Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009577.1 Kokia drynarioides strain JFW-HI SEQ_124291, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 75576
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Warning! 28 characters in sequence are not A, C, G, or T
Found at i:356 original size:103 final size:103
Alignment explanation
Indices: 177--406 Score: 415
Period size: 103 Copynumber: 2.2 Consensus size: 103
167 TCTTTTGTCA
*
177 TTTCATTTGGATAAATTTCTATTTTAAAATCTTTGATATCTTCTAGTATTAAACTACTCTTTTGC
1 TTTCATTTGGATAAATTTCTATTTTAAAATCTTTGATATCTTCTAGCATTAAACTACTCTTTTGC
242 TTTTCTTTAATCAATTTAATTGTCTTGGTGATTGATAT
66 TTTTCTTTAATCAATTTAATTGTCTTGGTGATTGATAT
*
280 TTTCATTTGGATAAATTTCTATTTTAAAATCTTTGATATCTTCTAGCATTAAACTATTCTTTTGC
1 TTTCATTTGGATAAATTTCTATTTTAAAATCTTTGATATCTTCTAGCATTAAACTACTCTTTTGC
*
345 TTTTCTTTAATCAATTTAATTGTCTTGGTGGTTGATAT
66 TTTTCTTTAATCAATTTAATTGTCTTGGTGATTGATAT
* *
383 TTTCATTTGGATGAATTTTTATTT
1 TTTCATTTGGATAAATTTCTATTT
407 AGTCCTTTCT
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 122 1.00
ACGTcount: A:0.25, C:0.11, G:0.10, T:0.53
Consensus pattern (103 bp):
TTTCATTTGGATAAATTTCTATTTTAAAATCTTTGATATCTTCTAGCATTAAACTACTCTTTTGC
TTTTCTTTAATCAATTTAATTGTCTTGGTGATTGATAT
Found at i:1096 original size:26 final size:27
Alignment explanation
Indices: 1067--1184 Score: 109
Period size: 22 Copynumber: 4.9 Consensus size: 27
1057 AAACGGAACT
* * *
1067 AACAGGAAGTACATA-ACTGCTGGGGA
1 AACAGGAAGCACACACAATGCTGGGGA
1093 AACA-GAAGCACACACAATGCTGGGGA
1 AACAGGAAGCACACACAATGCTGGGGA
1119 AACA-GAAGCACACACAATGCT---G-
1 AACAGGAAGCACACACAATGCTGGGGA
1141 AACA-GAAGCACACACAATGCT----A
1 AACAGGAAGCACACACAATGCTGGGGA
*
1163 AACA-GAAGCACACACAGTGCTG
1 AACAGGAAGCACACACAATGCTG
1185 AACAGTAAGC
Statistics
Matches: 85, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
22 41 0.48
23 1 0.01
25 8 0.09
26 35 0.41
ACGTcount: A:0.43, C:0.24, G:0.23, T:0.10
Consensus pattern (27 bp):
AACAGGAAGCACACACAATGCTGGGGA
Found at i:1144 original size:22 final size:22
Alignment explanation
Indices: 1093--1194 Score: 141
Period size: 22 Copynumber: 4.4 Consensus size: 22
1083 CTGCTGGGGA
1093 AACAGAAGCACACACAATGCTGGGG
1 AACAGAAGCACACACAATGCT---G
1118 AAACAGAAGCACACACAATGCTG
1 -AACAGAAGCACACACAATGCTG
*
1141 AACAGAAGCACACACAATGCTA
1 AACAGAAGCACACACAATGCTG
*
1163 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAATGCTG
1185 AACAGTAAGC
1 AACAG-AAGC
1195 GCGCTAGCGT
Statistics
Matches: 72, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
22 46 0.64
23 5 0.07
26 21 0.29
ACGTcount: A:0.45, C:0.25, G:0.21, T:0.09
Consensus pattern (22 bp):
AACAGAAGCACACACAATGCTG
Found at i:10641 original size:15 final size:16
Alignment explanation
Indices: 10613--10645 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
