Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1605
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: 22041
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:1165 original size:14 final size:15
Alignment explanation
Indices: 1135--1179 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1125 ACCGATAAAG
*
1135 AAATCCAAGAATGAGA
1 AAATCC-AGAATAAGA
1151 AAAT-CAGAATAAG-
1 AAATCCAGAATAAGA
1164 AAATCCAG-ATAAGA
1 AAATCCAGAATAAGA
1178 AA
1 AA
1180 CCCAGATACG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 9 0.35
14 12 0.46
15 1 0.04
16 4 0.15
ACGTcount: A:0.60, C:0.11, G:0.16, T:0.13
Consensus pattern (15 bp):
AAATCCAGAATAAGA
Found at i:1175 original size:13 final size:14
Alignment explanation
Indices: 1132--1185 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
1122 GGAACCGATA
1132 AAGAAATCCAAGAAT
1 AAGAAATCC-AGAAT
*
1147 GAGAAAAT-CAGAAT
1 AAG-AAATCCAGAAT
1161 AAGAAATCCAG-AT
1 AAGAAATCCAGAAT
*
1174 AAGAAACCCAGA
1 AAGAAATCCAGA
1186 TACGATACTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 16 0.48
14 10 0.30
15 3 0.09
16 4 0.12
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (14 bp):
AAGAAATCCAGAAT
Found at i:7512 original size:46 final size:46
Alignment explanation
Indices: 7462--7637 Score: 205
Period size: 46 Copynumber: 3.8 Consensus size: 46
7452 ATGGTTGGCA
* *
7462 TCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
7508 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
7555 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
7601 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
7638 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
45 3 0.03
46 65 0.59
47 28 0.25
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:7617 original size:93 final size:93
Alignment explanation
Indices: 7458--7629 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
7448 TAGGATGGTT
* * *
7458 GGCATCCGAACTCGTTGAGTTGAGTTCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
7523 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
7551 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
7616 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
7630 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:10560 original size:15 final size:15
Alignment explanation
Indices: 10517--10580 Score: 80
Period size: 14 Copynumber: 4.4 Consensus size: 15
10507 GTATCTTGGG
10517 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
10532 -TTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
10546 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
10561 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
10575 TTTCTT
1 TTTCTT
10581 GTTATCTTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
14 24 0.56
15 17 0.40
16 2 0.05
ACGTcount: A:0.11, C:0.16, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:13081 original size:45 final size:46
Alignment explanation
Indices: 12936--13107 Score: 194
Period size: 45 Copynumber: 3.8 Consensus size: 46
12926 ATTTGGGCAT
* *
12936 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
* * * *
12982 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ACGC
*
13027 ATCC--ACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
*
13072 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
13108 GCGGGTTACA
Statistics
Matches: 105, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
43 8 0.08
45 57 0.54
46 33 0.31
47 7 0.07
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGC
Found at i:13094 original size:90 final size:92
Alignment explanation
Indices: 12931--13099 Score: 279
Period size: 90 Copynumber: 1.8 Consensus size: 92
12921 AGGATATTTG
* *
12931 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAG
1 GGCATCC-AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAG
12996 TTGAGTCCGAGTTCGTGAGATGTAACTA
65 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
13024 GGCATCC-ACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GGCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
13087 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
13100 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
90 39 0.54
91 26 0.36
93 7 0.10
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (92 bp):
GGCATCCAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTA
Done.