Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005393.1 Kokia drynarioides strain JFW-HI SEQ_119397, 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: 53504
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:5060 original size:46 final size:46
Alignment explanation
Indices: 5000--5102 Score: 138
Period size: 46 Copynumber: 2.2 Consensus size: 46
4990 ATAATATCTT
* *
5000 ATAATAT-CTAATTAAGAATCAAATTA-TTAAGAGATAATATCACATA
1 ATAATATCCT-ATTAAAAATCAAATTACTAAAGA-ATAATATCACATA
* *
5046 ATAATATCCTATTAAAAATTAAATTACTAAAGAATAATATCGCATA
1 ATAATATCCTATTAAAAATCAAATTACTAAAGAATAATATCACATA
5092 ATAATATCCTA
1 ATAATATCCTA
5103 ACCGTGATTG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 44 0.86
47 7 0.14
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (46 bp):
ATAATATCCTATTAAAAATCAAATTACTAAAGAATAATATCACATA
Found at i:6982 original size:21 final size:21
Alignment explanation
Indices: 6956--6997 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6946 TCAATTTGAT
*
6956 GGCAATGTGAATCCATCAAAA
1 GGCAATATGAATCCATCAAAA
*
6977 GGCAATATGGATCCATCAAAA
1 GGCAATATGAATCCATCAAAA
6998 TTCAAGCGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (21 bp):
GGCAATATGAATCCATCAAAA
Found at i:8404 original size:138 final size:138
Alignment explanation
Indices: 8156--8430 Score: 487
Period size: 138 Copynumber: 2.0 Consensus size: 138
8146 GATAAAGAGA
8156 GTGTCAAAACCACTTTGGCAGAGGAAGCGAGGTCATTAATGATTTCAGATGAGCGATGTCCGGAT
1 GTGTCAAAACCACTTTGGCAGAGGAAGCGAGGTCATTAATGATTTCAGATGAGCGATGTCCGGAT
*
8221 TCCCTGTTTGACAAGCATGATTTCCAGGTAGCCTTTAATGATGATGAAGATTGTGTGAAAGAGCA
66 TCCCTGTTTGACAAGCATGATTTCCAGGCAGCCTTTAATGATGATGAAGATTGTGTGAAAGAGCA
8286 TGATTCCT
131 TGATTCCT
* * * *
8294 GTGTCAAAACCACTTTGGCAGAGGAAGCGAGGTCATTAGTGGTTTCAGATGATCGATGTCTGGAT
1 GTGTCAAAACCACTTTGGCAGAGGAAGCGAGGTCATTAATGATTTCAGATGAGCGATGTCCGGAT
* *
8359 TCCCTGTTTGACAAGCATGATTTCCAGGCAGCTTTTAATGATGATGAAGATTTTGTGAAAGAGCA
66 TCCCTGTTTGACAAGCATGATTTCCAGGCAGCCTTTAATGATGATGAAGATTGTGTGAAAGAGCA
8424 TGATTCC
131 TGATTCC
8431 CAAGCAGCCT
Statistics
Matches: 130, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
138 130 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (138 bp):
GTGTCAAAACCACTTTGGCAGAGGAAGCGAGGTCATTAATGATTTCAGATGAGCGATGTCCGGAT
TCCCTGTTTGACAAGCATGATTTCCAGGCAGCCTTTAATGATGATGAAGATTGTGTGAAAGAGCA
TGATTCCT
Found at i:14280 original size:18 final size:19
Alignment explanation
Indices: 14257--14293 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
14247 GTTGATACGG
14257 ACTAAAAAC-ATAAAAATT
1 ACTAAAAACGATAAAAATT
*
14275 ACTAAAAACGATCAAAATT
1 ACTAAAAACGATAAAAATT
14294 TGCTTACCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.62, C:0.14, G:0.03, T:0.22
Consensus pattern (19 bp):
ACTAAAAACGATAAAAATT
Found at i:19974 original size:6 final size:6
Alignment explanation
Indices: 19963--20038 Score: 70
Period size: 6 Copynumber: 13.2 Consensus size: 6
19953 GACCCAAACA
* *
19963 AAATTT AAATTT AAATTT -ATTTT AAGTTT AAATTT --ATTT GAAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT
* * *
20009 AAATTT -ATTTT AAATGT AAGTTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT AAATTT A
20039 TTTAAATGTA
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
