Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012371.1 Corchorus olitorius cultivar O-4 contig12404, 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: 28958
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:2774 original size:21 final size:21
Alignment explanation
Indices: 2740--2779 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2730 AAGTTTGTGA
2740 TTTTCATTTCTCCTGTTTTCT
1 TTTTCATTTCTCCTGTTTTCT
* * *
2761 TTTTCTTTTTTCCTTTTTT
1 TTTTCATTTCTCCTGTTTT
2780 TGTCTTTGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.75
Consensus pattern (21 bp):
TTTTCATTTCTCCTGTTTTCT
Found at i:11913 original size:91 final size:90
Alignment explanation
Indices: 11754--11935 Score: 274
Period size: 91 Copynumber: 2.0 Consensus size: 90
11744 GCACTTGTTG
* * * * *
11754 TGGAGCCATTTGATGCATTCATTTTCCCCGACCGTCGAATATTAAAAGGTTTAGCTAATGGCTAT
1 TGGAGCCACTTGATGCATTCATTTTCCCCAACCATCGAATATTAAAAGGTTTAACCAATGGCTAT
*
11819 TATAAACTCCAACCTGTTTAGCCAT
66 TATAAACTCCAACCTATTTAGCCAT
* *
11844 TGGAGCCACTTGATGCATTCATTTTCCCCTAATCATCGGATATTAAAAGGTTTAACCAATGGCTA
1 TGGAGCCACTTGATGCATTCATTTTCCCC-AACCATCGAATATTAAAAGGTTTAACCAATGGCTA
*
11909 TTATAAACTCCAACCTATTTAGTCAT
65 TTATAAACTCCAACCTATTTAGCCAT
11935 T
1 T
11936 CTGTTTAGCC
Statistics
Matches: 82, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 28 0.34
91 54 0.66
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (90 bp):
TGGAGCCACTTGATGCATTCATTTTCCCCAACCATCGAATATTAAAAGGTTTAACCAATGGCTAT
TATAAACTCCAACCTATTTAGCCAT
Found at i:17300 original size:12 final size:12
Alignment explanation
Indices: 17265--17300 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
17255 GAGAAATCAT
17265 CAAACAAACTAA
1 CAAACAAACTAA
* *
17277 CAACCAAGCTAA
1 CAAACAAACTAA
17289 CAAACAAACTAA
1 CAAACAAACTAA
17301 TCTTTCTTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.61, C:0.28, G:0.03, T:0.08
Consensus pattern (12 bp):
CAAACAAACTAA
Found at i:18966 original size:31 final size:31
Alignment explanation
Indices: 18864--18968 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
18854 TAAGGCTAAT
*
18864 TGCTCAAATAAGAGCCTAACGTTTGCCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
* * * * **
18895 TACTCAAATAAGGGTCTGATC-TTT--TAATT
1 TGCTCAAATAAGGGCCT-AACGTTTGCCAAAA
18924 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGCCAAAA
18955 TGCTCAAATAAGGG
1 TGCTCAAATAAGGG
18969 TCTGGCATCG
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
28 2 0.04
29 18 0.33
30 3 0.05
31 30 0.55
32 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGCCAAAA
Found at i:19077 original size:29 final size:29
Alignment explanation
Indices: 19034--19141 Score: 78
Period size: 29 Copynumber: 3.7 Consensus size: 29
19024 GCATTTTGGC
* *
19034 AAAGGTTAGACCCTTATTTGGCCAAATTA
1 AAAGATTAGGCCCTTATTTGGCCAAATTA
* * **
19063 AAAGATTGGGCCCTTATTTAAG-CATTTTCA
1 AAAGATTAGGCCCTTATTT-GGCCAAATT-A
*
19093 ATAACG-TTAAGCCCTTATTTGGCCAAATTA
1 A-AA-GATTAGGCCCTTATTTGGCCAAATTA
*
19123 AAAGA-TCGGCTCCTTATTT
1 AAAGATTAGGC-CCTTATTT
19142 AAGCATTTTG
Statistics
Matches: 59, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
28 4 0.07
29 30 0.51
30 6 0.10
31 18 0.31
32 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (29 bp):
AAAGATTAGGCCCTTATTTGGCCAAATTA
Found at i:19087 original size:60 final size:59
Alignment explanation
Indices: 19013--19173 Score: 211
Period size: 60 Copynumber: 2.7 Consensus size: 59
19003 TGATGCCAGG
* * *
19013 TCCTTATTTGAGCATTTTGGCAAAGGTTAGACCCTTATTTGGCCAAATTAAAAGATTGGGC
1 TCCTTATTTAAGCATTTT-GCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGA-TCGGC
19074 -CCTTATTTAAGCATTTT-CAATAACGTTA-AGCCCTTATTTGGCCAAATTAAAAGATCGGC
1 TCCTTATTTAAGCATTTTGC-A-AACGTTAGA-CCCTTATTTGGCCAAATTAAAAGATCGGC
*
19133 TCCTTATTTAAGCATTTTGACAAACGTTAGGCCCTTATTTG
1 TCCTTATTTAAGCATTTTG-CAAACGTTAGACCCTTATTTG
19174 AGCAATTAGT
Statistics
Matches: 89, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
58 1 0.01
59 6 0.07
60 80 0.90
61 1 0.01
62 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (59 bp):
TCCTTATTTAAGCATTTTGCAAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGC
Found at i:19172 original size:31 final size:29
Alignment explanation
Indices: 19071--19177 Score: 83
Period size: 31 Copynumber: 3.6 Consensus size: 29
19061 TAAAAGATTG
19071 GGCCCTTATTTAAGCATTTTCAATAACGTTA
1 GGCCCTTATTTAAGCATTTT-AA-AACGTTA
* * ** * *
19102 AGCCCTTATTT-GGCCAAATTAAAA-GATC
1 GGCCCTTATTTAAG-CATTTTAAAACGTTA
19130 GGCTCCTTATTTAAGCATTTTGACAAACGTTA
1 GGC-CCTTATTTAAGCATTTT-A-AAACGTTA
*
19162 GGCCCTTATTTGAGCA
1 GGCCCTTATTTAAGCA
19178 ATTAGTCTAA
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
28 4 0.07
29 14 0.25
30 5 0.09
31 29 0.51
32 5 0.09
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.35
Consensus pattern (29 bp):
GGCCCTTATTTAAGCATTTTAAAACGTTA
Found at i:28011 original size:13 final size:15
Alignment explanation
Indices: 27969--28014 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
27959 TCATGCACCC
*
27969 AAAAATAATTTAATA
1 AAAAATCATTTAATA
27984 AAAAATCATTT-ATA
1 AAAAATCATTTAATA
*
27998 AAACA-C-TTTAATA
1 AAAAATCATTTAATA
28011 AAAA
1 AAAA
28015 CAATAACGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 3 0.11
13 7 0.26
14 7 0.26
15 10 0.37
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAATCATTTAATA
Found at i:28557 original size:19 final size:19
Alignment explanation
Indices: 28506--28559 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
28496 GTTTATTTTT
*
28506 GGTT-GGACCGAGTCAAATC
1 GGTTCGGACCGA-CCAAATC
* * *
28525 TGTTCGGTCTGACCAAATC
1 GGTTCGGACCGACCAAATC
28544 GGTTCGGACCGACCAA
1 GGTTCGGACCGACCAA
28560 GCTGGCTCGT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.24, C:0.26, G:0.28, T:0.22
Consensus pattern (19 bp):
GGTTCGGACCGACCAAATC
Done.