Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015110.1 Kokia drynarioides strain JFW-HI SEQ_130154, 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: 14906
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Found at i:6890 original size:6 final size:6
Alignment explanation
Indices: 6882--6920 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
6872 CCCTAATCTT
*
6882 AATCCT AATCCA AATCCA AATCCA AATCCA AATCCA AAT
1 AATCCA AATCCA AATCCA AATCCA AATCCA AATCCA AAT
6921 AACAAAGCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.21
Consensus pattern (6 bp):
AATCCA
Found at i:7452 original size:25 final size:24
Alignment explanation
Indices: 7423--7469 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
7413 CAGTCACTCT
*
7423 AATTTATAATAATAAAAATAGATAA
1 AATTTATAACAA-AAAAATAGATAA
* *
7448 AATTTTTAACAAACAAATAGAT
1 AATTTATAACAAAAAAATAGAT
7470 TATATTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (24 bp):
AATTTATAACAAAAAAATAGATAA
Found at i:8397 original size:32 final size:32
Alignment explanation
Indices: 8351--8415 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
8341 ATTAATTTAT
* * *
8351 ATATTTTTAATGATATTTTTTATTATCAAAAA
1 ATATTTGTAATGATATTTATTAATATCAAAAA
* *
8383 ATATTTGTAGTGATATTTATTAATATTAAAAA
1 ATATTTGTAATGATATTTATTAATATCAAAAA
8415 A
1 A
8416 AAAGTTAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (32 bp):
ATATTTGTAATGATATTTATTAATATCAAAAA
Found at i:8936 original size:10 final size:10
Alignment explanation
Indices: 8910--8943 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
8900 TTCCTTTTTT
8910 AAATATTAAA
1 AAATATTAAA
8920 AAA-ATTAAA
1 AAATATTAAA
8929 AAATATTAAA
1 AAATATTAAA
8939 AAATA
1 AAATA
8944 AAATTAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAATATTAAA
Found at i:9451 original size:27 final size:27
Alignment explanation
Indices: 9391--9481 Score: 92
Period size: 27 Copynumber: 3.4 Consensus size: 27
9381 TTATGACGGG
* *
9391 TGATGCCTTTGGGATAGGCGGTACTAA
1 TGATGCCTTTTGGATAGGCGGCACTAA
* * *
9418 CGGTGCCTTTTGGATAGGCGGCACCAA
1 TGATGCCTTTTGGATAGGCGGCACTAA
* * * *
9445 TGATGCCTATTGGGTAGACAGCACTAA
1 TGATGCCTTTTGGATAGGCGGCACTAA
*
9472 TGTTGCCTTT
1 TGATGCCTTT
9482 GTCAAAACTA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (27 bp):
TGATGCCTTTTGGATAGGCGGCACTAA
Found at i:12670 original size:26 final size:26
Alignment explanation
Indices: 12598--12671 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
12588 ATAAATAATA
* * * *
12598 TGTATGTAATTAATAATTTTTATGTT
1 TGTATTTAATTAATGATGTTTATATT
*
12624 TGTATTTAATTATTGATGTTTATATT
1 TGTATTTAATTAATGATGTTTATATT
*
12650 TGTATTTAATTAATGAGGTTTA
1 TGTATTTAATTAATGATGTTTA
12672 AGGTTTAAGG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.57
Consensus pattern (26 bp):
TGTATTTAATTAATGATGTTTATATT
Found at i:12730 original size:37 final size:36
Alignment explanation
Indices: 12689--12812 Score: 82
Period size: 37 Copynumber: 3.5 Consensus size: 36
12679 AGGTTCAGGA
12689 TTTTAGATTTTTAAAGGTTAAAATGATGAGTTTAGGG
1 TTTTAGATTTTTAAAGGTT-AAATGATGAGTTTAGGG
* * * * *
12726 TTTTACAATTGTAAGGGTT---T--TGAATTTAGGG
1 TTTTAGATTTTTAAAGGTTAAATGATGAGTTTAGGG
* * *
12757 TTTTA-AGTATTTAGAA-ATTAAAGTGATGAGTTTAAGG
1 TTTTAGA-TTTTTA-AAGGTTAAA-TGATGAGTTTAGGG
*
12794 TTTTAGATTTTTAAGGGTT
1 TTTTAGATTTTTAAAGGTT
12813 TTGAGTTTAA
Statistics
Matches: 62, Mismatches: 15, Indels: 20
0.64 0.15 0.21
Matches are distributed among these distances:
30 1 0.02
31 20 0.32
32 1 0.02
33 1 0.02
