Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010812.1 Kokia drynarioides strain JFW-HI SEQ_125779, 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: 56221
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 16 characters in sequence are not A, C, G, or T
Found at i:2322 original size:86 final size:84
Alignment explanation
Indices: 1902--3055 Score: 1648
Period size: 86 Copynumber: 13.6 Consensus size: 84
1892 ATTTAAAATC
* * * * *
1902 TGATAAAAATTGTAATATAATAATAATTGTTAAATTAAATATTTAAAATTAATAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
*
1967 GTCAAATCAACACAATATT
66 GTCAAATCAACACATTATT
* * * * *
1986 TGATAAAAATTGTAATATAATAATAATTGTTGATTTAAATATTTAAAATTAATAAATAATTTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
* *
2051 ATCAAATCAACATATTATT
66 GTCAAATCAACACATTATT
*
2070 TGATAAAAATTGTAATATAATAATATTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
*
2135 GTCAAATCAACATATTATT
66 GTCAAATCAACACATTATT
* * * * *
2154 TGATAAAAATTATAATATAATAATAATTATTGATTTAAATATTTAAAATTAATAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
* *
2219 GTCAAATCAATATATTATT
66 GTCAAATCAACACATTATT
* *
2238 TTATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAATTTAGTAAATAATATA
1 TGATAAAAATTGTAATATAATAATAAT--TTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
*
2303 TTGTCAAATTAACACATTATT
64 TTGTCAAATCAACACATTATT
* * * * * * *
2324 TGATAAAAATTTTAATATAATAATAATTATTGATTTAAATATTTAAAATTAATAAATAATATATC
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
*
2389 ATCAAATCAACACATTATT
66 GTCAAATCAACACATTATT
2408 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
1 TGATAAAAATTGTAATATAATAAT-A-ATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
*
2473 TTGTCAAATCAACATATTATT
64 TTGTCAAATCAACACATTATT
* * * *
2494 TGATAAAAATTGTAATATAATAATAATTGTTAATTTAAATATTTAAAATTAATAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
* *
2559 TTTAAATCAACACATTATT
66 GTCAAATCAACACATTATT
* *
2578 TGATAAAAATTGTAATATAATAATAATATTTTTTATTCAAATATTTAAATTGAGTAAATAATGTA
1 TGATAAAAATTGTAATATAATAAT-A-ATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
* *
2643 TTATGAAATCAACACATTATT
64 TTGTCAAATCAACACATTATT
*
2664 TGATAAAAATTATAATATAATAATAATCTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAA--TTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
2729 TTGTCAAATCAACACATTATT
64 TTGTCAAATCAACACATTATT
2750 TGATAAAAATTGTAATATAATAATAATCTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAA--TTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
2815 TTGTCAAATCAACACATTATT
64 TTGTCAAATCAACACATTATT
* *
2836 TGATAAGAATTGTAATATAATAATAATCTTTTTTATTTAAATATTTAAATTTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAA--TTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
2901 TTGTCAAATCAACACATTATT
64 TTGTCAAATCAACACATTATT
* * **
2922 TGATAAATATTGTAATATAAT-ATAA-TTTGTACTTTAAATATGAAAATTT-GATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATTTTTTA-TTTAAATATTTAAATTTAG-TAAATAATGTA
* *
2984 TTGTCAAATGAACACAATATT
64 TTGTCAAATCAACACATTATT
* *
3005 TGATATAAATTGTAATGTAATAATAATTTTTTATTTAAATAATGTTAAATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAAT-AT-TTAAATT
