Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017640.1 Corchorus olitorius cultivar O-4 contig17673, 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: 23329
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Found at i:4077 original size:28 final size:28
Alignment explanation
Indices: 4028--4117 Score: 87
Period size: 27 Copynumber: 3.3 Consensus size: 28
4018 AAACGACCAT
* * *
4028 AATGCCCCCT-GAAGCACAAATGACTAA
1 AATGCCCCCTGGACGTAAAAATGACTAA
* *
4055 AATGCCCCCTAGG-TGTAAAAATGACCAA
1 AATGCCCCCT-GGACGTAAAAATGACTAA
**
4083 AATG-CCCCTGGACGTGCAAATGACTAA
1 AATGCCCCCTGGACGTAAAAATGACTAA
4110 AATGCCCC
1 AATGCCCC
4118 TGAATTTTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
26 2 0.04
27 30 0.59
28 18 0.35
29 1 0.02
ACGTcount: A:0.37, C:0.29, G:0.18, T:0.17
Consensus pattern (28 bp):
AATGCCCCCTGGACGTAAAAATGACTAA
Found at i:4090 original size:27 final size:27
Alignment explanation
Indices: 4045--4119 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
4035 CCTGAAGCAC
*
4045 AAATGACTAAAATGCCCCCTAGG-TGTAA
1 AAATGACTAAAATG-CCCCT-GGACGTAA
* **
4073 AAATGACCAAAATGCCCCTGGACGTGC
1 AAATGACTAAAATGCCCCTGGACGTAA
4100 AAATGACTAAAATGCCCCTG
1 AAATGACTAAAATGCCCCTG
4120 AATTTTTGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.05
27 26 0.63
28 13 0.32
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGGACGTAA
Found at i:9740 original size:21 final size:21
Alignment explanation
Indices: 9714--9758 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
9704 GGGACGTTTA
9714 GAGCAAACTCAGGATTGACTG
1 GAGCAAACTCAGGATTGACTG
** * *
9735 GAGCAAGTTCGGGGTTGACTG
1 GAGCAAACTCAGGATTGACTG
9756 GAG
1 GAG
9759 TAGCAACTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.38, T:0.20
Consensus pattern (21 bp):
GAGCAAACTCAGGATTGACTG
Found at i:11953 original size:4 final size:4
Alignment explanation
Indices: 11939--12203 Score: 79
Period size: 4 Copynumber: 67.5 Consensus size: 4
11929 AATAAAAAGT
* * * *
11939 AATA GATA AATA AATA AATA AATA GAA-A AATA AGTA AAAA TAATA GATA
1 AATA AATA AATA AATA AATA AATA -AATA AATA AATA AATA -AATA AATA
** ** * * * ** **
11988 AATA AA-A AGATA AATA GGTA TGTA GATA ATTA GATA AATA GGTA GGTA
1 AATA AATA A-ATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * * ** *
12036 AA-A AA-A AGTA GATA ATAGTA AATA AATA GAT- AATA GCTA AATT AATA
1 AATA AATA AATA AATA A-A-TA AATA AATA AATA AATA AATA AATA AATA
* * ** *
12083 AATA AA-A AGATA AAT- AGTA AATA AATA GAT- AATA GTTA AATT AATA
1 AATA AATA A-ATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * ** *
12129 AATA AA-A AGATA AAT- AGTA AATA AATA GAT- AATA GTTA AATT AATA
1 AATA AATA A-ATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
*
12175 AATA AA-A ATATA AAT- AGTA AATA AATA AA
1 AATA AATA A-ATA AATA AATA AATA AATA AA
12204 AAAAATCTTT
Statistics
