Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1372
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: 22308
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.35
Found at i:2357 original size:13 final size:13
Alignment explanation
Indices: 2336--2379 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
2326 AAATAGTACC
2336 CAATGTATCGATA
1 CAATGTATCGATA
*
2349 CATTGTATCGATA
1 CAATGTATCGATA
2362 CAATGTATCGATA
1 CAATGTATCGATA
2375 CAATG
1 CAATG
2380 AATGTTGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:6335 original size:21 final size:21
Alignment explanation
Indices: 6309--6354 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
6299 CATGCAAGTT
*
6309 TTTATTTTTC-TTAGCTAATTC
1 TTTA-TTTTCATTAGCCAATTC
*
6330 TTTATTTTCATTAGCCAATTT
1 TTTATTTTCATTAGCCAATTC
6351 TTTA
1 TTTA
6355 ATATCTACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.22, C:0.13, G:0.04, T:0.61
Consensus pattern (21 bp):
TTTATTTTCATTAGCCAATTC
Found at i:8729 original size:33 final size:32
Alignment explanation
Indices: 8668--8732 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
8658 CAATTTGTCC
* * *
8668 ATGTATCGATACAATGAACATGTGTCGATACA
1 ATGTATCAATACAAAGAACATGTATCGATACA
*
8700 ATGTATCAATACAAAGCAGCATGTATCGATACA
1 ATGTATCAATACAAAG-AACATGTATCGATACA
8733 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCAATACAAAGAACATGTATCGATACA
Found at i:9820 original size:21 final size:21
Alignment explanation
Indices: 9796--9836 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9786 AGGTAAGTTC
9796 TTGTTCTTC-TTAGCCAATTCA
1 TTGTT-TTCATTAGCCAATTCA
*
9817 TTGTTTTCATTAGCTAATTC
1 TTGTTTTCATTAGCCAATTC
9837 TTTATTACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.20, C:0.20, G:0.10, T:0.51
Consensus pattern (21 bp):
TTGTTTTCATTAGCCAATTCA
Found at i:9908 original size:21 final size:21
Alignment explanation
Indices: 9853--9913 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
9843 ACCATCTTGC
* *
9853 AATTCAATTATCTTCTTTTCT
1 AATTCACTTATTTTCTTTTCT
9874 AATTCACTTATTTTCTTTTCT
1 AATTCACTTATTTTCTTTTCT
** *
9895 AATTCTTTTTTTTTCTTTT
1 AATTCACTTATTTTCTTTT
9914 TAAGCACATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (21 bp):
AATTCACTTATTTTCTTTTCT
Found at i:12044 original size:13 final size:13
Alignment explanation
Indices: 12026--12056 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12016 ACTTTTCACT
12026 ATGTATCGATACA
1 ATGTATCGATACA
*
12039 ATGTATTGATACA
1 ATGTATCGATACA
12052 ATGTA
1 ATGTA
12057 CCATGTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:12164 original size:32 final size:32
Alignment explanation
Indices: 12122--12183 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
12112 CAATTTGCTG
*
12122 TGTATCGATACTAAG-ATCATGTATCGATATAT
