Multiple sequence alignment - TraesCS2D01G412900

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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 TraesCS2D01G412900 chr2D 100.000 3037 0 0 1 3037 527545793 527548829 0.000000e+00 5609.0
1 TraesCS2D01G412900 chr2A 91.365 3011 108 56 114 3037 672414291 672417236 0.000000e+00 3980.0
2 TraesCS2D01G412900 chr2B 93.041 2644 82 42 450 3036 624890773 624893371 0.000000e+00 3770.0
3 TraesCS2D01G412900 chr2B 86.032 315 19 11 114 403 624890065 624890379 6.320000e-82 315.0
4 TraesCS2D01G412900 chr5D 88.205 195 15 5 1727 1920 344399996 344400183 3.050000e-55 226.0
5 TraesCS2D01G412900 chr5A 88.205 195 15 5 1727 1920 448091106 448091293 3.050000e-55 226.0
6 TraesCS2D01G412900 chr5B 86.275 204 20 5 1727 1929 407817231 407817035 6.590000e-52 215.0
7 TraesCS2D01G412900 chr1B 86.567 201 18 4 1729 1920 418106021 418105821 2.370000e-51 213.0
8 TraesCS2D01G412900 chr1A 86.567 201 18 4 1729 1920 387840975 387840775 2.370000e-51 213.0
9 TraesCS2D01G412900 chr1A 88.235 85 10 0 1325 1409 387841262 387841178 5.360000e-18 102.0
10 TraesCS2D01G412900 chr1D 86.070 201 19 5 1729 1920 308459629 308459429 1.100000e-49 207.0
11 TraesCS2D01G412900 chr4B 90.441 136 12 1 1727 1861 491465484 491465619 8.650000e-41 178.0
12 TraesCS2D01G412900 chr4A 92.683 123 9 0 1727 1849 56145033 56145155 8.650000e-41 178.0
13 TraesCS2D01G412900 chr4A 100.000 39 0 0 2244 2282 718536692 718536730 4.200000e-09 73.1


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 TraesCS2D01G412900 chr2D 527545793 527548829 3036 False 5609.0 5609 100.0000 1 3037 1 chr2D.!!$F1 3036
1 TraesCS2D01G412900 chr2A 672414291 672417236 2945 False 3980.0 3980 91.3650 114 3037 1 chr2A.!!$F1 2923
2 TraesCS2D01G412900 chr2B 624890065 624893371 3306 False 2042.5 3770 89.5365 114 3036 2 chr2B.!!$F1 2922

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
349 382 0.251165 TGTTTTCCCTGGCTGGCTAC 60.251 55.000 4.64 0.91 0.00 3.58 F
350 383 0.251165 GTTTTCCCTGGCTGGCTACA 60.251 55.000 4.64 0.00 0.00 2.74 F
667 1060 1.035923 TCAAAGCGAAAATGCCCACA 58.964 45.000 0.00 0.00 34.65 4.17 F
1221 1636 1.153208 CCTGGAGATGCCACTGCTC 60.153 63.158 0.00 0.00 43.33 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1578 2025 0.670546 CGCGTCTGTTCTGGAACCAT 60.671 55.000 10.44 0.0 40.46 3.55 R
1716 2166 1.063469 CTTCGTCCTGCGTTGTTGTTT 59.937 47.619 0.00 0.0 42.13 2.83 R
1719 2169 1.082756 GCTTCGTCCTGCGTTGTTG 60.083 57.895 0.00 0.0 42.13 3.33 R
2966 3430 0.532573 ACACCGACTGATGCTACTGG 59.467 55.000 0.00 0.0 0.00 4.00 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
40 41 9.995003 AAATTTTAATTCAGGCAAACTATGTCA 57.005 25.926 0.00 0.00 35.54 3.58
