Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1086
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: 33761
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Found at i:12007 original size:45 final size:45
Alignment explanation
Indices: 11958--12128 Score: 206
Period size: 45 Copynumber: 3.8 Consensus size: 45
11948 TGGTTGAGCA
11958 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
* * *
12003 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-T--G
*
12048 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AATG
* *
12095 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
12129 GGGGCGGGTT
Statistics
Matches: 108, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 6 0.06
43 1 0.01
44 2 0.02
45 58 0.54
46 3 0.03
47 32 0.30
49 4 0.04
50 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATG
Found at i:12112 original size:92 final size:92
Alignment explanation
Indices: 11955--12123 Score: 295
Period size: 92 Copynumber: 1.8 Consensus size: 92
11945 GGATGGTTGA
* *
11955 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGCCCGAACTCGTTGAGTT
12020 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
*
12047 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC-AACGCCCGAACTCGTTGAGT
12111 TGAGTCCGAGTTC
65 TGAGTCCGAGTTC
12124 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
91 10 0.14
92 63 0.86
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:12825 original size:18 final size:18
Alignment explanation
Indices: 12802--12839 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12792 TTGCTGCAGC
12802 AATGACATGAATTTGAAA
1 AATGACATGAATTTGAAA
12820 AATGACATGAATTTGAAA
1 AATGACATGAATTTGAAA
12838 AA
1 AA
12840 AAATAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (18 bp):
AATGACATGAATTTGAAA
Found at i:17822 original size:13 final size:13
Alignment explanation
Indices: 17806--17838 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17796 TTTAATTAAA
*
17806 TTAGTTAATTAGT
1 TTAGATAATTAGT
17819 TTAGATAATTAGT
1 TTAGATAATTAGT
17832 TTA-ATAA
1 TTAGATAA
17839 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:19839 original size:76 final size:76
Alignment explanation
Indices: 19746--19899 Score: 290
Period size: 76 Copynumber: 2.0 Consensus size: 76
19736 CTCGTGTGCC
*
19746 ATATCCTAAAGCGATGACGAAAGATAGAACAGAAGAAAAATTCGGTAAGTTTGTCAAACTCTTAA
1 ATATCCTAAAGCGATGACGAAAGACAGAACAGAAGAAAAATTCGGTAAGTTTGTCAAACTCTTAA
19811 AGAAATTACAT
66 AGAAATTACAT
*
19822 ATATCCTAAAGCGATGACGAAAGACAGAACAGAAGAACAATTCGGTAAGTTTGTCAAACTCTTAA
1 ATATCCTAAAGCGATGACGAAAGACAGAACAGAAGAAAAATTCGGTAAGTTTGTCAAACTCTTAA
19887 AGAAATTACAT
66 AGAAATTACAT
19898 AT
1 AT
19900 TAACTTACCA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.23
Consensus pattern (76 bp):
ATATCCTAAAGCGATGACGAAAGACAGAACAGAAGAAAAATTCGGTAAGTTTGTCAAACTCTTAA
AGAAATTACAT
Found at i:23031 original size:6 final size:6
Alignment explanation
Indices: 23020--23090 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
23010 TCCTCCTATC
* * * *
23020 TTTTTA TTTTTA TTTTTA TTCTTA TTTATTA TTCTTA -TTTT- CTTTTC
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA
* * *
23067 TTTTTC TTTTTC TTTTTC TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA
23091 CTTTCATCTC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
5 7 0.12
6 44 0.79
7 5 0.09
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:23051 original size:13 final size:12
Alignment explanation
Indices: 23020--23060 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
23010 TCCTCCTATC
*
23020 TTTTTATTTTTA
1 TTTTTATTCTTA
23032 TTTTTATTCTTA
1 TTTTTATTCTTA
23044 TTTATTATTCTTA
1 TTT-TTATTCTTA
23057 TTTT
1 TTTT
23061 CTTTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.17, C:0.05, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTATTCTTA
Found at i:23076 original size:5 final size:6
Alignment explanation
Indices: 23057--23094 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
23047 ATTATTCTTA
23057 TTTTC- TTTTCT TTTTCT TTTTCT TTTTCT TTTTACT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT-CT TT
23095 CATCTCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 22 0.71
7 4 0.13
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTCT
Done.