Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011247.1 Corchorus capsularis cultivar CVL-1 contig11268, 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: 26490
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:489 original size:113 final size:113
Alignment explanation
Indices: 289--513 Score: 396
Period size: 113 Copynumber: 2.0 Consensus size: 113
279 AAGCCCGTCC
289 AACGGGCTTCACATTTATGTCCAAACCCTCCCAAATATCGGGCGGACTTACAGGCTTGGACGGAC
1 AACGGGCTTCACATTTATGTCCAAACCCTCCCAAATATCGGGCGGACTTACAGGCTTGGACGGAC
* * *
354 GGCCCGACCCATGGACAGCTCTACCACCGGTGTATCAAATAAATACCT
66 GGCCAGACCCATAGACAACTCTACCACCGGTGTATCAAATAAATACCT
* *
402 AACGGGCTTCACATTTATGTCCAAACCCTCCCAAATATCGGGCGGATTTACGGGCTTGGACGGAC
1 AACGGGCTTCACATTTATGTCCAAACCCTCCCAAATATCGGGCGGACTTACAGGCTTGGACGGAC
*
467 GGCCAGGCCCATAGACAACTCTACCACCGGTGTATCAAATAAATACC
66 GGCCAGACCCATAGACAACTCTACCACCGGTGTATCAAATAAATACC
514 CTTGGATTTT
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 106 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (113 bp):
AACGGGCTTCACATTTATGTCCAAACCCTCCCAAATATCGGGCGGACTTACAGGCTTGGACGGAC
GGCCAGACCCATAGACAACTCTACCACCGGTGTATCAAATAAATACCT
Found at i:1817 original size:11 final size:11
Alignment explanation
Indices: 1801--1842 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
1791 ATACTATATC
1801 TAATTAATAGA
1 TAATTAATAGA
**
1812 TAATTAATATC
1 TAATTAATAGA
*
1823 TAATTAATAGT
1 TAATTAATAGA
1834 TAATTAATA
1 TAATTAATA
1843 ATGAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (11 bp):
TAATTAATAGA
Found at i:1821 original size:22 final size:22
Alignment explanation
Indices: 1796--1842 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1786 CCATTATACT
1796 ATATCTAATTAATAGATAATTA
1 ATATCTAATTAATAGATAATTA
*
1818 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGATAATTA
1840 ATA
1 ATA
1843 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGATAATTA
Found at i:4499 original size:24 final size:23
Alignment explanation
Indices: 4450--4502 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
4440 ATCATTATTC
* ** *
4450 ATAATCCAAAATAAAAAATTTTA
1 ATAATACAAAATAAAAAAAATGA
4473 ATAATACAATAATAAAAAAAATGA
1 ATAATACAA-AATAAAAAAAATGA
4497 ATAATA
1 ATAATA
4503 ATCACACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 8 0.32
24 17 0.68
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (23 bp):
ATAATACAAAATAAAAAAAATGA
Found at i:9337 original size:2 final size:2
Alignment explanation
Indices: 9330--9358 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9320 TATTCATAAG
9330 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9359 GTTAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20782 original size:199 final size:198
Alignment explanation
Indices: 20129--21194 Score: 1225
Period size: 199 Copynumber: 5.3 Consensus size: 198
20119 CTTTATAATA
*
20129 AGGATTATTATACAAATACACTGTCAATGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGA
1 AGGATTATTATAC-AATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGA
** * * * *
20194 CACATACTTCATTTCATAATTAACTAAATA--T-ATATTAGTACGTATTCCTTAAGGGGACACAT
65 CACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAA-GGGACACAT
** * * *
20256 GTCAATCC-TTAAACCATGCACATACAGTCTACTAAACTCCACTGACGGTGTATTGTATAATTTT
129 GTCAA-CCATTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTT
*
20320 TTTTAT
193 TCTTAT
* * * * *
20326 AGAATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAACCGAGTTAAGAAGTTCAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
* * * ** * *
20391 ACATACCCTATTTTATAATTAATTAGATATAAAATATTAATACATTTTCCTAACGCCTAAAAGGA
66 ACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACA-TAT--T--C-CCT-AAGGGA
* ** * * * * **
20456 CACATGTCAACCCTTATGCCCCGCGCGTGTAGTCTGTTAAACTCCATTGACAATGTATTGTAATA
124 CACATGTCAACCATTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGT-ATA
* *
20521 TTTTTTGTTTTAT
188 -ATTTT-TCTTAT
* *
20534 ATGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAATTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
* *
20599 ACATACCCCATTTCATAATTAATTAAATATTTAATATT-ACACATATTCCCTAAGGGATACATGT
66 ACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGACACATGT
20663 CAACCATTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACTGTGTGTATTGTATAATTTTT
131 CAACCATTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGAC-G-GTGTATTGTATAATTTTT
20728 CTTAT
194 CTTAT
* * * * *
20733 AGGATTATTATACAATACACTGTCATTATAAATTTTGGACTCCATAAGCGAGTTAAGAAGCTAAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
*
20798 ACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTTCCTAAGGGGACACATG
66 ACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAA-GGGACACATG
* * * *
20863 TCAACCCTTAAATCCCGCACGTGCAGTCTGCTAAAATCCACTAACGG-GTATTGTATAATTTTTC
130 TCAACCATTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTC
20927 TTAT
195 TTAT
* * *
20931 AGGATTATTATACATTATACTGTCAGTGTAAATTTTGGACTCCATAAACGGGTTAAGAAGTTGAC
1 AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
* * *
20996 ACATACCCTATTTCATAA-T-A--AAATATTTAATATTAATACATATTCCCTAAGTGTACAAATG
66 ACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAG-GGACACATG
* * * ** * *
21057 TCAACCCTTAAAATTAAAGCCTGCATGTATAGTCTGTTAAACTCCACTGACGGTGTATTATATAA
130 TCAA-CC-----ATTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAA
*
21122 ATTTTCTTAT
189 TTTTTCTTAT
* * * * *
21132 ATGATTATCATACAATACATTGTCAGTGCAAATTTTTGGACTTCATAAGCGGGTTAAGAAGTT
1 AGGATTATTATACAATACACTGTCAGTGTAAA-TTTTGGACTCCATAAGCGGGTTAAGAAGTT
21195 TTTGTGCCAA
Statistics
Matches: 738, Mismatches: 104, Indels: 49
0.83 0.12 0.05
Matches are distributed among these distances:
193 1 0.00
194 40 0.05
195 2 0.00
196 71 0.10
197 13 0.02
198 95 0.13
199 111 0.15
200 100 0.14
201 101 0.14
202 38 0.05
204 4 0.01
205 50 0.07
206 7 0.01
207 8 0.01
208 97 0.13
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (198 bp):
AGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGAC
ACATACCCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGACACATGT
CAACCATTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTGTATAATTTTTCT
TAT
Found at i:22795 original size:26 final size:24
Alignment explanation
Indices: 22760--22823 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 24
22750 AATTTTACAT
*
22760 AAATTTAATAACTTCTCATTTTTAG
1 AAATTTAATAACTT-GCATTTTTAG
*
22785 AAATTTCAATAACCTTGCATTTTTGG
1 AAATTT-AATAA-CTTGCATTTTTAG
22811 AAATTTTAATAAC
1 AAA-TTTAATAAC
22824 ATTTCAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 7 0.21
26 21 0.62
27 6 0.18
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (24 bp):
AAATTTAATAACTTGCATTTTTAG
Done.