Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015046.1 Corchorus olitorius cultivar O-4 contig15079, 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: 17096
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Found at i:728 original size:101 final size:101
Alignment explanation
Indices: 620--863 Score: 416
Period size: 101 Copynumber: 2.4 Consensus size: 101
610 ATTAAAGAGT
**
620 CGTCTTCCGCTTATCCTTTGAACTGTCTTTCAATTCAATCTCAAAAGGACCGTCTTCCGCTTATC
1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTCAAAAGGACCGTCTTCCGCTTATC
* * * *
685 CTTTGAATTGTCTTCCAATTCAGTCTTAAAAAGGAC
66 CTTTGAACTGTCTACCAATTCAATCTTAAAAAGAAC
*
721 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAGGACCGTCTTCCGCTTATC
1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTCAAAAGGACCGTCTTCCGCTTATC
786 CTTTGAACTGTCTACCAATTCAATCTTAAAAAGAAC
66 CTTTGAACTGTCTACCAATTCAATCTTAAAAAGAAC
*
822 CATCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTC
1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTC
864 GAGAAAACCA
Statistics
Matches: 134, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 134 1.00
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.36
Consensus pattern (101 bp):
CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTCAAAAGGACCGTCTTCCGCTTATC
CTTTGAACTGTCTACCAATTCAATCTTAAAAAGAAC
Found at i:738 original size:51 final size:51
Alignment explanation
Indices: 620--862 Score: 400
Period size: 51 Copynumber: 4.8 Consensus size: 51
610 ATTAAAGAGT
** *
620 CGTCTTCCGCTTATCCTTTGAACTGTCTTTCAATTCAATC-TCAAAAGGAC
1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAAGGAC
* * *
670 CGTCTTCCGCTTATCCTTTGAATTGTCTTCCAATTCAGTCTTAAAAAGGAC
1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAAGGAC
721 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTT-AAAAGGAC
1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAAGGAC
*
771 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAAGAAC
1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAAGGAC
*
822 CATCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
1 CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCT
863 CGAGAAAACC
Statistics
Matches: 182, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
50 87 0.48
51 95 0.52
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.36
Consensus pattern (51 bp):
CGTCTTCCGCTTATCCTTTGAACTGTCTACCAATTCAATCTTAAAAAGGAC
Found at i:1287 original size:64 final size:64
Alignment explanation
Indices: 1092--1705 Score: 798
Period size: 64 Copynumber: 9.6 Consensus size: 64
1082 CCGGTGCATC
* * * * * * * * *
1092 TCTTAACAAGATCGTCTTCCGACCCACTTCTGAAACCTTTTCGAGAAACTAACTTCTGGTGTGCT
1 TCTTGACAAGATCGTCTTCCGATCAACTTATGAAA-ATTTTTGAGAAACCATCTTCTGGTGTACT
* * * * * * * * * *
1157 TTTTAATAAGATCGTATTCCGACCGACTTTTGAAAA-TTTTGAGAATCCATCTTCTGGCGTAAT
1 TCTTGACAAGATCGTCTTCCGATCAACTTATGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
*
1220 TCTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTATGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
* ** * * *
1284 TCTTGACAAGATCATCTTCCGATCAACTCCTGAAAACTGTTGAGAAACCATCTTCTGATGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTATGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
* * * * * * *
1348 TTTTGACAAGATCATCTTCCGATCCACTTCTGAAAACTGTTGAGAAAACATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTATGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
*
1412 TCTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTATGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
* *
1476 TCTTGACAAGATCGTCTTCCGATCAACTTAGGGAAATTTTTGAGAAACCATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTATGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
** * * *
1540 TCTTGACAAGATCGTCTTCCGATCAACTCCTGAAAACTGTTGAGAAAACATCTTCTGGTGTACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTATGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
* * *
1604 TCTTGACAAGATCGTCTTTCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTATACT
1 TCTTGACAAGATCGTCTTCCGATCAACTTATGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
**
1668 TCTTGACAAGATCGTCTTCCGATCAACTCCTGAAAATT
1 TCTTGACAAGATCGTCTTCCGATCAACTTATGAAAATT
1706 CTTTCTAGCA
Statistics
Matches: 484, Mismatches: 64, Indels: 3
0.88 0.12 0.01
Matches are distributed among these distances:
63 48 0.10
64 406 0.84
65 30 0.06
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (64 bp):
TCTTGACAAGATCGTCTTCCGATCAACTTATGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
