Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017011.1 Corchorus olitorius cultivar O-4 contig17044, 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: 40919
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:5016 original size:25 final size:25
Alignment explanation
Indices: 4938--5009 Score: 144
Period size: 25 Copynumber: 2.9 Consensus size: 25
4928 TTAGTTGATT
4938 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
4963 AAATTAGATTTGAGCTACATGAATG
1 AAATTAGATTTGAGCTACATGAATG
4988 AAATTAGATTTGAGCTACATGA
1 AAATTAGATTTGAGCTACATGA
5010 TTAAAATGCG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.32
Consensus pattern (25 bp):
AAATTAGATTTGAGCTACATGAATG
Found at i:5101 original size:26 final size:26
Alignment explanation
Indices: 5065--5115 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5055 AAATATGTAA
5065 AAAAAAAAATGCCAAAGGCGAATATG
1 AAAAAAAAATGCCAAAGGCGAATATG
*
5091 AAAAAAAAATGCCAAAGGCGCATAT
1 AAAAAAAAATGCCAAAGGCGAATAT
5116 TAAGATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.57, C:0.14, G:0.18, T:0.12
Consensus pattern (26 bp):
AAAAAAAAATGCCAAAGGCGAATATG
Found at i:5235 original size:27 final size:27
Alignment explanation
Indices: 5191--5263 Score: 85
Period size: 26 Copynumber: 2.7 Consensus size: 27
5181 AAGTGGACTT
*
5191 AAAATGACCAATATGCCCCTGAATGCA
1 AAAATGACCAAAATGCCCCTGAATGCA
* * * * *
5218 TAAATGACCAAAA-GGCCCTTAGTGTA
1 AAAATGACCAAAATGCCCCTGAATGCA
5244 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
5264 AAGTGACCCT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGCA
Found at i:8870 original size:41 final size:41
Alignment explanation
Indices: 8807--9042 Score: 203
Period size: 41 Copynumber: 5.7 Consensus size: 41
8797 ATTGTCCTTC
*
8807 TGTTATAATTGTGTTT-AGGGACTTTAGTATGGATGCCTCTA
1 TGTTATAAATGTGTTTGA-GGACTTTAGTATGGATGCCTCTA
* ** *
8848 TGTTATAAATGTGTTTGAGGACTTTTAAAG-A-GAATTGCCAATG
1 TGTTATAAATGTGTTTGAGGAC-TTT--AGTATGGA-TGCCTCTA
* * * *
8891 TGTTATAAATGTGTTTGGGGACTTT-GATATAGATGTCTCTG
1 TGTTATAAATGTGTTTGAGGACTTTAG-TATGGATGCCTCTA
* * *
8932 TGTTATAAATGTGTTTGAGGACTTTGGAATAGAGGTGTCC-CTA
1 TGTTATAAATGTGTTTGAGGACTTTAGTAT-G-GATG-CCTCTA
* ** * *
8975 TGTTATAAATGTGTTTGAGGACTTTTGTATTAATGTCTCTT
1 TGTTATAAATGTGTTTGAGGACTTTAGTATGGATGCCTCTA
9016 TGTTATAAATGTGTTTGAGGACTTTAG
1 TGTTATAAATGTGTTTGAGGACTTTAG
9043 AAAGAGAATT
Statistics
Matches: 157, Mismatches: 25, Indels: 26
0.75 0.12 0.12
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 81 0.52
42 11 0.07
43 60 0.38
44 3 0.02
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.43
Consensus pattern (41 bp):
TGTTATAAATGTGTTTGAGGACTTTAGTATGGATGCCTCTA
Found at i:8904 original size:43 final size:41
Alignment explanation
Indices: 8839--9084 Score: 203
Period size: 43 Copynumber: 5.8 Consensus size: 41
8829 TTTAGTATGG
*
8839 ATGCCTCTATGTTATAAATGTGTTTGAGGACTTTTAAAGAGA
1 ATGCC-CTATGTTATAAATGTGTTTGAGGACTTTGAAAGAGA
* * * * *
8881 ATTGCCAATGTGTTATAAATGTGTTTGGGGACTTTGATATAG-
1 A-TGCC-CTATGTTATAAATGTGTTTGAGGACTTTGAAAGAGA
* *
8923 ATGTCTCTGTGTTATAAATGTGTTTGAGGACTTTGGAATAGAG-
1 ATG-CCCTATGTTATAAATGTGTTTGAGGACTTT-GAA-AGAGA
* * **
8966 GTGTCCCTATGTTATAAATGTGTTTGAGGACTTTTG-TA-TTA
1 ATG-CCCTATGTTATAAATGTGTTTGAGGAC-TTTGAAAGAGA
* *
9007 ATGTCTCTTTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGA
1 ATG-CCCTATGTTATAAATGTGTTTGAGGACTTT-GAAAGAGA
* * *
9050 ATTGTCCCTATGTTATAATTGTGTATGGGGACTTT
1 A-TG-CCCTATGTTATAAATGTGTTTGAGGACTTT
9085 TAGTTATTGG
Statistics
Matches: 165, Mismatches: 29, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
40 3 0.02
41 58 0.35
42 6 0.04
43 67 0.41
44 31 0.19
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (41 bp):
ATGCCCTATGTTATAAATGTGTTTGAGGACTTTGAAAGAGA
Found at i:8937 original size:84 final size:84
Alignment explanation
Indices: 8796--9084 Score: 343
Period size: 84 Copynumber: 3.4 Consensus size: 84
8786 GCCATATAGA
* * * * * *
