Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015184.1 Corchorus capsularis cultivar CVL-1 contig15205, 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: 147303
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:1508 original size:9 final size:9
Alignment explanation
Indices: 1494--1520 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1484 CGGTAAAGGA
1494 TGCTGCAGC
1 TGCTGCAGC
1503 TGCTGCAGC
1 TGCTGCAGC
1512 TGCTGCAGC
1 TGCTGCAGC
1521 CAATAGAGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.33, G:0.33, T:0.22
Consensus pattern (9 bp):
TGCTGCAGC
Found at i:22679 original size:6 final size:6
Alignment explanation
Indices: 22668--22698 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
22658 CTTCCATATC
22668 ATCATA ATCATA ATCATA ATCATA ATCATA A
1 ATCATA ATCATA ATCATA ATCATA ATCATA A
22699 ATAAATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATCATA
Found at i:54167 original size:75 final size:75
Alignment explanation
Indices: 54044--54193 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
54034 ATTAGATGTT
54044 CACTTTTGATCAATAAAGTCAAAATTAGATTAGTGAATATAAAAAATATATAAAATAAAATAATT
1 CACTTTTGATCAATAAAGTCAAAATTAGATTAGTGAATATAAAAAATATATAAAATAAAATAATT
54109 TTTAAAAATA
66 TTTAAAAATA
*
54119 CACTTTTGGTCAATAAAGTCAAAATTAGATTAGTGAATATAAAAAATATATAAAATAAAATAATT
1 CACTTTTGATCAATAAAGTCAAAATTAGATTAGTGAATATAAAAAATATATAAAATAAAATAATT
54184 TTTAAAAATA
66 TTTAAAAATA
54194 ATAAAACTTT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.33
Consensus pattern (75 bp):
CACTTTTGATCAATAAAGTCAAAATTAGATTAGTGAATATAAAAAATATATAAAATAAAATAATT
TTTAAAAATA
Found at i:60988 original size:3 final size:3
Alignment explanation
Indices: 60982--61024 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
60972 TATTATCCTC
60982 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
61025 TTTTTAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:72897 original size:33 final size:33
Alignment explanation
Indices: 72851--72936 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
72841 CGGACGGGGT
72851 GGTATGAGGGATGGTGGCTTTGGTAGCCGTGGC
1 GGTATGAGGGATGGTGGCTTTGGTAGCCGTGGC
* * * *
72884 GGTATGAGAGATGGTGGTTTTGGTGGGCGTGGC
1 GGTATGAGGGATGGTGGCTTTGGTAGCCGTGGC
72917 GGTATGAGGGATGGTGGCTT
1 GGTATGAGGGATGGTGGCTT
72937 CAGTGGTCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.13, C:0.08, G:0.50, T:0.29
Consensus pattern (33 bp):
GGTATGAGGGATGGTGGCTTTGGTAGCCGTGGC
Found at i:73348 original size:24 final size:24
Alignment explanation
Indices: 73311--73363 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
73301 CGCAGTCCGG
*
73311 GCCGTACTCGTAGTCAAAGCCATA
1 GCCGTACTCATAGTCAAAGCCATA
* ** *
73335 GCCGTAGTCATAGTCGTAGCCATG
1 GCCGTACTCATAGTCAAAGCCATA
73359 GCCGT
1 GCCGT
73364 GGACACAGTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (24 bp):
GCCGTACTCATAGTCAAAGCCATA
Found at i:73373 original size:24 final size:24
Alignment explanation
Indices: 73322--73385 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
73312 CCGTACTCGT
* * *
73322 AGTCAAAGCCATAGCCGTAGTCAT
1 AGTCGAAGCCATAGCCGTAGACAC
* * *
73346 AGTCGTAGCCATGGCCGTGGACAC
1 AGTCGAAGCCATAGCCGTAGACAC
*
73370 AGTCGAAGCCGTAGCC
1 AGTCGAAGCCATAGCC
73386 ATAGCTATGA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.17
Consensus pattern (24 bp):
AGTCGAAGCCATAGCCGTAGACAC
Found at i:76035 original size:6 final size:6
Alignment explanation
Indices: 76024--76051 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
76014 AAAATGAATG
76024 AATTCC AATTCC AATTCC AATTCC AATT
1 AATTCC AATTCC AATTCC AATTCC AATT
76052 GCACACTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (6 bp):
AATTCC
Found at i:87313 original size:7 final size:7
Alignment explanation
Indices: 87303--87329 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
87293 TCTCAAATCT
87303 CTGCTGC
1 CTGCTGC
87310 CTGCTGC
1 CTGCTGC
87317 CTGCTGC
1 CTGCTGC
87324 CTGCTG
1 CTGCTG
87330 GTGTTGTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.41, G:0.30, T:0.30
Consensus pattern (7 bp):
CTGCTGC
Found at i:88983 original size:2 final size:2
Alignment explanation
Indices: 88976--89000 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
88966 ACTTTCCCCT
88976 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
89001 TTCATGTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:93934 original size:3 final size:3
Alignment explanation
Indices: 93928--93966 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
93918 TCTTCTTCTT
93928 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TT
93967 TTAAGCTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:95551 original size:31 final size:31
Alignment explanation
Indices: 95513--95577 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
95503 ACGATAATTT
95513 TACTTATTGTGATACACCACCAATATATAAC
1 TACTTATTGTGATACACCACCAATATATAAC
95544 TACTTATTGTGATACACCACCAATATATAAC
1 TACTTATTGTGATACACCACCAATATATAAC
95575 TAC
1 TAC
95578 GATCTTCAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (31 bp):
TACTTATTGTGATACACCACCAATATATAAC
Found at i:131465 original size:2 final size:2
Alignment explanation
Indices: 131458--131496 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
131448 ATTTATACAT
131458 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
131497 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:131780 original size:28 final size:28
Alignment explanation
Indices: 131740--131822 Score: 166
Period size: 28 Copynumber: 3.0 Consensus size: 28
131730 TAAAATGCTT
131740 CTAGATTTTAAGTCTGAAATAACAGAAA
1 CTAGATTTTAAGTCTGAAATAACAGAAA
131768 CTAGATTTTAAGTCTGAAATAACAGAAA
1 CTAGATTTTAAGTCTGAAATAACAGAAA
131796 CTAGATTTTAAGTCTGAAATAACAGAA
1 CTAGATTTTAAGTCTGAAATAACAGAA
131823 TTTTCTGTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (28 bp):
CTAGATTTTAAGTCTGAAATAACAGAAA
Found at i:139186 original size:20 final size:20
Alignment explanation
Indices: 139161--139204 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
139151 TTATCCAGAG
139161 TTGTCAAACTGGTAAAGAAA
1 TTGTCAAACTGGTAAAGAAA
139181 TTGTCAAACTGGTAAAGAAA
1 TTGTCAAACTGGTAAAGAAA
139201 TTGT
1 TTGT
139205 TCTGGGGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (20 bp):
TTGTCAAACTGGTAAAGAAA
Found at i:141110 original size:21 final size:21
Alignment explanation
Indices: 141084--141126 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
141074 GGAAAAATGG
141084 GTTGAAGAAGGAAAAAGCCTT
1 GTTGAAGAAGGAAAAAGCCTT
141105 GTTGAAGAAGGAAAAAGCCTT
1 GTTGAAGAAGGAAAAAGCCTT
141126 G
1 G
141127 AACAACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.30, T:0.19
Consensus pattern (21 bp):
GTTGAAGAAGGAAAAAGCCTT
Done.