3056 AATTTTAAAT
Statistics
Matches: 971, Mismatches: 85, Indels: 26
0.90 0.08 0.02
Matches are distributed among these distances:
82 5 0.01
83 63 0.06
84 418 0.43
85 15 0.02
86 470 0.48
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (84 bp):
TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
GTCAAATCAACACATTATT
Found at i:2349 original size:170 final size:170
Alignment explanation
Indices: 1902--3058 Score: 1722
Period size: 170 Copynumber: 6.8 Consensus size: 170
1892 ATTTAAAATC
* * * * *
1902 TGATAAAAATTGTAATATAATAAT-A-ATTGTTAAATTAAATATTTAAAATTAATAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
* *
1965 TTGTCAAATCAACACAATATTTGATAAAAATTGTAATATAATAATAATTGTTGATTTAAATATTT
66 TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATATTT
* * *
2030 AAAATTAATAAATAATTTATTATCAAATCAACATATTATT
131 AAAATTAATAAATAATGTATTGTCAAATCAACACATTATT
2070 TGATAAAAATTGTAATATAATAAT-AT-TTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
* * *
2133 TTGTCAAATCAACATATTATTTGATAAAAATTATAATATAATAATAATTATTGATTTAAATATTT
66 TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATATTT
* *
2198 AAAATTAATAAATAATGTATTGTCAAATCAATATATTATT
131 AAAATTAATAAATAATGTATTGTCAAATCAACACATTATT
* * *
2238 TTATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAATTTAGTAAATAATATA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
* * *
2303 TTGTCAAATTAACACATTATTTGATAAAAATTTTAATATAATAATAATTATTGATTTAAATATTT
66 TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATATTT
* **
2368 AAAATTAATAAATAATATATCATCAAATCAACACATTATT
131 AAAATTAATAAATAATGTATTGTCAAATCAACACATTATT
2408 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
* * *
2473 TTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAATAATTGTTAATTTAAATATTT
66 TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATATTT
* *
2538 AAAATTAATAAATAATGTATTTTTAAATCAACACATTATT
131 AAAATTAATAAATAATGTATTGTCAAATCAACACATTATT
* *
2578 TGATAAAAATTGTAATATAATAATAATATTTTTTATTCAAATATTTAAATTGAGTAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
* * * *
2643 TTATGAAATCAACACATTATTTGATAAAAATTATAATATAATAATAATCTTTTTTATTTAAATAT
66 TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAA--TTTTTGATTTAAATAT
* *
2708 TTAAATTTAGTAAATAATGTATTGTCAAATCAACACATTATT
129 TTAAAATTAATAAATAATGTATTGTCAAATCAACACATTATT
*
2750 TGATAAAAATTGTAATATAATAATAATCTTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
1 TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
* *
2815 TTGTCAAATCAACACATTATTTGATAAGAATTGTAATATAATAATAATCTTTTTTATTTAAATAT
66 TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAA--TTTTTGATTTAAATAT
*
2880 TTAAATTTAATAAATAATGTATTGTCAAATCAACACATTATT
129 TTAAAATTAATAAATAATGTATTGTCAAATCAACACATTATT
* * **
2922 TGATAAATATTGTAATATAAT-AT-A-A-TTTGTACTTTAAATATGAAAATTT-GATAAATAATG
1 TGATAAAAATTGTAATATAATAATAATATTTTTTA-TTTAAATATTTAAATTTAG-TAAATAATG
* * * * *
2982 TATTGTCAAATGAACACAATATTTGATATAAATTGTAATGTAATAATAATTTTTTATTTAAATAA
64 TATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAAT-A
3047 TGTT-AAATTAAT
128 T-TTAAAATTAAT
3059 TTTAAATATA
Statistics
