Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010083.1 Kokia drynarioides strain JFW-HI SEQ_124862, 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: 61810
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2051 original size:17 final size:15
Alignment explanation
Indices: 2016--2049 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2006 GAATTTTTTT
2016 TATAATTAAAAAAAA
1 TATAATTAAAAAAAA
**
2031 TATAATTATTAAAAA
1 TATAATTAAAAAAAA
2046 TATA
1 TATA
2050 TACCAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TATAATTAAAAAAAA
Found at i:2631 original size:20 final size:22
Alignment explanation
Indices: 2596--2635 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
2586 TAGCAAATGC
2596 TTTTAAAATTATTAAAATTAAT
1 TTTTAAAATTATTAAAATTAAT
2618 TTTTAAAA-TA-TAAAATTA
1 TTTTAAAATTATTAAAATTA
2636 TCATCATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTAAAATTATTAAAATTAAT
Found at i:7100 original size:26 final size:26
Alignment explanation
Indices: 7070--7120 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
7060 TATACCGTAC
*
7070 CATATTATACTCTTT-TCTATATTACT
1 CATATT-TACACTTTCTCTATATTACT
*
7096 CATATTTACACTTTCTTTATATTAC
1 CATATTTACACTTTCTCTATATTAC
7121 ATTATACAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (26 bp):
CATATTTACACTTTCTCTATATTACT
Found at i:16480 original size:25 final size:24
Alignment explanation
Indices: 16426--16482 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
16416 TCCCTTAATT
* *
16426 TTTTTATATTTAATTTTTATTTTT
1 TTTTTATATTTAAGTTTTATTTTG
**
16450 TCTTTTATATTTTGGTTTTATTTTAG
1 T-TTTTATATTTAAGTTTTATTTT-G
16476 TTTTTAT
1 TTTTTAT
16483 CTGCTTTTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 25 0.93
26 1 0.04
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (24 bp):
TTTTTATATTTAAGTTTTATTTTG
Found at i:27148 original size:28 final size:28
Alignment explanation
Indices: 27117--27170 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
27107 AATTAACATT
*
27117 ATAAATAAA-AAAATCTTAAAAAATATTC
1 ATAAA-AAACAAAACCTTAAAAAATATTC
*
27145 ATAAAAAACAAAACCTTAAAACATAT
1 ATAAAAAACAAAACCTTAAAAAATAT
27171 CAATTAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.65, C:0.11, G:0.00, T:0.24
Consensus pattern (28 bp):
ATAAAAAACAAAACCTTAAAAAATATTC
Found at i:27603 original size:29 final size:28
Alignment explanation
Indices: 27545--27603 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
27535 ATTAACATTA
**
27545 TAAATAAAAAAACCTTAAAAATATTCAT
1 TAAATAAAAAAACCTTAAAAATATAAAT
27573 TAAA-AAACAAAACCTTAAAACATATAAAT
1 TAAATAAA-AAAACCTTAAAA-ATATAAAT
27602 TA
1 TA
27604 GAATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 3 0.11
28 16 0.59
29 8 0.30
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.25
Consensus pattern (28 bp):
TAAATAAAAAAACCTTAAAAATATAAAT
Found at i:34665 original size:17 final size:17
Alignment explanation
Indices: 34643--34675 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
34633 TAAAATAATT
34643 TTTTAAAATATAAAATA
1 TTTTAAAATATAAAATA
34660 TTTTAAAATATAAAAT
1 TTTTAAAATATAAAAT
34676 TGTTACAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTTAAAATATAAAATA
Found at i:34696 original size:29 final size:29
Alignment explanation
Indices: 34660--34719 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
34650 ATATAAAATA
* *
34660 TTTTAAAAT-ATAAAATTGTTACAATTATT
1 TTTTAAAATAATAAAATTATTA-AATAATT
34689 TTTTAAAATAATAAAATTATTAAATAATT
1 TTTTAAAATAATAAAATTATTAAATAATT
34718 TT
1 TT
34720 AATTTCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
TTTTAAAATAATAAAATTATTAAATAATT
Found at i:34751 original size:12 final size:12
Alignment explanation
