCAAGT 59.039 47.826 0.00 0.00 0.00 3.16
277 282 5.044846 AGCTCCACCAAGTAATAATCAGGTT 60.045 40.000 0.00 0.00 0.00 3.50
298 303 5.798934 GGTTAATAGTATCGGTACTGCATCG 59.201 44.000 18.74 0.00 41.22 3.84
304 309 2.665649 TCGGTACTGCATCGAAACAT 57.334 45.000 0.00 0.00 0.00 2.71
314 319 2.096909 GCATCGAAACATACCGGAATCG 60.097 50.000 9.46 8.64 0.00 3.34
327 332 1.296727 GGAATCGGAAACCTAAGCCG 58.703 55.000 0.00 0.00 46.08 5.52
339 344 3.882444 ACCTAAGCCGGTAAAATTCTCC 58.118 45.455 1.90 0.00 34.94 3.71
346 351 6.002653 AGCCGGTAAAATTCTCCTTAATCT 57.997 37.500 1.90 0.00 0.00 2.40
474 485 1.154488 CCACGTCAAAATGCCGTCG 60.154 57.895 0.00 0.00 31.46 5.12
553 565 8.700644 GTTTATACTTAGTTATGATCAGGCACG 58.299 37.037 0.09 0.00 0.00 5.34
578 590 2.727123 TGACCTGACTCTGCCAAAAA 57.273 45.000 0.00 0.00 0.00 1.94
609 621 8.621532 ATGACTCATAAAGAAAAAGTACTGCA 57.378 30.769 0.00 0.00 0.00 4.41
610 622 8.445275 TGACTCATAAAGAAAAAGTACTGCAA 57.555 30.769 0.00 0.00 0.00 4.08
611 623 8.898761 TGACTCATAAAGAAAAAGTACTGCAAA 58.101 29.630 0.00 0.00 0.00 3.68
612 624 9.730420 GACTCATAAAGAAAAAGTACTGCAAAA 57.270 29.630 0.00 0.00 0.00 2.44
613 625 9.736023 ACTCATAAAGAAAAAGTACTGCAAAAG 57.264 29.630 0.00 0.00 0.00 2.27
614 626 9.185192 CTCATAAAGAAAAAGTACTGCAAAAGG 57.815 33.333 0.00 0.00 0.00 3.11
655 672 2.361610 CCCTGCAAGCAATCCGGT 60.362 61.111 0.00 0.00 0.00 5.28
657 674 1.376609 CCCTGCAAGCAATCCGGTAC 61.377 60.000 0.00 0.00 0.00 3.34
658 675 1.376609 CCTGCAAGCAATCCGGTACC 61.377 60.000 0.16 0.16 0.00 3.34
659 676 1.705337 CTGCAAGCAATCCGGTACCG 61.705 60.000 27.68 27.68 39.44 4.02
749 780 2.740714 GACGCAGCAACGCCCTAAG 61.741 63.158 0.00 0.00 36.19 2.18
824 861 1.271127 GGAGAGGCTGCTTCCTTCCT 61.271 60.000 8.26 0.00 36.38 3.36
829 866 1.836802 AGGCTGCTTCCTTCCTAGAAG 59.163 52.381 0.00 0.00 42.99 2.85
909 946 3.453717 CCACCATTCTCCTCTCATTCTCA 59.546 47.826 0.00 0.00 0.00 3.27
910 947 4.102838 CCACCATTCTCCTCTCATTCTCAT 59.897 45.833 0.00 0.00 0.00 2.90
911 948 5.397672 CCACCATTCTCCTCTCATTCTCATT 60.398 44.000 0.00 0.00 0.00 2.57
912 949 5.759273 CACCATTCTCCTCTCATTCTCATTC 59.241 44.000 0.00 0.00 0.00 2.67
913 950 5.666718 ACCATTCTCCTCTCATTCTCATTCT 59.333 40.000 0.00 0.00 0.00 2.40
914 951 6.183360 ACCATTCTCCTCTCATTCTCATTCTC 60.183 42.308 0.00 0.00 0.00 2.87
958 995 3.706373 GGCCGGCTGTCTCCTTGA 61.706 66.667 28.56 0.00 0.00 3.02
