Multiple sequence alignment - TraesCS5D01G500200

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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 TraesCS5D01G500200 chr5D 100.000 2288 0 0 1 2288 528972962 528970675 0.000000e+00 4226.0
1 TraesCS5D01G500200 chr5B 89.922 2193 127 36 160 2288 666196980 666194818 0.000000e+00 2739.0
2 TraesCS5D01G500200 chr5B 80.645 186 28 7 785 968 28234946 28234767 1.100000e-28 137.0
3 TraesCS5D01G500200 chr1B 88.383 1558 108 33 764 2288 452565356 452566873 0.000000e+00 1807.0
4 TraesCS5D01G500200 chr5A 89.806 1442 86 25 892 2288 657199290 657197865 0.000000e+00 1792.0
5 TraesCS5D01G500200 chr5A 81.433 684 80 24 113 783 657200172 657199523 1.210000e-142 516.0
6 TraesCS5D01G500200 chr1D 89.907 1179 83 18 764 1928 337211153 337212309 0.000000e+00 1485.0
7 TraesCS5D01G500200 chr1D 94.737 285 10 1 2004 2288 337212571 337212850 2.700000e-119 438.0
8 TraesCS5D01G500200 chr1D 91.379 58 3 1 1940 1997 337212492 337212547 6.780000e-11 78.7
9 TraesCS5D01G500200 chr1A 91.335 854 60 6 764 1608 435375907 435376755 0.000000e+00 1155.0
10 TraesCS5D01G500200 chr1A 90.365 602 31 9 1634 2214 435376750 435377345 0.000000e+00 765.0
11 TraesCS5D01G500200 chr1A 96.341 82 3 0 2207 2288 435377422 435377503 3.960000e-28 135.0
12 TraesCS5D01G500200 chr7B 77.561 410 48 27 583 968 152782248 152782637 8.280000e-50 207.0
13 TraesCS5D01G500200 chr3A 78.571 322 42 17 658 967 744055514 744055820 1.080000e-43 187.0
14 TraesCS5D01G500200 chr2B 83.721 172 20 8 781 951 236703607 236703443 3.040000e-34 156.0
15 TraesCS5D01G500200 chr6D 82.759 174 21 9 779 950 152256278 152256444 1.830000e-31 147.0


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 TraesCS5D01G500200 chr5D 528970675 528972962 2287 True 4226.000000 4226 100.000000 1 2288 1 chr5D.!!$R1 2287
1 TraesCS5D01G500200 chr5B 666194818 666196980 2162 True 2739.000000 2739 89.922000 160 2288 1 chr5B.!!$R2 2128
2 TraesCS5D01G500200 chr1B 452565356 452566873 1517 False 1807.000000 1807 88.383000 764 2288 1 chr1B.!!$F1 1524
3 TraesCS5D01G500200 chr5A 657197865 657200172 2307 True 1154.000000 1792 85.619500 113 2288 2 chr5A.!!$R1 2175
4 TraesCS5D01G500200 chr1D 337211153 337212850 1697 False 667.233333 1485 92.007667 764 2288 3 chr1D.!!$F1 1524
5 TraesCS5D01G500200 chr1A 435375907 435377503 1596 False 685.000000 1155 92.680333 764 2288 3 chr1A.!!$F1 1524

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