41 42 9.995003 AATTTTAATTCAGGCAAACTATGTCAA 57.005 25.926 0.00 0.00 35.54 3.18
42 43 9.995003 ATTTTAATTCAGGCAAACTATGTCAAA 57.005 25.926 0.00 0.00 35.54 2.69
43 44 9.823647 TTTTAATTCAGGCAAACTATGTCAAAA 57.176 25.926 0.00 0.00 35.54 2.44
44 45 9.995003 TTTAATTCAGGCAAACTATGTCAAAAT 57.005 25.926 0.00 0.00 35.54 1.82
45 46 9.638239 TTAATTCAGGCAAACTATGTCAAAATC 57.362 29.630 0.00 0.00 35.54 2.17
46 47 6.899393 TTCAGGCAAACTATGTCAAAATCT 57.101 33.333 0.00 0.00 35.54 2.40
47 48 6.258230 TCAGGCAAACTATGTCAAAATCTG 57.742 37.500 0.00 0.00 35.54 2.90
48 49 5.769662 TCAGGCAAACTATGTCAAAATCTGT 59.230 36.000 0.00 0.00 35.54 3.41
49 50 6.939730 TCAGGCAAACTATGTCAAAATCTGTA 59.060 34.615 0.00 0.00 35.54 2.74
50 51 7.446931 TCAGGCAAACTATGTCAAAATCTGTAA 59.553 33.333 0.00 0.00 35.54 2.41
51 52 8.081633 CAGGCAAACTATGTCAAAATCTGTAAA 58.918 33.333 0.00 0.00 35.54 2.01
52 53 8.806146 AGGCAAACTATGTCAAAATCTGTAAAT 58.194 29.630 0.00 0.00 35.54 1.40
58 59 9.661563 ACTATGTCAAAATCTGTAAATAACCGA 57.338 29.630 0.00 0.00 0.00 4.69
60 61 7.372451 TGTCAAAATCTGTAAATAACCGAGG 57.628 36.000 0.00 0.00 0.00 4.63
61 62 7.162761 TGTCAAAATCTGTAAATAACCGAGGA 58.837 34.615 0.00 0.00 0.00 3.71
62 63 7.662258 TGTCAAAATCTGTAAATAACCGAGGAA 59.338 33.333 0.00 0.00 0.00 3.36
63 64 8.674607 GTCAAAATCTGTAAATAACCGAGGAAT 58.325 33.333 0.00 0.00 0.00 3.01
64 65 9.893634 TCAAAATCTGTAAATAACCGAGGAATA 57.106 29.630 0.00 0.00 0.00 1.75
70 71 9.706691 TCTGTAAATAACCGAGGAATATTCATC 57.293 33.333 18.04 18.04 34.86 2.92
71 72 9.712305 CTGTAAATAACCGAGGAATATTCATCT 57.288 33.333 23.45 10.53 35.96 2.90
72 73 9.706691 TGTAAATAACCGAGGAATATTCATCTC 57.293 33.333 23.45 16.60 35.96 2.75
73 74 9.930693 GTAAATAACCGAGGAATATTCATCTCT 57.069 33.333 23.45 9.56 35.96 3.10
77 78 6.597832 ACCGAGGAATATTCATCTCTAAGG 57.402 41.667 23.45 19.06 35.96 2.69
78 79 5.482175 ACCGAGGAATATTCATCTCTAAGGG 59.518 44.000 23.45 18.50 35.96 3.95
79 80 5.105146 CCGAGGAATATTCATCTCTAAGGGG 60.105 48.000 23.45 13.72 35.96 4.79
80 81 5.717178 CGAGGAATATTCATCTCTAAGGGGA 59.283 44.000 23.45 0.00 35.96 4.81
81 82 6.127479 CGAGGAATATTCATCTCTAAGGGGAG 60.127 46.154 23.45 4.71 35.96 4.30
82 83 6.638953 AGGAATATTCATCTCTAAGGGGAGT 58.361 40.000 17.07 0.00 35.11 3.85
83 84 6.500049 AGGAATATTCATCTCTAAGGGGAGTG 59.500 42.308 17.07 0.00 35.11 3.51
84 85 6.498651 GGAATATTCATCTCTAAGGGGAGTGA 59.501 42.308 17.07 0.00 35.11 3.41
85 86 6.926630 ATATTCATCTCTAAGGGGAGTGAC 57.073 41.667 0.00 0.00 35.11 3.67
86 87 2.656002 TCATCTCTAAGGGGAGTGACG 58.344 52.381 0.00 0.00 35.11 4.35
87 88 1.683917 CATCTCTAAGGGGAGTGACGG 59.316 57.143 0.00 0.00 35.11 4.79
88 89 0.702902 TCTCTAAGGGGAGTGACGGT 59.297 55.000 0.00 0.00 35.11 4.83
89 90 1.918262 TCTCTAAGGGGAGTGACGGTA 59.082 52.381 0.00 0.00 35.11 4.02
