Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006200.1 Kokia drynarioides strain JFW-HI SEQ_120770, 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: 121971
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:16678 original size:45 final size:45
Alignment explanation
Indices: 16614--16705 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
16604 CAAAGTTTAT
*
16614 ATTTATTATTATGCTTTATATACAAAAGCTCGAAATAAGCACTTA
1 ATTTATTATTATGCTTTATATACAAAAGCTCAAAATAAGCACTTA
16659 ATTTATTATTATGCTTTATATACAAAAGCTCAAAATAAGCACTTA
1 ATTTATTATTATGCTTTATATACAAAAGCTCAAAATAAGCACTTA
16704 AT
1 AT
16706 GGTCGAATTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (45 bp):
ATTTATTATTATGCTTTATATACAAAAGCTCAAAATAAGCACTTA
Found at i:17710 original size:22 final size:23
Alignment explanation
Indices: 17656--17711 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
17646 AATTTTTAAT
*
17656 TTAT-TTTTTATAATATATAAAA
1 TTATATTTTAATAATATATAAAA
* **
17678 TTTTAAATTAATAATA-ATAAAA
1 TTATATTTTAATAATATATAAAA
17700 TTATATTTTAAT
1 TTATATTTTAAT
17712 CTAAAAAATG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATATTTTAATAATATATAAAA
Found at i:17728 original size:28 final size:28
Alignment explanation
Indices: 17694--17762 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
17684 ATTAATAATA
*
17694 ATAAAATTATATTTTAATCTAAAAAATG
1 ATAAAATTATATTTAAATCTAAAAAATG
* * * *
17722 ATAAAATTTTGATTTAAATTTTAAAAATT
1 ATAAAATTAT-ATTTAAATCTAAAAAATG
*
17751 ATAAAAATATAT
1 ATAAAATTATAT
17763 AGATAATTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
28 11 0.33
29 22 0.67
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (28 bp):
ATAAAATTATATTTAAATCTAAAAAATG
Found at i:24474 original size:6 final size:6
Alignment explanation
Indices: 24463--24493 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
24453 GTGTCTTTGG
24463 GAGGCT GAGGCT GAGGCT GAGGCT GAGGCT G
1 GAGGCT GAGGCT GAGGCT GAGGCT GAGGCT G
24494 CAGATGGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GAGGCT
Found at i:30155 original size:21 final size:21
Alignment explanation
Indices: 30129--30168 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
30119 TTAATATTTA
30129 AAATTTAACTTTATTTAAAAT
1 AAATTTAACTTTATTTAAAAT
* *
30150 AAATTTAATTTTTTTTAAA
1 AAATTTAACTTTATTTAAA
30169 TTAAGGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATTTAACTTTATTTAAAAT
Found at i:30603 original size:2 final size:2
Alignment explanation
Indices: 30596--30624 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30586 CACCACCGTA
30596 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30625 GGTTCCTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34135 original size:16 final size:16
Alignment explanation
Indices: 34111--34144 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34101 TAGCCGTTGG
* *
34111 AATATATAAAATTTAA
1 AATACATAAAAATTAA
34127 AATACATAAAAATTAA
1 AATACATAAAAATTAA
34143 AA
1 AA
34145 GGTTTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AATACATAAAAATTAA
Found at i:40277 original size:14 final size:14
Alignment explanation
Indices: 40238--40284 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
40228 GCTTTTAATG
40238 AAATTATAAATTAA
1 AAATTATAAATTAA
40252 AAA--ATAAATTAA
1 AAATTATAAATTAA
*
40264 AAATTATCAATTAA
1 AAATTATAAATTAA
*
40278 AATTTAT
1 AAATTAT
40285 TATCAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 12 0.41
14 17 0.59
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATTATAAATTAA
Found at i:41624 original size:14 final size:14
Alignment explanation
Indices: 41603--41640 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
41593 TTGGACCTAG
*
41603 GATTCAAGATCTACT
1 GATTCAAGATCCA-T
41618 G-TTCAAGATCCAT
1 GATTCAAGATCCAT
41631 GATTCAAGAT
1 GATTCAAGAT
41641 TCAGGGTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 2 0.10
14 18 0.86
15 1 0.05
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (14 bp):
GATTCAAGATCCAT
Found at i:46398 original size:28 final size:27
Alignment explanation