Matches: 185, Mismatches: 56, Indels: 40
0.66 0.20 0.14
Matches are distributed among these distances:
3 27 0.15
4 140 0.76
5 15 0.08
6 3 0.02
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:12082 original size:19 final size:18
Alignment explanation
Indices: 12044--12179 Score: 86
Period size: 19 Copynumber: 7.4 Consensus size: 18
12034 TAAAAAAAAG
12044 TAGATAATAGTAAATAAA
1 TAGATAATAGTAAATAAA
*
12062 TAGATAATAGCTAAATTAA
1 TAGATAATAG-TAAATAAA
*
12081 TAAATAA-A--AAGATAAA
1 TAGATAATAGTAA-ATAAA
12097 TAG-TAA-A-TAAATAGATAA
1 TAGATAATAGTAAAT--A-AA
* *
12115 TAGTTAAATTAATAAATAAA
1 TAGAT-AA-TAGTAAATAAA
*
12135 AAGATAAATAGTAAATAAA
1 TAGAT-AATAGTAAATAAA
*
12154 TAGATAATAGTTAAATTAA
1 TAGATAATAG-TAAATAAA
*
12173 TAAATAA
1 TAGATAA
12180 AAATATAAAT
Statistics
Matches: 96, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
15 8 0.08
16 8 0.08
17 1 0.01
18 21 0.22
19 41 0.43
20 10 0.10
21 1 0.01
22 1 0.01
23 5 0.05
ACGTcount: A:0.62, C:0.01, G:0.09, T:0.29
Consensus pattern (18 bp):
TAGATAATAGTAAATAAA
Found at i:12093 original size:27 final size:27
Alignment explanation
Indices: 12054--12208 Score: 116
Period size: 27 Copynumber: 6.4 Consensus size: 27
12044 TAGATAATAG
*
12054 TAAATAAATAGAT-AATAGCTAAATTAA
1 TAAATAAAAAGATAAATAG-TAAATTAA
12081 TAAATAAAAAGATAAATAGT--A--AA
1 TAAATAAAAAGATAAATAGTAAATTAA
12104 TAAAT----AGAT-AATAGTTAAATTAA
1 TAAATAAAAAGATAAATAG-TAAATTAA
12127 TAAATAAAAAGATAAATAGT--A--AA
1 TAAATAAAAAGATAAATAGTAAATTAA
12150 TAAAT----AGAT-AATAGTTAAATTAA
1 TAAATAAAAAGATAAATAG-TAAATTAA
* *
12173 TAAATAAAAATATAAATAGTAAATAAA
1 TAAATAAAAAGATAAATAGTAAATTAA
12200 TAAA-AAAAA
1 TAAATAAAAA
12209 TCTTTTTTGG
Statistics
Matches: 104, Mismatches: 3, Indels: 43
0.69 0.02 0.29
Matches are distributed among these distances:
18 10 0.10
19 10 0.10
21 2 0.02
23 28 0.27
25 2 0.02
26 5 0.05
27 32 0.31
28 15 0.14
ACGTcount: A:0.65, C:0.01, G:0.07, T:0.27
Consensus pattern (27 bp):
TAAATAAAAAGATAAATAGTAAATTAA
Found at i:12102 original size:46 final size:46
Alignment explanation
Indices: 12045--12201 Score: 289
Period size: 46 Copynumber: 3.4 Consensus size: 46
12035 AAAAAAAAGT
*
12045 AGAT-AATAGTAAATAAATAGATAATAGCTAAATTAATAAATAAAA
1 AGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAA
12090 AGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAA
1 AGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAA
12136 AGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAA
1 AGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAA
*
12182 ATATAAATAGTAAATAAATA
1 AGATAAATAGTAAATAAATA
12202 AAAAAAATCT
Statistics
Matches: 109, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
45 4 0.04
46 105 0.96
ACGTcount: A:0.63, C:0.01, G:0.08, T:0.28
Consensus pattern (46 bp):
AGATAAATAGTAAATAAATAGATAATAGTTAAATTAATAAATAAAA