90 91 2.512896 TCTCTAAGGGGAGTGACGGTAT 59.487 50.000 0.00 0.00 35.11 2.73
91 92 2.885894 CTCTAAGGGGAGTGACGGTATC 59.114 54.545 0.00 0.00 0.00 2.24
92 93 2.242965 TCTAAGGGGAGTGACGGTATCA 59.757 50.000 0.00 0.00 33.79 2.15
93 94 2.176247 AAGGGGAGTGACGGTATCAT 57.824 50.000 0.00 0.00 40.28 2.45
94 95 3.323774 AAGGGGAGTGACGGTATCATA 57.676 47.619 0.00 0.00 40.28 2.15
95 96 3.323774 AGGGGAGTGACGGTATCATAA 57.676 47.619 0.00 0.00 40.28 1.90
96 97 2.963782 AGGGGAGTGACGGTATCATAAC 59.036 50.000 0.00 0.00 40.28 1.89
97 98 2.036862 GGGGAGTGACGGTATCATAACC 59.963 54.545 0.00 0.00 40.28 2.85
98 99 2.036862 GGGAGTGACGGTATCATAACCC 59.963 54.545 0.00 0.00 40.28 4.11
99 100 2.036862 GGAGTGACGGTATCATAACCCC 59.963 54.545 0.00 0.00 40.28 4.95
100 101 2.963782 GAGTGACGGTATCATAACCCCT 59.036 50.000 0.00 0.00 40.28 4.79
101 102 2.963782 AGTGACGGTATCATAACCCCTC 59.036 50.000 0.00 0.00 40.28 4.30
102 103 2.036862 GTGACGGTATCATAACCCCTCC 59.963 54.545 0.00 0.00 40.28 4.30
103 104 2.322658 GACGGTATCATAACCCCTCCA 58.677 52.381 0.00 0.00 36.03 3.86
104 105 2.701951 GACGGTATCATAACCCCTCCAA 59.298 50.000 0.00 0.00 36.03 3.53
105 106 3.116959 ACGGTATCATAACCCCTCCAAA 58.883 45.455 0.00 0.00 36.03 3.28
106 107 3.720002 ACGGTATCATAACCCCTCCAAAT 59.280 43.478 0.00 0.00 36.03 2.32
107 108 4.167307 ACGGTATCATAACCCCTCCAAATT 59.833 41.667 0.00 0.00 36.03 1.82
108 109 4.760204 CGGTATCATAACCCCTCCAAATTC 59.240 45.833 0.00 0.00 36.03 2.17
109 110 5.689031 CGGTATCATAACCCCTCCAAATTCA 60.689 44.000 0.00 0.00 36.03 2.57
110 111 5.770162 GGTATCATAACCCCTCCAAATTCAG 59.230 44.000 0.00 0.00 33.02 3.02
111 112 4.249638 TCATAACCCCTCCAAATTCAGG 57.750 45.455 0.00 0.00 0.00 3.86
112 113 2.525105 TAACCCCTCCAAATTCAGGC 57.475 50.000 0.00 0.00 0.00 4.85
124 125 4.414852 CAAATTCAGGCATTTGGACGTAG 58.585 43.478 0.00 0.00 39.53 3.51
145 147 7.082602 CGTAGTGCTATGTATAGTAACCAAGG 58.917 42.308 1.28 0.00 32.96 3.61
249 259 2.125106 CCGGTGGAGGTGCTAAGC 60.125 66.667 0.00 0.00 0.00 3.09
295 328 8.651588 GCTAGAATTATCTCAATATTCACGTGG 58.348 37.037 17.00 0.00 37.10 4.94
300 333 4.545208 TCTCAATATTCACGTGGTTCCA 57.455 40.909 17.00 0.00 0.00 3.53
301 334 4.503910 TCTCAATATTCACGTGGTTCCAG 58.496 43.478 17.00 3.82 0.00 3.86
328 361 7.650104 TGAATTGTGAATAAACTTTTCGAACCC 59.350 33.333 0.00 0.00 0.00 4.11
336 369 7.997107 ATAAACTTTTCGAACCCTTGTTTTC 57.003 32.000 0.00 0.00 33.97 2.29
349 382 0.251165 TGTTTTCCCTGGCTGGCTAC 60.251 55.000 4.64 0.91 0.00 3.58
350 383 0.251165 GTTTTCCCTGGCTGGCTACA 60.251 55.000 4.64 0.00 0.00 2.74
365 398 2.817258 GGCTACAAGTGCACATAAACCA 59.183 45.455 21.04 0.00 0.00 3.67
371 404 5.827666 ACAAGTGCACATAAACCAGTAAAC 58.172 37.500 21.04 0.00 0.00 2.01
