Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015801.1 Corchorus olitorius cultivar O-4 contig15834, 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: 9537
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:2041 original size:30 final size:30
Alignment explanation
Indices: 2005--2063 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
1995 TAATAAACCA
2005 TTAAAATTTGAGGGTATAAGAGAAAAGTCT
1 TTAAAATTTGAGGGTATAAGAGAAAAGTCT
*
2035 TTAAAATTTGAGGGTATAAGAGGAAAGTC
1 TTAAAATTTGAGGGTATAAGAGAAAAGTC
2064 AAGATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.29
Consensus pattern (30 bp):
TTAAAATTTGAGGGTATAAGAGAAAAGTCT
Found at i:2169 original size:31 final size:31
Alignment explanation
Indices: 2133--2194 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
2123 ATGCCATTCC
*
2133 CACCACTTTCCCACTTGAATGGGAAAGTGAT
1 CACCACTTTCCCACTTGAATGAGAAAGTGAT
2164 CACCACTTTCCCACTTGAATGAGAAAGTGAT
1 CACCACTTTCCCACTTGAATGAGAAAGTGAT
2195 GGGAATGACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.26
Consensus pattern (31 bp):
CACCACTTTCCCACTTGAATGAGAAAGTGAT
Found at i:8471 original size:18 final size:18
Alignment explanation
Indices: 8448--8505 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
8438 TCAGTGTTGG
8448 TATTCAATTTGTTTGTGT
1 TATTCAATTTGTTTGTGT
**
8466 TATTCAATCAGTGTTG-G-
1 TATTCAATTTGT-TTGTGT
*
8483 TATTCAATTTGTTTGTCT
1 TATTCAATTTGTTTGTGT
8501 TATTC
1 TATTC
8506 TTTTTGCTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 3 0.09
17 10 0.31
18 16 0.50
19 3 0.09
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (18 bp):
TATTCAATTTGTTTGTGT
Found at i:8476 original size:35 final size:35
Alignment explanation
Indices: 8430--8505 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
8420 TTCTCCCAAT
* *
8430 TTATTTAATCAGTGTTGGTATTCAATTTGTTTGTG
1 TTATTCAATCAGTGTTGGTATTCAATTTGTTTGTC
8465 TTATTCAATCAGTGTTGGTATTCAATTTGTTTGTC
1 TTATTCAATCAGTGTTGGTATTCAATTTGTTTGTC
8500 TTATTC
1 TTATTC
8506 TTTTTGCTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.20, C:0.09, G:0.17, T:0.54
Consensus pattern (35 bp):
TTATTCAATCAGTGTTGGTATTCAATTTGTTTGTC
Found at i:8488 original size:17 final size:17
Alignment explanation
Indices: 8431--8490 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
8421 TCTCCCAATT
*
8431 TATTTAATCAGTGTTGG
1 TATTCAATCAGTGTTGG
**
8448 TATTCAATTTGT-TTGTG
1 TATTCAATCAGTGTTG-G
8465 TTATTCAATCAGTGTTGG
1 -TATTCAATCAGTGTTGG
8483 TATTCAAT
1 TATTCAAT
8491 TTGTTTGTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 3 0.09
17 18 0.51
18 11 0.31
19 3 0.09
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.50
Consensus pattern (17 bp):
TATTCAATCAGTGTTGG
Found at i:8542 original size:14 final size:13
Alignment explanation
Indices: 8489--8545 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 13
8479 TTGGTATTCA
8489 ATTTGTTTGTCTT
1 ATTTGTTTGTCTT
* *
8502 ATTCTTTTTGCTACATA
1 ATT-TGTTTG-T-C-TT
8519 ATTTGTTTGTCTT
1 ATTTGTTTGTCTT
8532 ATTTGGTTTGTCTT
1 ATTT-GTTTGTCTT
8546 TTTAGACGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
13 8 0.23
14 15 0.43
15 2 0.06
16 6 0.17
17 4 0.11
ACGTcount: A:0.12, C:0.11, G:0.14, T:0.63
Consensus pattern (13 bp):
ATTTGTTTGTCTT
Found at i:9040 original size:45 final size:45
Alignment explanation
Indices: 8990--9116 Score: 202
Period size: 45 Copynumber: 2.8 Consensus size: 45
8980 AATTCTACTC
8990 CATCTCTAGGTAATTCATCAAAATAAAACTAATATTATACTCC-T
1 CATCTCTAGGTAATTCATCAAAATAAAACTAATATTATACTCCTT
* * *
9034 CTATCTCTAGGCAATTCATCAAAATAAAGCTAATATTCTACTCCTT
1 C-ATCTCTAGGTAATTCATCAAAATAAAACTAATATTATACTCCTT
*
9080 CATCTCTAGGTCATTCATCAAAATAAAACTAATATTA
1 CATCTCTAGGTAATTCATCAAAATAAAACTAATATTA
9117 ATTGTTGCTT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
44 1 0.01
45 71 0.96
46 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (45 bp):
CATCTCTAGGTAATTCATCAAAATAAAACTAATATTATACTCCTT
Done.