Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015164.1 Kokia drynarioides strain JFW-HI SEQ_130208, 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: 20557
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1612 original size:24 final size:22
Alignment explanation
Indices: 1575--1628 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 22
1565 TTACCTGCAA
1575 AAAATACAGAGAAAAAAAAATGAG
1 AAAA-ACAGAGAAAAAAAAAT-AG
*
1599 AAAGAACAGAGAAAGAAAAATAG
1 AAA-AACAGAGAAAAAAAAATAG
1622 AAAAACA
1 AAAAACA
1629 TAATATATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 4 0.14
23 5 0.18
24 18 0.64
25 1 0.04
ACGTcount: A:0.72, C:0.06, G:0.17, T:0.06
Consensus pattern (22 bp):
AAAAACAGAGAAAAAAAAATAG
Found at i:3003 original size:2 final size:2
Alignment explanation
Indices: 2996--3027 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2986 ACGGTGGATA
2996 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3028 TTCTTTTTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:14939 original size:55 final size:56
Alignment explanation
Indices: 14822--15267 Score: 262
Period size: 56 Copynumber: 8.1 Consensus size: 56
14812 TGAGATTTTG
* * * * * * *
14822 AAAAGAAAAATTTGGTGTTGGTCAATGCTTGACCAACATC-ACCCTTTTGATCAAAT
1 AAAA-AAAAATTTGGTGTTGGTCAATACTTGGCCGACACCAACCTTTTTTATCAGAT
*
14878 AAAAAAAAAATTTGGTGTTGGTCAATACTTGGCCGACA-CAACCTTTTTAATCAGAT
1 -AAAAAAAAATTTGGTGTTGGTCAATACTTGGCCGACACCAACCTTTTTTATCAGAT
* * * * * *
14934 AAAAAAAAATTTAGTGTTGGTCATCTA-TTGGCTGACACCAGCATTTTTTTATCAAAT
1 AAAAAAAAATTTGGTGTTGGTCA-ATACTTGGCCGACACCAAC-CTTTTTTATCAGAT
* * * * * *
14991 GACAAAAAATTTTGGTGTTAGCCAATACTTGACCGACACCAA-CTTTTTTATTAGAT
1 -AAAAAAAAATTTGGTGTTGGTCAATACTTGGCCGACACCAACCTTTTTTATCAGAT
* * * * * *
15047 --AAAAAAATTTGGTATTAGCCAATGCTTGGTCGACACCAA-CTTTTTTATTAGAT
1 AAAAAAAAATTTGGTGTTGGTCAATACTTGGCCGACACCAACCTTTTTTATCAGAT
** * * ** * *
15100 AAAAAAAAA-TT-GTGTT-CACCATGCATTGGTTGACACC-GCTTTTTTTATCA-A-
1 AAAAAAAAATTTGGTGTTGGTCAATAC-TTGGCCGACACCAACCTTTTTTATCAGAT
* * * * *
15151 ATAAAAAAA-TTGGTGTTGG-CCATGCATTAGCCGACACC-A-TTTTTTTATCAGAT
1 AAAAAAAAATTTGGTGTTGGTCAATAC-TTGGCCGACACCAACCTTTTTTATCAGAT
*** * * * * * *
15204 AAAAATATTTTTTTGTGTTGGCCAATGCTTGGCCGACATC-ACTTTTTTTATCTGAT
1 AAAAA-AAAATTTGGTGTTGGTCAATACTTGGCCGACACCAACCTTTTTTATCAGAT
15260 AAAAAAAA
1 AAAAAAAA
15268 TAATTTTTTT
Statistics
Matches: 316, Mismatches: 55, Indels: 38
0.77 0.13 0.09
Matches are distributed among these distances:
51 21 0.07
52 28 0.09
53 76 0.24
54 3 0.01
55 60 0.19
56 82 0.26
57 17 0.05
58 29 0.09
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (56 bp):
AAAAAAAAATTTGGTGTTGGTCAATACTTGGCCGACACCAACCTTTTTTATCAGAT
Found at i:15065 original size:53 final size:53
Alignment explanation
Indices: 14994--15106 Score: 181
Period size: 53 Copynumber: 2.1 Consensus size: 53
14984 ATCAAATGAC
* *
14994 AAAAAATTTTGGTGTTAGCCAATACTTGACCGACACCAACTTTTTTATTAGAT
1 AAAAAAATTTGGTATTAGCCAATACTTGACCGACACCAACTTTTTTATTAGAT
* **
15047 AAAAAAATTTGGTATTAGCCAATGCTTGGTCGACACCAACTTTTTTATTAGAT
1 AAAAAAATTTGGTATTAGCCAATACTTGACCGACACCAACTTTTTTATTAGAT
15100 AAAAAAA
1 AAAAAAA
15107 AATTGTGTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (53 bp):
AAAAAAATTTGGTATTAGCCAATACTTGACCGACACCAACTTTTTTATTAGAT
Found at i:15142 original size:52 final size:52
Alignment explanation