959 996 2.586792 GCCGGCTGTCTCCTTGAT 59.413 61.111 22.15 0.00 0.00 2.57
960 997 1.522580 GCCGGCTGTCTCCTTGATC 60.523 63.158 22.15 0.00 0.00 2.92
961 998 1.144936 CCGGCTGTCTCCTTGATCC 59.855 63.158 0.00 0.00 0.00 3.36
971 1008 1.834263 CTCCTTGATCCTCCTCCGTTT 59.166 52.381 0.00 0.00 0.00 3.60
994 1031 3.807538 CGTCGACGTGGATCGGGT 61.808 66.667 29.08 0.00 44.69 5.28
1329 1366 4.052159 AGAGTCGCATAGGATGTTTGAG 57.948 45.455 0.00 0.00 0.00 3.02
1445 1482 7.873505 CCCTTCCTACTGAAACATAATACTAGC 59.126 40.741 0.00 0.00 31.06 3.42
1484 1524 8.647226 GCTATTGAAATACCAACACACAATTTC 58.353 33.333 0.00 0.00 37.17 2.17
1495 1535 3.761218 ACACACAATTTCTGGACAACACA 59.239 39.130 0.00 0.00 0.00 3.72
1502 1542 8.017373 CACAATTTCTGGACAACACACTTATAG 58.983 37.037 0.00 0.00 0.00 1.31
1609 1649 6.053005 CGACTTATTAGGCAACCCATTAGAA 58.947 40.000 0.00 0.00 37.17 2.10
1693 1733 9.907576 CATACTAAAAAGATGTCATCTCGTTTC 57.092 33.333 15.75 0.00 39.08 2.78
1917 1957 7.782897 TGATATAGACACCCCTTTCAGATAG 57.217 40.000 0.00 0.00 0.00 2.08
1927 1967 5.015178 ACCCCTTTCAGATAGGAATCAACAA 59.985 40.000 8.45 0.00 34.56 2.83
1950 1990 6.426646 AGTAACAGACCAAGATTGAAGAGT 57.573 37.500 0.00 0.00 0.00 3.24
1963 2003 7.573968 AGATTGAAGAGTTTATGGGTAATGC 57.426 36.000 0.00 0.00 0.00 3.56
2036 2086 2.097036 GGGATCTTTTAACGTTGGGGG 58.903 52.381 11.99 0.00 0.00 5.40
2051 2101 4.160626 CGTTGGGGGAAATTTAAAGCCATA 59.839 41.667 0.00 0.00 0.00 2.74
2175 2225 6.919775 AAACTGTCCTAGACAAGTATCAGT 57.080 37.500 0.00 0.00 42.26 3.41
2281 2331 6.978659 CACATCAAATGAGCAGCAAATAAGAT 59.021 34.615 0.00 0.00 0.00 2.40
2288 2338 6.915544 TGAGCAGCAAATAAGATAAGACAG 57.084 37.500 0.00 0.00 0.00 3.51
2321 2371 2.677559 GCGAAGATAGCCAGATTTGC 57.322 50.000 0.00 0.00 0.00 3.68
2330 2380 0.681175 GCCAGATTTGCCTGTTTGGT 59.319 50.000 0.00 0.00 38.35 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.063806 CAAAGCACTCTCGAGGAACG 58.936 55.000 13.56 1.60 44.09 3.95
3 4 1.795286 CACAAAGCACTCTCGAGGAAC 59.205 52.381 13.56 0.00 0.00 3.62
4 5 1.412710 ACACAAAGCACTCTCGAGGAA 59.587 47.619 13.56 0.00 0.00 3.36
5 6 1.040646 ACACAAAGCACTCTCGAGGA 58.959 50.000 13.56 0.00 0.00 3.71
6 7 1.143305 CACACAAAGCACTCTCGAGG 58.857 55.000 13.56 5.96 0.00 4.63
7 8 1.789464 GACACACAAAGCACTCTCGAG 59.211 52.381 5.93 5.93 0.00 4.04
