Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008589.1 Corchorus capsularis cultivar CVL-1 contig08610, 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: 29045
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:827 original size:20 final size:20
Alignment explanation
Indices: 791--828 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
781 ATTATTGAGA
*
791 TTTGAGAGGACATGTAGGGC
1 TTTGAGAGGAAATGTAGGGC
811 TTTGA-AGGAAATAGTAGG
1 TTTGAGAGGAAAT-GTAGG
829 ATAAATGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.32, C:0.05, G:0.37, T:0.26
Consensus pattern (20 bp):
TTTGAGAGGAAATGTAGGGC
Found at i:1549 original size:29 final size:29
Alignment explanation
Indices: 1527--1592 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 29
1517 AATAAGCATT
1527 TGAACTCTAATTGCAGCCAAATAAGCTCC
1 TGAACTCTAATTGCAGCCAAATAAGCTCC
* * * *
1556 TGAACTCTAATTGTAGCAAAATAAACCCC
1 TGAACTCTAATTGCAGCCAAATAAGCTCC
1585 TGAACTCT
1 TGAACTCT
1593 TATTTCGCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (29 bp):
TGAACTCTAATTGCAGCCAAATAAGCTCC
Found at i:1604 original size:29 final size:29
Alignment explanation
Indices: 1527--1620 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 29
1517 AATAAGCATT
* * *
1527 TGAACTCTAATTGCAGCC-AAATAAGCTCC
1 TGAACTCTAATTTC-GCCAAAATAAACCCC
*
1556 TGAACTCTAATTGTAG-CAAAATAAACCCC
1 TGAACTCTAATT-TCGCCAAAATAAACCCC
* *
1585 TGAACTCTTATTTCGCCAAAA-AAAACCC
1 TGAACTCTAATTTCGCCAAAATAAACCCC
1613 TGAACTCT
1 TGAACTCT
1621 TAAAAAGGGC
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
28 17 0.31
29 38 0.69
ACGTcount: A:0.37, C:0.27, G:0.11, T:0.26
Consensus pattern (29 bp):
TGAACTCTAATTTCGCCAAAATAAACCCC
Found at i:10007 original size:93 final size:93
Alignment explanation
Indices: 9848--10027 Score: 261
Period size: 93 Copynumber: 1.9 Consensus size: 93
9838 AACCTTCAAC
** *
9848 TTTCTTAACATTTTATATGTAATTTTACATGGTGTCCACCCTTATATGGTCCTAGATGCCCACCC
1 TTTCTTAACATTTTATATGTAATTTTACATGGTACCCACCCTTATATGGTCCTAAATGCCCACCC
9913 TCAATTAATTAACTCGTCAAAATGTCCA
66 TCAATTAATTAACTCGTCAAAATGTCCA
** * * **
9941 TTTCTTATTATTTTGTATGTAATTTTACATGGTACCCACCCTTATTTGGTCCTAAATGTTCACCC
1 TTTCTTAACATTTTATATGTAATTTTACATGGTACCCACCCTTATATGGTCCTAAATGCCCACCC
* *
10006 TCAATTGATTAACTTGTCAAAA
66 TCAATTAATTAACTCGTCAAAA
10028 ATTCTATATT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (93 bp):
TTTCTTAACATTTTATATGTAATTTTACATGGTACCCACCCTTATATGGTCCTAAATGCCCACCC
TCAATTAATTAACTCGTCAAAATGTCCA
Found at i:13805 original size:11 final size:10
Alignment explanation
Indices: 13787--13820 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
13777 AATTGTCTTC
13787 AAATCTTCAA
1 AAATCTTCAA
13797 AATATCTTCAA
1 AA-ATCTTCAA
13808 GAAATCTTCAA
1 -AAATCTTCAA
13819 AA
1 AA
13821 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:22403 original size:11 final size:10
Alignment explanation
Indices: 22385--22418 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
22375 AATTGTCTTC
22385 AAATCTTCAA
1 AAATCTTCAA
22395 AATATCTTCAA
1 AA-ATCTTCAA
22406 GAAATCTTCAA
1 -AAATCTTCAA
22417 AA
1 AA
22419 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:23155 original size:45 final size:45
Alignment explanation
Indices: 23103--23189 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
23093 AGCTGAAGAA
23103 AGGATCTTAGAGGAAGCTTTGAAACGCTTAAAATGGTTTAAGTGT
1 AGGATCTTAGAGGAAGCTTTGAAACGCTTAAAATGGTTTAAGTGT
*
23148 AGGATCTTAGAGGAAGCTTTGAAACGTTTAAAATGGTTTAAG
1 AGGATCTTAGAGGAAGCTTTGAAACGCTTAAAATGGTTTAAG
23190 AAGGGGGGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.31
Consensus pattern (45 bp):
AGGATCTTAGAGGAAGCTTTGAAACGCTTAAAATGGTTTAAGTGT
Found at i:25130 original size:18 final size:18
Alignment explanation
Indices: 25102--25152 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
25092 TTTCCTTTAG
25102 TTTTG-TTTTGTTTCGTA
1 TTTTGTTTTTGTTTCGTA
*
25119 TTTTGTTTTTGTTTTTCGTT
1 TTTTGTTTTTG--TTTCGTA
25139 TTTGTGTTTTTGTT
1 TTT-TGTTTTTGTT
25153 AATTTTGCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
17 5 0.17
18 5 0.17
19 2 0.07
20 9 0.31
21 8 0.28
ACGTcount: A:0.02, C:0.04, G:0.18, T:0.76
Consensus pattern (18 bp):
TTTTGTTTTTGTTTCGTA
Found at i:27636 original size:15 final size:16
Alignment explanation
Indices: 27604--27637 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
27594 AAAGAAGAAT
*
27604 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
27620 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
27635 TAA
1 TAA
27638 GACAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Done.