Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020685.1 Corchorus olitorius cultivar O-4 contig20718, 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: 29479
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:12482 original size:23 final size:22
Alignment explanation
Indices: 12455--12506 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
12445 AATAGTTGTT
*
12455 AAGCAATCCAAAATTAAATAAAA
1 AAGCAATACAAAATTAAAT-AAA
* *
12478 AAGCAAAAGAAAATTAAATAAA
1 AAGCAATACAAAATTAAATAAA
12500 AAGCAAT
1 AAGCAAT
12507 TAAAATAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.67, C:0.10, G:0.08, T:0.15
Consensus pattern (22 bp):
AAGCAATACAAAATTAAATAAA
Found at i:16994 original size:93 final size:93
Alignment explanation
Indices: 16825--17000 Score: 235
Period size: 93 Copynumber: 1.9 Consensus size: 93
16815 TGCATGTTCT
* * * *
16825 CCTTTGTGCCAAGCTAGAAGTAAAAATATGACCTCATGGTTAAGCTAAAGATATGACATGAATCT
1 CCTTTGCGCCAAGCTAGAAGTAAAAATATGACCTCATGCTCAAGCTAAAGATATGACACGAATCT
* *
16890 GACGTTAGTTCCAAGCTAAACATTTTCA
66 CACCTTAGTTCCAAGCTAAACATTTTCA
* * * * * *
16918 CCTTTGCGCCAAGTTATAAGTAAAGATCTTACCTCATGCTCGAGCTAAAGATATGACACGAATCT
1 CCTTTGCGCCAAGCTAGAAGTAAAAATATGACCTCATGCTCAAGCTAAAGATATGACACGAATCT
*
16983 CACCTTGGTTCCAAGCTA
66 CACCTTAGTTCCAAGCTA
17001 TAAGTAAAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (93 bp):
CCTTTGCGCCAAGCTAGAAGTAAAAATATGACCTCATGCTCAAGCTAAAGATATGACACGAATCT
CACCTTAGTTCCAAGCTAAACATTTTCA
Found at i:17003 original size:67 final size:67
Alignment explanation
Indices: 16926--17067 Score: 232
Period size: 67 Copynumber: 2.1 Consensus size: 67
16916 CACCTTTGCG
* * * *
16926 CCAAGTTATAAGTAAAGATCTTACCTCAT-GCTCGAGCTAAAGATATGACACGAATCTCACCTTG
1 CCAAGCTATAAGTAAAAATCTGACCTCATGGC-CAAGCTAAAGATATGACACGAATCTCACCTTG
16990 GTT
65 GTT
16993 CCAAGCTATAAGTAAAAATCTGACCTCATGGCCAAGCTAAAGATATGACACGAATCTCACCTTGG
1 CCAAGCTATAAGTAAAAATCTGACCTCATGGCCAAGCTAAAGATATGACACGAATCTCACCTTGG
17058 TT
66 TT
17060 CCAAGCTA
1 CCAAGCTA
17068 AGAATATCAC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 68 0.97
68 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (67 bp):
CCAAGCTATAAGTAAAAATCTGACCTCATGGCCAAGCTAAAGATATGACACGAATCTCACCTTGG
TT
Found at i:17064 original size:36 final size:36
Alignment explanation
Indices: 16960--17068 Score: 126
Period size: 36 Copynumber: 3.2 Consensus size: 36
16950 CTCATGCTCG
16960 AGCTAAAGATATGACACGAATCTCACCTTGGTTCCA
1 AGCTAAAGATATGACACGAATCTCACCTTGGTTCCA
*
16996 AGCTATAAG-TA--A-A--AATCTGACCTCATGG--CCA
1 AGCTA-AAGATATGACACGAATCTCACCT--TGGTTCCA
17027 AGCTAAAGATATGACACGAATCTCACCTTGGTTCCA
1 AGCTAAAGATATGACACGAATCTCACCTTGGTTCCA
17063 AGCTAA
1 AGCTAA
17069 GAATATCACA
Statistics
Matches: 60, Mismatches: 2, Indels: 22
0.71 0.02 0.26
Matches are distributed among these distances:
30 3 0.05
31 19 0.32
33 5 0.08
34 5 0.08
36 25 0.42
37 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (36 bp):
AGCTAAAGATATGACACGAATCTCACCTTGGTTCCA
Found at i:19227 original size:30 final size:30
Alignment explanation
Indices: 19193--19253 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
19183 ATGTATACTA
*
19193 TGTTAACAACT-TGTTAACAACTATCATCAT
1 TGTTAA-AACTATGTTAACAACTATAATCAT
*
19223 TGTTAATACTATGTTAACAACTATAATCAT
1 TGTTAAAACTATGTTAACAACTATAATCAT
19253 T
1 T
19254 TAGGGTATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 3 0.11
30 25 0.89
