Multiple sequence alignment - TraesCS5B01G465800

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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 TraesCS5B01G465800 chr5B 100.000 2352 0 0 1 2352 640143415 640145766 0.000000e+00 4344.0
1 TraesCS5B01G465800 chr5D 94.645 1438 39 15 274 1691 509510066 509511485 0.000000e+00 2194.0
2 TraesCS5B01G465800 chr5D 89.062 640 51 10 1702 2331 509511653 509512283 0.000000e+00 776.0
3 TraesCS5B01G465800 chr5D 97.656 128 2 1 149 276 509509872 509509998 3.940000e-53 219.0
4 TraesCS5B01G465800 chr5D 83.186 113 12 7 147 256 509510310 509510418 1.920000e-16 97.1
5 TraesCS5B01G465800 chr5A 89.692 1300 87 19 967 2249 636648510 636649779 0.000000e+00 1615.0
6 TraesCS5B01G465800 chr5A 90.336 714 26 16 210 896 636647621 636648318 0.000000e+00 896.0
7 TraesCS5B01G465800 chr7B 97.333 150 4 0 1 150 735353246 735353097 3.000000e-64 255.0
8 TraesCS5B01G465800 chr7A 94.000 150 7 1 1 150 324907494 324907641 2.350000e-55 226.0
9 TraesCS5B01G465800 chr4B 90.260 154 11 3 1 153 445173437 445173287 5.130000e-47 198.0


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 TraesCS5B01G465800 chr5B 640143415 640145766 2351 False 4344.000 4344 100.00000 1 2352 1 chr5B.!!$F1 2351
1 TraesCS5B01G465800 chr5D 509509872 509512283 2411 False 821.525 2194 91.13725 147 2331 4 chr5D.!!$F1 2184
2 TraesCS5B01G465800 chr5A 636647621 636649779 2158 False 1255.500 1615 90.01400 210 2249 2 chr5A.!!$F1 2039

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
621 701 0.250038 TTGGCAGCACTCACTCACTC 60.25 55.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2045 2424 0.320334 TGTGATGGCGACGTGACAAT 60.32 50.0 0.0 0.0 40.63 2.71 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
23 24 6.991485 AATCTAACTTTTGCATGTTTCGTG 57.009 33.333 5.75 0.00 0.00 4.35
24 25 5.493133 TCTAACTTTTGCATGTTTCGTGT 57.507 34.783 5.75 0.00 0.00 4.49
25 26 5.507077 TCTAACTTTTGCATGTTTCGTGTC 58.493 37.500 5.75 0.00 0.00 3.67
26 27 4.370364 AACTTTTGCATGTTTCGTGTCT 57.630 36.364 0.00 0.00 0.00 3.41
27 28 3.952535 ACTTTTGCATGTTTCGTGTCTC 58.047 40.909 0.00 0.00 0.00 3.36
28 29 3.243068 ACTTTTGCATGTTTCGTGTCTCC 60.243 43.478 0.00 0.00 0.00 3.71
29 30 1.960417 TTGCATGTTTCGTGTCTCCA 58.040 45.000 0.00 0.00 0.00 3.86
30 31 1.225855 TGCATGTTTCGTGTCTCCAC 58.774 50.000 0.00 0.00 38.27 4.02
47 48 9.136952 GTGTCTCCACGTATTTACATAATATCC 57.863 37.037 0.00 0.00 0.00 2.59
48 49 9.085645 TGTCTCCACGTATTTACATAATATCCT 57.914 33.333 0.00 0.00 0.00 3.24
75 76 7.687941 ATAACTTCCATTTTCATGTCTTCGT 57.312 32.000 0.00 0.00 0.00 3.85
76 77 8.786826 ATAACTTCCATTTTCATGTCTTCGTA 57.213 30.769 0.00 0.00 0.00 3.43
77 78 7.687941 AACTTCCATTTTCATGTCTTCGTAT 57.312 32.000 0.00 0.00 0.00 3.06
