Multiple sequence alignment - TraesCS5A01G251100

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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 TraesCS5A01G251100 chr5A 100.000 3339 0 0 1 3339 466981406 466984744 0.000000e+00 6167.0
1 TraesCS5A01G251100 chr5B 87.561 3095 218 84 349 3339 431794322 431797353 0.000000e+00 3428.0
2 TraesCS5A01G251100 chr5B 85.902 305 31 9 1 294 431793900 431794203 6.950000e-82 315.0
3 TraesCS5A01G251100 chr5D 88.706 1824 125 42 349 2140 365320342 365322116 0.000000e+00 2152.0
4 TraesCS5A01G251100 chr5D 88.870 1195 84 23 2178 3339 365322112 365323290 0.000000e+00 1424.0
5 TraesCS5A01G251100 chr1A 76.243 181 28 7 87 255 140964626 140964449 7.680000e-12 82.4


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 TraesCS5A01G251100 chr5A 466981406 466984744 3338 False 6167.0 6167 100.0000 1 3339 1 chr5A.!!$F1 3338
1 TraesCS5A01G251100 chr5B 431793900 431797353 3453 False 1871.5 3428 86.7315 1 3339 2 chr5B.!!$F1 3338
2 TraesCS5A01G251100 chr5D 365320342 365323290 2948 False 1788.0 2152 88.7880 349 3339 2 chr5D.!!$F1 2990

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
197 209 0.037419 AACATCCATTGTTTGGCCGC 60.037 50.0 0.00 0.00 46.51 6.53 F
433 515 0.038159 AATCCGATACCGCAGCTAGC 60.038 55.0 6.62 6.62 40.87 3.42 F
1868 1984 0.102481 TCGCGTAGAGAAGGGCAATC 59.898 55.0 5.77 0.00 30.01 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1221 1318 0.031585 GCAGTGTGAGTGTACCGTGA 59.968 55.0 0.00 0.0 0.00 4.35 R
2063 2180 0.250424 CTGTGATGTGGCCAGTGTGA 60.250 55.0 5.11 0.0 0.00 3.58 R
3219 3431 0.457851 CCAGAGTGAGACCATCGTCC 59.542 60.0 0.00 0.0 40.12 4.79 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
25 26 6.426633 TCGACAACAACAATATCAACAGATGT 59.573 34.615 0.00 0.00 0.00 3.06
32 33 9.341078 ACAACAATATCAACAGATGTATATGCA 57.659 29.630 0.00 0.00 0.00 3.96
46 47 9.570468 AGATGTATATGCAACTTCTGAATGATT 57.430 29.630 0.00 0.00 32.05 2.57
121 123 9.787532 TTTGATTTTACAATTATGCACTAGAGC 57.212 29.630 5.07 5.07 0.00 4.09
124 126 7.880160 TTTTACAATTATGCACTAGAGCCAT 57.120 32.000 9.79 6.10 0.00 4.40
126 128 7.496529 TTACAATTATGCACTAGAGCCATTC 57.503 36.000 9.79 0.00 0.00 2.67
128 130 5.762218 ACAATTATGCACTAGAGCCATTCTC 59.238 40.000 9.79 0.00 42.21 2.87
129 131 5.557576 ATTATGCACTAGAGCCATTCTCA 57.442 39.130 9.79 0.00 44.35 3.27
130 132 5.557576 TTATGCACTAGAGCCATTCTCAT 57.442 39.130 9.79 0.00 44.35 2.90
131 133 3.465742 TGCACTAGAGCCATTCTCATC 57.534 47.619 9.79 0.00 44.35 2.92
135 137 4.272991 GCACTAGAGCCATTCTCATCTTTG 59.727 45.833 0.00 0.00 44.35 2.77
136 138 4.272991 CACTAGAGCCATTCTCATCTTTGC 59.727 45.833 0.00 0.00 44.35 3.68
137 139 3.361281 AGAGCCATTCTCATCTTTGCA 57.639 42.857 0.00 0.00 44.35 4.08
138 140 3.015327 AGAGCCATTCTCATCTTTGCAC 58.985 45.455 0.00 0.00 44.35 4.57
158 163 7.609760 TGCACTGTTTCGATTATGTATTCTT 57.390 32.000 0.00 0.00 0.00 2.52
197 209 0.037419 AACATCCATTGTTTGGCCGC 60.037 50.000 0.00 0.00 46.51 6.53
200 212 1.037030 ATCCATTGTTTGGCCGCGAT 61.037 50.000 8.23 0.00 46.01 4.58
