Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011878.1 Corchorus olitorius cultivar O-4 contig11911, 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: 17819
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:5860 original size:13 final size:13
Alignment explanation
Indices: 5842--5866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5832 TTTTTACCAC
5842 CTTAAAATTATTG
1 CTTAAAATTATTG
5855 CTTAAAATTATT
1 CTTAAAATTATT
5867 TTTTGGCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
CTTAAAATTATTG
Found at i:11879 original size:36 final size:36
Alignment explanation
Indices: 11802--11880 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 36
11792 GACACGGCGG
* * *
11802 TGGTGGCTATGGTGGTGGTGGTCACGGAGGAGGAAA
1 TGGTGGTTATGGTGGTGGCGGGCACGGAGGAGGAAA
* * **
11838 GGGTGGTTATGGTGGTGGCGGGCATGGAGGAGGTTA
1 TGGTGGTTATGGTGGTGGCGGGCACGGAGGAGGAAA
11874 TGGTGGT
1 TGGTGGT
11881 GGAGGTGGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.15, C:0.06, G:0.53, T:0.25
Consensus pattern (36 bp):
TGGTGGTTATGGTGGTGGCGGGCACGGAGGAGGAAA
Found at i:11885 original size:18 final size:18
Alignment explanation
Indices: 11862--11924 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
11852 GTGGCGGGCA
11862 TGGAGGAGGTTATGGTGG
1 TGGAGGAGGTTATGGTGG
* *
11880 TGGAGGTGGATATGGTGG
1 TGGAGGAGGTTATGGTGG
* *
11898 CGGAAGAGGTGGATATGGTGG
1 TGGAGGAGGT---TATGGTGG
11919 TGGAGG
1 TGGAGG
11925 GGGACGTGGC
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
18 22 0.65
21 12 0.35
ACGTcount: A:0.19, C:0.02, G:0.56, T:0.24
Consensus pattern (18 bp):
TGGAGGAGGTTATGGTGG
Found at i:11915 original size:39 final size:41
Alignment explanation
Indices: 11872--11966 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
11862 TGGAGGAGGT
* * *
11872 TATGGTGGTGGAGGTGGA-T-ATGGTGGCGGAAGAGGTGGA
1 TATGGTGGTGGAGGGGGACTGACGGTGGCAGAAGAGGTGGA
* *
11911 TATGGTGGTGGAGGGGGACGTGGCGGTGGCAGCAGAGGTGGA
1 TATGGTGGTGGAGGGGGAC-TGACGGTGGCAGAAGAGGTGGA
11953 TATGGTGGTGGAGG
1 TATGGTGGTGGAGG
11967 ACGTGGCGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 17 0.35
41 1 0.02
42 30 0.62
ACGTcount: A:0.18, C:0.05, G:0.56, T:0.21
Consensus pattern (41 bp):
TATGGTGGTGGAGGGGGACTGACGGTGGCAGAAGAGGTGGA
Found at i:11939 original size:42 final size:39
Alignment explanation
Indices: 11893--11981 Score: 133
Period size: 42 Copynumber: 2.2 Consensus size: 39
11883 AGGTGGATAT
11893 GGTGGCGGAAGAGGTGGATATGGTGGTGGAGGGGGACGTGGC
1 GGTGGCGGAAGAGGTGGATATGGTGGTGGA---GGACGTGGC
* *
11935 GGTGGCAGCAGAGGTGGATATGGTGGTGGAGGACGTGGC
1 GGTGGCGGAAGAGGTGGATATGGTGGTGGAGGACGTGGC
11974 GGTGGCGG
1 GGTGGCGG
11982 TGGCGGATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
39 16 0.36
42 28 0.64
ACGTcount: A:0.16, C:0.09, G:0.58, T:0.17
Consensus pattern (39 bp):
GGTGGCGGAAGAGGTGGATATGGTGGTGGAGGACGTGGC
Found at i:11972 original size:21 final size:20
Alignment explanation
Indices: 11872--11972 Score: 75
Period size: 21 Copynumber: 5.0 Consensus size: 20
11862 TGGAGGAGGT
11872 TATGGTGGTGGA-G-GTGGA
1 TATGGTGGTGGAGGAGTGGA
* *
11890 TATGGTGGCGGAAGAGGTGGA
1 TATGGTGGTGGAGGA-GTGGA
11911 TATGGTGGTGGAGG-G-GGA
1 TATGGTGGTGGAGGAGTGGA
** *
11929 CGTGGCGGTGGCAGCAGAGGTGGA
1 TATGGTGGTGG-AG--GA-GTGGA
11953 TATGGTGGTGGAGGACGTGG
1 TATGGTGGTGGAGGA-GTGG
11973 CGGTGGCGGT
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
18 22 0.34
19 4 0.06
