Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007830.1 Kokia drynarioides strain JFW-HI SEQ_122466, 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: 73359
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Found at i:1274 original size:16 final size:19
Alignment explanation
Indices: 1230--1272 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
1220 ACATAATACA
1230 AATATAAAATAAGATAAAT
1 AATATAAAATAAGATAAAT
1249 AAT-TAAAATAA-A-AAAT
1 AATATAAAATAAGATAAAT
1265 AATATAAA
1 AATATAAA
1273 TACAAGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.30
17 5 0.22
18 8 0.35
19 3 0.13
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AATATAAAATAAGATAAAT
Found at i:3266 original size:25 final size:26
Alignment explanation
Indices: 3211--3267 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
3201 TGTTACAATC
*
3211 TATTTAAAATTTTTATATTTTTTTGTA
1 TATTTAAAA-TTTTATATTTTTTTCTA
*
3238 TATTTAAAA-TTTA-ATTTTTTATCTT
1 TATTTAAAATTTTATATTTTTT-TCTA
3263 TATTT
1 TATTT
3268 TTAAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 7 0.26
25 11 0.41
27 9 0.33
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (26 bp):
TATTTAAAATTTTATATTTTTTTCTA
Found at i:4347 original size:22 final size:22
Alignment explanation
Indices: 4322--4364 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4312 GTTCATTTCT
* *
4322 AGGCTTATATGTCTCGAGAAAA
1 AGGCTTAAATGTCTCAAGAAAA
4344 AGGCTTAAATGTCTCAAGAAA
1 AGGCTTAAATGTCTCAAGAAA
4365 GTGTCATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.26
Consensus pattern (22 bp):
AGGCTTAAATGTCTCAAGAAAA
Found at i:4431 original size:22 final size:22
Alignment explanation
Indices: 4406--4461 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
4396 AGTTATCCTA
* *
4406 TCTCGAGACAAATGAGTGAATG
1 TCTCGAGACAAAAGAATGAATG
* **
4428 TCTCAAGACAAAAGAATTTATG
1 TCTCGAGACAAAAGAATGAATG
4450 TCTCGAGACAAA
1 TCTCGAGACAAA
4462 GTCTAATATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (22 bp):
TCTCGAGACAAAAGAATGAATG
Found at i:6754 original size:15 final size:17
Alignment explanation
Indices: 6731--6768 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
6721 AATTTAATCA
*
6731 TTTATACTTTT-A-TCT
1 TTTACACTTTTCACTCT
6746 TTTACACTTTTCACTCT
1 TTTACACTTTTCACTCT
6763 TTTACA
1 TTTACA
6769 ATTTAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 1 0.05
17 9 0.45
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTACACTTTTCACTCT
Found at i:8474 original size:15 final size:16
Alignment explanation
Indices: 8442--8477 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
8432 TTATTTTTTA
8442 TGAATTATAAATATTT
1 TGAATTATAAATATTT
*
8458 TGAATTTTAAA-ATTT
1 TGAATTATAAATATTT
8473 TGAAT
1 TGAAT
8478 ATTTTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (16 bp):
TGAATTATAAATATTT
Found at i:15151 original size:16 final size:16
Alignment explanation
Indices: 15132--15170 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
15122 ATCATCAACT
*
15132 TTTGTTTTTTTTTTAA
1 TTTGTTTTTTTTCTAA
15148 TTTGTTTTTTTTCTAA
1 TTTGTTTTTTTTCTAA
15164 TTT-TTTT
1 TTTGTTTT
15171 AATGAAAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.10, C:0.03, G:0.05, T:0.82
Consensus pattern (16 bp):
TTTGTTTTTTTTCTAA
Found at i:15332 original size:18 final size:19
Alignment explanation
Indices: 15311--15346 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15301 AAATAATATA
15311 TTTAA-TTAAAAAAATAAC
1 TTTAATTTAAAAAAATAAC
15329 TTTAATTTAAAAAAATAA
1 TTTAATTTAAAAAAATAA
15347 GTTTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TTTAATTTAAAAAAATAAC
Found at i:24168 original size:18 final size:19
Alignment explanation
Indices: 24136--24171 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
24126 ATTAATAGGA
*
24136 AAATATCTCTTCTTTTATC
1 AAATATCTCTCCTTTTATC
24155 AAAT-TCTCTCCTTTTAT
1 AAATATCTCTCCTTTTAT
24172 TTTTTTTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATATCTCTCCTTTTATC
Found at i:24952 original size:10 final size:10
Alignment explanation
Indices: 24931--24967 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
24921 TTAATATCCG
24931 TATTGTTATCT
1 TATTG-TATCT
24942 TATTGTATCT
1 TATTGTATCT
24952 TATTGTATCT
1 TATTGTATCT
*
24962 TCTTGT
1 TATTGT
24968 TTTATCATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 20 0.80
11 5 0.20
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.62
Consensus pattern (10 bp):
TATTGTATCT
Found at i:31936 original size:35 final size:35
Alignment explanation
Indices: 31890--31958 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
31880 AGAATTGCCT
31890 GAAAGCTTCTTTGATAACTCAAGGTTATAGGACCC
1 GAAAGCTTCTTTGATAACTCAAGGTTATAGGACCC
31925 GAAAGCTTCTTTGATAACTCAAGGTTATAGGACC
1 GAAAGCTTCTTTGATAACTCAAGGTTATAGGACC
31959 TAACAACATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (35 bp):
GAAAGCTTCTTTGATAACTCAAGGTTATAGGACCC
Found at i:38033 original size:20 final size:20
