Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012845.1 Kokia drynarioides strain JFW-HI SEQ_127858, 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: 5847
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1656 original size:97 final size:97
Alignment explanation
Indices: 1481--1674 Score: 277
Period size: 97 Copynumber: 2.0 Consensus size: 97
1471 AACTTTCGAA
*
1481 AAGGATATTCGATTATCTTGATTTGAAGAAAAGTTGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCA
* *
1546 GAATCAGAGAT-AAAGAAACATTGCCTCGATTT
66 AAATCAGAAATAAAAG-AACATTGCCTCGATTT
* *
1578 AAGGGTATTCGATTAT-TTCGATTTGAGGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTC
1 AAGGATATTCGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTC
* *
1642 AAAACTC-GAAATAAAAGAATATTGTCTCGATTT
65 AAAA-TCAGAAATAAAAGAACATTGCCTCGATTT
1675 TAAAGTTTTC
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
96 2 0.02
97 79 0.91
98 6 0.07
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (97 bp):
AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAATCAGAAATAAAAGAACATTGCCTCGATTT
Found at i:1966 original size:29 final size:27
Alignment explanation
Indices: 1934--2070 Score: 82
Period size: 28 Copynumber: 4.8 Consensus size: 27
1924 GGTCACTTGA
1934 GGGGT-AAAATGGTAATTTTGGGAAAGTTC
1 GGGGTAAAAATGG-AATTTT-GGAAA-TTC
* * *
1963 GGGGTAAAAAATTGAATTTTTAGATATTC
1 GGGGT-AAAAATGGAA-TTTTGGAAATTC
*
1992 GAGGGT-AAAATGGTAATTTTGGAAAAAT-
1 G-GGGTAAAAATGG-AATTTTGG-AAATTC
* * *
2020 GGGGTAAAAATGGAATTTTTAGAAGTTTG
1 GGGGTAAAAATGGAA-TTTTGGAA-ATTC
**
2049 GGGGTAAAAATATAATTTTGGA
1 GGGGTAAAAATGGAATTTTGGA
2071 TAGTTTAGGG
Statistics
Matches: 85, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
27 8 0.09
28 31 0.36
29 27 0.32
30 9 0.11
31 10 0.12
ACGTcount: A:0.37, C:0.01, G:0.28, T:0.33
Consensus pattern (27 bp):
GGGGTAAAAATGGAATTTTGGAAATTC
Found at i:2050 original size:28 final size:29
Alignment explanation
Indices: 1934--2067 Score: 86
Period size: 29 Copynumber: 4.7 Consensus size: 29
1924 GGTCACTTGA
**
1934 GGGGT-AAAATGGTAATTTTGGGAAAGTTC
1 GGGGTAAAAATGGTAATTTTTAG-AAGTTC
*
1963 GGGGTAAAAAATTG-AATTTTTAGATA-TTC
1 GGGGT-AAAAATGGTAATTTTTAGA-AGTTC
* **
1992 GAGGGT-AAAATGGTAA-TTTTGGAAAAAT-
1 G-GGGTAAAAATGGTAATTTTTAG-AAGTTC
*
2020 GGGGTAAAAATGG-AATTTTTAGAAGTTTG
1 GGGGTAAAAATGGTAATTTTTAGAAG-TTC
*
2049 GGGGTAAAAAT-ATAATTTT
1 GGGGTAAAAATGGTAATTTT
2068 GGATAGTTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
27 8 0.10
28 26 0.31
29 31 0.37
30 12 0.14
31 6 0.07
ACGTcount: A:0.37, C:0.01, G:0.28, T:0.34
Consensus pattern (29 bp):
GGGGTAAAAATGGTAATTTTTAGAAGTTC
Found at i:2054 original size:56 final size:58
Alignment explanation
Indices: 1934--2070 Score: 165
Period size: 56 Copynumber: 2.4 Consensus size: 58
1924 GGTCACTTGA
** *
1934 GGGGTAAAATGGTAATTTTGGGAAAGTTCGGGGTAAAAAATTGAATTTTTAGATATTCG
1 GGGGTAAAATGGTAATTTT-GGAAAAATCGGGGTAAAAAATGGAATTTTTAGATATTCG
* *
1993 AGGGTAAAATGGTAATTTTGGAAAAAT-GGGGT-AAAAATGGAATTTTTAGA-AGTTTG
1 GGGGTAAAATGGTAATTTTGGAAAAATCGGGGTAAAAAATGGAATTTTTAGATA-TTCG
*
2049 GGGGTAAAAAT-ATAATTTTGGA
1 GGGGT-AAAATGGTAATTTTGGA
2071 TAGTTTAGGG
Statistics
Matches: 69, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
55 1 0.01
56 34 0.49
57 10 0.14
58 6 0.09
59 18 0.26
ACGTcount: A:0.37, C:0.01, G:0.28, T:0.33
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGAAAAATCGGGGTAAAAAATGGAATTTTTAGATATTCG
Found at i:3214 original size:3 final size:3
Alignment explanation
Indices: 3155--3199 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
3145 TATTTAATAT
*
3155 TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3200 ATGAATTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3952 original size:22 final size:24
Alignment explanation
Indices: 3927--3983 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
3917 ATTGGACTTG
**
3927 TAAATTTGTACATTA-ATTTA-AA
1 TAAATTTAAACATTATATTTATAA
*
3949 TAAATTTAAACTTTATATTTATAA
1 TAAATTTAAACATTATATTTATAA
3973 TAAATTTAAAC
1 TAAATTTAAAC
3984 TCCAAATGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 12 0.40
23 5 0.17
24 13 0.43
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (24 bp):
TAAATTTAAACATTATATTTATAA
Found at i:4032 original size:17 final size:17
Alignment explanation
Indices: 3987--4034 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
3977 TTTAAACTCC
*
3987 AAATGGATTTAAATTTA
1 AAATGAATTTAAATTTA
* * *
4004 ATATAAACTTAAATTTA
1 AAATGAATTTAAATTTA
4021 AAATGAATTTAAAT
1 AAATGAATTTAAAT
4035 CTATTGAGCC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (17 bp):
AAATGAATTTAAATTTA
Done.