208 220 2.844072 TTTGGCCGCGATGATCGACA 62.844 55.000 20.25 8.32 43.74 4.35
211 223 2.849007 CCGCGATGATCGACATGC 59.151 61.111 20.25 0.00 43.74 4.06
242 254 8.505625 GTTTGCATGTATTTGATGTTCCAAAAT 58.494 29.630 0.00 0.00 39.20 1.82
269 281 4.222588 GGAATTGTGGATGGGTCATTTGAA 59.777 41.667 0.00 0.00 0.00 2.69
294 306 0.389948 GACGGTCACTGTCCATGGAC 60.390 60.000 33.97 33.97 44.77 4.02
304 316 2.736144 GTCCATGGACACGTACTTCA 57.264 50.000 35.21 0.00 44.02 3.02
305 317 3.247006 GTCCATGGACACGTACTTCAT 57.753 47.619 35.21 0.00 44.02 2.57
306 318 4.380841 GTCCATGGACACGTACTTCATA 57.619 45.455 35.21 0.00 44.02 2.15
308 320 4.097437 GTCCATGGACACGTACTTCATAGA 59.903 45.833 35.21 0.00 44.02 1.98
309 321 4.893524 TCCATGGACACGTACTTCATAGAT 59.106 41.667 11.44 0.00 0.00 1.98
310 322 4.984785 CCATGGACACGTACTTCATAGATG 59.015 45.833 5.56 0.00 0.00 2.90
312 324 4.993905 TGGACACGTACTTCATAGATGTG 58.006 43.478 0.00 0.00 0.00 3.21
314 326 5.359860 TGGACACGTACTTCATAGATGTGAT 59.640 40.000 0.00 0.00 0.00 3.06
316 328 6.238786 GGACACGTACTTCATAGATGTGATCT 60.239 42.308 0.00 0.00 43.33 2.75
358 434 7.807687 TTTTACACTCTATCGCTGAAACTAC 57.192 36.000 0.00 0.00 0.00 2.73
433 515 0.038159 AATCCGATACCGCAGCTAGC 60.038 55.000 6.62 6.62 40.87 3.42
465 547 0.390124 AGCACCAAAACAGCACCATG 59.610 50.000 0.00 0.00 0.00 3.66
468 550 1.120795 ACCAAAACAGCACCATGGGG 61.121 55.000 18.09 14.63 41.29 4.96
470 552 0.604578 CAAAACAGCACCATGGGGAG 59.395 55.000 21.28 12.15 38.05 4.30
496 578 0.386731 CCCACGCACGATTGTTTTCC 60.387 55.000 0.00 0.00 0.00 3.13
497 579 0.591170 CCACGCACGATTGTTTTCCT 59.409 50.000 0.00 0.00 0.00 3.36
499 581 2.412325 CCACGCACGATTGTTTTCCTAC 60.412 50.000 0.00 0.00 0.00 3.18
500 582 1.802365 ACGCACGATTGTTTTCCTACC 59.198 47.619 0.00 0.00 0.00 3.18
511 593 1.770749 TTTCCTACCCACACCCCACG 61.771 60.000 0.00 0.00 0.00 4.94
512 594 4.404098 CCTACCCACACCCCACGC 62.404 72.222 0.00 0.00 0.00 5.34
513 595 3.632080 CTACCCACACCCCACGCA 61.632 66.667 0.00 0.00 0.00 5.24
514 596 3.894547 CTACCCACACCCCACGCAC 62.895 68.421 0.00 0.00 0.00 5.34
556 638 2.343758 CGAGGACACCACCACCAG 59.656 66.667 0.00 0.00 0.00 4.00
557 639 2.032681 GAGGACACCACCACCAGC 59.967 66.667 0.00 0.00 0.00 4.85
559 641 2.594592 GGACACCACCACCAGCAC 60.595 66.667 0.00 0.00 0.00 4.40
560 642 2.594592 GACACCACCACCAGCACC 60.595 66.667 0.00 0.00 0.00 5.01
561 643 4.562425 ACACCACCACCAGCACCG 62.562 66.667 0.00 0.00 0.00 4.94
651 733 3.518068 CCCGCCTTCCAATTCCGC 61.518 66.667 0.00 0.00 0.00 5.54
755 844 2.417936 GGAGATCGCCCGAGGTTC 59.582 66.667 3.71 0.00 0.00 3.62
760 849 1.668101 GATCGCCCGAGGTTCTCTGT 61.668 60.000 0.00 0.00 0.00 3.41
761 850 0.395311 ATCGCCCGAGGTTCTCTGTA 60.395 55.000 0.00 0.00 0.00 2.74
858 947 2.058829 AAACGGGAAAGCGCACACAG 62.059 55.000 11.47 0.00 0.00 3.66
907 996 0.814457 GTGCCGGGTTTGAATATGCA 59.186 50.000 2.18 0.00 0.00 3.96
973 1062 1.812922 CTGAGCTGATCGGTGTGGC 60.813 63.158 2.89 0.00 0.00 5.01
1018 1109 5.135362 TCCTTGGTATATAAAACCCCTGCAT 59.865 40.000 5.43 0.00 36.06 3.96
