Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012248.1 Corchorus capsularis cultivar CVL-1 contig12269, 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: 20445
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Found at i:891 original size:33 final size:32
Alignment explanation
Indices: 817--892 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 32
807 CGCCAAGCAA
*
817 TGGCCGGTTGTGGCCGGACATGTCCATGTCGCG
1 TGGCCGG-TGTGGCCGGACATCTCCATGTCGCG
*
850 TGGCCGGTGATGGCCGGGCATCTCCGA-GTCGCG
1 TGGCCGGTG-TGGCCGGACATCTCC-ATGTCGCG
883 TGGCCGGTGT
1 TGGCCGGTGT
893 TGGTCGGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
32 3 0.08
33 35 0.90
34 1 0.03
ACGTcount: A:0.08, C:0.28, G:0.42, T:0.22
Consensus pattern (32 bp):
TGGCCGGTGTGGCCGGACATCTCCATGTCGCG
Found at i:3990 original size:33 final size:32
Alignment explanation
Indices: 3940--4045 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 32
3930 CATAAGTGAT
* *
3940 CGGCCACGCGACTTGGAGATGCCCGCGCAACAC
1 CGGCCACGCAACATGGAGATGCCCG-GCAACAC
* *
3973 CGGCCATGCAACATGGAGATGCCCGGCCATCAC
1 CGGCCACGCAACATGGAGATGCCCGG-CAACAC
* ** *
4006 CGGCCACGCGACATGGCCATGCCCGGCCACAC
1 CGGCCACGCAACATGGAGATGCCCGGCAACAC
4038 TCGGCCAC
1 -CGGCCAC
4046 ATGACTCGGC
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
32 5 0.08
33 56 0.92
ACGTcount: A:0.21, C:0.42, G:0.28, T:0.09
Consensus pattern (32 bp):
CGGCCACGCAACATGGAGATGCCCGGCAACAC
Found at i:4057 original size:33 final size:32
Alignment explanation
Indices: 3940--4069 Score: 109
Period size: 33 Copynumber: 4.0 Consensus size: 32
3930 CATAAGTGAT
* * ** *
3940 CGGCCACGCGACTTGGAGATGCCCGCGCAACAC
1 CGGCCACACGACATGGCCATGCCCG-GCCACAC
** * **
3973 CGGCCATGCAACATGGAGATGCCCGGCCATCAC
1 CGGCCACACGACATGGCCATGCCCGGCCA-CAC
*
4006 CGGCCACGCGACATGGCCATGCCCGGCCACAC
1 CGGCCACACGACATGGCCATGCCCGGCCACAC
*
4038 TCGGCCACATGAC-TCGGCCATGCCCGGCCACA
1 -CGGCCACACGACAT-GGCCATGCCCGGCCACA
4070 ACCGTCACAT
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
32 7 0.08
33 77 0.92
ACGTcount: A:0.21, C:0.42, G:0.28, T:0.10
Consensus pattern (32 bp):
CGGCCACACGACATGGCCATGCCCGGCCACAC
Found at i:12202 original size:34 final size:33
Alignment explanation
Indices: 12136--12245 Score: 175
Period size: 33 Copynumber: 3.3 Consensus size: 33
12126 TTCCTTTCAC
** *
12136 CCAAAACAGAATTATTTTTAATGCTATAATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
12169 CCAAAACAGAATTATTTGCCAATGCTATGATCAA
1 CCAAAACAGAATTATTTG-CAATGCTATGATCAA
*
12203 CCAAAACAGAATTACTTGCAATGCTATGATCAA
1 CCAAAACAGAATTATTTGCAATGCTATGATCAA
12236 CCAAAACAGA
1 CCAAAACAGA
12246 TTTGTTTTCA
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 42 0.58
34 30 0.42
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (33 bp):
CCAAAACAGAATTATTTGCAATGCTATGATCAA
Found at i:12308 original size:33 final size:33
Alignment explanation
Indices: 12271--12375 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
12261 ATTAGCATCC
*
12271 AAAACAGATTTAGTATCATCACAAACAACACTT
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
* * * *
12304 AAAACAGATTTAGTGTCATTGCAAAAAACACTC
1 AAAACAGATTTAGTATCATCGCAAACAACACTT
** * *
12337 AAATTAGGTTTAGAATCATCGCAAACAACA-TCT
1 AAAACAGATTTAGTATCATCGCAAACAACACT-T
12370 AAAACA
1 AAAACA
12376 CTCTTTGCAA
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
32 1 0.02
33 55 0.98
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCGCAAACAACACTT
Found at i:13409 original size:30 final size:30
Alignment explanation
Indices: 13375--13433 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
13365 GGTCGAATGG
* * *
13375 CCGGTTGTTGCCGGATGGCCCGTGCGATGA
1 CCGGTTATGGCCGGATGGCCCATGCGATGA
*
13405 CCGGTTATGGCCGGATGGCTCATGCGATG
1 CCGGTTATGGCCGGATGGCCCATGCGATG
13434 TCCCGTGCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.12, C:0.25, G:0.39, T:0.24
Consensus pattern (30 bp):
CCGGTTATGGCCGGATGGCCCATGCGATGA
Found at i:17893 original size:12 final size:13
Alignment explanation
Indices: 17852--17896 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
17842 AATTATTGTT
17852 TGCTTTATTAATC
1 TGCTTTATTAATC
*
17865 TGCTTTATTAATT
1 TGCTTTATTAATC
17878 TGCTTTA-TAATC
1 TGCTTTATTAATC
17890 TGCTTTA
1 TGCTTTA
17897 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:18570 original size:33 final size:33
Alignment explanation
Indices: 18528--18608 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 33
18518 GTGTTTTAGA
***
18528 TGTTGTTTGCGATGATGCTAAACCTAATTTGAG
1 TGTTGTTTGCGATGACAATAAACCTAATTTGAG
* * **
18561 TGTTGTTTGCAATGACAATAAATCTTTTTTGAG
1 TGTTGTTTGCGATGACAATAAACCTAATTTGAG
*
18594 TGTTGTTTGTGATGA
1 TGTTGTTTGCGATGA
18609 AACAAAATCT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.44
Consensus pattern (33 bp):
TGTTGTTTGCGATGACAATAAACCTAATTTGAG
Found at i:18617 original size:33 final size:33
Alignment explanation
Indices: 18555--18624 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
18545 CTAAACCTAA
* *
18555 TTTGAGTGTTGTTTGCAATGACAATAAATCTTT
1 TTTGAGTGTTGTTTGCAATGACAAAAAATCTGT
**
18588 TTTGAGTGTTGTTTGTGATGA-AACAAAATCTGT
1 TTTGAGTGTTGTTTGCAATGACAA-AAAATCTGT
18621 TTTG
1 TTTG
18625 GATTCTACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.46
Consensus pattern (33 bp):
TTTGAGTGTTGTTTGCAATGACAAAAAATCTGT
Found at i:19074 original size:30 final size:30
Alignment explanation
Indices: 19034--19092 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
19024 CAAGGGGGAG
19034 GGAATAATGCGCCCAAGG-CTTATCATGGAA
1 GGAATAATGCG-CCAAGGACTTATCATGGAA
* *
19064 GGAATGATGCGCCAAGGACTTATTATGGA
1 GGAATAATGCGCCAAGGACTTATCATGGA
19093 CTTGAAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (30 bp):
GGAATAATGCGCCAAGGACTTATCATGGAA
Done.