Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021274.1 Corchorus olitorius cultivar O-4 contig21307, 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: 20885
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2166 original size:31 final size:32
Alignment explanation
Indices: 2105--2176 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
2095 CCTCCGTCAA
*
2105 GAGGTAAAATGTCCTGAATTTGAGAAGTTCATG
1 GAGGCAAAATGTCCTGAATTTGAGAAGTTCA-G
*
2138 G-GGCAAAATGTCTTGAATTTG-GAAGTTCAG
1 GAGGCAAAATGTCCTGAATTTGAGAAGTTCAG
2168 GAGGCAAAA
1 GAGGCAAAA
2177 ATGTTCGGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
30 2 0.06
31 15 0.42
32 18 0.50
33 1 0.03
ACGTcount: A:0.35, C:0.10, G:0.29, T:0.26
Consensus pattern (32 bp):
GAGGCAAAATGTCCTGAATTTGAGAAGTTCAG
Found at i:2189 original size:31 final size:32
Alignment explanation
Indices: 2110--2190 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
2100 GTCAAGAGGT
2110 AAAATGTC-CTGAATTTGAGAAGTTCATGGGGC
1 AAAATGTCTC-GAATTTGAGAAGTTCATGGGGC
*
2142 AAAATGTCTTGAATTTG-GAAGTTCA-GGAGGC
1 AAAATGTCTCGAATTTGAGAAGTTCATGG-GGC
*
2173 AAAAATGT-TCGGATTTGA
1 -AAAATGTCTCGAATTTGA
2191 AATGCATTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
30 2 0.05
31 18 0.43
32 22 0.52
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (32 bp):
AAAATGTCTCGAATTTGAGAAGTTCATGGGGC
Found at i:2582 original size:17 final size:18
Alignment explanation
Indices: 2556--2591 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2546 AATCAATCTA
2556 TTCTTCTTTTT-TTCTTT
1 TTCTTCTTTTTATTCTTT
*
2573 TTCTTTTTTTTATTCTTT
1 TTCTTCTTTTTATTCTTT
2591 T
1 T
2592 GCCAGACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (18 bp):
TTCTTCTTTTTATTCTTT
Found at i:8936 original size:31 final size:31
Alignment explanation
Indices: 8901--8977 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
8891 GCCAAATTAC
* * *
8901 CAATTTGAGACTAAACCTTTCAAAATTTGAT
1 CAATTTGAGCCTAAACATTTCAAAAATTGAT
* * *
8932 CAATTTTAGCCTAAACATTTTAAAAATTGCT
1 CAATTTGAGCCTAAACATTTCAAAAATTGAT
8963 CAATTTGAGCCTAAA
1 CAATTTGAGCCTAAA
8978 AACAAAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (31 bp):
CAATTTGAGCCTAAACATTTCAAAAATTGAT
Found at i:9157 original size:32 final size:29
Alignment explanation
Indices: 9121--9180 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
9111 TAGGCCCAAA
*
9121 TTGGTGCATTTTGATAAGGTTTTAGACTCAAT
1 TTGGTGCAGTTT-A-AAGG-TTTAGACTCAAT
*
9153 TTGGTTCAGTTTAAAGGTTTAGACTCAA
1 TTGGTGCAGTTTAAAGGTTTAGACTCAA
9181 ATTAAGAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 4 0.15
31 1 0.04
32 10 0.38
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.42
Consensus pattern (29 bp):
TTGGTGCAGTTTAAAGGTTTAGACTCAAT
Found at i:15876 original size:199 final size:196
