Multiple sequence alignment - TraesCS7A01G534300

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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 TraesCS7A01G534300 chr7A 100.000 2264 0 0 1 2264 712359906 712362169 0.000000e+00 4181
1 TraesCS7A01G534300 chr7D 92.979 1168 58 14 634 1784 618714582 618715742 0.000000e+00 1681
2 TraesCS7A01G534300 chr7D 83.891 329 41 2 1019 1335 618378348 618378020 1.020000e-78 303
3 TraesCS7A01G534300 chr7D 79.714 419 66 11 999 1415 618333530 618333129 3.680000e-73 285
4 TraesCS7A01G534300 chr7D 93.122 189 8 1 2076 2264 618715747 618715930 2.870000e-69 272
5 TraesCS7A01G534300 chr7D 81.461 356 41 14 254 588 618714227 618714578 3.710000e-68 268
6 TraesCS7A01G534300 chr7B 90.451 1152 58 15 163 1276 713215829 713216966 0.000000e+00 1471
7 TraesCS7A01G534300 chr7B 96.187 577 17 3 1566 2140 713216961 713217534 0.000000e+00 939


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 TraesCS7A01G534300 chr7A 712359906 712362169 2263 False 4181.000000 4181 100.000000 1 2264 1 chr7A.!!$F1 2263
1 TraesCS7A01G534300 chr7D 618714227 618715930 1703 False 740.333333 1681 89.187333 254 2264 3 chr7D.!!$F1 2010
2 TraesCS7A01G534300 chr7B 713215829 713217534 1705 False 1205.000000 1471 93.319000 163 2140 2 chr7B.!!$F1 1977

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
384 399 0.459237 CTACTCCACCTCTTGCAGCG 60.459 60.0 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 2234 0.17924 CGCAACTGCAACTTAGCTCG 60.179 55.0 2.12 0.0 42.21 5.03 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
83 84 9.725019 AAAATATTTCTTGCTTTTCTTAAGGGG 57.275 29.630 0.10 0.00 0.00 4.79
84 85 8.435931 AATATTTCTTGCTTTTCTTAAGGGGT 57.564 30.769 1.85 0.00 0.00 4.95
85 86 6.747414 ATTTCTTGCTTTTCTTAAGGGGTT 57.253 33.333 1.85 0.00 0.00 4.11
86 87 6.553953 TTTCTTGCTTTTCTTAAGGGGTTT 57.446 33.333 1.85 0.00 0.00 3.27
87 88 6.553953 TTCTTGCTTTTCTTAAGGGGTTTT 57.446 33.333 1.85 0.00 0.00 2.43
88 89 5.912892 TCTTGCTTTTCTTAAGGGGTTTTG 58.087 37.500 1.85 0.00 0.00 2.44
89 90 4.681074 TGCTTTTCTTAAGGGGTTTTGG 57.319 40.909 1.85 0.00 0.00 3.28
90 91 4.034410 TGCTTTTCTTAAGGGGTTTTGGT 58.966 39.130 1.85 0.00 0.00 3.67
91 92 4.471747 TGCTTTTCTTAAGGGGTTTTGGTT 59.528 37.500 1.85 0.00 0.00 3.67
92 93 5.045505 TGCTTTTCTTAAGGGGTTTTGGTTT 60.046 36.000 1.85 0.00 0.00 3.27
93 94 5.883673 GCTTTTCTTAAGGGGTTTTGGTTTT 59.116 36.000 1.85 0.00 0.00 2.43
94 95 6.376018 GCTTTTCTTAAGGGGTTTTGGTTTTT 59.624 34.615 1.85 0.00 0.00 1.94
95 96 7.627513 GCTTTTCTTAAGGGGTTTTGGTTTTTG 60.628 37.037 1.85 0.00 0.00 2.44
96 97 6.375830 TTCTTAAGGGGTTTTGGTTTTTGT 57.624 33.333 1.85 0.00 0.00 2.83
97 98 6.375830 TCTTAAGGGGTTTTGGTTTTTGTT 57.624 33.333 1.85 0.00 0.00 2.83
98 99 6.408035 TCTTAAGGGGTTTTGGTTTTTGTTC 58.592 36.000 1.85 0.00 0.00 3.18
99 100 4.919774 AAGGGGTTTTGGTTTTTGTTCT 57.080 36.364 0.00 0.00 0.00 3.01
100 101 4.919774 AGGGGTTTTGGTTTTTGTTCTT 57.080 36.364 0.00 0.00 0.00 2.52
