Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002697.1 Kokia drynarioides strain JFW-HI SEQ_114978, 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: 31414
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:9728 original size:5 final size:5
Alignment explanation
Indices: 9714--9744 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
9704 TATATTTATT
9714 ATAT- ATATG ATATG ATATG ATATG ATATG AT
1 ATATG ATATG ATATG ATATG ATATG ATATG AT
9745 GATAGTGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (5 bp):
ATATG
Found at i:9736 original size:15 final size:14
Alignment explanation
Indices: 9698--9744 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 14
9688 GTGTTTAAAC
9698 ATATGATATAT-T-
1 ATATGATATATATG
*
9710 -TATTATATATATG
1 ATATGATATATATG
9723 ATATGATATGATATG
1 ATATGATAT-ATATG
9738 ATATGAT
1 ATATGAT
9745 GATAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
14 7 0.24
15 12 0.41
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
ATATGATATATATG
Found at i:10018 original size:2 final size:2
Alignment explanation
Indices: 10011--10040 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10001 ATAAAAGTAC
10011 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10041 TAAAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11108 original size:22 final size:20
Alignment explanation
Indices: 11083--11126 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
11073 AATCAAATCG
*
11083 TGGTAATATTTCTACACAAAAA
1 TGGTAATATAT-TAC-CAAAAA
*
11105 TGGTTATATATTACCAAAAA
1 TGGTAATATATTACCAAAAA
11125 TG
1 TG
11127 CTTCAGTGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 3 0.15
22 9 0.45
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (20 bp):
TGGTAATATATTACCAAAAA
Found at i:19229 original size:17 final size:16
Alignment explanation
Indices: 19204--19250 Score: 62
Period size: 14 Copynumber: 3.0 Consensus size: 16
19194 ACATTATAAA
*
19204 ATATAAAAATCAAATT
1 ATATAAAAATTAAATT
19220 ATATTAAAAATTAAA--
1 ATA-TAAAAATTAAATT
19235 ATATAAAAATTAAATT
1 ATATAAAAATTAAATT
19251 TTAATTTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 3 0.11
17 10 0.37
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAAAATTAAATT
Found at i:19722 original size:20 final size:19
Alignment explanation
Indices: 19674--19730 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
19664 ATAATTTTAT
*
19674 TATTTTTAAGAAATTAAAATA
1 TATTTTTAA-AAA-TAATATA
*
19695 TATATTTAAAAATAATATA
1 TATTTTTAAAAATAATATA
19714 TATCTTTTAAAAATAAT
1 TAT-TTTTAAAAATAAT
19731 TTCAAATGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.28
20 15 0.47
21 8 0.25
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
TATTTTTAAAAATAATATA
Found at i:22927 original size:30 final size:30
Alignment explanation
Indices: 22880--23019 Score: 144
Period size: 30 Copynumber: 4.7 Consensus size: 30
22870 TTGGATGCCT
22880 GGGG-TAAAATGGTAATTTTTGGAAAGTTTA
1 GGGGTTAAAAT-GTAATTTTTGGAAAGTTTA
*
22910 GGGGTTAAAATGCAATTTTT-GAGAAGTTT-
1 GGGGTTAAAATGTAATTTTTGGA-AAGTTTA
* **
22939 GAGGGTTAAAATATAATTTTTAAAAAGTTTA
1 G-GGGTTAAAATGTAATTTTTGGAAAGTTTA
* *
22970 AGGGTCAAAATGTAATTTTTGGAAAGTTT-
1 GGGGTTAAAATGTAATTTTTGGAAAGTTTA
* *
22999 GGAGGTCAAAATATAATTTTT
