Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007454.1 Corchorus capsularis cultivar CVL-1 contig07475, 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: 28933
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:76 original size:32 final size:31
Alignment explanation
Indices: 4--65 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 31
1 TAG
4 GGCCGCCCCAGGGAGGCGGCCTGGCCATGGTA
1 GGCCG-CCCAGGGAGGCGGCCTGGCCATGGTA
*
36 GTGCCGCCCA-GGAGGGCGGCTTGGCCATGG
1 G-GCCGCCCAGGGA-GGCGGCCTGGCCATGG
66 CTCAGCCGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 3 0.11
32 20 0.74
33 4 0.15
ACGTcount: A:0.11, C:0.32, G:0.45, T:0.11
Consensus pattern (31 bp):
GGCCGCCCAGGGAGGCGGCCTGGCCATGGTA
Found at i:210 original size:32 final size:32
Alignment explanation
Indices: 165--258 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
155 CCGAGCCGCT
* * *
165 CCACCGGGGCGGCCTGTCGTGGCGAAGCCACC
1 CCACCGGGACGGCCTGCCCTGGCGAAGCCACC
* *
197 CCACCGGGACGGCCTGCCCTGGCTAAGCCGCC
1 CCACCGGGACGGCCTGCCCTGGCGAAGCCACC
** * *
229 CCAGTGGGGCGGCCTGCCCATGGTGAAGCC
1 CCACCGGGACGGCCTGCCC-TGGCGAAGCC
259 GCCCTCTTGG
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 43 0.84
33 8 0.16
ACGTcount: A:0.13, C:0.40, G:0.36, T:0.11
Consensus pattern (32 bp):
CCACCGGGACGGCCTGCCCTGGCGAAGCCACC
Found at i:1213 original size:14 final size:14
Alignment explanation
Indices: 1194--1227 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
1184 ACAATTTTAG
1194 AACATTTAT-TATAT
1 AACATTTATGT-TAT
1208 AACATTTATGTTAT
1 AACATTTATGTTAT
1222 AACATT
1 AACATT
1228 GAATTTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (14 bp):
AACATTTATGTTAT
Found at i:6248 original size:72 final size:72
Alignment explanation
Indices: 6126--6268 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 72
6116 TACCAAAAAA
* * * *
6126 AAACATATTAGGTTCTTGTGATGGTGACTCAAAACAGATCACTTATTGTGATGGTGACCCAAAAC
1 AAACAGATTAGGTTCTTGTGATGGTAACTCAAAACAGATCACTCACTGTGATGGTGACCCAAAAC
6191 AAATCAT
66 AAATCAT
*
6198 AAACAGATTAGGTTCTTGTTATGGTAACTCAAAACAGATCACTCACTGTGATGGTGACCCAAAAC
1 AAACAGATTAGGTTCTTGTGATGGTAACTCAAAACAGATCACTCACTGTGATGGTGACCCAAAAC
*
6263 AGATCA
66 AAATCA
6269 CTTACTGATG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (72 bp):
AAACAGATTAGGTTCTTGTGATGGTAACTCAAAACAGATCACTCACTGTGATGGTGACCCAAAAC
AAATCAT
Found at i:6261 original size:30 final size:30
Alignment explanation
Indices: 6218--6275 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
6208 GGTTCTTGTT
*
6218 ATGGTAACTCAAAACAGATCACTCACTGTG
1 ATGGTAACCCAAAACAGATCACTCACTGTG
* *
6248 ATGGTGACCCAAAACAGATCACTTACTG
1 ATGGTAACCCAAAACAGATCACTCACTG
6276 ATGACCCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (30 bp):
ATGGTAACCCAAAACAGATCACTCACTGTG
Found at i:13424 original size:7 final size:7
Alignment explanation
Indices: 13412--13445 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
13402 TGTGATGCAT
13412 AGACAAG
1 AGACAAG
13419 AGACAAG
1 AGACAAG
13426 AGACAAG
1 AGACAAG
13433 AGACAAG
1 AGACAAG
13440 AG-CAAG
1 AGACAAG
13446 TACTGCAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.15
7 23 0.85
ACGTcount: A:0.56, C:0.15, G:0.29, T:0.00
Consensus pattern (7 bp):
AGACAAG
Found at i:15594 original size:14 final size:16
Alignment explanation
Indices: 15565--15598 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
15555 TGTGGCAGTT
15565 TTTTTTAAATGAGTAG
1 TTTTTTAAATGAGTAG
15581 TTTTTT-AATG-GTAG
1 TTTTTTAAATGAGTAG
15595 TTTT
1 TTTT
15599 ATTTAAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 4 0.22
16 6 0.33
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.59
Consensus pattern (16 bp):
TTTTTTAAATGAGTAG
Found at i:15603 original size:16 final size:16
Alignment explanation
Indices: 15564--15604 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
15554 TTGTGGCAGT
15564 TTTTTTTAAATGAGTAG
1 TTTTTTT-AATGAGTAG
15581 -TTTTTTAATG-GTAG
1 TTTTTTTAATGAGTAG
15595 TTTTATTTAA
1 TTTT-TTTAA
15605 GATGGGCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.18
15 7 0.32
16 11 0.50
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.59
Consensus pattern (16 bp):
TTTTTTTAATGAGTAG
Found at i:15940 original size:22 final size:22
Alignment explanation
Indices: 15915--15959 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
15905 AATAATTTTA
*
15915 TGGCTGTGTTTTAGGAGGGTAG
1 TGGCTGTGTTCTAGGAGGGTAG
15937 TGGCTGTGTTCTAGGAGGGTAG
1 TGGCTGTGTTCTAGGAGGGTAG
15959 T
1 T
15960 TTAGTTGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.13, C:0.07, G:0.44, T:0.36
Consensus pattern (22 bp):
TGGCTGTGTTCTAGGAGGGTAG
Done.