101 102 4.839121 AGGGGTTTTGGTTTTTGTTCTTC 58.161 39.130 0.00 0.00 0.00 2.87
102 103 3.619483 GGGGTTTTGGTTTTTGTTCTTCG 59.381 43.478 0.00 0.00 0.00 3.79
103 104 3.619483 GGGTTTTGGTTTTTGTTCTTCGG 59.381 43.478 0.00 0.00 0.00 4.30
104 105 3.619483 GGTTTTGGTTTTTGTTCTTCGGG 59.381 43.478 0.00 0.00 0.00 5.14
105 106 3.528597 TTTGGTTTTTGTTCTTCGGGG 57.471 42.857 0.00 0.00 0.00 5.73
106 107 2.146920 TGGTTTTTGTTCTTCGGGGT 57.853 45.000 0.00 0.00 0.00 4.95
107 108 2.025898 TGGTTTTTGTTCTTCGGGGTC 58.974 47.619 0.00 0.00 0.00 4.46
108 109 2.025898 GGTTTTTGTTCTTCGGGGTCA 58.974 47.619 0.00 0.00 0.00 4.02
109 110 2.427812 GGTTTTTGTTCTTCGGGGTCAA 59.572 45.455 0.00 0.00 0.00 3.18
110 111 3.490249 GGTTTTTGTTCTTCGGGGTCAAG 60.490 47.826 0.00 0.00 0.00 3.02
111 112 3.284793 TTTTGTTCTTCGGGGTCAAGA 57.715 42.857 0.00 0.00 0.00 3.02
112 113 2.543777 TTGTTCTTCGGGGTCAAGAG 57.456 50.000 0.00 0.00 31.48 2.85
113 114 1.420430 TGTTCTTCGGGGTCAAGAGT 58.580 50.000 0.00 0.00 31.48 3.24
114 115 1.766496 TGTTCTTCGGGGTCAAGAGTT 59.234 47.619 0.00 0.00 31.48 3.01
115 116 2.171870 TGTTCTTCGGGGTCAAGAGTTT 59.828 45.455 0.00 0.00 31.48 2.66
116 117 3.211865 GTTCTTCGGGGTCAAGAGTTTT 58.788 45.455 0.00 0.00 31.48 2.43
117 118 3.570912 TCTTCGGGGTCAAGAGTTTTT 57.429 42.857 0.00 0.00 0.00 1.94
143 144 8.486942 TTTTAGATATATCTTCGGGGTCAAGA 57.513 34.615 20.13 0.00 38.32 3.02
144 145 7.704578 TTAGATATATCTTCGGGGTCAAGAG 57.295 40.000 20.13 0.00 38.32 2.85
145 146 5.646215 AGATATATCTTCGGGGTCAAGAGT 58.354 41.667 9.57 0.00 33.36 3.24
146 147 5.478679 AGATATATCTTCGGGGTCAAGAGTG 59.521 44.000 9.57 0.00 33.36 3.51
147 148 1.938585 ATCTTCGGGGTCAAGAGTGA 58.061 50.000 0.00 0.00 33.36 3.41
148 149 8.660427 AGATATATCTTCGGGGTCAAGAGTGAC 61.660 44.444 9.57 0.00 43.09 3.67
196 197 0.838987 TTTCCGGCCCACTAGTTCCT 60.839 55.000 0.00 0.00 0.00 3.36
358 367 7.075148 AGATCTCAATCAACCTCTCTTCCTAT 58.925 38.462 0.00 0.00 34.07 2.57
359 368 6.477053 TCTCAATCAACCTCTCTTCCTATG 57.523 41.667 0.00 0.00 0.00 2.23
362 371 5.721480 TCAATCAACCTCTCTTCCTATGTCA 59.279 40.000 0.00 0.00 0.00 3.58
367 376 5.671463 ACCTCTCTTCCTATGTCATCCTA 57.329 43.478 0.00 0.00 0.00 2.94
377 386 3.697190 ATGTCATCCTACTCCACCTCT 57.303 47.619 0.00 0.00 0.00 3.69
381 396 1.833630 CATCCTACTCCACCTCTTGCA 59.166 52.381 0.00 0.00 0.00 4.08
384 399 0.459237 CTACTCCACCTCTTGCAGCG 60.459 60.000 0.00 0.00 0.00 5.18
457 492 7.068103 GTGTTGGATCCATGTATAAATTGGTCA 59.932 37.037 17.06 0.00 0.00 4.02
460 495 5.183904 GGATCCATGTATAAATTGGTCAGGC 59.816 44.000 6.95 0.00 0.00 4.85
561 598 4.837972 AGCTCTGTAGAAAGGATTTGGTC 58.162 43.478 0.00 0.00 39.27 4.02
562 599 4.287067 AGCTCTGTAGAAAGGATTTGGTCA 59.713 41.667 0.00 0.00 39.27 4.02
564 601 5.799213 CTCTGTAGAAAGGATTTGGTCACT 58.201 41.667 0.00 0.00 39.27 3.41
565 602 5.794894 TCTGTAGAAAGGATTTGGTCACTC 58.205 41.667 0.00 0.00 39.27 3.51
610 647 2.791383 TGGTACAAATGTGCAAGTGC 57.209 45.000 4.09 0.00 37.08 4.40
