Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023820.1 Corchorus olitorius cultivar O-4 contig23853, 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: 8238
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Found at i:1031 original size:36 final size:36
Alignment explanation
Indices: 984--1053 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
974 TTCAATAACC
* **
984 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTAATTATCATATTTCTTA
*
1020 TTACATTTTTTGTAATTTTAATTATCATATTTCT
1 TTACATCTTTTGTAATTTTAATTATCATATTTCT
1054 CCAAAATCTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTAATTATCATATTTCTTA
Found at i:1964 original size:204 final size:203
Alignment explanation
Indices: 1567--1978 Score: 745
Period size: 204 Copynumber: 2.0 Consensus size: 203
1557 GCTTAATAAC
1567 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAAAAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAAAAA
*
1632 GATACAACACATTATTATTATATATATAACTATACCAAAAAAAAATTAGTTGAACATTAGTGGTT
66 GATACAACACATTACTATTATATATATAACTATACCAAAAAAAAATTAGTTGAACATTAGTGGTT
1697 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
131 GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
1762 CCGATTTA
196 CCGATTTA
*
1770 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAAAAA
* *
1835 GATATAACACATTACTATTATATATATAGAACTATTCC-AAAAAAAATTAGTTGAACATTAGTGG
66 GATACAACACATTACTATTATATATAT--AACTATACCAAAAAAAAATTAGTTGAACATTAGTGG
*
1899 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATTTTAAAG
129 TTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAG
*
1964 ATCTGATTTA
194 ATCCGATTTA
1974 TTTAT
1 TTTAT
1979 TATTAAGAAA
Statistics
Matches: 201, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
203 89 0.44
204 104 0.52
205 8 0.04
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (203 bp):
TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAAAAA
GATACAACACATTACTATTATATATATAACTATACCAAAAAAAAATTAGTTGAACATTAGTGGTT
GATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGAT
CCGATTTA
Found at i:2083 original size:25 final size:24
Alignment explanation
Indices: 2049--2095 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
2039 ACGTTTGCAC
2049 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
2074 AAATACCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
2096 TGTAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.55, C:0.09, G:0.06, T:0.30
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:2140 original size:39 final size:40
Alignment explanation
Indices: 2086--2166 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
2076 ATACCTAAGA
*
2086 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
2125 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
2165 AT
1 AT
2167 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:2394 original size:2 final size:2
Alignment explanation
Indices: 2382--2424 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
2372 AGTTTAGACT
*
2382 TA TA TA GTA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2425 ATGGAAAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4913 original size:50 final size:50
Alignment explanation
Indices: 4838--4938 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
4828 GTATCCATGT
4838 TATAGTCACTGCACTATATATAAATGCATTTGGGAAACAATCACAGTTGC
1 TATAGTCACTGCACTATATATAAATGCATTTGGGAAACAATCACAGTTGC
4888 TATAGTCACTGCACTATATATAAATGCATTTGGGAAACAATCACAGTTGC
1 TATAGTCACTGCACTATATATAAATGCATTTGGGAAACAATCACAGTTGC
4938 T
1 T
4939 GATCACAGTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (50 bp):
TATAGTCACTGCACTATATATAAATGCATTTGGGAAACAATCACAGTTGC
Found at i:8166 original size:2 final size:2
Alignment explanation
Indices: 8161--8185 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8151 AGATGAAAAA
8161 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
8186 GTTAGAGAGA
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
Done.