Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012008.1 Kokia drynarioides strain JFW-HI SEQ_127006, 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: 87532
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Warning! 122 characters in sequence are not A, C, G, or T
Found at i:3368 original size:25 final size:23
Alignment explanation
Indices: 3325--3370 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
3315 CCAAATAGGG
3325 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
3348 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
3371 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:10027 original size:23 final size:21
Alignment explanation
Indices: 10001--10043 Score: 68
Period size: 23 Copynumber: 2.0 Consensus size: 21
9991 TATCTGTTTT
10001 ATTATCTATATTCAACATATGTA
1 ATTATCTATA-TCAACA-ATGTA
10024 ATTATCTATATCAACAATGT
1 ATTATCTATATCAACAATGT
10044 TGTATTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 6 0.30
23 10 0.50
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTATCTATATCAACAATGTA
Found at i:13517 original size:30 final size:30
Alignment explanation
Indices: 13483--13587 Score: 104
Period size: 30 Copynumber: 3.3 Consensus size: 30
13473 TTAGAAAGGT
13483 TTGGACAAAATTATTAGGCCCGAAATGGGC
1 TTGGACAAAATTATTAGGCCCGAAATGGGC
* * * * *
13513 TTGGACAAAA-AAATAGACCCGTTTAAAATAATGGT
1 TTGGACAAAATTATTAGGCCCG----AAAT--GGGC
13548 TTGGACAAAATTATTAGGCCCGAAATGGGC
1 TTGGACAAAATTATTAGGCCCGAAATGGGC
13578 TTGGACAAAA
1 TTGGACAAAA
13588 AAAAATAGAC
Statistics
Matches: 58, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
29 8 0.14
30 22 0.38
32 4 0.07
33 4 0.07
35 12 0.21
36 8 0.14
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.24
Consensus pattern (30 bp):
TTGGACAAAATTATTAGGCCCGAAATGGGC
Found at i:13584 original size:65 final size:65
Alignment explanation
Indices: 13480--13608 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
13470 AATTTAGAAA
*
13480 GGTTTGGACAAAATTATTAGGCCCGAAATGGGCTTGGAC-AAAAAAATAGACCCGTTTAAAATAA
1 GGTTTGGACAAAATTATTAGGCCCGAAATGGGCTTGGACAAAAAAAATAGACCC-ATTAAAATAA
13544 T
65 T
13545 GGTTTGGACAAAATTATTAGGCCCGAAATGGGCTTGGACAAAAAAAAATAGACCCATTAAAATA
1 GGTTTGGACAAAATTATTAGGCCCGAAATGGGCTTGGAC-AAAAAAAATAGACCCATTAAAATA
13609 TGAGACAGTT
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
65 39 0.64
66 8 0.13
67 14 0.23
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.23
Consensus pattern (65 bp):
GGTTTGGACAAAATTATTAGGCCCGAAATGGGCTTGGACAAAAAAAATAGACCCATTAAAATAAT
Found at i:13818 original size:21 final size:21
Alignment explanation
Indices: 13784--13826 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
13774 TTAATTAAAT
* *
13784 ATTATAATTGAAATTTTTTAA
1 ATTATAATTAAAATATTTTAA
*
13805 ATTATCATTAAAATATTTTAA
1 ATTATAATTAAAATATTTTAA
13826 A
1 A
13827 CATATTCAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTATAATTAAAATATTTTAA
Found at i:14434 original size:28 final size:30
Alignment explanation
Indices: 14376--14434 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
14366 TAATATATTC
* * *
