Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008833.1 Corchorus capsularis cultivar CVL-1 contig08854, 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: 55393
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:284 original size:33 final size:33
Alignment explanation
Indices: 247--370 Score: 135
Period size: 33 Copynumber: 3.7 Consensus size: 33
237 TAGACAAAGG
* * *
247 GTCGTGTGGCCGGTTGTGGCCGGGCATGGCCGA-
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCC-AT
** *
280 GTCGTTTGGCCGGTTGTAGCCGGACATGTCCAT
1 GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
*
313 GTCGCGTGGCCGG-TGATGGTCGGACATGTCCAT
1 GTCGCGTGGCCGGTTG-TGGCCGGACATGTCCAT
346 GTCGCGTGGCCGGTCTTGTGGCCGG
1 GTCGCGTGGCCGG--TTGTGGCCGG
371 TGTTGCGCGG
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
32 3 0.04
33 66 0.86
35 6 0.08
36 2 0.03
ACGTcount: A:0.08, C:0.25, G:0.42, T:0.25
Consensus pattern (33 bp):
GTCGCGTGGCCGGTTGTGGCCGGACATGTCCAT
Found at i:1304 original size:3 final size:3
Alignment explanation
Indices: 1296--1332 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1286 ACCCCATCTC
1296 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1333 ATCTGTGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:6766 original size:29 final size:27
Alignment explanation
Indices: 6704--6766 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 27
6694 ACTTGTAGCG
*
6704 TTTGGACATTTTCCCCTTAAACCTCAA
1 TTTGGACATTTTCCCCCTAAACCTCAA
*
6731 TCTTGGACATTTTGCCCCCTGAACTCTCAA
1 T-TTGGACATTTT-CCCCCTAAAC-CTCAA
6761 TTTGGA
1 TTTGGA
6767 TCCCAGTCCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 1 0.03
28 11 0.35
29 13 0.42
30 6 0.19
ACGTcount: A:0.22, C:0.29, G:0.13, T:0.37
Consensus pattern (27 bp):
TTTGGACATTTTCCCCCTAAACCTCAA
Found at i:6946 original size:30 final size:28
Alignment explanation
Indices: 6907--6971 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 28
6897 TTAACTGGGC
*
6907 TCCAAATTGAGAGTTCAGGGGGCAAAATG
1 TCCAAATTGA-AGTTCAGGGGGCAAAACG
*
6936 TCCAAGATTGAAGTTTAGGGGGCAAAACG
1 TCCAA-ATTGAAGTTCAGGGGGCAAAACG
6965 TCCAAAT
1 TCCAAAT
6972 GCTACAAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 2 0.06
29 26 0.79
30 5 0.15
ACGTcount: A:0.35, C:0.15, G:0.28, T:0.22
Consensus pattern (28 bp):
TCCAAATTGAAGTTCAGGGGGCAAAACG
Found at i:6987 original size:31 final size:29
Alignment explanation
Indices: 6918--6993 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
6908 CCAAATTGAG
* *
6918 AGTTCAGGGGGCAAAATGTCCAAGATTGA
1 AGTTCAGGGGGCAAAACGTCCAAGATTCA
*
6947 AGTTTAGGGGGCAAAACGTCCAA-ATGCTACA
1 AGTTCAGGGGGCAAAACGTCCAAGAT--T-CA
*
6978 AGTTCAGGGGGGAAAA
1 AGTTCAGGGGGCAAAA
6994 TGATACTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 21 0.54
30 1 0.03
31 15 0.38
ACGTcount: A:0.36, C:0.14, G:0.32, T:0.18
Consensus pattern (29 bp):
AGTTCAGGGGGCAAAACGTCCAAGATTCA
Found at i:7406 original size:46 final size:46
Alignment explanation
Indices: 7356--7444 Score: 151
Period size: 46 Copynumber: 1.9 Consensus size: 46
7346 TAAAATTAAA
7356 GAGGCCGTCTACATGTAGCTGAGCCAATTGAGCACTATGCACTAAT
1 GAGGCCGTCTACATGTAGCTGAGCCAATTGAGCACTATGCACTAAT
* * *
7402 GAGGCTGTCTACATGTAGCTTAGCCGATTGAGCACTATGCACT
1 GAGGCCGTCTACATGTAGCTGAGCCAATTGAGCACTATGCACT
7445 TGCATGTGCC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.26
Consensus pattern (46 bp):
GAGGCCGTCTACATGTAGCTGAGCCAATTGAGCACTATGCACTAAT
Found at i:29644 original size:13 final size:14
