Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008193.1 Kokia drynarioides strain JFW-HI SEQ_122853, 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: 19525
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:2903 original size:42 final size:43
Alignment explanation
Indices: 2844--2946 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 43
2834 GAAGAAGAGA
*
2844 AAATTGAT-TTTGGGTTTAGTTTATGAA-TG-TTTTTTAATAATG
1 AAATT-ATATTTGGGTTTAGTTTAT-AAGTGTTTTTTTAAGAATG
*
2886 AAATTATATTTGAGTTTAGTTTATAAGTGTTTTTTTAAGAATG
1 AAATTATATTTGGGTTTAGTTTATAAGTGTTTTTTTAAGAATG
*
2929 AAATTGTATTTGGGTTTA
1 AAATTATATTTGGGTTTA
2947 AAAATATTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
41 4 0.07
42 22 0.41
43 28 0.52
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.51
Consensus pattern (43 bp):
AAATTATATTTGGGTTTAGTTTATAAGTGTTTTTTTAAGAATG
Found at i:8949 original size:37 final size:37
Alignment explanation
Indices: 8903--8991 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
8893 CTTACACAAA
8903 TTCAAGCTTTGTGCCTAGTAGGATTTGTGCCGGTATT
1 TTCAAGCTTTGTGCCTAGTAGGATTTGTGCCGGTATT
* * * *
8940 TTCAGGCTTTGTGCTTAGTAGGCTTTGTGCCGGTGTT
1 TTCAAGCTTTGTGCCTAGTAGGATTTGTGCCGGTATT
8977 TTCAAGCTTTGTGCC
1 TTCAAGCTTTGTGCC
8992 GGTGTTTTCG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.12, C:0.18, G:0.28, T:0.42
Consensus pattern (37 bp):
TTCAAGCTTTGTGCCTAGTAGGATTTGTGCCGGTATT
Found at i:8952 original size:21 final size:21
Alignment explanation
Indices: 8926--9005 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
8916 CCTAGTAGGA
*
8926 TTTGTGCCGGTATTTTCAGGC
1 TTTGTGCCGGTGTTTTCAGGC
**
8947 TTTGTG-C--T-TAGT-AGGC
1 TTTGTGCCGGTGTTTTCAGGC
*
8963 TTTGTGCCGGTGTTTTCAAGC
1 TTTGTGCCGGTGTTTTCAGGC
*
8984 TTTGTGCCGGTGTTTTCGGGC
1 TTTGTGCCGGTGTTTTCAGGC
9005 T
1 T
9006 ATATGCCTAG
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
16 10 0.21
17 3 0.06
18 1 0.02
19 1 0.02
20 3 0.06
21 29 0.62
ACGTcount: A:0.07, C:0.17, G:0.31, T:0.44
Consensus pattern (21 bp):
TTTGTGCCGGTGTTTTCAGGC
Found at i:9012 original size:21 final size:21
Alignment explanation
Indices: 8967--9012 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
8957 GTAGGCTTTG
* *
8967 TGCCGGTGTTTTCAAGCTTTG
1 TGCCGGTGTTTTCAAGCTATA
**
8988 TGCCGGTGTTTTCGGGCTATA
1 TGCCGGTGTTTTCAAGCTATA
9009 TGCC
1 TGCC
9013 TAGTAGGCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.22, G:0.30, T:0.39
Consensus pattern (21 bp):
TGCCGGTGTTTTCAAGCTATA
Found at i:11321 original size:15 final size:17
Alignment explanation
Indices: 11301--11347 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
11291 ATATTTACTT
11301 TTTATAATTAT-TAA-A
1 TTTATAATTATATAATA
*
11316 TTTATATTTATATAATA
1 TTTATAATTATATAATA
* *
11333 TTTTTAATTGTATAA
1 TTTATAATTATATAA
11348 ATGCATGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 10 0.38
16 3 0.12
17 13 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTATAATTATATAATA
Found at i:12435 original size:22 final size:23
Alignment explanation
Indices: 12410--12472 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 23
12400 GTATTTAGTT
12410 TATAATAAATT-TTAATTTATCA
1 TATAATAAATTATTAATTTATCA
**
12432 TATAATAATATTATTTGTTTATCA
1 TATAATAA-ATTATTAATTTATCA
12456 TATTAAATAAATATATT
1 TA-T-AATAAAT-TATT
12473 TTTATTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 8 0.24
23 3 0.09
24 11 0.32
25 3 0.09
26 9 0.26
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (23 bp):
TATAATAAATTATTAATTTATCA
Done.