78 79 8.786826 AACTTCCATTTTCATGTCTTCGTATA 57.213 30.769 0.00 0.00 0.00 1.47
79 80 8.197988 ACTTCCATTTTCATGTCTTCGTATAC 57.802 34.615 0.00 0.00 0.00 1.47
80 81 8.041323 ACTTCCATTTTCATGTCTTCGTATACT 58.959 33.333 0.56 0.00 0.00 2.12
81 82 8.786826 TTCCATTTTCATGTCTTCGTATACTT 57.213 30.769 0.56 0.00 0.00 2.24
82 83 8.196802 TCCATTTTCATGTCTTCGTATACTTG 57.803 34.615 0.56 0.00 0.00 3.16
83 84 6.907212 CCATTTTCATGTCTTCGTATACTTGC 59.093 38.462 0.56 0.00 0.00 4.01
84 85 7.413988 CCATTTTCATGTCTTCGTATACTTGCA 60.414 37.037 0.56 0.00 0.00 4.08
85 86 7.428282 TTTTCATGTCTTCGTATACTTGCAA 57.572 32.000 0.00 0.00 0.00 4.08
86 87 7.428282 TTTCATGTCTTCGTATACTTGCAAA 57.572 32.000 0.00 0.00 0.00 3.68
87 88 7.428282 TTCATGTCTTCGTATACTTGCAAAA 57.572 32.000 0.00 0.00 0.00 2.44
88 89 7.428282 TCATGTCTTCGTATACTTGCAAAAA 57.572 32.000 0.00 0.00 0.00 1.94
89 90 8.039603 TCATGTCTTCGTATACTTGCAAAAAT 57.960 30.769 0.00 0.00 0.00 1.82
90 91 8.511321 TCATGTCTTCGTATACTTGCAAAAATT 58.489 29.630 0.00 0.00 0.00 1.82
91 92 8.788813 CATGTCTTCGTATACTTGCAAAAATTC 58.211 33.333 0.00 0.00 0.00 2.17
92 93 7.302524 TGTCTTCGTATACTTGCAAAAATTCC 58.697 34.615 0.00 0.00 0.00 3.01
93 94 7.174253 TGTCTTCGTATACTTGCAAAAATTCCT 59.826 33.333 0.00 0.00 0.00 3.36
94 95 8.662141 GTCTTCGTATACTTGCAAAAATTCCTA 58.338 33.333 0.00 0.00 0.00 2.94
95 96 8.662141 TCTTCGTATACTTGCAAAAATTCCTAC 58.338 33.333 0.00 0.00 0.00 3.18
96 97 7.311364 TCGTATACTTGCAAAAATTCCTACC 57.689 36.000 0.00 0.00 0.00 3.18
97 98 6.879993 TCGTATACTTGCAAAAATTCCTACCA 59.120 34.615 0.00 0.00 0.00 3.25
98 99 7.554835 TCGTATACTTGCAAAAATTCCTACCAT 59.445 33.333 0.00 0.00 0.00 3.55
99 100 8.188139 CGTATACTTGCAAAAATTCCTACCATT 58.812 33.333 0.00 0.00 0.00 3.16
100 101 9.869757 GTATACTTGCAAAAATTCCTACCATTT 57.130 29.630 0.00 0.00 0.00 2.32
101 102 8.776376 ATACTTGCAAAAATTCCTACCATTTG 57.224 30.769 0.00 0.00 34.84 2.32
102 103 6.825610 ACTTGCAAAAATTCCTACCATTTGA 58.174 32.000 0.00 0.00 33.86 2.69
103 104 7.452562 ACTTGCAAAAATTCCTACCATTTGAT 58.547 30.769 0.00 0.00 33.86 2.57
104 105 8.592809 ACTTGCAAAAATTCCTACCATTTGATA 58.407 29.630 0.00 0.00 33.86 2.15
105 106 9.090692 CTTGCAAAAATTCCTACCATTTGATAG 57.909 33.333 0.00 0.00 33.86 2.08
106 107 7.041107 TGCAAAAATTCCTACCATTTGATAGC 58.959 34.615 0.00 0.00 33.86 2.97
107 108 7.041107 GCAAAAATTCCTACCATTTGATAGCA 58.959 34.615 0.00 0.00 33.86 3.49
108 109 7.548780 GCAAAAATTCCTACCATTTGATAGCAA 59.451 33.333 0.00 0.00 33.86 3.91
109 110 9.603921 CAAAAATTCCTACCATTTGATAGCAAT 57.396 29.630 0.00 0.00 33.86 3.56
114 115 8.408043 TTCCTACCATTTGATAGCAATAATGG 57.592 34.615 18.58 18.58 43.41 3.16
115 116 7.754624 TCCTACCATTTGATAGCAATAATGGA 58.245 34.615 24.43 11.99 41.68 3.41
116 117 7.665559 TCCTACCATTTGATAGCAATAATGGAC 59.334 37.037 24.43 0.00 41.68 4.02