Matches: 914, Mismatches: 66, Indels: 18
0.92 0.07 0.02
Matches are distributed among these distances:
167 14 0.02
168 193 0.21
169 72 0.08
170 397 0.43
171 2 0.00
172 236 0.26
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (170 bp):
TGATAAAAATTGTAATATAATAATAATATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTA
TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTGATTTAAATATTT
AAAATTAATAAATAATGTATTGTCAAATCAACACATTATT
Found at i:6744 original size:31 final size:31
Alignment explanation
Indices: 6706--6765 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
6696 TTGCCACTTC
*
6706 ACATGACAGTATATAATTCAACTCCGAAAAT
1 ACATGACAGTATATAATTCAACCCCGAAAAT
*
6737 ACATGACAGTATATAGTTCAACCCCGAAA
1 ACATGACAGTATATAATTCAACCCCGAAA
6766 TTCGATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (31 bp):
ACATGACAGTATATAATTCAACCCCGAAAAT
Found at i:7042 original size:57 final size:57
Alignment explanation
Indices: 6958--7088 Score: 147
Period size: 56 Copynumber: 2.2 Consensus size: 57
6948 ATTACATGGT
** * *
6958 CAACACTAAAAAAATTTAAATTTTTATCAAATAAAAAGGGGGTGTCGGTCATGGCATAAC
1 CAACAC-AAAAAAA-TCGAATTTTTATCAAA-AAAAAGGGGATGTCAGTCATGGCATAAC
** * *
7018 CAACA-AAAAAAATCGAATTTTTATCTGACAAAAGGGGATGTCAGTCATGGCATGAC
1 CAACACAAAAAAATCGAATTTTTATCAAAAAAAAGGGGATGTCAGTCATGGCATAAC
7074 CAACACCAAAAAAAT
1 CAACA-CAAAAAAAT
7089 TTAAAATTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
56 29 0.48
57 12 0.20
58 15 0.25
60 5 0.08
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (57 bp):
CAACACAAAAAAATCGAATTTTTATCAAAAAAAAGGGGATGTCAGTCATGGCATAAC
Found at i:7113 original size:62 final size:61
Alignment explanation
Indices: 6965--7177 Score: 201
Period size: 62 Copynumber: 3.6 Consensus size: 61
6955 GGTCAACACT
** * * *
6965 AAAAAAATTT-AAA-TTTTTATCAAATAAAAAGGGGGTGTCGGTCATGGCATAACC-A-AC-A
1 AAAAAAATTTAAAATTTTTTATCTGA-AAAAA-GGGGTGTCAGCCATGGCATGACCAACACAA
** * * *
7023 AAAAAAA--TCGAA-TTTTTATCTGACAAAAGGGGATGTCAGTCATGGCATGACCAACAC-C
1 AAAAAAATTTAAAATTTTTTATCTGAAAAAAGGGG-TGTCAGCCATGGCATGACCAACACAA
* *
7081 AAAAAAATTTAAAATTTTTTTATCTGAAAAAAGGAGGTGTCGGCCATTGCATGACCAACACAA
1 AAAAAAATTTAAAA-TTTTTTATCTGAAAAAAGG-GGTGTCAGCCATGGCATGACCAACACAA
*
7144 AAAAAAATTTAAAATTTTTTATCTGAGAAAAGGG
1 AAAAAAATTTAAAATTTTTTATCTGAAAAAAGGG
7178 CCAACACCCA
Statistics
Matches: 130, Mismatches: 15, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
55 4 0.03
56 22 0.17
57 12 0.09
58 16 0.12
60 3 0.02
61 1 0.01
62 56 0.43
63 16 0.12
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (61 bp):
AAAAAAATTTAAAATTTTTTATCTGAAAAAAGGGGTGTCAGCCATGGCATGACCAACACAA
Found at i:7326 original size:108 final size:102
Alignment explanation
Indices: 7094--7457 Score: 387
Period size: 105 Copynumber: 3.5 Consensus size: 102
7084 AAAATTTAAA
* * * *
7094 ATTTTTTTATCTGA-AAAAAGGAGGTGTCGGCCATTGCATGACCAACACAAAAAAAAATTTAAAA
1 ATTTTTTTATCAGATAAATAGG-GGTGTCGGCCATTGTATGGCCAACAC-AAAAAAAA-TT-AAA
* *
7158 TTTTTTATCTG----AGAAAAGGGCCAACACCCAAAAATTTG
62 -TTTTTATCTGACAAAAAAAATGGCCAACACCCAAAAATTTG
*
7196 ATTTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGTATGGCCGACATCGACACCAAAAAATTA
