Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014503.1 Corchorus olitorius cultivar O-4 contig14536, 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: 7432
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Found at i:19 original size:2 final size:2
Alignment explanation
Indices: 13--42 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3 TCTCGACCTT
*
13 TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
43 CAGTGTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1536 original size:16 final size:16
Alignment explanation
Indices: 1512--1554 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1502 TCTTCACTTC
*
1512 TCTTCTCCTTTTTCTT
1 TCTTTTCCTTTTTCTT
1528 TCTTTTCCTTTTTCTT
1 TCTTTTCCTTTTTCTT
1544 T-TTTT-CTTTTT
1 TCTTTTCCTTTTT
1555 GAATTGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 6 0.23
15 4 0.15
16 16 0.62
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTTTCCTTTTTCTT
Found at i:3050 original size:103 final size:103
Alignment explanation
Indices: 2879--3086 Score: 371
Period size: 103 Copynumber: 2.0 Consensus size: 103
2869 CCTTTTTAAT
* *
2879 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTTTAAGATTCA
1 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAAATTTTAAGATTCA
*
2944 ATATGTAATTTCATTTATCAATTAAATTAAATATATTA
66 ATATATAATTTCATTTATCAATTAAATTAAATATATTA
* *
2982 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAAATTTTAAGGTTTA
1 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAAATTTTAAGATTCA
3047 ATATATAATTTCATTTATCAATTAAATTAAATATATTA
66 ATATATAATTTCATTTATCAATTAAATTAAATATATTA
3085 TT
1 TT
3087 ATATTAAAAT
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (103 bp):
TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAAATTTTAAGATTCA
ATATATAATTTCATTTATCAATTAAATTAAATATATTA
Found at i:3201 original size:39 final size:40
Alignment explanation
Indices: 3145--3225 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
3135 TTTAATTCCT
**
3145 ATGTAATATATATAATAACTAAAATGTTTACATCAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
* * *
3185 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
3224 AT
1 AT
3226 TCTTAGGTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATCAATTAA
Found at i:3683 original size:202 final size:202
Alignment explanation
Indices: 3337--3745 Score: 764
Period size: 202 Copynumber: 2.0 Consensus size: 202
3327 TTCCTTAATA
*
3337 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACACTGATCTAATTT
*
3402 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAGTA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
3467 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
131 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
3532 ACCATTG
196 ACCATTG
3539 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACACTGATCTAATTT
1 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACACTGATCTAATTT
* * * *
3604 AATTTAATAATTCAACCACTAATGTTTAACTAATTTTTTTTTGTATAGTTTTATATATAATAATA
66 AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
3669 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
131 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
3734 ACCATTG
196 ACCATTG
3741 ATAAA
1 ATAAA
3746 GTTATTAAGC
Statistics
Matches: 201, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
202 201 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (202 bp):
ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACACTGATCTAATTT
AATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATAATAATA
ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
ACCATTG
Found at i:4306 original size:36 final size:36
Alignment explanation
Indices: 4259--4328 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
4249 GAGATTTTGG
* *
4259 AGAAATATGATAATCAAAATTACAAAAGATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAATA
4295 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAGATGTAA
4329 GGTTATTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.59, C:0.09, G:0.11, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAGATGTAATA
Found at i:7211 original size:2 final size:2
Alignment explanation
Indices: 7204--7231 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7194 CTTTAACTAG
7204 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
7232 CTAGTAATGA
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:7321 original size:20 final size:21
Alignment explanation
Indices: 7276--7321 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
7266 AATTTATAAA
*
7276 ACATATAAAAAATATTAAAAT
1 ACATATAAAAAATAATAAAAT
* *
7297 A-ATAT-AAATATAATAAATT
1 ACATATAAAAAATAATAAAAT
7316 ACATAT
1 ACATAT
7322 TAATTTGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 12 0.57
20 8 0.38
21 1 0.05
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
ACATATAAAAAATAATAAAAT
Done.