Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014403.1 Corchorus olitorius cultivar O-4 contig14436, 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: 2156
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Found at i:232 original size:65 final size:65
Alignment explanation
Indices: 151--302 Score: 229
Period size: 65 Copynumber: 2.3 Consensus size: 65
141 CAATTTATAT
* *
151 ATATTAAATTGATTGATTGATTTGA-AT-ATATTTTGATCCAATTAGAATCAATTAGTACTAAAA
1 ATATTAAATTGATTGATTGATTTGATATAATATCTCGATCCAATTAGAATCAATTAGTACT--AA
214 TG
64 TG
*
216 ATATTAAATTGATTGATTGA-TTGATTTGAATATCTCGATCCAATTAGAATCAATTAGTACTAAT
1 ATATTAAATTGATTGATTGATTTGATAT-AATATCTCGATCCAATTAGAATCAATTAGTACTAAT
280 G
65 G
281 ATATTAAATTGATTGATTGATT
1 ATATTAAATTGATTGATTGATT
303 GATTGATTGA
Statistics
Matches: 80, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
64 4 0.05
65 45 0.56
66 1 0.01
67 30 0.38
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (65 bp):
ATATTAAATTGATTGATTGATTTGATATAATATCTCGATCCAATTAGAATCAATTAGTACTAATG
Found at i:297 original size:4 final size:4
Alignment explanation
Indices: 288--314 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
278 ATGATATTAA
288 ATTG ATTG ATTG ATTG ATTG ATTG ATT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATT
315 TGAATATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
ATTG
Found at i:1736 original size:167 final size:166
Alignment explanation
Indices: 1448--1764 Score: 460
Period size: 167 Copynumber: 1.9 Consensus size: 166
1438 TGAAAAATAT
* ** * *
1448 AAATTGATTGAACATGTAAAATAAATAAATGAATCAAGTTTGTTGTTAGTTAACTTTGCCAATCA
1 AAATTGATTGAACATGTAAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGCCAATCA
*
1513 AAGTTATAATTGATGGATGATTATTTAATTTTACCATAAATAAATAAATAAATTAGTAATTATGT
66 AAGTTATAATTGATGGATGATGATTTAATTTTACCATAAATAAATAAATAAATTAGTAATTATGT
*
1578 T-GTCAAAAAAATAACTTGATTTTTTTTGCCACTAAAA
131 TAG-C-AAAAAATAAATTGATTTTTTTTGCCACTAAAA
*
1615 AAATTGATTGAACATGCT-AAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGTCAATC
1 AAATTGATTGAACATG-TAAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGCCAATC
* * * * *
1679 AAAGTTATAATTGATTGATGATGATTTGATTTTGCTATAAATAAA-AGAATCAATTAGTAATTAT
65 AAAGTTATAATTGATGGATGATGATTTAATTTTACCATAAATAAATA-AATAAATTAGTAATTAT
1743 GTTAGCAAAAAATAAATTGATT
129 GTTAGCAAAAAATAAATTGATT
1765 GAACATACTA
Statistics
Matches: 134, Mismatches: 13, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
166 16 0.12
167 116 0.87
168 2 0.01
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (166 bp):
AAATTGATTGAACATGTAAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGCCAATCA
AAGTTATAATTGATGGATGATGATTTAATTTTACCATAAATAAATAAATAAATTAGTAATTATGT
TAGCAAAAAATAAATTGATTTTTTTTGCCACTAAAA
Found at i:1776 original size:141 final size:141
Alignment explanation
Indices: 1611--2132 Score: 608
Period size: 141 Copynumber: 3.8 Consensus size: 141
1601 TTTTGCCACT
