Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013010.1 Corchorus olitorius cultivar O-4 contig13043, 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: 22121
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:2278 original size:19 final size:19
Alignment explanation
Indices: 2256--2299 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2246 AAATGAGACA
*
2256 AATAATATAGGATGAAGAG
1 AATAATATAGGACGAAGAG
*
2275 AATAATATAGGACGGAGAG
1 AATAATATAGGACGAAGAG
2294 AATAAT
1 AATAAT
2300 TAATAAGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.25, T:0.20
Consensus pattern (19 bp):
AATAATATAGGACGAAGAG
Found at i:17918 original size:127 final size:126
Alignment explanation
Indices: 17677--17932 Score: 467
Period size: 127 Copynumber: 2.0 Consensus size: 126
17667 CACTAGAACA
**
17677 GAATTCAGATCATTTTTTGGCCCTCAGCCGCCTGATGGAGAGTGATGATATTCCTTTGCAACCTG
1 GAATTCAGATCATTTTTTGGCCCTCAGCCGCCTGATGGAGAGTGATGATATTCCTGAGCAACCTG
*
17742 ATACTGATAAGTTAAATGCTCTGTATGCTGATTTTTCAAAACTGATCCAGGACCAACCAAT
66 ATACTGATAAGTTAAATGCTCTGTATGCTGATTATTCAAAACTGATCCAGGACCAACCAAT
*
17803 GAATTCAGATCATTTGTTTGGCCCTCAGCTGCCTGATGGAGAGTGATGATATTCCTGAGCAACCT
1 GAATTCAGATCATTT-TTTGGCCCTCAGCCGCCTGATGGAGAGTGATGATATTCCTGAGCAACCT
17868 GATACTGATAAGTTAAATGCTCTGTATGCTGATTATTCAAAACTGATCCAGGACCAACCAAT
65 GATACTGATAAGTTAAATGCTCTGTATGCTGATTATTCAAAACTGATCCAGGACCAACCAAT
17930 GAA
1 GAA
17933 GCTTTAGATT
Statistics
Matches: 125, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
126 15 0.12
127 110 0.88
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (126 bp):
GAATTCAGATCATTTTTTGGCCCTCAGCCGCCTGATGGAGAGTGATGATATTCCTGAGCAACCTG
ATACTGATAAGTTAAATGCTCTGTATGCTGATTATTCAAAACTGATCCAGGACCAACCAAT
Found at i:20496 original size:13 final size:13
Alignment explanation
Indices: 20478--20504 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20468 CTCTATAACC
20478 TCATAAATCATAT
1 TCATAAATCATAT
20491 TCATAAATCATAT
1 TCATAAATCATAT
20504 T
1 T
20505 TATTATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TCATAAATCATAT
Found at i:20653 original size:19 final size:18
Alignment explanation
Indices: 20625--20660 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20615 TTTTTAAGTA
*
20625 AAAATGTAATATATAAATT
1 AAAATATAATAT-TAAATT
20644 AAAATATAATATTAAAT
1 AAAATATAATATTAAAT
20661 AATTAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAAATATAATATTAAATT
Found at i:21407 original size:16 final size:16
Alignment explanation
Indices: 21369--21401 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
21359 ATACCTACCT
21369 ACAAACCAAATATACAA
1 ACAAA-CAAATATACAA
21386 ACAAACAAAT-TACAA
1 ACAAACAAATATACAA
21401 A
1 A
21402 TTAAACTCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 5 0.31
17 5 0.31
ACGTcount: A:0.67, C:0.21, G:0.00, T:0.12
Consensus pattern (16 bp):
ACAAACAAATATACAA
Found at i:21913 original size:2 final size:2
Alignment explanation
Indices: 21898--21952 Score: 53
Period size: 2 Copynumber: 27.5 Consensus size: 2
21888 CGGCCCCGAA
*
21898 AT AT AT A- AT TT AT AT AT -T CAT A- AT AT AT AT AT AT AT AT CAT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT -AT
21939 AT ACT AT AT AT AT A
1 AT A-T AT AT AT AT A
21953 CTTTATTGGG
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
1 3 0.07
2 37 0.82
3 5 0.11
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:21925 original size:22 final size:21
Alignment explanation
Indices: 21897--21952 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
21887 CCGGCCCCGA
*
21897 AATATATAATTTATATATTCAT
1 AATATATAATATATATA-TCAT
21919 AATATAT-ATATATATATCAT
1 AATATATAATATATATATCAT
21939 -ATACTAT-ATATATA
1 AATA-TATAATATATA
21953 CTTTATTGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 3 0.09
20 14 0.44
21 8 0.25
22 7 0.22
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATATAATATATATATCAT
Found at i:21940 original size:11 final size:10
Alignment explanation
Indices: 21898--21952 Score: 53
Period size: 9 Copynumber: 5.5 Consensus size: 10
21888 CGGCCCCGAA
21898 ATATATA-AT
1 ATATATATAT
*
21907 TTATATAT-T
1 ATATATATAT
21916 CATA-ATATAT
1 -ATATATATAT
21926 ATATATATAT
1 ATATATATAT
21936 CATATACTATAT
1 -ATATA-TATAT
21948 ATATA
1 ATATA
21953 CTTTATTGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 14 0.37
10 9 0.24
11 10 0.26
12 5 0.13
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (10 bp):
ATATATATAT
Found at i:22112 original size:11 final size:11
Alignment explanation
Indices: 22072--22120 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
22062 TTATTTCATG
22072 AATTTTATTAT
1 AATTTTATTAT
*
22083 AATTATT-TAGAT
1 AATT-TTAT-TAT
*
22095 TATTTTATTAT
1 AATTTTATTAT
22106 AATTTTATTAT
1 AATTTTATTAT
22117 AATT
1 AATT
22121 A
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
11 23 0.74
12 8 0.26
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
AATTTTATTAT
Done.