Alignment explanation
Indices: 38002--38056 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
37992 ACACGGATAA
38002 TAATAT-TAAAAACATCTTT
1 TAATATATAAAAACATCTTT
* *
38021 TAATATATAAAAATATTTTTT
1 TAATATATAAAAACA-TCTTT
*
38042 TAA-AAATAAAAACAT
1 TAATATATAAAAACAT
38057 ATTCAATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 7 0.23
20 16 0.53
21 7 0.23
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATATATAAAAACATCTTT
Found at i:38343 original size:3 final size:3
Alignment explanation
Indices: 38335--38391 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
38325 ATTAAACTTC
38335 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38383 TAT TAT TAT
1 TAT TAT TAT
38392 CTAGGTGAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41586 original size:18 final size:18
Alignment explanation
Indices: 41560--41597 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
41550 TGAAGGGAAT
*
41560 CATCTTAAATCGAGAAAA
1 CATCGTAAATCGAGAAAA
41578 CATCGTAAATCGAGAAAA
1 CATCGTAAATCGAGAAAA
41596 CA
1 CA
41598 AGACTAGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.18
Consensus pattern (18 bp):
CATCGTAAATCGAGAAAA
Found at i:48289 original size:16 final size:15
Alignment explanation
Indices: 48267--48304 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
48257 TTGTAATTAA
48267 TTATATATATATATT
1 TTATATATATATATT
*
48282 TGTATATA-ATTTATT
1 T-TATATATATATATT
48297 TTATATAT
1 TTATATAT
48305 CAGTTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 6 0.30
15 8 0.40
16 6 0.30
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATATATATATATT
Found at i:48882 original size:23 final size:23
Alignment explanation
Indices: 48822--48871 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
48812 GCCATAAGGC
* * *
48822 AAAAGCATGCTACAATACAGAAG
1 AAAAACATGCCACAAGACAGAAG
48845 AAAAACATGCCACAAGACAG-AG
1 AAAAACATGCCACAAGACAGAAG
48867 AAAAA
1 AAAAA
48872 GCGTGTCACA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 7 0.29
23 17 0.71
ACGTcount: A:0.58, C:0.18, G:0.16, T:0.08
Consensus pattern (23 bp):
AAAAACATGCCACAAGACAGAAG
Found at i:49383 original size:21 final size:21
Alignment explanation
Indices: 49359--49414 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
49349 ATTTTTTTTA
49359 AGGATGAAAATACTGAAATTT
1 AGGATGAAAATACTGAAATTT
*
49380 AGGATGAAAATGCTGAAATTT
1 AGGATGAAAATACTGAAATTT
49401 AGGATGAAAATACT
1 AGGATGAAAATACT
49415 AACATGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.46, C:0.05, G:0.21, T:0.27
Consensus pattern (21 bp):
AGGATGAAAATACTGAAATTT
Found at i:58034 original size:12 final size:12
Alignment explanation
Indices: 58017--58042 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
58007 TGAGCTCATC
58017 TGGAAGAGGGAG
1 TGGAAGAGGGAG
58029 TGGAAGAGGGAG
1 TGGAAGAGGGAG
58041 TG
1 TG
58043 CCAAAGGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.58, T:0.12
Consensus pattern (12 bp):
TGGAAGAGGGAG
Found at i:60424 original size:50 final size:50
Alignment explanation
Indices: 60311--60412 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
60301 AAAATTGTTG
* * *
60311 TTGTATGGTTTTCTCTATTCGCACTATCTTAACCAATCGAAAGCTCTCAT
1 TTGTATGATTTTCTCTATTCGCACTATCTTAACCAATCAAAAACTCTCAT
* *
60361 TTGTATGATTTTCTCTATTCGCACTGTCTTAACCAATTAAAAACTCTCAT
1 TTGTATGATTTTCTCTATTCGCACTATCTTAACCAATCAAAAACTCTCAT
60411 TT
1 TT
60413 TCTTTTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (50 bp):
TTGTATGATTTTCTCTATTCGCACTATCTTAACCAATCAAAAACTCTCAT
Found at i:60943 original size:23 final size:23
Alignment explanation
Indices: 60896--60945 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
60886 ATATATTCGT
* * **
60896 GAACGTATTTGTTTAATTTTCAC
1 GAACATATTCGTTTAATTTAAAC
60919 GAACATATTCGTTTAATTTAAAC
1 GAACATATTCGTTTAATTTAAAC
60942 GAAC
1 GAAC
60946 GAACATGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (23 bp):
GAACATATTCGTTTAATTTAAAC
Found at i:60992 original size:24 final size:23
Alignment explanation
Indices: 60962--61010 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 23
60952 GAACACACAT
*
60962 AATTTTAAATAAACGAATACGAATA
1 AATTTAAAATAAAC-AA-ACGAATA
60987 AATTTAAAAATAAACAAACGAATA
1 AATTT-AAAATAAACAAACGAATA
61011 TAAATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 7 0.32
26 8 0.36
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.24
Consensus pattern (23 bp):
AATTTAAAATAAACAAACGAATA
Found at i:62012 original size:15 final size:15
Alignment explanation
Indices: 61969--62017 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
61959 AGAAATTTAA
*
61969 TAAAA-ATAATTTTA
1 TAAAATATAATTTTT
*
61983 TACAAATA-AA-ATTT
1 TA-AAATATAATTTTT
61997 TAAAATATAATTTTT
1 TAAAATATAATTTTT
62012 TAAAAT
1 TAAAAT
62018 TAAAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
13 5 0.18
14 8 0.29
15 14 0.50
16 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAATATAATTTTT
Done.