Multiple sequence alignment - TraesCS7A01G542600

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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 TraesCS7A01G542600 chr7A 100.000 2625 0 0 1 2625 719416796 719419420 0.000000e+00 4848.0
1 TraesCS7A01G542600 chr7D 89.011 2266 161 38 409 2623 622604616 622602388 0.000000e+00 2724.0
2 TraesCS7A01G542600 chr7D 85.950 363 32 12 409 761 622606416 622606063 1.150000e-98 370.0
3 TraesCS7A01G542600 chr7D 86.572 283 27 4 131 412 622606712 622606440 4.250000e-78 302.0
4 TraesCS7A01G542600 chr7D 87.611 113 10 4 132 240 622605795 622605683 7.630000e-26 128.0
5 TraesCS7A01G542600 chr7B 88.703 1735 125 36 409 2122 721056645 721058329 0.000000e+00 2052.0
6 TraesCS7A01G542600 chr4D 78.061 196 18 10 2241 2422 441511179 441510995 1.660000e-17 100.0
7 TraesCS7A01G542600 chrUn 76.168 214 31 11 2350 2552 92294266 92294470 7.730000e-16 95.3
8 TraesCS7A01G542600 chr2A 92.537 67 2 2 2233 2297 706327531 706327596 2.780000e-15 93.5
9 TraesCS7A01G542600 chr1D 94.643 56 3 0 2346 2401 44273019 44273074 1.290000e-13 87.9


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 TraesCS7A01G542600 chr7A 719416796 719419420 2624 False 4848 4848 100.000 1 2625 1 chr7A.!!$F1 2624
1 TraesCS7A01G542600 chr7D 622602388 622606712 4324 True 881 2724 87.286 131 2623 4 chr7D.!!$R1 2492
2 TraesCS7A01G542600 chr7B 721056645 721058329 1684 False 2052 2052 88.703 409 2122 1 chr7B.!!$F1 1713

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
899 2735 0.034477 CGCCTTTCCATTACCCACCT 60.034 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 3592 0.108992 ACAGCGGCTGCAATTGAATG 60.109 50.0 28.8 9.78 46.23 2.67 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
45 46 9.890352 TTTTTGTTTCTTTCTTGGTTTTCAATG 57.110 25.926 0.00 0.00 34.45 2.82
46 47 6.660887 TGTTTCTTTCTTGGTTTTCAATGC 57.339 33.333 0.00 0.00 34.45 3.56
47 48 6.405538 TGTTTCTTTCTTGGTTTTCAATGCT 58.594 32.000 0.00 0.00 34.45 3.79
48 49 6.878389 TGTTTCTTTCTTGGTTTTCAATGCTT 59.122 30.769 0.00 0.00 34.45 3.91
49 50 7.390162 TGTTTCTTTCTTGGTTTTCAATGCTTT 59.610 29.630 0.00 0.00 34.45 3.51
50 51 7.920160 TTCTTTCTTGGTTTTCAATGCTTTT 57.080 28.000 0.00 0.00 34.45 2.27
51 52 7.920160 TCTTTCTTGGTTTTCAATGCTTTTT 57.080 28.000 0.00 0.00 34.45 1.94
117 118 5.964887 TTGTTTTGCTTTCATTCTTTCCG 57.035 34.783 0.00 0.00 0.00 4.30
118 119 3.801594 TGTTTTGCTTTCATTCTTTCCGC 59.198 39.130 0.00 0.00 0.00 5.54
119 120 3.724508 TTTGCTTTCATTCTTTCCGCA 57.275 38.095 0.00 0.00 0.00 5.69
120 121 3.940209 TTGCTTTCATTCTTTCCGCAT 57.060 38.095 0.00 0.00 0.00 4.73
121 122 3.940209 TGCTTTCATTCTTTCCGCATT 57.060 38.095 0.00 0.00 0.00 3.56
122 123 4.255833 TGCTTTCATTCTTTCCGCATTT 57.744 36.364 0.00 0.00 0.00 2.32
123 124 3.989167 TGCTTTCATTCTTTCCGCATTTG 59.011 39.130 0.00 0.00 0.00 2.32
124 125 3.989817 GCTTTCATTCTTTCCGCATTTGT 59.010 39.130 0.00 0.00 0.00 2.83