611 648 2.027385 TGGTACAAATGTGCAAGTGCA 58.973 42.857 0.82 0.82 42.94 4.57
612 649 2.428530 TGGTACAAATGTGCAAGTGCAA 59.571 40.909 7.71 0.00 45.85 4.08
613 650 3.069300 TGGTACAAATGTGCAAGTGCAAT 59.931 39.130 7.71 1.71 45.85 3.56
614 651 4.279420 TGGTACAAATGTGCAAGTGCAATA 59.721 37.500 7.71 0.64 45.85 1.90
635 672 3.257469 TCAACAGCTAGCCAGATTCTG 57.743 47.619 12.13 6.70 0.00 3.02
718 755 2.032528 CTGGAAGGCAGCGGAACA 59.967 61.111 0.00 0.00 0.00 3.18
725 762 0.678048 AGGCAGCGGAACAATCTTCC 60.678 55.000 0.00 0.00 35.27 3.46
736 773 1.271054 ACAATCTTCCGCTGCAGAGTT 60.271 47.619 20.43 0.49 0.00 3.01
752 789 7.615582 TGCAGAGTTCATTATTAGTTTCAGG 57.384 36.000 0.00 0.00 0.00 3.86
757 794 8.261522 AGAGTTCATTATTAGTTTCAGGACTCC 58.738 37.037 0.00 0.00 0.00 3.85
760 797 7.252612 TCATTATTAGTTTCAGGACTCCACA 57.747 36.000 0.00 0.00 0.00 4.17
796 835 1.396653 ACTGCCTCTAATTGCCATGC 58.603 50.000 0.00 0.00 0.00 4.06
803 842 4.008330 CCTCTAATTGCCATGCTAGGATG 58.992 47.826 16.78 16.78 0.00 3.51
804 843 4.263199 CCTCTAATTGCCATGCTAGGATGA 60.263 45.833 24.39 6.20 0.00 2.92
805 844 5.498393 CTCTAATTGCCATGCTAGGATGAT 58.502 41.667 24.39 8.30 0.00 2.45
848 887 2.542595 CACCGGTGAACAGTTTACAGAC 59.457 50.000 31.31 0.00 0.00 3.51
872 911 3.219176 TCCCTGAATGAATGCTCCATC 57.781 47.619 0.00 0.00 0.00 3.51
1011 1050 1.134310 ACGATGGAGATGAATGCTGCA 60.134 47.619 4.13 4.13 38.10 4.41
1066 1105 1.065928 CTCGGAGGGGAATCGTTCG 59.934 63.158 0.00 0.00 33.84 3.95
1083 1122 2.183046 GCAGTCAGCTCCGAGTCC 59.817 66.667 0.00 0.00 41.15 3.85
1167 1206 2.590575 ACCAAGCACAACGTCCCG 60.591 61.111 0.00 0.00 0.00 5.14
1191 1230 3.137176 ACGATGTCCCTGATGAATCCATT 59.863 43.478 0.00 0.00 32.09 3.16
1215 1254 2.746359 CCATCGGATGAGGAGGGC 59.254 66.667 19.30 0.00 0.00 5.19
1271 1310 3.672808 AGAAGCAGAAGTGATTGTCCTG 58.327 45.455 0.00 0.00 30.57 3.86
1293 1332 6.128607 CCTGAATCTCATCTGATTTATCGTGC 60.129 42.308 0.00 0.00 36.86 5.34
1294 1333 5.698089 TGAATCTCATCTGATTTATCGTGCC 59.302 40.000 0.00 0.00 36.86 5.01
1304 1343 5.741011 TGATTTATCGTGCCCTTTCTTAGT 58.259 37.500 0.00 0.00 0.00 2.24
1307 1346 1.640917 TCGTGCCCTTTCTTAGTCCT 58.359 50.000 0.00 0.00 0.00 3.85
1356 1395 0.842467 ACCCCTTGCTAGCTGTTCCT 60.842 55.000 17.23 0.00 0.00 3.36
1364 1403 2.104792 TGCTAGCTGTTCCTTTGACACT 59.895 45.455 17.23 0.00 0.00 3.55
1368 1407 2.945668 AGCTGTTCCTTTGACACTGAAC 59.054 45.455 0.00 0.00 38.03 3.18
1369 1408 2.286418 GCTGTTCCTTTGACACTGAACG 60.286 50.000 0.00 0.00 39.89 3.95
1372 1411 2.234300 TCCTTTGACACTGAACGACC 57.766 50.000 0.00 0.00 0.00 4.79
1373 1412 1.483004 TCCTTTGACACTGAACGACCA 59.517 47.619 0.00 0.00 0.00 4.02
1374 1413 2.093394 TCCTTTGACACTGAACGACCAA 60.093 45.455 0.00 0.00 0.00 3.67
1378 1417 2.912771 TGACACTGAACGACCAACAAT 58.087 42.857 0.00 0.00 0.00 2.71
1388 1427 8.504005 ACTGAACGACCAACAATTTATTCTTAG 58.496 33.333 0.00 0.00 0.00 2.18
1391 1430 5.708230 ACGACCAACAATTTATTCTTAGGCA 59.292 36.000 0.00 0.00 0.00 4.75
