Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010578.1 Corchorus olitorius cultivar O-4 contig10610, 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: 4742
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Found at i:530 original size:27 final size:27
Alignment explanation
Indices: 488--561 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 27
478 AAGTGGACTT
* * *
488 AAAATGACCAACATGCCCCTGAATATG
1 AAAATGACTAAAATGCCCCTGAATATA
* * * *
515 CAAATGACTAAAATG-CCCTTAGTGTA
1 AAAATGACTAAAATGCCCCTGAATATA
541 AAAATGACTAAAATGCCCCTG
1 AAAATGACTAAAATGCCCCTG
562 GGTGACCCTA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.22
Consensus pattern (27 bp):
AAAATGACTAAAATGCCCCTGAATATA
Found at i:1004 original size:35 final size:35
Alignment explanation
Indices: 958--1279 Score: 454
Period size: 35 Copynumber: 9.2 Consensus size: 35
948 CGAGTTCATC
*
958 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATCT
1 TTGAAGATGCTACACCGAGTCATCTG-ATTCTAACT
* * **
993 TTGAAGATGCTACACCGAGTCATCCGAGATC-ATTT
1 TTGAAGATGCTACACCGAGTCATCTGA-TTCTAACT
* *
1028 TTGAAGATGCTACACCGAGTCATCTGAAGTC-ATCT
1 TTGAAGATGCTACACCGAGTCATCTG-ATTCTAACT
*
1063 TTAAAGATGCTACACCGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACCGAGTCATCTGATTCTAACT
* * *
1098 TTGAAGATGCTACGCTGAGTCATCCGATTCTAACT
1 TTGAAGATGCTACACCGAGTCATCTGATTCTAACT
1133 TTGAAGATGCTACACCGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACCGAGTCATCTGATTCTAACT
*
1168 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACCGAGTCATCTGATTCTAACT
*
1203 TTGAA-AGTGCTACACTGAGTCATCTGATTCTAACT
1 TTGAAGA-TGCTACACCGAGTCATCTGATTCTAACT
*
1238 TTGAAGATGCTACACTGAGTCATCTGATTCTAACT
1 TTGAAGATGCTACACCGAGTCATCTGATTCTAACT
1273 TTGAAGA
1 TTGAAGA
1280 AATTTCATTT
Statistics
Matches: 265, Mismatches: 17, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
34 5 0.02
35 258 0.97
36 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGATTCTAACT
Found at i:1543 original size:64 final size:64
Alignment explanation
Indices: 1461--1687 Score: 328
Period size: 64 Copynumber: 3.5 Consensus size: 64
1451 TCTGGTGTAT
* * * *
1461 CAAGATCGTCCTCTGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTAATTCTTGA
1 CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
* * *
1525 CAAGATCGTCTTCCGATCAATTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTTTTAA
1 CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
* * * *
1589 TAAGATCGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGA
1 CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
* * *
1653 CAAGATCGTTTTCCGATCAATTTTTGAAAACTCTT
1 CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTT
1688 TCTAGCAAAC
Statistics
Matches: 142, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 142 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (64 bp):
CAAGATCGTCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
Found at i:1750 original size:67 final size:67
Alignment explanation
Indices: 1675--1976 Score: 491
Period size: 67 Copynumber: 4.5 Consensus size: 67
1665 CCGATCAATT
* * * *
1675 TTTGAAAACTCTTTCTAGCAAACCGTCTTCCGATGTATTCTTTAATGAGATTGTCTTCCAATCAG
1 TTTGAAAACTCTTTCTAGCAAACCGTCTTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATCAA
1740 CA
66 CA
* *
1742 CTTGAAAACTCTTTCTAGCAAACCGTCCTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATCAA
1 TTTGAAAACTCTTTCTAGCAAACCGTCTTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATCAA
1807 CA
66 CA
*
1809 TTTGAAAACTGTTTCTAGCAAACCGTCTTCCGGTGTGTT-CTTAATGAGATTGTCTT-CAATCAA
1 TTTGAAAACTCTTTCTAGCAAACCGTCTTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATCAA
**
1872 TT
66 CA
*
1874 TTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATCAA
1 TTTGAAAACTCTTTCTAGCAAACCGTCTTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATCAA
1939 CA
66 CA
*
1941 TTTGAAAACTGTTTCTAGCAAACCGTCTTCCGGTGT
1 TTTGAAAACTCTTTCTAGCAAACCGTCTTCCGGTGT
1977 TCTTCTAAAA
Statistics
Matches: 216, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
65 44 0.20
66 34 0.16
67 138 0.64
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (67 bp):
TTTGAAAACTCTTTCTAGCAAACCGTCTTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATCAA
CA
Found at i:1911 original size:132 final size:134
Alignment explanation
Indices: 1675--1976 Score: 509
Period size: 132 Copynumber: 2.3 Consensus size: 134
1665 CCGATCAATT
* * *
1675 TTTGAAAACTCTTTCTAGCAAACCGTCTTCCGATGTATTCTTTAATGAGATTGTCTTCCAATCAG
1 TTTGAAAACTGTTTCTAGCAAACCGTCTTCCGGTGTATTCTTTAATGAGATTGTCTTCCAATCAA
1740 CACTTGAAAACTCTTTCTAGCAAACCGTCCTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATC
66 CACTTGAAAACTCTTTCTAGCAAACCGTCCTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATC
1805 AACA
131 AACA
*
1809 TTTGAAAACTGTTTCTAGCAAACCGTCTTCCGGTGTGTTC-TTAATGAGATTGTCTT-CAATCAA
1 TTTGAAAACTGTTTCTAGCAAACCGTCTTCCGGTGTATTCTTTAATGAGATTGTCTTCCAATCAA
*** * *
1872 TTTTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATC
66 CACTTGAAAACTCTTTCTAGCAAACCGTCCTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATC
1937 AACA
131 AACA
1941 TTTGAAAACTGTTTCTAGCAAACCGTCTTCCGGTGT
1 TTTGAAAACTGTTTCTAGCAAACCGTCTTCCGGTGT
1977 TCTTCTAAAA
Statistics
Matches: 159, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
132 106 0.67
133 16 0.10
134 37 0.23
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (134 bp):
TTTGAAAACTGTTTCTAGCAAACCGTCTTCCGGTGTATTCTTTAATGAGATTGTCTTCCAATCAA
CACTTGAAAACTCTTTCTAGCAAACCGTCCTCCGGTGTGTTCCTTAATGAGATTGTCTTCCAATC
AACA
Done.