Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010800.1 Kokia drynarioides strain JFW-HI SEQ_125767, 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: 13219
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:654 original size:30 final size:30
Alignment explanation
Indices: 610--673 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
600 CAATTTTTTG
* * *
610 TTTTTGTTCTTATTATATATGACTTCTAAT
1 TTTTTATTCGTATTATATATAACTTCTAAT
*
640 TTTTTATTCGTATTATATTTAACTTCTAAT
1 TTTTTATTCGTATTATATATAACTTCTAAT
670 TTTT
1 TTTT
674 GTTTTGGTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.09, G:0.05, T:0.62
Consensus pattern (30 bp):
TTTTTATTCGTATTATATATAACTTCTAAT
Found at i:798 original size:8 final size:9
Alignment explanation
Indices: 780--836 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
770 TACTAAAATG
780 TATGT-TGT
1 TATGTATGT
788 TAT-TATGT
1 TATGTATGT
*
796 TATGTATGC
1 TATGTATGT
805 TATGAATATG-
1 TATG--TATGT
815 TATGTTATG-
1 TATG-TATGT
824 TATGTATGT
1 TATGTATGT
833 TATG
1 TATG
837 AATATTACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
7 1 0.02
8 13 0.31
9 20 0.48
10 4 0.10
11 4 0.10
ACGTcount: A:0.25, C:0.02, G:0.21, T:0.53
Consensus pattern (9 bp):
TATGTATGT
Found at i:935 original size:31 final size:31
Alignment explanation
Indices: 899--960 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
889 ATGTCTGTTA
899 GTATGTTATGTAGTATATCACTATTATGTAT
1 GTATGTTATGTAGTATATCACTATTATGTAT
* * *
930 GTATGTTATGTGGTATATTACTGTTATGTAT
1 GTATGTTATGTAGTATATCACTATTATGTAT
961 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50
Consensus pattern (31 bp):
GTATGTTATGTAGTATATCACTATTATGTAT
Found at i:2034 original size:38 final size:38
Alignment explanation
Indices: 1992--2064 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
1982 CCATGGACAA
*
1992 TTATGTATATTTTTGTTTATGTATGTATATTATGTATG
1 TTATGTATATTATTGTTTATGTATGTATATTATGTATG
* *
2030 TTATGTTTATTATTGTTTATGTATGTATGTTATGT
1 TTATGTATATTATTGTTTATGTATGTATATTATGT
2065 TTAGCACTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (38 bp):
TTATGTATATTATTGTTTATGTATGTATATTATGTATG
Found at i:2054 original size:29 final size:28
Alignment explanation
Indices: 1991--2067 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 28
1981 ACCATGGACA
* *
1991 ATTATGTATATTTTTGTTTATGTATGTAT
1 ATTATGTAT-GTTATGTTTATGTATGTAT
*
2020 ATTATGTATGTTATGTTTAT-TATTGTTT
1 ATTATGTATGTTATGTTTATGTA-TGTAT
2048 ATGTATGTATGTTATGTTTA
1 AT-TATGTATGTTATGTTTA
2068 GCACTGTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 2 0.05
28 15 0.35
29 26 0.60
ACGTcount: A:0.23, C:0.00, G:0.16, T:0.61
Consensus pattern (28 bp):
ATTATGTATGTTATGTTTATGTATGTAT
Found at i:2075 original size:29 final size:29
Alignment explanation
Indices: 2022--2077 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
2012 GTATGTATAT
** *
2022 TATGTATGTTATGTTTATTATTGTTTATG
1 TATGTATGTTATGTTTAGCACTGTTTATG
2051 TATGTATGTTATGTTTAGCACTGTTTA
1 TATGTATGTTATGTTTAGCACTGTTTA
2078 AAATATGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.21, C:0.04, G:0.18, T:0.57
Consensus pattern (29 bp):
TATGTATGTTATGTTTAGCACTGTTTATG
Found at i:4953 original size:24 final size:24
Alignment explanation
Indices: 4905--4980 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
4895 CAGTTGGAGT
** *
4905 AGCTTCAGCAACTCCTTTTCCACC
1 AGCTTCAGCAACTCCTGCTCAACC
*
4929 AGCTTCAGTAACTCCTGCTCAACC
1 AGCTTCAGCAACTCCTGCTCAACC
* * * *
