Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009827.1 Kokia drynarioides strain JFW-HI SEQ_124548, 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: 9470
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Found at i:464 original size:158 final size:158
Alignment explanation
Indices: 176--498 Score: 493
Period size: 158 Copynumber: 2.0 Consensus size: 158
166 ATCTCTATAT
* * * *
176 CATGTAGTGCTCACATAAGCTGTAAAATGGGTCTGCTCACACAAGCTGTGGGTCATGATGTTAGG
1 CATGTAATGCTCACACAAGCTGTAAAATGGGTCTGCTAACACAAGCTGTGGGTCAAGATGTTAGG
* * *
241 CTACACGATGTTGCTCACACGAGCTATGGAGAATCCGCAACATATGTCGGATCTCAGCCATCGGT
66 CTACACGATGCTGCTCACACGAGCTATGGAGAATCCGCAACATATGCCGAATCTCAGCCATCGGT
306 AGGACATCTAAGACTAGCACCCACATAA
131 AGGACATCTAAGACTAGCACCCACATAA
* * ** *
334 CATGTAATGCTCACACGAGCTGTGAAATGGGTCTGCTAACATGAGTTGTGGGTCAAGATGTTAGG
1 CATGTAATGCTCACACAAGCTGTAAAATGGGTCTGCTAACACAAGCTGTGGGTCAAGATGTTAGG
* * *
399 CTACACGATGCTGCTCACATGAGCTGTGGAGAATTCGCAACATATGCCGAATCTCAGCCATCGGT
66 CTACACGATGCTGCTCACACGAGCTATGGAGAATCCGCAACATATGCCGAATCTCAGCCATCGGT
*
464 AGGACATCTAAGACTAGCACCCATATAA
131 AGGACATCTAAGACTAGCACCCACATAA
*
492 CTTGTAA
1 CATGTAA
499 ATCCCGAAAT
Statistics
Matches: 148, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
158 148 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (158 bp):
CATGTAATGCTCACACAAGCTGTAAAATGGGTCTGCTAACACAAGCTGTGGGTCAAGATGTTAGG
CTACACGATGCTGCTCACACGAGCTATGGAGAATCCGCAACATATGCCGAATCTCAGCCATCGGT
AGGACATCTAAGACTAGCACCCACATAA
Found at i:1680 original size:26 final size:26
Alignment explanation
Indices: 1650--1729 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 26
1640 ATTATCGGGA
1650 AATTGTTCATTTATATGAATTGAAAT
1 AATTGTTCATTTATATGAATTGAAAT
** *
1676 AATTGAACATGTGATA--AATTTG--A-
1 AATTGTTCAT-TTATATGAA-TTGAAAT
1699 AATTGTTCATTTATATGAATTGAAAT
1 AATTGTTCATTTATATGAATTGAAAT
1725 AATTG
1 AATTG
1730 AACATGTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 4 0.10
23 11 0.27
24 3 0.07
25 3 0.07
26 16 0.39
27 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (26 bp):
AATTGTTCATTTATATGAATTGAAAT
Found at i:1714 original size:49 final size:49
Alignment explanation
Indices: 1648--1747 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
1638 AAATTATCGG
1648 GAAATTGTTCATTTATATGAATTGAAATAATTGAACATGTGATAAATTT
1 GAAATTGTTCATTTATATGAATTGAAATAATTGAACATGTGATAAATTT
1697 GAAATTGTTCATTTATATGAATTGAAATAATTGAACATGTGATAAATTT
1 GAAATTGTTCATTTATATGAATTGAAATAATTGAACATGTGATAAATTT
1746 GA
1 GA
1748 CTTAGTCAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.40
Consensus pattern (49 bp):
GAAATTGTTCATTTATATGAATTGAAATAATTGAACATGTGATAAATTT
Found at i:1721 original size:23 final size:23
Alignment explanation
Indices: 1648--1724 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 23
1638 AAATTATCGG
1648 GAAATTGTTCATTTATATGAATT
1 GAAATTGTTCATTTATATGAATT
** *
1671 GAAATAATTGAACATGTGATA--AATTT
1 G--A-AATTGTTCAT-TTATATGAA-TT
1697 GAAATTGTTCATTTATATGAATT
1 GAAATTGTTCATTTATATGAATT
1720 GAAAT
1 GAAAT
1725 AATTGAACAT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 4 0.10
23 16 0.39
24 3 0.07
25 3 0.07
26 11 0.27
27 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (23 bp):
GAAATTGTTCATTTATATGAATT
Found at i:1747 original size:26 final size:26
Alignment explanation
Indices: 1669--1747 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
1659 TTTATATGAA
1669 TTGAAATAATTGAACATGTGATAAAT
1 TTGAAATAATTGAACATGTGATAAAT
** *
1695 TTG--A-AATTGTTCAT-TTATATGAA-
1 TTGAAATAATTGAACATGTGATA--AAT
1718 TTGAAATAATTGAACATGTGATAAAT
1 TTGAAATAATTGAACATGTGATAAAT
1744 TTGA
1 TTGA
1748 CTTAGTCAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 4 0.10
23 11 0.28
24 3 0.08
25 3 0.08
26 15 0.38
27 4 0.10
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (26 bp):
TTGAAATAATTGAACATGTGATAAAT
Found at i:3388 original size:24 final size:24
Alignment explanation
Indices: 3329--3389 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
3319 GACTAATAAG
* * * *
3329 AGTTTGACTCAAACAAATAAATAG
1 AGTTTAACTGAAACAAATAAACAA
*
3353 AGTTTAATTGAAACAAATAAACAA
1 AGTTTAACTGAAACAAATAAACAA
3377 AGTTTAACTGAAA
1 AGTTTAACTGAAA
3390 GATTATTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.26
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAA
Found at i:6147 original size:16 final size:17
Alignment explanation
Indices: 6128--6160 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6118 CACATTTGCA
*
6128 TTTATTTTTATT-TTTT
1 TTTAATTTTATTATTTT
6144 TTTAATTTTATTATTTT
1 TTTAATTTTATTATTTT
6161 CACAAGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTAATTTTATTATTTT
Found at i:8076 original size:15 final size:14
Alignment explanation
Indices: 8049--8078 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
8039 AACGAGCTTA
8049 ATAAAATTTAAAAT
1 ATAAAATTTAAAAT
8063 ATAAAATATTAAAAT
1 ATAAAAT-TTAAAAT
8078 A
1 A
8079 AAGTTTTACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAATTTAAAAT
Found at i:9202 original size:17 final size:18
Alignment explanation
Indices: 9182--9215 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9172 AATTCTTTCA
*
9182 TTTTTTTTCTT-TTTTAC
1 TTTTATTTCTTCTTTTAC
9199 TTTTATTTCTTCTTTTA
1 TTTTATTTCTTCTTTTA
9216 TAATGTATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTATTTCTTCTTTTAC
Done.