202 209 0.035725 TGCTTCACAGGGCTGATCTG 60.036 55.0 0.0 0.0 38.16 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2403 0.107214 ACAACCACTGGTGACTGGTG 60.107 55.0 0.0 0.0 37.88 4.17 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
35 36 8.969260 AAAACTTATATAGGTCGTTTTAGGGG 57.031 34.615 0.00 0.00 36.40 4.79
36 37 6.106648 ACTTATATAGGTCGTTTTAGGGGC 57.893 41.667 0.00 0.00 0.00 5.80
37 38 5.603813 ACTTATATAGGTCGTTTTAGGGGCA 59.396 40.000 0.00 0.00 0.00 5.36
38 39 6.100134 ACTTATATAGGTCGTTTTAGGGGCAA 59.900 38.462 0.00 0.00 0.00 4.52
39 40 3.945640 ATAGGTCGTTTTAGGGGCAAT 57.054 42.857 0.00 0.00 0.00 3.56
40 41 1.834188 AGGTCGTTTTAGGGGCAATG 58.166 50.000 0.00 0.00 0.00 2.82
41 42 1.353022 AGGTCGTTTTAGGGGCAATGA 59.647 47.619 0.00 0.00 0.00 2.57
42 43 2.164338 GGTCGTTTTAGGGGCAATGAA 58.836 47.619 0.00 0.00 0.00 2.57
43 44 2.163613 GGTCGTTTTAGGGGCAATGAAG 59.836 50.000 0.00 0.00 0.00 3.02
44 45 3.078837 GTCGTTTTAGGGGCAATGAAGA 58.921 45.455 0.00 0.00 0.00 2.87
45 46 3.504520 GTCGTTTTAGGGGCAATGAAGAA 59.495 43.478 0.00 0.00 0.00 2.52
46 47 3.756434 TCGTTTTAGGGGCAATGAAGAAG 59.244 43.478 0.00 0.00 0.00 2.85
47 48 3.506067 CGTTTTAGGGGCAATGAAGAAGT 59.494 43.478 0.00 0.00 0.00 3.01
48 49 4.022329 CGTTTTAGGGGCAATGAAGAAGTT 60.022 41.667 0.00 0.00 0.00 2.66
49 50 5.508994 CGTTTTAGGGGCAATGAAGAAGTTT 60.509 40.000 0.00 0.00 0.00 2.66
50 51 6.294286 CGTTTTAGGGGCAATGAAGAAGTTTA 60.294 38.462 0.00 0.00 0.00 2.01
51 52 6.834168 TTTAGGGGCAATGAAGAAGTTTAG 57.166 37.500 0.00 0.00 0.00 1.85
52 53 3.701664 AGGGGCAATGAAGAAGTTTAGG 58.298 45.455 0.00 0.00 0.00 2.69
53 54 3.076032 AGGGGCAATGAAGAAGTTTAGGT 59.924 43.478 0.00 0.00 0.00 3.08
54 55 3.193479 GGGGCAATGAAGAAGTTTAGGTG 59.807 47.826 0.00 0.00 0.00 4.00
55 56 4.079253 GGGCAATGAAGAAGTTTAGGTGA 58.921 43.478 0.00 0.00 0.00 4.02
56 57 4.156739 GGGCAATGAAGAAGTTTAGGTGAG 59.843 45.833 0.00 0.00 0.00 3.51
57 58 4.379918 GGCAATGAAGAAGTTTAGGTGAGC 60.380 45.833 0.00 0.00 0.00 4.26
58 59 4.670221 GCAATGAAGAAGTTTAGGTGAGCG 60.670 45.833 0.00 0.00 0.00 5.03
59 60 3.746045 TGAAGAAGTTTAGGTGAGCGT 57.254 42.857 0.00 0.00 0.00 5.07
60 61 3.390135 TGAAGAAGTTTAGGTGAGCGTG 58.610 45.455 0.00 0.00 0.00 5.34
61 62 3.181469 TGAAGAAGTTTAGGTGAGCGTGT 60.181 43.478 0.00 0.00 0.00 4.49
62 63 2.755650 AGAAGTTTAGGTGAGCGTGTG 58.244 47.619 0.00 0.00 0.00 3.82
63 64 2.102588 AGAAGTTTAGGTGAGCGTGTGT 59.897 45.455 0.00 0.00 0.00 3.72
64 65 2.150397 AGTTTAGGTGAGCGTGTGTC 57.850 50.000 0.00 0.00 0.00 3.67
65 66 1.411246 AGTTTAGGTGAGCGTGTGTCA 59.589 47.619 0.00 0.00 0.00 3.58
