Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021792.1 Corchorus olitorius cultivar O-4 contig21825, 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: 16781
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7668 original size:20 final size:20
Alignment explanation
Indices: 7640--7677 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7630 AAGAATTTTT
7640 GGCCAAATTATTGCAATTGA
1 GGCCAAATTATTGCAATTGA
* *
7660 GGCCGAATTGTTGCAATT
1 GGCCAAATTATTGCAATT
7678 AGGGTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.32
Consensus pattern (20 bp):
GGCCAAATTATTGCAATTGA
Found at i:10784 original size:30 final size:30
Alignment explanation
Indices: 10748--10838 Score: 173
Period size: 30 Copynumber: 3.0 Consensus size: 30
10738 TTTTACATTG
10748 GGTGTAAGTGGATCTCTCCTCATATATATA
1 GGTGTAAGTGGATCTCTCCTCATATATATA
10778 GGTGTAAGTGGATCTCTCCTCATATATATA
1 GGTGTAAGTGGATCTCTCCTCATATATATA
10808 GGTGTAAGTGGATCTCTCCTCATTATATATA
1 GGTGTAAGTGGATCTCTCCTCA-TATATATA
10839 TATATATATG
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
30 52 0.87
31 8 0.13
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.37
Consensus pattern (30 bp):
GGTGTAAGTGGATCTCTCCTCATATATATA
Found at i:14064 original size:16 final size:16
Alignment explanation
Indices: 14021--14071 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 16
14011 TAGATGAGAT
* * *
14021 ATCTCTGTAGAGACAT
1 ATCTCTTTAGAAACAC
14037 ATCTCTTT--AAACAC
1 ATCTCTTTAGAAACAC
14051 ATCTCTTTAGAAACAAC
1 ATCTCTTTAGAAAC-AC
14068 ATCT
1 ATCT
14072 ATCCACTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 12 0.41
16 11 0.38
17 6 0.21
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (16 bp):
ATCTCTTTAGAAACAC
Found at i:15017 original size:31 final size:30
Alignment explanation
Indices: 14980--15147 Score: 132
Period size: 31 Copynumber: 5.6 Consensus size: 30
14970 AATGGCTAAT
14980 TGCTCAAATAAGGGCCTAACGTTTCCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTT-CCAAAA
* * * * **
15011 TACTCAAATAAGGGCATGATC-TTT-TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTCCAAAA
15040 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTT-CCAAAA
* * * **
15071 TGCTCAAATAAGGGCTCGATC-TTT-TAATT
1 TGCTCAAATAAGGGC-CTAACGTTTCCAAAA
15100 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTT-CCAAAA
15131 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
15148 GGCATCGAAA
Statistics
Matches: 103, Mismatches: 22, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
28 5 0.05
29 35 0.34
30 7 0.07
31 51 0.50
32 5 0.05
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (30 bp):
TGCTCAAATAAGGGCCTAACGTTTCCAAAA
Found at i:15077 original size:60 final size:60
Alignment explanation
Indices: 14984--15145 Score: 290
Period size: 60 Copynumber: 2.7 Consensus size: 60
14974 GCTAATTGCT
* *
14984 CAAATAAGGGCCTAACGTTTCCCAAAATACTCAAATAAGGGCAT-GATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGC-TCGATCTTTTAATTTGGC
15044 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
15104 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGC
15146 CTGGCATCGA
Statistics
Matches: 99, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
59 1 0.01
60 98 0.99
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCTCGATCTTTTAATTTGGC
Found at i:15114 original size:29 final size:29
Alignment explanation
Indices: 15015--15114 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 29
15005 CCAAAATACT
15015 CAAATAAGGGCAT-GATCTTTTAATTTGGC
1 CAAATAAGGGC-TCGATCTTTTAATTTGGC
* * * **
15044 CAAATAAGGGC-CTAACGTTTGCCAAAAT-GC
1 CAAATAAGGGCTCGATC-TTT--TAATTTGGC
15074 TCAAATAAGGGCTCGATCTTTTAATTTGGC
1 -CAAATAAGGGCTCGATCTTTTAATTTGGC
15104 CAAATAAGGGC
1 CAAATAAGGGC
15115 CTAACGTTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
28 2 0.04
29 28 0.52
30 4 0.07
31 17 0.31
32 3 0.06
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCTCGATCTTTTAATTTGGC
Found at i:15224 original size:31 final size:30
Alignment explanation
Indices: 15183--15353 Score: 118
Period size: 31 Copynumber: 5.7 Consensus size: 30
15173 CAAAACTGAT
15183 GTTAGGCCCTTATTTGAGCATTTTGGCAAAC
1 GTTAGGCCCTTATTTGAGCATTTT-GCAAAC
* ** *
15214 GTTAGCCCCTTATTTG-GCCAAATT--AAAA
1 GTTAGGCCCTTATTTGAG-CATTTTGCAAAC
**
15242 GATCGGGCCCTTATTTGAGCATTTTGACAAAC
1 G-TTAGGCCCTTATTTGAGCATTTTG-CAAAC
* * ** *
15274 GTTAGGCCCTTATTTAACCAAATT--AAAA
1 GTTAGGCCCTTATTTGAGCATTTTGCAAAC
**
15302 GATCGGGCCCTTATTTGAGCATTTTGGCAAAC
1 G-TTAGGCCCTTATTTGAGCATTTT-GCAAAC
* *
15334 ATTAGGCCCTTATTTAAGCA
1 GTTAGGCCCTTATTTGAGCA
15354 ATTAGCCCTA
Statistics
Matches: 102, Mismatches: 28, Indels: 20
0.68 0.19 0.13
Matches are distributed among these distances:
28 8 0.08
29 33 0.32
30 2 0.02
31 52 0.51
32 7 0.07
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (30 bp):
GTTAGGCCCTTATTTGAGCATTTTGCAAAC
Found at i:15258 original size:29 final size:29
Alignment explanation
Indices: 15220--15318 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
15210 AAACGTTAGC
15220 CCCTTATTTGGCCAAATTAAAAGATCGGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGG
** **
15249 CCCTTATTTGAG-CATTTTGACAAACG-TTAGG
1 CCCTTATTTG-GCCAAATT-A-AAA-GATCGGG
**
15280 CCCTTATTTAACCAAATTAAAAGATCGGG
1 CCCTTATTTGGCCAAATTAAAAGATCGGG
15309 CCCTTATTTG
1 CCCTTATTTG
15319 AGCATTTTGG
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 1 0.02
29 29 0.55
30 3 0.06
31 19 0.36
32 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCGGG
Found at i:15260 original size:60 final size:60
Alignment explanation
Indices: 15187--15350 Score: 283
Period size: 60 Copynumber: 2.7 Consensus size: 60
15177 ACTGATGTTA
* **
15187 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGCCCCTTATTTGGCCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAACCAAATTAAAAGATCG
*
15247 GGCCCTTATTTGAGCATTTTGACAAACGTTAGGCCCTTATTTAACCAAATTAAAAGATCG
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAACCAAATTAAAAGATCG
*
15307 GGCCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTAA
1 GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAA
15351 GCAATTAGCC
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 98 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (60 bp):
GGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTAACCAAATTAAAAGATCG
Done.