125 126 4.448732 GCTTTCATTCTTTCCGCATTTGTT 59.551 37.500 0.00 0.00 0.00 2.83
126 127 5.050159 GCTTTCATTCTTTCCGCATTTGTTT 60.050 36.000 0.00 0.00 0.00 2.83
127 128 6.523676 TTTCATTCTTTCCGCATTTGTTTC 57.476 33.333 0.00 0.00 0.00 2.78
128 129 5.452078 TCATTCTTTCCGCATTTGTTTCT 57.548 34.783 0.00 0.00 0.00 2.52
129 130 5.841810 TCATTCTTTCCGCATTTGTTTCTT 58.158 33.333 0.00 0.00 0.00 2.52
138 139 3.254657 CGCATTTGTTTCTTTGGGAGGTA 59.745 43.478 0.00 0.00 0.00 3.08
141 142 5.528870 CATTTGTTTCTTTGGGAGGTACAC 58.471 41.667 0.00 0.00 0.00 2.90
156 157 6.352737 GGGAGGTACACTTTCTCCATCAATAA 60.353 42.308 14.67 0.00 46.55 1.40
160 161 8.993424 AGGTACACTTTCTCCATCAATAATACT 58.007 33.333 0.00 0.00 0.00 2.12
205 206 7.913789 ACAAATGTGGATAGGTACACTTTCTA 58.086 34.615 0.00 0.00 40.06 2.10
248 249 8.557592 AAACTTTTAGTTTAATACTCCCTCCG 57.442 34.615 3.13 0.00 45.75 4.63
251 252 5.859205 TTAGTTTAATACTCCCTCCGGTC 57.141 43.478 0.00 0.00 38.33 4.79
252 253 3.991683 AGTTTAATACTCCCTCCGGTCT 58.008 45.455 0.00 0.00 28.23 3.85
263 264 7.715266 ACTCCCTCCGGTCTATATTAATTAC 57.285 40.000 0.00 0.00 0.00 1.89
285 287 8.867112 TTACCGCTGATTTAGATAAGTTGTAG 57.133 34.615 0.00 0.00 0.00 2.74
330 332 8.723942 ATTGATAGGAGCGGATATAACATTTC 57.276 34.615 0.00 0.00 0.00 2.17
365 367 7.897575 AAGTACTGTTTCTTGATGCTAAGAG 57.102 36.000 0.00 0.00 37.91 2.85
366 368 5.872070 AGTACTGTTTCTTGATGCTAAGAGC 59.128 40.000 0.00 0.00 42.82 4.09
367 369 4.006319 ACTGTTTCTTGATGCTAAGAGCC 58.994 43.478 0.00 0.00 41.51 4.70
368 370 4.260170 CTGTTTCTTGATGCTAAGAGCCT 58.740 43.478 0.00 0.00 41.51 4.58
369 371 5.046304 ACTGTTTCTTGATGCTAAGAGCCTA 60.046 40.000 0.00 0.00 41.51 3.93
390 2184 9.566432 AGCCTAAGATTAATATGAGTTTCCAAG 57.434 33.333 0.00 0.00 0.00 3.61
431 2252 1.081840 GCTCTTTCAGCGCAACCAC 60.082 57.895 11.47 0.00 38.76 4.16
434 2255 0.662619 TCTTTCAGCGCAACCACTTG 59.337 50.000 11.47 0.00 0.00 3.16
435 2256 0.381801 CTTTCAGCGCAACCACTTGT 59.618 50.000 11.47 0.00 0.00 3.16
558 2392 1.343465 ACACGAAGGAGAAACGGTCAT 59.657 47.619 0.00 0.00 0.00 3.06
575 2409 5.106317 ACGGTCATATCAACATGTGGAAAAC 60.106 40.000 7.10 3.39 0.00 2.43
608 2442 1.211190 GTACGGCGTCCTTCGTTCT 59.789 57.895 19.21 0.00 42.13 3.01
657 2491 3.457380 AGTTGTCTGCTGGTGGATCATAT 59.543 43.478 0.00 0.00 0.00 1.78
660 2494 4.226384 TGTCTGCTGGTGGATCATATACT 58.774 43.478 0.00 0.00 0.00 2.12
661 2495 4.039609 TGTCTGCTGGTGGATCATATACTG 59.960 45.833 0.00 0.00 0.00 2.74
707 2542 6.338214 TCTCTCATCACATCTGCTATTACC 57.662 41.667 0.00 0.00 0.00 2.85
708 2543 5.835280 TCTCTCATCACATCTGCTATTACCA 59.165 40.000 0.00 0.00 0.00 3.25
777 2613 1.139734 ATGTCACGCGCTCGAGAAT 59.860 52.632 18.75 0.00 37.08 2.40
884 2720 2.715532 ATCACAGCACGTCAACGCCT 62.716 55.000 1.81 0.00 44.43 5.52
886 2722 1.817941 ACAGCACGTCAACGCCTTT 60.818 52.632 1.81 0.00 44.43 3.11
887 2723 1.082756 CAGCACGTCAACGCCTTTC 60.083 57.895 1.81 0.00 44.43 2.62
889 2725 2.539338 GCACGTCAACGCCTTTCCA 61.539 57.895 1.81 0.00 44.43 3.53