117 118 6.317789 ACCATTTGATAGCAATAATGGACG 57.682 37.500 24.43 5.41 41.68 4.79
118 119 5.241506 ACCATTTGATAGCAATAATGGACGG 59.758 40.000 24.43 1.97 41.68 4.79
119 120 5.335897 CCATTTGATAGCAATAATGGACGGG 60.336 44.000 16.21 0.00 41.68 5.28
120 121 2.778299 TGATAGCAATAATGGACGGGC 58.222 47.619 0.00 0.00 0.00 6.13
121 122 1.732259 GATAGCAATAATGGACGGGCG 59.268 52.381 0.00 0.00 0.00 6.13
122 123 0.882927 TAGCAATAATGGACGGGCGC 60.883 55.000 0.00 0.00 0.00 6.53
123 124 2.477176 GCAATAATGGACGGGCGCA 61.477 57.895 10.83 0.00 0.00 6.09
124 125 1.648720 CAATAATGGACGGGCGCAG 59.351 57.895 10.83 4.90 0.00 5.18
140 141 4.752879 AGCAACGCGCACCGGTAT 62.753 61.111 6.87 0.00 46.13 2.73
141 142 4.514569 GCAACGCGCACCGGTATG 62.515 66.667 6.87 3.28 42.52 2.39
142 143 2.811747 CAACGCGCACCGGTATGA 60.812 61.111 6.87 0.00 42.52 2.15
143 144 2.171079 CAACGCGCACCGGTATGAT 61.171 57.895 6.87 0.00 42.52 2.45
144 145 1.881252 AACGCGCACCGGTATGATC 60.881 57.895 6.87 0.00 42.52 2.92
145 146 2.027605 CGCGCACCGGTATGATCT 59.972 61.111 6.87 0.00 0.00 2.75
146 147 1.284715 CGCGCACCGGTATGATCTA 59.715 57.895 6.87 0.00 0.00 1.98
147 148 0.729478 CGCGCACCGGTATGATCTAG 60.729 60.000 6.87 0.00 0.00 2.43
148 149 0.314302 GCGCACCGGTATGATCTAGT 59.686 55.000 6.87 0.00 0.00 2.57
149 150 1.538512 GCGCACCGGTATGATCTAGTA 59.461 52.381 6.87 0.00 0.00 1.82
150 151 2.163815 GCGCACCGGTATGATCTAGTAT 59.836 50.000 6.87 0.00 0.00 2.12
151 152 3.376234 GCGCACCGGTATGATCTAGTATA 59.624 47.826 6.87 0.00 0.00 1.47
152 153 4.142534 GCGCACCGGTATGATCTAGTATAA 60.143 45.833 6.87 0.00 0.00 0.98
192 193 2.431419 TGATGATGCCGGAATGCAATTT 59.569 40.909 5.05 0.00 45.84 1.82
258 259 8.291740 TCACTCACATTATTCTTTGTCATGTTG 58.708 33.333 0.00 0.00 0.00 3.33
354 429 8.807948 AATCAGCAACCATTTACTTGTACTAT 57.192 30.769 0.00 0.00 0.00 2.12
357 432 9.899661 TCAGCAACCATTTACTTGTACTATAAT 57.100 29.630 0.00 0.00 0.00 1.28
444 519 1.069513 ACAAGTGTAGCTGCCGTTACA 59.930 47.619 0.00 0.75 34.94 2.41
519 597 1.004080 CTGCAGTCCTCCACCAGTG 60.004 63.158 5.25 0.00 0.00 3.66
527 605 4.024670 AGTCCTCCACCAGTGTAGATTAC 58.975 47.826 0.00 0.00 0.00 1.89
528 606 3.767673 GTCCTCCACCAGTGTAGATTACA 59.232 47.826 0.00 0.00 36.08 2.41
531 609 6.097839 GTCCTCCACCAGTGTAGATTACATAA 59.902 42.308 0.00 0.00 41.34 1.90
532 610 6.844388 TCCTCCACCAGTGTAGATTACATAAT 59.156 38.462 0.00 0.00 41.34 1.28
533 611 8.008332 TCCTCCACCAGTGTAGATTACATAATA 58.992 37.037 0.00 0.00 41.34 0.98
534 612 8.816894 CCTCCACCAGTGTAGATTACATAATAT 58.183 37.037 0.00 0.00 41.34 1.28
559 637 1.004595 CATGATAGCGATGATGCCGG 58.995 55.000 0.00 0.00 34.65 6.13
573 653 2.367030 TGCCGGAATGCAGATTTTTG 57.633 45.000 5.05 0.00 36.04 2.44
576 656 3.066380 GCCGGAATGCAGATTTTTGTTT 58.934 40.909 5.05 0.00 0.00 2.83
