Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022833.1 Corchorus olitorius cultivar O-4 contig22866, 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: 21087
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:7703 original size:2 final size:2
Alignment explanation
Indices: 7696--7728 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7686 TATAAATTAG
7696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7729 AACTTGCTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7870 original size:30 final size:31
Alignment explanation
Indices: 7797--7871 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
7787 GGCTTAAATA
* *
7797 CCAAATAAATCCCTTACCTTTTTATTTTTGG
1 CCAAATAAATCCCTCACCTTTTTATTTTGGG
* *
7828 ACAAATAAATCCCTCATCTTTTT-TTTTGGG
1 CCAAATAAATCCCTCACCTTTTTATTTTGGG
*
7858 CCAAAAAAATCCCT
1 CCAAATAAATCCCT
7872 TTGCTATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
30 18 0.47
31 20 0.53
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.39
Consensus pattern (31 bp):
CCAAATAAATCCCTCACCTTTTTATTTTGGG
Found at i:15025 original size:28 final size:28
Alignment explanation
Indices: 14961--15015 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
14951 GTAATCAGTA
* *
14961 AAATGGTATTAGTAATCAATAAAAGAGT
1 AAATAGTAATAGTAATCAATAAAAGAGT
* *
14989 AAATAGTAATAGTAATCAGTTAAAGAG
1 AAATAGTAATAGTAATCAATAAAAGAG
15016 CAATCAGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.51, C:0.04, G:0.18, T:0.27
Consensus pattern (28 bp):
AAATAGTAATAGTAATCAATAAAAGAGT
Found at i:15041 original size:7 final size:7
Alignment explanation
Indices: 15031--15164 Score: 66
Period size: 7 Copynumber: 19.1 Consensus size: 7
15021 AGTAAATGGT
15031 AAGAGTA
1 AAGAGTA
15038 AAGAGTAA
1 AAGAGT-A
15046 AAGAGT-
1 AAGAGTA
15052 -AGTAGTA
1 AAG-AGTA
*
15059 GTA-AGTA
1 -AAGAGTA
15066 AAGAGTA
1 AAGAGTA
15073 AAGAGTA
1 AAGAGTA
15080 ATCA-AG-A
1 A--AGAGTA
15087 AAGAGT-
1 AAGAGTA
*
15093 AATAGTA
1 AAGAGTA
** *
15100 ATCAGCAA
1 AAGAG-TA
15108 AAGAGTA
1 AAGAGTA
15115 AAGAGTA
1 AAGAGTA
**
15122 ATCAGTAA
1 AAGAGT-A
15130 AAGAGT-
1 AAGAGTA
*
15136 AATAGTA
1 AAGAGTA
**
15143 ATCAGTA
1 AAGAGTA
15150 AAGAGTA
1 AAGAGTA
15157 AAGAGTA
1 AAGAGTA
15164 A
1 A
15165 TCAGTTAAAT
Statistics
Matches: 96, Mismatches: 17, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
5 3 0.03
6 16 0.17
7 57 0.59
8 18 0.19
9 2 0.02
ACGTcount: A:0.54, C:0.04, G:0.24, T:0.19
Consensus pattern (7 bp):
AAGAGTA
Found at i:15079 original size:21 final size:21
Alignment explanation
Indices: 14971--15192 Score: 167
Period size: 21 Copynumber: 10.6 Consensus size: 21
14961 AAATGGTATT
* *
14971 AGTAATCAATAAAAGAGTAAAT
1 AGTAATCAGT-AAAGAGTAAAG
**
14993 AGTAAT-AGTAATCAGTTAAAG
1 AGTAATCAGTAAAGAG-TAAAG
*
15014 AGCAATCAGTAAATG-GT-AAG
1 AGTAATCAGTAAA-GAGTAAAG
**
15034 AGTAAAGAGTAAAAGAGT--AG
1 AGTAATCAGT-AAAGAGTAAAG
* *
15054 TAGTAGTAAGTAAAGAGTAAAG
1 -AGTAATCAGTAAAGAGTAAAG
*
15076 AGTAATCAAG-AAAGAGT-AAT
