Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015146.1 Corchorus olitorius cultivar O-4 contig15179, 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: 28577
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:115 original size:44 final size:45
Alignment explanation
Indices: 54--139 Score: 147
Period size: 44 Copynumber: 1.9 Consensus size: 45
44 TTTAATTCCT
54 ATGTAATATATATAATAACTAAAATACTTACATTAATTAAATGTA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAAATGTA
* *
99 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAAAT
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAAAT
140 TCTTAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 31 0.79
45 8 0.21
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (45 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAAATGTA
Found at i:166 original size:25 final size:24
Alignment explanation
Indices: 130--176 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
120 AATACTTACA
130 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
154 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
177 GTGCAAACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:1005 original size:36 final size:36
Alignment explanation
Indices: 958--1027 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
948 GAGATTTTGG
* *
958 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
994 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
1028 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:2397 original size:58 final size:58
Alignment explanation
Indices: 2299--2408 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
2289 ATCATGCCTC
*
2299 GGTCCTAAAACGTCTTTTTTAGACATCTAACAAAAAAACATGTCACTCGATAAATCTT
1 GGTCCGAAAACGTCTTTTTTAGACATCTAACAAAAAAACATGTCACTCGATAAATCTT
* * *
2357 GGTCCGAAAACGTCTTTTTTTATG-CATCTAA-TAAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC-TTTTTTA-GACATCTAACAAAAAAACATGTCACTCGATA
2409 TTTGATTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
58 31 0.67
59 14 0.30
60 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (58 bp):
GGTCCGAAAACGTCTTTTTTAGACATCTAACAAAAAAACATGTCACTCGATAAATCTT
Found at i:5048 original size:123 final size:128
Alignment explanation
Indices: 4850--5097 Score: 380
Period size: 123 Copynumber: 1.9 Consensus size: 128
4840 AATATATTCA
* *
4850 AAAAATTCTAATATATATAAGTTTTTTTAATTAAAATGGTAAAATGGTAAAAATAAAATAGGTAT
1 AAAAATTCTAATATATATAAGTTTTTTCAATTAAAATAGTAAAATGGTAAAAAT---ATA-GTAT
* *
4915 AAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAAAGTATATT
62 AAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATT
4980 TT
127 TT
4982 AAAAATTCTAATATATATAAG-TTTTTCAATTAAAATAGTAAAATGGTAAAAAT-TA-TA-AA-A
1 AAAAATTCTAATATATATAAGTTTTTTCAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGA
*
5042 ATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAGT
66 ATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGT
5098 TTAAACAATG
Statistics
Matches: 111, Mismatches: 5, Indels: 9
0.89 0.04 0.07
Matches are distributed among these distances:
123 54 0.49
124 2 0.02
125 2 0.02
127 2 0.02
131 30 0.27
132 21 0.19
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (128 bp):
AAAAATTCTAATATATATAAGTTTTTTCAATTAAAATAGTAAAATGGTAAAAATATAGTATAAGA
ATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAGTATATTTT
Found at i:8304 original size:11 final size:11
Alignment explanation
Indices: 8280--8319 Score: 73
Period size: 11 Copynumber: 3.7 Consensus size: 11
8270 ACCTGTTCAT
8280 GGGCCGGG-TC
1 GGGCCGGGTTC
8290 GGGCCGGGTTC
1 GGGCCGGGTTC
8301 GGGCCGGGTTC
1 GGGCCGGGTTC
8312 GGGCCGGG
1 GGGCCGGG
8320 CCTAGCCTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 8 0.28
11 21 0.72
ACGTcount: A:0.00, C:0.28, G:0.60, T:0.12
Consensus pattern (11 bp):
GGGCCGGGTTC
Found at i:11758 original size:27 final size:27
Alignment explanation
Indices: 11720--11772 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
11710 TCTATTGCGG
11720 CAATCACTGTTGATTGCAGAGGCGAGA
1 CAATCACTGTTGATTGCAGAGGCGAGA
* *
11747 CAATGACTGTTGATTGCGGAGGCGAG
1 CAATCACTGTTGATTGCAGAGGCGAG
11773 GTTAAAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.34, T:0.23
Consensus pattern (27 bp):
CAATCACTGTTGATTGCAGAGGCGAGA
Found at i:17155 original size:73 final size:73
Alignment explanation
Indices: 17010--17155 Score: 186
Period size: 73 Copynumber: 2.0 Consensus size: 73
17000 CGATCGATCA
* ** * * *
17010 GTTCGGTTTTCAAAATAATGGTTAATACTCTCTTTGTCCCTAAATATAAGTTCCCGTCTTGAATC
1 GTTCGGTTTTCAAAACAACAGTTAATACCCTCTTTGTCCCCAAATATAAGTTCCCGTCTAGAATC
*
17075 ATTTTTTG
66 ATATTTTG
* **
17083 GTTCGGTTTTCAAAACAACAGTTAGTACCCTCTTTGTCCCCAAATATAAGTTCCTTTCTAGAAGT
1 GTTCGGTTTTCAAAACAACAGTTAATACCCTCTTTGTCCCCAAATATAAGTTCCCGTCTAGAA-T
17148 -ATATTTTG
65 CATATTTTG
17156 TCCCAATTTA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
73 61 0.98
74 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (73 bp):
GTTCGGTTTTCAAAACAACAGTTAATACCCTCTTTGTCCCCAAATATAAGTTCCCGTCTAGAATC
ATATTTTG
Found at i:20163 original size:10 final size:10
Alignment explanation
Indices: 20148--20172 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20138 GAAGATATGA
20148 AGAACAGCCC
1 AGAACAGCCC
20158 AGAACAGCCC
1 AGAACAGCCC
20168 AGAAC
1 AGAAC
20173 GTCCCTAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.36, G:0.20, T:0.00
Consensus pattern (10 bp):
AGAACAGCCC
Found at i:21436 original size:24 final size:23
Alignment explanation
Indices: 21408--21453 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
21398 ACCCTTATCT
21408 TTTATTTTTCG-TTATTTTCTTTTC
1 TTTA-TTTTCGTTTATTTT-TTTTC
21432 TTTATTTTCGTTTATTTTTTTT
1 TTTATTTTCGTTTATTTTTTTT
21454 AGTTACTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.09, C:0.09, G:0.04, T:0.78
Consensus pattern (23 bp):
TTTATTTTCGTTTATTTTTTTTC
Found at i:27523 original size:4 final size:4
Alignment explanation
Indices: 27514--27540 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
27504 CTTTGAAAAA
27514 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
27541 AAAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Done.