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (30 bp):
TGTTAAAACTATGTTAACAACTATAATCAT
Found at i:20060 original size:21 final size:21
Alignment explanation
Indices: 20034--20089 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
20024 TATATGCATG
20034 GTCAAACCCCAAAAGATGATA
1 GTCAAACCCCAAAAGATGATA
***
20055 GTCAAACCCCAAATTTTGATA
1 GTCAAACCCCAAAAGATGATA
*
20076 GTCAAACCACAAAA
1 GTCAAACCCCAAAA
20090 AACATTTCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.46, C:0.25, G:0.11, T:0.18
Consensus pattern (21 bp):
GTCAAACCCCAAAAGATGATA
Found at i:20101 original size:78 final size:77
Alignment explanation
Indices: 20006--20236 Score: 309
Period size: 78 Copynumber: 3.0 Consensus size: 77
19996 ACAAAAGCTA
* * * *
20006 ACAAAAATCATTTCATTGTATATGCATGGTCAAACCCCAAAAGATGATAGTCAAACCCCAAATTT
1 ACAAAAAACATTTCATTGTACATGCATGGTCAAACCCC-AAAGTTGATAGTCAAACCCCAAAATT
20071 TGATAGTCAAACC
65 TGATAGTCAAACC
* * * *
20084 ACAAAAAACATTTCATTGTACATCCATGGTCAAACCCTAAATTTAGATAGGCAAACCCCAAAATT
1 ACAAAAAACATTTCATTGTACATGCATGGTCAAACCCCAAAGTT-GATAGTCAAACCCCAAAATT
*
20149 TGATTGTCAAACC
65 TGATAGTCAAACC
* * * * *
20162 ATAAAAAACATTTCACTATACATGCATGGTCAAACCCCAAAGTTTAATAGTCAAACCCCAAAGTT
1 ACAAAAAACATTTCATTGTACATGCATGGTCAAACCCCAAAG-TTGATAGTCAAACCCCAAAATT
20227 TGATAGTCAA
65 TGATAGTCAA
20237 CCCCTAAAAT
Statistics
Matches: 132, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
77 4 0.03
78 126 0.95
79 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.11, T:0.26
Consensus pattern (77 bp):
ACAAAAAACATTTCATTGTACATGCATGGTCAAACCCCAAAGTTGATAGTCAAACCCCAAAATTT
GATAGTCAAACC
Found at i:20167 original size:21 final size:22
Alignment explanation
Indices: 20112--20167 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
20102 TACATCCATG
20112 GTCAAACCCT-AAATTTAGATA
1 GTCAAACCCTAAAATTTAGATA
* * *
20133 GGCAAACCCCAAAATTT-GATT
1 GTCAAACCCTAAAATTTAGATA
*
20154 GTCAAACCATAAAA
1 GTCAAACCCTAAAA
20168 AACATTTCAC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.23
Consensus pattern (22 bp):
GTCAAACCCTAAAATTTAGATA
Found at i:20216 original size:21 final size:21
Alignment explanation
Indices: 20190--20260 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
20180 TACATGCATG
*
20190 GTCAAACCCCAAAGTTTAATA
1 GTCAAACCCCAAAGTTTGATA
20211 GTCAAACCCCAAAGTTTGATA
1 GTCAAACCCCAAAGTTTGATA
*
20232 GTC-AACCCCTAAAATTTGATA
1 GTCAAACCCC-AAAGTTTGATA
20253 GTCAAACC
1 GTCAAACC
20261 ACGCTAAACC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 6 0.13
21 36 0.78
22 4 0.09
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.24
Consensus pattern (21 bp):
GTCAAACCCCAAAGTTTGATA
Found at i:23375 original size:19 final size:19
Alignment explanation
Indices: 23327--23367 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
23317 CGAACCCGAT
23327 TATGAATATATAGAATATA
1 TATGAATATATAGAATATA
*
23346 TATGAAAATATA-ACATATA
1 TATGAATATATAGA-ATATA
23365 TAT
1 TAT
23368 ATATATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (19 bp):
TATGAATATATAGAATATA
Found at i:25897 original size:21 final size:21
Alignment explanation
Indices: 25871--25920 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
25861 TACATACATG
25871 GTCAAACCCTAAAATTTGATA
1 GTCAAACCCTAAAATTTGATA
* *
25892 GTCAAACTCTAAAGTTTGATA
1 GTCAAACCCTAAAATTTGATA
25913 GTCCAAAC
1 GT-CAAAC
25921 ACGTTGAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (21 bp):
GTCAAACCCTAAAATTTGATA
Done.