8 9 1.409064 AGACACACAAAGCACTCTCGA 59.591 47.619 0.00 0.00 0.00 4.04
9 10 1.789464 GAGACACACAAAGCACTCTCG 59.211 52.381 0.00 0.00 0.00 4.04
10 11 2.799412 CAGAGACACACAAAGCACTCTC 59.201 50.000 0.00 0.00 33.35 3.20
11 12 2.169352 ACAGAGACACACAAAGCACTCT 59.831 45.455 0.00 0.00 35.52 3.24
12 13 2.555199 ACAGAGACACACAAAGCACTC 58.445 47.619 0.00 0.00 0.00 3.51
13 14 2.698855 ACAGAGACACACAAAGCACT 57.301 45.000 0.00 0.00 0.00 4.40
14 15 3.458189 AGTACAGAGACACACAAAGCAC 58.542 45.455 0.00 0.00 0.00 4.40
15 16 3.819564 AGTACAGAGACACACAAAGCA 57.180 42.857 0.00 0.00 0.00 3.91
16 17 6.159988 AGAATAGTACAGAGACACACAAAGC 58.840 40.000 0.00 0.00 0.00 3.51
17 18 7.329717 GGAAGAATAGTACAGAGACACACAAAG 59.670 40.741 0.00 0.00 0.00 2.77
18 19 7.152645 GGAAGAATAGTACAGAGACACACAAA 58.847 38.462 0.00 0.00 0.00 2.83
19 20 6.266786 TGGAAGAATAGTACAGAGACACACAA 59.733 38.462 0.00 0.00 0.00 3.33
20 21 5.773176 TGGAAGAATAGTACAGAGACACACA 59.227 40.000 0.00 0.00 0.00 3.72
21 22 6.071840 ACTGGAAGAATAGTACAGAGACACAC 60.072 42.308 0.00 0.00 37.43 3.82
22 23 6.010850 ACTGGAAGAATAGTACAGAGACACA 58.989 40.000 0.00 0.00 37.43 3.72
23 24 6.518208 ACTGGAAGAATAGTACAGAGACAC 57.482 41.667 0.00 0.00 37.43 3.67
24 25 7.834681 ACATACTGGAAGAATAGTACAGAGACA 59.165 37.037 0.00 0.00 37.43 3.41
25 26 8.132362 CACATACTGGAAGAATAGTACAGAGAC 58.868 40.741 0.00 0.00 37.43 3.36
26 27 7.201830 GCACATACTGGAAGAATAGTACAGAGA 60.202 40.741 0.00 0.00 37.43 3.10
27 28 6.920758 GCACATACTGGAAGAATAGTACAGAG 59.079 42.308 0.00 0.00 37.43 3.35
28 29 6.607600 AGCACATACTGGAAGAATAGTACAGA 59.392 38.462 0.00 0.00 37.43 3.41
29 30 6.810911 AGCACATACTGGAAGAATAGTACAG 58.189 40.000 0.00 0.00 37.43 2.74
30 31 6.791867 AGCACATACTGGAAGAATAGTACA 57.208 37.500 0.00 0.00 37.43 2.90
31 32 7.265673 TGAAGCACATACTGGAAGAATAGTAC 58.734 38.462 0.00 0.00 37.43 2.73
32 33 7.124298 ACTGAAGCACATACTGGAAGAATAGTA 59.876 37.037 0.00 0.00 37.43 1.82
33 34 6.070538 ACTGAAGCACATACTGGAAGAATAGT 60.071 38.462 0.00 0.00 37.43 2.12
34 35 6.344500 ACTGAAGCACATACTGGAAGAATAG 58.656 40.000 0.00 0.00 37.43 1.73
35 36 6.299805 ACTGAAGCACATACTGGAAGAATA 57.700 37.500 0.00 0.00 37.43 1.75
36 37 5.171339 ACTGAAGCACATACTGGAAGAAT 57.829 39.130 0.00 0.00 37.43 2.40
37 38 4.569943 GACTGAAGCACATACTGGAAGAA 58.430 43.478 0.00 0.00 37.43 2.52
38 39 3.367395 CGACTGAAGCACATACTGGAAGA 60.367 47.826 0.00 0.00 37.43 2.87