386 424 4.235360 CAGTAAACGCTAGTACTGCACTT 58.765 43.478 5.39 6.01 40.44 3.16
396 434 3.477530 AGTACTGCACTTCAAAAGGGTC 58.522 45.455 0.00 0.00 31.59 4.46
667 1060 1.035923 TCAAAGCGAAAATGCCCACA 58.964 45.000 0.00 0.00 34.65 4.17
901 1303 4.184629 CCACTTCTTTATCACTTCCGAGG 58.815 47.826 0.00 0.00 0.00 4.63
979 1383 2.107552 AGAGAGAGATAGACGAAGGGGG 59.892 54.545 0.00 0.00 0.00 5.40
1020 1428 1.535202 GATGGAGAGGGCCGAGGAT 60.535 63.158 0.00 0.00 0.00 3.24
1109 1517 3.370978 CACGCTCCAGGTAAATGTTACTG 59.629 47.826 0.00 0.00 0.00 2.74
1110 1518 2.351726 CGCTCCAGGTAAATGTTACTGC 59.648 50.000 0.00 0.00 0.00 4.40
1111 1519 3.610911 GCTCCAGGTAAATGTTACTGCT 58.389 45.455 0.00 0.00 0.00 4.24
1112 1520 4.679639 CGCTCCAGGTAAATGTTACTGCTA 60.680 45.833 0.00 0.00 0.00 3.49
1113 1521 4.811557 GCTCCAGGTAAATGTTACTGCTAG 59.188 45.833 0.00 0.00 0.00 3.42
1182 1597 7.328737 CCTAATACTATACGAGATGTTGGCAAC 59.671 40.741 23.12 23.12 0.00 4.17
1221 1636 1.153208 CCTGGAGATGCCACTGCTC 60.153 63.158 0.00 0.00 43.33 4.26
1419 1834 4.669700 ACCCGGTAATTAGCCTTTTCTTT 58.330 39.130 9.01 0.00 0.00 2.52
1420 1835 4.703575 ACCCGGTAATTAGCCTTTTCTTTC 59.296 41.667 9.01 0.00 0.00 2.62
1422 1837 4.201881 CCGGTAATTAGCCTTTTCTTTCGG 60.202 45.833 9.01 0.00 0.00 4.30
1423 1838 4.632688 CGGTAATTAGCCTTTTCTTTCGGA 59.367 41.667 9.01 0.00 0.00 4.55
1424 1839 5.220605 CGGTAATTAGCCTTTTCTTTCGGAG 60.221 44.000 9.01 0.00 0.00 4.63
1426 1841 6.820152 GGTAATTAGCCTTTTCTTTCGGAGTA 59.180 38.462 3.16 0.00 0.00 2.59
1427 1842 7.498239 GGTAATTAGCCTTTTCTTTCGGAGTAT 59.502 37.037 3.16 0.00 0.00 2.12
1428 1843 7.555306 AATTAGCCTTTTCTTTCGGAGTATC 57.445 36.000 0.00 0.00 0.00 2.24
1429 1844 4.553330 AGCCTTTTCTTTCGGAGTATCA 57.447 40.909 0.00 0.00 36.25 2.15
1475 1913 6.622549 ACATGCAGTTCTTAGTACTGTCTAC 58.377 40.000 17.81 4.65 43.81 2.59
1477 1915 6.497785 TGCAGTTCTTAGTACTGTCTACTC 57.502 41.667 17.81 3.75 43.81 2.59
1479 1917 7.392418 TGCAGTTCTTAGTACTGTCTACTCTA 58.608 38.462 17.81 0.00 43.81 2.43
1511 1958 3.481903 CCTGCGTGCTGCTACGTG 61.482 66.667 19.91 14.63 46.63 4.49
1622 2069 3.869246 AGGTACGTATTAGCACATGCAAC 59.131 43.478 6.64 0.00 45.16 4.17
1669 2119 4.369182 GGATTTCCTTTAAGCTCGATCGA 58.631 43.478 18.32 18.32 0.00 3.59
1693 2143 4.155099 TGATCAGAACGAGTTCTCAGTCTC 59.845 45.833 14.86 8.48 46.13 3.36
1946 2396 6.425504 CAACAACAACAACAACAACAACAAT 58.574 32.000 0.00 0.00 0.00 2.71
1951 2401 7.344910 ACAACAACAACAACAACAATAACAG 57.655 32.000 0.00 0.00 0.00 3.16
2518 2978 7.038799 TGTCTCCAGAAAGCATGCATATATCTA 60.039 37.037 21.98 1.26 0.00 1.98
2553 3013 6.570571 GCAAAGGGTTCTTCCATAGTTCTTTC 60.571 42.308 0.00 0.00 38.11 2.62
2652 3112 3.281240 GGCCACCGACTACTCGAA 58.719 61.111 0.00 0.00 43.06 3.71