10603 AAAACACTAA
*
10613 AAAAACCCCGAAAAAG
1 AAAAACCCCAAAAAAG
10629 AAAAA-CCCAAAAAAG
1 AAAAACCCCAAAAAAG
10644 AA
1 AA
10646 GAGAACTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.70, C:0.21, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAACCCCAAAAAAG
Found at i:15781 original size:19 final size:19
Alignment explanation
Indices: 15740--15781 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
15730 TTATCACTTA
* *
15740 ATTTTTTTTACTTCTTTAT
1 ATTTTTTTTACTTCTTGAC
15759 ATTTTTTTTACTTCTTGAC
1 ATTTTTTTTACTTCTTGAC
15778 ATTT
1 ATTT
15782 ATATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.69
Consensus pattern (19 bp):
ATTTTTTTTACTTCTTGAC
Found at i:19144 original size:156 final size:156
Alignment explanation
Indices: 18971--19282 Score: 527
Period size: 156 Copynumber: 2.0 Consensus size: 156
18961 ATGACTTTAA
*
18971 AAAAAAAAAAAAAGTAAGAGAGAGCAACTAAGAGTATAAAAAGAGTTGTGGGACAGATTTGTTAG
1 AAAAAAAAAAAAAGTAAGAAAGAGCAACTAAGAGTATAAAAAGAGTTGTGGGACAGATTTGTTAG
* *
19036 TCCACTCAACTCAAAATTTTGAATTAAAAGAGAATAAAAGAAAATGAGAGGTGG-TCGTTCAAGG
66 TCCACTCAACTCAAAATTTTGAATTAAAAGAAAAGAAAAGAAAATGAGAGGTGGCT-GTTCAAGG
19100 TAAATAAATATAATTTTTATGTGAATT
130 TAAATAAATATAATTTTTATGTGAATT
* * *
19127 AAAAAAAAAAGAAGTAAGAAAGAGCAACTAAGAGTATAAAAAGAGTTGTGGGGCAGATTTGTTGG
1 AAAAAAAAAAAAAGTAAGAAAGAGCAACTAAGAGTATAAAAAGAGTTGTGGGACAGATTTGTTAG
* * *
19192 TCCGCTCAACTCAAAATTTTGAATTAGAAGAAAAGAGAAGAAAATGAGAGGTGGCTGTTCAAGGT
66 TCCACTCAACTCAAAATTTTGAATTAAAAGAAAAGAAAAGAAAATGAGAGGTGGCTGTTCAAGGT
19257 AAATAAATATAATTTTTATGTGAATT
131 AAATAAATATAATTTTTATGTGAATT
19283 TATTATATTA
Statistics
Matches: 146, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
156 145 0.99
157 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.21, T:0.25
Consensus pattern (156 bp):
AAAAAAAAAAAAAGTAAGAAAGAGCAACTAAGAGTATAAAAAGAGTTGTGGGACAGATTTGTTAG
TCCACTCAACTCAAAATTTTGAATTAAAAGAAAAGAAAAGAAAATGAGAGGTGGCTGTTCAAGGT
AAATAAATATAATTTTTATGTGAATT
Found at i:22143 original size:22 final size:22
Alignment explanation
Indices: 22118--22168 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
22108 GATTCATTCC
* *
22118 AATTTTAAGTGTTATGTCATAT
1 AATTTCAAGTGTTATGTAATAT
22140 AATTTCAAGTGTTATGTAATAT
1 AATTTCAAGTGTTATGTAATAT
*
22162 AACTTCA
1 AATTTCA
22169 CTAAATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (22 bp):
AATTTCAAGTGTTATGTAATAT
Found at i:25515 original size:19 final size:21
Alignment explanation
Indices: 25493--25535 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 21
25483 ATAATAATTT
*
25493 TAAAATTT-TAAATT-AAAAA
1 TAAAATTTAAAAATTAAAAAA
25512 T-AAATTTAAAAATTAAAAAA
1 TAAAATTTAAAAATTAAAAAA
25532 TAAA
1 TAAA
25536 TAATAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 6 0.30