620 700 0.399454 ATTGGCAGCACTCACTCACT 59.601 50.000 0.00 0.00 0.00 3.41
621 701 0.250038 TTGGCAGCACTCACTCACTC 60.250 55.000 0.00 0.00 0.00 3.51
622 702 1.368950 GGCAGCACTCACTCACTCA 59.631 57.895 0.00 0.00 0.00 3.41
623 703 0.669932 GGCAGCACTCACTCACTCAG 60.670 60.000 0.00 0.00 0.00 3.35
899 979 3.823304 CCCTTTTTGTTTCCTCTCCTCTG 59.177 47.826 0.00 0.00 0.00 3.35
907 987 4.962362 TGTTTCCTCTCCTCTGCATACATA 59.038 41.667 0.00 0.00 0.00 2.29
916 996 5.402630 TCCTCTGCATACATAACATCCCTA 58.597 41.667 0.00 0.00 0.00 3.53
986 1187 1.202582 CATAACCCTCGGGCTCTATCG 59.797 57.143 0.82 0.00 39.32 2.92
1088 1297 1.447317 TACCGTAAGATCGACCGGCC 61.447 60.000 16.53 0.00 44.14 6.13
1116 1325 3.065371 ACTTCTTCGCTTTGTTGTGGAAG 59.935 43.478 0.00 0.00 36.17 3.46
1122 1331 2.541588 CGCTTTGTTGTGGAAGTCTTGG 60.542 50.000 0.00 0.00 0.00 3.61
1206 1417 0.890683 ATTGCTGTTTGCTAGGCACC 59.109 50.000 0.00 0.00 38.71 5.01
1408 1619 2.120909 CCGGCGGCCATCATCTTTT 61.121 57.895 20.71 0.00 0.00 2.27
1411 1622 0.101219 GGCGGCCATCATCTTTTGTC 59.899 55.000 15.62 0.00 0.00 3.18
1475 1686 2.349886 CGAGCAGATACTTTCCTTGTGC 59.650 50.000 0.00 0.00 0.00 4.57
1685 1899 2.160615 TCGGTTGACTTGTGTGTTTGTG 59.839 45.455 0.00 0.00 0.00 3.33
1691 1905 4.294232 TGACTTGTGTGTTTGTGTTTGTG 58.706 39.130 0.00 0.00 0.00 3.33
1694 1908 5.112686 ACTTGTGTGTTTGTGTTTGTGTTT 58.887 33.333 0.00 0.00 0.00 2.83
1695 1909 5.006165 ACTTGTGTGTTTGTGTTTGTGTTTG 59.994 36.000 0.00 0.00 0.00 2.93
1696 1910 4.433615 TGTGTGTTTGTGTTTGTGTTTGT 58.566 34.783 0.00 0.00 0.00 2.83
1697 1911 5.588240 TGTGTGTTTGTGTTTGTGTTTGTA 58.412 33.333 0.00 0.00 0.00 2.41
1699 1913 6.701841 TGTGTGTTTGTGTTTGTGTTTGTATT 59.298 30.769 0.00 0.00 0.00 1.89
1700 1914 7.224753 TGTGTGTTTGTGTTTGTGTTTGTATTT 59.775 29.630 0.00 0.00 0.00 1.40
1735 2106 6.532657 GCTTTCAATTGTCTGTGGATATTTGG 59.467 38.462 5.13 0.00 30.42 3.28
1739 2110 7.774134 TCAATTGTCTGTGGATATTTGGATTG 58.226 34.615 5.13 0.00 30.42 2.67
1742 2113 7.624360 TTGTCTGTGGATATTTGGATTGTAC 57.376 36.000 0.00 0.00 0.00 2.90
1749 2120 7.141363 GTGGATATTTGGATTGTACATTGCTC 58.859 38.462 10.10 0.39 0.00 4.26
1750 2121 6.265196 TGGATATTTGGATTGTACATTGCTCC 59.735 38.462 10.10 8.52 0.00 4.70
1773 2144 5.710984 CGTAAGGATTTGTATAGCGGAGAT 58.289 41.667 0.00 0.00 0.00 2.75
1826 2198 6.871492 GTGGTTCTACCCATTTTGGTAATTTG 59.129 38.462 0.00 0.00 40.30 2.32
1853 2225 8.930846 TTAATAGCTACCTAACTAATCGACCT 57.069 34.615 0.00 0.00 0.00 3.85
1879 2258 8.764524 ACACATAATCTGAGAAGTAACAGAAC 57.235 34.615 0.00 0.00 44.47 3.01
1970 2349 1.344438 AGAACTTCCACAGCACATCGA 59.656 47.619 0.00 0.00 0.00 3.59
1978 2357 6.597672 ACTTCCACAGCACATCGAAATTTATA 59.402 34.615 0.00 0.00 0.00 0.98