39 40 2.926200 CGACTGAAGCACATACTGGAAG 59.074 50.000 0.00 0.00 42.29 3.46
40 41 2.299013 ACGACTGAAGCACATACTGGAA 59.701 45.455 0.00 0.00 0.00 3.53
41 42 1.893137 ACGACTGAAGCACATACTGGA 59.107 47.619 0.00 0.00 0.00 3.86
42 43 2.370281 ACGACTGAAGCACATACTGG 57.630 50.000 0.00 0.00 0.00 4.00
43 44 3.181540 CGAAACGACTGAAGCACATACTG 60.182 47.826 0.00 0.00 0.00 2.74
44 45 2.987149 CGAAACGACTGAAGCACATACT 59.013 45.455 0.00 0.00 0.00 2.12
45 46 2.092211 CCGAAACGACTGAAGCACATAC 59.908 50.000 0.00 0.00 0.00 2.39
46 47 2.333926 CCGAAACGACTGAAGCACATA 58.666 47.619 0.00 0.00 0.00 2.29
47 48 1.148310 CCGAAACGACTGAAGCACAT 58.852 50.000 0.00 0.00 0.00 3.21
48 49 0.878523 CCCGAAACGACTGAAGCACA 60.879 55.000 0.00 0.00 0.00 4.57
49 50 0.599204 TCCCGAAACGACTGAAGCAC 60.599 55.000 0.00 0.00 0.00 4.40
50 51 0.599204 GTCCCGAAACGACTGAAGCA 60.599 55.000 0.00 0.00 0.00 3.91
51 52 0.319641 AGTCCCGAAACGACTGAAGC 60.320 55.000 0.00 0.00 39.14 3.86
52 53 1.269998 AGAGTCCCGAAACGACTGAAG 59.730 52.381 0.00 0.00 40.67 3.02
53 54 1.000607 CAGAGTCCCGAAACGACTGAA 60.001 52.381 0.00 0.00 40.67 3.02
54 55 0.596577 CAGAGTCCCGAAACGACTGA 59.403 55.000 0.00 0.00 40.67 3.41
55 56 0.314302 ACAGAGTCCCGAAACGACTG 59.686 55.000 0.00 0.00 40.67 3.51
56 57 1.901591 TACAGAGTCCCGAAACGACT 58.098 50.000 0.00 0.00 43.28 4.18
101 102 6.188175 GCTTCATGTGAATTCGTCAATAGAC 58.812 40.000 0.04 0.00 38.23 2.59
110 111 0.378257 CCCGGCTTCATGTGAATTCG 59.622 55.000 0.00 3.95 33.01 3.34
111 112 1.401905 GACCCGGCTTCATGTGAATTC 59.598 52.381 0.00 0.00 33.01 2.17
150 151 4.341806 TCCGTTCTCACTTTTACCACACTA 59.658 41.667 0.00 0.00 0.00 2.74
151 152 3.133362 TCCGTTCTCACTTTTACCACACT 59.867 43.478 0.00 0.00 0.00 3.55
158 159 2.608752 GCGTCCTCCGTTCTCACTTTTA 60.609 50.000 0.00 0.00 39.32 1.52
179 183 5.349543 GGAAGAATAACTTGCAATTTGCCTG 59.650 40.000 18.27 12.83 44.23 4.85
189 193 3.596214 TCTGTCGGGAAGAATAACTTGC 58.404 45.455 0.00 0.00 44.40 4.01
198 203 0.608640 GGCTTCTTCTGTCGGGAAGA 59.391 55.000 10.64 10.64 46.57 2.87
205 210 0.915364 ATGGGAGGGCTTCTTCTGTC 59.085 55.000 0.00 0.00 0.00 3.51
207 212 0.622665 ACATGGGAGGGCTTCTTCTG 59.377 55.000 0.00 0.00 0.00 3.02
277 282 6.806388 TTCGATGCAGTACCGATACTATTA 57.194 37.500 0.00 0.00 39.80 0.98
314 319 4.703575 AGAATTTTACCGGCTTAGGTTTCC 59.296 41.667 0.00 0.00 43.00 3.13
