Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009666.1 Kokia drynarioides strain JFW-HI SEQ_124384, 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: 21872
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 66 characters in sequence are not A, C, G, or T
Found at i:5220 original size:63 final size:63
Alignment explanation
Indices: 5128--5318 Score: 269
Period size: 63 Copynumber: 3.0 Consensus size: 63
5118 CAAGAGTAAG
* * *
5128 CCTCCGAGCGCC-CCCACGCCTGGAACTCCGAACGCCACCCCGCGAGGAACTTCAAGTTCTCCT
1 CCTCCGACCGCCGCCC-CGCCTGGAACTCCGAACGCCACCCCGCGTGGAACTTCAAGTCCTCCT
* *
5191 CCTCCGACCGCCGCCCCGCGTGGATCTCCGAACGCCACCCCGCGTGGAACTTCAAGTCCTCCT
1 CCTCCGACCGCCGCCCCGCCTGGAACTCCGAACGCCACCCCGCGTGGAACTTCAAGTCCTCCT
* * * *
5254 CCTCCGAGCC-CCGCCACGCCTGGAACTCCGAGCACCACCGCGCGTGGAACTTCAAGTCCTCCT
1 CCTCCGA-CCGCCGCCCCGCCTGGAACTCCGAACGCCACCCCGCGTGGAACTTCAAGTCCTCCT
5317 CC
1 CC
5319 CGAGGCCAAC
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
63 110 0.96
64 5 0.04
ACGTcount: A:0.17, C:0.47, G:0.21, T:0.15
Consensus pattern (63 bp):
CCTCCGACCGCCGCCCCGCCTGGAACTCCGAACGCCACCCCGCGTGGAACTTCAAGTCCTCCT
Found at i:5226 original size:24 final size:24
Alignment explanation
Indices: 5192--5238 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5182 AGTTCTCCTC
* *
5192 CTCCGACCGCCGCCCCGCGTGGAT
1 CTCCGAACGCCACCCCGCGTGGAT
5216 CTCCGAACGCCACCCCGCGTGGA
1 CTCCGAACGCCACCCCGCGTGGA
5239 ACTTCAAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.49, G:0.28, T:0.11
Consensus pattern (24 bp):
CTCCGAACGCCACCCCGCGTGGAT
Found at i:5301 original size:24 final size:24
Alignment explanation
Indices: 5255--5304 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
5245 AGTCCTCCTC
* *
5255 CTCCGAGCCCCGCCACGCCTGGAA
1 CTCCGAGCACCACCACGCCTGGAA
* *
5279 CTCCGAGCACCACCGCGCGTGGAA
1 CTCCGAGCACCACCACGCCTGGAA
5303 CT
1 CT
5305 TCAAGTCCTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.26, T:0.10
Consensus pattern (24 bp):
CTCCGAGCACCACCACGCCTGGAA
Found at i:13732 original size:3 final size:3
Alignment explanation
Indices: 13724--13750 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
13714 ATAAATTAAA
13724 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
13751 ATGTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:15575 original size:42 final size:42
Alignment explanation
Indices: 15516--15618 Score: 179
Period size: 42 Copynumber: 2.5 Consensus size: 42
15506 TTAGTGCTGC
* *
15516 GGGTTCGTCTCCGGCTCCTCAGCCGTCAGCCGCTCCCCCTCA
1 GGGTTCGTCTCCGGCTCCTCAGCCATCAGCCGCTCCCCCACA
15558 GGGTTCGTCTCCGGCTCCTCAGCCATCAGCCGCTCCCCCACA
1 GGGTTCGTCTCCGGCTCCTCAGCCATCAGCCGCTCCCCCACA
*
15600 GGGTTCTTCTCCGGCTCCT
1 GGGTTCGTCTCCGGCTCCT
15619 TTGCCGTCTG
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.08, C:0.46, G:0.23, T:0.23
Consensus pattern (42 bp):
GGGTTCGTCTCCGGCTCCTCAGCCATCAGCCGCTCCCCCACA
Found at i:16391 original size:12 final size:12
Alignment explanation
Indices: 16370--16404 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
16360 AACAGCAACC
*
16370 TCACCTTCACCT
1 TCACCATCACCT
*
16382 TCAGCATCACCT
1 TCACCATCACCT
16394 TCACCATCACC
1 TCACCATCACC
16405 ATCGACGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.23, C:0.49, G:0.03, T:0.26
Consensus pattern (12 bp):
TCACCATCACCT
Found at i:16407 original size:18 final size:18
Alignment explanation
Indices: 16370--16407 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16360 AACAGCAACC
* *
16370 TCACCTTCACCTTCAGCA
1 TCACCTTCACCATCACCA
16388 TCACCTTCACCATCACCA
1 TCACCTTCACCATCACCA
16406 TC
1 TC
16408 GACGACAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.47, G:0.03, T:0.26
Consensus pattern (18 bp):
TCACCTTCACCATCACCA
Found at i:18218 original size:35 final size:35
Alignment explanation
Indices: 18179--18246 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
18169 TATAATATAT
* * *
18179 AAAATACACTTAACA-ACATTAAAACAAACTTTAAA
1 AAAATAAACTTAAAATACATTAAAA-AAAATTTAAA
*
18214 AAAATAAATTTAAAATACATTAAAAAAAATTTA
1 AAAATAAACTTAAAATACATTAAAAAAAATTTA
18247 TATTAAGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 19 0.68
36 9 0.32
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.26
Consensus pattern (35 bp):
AAAATAAACTTAAAATACATTAAAAAAAATTTAAA
Found at i:21767 original size:23 final size:23
Alignment explanation
Indices: 21715--21872 Score: 158
Period size: 23 Copynumber: 6.7 Consensus size: 23
21705 TATACGGAAC
* *
21715 AAACATAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
21737 AGGCAACAGAGAGCACACACAGTGCT
1 A---AACAGAGAGCACACACAGTGCT
* * *
21763 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
* * *
21786 AGACAGAGAGCACACAAAATGCT
1 AAACAGAGAGCACACACAGTGCT
*
21809 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
*
21832 AATAACAGAGAGCACGAGAC-GTGCT
1 -A-AACAGAGAGCAC-ACACAGTGCT
21857 AAACAGAGAGCACACA
1 AAACAGAGAGCACACA
Statistics
Matches: 113, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
22 3 0.03
23 69 0.61
24 2 0.02
25 29 0.26
26 10 0.09
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Done.