Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014437.1 Corchorus olitorius cultivar O-4 contig14470, 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: 11889
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--43 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
* *
1 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT TT 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
43 A
1 A
44 AATTTGGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1541 original size:24 final size:25
Alignment explanation
Indices: 1496--1544 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
1486 CCATGAATAT
*
1496 CCATCAAAGGGTATACCCTAAACAC
1 CCATCAAAGGGTATACCATAAACAC
*
1521 CCATCAAA-GTTATACCATAAACAC
1 CCATCAAAGGGTATACCATAAACAC
1545 ACCAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.43, C:0.31, G:0.08, T:0.18
Consensus pattern (25 bp):
CCATCAAAGGGTATACCATAAACAC
Found at i:1554 original size:26 final size:24
Alignment explanation
Indices: 1507--1554 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
1497 CATCAAAGGG
* *
1507 TATACCCTAAACACCCATCAAAGT
1 TATACCATAAACACCCACCAAAGT
1531 TATACCATAAACACACCAACCAAA
1 TATACCATAAACAC-CC-ACCAAA
1555 TATCATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 2 0.10
26 5 0.25
ACGTcount: A:0.48, C:0.33, G:0.02, T:0.17
Consensus pattern (24 bp):
TATACCATAAACACCCACCAAAGT
Found at i:8503 original size:3 final size:3
Alignment explanation
Indices: 8495--8520 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8485 GCCCCTTACA
8495 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
8521 AAGGTGCGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:9552 original size:36 final size:36
Alignment explanation
Indices: 9505--9640 Score: 229
Period size: 36 Copynumber: 3.8 Consensus size: 36
9495 TTGCGCCCTG
9505 CTCCTGGGGAGGAAGAAGTAAGGCGCACCCTATTAT
1 CTCCTGGGGAGGAAGAAGTAAGGCGCACCCTATTAT
9541 CTCCTGGGGAGGAAGAAGTAAGGCGCACCCTATTAT
1 CTCCTGGGGAGGAAGAAGTAAGGCGCACCCTATTAT
9577 C-CCTGGGGAGGAAGAAGTAAGGCGCACCCTATTAT
1 CTCCTGGGGAGGAAGAAGTAAGGCGCACCCTATTAT
* * **
9612 CCCCTGGAGAGGAAGAAGTGTGGCGCACC
1 CTCCTGGGGAGGAAGAAGTAAGGCGCACC
9641 TCAGGTTCAT
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
35 35 0.36
36 61 0.64
ACGTcount: A:0.27, C:0.24, G:0.32, T:0.17
Consensus pattern (36 bp):
CTCCTGGGGAGGAAGAAGTAAGGCGCACCCTATTAT
Found at i:9587 original size:71 final size:71
Alignment explanation
Indices: 9507--9640 Score: 232
Period size: 71 Copynumber: 1.9 Consensus size: 71
9497 GCGCCCTGCT
* *
9507 CCTGGGGAGGAAGAAGTAAGGCGCACCCTATTATCTCCTGGGGAGGAAGAAGTAAGGCGCACCCT
1 CCTGGGGAGGAAGAAGTAAGGCGCACCCTATTATCCCCTGGAGAGGAAGAAGTAAGGCGCACCCT
9572 ATTATC
66 ATTATC
**
9578 CCTGGGGAGGAAGAAGTAAGGCGCACCCTATTATCCCCTGGAGAGGAAGAAGTGTGGCGCACC
1 CCTGGGGAGGAAGAAGTAAGGCGCACCCTATTATCCCCTGGAGAGGAAGAAGTAAGGCGCACC
9641 TCAGGTTCAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.28, C:0.23, G:0.33, T:0.16
Consensus pattern (71 bp):
CCTGGGGAGGAAGAAGTAAGGCGCACCCTATTATCCCCTGGAGAGGAAGAAGTAAGGCGCACCCT
ATTATC
Found at i:9843 original size:12 final size:12
Alignment explanation
Indices: 9818--9851 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9808 ACTCCTACTC
*
9818 TCACCCTCATTT
1 TCACCCTCACTT
*
9830 TCACCGTCACTT
1 TCACCCTCACTT
9842 TCACCCTCAC
1 TCACCCTCAC
9852 CCTCACTCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.47, G:0.03, T:0.32
Consensus pattern (12 bp):
TCACCCTCACTT
Found at i:10069 original size:54 final size:56
Alignment explanation
Indices: 9984--10093 Score: 161
Period size: 54 Copynumber: 2.0 Consensus size: 56
9974 TCATGACGAG
9984 GTGAGGCAGCACCACTAGCATCATTGGAGGGAAGTGAAGTGATCTTTGTGGTAGGAA
1 GTGAGGCAGCACCAC-AGCATCATTGGAGGGAAGTGAAGTGATCTTTGTGGTAGGAA
* ** *
10041 GTGAGGCAGCATCA-A-CATCATTGGAGGGAAGTGGGGTGGTCTTTGTGGTAGGA
1 GTGAGGCAGCACCACAGCATCATTGGAGGGAAGTGAAGTGATCTTTGTGGTAGGA
10094 TCCCCGATGA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
54 35 0.71
55 1 0.02
57 13 0.27
ACGTcount: A:0.25, C:0.13, G:0.38, T:0.24
Consensus pattern (56 bp):
GTGAGGCAGCACCACAGCATCATTGGAGGGAAGTGAAGTGATCTTTGTGGTAGGAA
Done.