Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023867.1 Corchorus olitorius cultivar O-4 contig23900, 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: 65259
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8 original size:2 final size:2
Alignment explanation
Indices: 2--43 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1 C
2 AT AT AT AT AT AT 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 AT AT AT AT AT AT
44 TAAGGGTTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6271 original size:17 final size:16
Alignment explanation
Indices: 6217--6267 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
6207 GATCATCCCC
*
6217 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
6234 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
6251 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
6267 A
1 A
6268 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:23575 original size:9 final size:9
Alignment explanation
Indices: 23561--23585 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
23551 CAAAGCCATT
23561 TCCTTCTTC
1 TCCTTCTTC
23570 TCCTTCTTC
1 TCCTTCTTC
23579 TCCTTCT
1 TCCTTCT
23586 CCTCTTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (9 bp):
TCCTTCTTC
Found at i:37997 original size:7 final size:7
Alignment explanation
Indices: 37986--38033 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
37976 TTTTAAAAAT
*
37986 ATAATTT
1 ATAATTA
37993 ATAATTA
1 ATAATTA
*
38000 ATAAATA
1 ATAATTA
38007 ATAATTA
1 ATAATTA
38014 ATAATTAA
1 ATAATT-A
*
38022 ATAACTA
1 ATAATTA
38029 ATAAT
1 ATAAT
38034 AATTAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
7 29 0.83
8 6 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAATTA
Found at i:38011 original size:21 final size:21
Alignment explanation
Indices: 37978--38033 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
37968 GCTTCATTTT
*
37978 TTAA-AAAT-ATAATTTATAA
1 TTAATAAATAATAATTAATAA
37997 TTAATAAATAATAATTAATAA
1 TTAATAAATAATAATTAATAA
*
38018 TTAAATAACTAATAAT
1 TT-AATAAATAATAAT
38034 AATTAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 12 0.38
22 12 0.38
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAATAAATAATAATTAATAA
Found at i:38050 original size:18 final size:19
Alignment explanation
Indices: 37978--38048 Score: 81
Period size: 18 Copynumber: 3.7 Consensus size: 19
37968 GCTTCATTTT
* *
37978 TTAAAAATATAATTTATAA
1 TTAAAAAAATAATTAATAA
37997 TTAATAAATAATAATTAATAA
1 TTAA-AAA-AATAATTAATAA
* *
38018 TTAAATAACTAA-TAATAA
1 TTAAAAAAATAATTAATAA
38036 TTAAAAAAATAAT
1 TTAAAAAAATAAT
38049 AAAAAAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
18 16 0.37
19 8 0.19
20 5 0.12
21 14 0.33
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (19 bp):
TTAAAAAAATAATTAATAA
Found at i:61174 original size:3 final size:3
Alignment explanation
Indices: 61159--61197 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
61149 GTTGCTTTCT
* * *
61159 TTA TTA TTG TTA TTA TTA TTT TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
61198 CAATTCCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:65227 original size:2 final size:2
Alignment explanation
Indices: 65222--65259 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
65212 TCTCTCTCTC
65222 TA TA TA TA TA 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 TA TA TA TA TA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.