1409 1454 2.350522 GCACACTAGCTGCTTGTGTAT 58.649 47.619 36.38 20.81 45.34 2.29
1414 1459 5.122869 CACACTAGCTGCTTGTGTATCAAAT 59.877 40.000 36.38 18.43 45.34 2.32
1415 1460 5.352569 ACACTAGCTGCTTGTGTATCAAATC 59.647 40.000 36.25 0.00 45.29 2.17
1416 1461 4.568359 ACTAGCTGCTTGTGTATCAAATCG 59.432 41.667 15.68 0.00 35.48 3.34
1431 1480 0.443869 AATCGATGTGTGCAAGCGAC 59.556 50.000 0.00 0.00 37.95 5.19
1448 1497 2.348666 GCGACGCTCAATGTTGTTATCT 59.651 45.455 13.73 0.00 0.00 1.98
1529 1579 1.537202 GATGTTCTGCTTTTCGCTGGT 59.463 47.619 0.00 0.00 40.11 4.00
1549 1599 6.425210 TGGTAATATATGAGCTTCAGCACT 57.575 37.500 0.75 0.00 45.16 4.40
1555 1605 8.600449 AATATATGAGCTTCAGCACTAAAGTC 57.400 34.615 0.75 0.00 45.16 3.01
1557 1607 2.368548 TGAGCTTCAGCACTAAAGTCCA 59.631 45.455 0.75 0.00 45.16 4.02
1652 1702 5.500234 TCATCCTAATCTGGTTTGACTTGG 58.500 41.667 0.00 0.00 0.00 3.61
1699 1749 3.540314 AGGTCAGAGAACATGCTGATC 57.460 47.619 4.38 4.08 42.51 2.92
1718 1770 1.028868 CCCCTTGCTAGCTGCTGTTC 61.029 60.000 17.23 1.56 43.37 3.18
1786 1841 2.095059 GTGTAGGAAATTGCTGCTGGTG 60.095 50.000 4.20 0.00 0.00 4.17
1818 1873 2.805671 CGGTGCTCAATGTTGTTGTCTA 59.194 45.455 0.00 0.00 0.00 2.59
1827 1882 7.859377 GCTCAATGTTGTTGTCTAATATGATGG 59.141 37.037 0.00 0.00 0.00 3.51
1839 1894 1.434188 TATGATGGTAGGTGCAGGGG 58.566 55.000 0.00 0.00 0.00 4.79
1858 1913 2.937149 GGGAATTCGCTCCTTTCTGTAC 59.063 50.000 14.84 0.00 35.63 2.90
1897 1952 6.885918 TGTGATGATTTGCTTTGAGGAGAATA 59.114 34.615 0.00 0.00 0.00 1.75
1939 1994 7.358683 GCACATGAGTTCTTAATTTTCTGTTGC 60.359 37.037 0.00 0.00 0.00 4.17
1965 2020 2.032054 CCATGTTATGTGCAGTAAGGCG 59.968 50.000 0.00 0.00 36.28 5.52
1966 2021 2.465860 TGTTATGTGCAGTAAGGCGT 57.534 45.000 0.00 0.00 36.28 5.68
2175 2230 7.063780 GGCACAAGTCCAAAGATCAAATTATTG 59.936 37.037 0.00 0.00 37.92 1.90
2184 2239 8.184192 CCAAAGATCAAATTATTGTTACGAGCT 58.816 33.333 0.00 0.00 37.79 4.09
2188 2243 9.601217 AGATCAAATTATTGTTACGAGCTAAGT 57.399 29.630 0.00 0.00 37.79 2.24
2252 2307 8.605065 TGATGCTCAATGTTATCCCTTGATATA 58.395 33.333 0.00 0.00 33.54 0.86
2255 2310 7.337689 TGCTCAATGTTATCCCTTGATATATGC 59.662 37.037 0.00 0.00 33.54 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 9.725019 CCCCTTAAGAAAAGCAAGAAATATTTT 57.275 29.630 3.36 0.00 0.00 1.82
58 59 8.880244 ACCCCTTAAGAAAAGCAAGAAATATTT 58.120 29.630 3.36 0.00 0.00 1.40
59 60 8.435931 ACCCCTTAAGAAAAGCAAGAAATATT 57.564 30.769 3.36 0.00 0.00 1.28
60 61 8.435931 AACCCCTTAAGAAAAGCAAGAAATAT 57.564 30.769 3.36 0.00 0.00 1.28
61 62 7.849322 AACCCCTTAAGAAAAGCAAGAAATA 57.151 32.000 3.36 0.00 0.00 1.40
62 63 6.747414 AACCCCTTAAGAAAAGCAAGAAAT 57.253 33.333 3.36 0.00 0.00 2.17
63 64 6.553953 AAACCCCTTAAGAAAAGCAAGAAA 57.446 33.333 3.36 0.00 0.00 2.52
64 65 6.345298 CAAAACCCCTTAAGAAAAGCAAGAA 58.655 36.000 3.36 0.00 0.00 2.52
65 66 5.163353 CCAAAACCCCTTAAGAAAAGCAAGA 60.163 40.000 3.36 0.00 0.00 3.02