1 GG-GGTTAAAATGTAATTTTT
23020 AAGAAGTTTT
Statistics
Matches: 93, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
29 4 0.04
30 82 0.88
31 7 0.08
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTTGGAAAGTTTA
Found at i:22958 original size:60 final size:60
Alignment explanation
Indices: 22892--23038 Score: 183
Period size: 60 Copynumber: 2.5 Consensus size: 60
22882 GGTAAAATGG
** * * *
22892 TAATTTTTGGAAAGTTTAGGGGTTAAAATGCAATTTTT-GAGAAGTTT-GAGGGTTAAAATA
1 TAATTTTTAAAAAGTTTAAGGGTCAAAATGCAATTTTTGGA-AAGTTTGGA-GGTCAAAATA
*
22952 TAATTTTTAAAAAGTTTAAGGGTCAAAATGTAATTTTTGGAAAGTTTGGAGGTCAAAATA
1 TAATTTTTAAAAAGTTTAAGGGTCAAAATGCAATTTTTGGAAAGTTTGGAGGTCAAAATA
*
23012 TAATTTTTAAGAAGTTTTAA-GGTCAAA
1 TAATTTTTAAAAAG-TTTAAGGGTCAAA
23039 TTAAAATTGG
Statistics
Matches: 77, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
60 68 0.88
61 9 0.12
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (60 bp):
TAATTTTTAAAAAGTTTAAGGGTCAAAATGCAATTTTTGGAAAGTTTGGAGGTCAAAATA
Found at i:23027 original size:30 final size:30
Alignment explanation
Indices: 22903--23038 Score: 125
Period size: 30 Copynumber: 4.5 Consensus size: 30
22893 AATTTTTGGA
* * ** *
22903 AAGTTTAGGGGTTAAAATGCAATTTTTGAG
1 AAGTTTAAGGGTCAAAATATAATTTTTAAG
* * *
22933 AAGTTTGAGGGTTAAAATATAATTTTTAAA
1 AAGTTTAAGGGTCAAAATATAATTTTTAAG
* *
22963 AAGTTTAAGGGTCAAAATGTAATTTTT-GG
1 AAGTTTAAGGGTCAAAATATAATTTTTAAG
*
22992 AAAGTTT-GGAGGTCAAAATATAATTTTTAAG
1 -AAGTTTAAG-GGTCAAAATATAATTTTTAAG
23023 AAGTTTTAA-GGTCAAA
1 AAG-TTTAAGGGTCAAA
23039 TTAAAATTGG
Statistics
Matches: 86, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
29 1 0.01
30 81 0.94
31 4 0.05
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (30 bp):
AAGTTTAAGGGTCAAAATATAATTTTTAAG
Found at i:23193 original size:17 final size:17
Alignment explanation
Indices: 23122--23201 Score: 81
Period size: 17 Copynumber: 4.7 Consensus size: 17
23112 TATTTTCAAT
*
23122 TTAAAATAAATTTAAA-
1 TTAAAATAAATTCAAAC
*
23138 TCTAAAGTAAATTCAAAC
1 T-TAAAATAAATTCAAAC
* * * * *
23156 TCAAAATGAGTTTAAAT
1 TTAAAATAAATTCAAAC
23173 TTAAAATAAATTCAAAC
1 TTAAAATAAATTCAAAC
23190 TTAAAATAAATT
1 TTAAAATAAATT
23202 AAAATTTTGA
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
16 1 0.02
17 47 0.96
18 1 0.02
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.34
Consensus pattern (17 bp):
TTAAAATAAATTCAAAC
Found at i:23207 original size:34 final size:34
Alignment explanation
Indices: 23122--23208 Score: 120
Period size: 34 Copynumber: 2.6 Consensus size: 34
23112 TATTTTCAAT
* *
23122 TTAAAATAAATTTAAATCTAAAGTAAATTCAAAC
1 TTAAAATAAATTTAAATTTAAAATAAATTCAAAC
* * *
23156 TCAAAATGAGTTTAAATTTAAAATAAATTCAAAC
1 TTAAAATAAATTTAAATTTAAAATAAATTCAAAC
*
23190 TTAAAATAAATTAAAATTT
1 TTAAAATAAATTTAAATTT
23209 TGACTCAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.34
Consensus pattern (34 bp):
TTAAAATAAATTTAAATTTAAAATAAATTCAAAC
Found at i:25257 original size:14 final size:13
Alignment explanation
Indices: 25232--25256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25222 ACATCTTCAA
25232 AAAATACTTTTTC
1 AAAATACTTTTTC
25245 AAAATACTTTTT
1 AAAATACTTTTT
25257 TTGTAGAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATACTTTTTC
Done.