35 1 0.02
36 1 0.02
37 36 0.58
38 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.45
Consensus pattern (36 bp):
TTTTAGATTTTTAAAGGTTAAATGATGAGTTTAGGG
Found at i:12784 original size:68 final size:67
Alignment explanation
Indices: 12706--12952 Score: 282
Period size: 68 Copynumber: 3.6 Consensus size: 67
12696 TTTTTAAAGG
* * * *
12706 TTAAAATGATGAGTTTAGGGTTTTACAATTGTAAGGGTTTTGAATTTAGGGTTTTAAGTATTTAG
1 TTAAAGTGATGAGTTTAGGGTTTTAGAATTTTAAGGGTTTTGAATTTA-GGTTTTAAGGATTTAG
*
12771 AAA
65 AAT
* * *
12774 TTAAAGTGATGAGTTTAAGGTTTTAGATTTTTAAGGGTTTTGAGTTTAAGGTTTTAAGGATTTAG
1 TTAAAGTGATGAGTTTAGGGTTTTAGAATTTTAAGGGTTTTGAATTT-AGGTTTTAAGGATTTAG
*
12839 GAT
65 AAT
* * * * * *
12842 TTAAAGTGATTAGTTTAGAGTTTTAGATTTTTAAGGATTTTGATTTTCAAGTTTTAAGGATTTA-
1 TTAAAGTGATGAGTTTAGGGTTTTAGAATTTTAAGGGTTTTGAATTT-AGGTTTTAAGGATTTAG
12906 ATAT
65 A-AT
* *
12910 TTAAATTGACGAGTTTAGGGTTTTAG-ATTTTCAAGGGTTTTGA
1 TTAAAGTGATGAGTTTAGGGTTTTAGAATTTT-AAGGGTTTTGA
12953 GTCTAAGGTT
Statistics
Matches: 153, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
67 4 0.03
68 148 0.97
69 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.46
Consensus pattern (67 bp):
TTAAAGTGATGAGTTTAGGGTTTTAGAATTTTAAGGGTTTTGAATTTAGGTTTTAAGGATTTAGA
AT
Found at i:12808 original size:16 final size:15
Alignment explanation
Indices: 12784--12829 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
12774 TTAAAGTGAT
12784 GAGTTTAAGGTTTTA
1 GAGTTTAAGGTTTTA
*
12799 GATTTTTAAGGGTTTT-
1 GA-GTTTAA-GGTTTTA
12815 GAGTTTAAGGTTTTA
1 GAGTTTAAGGTTTTA
12830 AGGATTTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 6 0.23
15 7 0.27
16 7 0.27
17 6 0.23
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (15 bp):
GAGTTTAAGGTTTTA
Found at i:12859 original size:136 final size:136
Alignment explanation
Indices: 12706--12963 Score: 340
Period size: 136 Copynumber: 1.9 Consensus size: 136
12696 TTTTTAAAGG
* * * *
12706 TTAAAATGATGAGTTTAGGGTTTTACAATTGTAAGGGTTTTGAATTT-AGGGTTTTAAGTATTTA
1 TTAAAATGATGAGTTTAGAGTTTTACAATTGTAAGGATTTTGAATTTCA-AGTTTTAAGGATTTA
* * *
12770 GA-AATTAAAGTGATGAGTTTAAGGTTTTAGATTTTTAAGGGTTTTGAGTTTAAGGTTTTAAGGA
65 -ATAATTAAAGTGACGAGTTTAAGGTTTTAGATTTTCAAGGGTTTTGAGTCTAAGGTTTTAAGGA
12834 TTTAGGAT
129 TTTAGGAT
* * * * * *
12842 TTAAAGTGATTAGTTTAGAGTTTTAGATTTTTAAGGATTTTGATTTTCAAGTTTTAAGGATTTAA
1 TTAAAATGATGAGTTTAGAGTTTTACAATTGTAAGGATTTTGAATTTCAAGTTTTAAGGATTTAA
* * *
12907 TATTTAAATTGACGAGTTTAGGGTTTTAGATTTTCAAGGGTTTTGAGTCTAAGGTTT
66 TAATTAAAGTGACGAGTTTAAGGTTTTAGATTTTCAAGGGTTTTGAGTCTAAGGTTT
12964 AAAGTGATGA
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
135 1 0.01
136 102 0.98
137 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.23, T:0.46
Consensus pattern (136 bp):
TTAAAATGATGAGTTTAGAGTTTTACAATTGTAAGGATTTTGAATTTCAAGTTTTAAGGATTTAA
TAATTAAAGTGACGAGTTTAAGGTTTTAGATTTTCAAGGGTTTTGAGTCTAAGGTTTTAAGGATT
TAGGAT
Found at i:13023 original size:14 final size:15
Alignment explanation
Indices: 12970--13043 Score: 57
Period size: 14 Copynumber: 5.0 Consensus size: 15
12960 GTTTAAAGTG
*
12970 ATGAGTTTAGGGTTTT
1 ATGATTTTAGGG-TTT
12986 ATGATTTTAAGGGTTGT
1 ATGATTTT-AGGGTT-T
13003 A--ATTTTAGGGTTT
1 ATGATTTTAGGGTTT
**
13016 ATGA-TTTAAAGTTT
1 ATGATTTTAGGGTTT
*
13030 AGGA-TTTAGGGTTT
1 ATGATTTTAGGGTTT
13044 TAATTAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
13 2 0.04
14 25 0.52
15 6 0.12
16 9 0.19
17 6 0.12
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (15 bp):
ATGATTTTAGGGTTT
Done.