Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006283.1 Kokia drynarioides strain JFW-HI SEQ_120855, 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: 14780
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:1224 original size:17 final size:17
Alignment explanation
Indices: 1202--1237 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1192 AGCAGCCTCA
1202 GGATCCGAAACGTCTCG
1 GGATCCGAAACGTCTCG
1219 GGATCCGAAACGTCTCG
1 GGATCCGAAACGTCTCG
1236 GG
1 GG
1238 CAGAGGAGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.28, G:0.33, T:0.17
Consensus pattern (17 bp):
GGATCCGAAACGTCTCG
Found at i:2451 original size:14 final size:16
Alignment explanation
Indices: 2413--2453 Score: 50
Period size: 14 Copynumber: 2.6 Consensus size: 16
2403 AAACTCAACC
2413 TTTAAATATTTTCAATA
1 TTTAAA-ATTTTCAATA
2430 TATTAAAATTTTC-AT-
1 T-TTAAAATTTTCAATA
2445 TTTAAAATT
1 TTTAAAATT
2454 AAAAAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 8 0.35
15 1 0.04
16 2 0.09
17 7 0.30
18 5 0.22
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTAAAATTTTCAATA
Found at i:4955 original size:21 final size:20
Alignment explanation
Indices: 4929--4968 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4919 TTAACAATCA
4929 ATAGTTATACATTATGTCAAT
1 ATAGTT-TACATTATGTCAAT
**
4950 ATAGTTTTTATTATGTCAA
1 ATAGTTTACATTATGTCAA
4969 CTTTATCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (20 bp):
ATAGTTTACATTATGTCAAT
Found at i:9664 original size:12 final size:13
Alignment explanation
Indices: 9640--9672 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
9630 TATAAGTTAC
*
9640 ATAATATATAAAA
1 ATAATATAAAAAA
9653 AT-ATATAAAAAA
1 ATAATATAAAAAA
9665 ATAATATA
1 ATAATATA
9673 TTATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAATATAAAAAA
Found at i:11655 original size:26 final size:25
Alignment explanation
Indices: 11618--11668 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
11608 CGTTTGGGTA
* *
11618 TTGAGCTATTTTGGTTTTTAATTTTT
1 TTGAGCTATTTT-ATATTTAATTTTT
11644 TTGAGC-ATTTTTATATTTAATTTTT
1 TTGAGCTA-TTTTATATTTAATTTTT
11669 ATTTTTTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.65
Consensus pattern (25 bp):
TTGAGCTATTTTATATTTAATTTTT
Found at i:13641 original size:51 final size:51
Alignment explanation
Indices: 13530--13644 Score: 126
Period size: 51 Copynumber: 2.3 Consensus size: 51
13520 AATTTCATCT
*
13530 CAATATTTACATATTATGTCAATTTCAAACTGATTTAACAAATTTAGTCCA
1 CAATATTTACATAATATGTCAATTTCAAACTGATTTAACAAATTTAGTCCA
* * * * ***
13581 CAGCT-TTTACATAATCTGTCAATTT-GATCTTGATTTAACAAATTTAGTTTG
1 CA-ATATTTACATAATATGTCAATTTCAAAC-TGATTTAACAAATTTAGTCCA
13632 CAATATTTACATA
1 CAATATTTACATA
13645 GTCAATCAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
50 3 0.06
51 48 0.92
52 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (51 bp):
CAATATTTACATAATATGTCAATTTCAAACTGATTTAACAAATTTAGTCCA
Done.