66 67 1.525619 GTTTAGGTGAGCGTGTGTCAC 59.474 52.381 0.00 0.00 43.12 3.67
67 68 1.037493 TTAGGTGAGCGTGTGTCACT 58.963 50.000 4.27 0.00 43.34 3.41
68 69 1.900245 TAGGTGAGCGTGTGTCACTA 58.100 50.000 4.27 0.00 43.34 2.74
69 70 1.257743 AGGTGAGCGTGTGTCACTAT 58.742 50.000 4.27 0.00 43.34 2.12
70 71 1.618837 AGGTGAGCGTGTGTCACTATT 59.381 47.619 4.27 0.00 43.34 1.73
71 72 2.823747 AGGTGAGCGTGTGTCACTATTA 59.176 45.455 4.27 0.00 43.34 0.98
72 73 3.447586 AGGTGAGCGTGTGTCACTATTAT 59.552 43.478 4.27 0.00 43.34 1.28
73 74 3.551890 GGTGAGCGTGTGTCACTATTATG 59.448 47.826 4.27 0.00 43.34 1.90
74 75 4.421058 GTGAGCGTGTGTCACTATTATGA 58.579 43.478 4.27 0.00 41.05 2.15
75 76 5.043903 GTGAGCGTGTGTCACTATTATGAT 58.956 41.667 4.27 0.00 41.05 2.45
76 77 5.520288 GTGAGCGTGTGTCACTATTATGATT 59.480 40.000 4.27 0.00 41.05 2.57
77 78 6.036083 GTGAGCGTGTGTCACTATTATGATTT 59.964 38.462 4.27 0.00 41.05 2.17
78 79 6.255670 TGAGCGTGTGTCACTATTATGATTTC 59.744 38.462 4.27 0.00 31.34 2.17
79 80 6.341316 AGCGTGTGTCACTATTATGATTTCT 58.659 36.000 4.27 0.00 31.34 2.52
80 81 6.818644 AGCGTGTGTCACTATTATGATTTCTT 59.181 34.615 4.27 0.00 31.34 2.52
81 82 7.334421 AGCGTGTGTCACTATTATGATTTCTTT 59.666 33.333 4.27 0.00 31.34 2.52
82 83 7.962918 GCGTGTGTCACTATTATGATTTCTTTT 59.037 33.333 4.27 0.00 31.34 2.27
83 84 9.825972 CGTGTGTCACTATTATGATTTCTTTTT 57.174 29.630 4.27 0.00 31.34 1.94
97 98 7.620215 TGATTTCTTTTTGTTGAGAAAATGCG 58.380 30.769 3.05 0.00 42.99 4.73
98 99 6.959671 TTTCTTTTTGTTGAGAAAATGCGT 57.040 29.167 0.00 0.00 38.53 5.24
99 100 5.947503 TCTTTTTGTTGAGAAAATGCGTG 57.052 34.783 0.00 0.00 0.00 5.34
100 101 5.406649 TCTTTTTGTTGAGAAAATGCGTGT 58.593 33.333 0.00 0.00 0.00 4.49
101 102 5.514914 TCTTTTTGTTGAGAAAATGCGTGTC 59.485 36.000 0.00 0.00 0.00 3.67
102 103 4.362932 TTTGTTGAGAAAATGCGTGTCA 57.637 36.364 0.00 0.00 0.00 3.58
103 104 3.332761 TGTTGAGAAAATGCGTGTCAC 57.667 42.857 0.00 0.00 0.00 3.67
104 105 2.942376 TGTTGAGAAAATGCGTGTCACT 59.058 40.909 0.65 0.00 0.00 3.41
105 106 3.242706 TGTTGAGAAAATGCGTGTCACTG 60.243 43.478 0.65 0.00 0.00 3.66
106 107 2.560504 TGAGAAAATGCGTGTCACTGT 58.439 42.857 0.65 0.00 0.00 3.55
107 108 2.543848 TGAGAAAATGCGTGTCACTGTC 59.456 45.455 0.65 0.00 0.00 3.51
108 109 2.543848 GAGAAAATGCGTGTCACTGTCA 59.456 45.455 0.65 0.00 0.00 3.58
109 110 2.942376 AGAAAATGCGTGTCACTGTCAA 59.058 40.909 0.65 0.00 0.00 3.18
110 111 3.565482 AGAAAATGCGTGTCACTGTCAAT 59.435 39.130 0.65 0.00 0.00 2.57
111 112 3.988379 AAATGCGTGTCACTGTCAATT 57.012 38.095 0.65 0.00 0.00 2.32