Alignment explanation
Indices: 29628--29659 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
29618 TAAAAATCGA
29628 AAAAACCGA-ACCG
1 AAAAACCGACACCG
29641 AAAAACCGACACCG
1 AAAAACCGACACCG
29655 AAAAA
1 AAAAA
29660 TGAGCAACCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.59, C:0.28, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAACCGACACCG
Found at i:35170 original size:25 final size:25
Alignment explanation
Indices: 35136--35186 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
35126 TTGTGTTCAC
35136 AGGTATTGAAGAGAAGAAAAGTGCA
1 AGGTATTGAAGAGAAGAAAAGTGCA
*
35161 AGGTATTGAAGAGAAGGAAAGTGCA
1 AGGTATTGAAGAGAAGAAAAGTGCA
35186 A
1 A
35187 AAGTGATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.47, C:0.04, G:0.33, T:0.16
Consensus pattern (25 bp):
AGGTATTGAAGAGAAGAAAAGTGCA
Found at i:36177 original size:6 final size:6
Alignment explanation
Indices: 36168--36226 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
36158 TTAATCCCTG
* * *
36168 TGATGA TGATCA TGATTA TGATTA TGA-TA T--TTAA GTGATTA TGGTTA
1 TGATTA TGATTA TGATTA TGATTA TGATTA TGATT-A -TGATTA TGATTA
36215 TGATTA TGATTA
1 TGATTA TGATTA
36227 AGATCATGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
4 1 0.02
5 4 0.09
6 36 0.82
7 1 0.02
8 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (6 bp):
TGATTA
Found at i:45997 original size:30 final size:29
Alignment explanation
Indices: 45952--46008 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
45942 CTCGAAATTA
*
45952 AATTCCTTTCCTTGTTAATCCTTTTTGTT
1 AATTCCATTCCTTGTTAATCCTTTTTGTT
* *
45981 AATTCCATTCTCTTGTTTATCTTTTTTG
1 AATTCCATTC-CTTGTTAATCCTTTTTG
46009 CCCCCTCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.14, C:0.19, G:0.07, T:0.60
Consensus pattern (29 bp):
AATTCCATTCCTTGTTAATCCTTTTTGTT
Found at i:54034 original size:123 final size:123
Alignment explanation
Indices: 53822--54316 Score: 882
Period size: 123 Copynumber: 4.0 Consensus size: 123
53812 TTTCCATATC
* * * * *
53822 TGGTCAAGGATGGTTCGTGCAGATCTCTTGCCAGTCGGGAGCCAGACTTCGATTCGAGGCCAGCT
1 TGGTCAGGGATGGTTCGTGCCGATCTCCTGCCAGTTGGGGGCCAGACTTCGATTCGAGGCCAGCT
*
53887 TTTGCTTGGCGCTCGTCGGTTGGCGTTGAGCCCATTTGGGGCGTTATTTTCCCATACT
66 TTTGCTCGGCGCTCGTCGGTTGGCGTTGAGCCCATTTGGGGCGTTATTTTCCCATACT
* * *
53945 TGGTCAGGGATGGTTCATGCCGATCTCTTGCCAGTTGGGGGCCAAACTTCGATTCGAGGCCAGCT
1 TGGTCAGGGATGGTTCGTGCCGATCTCCTGCCAGTTGGGGGCCAGACTTCGATTCGAGGCCAGCT
* *
54010 TTTGCTCGGTGCTCGTCGGTTGGCGTTGAGCCCATTTGGGGCGTCATTTTCCCATACT
66 TTTGCTCGGCGCTCGTCGGTTGGCGTTGAGCCCATTTGGGGCGTTATTTTCCCATACT
54068 TGGTCAGGGATGGTTCGTGCCGATCTCCTGCCAGTTGGGGGCCAGACTTCGATTCGAGGCCAGCT
1 TGGTCAGGGATGGTTCGTGCCGATCTCCTGCCAGTTGGGGGCCAGACTTCGATTCGAGGCCAGCT
54133 TTTGCTCGGCGCTCGTCGGTTGGCGTTGAGCCCATTTGGGGCGTTATTTTCCCATACT
66 TTTGCTCGGCGCTCGTCGGTTGGCGTTGAGCCCATTTGGGGCGTTATTTTCCCATACT
54191 TGGTCAGGGATGGTTCGTGCCGATCTCCTGCCAGTTGGGGGCCAGACTTCGATTCGAGGCCAGCT
1 TGGTCAGGGATGGTTCGTGCCGATCTCCTGCCAGTTGGGGGCCAGACTTCGATTCGAGGCCAGCT
*
54256 TTTGCTTGGCGCTCGTCGGTTGGCGTTGAGCCCATTTGGGGCGTTATTTTCCCATACT
66 TTTGCTCGGCGCTCGTCGGTTGGCGTTGAGCCCATTTGGGGCGTTATTTTCCCATACT
54314 TGG
1 TGG
54317 GATATTATTC
Statistics
Matches: 357, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 357 1.00
ACGTcount: A:0.12, C:0.25, G:0.32, T:0.31
Consensus pattern (123 bp):
TGGTCAGGGATGGTTCGTGCCGATCTCCTGCCAGTTGGGGGCCAGACTTCGATTCGAGGCCAGCT
TTTGCTCGGCGCTCGTCGGTTGGCGTTGAGCCCATTTGGGGCGTTATTTTCCCATACT
Done.