Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012513.1 Corchorus olitorius cultivar O-4 contig12546, 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: 32063
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:3711 original size:3 final size:3
Alignment explanation
Indices: 3703--3732 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3693 GATTCCGCTG
3703 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
3733 ATGGTCCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
CCT
Found at i:13540 original size:7 final size:7
Alignment explanation
Indices: 13530--13565 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
13520 TCTCCTCATT
13530 CCTCAAC
1 CCTCAAC
13537 CCTCAAC
1 CCTCAAC
13544 CCTCAAC
1 CCTCAAC
13551 CCTCAAC
1 CCTCAAC
13558 CCTCAAC
1 CCTCAAC
13565 C
1 C
13566 AAACATGTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.58, G:0.00, T:0.14
Consensus pattern (7 bp):
CCTCAAC
Found at i:14520 original size:2 final size:2
Alignment explanation
Indices: 14509--14546 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
14499 AAGAAACTAG
14509 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14547 TGTATCAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15141 original size:11 final size:10
Alignment explanation
Indices: 15111--15135 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15101 GACAAGTGAG
15111 AAAAGACAAA
1 AAAAGACAAA
15121 AAAAGACAAA
1 AAAAGACAAA
15131 AAAAG
1 AAAAG
15136 TTCAAATAGA
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:0.80, C:0.08, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAGACAAA
Found at i:15514 original size:39 final size:40
Alignment explanation
Indices: 15450--15530 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
15440 TTTAATTCCT
*
15450 ATGTAATATATATAATCACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
15490 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
15529 AT
1 AT
15531 TCTTAGGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:15557 original size:25 final size:24
Alignment explanation
Indices: 15521--15567 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
15511 AATACTTACA
15521 TTAATTAAATTCTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
15545 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
15568 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:15900 original size:203 final size:205
Alignment explanation
Indices: 15639--16051 Score: 778
Period size: 204 Copynumber: 2.0 Consensus size: 205
15629 TTCCTTAATA
*
15639 ATAAATAAATCGGGTCTTAATATCTTTTTATAATTTTTGAAATTTTGTTTGACATTGATCTAATT
1 ATAAATAAATCGGATCTTAATATCTTTTTATAATTTTTGAAATTTTGTTTGACATTGATCTAATT
15704 TAATTTAAT-AATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATA
66 TAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATA
15768 GTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
131 GTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
*
15833 TTCACCATTG
196 TTCACCAGTG
15843 ATAAATAAATCGGATCTTTAATATC-TTTTATAA-TTTTGAAATTTTGTTTGACATTGATCTAAT
1 ATAAATAAATCGGATC-TTAATATCTTTTTATAATTTTTGAAATTTTGTTTGACATTGATCTAAT
15906 TTAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAAT
65 TTAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAAT
15971 AGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
130 AGTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAAC
16036 ATTCACCAGTG
195 ATTCACCAGTG
16047 ATAAA
1 ATAAA
16052 GTTATTAAGC
Statistics
Matches: 205, Mismatches: 2, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
203 40 0.20
204 157 0.77
205 8 0.04
ACGTcount: A:0.36, C:0.11, G:0.09, T:0.44
Consensus pattern (205 bp):
ATAAATAAATCGGATCTTAATATCTTTTTATAATTTTTGAAATTTTGTTTGACATTGATCTAATT
TAATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATA
GTAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
TTCACCAGTG
Found at i:19094 original size:6 final size:6
Alignment explanation
Indices: 19083--19117 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
19073 AAGAAGCAGA
19083 GCCAAC GCCAAC GCCAAC GCCAAC GCCAAC GCCAA
1 GCCAAC GCCAAC GCCAAC GCCAAC GCCAAC GCCAA
19118 AGGTTCCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
GCCAAC
Found at i:22485 original size:72 final size:72
Alignment explanation
Indices: 22368--22508 Score: 264
Period size: 72 Copynumber: 2.0 Consensus size: 72
22358 TCTTTCTGGA
22368 TCCATGTTTCAACTTTTCTTCATTTTAGAATGAAGATGTTTGCTTTTGCATCTCAAGATATAGAC
1 TCCATGTTTCAACTTTTCTTCATTTTAGAATGAAGATGTTTGCTTTTGCATCTCAAGATATAGAC
22433 TCTTGGT
66 TCTTGGT
* *
22440 TCCATGTTTCCACTTTTCTTCATTTTAGAATGAAGATGTTTGCTTTTGTATCTCAAGATATAGAC
1 TCCATGTTTCAACTTTTCTTCATTTTAGAATGAAGATGTTTGCTTTTGCATCTCAAGATATAGAC
22505 TCTT
66 TCTT
22509 AATTTGTCAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.23, C:0.17, G:0.14, T:0.45
Consensus pattern (72 bp):
TCCATGTTTCAACTTTTCTTCATTTTAGAATGAAGATGTTTGCTTTTGCATCTCAAGATATAGAC
TCTTGGT
Found at i:25424 original size:4 final size:4
Alignment explanation
Indices: 25415--25471 Score: 114
Period size: 4 Copynumber: 14.2 Consensus size: 4
25405 AAATTAAGCA
25415 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
25463 ATGT ATGT A
1 ATGT ATGT A
25472 CCTCTTTGCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Done.