1189 1280 1.134340 AGCACACAACAAGGTCGGTAA 60.134 47.619 0.00 0.00 0.00 2.85
1213 1310 6.131544 ACAATTTCGCAGTAACTTCTTGTT 57.868 33.333 0.00 0.00 42.31 2.83
1214 1311 6.199393 ACAATTTCGCAGTAACTTCTTGTTC 58.801 36.000 0.00 0.00 39.89 3.18
1215 1312 6.183360 ACAATTTCGCAGTAACTTCTTGTTCA 60.183 34.615 0.00 0.00 39.89 3.18
1216 1313 4.789095 TTCGCAGTAACTTCTTGTTCAC 57.211 40.909 0.00 0.00 39.89 3.18
1217 1314 2.792674 TCGCAGTAACTTCTTGTTCACG 59.207 45.455 0.00 0.00 39.89 4.35
1218 1315 2.659291 CGCAGTAACTTCTTGTTCACGC 60.659 50.000 0.00 0.00 39.89 5.34
1219 1316 2.349532 GCAGTAACTTCTTGTTCACGCC 60.350 50.000 0.00 0.00 39.89 5.68
1220 1317 3.131396 CAGTAACTTCTTGTTCACGCCT 58.869 45.455 0.00 0.00 39.89 5.52
1221 1318 3.560068 CAGTAACTTCTTGTTCACGCCTT 59.440 43.478 0.00 0.00 39.89 4.35
1227 1324 1.153329 TTGTTCACGCCTTCACGGT 60.153 52.632 0.00 0.00 37.37 4.83
1230 1327 0.598158 GTTCACGCCTTCACGGTACA 60.598 55.000 0.00 0.00 37.37 2.90
1246 1343 0.179097 TACACTCACACTGCGTGCAA 60.179 50.000 8.31 0.00 45.92 4.08
1316 1429 1.396301 CGTGAAAATGCAGGAGAGCTC 59.604 52.381 5.27 5.27 34.99 4.09
1472 1585 3.890674 CCGCGGAGGGAAGAAAAG 58.109 61.111 24.07 0.00 46.37 2.27
1482 1595 2.638363 AGGGAAGAAAAGCGTAGAGGTT 59.362 45.455 0.00 0.00 43.26 3.50
1590 1703 1.227263 CGATTACCGCACTCCCAGG 60.227 63.158 0.00 0.00 0.00 4.45
1602 1715 4.856801 CCCAGGGTTCATCCGCCG 62.857 72.222 0.00 0.00 37.00 6.46
1664 1778 2.490509 TGCTTCTTGCCACTGATTGATG 59.509 45.455 0.00 0.00 42.00 3.07
1666 1780 3.380637 GCTTCTTGCCACTGATTGATGAT 59.619 43.478 0.00 0.00 35.15 2.45
1667 1781 4.142227 GCTTCTTGCCACTGATTGATGATT 60.142 41.667 0.00 0.00 35.15 2.57
1668 1782 5.066893 GCTTCTTGCCACTGATTGATGATTA 59.933 40.000 0.00 0.00 35.15 1.75
1697 1811 5.430007 AGTGGTACAGTAGTAGTAGCTCTG 58.570 45.833 0.00 0.00 42.13 3.35
1703 1817 8.734386 GGTACAGTAGTAGTAGCTCTGTTTTTA 58.266 37.037 7.22 0.00 39.54 1.52
1707 1823 9.856488 CAGTAGTAGTAGCTCTGTTTTTAATCA 57.144 33.333 0.00 0.00 0.00 2.57
1741 1857 1.738099 GTGGTAGTGCAGTGCTCCG 60.738 63.158 17.60 0.00 0.00 4.63
1753 1869 1.076332 GTGCTCCGCGTCTGTTAAAT 58.924 50.000 4.92 0.00 0.00 1.40
1763 1879 4.548346 CGCGTCTGTTAAATAAGCTAGTGC 60.548 45.833 0.00 0.00 40.05 4.40
1822 1938 1.203050 ACCCCATCACCCAAACTTGAG 60.203 52.381 0.00 0.00 0.00 3.02
1837 1953 6.373779 CAAACTTGAGCCTGTAATTAGTGTG 58.626 40.000 0.00 0.00 0.00 3.82
1868 1984 0.102481 TCGCGTAGAGAAGGGCAATC 59.898 55.000 5.77 0.00 30.01 2.67
1870 1986 1.739035 CGCGTAGAGAAGGGCAATCAA 60.739 52.381 0.00 0.00 0.00 2.57
1883 1999 4.080356 AGGGCAATCAATTAGCTGTACTGA 60.080 41.667 3.61 0.00 0.00 3.41
1885 2001 5.300286 GGGCAATCAATTAGCTGTACTGATT 59.700 40.000 3.61 2.99 37.24 2.57
1886 2002 6.183360 GGGCAATCAATTAGCTGTACTGATTT 60.183 38.462 3.61 0.00 35.15 2.17
1887 2003 7.260603 GGCAATCAATTAGCTGTACTGATTTT 58.739 34.615 3.61 0.00 35.15 1.82
1888 2004 8.405531 GGCAATCAATTAGCTGTACTGATTTTA 58.594 33.333 3.61 0.00 35.15 1.52
1898 2014 7.820648 AGCTGTACTGATTTTATTTTGTCTGG 58.179 34.615 3.61 0.00 0.00 3.86
1926 2042 1.409241 CCACTGGACCCTGAATGATGG 60.409 57.143 0.00 0.00 0.00 3.51