112 113 3.988379 AATGCGTGTCACTGTCAATTT 57.012 38.095 0.65 0.00 0.00 1.82
113 114 3.988379 ATGCGTGTCACTGTCAATTTT 57.012 38.095 0.65 0.00 0.00 1.82
114 115 3.773860 TGCGTGTCACTGTCAATTTTT 57.226 38.095 0.65 0.00 0.00 1.94
158 162 0.323725 GCATGTGGGACCATCCTTGT 60.324 55.000 0.00 0.00 36.57 3.16
162 166 1.281867 TGTGGGACCATCCTTGTGATC 59.718 52.381 0.00 0.00 36.57 2.92
169 173 1.069823 CCATCCTTGTGATCTCCTCGG 59.930 57.143 0.00 0.00 0.00 4.63
175 179 3.369892 CCTTGTGATCTCCTCGGTGAAAT 60.370 47.826 0.00 0.00 0.00 2.17
185 189 1.079888 CGGTGAAATGGGGCTTTGC 60.080 57.895 0.00 0.00 0.00 3.68
191 195 1.344114 GAAATGGGGCTTTGCTTCACA 59.656 47.619 0.00 0.00 0.00 3.58
202 209 0.035725 TGCTTCACAGGGCTGATCTG 60.036 55.000 0.00 0.00 38.16 2.90
207 214 1.614525 ACAGGGCTGATCTGCAGGA 60.615 57.895 23.84 0.57 45.03 3.86
328 335 0.772124 TCCTTGGTTCCCCTCTGCTT 60.772 55.000 0.00 0.00 0.00 3.91
335 342 0.911525 TTCCCCTCTGCTTCCCTCTG 60.912 60.000 0.00 0.00 0.00 3.35
343 350 3.080121 CTTCCCTCTGCGGCTCCT 61.080 66.667 0.00 0.00 0.00 3.69
404 418 2.649034 GTTCGTGCCTCTCCGACA 59.351 61.111 0.00 0.00 31.95 4.35
405 419 1.444553 GTTCGTGCCTCTCCGACAG 60.445 63.158 0.00 0.00 31.95 3.51
652 706 4.323792 CGGCTATCTATCAACATTCCCCAT 60.324 45.833 0.00 0.00 0.00 4.00
718 773 7.755591 TCATTTTCTGCTGTTCAGTTATGATC 58.244 34.615 1.78 0.00 43.32 2.92
725 780 7.287696 TCTGCTGTTCAGTTATGATCCATACTA 59.712 37.037 1.78 0.00 43.32 1.82
739 794 7.914859 TGATCCATACTAATGCAGAGATTGAT 58.085 34.615 5.45 2.55 0.00 2.57
741 796 9.311916 GATCCATACTAATGCAGAGATTGATAC 57.688 37.037 5.45 0.00 0.00 2.24
748 803 9.486497 ACTAATGCAGAGATTGATACAATGTAG 57.514 33.333 5.45 0.00 0.00 2.74
753 808 8.424133 TGCAGAGATTGATACAATGTAGTGTAT 58.576 33.333 4.82 4.82 45.34 2.29
819 917 5.532557 AGGCTTCTTTTATGCAAAACTGAC 58.467 37.500 0.00 0.00 30.52 3.51
919 1108 5.111989 AGAACGTTCACATGTCATATCTGG 58.888 41.667 28.78 0.00 0.00 3.86
925 1114 4.758688 TCACATGTCATATCTGGTGTCAC 58.241 43.478 0.00 0.00 0.00 3.67
984 1181 3.597728 GGCTACCGGAGAGCGGAG 61.598 72.222 21.43 4.23 41.06 4.63
1017 1233 0.104725 AGATGGGGATGGAGGAGTCC 60.105 60.000 0.00 0.00 44.24 3.85
1336 1552 5.328565 CCTTCTTCTTTTTCCTCCCAGATT 58.671 41.667 0.00 0.00 0.00 2.40
1337 1553 5.184671 CCTTCTTCTTTTTCCTCCCAGATTG 59.815 44.000 0.00 0.00 0.00 2.67
1338 1554 5.582950 TCTTCTTTTTCCTCCCAGATTGA 57.417 39.130 0.00 0.00 0.00 2.57
1351 1572 5.573219 TCCCAGATTGATTGTCACTTGATT 58.427 37.500 0.00 0.00 0.00 2.57