Alignment explanation
Indices: 15442--15858 Score: 671
Period size: 199 Copynumber: 2.1 Consensus size: 196
15432 TACAATCACT
** *
15442 AATCATAACAATCTCTCTAGGAAACTCTCAATCTAATCAACCCAACATCATGTGTGATTCTCTCA
1 AATCATAACAA-CTCTCTAAAAAACTATCAATCTAATCAACCCAACATCATGTGTGATTCTCTCA
15507 CACCAACATAAAGATATCTCAGCTTTTTCTCTCACACAATAATTAAAAAAAAAAAAAACTAAACA
65 CACCAACATAAAGATATCTCAGCTTTTTCTCTCACACAATAATT--AAAAAAAAAAAACTAAACA
*
15572 CAAACTGCTTATTTATACTGACACAAACTTAGACTCCAAGAATCCCTTTCCTATTAGGATTCTTG
128 CAAACTGCTTATTTATACTGACACAAACTTAAACTCCAAGAATCCCTTTCCTATTAGGATTCTTG
* *
15637 GACT
193 CACC
** *
15641 AATCATAACAATCTCTCTAGGAAACTCTCAATCTAATCAACCCAACATCATGTGTGATTCTCTCA
1 AATCATAACAA-CTCTCTAAAAAACTATCAATCTAATCAACCCAACATCATGTGTGATTCTCTCA
15706 CACCAACATAAAGATATCTCAGCTTTTTCTCTCACACAATAATT-AAAAAAAAAAACTAAACACA
65 CACCAACATAAAGATATCTCAGCTTTTTCTCTCACACAATAATTAAAAAAAAAAAACTAAACACA
15770 AACTGCTTATTTATACTGACACAAACTTAAACTCCAAGAATCCCTTTCCTATTAGGATTCTTGTC
130 AACTGCTTATTTATACTGACACAAACTTAAACTCCAAGAATCCCTTTCCTATTAGGATTCTTG--
15835 CACC
193 CACC
15839 AATCA-AA-AA-TCTCTAAAAAA
1 AATCATAACAACTCTCTAAAAAA
15859 TCCTAATCCA
Statistics
Matches: 211, Mismatches: 5, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
194 9 0.04
196 84 0.40
197 2 0.01
198 7 0.03
199 109 0.52
ACGTcount: A:0.40, C:0.25, G:0.07, T:0.28
Consensus pattern (196 bp):
AATCATAACAACTCTCTAAAAAACTATCAATCTAATCAACCCAACATCATGTGTGATTCTCTCAC
ACCAACATAAAGATATCTCAGCTTTTTCTCTCACACAATAATTAAAAAAAAAAAACTAAACACAA
ACTGCTTATTTATACTGACACAAACTTAAACTCCAAGAATCCCTTTCCTATTAGGATTCTTGCAC
C
Found at i:15983 original size:48 final size:49
Alignment explanation
Indices: 15912--16012 Score: 159
Period size: 48 Copynumber: 2.1 Consensus size: 49
15902 GAGTTGGTGC
*
15912 CTTGGTGGGTGCCAAAAAGATATAATGCAGCTTAAAAGAGGGATTG-TT
1 CTTGGTGGGTGCCAAAAAGATATAATGCAGCTTAAAAGAGGAATTGTTT
* **
15960 CTTGGTGGGTGGCGGAAAGATATAATGCAGCTTAAAAGAGGAATTGTTT
1 CTTGGTGGGTGCCAAAAAGATATAATGCAGCTTAAAAGAGGAATTGTTT
16009 CTTG
1 CTTG
16013 AATAGCCAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
48 42 0.88
49 6 0.12
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (49 bp):
CTTGGTGGGTGCCAAAAAGATATAATGCAGCTTAAAAGAGGAATTGTTT
Found at i:19727 original size:27 final size:27
Alignment explanation
Indices: 19697--19795 Score: 189
Period size: 27 Copynumber: 3.7 Consensus size: 27
19687 GGTCATCTAT
19697 GGGGCATTTTGGTCATTTACACATTCA
1 GGGGCATTTTGGTCATTTACACATTCA
19724 GGGGCATTTTGGTCATTTACACATTCA
1 GGGGCATTTTGGTCATTTACACATTCA
19751 GGGGCATTTTGGTCATTTACACATTCA
1 GGGGCATTTTGGTCATTTACACATTCA
*
19778 TGGGCATTTTGGTCATTT
1 GGGGCATTTTGGTCATTT
19796 TAAGTTCAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.39
Consensus pattern (27 bp):
GGGGCATTTTGGTCATTTACACATTCA
Done.