Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018385.1 Corchorus olitorius cultivar O-4 contig18418, 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: 38120
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:537 original size:2 final size:2
Alignment explanation
Indices: 530--557 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
520 ATTCAACTTT
530 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
558 CAAAATGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1255 original size:41 final size:41
Alignment explanation
Indices: 1161--1282 Score: 219
Period size: 41 Copynumber: 3.0 Consensus size: 41
1151 ACTTGACCCT
* *
1161 CCTAATAATTAAGGAAATAAATTAAATCCAGATTTAG-CCC
1 CCTAATAATTAAGGTAATAAATTAAATCCAGGTTTAGCCCC
1201 CCTAATAATTAAGGTAATAAATTAAATCCAGGTTTAGCCCC
1 CCTAATAATTAAGGTAATAAATTAAATCCAGGTTTAGCCCC
1242 CCTAATAATTAAGGTAATAAATTAAATCCAGGTTTAGCCCC
1 CCTAATAATTAAGGTAATAAATTAAATCCAGGTTTAGCCCC
1283 TAGTTATATA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
40 35 0.44
41 44 0.56
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (41 bp):
CCTAATAATTAAGGTAATAAATTAAATCCAGGTTTAGCCCC
Found at i:8516 original size:21 final size:21
Alignment explanation
Indices: 8500--8600 Score: 103
Period size: 21 Copynumber: 4.8 Consensus size: 21
8490 ACTCCACCTT
8500 CAAGAGGAGTCAGTCCAACTC
1 CAAGAGGAGTCAGTCCAACTC
* * *
8521 CAAGGGGCGTCAGTCCAACCC
1 CAAGAGGAGTCAGTCCAACTC
* * *
8542 CAAGGGGTGTCAGTCCAACCC
1 CAAGAGGAGTCAGTCCAACTC
* * *
8563 CAAGGGGCGTCAGTCCAACGC
1 CAAGAGGAGTCAGTCCAACTC
* *
8584 CAAGGGGTGTCAGTCCA
1 CAAGAGGAGTCAGTCCA
8601 TCTCGGATAA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 73 1.00
ACGTcount: A:0.26, C:0.32, G:0.30, T:0.13
Consensus pattern (21 bp):
CAAGAGGAGTCAGTCCAACTC
Found at i:8554 original size:42 final size:42
Alignment explanation
Indices: 8508--8600 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
8498 TTCAAGAGGA
*
8508 GTCAGTCCAACTCCAAGGGGCGTCAGTCCAACCCCAAGGGGT
1 GTCAGTCCAACCCCAAGGGGCGTCAGTCCAACCCCAAGGGGT
*
8550 GTCAGTCCAACCCCAAGGGGCGTCAGTCCAACGCCAAGGGGT
1 GTCAGTCCAACCCCAAGGGGCGTCAGTCCAACCCCAAGGGGT
8592 GTCAGTCCA
1 GTCAGTCCA
8601 TCTCGGATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.24, C:0.33, G:0.29, T:0.14
Consensus pattern (42 bp):
GTCAGTCCAACCCCAAGGGGCGTCAGTCCAACCCCAAGGGGT
Found at i:10244 original size:20 final size:20
Alignment explanation
Indices: 10215--10256 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
10205 GGATTGGTCC
* *
10215 TTCCCTTCCTTTCCTCTCCT
1 TTCCCATCCTATCCTCTCCT
*
10235 TTCCCATCCTATCCTGTCCT
1 TTCCCATCCTATCCTCTCCT
10255 TT
1 TT
10257 ACTGATCCCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.05, C:0.45, G:0.02, T:0.48
Consensus pattern (20 bp):
TTCCCATCCTATCCTCTCCT
Found at i:13985 original size:17 final size:17
Alignment explanation
Indices: 13963--14021 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
13953 GCCTTATTGG
13963 CATAGAAATCGCTTTCT
1 CATAGAAATCGCTTTCT
* *
13980 CATAGAGTATGCTGACATT-T
1 CATAGA-AAT-C-G-CTTTCT
14000 -ATAGAAATCGCTTTCT
1 CATAGAAATCGCTTTCT
14016 CATAGA
1 CATAGA
14022 GTATGCTGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
15 3 0.09
16 2 0.06
17 12 0.38
18 4 0.12
19 6 0.19
20 2 0.06
21 3 0.09
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (17 bp):
CATAGAAATCGCTTTCT
Found at i:14011 original size:36 final size:36
Alignment explanation
Indices: 13964--14036 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
13954 CCTTATTGGC
13964 ATAGAAATCGCTTTCTCATAGAGTATGCTGACATTT
1 ATAGAAATCGCTTTCTCATAGAGTATGCTGACATTT
14000 ATAGAAATCGCTTTCTCATAGAGTATGCTGACATTT
1 ATAGAAATCGCTTTCTCATAGAGTATGCTGACATTT
14036 A
1 A
14037 CACTGCCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (36 bp):
ATAGAAATCGCTTTCTCATAGAGTATGCTGACATTT
Found at i:19181 original size:44 final size:44
Alignment explanation
Indices: 19131--19218 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
19121 GTTGGATGGA
19131 ACTGTTTATGTCAATGTTAATTAAGTGAATACAATCACTCTATG
1 ACTGTTTATGTCAATGTTAATTAAGTGAATACAATCACTCTATG
19175 ACTGTTTATGTCAATGTTAATTAAGTGAATACAATCACTCTATG
1 ACTGTTTATGTCAATGTTAATTAAGTGAATACAATCACTCTATG
19219 TTCTGGAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (44 bp):
ACTGTTTATGTCAATGTTAATTAAGTGAATACAATCACTCTATG
Done.