4 4 0.07
5 8 0.14
6 40 0.71
7 4 0.07
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:20007 original size:40 final size:39
Alignment explanation
Indices: 19963--20045 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 39
19953 GACCCAAACA
* *
19963 AAATTTAAATTTAAATTT-ATTTTAAGTTTAAATTTATTT
1 AAATTTAAATTT-AATTTAAATGTAAGTTTAAATTTATTT
*
20002 GAAATTTAAATTTATTTTAAATGTAAGTTTAAATTTATTT
1 -AAATTTAAATTTAATTTAAATGTAAGTTTAAATTTATTT
20042 AAAT
1 AAAT
20046 GTATTAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 8 0.21
40 31 0.79
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (39 bp):
AAATTTAAATTTAATTTAAATGTAAGTTTAAATTTATTT
Found at i:20009 original size:23 final size:21
Alignment explanation
Indices: 19966--20045 Score: 69
Period size: 23 Copynumber: 3.8 Consensus size: 21
19956 CCAAACAAAA
**
19966 TTTAAATTTAAATTTATTTTAAG
1 TTTAAATTT--ATTTAAATTAAG
*
19989 TTTAAATTTATTT-GA--AA-
1 TTTAAATTTATTTAAATTAAG
20006 TTTAAATTTATTTTAAATGTAAG
1 TTTAAATTTA-TTTAAAT-TAAG
20029 TTTAAATTTATTTAAAT
1 TTTAAATTTATTTAAAT
20046 GTATTAATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
17 10 0.21
18 5 0.10
19 1 0.02
21 4 0.08
22 9 0.19
23 19 0.40
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTAAATTTATTTAAATTAAG
Found at i:20032 original size:17 final size:17
Alignment explanation
Indices: 19966--20023 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
19956 CCAAACAAAA
19966 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
19983 TTTAAGTTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
20000 TTGAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
20017 TTTAAAT
1 TTTAAAT
20024 GTAAGTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:20045 original size:22 final size:23
Alignment explanation
Indices: 20006--20048 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
19996 TTATTTGAAA
20006 TTTAAATTTATTTTAAATGTAAG
1 TTTAAATTTATTTTAAATGTAAG
20029 TTTAAATTTA-TTTAAATGTA
1 TTTAAATTTATTTTAAATGTA
20049 TTAATATCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (23 bp):
TTTAAATTTATTTTAAATGTAAG
Found at i:21763 original size:30 final size:30
Alignment explanation
Indices: 21707--22070 Score: 266
Period size: 30 Copynumber: 12.1 Consensus size: 30
21697 AAAGGCCTCG
* *
21707 AACTTT-TCAAAAATCACATTTTTTAACCCCTA
1 AACTTTCTCCAAAATCACA--TTTTGACCCC-A
* * *
21739 AACTTTCT-AAAAATAACATTTTAACCCTCA
1 AACTTTCTCCAAAATCACATTTTGACCC-CA
**
21769 AAC-TTCTTAAAAAATCACATTTTGACCACCA
1 AACTTTC-TCCAAAATCACATTTTGACC-CCA
* *
21800 AAC-TTCTCAAAAATCACATTTTGACTTCCA
1 AACTTTCTCCAAAATCACATTTTGAC-CCCA
*
21830 AAGCTTTCT--AAAATCACATTTTAACCCCA
1 AA-CTTTCTCCAAAATCACATTTTGACCCCA
* * * *
21859 AAATTTTTCTAAAATCACATTTTGACCCTTA
1 AACTTTCTCCAAAATCACATTTTGACCC-CA
* * *
21890 AACTTT-TCCAAAATAATATTTTCACCCCCA
1 AACTTTCTCCAAAATCACATTTTGA-CCCCA
21920 AAC-TTCTCCAAAATCACATTTTGACCACCA
1 AACTTTCTCCAAAATCACATTTTGACC-CCA
* *
21950 AACCTTCT-CGAAATCACATTTTGACCCCA
1 AACTTTCTCCAAAATCACATTTTGACCCCA
* *
21979 AAC-TTCTCCAAAATCACCTTTTGACTCCA
1 AACTTTCTCCAAAATCACATTTTGACCCCA
* * *
22008 AACTTTC-CTAAAATTACATTTTTA-CCCA
1 AACTTTCTCCAAAATCACATTTTGACCCCA
* * * ** *
22036 TAAATTTTTCCAAAATTATGTTTTAACCCCA
1 -AACTTTCTCCAAAATCACATTTTGACCCCA
22067 AACT