323 328 6.002653 AGATTAAGGAGAATTTTACCGGCT 57.997 37.500 0.00 0.00 0.00 5.52
327 332 8.070769 GCGATGAAGATTAAGGAGAATTTTACC 58.929 37.037 0.00 0.00 0.00 2.85
339 344 8.127327 ACTTGATGATTTGCGATGAAGATTAAG 58.873 33.333 0.00 0.00 0.00 1.85
346 351 4.455190 TCACACTTGATGATTTGCGATGAA 59.545 37.500 0.00 0.00 0.00 2.57
404 410 4.031765 CGTTCAGTTGATATGTGTTCGAGG 59.968 45.833 0.00 0.00 0.00 4.63
474 485 8.736751 TTTATTTCCGATTTGTTTAGCTGTTC 57.263 30.769 0.00 0.00 0.00 3.18
549 561 1.207593 GTCAGGTCAATGTGCGTGC 59.792 57.895 0.00 0.00 0.00 5.34
553 565 0.801251 GCAGAGTCAGGTCAATGTGC 59.199 55.000 0.00 0.00 0.00 4.57
607 619 0.961019 TGATGTGTGCCTCCTTTTGC 59.039 50.000 0.00 0.00 0.00 3.68
608 620 2.821378 TGATGATGTGTGCCTCCTTTTG 59.179 45.455 0.00 0.00 0.00 2.44
609 621 2.821969 GTGATGATGTGTGCCTCCTTTT 59.178 45.455 0.00 0.00 0.00 2.27
610 622 2.224843 TGTGATGATGTGTGCCTCCTTT 60.225 45.455 0.00 0.00 0.00 3.11
611 623 1.352017 TGTGATGATGTGTGCCTCCTT 59.648 47.619 0.00 0.00 0.00 3.36
612 624 0.986527 TGTGATGATGTGTGCCTCCT 59.013 50.000 0.00 0.00 0.00 3.69
613 625 1.674441 CATGTGATGATGTGTGCCTCC 59.326 52.381 0.00 0.00 0.00 4.30
614 626 2.612672 CTCATGTGATGATGTGTGCCTC 59.387 50.000 0.00 0.00 38.85 4.70
655 672 1.614241 GGAGGCTTGCTTCTCCGGTA 61.614 60.000 0.00 0.00 39.95 4.02
657 674 2.124942 GGAGGCTTGCTTCTCCGG 60.125 66.667 0.00 0.00 39.95 5.14
659 676 3.167189 GAAGGAGGCTTGCTTCTCC 57.833 57.895 20.64 9.34 45.31 3.71
663 680 0.038890 GGAAGGAAGGAGGCTTGCTT 59.961 55.000 1.16 1.16 45.38 3.91
664 681 1.688211 GGAAGGAAGGAGGCTTGCT 59.312 57.895 0.00 0.00 36.57 3.91
665 682 1.746991 CGGAAGGAAGGAGGCTTGC 60.747 63.158 0.00 0.00 0.00 4.01
743 774 3.051081 CTGGCTTAGCTATGCTTAGGG 57.949 52.381 25.58 11.39 40.44 3.53
824 861 3.034635 GGAAGGAGTCCATGAGCTTCTA 58.965 50.000 12.86 0.00 46.97 2.10
909 946 2.821969 GCAACAGTGGTGAATGGAGAAT 59.178 45.455 13.73 0.00 0.00 2.40
910 947 2.229792 GCAACAGTGGTGAATGGAGAA 58.770 47.619 13.73 0.00 0.00 2.87
911 948 1.142667 TGCAACAGTGGTGAATGGAGA 59.857 47.619 13.73 0.00 0.00 3.71
912 949 1.608055 TGCAACAGTGGTGAATGGAG 58.392 50.000 13.73 0.00 0.00 3.86
913 950 2.291209 ATGCAACAGTGGTGAATGGA 57.709 45.000 13.73 0.00 0.00 3.41
914 951 2.679450 CAATGCAACAGTGGTGAATGG 58.321 47.619 13.73 0.00 0.00 3.16
943 980 1.144936 GGATCAAGGAGACAGCCGG 59.855 63.158 0.00 0.00 0.00 6.13