890 2726 1.852067 GCACGTCAACGCCTTTCCAT 61.852 55.000 1.81 0.00 44.43 3.41
892 2728 1.801771 CACGTCAACGCCTTTCCATTA 59.198 47.619 1.81 0.00 44.43 1.90
893 2729 1.802365 ACGTCAACGCCTTTCCATTAC 59.198 47.619 1.81 0.00 44.43 1.89
895 2731 1.471287 GTCAACGCCTTTCCATTACCC 59.529 52.381 0.00 0.00 0.00 3.69
896 2732 1.074084 TCAACGCCTTTCCATTACCCA 59.926 47.619 0.00 0.00 0.00 4.51
897 2733 1.201414 CAACGCCTTTCCATTACCCAC 59.799 52.381 0.00 0.00 0.00 4.61
898 2734 0.323087 ACGCCTTTCCATTACCCACC 60.323 55.000 0.00 0.00 0.00 4.61
899 2735 0.034477 CGCCTTTCCATTACCCACCT 60.034 55.000 0.00 0.00 0.00 4.00
900 2736 1.210967 CGCCTTTCCATTACCCACCTA 59.789 52.381 0.00 0.00 0.00 3.08
901 2737 2.356330 CGCCTTTCCATTACCCACCTAA 60.356 50.000 0.00 0.00 0.00 2.69
902 2738 3.021695 GCCTTTCCATTACCCACCTAAC 58.978 50.000 0.00 0.00 0.00 2.34
903 2739 3.628008 CCTTTCCATTACCCACCTAACC 58.372 50.000 0.00 0.00 0.00 2.85
904 2740 3.275999 CTTTCCATTACCCACCTAACCG 58.724 50.000 0.00 0.00 0.00 4.44
905 2741 2.250921 TCCATTACCCACCTAACCGA 57.749 50.000 0.00 0.00 0.00 4.69
906 2742 2.112998 TCCATTACCCACCTAACCGAG 58.887 52.381 0.00 0.00 0.00 4.63
907 2743 2.112998 CCATTACCCACCTAACCGAGA 58.887 52.381 0.00 0.00 0.00 4.04
908 2744 2.704065 CCATTACCCACCTAACCGAGAT 59.296 50.000 0.00 0.00 0.00 2.75
909 2745 3.899360 CCATTACCCACCTAACCGAGATA 59.101 47.826 0.00 0.00 0.00 1.98
910 2746 4.530946 CCATTACCCACCTAACCGAGATAT 59.469 45.833 0.00 0.00 0.00 1.63
911 2747 5.337330 CCATTACCCACCTAACCGAGATATC 60.337 48.000 0.00 0.00 0.00 1.63
912 2748 3.614568 ACCCACCTAACCGAGATATCT 57.385 47.619 4.47 4.47 0.00 1.98
925 2761 5.074790 ACCGAGATATCTCTACCTAACCCTT 59.925 44.000 26.29 0.00 40.75 3.95
954 2790 3.059597 AGCTCGATCAACAAGTTTTGTCG 60.060 43.478 0.00 5.52 44.59 4.35
956 2792 4.551990 GCTCGATCAACAAGTTTTGTCGAA 60.552 41.667 12.16 2.28 44.59 3.71
985 2821 0.302890 CTCGATCAACAAGCATCCGC 59.697 55.000 0.00 0.00 38.99 5.54
988 2824 1.078497 ATCAACAAGCATCCGCCGA 60.078 52.632 0.00 0.00 39.83 5.54
1019 2855 4.357947 GTCGCCGTCTCACTGCCA 62.358 66.667 0.00 0.00 0.00 4.92
1020 2856 3.381983 TCGCCGTCTCACTGCCAT 61.382 61.111 0.00 0.00 0.00 4.40
1137 2973 2.345991 GGCACCAACTACGCCTCA 59.654 61.111 0.00 0.00 42.78 3.86
1160 2996 4.443266 GCAGAGCCGCTCCTTCGT 62.443 66.667 16.99 0.00 0.00 3.85
1198 3034 3.964031 AGGTCAGTATCTCCATCAACCTC 59.036 47.826 0.00 0.00 30.12 3.85
1295 3131 1.714460 CAGTGTTCGAGTACGTCAAGC 59.286 52.381 0.00 0.00 40.69 4.01
1496 3332 2.995872 AACGTCTCTGCGGGCTCTC 61.996 63.158 0.00 0.00 35.98 3.20
1554 3390 3.755628 GTCAGCCGGAGCCACGTA 61.756 66.667 5.05 0.00 41.25 3.57
1575 3411 4.792804 GAGCAGCTGGGTGGCCTC 62.793 72.222 17.12 8.41 0.00 4.70
1597 3433 4.715523 GCCGGCTTGGTGGTGCTA 62.716 66.667 22.15 0.00 41.21 3.49
1673 3509 3.075148 CGCTCCTGTATGCTACTAGCTA 58.925 50.000 9.49 0.00 42.97 3.32
1756 3592 7.558161 TCATGATTCACAGATACAACATTCC 57.442 36.000 0.00 0.00 0.00 3.01