1978 2094 3.336468 AGCAAGTCAAGAAGCAGATCAG 58.664 45.455 0.00 0.00 0.00 2.90
2012 2128 6.209192 TGAATTTGTACATGATGAGGCAAGTT 59.791 34.615 0.00 4.45 0.00 2.66
2044 2161 4.665212 CACGCTTTACATGATTCAGCATT 58.335 39.130 0.00 0.00 0.00 3.56
2082 2209 0.250424 TCACACTGGCCACATCACAG 60.250 55.000 0.00 0.00 38.19 3.66
2145 2272 3.365565 CGGTTTCATTTCCAGGGTAAACG 60.366 47.826 0.00 0.00 0.00 3.60
2153 2280 0.323629 CCAGGGTAAACGGAGCAAGA 59.676 55.000 0.00 0.00 0.00 3.02
2155 2282 0.613777 AGGGTAAACGGAGCAAGAGG 59.386 55.000 0.00 0.00 0.00 3.69
2156 2283 1.025113 GGGTAAACGGAGCAAGAGGC 61.025 60.000 0.00 0.00 45.30 4.70
2161 2288 4.093291 CGGAGCAAGAGGCCAGCT 62.093 66.667 5.01 8.83 46.50 4.24
2197 2324 4.838152 GGAGCAAGCGGCCATCGA 62.838 66.667 2.24 0.00 46.50 3.59
2331 2458 2.699321 TGGATGAGCTCATGGAGAAGAG 59.301 50.000 33.33 0.00 36.57 2.85
2335 2462 1.148048 GCTCATGGAGAAGAGGCCC 59.852 63.158 0.00 0.00 32.54 5.80
2358 2485 2.449031 CTAGCTGCCGGTCCACACAA 62.449 60.000 1.90 0.00 0.00 3.33
2372 2499 1.016130 ACACAAGCGAGAAGATGCGG 61.016 55.000 0.00 0.00 35.87 5.69
2379 2506 0.385751 CGAGAAGATGCGGCTCCTAA 59.614 55.000 0.00 0.00 0.00 2.69
2383 2510 0.179108 AAGATGCGGCTCCTAACGAC 60.179 55.000 0.00 0.00 0.00 4.34
2398 2530 7.612668 TCCTAACGACATAGATACAGATAGC 57.387 40.000 0.00 0.00 0.00 2.97
2439 2599 2.117051 GTTAGCTTGGCTAGGTAGGGT 58.883 52.381 7.83 0.00 42.34 4.34
2483 2643 1.087501 GCCCATTTCTGAACCTCGAC 58.912 55.000 0.00 0.00 0.00 4.20
2497 2657 1.137086 CCTCGACCGATCAATGGAACT 59.863 52.381 0.00 0.00 0.00 3.01
2560 2720 3.682292 CTTGGAGGGGTAGTGGCGC 62.682 68.421 0.00 0.00 0.00 6.53
2567 2727 1.525442 GGGTAGTGGCGCCTGTAAT 59.475 57.895 29.70 9.51 0.00 1.89
2568 2728 0.532196 GGGTAGTGGCGCCTGTAATC 60.532 60.000 29.70 10.63 0.00 1.75
2569 2729 0.532196 GGTAGTGGCGCCTGTAATCC 60.532 60.000 29.70 17.65 0.00 3.01
2570 2730 0.874607 GTAGTGGCGCCTGTAATCCG 60.875 60.000 29.70 0.00 0.00 4.18
2583 2743 1.134965 GTAATCCGTCTGTCAGCAGCT 60.135 52.381 0.00 0.00 42.29 4.24
2584 2744 0.322975 AATCCGTCTGTCAGCAGCTT 59.677 50.000 0.00 0.00 42.29 3.74
2603 2763 3.690475 TTCATCTCTGAAGCTGCAGAA 57.310 42.857 24.86 15.81 43.75 3.02
2606 2766 3.750130 TCATCTCTGAAGCTGCAGAAAAC 59.250 43.478 24.86 5.80 43.75 2.43
2610 2770 3.136763 TCTGAAGCTGCAGAAAACAGAG 58.863 45.455 22.83 3.10 41.65 3.35
2627 2798 4.270834 ACAGAGCTCATGATTTTCAGCAT 58.729 39.130 17.77 0.00 0.00 3.79
2650 2821 0.449388 GCTGTGGCAAGCAGTATGTC 59.551 55.000 14.15 0.00 43.01 3.06
2719 2898 2.109181 GGTCAGCCCATCGTAGCC 59.891 66.667 0.00 0.00 0.00 3.93
2732 2916 0.166597 CGTAGCCGTTACACGTCTCA 59.833 55.000 0.00 0.00 40.58 3.27
2737 2921 0.456312 CCGTTACACGTCTCAGAGCC 60.456 60.000 0.00 0.00 40.58 4.70
2779 2963 1.493861 TCTCAGGGCTCAGATCCTTG 58.506 55.000 0.00 0.00 32.57 3.61
2789 2973 1.918262 TCAGATCCTTGCAGACCCAAT 59.082 47.619 0.00 0.00 0.00 3.16
2949 3157 1.339151 GGCCGGCCAATAATAGAGGAG 60.339 57.143 40.73 0.00 35.81 3.69
2951 3159 1.625818 CCGGCCAATAATAGAGGAGCT 59.374 52.381 2.24 0.00 0.00 4.09
