Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023191.1 Corchorus olitorius cultivar O-4 contig23224, 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: 16499
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:5067 original size:27 final size:27
Alignment explanation
Indices: 5029--5082 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
5019 GCTTGTGACA
5029 AGATCAAAGAAGGTGCCATTTGATCCT
1 AGATCAAAGAAGGTGCCATTTGATCCT
5056 AGATCAAAGAAGGTGCCATTTGATCCT
1 AGATCAAAGAAGGTGCCATTTGATCCT
5083 TTGAGTATGC
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:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (27 bp):
AGATCAAAGAAGGTGCCATTTGATCCT
Found at i:6756 original size:94 final size:95
Alignment explanation
Indices: 6648--6835 Score: 351
Period size: 95 Copynumber: 2.0 Consensus size: 95
6638 GAGAACATAG
6648 GTGTGTGTGTGTGCGCTTGTGAGGATTTTTCTTTATCTTTACT-ATCTTTTCTTGCAAGTACAAT
1 GTGTGTGTGTGTGCGCTTGTGAGGATTTTTCTTTATCTTTACTAATCTTTTCTTGCAAGTACAAT
6712 GGGAAATAGAATGGATGGAGAAAATCAGGT
66 GGGAAATAGAATGGATGGAGAAAATCAGGT
*
6742 GTGTGTGTGTGTGCGCTTGTGAGGATTTTTCTTTATCTTTACTAATCTTTTCTTGCAGGTACAAT
1 GTGTGTGTGTGTGCGCTTGTGAGGATTTTTCTTTATCTTTACTAATCTTTTCTTGCAAGTACAAT
*
6807 GGGAAATAGAGTGGATGGAGAAAATCAGG
66 GGGAAATAGAATGGATGGAGAAAATCAGG
6836 CCGATTTGGC
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
94 43 0.47
95 48 0.53
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.38
Consensus pattern (95 bp):
GTGTGTGTGTGTGCGCTTGTGAGGATTTTTCTTTATCTTTACTAATCTTTTCTTGCAAGTACAAT
GGGAAATAGAATGGATGGAGAAAATCAGGT
Found at i:8071 original size:37 final size:38
Alignment explanation
Indices: 7966--8109 Score: 141
Period size: 38 Copynumber: 3.8 Consensus size: 38
7956 CTGTACATAA
* * * *
7966 TGGACTCGTGCCTTATGTGCTTAAACTGTTGGTAAGAG
1 TGGACTCATGCCTTAGGGGGTTAAACTGTTGGTAAGAG
* * * * *
8004 TGGCCCCATACCTCAAGGGGTTAAACTGTTGGTAAGAG
1 TGGACTCATGCCTTAGGGGGTTAAACTGTTGGTAAGAG
* *
8042 TGGACTCGTGCCTTA-GGGGTTAAATTGTTGGTAAGAG
1 TGGACTCATGCCTTAGGGGGTTAAACTGTTGGTAAGAG
* *
8079 TAGAAC-CATGTCTTAGGGGGTTAAA-TGTTGG
1 T-GGACTCATGCCTTAGGGGGTTAAACTGTTGG
8110 CTAGACTTGA
Statistics
Matches: 87, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
37 35 0.40
38 52 0.60
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.31
Consensus pattern (38 bp):
TGGACTCATGCCTTAGGGGGTTAAACTGTTGGTAAGAG
Found at i:8099 original size:75 final size:75
Alignment explanation
Indices: 7966--8109 Score: 182
Period size: 75 Copynumber: 1.9 Consensus size: 75
7956 CTGTACATAA
* * **
7966 TGGACTCGTGCCTTATGTGCTTAAACTGTTGGTAAGAGTGGCCCCATACCTCAAGGGGTTAAACT
1 TGGACTCGTGCCTTATGGGCTTAAACTGTTGGTAAGAGTAGAACCATACCTCAAGGGGTTAAA-T
8031 GTTGGTAAGAG
65 GTTGGTAAGAG
* * ** * *
8042 TGGACTCGTGCCTTA-GGGGTTAAATTGTTGGTAAGAGTAGAACCATGTCTTAGGGGGTTAAATG
1 TGGACTCGTGCCTTATGGGCTTAAACTGTTGGTAAGAGTAGAACCATACCTCAAGGGGTTAAATG
8106 TTGG
66 TTGG
8110 CTAGACTTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
74 6 0.10
75 37 0.64
76 15 0.26
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.31
Consensus pattern (75 bp):
TGGACTCGTGCCTTATGGGCTTAAACTGTTGGTAAGAGTAGAACCATACCTCAAGGGGTTAAATG
TTGGTAAGAG
Found at i:9073 original size:44 final size:44
Alignment explanation
Indices: 9024--9139 Score: 196
Period size: 44 Copynumber: 2.6 Consensus size: 44
9014 ATATGTCTAG
9024 AATGATATTAAGTTTAAATTTTATGATTTTATGTAACTGTCTTT
1 AATGATATTAAGTTTAAATTTTATGATTTTATGTAACTGTCTTT
* *
9068 GATGATATTAAGTTTAAATTTTATGATTTTGTGTAACTGTCTTT
1 AATGATATTAAGTTTAAATTTTATGATTTTATGTAACTGTCTTT