1 A-TTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGTATGGCC-A-A-C-ACA-AAAAAAATTA
* *
7261 AATTTTTTATCTGATAAAAAAAATGGCCAACACCAAAAAATTTG
60 AA-TTTTTATCTGACAAAAAAAATGGCCAACACCCAAAAATTTG
* * **
7305 ATTTTTTTATCAGATGAATAGGGGTGTCGACCATTGTATGGCCAACACAAAAAAAATTGTATTTT
1 ATTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGTATGGCCAACACAAAAAAAATTAAATTTT
*
7370 TATCTGACAAAAAAGGCAATGGCCGACACCCAAAAATTTG
66 TATCTGACAAAAAA---AATGGCCAACACCCAAAAATTTG
* * * *
7410 ATTTTTTTATCAAATTAAAAAGGGGTGTCGGCCATTGCATGACCAACA
1 ATTTTTTTATCAGA-TAAATAGGGGTGTCGGCCATTGTATGGCCAACA
7458 TCCAAATTTT
Statistics
Matches: 225, Mismatches: 22, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
102 18 0.08
103 40 0.18
104 10 0.04
105 50 0.22
106 33 0.15
107 9 0.04
108 40 0.18
109 25 0.11
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (102 bp):
ATTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGTATGGCCAACACAAAAAAAATTAAATTTT
TATCTGACAAAAAAAATGGCCAACACCCAAAAATTTG
Found at i:8086 original size:21 final size:21
Alignment explanation
Indices: 8061--8101 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
8051 TTCAAATCTA
*
8061 AAAAATAGATTAACTAATTTT
1 AAAAATAGATCAACTAATTTT
8082 AAAAATAGATCAACTAATTT
1 AAAAATAGATCAACTAATTT
8102 CCAAATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAAATAGATCAACTAATTTT
Found at i:14426 original size:86 final size:83
Alignment explanation
Indices: 14281--14558 Score: 398
Period size: 86 Copynumber: 3.3 Consensus size: 83
14271 NNNNNNNNNN
*
14281 TTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAG
1 TTTTTTATTTAAATATTTAAATTTAATAAATAATGTATTGTCAAATCAACACATTATTTGATAA-
14346 AATTGTAATATAATAATAA
65 AATTGTAATATAATAATAA
14365 TCTTTTTTATTTAAATATTTAAATTTAATAAATAATGTATTGTCAAATCAACACATTATTTGATA
1 --TTTTTTATTTAAATATTTAAATTTAATAAATAATGTATTGTCAAATCAACACATTATTTGATA
14430 AATATTGTAATATAAT-ATAA
64 AA-ATTGTAATATAATAATAA
* ** * * *
14450 -TTTGTACTTTAAATATGAAAATTTGATAAATAATGTATTGTCAAATGAACACAATATTTGATAT
1 TTTTTTA-TTTAAATATTTAAATTTAATAAATAATGTATTGTCAAATCAACACATTATTTGATA-
*
14514 AAATTGTAATGTAATAATAA
64 AAATTGTAATATAATAATAA
14534 TTTTTTATTTAAATAATGTTAAATT
1 TTTTTTATTTAAAT-AT-TTAAATT
14559 AATTTTAAAT
Statistics
Matches: 174, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
82 5 0.03
83 63 0.36
84 13 0.07
85 12 0.07
86 81 0.47
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (83 bp):
TTTTTTATTTAAATATTTAAATTTAATAAATAATGTATTGTCAAATCAACACATTATTTGATAAA
ATTGTAATATAATAATAA
Found at i:18229 original size:31 final size:31
Alignment explanation
Indices: 18191--18250 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
18181 TTGCCACTTC
*
18191 ACATGACAGTATATAATTCAACTCCGAAAAT
1 ACATGACAGTATATAATTCAACCCCGAAAAT
*
18222 ACATGACAGTATATAGTTCAACCCCGAAA
1 ACATGACAGTATATAATTCAACCCCGAAA
18251 TTCGATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (31 bp):
ACATGACAGTATATAATTCAACCCCGAAAAT
Found at i:18527 original size:57 final size:57
Alignment explanation
Indices: 18443--18573 Score: 147
Period size: 56 Copynumber: 2.2 Consensus size: 57
18433 ATTACATGGT
** * *
18443 CAACACTAAAAAAATTTAAATTTTTATCAAATAAAAAGGGGGTGTCGGTCATGGCATAAC