2952 3160 2.039084 CCGGCCAATAATAGAGGAGCTT 59.961 50.000 2.24 0.00 0.00 3.74
2960 3168 6.450545 CAATAATAGAGGAGCTTGACGATCA 58.549 40.000 0.00 0.00 0.00 2.92
2965 3173 2.165437 GAGGAGCTTGACGATCAGAGTT 59.835 50.000 0.00 0.00 0.00 3.01
2966 3174 2.165437 AGGAGCTTGACGATCAGAGTTC 59.835 50.000 0.00 0.00 0.00 3.01
2970 3178 2.254459 CTTGACGATCAGAGTTCACGG 58.746 52.381 0.00 0.00 0.00 4.94
3111 3323 4.295119 ACTGCACCCACGACCGTC 62.295 66.667 0.00 0.00 0.00 4.79
3135 3347 5.062809 CCTCGCTTGAAGTTTTCTGATCTAC 59.937 44.000 0.00 0.00 0.00 2.59
3136 3348 5.784177 TCGCTTGAAGTTTTCTGATCTACT 58.216 37.500 0.00 0.00 0.00 2.57
3137 3349 6.920817 TCGCTTGAAGTTTTCTGATCTACTA 58.079 36.000 0.00 0.00 0.00 1.82
3138 3350 7.375834 TCGCTTGAAGTTTTCTGATCTACTAA 58.624 34.615 0.00 0.00 0.00 2.24
3163 3375 1.339055 TGATGGGCTTGGACTTCTTCG 60.339 52.381 0.00 0.00 0.00 3.79
3166 3378 0.955919 GGGCTTGGACTTCTTCGGTG 60.956 60.000 0.00 0.00 0.00 4.94
3167 3379 1.578206 GGCTTGGACTTCTTCGGTGC 61.578 60.000 0.00 0.00 0.00 5.01
3174 3386 2.031944 GGACTTCTTCGGTGCAGTTTTC 60.032 50.000 0.00 0.00 0.00 2.29
3206 3418 1.004044 ACAGTCCAGATGCAGGAAAGG 59.996 52.381 0.00 0.00 36.80 3.11
3219 3431 0.615850 GGAAAGGGACCTCCACTGAG 59.384 60.000 0.00 0.00 38.24 3.35
3246 3458 0.244994 GTCTCACTCTGGCGTGTGAT 59.755 55.000 12.18 0.00 41.29 3.06
3247 3459 0.244721 TCTCACTCTGGCGTGTGATG 59.755 55.000 12.18 8.47 41.29 3.07
3272 3484 2.436115 GCCACCTAACCTGACGGC 60.436 66.667 0.00 0.00 0.00 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.565090 AGTTGCATATACATCTGTTGATATTGT 57.435 29.630 0.00 0.00 0.00 2.71
32 33 9.512588 ACATACTCAGAAAATCATTCAGAAGTT 57.487 29.630 0.00 0.00 0.00 2.66
46 47 5.189539 TGGATGATCCACACATACTCAGAAA 59.810 40.000 10.75 0.00 42.67 2.52
49 50 4.677673 TGGATGATCCACACATACTCAG 57.322 45.455 10.75 0.00 42.67 3.35
104 106 5.688807 AGAATGGCTCTAGTGCATAATTGT 58.311 37.500 17.89 9.99 30.22 2.71
120 122 2.490903 ACAGTGCAAAGATGAGAATGGC 59.509 45.455 0.00 0.00 0.00 4.40
121 123 4.778534 AACAGTGCAAAGATGAGAATGG 57.221 40.909 0.00 0.00 0.00 3.16
124 126 4.126437 TCGAAACAGTGCAAAGATGAGAA 58.874 39.130 0.00 0.00 0.00 2.87
126 128 4.675190 ATCGAAACAGTGCAAAGATGAG 57.325 40.909 0.00 0.00 0.00 2.90
128 130 6.317088 ACATAATCGAAACAGTGCAAAGATG 58.683 36.000 0.00 0.00 0.00 2.90
129 131 6.500684 ACATAATCGAAACAGTGCAAAGAT 57.499 33.333 0.00 0.00 0.00 2.40
130 132 5.940192 ACATAATCGAAACAGTGCAAAGA 57.060 34.783 0.00 0.00 0.00 2.52
131 133 8.177663 AGAATACATAATCGAAACAGTGCAAAG 58.822 33.333 0.00 0.00 0.00 2.77
135 137 9.638300 CTTAAGAATACATAATCGAAACAGTGC 57.362 33.333 0.00 0.00 0.00 4.40
197 209 1.929169 ACACTTGCATGTCGATCATCG 59.071 47.619 0.00 0.00 42.10 3.84
200 212 3.541071 CAAACACTTGCATGTCGATCA 57.459 42.857 1.56 0.00 30.55 2.92
211 223 7.359431 GGAACATCAAATACATGCAAACACTTG 60.359 37.037 0.00 0.00 35.49 3.16
242 254 4.666412 TGACCCATCCACAATTCCTTAA 57.334 40.909 0.00 0.00 0.00 1.85
247 259 5.185635 TCTTCAAATGACCCATCCACAATTC 59.814 40.000 0.00 0.00 0.00 2.17
