Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023527.1 Corchorus olitorius cultivar O-4 contig23560, 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: 41151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:162 original size:21 final size:21
Alignment explanation
Indices: 138--208 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
128 TAAAATCAAA
*
138 AATAAGATTACTAAAAATCTT
1 AATAAGATTACTAAAAAACTT
* *
159 AATAAGGTTAGGTAAAAACACTT
1 AATAAGATTA-CTAAAAA-ACTT
*
182 AATAAGATGACTAAAAAACTT
1 AATAAGATTACTAAAAAACTT
*
203 TATAAG
1 AATAAG
209 GCCAAAAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
21 18 0.44
22 12 0.29
23 11 0.27
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (21 bp):
AATAAGATTACTAAAAAACTT
Found at i:684 original size:31 final size:31
Alignment explanation
Indices: 646--716 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
636 ATAATTATTC
**
646 ATTATAAAGAAATAACAATGTTTTTCTACAA
1 ATTATAAAGAAATAACAATACTTTTCTACAA
** **
677 ATTATAAAGATTTAGTAATACTTTTCTACAA
1 ATTATAAAGAAATAACAATACTTTTCTACAA
708 ATTATAAAG
1 ATTATAAAG
717 GTTTTACATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.38
Consensus pattern (31 bp):
ATTATAAAGAAATAACAATACTTTTCTACAA
Found at i:17966 original size:41 final size:41
Alignment explanation
Indices: 17917--17998 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
17907 CTAACAATGT
17917 CTCCAATGAATTCTGATTCATGTCTACAAATAGAACAAAGA
1 CTCCAATGAATTCTGATTCATGTCTACAAATAGAACAAAGA
17958 CTCCAATGAATTCTGATTCATGTCTACAAATAGAACAAAGA
1 CTCCAATGAATTCTGATTCATGTCTACAAATAGAACAAAGA
17999 TATAAAACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (41 bp):
CTCCAATGAATTCTGATTCATGTCTACAAATAGAACAAAGA
Found at i:21272 original size:210 final size:210
Alignment explanation
Indices: 20901--21279 Score: 503
Period size: 210 Copynumber: 1.8 Consensus size: 210
20891 TCAATCTGAG
* * * *
20901 CTGGTAACCTTTCAAGATTCGAGCAGCCTGAAAGAATTAATATCTCAAGAGATTCCATTCTAATT
1 CTGGTAACCTTTCAAGATTCGAGCAACCTGAAAGAATCAATATCTCAAGAGATACCATTCTAAAT
* * * * * *
20966 TTGGTTGGAAGACTCCTAAGACTTTTGCAGTCTCTTAAATTCAGGATTTTAAGACTCCTTAGAAG
66 TTGGTAGGAAGACTCCCAAGACTTCTGCAATCTCTTAAATTCAGAAGTTTAAGACTCCTTAGAAG
* * * *
21031 TCCGATGGATGGATGAACATCTACTATCTTGACACAACCAACCGTAATCAAATGTTTGAGATTTG
131 TCCAATAGACGGATGAACATCTACCATCTTGACACAACCAACCGTAATCAAATGTTTGAGATTTG
21096 GGGCCATTGTAAAGT
196 GGGCCATTGTAAAGT
* * * * **
21111 CTGGTAACCTGTT-GAGATTTGTGCAACCTGAAAGAATCAATGTCTCAAGAGATACTGTT-TCAA
1 CTGGTAACCT-TTCAAGATTCGAGCAACCTGAAAGAATCAATATCTCAAGAGATACCATTCT-AA
*
21174 ATTTGGTAGGAAGACTCCCAAGACTTCTGCAATCTCTTAAA-TCAAGAAGTTTAAGTCTCCTTAG
64 ATTTGGTAGGAAGACTCCCAAGACTTCTGCAATCTCTTAAATTC-AGAAGTTTAAGACTCCTTAG
* *
21238 AAGTCCAATAGACGGATGAATATCTACCATCTTGATACAACC
128 AAGTCCAATAGACGGATGAACATCTACCATCTTGACACAACC
21280 TGTCAAAACC
Statistics
Matches: 143, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
209 3 0.02
210 138 0.97
211 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (210 bp):
CTGGTAACCTTTCAAGATTCGAGCAACCTGAAAGAATCAATATCTCAAGAGATACCATTCTAAAT
