Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022291.1 Corchorus olitorius cultivar O-4 contig22324, 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: 24941
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Found at i:5162 original size:17 final size:16
Alignment explanation
Indices: 5137--5170 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5127 GATCAAGTGT
*
5137 AGAAGTAAAAAGGAAAA
1 AGAAATAAAAA-GAAAA
5154 AGAAATAAAAAGAAAA
1 AGAAATAAAAAGAAAA
5170 A
1 A
5171 CAACTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (16 bp):
AGAAATAAAAAGAAAA
Found at i:11798 original size:10 final size:10
Alignment explanation
Indices: 11785--11821 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
11775 AGTAGAACTT
11785 AGAAAAGTAA
1 AGAAAAGTAA
*
11795 AGAAAAGAAA
1 AGAAAAGTAA
11805 AGAAAAAGTAA
1 AG-AAAAGTAA
11816 AGAAAA
1 AGAAAA
11822 TATACCCTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (10 bp):
AGAAAAGTAA
Found at i:13866 original size:19 final size:18
Alignment explanation
Indices: 13817--13862 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
13807 AGATGATGAT
13817 TTTAATAATAATTATTCA
1 TTTAATAATAATTATTCA
** *
13835 TAAAAATAATAATTATTTA
1 T-TTAATAATAATTATTCA
13854 TTTAATAAT
1 TTTAATAAT
13863 TAATAAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAATAATAATTATTCA
Found at i:14096 original size:24 final size:24
Alignment explanation
Indices: 14061--14108 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
14051 TATTGTTGAA
*
14061 GAGGTTGGTTGAGATTAAAATTGG
1 GAGGTTGATTGAGATTAAAATTGG
14085 GAGGTTGATTGAGATTAAAATTGG
1 GAGGTTGATTGAGATTAAAATTGG
14109 TCAAGAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.33
Consensus pattern (24 bp):
GAGGTTGATTGAGATTAAAATTGG
Found at i:22738 original size:12 final size:12
Alignment explanation
Indices: 22721--22753 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
22711 TTTTCATAAT
22721 ATGTTTAATTTA
1 ATGTTTAATTTA
22733 ATGTTTAA-TTA
1 ATGTTTAATTTA
22744 AT-TTTAATTT
1 ATGTTTAATTT
22754 GAAATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.25
11 7 0.35
12 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (12 bp):
ATGTTTAATTTA
Found at i:22956 original size:16 final size:15
Alignment explanation
Indices: 22932--22965 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
22922 TTGATTCTTA
22932 TATAATATAATATATG
1 TATAATATAA-ATATG
*
22948 TATACTATAAATATG
1 TATAATATAAATATG
22963 TAT
1 TAT
22966 TTGTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (15 bp):
TATAATATAAATATG
Found at i:23159 original size:2 final size:2
Alignment explanation
Indices: 23148--23190 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
23138 AAAAGCCTAT
23148 TA TA TA -A TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
23189 TA
1 TA
23191 AATCAGAGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:23168 original size:15 final size:15
Alignment explanation
Indices: 23148--23190 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
23138 AAAAGCCTAT
23148 TATATA-AT-ATATA
1 TATATATATAATATA
23161 TATATATATAATATA
1 TATATATATAATATA
*
23176 TATATATATAGTATA
1 TATATATATAATATA
23191 AATCAGAGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 6 0.22
14 2 0.07
15 19 0.70
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (15 bp):
TATATATATAATATA
Found at i:23170 original size:17 final size:17
Alignment explanation
Indices: 23148--23185 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
23138 AAAAGCCTAT
23148 TATATAATATATATATA
1 TATATAATATATATATA
23165 TATATAATATATATATA
1 TATATAATATATATATA
23182 TATA
1 TATA
23186 GTATAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATAATATATATATA
Found at i:23847 original size:15 final size:17
Alignment explanation
Indices: 23812--23849 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
23802 AACCGAAAAC
23812 GACCC-AACCCAGAATT
1 GACCCGAACCCAGAATT
23828 GACCCGAACCCA-AA-T
1 GACCCGAACCCAGAATT
23843 GACCCGA
1 GACCCGA
23850 TATTTGAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 7 0.33
17 6 0.29
ACGTcount: A:0.37, C:0.39, G:0.16, T:0.08
Consensus pattern (17 bp):
GACCCGAACCCAGAATT
Found at i:23998 original size:2 final size:2
Alignment explanation
Indices: 23991--24025 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
23981 TATAGAGTGA
23991 AT AT AT AT AT 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 AT AT AT AT AT A
24026 CACTATTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24669 original size:132 final size:133
Alignment explanation
Indices: 24499--24751 Score: 409
Period size: 132 Copynumber: 1.9 Consensus size: 133
24489 TCAAGCAATC
*** *
24499 CTTGCTTTTCAGACCGTGTTCATCAGTTCATCGAACCAATCAGCCAGGTTATTCATTATCATCTC
1 CTTGCTTTTCAGACCACCTTCATCAGTTCATCGAACCAATCAGCCAGGTTATTCACTATCATCTC
**
24564 ACTATTTGAAGAATTT-CATTTTCCTGTGCTTAGGGATTTAACTCCAATATTCTCATCTCCGTTT
66 ACTACCTGAAGAATTTGCATTTTCCTGTGCTTAGGGATTTAACTCCAATATTCTCATCTCCGTTT
24628 ATT
131 ATT
* *
24631 CTTGCTTTTCTGACCACCTTCATTAGTTCATCGAACCAATCAGCCAGGTTATTCACTATCATCTC
1 CTTGCTTTTCAGACCACCTTCATCAGTTCATCGAACCAATCAGCCAGGTTATTCACTATCATCTC
* *
24696 ACTACCTGAAGAATTTGCTTTTTCCTGTGTTTAGGGATTTAACTCCAATATTCTCA
66 ACTACCTGAAGAATTTGCATTTTCCTGTGCTTAGGGATTTAACTCCAATATTCTCA
24752 ACGTTCCCTA
Statistics
Matches: 110, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
132 73 0.66
133 37 0.34
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.39
Consensus pattern (133 bp):
CTTGCTTTTCAGACCACCTTCATCAGTTCATCGAACCAATCAGCCAGGTTATTCACTATCATCTC
ACTACCTGAAGAATTTGCATTTTCCTGTGCTTAGGGATTTAACTCCAATATTCTCATCTCCGTTT
ATT
Done.