Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010331.1 Corchorus olitorius cultivar O-4 contig10363, 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: 11343
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1136 original size:21 final size:24
Alignment explanation
Indices: 1107--1157 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
1097 TTTTGAACTC
1107 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
1130 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
1153 ATTAT
1 ATTAT
1158 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:1152 original size:25 final size:25
Alignment explanation
Indices: 1107--1155 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1097 TTTTGAACTC
*
1107 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
1132 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
1156 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:1636 original size:258 final size:254
Alignment explanation
Indices: 1175--1692 Score: 797
Period size: 258 Copynumber: 2.0 Consensus size: 254
1165 ATAGTAAAGT
1175 TTAATTAACATATATATTTTTATCAAAATAATTAATTTACACATCTAATGAATATTTTAACTAGT
1 TTAATTAACATATATATTTTTATCAAAATAATTAATTTACACATCTAATGAATATTTTAACTAGT
*
1240 CAATCTAATTAAAAAAAATAAAATATTCTAATTATTTAAGTATACAGGCCGGGCTCGGGCTGGAC
66 CAATCTAATTAAAAAAAATAAAATATTCTAATTATTTAAGTATACAGGCCGGGCTCGGGCCGGAC
* *
1305 TTTTATGGTTAAGACCATACCCGAGCCCGGCGCATTTTGTAAGTGGGCCTTAAAATTTTATCCAA
131 TTTTATGGTTAAGACCA-A--C-AGCCCGGCCCATTTTATAAGTGGGCCTTAAAATTTTATCCAA
* **
1370 ATCCGTCCAATGGGCTTCAAATTTTTGTCCAAACCCTCCCAAATATCAGACGGGCTTACGGGC
192 ACCCGTCCAATGAACTTCAAATTTTTGTCCAAACCCTCCCAAATATCAGACGGGCTTACGGGC
*
1433 TTAATTAACATATATATTTTTATCAAAATAATTCATTTACACATCTAATGAATATTTTAACTAGT
1 TTAATTAACATATATATTTTTATCAAAATAATTAATTTACACATCTAATGAATATTTTAACTAGT
*
1498 CAATCTAATTAAAAACAAATAAAATATTCTAATTATTTAAGTATACGGAACAGGTCGGGCTCGGG
66 CAATCTAATTAAAAA-AAATAAAATATTCTAATTATTTAAGTAT-----ACAGGCCGGGCTCGGG
* *
1563 CCGGGCTTTTATGGTTAAGACC-A-AGCCCGGCCCATTTTATAAGTGGGCCTTAAAATTTTGTCC
125 CCGGACTTTTATGGTTAAGACCAACAGCCCGGCCCATTTTATAAGTGGGCCTTAAAATTTTATCC
* * * * *
1626 AAGCCCGTCCAATGAACTTCAATTTTTTGTCCAAGCCCTCCCAAATATCGGGCGGGCTTACGGGC
190 AAACCCGTCCAATGAACTTCAAATTTTTGTCCAAACCCTCCCAAATATCAGACGGGCTTACGGGC
1691 TT
1 TT
1693 GGACGGGTAG
Statistics
Matches: 239, Mismatches: 15, Indels: 12
0.90 0.06 0.05
Matches are distributed among these distances:
258 175 0.73
259 28 0.12
262 1 0.00
264 35 0.15
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (254 bp):
TTAATTAACATATATATTTTTATCAAAATAATTAATTTACACATCTAATGAATATTTTAACTAGT
CAATCTAATTAAAAAAAATAAAATATTCTAATTATTTAAGTATACAGGCCGGGCTCGGGCCGGAC
TTTTATGGTTAAGACCAACAGCCCGGCCCATTTTATAAGTGGGCCTTAAAATTTTATCCAAACCC
GTCCAATGAACTTCAAATTTTTGTCCAAACCCTCCCAAATATCAGACGGGCTTACGGGC
Found at i:1976 original size:14 final size:14
Alignment explanation
Indices: 1957--1984 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1947 GTTGTTGAGG
1957 ATAAATGATAAAGC
1 ATAAATGATAAAGC
1971 ATAAATGATAAAGC
1 ATAAATGATAAAGC
1985 GGGGGATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
ATAAATGATAAAGC
Found at i:2464 original size:41 final size:41
Alignment explanation
Indices: 2407--2492 Score: 172
Period size: 41 Copynumber: 2.1 Consensus size: 41
2397 TACATCCATA
2407 CTTTAATATATAGATATAGATATAAATATTATGTACCTGTT