1 AGTAATC-AGTAAAGAGTAAAG
*
15096 AGTAATCAGCAAAAGAGTAAAG
1 AGTAATCAG-TAAAGAGTAAAG
*
15118 AGTAATCAGTAAAAGAGT-AAT
1 AGTAATCAGT-AAAGAGTAAAG
15139 AGTAATCAGTAAAGAGTAAAG
1 AGTAATCAGTAAAGAGTAAAG
*
15160 AGTAATCAGTTAAATG-GTAATG
1 AGTAATCAG-TAAA-GAGTAAAG
15182 -GTAATCAGTAA
1 AGTAATCAGTAA
15193 TTAAAATTCA
Statistics
Matches: 163, Mismatches: 21, Indels: 34
0.75 0.10 0.16
Matches are distributed among these distances:
19 2 0.01
20 43 0.26
21 74 0.45
22 43 0.26
23 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (21 bp):
AGTAATCAGTAAAGAGTAAAG
Found at i:15165 original size:42 final size:41
Alignment explanation
Indices: 15017--15192 Score: 189
Period size: 42 Copynumber: 4.2 Consensus size: 41
15007 GTTAAAGAGC
** *
15017 AATCAGTAAATG-GT-AAGAGTAAAGAGTAAAAGAGTAGTAGT
1 AATCAGTAAA-GAGTAAAGAGTAATCAGTAAAAG-GTAATAGT
* *
15058 AGTAAGTAAAGAGTAAAGAGTAATCA--AGAAAGAGTAATAGT
1 AATCAGTAAAGAGTAAAGAGTAATCAGTA-AAAG-GTAATAGT
*
15099 AATCAGCAAAAGAGTAAAGAGTAATCAGTAAAAGAGTAATAGT
1 AATCAG-TAAAGAGTAAAGAGTAATCAGTAAAAG-GTAATAGT
* *
15142 AATCAGTAAAGAGTAAAGAGTAATCAGTTAAATGGTAATGGT
1 AATCAGTAAAGAGTAAAGAGTAATCAG-TAAAAGGTAATAGT
15184 AATCAGTAA
1 AATCAGTAA
15193 TTAAAATTCA
Statistics
Matches: 117, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
40 2 0.02
41 26 0.22
42 64 0.55
43 24 0.21
44 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.22
Consensus pattern (41 bp):
AATCAGTAAAGAGTAAAGAGTAATCAGTAAAAGGTAATAGT
Found at i:15318 original size:35 final size:34
Alignment explanation
Indices: 15226--15333 Score: 146
Period size: 35 Copynumber: 3.1 Consensus size: 34
15216 GAAAAAAGAT
*
15226 TAAAAAGAGTAAAAATGGTATTTAGTAATTAAAG
1 TAAAAAGAGTAAAAATGGTATTCAGTAATTAAAG
** * *
15260 TTAAAAA-TTTAAAAATGGCATTCAGTAACTAAAG
1 -TAAAAAGAGTAAAAATGGTATTCAGTAATTAAAG
15294 TAAAAAGGAGTAAAAATGGTATTCAGTAATTAAAG
1 TAAAAA-GAGTAAAAATGGTATTCAGTAATTAAAG
15329 TAAAA
1 TAAAA
15334 CAGGCAAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
33 6 0.10
34 22 0.35
35 34 0.55
ACGTcount: A:0.53, C:0.04, G:0.16, T:0.28
Consensus pattern (34 bp):
TAAAAAGAGTAAAAATGGTATTCAGTAATTAAAG
Found at i:15344 original size:35 final size:33
Alignment explanation
Indices: 15226--15347 Score: 127
Period size: 35 Copynumber: 3.5 Consensus size: 33
15216 GAAAAAAGAT
* *
15226 TAAAAAGAGTAAAAATGGTATTTAGTAATTAAAG
1 TAAAAAG-GAAAAAATGGTATTCAGTAATTAAAG
*** * *
15260 TTAAAAATTTAAAAATGGCATTCAGTAACTAAAG
1 -TAAAAAGGAAAAAATGGTATTCAGTAATTAAAG
15294 TAAAAAGGAGTAAAAATGGTATTCAGTAATTAAAG
1 TAAAAAGGA--AAAAATGGTATTCAGTAATTAAAG
15329 TAAAACAGGCAAAAAATGG
1 TAAAA-AGG-AAAAAATGG
15348 AAACCAGTAA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
33 6 0.08
34 22 0.30
35 41 0.56
36 3 0.04
37 1 0.01
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.25
Consensus pattern (33 bp):
TAAAAAGGAAAAAATGGTATTCAGTAATTAAAG
Found at i:15356 original size:35 final size:34
Alignment explanation