1779 3615 0.318869 CAATTGCAGCCGCTGTTTGA 60.319 50.000 21.29 6.00 39.64 2.69
1803 3639 5.972382 ACACAAACATTTGCATGAAATTTGC 59.028 32.000 9.87 0.00 41.79 3.68
1829 3665 6.162079 TCTTCAATTGAATTTATGCGGCAAA 58.838 32.000 20.76 0.00 33.01 3.68
1886 3730 6.869315 TCAACCACAAATCTTCGTCATTTA 57.131 33.333 0.00 0.00 0.00 1.40
1888 3732 7.359595 TCAACCACAAATCTTCGTCATTTAAG 58.640 34.615 0.00 0.00 0.00 1.85
1894 3738 9.672086 CACAAATCTTCGTCATTTAAGGTTTTA 57.328 29.630 0.00 0.00 34.58 1.52
1908 3752 8.922058 TTTAAGGTTTTAACGTATGCAAAACA 57.078 26.923 19.34 4.82 41.65 2.83
1909 3753 8.922058 TTAAGGTTTTAACGTATGCAAAACAA 57.078 26.923 19.34 8.83 41.65 2.83
1944 3790 3.756434 GCCAGTGCAAACTCCAATTACTA 59.244 43.478 0.00 0.00 37.47 1.82
1946 3792 5.677091 GCCAGTGCAAACTCCAATTACTATG 60.677 44.000 0.00 0.00 37.47 2.23
1954 3800 6.909550 AACTCCAATTACTATGTTTGCCAA 57.090 33.333 0.00 0.00 0.00 4.52
1964 3810 6.902224 ACTATGTTTGCCAACAAAAGTTTC 57.098 33.333 7.52 0.00 46.94 2.78
1992 3838 4.694509 ACTGTCAATGAGATGAGAAGTTGC 59.305 41.667 0.00 0.00 28.09 4.17
1994 3840 4.934001 TGTCAATGAGATGAGAAGTTGCTC 59.066 41.667 0.00 0.00 35.46 4.26
2037 3883 3.244526 TGTGCGCTGGGATAACATGATAT 60.245 43.478 9.73 0.00 0.00 1.63
2129 3995 4.925054 CCATTGCTTACCACAATTTGACAG 59.075 41.667 2.79 0.00 35.58 3.51
2173 4039 6.966021 ACATGTTTGATAAGTTTAACGCACT 58.034 32.000 0.00 0.00 0.00 4.40
2174 4040 7.075741 ACATGTTTGATAAGTTTAACGCACTC 58.924 34.615 0.00 0.00 0.00 3.51
2196 4062 3.126858 CGTGGCGGCTGCATTATTAATAT 59.873 43.478 21.31 0.00 45.35 1.28
2219 4085 1.839994 TGAGCATAACAGAGAAGGGGG 59.160 52.381 0.00 0.00 0.00 5.40
2237 4106 3.108376 GGGGGCAATGGTGGTAAAAATA 58.892 45.455 0.00 0.00 0.00 1.40
2270 4141 1.207390 GTGCTCGAGCTCACATGATC 58.793 55.000 35.27 12.17 42.66 2.92
2344 4216 5.580297 TCTGAATGTTTTTGGCAAGAAACAC 59.420 36.000 27.17 20.49 45.33 3.32
2351 4234 2.719531 TGGCAAGAAACACCTACACA 57.280 45.000 0.00 0.00 0.00 3.72
2365 4248 4.382457 CACCTACACACATGCAAATTTTCG 59.618 41.667 0.00 0.00 0.00 3.46
2374 4257 3.229276 TGCAAATTTTCGCGATGGAAT 57.771 38.095 10.88 8.35 0.00 3.01
2395 4278 3.213506 TCACATTTGTGGAGGTGTGAAG 58.786 45.455 10.60 0.00 45.50 3.02
2401 4284 4.712122 TTGTGGAGGTGTGAAGAAAAAC 57.288 40.909 0.00 0.00 0.00 2.43
2417 4300 4.405358 AGAAAAACCAAAGTTGATGCTCCA 59.595 37.500 0.00 0.00 35.97 3.86
2419 4302 4.326504 AAACCAAAGTTGATGCTCCAAG 57.673 40.909 0.00 0.00 35.97 3.61
2428 4311 1.627329 TGATGCTCCAAGAAGAGTGCT 59.373 47.619 0.00 0.00 36.20 4.40
2504 4388 6.426980 TCATGAAAAGTAGCAAGCATGTAG 57.573 37.500 0.00 0.00 35.75 2.74
2506 4390 6.314648 TCATGAAAAGTAGCAAGCATGTAGAG 59.685 38.462 0.00 0.00 35.75 2.43
2603 4487 6.402222 ACTGTTTATCTAAGCTCAGGTGAAG 58.598 40.000 0.00 0.00 0.00 3.02
2623 4507 5.470098 TGAAGTTGAGCTTACAAACTCCATC 59.530 40.000 0.00 0.00 37.59 3.51