Indices: 46362--46422 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
46352 TGTAATTTTT
46362 ATTTATAAAAAATCTAAAACATTAATAAA
1 ATTT-TAAAAAATCTAAAA-ATTAATAAA
* * *
46391 ATTTTAAAAATTCTAAAAATTATTTAA
1 ATTTTAAAAAATCTAAAAATTAATAAA
46418 ATTTT
1 ATTTT
46423 TAAGTATTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 12 0.41
28 13 0.45
29 4 0.14
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTTTAAAAAATCTAAAAATTAATAAA
Found at i:47687 original size:32 final size:30
Alignment explanation
Indices: 47635--47717 Score: 105
Period size: 32 Copynumber: 2.7 Consensus size: 30
47625 TTTTATTATT
* *
47635 ATTTATATTTATTTGTTTATTTTGACATTTA
1 ATTTTTATTTA-TTGTTTATTTTAACATTTA
47666 ATTTATTTATTTATTGTTTATTTTAACATTTA
1 A-TT-TTTATTTATTGTTTATTTTAACATTTA
*
47698 ATTTTTATTT-TTATTTATTT
1 ATTTTTATTTATTGTTTATTT
47718 ATCTATTTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 9 0.19
30 7 0.15
31 3 0.06
32 21 0.45
33 7 0.15
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (30 bp):
ATTTTTATTTATTGTTTATTTTAACATTTA
Found at i:47690 original size:25 final size:25
Alignment explanation
Indices: 47626--47737 Score: 74
Period size: 25 Copynumber: 4.6 Consensus size: 25
47616 TCGGAGTTTT
* * *
47626 TTTATTATTA-TTTATATTTATTTG
1 TTTATTTTTATTTTACATTTATTTA
* *
47650 TTTATTTTGACATTTA-ATTTATTTA
1 TTTATTTTTA-TTTTACATTTATTTA
*
47675 TTTATTGTTTATTTTAACATTTAATT-
1 TTTATT-TTTATTTT-ACATTTATTTA
*
47701 TTTATTTTTA-TTT--ATTTATCTA
1 TTTATTTTTATTTTACATTTATTTA
*
47723 TTTGTTATTTATTTT
1 TTTATT-TTTATTTT
47738 CATATCATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
21 6 0.08
22 5 0.07
23 4 0.06
24 14 0.20
25 21 0.30
26 14 0.20
27 7 0.10
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTATTTTTATTTTACATTTATTTA
Found at i:47913 original size:21 final size:20
Alignment explanation
Indices: 47889--47928 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
47879 AATTATATAG
*
47889 ATATTTTTATGATTGTATTAC
1 ATATATTTATGATT-TATTAC
*
47910 ATATATTTATTATTTATTA
1 ATATATTTATGATTTATTA
47929 TTATTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (20 bp):
ATATATTTATGATTTATTAC
Found at i:47996 original size:71 final size:69
Alignment explanation
Indices: 47919--48088 Score: 157
Period size: 71 Copynumber: 2.4 Consensus size: 69
47909 CATATATTTA
* *
47919 TTATTTATTATTATTTATTTATTTATTGGTTAATCATTTTT-TGTTATTTACA-TCCTCGCTTTT
1 TTATTTATTATTATTTATTTATTTATTGGTT-AT--TTTTTATGCTATTTACATTCCTC-CTTTC
47982 ATTTAATT
62 ATTTAATT
* * * * * **
47990 TTATTTATTGTTTTATGTATTTTTTTATTTGTTATTTTTTATGCTATTTATATTTTTCCTTTCAT
1 TTATTTA-T-TATTATTTATTTATTTATTGGTTATTTTTTATGCTATTTACATTCCTCCTTTCAT
48055 TTAATT
64 TTAATT
48061 TTATTTATTCATTGATATT-TTTATTTAT
1 TTATTTATT-ATT-AT-TTATTTATTTAT
48089 ATGCCATATT
Statistics
Matches: 80, Mismatches: 12, Indels: 14
0.75 0.11 0.13
Matches are distributed among these distances:
69 1 0.01
70 8 0.10
71 45 0.56
72 7 0.09
73 19 0.24
ACGTcount: A:0.21, C:0.06, G:0.05, T:0.67
Consensus pattern (69 bp):
TTATTTATTATTATTTATTTATTTATTGGTTATTTTTTATGCTATTTACATTCCTCCTTTCATTT
AATT
Found at i:48022 original size:21 final size:22
Alignment explanation
Indices: 47978--48018 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
47968 ACATCCTCGC
*
47978 TTTTATTTAATTTTATTTATTG
1 TTTTATGTAATTTTATTTATTG
48000 TTTTATGT-ATTTT-TTTATT
1 TTTTATGTAATTTTATTTATT
48019 TGTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.76
Consensus pattern (22 bp):
TTTTATGTAATTTTATTTATTG
Found at i:48027 original size:12 final size:12
Alignment explanation
Indices: 47978--48027 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
47968 ACATCCTCGC
47978 TTTTATTTA--A
1 TTTTATTTATTA
*
47988 TTTTATTTATTG
1 TTTTATTTATTA
* *
48000 TTTTATGTATTT
1 TTTTATTTATTA
*
48012 TTTTATTTGTTA
1 TTTTATTTATTA
48024 TTTT
1 TTTT
48028 TTATGCTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
10 9 0.28
12 23 0.72
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:51817 original size:2 final size:2
Alignment explanation
Indices: 51810--51842 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
