Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018639.1 Corchorus olitorius cultivar O-4 contig18672, 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: 26817
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Found at i:2237 original size:21 final size:21
Alignment explanation
Indices: 2170--2237 Score: 50
Period size: 21 Copynumber: 3.1 Consensus size: 21
2160 ACCAACAATT
2170 AATATTAGCTTTATTTTGATG
1 AATATTAGCTTTATTTTGATG
* ***
2191 AATTATCTAG--ATATGAGGAGTAG
1 AA-TAT-TAGCTTTATTTTGA-T-G
2214 AATATTAGCTTTATTTTGATG
1 AATATTAGCTTTATTTTGATG
2235 AAT
1 AAT
2238 TACCTAGAGA
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
21 14 0.42
22 8 0.24
23 11 0.33
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (21 bp):
AATATTAGCTTTATTTTGATG
Found at i:2705 original size:44 final size:44
Alignment explanation
Indices: 2625--2726 Score: 136
Period size: 44 Copynumber: 2.3 Consensus size: 44
2615 CTAAAAGTGC
* *
2625 ATTACCTAA-ATTATACTTCCTCATCTCAAGGTAATTCATCAAA
1 ATTAACTAATATTATACTTCCTCATCTCAAGGCAATTCATCAAA
*
2668 ATTAACTAATATTATAC-TCCTTCATCTCTAGGCAATTCATCAAA
1 ATTAACTAATATTATACTTCC-TCATCTCAAGGCAATTCATCAAA
*
2712 ATAAATCTAATATTA
1 ATTAA-CTAATATTA
2727 AATGTTGCTT
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
43 11 0.21
44 32 0.62
45 9 0.17
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (44 bp):
ATTAACTAATATTATACTTCCTCATCTCAAGGCAATTCATCAAA
Found at i:9173 original size:24 final size:24
Alignment explanation
Indices: 9140--9186 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
9130 TGGACTTGAA
9140 GATGACAATGGAGAGCAAGGAGAG
1 GATGACAATGGAGAGCAAGGAGAG
* * *
9164 GATGAGAATGGAGTGCATGGAGA
1 GATGACAATGGAGAGCAAGGAGA
9187 CATGGAGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.06, G:0.43, T:0.13
Consensus pattern (24 bp):
GATGACAATGGAGAGCAAGGAGAG
Found at i:9200 original size:18 final size:18
Alignment explanation
Indices: 9167--9214 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
9157 AGGAGAGGAT
9167 GAGA-ATGGAG-TGCATG
1 GAGACATGGAGATGCATG
9183 GAGACATGGAGATGCATG
1 GAGACATGGAGATGCATG
9201 GAGACCATGGAGAT
1 GAGA-CATGGAGAT
9215 AACGATGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 4 0.14
17 6 0.21
18 10 0.34
19 9 0.31
ACGTcount: A:0.33, C:0.10, G:0.40, T:0.17
Consensus pattern (18 bp):
GAGACATGGAGATGCATG
Found at i:12560 original size:13 final size:13
Alignment explanation
Indices: 12507--12561 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
12497 TTGAGGAACT
*
12507 ATTTTATT-ACTG
1 ATTTTATTAAATG
12519 -TTTTATTAAATTG
1 ATTTTATTAAA-TG
* *
12532 TTTTTA-TAAATA
1 ATTTTATTAAATG
12544 ATTTTATTAAATG
1 ATTTTATTAAATG
12557 ATTTT
1 ATTTT
12562 GGGTGCATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 7 0.20
12 7 0.20
13 16 0.46
14 5 0.14
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (13 bp):
ATTTTATTAAATG
Found at i:18350 original size:2 final size:2
Alignment explanation
Indices: 18343--18380 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
18333 ATGTTCCTTA
* *
18343 AT AT AT AT AT AT AT AT AT AA AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18381 TGAATGGAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21104 original size:21 final size:21
Alignment explanation
Indices: 21080--21150 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
21070 CTTAGGCAAT
*
21080 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
21101 TCCAATGAGATTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
21122 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
21143 TCCAATGA
1 TCCAATGA
21151 ACTCCTAGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 3 0.07
21 43 0.93
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:22873 original size:33 final size:33
Alignment explanation
Indices: 22836--22925 Score: 108
Period size: 33 Copynumber: 2.7 Consensus size: 33
22826 AGAATTTGTT
22836 TCATCACAAACAACACCTAAAACAGATTTAGTA
1 TCATCACAAACAACACCTAAAACAGATTTAGTA
* ** *
22869 TCATCACAAACAACACTTAAATTAGGTTTAGTA
1 TCATCACAAACAACACCTAAAACAGATTTAGTA
* * * *
22902 TCATTACTAACAACATCTAGAACA
1 TCATCACAAACAACACCTAAAACA
22926 CTCTTTGCAA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.26
Consensus pattern (33 bp):
TCATCACAAACAACACCTAAAACAGATTTAGTA
Done.