1 AACT
22071 CTCCGAAACT
Statistics
Matches: 276, Mismatches: 36, Indels: 42
0.78 0.10 0.12
Matches are distributed among these distances:
28 11 0.04
29 57 0.21
30 144 0.52
31 43 0.16
32 20 0.07
33 1 0.00
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (30 bp):
AACTTTCTCCAAAATCACATTTTGACCCCA
Found at i:21893 original size:90 final size:86
Alignment explanation
Indices: 21707--22070 Score: 316
Period size: 90 Copynumber: 4.0 Consensus size: 86
21697 AAAGGCCTCG
* * * *
21707 AACTTTTCAAAAATCACATTTTTTAACCCCTAAACTTTCTAAAAATAACATTTTAACCCTCAAAC
1 AACTTCTCAAAAATCACA--TTTTGACCCC-AAACTTTCT-AAAATCACATTTTAACCC-CAAAA
**
21772 TTCTTAAAAAATCACATTTTGACCACCA
61 TT-TTTCAAAATCACATTTTGACC-CCA
*
21800 AACTTCTCAAAAATCACATTTTGACTTCCAAAGCTTTCTAAAATCACATTTTAACCCCAAAATTT
1 AACTTCTCAAAAATCACATTTTGAC-CCCAAA-CTTTCTAAAATCACATTTTAACCCCAAAATTT
*
21865 TTCTAAAATCACATTTTGACCCTTA
64 TTC-AAAATCACATTTTGACCC-CA
* * * * * * * **
21890 AACTTTTCCAAAATAATATTTTCACCCCCAAACTTCTCCAAAATCACATTTTGACCACCAAACCT
1 AACTTCTCAAAAATCACATTTTGA-CCCCAAACTT-TCTAAAATCACATTTTAACC-CCAAAATT
* *
21955 TCTCGAAATCACATTTTGACCCCA
63 TTTCAAAATCACATTTTGACCCCA
* * * * *
21979 AACTTCTCCAAAATCACCTTTTGACTCCAAACTTTCCTAAAATTACATTTTTA-CCCATAAATTT
1 AACTTCTCAAAAATCACATTTTGACCCCAAACTTT-CTAAAATCACATTTTAACCCCA-AAATTT
* ** *
22043 TTCCAAAATTATGTTTTAACCCCA
64 TT-CAAAATCACATTTTGACCCCA
22067 AACT
1 AACT
22071 CTCCGAAACT
Statistics
Matches: 223, Mismatches: 38, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
86 3 0.01
87 7 0.03
88 43 0.19
89 26 0.12
90 83 0.37
91 36 0.16
92 8 0.04
93 17 0.08
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.34
Consensus pattern (86 bp):
AACTTCTCAAAAATCACATTTTGACCCCAAACTTTCTAAAATCACATTTTAACCCCAAAATTTTT
CAAAATCACATTTTGACCCCA
Found at i:27117 original size:6 final size:6
Alignment explanation
Indices: 27108--27133 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27098 ATACCCGAAA
27108 CCTGAC CCTGAC CCTGAC CCTGAC CC
1 CCTGAC CCTGAC CCTGAC CCTGAC CC
27134 AAACCCAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.54, G:0.15, T:0.15
Consensus pattern (6 bp):
CCTGAC
Found at i:28052 original size:10 final size:10
Alignment explanation
Indices: 28038--28136 Score: 53
Period size: 10 Copynumber: 9.5 Consensus size: 10
28028 AAAATTGTAA
28038 AAAAAGTTATT
1 AAAAA-TTATT
*
28049 AAAAATTA-A
1 AAAAATTATT
28058 AAAACATTATT
1 AAAA-ATTATT
* * *
28069 TAAATTTTTT
1 AAAAATTATT
28079 AAAAAGTTATT
1 AAAAA-TTATT
*
28090 -AAAA-TAAT
1 AAAAATTATT
28098 AAAATATTATTT
1 AAAA-ATTA-TT
28110 AAAATATTA-T
1 AAAA-ATTATT
28120 AAATAATTATT
1 AAA-AATTATT
28131 AGAAAA
1 A-AAAA
28137 ATGTAAATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 20
0.69 0.10 0.20
Matches are distributed among these distances:
8 3 0.04
9 7 0.10
10 27 0.40
11 19 0.28
12 12 0.18
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (10 bp):
AAAAATTATT
Found at i:28071 original size:21 final size:22
Alignment explanation
Indices: 28025--28072 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
28015 GCTAAAATGT
*
28025 TTTAAAATTGTAAAAAAAGTTA
1 TTTAAAAATGTAAAAAAAGTTA
28047 -TTAAAAAT-TAAAAAACA-TTA
1 TTTAAAAATGTAAAAAA-AGTTA
28067 TTTAAA
1 TTTAAA
28073 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.35