51800 TCAGAAAAAC
51810 AG AG AG AG 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 AG AG AG AG A
51843 ACTCATTACC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:57049 original size:2 final size:2
Alignment explanation
Indices: 57042--57067 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57032 TCACATGCTA
57042 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
57068 TACACAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61697 original size:2 final size:2
Alignment explanation
Indices: 61690--61723 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61680 GTAAATATTT
61690 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
61724 TTATATGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:62299 original size:8 final size:8
Alignment explanation
Indices: 62280--62313 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
62270 TTGGGTTCTC
62280 AAAAAAAT
1 AAAAAAAT
62288 --AAAAAT
1 AAAAAAAT
62294 AAAAAAAT
1 AAAAAAAT
62302 AAAAAAAT
1 AAAAAAAT
62310 AAAA
1 AAAA
62314 TAGGCTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
8 18 0.75
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:62299 original size:14 final size:13
Alignment explanation
Indices: 62280--62315 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
62270 TTGGGTTCTC
62280 AAAAAAATAAAAA
1 AAAAAAATAAAAA
62293 TAAAAAAATAAAAA
1 -AAAAAAATAAAAA
*
62307 AATAAAATA
1 AAAAAAATA
62316 GGCTATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAAAATAAAAA
Found at i:82968 original size:210 final size:211
Alignment explanation
Indices: 82601--83018 Score: 748
Period size: 210 Copynumber: 2.0 Consensus size: 211
82591 TAGCATGTGG
*
82601 CCCCATTATTGATTCAGTTGCATTGAAGACCTTGTACAATCCAAAACGTACTCGAGGTATATAAA
1 CCCCATTATTGATTCAGTTGCATTGAAGACCTTGTACAAT----AACATACTCGAGGTATATAAA
*
82666 ATCGATCACATTGACATCTGATGTTTGTGTTTGATGATTGAAATACAAGTTCATACTTCACTAAC
62 ATCGATCACATTGACATCTGATGTTTGTGTTTGATGATTGAAATACAAGTTCATAATTCACTAAC
82731 CTGTTGTTTGATTCAACAATTTGCAACCAATCTATACTAAATAATGGAAACTTCAAAGAAGGTCC
127 CTGTTGTTTGATTCAACAATTTGCAACCAATCTATACTAAATAATGGAAACTTCAAAGAAGGTCC
82796 TTATATCTTCCCAAGACCAA
192 TTATATCTTCCCAAGACCAA
82816 CCCCATTATTGATTCAGTTGCATTGAAGACCTTGTACAAT-ACATACTCGAGGTATATAAAATCG
1 CCCCATTATTGATTCAGTTGCATTGAAGACCTTGTACAATAACATACTCGAGGTATATAAAATCG
*
82880 ATCACATTGACATTTGATGTTTGTGTTTGATGATTGAAATACAAGTTCATAATTCACTAACCTGT
66 ATCACATTGACATCTGATGTTTGTGTTTGATGATTGAAATACAAGTTCATAATTCACTAACCTGT
* *
82945 TGTTTGGTTCAACAATTTGCAACCAATCTATACTAAATAATGGAAACTTCAAAGACGGTCCTTAT
131 TGTTTGATTCAACAATTTGCAACCAATCTATACTAAATAATGGAAACTTCAAAGAAGGTCCTTAT
83010 ATCTTCCCA
196 ATCTTCCCA
83019 TGAAGATGAT
Statistics
Matches: 198, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
210 158 0.80
215 40 0.20
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (211 bp):
CCCCATTATTGATTCAGTTGCATTGAAGACCTTGTACAATAACATACTCGAGGTATATAAAATCG
ATCACATTGACATCTGATGTTTGTGTTTGATGATTGAAATACAAGTTCATAATTCACTAACCTGT
TGTTTGATTCAACAATTTGCAACCAATCTATACTAAATAATGGAAACTTCAAAGAAGGTCCTTAT
ATCTTCCCAAGACCAA
Found at i:89081 original size:19 final size:19
Alignment explanation
Indices: 89057--89093 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
89047 GATGAATTCA
*
89057 TCAAATCAAATCCTAAAAC
1 TCAAATCAAATACTAAAAC
*
89076 TCAAATTAAATACTAAAA
1 TCAAATCAAATACTAAAA
89094 GTTAACATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.19, G:0.00, T:0.24
Consensus pattern (19 bp):
TCAAATCAAATACTAAAAC
Found at i:119927 original size:29 final size:30
Alignment explanation
Indices: 119864--119929 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
119854 ACGAACGTAA
119864 TCTTAAATTTTAGATCAATTTATCTTTTGT
1 TCTTAAATTTTAGATCAATTTATCTTTTGT
*
119894 T-TT-AATATTTA-ATCAATTTAGT-TTTTTT
1 TCTTAAAT-TTTAGATCAATTTA-TCTTTTGT
119922 TCTTAAAT
1 TCTTAAAT
119930 AAAATTTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
28 18 0.58
29 9 0.29
30 4 0.13
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.59
Consensus pattern (30 bp):
TCTTAAATTTTAGATCAATTTATCTTTTGT
Done.