248 260 5.047092 GTCTTCAAATGACCCATCCACAATT 60.047 40.000 0.00 0.00 0.00 2.32
250 262 3.826157 GTCTTCAAATGACCCATCCACAA 59.174 43.478 0.00 0.00 0.00 3.33
276 288 1.671742 GTCCATGGACAGTGACCGT 59.328 57.895 35.21 3.74 44.02 4.83
290 302 4.703093 TCACATCTATGAAGTACGTGTCCA 59.297 41.667 0.00 0.00 0.00 4.02
294 306 9.684448 ATTTAGATCACATCTATGAAGTACGTG 57.316 33.333 0.00 0.00 41.23 4.49
295 307 9.684448 CATTTAGATCACATCTATGAAGTACGT 57.316 33.333 0.00 0.00 41.23 3.57
296 308 8.642885 GCATTTAGATCACATCTATGAAGTACG 58.357 37.037 0.00 0.00 41.23 3.67
297 309 9.703892 AGCATTTAGATCACATCTATGAAGTAC 57.296 33.333 0.00 0.00 41.23 2.73
333 389 8.086522 AGTAGTTTCAGCGATAGAGTGTAAAAA 58.913 33.333 0.00 0.00 39.76 1.94
334 390 7.541091 CAGTAGTTTCAGCGATAGAGTGTAAAA 59.459 37.037 0.00 0.00 39.76 1.52
336 392 6.373495 TCAGTAGTTTCAGCGATAGAGTGTAA 59.627 38.462 0.00 0.00 39.76 2.41
337 393 5.878669 TCAGTAGTTTCAGCGATAGAGTGTA 59.121 40.000 0.00 0.00 39.76 2.90
338 394 4.700692 TCAGTAGTTTCAGCGATAGAGTGT 59.299 41.667 0.00 0.00 39.76 3.55
339 395 5.236655 TCAGTAGTTTCAGCGATAGAGTG 57.763 43.478 0.00 0.00 39.76 3.51
340 396 5.899120 TTCAGTAGTTTCAGCGATAGAGT 57.101 39.130 0.00 0.00 39.76 3.24
341 397 5.174761 GCATTCAGTAGTTTCAGCGATAGAG 59.825 44.000 0.00 0.00 39.76 2.43
342 398 5.043903 GCATTCAGTAGTTTCAGCGATAGA 58.956 41.667 0.00 0.00 39.76 1.98
343 399 4.085363 CGCATTCAGTAGTTTCAGCGATAG 60.085 45.833 0.00 0.00 46.01 2.08
344 400 3.796717 CGCATTCAGTAGTTTCAGCGATA 59.203 43.478 0.00 0.00 46.01 2.92
346 402 1.992667 CGCATTCAGTAGTTTCAGCGA 59.007 47.619 0.00 0.00 46.01 4.93
347 403 1.992667 TCGCATTCAGTAGTTTCAGCG 59.007 47.619 0.00 0.00 44.66 5.18
358 434 1.201769 CCAACGTACGTTCGCATTCAG 60.202 52.381 29.67 15.90 36.00 3.02
395 477 3.489180 TTCCTTCGAATCAGACGTCTC 57.511 47.619 16.96 3.53 0.00 3.36
433 515 0.824109 TGGTGCTTGTAGGGAGATCG 59.176 55.000 0.00 0.00 0.00 3.69
482 564 2.095415 GTGGGTAGGAAAACAATCGTGC 60.095 50.000 0.00 0.00 0.00 5.34
496 578 3.632080 TGCGTGGGGTGTGGGTAG 61.632 66.667 0.00 0.00 0.00 3.18
497 579 3.943691 GTGCGTGGGGTGTGGGTA 61.944 66.667 0.00 0.00 0.00 3.69
858 947 1.534595 CGCCCAATATCAAACTGCTGC 60.535 52.381 0.00 0.00 0.00 5.25
907 996 1.377994 CTGGTCAAAGGGAGCTGCT 59.622 57.895 0.00 0.00 44.40 4.24
973 1062 2.301296 AGGCAGATTAGATCCATCCACG 59.699 50.000 0.00 0.00 0.00 4.94
1018 1109 4.202430 GGAAAGGAGAGGTTTAGGTGACAA 60.202 45.833 0.00 0.00 0.00 3.18
1057 1148 1.260538 TACCTGCTGGCACCTCTGAG 61.261 60.000 9.95 0.00 36.63 3.35
1173 1264 4.561735 ATTGTTTACCGACCTTGTTGTG 57.438 40.909 0.00 0.00 0.00 3.33
1189 1280 6.131544 ACAAGAAGTTACTGCGAAATTGTT 57.868 33.333 0.00 0.00 0.00 2.83
1213 1310 1.007038 GTGTACCGTGAAGGCGTGA 60.007 57.895 0.00 0.00 46.52 4.35
1214 1311 1.006571 AGTGTACCGTGAAGGCGTG 60.007 57.895 0.00 0.00 46.52 5.34
1215 1312 1.288127 GAGTGTACCGTGAAGGCGT 59.712 57.895 0.00 0.00 46.52 5.68
1216 1313 1.007336 GTGAGTGTACCGTGAAGGCG 61.007 60.000 0.00 0.00 46.52 5.52
1217 1314 0.032952 TGTGAGTGTACCGTGAAGGC 59.967 55.000 0.00 0.00 46.52 4.35