19 6 0.30
20 6 0.30
21 2 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAATTTAAAAATTAAAAAA
Found at i:25535 original size:26 final size:26
Alignment explanation
Indices: 25475--25542 Score: 66
Period size: 26 Copynumber: 2.5 Consensus size: 26
25465 TAGCTCTACC
* **
25475 AAAAT-AAAATAATAATTTTAAAATTTT
1 AAAATAAAAAT-A-AATTTAAAAATTAA
*
25502 AAATTAAAAATAAATTTAAAAATTAA
1 AAAATAAAAATAAATTTAAAAATTAA
25528 AAAATAAATAATAAA
1 AAAATAAA-AATAAA
25543 CAAAAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
26 18 0.53
27 11 0.32
28 5 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (26 bp):
AAAATAAAAATAAATTTAAAAATTAA
Found at i:25636 original size:20 final size:18
Alignment explanation
Indices: 25597--25632 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
25587 CCACCAAAAA
25597 TAAAATATATATTTAAAT
1 TAAAATATATATTTAAAT
*
25615 TAAACTATATATTTAAAT
1 TAAAATATATATTTAAAT
25633 ATTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATATATTTAAAT
Found at i:25758 original size:94 final size:93
Alignment explanation
Indices: 25641--25958 Score: 430
Period size: 95 Copynumber: 3.4 Consensus size: 93
25631 ATATTATATA
* * ** *
25641 ATAAATAAAAAATCGTTTAAAAAATTCATTTAATTAAAGTAATGGCGTAATTTAATATGACATCA
1 ATAAATAATAAATTGTTTAAAAAATTCATTTAATTAAAGTGGTGACGT-ATTTAATATGACATCA
* *
25706 CCAAAAAAATTTTAAATTTATTTTAATAAT
65 -CAAAAAAAATTTAAATTTATTTTAAAAAT
*
25736 ATAAATAATAAATTGTTTAAAAAATTCATTTAATTAAAGTGGTGACGCTATTTAATATGACACCA
1 ATAAATAATAAATTGTTTAAAAAATTCATTTAATTAAAGTGGTGACG-TATTTAATATGACATCA
*
25801 AAAAAAAAATTT-AATTTATTTTAAAAAT
65 CAAAAAAAATTTAAATTTATTTTAAAAAT
* * *
25829 ATAAATAATAAATAAT-TTTAAAAAATTCATTTAATTAAGGTGGTGACGCCA--TAATATGGCAT
1 ATAAATAATAAAT--TGTTTAAAAAATTCATTTAATTAAAGTGGTGACG-TATTTAATATGACAT
*
25891 CACAAAAAAAAATTAAATTTATTTTAAAAAT
63 CACAAAAAAAATTTAAATTTATTTTAAAAAT
25922 ATAAATAATAAATTGTTTAAAAAATT-ATTTAATTAAA
1 ATAAATAATAAATTGTTTAAAAAATTCATTTAATTAAA
25959 AAGGTGACAC
Statistics
Matches: 202, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
91 11 0.05
92 32 0.16
93 57 0.28
94 43 0.21
95 58 0.29
96 1 0.00
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.36
Consensus pattern (93 bp):
ATAAATAATAAATTGTTTAAAAAATTCATTTAATTAAAGTGGTGACGTATTTAATATGACATCAC
AAAAAAAATTTAAATTTATTTTAAAAAT
Found at i:25992 original size:93 final size:93
Alignment explanation
Indices: 25641--26022 Score: 438
Period size: 93 Copynumber: 4.1 Consensus size: 93
25631 ATATTATATA
* * ** * ** *
25641 ATAAATAAAAAATCGTTTAAAAAATTCATTTAATTAAAGTAATGGCGTAATTTAATATGACATCA
1 ATAAATAATAAATTGTTTAAAAAATTCATTTAATTAAAGTGGTGACGCCATTTAATATGGCA-C-
* ** *
25706 CCAAAAAAATTTTAAATTTATTTTAATAAT
64 CAAAAAAAAAATTAAATTTATTTTAAAAAT
* *
25736 ATAAATAATAAATTGTTTAAAAAATTCATTTAATTAAAGTGGTGACGCTATTTAATATGACACCA