2624 4508 5.234466 AGTTGAGCTTACAAACTCCATCT 57.766 39.130 0.00 0.00 31.65 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.890352 CATTGAAAACCAAGAAAGAAACAAAAA 57.110 25.926 0.00 0.00 38.31 1.94
20 21 8.020244 GCATTGAAAACCAAGAAAGAAACAAAA 58.980 29.630 0.00 0.00 38.31 2.44
21 22 7.390162 AGCATTGAAAACCAAGAAAGAAACAAA 59.610 29.630 0.00 0.00 38.31 2.83
22 23 6.878389 AGCATTGAAAACCAAGAAAGAAACAA 59.122 30.769 0.00 0.00 38.31 2.83
23 24 6.405538 AGCATTGAAAACCAAGAAAGAAACA 58.594 32.000 0.00 0.00 38.31 2.83
24 25 6.908870 AGCATTGAAAACCAAGAAAGAAAC 57.091 33.333 0.00 0.00 38.31 2.78
25 26 7.920160 AAAGCATTGAAAACCAAGAAAGAAA 57.080 28.000 0.00 0.00 38.31 2.52
26 27 7.920160 AAAAGCATTGAAAACCAAGAAAGAA 57.080 28.000 0.00 0.00 38.31 2.52
27 28 7.920160 AAAAAGCATTGAAAACCAAGAAAGA 57.080 28.000 0.00 0.00 38.31 2.52
92 93 7.239972 CGGAAAGAATGAAAGCAAAACAAAAA 58.760 30.769 0.00 0.00 0.00 1.94
93 94 6.674278 GCGGAAAGAATGAAAGCAAAACAAAA 60.674 34.615 0.00 0.00 0.00 2.44
94 95 5.220567 GCGGAAAGAATGAAAGCAAAACAAA 60.221 36.000 0.00 0.00 0.00 2.83
95 96 4.269844 GCGGAAAGAATGAAAGCAAAACAA 59.730 37.500 0.00 0.00 0.00 2.83
96 97 3.801594 GCGGAAAGAATGAAAGCAAAACA 59.198 39.130 0.00 0.00 0.00 2.83
97 98 3.801594 TGCGGAAAGAATGAAAGCAAAAC 59.198 39.130 0.00 0.00 0.00 2.43
98 99 4.052159 TGCGGAAAGAATGAAAGCAAAA 57.948 36.364 0.00 0.00 0.00 2.44
99 100 3.724508 TGCGGAAAGAATGAAAGCAAA 57.275 38.095 0.00 0.00 0.00 3.68
100 101 3.940209 ATGCGGAAAGAATGAAAGCAA 57.060 38.095 0.00 0.00 36.69 3.91
101 102 3.940209 AATGCGGAAAGAATGAAAGCA 57.060 38.095 0.00 0.00 37.54 3.91
102 103 3.989817 ACAAATGCGGAAAGAATGAAAGC 59.010 39.130 0.00 0.00 0.00 3.51
103 104 6.421801 AGAAACAAATGCGGAAAGAATGAAAG 59.578 34.615 0.00 0.00 0.00 2.62
104 105 6.279882 AGAAACAAATGCGGAAAGAATGAAA 58.720 32.000 0.00 0.00 0.00 2.69
105 106 5.841810 AGAAACAAATGCGGAAAGAATGAA 58.158 33.333 0.00 0.00 0.00 2.57
106 107 5.452078 AGAAACAAATGCGGAAAGAATGA 57.548 34.783 0.00 0.00 0.00 2.57
107 108 6.357198 CAAAGAAACAAATGCGGAAAGAATG 58.643 36.000 0.00 0.00 0.00 2.67
108 109 5.466393 CCAAAGAAACAAATGCGGAAAGAAT 59.534 36.000 0.00 0.00 0.00 2.40
109 110 4.808364 CCAAAGAAACAAATGCGGAAAGAA 59.192 37.500 0.00 0.00 0.00 2.52
110 111 4.367450 CCAAAGAAACAAATGCGGAAAGA 58.633 39.130 0.00 0.00 0.00 2.52
111 112 3.494251 CCCAAAGAAACAAATGCGGAAAG 59.506 43.478 0.00 0.00 0.00 2.62
112 113 3.133003 TCCCAAAGAAACAAATGCGGAAA 59.867 39.130 0.00 0.00 0.00 3.13
113 114 2.695666 TCCCAAAGAAACAAATGCGGAA 59.304 40.909 0.00 0.00 0.00 4.30
114 115 2.295909 CTCCCAAAGAAACAAATGCGGA 59.704 45.455 0.00 0.00 0.00 5.54
115 116 2.610232 CCTCCCAAAGAAACAAATGCGG 60.610 50.000 0.00 0.00 0.00 5.69
116 117 2.035832 ACCTCCCAAAGAAACAAATGCG 59.964 45.455 0.00 0.00 0.00 4.73
117 118 3.751479 ACCTCCCAAAGAAACAAATGC 57.249 42.857 0.00 0.00 0.00 3.56
118 119 5.301805 AGTGTACCTCCCAAAGAAACAAATG 59.698 40.000 0.00 0.00 0.00 2.32
119 120 5.454966 AGTGTACCTCCCAAAGAAACAAAT 58.545 37.500 0.00 0.00 0.00 2.32
