Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013914.1 Corchorus olitorius cultivar O-4 contig13947, 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: 23606
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:55 original size:17 final size:17
Alignment explanation
Indices: 33--86 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
23 ATCACCCCCG
* *
33 GATCACTAGTGATCTAA
1 GATCACCAGTGATCAAA
*
50 GATCACCAGTGATAAAA
1 GATCACCAGTGATCAAA
*
67 GATCACCGGTGATCAAA
1 GATCACCAGTGATCAAA
84 GAT
1 GAT
87 TACATGGGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (17 bp):
GATCACCAGTGATCAAA
Found at i:221 original size:12 final size:13
Alignment explanation
Indices: 192--224 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
182 GGGTGATCTG
*
192 AGATCACCTGCCA
1 AGATCACCTGCAA
205 AGATCACC-GCAA
1 AGATCACCTGCAA
217 AGATCACC
1 AGATCACC
225 CCCAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.36, G:0.15, T:0.12
Consensus pattern (13 bp):
AGATCACCTGCAA
Found at i:1958 original size:12 final size:12
Alignment explanation
Indices: 1937--1966 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1927 TATATGATAA
*
1937 AAATAAATAAAT
1 AAATATATAAAT
1949 AAATATATAAAT
1 AAATATATAAAT
1961 AAATAT
1 AAATAT
1967 TTTCTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAATATATAAAT
Found at i:9056 original size:2 final size:2
Alignment explanation
Indices: 9051--9075 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9041 ATATCTTAGA
9051 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
9076 CTCATTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13814 original size:14 final size:14
Alignment explanation
Indices: 13797--13834 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
13787 CTCTAAGTAA
13797 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
13811 AAAAAAAGAGAAAG
1 AAAAAAAAAGAAAG
13825 AAAGAAAAAA
1 AAA-AAAAAA
13835 TAAAAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:13816 original size:18 final size:18
Alignment explanation
Indices: 13795--13843 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
13785 GTCTCTAAGT
13795 AAAAAAAAAAAGAAAGAA
1 AAAAAAAAAAAGAAAGAA
* *
13813 AAAAAGAGAAAGAAAGAA
1 AAAAAAAAAAAGAAAGAA
13831 AAAATAAAAAAAG
1 AAAA-AAAAAAAG
13844 GGCAAGGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAAAGAAAGAA
Found at i:14022 original size:31 final size:31
Alignment explanation
Indices: 13984--14045 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
13974 TGGAGGGTAA
13984 AGATAAAAGGGAAAATTAAAAAGTAACAAAT
1 AGATAAAAGGGAAAATTAAAAAGTAACAAAT
14015 AGATAAAAGGGAAAATTAAAAAGTAACAAAT
1 AGATAAAAGGGAAAATTAAAAAGTAACAAAT
14046 TGAAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.65, C:0.03, G:0.16, T:0.16
Consensus pattern (31 bp):
AGATAAAAGGGAAAATTAAAAAGTAACAAAT
Found at i:16158 original size:29 final size:29
Alignment explanation
Indices: 16105--16166 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
16095 ATTTATATAA
*
16105 TTTAATAACAAATTAAATCAAAAT-AAGT
1 TTTAATAAAAAATTAAATCAAAATAAAGT
*
16133 TTTAATAAAAAGATTAAAT-ATTAATAAAGT
1 TTTAATAAAAA-ATTAAATCA-AAATAAAGT
16163 TTTA
1 TTTA
16167 CAATTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 11 0.38
29 10 0.34
30 8 0.28
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (29 bp):
TTTAATAAAAAATTAAATCAAAATAAAGT
Found at i:16964 original size:56 final size:56
Alignment explanation
Indices: 16866--16979 Score: 185
Period size: 56 Copynumber: 2.0 Consensus size: 56
16856 TATCTGTTTC
* *
16866 CTTTCACACAATAAATGTTAAAATAAATCTTATCCCCATATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTAAAATAAATCCTATCCCCATATCTCTACTTAATTATT
*
16922 CTTTCACACAATAAATATTATAATAAATCCTATCTCCC-TATCTCTACTTAATTATT
1 CTTTCACACAATAAATATTAAAATAAATCCTATC-CCCATATCTCTACTTAATTATT
16978 CT
1 CT
16980 ACAAAATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 51 0.94
57 3 0.06
ACGTcount: A:0.36, C:0.23, G:0.01, T:0.40
Consensus pattern (56 bp):
CTTTCACACAATAAATATTAAAATAAATCCTATCCCCATATCTCTACTTAATTATT
Found at i:21587 original size:42 final size:44
Alignment explanation
Indices: 21537--21630 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
21527 AATGCATTAC
*
21537 CTAA-ATTCTACT-TC-ATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCTATCTCTAGATAATTCATCAAAATAAAG
21578 CTAATATTCTACTCCTCTATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT-CTCTATCTCTAGATAATTCATCAAAATAAAG
*
21623 TTAATATT
1 CTAATATT
21631 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 2 0.04
45 33 0.70
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (44 bp):
CTAATATTCTACTCTCTATCTCTAGATAATTCATCAAAATAAAG
Done.