66 67 5.056480 CCAAAACCCCTTAAGAAAAGCAAG 58.944 41.667 3.36 0.00 0.00 4.01
67 68 4.471747 ACCAAAACCCCTTAAGAAAAGCAA 59.528 37.500 3.36 0.00 0.00 3.91
68 69 4.034410 ACCAAAACCCCTTAAGAAAAGCA 58.966 39.130 3.36 0.00 0.00 3.91
69 70 4.682778 ACCAAAACCCCTTAAGAAAAGC 57.317 40.909 3.36 0.00 0.00 3.51
70 71 7.392113 ACAAAAACCAAAACCCCTTAAGAAAAG 59.608 33.333 3.36 0.00 0.00 2.27
71 72 7.232188 ACAAAAACCAAAACCCCTTAAGAAAA 58.768 30.769 3.36 0.00 0.00 2.29
72 73 6.780901 ACAAAAACCAAAACCCCTTAAGAAA 58.219 32.000 3.36 0.00 0.00 2.52
73 74 6.375830 ACAAAAACCAAAACCCCTTAAGAA 57.624 33.333 3.36 0.00 0.00 2.52
74 75 6.213802 AGAACAAAAACCAAAACCCCTTAAGA 59.786 34.615 3.36 0.00 0.00 2.10
75 76 6.411376 AGAACAAAAACCAAAACCCCTTAAG 58.589 36.000 0.00 0.00 0.00 1.85
76 77 6.375830 AGAACAAAAACCAAAACCCCTTAA 57.624 33.333 0.00 0.00 0.00 1.85
77 78 6.375830 AAGAACAAAAACCAAAACCCCTTA 57.624 33.333 0.00 0.00 0.00 2.69
78 79 4.919774 AGAACAAAAACCAAAACCCCTT 57.080 36.364 0.00 0.00 0.00 3.95
79 80 4.621983 CGAAGAACAAAAACCAAAACCCCT 60.622 41.667 0.00 0.00 0.00 4.79
80 81 3.619483 CGAAGAACAAAAACCAAAACCCC 59.381 43.478 0.00 0.00 0.00 4.95
81 82 3.619483 CCGAAGAACAAAAACCAAAACCC 59.381 43.478 0.00 0.00 0.00 4.11
82 83 3.619483 CCCGAAGAACAAAAACCAAAACC 59.381 43.478 0.00 0.00 0.00 3.27
83 84 3.619483 CCCCGAAGAACAAAAACCAAAAC 59.381 43.478 0.00 0.00 0.00 2.43
84 85 3.261137 ACCCCGAAGAACAAAAACCAAAA 59.739 39.130 0.00 0.00 0.00 2.44
85 86 2.832733 ACCCCGAAGAACAAAAACCAAA 59.167 40.909 0.00 0.00 0.00 3.28
86 87 2.427812 GACCCCGAAGAACAAAAACCAA 59.572 45.455 0.00 0.00 0.00 3.67
87 88 2.025898 GACCCCGAAGAACAAAAACCA 58.974 47.619 0.00 0.00 0.00 3.67
88 89 2.025898 TGACCCCGAAGAACAAAAACC 58.974 47.619 0.00 0.00 0.00 3.27
89 90 3.379057 TCTTGACCCCGAAGAACAAAAAC 59.621 43.478 0.00 0.00 0.00 2.43
90 91 3.622630 TCTTGACCCCGAAGAACAAAAA 58.377 40.909 0.00 0.00 0.00 1.94
91 92 3.211045 CTCTTGACCCCGAAGAACAAAA 58.789 45.455 0.00 0.00 0.00 2.44
92 93 2.171870 ACTCTTGACCCCGAAGAACAAA 59.828 45.455 0.00 0.00 0.00 2.83
93 94 1.766496 ACTCTTGACCCCGAAGAACAA 59.234 47.619 0.00 0.00 0.00 2.83
94 95 1.420430 ACTCTTGACCCCGAAGAACA 58.580 50.000 0.00 0.00 0.00 3.18
95 96 2.545537 AACTCTTGACCCCGAAGAAC 57.454 50.000 0.00 0.00 0.00 3.01
96 97 3.570912 AAAACTCTTGACCCCGAAGAA 57.429 42.857 0.00 0.00 0.00 2.52
97 98 3.570912 AAAAACTCTTGACCCCGAAGA 57.429 42.857 0.00 0.00 0.00 2.87
117 118 8.930527 TCTTGACCCCGAAGATATATCTAAAAA 58.069 33.333 15.64 2.59 35.76 1.94
118 119 8.486942 TCTTGACCCCGAAGATATATCTAAAA 57.513 34.615 15.64 2.14 35.76 1.52
119 120 7.728981 ACTCTTGACCCCGAAGATATATCTAAA 59.271 37.037 15.64 1.25 35.76 1.85
120 121 7.176865 CACTCTTGACCCCGAAGATATATCTAA 59.823 40.741 15.64 3.32 35.76 2.10
121 122 6.659668 CACTCTTGACCCCGAAGATATATCTA 59.340 42.308 15.64 0.00 35.76 1.98
122 123 5.478679 CACTCTTGACCCCGAAGATATATCT 59.521 44.000 9.57 9.57 39.22 1.98
123 124 5.477291 TCACTCTTGACCCCGAAGATATATC 59.523 44.000 4.42 4.42 0.00 1.63