2664 3126 1.266175 CTACTCGAACGTGTGGACTGT 59.734 52.381 11.24 0.00 0.00 3.55
2686 3148 1.541147 CAATCAAACTGCCACACGGAT 59.459 47.619 0.00 0.00 0.00 4.18
2966 3430 3.056179 GCCATCTCCATCTTCTAGTAGCC 60.056 52.174 0.00 0.00 0.00 3.93
2995 3459 0.457851 CAGTCGGTGTCATCTCCCTC 59.542 60.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.995003 TGACATAGTTTGCCTGAATTAAAATTT 57.005 25.926 0.00 0.00 0.00 1.82
15 16 9.995003 TTGACATAGTTTGCCTGAATTAAAATT 57.005 25.926 0.00 0.00 0.00 1.82
16 17 9.995003 TTTGACATAGTTTGCCTGAATTAAAAT 57.005 25.926 0.00 0.00 0.00 1.82
17 18 9.823647 TTTTGACATAGTTTGCCTGAATTAAAA 57.176 25.926 0.00 0.00 0.00 1.52
18 19 9.995003 ATTTTGACATAGTTTGCCTGAATTAAA 57.005 25.926 0.00 0.00 0.00 1.52
19 20 9.638239 GATTTTGACATAGTTTGCCTGAATTAA 57.362 29.630 0.00 0.00 0.00 1.40
20 21 9.023962 AGATTTTGACATAGTTTGCCTGAATTA 57.976 29.630 0.00 0.00 0.00 1.40
21 22 7.816031 CAGATTTTGACATAGTTTGCCTGAATT 59.184 33.333 0.00 0.00 0.00 2.17
22 23 7.039504 ACAGATTTTGACATAGTTTGCCTGAAT 60.040 33.333 0.00 0.00 0.00 2.57
23 24 6.265196 ACAGATTTTGACATAGTTTGCCTGAA 59.735 34.615 0.00 0.00 0.00 3.02
24 25 5.769662 ACAGATTTTGACATAGTTTGCCTGA 59.230 36.000 0.00 0.00 0.00 3.86
25 26 6.017400 ACAGATTTTGACATAGTTTGCCTG 57.983 37.500 0.00 0.00 0.00 4.85
26 27 7.759489 TTACAGATTTTGACATAGTTTGCCT 57.241 32.000 0.00 0.00 0.00 4.75
27 28 8.986477 ATTTACAGATTTTGACATAGTTTGCC 57.014 30.769 0.00 0.00 0.00 4.52
32 33 9.661563 TCGGTTATTTACAGATTTTGACATAGT 57.338 29.630 0.00 0.00 0.00 2.12
34 35 9.104965 CCTCGGTTATTTACAGATTTTGACATA 57.895 33.333 0.00 0.00 30.42 2.29
35 36 7.827236 TCCTCGGTTATTTACAGATTTTGACAT 59.173 33.333 0.00 0.00 30.42 3.06
36 37 7.162761 TCCTCGGTTATTTACAGATTTTGACA 58.837 34.615 0.00 0.00 30.42 3.58
37 38 7.605410 TCCTCGGTTATTTACAGATTTTGAC 57.395 36.000 0.00 0.00 30.42 3.18
38 39 8.801882 ATTCCTCGGTTATTTACAGATTTTGA 57.198 30.769 0.00 0.00 30.42 2.69
44 45 9.706691 GATGAATATTCCTCGGTTATTTACAGA 57.293 33.333 12.90 0.00 0.00 3.41
45 46 9.712305 AGATGAATATTCCTCGGTTATTTACAG 57.288 33.333 12.90 0.00 0.00 2.74
46 47 9.706691 GAGATGAATATTCCTCGGTTATTTACA 57.293 33.333 12.90 0.00 0.00 2.41
47 48 9.930693 AGAGATGAATATTCCTCGGTTATTTAC 57.069 33.333 12.90 0.66 0.00 2.01
51 52 8.754080 CCTTAGAGATGAATATTCCTCGGTTAT 58.246 37.037 12.90 0.00 0.00 1.89
52 53 7.178628 CCCTTAGAGATGAATATTCCTCGGTTA 59.821 40.741 12.90 5.68 0.00 2.85
53 54 6.014156 CCCTTAGAGATGAATATTCCTCGGTT 60.014 42.308 12.90 6.49 0.00 4.44
54 55 5.482175 CCCTTAGAGATGAATATTCCTCGGT 59.518 44.000 12.90 7.77 0.00 4.69
55 56 5.105146 CCCCTTAGAGATGAATATTCCTCGG 60.105 48.000 12.90 8.36 0.00 4.63
56 57 5.717178 TCCCCTTAGAGATGAATATTCCTCG 59.283 44.000 12.90 0.37 0.00 4.63
