Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013713.1 Corchorus olitorius cultivar O-4 contig13746, 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: 32201
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:118 original size:42 final size:43
Alignment explanation
Indices: 67--160 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 43
57 AGTGCATTAT
**
67 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCAACAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAAATAATTCAACAAAATAAAG
**
108 CTAATATTCTACTCCTCCATCTCTAAATAATTCGTCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAAATAATTCAACAAAATAAAG
*
153 CTTATATT
1 CTAATATT
161 AATTGTTGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.14
45 34 0.77
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAAATAATTCAACAAAATAAAG
Found at i:1110 original size:5 final size:5
Alignment explanation
Indices: 1102--1136 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
1092 ACTTCCCTCC
*
1102 CCTTT CCTTT CCTTT CCTTT CCTTC CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
1137 AATTACTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (5 bp):
CCTTT
Found at i:1687 original size:20 final size:19
Alignment explanation
Indices: 1664--1703 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1654 ATTAAATTTT
*
1664 TTTAATTATTTTTAAGTATA
1 TTTAATTAATTTTAA-TATA
*
1684 TTTATTTAATTTTAATATA
1 TTTAATTAATTTTAATATA
1703 T
1 T
1704 CTTTTATGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTAATTAATTTTAATATA
Found at i:26332 original size:16 final size:16
Alignment explanation
Indices: 26311--26342 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
26301 CTAAAAAAGC
26311 ACAATATTCTTTGTGT
1 ACAATATTCTTTGTGT
26327 ACAATATTCTTTGTGT
1 ACAATATTCTTTGTGT
26343 GTGTGTGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (16 bp):
ACAATATTCTTTGTGT
Found at i:27580 original size:82 final size:82
Alignment explanation
Indices: 27443--27606 Score: 231
Period size: 82 Copynumber: 2.0 Consensus size: 82
27433 ATGACTTGAA
* * * ** *
27443 AAATGAAAATGATCTTACTTACTATTGAATTATTACATGTATTATATTTATAACTAAGTAACATT
1 AAATGAAAATGATCGTACTTACTATTGAAATATTACATGTACTATATCCATAACTAAGTAACATG
* *
27508 GATCTATCATCATATGT
66 GAACTATCATCAAATGT
*
27525 AAATGAAAATGATCGTACTTTCTA-TGAAAATATTACATGTACTATATCCATAACTAAGTAACAT
1 AAATGAAAATGATCGTACTTACTATTG-AAATATTACATGTACTATATCCATAACTAAGTAACAT
27589 GGAACTATCATCAAATGT
65 GGAACTATCATCAAATGT
27607 GTATAACATG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 2 0.03
82 70 0.97
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (82 bp):
AAATGAAAATGATCGTACTTACTATTGAAATATTACATGTACTATATCCATAACTAAGTAACATG
GAACTATCATCAAATGT
Found at i:28219 original size:188 final size:187
Alignment explanation
Indices: 27796--28351 Score: 900
Period size: 188 Copynumber: 3.0 Consensus size: 187
27786 GTTTACATTG
*
27796 TCGGGGAGGGGAGAGCCCGGGATCGAACCCGTTCCTTTTATGAAC-TCTCTAAGCCTCTTTGGCC
1 TCGGGGAGGGGAGAGCCTGGGATCGAACCCGTTCCTTTTATGAACTTC-CTAAGCCTCTTTGGCC
* *
27860 ACTCAGCCAAGAGGCTGAGTTCCCTCCTTTTCTTTATTTGGTACTTATATATATATCTTACCTTA
65 ACTCGGCCAAGAGGTTGAGTTCCCTCCTTTTCTTTATTTGGTAC-T-TATATATATCTTA-CTTA
* * ***
27925 ATCATTCATAAAACTTTTATCT-AAACTTACCCGAAAATATAATCAAATCGGTTCTATGAA
127 ATCATTCATAAAACTTATATCTAAAACTTACCCTAAAATATAATCAAATCGAAACTATGAA
* *
27985 TCGGGGAGGGGAGAGCGTAGGATCGAACCCGTTCCTTTTATGAACTTCCTAAGCCTCTTTGGCCA
1 TCGGGGAGGGGAGAGCCTGGGATCGAACCCGTTCCTTTTATGAACTTCCTAAGCCTCTTTGGCCA
*
28050 CTCGGCCAAGAGGTTGAGTTCCCTCCTTTTCTTTATTTGGTACTTATATACATCTTATCTTAATC
66 CTCGGCCAAGAGGTTGAGTTCCCTCCTTTTCTTTATTTGGTACTTATATATATCTTA-CTTAATC
28115 ATTCATAAAACTTATATCTAAAACTTACCCTAAAATATAATCAAATCGAAACTATGAA
130 ATTCATAAAACTTATATCTAAAACTTACCCTAAAATATAATCAAATCGAAACTATGAA
*
28173 TCGGGGAAGGGAGAGCCTGGGATCGAACCCGTTCCTTTTATGAACTTCCTAAGCCTCTTTGGCCA
1 TCGGGGAGGGGAGAGCCTGGGATCGAACCCGTTCCTTTTATGAACTTCCTAAGCCTCTTTGGCCA
* *
28238 CTCGGCCAAGAGGTTGAGTTCCTTCCTTTTCTTTATTTGGTACTTAAATATATCTTACTTTAATC
66 CTCGGCCAAGAGGTTGAGTTCCCTCCTTTTCTTTATTTGGTACTTATATATATCTTAC-TTAATC
* *
28303 ATTCATAGAACTTAAATCTAAAACTTACCCTAAAATATAATCAAATCGA
130 ATTCATAAAACTTATATCTAAAACTTACCCTAAAATATAATCAAATCGA
28352 TTCAATCAAT
Statistics
Matches: 344, Mismatches: 20, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
187 38 0.11
188 204 0.59
189 100 0.29
190 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.33
Consensus pattern (187 bp):
TCGGGGAGGGGAGAGCCTGGGATCGAACCCGTTCCTTTTATGAACTTCCTAAGCCTCTTTGGCCA
CTCGGCCAAGAGGTTGAGTTCCCTCCTTTTCTTTATTTGGTACTTATATATATCTTACTTAATCA
TTCATAAAACTTATATCTAAAACTTACCCTAAAATATAATCAAATCGAAACTATGAA
Done.