1 TGTATCGATACAAAGAAT-ATGTATCGATATAT
*
12154 TGTATTGATACAAAGCAATATGTATCGATA
1 TGTATCGATACAAAG-AATATGTATCGATA
12184 CGTCTAGGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 13 0.50
33 11 0.42
34 2 0.08
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAGAATATGTATCGATATAT
Found at i:14848 original size:20 final size:21
Alignment explanation
Indices: 14817--14855 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
14807 AGGTCAAAAC
14817 CCTAGAATGTATCGATACACA
1 CCTAGAATGTATCGATACACA
14838 CCTAG-ATGTATCGATACA
1 CCTAGAATGTATCGATACA
14856 TATTGCTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (21 bp):
CCTAGAATGTATCGATACACA
Found at i:14906 original size:32 final size:33
Alignment explanation
Indices: 14844--14907 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
14834 CACACCTAGA
14844 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
* * *
14877 TGTATCGGTACATGTT-CTTTGTATCGATACA
1 TGTATCGATACATATTGCTTAGTATCGATACA
14908 ACATGAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATATTGCTTAGTATCGATACAT
Found at i:14975 original size:20 final size:20
Alignment explanation
Indices: 14950--14987 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
14940 TAACTACCCA
*
14950 AGTAAATTGTATTGATACAT
1 AGTAAATTGTATCGATACAT
14970 AGTAAATTGTATCGATAC
1 AGTAAATTGTATCGATAC
14988 GTTGAGCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (20 bp):
AGTAAATTGTATCGATACAT
Found at i:21165 original size:58 final size:57
Alignment explanation
Indices: 21029--21509 Score: 265
Period size: 58 Copynumber: 8.3 Consensus size: 57
21019 TAGGGATTTG
* *
21029 GATGTAATTTTATGAATTTTGATGCCATTTAGGTCATTTTTTCATG-TTTAAAGGACTTT
1 GATGTAATTTTATGAATTTTGATGCCATTTAGGTCA-TTTTCCATGATAT-AAGGAC-TT
* * * * *** *
21088 TATGTCATTTTATGCATTTTAATATTATTTAGGTCATTTTCTATGATATAAGGACTT
1 GATGTAATTTTATGAATTTTGATGCCATTTAGGTCATTTTCCATGATATAAGGACTT
* * * * * *
21145 AGATGTAATTTTATGAATTTTGATGTCATCTAGATCATTTACCATGATCTAGGGACTT
1 -GATGTAATTTTATGAATTTTGATGCCATTTAGGTCATTTTCCATGATATAAGGACTT
* * ** *
21203 GTGTGTAATTTTATAAATTTTGATGCCATTTAGGTCATTTTCCATGATCGAATGACTTT
1 G-ATGTAATTTTATGAATTTTGATGCCATTTAGGTCATTTTCCATGATATAAGGAC-TT
* * * * ** *
21262 AATGTCAA-TTAATGCATTTTGATGTCATTTAAATCATTTTCCATGA-ACTAGGGACTT
1 GATGT-AATTTTATGAATTTTGATGCCATTTAGGTCATTTTCCATGATA-TAAGGACTT
* * * * ** * * * *
21319 GGATGTAATTTTGTAAATTTTGTTGTCATTTAAATCATTTACCTTGATCT-CGAGAC-T
1 -GATGTAATTTTATGAATTTTGATGCCATTTAGGTCATTTTCCATGATATAAG-GACTT
* * * ** * * * *
21376 CAGGTACAATCTCGTGAATTTTGATGCCATTTAGGTTA-TTTCTATGATCTACGGACTTT
1 GATGT--AATTTTATGAATTTTGATGCCATTTAGGTCATTTTCCATGATATAAGGAC-TT
* * * * * ** * *
21435 TAAGTCATTTCATGCATTTTGATATCATTTAGG-CTATTTTTCATGATCTAAGGACTTT
1 GATGTAATTTTATGAATTTTGATGCCATTTAGGTC-ATTTTCCATGATATAAGGAC-TT
*
21493 TATGTAATTTTATGAAT