57 58 6.728632 ACTCCCCTTAGAGATGAATATTCCTC 59.271 42.308 12.90 12.18 37.33 3.71
58 59 6.500049 CACTCCCCTTAGAGATGAATATTCCT 59.500 42.308 12.90 2.79 37.33 3.36
59 60 6.498651 TCACTCCCCTTAGAGATGAATATTCC 59.501 42.308 12.90 0.00 37.33 3.01
60 61 7.382898 GTCACTCCCCTTAGAGATGAATATTC 58.617 42.308 8.60 8.60 37.33 1.75
61 62 6.015010 CGTCACTCCCCTTAGAGATGAATATT 60.015 42.308 0.00 0.00 37.33 1.28
62 63 5.478679 CGTCACTCCCCTTAGAGATGAATAT 59.521 44.000 0.00 0.00 37.33 1.28
63 64 4.827835 CGTCACTCCCCTTAGAGATGAATA 59.172 45.833 0.00 0.00 37.33 1.75
64 65 3.639094 CGTCACTCCCCTTAGAGATGAAT 59.361 47.826 0.00 0.00 37.33 2.57
65 66 3.024547 CGTCACTCCCCTTAGAGATGAA 58.975 50.000 0.00 0.00 37.33 2.57
66 67 2.656002 CGTCACTCCCCTTAGAGATGA 58.344 52.381 0.00 0.00 37.33 2.92
67 68 1.683917 CCGTCACTCCCCTTAGAGATG 59.316 57.143 0.00 0.00 37.33 2.90
68 69 1.288335 ACCGTCACTCCCCTTAGAGAT 59.712 52.381 0.00 0.00 37.33 2.75
69 70 0.702902 ACCGTCACTCCCCTTAGAGA 59.297 55.000 0.00 0.00 37.33 3.10
70 71 2.431954 TACCGTCACTCCCCTTAGAG 57.568 55.000 0.00 0.00 39.91 2.43
71 72 2.242965 TGATACCGTCACTCCCCTTAGA 59.757 50.000 0.00 0.00 0.00 2.10
72 73 2.662866 TGATACCGTCACTCCCCTTAG 58.337 52.381 0.00 0.00 0.00 2.18
73 74 2.832643 TGATACCGTCACTCCCCTTA 57.167 50.000 0.00 0.00 0.00 2.69
74 75 2.176247 ATGATACCGTCACTCCCCTT 57.824 50.000 0.00 0.00 40.28 3.95
75 76 2.963782 GTTATGATACCGTCACTCCCCT 59.036 50.000 0.00 0.00 40.28 4.79
76 77 2.036862 GGTTATGATACCGTCACTCCCC 59.963 54.545 0.00 0.00 40.28 4.81
77 78 2.036862 GGGTTATGATACCGTCACTCCC 59.963 54.545 0.00 0.00 40.28 4.30
78 79 2.036862 GGGGTTATGATACCGTCACTCC 59.963 54.545 0.00 0.00 40.28 3.85
79 80 2.963782 AGGGGTTATGATACCGTCACTC 59.036 50.000 0.00 0.00 40.28 3.51
80 81 2.963782 GAGGGGTTATGATACCGTCACT 59.036 50.000 0.00 0.00 40.28 3.41
81 82 2.036862 GGAGGGGTTATGATACCGTCAC 59.963 54.545 0.00 0.00 40.28 3.67
82 83 2.322658 GGAGGGGTTATGATACCGTCA 58.677 52.381 0.00 0.00 40.08 4.35
83 84 2.322658 TGGAGGGGTTATGATACCGTC 58.677 52.381 0.00 0.00 39.18 4.79
84 85 2.482414 TGGAGGGGTTATGATACCGT 57.518 50.000 0.00 0.00 39.18 4.83
85 86 3.849563 TTTGGAGGGGTTATGATACCG 57.150 47.619 0.00 0.00 39.18 4.02
86 87 5.701224 TGAATTTGGAGGGGTTATGATACC 58.299 41.667 0.00 0.00 37.47 2.73
87 88 5.770162 CCTGAATTTGGAGGGGTTATGATAC 59.230 44.000 0.00 0.00 0.00 2.24
88 89 5.692781 GCCTGAATTTGGAGGGGTTATGATA 60.693 44.000 3.03 0.00 0.00 2.15
89 90 4.808042 CCTGAATTTGGAGGGGTTATGAT 58.192 43.478 0.00 0.00 0.00 2.45
90 91 3.627237 GCCTGAATTTGGAGGGGTTATGA 60.627 47.826 3.03 0.00 0.00 2.15
91 92 2.695147 GCCTGAATTTGGAGGGGTTATG 59.305 50.000 3.03 0.00 0.00 1.90
92 93 2.314549 TGCCTGAATTTGGAGGGGTTAT 59.685 45.455 3.03 0.00 0.00 1.89
93 94 1.713647 TGCCTGAATTTGGAGGGGTTA 59.286 47.619 3.03 0.00 0.00 2.85