TTGGTAGGAAGACTCCCAAGACTTCTGCAATCTCTTAAATTCAGAAGTTTAAGACTCCTTAGAAG
TCCAATAGACGGATGAACATCTACCATCTTGACACAACCAACCGTAATCAAATGTTTGAGATTTG
GGGCCATTGTAAAGT
Found at i:21308 original size:210 final size:210
Alignment explanation
Indices: 20901--21332 Score: 489
Period size: 210 Copynumber: 2.1 Consensus size: 210
20891 TCAATCTGAG
* * * *
20901 CTGGTAACCTTTCAAGATTCGAGCAGCCTGAAAGAATTAATATCTCAAGAGATTCCATTCTAATT
1 CTGGTAACCTTTCAAGATTCGAGCAACCTGAAAGAATCAATATCTCAAGAGATACCATTCTAAAT
* * * * * *
20966 TTGGTTGGAAGACTCCTAAGACTTTTGCAGTCTCTTAAATTCAGGATTTTAAGACTCCTTAGAAG
66 TTGGTAGGAAGACTCCCAAGACTTCTGCAATCTCTTAAATTCAGAAGTTTAAGACTCCTTAGAAG
* * * * * * *
21031 TCCGATGGATGGATGAACATCTACTATCTTGACACAACCAACCGTAATCAAATGTTTGAGATTTG
131 TCCAATAGACGGATGAACATCTACCATCTTGACACAACCAACCGAAAACAAATGTTTAAGATTTG
21096 GGGCCATTGTAAAGT
196 GGGCCATTGTAAAGT
* * * * **
21111 CTGGTAACCTGTT-GAGATTTGTGCAACCTGAAAGAATCAATGTCTCAAGAGATACTGTT-TCAA
1 CTGGTAACCT-TTCAAGATTCGAGCAACCTGAAAGAATCAATATCTCAAGAGATACCATTCT-AA
*
21174 ATTTGGTAGGAAGACTCCCAAGACTTCTGCAATCTCTTAAA-TCAAGAAGTTTAAGTCTCCTTAG
64 ATTTGGTAGGAAGACTCCCAAGACTTCTGCAATCTCTTAAATTC-AGAAGTTTAAGACTCCTTAG
* * *** *
21238 AAGTCCAATAGACGGATGAATATCTACCATCTTGATACAACCTGTC-AAAACCAA-GCTTTCAAG
128 AAGTCCAATAGACGGATGAACATCTACCATCTTGACACAACCAACCGAAAACAAATG-TTT-AAG
*
21301 GTTTGGGGCCATTGTAAAGT
191 ATTTGGGGCCATTGTAAAGT
*
21321 CTGG-AATCTTTC
1 CTGGTAACCTTTC
21333 TCAGTTTTTT
Statistics
Matches: 184, Mismatches: 32, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
208 3 0.02
209 15 0.08
210 164 0.89
211 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (210 bp):
CTGGTAACCTTTCAAGATTCGAGCAACCTGAAAGAATCAATATCTCAAGAGATACCATTCTAAAT
TTGGTAGGAAGACTCCCAAGACTTCTGCAATCTCTTAAATTCAGAAGTTTAAGACTCCTTAGAAG
TCCAATAGACGGATGAACATCTACCATCTTGACACAACCAACCGAAAACAAATGTTTAAGATTTG
GGGCCATTGTAAAGT
Found at i:27387 original size:29 final size:30
Alignment explanation
Indices: 27324--27399 Score: 100
Period size: 29 Copynumber: 2.5 Consensus size: 30
27314 GGCGGCTGAT
* * *
27324 GTGGCATGCCACGTATACTAAAAAATGACAT
1 GTGGCATGCCACGTGTAC-AAAAAAGGACAC
*
27355 GTGGCACGCCACGTGTAC-AAAAAGGACAC
1 GTGGCATGCCACGTGTACAAAAAAGGACAC
27384 GTGGCATGCCACGTGT
1 GTGGCATGCCACGTGT
27400 TAGAAATACC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 24 0.60
31 16 0.40
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (30 bp):
GTGGCATGCCACGTGTACAAAAAAGGACAC
Found at i:29076 original size:2 final size:2
Alignment explanation
Indices: 29069--29098 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29059 TCTAGAGTGA
29069 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29099 GAAAGAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40839 original size:12 final size:12
Alignment explanation
Indices: 40822--40846 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40812 TTTATATTTC
40822 TTGTGTTTATAT
1 TTGTGTTTATAT
40834 TTGTGTTTATAT
1 TTGTGTTTATAT
40846 T
1 T
40847 CAAAATTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TTGTGTTTATAT
Done.