4953 AG-TCACAACAACTCTTGCTCCACC
1 AGCT-TCAGCAACTCCTGCTCAACC
4977 AGCT
1 AGCT
4981 CCTTCTGATC
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
23 1 0.02
24 39 0.95
25 1 0.02
ACGTcount: A:0.25, C:0.39, G:0.11, T:0.25
Consensus pattern (24 bp):
AGCTTCAGCAACTCCTGCTCAACC
Found at i:5347 original size:21 final size:21
Alignment explanation
Indices: 5321--5374 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
5311 AGTAGCAGAC
5321 TTCTACCGATACTTGTGATGG
1 TTCTACCGATACTTGTGATGG
5342 TTCTACCGATACTTGTGATGG
1 TTCTACCGATACTTGTGATGG
5363 TTCTACCGATAC
1 TTCTACCGATAC
5375 AAGTGTACCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.22, G:0.20, T:0.37
Consensus pattern (21 bp):
TTCTACCGATACTTGTGATGG
Found at i:7718 original size:14 final size:13
Alignment explanation
Indices: 7685--7724 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
7675 ATAGACGGTT
*
7685 TTATTTTGTTGGA
1 TTATTTTGATGGA
7698 TTATTTTGATGGA
1 TTATTTTGATGGA
7711 TGTATTTTGATGGA
1 T-TATTTTGATGGA
7725 CAATTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.55
Consensus pattern (13 bp):
TTATTTTGATGGA
Found at i:7740 original size:45 final size:45
Alignment explanation
Indices: 7683--7780 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 45
7673 TGATAGACGG
* * * * *
7683 TTTTATTTTGTTGGATTATTTTGATGGATGTATTTTGATGGACAA
1 TTTTATTATGTTGAATCATTCTAATGGATGTATTTTGATGGACAA
*
7728 TTTTATTATGTTGAATCATTCTAATGGTTGTATTTTGATGGACAA
1 TTTTATTATGTTGAATCATTCTAATGGATGTATTTTGATGGACAA
7773 TTTATATT
1 TTT-TATT
7781 TATCCTTTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 42 0.91
46 4 0.09
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.53
Consensus pattern (45 bp):
TTTTATTATGTTGAATCATTCTAATGGATGTATTTTGATGGACAA
Found at i:9153 original size:9 final size:9
Alignment explanation
Indices: 9139--9168 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
9129 AATCTAATCA
9139 AGTTATTCG
1 AGTTATTCG
9148 AGTTATTCG
1 AGTTATTCG
*
9157 AATTATTCG
1 AGTTATTCG
9166 AGT
1 AGT
9169 CAACTCGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (9 bp):
AGTTATTCG
Found at i:9491 original size:3 final size:3
Alignment explanation
Indices: 9483--9526 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
9473 TAAAACATAT
*
9483 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9527 TTGTTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:10332 original size:14 final size:14
Alignment explanation
Indices: 10302--10331 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
10292 ATTTTTAGGG
10302 TTTGTGATAAAAAT
1 TTTGTGATAAAAAT
10316 TTTGTGAT-AAAAT
1 TTTGTGATAAAAAT
10329 TTT
1 TTT
10332 TAGGGGGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TTTGTGATAAAAAT
Found at i:10362 original size:4 final size:4
Alignment explanation
Indices: 10353--10404 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
10343 AAATAAACGG
* * * *
10353 GAAA GAAA GAAA GAAAA GAAA GAAA GGAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
10403 GA
1 GA
10405 TAATGTGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 34 0.81
5 8 0.19
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:10372 original size:13 final size:13
Alignment explanation
Indices: 10354--10378 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10344 AATAAACGGG
10354 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
10367 AAAGAAAGAAAG
1 AAAGAAAGAAAG
10379 GAAGGAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Done.