Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_47 ID=scaffold_47-JGI_221_v2.0
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: 28103
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.29
Warning! 3881 characters in sequence are not A, C, G, or T
Found at i:2196 original size:22 final size:23
Alignment explanation
Indices: 2169--2211 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2159 ATTATTCCAT
2169 TTGTG-AATATT-TTTCTCCATTG
1 TTGTGAAATATTATTT-TCCATTG
2191 TTGTGAAATATTATTTTCCAT
1 TTGTGAAATATTATTTTCCAT
2212 CTCGAACCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 11 0.58
24 3 0.16
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (23 bp):
TTGTGAAATATTATTTTCCATTG
Found at i:3191 original size:35 final size:35
Alignment explanation
Indices: 3151--3220 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
3141 GTATTAGTGC
3151 ATTAATTGCTATCATACTTGATCTATATTAAATAT
1 ATTAATTGCTATCATACTTGATCTATATTAAATAT
3186 ATTAATTGCTATCATACTTGATCTATATTAAATAT
1 ATTAATTGCTATCATACTTGATCTATATTAAATAT
3221 GGCGCATTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (35 bp):
ATTAATTGCTATCATACTTGATCTATATTAAATAT
Found at i:3756 original size:47 final size:47
Alignment explanation
Indices: 3687--3780 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
3677 TCTTAAAATG
3687 TATGTGCAGGAAAACAGTAACTGAATTTGGTATCGATACTTTTTTAC
1 TATGTGCAGGAAAACAGTAACTGAATTTGGTATCGATACTTTTTTAC
3734 TATGTGCAGGAAAACAGTAACTGAATTTGGTATCGATACTTTTTTAC
1 TATGTGCAGGAAAACAGTAACTGAATTTGGTATCGATACTTTTTTAC
3781 AAGTATCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (47 bp):
TATGTGCAGGAAAACAGTAACTGAATTTGGTATCGATACTTTTTTAC
Found at i:6440 original size:26 final size:29
Alignment explanation
Indices: 6397--6452 Score: 82
Period size: 27 Copynumber: 2.0 Consensus size: 29
6387 CATAAAATCC
6397 AATTACAACCCAAACCCAAA-ACCCAACA
1 AATTACAACCCAAACCCAAATACCCAACA
*
6425 AATTA-AA-CCAAGCCCAAATACCCAACA
1 AATTACAACCCAAACCCAAATACCCAACA
6452 A
1 A
6453 GCCCAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 10 0.38
27 11 0.42
28 5 0.19
ACGTcount: A:0.54, C:0.36, G:0.02, T:0.09
Consensus pattern (29 bp):
AATTACAACCCAAACCCAAATACCCAACA
Found at i:7628 original size:2 final size:2
Alignment explanation
Indices: 7623--7647 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7613 ATTTTAGCTT
7623 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 T
7648 GGATGTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8054 original size:22 final size:22
Alignment explanation
Indices: 8024--8068 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
8014 ATTTTAAAAT
*
8024 ATATGCATACATTTT-TTATATA
1 ATATACATAC-TTTTATTATATA
*
8046 ATATACATACTTTTATTTTATA
1 ATATACATACTTTTATTATATA
8068 A
1 A
8069 CTTTCGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (22 bp):
ATATACATACTTTTATTATATA
Found at i:21784 original size:26 final size:25
Alignment explanation
Indices: 21748--21807 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 25
21738 GATTGAGAAG
*
21748 GCTACATTAGCCACTGAAATGGCTAA
1 GCTATATTAGCCACTGAAATGGCT-A
21774 GCTATATTAGCCACTGAAATGGCTA
1 GCTATATTAGCCACTGAAATGGCTA
21799 GTCTATATT
1 G-CTATATT
21808 GGGGGTGAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 2 0.06
26 30 0.94
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (25 bp):
GCTATATTAGCCACTGAAATGGCTA
Found at i:22269 original size:22 final size:23
Alignment explanation
Indices: 22224--22271 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
22214 GAAAATTCTT
*
22224 CCAATAAAAATGCAGACTAGTTG
1 CCAATAAAAATGCAGACTAATTG
22247 CCAATAAAAATGC-GA-TAAATTG
1 CCAATAAAAATGCAGACT-AATTG
22269 CCA
1 CCA
22272 TTCCCCTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 1 0.04
22 9 0.39
23 13 0.57
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.21
Consensus pattern (23 bp):
CCAATAAAAATGCAGACTAATTG
Done.