Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001355.1 Kokia drynarioides strain JFW-HI SEQ_112804, 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: 41257
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5447 original size:15 final size:17
Alignment explanation
Indices: 5417--5458 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
5407 TAGTAAAAAT
5417 ATAATTTTATTATTTTA
1 ATAATTTTATTATTTTA
*
5434 ATAA-TTTA-TATTTTT
1 ATAATTTTATTATTTTA
5449 ATAACTTTTA
1 ATAA-TTTTA
5459 AAGGTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 10 0.45
16 4 0.18
17 8 0.36
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
ATAATTTTATTATTTTA
Found at i:22137 original size:12 final size:12
Alignment explanation
Indices: 22093--22138 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
22083 CTGTAGCGAC
22093 AAAAACCAAAGA
1 AAAAACCAAAGA
*
22105 AGAAA-CAAAGA
1 AAAAACCAAAGA
*
22116 AAACAACCAAACA
1 AAA-AACCAAAGA
22129 AAAAACCAAA
1 AAAAACCAAA
22139 ACCAGAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 8 0.28
12 13 0.45
13 8 0.28
ACGTcount: A:0.74, C:0.20, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAACCAAAGA
Found at i:22172 original size:22 final size:23
Alignment explanation
Indices: 22142--22192 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
22132 AACCAAAACC
22142 AGAATAACCATGCTAATAAGCAG
1 AGAATAACCATGCTAATAAGCAG
* *
22165 AGAA-AACCGTGCTAATAAGTAG
1 AGAATAACCATGCTAATAAGCAG
22187 AGAATA
1 AGAATA
22193 GTTAAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.49, C:0.14, G:0.20, T:0.18
Consensus pattern (23 bp):
AGAATAACCATGCTAATAAGCAG
Found at i:27236 original size:30 final size:29
Alignment explanation
Indices: 27173--27238 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
27163 CAACACTTAC
* *
27173 AATTTAATCTTTTTATTTTTATTTTAAAG
1 AATTTAATCTTTTAATTTTTAATTTAAAG
*
27202 AATTTAATCTCTTTAATTTTTAAATTTCAA-
1 AATTTAATCT-TTTAATTTTT-AATTTAAAG
27232 AATTTAA
1 AATTTAA
27239 ATTTAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 10 0.31
30 16 0.50
31 6 0.19
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (29 bp):
AATTTAATCTTTTAATTTTTAATTTAAAG
Found at i:30282 original size:32 final size:32
Alignment explanation
Indices: 30246--30310 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
30236 AGTATGTAAG
30246 TATGTATACTGGTTTTGGCAATGCAACTACTT
1 TATGTATACTGGTTTTGGCAATGCAACTACTT
* *
30278 TATGTGTACTGGTTTTGGCAATGTAACTACTT
1 TATGTATACTGGTTTTGGCAATGCAACTACTT
30310 T
1 T
30311 TATGCAGACG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (32 bp):
TATGTATACTGGTTTTGGCAATGCAACTACTT
Found at i:33747 original size:38 final size:40
Alignment explanation
Indices: 33675--33758 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 40
33665 TAAAAAGTAT
**
33675 TTATATTAAAAAAATACTACCATAAATATAATAAATGTTTTA
1 TTATATTAAAAAAATAC-A-CATAAATATAATAAACATTTTA
33717 TTATATTAAAAAAATA-A-ATAAATATAATAAACATTTTA
1 TTATATTAAAAAAATACACATAAATATAATAAACATTTTA
33755 TTAT
1 TTAT
33759 TAATATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
38 23 0.57
40 1 0.03
42 16 0.40
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (40 bp):
TTATATTAAAAAAATACACATAAATATAATAAACATTTTA
Found at i:37373 original size:110 final size:110
Alignment explanation
Indices: 37180--37458 Score: 504
Period size: 110 Copynumber: 2.5 Consensus size: 110
37170 CATGATCGGA
* * *
37180 AGAAAAGTCGTCGATTTCACCTGCGTTAATTTTAGATATTTTTATTGATTAATATAAAGAAGGTG
1 AGAAAAGTCGTCCATTTGACCTGTGTTAATTTTAGATATTTTTATTGATTAATATAAAGAAGGTG
*
37245 GAGCGGCCGCTTTCAGTGATGTATACTCCAGATATGCTTGGACAG
66 GAGCGGCCGCTTTCAGTGATGTATACTCCAGATATGCTTGGAAAG
37290 AGAAAAGTCGTCCATTTGACCTGTGTTAATTTTAGATATTTTTATTGATTAATATAAAGAAGGTG
1 AGAAAAGTCGTCCATTTGACCTGTGTTAATTTTAGATATTTTTATTGATTAATATAAAGAAGGTG
*
37355 GAGGGGCCGCTTTCAGTGATGTATACTCCAGATATGCTTGGAAAG
66 GAGCGGCCGCTTTCAGTGATGTATACTCCAGATATGCTTGGAAAG
*
37400 AGAAAAGTCGTCCATTTGACCTGTGTTAATTTTAGATATTTTTATTGGTTAATATAAAG
1 AGAAAAGTCGTCCATTTGACCTGTGTTAATTTTAGATATTTTTATTGATTAATATAAAG
37459 GGGTTCTTTT
Statistics
Matches: 163, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 163 1.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (110 bp):
AGAAAAGTCGTCCATTTGACCTGTGTTAATTTTAGATATTTTTATTGATTAATATAAAGAAGGTG
GAGCGGCCGCTTTCAGTGATGTATACTCCAGATATGCTTGGAAAG
Found at i:40525 original size:29 final size:30
Alignment explanation
Indices: 40493--40560 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
40483 TAGATGGGTT
40493 TTAAATTTA-TTTCTAAAATTAAATTTACC
1 TTAAATTTATTTTCTAAAATTAAATTTACC
* * * **
40522 TTAAATTCATTTTTTAAATTTAAATTTATT
1 TTAAATTTATTTTCTAAAATTAAATTTACC
40552 TTAAATTTA
1 TTAAATTTA
40561 AATTTAGTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (30 bp):
TTAAATTTATTTTCTAAAATTAAATTTACC
Found at i:40545 original size:6 final size:6
Alignment explanation
Indices: 40534--40602 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
40524 AAATTCATTT
* * *
40534 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AG TCTAAA TTTGAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
* *
40581 --TAAT TTTAAA CTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
40603 ATCAATTACA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
4 2 0.04
5 8 0.17
6 35 0.73
7 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:40555 original size:17 final size:17
Alignment explanation
Indices: 40492--40600 Score: 93
Period size: 17 Copynumber: 6.6 Consensus size: 17
40482 TTAGATGGGT
40492 TTTAAATTTATTTCTAAA
1 TTTAAATTTATTT-TAAA
* **
40510 ATTAAATTTACCTTAAA
1 TTTAAATTTATTTTAAA
*
40527 -TT-CA-TT-TTTTAAA
1 TTTAAATTTATTTTAAA
40540 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
40557 TTTAAATTTAGTCTAAA
1 TTTAAATTTATTTTAAA
*
40574 TTTGAAA-TAATTTTAAA
1 TTT-AAATTTATTTTAAA
*
40591 CTTAAATTTA
1 TTTAAATTTA
40601 AAATCAATTA
Statistics
Matches: 71, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
13 5 0.07
14 4 0.06
15 2 0.03
16 7 0.10
17 40 0.56
18 13 0.18
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Done.