9112 AATGATATTAAGTTTAAATATTTTATGA
1 AATGATATTAAGTTT-AA-ATTTTATGA
9140 AGTTAAGTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
44 56 0.84
45 2 0.03
46 9 0.13
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (44 bp):
AATGATATTAAGTTTAAATTTTATGATTTTATGTAACTGTCTTT
Found at i:9139 original size:23 final size:23
Alignment explanation
Indices: 9025--9160 Score: 83
Period size: 23 Copynumber: 6.1 Consensus size: 23
9015 TATGTCTAGA
9025 ATGATATTAAGTTT-AA-ATTTT
1 ATGATATTAAGTTTAAATATTTT
* * * *
9046 ATGAT-TTTA-TGTAACTGTCTTT
1 ATGATATTAAGTTTAAATAT-TTT
9068 GATGATATTAAGTTT-AA-ATTTT
1 -ATGATATTAAGTTTAAATATTTT
* * * *
9090 ATGAT-TT-TGTGTAACTGTCTTT
1 ATGATATTAAGTTTAAATAT-TTT
9112 AATGATATTAAGTTTAAATATTTT
1 -ATGATATTAAGTTTAAATATTTT
*
9136 ATGA-AGTTAAGTTTAAATCTTTT
1 ATGATA-TTAAGTTTAAATATTTT
9159 AT
1 AT
9161 ATAACTGTCT
Statistics
Matches: 85, Mismatches: 17, Indels: 24
0.67 0.13 0.19
Matches are distributed among these distances:
19 5 0.06
20 7 0.08
21 12 0.14
22 10 0.12
23 33 0.39
24 9 0.11
25 9 0.11
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.51
Consensus pattern (23 bp):
ATGATATTAAGTTTAAATATTTT
Found at i:9217 original size:39 final size:39
Alignment explanation
Indices: 9131--9236 Score: 135
Period size: 39 Copynumber: 2.7 Consensus size: 39
9121 AAGTTTAAAT
* *
9131 ATTTTATGAAGTTAAGTTTAAATCTTTTATATAACTGTC
1 ATTTAATGATGTTAAGTTTAAATCTTTTATATAACTGTC
* *
9170 -TTTAATGATGTTAAGTTTAAATGTCTTTGTATAACTG-C
1 ATTTAATGATGTTAAGTTTAAATCT-TTTATATAACTGTC
* *
9208 ATTTGATGATGTTAAGTTTAAATATTTTA
1 ATTTAATGATGTTAAGTTTAAATCTTTTA
9237 AGCATTTTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
38 25 0.43
39 33 0.57
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (39 bp):
ATTTAATGATGTTAAGTTTAAATCTTTTATATAACTGTC
Found at i:9236 original size:100 final size:102
Alignment explanation
Indices: 9050--9236 Score: 247
Period size: 100 Copynumber: 1.8 Consensus size: 102
9040 AATTTTATGA
* * *
9050 TTTTATGTAACTGTCTTTGATGATATTAAGTTTAAATTTTATGATTTTGTGTAACTGTCTTTAAT
1 TTTTATATAACTGTCTTTAATGATATTAAGTTTAAA---TATGATTTTGTATAACTGTCTTTAAT
9115 GATATTAAGTTTAAATATTTTATGAAGTTAAGTTTAAATC
63 GATATTAAGTTTAAATATTTTATGAAGTTAAGTTTAAATC
* *
9155 TTTTATATAACTGTCTTTAATGATGTTAAGTTT-AA-ATG-TCTTTGTATAACTG-CATTTGATG
1 TTTTATATAACTGTCTTTAATGATATTAAGTTTAAATATGAT-TTTGTATAACTGTC-TTTAATG
*
9216 ATGTTAAGTTTAAATATTTTA
64 ATATTAAGTTTAAATATTTTA
9237 AGCATTTTGA
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
99 2 0.03
100 40 0.54
104 2 0.03
105 30 0.41
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.50
Consensus pattern (102 bp):
TTTTATATAACTGTCTTTAATGATATTAAGTTTAAATATGATTTTGTATAACTGTCTTTAATGAT
ATTAAGTTTAAATATTTTATGAAGTTAAGTTTAAATC
Found at i:12766 original size:21 final size:21
Alignment explanation
Indices: 12749--12799 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
12739 ATGAGATAGG
12749 TACAAAAATGACAAAGATAAA
1 TACAAAAATGACAAAGATAAA
* * *
12770 TACATAAATGATAAAGAAAAA
1 TACAAAAATGACAAAGATAAA
12791 TACAAAAAT
1 TACAAAAAT
12800 AAAGATTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.18
Consensus pattern (21 bp):
TACAAAAATGACAAAGATAAA
Found at i:14293 original size:21 final size:20
Alignment explanation
Indices: 14265--14303 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
14255 ATGGGTTAGT
* *
14265 TTTAATATTATAATAATATA
1 TTTAATATAATAAAAATATA
14285 TTTATATATAATAAAAATA
1 TTTA-ATATAATAAAAATA
14304 AAAAAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTAATATAATAAAAATATA
Done.