Indices: 15282--15357 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
15272 AAATGGCATT
* **
15282 CAGTAACTAAAGTAAAAAGGAGTAAAAATGGTATT
1 CAGTAACTAAAGTAAAAAGGAG-AAAAATGGAAAC
*
15317 CAGTAATTAAAGTAAAACAGGCA-AAAAATGGAAAC
1 CAGTAACTAAAGTAAAA-AGG-AGAAAAATGGAAAC
15352 CAGTAA
1 CAGTAA
15358 AAAAGGTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
35 31 0.89
36 3 0.09
37 1 0.03
ACGTcount: A:0.54, C:0.09, G:0.18, T:0.18
Consensus pattern (34 bp):
CAGTAACTAAAGTAAAAAGGAGAAAAATGGAAAC
Found at i:15393 original size:25 final size:26
Alignment explanation
Indices: 15365--15427 Score: 85
Period size: 25 Copynumber: 2.4 Consensus size: 26
15355 TAAAAAAGGT
15365 AAAGTAAGAAAATGATAATGAGTAAA
1 AAAGTAAGAAAATGATAATGAGTAAA
*
15391 AAGAGT-A-AAAATGGTAATGAGTAAA
1 AA-AGTAAGAAAATGATAATGAGTAAA
15416 AAGAGTAAGAAA
1 AA-AGTAAGAAA
15428 TGGTAATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
25 23 0.70
26 4 0.12
27 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.22, T:0.17
Consensus pattern (26 bp):
AAAGTAAGAAAATGATAATGAGTAAA
Found at i:17265 original size:39 final size:38
Alignment explanation
Indices: 17153--17290 Score: 197
Period size: 39 Copynumber: 3.6 Consensus size: 38
17143 GTGGATCCAA
* *
17153 GCCTTAGGGAGTTAAACTGATTGGTAAGAGTGGACCCGT
1 GCCTCAGGGGGTTAAACTG-TTGGTAAGAGTGGACCCGT
* * *
17192 GCCTCAGGGGGTTCAAGTGTTGGTAAGAGCGGACCCGT
1 GCCTCAGGGGGTTAAACTGTTGGTAAGAGTGGACCCGT
*
17230 GCCTTAGGGGGTTAAACTGATTGGTAAGAGTGGACCCGT
1 GCCTCAGGGGGTTAAACTG-TTGGTAAGAGTGGACCCGT
17269 GCCTCAGGGGGTT-AACTGTTGG
1 GCCTCAGGGGGTTAAACTGTTGG
17291 CTAGACTCGA
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
37 4 0.05
38 39 0.44
39 45 0.51
ACGTcount: A:0.21, C:0.17, G:0.37, T:0.25
Consensus pattern (38 bp):
GCCTCAGGGGGTTAAACTGTTGGTAAGAGTGGACCCGT
Found at i:17331 original size:6 final size:6
Alignment explanation
Indices: 17320--17369 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
17310 CGTTAACGAA
17320 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG
1 TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG TGATTG
17368 TG
1 TG
17370 GTGCAGCCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.16, C:0.00, G:0.34, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:20191 original size:32 final size:32
Alignment explanation
Indices: 20150--20214 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
20140 GCTCCACAGC
20150 AAAAATTAAAAAGAGCTTTTAGTAACTTTGGT
1 AAAAATTAAAAAGAGCTTTTAGTAACTTTGGT
20182 AAAAATTAAAAAGAGCTTTTAGTAACTTTGGT
1 AAAAATTAAAAAGAGCTTTTAGTAACTTTGGT
20214 A
1 A
20215 GGGGTTACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (32 bp):
AAAAATTAAAAAGAGCTTTTAGTAACTTTGGT
Found at i:21058 original size:2 final size:2
Alignment explanation
Indices: 21051--21086 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
21041 AAATATTTCT
21051 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21087 C
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.