1981 2360 6.765512 TCCACAGCACATCGAAATTTATATCA 59.234 34.615 0.00 0.00 0.00 2.15
2127 2507 1.582968 GGACTAACGGCTCGTCACA 59.417 57.895 0.69 0.00 39.99 3.58
2128 2508 0.172803 GGACTAACGGCTCGTCACAT 59.827 55.000 0.69 0.00 39.99 3.21
2139 2519 3.126073 GCTCGTCACATGCTATGATCAA 58.874 45.455 0.00 0.00 0.00 2.57
2146 2526 5.583854 GTCACATGCTATGATCAACTCACTT 59.416 40.000 0.00 0.00 36.48 3.16
2167 2547 3.726291 ATGTTTGCGCTTTACCTTTGT 57.274 38.095 9.73 0.00 0.00 2.83
2184 2564 6.801575 ACCTTTGTCGTGTTGTAAATTCATT 58.198 32.000 0.00 0.00 0.00 2.57
2308 2689 7.007723 TGTAATCCAAAGAGGCCTTAAAGAAA 58.992 34.615 6.77 0.00 37.29 2.52
2309 2690 6.994421 AATCCAAAGAGGCCTTAAAGAAAA 57.006 33.333 6.77 0.00 37.29 2.29
2310 2691 6.994421 ATCCAAAGAGGCCTTAAAGAAAAA 57.006 33.333 6.77 0.00 37.29 1.94
2311 2692 6.405278 TCCAAAGAGGCCTTAAAGAAAAAG 57.595 37.500 6.77 0.00 37.29 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.503524 ACACGAAACATGCAAAAGTTAGATT 58.496 32.000 0.00 0.00 0.00 2.40
3 4 5.510671 AGACACGAAACATGCAAAAGTTAG 58.489 37.500 0.00 0.00 0.00 2.34
4 5 5.493133 AGACACGAAACATGCAAAAGTTA 57.507 34.783 0.00 0.00 0.00 2.24
5 6 4.351192 GAGACACGAAACATGCAAAAGTT 58.649 39.130 0.00 0.00 0.00 2.66
6 7 3.243068 GGAGACACGAAACATGCAAAAGT 60.243 43.478 0.00 0.00 0.00 2.66
7 8 3.243035 TGGAGACACGAAACATGCAAAAG 60.243 43.478 0.00 0.00 33.40 2.27
8 9 2.685388 TGGAGACACGAAACATGCAAAA 59.315 40.909 0.00 0.00 33.40 2.44
9 10 2.293170 TGGAGACACGAAACATGCAAA 58.707 42.857 0.00 0.00 33.40 3.68
10 11 1.960417 TGGAGACACGAAACATGCAA 58.040 45.000 0.00 0.00 33.40 4.08
11 12 3.696306 TGGAGACACGAAACATGCA 57.304 47.368 0.00 0.00 33.40 3.96
22 23 9.085645 AGGATATTATGTAAATACGTGGAGACA 57.914 33.333 0.00 0.00 38.70 3.41
49 50 9.396022 ACGAAGACATGAAAATGGAAGTTATAT 57.604 29.630 0.00 0.00 0.00 0.86
50 51 8.786826 ACGAAGACATGAAAATGGAAGTTATA 57.213 30.769 0.00 0.00 0.00 0.98
51 52 7.687941 ACGAAGACATGAAAATGGAAGTTAT 57.312 32.000 0.00 0.00 0.00 1.89
52 53 8.786826 ATACGAAGACATGAAAATGGAAGTTA 57.213 30.769 0.00 0.00 0.00 2.24
53 54 7.687941 ATACGAAGACATGAAAATGGAAGTT 57.312 32.000 0.00 0.00 0.00 2.66
54 55 8.041323 AGTATACGAAGACATGAAAATGGAAGT 58.959 33.333 0.00 0.00 0.00 3.01
55 56 8.425577 AGTATACGAAGACATGAAAATGGAAG 57.574 34.615 0.00 0.00 0.00 3.46
56 57 8.664798 CAAGTATACGAAGACATGAAAATGGAA 58.335 33.333 0.00 0.00 0.00 3.53
57 58 7.201609 GCAAGTATACGAAGACATGAAAATGGA 60.202 37.037 0.00 0.00 0.00 3.41
58 59 6.907212 GCAAGTATACGAAGACATGAAAATGG 59.093 38.462 0.00 0.00 0.00 3.16
59 60 7.463544 TGCAAGTATACGAAGACATGAAAATG 58.536 34.615 0.00 0.00 0.00 2.32
60 61 7.609760 TGCAAGTATACGAAGACATGAAAAT 57.390 32.000 0.00 0.00 0.00 1.82
61 62 7.428282 TTGCAAGTATACGAAGACATGAAAA 57.572 32.000 0.00 0.00 0.00 2.29
62 63 7.428282 TTTGCAAGTATACGAAGACATGAAA 57.572 32.000 0.00 0.00 0.00 2.69