14376 AACATGCAAAATAGTTTTTTTTTTGTGATA
1 AACATACAAAATAGTTTTTATTTTGAGATA
14406 AACATACAAAATAG-TTTTATTTT-AGATA
1 AACATACAAAATAGTTTTTATTTTGAGATA
14434 A
1 A
14435 TTAATGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 5 0.19
29 8 0.31
30 13 0.50
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (30 bp):
AACATACAAAATAGTTTTTATTTTGAGATA
Found at i:14611 original size:6 final size:6
Alignment explanation
Indices: 14587--14636 Score: 66
Period size: 6 Copynumber: 8.3 Consensus size: 6
14577 GTCAAAAATA
* *
14587 ATAATT GTAATTT ATAATT ACAATT A-AATT ATAATT ATAATT ATAATT
1 ATAATT ATAA-TT ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT
14635 AT
1 AT
14637 CACAAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
5 5 0.13
6 29 0.74
7 5 0.13
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:14628 original size:23 final size:24
Alignment explanation
Indices: 14589--14635 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
14579 CAAAAATAAT
*
14589 AATTGTAATTTATAATTACAATTA
1 AATTATAATTTATAATTACAATTA
*
14613 AATTATAA-TTATAATTATAATTA
1 AATTATAATTTATAATTACAATTA
14636 TCACAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (24 bp):
AATTATAATTTATAATTACAATTA
Found at i:17590 original size:27 final size:28
Alignment explanation
Indices: 17525--17605 Score: 94
Period size: 27 Copynumber: 2.9 Consensus size: 28
17515 ACATTAAAAT
17525 AATATTAAAATGACTATATAAAAAT-TTAC
1 AATATTAAAAT-A-TATATAAAAATATTAC
*
17554 AATAAATAAAATATATATAAAAATATTA-
1 AAT-ATTAAAATATATATAAAAATATTAC
* *
17582 AATATTAAAATAAATTTAAAAATA
1 AATATTAAAATATATATAAAAATA
17606 ATATAGACGA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
27 18 0.39
28 14 0.30
29 7 0.15
30 7 0.15
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (28 bp):
AATATTAAAATATATATAAAAATATTAC
Found at i:18022 original size:21 final size:20
Alignment explanation
Indices: 17998--18036 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17988 TTAATTTAAA
17998 ATTTTAAAAAAATTAAAAACT
1 ATTTT-AAAAAATTAAAAACT
*
18019 ATTTTTAAAAATTAAAAA
1 ATTTTAAAAAATTAAAAA
18037 TCATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTTTAAAAAATTAAAAACT
Found at i:18435 original size:15 final size:14
Alignment explanation
Indices: 18415--18466 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
18405 CAATCTTTCT
18415 ATTTTAATTTAGTTA
1 ATTTTAATTT-GTTA
18430 ATTTTAATTT-TATA
1 ATTTTAATTTGT-TA
*
18444 ATTTTAAATTGGTTA
1 ATTTT-AATTTGTTA
18459 ATTTTAAT
1 ATTTTAAT
18467 GTTTGTACCT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
13 1 0.03
14 10 0.30
15 21 0.64
16 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (14 bp):
ATTTTAATTTGTTA
Found at i:23356 original size:2 final size:2
Alignment explanation
Indices: 23349--23381 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
23339 ATGATAGGGG
23349 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
23382 GGGAGCTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:24340 original size:2 final size:2
Alignment explanation
Indices: 24335--24359 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24325 ATATATATAT