1368 1591 2.487372 TGATTGCGTTGTATGTGTGCAT 59.513 40.909 0.00 0.00 39.03 3.96
1422 1652 6.655003 TGGTTCCTGATTTGTATTCTCAAGAC 59.345 38.462 0.00 0.00 0.00 3.01
1518 1749 3.274288 GCTTCCTGGTTTGTATCCTCAG 58.726 50.000 0.00 0.00 0.00 3.35
1645 1881 6.552859 TGCAGAGACGAATTTGAAATACAA 57.447 33.333 0.00 0.00 36.65 2.41
1733 1969 8.393366 CCATGAGTAGAATTGTTGTTATGTCAG 58.607 37.037 0.00 0.00 0.00 3.51
1791 2030 6.869315 TCTTTATCATTCGTTTGGTTGTGA 57.131 33.333 0.00 0.00 0.00 3.58
1945 2354 3.214328 AGCTCGTTGTCCTTGAACAAAT 58.786 40.909 0.00 0.00 40.62 2.32
1995 2408 2.512896 GCCTATGCCCCTCACCAG 59.487 66.667 0.00 0.00 0.00 4.00
2118 2556 2.213499 GCCCATCGTAGAATTGTGAGG 58.787 52.381 0.00 0.00 43.58 3.86
2237 2759 5.004922 TCTTTGTCATTGGTTTGGTTGAC 57.995 39.130 0.00 0.00 39.11 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.399797 CCCCTAAAACGACCTATATAAGTTTTT 57.600 33.333 16.23 9.50 42.59 1.94
10 11 7.500227 GCCCCTAAAACGACCTATATAAGTTTT 59.500 37.037 15.72 15.72 44.15 2.43
11 12 6.994496 GCCCCTAAAACGACCTATATAAGTTT 59.006 38.462 0.00 0.00 36.70 2.66
12 13 6.100134 TGCCCCTAAAACGACCTATATAAGTT 59.900 38.462 0.00 0.00 0.00 2.66
13 14 5.603813 TGCCCCTAAAACGACCTATATAAGT 59.396 40.000 0.00 0.00 0.00 2.24
14 15 6.105397 TGCCCCTAAAACGACCTATATAAG 57.895 41.667 0.00 0.00 0.00 1.73
15 16 6.497624 TTGCCCCTAAAACGACCTATATAA 57.502 37.500 0.00 0.00 0.00 0.98
16 17 6.270463 TCATTGCCCCTAAAACGACCTATATA 59.730 38.462 0.00 0.00 0.00 0.86
17 18 5.072600 TCATTGCCCCTAAAACGACCTATAT 59.927 40.000 0.00 0.00 0.00 0.86
18 19 4.409574 TCATTGCCCCTAAAACGACCTATA 59.590 41.667 0.00 0.00 0.00 1.31
19 20 3.201266 TCATTGCCCCTAAAACGACCTAT 59.799 43.478 0.00 0.00 0.00 2.57
20 21 2.572556 TCATTGCCCCTAAAACGACCTA 59.427 45.455 0.00 0.00 0.00 3.08
21 22 1.353022 TCATTGCCCCTAAAACGACCT 59.647 47.619 0.00 0.00 0.00 3.85
22 23 1.828979 TCATTGCCCCTAAAACGACC 58.171 50.000 0.00 0.00 0.00 4.79
23 24 3.078837 TCTTCATTGCCCCTAAAACGAC 58.921 45.455 0.00 0.00 0.00 4.34
24 25 3.426787 TCTTCATTGCCCCTAAAACGA 57.573 42.857 0.00 0.00 0.00 3.85
25 26 3.506067 ACTTCTTCATTGCCCCTAAAACG 59.494 43.478 0.00 0.00 0.00 3.60
26 27 5.468540 AACTTCTTCATTGCCCCTAAAAC 57.531 39.130 0.00 0.00 0.00 2.43
27 28 6.210584 CCTAAACTTCTTCATTGCCCCTAAAA 59.789 38.462 0.00 0.00 0.00 1.52
28 29 5.714806 CCTAAACTTCTTCATTGCCCCTAAA 59.285 40.000 0.00 0.00 0.00 1.85
29 30 5.222254 ACCTAAACTTCTTCATTGCCCCTAA 60.222 40.000 0.00 0.00 0.00 2.69
30 31 4.291249 ACCTAAACTTCTTCATTGCCCCTA 59.709 41.667 0.00 0.00 0.00 3.53