Indices: 34734--34758 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34724 TCCAATTTCA
34734 TCATCTTCTTCT
1 TCATCTTCTTCT
34746 TCATCTTCTTCT
1 TCATCTTCTTCT
34758 T
1 T
34759 AATCATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATCTTCTTCT
Found at i:35763 original size:24 final size:24
Alignment explanation
Indices: 35735--35797 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
35725 AGAAATAATC
*
35735 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTATTTAATTG
* * *
35759 TTTCAATTAAACTTTATTTATTTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
35783 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
35798 TATTAGTTTA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAATTG
Found at i:38292 original size:30 final size:29
Alignment explanation
Indices: 38256--38327 Score: 119
Period size: 29 Copynumber: 2.4 Consensus size: 29
38246 ATTAAAATTA
38256 TTTAATAATTTTAT-TATTTAAAAAAATAAT
1 TTTAATAATTTTATGT-TTT-AAAAAATAAT
38286 TTTAATAATTTTATGTTTTAAAAAATAAT
1 TTTAATAATTTTATGTTTTAAAAAATAAT
38315 TTTAATAATTTTA
1 TTTAATAATTTTA
38328 AAATCATTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
29 23 0.56
30 17 0.41
31 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
TTTAATAATTTTATGTTTTAAAAAATAAT
Found at i:48129 original size:30 final size:30
Alignment explanation
Indices: 48095--48154 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
48085 TGTTTTAAAA
48095 TTTTAAAAATAAAGAAATTA-TAAAAAATAT
1 TTTTAAAAATAAA-AAATTATTAAAAAATAT
* *
48125 TTTTAAATATTAAAAATTATTAAAAAATAT
1 TTTTAAAAATAAAAAATTATTAAAAAATAT
48155 AAAAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (30 bp):
TTTTAAAAATAAAAAATTATTAAAAAATAT
Found at i:48157 original size:9 final size:10
Alignment explanation
Indices: 48115--48166 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
48105 AAAGAAATTA
48115 TAAAAAATAT
1 TAAAAAATAT
***
48125 TTTTAAATAT
1 TAAAAAATAT
*
48135 TAAAAATTAT
1 TAAAAAATAT
48145 TAAAAAATAT
1 TAAAAAATAT
*
48155 AAAAAAAT-T
1 TAAAAAATAT
48164 TAA
1 TAA
48167 TTAAATGTTA
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
9 3 0.09
10 29 0.91
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TAAAAAATAT
Found at i:48172 original size:20 final size:20
Alignment explanation
Indices: 48113--48172 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
48103 ATAAAGAAAT
48113 TATAAAAAATATTT--TTAAA
1 TATAAAAAA-ATTTAATTAAA
* * *
48132 TATTAAAAATTATTAA-AAAA
1 TATAAAAAAAT-TTAATTAAA
48152 TATAAAAAAATTTAATTAAA
1 TATAAAAAAATTTAATTAAA
48172 T
1 T
48173 GTTAACATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
20 16 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TATAAAAAAATTTAATTAAA
Found at i:56309 original size:2 final size:2
Alignment explanation
Indices: 56302--56332 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
56292 AAGGGGGACT
*
56302 GA GA GA GA AA 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 G
56333 GAGGGGGGNG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:61034 original size:20 final size:20
Alignment explanation
Indices: 61002--61039 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
60992 TCAATCTCTA
*
61002 ATTTTGATATTTATATTTCT
1 ATTTTGATATTTAAATTTCT
61022 ATTTTGA-ATTTTAAATTT
1 ATTTTGATA-TTTAAATTT
61040 GCTAGCTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
ATTTTGATATTTAAATTTCT
Found at i:61533 original size:2 final size:2
Alignment explanation
Indices: 61526--61584 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
61516 CTTTTGACTT
61526 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61568 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
61585 TAAATCACAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.