Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010908.1 Corchorus olitorius cultivar O-4 contig10940, 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: 45146
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:151 original size:24 final size:21
Alignment explanation
Indices: 102--150 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
92 TTCACCATGA
102 CACCACCGGTTAAGCCCGTGC
1 CACCACCGGTTAAGCCCGTGC
*
123 CACCACCGGTTATGCCCGTGC
1 CACCACCGGTTAAGCCCGTGC
*
144 CATCACC
1 CACCACC
151 ATTCCAAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.45, G:0.20, T:0.16
Consensus pattern (21 bp):
CACCACCGGTTAAGCCCGTGC
Found at i:3795 original size:32 final size:32
Alignment explanation
Indices: 3759--3903 Score: 202
Period size: 32 Copynumber: 4.5 Consensus size: 32
3749 CGTTTCAGTT
*
3759 CTGAAACGCCACTATTTCGCGGCGTCTCAGAA
1 CTGAAACGCCACTATTTCGCGGCGTCTCAGCA
* *
3791 CTGAATCGCCACTATTTCGCGGCGTCTTAGCA
1 CTGAAACGCCACTATTTCGCGGCGTCTCAGCA
*
3823 CTGAAACGCCACTATTTCGCGGCGTCTCCGCA
1 CTGAAACGCCACTATTTCGCGGCGTCTCAGCA
* * * *
3855 CTGAAACGCCACAATTTAGCGGCGTTTTCA-TA
1 CTGAAACGCCACTATTTCGCGGCG-TCTCAGCA
3887 CTGAAACGCCACTATTT
1 CTGAAACGCCACTATTT
3904 TGAAATCAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
32 97 0.97
33 3 0.03
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (32 bp):
CTGAAACGCCACTATTTCGCGGCGTCTCAGCA
Found at i:6654 original size:15 final size:16
Alignment explanation
Indices: 6624--6663 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
6614 TTACTTTGCT
6624 TTGTTTTCTAGTTTAA
1 TTGTTTTCTAGTTTAA
*
6640 TTGTTTT-TTGTTTAA
1 TTGTTTTCTAGTTTAA
*
6655 TTGCTTTCT
1 TTGTTTTCT
6664 GTCAATCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.68
Consensus pattern (16 bp):
TTGTTTTCTAGTTTAA
Found at i:11609 original size:41 final size:43
Alignment explanation
Indices: 11559--11849 Score: 293
Period size: 41 Copynumber: 6.9 Consensus size: 43
11549 GCCATATAGA
* *
11559 AATTGCCTCTGTGTTATAATTGTGTTTAAGGACTTTAGCATG-G
1 AATTGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAG-ATGAG
11602 -A-TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTAGA-GAG
1 AATTGCCTCTGTGTTATAAATGTGTTTGAGGAC-TTTAGATGAG
* * * * *
11643 AATTGCCCCTGTGTTATAATTGTATTTGGGGACTTT-GAT-AT
1 AATTGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGATGAG
*
11684 AGA-TGCCTCTGTGTTATAAATGTGTTTGAAGACTTTTAGATAGAG
1 A-ATTGCCTCTGTGTTATAAATGTGTTTGAGGAC-TTTAGAT-GAG
* * *
11729 AATTACC-CTGTGTTATAAATATGTTTG-GGACTTTGGTAT-AG
1 AATTGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAG-ATGAG
* *
11770 -A-TGCCTCTCTGTTATAAATGTGTTTGAGGACTTTAGAAAGAG
1 AATTGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAG-ATGAG
*
11812 AATTGCC-CATGTGTTATAAATGTGTTTGGGGACTTTAG
1 AATTGCCTC-TGTGTTATAAATGTGTTTGAGGACTTTAG
11850 TTATTGGGTA
Statistics
Matches: 205, Mismatches: 25, Indels: 35
0.77 0.09 0.13
Matches are distributed among these distances:
39 3 0.01
40 20 0.10
41 70 0.34
42 20 0.10
43 36 0.18
44 51 0.25
45 5 0.02
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.40
Consensus pattern (43 bp):
AATTGCCTCTGTGTTATAAATGTGTTTGAGGACTTTAGATGAG
Found at i:11700 original size:84 final size:85
Alignment explanation
Indices: 11559--11847 Score: 390
Period size: 84 Copynumber: 3.4 Consensus size: 85
11549 GCCATATAGA
* * ** * *
11559 AATTGCCTCTGTGTTATAATTGTGTTTAAGGACTTT-AGCATGGATGCCTCTGTGTTATAAATGT
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGA-TATAGATGCCTCTGTGTTATAAATGT
11623 GTTTGAGGACTTTTAG-AGAG
65 GTTTGAGGACTTTTAGAAGAG
* *
11643 AATTGCCCCTGTGTTATAATTGTATTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTG
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTG
*
11708 TTTGAAGACTTTTAGATAGAG
66 TTTGAGGACTTTTAGA-AGAG
* * * *