*
1611 AAAA-AAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGTC
1 AAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGCC
* * * *
1675 AATCAAAGTTATAATTGATTGATGATGATTTGATTTTGCTATAAATAAAAGAATCAATTAGTAAT
66 AATCAAAGTTATAACTGATTGATGATTATTTAATTTTGCCATAAATAAAAGAATCAATTAGTAAT
1740 TATGTTAGCAA
131 TATGTTAGCAA
* * * * *
1751 AAAATAAATTGATTGAACATACTAAATAAATAAATAAATCAAATTAGTCGTTAATTAACTTTGCC
1 AAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGCC
* * *
1816 AATCAAAGTTATAACTAATTGATGATTATTAAATTTTGCCATAAATAAATGAATCAATTAGTAAT
66 AATCAAAGTTATAACTGATTGATGATTATTTAATTTTGCCATAAATAAAAGAATCAATTAGTAAT
1881 TATGTTAGC-A
131 TATGTTAGCAA
* * * *
1891 AAAATAAACTGATTCAACATGCTAAATAAACAAATGAACCAAGTTAGTCC-TAAGTCAACTTTGC
1 AAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAA-TCAACTTTGC
* ** * *
1955 CAATAAAAG-T-T-ACT-CCT-AT-A--A--T--TTTT-CCATGAATAAACGAATCAATTAGTAA
65 CAATCAAAGTTATAACTGATTGATGATTATTTAATTTTGCCATAAATAAAAGAATCAATTAGTAA
*
2007 TTATATTAGCAAAA
130 TTATGTTAGC--AA
* * * * * *
2021 AAAATAAAATCGATTAAACATGCTAAATAAATAAATGAATCAAGTTAGTCGTTAGTTAATTTTGC
1 AAAAT-AAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGC
* * *
2086 CAATCAAAGTTGTAATTGATTGATGATTATTTAATTTTACCATAAAT
65 CAATCAAAGTTATAACTGATTGATGATTATTTAATTTTGCCATAAAT
2133 CGCTACCAAA
Statistics
Matches: 319, Mismatches: 43, Indels: 36
0.80 0.11 0.09
Matches are distributed among these distances:
127 33 0.10
128 4 0.01
130 6 0.02
131 55 0.17
132 4 0.01
133 1 0.00
134 3 0.01
135 3 0.01
136 3 0.01
137 4 0.01
138 1 0.00
139 5 0.02
140 64 0.20
141 122 0.38
143 4 0.01
144 7 0.02
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (141 bp):
AAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTCCTTAATCAACTTTGCC
AATCAAAGTTATAACTGATTGATGATTATTTAATTTTGCCATAAATAAAAGAATCAATTAGTAAT
TATGTTAGCAA
Found at i:2085 original size:131 final size:127
Alignment explanation
Indices: 1847--2096 Score: 347
Period size: 131 Copynumber: 1.9 Consensus size: 127
1837 ATGATTATTA
* * * *
1847 AATTTTGCCATAAATAAATGAATCAATTAGTAATTATGTTAGCAAAAATAAACTGATTCAACATG
1 AATTTTGCCATAAATAAACGAATCAATTAGTAATTATATTAGCAAAAATAAAATGATTAAACATG
1912 CTAAATAAACAAATGAACCAAGTTAGTCCTAAGTCAACTTTGCCAATAAAAGTTACTCCTAT
66 CTAAATAAACAAATGAACCAAGTTAGTCCTAAGTCAACTTTGCCAATAAAAGTTACTCCTAT
* *
1974 AATTTTTCCATGAATAAACGAATCAATTAGTAATTATATTAGCAAAAAAAATAAAATCGATTAAA
1 AATTTTGCCATAAATAAACGAATCAATTAGTAATTATATTAGC---AAAAATAAAAT-GATTAAA
* * * * * * *
2039 CATGCTAAATAAATAAATGAATCAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTT
62 CATGCTAAATAAACAAATGAACCAAGTTAGTCCTAAGTCAACTTTGCCAATAAAAGTT
2097 GTAATTGATT
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
127 39 0.37
130 10 0.09
131 57 0.54
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (127 bp):
AATTTTGCCATAAATAAACGAATCAATTAGTAATTATATTAGCAAAAATAAAATGATTAAACATG
CTAAATAAACAAATGAACCAAGTTAGTCCTAAGTCAACTTTGCCAATAAAAGTTACTCCTAT
Done.