Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008388.1 Kokia drynarioides strain JFW-HI SEQ_123056, 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: 12462
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4591 original size:2 final size:2
Alignment explanation
Indices: 4584--4608 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4574 CCCATAGGGA
4584 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4609 GAATGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11164 original size:29 final size:29
Alignment explanation
Indices: 11130--11193 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
11120 AAATGAGACT
*
11130 TTTTGGACACCCGAGGGGCAAAATGGTAA
1 TTTTGGACACCCGAGGGGCAAAATGATAA
* * *
11159 TTTTGGACTCTCGGGGGGCAAAATGATAA
1 TTTTGGACACCCGAGGGGCAAAATGATAA
11188 TTTTGG
1 TTTTGG
11194 GGTTAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.27, C:0.14, G:0.31, T:0.28
Consensus pattern (29 bp):
TTTTGGACACCCGAGGGGCAAAATGATAA
Found at i:11318 original size:58 final size:58
Alignment explanation
Indices: 11256--11561 Score: 311
Period size: 58 Copynumber: 5.3 Consensus size: 58
11246 AATCGAGATC
11256 AAAAATGGAATTTTTGGACA-TTCGGGGGTAAAATGGTAACTTTTGAAAGTTTTGGGGTA
1 AAAAATGGAATTTTTGGA-AGTTCGGGGGTAAAATGGTAA-TTTTGAAAGTTTTGGGGTA
* *
11315 AAAAATGGAAGCTTTTGGACA-TTCAGGGGTAAAATGGTAATTTTGAAAG-TTTGGGGTA
1 AAAAATGGAA-TTTTTGGA-AGTTCGGGGGTAAAATGGTAATTTTGAAAGTTTTGGGGTA
* * * * *
11373 AAAAATGGAA-TTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGAAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGTAA-TTTTGAAAGTTTTGGGGTA
* * *** *
11431 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAAT-ATAATTTTTAGAAGTTTCAAGGTT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT-AAAATGGTAATTTTGA-AAGTTTTGGGGTA
* ** * * * *
11490 AAGAAT-GAATTTTTGGAAGTTTAGGGGTAACAT-GTAATTTTTAGAAGTTTTGAGGTC
1 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTGA-AAGTTTTGGGGTA
11547 AAAAATGGAATTTTT
1 AAAAATGGAATTTTT
11562 AGACAGTTGA
Statistics
Matches: 217, Mismatches: 22, Indels: 17
0.85 0.09 0.07
Matches are distributed among these distances:
55 1 0.00
56 23 0.11
57 38 0.18
58 68 0.31
59 55 0.25
60 32 0.15
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTGAAAGTTTTGGGGTA
Found at i:11529 original size:28 final size:28
Alignment explanation
Indices: 11257--11539 Score: 166
Period size: 29 Copynumber: 9.8 Consensus size: 28
11247 ATCGAGATCA
* **
11257 AAAATGGAATTTTTGGACA-TTCGGGGGT
1 AAAATGTAATTTTTGGA-AGTTTAGGGGT
* * *
11285 AAAATGGTAACTTTTGAAAGTTTTGGGGT
1 AAAAT-GTAATTTTTGGAAGTTTAGGGGT
* * *
11314 AAAAAATGGAAGCTTTTGGACA-TTCAGGGGT
1 --AAAATGTAA-TTTTTGGA-AGTTTAGGGGT
*
11345 AAAATGGTAA-TTTTGAAAGTTT-GGGGT
1 AAAAT-GTAATTTTTGGAAGTTTAGGGGT
*
11372 AAAAAATGGAA-TTTTGGAAGTTT-GAGGGT
1 --AAAATGTAATTTTTGGAAGTTTAG-GGGT
* * *
11401 AAAATGGTAATTTTTGAAAGTTTCGAGGTT
1 AAAAT-GTAATTTTTGGAAGTTTAG-GGGT
* **
11431 AAAAATGGAATTTTTGGAAGTTCGGGGGT
1 -AAAATGTAATTTTTGGAAGTTTAGGGGT
* * * *
11460 AAAAATATAATTTTTAGAAGTTTCAAGGTT
1 -AAAATGTAATTTTTGGAAGTTT-AGGGGT
11490 AAGAATG-AATTTTTGGAAGTTTAGGGGT
1 AA-AATGTAATTTTTGGAAGTTTAGGGGT
* *
11518 AACATGTAATTTTTAGAAGTTT
1 AAAATGTAATTTTTGGAAGTTT
11540 TGAGGTCAAA
Statistics
Matches: 202, Mismatches: 35, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
27 14 0.07
28 52 0.26
29 79 0.39
30 32 0.16
31 24 0.12
32 1 0.00
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (28 bp):
AAAATGTAATTTTTGGAAGTTTAGGGGT
Found at i:11572 original size:29 final size:28
Alignment explanation
Indices: 11345--11573 Score: 157
Period size: 29 Copynumber: 7.9 Consensus size: 28
11335 ATTCAGGGGT
* *
11345 AAAATGGTAATTTTGA-AAGTTTGGGGTAA
1 AAAATGG-AATTTTTAGAAGTTTGAGGT-A
*
11374 AAAATGGAA-TTTTGGAAGTTTGAGGGT-
1 AAAATGGAATTTTTAGAAGTTTGA-GGTA
11401 AAAATGGTAATTTTT-GAAAGTTTCGAGGTTA
1 AAAATGG-AATTTTTAG-AAGTTT-GAGG-TA
* * *
11432 AAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTAGAAGTT-TGAGGTA
** *
11461 AAAATATAATTTTTAGAAGTTTCAAGGTTA
1 AAAATGGAATTTTTAGAAGTTT-GAGG-TA
* * *
11491 AGAAT-GAATTTTTGGAAGTTTAGGGGT-
1 AAAATGGAATTTTTAGAAGTTT-GAGGTA
* *
11518 AACATGTAATTTTTAGAAGTTTTGAGGTCA
1 AAAATGGAATTTTTAGAAG-TTTGAGGT-A
11548 AAAATGGAATTTTTAGACAG-TTGAGG
1 AAAATGGAATTTTTAGA-AGTTTGAGG
11574 GACCTTCAGG
Statistics
Matches: 159, Mismatches: 24, Indels: 34
0.73 0.11 0.16
Matches are distributed among these distances:
27 13 0.08
28 28 0.18
29 69 0.43
30 39 0.25
31 10 0.06
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
AAAATGGAATTTTTAGAAGTTTGAGGTA
Done.