120 121 4.862371 AGTGTACCTCCCAAAGAAACAAA 58.138 39.130 0.00 0.00 0.00 2.83
121 122 4.513406 AGTGTACCTCCCAAAGAAACAA 57.487 40.909 0.00 0.00 0.00 2.83
122 123 4.513406 AAGTGTACCTCCCAAAGAAACA 57.487 40.909 0.00 0.00 0.00 2.83
123 124 5.131067 AGAAAGTGTACCTCCCAAAGAAAC 58.869 41.667 0.00 0.00 0.00 2.78
124 125 5.374071 GAGAAAGTGTACCTCCCAAAGAAA 58.626 41.667 0.00 0.00 0.00 2.52
125 126 4.202430 GGAGAAAGTGTACCTCCCAAAGAA 60.202 45.833 4.26 0.00 40.35 2.52
126 127 3.326880 GGAGAAAGTGTACCTCCCAAAGA 59.673 47.826 4.26 0.00 40.35 2.52
127 128 3.072476 TGGAGAAAGTGTACCTCCCAAAG 59.928 47.826 11.29 0.00 44.41 2.77
128 129 3.050089 TGGAGAAAGTGTACCTCCCAAA 58.950 45.455 11.29 0.00 44.41 3.28
129 130 2.696775 TGGAGAAAGTGTACCTCCCAA 58.303 47.619 11.29 0.00 44.41 4.12
164 165 6.147000 CCACATTTGTATAAAAAGTGGGCAAC 59.853 38.462 21.85 0.00 44.19 4.17
178 179 8.548877 AGAAAGTGTACCTATCCACATTTGTAT 58.451 33.333 0.00 0.00 33.99 2.29
180 181 6.779860 AGAAAGTGTACCTATCCACATTTGT 58.220 36.000 0.00 0.00 33.99 2.83
263 264 8.867112 TTACTACAACTTATCTAAATCAGCGG 57.133 34.615 0.00 0.00 0.00 5.52
291 293 8.491152 CGCTCCTATCAATATTAACTTTCACTG 58.509 37.037 0.00 0.00 0.00 3.66
294 296 7.732025 TCCGCTCCTATCAATATTAACTTTCA 58.268 34.615 0.00 0.00 0.00 2.69
295 297 8.779354 ATCCGCTCCTATCAATATTAACTTTC 57.221 34.615 0.00 0.00 0.00 2.62
325 327 6.924111 ACAGTACTTTGCTTATTGGGAAATG 58.076 36.000 0.00 0.00 0.00 2.32
327 329 6.969993 AACAGTACTTTGCTTATTGGGAAA 57.030 33.333 0.00 0.00 0.00 3.13
330 332 6.575162 AGAAACAGTACTTTGCTTATTGGG 57.425 37.500 0.00 0.00 0.00 4.12
346 348 4.260170 AGGCTCTTAGCATCAAGAAACAG 58.740 43.478 0.78 0.00 44.75 3.16
365 367 8.787852 CCTTGGAAACTCATATTAATCTTAGGC 58.212 37.037 0.00 0.00 0.00 3.93
366 368 9.853177 ACCTTGGAAACTCATATTAATCTTAGG 57.147 33.333 0.00 0.00 0.00 2.69
369 371 9.401058 CTGACCTTGGAAACTCATATTAATCTT 57.599 33.333 0.00 0.00 0.00 2.40
390 2184 2.560542 TGTGCTTCTCTTCTCTCTGACC 59.439 50.000 0.00 0.00 0.00 4.02
394 2188 3.249986 GCATGTGCTTCTCTTCTCTCT 57.750 47.619 0.00 0.00 38.21 3.10
446 2270 4.461781 AGACAAGAGGCCAAGATGAATTTG 59.538 41.667 5.01 0.00 0.00 2.32
449 2273 3.618351 CAGACAAGAGGCCAAGATGAAT 58.382 45.455 5.01 0.00 0.00 2.57
507 2336 8.178964 TGTAGTTTTGTGTCTTGTGTTGTTATC 58.821 33.333 0.00 0.00 0.00 1.75
512 2346 5.567534 GTGTGTAGTTTTGTGTCTTGTGTTG 59.432 40.000 0.00 0.00 0.00 3.33
558 2392 8.356657 CAAGGTTAAGTTTTCCACATGTTGATA 58.643 33.333 0.00 0.00 0.00 2.15
575 2409 2.676342 GCCGTACATGGACAAGGTTAAG 59.324 50.000 9.21 0.00 0.00 1.85
661 2495 6.868864 AGATGATGTCAAAGCGTATATGGTAC 59.131 38.462 0.00 0.00 0.00 3.34
870 2706 2.251642 GGAAAGGCGTTGACGTGCT 61.252 57.895 0.00 0.00 42.22 4.40
884 2720 2.911636 TCGGTTAGGTGGGTAATGGAAA 59.088 45.455 0.00 0.00 0.00 3.13
886 2722 2.112998 CTCGGTTAGGTGGGTAATGGA 58.887 52.381 0.00 0.00 0.00 3.41
887 2723 2.112998 TCTCGGTTAGGTGGGTAATGG 58.887 52.381 0.00 0.00 0.00 3.16