24335 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
24360 AAGAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25366 original size:21 final size:21
Alignment explanation
Indices: 25342--25385 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
25332 AAACTACAAC
25342 AAGC-CAAATATAAAAGTGAAA
1 AAGCACAAATAT-AAAGTGAAA
* *
25363 AAGCAGAAATATAAAGTTAAA
1 AAGCACAAATATAAAGTGAAA
25384 AA
1 AA
25386 AGAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.16
Consensus pattern (21 bp):
AAGCACAAATATAAAGTGAAA
Found at i:29189 original size:141 final size:146
Alignment explanation
Indices: 28920--29228 Score: 359
Period size: 141 Copynumber: 2.2 Consensus size: 146
28910 GGGGTTTTGG
** *
28920 GAGTAAAA-TTTTGAGGGAAAGTAAATAGGGGGAGTAAAATTTTAGAAGGAAAATATTCAAAAAA
1 GAGTAAAAGTTTT-AGGGAAAAAAAATAGGGGGAGTAAAATTTTAGAAGAAAAATATTCAAAAAA
* * * * * *
28984 AATTTGGGAGGGGGGAATGGGTTTGGGGTAGATAGAGGGTTGGATAGGAGGGGAATAAAAGTTTT
65 AATATGGGAGGAGGAAATGAGTTTGGGGTAGATAGAGGGGTGGATAGCAGGGGAATAAAAGTTTT
29049 AGGGGG-AAAGTGAG-AAA
130 -GGGGGAAAAGTG-GTAAA
* * * *
29066 GAGTAGAAGTTTT-GGGAAAAAAAATTGGGGGAGTAAAATTTTGGATGAAAAATATT-AAAAAAA
1 GAGTAAAAGTTTTAGGGAAAAAAAATAGGGGGAGTAAAATTTTAGAAGAAAAATATTCAAAAAAA
* *
29129 A-AT-GG-GGAGGAAATGAGTTTGGGGTAGAT-GGGGGGTGAGAT-GACAGGGGAGTAAAAGTTT
66 ATATGGGAGGAGGAAATGAGTTTGGGGTAGATAGAGGGGTG-GATAG-CAGGGGAATAAAAGTTT
*
29189 TGGGGGAAAAGTGGTAAG
129 TGGGGGAAAAGTGGTAAA
29207 GAGTAAAAGTTTTAGGGAAAAA
1 GAGTAAAAGTTTTAGGGAAAAA
29229 GTAAAAAATA
Statistics
Matches: 140, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
140 13 0.09
141 60 0.43
142 10 0.07
143 1 0.01
144 8 0.06
145 37 0.26
146 7 0.05
147 4 0.03
ACGTcount: A:0.40, C:0.01, G:0.37, T:0.23
Consensus pattern (146 bp):
GAGTAAAAGTTTTAGGGAAAAAAAATAGGGGGAGTAAAATTTTAGAAGAAAAATATTCAAAAAAA
ATATGGGAGGAGGAAATGAGTTTGGGGTAGATAGAGGGGTGGATAGCAGGGGAATAAAAGTTTTG
GGGGAAAAGTGGTAAA
Found at i:29193 original size:16 final size:16
Alignment explanation
Indices: 29175--29224 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
29165 GAGATGACAG
29175 GGGAGTAAAAGTTTT-
1 GGGAGTAAAAGTTTTA
* **
29190 GGG-GGAAAAGTGGTA
1 GGGAGTAAAAGTTTTA
*
29205 AGGAGTAAAAGTTTTA
1 GGGAGTAAAAGTTTTA
29221 GGGA
1 GGGA
29225 AAAAGTAAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 3
0.69 0.22 0.08
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 12 0.48
ACGTcount: A:0.36, C:0.00, G:0.40, T:0.24
Consensus pattern (16 bp):
GGGAGTAAAAGTTTTA
Found at i:32675 original size:24 final size:26
Alignment explanation
Indices: 32633--32681 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
32623 TACATATTGC
32633 ATATAAAAATAATTATATTAATTTAA
1 ATATAAAAATAATTATATTAATTTAA
* *
32659 ATATAAATA-AATT-TATTTATTTA
1 ATATAAAAATAATTATATTAATTTA
32682 TTTTTATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 4 0.19
26 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATATAAAAATAATTATATTAATTTAA
Found at i:37170 original size:45 final size:45
Alignment explanation
Indices: 37106--37198 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