1219 1316 2.394708 CAGTGTGAGTGTACCGTGAAG 58.605 52.381 0.00 0.00 0.00 3.02
1220 1317 1.537348 GCAGTGTGAGTGTACCGTGAA 60.537 52.381 0.00 0.00 0.00 3.18
1221 1318 0.031585 GCAGTGTGAGTGTACCGTGA 59.968 55.000 0.00 0.00 0.00 4.35
1271 1384 3.735240 CGAGAAGCAAGATATCAGCACTC 59.265 47.826 21.98 21.98 33.78 3.51
1397 1510 3.554342 CCTCATCCCTCCCCGCTG 61.554 72.222 0.00 0.00 0.00 5.18
1472 1585 1.622232 GACAACGGTAACCTCTACGC 58.378 55.000 0.00 0.00 0.00 4.42
1590 1703 2.234300 TATTCTTCGGCGGATGAACC 57.766 50.000 20.20 0.00 38.63 3.62
1602 1715 0.931005 CCGCGCCTCAGTTATTCTTC 59.069 55.000 0.00 0.00 0.00 2.87
1664 1778 6.696441 ACTACTGTACCACTAGCAGTAATC 57.304 41.667 8.07 0.00 42.74 1.75
1666 1780 6.715280 ACTACTACTGTACCACTAGCAGTAA 58.285 40.000 8.07 0.00 42.74 2.24
1667 1781 6.305272 ACTACTACTGTACCACTAGCAGTA 57.695 41.667 6.89 6.89 42.60 2.74
1668 1782 5.176741 ACTACTACTGTACCACTAGCAGT 57.823 43.478 5.46 5.46 44.49 4.40
1688 1802 8.854614 ACTTCATGATTAAAAACAGAGCTACT 57.145 30.769 0.00 0.00 0.00 2.57
1707 1823 9.899661 TGCACTACCACTATAATTTTACTTCAT 57.100 29.630 0.00 0.00 0.00 2.57
1718 1834 3.132289 GGAGCACTGCACTACCACTATAA 59.868 47.826 3.30 0.00 0.00 0.98
1720 1836 1.482593 GGAGCACTGCACTACCACTAT 59.517 52.381 3.30 0.00 0.00 2.12
1721 1837 0.895530 GGAGCACTGCACTACCACTA 59.104 55.000 3.30 0.00 0.00 2.74
1741 1857 4.823204 GCACTAGCTTATTTAACAGACGC 58.177 43.478 0.00 0.00 37.91 5.19
1763 1879 7.319646 AGAATCTCTACAGTACAAGCAAAGAG 58.680 38.462 0.00 1.90 0.00 2.85
1799 1915 1.155155 GTTTGGGTGATGGGGTGGT 59.845 57.895 0.00 0.00 0.00 4.16
1822 1938 2.083774 TGCAGCACACTAATTACAGGC 58.916 47.619 0.00 0.00 0.00 4.85
1837 1953 2.309764 CTACGCGACCCATTTGCAGC 62.310 60.000 15.93 0.00 33.55 5.25
1883 1999 5.469760 GGTTTGCTGCCAGACAAAATAAAAT 59.530 36.000 13.36 0.00 37.50 1.82
1885 2001 4.141846 TGGTTTGCTGCCAGACAAAATAAA 60.142 37.500 13.36 1.62 37.50 1.40
1886 2002 3.386078 TGGTTTGCTGCCAGACAAAATAA 59.614 39.130 13.36 3.42 37.50 1.40
1887 2003 2.961741 TGGTTTGCTGCCAGACAAAATA 59.038 40.909 13.36 5.80 37.50 1.40
1888 2004 1.761784 TGGTTTGCTGCCAGACAAAAT 59.238 42.857 13.36 0.00 37.50 1.82
1898 2014 2.564721 GGGTCCAGTGGTTTGCTGC 61.565 63.158 9.54 0.00 32.93 5.25
1927 2043 2.009774 ACAGAAATGGCACGTATCAGC 58.990 47.619 0.00 0.00 0.00 4.26
1962 2078 1.005340 CGCCTGATCTGCTTCTTGAC 58.995 55.000 6.30 0.00 0.00 3.18
1978 2094 1.804151 TGTACAAATTCAGCAGACGCC 59.196 47.619 0.00 0.00 39.83 5.68
2063 2180 0.250424 CTGTGATGTGGCCAGTGTGA 60.250 55.000 5.11 0.00 0.00 3.58
2082 2209 2.284417 GGAACTGAAGTTGTGTGTCGAC 59.716 50.000 9.11 9.11 38.56 4.20
2145 2272 2.438075 CAGCTGGCCTCTTGCTCC 60.438 66.667 5.57 0.00 40.92 4.70
2161 2288 3.982316 CTGAAGCATGGGCCGAGCA 62.982 63.158 20.13 0.00 42.56 4.26
2240 2367 1.410882 GGAGTAGTCCATCCTCAGCAC 59.589 57.143 12.02 0.00 43.31 4.40
2321 2448 0.267356 AGCTAGGGCCTCTTCTCCAT 59.733 55.000 10.74 0.00 39.73 3.41
2322 2449 0.934446 TAGCTAGGGCCTCTTCTCCA 59.066 55.000 10.74 0.00 39.73 3.86
2331 2458 4.306967 CGGCAGCTAGCTAGGGCC 62.307 72.222 26.98 26.98 44.79 5.80