8796 AATTGTCCTTCTGTTATAATTGTGTTTAGGGACTTT-AGTATGGATGCCTCTATGTTATAAATGT
1 AATTGTCCCTATGTTATAAATGTGTTTGGGGACTTTGA-TATAGATGTCTCTATGTTATAAATGT
*
8860 GTTTGAGGACTTTTAAAGAG
65 GTTTGAGGACTTTGAAAGAG
* * *
8880 AATTG-CCAATGTGTTATAAATGTGTTTGGGGACTTTGATATAGATGTCTCTGTGTTATAAATGT
1 AATTGTCC-CTATGTTATAAATGTGTTTGGGGACTTTGATATAGATGTCTCTATGTTATAAATGT
* *
8944 GTTTGAGGACTTTGGAATAG
65 GTTTGAGGACTTTGAAAGAG
** * *
8964 AGGTGTCCCTATGTTATAAATGTGTTTGAGGACTTTTG-TATTA-ATGTCTCTTTGTTATAAATG
1 AATTGTCCCTATGTTATAAATGTGTTTGGGGAC-TTTGATA-TAGATGTCTCTATGTTATAAATG
9027 TGTTTGAGGACTTTAGAAAGAG
64 TGTTTGAGGACTTT-GAAAGAG
* *
9049 AATTGTCCCTATGTTATAATTGTGTATGGGGACTTT
1 AATTGTCCCTATGTTATAAATGTGTTTGGGGACTTT
9085 TAGTTATTGG
Statistics
Matches: 176, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
83 2 0.01
84 132 0.75
85 42 0.24
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.42
Consensus pattern (84 bp):
AATTGTCCCTATGTTATAAATGTGTTTGGGGACTTTGATATAGATGTCTCTATGTTATAAATGTG
TTTGAGGACTTTGAAAGAG
Found at i:10645 original size:28 final size:28
Alignment explanation
Indices: 10578--10664 Score: 77
Period size: 30 Copynumber: 3.0 Consensus size: 28
10568 ACGGGGCAAA
* * *
10578 AAAAAGTCCAAAATTAAGAGTTTATGTGGT
1 AAAATGTCCAAAATTAA-AGTTCA-GGGGT
10608 AAAATGTCCAAAATTAAAGTTCAGGGGT
1 AAAATGTCCAAAATTAAAGTTCAGGGGT
* *
10636 -AAATCGTCCAAGCATTACAAGTTGAGGGG
1 AAAAT-GTCCAA-AATTA-AAGTTCAGGGG
10665 GTCAAAAGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.08
28 10 0.20
29 9 0.18
30 26 0.53
ACGTcount: A:0.40, C:0.11, G:0.23, T:0.25
Consensus pattern (28 bp):
AAAATGTCCAAAATTAAAGTTCAGGGGT
Found at i:12588 original size:17 final size:17
Alignment explanation
Indices: 12568--12601 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12558 TTACAAGGGA
12568 GGAAGTTAAGCAAGCAG
1 GGAAGTTAAGCAAGCAG
12585 GGAAGTTAAGCAAGCAG
1 GGAAGTTAAGCAAGCAG
12602 TGTTTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.35, T:0.12
Consensus pattern (17 bp):
GGAAGTTAAGCAAGCAG
Found at i:16310 original size:15 final size:15
Alignment explanation
Indices: 16290--16322 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
16280 AAAACAAACT
16290 AACTAAACTAACTCA
1 AACTAAACTAACTCA
16305 AACTAAACTAACTCA
1 AACTAAACTAACTCA
16320 AAC
1 AAC
16323 ATTCAAGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.55, C:0.27, G:0.00, T:0.18
Consensus pattern (15 bp):
AACTAAACTAACTCA
Found at i:17028 original size:19 final size:20
Alignment explanation
Indices: 16981--17028 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
16971 TTTAATGTGG
*
16981 GTATACTTATTTATACATGT
1 GTATACTTGTTTATACATGT
17001 -TAT--TTGTTT-TACATGT
1 GTATACTTGTTTATACATGT
17017 GTATACTTGTTT
1 GTATACTTGTTT
17029 CCACATCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
16 7 0.29
17 8 0.33
19 9 0.38
ACGTcount: A:0.23, C:0.08, G:0.12, T:0.56
Consensus pattern (20 bp):
GTATACTTGTTTATACATGT
Found at i:27835 original size:42 final size:43
Alignment explanation
Indices: 27788--27873 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 43
27778 TATTATCTTA
*
27788 ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAGCTAAC
1 ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAC
27830 ATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCTAA
1 ATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAGCTAA
27874 TATTAATTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 6 0.15
45 34 0.85
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.31
Consensus pattern (43 bp):
ATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAGCTAAC
Found at i:35449 original size:11 final size:11
Alignment explanation
Indices: 35433--35458 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35423 TCTTTTTGGC
35433 AAAAAAAAATA
1 AAAAAAAAATA
35444 AAAAAAAAATA
1 AAAAAAAAATA
35455 AAAA
1 AAAA
35459 TTGAATGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAAAAAAATA
Done.