Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019150.1 Corchorus olitorius cultivar O-4 contig19183, 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: 13887
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Found at i:844 original size:31 final size:31
Alignment explanation
Indices: 806--916 Score: 120
Period size: 32 Copynumber: 3.6 Consensus size: 31
796 TTAGGCTAAT
806 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
** * * **
837 TGCTCAAATAAGGGCCCCGATCTTT--TAATT
1 TGCTCAAATAAGGG-CCTAATGTTTGCCAAAA
867 TGGC-CAAATAAGGGCCTAATGTTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAATG-TTTGCCAAAA
899 TGCTCAAATAAGGGCCTA
1 TGCTCAAATAAGGGCCTA
917 GCGTCGAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
29 4 0.06
30 16 0.26
31 18 0.29
32 24 0.39
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAATGTTTGCCAAAA
Found at i:995 original size:31 final size:29
Alignment explanation
Indices: 953--1121 Score: 130
Period size: 31 Copynumber: 5.6 Consensus size: 29
943 AAATTGACGC
953 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTT-G-AAACGT
* ** *
984 TAGACCCTTATTTG-GCCAAATT-AAAAGAT
1 TAGGCCCTTATTTGAG-CATTTTGAAACG-T
**
1013 CGGGCCCTTATTTGAGCATTTTCGATAACGT
1 TAGGCCCTTATTTGAGCATTTT-GA-AACGT
** *
1044 TAGGCCCTTATTTG-GCCAAATT-AAAAGAT
1 TAGGCCCTTATTTGAG-CATTTTGAAACG-T
*
1073 TAGGCCCTTATTTGAGTATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTT-G-AAACGT
1104 TAGGCCCTTATTTGAGCA
1 TAGGCCCTTATTTGAGCA
1122 ATTAGCCTAA
Statistics
Matches: 106, Mismatches: 20, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
28 7 0.07
29 35 0.33
30 4 0.04
31 53 0.50
32 7 0.07
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (29 bp):
TAGGCCCTTATTTGAGCATTTTGAAACGT
Found at i:1026 original size:29 final size:29
Alignment explanation
Indices: 983--1086 Score: 104
Period size: 29 Copynumber: 3.5 Consensus size: 29
973 TTGGCAAACG
*
983 TTAGACCCTTATTTGGCCAAATTAAAAGA
1 TTAGGCCCTTATTTGGCCAAATTAAAAGA
** ** *
1012 TCGGGCCCTTATTTGAG-CATTTTCGATAACG-
1 TTAGGCCCTTATTTG-GCCAAATT--A-AAAGA
1043 TTAGGCCCTTATTTGGCCAAATTAAAAGA
1 TTAGGCCCTTATTTGGCCAAATTAAAAGA
1072 TTAGGCCCTTATTTG
1 TTAGGCCCTTATTTG
1087 AGTATTTTGG
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
28 3 0.05
29 32 0.55
30 2 0.03
31 18 0.31
32 3 0.05
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (29 bp):
TTAGGCCCTTATTTGGCCAAATTAAAAGA
Found at i:1032 original size:60 final size:60
Alignment explanation
Indices: 954--1117 Score: 267
Period size: 60 Copynumber: 2.7 Consensus size: 60
944 AATTGACGCT
*
954 AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
* * *
1014 GGGCCCTTATTTGAGCATTTTCG-ATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATT
1 AGGCCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
*
1074 AGGCCCTTATTTGAGTATTTTGGCAAACGTTAGGCCCTTATTTG
1 AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
1118 AGCAATTAGC
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
59 1 0.01
60 93 0.98
61 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (60 bp):
AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
Found at i:1527 original size:22 final size:22
Alignment explanation
Indices: 1494--1535 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
1484 GGTATGATAG
1494 TGGGTAATTTTGTGTT-TCTTTT
1 TGGGTAATTTTG-GTTCTCTTTT
1516 TGGGTTAA-TTTGGTTCTCTT
1 TGGG-TAATTTTGGTTCTCTT
1536 CTCCACCGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
21 3 0.17
22 12 0.67
23 3 0.17
ACGTcount: A:0.10, C:0.07, G:0.24, T:0.60
Consensus pattern (22 bp):
TGGGTAATTTTGGTTCTCTTTT
Found at i:6711 original size:24 final size:22
Alignment explanation
Indices: 6676--6723 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
6666 ACTGAAAACA
6676 TTAAGTTTTTTCTTTTTCATTTTT
1 TTAAGTTTTTTC-TTTT-ATTTTT
6700 TTAA-TTTGTTTCTTTTATTTTT
1 TTAAGTTT-TTTCTTTTATTTTT
6722 TT
1 TT
6724 TTTTTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.35
23 7 0.30
24 8 0.35
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.77
Consensus pattern (22 bp):
TTAAGTTTTTTCTTTTATTTTT
Found at i:9782 original size:42 final size:44
Alignment explanation
Indices: 9731--9824 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 44
9721 AGTGCATTAT
9731 CTAA-ATTCTA-C-TCCATCTCTA-AGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTTCCATCTCTAGA-TAATTCATCAAAATAAAG
*
9772 CTAATATTCTACTCTTCCATCTCTAGATAATTCATCAAAATAAAT
1 CTAATATTCTAC-CTTCCATCTCTAGATAATTCATCAAAATAAAG
9817 CTAATATT
1 CTAATATT
9825 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 1 0.02
45 35 0.74
46 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAAAG
Done.