Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014281.1 Corchorus capsularis cultivar CVL-1 contig14302, 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: 15435
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Found at i:7942 original size:21 final size:22
Alignment explanation
Indices: 7916--7960 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
7906 TTCTATTGAA
7916 TTGCTAAAT-ACCGCCCCA-TTT
1 TTGCT-AATCACCGCCCCACTTT
*
7937 TTGCTATTCACCGCCCCACTTT
1 TTGCTAATCACCGCCCCACTTT
7959 TT
1 TT
7961 ATATTTTTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 14 0.67
22 5 0.24
ACGTcount: A:0.18, C:0.36, G:0.09, T:0.38
Consensus pattern (22 bp):
TTGCTAATCACCGCCCCACTTT
Found at i:7965 original size:21 final size:21
Alignment explanation
Indices: 7925--7965 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
7915 ATTGCTAAAT
*
7925 ACCGCCCCATTTTTGCTATTC
1 ACCGCCCCATTTTTGATATTC
7946 ACCGCCCCACTTTTT-ATATT
1 ACCGCCCCA-TTTTTGATATT
7966 TTTGCCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.37, G:0.07, T:0.39
Consensus pattern (21 bp):
ACCGCCCCATTTTTGATATTC
Found at i:8064 original size:15 final size:14
Alignment explanation
Indices: 8044--8075 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
8034 AACTAAAATC
8044 TTTACTTCAAACATA
1 TTTACTTCAAACA-A
8059 TTTACTTCAAACAA
1 TTTACTTCAAACAA
8073 TTT
1 TTT
8076 TTTCATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTACTTCAAACAA
Found at i:8236 original size:14 final size:14
Alignment explanation
Indices: 8213--8251 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
8203 TTTGTAGATC
8213 TAGATCTAGAGAAA
1 TAGATCTAGAGAAA
*
8227 TAGATGTAGAGAAA
1 TAGATCTAGAGAAA
8241 TAGATCTAGAG
1 TAGATCTAGAG
8252 TTTTTCGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.05, G:0.26, T:0.23
Consensus pattern (14 bp):
TAGATCTAGAGAAA
Found at i:8689 original size:21 final size:20
Alignment explanation
Indices: 8653--8705 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
8643 GCTGAGCTTC
* * *
8653 AGAGGGAGAGAAAGGCTTAG
1 AGAGAGAGAGAGAGGCTCAG
8673 AGAGAGCAGAGAGAGGCTCAG
1 AGAGAG-AGAGAGAGGCTCAG
*
8694 AGGGAGAGAGAG
1 AGAGAGAGAGAG
8706 CTTCAAAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.40, C:0.08, G:0.47, T:0.06
Consensus pattern (20 bp):
AGAGAGAGAGAGAGGCTCAG
Found at i:8818 original size:27 final size:27
Alignment explanation
Indices: 8780--8833 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
8770 AGTTGCAGCA
8780 TGCTCAGCCGGGTTATTATGATGGGGC
1 TGCTCAGCCGGGTTATTATGATGGGGC
8807 TGCTCAGCCGGGTTATTATGATGGGGC
1 TGCTCAGCCGGGTTATTATGATGGGGC
8834 CGAGGACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.30
Consensus pattern (27 bp):
TGCTCAGCCGGGTTATTATGATGGGGC
Found at i:8992 original size:12 final size:12
Alignment explanation
Indices: 8977--9044 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 12
8967 ATTTGTTACA
8977 AATTTAGTTATT
1 AATTTAGTTATT
*
8989 AATTTTATATTATT
1 AA-TTTA-GTTATT
*
9003 AGA-TTAGTAAATT
1 A-ATTTAGT-TATT
9016 AATTTAGTTATT
1 AATTTAGTTATT
* *
9028 AATTCATTTATT
1 AATTTAGTTATT
9040 AATTT
1 AATTT
9045 TAGGGAGTAC
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
12 21 0.48
13 16 0.36
14 6 0.14
15 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (12 bp):
AATTTAGTTATT
Found at i:12114 original size:9 final size:9
Alignment explanation
Indices: 12096--12135 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
12086 ATTGATTTGT
*
12096 ATTTTTAAC
1 ATTTATAAC
*
12105 ATTTAGAAC
1 ATTTATAAC
12114 ATTTATAAC
1 ATTTATAAC
*
12123 ATGTATAAC
1 ATTTATAAC
12132 ATTT
1 ATTT
12136 GATTTTGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (9 bp):
ATTTATAAC
Found at i:12656 original size:28 final size:26
Alignment explanation
Indices: 12624--12681 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
12614 TGTTAATAAT
12624 AATTAATCTTAATTAAA-ATGGATAAAAA
1 AATTAATCTTAA-TAAATAT--ATAAAAA
* *
12652 AATTATTTTTAATAAATATATAAAAA
1 AATTAATCTTAATAAATATATAAAAA
12678 AATT
1 AATT
12682 GCATGTGCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 11 0.41
27 4 0.15
28 12 0.44
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (26 bp):
AATTAATCTTAATAAATATATAAAAA
Found at i:15023 original size:15 final size:15
Alignment explanation
Indices: 14987--15023 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
14977 CGTCGTTTTG
14987 TATA-ATATATATTA
1 TATATATATATATTA
15001 TA-ATTATATATATTA
1 TATA-TATATATATTA
15016 TATATATA
1 TATATATA
15024 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 1 0.05
14 2 0.10
15 16 0.80
16 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATATATATATTA
Found at i:15053 original size:20 final size:20
Alignment explanation
Indices: 14990--15057 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
14980 CGTTTTGTAT
*
14990 AATATATATTATAATTATATAT
1 AATATATA-TATAA-TATATAA
* * *
15012 ATTATATATATAAAATAAAA
1 AATATATATATAATATATAA
*
15032 AATATATATATAATATTTAA
1 AATATATATATAATATATAA
15052 AATATA
1 AATATA
15058 AATACCTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 26 0.68
21 5 0.13
22 7 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
AATATATATATAATATATAA
Done.