Found at i:1425 original size:192 final size:192
Alignment explanation
Indices: 1092--1703 Score: 913
Period size: 192 Copynumber: 3.2 Consensus size: 192
1082 CCGGTGCATC
* * * * * * * *
1092 TCTTAACAAGATCGTCTTCCGACCCACTTCTGAAACCTTTTCGAGAAACTAACTTCTGGTGTGCT
1 TCTTGACAAGATCGTCTTCCGATCAACTCCTGAAAACTTTT-GAGAAACCATCTTCTGGTGTACT
* * * * * ** * *
1157 TTTTAATAAGATCGTATTCCGA-CCGACTTTTGAAAA-TTTTGAGAATCCATCTTCTGGCGTAAT
65 TTTTGACAAGATCGTCTTCCGATCC-ACTTCTGAAAACTGTTGAGAAAACATCTTCTGGTGTACT
1220 TCTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
129 TCTTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
* * *
1284 TCTTGACAAGATCATCTTCCGATCAACTCCTGAAAACTGTTGAGAAACCATCTTCTGATGTACTT
1 TCTTGACAAGATCGTCTTCCGATCAACTCCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTT
*
1349 TTTGACAAGATCATCTTCCGATCCACTTCTGAAAACTGTTGAGAAAACATCTTCTGGTGTACTTC
66 TTTGACAAGATCGTCTTCCGATCCACTTCTGAAAACTGTTGAGAAAACATCTTCTGGTGTACTTC
1414 TTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
131 TTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
*** * *
1476 TCTTGACAAGATCGTCTTCCGATCAACTTAGGGAAATTTTTGAGAAACCATCTTCTGGTGTACTT
1 TCTTGACAAGATCGTCTTCCGATCAACTCCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTT
* * *
1541 CTTGACAAGATCGTCTTCCGATCAACTCCTGAAAACTGTTGAGAAAACATCTTCTGGTGTACTTC
66 TTTGACAAGATCGTCTTCCGATCCACTTCTGAAAACTGTTGAGAAAACATCTTCTGGTGTACTTC
* *
1606 TTGACAAGATCGTCTTTCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTATACT
131 TTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
1668 TCTTGACAAGATCGTCTTCCGATCAACTCCTGAAAA
1 TCTTGACAAGATCGTCTTCCGATCAACTCCTGAAAA
1704 TTCTTTCTAG
Statistics
Matches: 379, Mismatches: 39, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
191 47 0.12
192 332 0.88
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (192 bp):
TCTTGACAAGATCGTCTTCCGATCAACTCCTGAAAACTTTTGAGAAACCATCTTCTGGTGTACTT
TTTGACAAGATCGTCTTCCGATCCACTTCTGAAAACTGTTGAGAAAACATCTTCTGGTGTACTTC
TTGACAAGATCGTCTTCCGATCAACTTAGGAAAATTTTTGAGAAACCATCTTCTGGTGTACT
Found at i:1770 original size:55 final size:55
Alignment explanation
Indices: 1676--1837 Score: 245
Period size: 55 Copynumber: 2.9 Consensus size: 55
1666 CTTCTTGACA
* * * *
1676 AGATCGTCTTCCGATCAAC-TCCTGAAAATTCTTTCTAGCAAACCGTCTTCCGATG
1 AGATTGTCTTCCAATCAACAT-TTGAAAATCCTTTCTAGCAAACCGTCTTCCGATG
* *
1731 AGATTGTCTTCCAATCAACATTTGAAAATCCTTTTTAGCAAACCGTATTCCGATG
1 AGATTGTCTTCCAATCAACATTTGAAAATCCTTTCTAGCAAACCGTCTTCCGATG
*
1786 AGATTGTCTTCCAACCAACATTTGAAAATCCTTTCTAGCAAACCGTCTTCCG
1 AGATTGTCTTCCAATCAACATTTGAAAATCCTTTCTAGCAAACCGTCTTCCG
1838 GTGTTCTCCT
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
55 96 0.99
56 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (55 bp):
AGATTGTCTTCCAATCAACATTTGAAAATCCTTTCTAGCAAACCGTCTTCCGATG
Found at i:2115 original size:67 final size:67
Alignment explanation
Indices: 1782--2112 Score: 500
Period size: 67 Copynumber: 4.9 Consensus size: 67
1772 ACCGTATTCC
* * * *
1782 GATGAGATTGTCTTCCAACCAACATTTGAAAATCCTTTCTAGCAAACCGTCTTCCGGTGTTCTCC
1 GATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAGACCGTCTTCCGGTGTACTCC
1847 TT
66 TT
* *
1849 AATGAGATTGTCTTCCAATCAACCTTTGAAAATTCTTTCTAGCAGACCGTCTTCCGGTGTACTCC
1 GATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAGACCGTCTTCCGGTGTACTCC
1914 TT
66 TT
* * * *
1916 AATGAGATTGTCTTCCAATCAACCTTTGAAAATTCTTTCTAGCAGACAGTCTTCCGGTGTACCCC
1 GATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAGACCGTCTTCCGGTGTACTCC
1981 TT
66 TT
* *
1983 GATGAGATTGTCCTCCAATCAACATTTGAAAATTCTTTCTAGCAGACCGTCTTCCGGTGTACTTC
1 GATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAGACCGTCTTCCGGTGTACTCC
2048 TT
66 TT
* * * * * *
2050 GATGAGATTGCCTTCCAATCATCTTTTGAAAATTCTTTCTATCAAACCATCTTCCGGTGTACT
1 GATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAGACCGTCTTCCGGTGTACT
2113 TCTAAAATCC
Statistics
Matches: 243, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 243 1.00
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.36
Consensus pattern (67 bp):
GATGAGATTGTCTTCCAATCAACATTTGAAAATTCTTTCTAGCAGACCGTCTTCCGGTGTACTCC
TT
Found at i:10941 original size:13 final size:13
Alignment explanation
Indices: 10923--10947 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10913 ATGGTAACAA
10923 CAAAAATCATCAC
1 CAAAAATCATCAC
10936 CAAAAATCATCA
1 CAAAAATCATCA
10948 TCCATGCCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (13 bp):
CAAAAATCATCAC
Done.