2335 2462 2.127869 TGGACCGGCAGCTAGCTAG 61.128 63.158 18.86 16.84 44.79 3.42
2358 2485 2.105930 GAGCCGCATCTTCTCGCT 59.894 61.111 0.00 0.00 0.00 4.93
2372 2499 5.943706 TCTGTATCTATGTCGTTAGGAGC 57.056 43.478 0.00 0.00 0.00 4.70
2379 2506 5.943706 AACGCTATCTGTATCTATGTCGT 57.056 39.130 0.00 0.00 0.00 4.34
2427 2584 1.765255 GGTCCCACCCTACCTAGCC 60.765 68.421 0.00 0.00 32.72 3.93
2461 2621 1.756430 GAGGTTCAGAAATGGGCTCC 58.244 55.000 0.00 0.00 0.00 4.70
2497 2657 1.405463 CCAACTCACCTCGATCGATCA 59.595 52.381 24.40 11.08 0.00 2.92
2560 2720 1.204704 TGCTGACAGACGGATTACAGG 59.795 52.381 6.65 0.00 0.00 4.00
2583 2743 3.690475 TTCTGCAGCTTCAGAGATGAA 57.310 42.857 15.69 0.00 41.81 2.57
2584 2744 3.690475 TTTCTGCAGCTTCAGAGATGA 57.310 42.857 15.69 0.00 41.81 2.92
2603 2763 4.521639 TGCTGAAAATCATGAGCTCTGTTT 59.478 37.500 16.19 9.03 0.00 2.83
2606 2766 4.096532 ACATGCTGAAAATCATGAGCTCTG 59.903 41.667 16.19 10.75 41.82 3.35
2610 2770 3.444916 CCACATGCTGAAAATCATGAGC 58.555 45.455 0.09 0.00 41.82 4.26
2627 2798 2.336484 TACTGCTTGCCACAGCCACA 62.336 55.000 0.00 0.00 39.25 4.17
2650 2821 0.815734 TTCTTTACGGCGAGGAGAGG 59.184 55.000 16.62 0.00 0.00 3.69
2732 2916 2.301296 CAACTATGATGATCGGGGCTCT 59.699 50.000 0.00 0.00 0.00 4.09
2737 2921 3.070018 GGAAGCAACTATGATGATCGGG 58.930 50.000 0.00 0.00 0.00 5.14
2779 2963 1.337167 GGCACTTTTCATTGGGTCTGC 60.337 52.381 0.00 0.00 0.00 4.26
2789 2973 2.202395 GGCAGGCAGGCACTTTTCA 61.202 57.895 0.00 0.00 43.51 2.69
2881 3086 2.112297 GGGAGTTTGCGTGGTCCA 59.888 61.111 0.00 0.00 0.00 4.02
2949 3157 1.651138 CGTGAACTCTGATCGTCAAGC 59.349 52.381 0.00 0.00 0.00 4.01
2951 3159 1.611977 ACCGTGAACTCTGATCGTCAA 59.388 47.619 0.00 0.00 0.00 3.18
2952 3160 1.199327 GACCGTGAACTCTGATCGTCA 59.801 52.381 0.00 0.00 0.00 4.35
2960 3168 2.050351 CGTGCGACCGTGAACTCT 60.050 61.111 0.00 0.00 0.00 3.24
2983 3191 3.880846 CTCCCAATGCTTCGCCGC 61.881 66.667 0.00 0.00 0.00 6.53
2984 3192 3.204827 CCTCCCAATGCTTCGCCG 61.205 66.667 0.00 0.00 0.00 6.46
2985 3193 3.521796 GCCTCCCAATGCTTCGCC 61.522 66.667 0.00 0.00 0.00 5.54
3035 3245 2.639839 AGGATAACAGCAACAGGTGTCT 59.360 45.455 0.48 0.00 42.66 3.41
3109 3321 3.131396 TCAGAAAACTTCAAGCGAGGAC 58.869 45.455 0.00 0.00 0.00 3.85
3111 3323 3.999663 AGATCAGAAAACTTCAAGCGAGG 59.000 43.478 0.00 0.00 0.00 4.63
3135 3347 3.131396 GTCCAAGCCCATCACGTATTAG 58.869 50.000 0.00 0.00 0.00 1.73
3136 3348 2.769663 AGTCCAAGCCCATCACGTATTA 59.230 45.455 0.00 0.00 0.00 0.98
3137 3349 1.559682 AGTCCAAGCCCATCACGTATT 59.440 47.619 0.00 0.00 0.00 1.89
3138 3350 1.204146 AGTCCAAGCCCATCACGTAT 58.796 50.000 0.00 0.00 0.00 3.06
3163 3375 4.515191 TGAACTACAGATGAAAACTGCACC 59.485 41.667 0.00 0.00 40.90 5.01
3166 3378 5.673337 TGTGAACTACAGATGAAAACTGC 57.327 39.130 0.00 0.00 40.90 4.40
3219 3431 0.457851 CCAGAGTGAGACCATCGTCC 59.542 60.000 0.00 0.00 40.12 4.79
3222 3434 1.226802 CGCCAGAGTGAGACCATCG 60.227 63.158 0.00 0.00 0.00 3.84
3272 3484 2.079925 CTTCTCCGAGCCCTTCTTTTG 58.920 52.381 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.