Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007658.1 Corchorus capsularis cultivar CVL-1 contig07679, 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: 10572
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Found at i:773 original size:26 final size:24
Alignment explanation
Indices: 734--782 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
724 TATGATTAAA
734 ATGCAACAATATTAAGCTAAATGAAG
1 ATGCAACAATATT-A-CTAAATGAAG
760 ATGCAACTAA-ATTACTAAATGAA
1 ATGCAAC-AATATTACTAAATGAA
783 AATATGCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 9 0.41
25 1 0.05
26 10 0.45
27 2 0.09
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.24
Consensus pattern (24 bp):
ATGCAACAATATTACTAAATGAAG
Found at i:1799 original size:63 final size:64
Alignment explanation
Indices: 1680--1800 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 64
1670 GAATTTTGGT
* *
1680 AACTTTCCTATGAAATGTTGGTAACCACACTATGAAATTTTGGTAACCTCGCTATGAAGTTACCA
1 AACTTTCCTATGAAATGTTGATAACCACAC-ATGAAATTCTGGTAACCTCGCTATGAAGTTACCA
* *
1745 AACTTTCCTATGGAATTTTGATAACCACAC-TGAAATTCTGGTAACCTAC-CTATGAA
1 AACTTTCCTATGAAATGTTGATAACCACACATGAAATTCTGGTAACCT-CGCTATGAA
1801 ATTTTAGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
63 23 0.45
64 1 0.02
65 27 0.53
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (64 bp):
AACTTTCCTATGAAATGTTGATAACCACACATGAAATTCTGGTAACCTCGCTATGAAGTTACCA
Found at i:1801 original size:22 final size:22
Alignment explanation
Indices: 1598--1833 Score: 117
Period size: 22 Copynumber: 10.8 Consensus size: 22
1588 ATAACTTTTT
* ** *
1598 CCTATGAAATTTTGGGAATATT
1 CCTATGAAATTTTGGTAACCTA
* *
1620 CTTATGAAATTTTGGTAACTTA
1 CCTATGAAATTTTGGTAACCTA
* * * *
1642 CCTATCAAATTTTGATAA-TTG
1 CCTATGAAATTTTGGTAACCTA
* * * *
1663 CGCCATGGAATTTTGGTAACTTT
1 C-CTATGAAATTTTGGTAACCTA
*
1686 CCTATGAAATGTTGGTAACC-A
1 CCTATGAAATTTTGGTAACCTA
1707 CACTATGAAATTTTGGTAACCT-
1 C-CTATGAAATTTTGGTAACCTA
* **** * *
1729 CGCTATG-AAGTTACCAAACTTT
1 C-CTATGAAATTTTGGTAACCTA
* *
1751 CCTATGGAATTTTGATAACC-A
1 CCTATGAAATTTTGGTAACCTA
*
1772 -C-ACTGAAATTCTGGTAACCTA
1 CCTA-TGAAATTTTGGTAACCTA
* * * *
1793 CCTATGAAATTTTAGAAACGTC
1 CCTATGAAATTTTGGTAACCTA
1815 CCTTATGAAATTTTGGTAA
1 CC-TATGAAATTTTGGTAA
1834 GCTCACTGTG
Statistics
Matches: 159, Mismatches: 44, Indels: 21
0.71 0.20 0.09
Matches are distributed among these distances:
19 1 0.01
20 14 0.09
21 18 0.11
22 108 0.68
23 18 0.11
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (22 bp):
CCTATGAAATTTTGGTAACCTA
Found at i:2104 original size:23 final size:23
Alignment explanation
Indices: 2078--2123 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2068 CCAAGAGAGC
* * *
2078 CAAAATAATTCGTTGCAATTTGT
1 CAAAAAAATCCGTTACAATTTGT
2101 CAAAAAAATCCGTTACAATTTGT
1 CAAAAAAATCCGTTACAATTTGT
2124 GCAATGGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (23 bp):
CAAAAAAATCCGTTACAATTTGT
Found at i:7039 original size:10 final size:10
Alignment explanation
Indices: 7024--7068 Score: 54
Period size: 10 Copynumber: 4.2 Consensus size: 10
7014 CTAATGATCT
7024 ATAAATTTTC
1 ATAAATTTTC
7034 ATAAATTTTC
1 ATAAATTTTC
7044 ATTAAAATTTTC
1 A-T-AAATTTTC
*
7056 ATTAAATCTTC
1 A-TAAATTTTC
7067 AT
1 AT
7069 TAGTGATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 12 0.38
11 9 0.28
12 11 0.34
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (10 bp):
ATAAATTTTC
Found at i:7062 original size:11 final size:11
Alignment explanation
Indices: 7025--7070 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
7015 TAATGATCTA
7025 TAAATTTTCA-
1 TAAATTTTCAT
7035 TAAATTTTCAT
1 TAAATTTTCAT
7046 TAAAATTTTCAT
1 T-AAATTTTCAT
*
7058 TAAATCTTCAT
1 TAAATTTTCAT
7069 TA
1 TA
7071 GTGATAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
10 10 0.30
11 12 0.36
12 11 0.33
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (11 bp):
TAAATTTTCAT
Found at i:7067 original size:23 final size:22
Alignment explanation
Indices: 7026--7070 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
7016 AATGATCTAT
*
7026 AAATTTTCATAAATTTTCATTA
1 AAATTTTCATAAATCTTCATTA
7048 AAATTTTCATTAAATCTTCATTA
1 AAATTTTCA-TAAATCTTCATTA
7071 GTGATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (22 bp):
AAATTTTCATAAATCTTCATTA
Found at i:7891 original size:10 final size:11
Alignment explanation
Indices: 7850--7890 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
7840 GGCAATTAAT
7850 TTTGGATTTTG
1 TTTGGATTTTG
**
7861 TTTGGA-TACG
1 TTTGGATTTTG
7871 TTTGGATTTTG
1 TTTGGATTTTG
7882 TTTGGATTT
1 TTTGGATTT
7891 GATTTCCATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.12, C:0.02, G:0.27, T:0.59
Consensus pattern (11 bp):
TTTGGATTTTG
Done.