37096 AATGGAAGAC
37106 AATAATGATTTTGTTCATATAAGCGAACGATCTTACCGTATGAGA
1 AATAATGATTTTGTTCATATAAGCGAACGATCTTACCGTATGAGA
*
37151 AATAATGATTTTGTTCATATAAGCGAATGATCTTACCGTATGAGA
1 AATAATGATTTTGTTCATATAAGCGAACGATCTTACCGTATGAGA
37196 AAT
1 AAT
37199 CATTATGGAC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (45 bp):
AATAATGATTTTGTTCATATAAGCGAACGATCTTACCGTATGAGA
Found at i:46962 original size:16 final size:14
Alignment explanation
Indices: 46928--46974 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
46918 TTATGAAAGT
* *
46928 TTAT-AATTTTTTT
1 TTATAAATTTTATA
46941 TTATAAATATTATATA
1 TTATAAAT-TT-TATA
46957 TTATAAATTTTATA
1 TTATAAATTTTATA
46971 TTAT
1 TTAT
46975 TTTTTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 4 0.14
14 11 0.38
15 4 0.14
16 10 0.34
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATAAATTTTATA
Found at i:52734 original size:17 final size:17
Alignment explanation
Indices: 52706--52740 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
52696 GTATATTACC
52706 TAAAATTAATTA-ATTA
1 TAAAATTAATTAGATTA
52722 TAAAATATAATTAGATTA
1 TAAAAT-TAATTAGATTA
52740 T
1 T
52741 TTTATAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 6 0.35
18 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TAAAATTAATTAGATTA
Found at i:55834 original size:14 final size:14
Alignment explanation
Indices: 55811--55840 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55801 TTTGTTTTAA
*
55811 TTAAATTTAGGGTT
1 TTAAAATTAGGGTT
55825 TTAAAATTAGGGTT
1 TTAAAATTAGGGTT
55839 TT
1 TT
55841 GGTATTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (14 bp):
TTAAAATTAGGGTT
Found at i:55857 original size:21 final size:22
Alignment explanation
Indices: 55823--55880 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
55813 AAATTTAGGG
*
55823 TTTTAAAATTAGGGTTTTG-GTA
1 TTTT-AAATAAGGGTTTTGAGTA
55845 TTTTAAATAAGGG--TTGAGTA
1 TTTTAAATAAGGGTTTTGAGTA
55865 TTTTAAATTAAGGGTT
1 TTTTAAA-TAAGGGTT
55881 ATGAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.10
20 10 0.32
21 14 0.45
22 4 0.13
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (22 bp):
TTTTAAATAAGGGTTTTGAGTA
Found at i:55867 original size:20 final size:21
Alignment explanation
Indices: 55842--55880 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
55832 TAGGGTTTTG
55842 GTATTTTAAA-TAAGGGTTGA
1 GTATTTTAAATTAAGGGTTGA
55862 GTATTTTAAATTAAGGGTT
1 GTATTTTAAATTAAGGGTT
55881 ATGAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.44
Consensus pattern (21 bp):
GTATTTTAAATTAAGGGTTGA
Found at i:59183 original size:62 final size:63
Alignment explanation
Indices: 59083--59211 Score: 206
Period size: 62 Copynumber: 2.1 Consensus size: 63
59073 TTGGTTCTCA
*
59083 ATTAAATGAAACAATATGTTAAAAACTAATGTGTACAAAAATATTCAAATGAACTTAAATTTT
1 ATTAAATGAAACAATATGTCAAAAACTAATGTGTACAAAAATATTCAAATGAACTTAAATTTT
* * **
59146 ATTAAATGAAACAATATG-CCAAAACTAATGTGTACAAAAATATTCAAATGAATTTCGATTTT
1 ATTAAATGAAACAATATGTCAAAAACTAATGTGTACAAAAATATTCAAATGAACTTAAATTTT
59208 ATTA
1 ATTA
