Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018270.1 Corchorus olitorius cultivar O-4 contig18303, 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: 23248
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:715 original size:2 final size:2
Alignment explanation
Indices: 703--757 Score: 66
Period size: 2 Copynumber: 30.0 Consensus size: 2
693 TTATAATTAG
*
703 TA TA GA TA TA TA TA TA TA TA TA -A T- TA TA TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
741 T- TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
758 CACAAATATA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
1 5 0.11
2 41 0.89
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1360 original size:42 final size:44
Alignment explanation
Indices: 1309--1402 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
1299 AGTGCATTAC
*
1309 CTAA-ATTCTA-T-TCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
*
1350 CTAATATTCTACTCCTCCATCTCTAGATAATTTATCAAAATAAAG
1 CTAATATTCTACT-CTCCATCTCTAGATAATTCATCAAAATAAAG
*
1395 TTAATATT
1 CTAATATT
1403 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
43 1 0.02
45 35 0.76
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.37
Consensus pattern (44 bp):
CTAATATTCTACTCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:11374 original size:19 final size:19
Alignment explanation
Indices: 11350--11391 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
11340 AAATACAGGT
11350 ACAAATATTCACCAAGTAC
1 ACAAATATTCACCAAGTAC
11369 ACAAATATTCACCAAGTAC
1 ACAAATATTCACCAAGTAC
11388 ACAA
1 ACAA
11392 GACCATAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.50, C:0.26, G:0.05, T:0.19
Consensus pattern (19 bp):
ACAAATATTCACCAAGTAC
Found at i:18388 original size:18 final size:18
Alignment explanation
Indices: 18352--18390 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
18342 AAAGTTTTCA
*
18352 AAATGGGATTTTCGCTTG
1 AAATGGGATTTTAGCTTG
* *
18370 AAATTGGATTTTAGTTTG
1 AAATGGGATTTTAGCTTG
18388 AAA
1 AAA
18391 ACTTTGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (18 bp):
AAATGGGATTTTAGCTTG
Found at i:18841 original size:7 final size:8
Alignment explanation
Indices: 18817--18844 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
18807 AATGATGATG
18817 AAATGAAA
1 AAATGAAA
18825 AAATGAAA
1 AAATGAAA
18833 AAATGAAA
1 AAATGAAA
18841 AAAT
1 AAAT
18845 TAAGGCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (8 bp):
AAATGAAA
Found at i:19242 original size:16 final size:16
Alignment explanation
Indices: 19221--19291 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
19211 CAAGAAATTC
19221 CAAAAAAAACAAAGAA-
1 CAAAAAAAACAAA-AAT
*
19237 CAAAAAAATCAAAAAT
1 CAAAAAAAACAAAAAT
*
19253 C-AAAAATACAAAAA-
1 CAAAAAAAACAAAAAT
*
19267 -AATAAACAA-AAAAAT
1 CAA-AAAAAACAAAAAT
19282 CAAATAAAAA
1 CAAA-AAAAA
19292 ACGAAGTCGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
14 6 0.14
15 18 0.42
16 19 0.44
ACGTcount: A:0.79, C:0.11, G:0.01, T:0.08
Consensus pattern (16 bp):
CAAAAAAAACAAAAAT
Found at i:19243 original size:15 final size:15
Alignment explanation
Indices: 19223--19266 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
19213 AGAAATTCCA
19223 AAAAAAACAAAGAA-C
1 AAAAAAACAAA-AATC
19238 AAAAAAATCAAAAATC
1 AAAAAAA-CAAAAATC
*
19254 AAAAATACAAAAA
1 AAAAAAACAAAAA
19267 AATAAACAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.80, C:0.11, G:0.02, T:0.07
Consensus pattern (15 bp):
AAAAAAACAAAAATC
Found at i:19250 original size:24 final size:25
Alignment explanation
Indices: 19222--19278 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 25
19212 AAGAAATTCC
*
19222 AAAAAAAACAAAGA-ACAAAAAAAT
1 AAAAAAAACAAAAATACAAAAAAAT
* *
19246 -CAAAAATCAAAAATACAAAAAAAT
1 AAAAAAAACAAAAATACAAAAAAAT
19270 AAACAAAAA
1 AAA-AAAAA
19279 AATCAAATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
23 10 0.40
24 10 0.40
25 1 0.04
26 4 0.16
ACGTcount: A:0.81, C:0.11, G:0.02, T:0.07
Consensus pattern (25 bp):
AAAAAAAACAAAAATACAAAAAAAT
Found at i:19290 original size:13 final size:12
Alignment explanation
Indices: 19235--19292 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
19225 AAAAACAAAG
19235 AACAAAAAAATCA
1 AACAAAAAAAT-A
19248 AA-AATCAAAAAT-
1 AACAA--AAAAATA
19260 -ACAAAAAAATA
1 AACAAAAAAATA
19271 AACAAAAAAATCA
1 AACAAAAAAAT-A
*
19284 AATAAAAAA
1 AACAAAAAA
19293 CGAAGTCGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
10 6 0.16
11 1 0.03
12 14 0.37
13 11 0.29
14 6 0.16
ACGTcount: A:0.79, C:0.10, G:0.00, T:0.10
Consensus pattern (12 bp):
AACAAAAAAATA
Found at i:21035 original size:110 final size:110
Alignment explanation
Indices: 20838--21060 Score: 392
Period size: 110 Copynumber: 2.0 Consensus size: 110
20828 TCAGATTCAA
20838 TTTTCAAGATTTTTCATCGGCTCCATCTGAATGATTAGGCTTTTCCACAAGCCAAACTCGTTTCC
1 TTTTCAAGATTTTTCATCGGCTCCATCTGAATGATTAGGCTTTTCCACAAGCCAAACTCGTTTCC
