Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010801.1 Kokia drynarioides strain JFW-HI SEQ_125768, 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: 35066
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 13 characters in sequence are not A, C, G, or T
Found at i:1044 original size:17 final size:16
Alignment explanation
Indices: 1022--1084 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
1012 TTGATTTTTC
1022 TAAATTTAATTTTATAA
1 TAAATTTAATTTTA-AA
*
1039 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTTAAA
* *
1056 TAAACTTAAATTTAAAA
1 TAAA-TTTAATTTTAAA
*
1073 TAAATTCAATTT
1 TAAATTTAATTT
1085 CCAACAGGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 7 0.17
17 25 0.62
18 8 0.20
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTTAAA
Found at i:8039 original size:26 final size:25
Alignment explanation
Indices: 7996--8092 Score: 76
Period size: 24 Copynumber: 3.9 Consensus size: 25
7986 ATTATTAAAT
* *
7996 ATAATTTAATA-AAATTAATAATAA
1 ATAATTAAATATAATTTAATAATAA
* *
8020 ATAATTTAATCATATTTTAAT-ATAA
1 ATAATTAAAT-ATAATTTAATAATAA
*
8045 TTATTATTAAATATAATTTAATAA-AA
1 --ATAATTAAATATAATTTAATAATAA
*
8071 ATAA-AAATATATAATTTAATAA
1 ATAATTAA-ATATAATTTAATAA
8093 CATTCTTAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
23 2 0.03
24 27 0.45
25 5 0.08
26 17 0.28
27 9 0.15
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
ATAATTAAATATAATTTAATAATAA
Found at i:8048 original size:61 final size:62
Alignment explanation
Indices: 7983--8108 Score: 200
Period size: 61 Copynumber: 2.0 Consensus size: 62
7973 ATATAATAGG
* * * *
7983 ATTATTATTAAATATAATTTAATAAAATTAATAATAAATAATTTAATCATATT-TTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATAACATTCTTAATATA
*
8044 ATTATTATTAAATATAATTTAATAAAAATAAAAATATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATAACATTCTTAATATA
8106 ATT
1 ATT
8109 TTTTATATAT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
61 48 0.81
62 11 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (62 bp):
ATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATAACATTCTTAATATA
Found at i:8061 original size:21 final size:21
Alignment explanation
Indices: 7962--8066 Score: 74
Period size: 21 Copynumber: 5.1 Consensus size: 21
7952 ATTATTTGTT
**
7962 ATTATTATTAAATATAATAGG
1 ATTATTATTAAATATAATATA
*
7983 ATTATTATTAAATATAATTTA
1 ATTATTATTAAATATAATATA
**
8004 A-TAAAATT-AATAATAA-ATA
1 ATTATTATTAAAT-ATAATATA
* * * *
8023 ATT-TAATCATATTTTAATATA
1 ATTATTATTA-AATATAATATA
*
8044 ATTATTATTAAATATAATTTA
1 ATTATTATTAAATATAATATA
8065 AT
1 AT
8067 AAAAATAAAA
Statistics
Matches: 63, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
19 9 0.14
20 13 0.21
21 37 0.59
22 4 0.06
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTATTATTAAATATAATATA
Found at i:24536 original size:19 final size:18
Alignment explanation
Indices: 24512--24547 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
24502 AATGAAATTA
*
24512 TTTAATATTACAATTTTAT
1 TTTAATAATA-AATTTTAT
24531 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
24548 ACATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:24586 original size:20 final size:20
Alignment explanation
Indices: 24528--24593 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 20
24518 ATTACAATTT
*
24528 TATTTTAATAATAAATTTTAA
1 TATTTTAAAAAT-AATTTTAA
*
24549 CA--TTAAAAATAATTTTAA
1 TATTTTAAAAATAATTTTAA
*
24567 -ATTTTAAAAGATATTTTTAA
1 TATTTTAAAA-ATAATTTTAA
24587 TATTTTA
1 TATTTTA
24594 TTGAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 1 0.03
18 8 0.21
19 13 0.34
20 9 0.24
21 7 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TATTTTAAAAATAATTTTAA
Found at i:24684 original size:114 final size:114
Alignment explanation
Indices: 24550--24777 Score: 447
Period size: 114 Copynumber: 2.0 Consensus size: 114
24540 AAATTTTAAC
24550 ATTAAAAATAATTTTAAATTTTAAAAGATATTTTTAATATTTTATTGAAAAATATGTTATATTAA
1 ATTAAAAATAATTTTAAATTTTAAAAGATATTTTTAATATTTTATTGAAAAATATGTTATATTAA
*
24615 TATTTCAATAATAGATATATATTATGGTTTATAAATATTCAATAATAAA
66 CATTTCAATAATAGATATATATTATGGTTTATAAATATTCAATAATAAA
24664 ATTAAAAATAATTTTAAATTTTAAAAGATATTTTTAATATTTTATTGAAAAATATGTTATATTAA
1 ATTAAAAATAATTTTAAATTTTAAAAGATATTTTTAATATTTTATTGAAAAATATGTTATATTAA
24729 CATTTCAATAATAGATATATATTATGGTTTATAAATATTCAATAATAAA
66 CATTTCAATAATAGATATATATTATGGTTTATAAATATTCAATAATAAA
24778 TGTTTTTATA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (114 bp):
ATTAAAAATAATTTTAAATTTTAAAAGATATTTTTAATATTTTATTGAAAAATATGTTATATTAA
