Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009696.1 Kokia drynarioides strain JFW-HI SEQ_124415, 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: 58083
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:3045 original size:14 final size:14
Alignment explanation
Indices: 3026--3052 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3016 AGTCACTTAT
3026 AATATATGTGTTGG
1 AATATATGTGTTGG
3040 AATATATGTGTTG
1 AATATATGTGTTG
3053 ATTACTGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.44
Consensus pattern (14 bp):
AATATATGTGTTGG
Found at i:3256 original size:27 final size:28
Alignment explanation
Indices: 3225--3295 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
3215 TCTTTTATGT
**
3225 TTTTTCAACTATCTTTTTTTTTTC-TTTA
1 TTTTTC-ACTATCTTTTGCTTTTCTTTTA
*
3253 TTTTTCATTATCTTTTGCTTTTCTTTTA
1 TTTTTCACTATCTTTTGCTTTTCTTTTA
*
3281 TTTTTCTCTAT-TTTT
1 TTTTTCACTATCTTTT
3296 CGTATGTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 18 0.49
28 19 0.51
ACGTcount: A:0.11, C:0.14, G:0.01, T:0.73
Consensus pattern (28 bp):
TTTTTCACTATCTTTTGCTTTTCTTTTA
Found at i:24337 original size:25 final size:25
Alignment explanation
Indices: 24304--24353 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
24294 CGAATCATAA
24304 ACAACACTA-ATATAACAATATTACAT
1 ACAACACTATA-ATAA-AATATTACAT
24330 ACAA-ACTATGAATAAAATATTACA
1 ACAACACTAT-AATAAAATATTACA
24354 AATTATTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
25 13 0.59
26 8 0.36
27 1 0.05
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.26
Consensus pattern (25 bp):
ACAACACTATAATAAAATATTACAT
Found at i:35190 original size:14 final size:15
Alignment explanation
Indices: 35161--35193 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
35151 AAATCCAAAG
35161 ATAAAATCAAAGGAT
1 ATAAAATCAAAGGAT
*
35176 ATAAAA-CATAGGAT
1 ATAAAATCAAAGGAT
35190 ATAA
1 ATAA
35194 GTCGAACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.21
Consensus pattern (15 bp):
ATAAAATCAAAGGAT
Found at i:39616 original size:29 final size:31
Alignment explanation
Indices: 39559--39618 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
39549 ATTATAAAAA
*
39559 TAATCACTCAATTATTAAAATATTTTTATTT
1 TAATCACTCAAGTATTAAAATATTTTTATTT
*
39590 TAATCACTCAAGT-TT-AAATTTTTTTATTT
1 TAATCACTCAAGTATTAAAATATTTTTATTT
39619 AATTGCTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 13 0.48
30 2 0.07
31 12 0.44
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (31 bp):
TAATCACTCAAGTATTAAAATATTTTTATTT
Found at i:39771 original size:30 final size:30
Alignment explanation
Indices: 39736--39804 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
39726 ATATTCTATC
*
39736 AATTTAATCCTAAATTTAACAAACTTAACA
1 AATTTAATCCTAAATTTAACAAACTTAAAA
* * * * *
39766 AATTTAACCCTCAATTTTACACATTTAAAA
1 AATTTAATCCTAAATTTAACAAACTTAAAA
39796 AATTTAATC
1 AATTTAATC
39805 TTGATTCTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.36
Consensus pattern (30 bp):
AATTTAATCCTAAATTTAACAAACTTAAAA
Found at i:40282 original size:21 final size:21
Alignment explanation
Indices: 40257--40310 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
40247 TAACATGAAA
* *
40257 TTTATTCATTAAAATAATAAG
1 TTTATTAAATAAAATAATAAG
*
40278 TTTA-TAAATAAAATAATAAT
1 TTTATTAAATAAAATAATAAG
40298 TTTA-TAAATAAAA
1 TTTATTAAATAAAA
40311 CAATTTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TTTATTAAATAAAATAATAAG
Found at i:40291 original size:20 final size:20
Alignment explanation
Indices: 40266--40310 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
40256 ATTTATTCAT
40266 TAAAATAATAAGTTTATAAA
1 TAAAATAATAAGTTTATAAA
*
40286 TAAAATAATAATTTTATAAA
1 TAAAATAATAAGTTTATAAA
40306 TAAAA
1 TAAAA
40311 CAATTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAATAATAAGTTTATAAA
Found at i:43135 original size:17 final size:17
Alignment explanation
Indices: 43104--43138 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43094 TGGACCCAAG
*
43104 CTTTCTTTTTCCTATTA
1 CTTTCTTTTACCTATTA
*
43121 CTTTCTTTTAGCTATTA
1 CTTTCTTTTACCTATTA
43138 C
1 C
43139 CAAACTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.23, G:0.03, T:0.60
Consensus pattern (17 bp):
CTTTCTTTTACCTATTA
Found at i:47127 original size:58 final size:56
Alignment explanation
Indices: 47035--47148 Score: 183
Period size: 58 Copynumber: 2.0 Consensus size: 56
47025 GACTTGGCTC
* * *
47035 AAGAAGCAGATCATGACAACTTTTTTTCATGTCAGAGCCAGTGGTTGTAAGAACTG
1 AAGAAGCAGATCATGACAACATTTTTCCATGTCAGAGCCAGTGGCTGTAAGAACTG
47091 AAGAAGCAGATCATGACACAACATTTTTCCATGTCAGAGCCAGTGGCTGTAAGAACTG
1 AAGAAGCAGATCATG--ACAACATTTTTCCATGTCAGAGCCAGTGGCTGTAAGAACTG
47149 CGGGGTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
56 15 0.28
58 38 0.72
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.25
Consensus pattern (56 bp):
AAGAAGCAGATCATGACAACATTTTTCCATGTCAGAGCCAGTGGCTGTAAGAACTG
Found at i:47245 original size:4 final size:4
Alignment explanation
Indices: 47221--47260 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
47211 ATTTAGTATC
* * *
47221 ATAT TTAT AAAT ATTT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
47261 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (4 bp):
ATAT
Found at i:47245 original size:6 final size:6
Alignment explanation
Indices: 47221--47260 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
47211 ATTTAGTATC
* * *
47221 ATATTT ATAAAT ATTTAT ATATAT ATATAT ATATAT ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
47261 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
ATATAT
Done.