889 2725 5.652324 AGATATCTCGGTTAGGTGGGTAAT 58.348 41.667 0.00 0.00 0.00 1.89
890 2726 5.070823 AGATATCTCGGTTAGGTGGGTAA 57.929 43.478 0.00 0.00 0.00 2.85
892 2728 3.498334 GAGATATCTCGGTTAGGTGGGT 58.502 50.000 16.77 0.00 32.78 4.51
904 2740 8.658840 ATGAAAGGGTTAGGTAGAGATATCTC 57.341 38.462 22.92 22.92 43.17 2.75
905 2741 8.235230 TGATGAAAGGGTTAGGTAGAGATATCT 58.765 37.037 4.47 4.47 0.00 1.98
906 2742 8.423906 TGATGAAAGGGTTAGGTAGAGATATC 57.576 38.462 0.00 0.00 0.00 1.63
907 2743 8.798975 TTGATGAAAGGGTTAGGTAGAGATAT 57.201 34.615 0.00 0.00 0.00 1.63
908 2744 7.202011 GCTTGATGAAAGGGTTAGGTAGAGATA 60.202 40.741 0.00 0.00 36.30 1.98
909 2745 6.408662 GCTTGATGAAAGGGTTAGGTAGAGAT 60.409 42.308 0.00 0.00 36.30 2.75
910 2746 5.104900 GCTTGATGAAAGGGTTAGGTAGAGA 60.105 44.000 0.00 0.00 36.30 3.10
911 2747 5.104735 AGCTTGATGAAAGGGTTAGGTAGAG 60.105 44.000 0.00 0.00 36.30 2.43
912 2748 4.783227 AGCTTGATGAAAGGGTTAGGTAGA 59.217 41.667 0.00 0.00 36.30 2.59
925 2761 4.318332 ACTTGTTGATCGAGCTTGATGAA 58.682 39.130 21.56 16.26 0.00 2.57
954 2790 6.032880 GCTTGTTGATCGAGCTTATGTTTTTC 59.967 38.462 0.90 0.00 46.89 2.29
956 2792 5.393962 GCTTGTTGATCGAGCTTATGTTTT 58.606 37.500 0.90 0.00 46.89 2.43
985 2821 1.268083 CGACATATCGGATCGGATCGG 60.268 57.143 18.10 16.83 44.99 4.18
1198 3034 7.113684 GCGAGTTAGCTAATTGGCTATATATCG 59.886 40.741 22.36 24.38 43.21 2.92
1295 3131 2.549282 GTACACGTTGTGCTGGCG 59.451 61.111 0.00 0.00 36.98 5.69
1309 3145 2.577593 GCCTCCGTCACCTGGTAC 59.422 66.667 0.00 0.00 0.00 3.34
1369 3205 4.446413 CCGGTGTCGTAGGTGGCC 62.446 72.222 0.00 0.00 33.95 5.36
1552 3388 3.391382 ACCCAGCTGCTCCGGTAC 61.391 66.667 14.67 0.00 0.00 3.34
1597 3433 4.609018 AAGACGTGCAGTGCGCCT 62.609 61.111 22.40 11.52 41.33 5.52
1604 3440 0.583438 CAGTTGACCAAGACGTGCAG 59.417 55.000 0.00 0.00 0.00 4.41
1652 3488 1.883275 AGCTAGTAGCATACAGGAGCG 59.117 52.381 23.77 0.00 46.26 5.03
1673 3509 9.539194 AAAATGGAGAAGGACAGAAGAATAAAT 57.461 29.630 0.00 0.00 0.00 1.40
1756 3592 0.108992 ACAGCGGCTGCAATTGAATG 60.109 50.000 28.80 9.78 46.23 2.67
1779 3615 5.972382 GCAAATTTCATGCAAATGTTTGTGT 59.028 32.000 7.26 0.00 43.29 3.72
1803 3639 5.749588 TGCCGCATAAATTCAATTGAAGATG 59.250 36.000 24.17 23.75 37.48 2.90
1806 3642 6.406093 TTTGCCGCATAAATTCAATTGAAG 57.594 33.333 24.17 12.45 37.48 3.02
1829 3665 7.246027 AGATAGGTAGGGTGGAAAACAAAAAT 58.754 34.615 0.00 0.00 0.00 1.82
1886 3730 7.829378 TTTGTTTTGCATACGTTAAAACCTT 57.171 28.000 18.65 0.00 41.30 3.50
1888 3732 6.571887 GCATTTGTTTTGCATACGTTAAAACC 59.428 34.615 18.65 7.21 41.30 3.27
1894 3738 3.722147 TGGCATTTGTTTTGCATACGTT 58.278 36.364 0.00 0.00 41.95 3.99
1895 3739 3.377346 TGGCATTTGTTTTGCATACGT 57.623 38.095 0.00 0.00 41.95 3.57
1908 3752 1.276989 CACTGGCTGGATTTGGCATTT 59.723 47.619 0.00 0.00 39.24 2.32
1909 3753 0.899720 CACTGGCTGGATTTGGCATT 59.100 50.000 0.00 0.00 39.24 3.56
1944 3790 4.875536 GGAGAAACTTTTGTTGGCAAACAT 59.124 37.500 7.67 0.00 45.54 2.71