11729 AATT-ACCCTGTGTTATAAATATGTTT-GGGACTTTGGTATAGATGCCTCTCTGTTATAAATGTG
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTG
11792 TTTGAGGAC-TTTAGAAAGAG
66 TTTGAGGACTTTTAG-AAGAG
*
11812 AATTGCCCATGTGTTATAAATGTGTTTGGGGACTTT
1 AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTT
11848 AGTTATTGGG
Statistics
Matches: 182, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
83 13 0.07
84 134 0.74
85 27 0.15
86 8 0.04
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.40
Consensus pattern (85 bp):
AATTGCCCCTGTGTTATAAATGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTG
TTTGAGGACTTTTAGAAGAG
Found at i:11847 original size:128 final size:128
Alignment explanation
Indices: 11562--11839 Score: 299
Period size: 125 Copynumber: 2.2 Consensus size: 128
11552 ATATAGAAAT
* *
11562 TGCCTCTGTGTTATAATTGTGTTT-AAGGAC-TTTAGCAT-G-G-A-TGCCTCTGTGTTATAAAT
1 TGCCTCTGTGTTATAAATGTGTTTGAA-GACTTTTAG-ATAGAGAATTACC-CTGTGTTATAAAT
* * * * * *
11621 GTGTTTGAGGACTTTTAGAGAGAATTGCCCCTGTGTTATAATTGTATTTGGGGACTTTGATATAG
63 ATGTTTGAGGACTTTTAGAGAGAATTGCCCCTCTGTTATAAATGTATTTGAGGACTTTGAAAGAG
11686 A
128 A
11687 TGCCTCTGTGTTATAAATGTGTTTGAAGACTTTTAGATAGAGAATTACCCTGTGTTATAAATATG
1 TGCCTCTGTGTTATAAATGTGTTTGAAGACTTTTAGATAGAGAATTACCCTGTGTTATAAATATG
* * * *
11752 TTTG-GGAC-TTTGGTATAG-A-TGCCTCTCTGTTATAAATGTGTTTGAGGACTTTAGAAAGAGA
66 TTTGAGGACTTTTAG-AGAGAATTGCCCCTCTGTTATAAATGTATTTGAGGACTTT-GAAAGAG-
11813 A
128 A
11814 TTGCC-CATGTGTTATAAATGTGTTTG
1 -TGCCTC-TGTGTTATAAATGTGTTTG
11840 GGGACTTTAG
Statistics
Matches: 130, Mismatches: 12, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
125 56 0.43
126 18 0.14
127 10 0.08
128 43 0.33
129 3 0.02
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.40
Consensus pattern (128 bp):
TGCCTCTGTGTTATAAATGTGTTTGAAGACTTTTAGATAGAGAATTACCCTGTGTTATAAATATG
TTTGAGGACTTTTAGAGAGAATTGCCCCTCTGTTATAAATGTATTTGAGGACTTTGAAAGAGA
Found at i:12754 original size:4 final size:4
Alignment explanation
Indices: 12745--12775 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
12735 CAAATGATTG
*
12745 AATA AATA AATA AATA AGTA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AAT
12776 TAATTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:12899 original size:15 final size:13
Alignment explanation
Indices: 12871--12929 Score: 68
Period size: 12 Copynumber: 4.5 Consensus size: 13
12861 GCACCTCGAG
*
12871 TATTTTTTATTTATT
1 TATTTATTA-TTA-T
12886 TATTTATTTATTAT
1 TATTTA-TTATTAT
12900 TA-TTATTATTAT
1 TATTTATTATTAT
12912 TA-TTATTATTAT
1 TATTTATTATTAT
12924 TATTTA
1 TATTTA
12930 AAAAAATTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
12 21 0.51
13 6 0.15
14 3 0.07
15 8 0.20
16 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTATTATTAT
Found at i:12901 original size:3 final size:3
Alignment explanation
Indices: 12893--12927 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12883 ATTTATTTAT
12893 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12928 TAAAAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31343 original size:21 final size:21
Alignment explanation
Indices: 31317--31358 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
31307 GCATCTTAGG
31317 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
31338 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
31359 TTCTTTGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:37508 original size:21 final size:21
Alignment explanation
Indices: 37482--37523 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
37472 GCATCTTAGG
* *
37482 CAACTCCGATGAGCTTGAAAC
1 CAACTCCAAAGAGCTTGAAAC
37503 CAACTCCAAAGAGCTTGAAAC
1 CAACTCCAAAGAGCTTGAAAC
37524 TTCTTTGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.29, G:0.17, T:0.17
Consensus pattern (21 bp):
CAACTCCAAAGAGCTTGAAAC
Done.