Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010662.1 Kokia drynarioides strain JFW-HI SEQ_125607, 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: 10434
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Found at i:1221 original size:61 final size:59
Alignment explanation
Indices: 1147--1281 Score: 225
Period size: 61 Copynumber: 2.3 Consensus size: 59
1137 ATTTTTTACC
1147 ATTTTGGTAAATAATATGATGGGGATATTATTTTACATAATTAATTATTTTTTTATATTAT
1 ATTTTGGTAAATAATATGATGGGGATATTATTTT-CATAATTAATTA-TTTTTTATATTAT
* *
1208 ATTTTGGTCAATAATATGATGGGGATATTATTTTGATAATTAATTATTTTTTATATTAT
1 ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAT
*
1267 ATTTTGGTAATTAAT
1 ATTTTGGTAAATAAT
1282 TATCTAAGTT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 26 0.37
60 11 0.16
61 33 0.47
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (59 bp):
ATTTTGGTAAATAATATGATGGGGATATTATTTTCATAATTAATTATTTTTTATATTAT
Found at i:1255 original size:16 final size:16
Alignment explanation
Indices: 1234--1284 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1224 TGATGGGGAT
1234 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
1250 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
1265 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
1280 ATTAT
1 ATTAT
1285 CTAAGTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.31
15 6 0.21
16 14 0.48
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:1568 original size:20 final size:21
Alignment explanation
Indices: 1543--1585 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1533 TACTTACTAC
1543 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
1563 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
1584 TA
1 TA
1586 AAGGAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:1975 original size:4 final size:4
Alignment explanation
Indices: 1968--2006 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
1958 TTCTTCCTTC
*
1968 TTCT TTCT TTCT TTCT TTCT CTTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TTCT TTCT TTC
2007 CTTCATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:1995 original size:21 final size:20
Alignment explanation
Indices: 1966--2010 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1956 CCTTCTTCCT
1966 TCTTCTTTCTTTCTTTCTTTC
1 TCTTCTTTCTTTCTTT-TTTC
*
1987 TCTTTTTTCTTTCTTTTTTC
1 TCTTCTTTCTTTCTTTTTTC
2007 -CTTC
1 TCTTC
2011 ATTTTTCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 3 0.14
20 4 0.18
21 15 0.68
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (20 bp):
TCTTCTTTCTTTCTTTTTTC
Found at i:2003 original size:11 final size:11
Alignment explanation
Indices: 1965--2017 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
1955 TCCTTCTTCC
*
1965 TTCTTCTTTCT
1 TTCTTTTTTCT
1976 TTCTTTCTTTC-
1 TTCTTT-TTTCT
1987 -TCTTTTTTCT
1 TTCTTTTTTCT
*
1997 TTCTTTTTTCC
1 TTCTTTTTTCT
*
2008 TTCATTTTTC
1 TTCTTTTTTC
2018 GTTGGTCCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 23 0.64
12 4 0.11
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.74
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:2015 original size:21 final size:21
Alignment explanation
Indices: 1961--2015 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 21
1951 ATTCTCCTTC
1961 TTCCTTCTTCTTTCTTTCTTTCT
1 TTCCTTC-T-TTTCTTTCTTTCT
1984 TTCTCTT-TTTTCTTTCTTT-T
1 TTC-CTTCTTTTCTTTCTTTCT
2004 TTCCTTCATTTT
1 TTCCTTC-TTTT
2016 TCGTTGGTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.10
20 4 0.14
21 15 0.52
22 1 0.03
23 3 0.10
24 3 0.10
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCCTTCTTTTCTTTCTTTCT
Found at i:3940 original size:30 final size:30
Alignment explanation
Indices: 3884--3940 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3874 AATTTTAAAA
* * *
3884 AAATTAAATTTAATTTTTATCATATTAGAG
1 AAATAAAATGTAATTTTTACCATATTAGAG
3914 AAATAAAATGTAA-TTTTACCATTATTA
1 AAATAAAATGTAATTTTTACCA-TATTA
3941 ATTTAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (30 bp):
AAATAAAATGTAATTTTTACCATATTAGAG
Found at i:4497 original size:23 final size:21
Alignment explanation
Indices: 4466--4507 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
4456 TACATAAAAA
*
4466 AAATTAACTTTTAAATTATAAAT
1 AAATAAAC-TTTAAA-TATAAAT
4489 AAATAAACTTTAAATATAA
1 AAATAAACTTTAAATATAA
4508 CTAATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATAAACTTTAAATATAAAT
Found at i:4503 original size:22 final size:22
Alignment explanation
Indices: 4453--4507 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
4443 TAACTCTTAA
* * *
4453 TTTTACATA-AAAAAAATTAAC
1 TTTTAAATATAAATAAATAAAC
4474 TTTTAAATTATAAATAAATAAAC
1 TTTTAAA-TATAAATAAATAAAC
4497 -TTTAAATATAA
1 TTTTAAATATAA
4508 CTAATTTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 11 0.38
22 8 0.28
23 10 0.34
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTTAAATATAAATAAATAAAC
Found at i:5198 original size:21 final size:19
Alignment explanation
Indices: 5161--5200 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
5151 TTATTTTTAC
*
5161 ACTACTCATAAATAAACCT
1 ACTACTCATAAAAAAACCT
5180 ACTACTCATCTAAAAAAACCT
1 ACTACTCA--TAAAAAAACCT
5201 TGAAGACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (19 bp):
ACTACTCATAAAAAAACCT
Done.