1 ATAAATAATAAATTGTTTAAAAAATTCATTTAATTAAAGTGGTGACGCCATTTAATATGGCACCA
*
25801 AAAAAAAAATTTAATTTATTTTAAAAAT
66 AAAAAAAAATTAAATTTATTTTAAAAAT
* *
25829 ATAAATAATAAATAAT-TTTAAAAAATTCATTTAATTAAGGTGGTGACGCCA--TAATATGGCAT
1 ATAAATAATAAAT--TGTTTAAAAAATTCATTTAATTAAAGTGGTGACGCCATTTAATATGGCAC
25891 CACAAAAAAAAATTAAATTTATTTTAAAAAT
64 CA-AAAAAAAAATTAAATTTATTTTAAAAAT
** * *
25922 ATAAATAATAAATTGTTTAAAAAATT-ATTTAATTAAAAAGGTGACACCATTTAATATGGTACCA
1 ATAAATAATAAATTGTTTAAAAAATTCATTTAATTAAAGTGGTGACGCCATTTAATATGGCACCA
** *
25986 TTAAAAAATTTAAA--T-TTTTAAAAA-
66 AAAAAAAAATTAAATTTATTTTAAAAAT
*
26010 ATAAATATTAAAT
1 ATAAATAATAAAT
26023 AATGAAAAAA
Statistics
Matches: 254, Mismatches: 27, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
88 12 0.05
89 9 0.04
90 1 0.00
91 20 0.08
92 33 0.13
93 89 0.35
94 34 0.13
95 56 0.22
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (93 bp):
ATAAATAATAAATTGTTTAAAAAATTCATTTAATTAAAGTGGTGACGCCATTTAATATGGCACCA
AAAAAAAAATTAAATTTATTTTAAAAAT
Found at i:26334 original size:28 final size:27
Alignment explanation
Indices: 26269--26334 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
26259 GATAGATTTT
* *
26269 AAGTTATTTTTCGTATTTAATAAAAAA
1 AAGTTATTTTTAGTAATTAATAAAAAA
* * *
26296 AAATT-TATTTAGATAATTAATTAAAAA
1 AAGTTATTTTTAG-TAATTAATAAAAAA
26323 AAGTTATTTTTA
1 AAGTTATTTTTA
26335 TAAAAAAGCC
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
26 5 0.17
27 20 0.67
28 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (27 bp):
AAGTTATTTTTAGTAATTAATAAAAAA
Found at i:26337 original size:26 final size:27
Alignment explanation
Indices: 26269--26337 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
26259 GATAGATTTT
* *
26269 AAGTTATTTTTCGTATTTAATAAAAAAA
1 AAGTTATTTTT-ATAATTAATAAAAAAA
* ** *
26297 AATTTATTTAGATAATTAAT-TAAAAA
1 AAGTTATTTTTATAATTAATAAAAAAA
26323 AAGTTATTTTTATAA
1 AAGTTATTTTTATAA
26338 AAAAGCCTAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
26 17 0.53
27 7 0.22
28 8 0.25
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (27 bp):
AAGTTATTTTTATAATTAATAAAAAAA
Found at i:27898 original size:31 final size:31
Alignment explanation
Indices: 27858--27933 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
27848 AAAAATATAT
27858 TATTTTAGTCACTCT-GATTAACTAAATTTCA
1 TATTTTAGTCACTCTCG-TTAACTAAATTTCA
* ** *
27889 TGTTTTAGTCACTCTCGTTAGTTAAATTTCC
1 TATTTTAGTCACTCTCGTTAACTAAATTTCA
27920 TATTTTAGTCACTC
1 TATTTTAGTCACTC
27934 CCCGGTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.47
Consensus pattern (31 bp):
TATTTTAGTCACTCTCGTTAACTAAATTTCA
Found at i:38767 original size:43 final size:43
Alignment explanation
Indices: 38677--38766 Score: 155
Period size: 43 Copynumber: 2.1 Consensus size: 43