63 64 7.428282 TTTTGCAAGTATACGAAGACATGAA 57.572 32.000 0.00 0.00 0.00 2.57
64 65 7.428282 TTTTTGCAAGTATACGAAGACATGA 57.572 32.000 0.00 0.00 0.00 3.07
65 66 8.673626 AATTTTTGCAAGTATACGAAGACATG 57.326 30.769 0.00 0.00 0.00 3.21
66 67 7.968405 GGAATTTTTGCAAGTATACGAAGACAT 59.032 33.333 0.00 0.00 0.00 3.06
67 68 7.174253 AGGAATTTTTGCAAGTATACGAAGACA 59.826 33.333 0.00 0.00 0.00 3.41
68 69 7.527457 AGGAATTTTTGCAAGTATACGAAGAC 58.473 34.615 0.00 0.00 0.00 3.01
69 70 7.681939 AGGAATTTTTGCAAGTATACGAAGA 57.318 32.000 0.00 0.00 0.00 2.87
70 71 7.908601 GGTAGGAATTTTTGCAAGTATACGAAG 59.091 37.037 0.00 0.00 0.00 3.79
71 72 7.390996 TGGTAGGAATTTTTGCAAGTATACGAA 59.609 33.333 0.00 0.00 0.00 3.85
72 73 6.879993 TGGTAGGAATTTTTGCAAGTATACGA 59.120 34.615 0.00 0.00 0.00 3.43
73 74 7.079182 TGGTAGGAATTTTTGCAAGTATACG 57.921 36.000 0.00 0.00 0.00 3.06
74 75 9.869757 AAATGGTAGGAATTTTTGCAAGTATAC 57.130 29.630 0.00 0.00 0.00 1.47
75 76 9.868277 CAAATGGTAGGAATTTTTGCAAGTATA 57.132 29.630 0.00 0.00 0.00 1.47
76 77 8.592809 TCAAATGGTAGGAATTTTTGCAAGTAT 58.407 29.630 0.00 0.00 0.00 2.12
77 78 7.957002 TCAAATGGTAGGAATTTTTGCAAGTA 58.043 30.769 0.00 0.00 0.00 2.24
78 79 6.825610 TCAAATGGTAGGAATTTTTGCAAGT 58.174 32.000 0.00 0.00 0.00 3.16
79 80 7.910441 ATCAAATGGTAGGAATTTTTGCAAG 57.090 32.000 0.00 0.00 0.00 4.01
80 81 7.548780 GCTATCAAATGGTAGGAATTTTTGCAA 59.451 33.333 0.00 0.00 0.00 4.08
81 82 7.041107 GCTATCAAATGGTAGGAATTTTTGCA 58.959 34.615 3.07 0.00 0.00 4.08
82 83 7.041107 TGCTATCAAATGGTAGGAATTTTTGC 58.959 34.615 3.07 0.00 0.00 3.68
83 84 9.603921 ATTGCTATCAAATGGTAGGAATTTTTG 57.396 29.630 12.90 0.00 36.09 2.44
88 89 9.028284 CCATTATTGCTATCAAATGGTAGGAAT 57.972 33.333 19.82 19.82 40.54 3.01
89 90 8.224025 TCCATTATTGCTATCAAATGGTAGGAA 58.776 33.333 17.04 9.63 39.71 3.36
90 91 7.665559 GTCCATTATTGCTATCAAATGGTAGGA 59.334 37.037 17.04 0.00 39.71 2.94
91 92 7.361201 CGTCCATTATTGCTATCAAATGGTAGG 60.361 40.741 17.04 9.50 39.71 3.18
92 93 7.361201 CCGTCCATTATTGCTATCAAATGGTAG 60.361 40.741 17.04 13.27 39.71 3.18
93 94 6.429692 CCGTCCATTATTGCTATCAAATGGTA 59.570 38.462 17.04 6.63 39.71 3.25
94 95 5.241506 CCGTCCATTATTGCTATCAAATGGT 59.758 40.000 17.04 0.00 39.71 3.55
95 96 5.335897 CCCGTCCATTATTGCTATCAAATGG 60.336 44.000 13.46 13.46 39.92 3.16
96 97 5.702865 CCCGTCCATTATTGCTATCAAATG 58.297 41.667 0.00 0.00 35.56 2.32
97 98 4.218417 GCCCGTCCATTATTGCTATCAAAT 59.782 41.667 0.00 0.00 35.56 2.32
98 99 3.568007 GCCCGTCCATTATTGCTATCAAA 59.432 43.478 0.00 0.00 35.56 2.69
99 100 3.146066 GCCCGTCCATTATTGCTATCAA 58.854 45.455 0.00 0.00 36.51 2.57
100 101 2.778299 GCCCGTCCATTATTGCTATCA 58.222 47.619 0.00 0.00 0.00 2.15
101 102 1.732259 CGCCCGTCCATTATTGCTATC 59.268 52.381 0.00 0.00 0.00 2.08