31 32 3.076032 ACCTAAACTTCTTCATTGCCCCT 59.924 43.478 0.00 0.00 0.00 4.79
32 33 3.193479 CACCTAAACTTCTTCATTGCCCC 59.807 47.826 0.00 0.00 0.00 5.80
33 34 4.079253 TCACCTAAACTTCTTCATTGCCC 58.921 43.478 0.00 0.00 0.00 5.36
34 35 4.379918 GCTCACCTAAACTTCTTCATTGCC 60.380 45.833 0.00 0.00 0.00 4.52
35 36 4.670221 CGCTCACCTAAACTTCTTCATTGC 60.670 45.833 0.00 0.00 0.00 3.56
36 37 4.452455 ACGCTCACCTAAACTTCTTCATTG 59.548 41.667 0.00 0.00 0.00 2.82
37 38 4.452455 CACGCTCACCTAAACTTCTTCATT 59.548 41.667 0.00 0.00 0.00 2.57
38 39 3.997021 CACGCTCACCTAAACTTCTTCAT 59.003 43.478 0.00 0.00 0.00 2.57
39 40 3.181469 ACACGCTCACCTAAACTTCTTCA 60.181 43.478 0.00 0.00 0.00 3.02
40 41 3.184581 CACACGCTCACCTAAACTTCTTC 59.815 47.826 0.00 0.00 0.00 2.87
41 42 3.131396 CACACGCTCACCTAAACTTCTT 58.869 45.455 0.00 0.00 0.00 2.52
42 43 2.102588 ACACACGCTCACCTAAACTTCT 59.897 45.455 0.00 0.00 0.00 2.85
43 44 2.475487 GACACACGCTCACCTAAACTTC 59.525 50.000 0.00 0.00 0.00 3.01
44 45 2.159014 TGACACACGCTCACCTAAACTT 60.159 45.455 0.00 0.00 0.00 2.66
45 46 1.411246 TGACACACGCTCACCTAAACT 59.589 47.619 0.00 0.00 0.00 2.66
46 47 1.525619 GTGACACACGCTCACCTAAAC 59.474 52.381 0.00 0.00 33.23 2.01
47 48 1.411246 AGTGACACACGCTCACCTAAA 59.589 47.619 8.59 0.00 39.15 1.85
48 49 1.037493 AGTGACACACGCTCACCTAA 58.963 50.000 8.59 0.00 39.15 2.69
49 50 1.900245 TAGTGACACACGCTCACCTA 58.100 50.000 8.59 0.00 39.15 3.08
50 51 1.257743 ATAGTGACACACGCTCACCT 58.742 50.000 8.59 0.00 39.15 4.00
51 52 2.080286 AATAGTGACACACGCTCACC 57.920 50.000 8.59 0.00 39.15 4.02
52 53 4.421058 TCATAATAGTGACACACGCTCAC 58.579 43.478 8.59 0.00 39.64 3.51
53 54 4.712122 TCATAATAGTGACACACGCTCA 57.288 40.909 8.59 0.00 39.64 4.26
54 55 6.477033 AGAAATCATAATAGTGACACACGCTC 59.523 38.462 8.59 0.00 39.64 5.03
55 56 6.341316 AGAAATCATAATAGTGACACACGCT 58.659 36.000 8.59 0.00 39.64 5.07
56 57 6.589830 AGAAATCATAATAGTGACACACGC 57.410 37.500 8.59 0.00 39.64 5.34
57 58 9.825972 AAAAAGAAATCATAATAGTGACACACG 57.174 29.630 8.59 0.00 39.64 4.49
71 72 8.277713 CGCATTTTCTCAACAAAAAGAAATCAT 58.722 29.630 0.00 0.00 40.25 2.45
72 73 7.277539 ACGCATTTTCTCAACAAAAAGAAATCA 59.722 29.630 0.00 0.00 40.25 2.57
73 74 7.580165 CACGCATTTTCTCAACAAAAAGAAATC 59.420 33.333 0.00 0.00 40.25 2.17
74 75 7.064490 ACACGCATTTTCTCAACAAAAAGAAAT 59.936 29.630 0.00 0.00 40.25 2.17
75 76 6.367422 ACACGCATTTTCTCAACAAAAAGAAA 59.633 30.769 0.00 0.00 39.18 2.52
76 77 5.866633 ACACGCATTTTCTCAACAAAAAGAA 59.133 32.000 0.00 0.00 0.00 2.52