1 CAACAC-AAAAAAA-TCGAATTTTTATCAAA-AAAAAGGGGATGTCAGTCATGGCATAAC
** * *
18503 CAACA-AAAAAAATCGAATTTTTATCTGACAAAAGGGGATGTCAGTCATGGCATGAC
1 CAACACAAAAAAATCGAATTTTTATCAAAAAAAAGGGGATGTCAGTCATGGCATAAC
18559 CAACACCAAAAAAAT
1 CAACA-CAAAAAAAT
18574 TTAAAATTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
56 29 0.48
57 12 0.20
58 15 0.25
60 5 0.08
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.23
Consensus pattern (57 bp):
CAACACAAAAAAATCGAATTTTTATCAAAAAAAAGGGGATGTCAGTCATGGCATAAC
Found at i:18598 original size:62 final size:61
Alignment explanation
Indices: 18450--18662 Score: 201
Period size: 62 Copynumber: 3.6 Consensus size: 61
18440 GGTCAACACT
** * * *
18450 AAAAAAATTT-AAA-TTTTTATCAAATAAAAAGGGGGTGTCGGTCATGGCATAACC-A-AC-A
1 AAAAAAATTTAAAATTTTTTATCTGA-AAAAA-GGGGTGTCAGCCATGGCATGACCAACACAA
** * * *
18508 AAAAAAA--TCGAA-TTTTTATCTGACAAAAGGGGATGTCAGTCATGGCATGACCAACAC-C
1 AAAAAAATTTAAAATTTTTTATCTGAAAAAAGGGG-TGTCAGCCATGGCATGACCAACACAA
* *
18566 AAAAAAATTTAAAATTTTTTTATCTGAAAAAAGGAGGTGTCGGCCATTGCATGACCAACACAA
1 AAAAAAATTTAAAA-TTTTTTATCTGAAAAAAGG-GGTGTCAGCCATGGCATGACCAACACAA
*
18629 AAAAAAATTTAAAATTTTTTATCTGAGAAAAGGG
1 AAAAAAATTTAAAATTTTTTATCTGAAAAAAGGG
18663 CCAACACCCA
Statistics
Matches: 130, Mismatches: 15, Indels: 17
0.80 0.09 0.10
Matches are distributed among these distances:
55 4 0.03
56 22 0.17
57 12 0.09
58 16 0.12
60 3 0.02
61 1 0.01
62 56 0.43
63 16 0.12
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.26
Consensus pattern (61 bp):
AAAAAAATTTAAAATTTTTTATCTGAAAAAAGGGGTGTCAGCCATGGCATGACCAACACAA
Found at i:18811 original size:108 final size:102
Alignment explanation
Indices: 18579--18942 Score: 387
Period size: 105 Copynumber: 3.5 Consensus size: 102
18569 AAAATTTAAA
* * * *
18579 ATTTTTTTATCTGA-AAAAAGGAGGTGTCGGCCATTGCATGACCAACACAAAAAAAAATTTAAAA
1 ATTTTTTTATCAGATAAATAGG-GGTGTCGGCCATTGTATGGCCAACAC-AAAAAAAA-TT-AAA
* *
18643 TTTTTTATCTG----AGAAAAGGGCCAACACCCAAAAATTTG
62 -TTTTTATCTGACAAAAAAAATGGCCAACACCCAAAAATTTG
*
18681 ATTTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGTATGGCCGACATCGACACCAAAAAATTA
1 A-TTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGTATGGCC-A-A-C-ACA-AAAAAAATTA
* *
18746 AATTTTTTATCTGATAAAAAAAATGGCCAACACCAAAAAATTTG
60 AA-TTTTTATCTGACAAAAAAAATGGCCAACACCCAAAAATTTG
* * **
18790 ATTTTTTTATCAGATGAATAGGGGTGTCGACCATTGTATGGCCAACACAAAAAAAATTGTATTTT
1 ATTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGTATGGCCAACACAAAAAAAATTAAATTTT
*
18855 TATCTGACAAAAAAGGCAATGGCCGACACCCAAAAATTTG
66 TATCTGACAAAAAA---AATGGCCAACACCCAAAAATTTG
* * * *
18895 ATTTTTTTATCAAATTAAAAAGGGGTGTCGGCCATTGCATGACCAACA
1 ATTTTTTTATCAGA-TAAATAGGGGTGTCGGCCATTGTATGGCCAACA
18943 TCCAAATTTT
Statistics
Matches: 225, Mismatches: 22, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
102 18 0.08
103 40 0.18
104 10 0.04
105 50 0.22
106 33 0.15
107 9 0.04
108 40 0.18
109 25 0.11
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (102 bp):
ATTTTTTTATCAGATAAATAGGGGTGTCGGCCATTGTATGGCCAACACAAAAAAAATTAAATTTT
TATCTGACAAAAAAAATGGCCAACACCCAAAAATTTG
Found at i:19571 original size:21 final size:21