102 103 1.808411 CGCCCGTCCATTATTGCTAT 58.192 50.000 0.00 0.00 0.00 2.97
103 104 0.882927 GCGCCCGTCCATTATTGCTA 60.883 55.000 0.00 0.00 0.00 3.49
104 105 2.186826 GCGCCCGTCCATTATTGCT 61.187 57.895 0.00 0.00 0.00 3.91
105 106 2.331451 GCGCCCGTCCATTATTGC 59.669 61.111 0.00 0.00 0.00 3.56
106 107 1.648720 CTGCGCCCGTCCATTATTG 59.351 57.895 4.18 0.00 0.00 1.90
107 108 2.186826 GCTGCGCCCGTCCATTATT 61.187 57.895 4.18 0.00 0.00 1.40
108 109 2.591715 GCTGCGCCCGTCCATTAT 60.592 61.111 4.18 0.00 0.00 1.28
109 110 3.613877 TTGCTGCGCCCGTCCATTA 62.614 57.895 4.18 0.00 0.00 1.90
123 124 4.752879 ATACCGGTGCGCGTTGCT 62.753 61.111 19.93 0.00 46.63 3.91
124 125 4.514569 CATACCGGTGCGCGTTGC 62.515 66.667 19.93 0.00 46.70 4.17
125 126 2.089433 GATCATACCGGTGCGCGTTG 62.089 60.000 19.93 5.30 0.00 4.10
126 127 1.881252 GATCATACCGGTGCGCGTT 60.881 57.895 19.93 0.00 0.00 4.84
127 128 1.449726 TAGATCATACCGGTGCGCGT 61.450 55.000 19.93 0.00 0.00 6.01
128 129 0.729478 CTAGATCATACCGGTGCGCG 60.729 60.000 19.93 0.00 0.00 6.86
129 130 0.314302 ACTAGATCATACCGGTGCGC 59.686 55.000 19.93 0.00 0.00 6.09
130 131 5.556355 TTATACTAGATCATACCGGTGCG 57.444 43.478 19.93 8.20 0.00 5.34
161 162 1.269778 CGGCATCATCACTATCGTGGT 60.270 52.381 0.00 0.00 41.53 4.16
192 193 2.512056 TCCCCACTTCCAAGACAAAAGA 59.488 45.455 0.00 0.00 0.00 2.52
258 259 5.567138 AGGAGCACATTTTACAAGTATGC 57.433 39.130 0.00 0.00 0.00 3.14
354 429 7.040478 GCATGGCAGTTCAATATTGGTAGATTA 60.040 37.037 15.36 0.00 0.00 1.75
357 432 4.580167 GCATGGCAGTTCAATATTGGTAGA 59.420 41.667 15.36 0.00 0.00 2.59
361 436 5.717078 ATAGCATGGCAGTTCAATATTGG 57.283 39.130 15.36 0.58 0.00 3.16
362 437 6.154445 GGAATAGCATGGCAGTTCAATATTG 58.846 40.000 9.29 9.29 0.00 1.90
482 560 6.319658 ACTGCAGATGAACTTTCTTTTTCTCA 59.680 34.615 23.35 0.00 0.00 3.27
531 609 7.374272 GCATCATCGCTATCATGGTACTATAT 58.626 38.462 0.00 0.00 0.00 0.86
532 610 6.239036 GGCATCATCGCTATCATGGTACTATA 60.239 42.308 0.00 0.00 0.00 1.31
533 611 5.452496 GGCATCATCGCTATCATGGTACTAT 60.452 44.000 0.00 0.00 0.00 2.12
534 612 4.142160 GGCATCATCGCTATCATGGTACTA 60.142 45.833 0.00 0.00 0.00 1.82
535 613 3.368843 GGCATCATCGCTATCATGGTACT 60.369 47.826 0.00 0.00 0.00 2.73
536 614 2.932614 GGCATCATCGCTATCATGGTAC 59.067 50.000 0.00 0.00 0.00 3.34
537 615 2.417243 CGGCATCATCGCTATCATGGTA 60.417 50.000 0.00 0.00 0.00 3.25
538 616 1.673923 CGGCATCATCGCTATCATGGT 60.674 52.381 0.00 0.00 0.00 3.55
539 617 1.004595 CGGCATCATCGCTATCATGG 58.995 55.000 0.00 0.00 0.00 3.66
540 618 1.004595 CCGGCATCATCGCTATCATG 58.995 55.000 0.00 0.00 0.00 3.07
620 700 9.753674 ACCTAACCATGAAAAAGAATAATCTGA 57.246 29.630 0.00 0.00 35.59 3.27
754 834 1.589716 CTTGGGCTTCCTTCCTTGCG 61.590 60.000 0.00 0.00 0.00 4.85