945 982 0.467804 GGAGGATCAAGGAGACAGCC 59.532 60.000 0.00 0.00 36.25 4.85
947 984 2.038659 GGAGGAGGATCAAGGAGACAG 58.961 57.143 0.00 0.00 36.25 3.51
948 985 1.686428 CGGAGGAGGATCAAGGAGACA 60.686 57.143 0.00 0.00 36.25 3.41
949 986 1.036707 CGGAGGAGGATCAAGGAGAC 58.963 60.000 0.00 0.00 36.25 3.36
950 987 0.631753 ACGGAGGAGGATCAAGGAGA 59.368 55.000 0.00 0.00 36.25 3.71
951 988 1.490574 AACGGAGGAGGATCAAGGAG 58.509 55.000 0.00 0.00 36.25 3.69
956 993 1.674817 GCGAAAAACGGAGGAGGATCA 60.675 52.381 0.00 0.00 42.83 2.92
957 994 1.007580 GCGAAAAACGGAGGAGGATC 58.992 55.000 0.00 0.00 42.83 3.36
958 995 0.392595 GGCGAAAAACGGAGGAGGAT 60.393 55.000 0.00 0.00 42.83 3.24
959 996 1.004200 GGCGAAAAACGGAGGAGGA 60.004 57.895 0.00 0.00 42.83 3.71
960 997 2.388232 CGGCGAAAAACGGAGGAGG 61.388 63.158 0.00 0.00 42.83 4.30
961 998 1.623973 GACGGCGAAAAACGGAGGAG 61.624 60.000 16.62 0.00 42.83 3.69
1193 1230 2.752238 CCTGGAGCTCGTCGTCCT 60.752 66.667 7.83 0.00 33.57 3.85
1329 1366 9.006215 GTAACAAAAGTCAAGTTACATCAACAC 57.994 33.333 9.15 0.00 44.20 3.32
1445 1482 3.136009 TCAATAGCATGATCAGCCAGG 57.864 47.619 0.09 0.00 0.00 4.45
1484 1524 7.441157 TCTGTTTTCTATAAGTGTGTTGTCCAG 59.559 37.037 0.00 0.00 0.00 3.86
1495 1535 6.311445 CGTGCTGTGATCTGTTTTCTATAAGT 59.689 38.462 0.00 0.00 0.00 2.24
1502 1542 1.264020 TGCGTGCTGTGATCTGTTTTC 59.736 47.619 0.00 0.00 0.00 2.29
1625 1665 3.560636 AAGGAGTTGTTGTACTGCACT 57.439 42.857 0.00 0.00 38.77 4.40
1677 1717 3.775202 CGAAGGAAACGAGATGACATCT 58.225 45.455 17.98 17.98 43.70 2.90
1693 1733 1.128692 GACAACATTTCTCGGCGAAGG 59.871 52.381 12.13 0.00 32.21 3.46
1917 1957 5.763204 TCTTGGTCTGTTACTTGTTGATTCC 59.237 40.000 0.00 0.00 0.00 3.01
1927 1967 6.426646 ACTCTTCAATCTTGGTCTGTTACT 57.573 37.500 0.00 0.00 0.00 2.24
1963 2003 9.965748 CCAAGTGTTTGTTTAAATTTAACTGTG 57.034 29.630 10.18 5.21 32.21 3.66
2036 2086 8.435430 GTGCTTTTCAGTATGGCTTTAAATTTC 58.565 33.333 0.00 0.00 36.16 2.17
2051 2101 3.305608 GCTATGGCTTTGTGCTTTTCAGT 60.306 43.478 0.00 0.00 42.39 3.41
2175 2225 5.505780 AGTTGGGCTTGCTATTATGTTACA 58.494 37.500 0.00 0.00 0.00 2.41
2281 2331 2.766263 CCTGTGAGGTATGGCTGTCTTA 59.234 50.000 0.00 0.00 0.00 2.10
2288 2338 0.811616 CTTCGCCTGTGAGGTATGGC 60.812 60.000 0.00 0.00 37.80 4.40


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

AutoCloner maintained by Alex Coulton.