Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024274.1 Corchorus olitorius cultivar O-4 contig24307, 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: 37839
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:13662 original size:13 final size:13
Alignment explanation
Indices: 13644--13669 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13634 CTTGGCATGA
13644 GTGATGATTTTTG
1 GTGATGATTTTTG
13657 GTGATGATTTTTG
1 GTGATGATTTTTG
13670 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:14043 original size:19 final size:19
Alignment explanation
Indices: 14021--14072 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
14011 GGGCTGAAAT
14021 TAATTAATTATTAAATAAA
1 TAATTAATTATTAAATAAA
* * *
14040 TAA-TAATTATTTTATTGAA
1 TAATTAATTA-TTAAATAAA
14059 TAATT-ATTATTAAA
1 TAATTAATTATTAAA
14073 AACACCACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TAATTAATTATTAAATAAA
Found at i:24652 original size:21 final size:21
Alignment explanation
Indices: 24623--24672 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
24613 GAGCCATGAC
* * *
24623 ACAACCCACCTGGGTGATTAG
1 ACAAACCACATGGGTCATTAG
* *
24644 GCAAACCACATGGGTCTTTAG
1 ACAAACCACATGGGTCATTAG
24665 ACAAACCA
1 ACAAACCA
24673 TGTGGGCACC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (21 bp):
ACAAACCACATGGGTCATTAG
Found at i:29032 original size:28 final size:29
Alignment explanation
Indices: 28996--29073 Score: 72
Period size: 28 Copynumber: 2.8 Consensus size: 29
28986 TTCAAAGTAC
* *
28996 AAGGTTAAAACTGTAAATTTA-ACCTTCT
1 AAGGGTAAAACTGTAAATTTATACATTCT
*
29024 AAGGGTAAAA-TGGT-AATTTATTCATTCT
1 AAGGGTAAAACT-GTAAATTTATACATTCT
* * *
29052 TAGGGTAAAACGGTAATTTTAT
1 AAGGGTAAAACTGTAAATTTAT
29074 GCCCATACGG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
27 7 0.17
28 27 0.68
29 6 0.15
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (29 bp):
AAGGGTAAAACTGTAAATTTATACATTCT
Found at i:29915 original size:7 final size:6
Alignment explanation
Indices: 29889--29947 Score: 75
Period size: 6 Copynumber: 9.7 Consensus size: 6
29879 TTTTATTTTA
* *
29889 TTTTCT TTTTCC TTTTCT TTTTCC TTTTCTT TTTTCT TTTTCT TTTCTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTT-TCT
29939 TTTT-T TTTT
1 TTTTCT TTTT
29948 ATTCTCATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
5 5 0.11
6 31 0.66
7 11 0.23
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:29923 original size:19 final size:19
Alignment explanation
Indices: 29889--29947 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
29879 TTTTATTTTA
*
29889 TTTTCTTTT-TCCTTTTCT
1 TTTTCTTTTCTCTTTTTCT
29907 TTTTCCTTTTCT-TTTTTCT
1 TTTT-CTTTTCTCTTTTTCT
29926 TTTTCTTTTCTCTTTTT-T
1 TTTTCTTTTCTCTTTTTCT
29944 TTTT
1 TTTT
29948 ATTCTCATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 16 0.43
19 20 0.54
20 1 0.03
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTCTTTTCTCTTTTTCT
Found at i:31604 original size:16 final size:16
Alignment explanation
Indices: 31585--31617 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31575 CCCGAAAAAT
31585 CCAAAACCCAAATGAC
1 CCAAAACCCAAATGAC
*
31601 CCAAAACCCAAGTGAC
1 CCAAAACCCAAATGAC
31617 C
1 C
31618 TGAGGCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.39, G:0.09, T:0.06
Consensus pattern (16 bp):
CCAAAACCCAAATGAC
Found at i:33423 original size:31 final size:31
Alignment explanation
Indices: 33385--33447 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
33375 ATATGTTAGA
*
33385 TAAATAAG-GATATAATAGGCTTTTCAAAAGT
1 TAAATAAGAG-TATAATAGGCGTTTCAAAAGT
33416 TAAATAAGAGTATAATAGGCGTTTCAAAAGT
1 TAAATAAGAGTATAATAGGCGTTTCAAAAGT
33447 T
1 T
33448 TTACAAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.32
Consensus pattern (31 bp):
TAAATAAGAGTATAATAGGCGTTTCAAAAGT
Found at i:33899 original size:53 final size:53
Alignment explanation
Indices: 33823--33931 Score: 200
Period size: 53 Copynumber: 2.1 Consensus size: 53
33813 AAACTTCATG
*
33823 AATATATATACTATATATTATTTTTAGTTACCAGGGAAATTACTAAAAGGCCA
1 AATACATATACTATATATTATTTTTAGTTACCAGGGAAATTACTAAAAGGCCA
*
33876 AATACATATACTATATATTATTTTTAGTTACCAGGGAAATTACTAAATGGCCA
1 AATACATATACTATATATTATTTTTAGTTACCAGGGAAATTACTAAAAGGCCA
33929 AAT
1 AAT
33932 TGAGGATTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (53 bp):
AATACATATACTATATATTATTTTTAGTTACCAGGGAAATTACTAAAAGGCCA
Found at i:35950 original size:110 final size:107
Alignment explanation
Indices: 35747--35962 Score: 342
Period size: 110 Copynumber: 2.0 Consensus size: 107
35737 TTCAAAAACC
* *
35747 TTGACCTGAAATATCTAAAATACCTTTTTAAATTTTTAAATTTTAATTATATTTTAAAGATTAAT
1 TTGACCTGAAATATCTAAAATACCCTTTTAAAGTTTTAAATTTTAATTATATTTTAAAGATTAAT
35812 ATGTAATCTATCAAACCAGATTTCATTTCCATATTAAAAAAA
66 ATGTAATCTATCAAACCAGATTTCATTTCCATATTAAAAAAA
*
35854 TTGACCTGAAATATCTAAAATACCCTTTTAAAGTTTTAAATTTTTTTAATTATATTTTAAAGGTT
1 TTGACCTGAAATATCTAAAATACCCTTTTAAAGTTTTAAA---TTTTAATTATATTTTAAAGATT
* * * *
35919 AATATGTAATCTATCCAGCTAGATTTTATTTCCATATTAAAAAA
63 AATATGTAATCTATCAAACCAGATTTCATTTCCATATTAAAAAA
35963 GTCTAAAATA
Statistics
Matches: 99, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
107 38 0.38
110 61 0.62
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (107 bp):
TTGACCTGAAATATCTAAAATACCCTTTTAAAGTTTTAAATTTTAATTATATTTTAAAGATTAAT
ATGTAATCTATCAAACCAGATTTCATTTCCATATTAAAAAAA
Found at i:37017 original size:32 final size:32
Alignment explanation
Indices: 36981--37042 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
36971 CGATTCTATT
* *
36981 AATTTAACAATTACAGTCAAGATTATAAAATG
1 AATTTAACAATTACAATCAAGATTAAAAAATG
**
37013 AATTTAACAATTGTAATCAAGATTAAAAAA
1 AATTTAACAATTACAATCAAGATTAAAAAA
37043 ATGACCGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (32 bp):
AATTTAACAATTACAATCAAGATTAAAAAATG
Done.