1 CTTTAATATATAGATATAGATATAAATATTATGTACCTGTT
2448 CTTTAATATATAGATATAGATATAAATATTATGTACCTGTT
1 CTTTAATATATAGATATAGATATAAATATTATGTACCTGTT
2489 CTTT
1 CTTT
2493 GATGTAGGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.45
Consensus pattern (41 bp):
CTTTAATATATAGATATAGATATAAATATTATGTACCTGTT
Found at i:4184 original size:2 final size:2
Alignment explanation
Indices: 4177--4205 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4167 CTAAAATCGA
4177 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4206 TAATTAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5213 original size:5 final size:5
Alignment explanation
Indices: 5203--5231 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
5193 CTTTTAAAGT
5203 TATAA TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATAA TATA
5232 TTAGTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:7253 original size:26 final size:28
Alignment explanation
Indices: 7205--7260 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
7195 AATTAGTAAA
*
7205 ATGATAAAAATAAAATAGGTATAAGGAT
1 ATGATAAAAATAAAATAGATATAAGGAT
*
7233 ATGATGAAAA-AAAA-AGATATAAGGAT
1 ATGATAAAAATAAAATAGATATAAGGAT
7259 AT
1 AT
7261 CAGATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 13 0.50
27 4 0.15
28 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (28 bp):
ATGATAAAAATAAAATAGATATAAGGAT
Found at i:8141 original size:124 final size:124
Alignment explanation
Indices: 7940--8192 Score: 371
Period size: 124 Copynumber: 2.0 Consensus size: 124
7930 CATTGTTTAA
*
7940 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATAAT
**
8005 TTTTACCATTTTACTATTTTAATTAAAAAAACGTATATATATTAGAATTTTTTAAATAT
66 TTTTATAATTTTACTATTTTAATTAAAAAAACGTATATATATTAGAATTTTTTAAATAT
*
8064 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATA--
* * *
8129 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTTTATATATTAGAATTTTTTAAA
64 -A--TT-TTTATA--ATTTTACTATTTTAATTAAAAAAACGTATATATATTAGAATTTTTTAAA
8193 AATATTTCTT
Statistics
Matches: 114, Mismatches: 7, Indels: 8
0.88 0.05 0.06
Matches are distributed among these distances:
124 61 0.54
127 1 0.01
129 2 0.02
130 3 0.03
132 47 0.41
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (124 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATAAT
TTTTATAATTTTACTATTTTAATTAAAAAAACGTATATATATTAGAATTTTTTAAATAT
Found at i:8187 original size:132 final size:124
Alignment explanation
Indices: 7940--8192 Score: 398
Period size: 132 Copynumber: 2.0 Consensus size: 124
7930 CATTGTTTAA
*
7940 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATAAT
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATAAT
8005 TTTTACCATTTTACTATTTTAATTAAAAAAACGTATATATATTAGAATTTTTTAAATAT
66 TTTTACCATTTTACTATTTTAATTAAAAAAACGTATATATATTAGAATTTTTTAAATAT
8064 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATAT-C--AT---
* * *
8129 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTTTATATATTAGAATTTTTTAAA
60 TA--TAATTTTTACCATTTTACTATTTTAATTAAAAAAACGTATATATATTAGAATTTTTTAAA
8193 AATATTTCTT
Statistics
Matches: 117, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
124 55 0.47
125 1 0.01
127 2 0.02
130 2 0.02
132 57 0.49
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (124 bp):
ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCATTATAAT
TTTTACCATTTTACTATTTTAATTAAAAAAACGTATATATATTAGAATTTTTTAAATAT
Done.