59212 TCGACAGAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
62 43 0.70
63 18 0.30
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (63 bp):
ATTAAATGAAACAATATGTCAAAAACTAATGTGTACAAAAATATTCAAATGAACTTAAATTTT
Found at i:59304 original size:19 final size:19
Alignment explanation
Indices: 59280--59321 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
59270 TCAAAATTTT
59280 GAGAATTTTGAAAGCTTTA
1 GAGAATTTTGAAAGCTTTA
*
59299 GAGAATTTTGAGAGCTTTA
1 GAGAATTTTGAAAGCTTTA
59318 GAGA
1 GAGA
59322 GAAATTGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (19 bp):
GAGAATTTTGAAAGCTTTA
Found at i:59357 original size:23 final size:23
Alignment explanation
Indices: 59314--59359 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
59304 TTTTGAGAGC
*
59314 TTTAGAGAGAAATTGGTGTGAAA
1 TTTAGAGAGAAATTGGAGTGAAA
59337 TTTAGAGAGAAAATT-GAGTGAAA
1 TTTAGAGAG-AAATTGGAGTGAAA
59360 ATAATAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.28
Consensus pattern (23 bp):
TTTAGAGAGAAATTGGAGTGAAA
Found at i:62186 original size:17 final size:18
Alignment explanation
Indices: 62152--62186 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
62142 ATCTTAGTTT
*
62152 AGGATTTTTATCATTTAA
1 AGGAGTTTTATCATTTAA
62170 AGGAGTTTTAT-ATTTAA
1 AGGAGTTTTATCATTTAA
62187 TTATTAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (18 bp):
AGGAGTTTTATCATTTAA
Found at i:71391 original size:93 final size:94
Alignment explanation
Indices: 71130--71414 Score: 434
Period size: 97 Copynumber: 3.0 Consensus size: 94
71120 CAACTTGCTG
71130 AGGCCTAAGGTGGTCGGTTTTGCAATAAACATACAGTGTTCTGCACCAATGGTCCTTTTGTTGCT
1 AGGCCTAAGGTGGTCGGTTTTGCAATAAACATACAGTGTTCTGCACCAATGGTCCTTTTGTTGCT
71195 AGTATTTTCTGTTTAAACCTCGGTGAATGATGCTA
66 AGTATTTTCTGTTTAAACCTCGGTG-A--A---TA
* *
71230 AGGCCTAAGGTGGT-TGTTTTGCAATAAACATACA--GTTCTGCACTAATGGTCCTTTTGTTGCT
1 AGGCCTAAGGTGGTCGGTTTTGCAATAAACATACAGTGTTCTGCACCAATGGTCCTTTTGTTGCT
71292 AGTA-TTTCTGTTTAAACCTCGGTGAATA
66 AGTATTTTCTGTTTAAACCTCGGTGAATA
* *
71320 AGGCCTAAGGTGGTCGGTTTTGCAATAAACAGACAGTGTTCTGCACCAATGGTCCTTTTGTTGCC
1 AGGCCTAAGGTGGTCGGTTTTGCAATAAACATACAGTGTTCTGCACCAATGGTCCTTTTGTTGCT
* *
71385 ATTATTTTCTGTTTAAACCTTGGTGAATA
66 AGTATTTTCTGTTTAAACCTCGGTGAATA
71414 A
1 A
71415 TTTTAACTGT
Statistics
Matches: 173, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
90 16 0.09
91 18 0.10
93 30 0.17
94 24 0.14
95 1 0.01
96 20 0.12
97 31 0.18
99 19 0.11
100 14 0.08
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (94 bp):
AGGCCTAAGGTGGTCGGTTTTGCAATAAACATACAGTGTTCTGCACCAATGGTCCTTTTGTTGCT
AGTATTTTCTGTTTAAACCTCGGTGAATA
Found at i:72229 original size:12 final size:12
Alignment explanation
Indices: 72212--72241 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
72202 CCGGTGACGG
72212 TTGCATCTGACA
1 TTGCATCTGACA
72224 TTGCATCTGACA
1 TTGCATCTGACA
72236 TGTGCA
1 T-TGCA
72242 AGTTCGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (12 bp):
TTGCATCTGACA
Found at i:72837 original size:36 final size:36
Alignment explanation
Indices: 72769--72840 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