38667 AAAAAATCTT
**
38677 AAAAATATTCACAAGTATTCACTCCCCCACCTTTTTTAAAAAA
1 AAAAATATTCACAAGTATTCACTCCCCCACCTTTTAAAAAAAA
38720 AAAAATATTCACAAGTATTCACTCCCCCA-CTTTTAAAAAAAA
1 AAAAATATTCACAAGTATTCACTCCCCCACCTTTTAAAAAAAA
38762 AAAAA
1 AAAAA
38767 AAAATCATCT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 16 0.36
43 29 0.64
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (43 bp):
AAAAATATTCACAAGTATTCACTCCCCCACCTTTTAAAAAAAA
Found at i:62192 original size:283 final size:283
Alignment explanation
Indices: 61685--62241 Score: 1105
Period size: 283 Copynumber: 2.0 Consensus size: 283
61675 ACAAATAAAA
61685 TGAACTGCATCATTCTAGAAAGGGAAGAGTGATAGTTCACCCAACATATTTCCAACCAACCTCAG
1 TGAACTGCATCATTCTAGAAAGGGAAGAGTGATAGTTCACCCAACATATTTCCAACCAACCTCAG
61750 TGAGGCATATAGCTTTACATGGGTTAATGTATCCAAATGCATAATGGAGAAATGCATAATCCATA
66 TGAGGCATATAGCTTTACATGGGTTAATGTATCCAAATGCATAATGGAGAAATGCATAATCCATA
61815 AAAGGTTCGCAAAGTCAAGTCAAAAACCAGCCTTCATAAGGTGTGTAGCATTTGGAAGTGTTCAT
131 AAAGGTTCGCAAAGTCAAGTCAAAAACCAGCCTTCATAAGGTGTGTAGCATTTGGAAGTGTTCAT
61880 GATGCAAATGCATGCATATATGTAACAGAGAGTGGCTAAGAGAGAAACAAAACACTTCAAATTTC
196 GATGCAAATGCATGCATATATGTAACAGAGAGTGGCTAAGAGAGAAACAAAACACTTCAAATTTC
*
61945 TTAAAGAACAATTAAGGGAAGAG
261 TTAAAGAAAAATTAAGGGAAGAG
61968 TGAACTGCATCATTCTAGAAAGGGAAGAGTGATAGTTCACCCAACATATTTCCAACCAACCTCAG
1 TGAACTGCATCATTCTAGAAAGGGAAGAGTGATAGTTCACCCAACATATTTCCAACCAACCTCAG
62033 TGAGGCATATAGCTTTACATGGGTTAATGTATCCAAATGCATAATGGAGAAATGCATAATCCATA
66 TGAGGCATATAGCTTTACATGGGTTAATGTATCCAAATGCATAATGGAGAAATGCATAATCCATA
62098 AAAGGTTCGCAAAGTCAAGTCAAAAACCAGCCTTCATAAGGTGTGTAGCATTTGGAAGTGTTCAT
131 AAAGGTTCGCAAAGTCAAGTCAAAAACCAGCCTTCATAAGGTGTGTAGCATTTGGAAGTGTTCAT
62163 GATGCAAATGCATGCATATATGTAACAGAGAGTGGCTAAGAGAGAAACAAAACACTTCAAATTTC
196 GATGCAAATGCATGCATATATGTAACAGAGAGTGGCTAAGAGAGAAACAAAACACTTCAAATTTC
62228 TTAAAGAAAAATTA
261 TTAAAGAAAAATTA
62242 GGATTGCAAG
Statistics
Matches: 273, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
283 273 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.25
Consensus pattern (283 bp):
TGAACTGCATCATTCTAGAAAGGGAAGAGTGATAGTTCACCCAACATATTTCCAACCAACCTCAG
TGAGGCATATAGCTTTACATGGGTTAATGTATCCAAATGCATAATGGAGAAATGCATAATCCATA
AAAGGTTCGCAAAGTCAAGTCAAAAACCAGCCTTCATAAGGTGTGTAGCATTTGGAAGTGTTCAT
GATGCAAATGCATGCATATATGTAACAGAGAGTGGCTAAGAGAGAAACAAAACACTTCAAATTTC
TTAAAGAAAAATTAAGGGAAGAG
Found at i:66059 original size:5 final size:5
Alignment explanation
Indices: 66051--66084 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
66041 GAAAAAATTA
66051 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
66085 AACTTTGCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:66312 original size:15 final size:16
Alignment explanation
