Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_140 ID=scaffold_140-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: 11164
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1117 original size:3 final size:3
Alignment explanation
Indices: 1100--1168 Score: 75
Period size: 3 Copynumber: 23.0 Consensus size: 3
1090 AACTAATATA
* * * * * * *
1100 AAT AAT AAC ACT AAT AAT AGT AGT AGT AGT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1148 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
1169 GATGATGATA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.58, C:0.03, G:0.07, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2691 original size:50 final size:48
Alignment explanation
Indices: 2637--2797 Score: 133
Period size: 50 Copynumber: 3.2 Consensus size: 48
2627 GTGATGTCGA
*
2637 GGAAGCAAGATTCACCGTTGTGGCTTCAATCTATTCCACTGCACCGCCTG
1 GGAAGCAAGATTCACTGTTGTGGCTT-AATCT-TTCCACTGCACCGCCTG
* * * ** ** * *
2687 GGAAGTAAGATTCACTATTGTAGCTTTAATCCTTTTAACTGCAATGTCGG
1 GGAAGCAAGATTCACTGTTGTGGC-TTAAT-CTTTCCACTGCACCGCCTG
** *
2737 GGAAGCAAGATTCGTTGTTGTGGCGTTAATCTGTTCCACTGCACCGCTTG
1 GGAAGCAAGATTCACTGTTGTGGC-TTAATCT-TTCCACTGCACCGCCTG
* *
2787 AGAAGTAAGAT
1 GGAAGCAAGAT
2798 CTGTAATTCT
Statistics
Matches: 83, Mismatches: 25, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
49 2 0.02
50 77 0.93
51 4 0.05
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (48 bp):
GGAAGCAAGATTCACTGTTGTGGCTTAATCTTTCCACTGCACCGCCTG
Found at i:2948 original size:44 final size:44
Alignment explanation
Indices: 2895--3017 Score: 165
Period size: 44 Copynumber: 2.8 Consensus size: 44
2885 CCTTTATTTT
* * *
2895 AATCCGCTCCACTGTAATCTCAAGGAAATAGGATTGCTGGCTTC
1 AATCTGCTCCACTGTAATATCAAGGAAATAAGATTGCTGGCTTC
* * * *
2939 AATCTGCTCCGCTGTAATATCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATATCAAGGAAATAAGATTGCTGGCTTC
* *
2983 AATCTGCTCCACTGTAATATCAGGGAGATAAGATT
1 AATCTGCTCCACTGTAATATCAAGGAAATAAGATT
3018 CACCATTTTC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 71 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.29
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATATCAAGGAAATAAGATTGCTGGCTTC
Found at i:4946 original size:7 final size:7
Alignment explanation
Indices: 4926--4974 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
4916 TTAGCCTCTC
4926 CATTTTT
1 CATTTTT
*
4933 ACTTTTTT
1 -CATTTTT
4941 CATTTTT
1 CATTTTT
4948 CA-TTTT
1 CATTTTT
4954 CA-TTTT
1 CATTTTT
4960 CATTTTT
1 CATTTTT
4967 CATCTTTT
1 CAT-TTTT
4975 TTTTACTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 12 0.32
7 15 0.41
8 10 0.27
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:4955 original size:13 final size:13
Alignment explanation
Indices: 4936--4969 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
4926 CATTTTTACT
4936 TTTTTCATTTTTCA
1 TTTTTCA-TTTTCA
4950 -TTTTCATTTTCA
1 TTTTTCATTTTCA
4962 TTTTTCAT
1 TTTTTCAT
4970 CTTTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTCATTTTCA
Found at i:4978 original size:19 final size:18
Alignment explanation
Indices: 4935--4978 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
4925 CCATTTTTAC
4935 TTTTTTCATTTTTCATTT
1 TTTTTTCATTTTTCATTT
*
4953 TCATTTTCATTTTTCATCTT
1 T-TTTTTCATTTTTCAT-TT
4973 TTTTTT
1 TTTTTT
4979 ACTCAAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 1 0.05
19 18 0.82
20 3 0.14
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTTCATTTTTCATTT
Found at i:5902 original size:17 final size:18
Alignment explanation
Indices: 5875--5917 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
5865 TCTTATTTTA
*
5875 TTTTGATTTTTTTAATTT
1 TTTTGAATTTTTTAATTT
*
5893 TTTT-AA-TTTTTATTTT
1 TTTTGAATTTTTTAATTT
5909 TTTTGAATT
1 TTTTGAATT
5918 GGATCTGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 13 0.62
17 3 0.14
18 5 0.24
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTGAATTTTTTAATTT
Found at i:10736 original size:2 final size:2
Alignment explanation
Indices: 10729--10759 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
10719 GTTTAAAATA
*
10729 AT AT AT AT TT 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 A
10760 CATAAAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:10928 original size:12 final size:13
Alignment explanation
Indices: 10910--10951 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
10900 AGGAAAGATT
10910 TAATAATAATATA
1 TAATAATAATATA
10923 -AATAATAACGTATA
1 TAATAATAA--TATA
10937 TACATAATAATATA
1 TA-ATAATAATATA
10951 T
1 T
10952 TAAAGTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 8 0.32
14 9 0.36
15 1 0.04
16 7 0.28
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (13 bp):
TAATAATAATATA
Done.