72759 GCACATCAAT
72769 ATTTTCGATAATTAATTTTCAAAAGAAAATATTTTCG
1 ATTTTCGATAATT-ATTTTCAAAAGAAAATATTTTCG
*
72806 ATTTTTGATAATT-TTATTCAAAA-AAATATATTTTC
1 ATTTTCGATAATTATT-TTCAAAAGAAA-ATATTTTC
72841 AATAATTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
35 5 0.16
36 15 0.47
37 12 0.38
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (36 bp):
ATTTTCGATAATTATTTTCAAAAGAAAATATTTTCG
Found at i:76970 original size:22 final size:24
Alignment explanation
Indices: 76932--76988 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 24
76922 AAATTTTAAA
76932 TATTAAAAATATATTTTTAT-AATT
1 TATTAAAAATATATTTTT-TGAATT
76956 T-TTAAAAATAT-TTTTTTGAATT
1 TATTAAAAATATATTTTTTGAATT
76978 TAATTAAAAAT
1 T-ATTAAAAAT
76989 TTAAAATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.03
22 10 0.33
23 10 0.33
24 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TATTAAAAATATATTTTTTGAATT
Found at i:83734 original size:57 final size:57
Alignment explanation
Indices: 83660--83767 Score: 207
Period size: 57 Copynumber: 1.9 Consensus size: 57
83650 GATATCATTA
83660 ATCTCTTTAGGAAAATTTTGTTCATCTAATATGATCTTATTTTATCTCATGGCAACT
1 ATCTCTTTAGGAAAATTTTGTTCATCTAATATGATCTTATTTTATCTCATGGCAACT
*
83717 ATCTCTTTAGGATAATTTTGTTCATCTAATATGATCTTATTTTATCTCATG
1 ATCTCTTTAGGAAAATTTTGTTCATCTAATATGATCTTATTTTATCTCATG
83768 AAAACAATTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (57 bp):
ATCTCTTTAGGAAAATTTTGTTCATCTAATATGATCTTATTTTATCTCATGGCAACT
Found at i:84823 original size:223 final size:223
Alignment explanation
Indices: 84431--84865 Score: 719
Period size: 223 Copynumber: 2.0 Consensus size: 223
84421 TCACGGATCA
* * * * *
84431 TGGATCAAAGCCCGTGATTATTATGCATGAAACATCCTATGGAGGTTAATTGATGTTCTTTTTTA
1 TGGATCAAAGCCCGTGATCATTATGAATGAAACATCCCATGGAGGTTAACTGATGTTCCTTTTTA
* *
84496 TAATGATAGTCCTCAAAGGCTAATTGTTAAGGCAATTTGGAAGATTTCATGCTAACCGAAGATCC
66 TAATGATAGTCCTCAAAGGCCAATTGTTAAGGCAATTTGGAAGATTTCATGCCAACCGAAGATCC
** * *
84561 AACACTTTTTTTGGTTGGATTGGAAAGATATGACTCATGACAAATACAAGTCGTATATTTTGACG
131 AACACTTCCTTCGGTTGGATTGGAAAGATAAGACTCATGACAAATACAAGTCGTATATTTTGACG
84626 TCTAACTATAGATGAGACTCATGGATTG
196 TCTAACTATAGATGAGACTCATGGATTG
*
84654 TGGATCAAAGCCCGTGATCATTGTGAATGAAACATCCCATGGAGGTTAACTGATGTTCCTTTTTA
1 TGGATCAAAGCCCGTGATCATTATGAATGAAACATCCCATGGAGGTTAACTGATGTTCCTTTTTA
*
84719 TAATGATAGTCCTCAATGGCCAATTGTTAAGGCAATTTGGAAGATTTCATGCCAACCGAAGATCC
66 TAATGATAGTCCTCAAAGGCCAATTGTTAAGGCAATTTGGAAGATTTCATGCCAACCGAAGATCC
*
84784 AACACTTCCTTCGGTTGGATTGGAAAGATAA-AGCTCATGATAAATACAAGTCGTATATTTTGAC
131 AACACTTCCTTCGGTTGGATTGGAAAGATAAGA-CTCATGACAAATACAAGTCGTATATTTTGAC
*
84848 GTTTAACTATAGATGAGA
195 GTCTAACTATAGATGAGA
84866 GTTGTAATAT
Statistics
Matches: 196, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
222 1 0.01
223 195 0.99
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (223 bp):
TGGATCAAAGCCCGTGATCATTATGAATGAAACATCCCATGGAGGTTAACTGATGTTCCTTTTTA
TAATGATAGTCCTCAAAGGCCAATTGTTAAGGCAATTTGGAAGATTTCATGCCAACCGAAGATCC
AACACTTCCTTCGGTTGGATTGGAAAGATAAGACTCATGACAAATACAAGTCGTATATTTTGACG
TCTAACTATAGATGAGACTCATGGATTG
Done.