21 24 0.38
23 3 0.05
24 11 0.17
ACGTcount: A:0.18, C:0.06, G:0.55, T:0.21
Consensus pattern (20 bp):
TATGGTGGTGGAGGAGTGGA
Found at i:12531 original size:12 final size:12
Alignment explanation
Indices: 12508--12543 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
12498 TTCCTAGATC
12508 CATTCCAAAAACT
1 CATTCC-AAAACT
*
12521 CATTCCTAAACT
1 CATTCCAAAACT
12533 CATTCCAAAAC
1 CATTCCAAAAC
12544 CCGTTGCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.42, C:0.33, G:0.00, T:0.25
Consensus pattern (12 bp):
CATTCCAAAACT
Found at i:13397 original size:173 final size:172
Alignment explanation
Indices: 13087--13486 Score: 491
Period size: 173 Copynumber: 2.3 Consensus size: 172
13077 TGATTTGTTT
* * * *
13087 TAGATCATGAAAAAACCTTGTAATAGACACTCGAATCACCTTAATCGGACATTTAGAGCGAAAAT
1 TAGATCATGGAACAACCTTTTAATAGACACTCGAATCACCTCAATCGGAC----AGAGCGAAAAT
* * * *
13152 TATGATATTAAGTAGATCGCCCATTCCTACTAACCGAAACACCTAATTTTTCGGAAGCATTTTGG
62 CATGATATTAAGTAGACCGCCCATTCCCACTAACCGAAACAACTAATTTTTCGGAAGCATTTTGG
* *
13217 ATACTTGAGACATCAAATTTAACTTTCGAGTCCATCATGAAAGTTG
127 ATACTTGAAACATCAAATTTAACTTTCGAGTCCATAATGAAAGTTG
*
13263 TAGATCATGGAACAACCTTTTAATAGACACTTGAATCACCTCAATCGGACA-AGC-AAAACTCAT
1 TAGATCATGGAACAACCTTTTAATAGACACTCGAATCACCTCAATCGGACAGAGCGAAAA-TCAT
* * * * *
13326 GTAATATTAATTGGACCGTCCATTCCCACTAACCGAAACAACTAATTTTTTGGAATCATTTT-GA
65 G--ATATTAAGTAGACCGCCCATTCCCACTAACCGAAACAACTAATTTTTCGGAAGCATTTTGGA
* * * *
13390 CTACTTGAAACATCAAATTTAGCTTTCTAGTTCTTAATGAAAGTTG
128 -TACTTGAAACATCAAATTTAACTTTCGAGTCCATAATGAAAGTTG
* * * *
13436 TAGATCATAGAACAACCTTTAAATAGACTCTCGAATCAGCTCAATCGGACA
1 TAGATCATGGAACAACCTTTTAATAGACACTCGAATCACCTCAATCGGACA
13487 TTTACATATA
Statistics
Matches: 195, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
170 4 0.02
171 7 0.04
172 3 0.02
173 136 0.70
176 45 0.23
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (172 bp):
TAGATCATGGAACAACCTTTTAATAGACACTCGAATCACCTCAATCGGACAGAGCGAAAATCATG
ATATTAAGTAGACCGCCCATTCCCACTAACCGAAACAACTAATTTTTCGGAAGCATTTTGGATAC
TTGAAACATCAAATTTAACTTTCGAGTCCATAATGAAAGTTG
Found at i:17451 original size:42 final size:42
Alignment explanation
Indices: 17392--17472 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
17382 GCTAAGTCTT
* *
17392 GAAAATTCTCTGTAAATTAAGAAATACTCAATTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTAAACTCAAATCATA
*
17434 GAAAATTCTTTGTAAATTAAGAAATACTAAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTAAACTCAAATC
17473 CTAAGTCCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.31
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTAAACTCAAATCATA
Found at i:17624 original size:57 final size:59
Alignment explanation
Indices: 17530--17648 Score: 188
Period size: 57 Copynumber: 2.0 Consensus size: 59
17520 TTTATTTTGT
* *
17530 AGAATAATTAAATAGAGATATATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAATAGAGA-ATAGAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
*
17590 AGAATAATTAAGTAGAG-ATAGA-GGGGATAAGATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAATAGAGAATAGAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
17647 AG
1 AG
17649 GAAACGGATA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 36 0.64
58 4 0.07
60 16 0.29
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.34
Consensus pattern (59 bp):
AGAATAATTAAATAGAGAATAGAGGGGGATAAGATTTATTATAACATTTATTGTGTGAA
Done.