Alignment explanation
Indices: 19546--19586 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
19536 TTCAAATCTA
*
19546 AAAAATAGATTAACTAATTTT
1 AAAAATAGATCAACTAATTTT
19567 AAAAATAGATCAACTAATTT
1 AAAAATAGATCAACTAATTT
19587 CCAAATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (21 bp):
AAAAATAGATCAACTAATTTT
Found at i:28918 original size:16 final size:16
Alignment explanation
Indices: 28869--28920 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
28859 TTAAAAAATC
28869 TATAAAAATATTTTAAA
1 TATAAAAATA-TTTAAA
* * *
28886 AAT-AATATTTTTAAAA
1 TATAAAAATATTT-AAA
28902 TATAAAAATATTTAAA
1 TATAAAAATATTTAAA
28918 TAT
1 TAT
28921 GTATAAATCT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
15 3 0.11
16 15 0.56
17 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATAAAAATATTTAAA
Found at i:28951 original size:26 final size:25
Alignment explanation
Indices: 28905--28969 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 25
28895 TTTAAAATAT
28905 AAAAATATTTAAATATGTATAAATCTAA
1 AAAAAT-TTTAAATATGTAT-AA-CTAA
28933 AAAAATTCTTAAA-AT-TATAACTAA
1 AAAAATT-TTAAATATGTATAACTAA
28957 AAAAACTTTTAAA
1 AAAAA-TTTTAAA
28970 CTAACATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
24 14 0.40
25 4 0.11
26 3 0.09
27 3 0.09
28 11 0.31
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (25 bp):
AAAAATTTTAAATATGTATAACTAA
Found at i:35587 original size:6 final size:6
Alignment explanation
Indices: 35576--35607 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
35566 AGATTCTGAT
*
35576 GACCAA GACCAA GACCAA GACCAA GACGAA GA
1 GACCAA GACCAA GACCAA GACCAA GACCAA GA
35608 AGAAGCAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.50, C:0.28, G:0.22, T:0.00
Consensus pattern (6 bp):
GACCAA
Found at i:38245 original size:13 final size:14
Alignment explanation
Indices: 38227--38278 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
38217 AAATTCCAAC
38227 TATAATA-ATATAA
1 TATAATATATATAA
*
38240 TATAATTTA-ATAA
1 TATAATATATATAA
*
38253 TATAATATTATATAT
1 TATAATA-TATATAA
*
38268 TATAGTATATA
1 TATAATATATA
38279 ATGTTGGGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 16 0.50
14 7 0.22
15 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (14 bp):
TATAATATATATAA
Found at i:50316 original size:89 final size:91
Alignment explanation
Indices: 50223--50389 Score: 216
Period size: 89 Copynumber: 1.9 Consensus size: 91
50213 GAAAATAAAA
* * *
50223 ATTAAGTTCAAAATTTATGAATTTAATTATTATTGTTTGGATCA-AG-A-GTAAAATTATAAAAA
1 ATTAAATTCAAAACTTATAAATTTAATTATTATTGTTTGGATCATAGAATGTAAAATTATAAAAA
50285 TTAAAAAAAT-CAAATTAAAGAACATAG
66 --AAAAAAATACAAATTAAAGAACATAG
** * * *
50312 ATTAAATTTGAAACTTATAAATTTAATTGTTATTGTTTGGATCATAGAATTTAAAATTTTAAAAA
1 ATTAAATTCAAAACTTATAAATTTAATTATTATTGTTTGGATCATAGAATGTAAAATTATAAAAA
50377 AAAAAAATACAAA
66 AAAAAAATACAAA
50390 AGCTAAAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
89 38 0.58
90 10 0.15
91 5 0.08
92 13 0.20
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (91 bp):
ATTAAATTCAAAACTTATAAATTTAATTATTATTGTTTGGATCATAGAATGTAAAATTATAAAAA
AAAAAAATACAAATTAAAGAACATAG
Done.