Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013078.1 Corchorus olitorius cultivar O-4 contig13111, 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: 26464
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Found at i:1594 original size:21 final size:21
Alignment explanation
Indices: 1554--1594 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1544 ATCGATAAAA
1554 AAAGAAAACCTAATAAATATAG
1 AAAGAAAA-CTAATAAATATAG
1576 AAAGAAAA-TAATCAAATAT
1 AAAGAAAACTAAT-AAATAT
1595 CCAACCGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.20
Consensus pattern (21 bp):
AAAGAAAACTAATAAATATAG
Found at i:2080 original size:13 final size:13
Alignment explanation
Indices: 2062--2096 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
2052 GATGTTTATA
2062 GCTTTGGGATTGT
1 GCTTTGGGATTGT
2075 GCTTTGGGATTGT
1 GCTTTGGGATTGT
2088 GCTTTGGGA
1 GCTTTGGGA
2097 GTTGATGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.09, C:0.09, G:0.40, T:0.43
Consensus pattern (13 bp):
GCTTTGGGATTGT
Found at i:11110 original size:162 final size:162
Alignment explanation
Indices: 10837--11277 Score: 645
Period size: 162 Copynumber: 2.7 Consensus size: 162
10827 ACGGACACCT
* *
10837 TTCTTAGAACGACCGCACTGGATCAATTTGGAGATCAACTCTGATCATCAAAACTTCTTGCCACG
1 TTCTTGGAACGACCGCACTGGATCAATTTGGAGATCAACTCTGACCATCAAAACTTCTTGCCACG
* *
10902 ACCGCACTGGATCAATTGGAGATCAACTCTGATCATCGAAAACTTATTGGAAAGACCACACTGGA
66 ACCGCAATGGATCAATTGGAGATCAACTTTGATCATCGAAAACTTATTGGAAAGACCACACTGGA
* *
10967 TCATCTGGAGATCAACTCTGATCCTTGAAAAC
131 TCATCTGGAAATCAACTCTGATCATTGAAAAC
* * *
10999 TTCTTGGAACGACCGCACTGGATCAATTTGAAGATCAACTCTAACCATCAAAACTTTTTGCCACG
1 TTCTTGGAACGACCGCACTGGATCAATTTGGAGATCAACTCTGACCATCAAAACTTCTTGCCACG
*
11064 ACCGCAATGGATCAATTGGAGATCAACTTTGATCATCAAAAACTTATTGGAAAGACCACACTGGA
66 ACCGCAATGGATCAATTGGAGATCAACTTTGATCATCGAAAACTTATTGGAAAGACCACACTGGA
11129 TCATCTGGAAATCAACTCTGATCATTGAAAAC
131 TCATCTGGAAATCAACTCTGATCATTGAAAAC
** * ** *
11161 TTCTTGGAACGACCGCACTGGATC-ACCTGGAGATCAACTCTGACCAATGAAAACTTCTTGGAAT
1 TTCTTGGAACGACCGCACTGGATCAATTTGGAGATCAACTCTGACC-ATCAAAACTTCTTGCCAC
* * * * *
11225 GACCGCATTGGATC-TTCTAGG-GATCAACTTTGACCATTGAAAACTTCTTGGAA
65 GACCGCAATGGATCAAT-T-GGAGATCAACTTTGATCATCGAAAACTTATTGGAA
11278 TGACAACTGG
Statistics
Matches: 251, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
161 18 0.07
162 231 0.92
163 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (162 bp):
TTCTTGGAACGACCGCACTGGATCAATTTGGAGATCAACTCTGACCATCAAAACTTCTTGCCACG
ACCGCAATGGATCAATTGGAGATCAACTTTGATCATCGAAAACTTATTGGAAAGACCACACTGGA
TCATCTGGAAATCAACTCTGATCATTGAAAAC
Found at i:11281 original size:54 final size:54
Alignment explanation
Indices: 10837--11277 Score: 480
Period size: 54 Copynumber: 8.2 Consensus size: 54
10827 ACGGACACCT
* * * *
10837 TTCTTAGAACGACCGCACTGGATCAATTTGGAGATCAACTCTGATCA-TCAAAAC
1 TTCTTGGAACGACCGCACTGGATC-ATCTGGAGATCAACTCTGACCATTGAAAAC
** * *
10891 TTCTTGCCACGACCGCACTGGATCAAT-TGGAGATCAACTCTGATCATCGAAAAC
1 TTCTTGGAACGACCGCACTGGATC-ATCTGGAGATCAACTCTGACCATTGAAAAC
* * *
10945 TTATTGGAAAGACCACACTGGATCATCTGGAGATCAACTCTGATCC-TTGAAAAC
1 TTCTTGGAACGACCGCACTGGATCATCTGGAGATCAACTCTGA-CCATTGAAAAC
* * * *
10999 TTCTTGGAACGACCGCACTGGATCAATTTGAAGATCAACTCTAACCA-TCAAAAC
1 TTCTTGGAACGACCGCACTGGATC-ATCTGGAGATCAACTCTGACCATTGAAAAC
* ** * * * **
11053 TTTTTGCCACGACCGCAATGGATCAAT-TGGAGATCAACTTTGATCATCAAAAAC
1 TTCTTGGAACGACCGCACTGGATC-ATCTGGAGATCAACTCTGACCATTGAAAAC
* * * * *
11107 TTATTGGAAAGACCACACTGGATCATCTGGAAATCAACTCTGATCATTGAAAAC
1 TTCTTGGAACGACCGCACTGGATCATCTGGAGATCAACTCTGACCATTGAAAAC
* *
11161 TTCTTGGAACGACCGCACTGGATCACCTGGAGATCAACTCTGACCAATGAAAAC
1 TTCTTGGAACGACCGCACTGGATCATCTGGAGATCAACTCTGACCATTGAAAAC
* * * *
11215 TTCTTGGAATGACCGCATTGGATCTTCTAGG-GATCAACTTTGACCATTGAAAAC
1 TTCTTGGAACGACCGCACTGGATCATCT-GGAGATCAACTCTGACCATTGAAAAC
11269 TTCTTGGAA
1 TTCTTGGAA
11278 TGACAACTGG
Statistics
Matches: 327, Mismatches: 52, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
53 38 0.12
54 270 0.83
55 19 0.06
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (54 bp):
TTCTTGGAACGACCGCACTGGATCATCTGGAGATCAACTCTGACCATTGAAAAC
Done.