94 95 0.486879 TGCCTGAATTTGGAGGGGTT 59.513 50.000 3.03 0.00 0.00 4.11
95 96 0.712380 ATGCCTGAATTTGGAGGGGT 59.288 50.000 3.03 0.00 0.00 4.95
96 97 1.870064 AATGCCTGAATTTGGAGGGG 58.130 50.000 3.03 0.00 0.00 4.79
97 98 3.255969 CAAATGCCTGAATTTGGAGGG 57.744 47.619 3.07 0.00 41.71 4.30
102 103 3.302365 ACGTCCAAATGCCTGAATTTG 57.698 42.857 3.93 3.93 43.94 2.32
103 104 4.079253 ACTACGTCCAAATGCCTGAATTT 58.921 39.130 0.00 0.00 0.00 1.82
104 105 3.440173 CACTACGTCCAAATGCCTGAATT 59.560 43.478 0.00 0.00 0.00 2.17
105 106 3.009723 CACTACGTCCAAATGCCTGAAT 58.990 45.455 0.00 0.00 0.00 2.57
106 107 2.422597 CACTACGTCCAAATGCCTGAA 58.577 47.619 0.00 0.00 0.00 3.02
107 108 1.943968 GCACTACGTCCAAATGCCTGA 60.944 52.381 0.00 0.00 0.00 3.86
108 109 0.447801 GCACTACGTCCAAATGCCTG 59.552 55.000 0.00 0.00 0.00 4.85
109 110 0.324943 AGCACTACGTCCAAATGCCT 59.675 50.000 0.00 0.00 36.96 4.75
110 111 2.018542 TAGCACTACGTCCAAATGCC 57.981 50.000 0.00 0.00 36.96 4.40
111 112 2.936498 ACATAGCACTACGTCCAAATGC 59.064 45.455 0.00 0.00 36.52 3.56
112 113 7.145985 ACTATACATAGCACTACGTCCAAATG 58.854 38.462 0.00 0.00 33.68 2.32
124 125 6.874134 CCATCCTTGGTTACTATACATAGCAC 59.126 42.308 0.00 0.00 38.30 4.40
145 147 4.338795 TCCCTACATAGATCCTCCCATC 57.661 50.000 0.00 0.00 0.00 3.51
228 236 1.485066 CTTAGCACCTCCACCGGTTAT 59.515 52.381 2.97 0.00 34.29 1.89
249 259 7.891782 TCTAGCATACGTTTGAATTTTAGACG 58.108 34.615 10.37 3.21 39.43 4.18
295 328 8.871686 AAAGTTTATTCACAATTCACTGGAAC 57.128 30.769 0.00 0.00 35.46 3.62
300 333 9.233232 GTTCGAAAAGTTTATTCACAATTCACT 57.767 29.630 0.00 0.00 0.00 3.41
301 334 8.476925 GGTTCGAAAAGTTTATTCACAATTCAC 58.523 33.333 0.00 0.00 0.00 3.18
328 361 0.829182 AGCCAGCCAGGGAAAACAAG 60.829 55.000 0.00 0.00 38.09 3.16
336 369 1.377725 CACTTGTAGCCAGCCAGGG 60.378 63.158 0.00 0.00 38.09 4.45
349 382 4.909305 CGTTTACTGGTTTATGTGCACTTG 59.091 41.667 19.41 1.22 0.00 3.16
350 383 4.555906 GCGTTTACTGGTTTATGTGCACTT 60.556 41.667 19.41 14.68 0.00 3.16
365 398 4.022589 TGAAGTGCAGTACTAGCGTTTACT 60.023 41.667 0.00 0.00 39.18 2.24
371 404 3.123621 CCTTTTGAAGTGCAGTACTAGCG 59.876 47.826 0.00 0.00 39.18 4.26
386 424 6.621931 TGTTCCCATATATAGGACCCTTTTGA 59.378 38.462 0.00 0.00 0.00 2.69
527 919 4.033587 ACGTGCAAAATAGAATAATCGCGT 59.966 37.500 5.77 0.00 35.10 6.01
691 1089 3.895041 TCCACTCAAACCAGGATTTTTCC 59.105 43.478 0.00 0.00 0.00 3.13
743 1141 1.079405 CCACCGCTAAAGGCTCGAA 60.079 57.895 0.00 0.00 39.13 3.71
901 1303 0.104120 GTTTGCAGTTGGGGTTGGAC 59.896 55.000 0.00 0.00 0.00 4.02
979 1383 1.817740 CGATCTCCCTGACCTCTCTCC 60.818 61.905 0.00 0.00 0.00 3.71
1113 1521 4.627900 GGAGTTGAAGAAGTAAGCACTAGC 59.372 45.833 0.00 0.00 42.56 3.42
