Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014937.1 Kokia drynarioides strain JFW-HI SEQ_129980, 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: 98995
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:1050 original size:24 final size:25
Alignment explanation
Indices: 1004--1051 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
994 ATAACTTTTT
* *
1004 ATTTTCTTTTAATTTAAATTTAATA
1 ATTTTATTTTAATATAAATTTAATA
1029 ATTTTATTTTAA-ATAAATTTAAT
1 ATTTTATTTTAATATAAATTTAAT
1052 TATCATGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
ATTTTATTTTAATATAAATTTAATA
Found at i:2813 original size:25 final size:25
Alignment explanation
Indices: 2785--2848 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
2775 GAGCAATTTA
2785 ATTTTTTTTTGTTTATGTT-CTTTTC
1 ATTTTTTTTTGTTTAT-TTACTTTTC
* *
2810 ATTTTTATTTT-TTTCTTTATTTTTC
1 ATTTTT-TTTTGTTTATTTACTTTTC
*
2835 ATTCTTTTTTGTTT
1 ATTTTTTTTTGTTT
2849 CTCCATCTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 6 0.18
25 23 0.70
26 4 0.12
ACGTcount: A:0.09, C:0.08, G:0.05, T:0.78
Consensus pattern (25 bp):
ATTTTTTTTTGTTTATTTACTTTTC
Found at i:2839 original size:14 final size:14
Alignment explanation
Indices: 2805--2841 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
2795 GTTTATGTTC
2805 TTTTCATT-TTTAT
1 TTTTCATTCTTTAT
2818 TTTT--TTCTTTAT
1 TTTTCATTCTTTAT
2830 TTTTCATTCTTT
1 TTTTCATTCTTT
2842 TTTGTTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.10
12 9 0.43
13 4 0.19
14 6 0.29
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCATTCTTTAT
Found at i:12953 original size:16 final size:16
Alignment explanation
Indices: 12933--12985 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
12923 AAAAATTATG
* *
12933 TTTTCCAGCCTTCTAG
1 TTTTCCACCCTTCTAA
*
12949 TTTTCTACCCCTTC-AA
1 TTTTCCA-CCCTTCTAA
*
12965 TTTTCCATCCTTCTAA
1 TTTTCCACCCTTCTAA
12981 TTTTC
1 TTTTC
12986 TTTCCAGTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 20 0.67
17 5 0.17
ACGTcount: A:0.15, C:0.32, G:0.04, T:0.49
Consensus pattern (16 bp):
TTTTCCACCCTTCTAA
Found at i:23299 original size:20 final size:20
Alignment explanation
Indices: 23271--23310 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
23261 CTCTAATTAG
* *
23271 AATCTCTAAAAATTAGCTAT
1 AATCCCTAAAAACTAGCTAT
*
23291 AATCCCTAAAGACTAGCTAT
1 AATCCCTAAAAACTAGCTAT
23311 TCAATGCTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (20 bp):
AATCCCTAAAAACTAGCTAT
Found at i:39370 original size:2 final size:2
Alignment explanation
Indices: 39363--39394 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39353 GCACGCGTGT
39363 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
39395 TCTTTGTCTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41840 original size:18 final size:18
Alignment explanation
Indices: 41819--41865 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
41809 TTAAAAACAC
41819 TTTTGAAATAAAAAATAT
1 TTTTGAAATAAAAAATAT
*
41837 TTTTGAGAT-AAAAATAT
1 TTTTGAAATAAAAAATAT
*
41854 TATT-AAATAAAA
1 TTTTGAAATAAAA
41866 TATTTTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 3 0.12
17 14 0.56
18 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TTTTGAAATAAAAAATAT
Found at i:41976 original size:16 final size:17
Alignment explanation
Indices: 41955--41994 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
41945 AAAAAATTGA
*
41955 ACTTTTT-CTCAAAAAT
1 ACTTTTTACTCAAAAAC
41971 ACTTTTTGACTCAAAAAC
1 ACTTTTT-ACTCAAAAAC
41989 ACTTTT
1 ACTTTT
41995 AAAAAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
18 14 0.67
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (17 bp):
ACTTTTTACTCAAAAAC
Found at i:43187 original size:23 final size:24
Alignment explanation
Indices: 43155--43199 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
43145 CTAATAGAAG
43155 TACCAACTTGGGAAAAAAAAAAAT
1 TACCAACTTGGGAAAAAAAAAAAT
* *
43179 TACC-ACTTGTGACAAAAAAAA
1 TACCAACTTGGGAAAAAAAAAA
43200 TTTAGGTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.56, C:0.16, G:0.11, T:0.18