124 125 5.244178 GTCACTCTTGACCCCGAAGATATAT 59.756 44.000 0.00 0.00 45.77 0.86
125 126 4.583489 GTCACTCTTGACCCCGAAGATATA 59.417 45.833 0.00 0.00 45.77 0.86
126 127 3.385111 GTCACTCTTGACCCCGAAGATAT 59.615 47.826 0.00 0.00 45.77 1.63
127 128 2.758979 GTCACTCTTGACCCCGAAGATA 59.241 50.000 0.00 0.00 45.77 1.98
128 129 1.550976 GTCACTCTTGACCCCGAAGAT 59.449 52.381 0.00 0.00 45.77 2.40
129 130 0.966920 GTCACTCTTGACCCCGAAGA 59.033 55.000 0.00 0.00 45.77 2.87
130 131 3.516578 GTCACTCTTGACCCCGAAG 57.483 57.895 0.00 0.00 45.77 3.79
138 139 1.924731 ATCCGTGGAGTCACTCTTGA 58.075 50.000 4.40 0.00 41.53 3.02
139 140 2.289072 ACAATCCGTGGAGTCACTCTTG 60.289 50.000 4.40 2.77 41.53 3.02
140 141 1.971357 ACAATCCGTGGAGTCACTCTT 59.029 47.619 4.40 0.00 41.53 2.85
141 142 1.273606 CACAATCCGTGGAGTCACTCT 59.726 52.381 4.40 0.00 42.34 3.24
142 143 1.714794 CACAATCCGTGGAGTCACTC 58.285 55.000 0.00 0.00 42.34 3.51
143 144 0.320771 GCACAATCCGTGGAGTCACT 60.321 55.000 0.00 0.00 46.45 3.41
144 145 1.298859 GGCACAATCCGTGGAGTCAC 61.299 60.000 0.00 0.00 46.45 3.67
145 146 1.003839 GGCACAATCCGTGGAGTCA 60.004 57.895 0.00 0.00 46.45 3.41
146 147 1.003839 TGGCACAATCCGTGGAGTC 60.004 57.895 0.00 0.00 46.45 3.36
147 148 1.003355 CTGGCACAATCCGTGGAGT 60.003 57.895 0.00 0.00 46.45 3.85
148 149 2.401766 GCTGGCACAATCCGTGGAG 61.402 63.158 0.00 0.00 46.45 3.86
149 150 2.359850 GCTGGCACAATCCGTGGA 60.360 61.111 0.00 0.00 46.45 4.02
150 151 2.535485 TAGGCTGGCACAATCCGTGG 62.535 60.000 3.38 0.00 46.45 4.94
152 153 0.676782 GTTAGGCTGGCACAATCCGT 60.677 55.000 3.38 0.00 38.70 4.69
153 154 0.392998 AGTTAGGCTGGCACAATCCG 60.393 55.000 3.38 0.00 38.70 4.18
154 155 1.745653 GAAGTTAGGCTGGCACAATCC 59.254 52.381 3.38 0.00 38.70 3.01
155 156 1.398390 CGAAGTTAGGCTGGCACAATC 59.602 52.381 3.38 0.00 38.70 2.67
156 157 1.453155 CGAAGTTAGGCTGGCACAAT 58.547 50.000 3.38 0.00 38.70 2.71
157 158 1.234615 GCGAAGTTAGGCTGGCACAA 61.235 55.000 3.38 0.00 38.70 3.33
158 159 1.671054 GCGAAGTTAGGCTGGCACA 60.671 57.895 3.38 0.00 0.00 4.57
159 160 0.955919 AAGCGAAGTTAGGCTGGCAC 60.956 55.000 3.38 0.00 39.93 5.01
160 161 0.250727 AAAGCGAAGTTAGGCTGGCA 60.251 50.000 3.38 0.00 39.93 4.92
161 162 0.448197 GAAAGCGAAGTTAGGCTGGC 59.552 55.000 0.00 0.00 39.93 4.85
215 216 0.755327 GAGGTGAGGAGGAGAGGAGC 60.755 65.000 0.00 0.00 0.00 4.70
219 220 0.628522 TGGAGAGGTGAGGAGGAGAG 59.371 60.000 0.00 0.00 0.00 3.20
319 328 1.951631 GATCTTACGCTCGGGCTGC 60.952 63.158 5.36 0.00 36.09 5.25
341 350 5.306678 GGATGACATAGGAAGAGAGGTTGAT 59.693 44.000 0.00 0.00 0.00 2.57
358 367 3.099905 CAAGAGGTGGAGTAGGATGACA 58.900 50.000 0.00 0.00 0.00 3.58
359 368 2.159028 GCAAGAGGTGGAGTAGGATGAC 60.159 54.545 0.00 0.00 0.00 3.06
362 371 2.114616 CTGCAAGAGGTGGAGTAGGAT 58.885 52.381 0.00 0.00 40.67 3.24
367 376 2.345244 CGCTGCAAGAGGTGGAGT 59.655 61.111 0.00 0.00 46.94 3.85
377 386 2.899838 AAGCAACGGACGCTGCAA 60.900 55.556 20.20 0.00 40.35 4.08