77 78 5.406649 ACACGCATTTTCTCAACAAAAAGA 58.593 33.333 0.00 0.00 0.00 2.52
78 79 5.288232 TGACACGCATTTTCTCAACAAAAAG 59.712 36.000 0.00 0.00 0.00 2.27
79 80 5.061560 GTGACACGCATTTTCTCAACAAAAA 59.938 36.000 0.00 0.00 0.00 1.94
80 81 4.560819 GTGACACGCATTTTCTCAACAAAA 59.439 37.500 0.00 0.00 0.00 2.44
81 82 4.101942 GTGACACGCATTTTCTCAACAAA 58.898 39.130 0.00 0.00 0.00 2.83
82 83 3.376859 AGTGACACGCATTTTCTCAACAA 59.623 39.130 0.00 0.00 0.00 2.83
83 84 2.942376 AGTGACACGCATTTTCTCAACA 59.058 40.909 0.00 0.00 0.00 3.33
84 85 3.242739 ACAGTGACACGCATTTTCTCAAC 60.243 43.478 0.00 0.00 0.00 3.18
85 86 2.942376 ACAGTGACACGCATTTTCTCAA 59.058 40.909 0.00 0.00 0.00 3.02
86 87 2.543848 GACAGTGACACGCATTTTCTCA 59.456 45.455 0.00 0.00 0.00 3.27
87 88 2.543848 TGACAGTGACACGCATTTTCTC 59.456 45.455 0.00 0.00 0.00 2.87
88 89 2.560504 TGACAGTGACACGCATTTTCT 58.439 42.857 0.00 0.00 0.00 2.52
89 90 3.332761 TTGACAGTGACACGCATTTTC 57.667 42.857 0.00 0.00 0.00 2.29
90 91 3.988379 ATTGACAGTGACACGCATTTT 57.012 38.095 0.00 0.00 0.00 1.82
91 92 3.988379 AATTGACAGTGACACGCATTT 57.012 38.095 0.00 1.16 0.00 2.32
92 93 3.988379 AAATTGACAGTGACACGCATT 57.012 38.095 0.00 0.00 0.00 3.56
93 94 3.988379 AAAATTGACAGTGACACGCAT 57.012 38.095 0.00 0.00 0.00 4.73
94 95 3.773860 AAAAATTGACAGTGACACGCA 57.226 38.095 0.00 0.00 0.00 5.24
115 116 6.442952 CCGGTGATACACATTTTCTCAAAAA 58.557 36.000 0.00 0.00 38.66 1.94
116 117 5.563867 GCCGGTGATACACATTTTCTCAAAA 60.564 40.000 1.90 0.00 35.86 2.44
117 118 4.083003 GCCGGTGATACACATTTTCTCAAA 60.083 41.667 1.90 0.00 35.86 2.69
120 121 3.006940 TGCCGGTGATACACATTTTCTC 58.993 45.455 1.90 0.00 35.86 2.87
132 133 2.272146 GTCCCACATGCCGGTGAT 59.728 61.111 1.90 0.00 41.32 3.06
137 138 2.516930 GGATGGTCCCACATGCCG 60.517 66.667 0.00 0.00 33.64 5.69
158 162 1.486310 CCCATTTCACCGAGGAGATCA 59.514 52.381 0.00 0.00 0.00 2.92
162 166 1.452108 GCCCCATTTCACCGAGGAG 60.452 63.158 0.00 0.00 0.00 3.69
169 173 1.344114 TGAAGCAAAGCCCCATTTCAC 59.656 47.619 0.00 0.00 0.00 3.18
175 179 1.531365 CCTGTGAAGCAAAGCCCCA 60.531 57.895 0.00 0.00 0.00 4.96
185 189 0.035725 TGCAGATCAGCCCTGTGAAG 60.036 55.000 7.72 0.00 34.29 3.02
191 195 1.706995 CCATCCTGCAGATCAGCCCT 61.707 60.000 17.39 0.00 41.50 5.19
224 231 1.140652 CCCATCTCCTCTTCAAGCCTC 59.859 57.143 0.00 0.00 0.00 4.70
227 234 0.545646 AGCCCATCTCCTCTTCAAGC 59.454 55.000 0.00 0.00 0.00 4.01
231 238 0.467804 GTCCAGCCCATCTCCTCTTC 59.532 60.000 0.00 0.00 0.00 2.87
343 350 2.798689 CGGCGAGTTCAGATCGGA 59.201 61.111 0.00 0.00 40.50 4.55
