Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_245 ID=scaffold_245-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: 9005
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:4981 original size:6 final size:6
Alignment explanation
Indices: 4972--5020 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
4962 GATTCAAAAA
*
4972 AAAATC AAAATC AAAATC ACAATC AAAATC AAAATC AAAAT- AAAA-C
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
5018 AAA
1 AAA
5021 GAAAGAAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
5 7 0.17
6 33 0.82
ACGTcount: A:0.69, C:0.16, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATC
Found at i:5062 original size:21 final size:19
Alignment explanation
Indices: 5022--5070 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
5012 TAAAACAAAG
5022 AAAG-AAAAGAGAAAAATC
1 AAAGCAAAAGAGAAAAATC
5040 AAAGCAAAAGAGAAATCAATC
1 AAAGCAAAAGAGAAA--AATC
5061 AAAGTCAAAA
1 AAAG-CAAAA
5071 TAAAACATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.15
19 10 0.37
21 8 0.30
22 5 0.19
ACGTcount: A:0.67, C:0.10, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAGCAAAAGAGAAAAATC
Found at i:6844 original size:43 final size:43
Alignment explanation
Indices: 6797--6928 Score: 110
Period size: 43 Copynumber: 3.1 Consensus size: 43
6787 AGAAGCAGAT
*
6797 CTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAGCGGAGCAGATCGAAAACAAAGC
* * * * * ** * *
6840 CTTGCC-TCCAT-CGGTT-GCAGTGGAGCTGGTTAAAGAAGCAGA-T
1 CTTGCCTTCC-TGC-ATTAACAGCGGAGCAGATCGAA-AA-CAAAGC
6883 CTTGCCTTCCTGCATTAACAGCGGAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCATTAACAGCGGAGCAGATCGAAAACAAAGC
6926 CTT
1 CTT
6929 ACCTCCATCG
Statistics
Matches: 62, Mismatches: 19, Indels: 16
0.64 0.20 0.16
Matches are distributed among these distances:
42 18 0.29
43 25 0.40
44 19 0.31
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.22
Consensus pattern (43 bp):
CTTGCCTTCCTGCATTAACAGCGGAGCAGATCGAAAACAAAGC
Found at i:6852 original size:86 final size:86
Alignment explanation
Indices: 6707--7001 Score: 473
Period size: 86 Copynumber: 3.4 Consensus size: 86
6697 TGAAGATAGT
* * * *
6707 AGATCTTTCCTTCCTGCATTGACAGCAAAGTAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGC
6772 AGTGGAGCTGGTTAAAGAAGC
66 AGTGGAGCTGGTTAAAGAAGC
6793 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGC
6858 AGTGGAGCTGGTTAAAGAAGC
66 AGTGGAGCTGGTTAAAGAAGC
* *
6879 AGATCTTGCCTTCCTGCATTAACAGCGGAGCAGATCGAAAACAAAGCCTTACCTCCATCGGTTGC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGC
*
6944 AGTGGAGCTGGTTGAAGATAGC
66 AGTGGAGCTGGTTAAAGA-AGC
* * ** *
6966 AGATCTTGCCCTCCTGCGTCGACAGTGAAGCAGATC
1 AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATC
7002 AAAGATTACA
Statistics
Matches: 195, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
86 162 0.83
87 33 0.17
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (86 bp):
AGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGC
AGTGGAGCTGGTTAAAGAAGC
Found at i:7209 original size:44 final size:44
Alignment explanation
Indices: 7098--7305 Score: 156
Period size: 44 Copynumber: 4.7 Consensus size: 44
7088 TCGCATCGGG
* *
7098 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGAAAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGAAAACAAA
* ** * * *
7142 TCTTATCACCCTGAAGTCACAGTGGGGTAGACTGA-AGAAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGA-AAACAAA
* * * **
7186 TCTTCTCTCCCTGAGGTTGCAGTGGAGCAGA-T-TGAATTCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGAAAAC-A-AA
* * * * *
7230 TCCTATCTCTCTGAAGTTGTAGTGGAGCAGA-TTA-AAGTAATAAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGAA--AACAA-A
*
7275 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
7306 TCGCATCAAG
Statistics
Matches: 125, Mismatches: 31, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
42 2 0.02
43 4 0.03
44 90 0.72
45 29 0.23
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAGAAAACAAA
Found at i:8836 original size:26 final size:25
Alignment explanation
Indices: 8807--8861 Score: 58
Period size: 26 Copynumber: 2.1 Consensus size: 25
8797 TACTATTTAG
*
8807 TTAAGTCA-TTTATTTTATATGTTATT
1 TTAAATCAGTTTATTTTA-AT-TTATT
*
8833 TTAAAATTAGTTTATTTTAATTTATT
1 TT-AAATCAGTTTATTTTAATTTATT
8859 TTA
1 TTA
8862 TTTAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
25 1 0.04
26 9 0.36
27 6 0.24
28 9 0.36
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (25 bp):
TTAAATCAGTTTATTTTAATTTATT
Found at i:8863 original size:15 final size:16
Alignment explanation
Indices: 8828--8870 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
8818 ATTTTATATG
8828 TTATTTTAAAATTAGT
1 TTATTTTAAAATTAGT
* *
8844 TTATTTT-AATTTATT
1 TTATTTTAAAATTAGT
8859 TTA-TTTAAAATT
1 TTATTTTAAAATT
8871 TCCCGTGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
14 3 0.13
15 13 0.57
16 7 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTATTTTAAAATTAGT
Done.