409 424 1.758514 GATGAGAGCCCCCGTCAGA 60.759 63.158 0.00 0.00 0.00 3.27
411 426 2.060383 CAGATGAGAGCCCCCGTCA 61.060 63.158 0.00 0.00 0.00 4.35
412 427 2.060980 ACAGATGAGAGCCCCCGTC 61.061 63.158 0.00 0.00 0.00 4.79
414 429 2.362369 ACACAGATGAGAGCCCCCG 61.362 63.158 0.00 0.00 0.00 5.73
457 492 0.524862 CAGAATTTTGCAGCTCGCCT 59.475 50.000 5.82 0.00 41.33 5.52
460 495 4.973396 TGATTACAGAATTTTGCAGCTCG 58.027 39.130 0.00 0.00 0.00 5.03
561 598 2.368875 ACCCCTTACAGAACACAGAGTG 59.631 50.000 0.00 0.00 39.75 3.51
562 599 2.690840 ACCCCTTACAGAACACAGAGT 58.309 47.619 0.00 0.00 0.00 3.24
564 601 2.565834 GCTACCCCTTACAGAACACAGA 59.434 50.000 0.00 0.00 0.00 3.41
565 602 2.567615 AGCTACCCCTTACAGAACACAG 59.432 50.000 0.00 0.00 0.00 3.66
607 644 2.945008 TGGCTAGCTGTTGATATTGCAC 59.055 45.455 15.72 0.00 0.00 4.57
608 645 3.118298 TCTGGCTAGCTGTTGATATTGCA 60.118 43.478 15.72 0.00 0.00 4.08
609 646 3.470709 TCTGGCTAGCTGTTGATATTGC 58.529 45.455 15.72 0.00 0.00 3.56
610 647 5.996513 AGAATCTGGCTAGCTGTTGATATTG 59.003 40.000 15.72 0.00 0.00 1.90
611 648 5.996513 CAGAATCTGGCTAGCTGTTGATATT 59.003 40.000 15.72 5.35 0.00 1.28
612 649 5.306419 TCAGAATCTGGCTAGCTGTTGATAT 59.694 40.000 15.72 3.86 31.51 1.63
613 650 4.651045 TCAGAATCTGGCTAGCTGTTGATA 59.349 41.667 15.72 0.00 31.51 2.15
614 651 3.453717 TCAGAATCTGGCTAGCTGTTGAT 59.546 43.478 15.72 10.05 31.51 2.57
621 658 1.003003 GGGGATCAGAATCTGGCTAGC 59.997 57.143 10.71 6.04 31.51 3.42
635 672 5.104735 AGTGAAAGAAGTACTGATGGGGATC 60.105 44.000 0.00 0.00 0.00 3.36
718 755 1.002430 TGAACTCTGCAGCGGAAGATT 59.998 47.619 9.47 0.02 0.00 2.40
725 762 5.725110 AACTAATAATGAACTCTGCAGCG 57.275 39.130 9.47 5.22 0.00 5.18
736 773 7.252612 TGTGGAGTCCTGAAACTAATAATGA 57.747 36.000 11.33 0.00 0.00 2.57
796 835 3.758755 TGCTGCTGGTTATCATCCTAG 57.241 47.619 0.00 0.00 0.00 3.02
872 911 4.097741 TGCCGATTCCACAATTTCATTAGG 59.902 41.667 0.00 0.00 0.00 2.69
1011 1050 6.420913 TTTGCTCTAGGTTCTAGACTTGTT 57.579 37.500 0.00 0.00 0.00 2.83
1038 1077 1.001248 CCCTCCGAGAACCAGGGTA 59.999 63.158 0.00 0.00 42.02 3.69
1066 1105 2.183046 GGACTCGGAGCTGACTGC 59.817 66.667 4.58 0.00 43.29 4.40
1167 1206 3.134458 GGATTCATCAGGGACATCGTTC 58.866 50.000 0.00 0.00 0.00 3.95
1191 1230 2.040988 TCATCCGATGGGCCCTCA 60.041 61.111 25.70 2.97 0.00 3.86
1215 1254 1.068541 GGGTTTTTAGCAAGTGCCTCG 60.069 52.381 0.00 0.00 43.38 4.63
1271 1310 5.121454 GGGCACGATAAATCAGATGAGATTC 59.879 44.000 0.00 0.00 37.24 2.52
1293 1332 3.261897 TGCAAGAGAGGACTAAGAAAGGG 59.738 47.826 0.00 0.00 0.00 3.95
1294 1333 4.543590 TGCAAGAGAGGACTAAGAAAGG 57.456 45.455 0.00 0.00 0.00 3.11
1304 1343 4.092279 TCTCAGATCTTTGCAAGAGAGGA 58.908 43.478 9.15 8.81 41.61 3.71
1307 1346 5.219343 TGTTCTCAGATCTTTGCAAGAGA 57.781 39.130 9.15 9.15 41.61 3.10
1356 1395 2.701107 TGTTGGTCGTTCAGTGTCAAA 58.299 42.857 0.00 0.00 0.00 2.69
1364 1403 7.574217 GCCTAAGAATAAATTGTTGGTCGTTCA 60.574 37.037 0.00 0.00 0.00 3.18
