Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010986.1 Kokia drynarioides strain JFW-HI SEQ_125956, 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: 13564
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:2806 original size:29 final size:28
Alignment explanation
Indices: 2719--2800 Score: 110
Period size: 29 Copynumber: 2.9 Consensus size: 28
2709 AATTGGGGTT
*
2719 TTGGATCCCTTAAAAGTTGAAAAAAAAA
1 TTGGATCCCTTAAAAATTGAAAAAAAAA
** *
2747 TTTAAGCCCTTAAAAATTGAAAAAAAAAA
1 TTGGATCCCTTAAAAATTG-AAAAAAAAA
*
2776 TTGGATCCCTTAAAAACTGAAAAAA
1 TTGGATCCCTTAAAAATTGAAAAAA
2801 TTAATTTTCG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
28 21 0.47
29 24 0.53
ACGTcount: A:0.52, C:0.12, G:0.11, T:0.24
Consensus pattern (28 bp):
TTGGATCCCTTAAAAATTGAAAAAAAAA
Found at i:5095 original size:31 final size:34
Alignment explanation
Indices: 5033--5096 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
5023 TTTTTATTAT
*
5033 TTTAAAAATAAATTAAAAATATAAAATTATTTTA
1 TTTAAAAATAAATTAAAAACATAAAATTATTTTA
*
5067 TTTAATAA-AAATTAAAAACA-AAAA-TATTTT
1 TTTAAAAATAAATTAAAAACATAAAATTATTTT
5097 TAGCCCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 6 0.21
32 4 0.14
33 11 0.39
34 7 0.25
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (34 bp):
TTTAAAAATAAATTAAAAACATAAAATTATTTTA
Found at i:6124 original size:21 final size:21
Alignment explanation
Indices: 6099--6159 Score: 86
Period size: 23 Copynumber: 2.8 Consensus size: 21
6089 ATTATATTGC
6099 TATATTTTACTGTTTTGGTGAT
1 TATATTTTACTGTTTTGGT-AT
*
6121 ATATTTTTTACTGTTTTGGTAT
1 -TATATTTTACTGTTTTGGTAT
*
6143 TATTTTTTACTGTTTTG
1 TATATTTTACTGTTTTG
6160 ATGCTGCTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
21 17 0.46
22 2 0.05
23 18 0.49
ACGTcount: A:0.16, C:0.05, G:0.15, T:0.64
Consensus pattern (21 bp):
TATATTTTACTGTTTTGGTAT
Found at i:6133 original size:23 final size:21
Alignment explanation
Indices: 6103--6159 Score: 96
Period size: 21 Copynumber: 2.6 Consensus size: 21
6093 TATTGCTATA
6103 TTTTACTGTTTTGGTGATATATT
1 TTTTACTGTTTTGGT-AT-TATT
6126 TTTTACTGTTTTGGTATTATT
1 TTTTACTGTTTTGGTATTATT
6147 TTTTACTGTTTTG
1 TTTTACTGTTTTG
6160 ATGCTGCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 17 0.50
22 2 0.06
23 15 0.44
ACGTcount: A:0.14, C:0.05, G:0.16, T:0.65
Consensus pattern (21 bp):
TTTTACTGTTTTGGTATTATT
Found at i:6187 original size:3 final size:3
Alignment explanation
Indices: 6181--6257 Score: 56
Period size: 3 Copynumber: 26.7 Consensus size: 3
6171 GCTATTATTT
* *
6181 TTG TTG TTG TT- TTG TTG TTA TT- TTCG TTG TTG TT- TTG TTG TTA
1 TTG TTG TTG TTG TTG TTG TTG TTG TT-G TTG TTG TTG TTG TTG TTG
* * *
6224 TTT TTG CTG CTG TT- TTGG TTG TTG TT- TTG TTG TT
1 TTG TTG TTG TTG TTG TT-G TTG TTG TTG TTG TTG TT
6258 TGGATGTTAT
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
2 10 0.16
3 47 0.77
4 4 0.07
ACGTcount: A:0.03, C:0.04, G:0.25, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:6193 original size:11 final size:11
Alignment explanation
Indices: 6179--6257 Score: 95
Period size: 11 Copynumber: 6.9 Consensus size: 11
6169 TTGCTATTAT
6179 TTTTGTTGTTG
1 TTTTGTTGTTG
*
6190 TTTTGTTGTTA
1 TTTTGTTGTTG
6201 TTTTCGTTGTTG
1 TTTT-GTTGTTG
*
6213 TTTTGTTGTTAT
1 TTTTGTTGTT-G
* *
6225 TTTTGCTGCTG
1 TTTTGTTGTTG
6236 TTTTGGTTGTTG
1 TTTT-GTTGTTG
6248 TTTTGTTGTT
1 TTTTGTTGTT
6258 TGGATGTTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
11 30 0.53
12 27 0.47
ACGTcount: A:0.03, C:0.04, G:0.24, T:0.70
Consensus pattern (11 bp):
TTTTGTTGTTG
Found at i:6193 original size:23 final size:23
Alignment explanation
Indices: 6175--6257 Score: 114
Period size: 23 Copynumber: 3.6 Consensus size: 23
6165 GCTTTTGCTA
6175 TTATTTTTGTTGTTGTTTTGTTG
1 TTATTTTTGTTGTTGTTTTGTTG
*
6198 TTATTTTCGTTGTTGTTTTGTTG
1 TTATTTTTGTTGTTGTTTTGTTG
* *
6221 TTATTTTTGCTGCTGTTTTGGTTG
1 TTATTTTTGTTGTTGTTTT-GTTG
*
6245 TT-GTTTTGTTGTT
1 TTATTTTTGTTGTT
6258 TGGATGTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
23 46 0.88
24 6 0.12
ACGTcount: A:0.04, C:0.04, G:0.23, T:0.70
Consensus pattern (23 bp):
TTATTTTTGTTGTTGTTTTGTTG
Done.