CATTTCAATAATAGATATATATTATGGTTTATAAATATTCAATAATAAA
Found at i:24689 original size:19 final size:21
Alignment explanation
Indices: 24665--24707 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
24655 AATAATAAAA
24665 TTAAAA-ATAATTTTAA-ATT
1 TTAAAAGATAATTTTAATATT
*
24684 TTAAAAGATATTTTTAATATT
1 TTAAAAGATAATTTTAATATT
24705 TTA
1 TTA
24708 TTGAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 9 0.43
21 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTAAAAGATAATTTTAATATT
Found at i:25197 original size:14 final size:14
Alignment explanation
Indices: 25178--25211 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
25168 AAAATCAATC
25178 TATTTTTTAAAAAT
1 TATTTTTTAAAAAT
*
25192 TATTTTTTAGAAAT
1 TATTTTTTAAAAAT
*
25206 TGTTTT
1 TATTTT
25212 CAATGAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (14 bp):
TATTTTTTAAAAAT
Found at i:29675 original size:22 final size:22
Alignment explanation
Indices: 29647--29691 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29637 TGGCTACTTT
29647 TGAACATAATACTATCTCAAAG
1 TGAACATAATACTATCTCAAAG
29669 TGAACATAATACTATCTCAAAG
1 TGAACATAATACTATCTCAAAG
29691 T
1 T
29692 ATCTAACTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.18, G:0.09, T:0.29
Consensus pattern (22 bp):
TGAACATAATACTATCTCAAAG
Found at i:33110 original size:18 final size:20
Alignment explanation
Indices: 33068--33111 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
33058 ATACAATAAT
33068 AATATATTTTAATTTTAGAA
1 AATATATTTTAATTTTAGAA
*
33088 CATATATTTT-ATTTTA-AA
1 AATATATTTTAATTTTAGAA
33106 AATATA
1 AATATA
33112 ATTATATATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 6 0.27
20 9 0.41
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
AATATATTTTAATTTTAGAA
Found at i:33276 original size:21 final size:21
Alignment explanation
Indices: 33246--33294 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
33236 TTTTTGTATG
33246 AAAATTCTATCATAA-AAGTTAT
1 AAAA-TCTATCA-AACAAGTTAT
* *
33268 AAAATCTATTAAACAATTTAT
1 AAAATCTATCAAACAAGTTAT
33289 AAAATC
1 AAAATC
33295 CTTCTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 18 0.75
22 4 0.17
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (21 bp):
AAAATCTATCAAACAAGTTAT
Found at i:34684 original size:11 final size:11
Alignment explanation
Indices: 34668--34727 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
34658 GGGGACCAAC
* *
34668 GAAAAATGAAG
1 GAAAAAAGAAA
34679 GAAAAAAGAAA
1 GAAAAAAGAAA
34690 GAAAAAAG--A
1 GAAAAAAGAAA
34699 GAAAGAAAGAAA
1 GAAA-AAAGAAA
* *
34711 GAAAGAAGAAG
1 GAAAAAAGAAA
34722 GAAAAA
1 GAAAAA
34728 GGAGAAGAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
9 5 0.12
10 4 0.10
11 27 0.66
12 5 0.12
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:34692 original size:4 final size:4
Alignment explanation
Indices: 34679--34717 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
34669 AAAAATGAAG
*
34679 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAA
34718 GAAGGAAAAA
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:34728 original size:25 final size:24
Alignment explanation
Indices: 34679--34728 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
34669 AAAAATGAAG
*
34679 GAAAAAAGAAAGAAAAAAGAGAAA
1 GAAAAAAGAAAGAAAAAAGAAAAA
* *
34703 GAAAGAAAGAAAGAAGAAGGAAAAA
1 GAAA-AAAGAAAGAAAAAAGAAAAA
34728 G
1 G
34729 GAGAAGAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (24 bp):
GAAAAAAGAAAGAAAAAAGAAAAA
Found at i:34736 original size:31 final size:33
Alignment explanation
Indices: 34679--34759 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 33
34669 AAAAATGAAG
* *
34679 GAAAAAAGAAAGAAAAAAGAGAAAGAA-AGAAA
1 GAAAGAAGAAGGAAAAAAGAGAAAGAAGAGAAA
* * *
34711 GAAAGAAGAAGGAAAAAGGAG-AAGAAGGGGAA
1 GAAAGAAGAAGGAAAAAAGAGAAAGAAGAGAAA
*
34743 G-AAGGAGAAGGAAAAAA
1 GAAAGAAGAAGGAAAAAA
34760 AAAGTAACGT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 19 0.46
32 22 0.54
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (33 bp):
GAAAGAAGAAGGAAAAAAGAGAAAGAAGAGAAA
Found at i:34743 original size:9 final size:9
Alignment explanation
Indices: 34714--34752 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
34704 AAAGAAAGAA
34714 AGAAGAAGG
1 AGAAGAAGG
34723 A-AA-AAGG
1 AGAAGAAGG
34730 AGAAGAAGG
1 AGAAGAAGG
*
34739 GGAAGAAGG
1 AGAAGAAGG
34748 AGAAG
1 AGAAG
34753 GAAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 5 0.19
8 4 0.15
9 17 0.65
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (9 bp):
AGAAGAAGG
Done.