Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013472.1 Corchorus capsularis cultivar CVL-1 contig13493, 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: 23385
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:1168 original size:29 final size:29
Alignment explanation
Indices: 1135--1190 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1125 ACAAACTAAA
*
1135 GAATTATGTAACACGTTTATTGGTAGATG
1 GAATTATGTAACACGTGTATTGGTAGATG
*
1164 GAATTATGTAACACGTGTGTTGGTAGA
1 GAATTATGTAACACGTGTATTGGTAGA
1191 CGAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (29 bp):
GAATTATGTAACACGTGTATTGGTAGATG
Found at i:1197 original size:29 final size:29
Alignment explanation
Indices: 1136--1197 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
1126 CAAACTAAAG
* * *
1136 AATTATGTAACACGTTTATTGGTAGATGG
1 AATTATGTAACACGTGTATTGGTAGACGA
*
1165 AATTATGTAACACGTGTGTTGGTAGACGA
1 AATTATGTAACACGTGTATTGGTAGACGA
1194 AATT
1 AATT
1198 TTAATGATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.35
Consensus pattern (29 bp):
AATTATGTAACACGTGTATTGGTAGACGA
Found at i:2049 original size:38 final size:38
Alignment explanation
Indices: 1998--2075 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 38
1988 TAAAATTGCC
*
1998 AAAAATTCAAAGTATTAAGTAAGAATGTAAGATTGTTG
1 AAAAATTCAAAGTATTAAGTAAGAATGTAAGATAGTTG
2036 AAAAATGT-AAAGTATTAAGTAAGAATGTAAGATAGTTG
1 AAAAAT-TCAAAGTATTAAGTAAGAATGTAAGATAGTTG
2074 AA
1 AA
2076 TTTGTTGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 37 0.97
39 1 0.03
ACGTcount: A:0.50, C:0.01, G:0.19, T:0.29
Consensus pattern (38 bp):
AAAAATTCAAAGTATTAAGTAAGAATGTAAGATAGTTG
Found at i:3066 original size:18 final size:17
Alignment explanation
Indices: 3036--3108 Score: 53
Period size: 17 Copynumber: 4.2 Consensus size: 17
3026 TTATTATGCG
3036 ATTTATTATATTTATTT
1 ATTTATTATATTTATTT
*
3053 ATTTTTTATGATTTA-TT
1 ATTTATTAT-ATTTATTT
* * *
3070 A-TTA-CAAATTAATATGTG
1 ATTTATTATATT--TAT-TT
3088 ATTTATTATATTTATTT
1 ATTTATTATATTTATTT
3105 ATTT
1 ATTT
3109 GTTTTTTATG
Statistics
Matches: 41, Mismatches: 8, Indels: 14
0.65 0.13 0.22
Matches are distributed among these distances:
14 3 0.07
15 1 0.02
16 4 0.10
17 16 0.39
18 10 0.24
19 3 0.07
20 4 0.10
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (17 bp):
ATTTATTATATTTATTT
Found at i:20801 original size:68 final size:67
Alignment explanation
Indices: 20690--20860 Score: 281
Period size: 68 Copynumber: 2.6 Consensus size: 67
20680 AATTGTCCTC
**
20690 TGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAGTTTGATTTGATTTGA
1 TGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTGATTTGA
20755 TT
66 TT
* *
20757 TGATTCAAGGGTCGAACGACTTTGATCTTGAACTTGATGGTAATTTGAGAACTTGATTTGATTTG
1 TGATTCAAGGGTCGAATGAC-TTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTGATTTG
20822 ATT
65 ATT
*
20825 TGATTCAAGGGTCGAATGACTTGGTCTTGAA-TTGAT
1 TGATTCAAGGGTCGAATGACTTGATCTTGAACTTGAT
20861 AATTTAATTA
Statistics
Matches: 97, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
66 5 0.05
67 29 0.30
68 63 0.65
ACGTcount: A:0.26, C:0.09, G:0.25, T:0.40
Consensus pattern (67 bp):
TGATTCAAGGGTCGAATGACTTGATCTTGAACTTGATGATAATTTGAGAACTTGATTTGATTTGA
TT
Found at i:20916 original size:94 final size:96
Alignment explanation
Indices: 20817--20995 Score: 231
Period size: 99 Copynumber: 1.9 Consensus size: 96
20807 ACTTGATTTG
* *
20817 ATTTGATTTGATTCAAGGGTC-GAATGACTTGGTCTTGAA-T-TGATAATTTAATTAAAGGGTCT
1 ATTTGATTTGATTCAAGGGTCTG-ATGACTTGATCTCGAATTATGATAATTTAATTAAAGGGTCT
20879 T-GACGACTTGATCTTGAATTGATGACTTGGGA
65 TAG-CGACTTGATCTTGAATTGATGACTTGGGA
* * *
20911 ATTTGATTTGATTCGAGGGTCTTTGATGACTTGATCTCGAATTGATGATAATTTGATTCAAGGGT
1 ATTTGATTTGATTCAAGGGTC--TGATGACTTGATCTCGAATT-ATGATAATTTAATTAAAGGGT
*
20976 CTTAGTGACTTGATCTTGAA
63 CTTAGCGACTTGATCTTGAA
20996 CAAACAAAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
94 20 0.28
96 14 0.19
97 2 0.03
99 35 0.49
100 1 0.01
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (96 bp):
ATTTGATTTGATTCAAGGGTCTGATGACTTGATCTCGAATTATGATAATTTAATTAAAGGGTCTT
AGCGACTTGATCTTGAATTGATGACTTGGGA
Found at i:21278 original size:16 final size:16
Alignment explanation
Indices: 21257--21291 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
21247 ATCTGAAATA
21257 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
21273 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
21289 CTT
1 CTT
21292 TTTTGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:23289 original size:29 final size:31
Alignment explanation
Indices: 23235--23293 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
23225 TACTTGATAC
*
23235 AAAAAGTAAACTATATTTCTGTCCAAAAAAA
1 AAAAAGTAAACTATATTTCTGGCCAAAAAAA
23266 AAAAAGTAAACTATA-TT-TGGCCAAAAAA
1 AAAAAGTAAACTATATTTCTGGCCAAAAAA
23294 TACAATAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 2 0.07
31 15 0.56
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (31 bp):
AAAAAGTAAACTATATTTCTGGCCAAAAAAA
Done.