Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015424.1 Corchorus olitorius cultivar O-4 contig15457, 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: 38424
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--40 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
41 TCATATATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:8102 original size:17 final size:16
Alignment explanation
Indices: 8076--8107 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
8066 TGGTTGGGGG
8076 GTTTAAGCCCAATTAA
1 GTTTAAGCCCAATTAA
8092 GTTTCAAGCCCAATTA
1 GTTT-AAGCCCAATTA
8108 GAACAGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.31
Consensus pattern (16 bp):
GTTTAAGCCCAATTAA
Found at i:14617 original size:14 final size:16
Alignment explanation
Indices: 14587--14619 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
14577 TTGGTGCTCT
14587 GCCCAGTAGGCCCAGA
1 GCCCAGTAGGCCCAGA
14603 GCCCAG-AGG-CCAGA
1 GCCCAGTAGGCCCAGA
14617 GCC
1 GCC
14620 AATTTAGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.24, C:0.39, G:0.33, T:0.03
Consensus pattern (16 bp):
GCCCAGTAGGCCCAGA
Found at i:18320 original size:72 final size:72
Alignment explanation
Indices: 18233--18375 Score: 216
Period size: 72 Copynumber: 2.0 Consensus size: 72
18223 ACTGGGTTTG
* * * * *
18233 TTTGTTGGGGAAGGGGTTTGTTGGCTCATAGATTAACATTTCGGTAATG-TAGCTAATCATGTAG
1 TTTGTTAGGGAAGGGGTTTGTTGACTCATAGATTAACATTTCGATAA-GCTAACTAATCATGTAA
18297 CGGTGTAA
65 CGGTGTAA
*
18305 TTTGTTAGGGAAGGGGTTTGTTGACTCATAGATTAGCATTTCGATAAGCTAACTAATCATGTAAC
1 TTTGTTAGGGAAGGGGTTTGTTGACTCATAGATTAACATTTCGATAAGCTAACTAATCATGTAAC
18370 GGTGTA
66 GGTGTA
18376 CGGGTCTTCC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 1 0.02
72 63 0.98
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (72 bp):
TTTGTTAGGGAAGGGGTTTGTTGACTCATAGATTAACATTTCGATAAGCTAACTAATCATGTAAC
GGTGTAA
Found at i:18523 original size:74 final size:74
Alignment explanation
Indices: 18403--18550 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 74
18393 TTGTAATCCC
*
18403 AATCTTTTAAAAAAATGAAAATGATTCTTATCTGAAAAAACAAAACTTTCATTTGTTTAAATCAG
1 AATCTCTTAAAAAAATGAAAATGATTCTTATCTGAAAAAACAAAACTTTCATTTGTTTAAATCAG
18468 AATGCTACT
66 AATGCTACT
* *
18477 AATCTCTTAAAGAAATGAAAATTATTCTTATCTGAAAAAACAAAACTTTCATTTGTTTAAATCAG
1 AATCTCTTAAAAAAATGAAAATGATTCTTATCTGAAAAAACAAAACTTTCATTTGTTTAAATCAG
18542 AATGCTACT
66 AATGCTACT
18551 GCTTGATGCG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (74 bp):
AATCTCTTAAAAAAATGAAAATGATTCTTATCTGAAAAAACAAAACTTTCATTTGTTTAAATCAG
AATGCTACT
Found at i:19642 original size:21 final size:19
Alignment explanation
Indices: 19610--19668 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
19600 CGTTACTCTA
*
19610 ATAATCTTATCTGTACAGT
1 ATAATCTAATCTGTACAGT
*
19629 ACCTGATCTAATCTGTACAGT
1 A--TAATCTAATCTGTACAGT
*
19650 ATAATCTCATCTGTACAGT
1 ATAATCTAATCTGTACAGT
19669 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (19 bp):
ATAATCTAATCTGTACAGT
Found at i:20637 original size:3 final size:3
Alignment explanation
Indices: 20626--20666 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
20616 TCACCACCCT
20626 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20667 GTAGTAAGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:24559 original size:2 final size:2
Alignment explanation
Indices: 24552--24578 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
24542 AGTAATCAAC
24552 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 A
24579 GTAATTAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26109 original size:11 final size:11
Alignment explanation
Indices: 26093--26117 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
26083 ATTTGGTCGT
26093 TGTATCATGTA
1 TGTATCATGTA
26104 TGTATCATGTA
1 TGTATCATGTA
26115 TGT
1 TGT
26118 TTGTAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (11 bp):
TGTATCATGTA
Found at i:33996 original size:9 final size:9
Alignment explanation
Indices: 33982--34043 Score: 124
Period size: 9 Copynumber: 6.9 Consensus size: 9
33972 TTGCCATGAC
33982 TATGACCAA
1 TATGACCAA
33991 TATGACCAA
1 TATGACCAA
34000 TATGACCAA
1 TATGACCAA
34009 TATGACCAA
1 TATGACCAA
34018 TATGACCAA
1 TATGACCAA
34027 TATGACCAA
1 TATGACCAA
34036 TATGACCA
1 TATGACCA
34044 TGACCAAAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.23
Consensus pattern (9 bp):
TATGACCAA
Found at i:37248 original size:13 final size:13
Alignment explanation
Indices: 37230--37255 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37220 ACTTGATTAG
37230 ATATTACATATAT
1 ATATTACATATAT
37243 ATATTACATATAT
1 ATATTACATATAT
37256 TTAATTTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATTACATATAT
Found at i:38351 original size:14 final size:14
Alignment explanation
Indices: 38332--38358 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38322 ATTAATAGAA
38332 CTAGAACTAGAAGT
1 CTAGAACTAGAAGT
38346 CTAGAACTAGAAG
1 CTAGAACTAGAAG
38359 AATTTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (14 bp):
CTAGAACTAGAAGT
Done.