Indices: 66292--66324 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
66282 AAATTTTTTT
66292 AAAAA-TAAAATAATA
1 AAAAATTAAAATAATA
*
66307 AAAAATTAAAATGATA
1 AAAAATTAAAATAATA
66323 AA
1 AA
66325 TTTGAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAAATTAAAATAATA
Found at i:68786 original size:29 final size:29
Alignment explanation
Indices: 68739--68811 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
68729 GTTAATAATT
* * *
68739 TATAAGAATTGGATCAAATTAAAATTTCATG
1 TATAA-AATTGCA-CAAAATAAAAGTTCATG
*
68770 -ATAAAATTGCACAAAATCAAAGTTCATG
1 TATAAAATTGCACAAAATAAAAGTTCATG
*
68798 TATATAATTGCACA
1 TATAAAATTGCACA
68812 TCAAACCATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 14 0.39
29 18 0.50
30 4 0.11
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (29 bp):
TATAAAATTGCACAAAATAAAAGTTCATG
Found at i:71343 original size:26 final size:26
Alignment explanation
Indices: 71310--71363 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
71300 ATCAAAGTAT
71310 GGATTTTAACAATATTCATATCATCA
1 GGATTTTAACAATATTCATATCATCA
71336 GGATTTTAACAATATTCATATCATCA
1 GGATTTTAACAATATTCATATCATCA
71362 GG
1 GG
71364 GACTTAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (26 bp):
GGATTTTAACAATATTCATATCATCA
Found at i:73042 original size:30 final size:30
Alignment explanation
Indices: 73008--73076 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
72998 AAATTAAATC
*
73008 AAATCAAAATTCCATATATAAAATTGGACA-
1 AAATCAAAATT-CATATATAAAATTGCACAT
* * *
73038 AAATCAAAGTTCATGTATAACATTGCACATT
1 AAATCAAAATTCATATATAAAATTGCACA-T
73069 AAATCAAA
1 AAATCAAA
73077 GTTTATGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 15 0.45
30 10 0.30
31 8 0.24
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (30 bp):
AAATCAAAATTCATATATAAAATTGCACAT
Found at i:73057 original size:29 final size:30
Alignment explanation
Indices: 73008--73089 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
72998 AAATTAAATC
* * *
73008 AAATCAAAATTCCATATATAAAATTGGACA-
1 AAATCAAAGTT-CATGTATAAAATTGCACAT
*
73038 AAATCAAAGTTCATGTATAACATTGCACATT
1 AAATCAAAGTTCATGTATAAAATTGCACA-T
*
73069 AAATCAAAGTTTATGTATAAA
1 AAATCAAAGTTCATGTATAAA
73090 TTTAATATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 15 0.34
30 10 0.23
31 19 0.43
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTGCACAT
Found at i:73504 original size:21 final size:19
Alignment explanation
Indices: 73464--73506 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
73454 ACTATTTTTT
**
73464 AAATTTTAAAAAATTCAAA
1 AAATTTTAAAAAATAAAAA
73483 AAATTATTACAAAAATAAAAA
1 AAATT-TTA-AAAAATAAAAA
73504 AAA
1 AAA
73507 ATACTAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 3 0.15
21 12 0.60
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATTTTAAAAAATAAAAA
Done.