Consensus pattern (24 bp):
TACCAACTTGGGAAAAAAAAAAAT
Found at i:47948 original size:12 final size:14
Alignment explanation
Indices: 47927--47959 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
47917 CTAAATTTTT
*
47927 TTATTTTTAAATAA
1 TTATTTTAAAATAA
47941 -TATTTTAAAATAA
1 TTATTTTAAAATAA
47954 TTATTT
1 TTATTT
47960 CACATACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTATTTTAAAATAA
Found at i:48017 original size:20 final size:19
Alignment explanation
Indices: 47980--48018 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
47970 GATTAAAAAA
*
47980 TTATTTAAAATATTTATTT
1 TTATTTAAAATATGTATTT
*
47999 TTATTTTAAATAGTGTATTT
1 TTATTTAAAATA-TGTATTT
48019 AAAATGGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
TTATTTAAAATATGTATTT
Found at i:49706 original size:20 final size:20
Alignment explanation
Indices: 49667--49707 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
49657 ACATTTTACA
*
49667 AATAAAATATAATTATATTT
1 AATAAAATATAATTAAATTT
* *
49687 AATAAAATTTAGTTAAATTT
1 AATAAAATATAATTAAATTT
49707 A
1 A
49708 TTTGTACTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AATAAAATATAATTAAATTT
Found at i:54375 original size:2 final size:2
Alignment explanation
Indices: 54368--54402 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
54358 GTGATGTATC
*
54368 AT AT AT AT AT AT AT AT AT AT AT -T AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54403 TCAAATAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:66569 original size:27 final size:27
Alignment explanation
Indices: 66539--66593 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
66529 TCCTTTTTTT
* *
66539 TTATTCTTTTATATATATTAAAAAAAA
1 TTATTCATTTATATATATAAAAAAAAA
*
66566 TTATTCATTTATGTATATAAAAAAAAA
1 TTATTCATTTATATATATAAAAAAAAA
66593 T
1 T
66594 GTCAATGTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (27 bp):
TTATTCATTTATATATATAAAAAAAAA
Found at i:68312 original size:29 final size:29
Alignment explanation
Indices: 68243--68312 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
68233 TAAAAATATC
***
68243 CATAAATATTTTTTAAAAACGTTTATTTT
1 CATAAATATTTTTTAAAAACACCTATTTT
*
68272 TATAAATA-TTTTTAAAAACACCTATTTT
1 CATAAATATTTTTTAAAAACACCTATTTT
*
68300 CGTAAATATTTTT
1 CATAAATATTTTT
68313 ATCTTAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 23 0.68
29 11 0.32
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.50
Consensus pattern (29 bp):
CATAAATATTTTTTAAAAACACCTATTTT
Found at i:68425 original size:43 final size:45
Alignment explanation
Indices: 68362--68448 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 45
68352 CGAAAAAATT
*
68362 TAAGAACACTTATTTCCATAAATATTTTCA-AAAA-GTTTATTTC
1 TAAGAACACTTATTTCCATAAATATTTTCAGAAAACGCTTATTTC
* * *
68405 TAAGAACGCTTATTTTCATAATTATTTTCAGAAAACGCTTATTT
1 TAAGAACACTTATTTCCATAAATATTTTCAGAAAACGCTTATTT
68449 TCGTAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 27 0.71
44 4 0.11
45 7 0.18
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.43
Consensus pattern (45 bp):
TAAGAACACTTATTTCCATAAATATTTTCAGAAAACGCTTATTTC
Found at i:68493 original size:31 final size:31
Alignment explanation
Indices: 68427--68511 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
68417 TTTTCATAAT
* * *
68427 TATTTTCAGAAAACGCTTA--TTT-TCGTAAT
1 TATTTTTA-AAAACGCTTATTTTTATTGTAAA
*
68456 TATTTTT-AACACGCTTAGTTTTTATTGTAAA
1 TATTTTTAAAAACGCTTA-TTTTTATTGTAAA
68487 TATTTTTAAAAACGCTTATTTTTAT
1 TATTTTTAAAAACGCTTATTTTTAT
68512 AAATAATTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
27 9 0.20
29 6 0.13
30 3 0.07
31 19 0.41
32 9 0.20
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (31 bp):
TATTTTTAAAAACGCTTATTTTTATTGTAAA
Found at i:74370 original size:29 final size:29
Alignment explanation
Indices: 74301--74370 Score: 88
Period size: 28 Copynumber: 2.4 Consensus size: 29
74291 TAAAAATATC
***
74301 CATAAATATTTTTTAAAAACGTTTATTTT
1 CATAAATATTTTTTAAAAACACCTATTTT
*
74330 TATAAATA-TTTTTAAAAACACCTATTTT
1 CATAAATATTTTTTAAAAACACCTATTTT
*
74358 CGTAAATATTTTT
1 CATAAATATTTTT
