Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014524.1 Kokia drynarioides strain JFW-HI SEQ_129563, 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: 18363
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:2279 original size:12 final size:12
Alignment explanation
Indices: 2262--2303 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
2252 ATAACAACTT
2262 ATAAAATAAAAA
1 ATAAAATAAAAA
2274 ATAAAAATAAAAA
1 AT-AAAATAAAAA
2287 CA-AAAATAAGAAA
1 -ATAAAATAA-AAA
2300 ATAA
1 ATAA
2304 CAATTTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 10 0.38
13 15 0.58
14 1 0.04
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:2282 original size:13 final size:13
Alignment explanation
Indices: 2264--2303 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
2254 AACAACTTAT
2264 AAAATAAAAAATA
1 AAAATAAAAAATA
*
2277 AAAAT-AAAAACA
1 AAAATAAAAAATA
2289 AAAATAAGAAAATA
1 AAAATAA-AAAATA
2303 A
1 A
2304 CAATTTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 11 0.48
13 6 0.26
14 6 0.26
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAATAAAAAATA
Found at i:4055 original size:27 final size:27
Alignment explanation
Indices: 4017--4071 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
4007 AATGACCAAA
*
4017 ATGTAAATTTACTCATCCCCACATTTG
1 ATGTAAATTTACCCATCCCCACATTTG
**
4044 ATGTAAATTTACCCATCCCTGCATTTG
1 ATGTAAATTTACCCATCCCCACATTTG
4071 A
1 A
4072 CGCCTATTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.36
Consensus pattern (27 bp):
ATGTAAATTTACCCATCCCCACATTTG
Found at i:6160 original size:14 final size:14
Alignment explanation
Indices: 6143--6192 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 14
6133 AAATTTTGAG
*
6143 ATTTAATCTTTATA
1 ATTTAATTTTTATA
6157 ATTTAATTTTTAACATA
1 ATTTAATTTTT---ATA
6174 ATTTAATTTTTATA
1 ATTTAATTTTTATA
6188 TATTT
1 -ATTT
6193 TAATGTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 13 0.42
15 4 0.13
17 14 0.45
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTTAATTTTTATA
Found at i:6909 original size:24 final size:28
Alignment explanation
Indices: 6859--6910 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 28
6849 ATCTTAAACC
*
6859 ATTTCATATATAATTAATCTTACAAATA
1 ATTTCATATATAATTAATCTTAAAAATA
6887 ATTT-ATAT-TAATT-A-CTTAAAAATA
1 ATTTCATATATAATTAATCTTAAAAATA
6911 TATAAAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 9 0.39
25 1 0.04
26 5 0.22
27 4 0.17
28 4 0.17
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (28 bp):
ATTTCATATATAATTAATCTTAAAAATA
Found at i:7072 original size:13 final size:14
Alignment explanation
Indices: 7046--7073 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
7036 AGAATATAAT
7046 AAAATATTTAAAAA
1 AAAATATTTAAAAA
7060 AAAATATTTAAAAA
1 AAAATATTTAAAAA
7074 TAAGGAGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATATTTAAAAA
Found at i:17097 original size:60 final size:62
Alignment explanation
Indices: 16993--17158 Score: 162
Period size: 61 Copynumber: 2.7 Consensus size: 62
16983 CAAAATTAGC
* * * * *
16993 CCTCTAATATTTACAGATTCTATCAA-TTGGATCCTAAATATAAAAAAATT-AATAAATTT-AG
1 CCTC-AATATTTACAAAATCTATCAATTTAG-TCCTAACTCTAAAAAAATTCAATAAATTTAAG
* * * * * *
17054 CCTCAATGTTTACAAAAAT-TTTCATTTTAGTTCTAATTCT-AAAAAATTCAATAAATTTAAT
1 CCTCAATATTTAC-AAAATCTATCAATTTAGTCCTAACTCTAAAAAAATTCAATAAATTTAAG
*
17115 CCTCGATATTTACAAAATCTATCAATTTAGTCCTAACTCTAAAA
1 CCTCAATATTTACAAAATCTATCAATTTAGTCCTAACTCTAAAA
17159 TTAGAAAAAA
Statistics
Matches: 83, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
59 8 0.10
60 33 0.40
61 39 0.47
62 3 0.04
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.38
Consensus pattern (62 bp):
CCTCAATATTTACAAAATCTATCAATTTAGTCCTAACTCTAAAAAAATTCAATAAATTTAAG
Done.