1126 1534 0.894184 AGTCTCGCCGGAGTTGAAGA 60.894 55.000 5.05 0.00 41.26 2.87
1169 1584 3.503363 TGATCAACAGTTGCCAACATCTC 59.497 43.478 10.69 0.00 0.00 2.75
1170 1585 3.489355 TGATCAACAGTTGCCAACATCT 58.511 40.909 10.69 0.00 0.00 2.90
1176 1591 2.289882 CCTCTCTGATCAACAGTTGCCA 60.290 50.000 8.58 8.01 45.86 4.92
1182 1597 4.650588 AGGAATCTCCTCTCTGATCAACAG 59.349 45.833 0.00 0.00 45.66 3.16
1437 1852 7.669427 AGAACTGCATGTTTCATGGAAATAAA 58.331 30.769 10.96 0.00 39.30 1.40
1475 1913 7.169982 CACGCAGGGTTTAGAAAGATTATAGAG 59.830 40.741 0.00 0.00 0.00 2.43
1477 1915 6.292919 GCACGCAGGGTTTAGAAAGATTATAG 60.293 42.308 0.00 0.00 0.00 1.31
1479 1917 4.335594 GCACGCAGGGTTTAGAAAGATTAT 59.664 41.667 0.00 0.00 0.00 1.28
1482 1920 2.084546 GCACGCAGGGTTTAGAAAGAT 58.915 47.619 0.00 0.00 0.00 2.40
1511 1958 1.079819 TTCTGCCTCTGCACGTAGC 60.080 57.895 0.00 0.00 44.23 3.58
1578 2025 0.670546 CGCGTCTGTTCTGGAACCAT 60.671 55.000 10.44 0.00 40.46 3.55
1622 2069 9.224267 CCCATCCAAAGAACATATAAGATACTG 57.776 37.037 0.00 0.00 0.00 2.74
1646 2096 3.495001 CGATCGAGCTTAAAGGAAATCCC 59.505 47.826 10.26 0.00 36.42 3.85
1711 2161 3.238798 CGTCCTGCGTTGTTGTTTAAAAC 59.761 43.478 0.00 0.00 35.54 2.43
1716 2166 1.063469 CTTCGTCCTGCGTTGTTGTTT 59.937 47.619 0.00 0.00 42.13 2.83
1719 2169 1.082756 GCTTCGTCCTGCGTTGTTG 60.083 57.895 0.00 0.00 42.13 3.33
1946 2396 2.740826 GCGGCGTTGGAGCTGTTA 60.741 61.111 9.37 0.00 44.91 2.41
2180 2638 3.118555 TCGTGTTCCTTCCTGACAAAGAA 60.119 43.478 0.00 0.00 0.00 2.52
2181 2639 2.432874 TCGTGTTCCTTCCTGACAAAGA 59.567 45.455 0.00 0.00 0.00 2.52
2333 2793 4.072088 GCGACAGGACAAACCGCG 62.072 66.667 0.00 0.00 44.74 6.46
2334 2794 2.251642 AAGCGACAGGACAAACCGC 61.252 57.895 0.00 0.00 44.74 5.68
2335 2795 1.569493 CAAGCGACAGGACAAACCG 59.431 57.895 0.00 0.00 44.74 4.44
2336 2796 1.949257 CCAAGCGACAGGACAAACC 59.051 57.895 0.00 0.00 39.35 3.27
2518 2978 7.125391 TGGAAGAACCCTTTGCATAGATTAAT 58.875 34.615 5.65 0.00 38.00 1.40
2534 2994 5.249420 AGCAGAAAGAACTATGGAAGAACC 58.751 41.667 0.00 0.00 39.54 3.62
2538 2998 4.328440 CGTGAGCAGAAAGAACTATGGAAG 59.672 45.833 0.00 0.00 0.00 3.46
2553 3013 7.997107 TTAAATTAGGTACATACGTGAGCAG 57.003 36.000 0.00 0.00 0.00 4.24
2604 3064 7.827729 GTGTTTAGTTGTCTATATCCAAACCCT 59.172 37.037 0.00 0.00 0.00 4.34
2652 3112 3.462483 TTGATTGTACAGTCCACACGT 57.538 42.857 15.02 0.00 0.00 4.49
2664 3126 1.876799 CCGTGTGGCAGTTTGATTGTA 59.123 47.619 0.00 0.00 0.00 2.41
2686 3148 2.295904 TGATCCCGGATCAGTTGCA 58.704 52.632 23.92 3.23 43.11 4.08
2966 3430 0.532573 ACACCGACTGATGCTACTGG 59.467 55.000 0.00 0.00 0.00 4.00
2995 3459 4.625972 ATAAAGTGGCGAAAATTACCCG 57.374 40.909 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.