1946 3792 3.621268 GGGAGAAACTTTTGTTGGCAAAC 59.379 43.478 0.00 0.00 43.47 2.93
1954 3800 3.963129 TGACAGTGGGAGAAACTTTTGT 58.037 40.909 0.00 0.00 0.00 2.83
1964 3810 3.450096 TCTCATCTCATTGACAGTGGGAG 59.550 47.826 6.67 5.43 27.89 4.30
1992 3838 4.097892 ACCTTTGCACCTTTGTTTGTAGAG 59.902 41.667 0.00 0.00 0.00 2.43
1994 3840 4.111916 CACCTTTGCACCTTTGTTTGTAG 58.888 43.478 0.00 0.00 0.00 2.74
2022 3868 5.542251 TCTGAACGGATATCATGTTATCCCA 59.458 40.000 26.64 20.25 43.20 4.37
2037 3883 2.176045 TGGAAGCACTATCTGAACGGA 58.824 47.619 0.00 0.00 0.00 4.69
2096 3962 3.964031 TGGTAAGCAATGGGTTTGTTCTT 59.036 39.130 0.00 0.00 37.65 2.52
2145 4011 9.088512 TGCGTTAAACTTATCAAACATGTTTTT 57.911 25.926 21.10 13.77 33.63 1.94
2173 4039 0.179070 TAATAATGCAGCCGCCACGA 60.179 50.000 0.00 0.00 37.32 4.35
2174 4040 0.660488 TTAATAATGCAGCCGCCACG 59.340 50.000 0.00 0.00 37.32 4.94
2196 4062 4.103153 CCCCCTTCTCTGTTATGCTCATAA 59.897 45.833 0.00 0.00 0.00 1.90
2216 4082 1.353091 TTTTTACCACCATTGCCCCC 58.647 50.000 0.00 0.00 0.00 5.40
2217 4083 3.429684 CGTATTTTTACCACCATTGCCCC 60.430 47.826 0.00 0.00 0.00 5.80
2219 4085 4.705337 TCGTATTTTTACCACCATTGCC 57.295 40.909 0.00 0.00 0.00 4.52
2220 4086 6.088883 CACTTTCGTATTTTTACCACCATTGC 59.911 38.462 0.00 0.00 0.00 3.56
2221 4087 6.088883 GCACTTTCGTATTTTTACCACCATTG 59.911 38.462 0.00 0.00 0.00 2.82
2237 4106 1.726791 CGAGCACAATAGCACTTTCGT 59.273 47.619 0.00 0.00 36.85 3.85
2252 4121 1.109609 AGATCATGTGAGCTCGAGCA 58.890 50.000 36.87 18.69 45.16 4.26
2270 4141 8.925161 TTTTTGGAATTTACTGTTCACTCAAG 57.075 30.769 0.00 0.00 0.00 3.02
2333 4204 2.294074 TGTGTGTAGGTGTTTCTTGCC 58.706 47.619 0.00 0.00 0.00 4.52
2344 4216 3.364621 GCGAAAATTTGCATGTGTGTAGG 59.635 43.478 0.00 0.00 37.52 3.18
2351 4234 2.094803 TCCATCGCGAAAATTTGCATGT 60.095 40.909 15.24 0.00 37.43 3.21
2393 4276 5.104982 TGGAGCATCAACTTTGGTTTTTCTT 60.105 36.000 0.00 0.00 36.25 2.52
2395 4278 4.692228 TGGAGCATCAACTTTGGTTTTTC 58.308 39.130 0.00 0.00 36.25 2.29
2401 4284 3.822735 TCTTCTTGGAGCATCAACTTTGG 59.177 43.478 0.00 0.00 36.25 3.28
2419 4302 6.492007 TTGATGATTCAAGAAGCACTCTTC 57.508 37.500 2.55 0.00 42.84 2.87
2455 4339 1.680735 TCACATTTGTGGAAGTGTGGC 59.319 47.619 10.60 0.00 45.65 5.01
2481 4365 6.172630 TCTACATGCTTGCTACTTTTCATGA 58.827 36.000 6.98 0.00 36.23 3.07
2483 4367 6.409704 TCTCTACATGCTTGCTACTTTTCAT 58.590 36.000 0.00 0.00 0.00 2.57
2573 4457 9.740710 ACCTGAGCTTAGATAAACAGTAAAATT 57.259 29.630 7.16 0.00 0.00 1.82
2578 4462 7.178628 ACTTCACCTGAGCTTAGATAAACAGTA 59.821 37.037 7.16 0.00 0.00 2.74
2585 4469 6.214191 CTCAACTTCACCTGAGCTTAGATA 57.786 41.667 7.16 0.00 33.17 1.98
2596 4480 4.781934 AGTTTGTAAGCTCAACTTCACCT 58.218 39.130 0.00 0.00 39.97 4.00
2597 4481 4.023963 GGAGTTTGTAAGCTCAACTTCACC 60.024 45.833 10.04 0.00 39.97 4.02


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

AutoCloner maintained by Alex Coulton.