Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016632.1 Corchorus olitorius cultivar O-4 contig16665, 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: 25380
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Found at i:275 original size:15 final size:15
Alignment explanation
Indices: 255--286 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
245 CAATAAGCCA
255 ATATTTTAATGGCTT
1 ATATTTTAATGGCTT
270 ATATTTTAATGGCTT
1 ATATTTTAATGGCTT
285 AT
1 AT
287 TAGCTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.53
Consensus pattern (15 bp):
ATATTTTAATGGCTT
Found at i:2016 original size:31 final size:29
Alignment explanation
Indices: 1973--2140 Score: 97
Period size: 31 Copynumber: 5.6 Consensus size: 29
1963 TTCGGCTAAT
*
1973 TGCTTAAATAAGGGTCTAATGTTTGTCAAAA
1 TGCTCAAATAAGGGTCTAATGTTT-T-AAAA
* * **
2004 TGCTCAAATAAGGGTCCAATCTTTTAATT
1 TGCTCAAATAAGGGTCTAATGTTTTAAAA
* *
2033 TGGC-CAAATAAGGGCCTAACGTTATTGAAAA
1 T-GCTCAAATAAGGGTCTAATGTT-TT-AAAA
* ** * **
2064 TGCTCAAATAAGGGCCCGATCTTTTAATT
1 TGCTCAAATAAGGGTCTAATGTTTTAAAA
* ** *
2093 TGGC-CAAATAAGGGCCTAACCTTATCGAAAA
1 T-GCTCAAATAAGGGTCTAATGTT-T-TAAAA
2124 TGCTCAAATAAGGGTCT
1 TGCTCAAATAAGGGTCT
2141 GACATCAGTT
Statistics
Matches: 105, Mismatches: 24, Indels: 16
0.72 0.17 0.11
Matches are distributed among these distances:
29 37 0.35
30 14 0.13
31 54 0.51
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (29 bp):
TGCTCAAATAAGGGTCTAATGTTTTAAAA
Found at i:2064 original size:60 final size:60
Alignment explanation
Indices: 1978--2139 Score: 245
Period size: 60 Copynumber: 2.7 Consensus size: 60
1968 CTAATTGCTT
* * *
1978 AAATAAGGGTCTAATGTT-TGTCAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGCC
1 AAATAAGGGCCTAACGTTAT-TGAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGCC
* *
2038 AAATAAGGGCCTAACGTTATTGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCC
1 AAATAAGGGCCTAACGTTATTGAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGCC
* *
2098 AAATAAGGGCCTAACCTTATCGAAAATGCTCAAATAAGGGTC
1 AAATAAGGGCCTAACGTTATTGAAAATGCTCAAATAAGGGTC
2140 TGACATCAGT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 92 0.99
61 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (60 bp):
AAATAAGGGCCTAACGTTATTGAAAATGCTCAAATAAGGGTCCAATCTTTTAATTTGGCC
Found at i:2108 original size:29 final size:29
Alignment explanation
Indices: 2008--2108 Score: 107
Period size: 29 Copynumber: 3.4 Consensus size: 29
1998 TCAAAATGCT
*
2008 CAAATAAGGGTCCAATCTTTTAATTTGGC
1 CAAATAAGGGCCCAATCTTTTAATTTGGC
* **
2037 CAAATAAGGGCCTAA-CGTTATTGAAAAT-GC
1 CAAATAAGGGCCCAATC-TT-TT-AATTTGGC
*
2067 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCAATCTTTTAATTTGGC
2097 CAAATAAGGGCC
1 CAAATAAGGGCC
2109 TAACCTTATC
Statistics
Matches: 58, Mismatches: 8, Indels: 12
0.74 0.10 0.15
Matches are distributed among these distances:
28 1 0.02
29 30 0.52
30 8 0.14
31 18 0.31
32 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCCCAATCTTTTAATTTGGC
Found at i:2280 original size:60 final size:60
Alignment explanation
Indices: 2180--2319 Score: 217
Period size: 60 Copynumber: 2.3 Consensus size: 60
2170 TTCGACGTCA
*
2180 GGCCCTTATTTGAGCATTTTCAATAACATTAGACCCTTATTCGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCAATAACATTAGACCATTATTCGGCCAAATTAAAAGATCG
* ** * * *
2240 GGCCCTTATTTGAGCATTTTCGATAATGTTAGGCCATTATTTGGTCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTCAATAACATTAGACCATTATTCGGCCAAATTAAAAGATCG
2300 GGCCCTTATTTGAGCATTTT
1 GGCCCTTATTTGAGCATTTT
2320 GGCAAATGTT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTCAATAACATTAGACCATTATTCGGCCAAATTAAAAGATCG
Found at i:2308 original size:29 final size:28
Alignment explanation
Indices: 2213--2311 Score: 74
Period size: 29 Copynumber: 3.4 Consensus size: 28
2203 TAACATTAGA
*
2213 CCCTTATTCGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGG-CAAATTAAAAGATCGGG
** * **
2242 CCCTTATTTGAGCATTTTCGATAATG-TTAGG
1 CCCTTATTTG-GCAAATT--A-AAAGATCGGG
*
2273 CCATTATTTGGTCAAATTAAAAGATCGGG
1 CCCTTATTTGG-CAAATTAAAAGATCGGG
2302 CCCTTATTTG
1 CCCTTATTTG
2312 AGCATTTTGG
Statistics
Matches: 51, Mismatches: 13, Indels: 12
0.67 0.17 0.16
Matches are distributed among these distances:
28 3 0.06
29 26 0.51
30 2 0.04
31 17 0.33
32 3 0.06
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (28 bp):
CCCTTATTTGGCAAATTAAAAGATCGGG
Found at i:2341 original size:60 final size:60
Alignment explanation
Indices: 2180--2341 Score: 213
Period size: 60 Copynumber: 2.7 Consensus size: 60
2170 TTCGACGTCA
** *
2180 GGCCCTTATTTGAGCATTTT-CAATAACATTAGACCCTTATTCGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTGC-ATAATGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
* * *
2240 GGCCCTTATTTGAGCATTTT-CGATAATGTTAGGCCATTATTTGGTCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTGC-ATAATGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
*
2300 GGCCCTTATTTGAGCATTTTGGCA-AATGTTACACCCTTATTT
1 GGCCCTTATTTGAGCATTTT-GCATAATGTTAGACCCTTATTT
2342 AAGCAATTAG
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
60 88 0.98
61 1 0.01
62 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTGCATAATGTTAGACCCTTATTTGGCCAAATTAAAAGATCG
Found at i:4554 original size:2 final size:2
Alignment explanation
Indices: 4547--4585 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4537 TGTCAGTGTT
4547 TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC T
4586 TTCCTTCTCT
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:9623 original size:20 final size:20
Alignment explanation
Indices: 9598--9639 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
9588 TGCACTTTCC
9598 TCCCTACTACAAACATCACT
1 TCCCTACTACAAACATCACT
9618 TCCCTACTACAAACATCACT
1 TCCCTACTACAAACATCACT
9638 TC
1 TC
9640 AGACTTTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.26
Consensus pattern (20 bp):
TCCCTACTACAAACATCACT
Found at i:16089 original size:6 final size:6
Alignment explanation
Indices: 16078--16104 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
16068 AGAACTTGAA
16078 GTCTTC GTCTTC GTCTTC GTCTTC GTC
1 GTCTTC GTCTTC GTCTTC GTCTTC GTC
16105 ATGAAAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.19, T:0.48
Consensus pattern (6 bp):
GTCTTC
Done.