Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002547.1 Kokia drynarioides strain JFW-HI SEQ_114732, 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: 29673
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:74 original size:31 final size:31
Alignment explanation
Indices: 39--97 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
29 ATATGTATGT
39 TTAATAATATTAAAAAATAT-AATATTTTATA
1 TTAAT-ATATTAAAAAATATAAATATTTTATA
* * *
70 TTAATATTTTAATAAATTTAAATATTTT
1 TTAATATATTAAAAAATATAAATATTTT
98 TAAAAATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
TTAATATATTAAAAAATATAAATATTTTATA
Found at i:4879 original size:34 final size:34
Alignment explanation
Indices: 4836--4904 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
4826 TCTAGTCACT
* *
4836 TCCATGAATAGCTTTTGACAGTCTCCAAGCTATC
1 TCCATGAATAGCGTTTAACAGTCTCCAAGCTATC
4870 TCCATGAATAGCGTTTAACAGTCTCCAAGCTATC
1 TCCATGAATAGCGTTTAACAGTCTCCAAGCTATC
4904 T
1 T
4905 AATTGGATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (34 bp):
TCCATGAATAGCGTTTAACAGTCTCCAAGCTATC
Found at i:12117 original size:15 final size:15
Alignment explanation
Indices: 12092--12160 Score: 68
Period size: 15 Copynumber: 4.7 Consensus size: 15
12082 TTTACATACA
12092 AACT-TTTATATGTG
1 AACTGTTTATATGTG
* *
12106 AACTGCTTATATGAG
1 AACTGTTTATATGTG
* *
12121 AATTGTTTATATGCG
1 AACTGTTTATATGTG
** *
12136 AACTAATTGTATGTG
1 AACTGTTTATATGTG
12151 AACTGTTTAT
1 AACTGTTTAT
12161 GTTTTAGCTA
Statistics
Matches: 41, Mismatches: 13, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
14 4 0.10
15 37 0.90
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (15 bp):
AACTGTTTATATGTG
Found at i:12158 original size:30 final size:30
Alignment explanation
Indices: 12092--12160 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
12082 TTTACATACA
* **
12092 AACT-TTTATATGTGAACTGCTTATATGAG
1 AACTGTTTATATGCGAACTAATTATATGAG
* * *
12121 AATTGTTTATATGCGAACTAATTGTATGTG
1 AACTGTTTATATGCGAACTAATTATATGAG
12151 AACTGTTTAT
1 AACTGTTTAT
12161 GTTTTAGCTA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 3 0.09
30 29 0.91
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.43
Consensus pattern (30 bp):
AACTGTTTATATGCGAACTAATTATATGAG
Found at i:28400 original size:18 final size:18
Alignment explanation
Indices: 28377--28426 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
28367 AAAATGCAGG
28377 AAATGATGTTAACACTTC
1 AAATGATGTTAACACTTC
*
28395 AAATGATGTTCAA-ATTTC
1 AAATGATGTT-AACACTTC
*
28413 AAATGACGTTAACA
1 AAATGATGTTAACA
28427 TTGATGGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 24 0.86
19 2 0.07
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (18 bp):
AAATGATGTTAACACTTC
Found at i:28944 original size:72 final size:72
Alignment explanation
Indices: 28858--29030 Score: 292
Period size: 72 Copynumber: 2.4 Consensus size: 72
28848 CAATGCTAAA
*
28858 CTAGTTTTACCAATAGTTGTTTATGTTTGGTTTTTAGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTAGATATTGAATTTATGTTCTACTTATTTAT
28923 GTGCAAT
66 GTGCAAT
* *
28930 CTAGTTTTATCAATAGTTGTTTTTGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTAGATATTGAATTTATGTTCTACTTATTTAT
*
28995 GTGTAAT
66 GTGCAAT
* *
29002 TTAGTTTTATCAATAGTTGTTTATATTTG
1 CTAGTTTTATCAATAGTTGTTTATGTTTG
29031 ATTTCGGATA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 94 1.00
ACGTcount: A:0.23, C:0.06, G:0.16, T:0.55
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTAGATATTGAATTTATGTTCTACTTATTTAT
GTGCAAT
Found at i:29256 original size:30 final size:30
Alignment explanation
Indices: 29222--29311 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 30
29212 GAATTGAGAA
29222 TTAGACTATATAGCTAAAATAAGAAAATAG
1 TTAGACTATATAGCTAAAATAAGAAAATAG
** * * *
29252 TTAGAAAAT-TAAG-TAGAAT-TG-AGA-A-
1 TTAGACTATAT-AGCTAAAATAAGAAAATAG
29277 TTAGACTATATAGCTAAAATAAGAAAATAG
1 TTAGACTATATAGCTAAAATAAGAAAATAG
29307 TTAGA
1 TTAGA
29312 AAATTAAGGA
Statistics
Matches: 43, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 9 0.21
26 7 0.16
27 3 0.07
28 3 0.07
29 7 0.16
30 14 0.33
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.28
Consensus pattern (30 bp):
TTAGACTATATAGCTAAAATAAGAAAATAG
Found at i:29276 original size:55 final size:55
Alignment explanation
Indices: 29208--29319 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
29198 ATAGTAATAG
29208 AGTAGAATTGAGAATTAGACTATATAGCTAAAATAAGAAAATAGTTAGAAAATTA
1 AGTAGAATTGAGAATTAGACTATATAGCTAAAATAAGAAAATAGTTAGAAAATTA
29263 AGTAGAATTGAGAATTAGACTATATAGCTAAAATAAGAAAATAGTTAGAAAATTA
1 AGTAGAATTGAGAATTAGACTATATAGCTAAAATAAGAAAATAGTTAGAAAATTA
29318 AG
1 AG
29320 GATTAATTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.27
Consensus pattern (55 bp):
AGTAGAATTGAGAATTAGACTATATAGCTAAAATAAGAAAATAGTTAGAAAATTA
Done.