Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014431.1 Corchorus olitorius cultivar O-4 contig14464, 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: 28370
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:50 original size:11 final size:10
Alignment explanation
Indices: 33--85 Score: 52
Period size: 11 Copynumber: 4.9 Consensus size: 10
23 TGCTCGATTA
33 ATGTTCGTTT
1 ATGTTCGTTT
43 AGTGTTCGTTT
1 A-TGTTCGTTT
*
54 ATTGTTCGTTCA
1 A-TGTTCGTT-T
*
66 ATAGCTCGTTT
1 AT-GTTCGTTT
77 ATGTTCGTT
1 ATGTTCGTT
86 AATTAAGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 7 0.20
11 21 0.60
12 7 0.20
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (10 bp):
ATGTTCGTTT
Found at i:210 original size:30 final size:30
Alignment explanation
Indices: 150--214 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
140 ATTCAAATTT
**
150 TATTAGAAATATTTATTAATATGTAATAAA
1 TATTAGAAATATTTATTAATATACAATAAA
*
180 TATTA-AAATATTTATTTAATATACAGTAAA
1 TATTAGAAATATTTA-TTAATATACAATAAA
210 TATTA
1 TATTA
215 TTAAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.45
Consensus pattern (30 bp):
TATTAGAAATATTTATTAATATACAATAAA
Found at i:217 original size:33 final size:29
Alignment explanation
Indices: 136--220 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 29
126 TTATTTCAAA
*
136 TAATAT-TCAAATTTTATTAGAAATATTTAT
1 TAATATGT-AAATATTATTA-AAATATTTAT
*
166 TAATATGT-AATAAATATTAAAATATTTATT
1 TAATATGTAAAT-ATTATTAAAATATTTA-T
196 TAATATACAGTAAATATTATTAAAA
1 TAATAT---GTAAATATTATTAAAA
221 ATAATATGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
29 12 0.27
30 18 0.40
31 1 0.02
33 11 0.24
34 3 0.07
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (29 bp):
TAATATGTAAATATTATTAAAATATTTAT
Found at i:2684 original size:19 final size:19
Alignment explanation
Indices: 2660--2704 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
2650 TTGTAGTTTA
2660 GAAAATGAAAACGGAATTG
1 GAAAATGAAAACGGAATTG
2679 GAAAATGAAAACGGAATTG
1 GAAAATGAAAACGGAATTG
2698 GAAAATG
1 GAAAATG
2705 TTTTTGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.27, T:0.16
Consensus pattern (19 bp):
GAAAATGAAAACGGAATTG
Found at i:4673 original size:3 final size:3
Alignment explanation
Indices: 4667--4700 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
4657 CTTCTTCACT
4667 TTC TTC TTC TTC TTC TTC TTC TTC TTTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC
4701 ATTTGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5862 original size:5 final size:5
Alignment explanation
Indices: 5852--5881 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
5842 GATCTAATTA
5852 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG
5882 ATGTAGGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:11987 original size:6 final size:7
Alignment explanation
Indices: 11957--11987 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
11947 TTACAAACCC
11957 AAAGCCA
1 AAAGCCA
11964 AAAGCCA
1 AAAGCCA
11971 AAAGCCA
1 AAAGCCA
11978 AAAG-CA
1 AAAGCCA
11984 AAAG
1 AAAG
11988 GCAGAAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.61, C:0.23, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAGCCA
Found at i:15293 original size:28 final size:29
Alignment explanation
Indices: 15230--15304 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 29
15220 ACCCTGATGG
*
15230 AGGGGGAAAATTGTCCTGGATTTGGGAAGTTC
1 AGGGGGCAAATTGT-CTGGATTT--GAAGTTC
* *
15262 AGGGGGCAAATTGTCTGGATTT-TAGTTT
1 AGGGGGCAAATTGTCTGGATTTGAAGTTC
15290 AGGGGGCAAATTGTC
1 AGGGGGCAAATTGTC
15305 CTTAGCCCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 19 0.47
31 8 0.20
32 13 0.32
ACGTcount: A:0.24, C:0.09, G:0.36, T:0.31
Consensus pattern (29 bp):
AGGGGGCAAATTGTCTGGATTTGAAGTTC
Found at i:17087 original size:14 final size:14
Alignment explanation
Indices: 17068--17098 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17058 ATCTATCTAG
17068 TTACTATAAAAAAA
1 TTACTATAAAAAAA
*
17082 TTACTATAAAAGAA
1 TTACTATAAAAAAA
17096 TTA
1 TTA
17099 GTAAGTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (14 bp):
TTACTATAAAAAAA
Done.