74371 ATCTTAATTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 23 0.68
29 11 0.32
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.50
Consensus pattern (29 bp):
CATAAATATTTTTTAAAAACACCTATTTT
Found at i:74483 original size:43 final size:45
Alignment explanation
Indices: 74420--74506 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 45
74410 CGAAAAAATT
*
74420 TAAGAACACTTATTTCCATAAATATTTTCA-AAAA-GTTTATTTC
1 TAAGAACACTTATTTCCATAAATATTTTCAGAAAACGCTTATTTC
* * *
74463 TAAGAACGCTTATTTTCATAATTATTTTCAGAAAACGCTTATTT
1 TAAGAACACTTATTTCCATAAATATTTTCAGAAAACGCTTATTT
74507 TCGTAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 27 0.71
44 4 0.11
45 7 0.18
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.43
Consensus pattern (45 bp):
TAAGAACACTTATTTCCATAAATATTTTCAGAAAACGCTTATTTC
Found at i:74551 original size:31 final size:31
Alignment explanation
Indices: 74485--74569 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 31
74475 TTTTCATAAT
* * *
74485 TATTTTCAGAAAACGCTTA--TTT-TCGTAAT
1 TATTTTTA-AAAACGCTTATTTTTATTGTAAA
*
74514 TATTTTT-AACACGCTTAGTTTTTATTGTAAA
1 TATTTTTAAAAACGCTTA-TTTTTATTGTAAA
74545 TATTTTTAAAAACGCTTATTTTTAT
1 TATTTTTAAAAACGCTTATTTTTAT
74570 AAATAATTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
27 9 0.20
29 6 0.13
30 3 0.07
31 19 0.41
32 9 0.20
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (31 bp):
TATTTTTAAAAACGCTTATTTTTATTGTAAA
Found at i:81776 original size:23 final size:24
Alignment explanation
Indices: 81744--81789 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
81734 TGTAGCATGT
*
81744 TTAATTATATTTTAT-ATATTATG
1 TTAATAATATTTTATGATATTATG
81767 TTAATAATATTTTATGATATTAT
1 TTAATAATATTTTATGATATTAT
81790 TATACATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
TTAATAATATTTTATGATATTATG
Found at i:82358 original size:19 final size:21
Alignment explanation
Indices: 82318--82358 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
82308 TAATATATTT
82318 AATATAGATTTATTACTATAC
1 AATATAGATTTATTACTATAC
*
82339 AATATA-ATTTTTTA-TATAC
1 AATATAGATTTATTACTATAC
82358 A
1 A
82359 TTAATAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 7 0.37
21 6 0.32
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (21 bp):
AATATAGATTTATTACTATAC
Found at i:82832 original size:20 final size:23
Alignment explanation
Indices: 82807--82873 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
82797 AATTTATCAG
*
82807 AATTAT-TATAT-TAAAT-TTTA
1 AATTATGTATATAAAAATATTTA
82827 AATTATGTATATAAAAATATTTA
1 AATTATGTATATAAAAATATTTA
* *
82850 AA-TATGTAAATAACAATTATTTA
1 AATTATGTATATAA-AAATATTTA
82873 A
1 A
82874 TATAATTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
20 6 0.15
21 5 0.12
22 14 0.35
23 15 0.38
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (23 bp):
AATTATGTATATAAAAATATTTA
Found at i:82855 original size:22 final size:24
Alignment explanation
Indices: 82819--82873 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
82809 TTATTATATT
*
82819 AAAT-TTTAAATTATGTATATAA-
1 AAATATTTAAATTATGTAAATAAC
82841 AAATATTTAAA-TATGTAAATAAC
1 AAATATTTAAATTATGTAAATAAC
*
82864 AATTATTTAA
1 AAATATTTAA
82874 TATAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
AAATATTTAAATTATGTAAATAAC
Found at i:86694 original size:25 final size:26
Alignment explanation
Indices: 86650--86699 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
86640 AAATTTCTAA
*
86650 ATATTTATAAAAATTCTAAAAATTAT
1 ATATTTATAAAAATTATAAAAATTAT
*
86676 ATATTT-TTAAAATTATAAAAATTA
1 ATATTTATAAAAATTATAAAAATTA
86700 AAAAATTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
ATATTTATAAAAATTATAAAAATTAT
Found at i:86711 original size:25 final size:25
Alignment explanation
Indices: 86659--86711 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
86649 AATATTTATA
* * * * *
86659 AAAATTCTAAAAATTATATATTTTT
1 AAAATTATAAAAATTAAAAAATTCT
86684 AAAATTATAAAAATTAAAAAATTCT
1 AAAATTATAAAAATTAAAAAATTCT
86709 AAA
1 AAA
86712 GAATATATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAATTATAAAAATTAAAAAATTCT
Done.