Consensus pattern (22 bp):
TTTAAAAATGTAAAAAAAGTTA
Found at i:28074 original size:41 final size:40
Alignment explanation
Indices: 28029--28112 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
28019 AAATGTTTTA
28029 AAATTGTAAAAAAAGTTATTAAAAATTAA-AAAACATTATTT
1 AAATTGTAAAAAAAGTTATT-AAAA-TAATAAAACATTATTT
* ** *
28070 AAATTTTTTAAAAAGTTATTAAAATAATAAAATATTATTT
1 AAATTGTAAAAAAAGTTATTAAAATAATAAAACATTATTT
28110 AAA
1 AAA
28113 ATATTATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
39 3 0.08
40 18 0.47
41 17 0.45
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (40 bp):
AAATTGTAAAAAAAGTTATTAAAATAATAAAACATTATTT
Found at i:28130 original size:41 final size:41
Alignment explanation
Indices: 28025--28159 Score: 122
Period size: 41 Copynumber: 3.3 Consensus size: 41
28015 GCTAAAATGT
* *
28025 TTTAAAAT-TGTAAAAAAAGTTATTAAAAATTAA-AAAACATTA
1 TTTAAAATAT-TATAAAAAGTTATT-AAAA-TAATAAAATATTA
* *
28067 TTT-AAATTTTTTAAAAAGTTATTAAAATAATAAAATATTA
1 TTTAAAATATTATAAAAAGTTATTAAAATAATAAAATATTA
*
28107 TTTAAAATATTATAAATAA-TTATTAGAAA-AATGTAAAT-TTA
1 TTTAAAATATTATAAA-AAGTTATTA-AAATAAT-AAAATATTA
28148 TTTAAAA-ATTAT
1 TTTAAAATATTAT
28160 GGACCAGTGG
Statistics
Matches: 81, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
39 3 0.04
40 20 0.25
41 45 0.56
42 13 0.16
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.41
Consensus pattern (41 bp):
TTTAAAATATTATAAAAAGTTATTAAAATAATAAAATATTA
Found at i:28359 original size:3 final size:3
Alignment explanation
Indices: 28351--28437 Score: 174
Period size: 3 Copynumber: 29.0 Consensus size: 3
28341 AGATAAAATT
28351 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
28399 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
28438 TTTGATTTGT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29155 original size:82 final size:82
Alignment explanation
Indices: 29063--29226 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
29053 TATAAATGTG
*
29063 GGTAATTTTCAATTTTGATTCTTCTAATAGATTTAAACTTAGAGATTTAATCTTTATACTTCAAT
1 GGTAAATTTCAATTTTGATTCTTCTAATAGATTTAAACTTAGAGATTTAATCTTTATACTTCAAT
29128 TTTTAACATAATTTCAT
66 TTTTAACATAATTTCAT
29145 GGTAAATTTCAATTTTGATTCTTCTAATAGATTTAAACTTAGAGATTTAATCTTTATACTTCAAT
1 GGTAAATTTCAATTTTGATTCTTCTAATAGATTTAAACTTAGAGATTTAATCTTTATACTTCAAT
29210 TTTTAACATAATTTCAT
66 TTTTAACATAATTTCAT
29227 CTTTACATTT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (82 bp):
GGTAAATTTCAATTTTGATTCTTCTAATAGATTTAAACTTAGAGATTTAATCTTTATACTTCAAT
TTTTAACATAATTTCAT
Found at i:36126 original size:25 final size:26
Alignment explanation
Indices: 36080--36133 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
36070 TTATTATTTT
* *
36080 AAATATTCAAAAATTTATAATTATAA
1 AAATATTCAAAAAATTAAAATTATAA
36106 AAATATT-AAAAAATTAAAATTATAA
1 AAATATTCAAAAAATTAAAATTATAA
36131 AAA
1 AAA
36134 CAAAACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATATTCAAAAAATTAAAATTATAA
Found at i:53456 original size:2 final size:2
Alignment explanation
Indices: 53449--53504 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
53439 CAATCAATTA
53449 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
53491 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.