380 394 4.011517 GAGGCACGAACCCCGGAA 62.012 66.667 0.73 0.00 43.93 4.30
389 403 3.749064 GCTGTCGGAGAGGCACGA 61.749 66.667 4.18 0.00 36.95 4.35
536 588 3.984193 CTGTAGTGCAGGGCAGGGC 62.984 68.421 0.00 0.00 40.08 5.19
611 664 0.859232 CGTACCTGTGTGCTGTGTTC 59.141 55.000 0.00 0.00 0.00 3.18
652 706 6.345298 GGTTTGAATCAGAAACTGGGAAAAA 58.655 36.000 0.00 0.00 34.36 1.94
718 773 8.837788 TTGTATCAATCTCTGCATTAGTATGG 57.162 34.615 0.00 0.00 32.15 2.74
725 780 7.772292 ACACTACATTGTATCAATCTCTGCATT 59.228 33.333 0.00 0.00 0.00 3.56
780 874 6.651975 AGAAGCCTACATAGTACATACCAC 57.348 41.667 0.00 0.00 0.00 4.16
819 917 9.912634 ACACCAAAATTCTCAATTATACAAGTG 57.087 29.630 0.00 0.00 0.00 3.16
939 1128 7.332433 TCTAGGAATTTAAAACAGGGTGGTA 57.668 36.000 0.00 0.00 0.00 3.25
1005 1221 3.917760 CCCGCGGACTCCTCCATC 61.918 72.222 30.73 0.00 36.12 3.51
1282 1498 3.488890 GCACGAACCTTAGTAGCCTAGAC 60.489 52.174 0.00 0.00 0.00 2.59
1295 1511 3.692406 GGTCGAGGGCACGAACCT 61.692 66.667 9.58 0.00 43.08 3.50
1336 1552 3.314913 ACAACGCAATCAAGTGACAATCA 59.685 39.130 0.00 0.00 0.00 2.57
1337 1553 3.888934 ACAACGCAATCAAGTGACAATC 58.111 40.909 0.00 0.00 0.00 2.67
1338 1554 3.988379 ACAACGCAATCAAGTGACAAT 57.012 38.095 0.00 0.00 0.00 2.71
1351 1572 1.233919 ACATGCACACATACAACGCA 58.766 45.000 0.00 0.00 33.67 5.24
1422 1652 0.625849 AGACCCCCTTGCATTACCAG 59.374 55.000 0.00 0.00 0.00 4.00
1518 1749 7.012704 ACACAGACTCCATTGCATTATCAATAC 59.987 37.037 0.00 0.00 35.12 1.89
1733 1969 1.239347 GCCTCCAGAACAAGGAACAC 58.761 55.000 0.00 0.00 34.35 3.32
1791 2030 2.248280 TGAAACACGTGTGCCTACAT 57.752 45.000 24.16 0.52 39.39 2.29
1945 2354 5.069648 TGTGTTATTTCCATTTGCTTCCACA 59.930 36.000 0.00 0.00 0.00 4.17
1989 2402 0.180171 CAACCACTGGTGACTGGTGA 59.820 55.000 0.00 0.00 37.88 4.02
1990 2403 0.107214 ACAACCACTGGTGACTGGTG 60.107 55.000 0.00 0.00 37.88 4.17
1991 2404 1.502690 TACAACCACTGGTGACTGGT 58.497 50.000 0.00 0.00 40.38 4.00
1992 2405 2.494059 CTTACAACCACTGGTGACTGG 58.506 52.381 0.00 0.00 35.34 4.00
1993 2406 2.158813 ACCTTACAACCACTGGTGACTG 60.159 50.000 0.00 0.00 35.34 3.51
1994 2407 2.124411 ACCTTACAACCACTGGTGACT 58.876 47.619 0.00 0.00 35.34 3.41
1995 2408 2.632987 ACCTTACAACCACTGGTGAC 57.367 50.000 0.00 0.00 35.34 3.67
2118 2556 4.329256 GCTCCCTGTAGTTAAAATGTCGAC 59.671 45.833 9.11 9.11 0.00 4.20
2237 2759 0.650512 GGAACATCCGTGCATGTACG 59.349 55.000 26.79 26.79 43.35 3.67


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

AutoCloner maintained by Alex Coulton.