Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014767.1 Corchorus capsularis cultivar CVL-1 contig14788, 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: 5609
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:3861 original size:69 final size:69
Alignment explanation
Indices: 3777--3943 Score: 237
Period size: 69 Copynumber: 2.4 Consensus size: 69
3767 AAGACCACCC
* * * * **
3777 TGGATCAACTGGAAACAACTTATGAAAAACCGCCCTGGGTCGACTGAATCGATCGTTCTGACATA
1 TGGATAAACTTGAAACAACTGAAGAAAAACCGCCCTGGGTCGACTGAATCGATAATTCTGACATA
3842 AACT
66 AACT
*
3846 TGGATAAACTTGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATAATTCTGACATA
1 TGGATAAACTTGAAACAACTGAAGAAAAACCGCCCTGGGTCGACTGAATCGATAATTCTGACATA
3911 AACT
66 AACT
*
3915 TCGAATAAACTTGAAAACAACTGAA-AAAA
1 T-GGATAAACTTG-AAACAACTGAAGAAAA
3944 GAAAAGAAAA
Statistics
Matches: 87, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
69 63 0.72
70 13 0.15
71 11 0.13
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.22
Consensus pattern (69 bp):
TGGATAAACTTGAAACAACTGAAGAAAAACCGCCCTGGGTCGACTGAATCGATAATTCTGACATA
AACT
Found at i:4028 original size:49 final size:49
Alignment explanation
Indices: 3968--4148 Score: 290
Period size: 49 Copynumber: 3.7 Consensus size: 49
3958 AAGACCATCA
*
3968 TGGGTCGACTGAATCGATCATTCTGACACAAACTGAAGAAAGACCGCCC
1 TGGGTCAACTGAATCGATCATTCTGACACAAACTGAAGAAAGACCGCCC
* * * * **
4017 TGGGTCAACTGAATCGATGATTCTGTCATAAACTTAAGAAAGACCATCC
1 TGGGTCAACTGAATCGATCATTCTGACACAAACTGAAGAAAGACCGCCC
4066 TGGGTCAACTGAATCGATCATTCTGACACAAACTGAAGAAAGACCGCCC
1 TGGGTCAACTGAATCGATCATTCTGACACAAACTGAAGAAAGACCGCCC
*
4115 TGGGTCAACTGAATCGATCATTCTGACATAAACT
1 TGGGTCAACTGAATCGATCATTCTGACACAAACT
4149 TCGAATAAAC
Statistics
Matches: 118, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 118 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.23
Consensus pattern (49 bp):
TGGGTCAACTGAATCGATCATTCTGACACAAACTGAAGAAAGACCGCCC
Found at i:4126 original size:98 final size:98
Alignment explanation
Indices: 3957--4149 Score: 350
Period size: 98 Copynumber: 2.0 Consensus size: 98
3947 AAGAAAAGAA
*
3957 AAAGACCATCATGGGTCGACTGAATCGATCATTCTGACACAAACTGAAGAAAGACCGCCCTGGGT
1 AAAGACCATCATGGGTCAACTGAATCGATCATTCTGACACAAACTGAAGAAAGACCGCCCTGGGT
* *
4022 CAACTGAATCGATGATTCTGTCATAAACTTAAG
66 CAACTGAATCGATCATTCTGACATAAACTTAAG
*
4055 AAAGACCATCCTGGGTCAACTGAATCGATCATTCTGACACAAACTGAAGAAAGACCGCCCTGGGT
1 AAAGACCATCATGGGTCAACTGAATCGATCATTCTGACACAAACTGAAGAAAGACCGCCCTGGGT
4120 CAACTGAATCGATCATTCTGACATAAACTT
66 CAACTGAATCGATCATTCTGACATAAACTT
4150 CGAATAAACT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (98 bp):
AAAGACCATCATGGGTCAACTGAATCGATCATTCTGACACAAACTGAAGAAAGACCGCCCTGGGT
CAACTGAATCGATCATTCTGACATAAACTTAAG
Found at i:4214 original size:70 final size:70
Alignment explanation
Indices: 4096--4433 Score: 437
Period size: 70 Copynumber: 4.8 Consensus size: 70
4086 TTCTGACACA
* *
4096 AACTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAAC-T
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT-GAATAAACAT
4160 TGAAAC
65 TGAAAC
* * * *
4166 AACTAAAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAATAATCTT
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT-GAATAAACAT
4231 TGAAAC
65 TGAAAC
* * * * *
4237 AATTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACAAAAACTTGGATAAACATG
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGAATAAACATT
4302 GAAAC
66 GAAAC
* *
4307 TACTGAAGAAAGACCACCGTGGGTCGACTGAATCGATCATTCTGACATAAACTTGTAATAAAC-T
1 AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTG-AATAAACAT
* *
4371 TAAAAAAA
65 T--GAAAC
* * *
4379 AACTGAAAAAAAAGACCATCCTGGGTCGACTGAATCGATCATTCTGACACAAACT
1 AACTG--AAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
4434 GAAGAAAGAC
Statistics
Matches: 235, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
70 122 0.52
71 62 0.26
72 7 0.03
74 44 0.19
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (70 bp):
AACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGAATAAACATT
GAAAC
Found at i:4268 original size:141 final size:142
Alignment explanation
Indices: 4095--4433 Score: 475
Period size: 141 Copynumber: 2.4 Consensus size: 142
4085 ATTCTGACAC
* *
4095 AAACTGAAGAAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTCGAATAAAC-
1 AAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACAAAAACTT-GAATAAACA
*
4159 TTGAAACAACTAAAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAA
65 TGGAAACAACTAAAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAA
* **
4224 TAATCTT-TGAAA
130 TAAACTTAAAAAA
* * *
4236 CAATTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACAAAAACTTGGATAAACAT
1 AAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACAAAAACTTGAATAAACAT
* * * * *
4301 GGAAACTACTGAAGAAAGACCACCGTGGGTCGACTGAATCGATCATTCTGACATAAACTTGTAAT
66 GGAAACAACTAAAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAAT
4366 AAACTTAAAAAA
131 AAACTTAAAAAA
* ** *
4378 AAACTGAAAAAAAAGACCATCCTGGGTCGACTGAATCGATCATTCTGACACAAACT
1 AAACTG--AAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACAAAAACT
4434 GAAGAAAGAC
Statistics
Matches: 174, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
140 7 0.04
141 116 0.67
142 7 0.04
144 44 0.25
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (142 bp):
AAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACAAAAACTTGAATAAACAT
GGAAACAACTAAAGAAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGGAAT
AAACTTAAAAAA
Found at i:4452 original size:49 final size:49
Alignment explanation
Indices: 4389--4513 Score: 196
Period size: 49 Copynumber: 2.6 Consensus size: 49
4379 AACTGAAAAA
* *
4389 AAAGACCATCCTGGGTCGACTGAATCGATCATTCTGACACAAACTGAAG
1 AAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACACAAACTGAAG
* * * *
4438 AAAGACCGCCCTGGGTCAACTGAATCGATCATTCTGCCATAAACTTAAG
1 AAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACACAAACTGAAG
4487 AAAGACCACCCTGGGTCAACTGAATCG
1 AAAGACCACCCTGGGTCAACTGAATCG
4514 CATTGAAGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 69 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (49 bp):
AAAGACCACCCTGGGTCAACTGAATCGATCATTCTGACACAAACTGAAG
Done.