1368 1407 6.027749 GTGCCTAAGAATAAATTGTTGGTCG 58.972 40.000 0.00 0.00 0.00 4.79
1369 1408 6.806739 GTGTGCCTAAGAATAAATTGTTGGTC 59.193 38.462 0.00 0.00 0.00 4.02
1372 1411 7.698130 GCTAGTGTGCCTAAGAATAAATTGTTG 59.302 37.037 0.00 0.00 0.00 3.33
1373 1412 7.611855 AGCTAGTGTGCCTAAGAATAAATTGTT 59.388 33.333 0.00 0.00 0.00 2.83
1374 1413 7.066284 CAGCTAGTGTGCCTAAGAATAAATTGT 59.934 37.037 0.00 0.00 0.00 2.71
1378 1417 4.876107 GCAGCTAGTGTGCCTAAGAATAAA 59.124 41.667 7.75 0.00 34.67 1.40
1388 1427 0.886490 ACACAAGCAGCTAGTGTGCC 60.886 55.000 22.20 0.00 45.23 5.01
1409 1454 1.136000 CGCTTGCACACATCGATTTGA 60.136 47.619 18.08 0.00 0.00 2.69
1414 1459 2.371923 CGTCGCTTGCACACATCGA 61.372 57.895 0.00 0.00 0.00 3.59
1415 1460 2.094539 CGTCGCTTGCACACATCG 59.905 61.111 0.00 0.00 0.00 3.84
1416 1461 2.202222 GCGTCGCTTGCACACATC 60.202 61.111 10.68 0.00 0.00 3.06
1431 1480 9.750882 CATATTATCAGATAACAACATTGAGCG 57.249 33.333 4.91 0.00 0.00 5.03
1448 1497 6.658816 ACTTTCCTTGCACACACATATTATCA 59.341 34.615 0.00 0.00 0.00 2.15
1529 1579 9.698309 GACTTTAGTGCTGAAGCTCATATATTA 57.302 33.333 3.61 0.00 42.66 0.98
1549 1599 9.421806 CAAATGATTTAACTGCAATGGACTTTA 57.578 29.630 0.00 0.00 0.00 1.85
1555 1605 7.092079 TCTGACAAATGATTTAACTGCAATGG 58.908 34.615 0.00 0.00 0.00 3.16
1557 1607 8.308931 ACATCTGACAAATGATTTAACTGCAAT 58.691 29.630 0.00 0.00 0.00 3.56
1795 1850 1.748493 ACAACAACATTGAGCACCGTT 59.252 42.857 0.00 0.00 0.00 4.44
1818 1873 2.376518 CCCCTGCACCTACCATCATATT 59.623 50.000 0.00 0.00 0.00 1.28
1827 1882 1.095807 GCGAATTCCCCTGCACCTAC 61.096 60.000 0.00 0.00 0.00 3.18
1839 1894 3.303760 GTCGTACAGAAAGGAGCGAATTC 59.696 47.826 0.00 0.00 0.00 2.17
1858 1913 4.123497 TCATCACATACCCAAAGAGTCG 57.877 45.455 0.00 0.00 0.00 4.18
1897 1952 1.561076 TGTGCTGAAGCCCAGTCATAT 59.439 47.619 0.00 0.00 44.71 1.78
1918 1973 7.771183 ACAAGCAACAGAAAATTAAGAACTCA 58.229 30.769 0.00 0.00 0.00 3.41
1939 1994 5.163723 CCTTACTGCACATAACATGGACAAG 60.164 44.000 0.00 0.00 33.60 3.16
1965 2020 4.647424 TGTTGGATTTCAGGTTGTTGAC 57.353 40.909 0.00 0.00 0.00 3.18
1966 2021 4.441356 GCTTGTTGGATTTCAGGTTGTTGA 60.441 41.667 0.00 0.00 0.00 3.18
2175 2230 3.664537 GCAACTGCAACTTAGCTCGTAAC 60.665 47.826 0.00 0.00 41.59 2.50
2179 2234 0.179240 CGCAACTGCAACTTAGCTCG 60.179 55.000 2.12 0.00 42.21 5.03
2184 2239 3.120683 CGATTTCTCGCAACTGCAACTTA 60.121 43.478 2.12 0.00 42.21 2.24
2185 2240 2.349817 CGATTTCTCGCAACTGCAACTT 60.350 45.455 2.12 0.00 42.21 2.66
2186 2241 1.195448 CGATTTCTCGCAACTGCAACT 59.805 47.619 2.12 0.00 42.21 3.16
2187 2242 1.595609 CGATTTCTCGCAACTGCAAC 58.404 50.000 2.12 0.00 42.21 4.17
2226 2281 5.698104 ATCAAGGGATAACATTGAGCATCA 58.302 37.500 1.09 0.00 35.82 3.07
2227 2282 7.934855 ATATCAAGGGATAACATTGAGCATC 57.065 36.000 1.09 0.00 39.36 3.91
2240 2295 6.319048 CTTACCCTGCATATATCAAGGGAT 57.681 41.667 26.30 16.65 39.73 3.85


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

AutoCloner maintained by Alex Coulton.