Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006781.1 Kokia drynarioides strain JFW-HI SEQ_121380, 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: 11925
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5225 original size:29 final size:27
Alignment explanation
Indices: 5194--5404 Score: 145
Period size: 29 Copynumber: 7.3 Consensus size: 27
5184 TTTGGAGTCA
5194 AAAATGAGATTTTTAGAAGTTCGGGGGT
1 AAAATG-GATTTTTAGAAGTTCGGGGGT
* *
5222 AAAATGGTAATTTTTAGAAAGTTAGGGGTT
1 AAAATGG--ATTTTTAG-AAGTTCGGGGGT
* *
5252 AAGAATGGGATTTTTGGAAGTTTGGGGGT
1 AA-AAT-GGATTTTTAGAAGTTCGGGGGT
* * **
5281 AAAATGGTAATTTTCAAAAGTT-TAGGGT
1 AAAATGG--ATTTTTAGAAGTTCGGGGGT
*
5309 CAAAAATGGGATTTTTTGAAGTTCGGGGGT
1 --AAAAT-GGATTTTTAGAAGTTCGGGGGT
*
5339 AAAATGGTAATTTTTAGAAGATTCGGGGTT
1 AAAATGG--ATTTTTAGAAG-TTCGGGGGT
* ***
5369 GAAAATGGGATTTTTGGAAGTTTTTGGGT
1 -AAAAT-GGATTTTTAGAAGTTCGGGGGT
5398 AAAATGG
1 AAAATGG
5405 TAATTTTTGA
Statistics
Matches: 145, Mismatches: 22, Indels: 33
0.73 0.11 0.17
Matches are distributed among these distances:
27 7 0.05
28 23 0.16
29 55 0.38
30 46 0.32
31 10 0.07
32 4 0.03
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.35
Consensus pattern (27 bp):
AAAATGGATTTTTAGAAGTTCGGGGGT
Found at i:5279 original size:59 final size:59
Alignment explanation
Indices: 5194--5425 Score: 294
Period size: 59 Copynumber: 3.9 Consensus size: 59
5184 TTTGGAGTCA
* *
5194 AAAATGAGATTTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAG-TTAGGGGTT
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGGTT
* * *
5252 AAGAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTCA-AAAGTTTA-GGGTCA
1 AA-AATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGGT-T
* * *
5311 AAAATGGGATTTTTTGAAGTTCGGGGGTAAAATGGTAATTTTTAG-AAGATTCGGGGTT
1 AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGGTT
***
5369 GAAAATGGGATTTTTGGAAGTTTTTGGGTAAAATGGTAATTTTT-GAAAAGTTTAGGG
1 -AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAG-AAAGTTTAGGG
5426 ACTTTCGGGG
Statistics
Matches: 149, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
58 55 0.37
59 86 0.58
60 8 0.05
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (59 bp):
AAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTTAGGGGTT
Found at i:5367 original size:117 final size:118
Alignment explanation
Indices: 5190--5425 Score: 379
Period size: 117 Copynumber: 2.0 Consensus size: 118
5180 AAGGTTTGGA
5190 GTCAAAAATGAGATTTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTAGGGGTT-AA
1 GTCAAAAATGAGATTTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTAGGGGTTGAA
5254 GAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAA-TTTTCAAAAGTTTAGG
66 -AATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTCAAAAGTTTAGG
* * *
5307 GTCAAAAATGGGATTTTTTGAAGTTCGGGGGTAAAATGGTAATTTTTAG-AAGATTCGGGGTTGA
1 GTCAAAAATGAGATTTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAG-TTAGGGGTTGA
** *
5371 AAATGGGATTTTTGGAAGTTTTTGGGTAAAATGGTAATTTTTGAAAAGTTTAGG
65 AAATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTCAAAAGTTTAGG
5425 G
1 G
5426 ACTTTCGGGG
Statistics
Matches: 110, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
116 3 0.03
117 89 0.81
118 18 0.16
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.36
Consensus pattern (118 bp):
GTCAAAAATGAGATTTTTAGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAAGTTAGGGGTTGAA
AATGGGATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTCAAAAGTTTAGG
Found at i:7201 original size:17 final size:17
Alignment explanation
Indices: 7156--7218 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
7146 TTAGACATTT
*
7156 TAAATTTTAAATTTATAAGC
1 TAAA-TTTAAATTTA-AA-A
*
7176 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTAAAA
* *
7193 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
7210 TAAATTTAA
1 TAAATTTAA
7219 GTTCATTGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 22 0.59
18 1 0.03
19 10 0.27
20 4 0.11
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:7661 original size:16 final size:17
Alignment explanation
Indices: 7636--7668 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
7626 ATAATTATTA
7636 AAAAATATATAAAATAT
1 AAAAATATATAAAATAT
*
7653 AAAAA-ATATTAAATAT
1 AAAAATATATAAAATAT
7669 GATTAAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAATATATAAAATAT
Found at i:7717 original size:18 final size:16
Alignment explanation
Indices: 7685--7736 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 16
7675 GAATGATAAG
7685 AAATTATAAATAATTATT
1 AAATTA-AAA-AATTATT
*
7703 AAACTTTAAAAAATTAAT
1 AAA--TTAAAAAATTATT
7721 -AATTAAAAAATTATT
1 AAATTAAAAAATTATT
7736 A
1 A
7737 TGAAAGGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 12 0.41
17 2 0.07
18 9 0.31
19 3 0.10
20 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTAAAAAATTATT
Found at i:8124 original size:39 final size:40
Alignment explanation
Indices: 8037--8138 Score: 97
Period size: 39 Copynumber: 2.6 Consensus size: 40
8027 TATATGTGTA
* * *
8037 TATATATAGTTTTA-ATAA-TTTTTAAAATTTTAAATAAT
1 TATATCTAATTTTATATAACTTTTTAAAATTTTAAACAAT
* * *
8075 TATTTTTAATTTCT-TAT-ACTTTTTAATATTTTAAACAAT
1 TATATCTAATTT-TATATAACTTTTTAAAATTTTAAACAAT
8114 T-TCATCTAATTTTATATAACTTTTT
1 TAT-ATCTAATTTTATATAACTTTTT
8139 TATAATTATT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
38 12 0.24
39 32 0.63
40 7 0.14
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (40 bp):
TATATCTAATTTTATATAACTTTTTAAAATTTTAAACAAT
Found at i:11900 original size:2 final size:2
Alignment explanation
Indices: 11893--11925 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11883 TGATGAAACC
11893 AT AT AT AT 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 AT AT AT AT A
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.