Indices: 15024--15208 Score: 164
Period size: 53 Copynumber: 3.5 Consensus size: 52
15014 AATACTTGAC
* * *
15024 CGACACCAACTTTTTTATTAGAT-AAAAAAATTTG-GTATTAGCCAATGC-TTGGT
1 CGACACC-ACTTTTTTATCAGATAAAAAAAAATTGTGT-TCA-CC-ATGCATTGGT
*
15077 CGACACCAACTTTTTTATTAGATAAAAAAAAATTGTGTTCACCATGCATTGGT
1 CGACACC-ACTTTTTTATCAGATAAAAAAAAATTGTGTTCACCATGCATTGGT
* * * ** * *
15130 TGACACCGCTTTTTTTATCA-A-ATAAAAAAATTGGTGTTGGCCATGCATTAGC
1 CGACACCAC-TTTTTTATCAGATAAAAAAAAATT-GTGTTCACCATGCATTGGT
*
15182 CGACACCATTTTTTTATCAGATAAAAA
1 CGACACCACTTTTTTATCAGATAAAAA
15209 TATTTTTTTG
Statistics
Matches: 111, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
51 20 0.18
52 28 0.25
53 49 0.44
54 12 0.11
55 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (52 bp):
CGACACCACTTTTTTATCAGATAAAAAAAAATTGTGTTCACCATGCATTGGT
Found at i:15302 original size:62 final size:55
Alignment explanation
Indices: 15163--15311 Score: 174
Period size: 62 Copynumber: 2.6 Consensus size: 55
15153 AAAAAAATTG
15163 GTGTTGGCCATGCATTAGCCGACACCATTTTTTTATCAGATAAAAATATTTTTTT
1 GTGTTGGCCATGCATTAGCCGACACCATTTTTTTATCAGATAAAAATATTTTTTT
* * *
15218 GTGTTGGCCAATGC-TTGGCCGACATCACTTTTTTTATCTGATAAAAAAAATAATTTTTTTTT
1 GTGTTGGCC-ATGCATTAGCCGACACCA-TTTTTTTATCAGAT---AAAAAT-A--TTTTTTT
* *
15280 GTGTTGGCCATGCATTAACCGACACCAATTTT
1 GTGTTGGCCATGCATTAGCCGACACCATTTTT
15312 CCCTCATTTC
Statistics
Matches: 78, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
55 20 0.26
56 17 0.22
59 6 0.08
60 1 0.01
61 8 0.10
62 26 0.33
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (55 bp):
GTGTTGGCCATGCATTAGCCGACACCATTTTTTTATCAGATAAAAATATTTTTTT
Found at i:16145 original size:22 final size:21
Alignment explanation
Indices: 16102--16146 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
16092 AAATAAATAT
* * *
16102 TATTGAAAAAGATTATATAAA
1 TATTGAAAAAAATAATAGAAA
16123 TATTGAAAAAAATAATTAGAAA
1 TATTGAAAAAAATAA-TAGAAA
16145 TA
1 TA
16147 AAATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (21 bp):
TATTGAAAAAAATAATAGAAA
Found at i:16229 original size:31 final size:30
Alignment explanation
Indices: 16136--16258 Score: 183
Period size: 30 Copynumber: 4.1 Consensus size: 30
16126 TGAAAAAAAT
* *
16136 AATTAGAAATAAAATTTAAAATATAAACAA
1 AATTAGAAATTAAATTTAAAATATAAACGA
*
16166 AATTAGAAATTAAATTCAAAATATAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
*
16196 AATTAGAAATTAAATTTAAAATATGTAACGA
1 AATTAGAAATTAAATTTAAAATAT-AAACGA
* *
16227 AATTACAAATTAAATTTAAAAAATAAACGA
1 AATTAGAAATTAAATTTAAAATATAAACGA
16257 AA
1 AA
16259 AAAATCAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
30 57 0.68
31 27 0.32
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.28
Consensus pattern (30 bp):
AATTAGAAATTAAATTTAAAATATAAACGA
Found at i:16255 original size:61 final size:60
Alignment explanation
Indices: 16136--16258 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 60
16126 TGAAAAAAAT
* *
16136 AATTAGAAATAAAATTTAAAATATAAACAAAATTAGAAATTAAATTCAAAATATAAACGA
1 AATTAGAAATAAAATTTAAAATATAAACAAAATTACAAATTAAATTCAAAAAATAAACGA
* * * *
16196 AATTAGAAATTAAATTTAAAATATGTAACGAAATTACAAATTAAATTTAAAAAATAAACGA
1 AATTAGAAATAAAATTTAAAATAT-AAACAAAATTACAAATTAAATTCAAAAAATAAACGA
16257 AA
1 AA
16259 AAAATCAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
60 23 0.41
61 33 0.59
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.28
