Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007441.1 Corchorus olitorius cultivar O-4 contig07466, 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: 4415
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Found at i:891 original size:20 final size:20
Alignment explanation
Indices: 866--910 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
856 TCAGCGGACA
*
866 CTTAAGTCATTGCGTTAGAT
1 CTTAAGTCATTGCATTAGAT
*
886 CTTAAGTCGTTGCATTAGAT
1 CTTAAGTCATTGCATTAGAT
*
906 ATTAA
1 CTTAA
911 ACAATGGAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (20 bp):
CTTAAGTCATTGCATTAGAT
Found at i:1583 original size:17 final size:18
Alignment explanation
Indices: 1555--1589 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1545 TATCTATACA
1555 CAAACAAAAAAAAATCTT
1 CAAACAAAAAAAAATCTT
1573 CAAAC-AAAAAAAATCTT
1 CAAACAAAAAAAAATCTT
1590 TGATCACCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (18 bp):
CAAACAAAAAAAAATCTT
Found at i:1659 original size:48 final size:49
Alignment explanation
Indices: 1566--1661 Score: 133
Period size: 49 Copynumber: 2.0 Consensus size: 49
1556 AAACAAAAAA
1566 AAATCTTCAAACAAAAAAAATCTTTGATCACCCATTAAAACTTAATAAT
1 AAATCTTCAAACAAAAAAAATCTTTGATCACCCATTAAAACTTAATAAT
* * * *
1615 AAATCTTCGAAA-ACAAAAAATCTTTGATTATCGATT-AAACTTAATAA
1 AAATCTTC-AAACAAAAAAAATCTTTGATCACCCATTAAAACTTAATAA
1662 CAATCTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
48 11 0.26
49 28 0.67
50 3 0.07
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (49 bp):
AAATCTTCAAACAAAAAAAATCTTTGATCACCCATTAAAACTTAATAAT
Found at i:1669 original size:30 final size:31
Alignment explanation
Indices: 1633--1695 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
1623 GAAAACAAAA
*
1633 AATCTTTGATTATCGATT-AAACTTAATAAC
1 AATCTTTGATTACCGATTAAAACTTAATAAC
*
1663 AATCTTTGATTACCGATTAAAACTTAGTAAC
1 AATCTTTGATTACCGATTAAAACTTAATAAC
1694 AA
1 AA
1696 AGATTAGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 17 0.57
31 13 0.43
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (31 bp):
AATCTTTGATTACCGATTAAAACTTAATAAC
Found at i:2000 original size:108 final size:106
Alignment explanation
Indices: 1869--2083 Score: 378
Period size: 108 Copynumber: 2.0 Consensus size: 106
1859 TAACAGAAAC
*
1869 AAAAAGCATTTTGAAAG-AAAAAAAATCACCAAAGCACTATAATATATTCCGATTAAAAGAAAGA
1 AAAAAGCATTTTGAAAGAAAAAAAAATCACCAAAACACTAT-A-ATATTCCGATTAAAAGAAAGA
1933 ATAAATAATAACTAAATCTGAAAGCAAGAACATGTTAACCTAAA
64 ATAAATAATAACTAAATCTGAAAGCAAGAACATGTTAA-CTAAA
1977 AAAAAGCATTTTGAAAGAAAAAAAAAATCACCAAAACACTATAATATTCCGATTAAAAGAAAGAA
1 AAAAAGCATTTTGAAAG-AAAAAAAAATCACCAAAACACTATAATATTCCGATTAAAAGAAAGAA
2042 TAAATAATAACTAAATCTGAAAGCAAGAACATGTTAACTAAA
65 TAAATAATAACTAAATCTGAAAGCAAGAACATGTTAACTAAA
2084 GGTACATGTT
Statistics
Matches: 104, Mismatches: 1, Indels: 5
0.95 0.01 0.05
Matches are distributed among these distances:
107 5 0.05
108 76 0.73
109 1 0.01
110 22 0.21
ACGTcount: A:0.57, C:0.13, G:0.10, T:0.21
Consensus pattern (106 bp):
AAAAAGCATTTTGAAAGAAAAAAAAATCACCAAAACACTATAATATTCCGATTAAAAGAAAGAAT
AAATAATAACTAAATCTGAAAGCAAGAACATGTTAACTAAA
Found at i:2343 original size:57 final size:57
Alignment explanation
Indices: 2255--2369 Score: 212
Period size: 57 Copynumber: 2.0 Consensus size: 57
2245 TAAACCTGAG
*
2255 CCATGATCACCATGTAAGATTACTTTAAAAAGCATAAAGTTGACTCCTTTGTTTCTT
1 CCATGATCACCATGTAAGATTACTTTAAAAAGCACAAAGTTGACTCCTTTGTTTCTT
*
2312 CCATGATCACCATGTAAGATTACTTTAAAAAGCCCAAAGTTGACTCCTTTGTTTCTT
1 CCATGATCACCATGTAAGATTACTTTAAAAAGCACAAAGTTGACTCCTTTGTTTCTT
2369 C
1 C
2370 ATTTCATATC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (57 bp):
CCATGATCACCATGTAAGATTACTTTAAAAAGCACAAAGTTGACTCCTTTGTTTCTT
Found at i:2813 original size:2 final size:2
Alignment explanation
Indices: 2806--2835 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2796 TGTTAATTAC
2806 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
2836 ACAAGGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3247 original size:42 final size:43
Alignment explanation
Indices: 3188--3288 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 43
3178 ATTCGTATAT
* *
3188 ATAAAGCTAA-ATATCTA-CTCCATCTCTAGGTAATTCATCAAA
1 ATAAAGCTAATAT-TCTACCTCCATCTCTAGATAATTAATCAAA
*
3230 ATAAAACTAATATTCTACTCCTCCATCTCTAGATAATTAATCAAA
1 ATAAAGCTAATATTCTA--CCTCCATCTCTAGATAATTAATCAAA
3275 ATAAAGCTAATATT
1 ATAAAGCTAATATT
3289 AATTTTTGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
42 13 0.25
43 2 0.04
45 36 0.71
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (43 bp):
ATAAAGCTAATATTCTACCTCCATCTCTAGATAATTAATCAAA
Done.