Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013456.1 Kokia drynarioides strain JFW-HI SEQ_128482, 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: 4462
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.32
Warning! 378 characters in sequence are not A, C, G, or T
Found at i:577 original size:29 final size:28
Alignment explanation
Indices: 530--664 Score: 132
Period size: 29 Copynumber: 4.7 Consensus size: 28
520 AGATACCCGG
* **
530 GGGGT-AAAATGTAA-TTTTGGATTTTT
1 GGGGTCAAAATGGAATTTTTGGAAGTTT
556 AGGGG-CAAAATGGTAATTTTTGGAAAGTTT
1 -GGGGTCAAAATGG-AATTTTTGG-AAGTTT
586 GGGGTCAAAAATGGAATTTTTGGAAGTTT
1 GGGGTC-AAAATGGAATTTTTGGAAGTTT
*
615 CGGGGTTAAAATGGAATTTTTGGAAGTTT
1 -GGGGTCAAAATGGAATTTTTGGAAGTTT
* *
644 CGAGGGTAAAAATTGAATTTT
1 -G-GGGTCAAAATGGAATTTT
665 CGCGATCAAA
Statistics
Matches: 94, Mismatches: 6, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
27 10 0.11
28 2 0.02
29 40 0.43
30 35 0.37
31 7 0.07
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (28 bp):
GGGGTCAAAATGGAATTTTTGGAAGTTT
Found at i:604 original size:30 final size:29
Alignment explanation
Indices: 562--664 Score: 145
Period size: 29 Copynumber: 3.4 Consensus size: 29
552 TTTTAGGGGC
562 AAAATGGTAATTTTTGGAAAGTTT-GGGGTCA
1 AAAATGG-AATTTTTGG-AAGTTTCGGGGT-A
*
593 AAAATGGAATTTTTGGAAGTTTCGGGGTT
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
622 AAAATGGAATTTTTGGAAGTTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
*
652 AAAATTGAATTTT
1 AAAATGGAATTTT
665 CGCGATCAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
29 30 0.45
30 30 0.45
31 7 0.10
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:1323 original size:10 final size:10
Alignment explanation
Indices: 1309--1343 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1299 GTCGTCCACA
1309 GTCGCGCGTC
1 GTCGCGCGTC
* *
1319 ATCGCCCGTC
1 GTCGCGCGTC
1329 GTCGCGCGTC
1 GTCGCGCGTC
1339 GTCGC
1 GTCGC
1344 CGCGCCTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.03, C:0.43, G:0.34, T:0.20
Consensus pattern (10 bp):
GTCGCGCGTC
Found at i:1826 original size:16 final size:16
Alignment explanation
Indices: 1805--1835 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1795 TCTTTTATTT
*
1805 TTATTTAATATTTATA
1 TTATTTAATACTTATA
1821 TTATTTAATACTTAT
1 TTATTTAATACTTAT
1836 TATTTATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTTAATACTTATA
Found at i:2584 original size:17 final size:17
Alignment explanation
Indices: 2558--2610 Score: 81
Period size: 17 Copynumber: 3.2 Consensus size: 17
2548 ATTGGACATT
2558 ATTT-AAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
2574 ATTTAAAATAAACTTAA
1 ATTTAAAATAAATTTAA
*
2591 TTTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
2608 ATT
1 ATT
2611 CTGTTGGGCC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 4 0.12
17 28 0.88
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:4132 original size:21 final size:19
Alignment explanation
Indices: 4101--4140 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 19
4091 TTTTATCAAA
4101 TTTTAATTTTTAAATAAATT
1 TTTTAATTTTTAAA-AAATT
4121 TTTTATATTTTTAAAAAATT
1 TTTTA-ATTTTTAAAAAATT
4141 AATTAGTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAATTTTTAAAAAATT
Found at i:4340 original size:76 final size:76
Alignment explanation
Indices: 4210--4362 Score: 270
Period size: 76 Copynumber: 2.0 Consensus size: 76
4200 TGACAAATAT
* * * *
4210 TAACTTTTCCATACATTTTAGGTGTTTTGACAAACAATGCAAGTTTAAGGACTAAAATAGATAAT
1 TAACTTTTCCATACATTTTAGGTGGTTTGACAAACAACGCAAATTTAAGAACTAAAATAGATAAT
4275 AAAAAATTAGA
66 AAAAAATTAGA
4286 TAACTTTTCCATACATTTTAGGTGGTTTGACAAACAACGCAAATTTAAGAACTAAAATAGATAAT
1 TAACTTTTCCATACATTTTAGGTGGTTTGACAAACAACGCAAATTTAAGAACTAAAATAGATAAT
4351 AAAAAATTAGA
66 AAAAAATTAGA
4362 T
1 T
4363 GGATAATTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 73 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.32
Consensus pattern (76 bp):
TAACTTTTCCATACATTTTAGGTGGTTTGACAAACAACGCAAATTTAAGAACTAAAATAGATAAT
AAAAAATTAGA
Done.