899 979 4.455877 GCAAGGTAGGGATGTTATGTATGC 59.544 45.833 0.00 0.00 0.00 3.14
907 987 0.034089 GGCTGCAAGGTAGGGATGTT 60.034 55.000 0.50 0.00 0.00 2.71
986 1187 0.394899 CCCCATGAGGAAGCCTTGAC 60.395 60.000 0.00 0.00 38.24 3.18
1088 1297 4.034510 ACAACAAAGCGAAGAAGTTGAGAG 59.965 41.667 10.18 0.00 41.41 3.20
1116 1325 4.112634 GCCACAAAAGAAGAAACCAAGAC 58.887 43.478 0.00 0.00 0.00 3.01
1122 1331 4.270808 CCACAATGCCACAAAAGAAGAAAC 59.729 41.667 0.00 0.00 0.00 2.78
1206 1417 2.653890 CCAAGAAGCACAACAATGTCG 58.346 47.619 0.00 0.00 37.82 4.35
1475 1686 2.319707 GTGTCACACACGCACACG 59.680 61.111 2.00 0.00 39.53 4.49
1685 1899 6.245296 CGCAAACACAAAATACAAACACAAAC 59.755 34.615 0.00 0.00 0.00 2.93
1691 1905 4.770351 AGCGCAAACACAAAATACAAAC 57.230 36.364 11.47 0.00 0.00 2.93
1694 1908 4.424626 TGAAAGCGCAAACACAAAATACA 58.575 34.783 11.47 0.00 0.00 2.29
1695 1909 5.382573 TTGAAAGCGCAAACACAAAATAC 57.617 34.783 11.47 0.00 0.00 1.89
1696 1910 6.036517 ACAATTGAAAGCGCAAACACAAAATA 59.963 30.769 13.59 0.00 0.00 1.40
1697 1911 5.163774 ACAATTGAAAGCGCAAACACAAAAT 60.164 32.000 13.59 0.00 0.00 1.82
1699 1913 3.681897 ACAATTGAAAGCGCAAACACAAA 59.318 34.783 13.59 0.00 0.00 2.83
1700 1914 3.257393 ACAATTGAAAGCGCAAACACAA 58.743 36.364 13.59 8.99 0.00 3.33
1735 2106 4.439057 TCCTTACGGAGCAATGTACAATC 58.561 43.478 0.00 0.00 33.30 2.67
1739 2110 4.634443 ACAAATCCTTACGGAGCAATGTAC 59.366 41.667 0.00 0.00 44.06 2.90
1742 2113 6.347725 GCTATACAAATCCTTACGGAGCAATG 60.348 42.308 0.00 0.00 44.06 2.82
1749 2120 4.022589 TCTCCGCTATACAAATCCTTACGG 60.023 45.833 0.00 0.00 39.44 4.02
1750 2121 5.117355 TCTCCGCTATACAAATCCTTACG 57.883 43.478 0.00 0.00 0.00 3.18
1826 2198 9.404348 GGTCGATTAGTTAGGTAGCTATTAAAC 57.596 37.037 1.80 0.00 0.00 2.01
1853 2225 9.856488 GTTCTGTTACTTCTCAGATTATGTGTA 57.144 33.333 0.00 0.00 39.85 2.90
1879 2258 8.547894 AGCTTTTAAAATCCTTTAACGCTTTTG 58.452 29.630 0.09 0.00 39.04 2.44
1948 2327 1.728971 GATGTGCTGTGGAAGTTCTCG 59.271 52.381 2.25 0.00 0.00 4.04
2038 2417 2.173382 GACGTGACAATGTGCGCC 59.827 61.111 4.18 0.00 0.00 6.53
2045 2424 0.320334 TGTGATGGCGACGTGACAAT 60.320 50.000 0.00 0.00 40.63 2.71
2120 2500 4.142182 TGAGTTGATCATAGCATGTGACGA 60.142 41.667 0.00 0.00 31.12 4.20
2127 2507 8.618677 CAAACATAAGTGAGTTGATCATAGCAT 58.381 33.333 0.00 0.00 40.92 3.79
2128 2508 7.414429 GCAAACATAAGTGAGTTGATCATAGCA 60.414 37.037 0.00 0.00 40.92 3.49
2139 2519 4.083484 GGTAAAGCGCAAACATAAGTGAGT 60.083 41.667 11.47 0.00 0.00 3.41
2146 2526 4.611807 CGACAAAGGTAAAGCGCAAACATA 60.612 41.667 11.47 0.00 0.00 2.29
2284 2665 7.462571 TTTCTTTAAGGCCTCTTTGGATTAC 57.537 36.000 5.23 0.00 38.35 1.89


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

AutoCloner maintained by Alex Coulton.