Found at i:12195 original size:19 final size:19
Alignment explanation
Indices: 12081--12199 Score: 65
Period size: 19 Copynumber: 6.4 Consensus size: 19
12071 GCTAAATTAA
*
12081 TAAATAAAAAGATAAATAG
1 TAAATAAAAATATAAATAG
* *
12100 TAAATAAATAGAT-AATAG
1 TAAATAAAAATATAAATAG
12118 TTAAATTAATAAATA-AAA-AG
1 -TAAA-TAA-AAATATAAATAG
**
12138 ATAAATAGTAA-ATAAATAG
1 -TAAATAAAAATATAAATAG
* * *
12157 ---ATAATAGT-TAAATTAA
1 TAAATAAAAATATAAA-TAG
12173 TAAATAAAAATATAAATAG
1 TAAATAAAAATATAAATAG
12192 TAAATAAA
1 TAAATAAA
12200 TAAAAAAAAT
Statistics
Matches: 76, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
15 9 0.12
16 2 0.03
17 1 0.01
18 10 0.13
19 36 0.47
20 13 0.17
21 5 0.07
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.28
Consensus pattern (19 bp):
TAAATAAAAATATAAATAG
Found at i:20132 original size:90 final size:91
Alignment explanation
Indices: 19965--20135 Score: 231
Period size: 90 Copynumber: 1.9 Consensus size: 91
19955 ACGATTCAAC
* * * * *
19965 GCAATATTTCTCCAAAGATTGGAGCTCGGTGAGCTCGGTGCAGCATGTTTTCAAACATATTAGGT
1 GCAATATTTCTCCAAAGATTGGAACTCGGTAAGCTCAGTGCAACATGTTTTCAAACATATTAGGG
20030 TGATTCGGTGAATCAATTTGGTACAG
66 TGATTCGGTGAATCAATTTGGTACAG
* * *
20056 GCAATATTTCGT-C-AAGATTGGAATTCGGTAAGCTCAGTGCAACATGTTTTCAGATA-ATTCAG
1 GCAATATTTC-TCCAAAGATTGGAACTCGGTAAGCTCAGTGCAACATGTTTTCAAACATATT-AG
20118 GGTGATTCGGTGAATCAA
64 GGTGATTCGGTGAATCAA
20136 GTTGATGGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
89 3 0.04
90 55 0.79
91 11 0.16
92 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.32
Consensus pattern (91 bp):
GCAATATTTCTCCAAAGATTGGAACTCGGTAAGCTCAGTGCAACATGTTTTCAAACATATTAGGG
TGATTCGGTGAATCAATTTGGTACAG
Found at i:20205 original size:88 final size:89
Alignment explanation
Indices: 19990--20251 Score: 273
Period size: 90 Copynumber: 2.9 Consensus size: 89
19980 AGATTGGAGC
* * * *
19990 TCGGTGAGCTCGGTGCAGCATGTTTTCAAACATATTAGGTTGATTCGGTGAATCAATTTGGTACA
1 TCGGTGAGCTCGGTGCAGCATGTTTTCAAACAT-TCAGGATGATTCGGTGAATCAAGTT-GTACG
* * *
20055 G-GCAATATTTCGTCAAGATTGGAAT
64 GTGCATTATTTCTTCAAGGTTGGAAT
* * * * *
20080 TCGGTAAGCTCAGTGCAACATGTTTTCAGATA-ATTCAGGGTGATTCGGTGAATCAAGTTG-ATG
1 TCGGTGAGCTCGGTGCAGCATGTTTTCA-A-ACATTCAGGATGATTCGGTGAATCAAGTTGTACG
20143 GTGCATTACTTT-TTCAAGGTTGG-AT
64 GTGCATTA-TTTCTTCAAGGTTGGAAT
*** * *
20168 TCGGTGAGCTCGGTGCAGCGCATTTTCAAACAGTTCAGGATGGTTCGGTGAATCAAGCTAGTACG
1 TCGGTGAGCTCGGTGCAGCATGTTTTCAAACA-TTCAGGATGATTCGGTGAATCAAG-TTGTACG
20233 GTGCATTATTTCTTCAAGG
64 GTGCATTATTTCTTCAAGG
20252 ATCAATTCGG
Statistics
Matches: 142, Mismatches: 21, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
86 1 0.01
87 2 0.01
88 48 0.34
89 20 0.14
90 67 0.47
91 3 0.02
92 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (89 bp):
TCGGTGAGCTCGGTGCAGCATGTTTTCAAACATTCAGGATGATTCGGTGAATCAAGTTGTACGGT
GCATTATTTCTTCAAGGTTGGAAT
Done.