Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016887.1 Corchorus olitorius cultivar O-4 contig16920, 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: 24971
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:75 original size:23 final size:20
Alignment explanation
Indices: 19--75 Score: 51
Period size: 23 Copynumber: 2.6 Consensus size: 20
9 ACCCGCTATT
19 TTTTTATGCGTTTTTTTTAATC
1 TTTTTAT-C-TTTTTTTTAATC
**
41 TTTTTAGATTTTCTTTTAATTTC
1 TTTTTATCTTTT-TTTTAA--TC
64 TTTTTATCTTTT
1 TTTTTATCTTTT
76 AATAAGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 4 0.14
21 6 0.21
22 6 0.21
23 12 0.43
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTATCTTTTTTTTAATC
Found at i:1313 original size:80 final size:80
Alignment explanation
Indices: 1180--1337 Score: 262
Period size: 80 Copynumber: 2.0 Consensus size: 80
1170 AGTGGTTTCG
* *
1180 GATCTTAGACGACTTTTGAAGATAAGTTGGCTGGAAAACCTATTTTGGGAAGGGAAATAAAAACG
1 GATCTTAGACGACTTTTCAAGATAAGTTGGCTGGAAAACCTATTTTGGGAAGGGAAATAAAAACA
1245 AGGGGGAGTTGCACC
66 AGGGGGAGTTGCACC
* ** *
1260 GATCTTAGACGACTTTTCAATATGGGTTGGCTGGAAAACCTATTTTGGGAAGGGAAATGAAAACA
1 GATCTTAGACGACTTTTCAAGATAAGTTGGCTGGAAAACCTATTTTGGGAAGGGAAATAAAAACA
1325 AGGGGGAGTTGCA
66 AGGGGGAGTTGCA
1338 TAACGAATGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.33, C:0.12, G:0.30, T:0.25
Consensus pattern (80 bp):
GATCTTAGACGACTTTTCAAGATAAGTTGGCTGGAAAACCTATTTTGGGAAGGGAAATAAAAACA
AGGGGGAGTTGCACC
Found at i:1937 original size:20 final size:22
Alignment explanation
Indices: 1891--1940 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
1881 AAATTATTTC
1891 TCAAAAT-ATCTTTATAAACTA
1 TCAAAATAATCTTTATAAACTA
* *
1912 TTAAAATAAT-TTT-TAAATTA
1 TCAAAATAATCTTTATAAACTA
1932 TCAAAATAA
1 TCAAAATAA
1941 AATTCATAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 14 0.56
21 9 0.36
22 2 0.08
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
TCAAAATAATCTTTATAAACTA
Found at i:12089 original size:29 final size:30
Alignment explanation
Indices: 12054--12113 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
12044 TATATAAATA
* *
12054 ATATAATATAATAAAATAA-TTATATTTAT
1 ATATAATAAAATAAAATAATTTATATGTAT
**
12083 ATATAATAAAATTGAATAATTTATATGTAT
1 ATATAATAAAATAAAATAATTTATATGTAT
12113 A
1 A
12114 CGTTAATTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (30 bp):
ATATAATAAAATAAAATAATTTATATGTAT
Found at i:12104 original size:24 final size:22
Alignment explanation
Indices: 12050--12108 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 22
12040 ATTATATATA
*
12050 AATAATATA-ATATAATAAAAT
1 AATAATTTATATATAATAAAAT
12071 AATTATATTTATATATAATAAAATT
1 AA-TA-ATTTATATATAATAAAA-T
12096 GAATAATTTATAT
1 -AATAATTTATAT
12109 GTATACGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 2 0.06
22 2 0.06
23 4 0.12
24 19 0.59
25 3 0.09
26 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AATAATTTATATATAATAAAAT
Found at i:12240 original size:26 final size:26
Alignment explanation
Indices: 12215--12263 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
12205 TTAATGTTTA
12215 AATT-TTATTTT-TTATTAAAAAATTT
1 AATTATTATTTTATT-TTAAAAAATTT
12240 AATTATTATTTTATTTTAAAAAAT
1 AATTATTATTTTATTTTAAAAAAT
12264 AAATATGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.18
26 16 0.73
27 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATTATTATTTTATTTTAAAAAATTT
Found at i:12712 original size:22 final size:22
Alignment explanation
Indices: 12671--12712 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12661 GACAAACTTG
**
12671 TAACCTAAATGACCTGAGAAGT
1 TAACCTAAATGACCCAAGAAGT
*
12693 TAACCTGAATGACCCAAGAA
1 TAACCTAAATGACCCAAGAA
12713 TATTATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (22 bp):
TAACCTAAATGACCCAAGAAGT
Found at i:19077 original size:2 final size:2
Alignment explanation
Indices: 19070--19107 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
19060 GGACGAAAGT
19070 TA TA TA TA TA 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 TA TA TA TA TA
19108 CTTACTGTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.