* *
20903 ATACAAGTAAGTTTAAGTCTTGGTTCCATCCAAGCCATATAGACT
66 ATACAAGTAAGTTTAAGCCTTGGTTCCATCCAAGCCACATAGACT
20948 TTTTCAAGATTTTTCATCGGCTCCATCTGAATGATTAGGCTTTTCCACAAGCCAAACTCGTTTCC
1 TTTTCAAGATTTTTCATCGGCTCCATCTGAATGATTAGGCTTTTCCACAAGCCAAACTCGTTTCC
* * * *
21013 ATACGAGTCAGTTTAAGCCTTGGTTCCGTCCAAGCCACATAGGCT
66 ATACAAGTAAGTTTAAGCCTTGGTTCCATCCAAGCCACATAGACT
21058 TTT
1 TTT
21061 CCACAAGCCG
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 107 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (110 bp):
TTTTCAAGATTTTTCATCGGCTCCATCTGAATGATTAGGCTTTTCCACAAGCCAAACTCGTTTCC
ATACAAGTAAGTTTAAGCCTTGGTTCCATCCAAGCCACATAGACT
Found at i:21309 original size:102 final size:102
Alignment explanation
Indices: 21131--21456 Score: 492
Period size: 102 Copynumber: 3.2 Consensus size: 102
21121 CTTATTTCCA
* * * * * *
21131 ATTGATAAAACCTCCGAGTACCATTTGATTTCATTAAATTTTTCATCAAAAGATTCATGTTGAAG
1 ATTGATAAAACCTCCGGGTATCATTTCATTTCA-TCAAGTTTTCATC-AAAGATTCATGTTTAAG
21196 TTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTTGC
64 TTTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTTGC
* *
21235 ATTGATAAAACCTCCGGGTATCATTTCATTTTATCAAGTTCTCATCAAAGATTCATGTTTAAGTT
1 ATTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTCATCAAAGATTCATGTTTAAGTT
21300 TAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTTGC
66 TAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTTGC
*
21337 ATTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTTCATCAAAAATTCATGTTTAAGT
1 ATTGATAAAACCTCCGGGTATCATTTCATTTCATCAAG-TTTTCATCAAAGATTCATGTTTAAGT
* *
21402 TCAAAATCCTTGGTCAAGGTCTCTATTCAGAG-TTTGC
65 TTAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTTGC
* **
21439 ATTGGTAAGTCCTCCGGG
1 ATTGATAAAACCTCCGGG
21457 CACAAATTCA
Statistics
Matches: 205, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
102 112 0.55
103 64 0.31
104 29 0.14
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.39
Consensus pattern (102 bp):
ATTGATAAAACCTCCGGGTATCATTTCATTTCATCAAGTTTTCATCAAAGATTCATGTTTAAGTT
TAAAATCCTTGTTCAAGGTCTCTATTCAGAGTTTTGC
Found at i:21544 original size:25 final size:25
Alignment explanation
Indices: 21471--21545 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
21461 AATTCAGAAA
*
21471 CCTCCGGGTATTAATTCCGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
* * **
21496 CCTCAGGG---CAA-T-TGATAAAA
1 CCTCCGGGTATTAATTCTGATAAGT
21516 CCTCCGGGTATTAATTCTGATAAGT
1 CCTCCGGGTATTAATTCTGATAAGT
21541 CCTCC
1 CCTCC
21546 AGGCATTGGA
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
20 12 0.33
21 1 0.03
22 2 0.06
23 2 0.06
24 1 0.03
25 18 0.50
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (25 bp):
CCTCCGGGTATTAATTCTGATAAGT
Found at i:21842 original size:30 final size:30
Alignment explanation
Indices: 21792--22276 Score: 675
Period size: 30 Copynumber: 16.2 Consensus size: 30
21782 ACTTTATCAG
* * *
21792 TTTACTTTGATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * **
21822 TTCATTTTAACCCCAGTTGAGGAT-ATTTGC
1 TTTATTTTAATCCTGGTTGAGGATCA-TTGC
*
21852 TTTATTTTAATCCTGTTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
21882 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
21912 ATCATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
21942 ATCATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
21972 TTTGTTTTAATCCTGTTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
22002 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
22032 TTTGTTTTAGTCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
22062 TTTGTTTTAATCCTGGTTGAGGATCATTGA
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * *
22092 TTTGTTTTAATCCTGTTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
22122 TTTATTCTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* * * * *
22152 TTTATTTCAGTCCTGATTTAGGGTCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
*
22182 TTCATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
* *
22212 TTTGTTTTAATCATGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
22242 TTTATTTTAATCCTGGTTGAGGATCATTGC
1 TTTATTTTAATCCTGGTTGAGGATCATTGC
22272 TTTAT
1 TTTAT
22277 CAGATTATTG
Statistics
Matches: 402, Mismatches: 51, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
29 1 0.00
30 400 1.00
31 1 0.00
ACGTcount: A:0.19, C:0.14, G:0.21, T:0.46
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTGAGGATCATTGC
Found at i:22854 original size:26 final size:26
Alignment explanation
Indices: 22804--22855 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
22794 CAAAATCCAA
*
22804 GGGCATTTTGGTCATTTGCTTGTTCAG
1 GGGCATTTTGGTCATTT-CTAGTTCAG
22831 GGGCATTTTGGTCATTT-TAAGTTCA
1 GGGCATTTTGGTCATTTCT-AGTTCA
22856 CTTTTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 1 0.04
26 5 0.22
27 17 0.74
ACGTcount: A:0.15, C:0.13, G:0.27, T:0.44
Consensus pattern (26 bp):
GGGCATTTTGGTCATTTCTAGTTCAG
Done.