Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019546.1 Corchorus olitorius cultivar O-4 contig19579, 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: 13631
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:3840 original size:5 final size:6
Alignment explanation
Indices: 3818--3866 Score: 62
Period size: 6 Copynumber: 7.7 Consensus size: 6
3808 CAAAAATACA
*
3818 AAAACAC AAAAAC AAAAAC AAAAAC AAAATAC GAAAAAT AAAAAC AAAA
1 AAAA-AC AAAAAC AAAAAC AAAAAC AAAA-AC -AAAAAC AAAAAC AAAA
3867 TTAAAGGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
6 27 0.71
7 7 0.18
8 4 0.11
ACGTcount: A:0.80, C:0.14, G:0.02, T:0.04
Consensus pattern (6 bp):
AAAAAC
Found at i:3844 original size:26 final size:27
Alignment explanation
Indices: 3810--3867 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
3800 AAAATTAACA
3810 AAAATACAAAA-ACACAAAAACAAAAAC
1 AAAATACAAAATAC-CAAAAACAAAAAC
* *
3837 AAAA-ACAAAATACGAAAAATAAAAAC
1 AAAATACAAAATACCAAAAACAAAAAC
3863 AAAAT
1 AAAAT
3868 TAAAGGAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.78, C:0.14, G:0.02, T:0.07
Consensus pattern (27 bp):
AAAATACAAAATACCAAAAACAAAAAC
Found at i:3867 original size:20 final size:19
Alignment explanation
Indices: 3810--3867 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
3800 AAAATTAACA
*
3810 AAAATACAAAAACACAAAAAC
1 AAAA-ACAAAAACA-AAATAC
3831 AAAAACAAAAACAAAATAC
1 AAAAACAAAAACAAAATAC
*
3850 GAAAAATAAAAACAAAAT
1 -AAAAACAAAAACAAAAT
3868 TAAAGGAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.74
21 4 0.12
ACGTcount: A:0.78, C:0.14, G:0.02, T:0.07
Consensus pattern (19 bp):
AAAAACAAAAACAAAATAC
Found at i:5953 original size:31 final size:31
Alignment explanation
Indices: 5918--6021 Score: 92
Period size: 31 Copynumber: 3.4 Consensus size: 31
5908 TTAATTTGGC
5918 CAAATAAGGGCCTAACGTTTGCTAAAATGCT
1 CAAATAAGGGCCTAACGTTTGCTAAAATGCT
* **
5949 CAAATAAGGGCC---CGGTCTT-TTAATTTGGC-
1 CAAATAAGGGCCTAAC-GT-TTGCTAAAAT-GCT
* * *
5978 CAAATAAGGGTCTAACGTTTGCCAAAATGTT
1 CAAATAAGGGCCTAACGTTTGCTAAAATGCT
6009 CAAATAAGGGCCT
1 CAAATAAGGGCCT
6022 GGCATCGAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
28 1 0.02
29 17 0.31
30 7 0.13
31 29 0.53
32 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTTGCTAAAATGCT
Found at i:5971 original size:60 final size:60
Alignment explanation
Indices: 5904--6020 Score: 207
Period size: 60 Copynumber: 1.9 Consensus size: 60
5894 AAAGGCCCAA
*
5904 TCTTTTAATTTGGCCAAATAAGGGCCTAACGTTTGCTAAAATGCTCAAATAAGGGCCCGG
1 TCTTTTAATTTGGCCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGG
* *
5964 TCTTTTAATTTGGCCAAATAAGGGTCTAACGTTTGCCAAAATGTTCAAATAAGGGCC
1 TCTTTTAATTTGGCCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
6021 TGGCATCGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (60 bp):
TCTTTTAATTTGGCCAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGG
Found at i:6098 original size:31 final size:28
Alignment explanation
Indices: 6060--6227 Score: 106
Period size: 31 Copynumber: 5.6 Consensus size: 28
6050 AACTGATGCC
*
6060 AGGCCCTTATTTGAGCATTTTGGCAAATGTT
1 AGGCCCTTATTTGAGCATTTT---AAAAGTT
** *
6091 AGGCCCTTATTTG-GCCAAATTAAAAGAT
1 AGGCCCTTATTTGAG-CATTTTAAAAGTT
*
6119 CGGACCCTTATTTGAGCATTTTTAATAACGTT
1 AGG-CCCTTATTTGAGCA-TTTTAA-AA-GTT
** *
6151 AGGCCCTTATTTG-GCCAAATTAAAAGATC
1 AGGCCCTTATTTGAG-CATTTTAAAAG-TT
* *
6180 AGGCCCTTTTTTGAGCATTTTGGCAAACGTT
1 AGGCCCTTATTTGAGCATTTT---AAAAGTT
*
6211 AGACCCTTATTTGAGCA
1 AGGCCCTTATTTGAGCA
6228 ATTAACCATC
Statistics
Matches: 106, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
28 8 0.08
29 31 0.29
30 12 0.11
31 47 0.44
32 8 0.08
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (28 bp):
AGGCCCTTATTTGAGCATTTTAAAAGTT
Found at i:6131 original size:60 final size:60
Alignment explanation
Indices: 6059--6223 Score: 253
Period size: 60 Copynumber: 2.8 Consensus size: 60
6049 AAACTGATGC
*
6059 CAGGCCCTTATTTGAGCATTTTGGCAAATGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
**
6119 C-GGACCCTTATTTGAGCATTTT-TAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
1 CAGG-CCCTTATTTGAGCATTTTGGCA-AACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* *
6179 CAGGCCCTTTTTTGAGCATTTTGGCAAACGTTAGACCCTTATTTG
1 CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
6224 AGCAATTAAC
Statistics
Matches: 94, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
59 3 0.03
60 88 0.94
61 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (60 bp):
CAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:6192 original size:29 final size:29
Alignment explanation
Indices: 6091--6192 Score: 102
Period size: 29 Copynumber: 3.4 Consensus size: 29
6081 GGCAAATGTT
6091 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
** *
6120 -GGACCCTTATTTGAG-CATTTTTAATAACG-TT
1 AGG-CCCTTATTTG-GCCA-AATTAA-AA-GATC
6151 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCAAATTAAAAGATC
*
6180 AGGCCCTTTTTTG
1 AGGCCCTTATTTG
6193 AGCATTTTGG
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
28 3 0.05
29 27 0.47
30 10 0.17
31 15 0.26
32 3 0.05
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCAAATTAAAAGATC
Done.