Consensus pattern (60 bp):
AATTAGAAATAAAATTTAAAATATAAACAAAATTACAAATTAAATTCAAAAAATAAACGA
Found at i:17455 original size:18 final size:17
Alignment explanation
Indices: 17417--17458 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
17407 AAATAATTTT
*
17417 TAAAAAAATCGAAAAGC
1 TAAAAAAATCGAAAAGA
*
17434 TAAAAAAATTCGAAAATA
1 TAAAAAAA-TCGAAAAGA
17452 TAAAAAA
1 TAAAAAA
17459 TATATGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (17 bp):
TAAAAAAATCGAAAAGA
Found at i:17556 original size:22 final size:21
Alignment explanation
Indices: 17500--17549 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
17490 TTTAAAAGAA
*
17500 TTCAAAAA-ATAAAAAAACAT
1 TTCAAAAATAGAAAAAAACAT
*
17520 TTCAAAAATAGAAAAAAATAT
1 TTCAAAAATAGAAAAAAACAT
*
17541 TTTAAAAAT
1 TTCAAAAAT
17550 TCGAAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (21 bp):
TTCAAAAATAGAAAAAAACAT
Found at i:17922 original size:33 final size:33
Alignment explanation
Indices: 17880--17945 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
17870 TACAATGTAA
17880 CTTAATTTCCTGGCTGCCTTCATATCAACCAGT
1 CTTAATTTCCTGGCTGCCTTCATATCAACCAGT
17913 CTTAATTTCCTGGCTGCCTTCATATCAACCAGT
1 CTTAATTTCCTGGCTGCCTTCATATCAACCAGT
17946 AATAGGAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.36
Consensus pattern (33 bp):
CTTAATTTCCTGGCTGCCTTCATATCAACCAGT
Found at i:18901 original size:93 final size:92
Alignment explanation
Indices: 18800--19441 Score: 980
Period size: 93 Copynumber: 6.9 Consensus size: 92
18790 TTAAGGGTAT
18800 TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATT
1 TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATT
18865 TTTTATTTAAAAAATTTTAAAATTTGAA
66 TTTTATTTAAAAAA-TTTAAAATTTGAA
*
18893 TTTGGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATT
1 TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATT
18958 TTTTATTTAAAAAAATTTAAAATTTGAA
66 TTTTATTT-AAAAAATTTAAAATTTGAA
*
18986 TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTAATAAAAATTGAAATATTATAATAATT
1 TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATT
19051 TTTTATTTAAATAAATTTAAAATTTGAA
66 TTTTATTTAAA-AAATTTAAAATTTGAA
* * * * * *
19079 TTAGATAAATAATGTATTGTCAAATCAAAACTTTATTTGATAAAAATTAAAATATTATAATAAAT
1 TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATT
19144 TTTTATTTAAATAAATTTAAAATTTGAA
66 TTTTATTTAAA-AAATTTAAAATTTGAA
* * * *
19172 TTAGGTAAATAATTTATTGTCAAATCAACACATTATTTGATAAAAATTAAAATATTATAATTATT
1 TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATT
19237 TTTTATTTAAATAAATTTAAAATTTGAA
66 TTTTATTTAAA-AAATTTAAAATTTGAA
** * * *
19265 TTTAATAAATAATGTATTGTCAAAT-AACACATTATTTTATAAAAATTGAAATATTATAGTAGTC
1 TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATA--A
*
19329 TTTTTTATTTAAATAATTTTAAAATTTGAA
64 TTTTTTATTTAAA-AAATTTAAAATTTGAA
* * * *
19359 TTTGGTAAATAATATATTGTCAAATCAACACATTATTTGATATAAATTAAAATATTATACTAATA
1 TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAAT-A-A
*
19424 TTTTTTATTTAAATAATT
64 TTTTTTATTTAAAAAATT
19442 AATTTTAAAA
Statistics
Matches: 507, Mismatches: 36, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
92 35 0.07
93 366 0.72
94 60 0.12
95 45 0.09
96 1 0.00
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (92 bp):
TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATT
TTTTATTTAAAAAATTTAAAATTTGAA
Done.