1 GATGTAATTTTATGAAT
21510 AATGGGGTCA
Statistics
Matches: 323, Mismatches: 82, Indels: 35
0.73 0.19 0.08
Matches are distributed among these distances:
56 3 0.01
57 44 0.14
58 237 0.73
59 39 0.12
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (57 bp):
GATGTAATTTTATGAATTTTGATGCCATTTAGGTCATTTTCCATGATATAAGGACTT
Found at i:21241 original size:116 final size:117
Alignment explanation
Indices: 21029--21350 Score: 339
Period size: 116 Copynumber: 2.8 Consensus size: 117
21019 TAGGGATTTG
* * * * * * *
21029 GATGTAATTTTATGAATTTTGATGCCATTTAGGTCATTTTTTCATG-TTTAAAGGACTTTTATGT
1 GATGTAATTTTATGAATTTTGATGTCATTTAGATCA-TTTTCCATGATCT-AGGGACTTGTGTGT
* ** * * * * *
21093 CATTTTATGCATTTTAATATTATTTAGGTCATTTTCTATGATATAAGGAC-TTA
64 AATTTTATAAATTTTGATGTCATTTAGGTCATTTTCCATGATAGAAGGACTTTA
* *
21146 GATGTAATTTTATGAATTTTGATGTCATCTAGATCATTTACCATGATCTAGGGACTTGTGTGTAA
1 GATGTAATTTTATGAATTTTGATGTCATTTAGATCATTTTCCATGATCTAGGGACTTGTGTGTAA
* * *
21211 TTTTATAAATTTTGATGCCATTTAGGTCATTTTCCATGATCGAATGACTTTA
66 TTTTATAAATTTTGATGTCATTTAGGTCATTTTCCATGATAGAAGGACTTTA
* * * *
21263 -ATGTCAA-TTAATGCATTTTGATGTCATTTAAATCATTTTCCATGAACTAGGGACTTG-GATGT
1 GATGT-AATTTTATGAATTTTGATGTCATTTAGATCATTTTCCATGATCTAGGGACTTGTG-TGT
* *
21325 AATTTTGTAAATTTTGTTGTCATTTA
64 AATTTTATAAATTTTGATGTCATTTA
21351 AATCATTTAC
Statistics
Matches: 172, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
115 1 0.01
116 131 0.76
117 40 0.23
ACGTcount: A:0.28, C:0.10, G:0.16, T:0.46
Consensus pattern (117 bp):
GATGTAATTTTATGAATTTTGATGTCATTTAGATCATTTTCCATGATCTAGGGACTTGTGTGTAA
TTTTATAAATTTTGATGTCATTTAGGTCATTTTCCATGATAGAAGGACTTTA
Found at i:21398 original size:174 final size:174
Alignment explanation
Indices: 21040--21505 Score: 474
Period size: 174 Copynumber: 2.7 Consensus size: 174
21030 ATGTAATTTT
* * * * *
21040 ATGAATTTTGATGCCATTTAGGTCATTTTTTCATGTTTAAAGGACTTTTATGTCATTTTATGCAT
1 ATGAATTTTGATGCCATTTAGGTCA-TTTTCCATGATCAAAGGACTTTAATGTCATTTAATGCAT
* * ** * *
21105 TTTAATATTATTTAGGTCATTTTCTATGATATAAGGACTTAGATGTAATTTTATGAATTTTGATG
65 TTTGATATCATTTAAATCATTTTCCATGATATAAGGACTTAGATGTAATTTTATAAATTTTGATG
* * * ** * *
21170 TCATCTAGATCATTTACCATGATCTAGGGACTTGTGTGTAATTTT
130 TCATCTAAATCATTTACCATGATCTAGAGACTAGTGTACAATCTC
* * * *
21215 ATAAATTTTGATGCCATTTAGGTCATTTTCCATGATCGAATGACTTTAATGTCAATTAATGCATT
1 ATGAATTTTGATGCCATTTAGGTCATTTTCCATGATCAAAGGACTTTAATGTCATTTAATGCATT
* * * * *
21280 TTGATGTCATTTAAATCATTTTCCATGA-ACTAGGGACTTGGATGTAATTTTGTAAATTTTGTTG
66 TTGATATCATTTAAATCATTTTCCATGATA-TAAGGACTTAGATGTAATTTTATAAATTTTGATG
* * *
21344 TCATTTAAATCATTTACCTTGATCTCGAGACTCAG-GTACAATCTC
130 TCATCTAAATCATTTACCATGATCTAGAGACT-AGTGTACAATCTC
* * * * * *
21389 GTGAATTTTGATGCCATTTAGGTTA-TTTCTATGATCTACGGACTTTTAA-GTCATTTCATGCAT
1 ATGAATTTTGATGCCATTTAGGTCATTTTCCATGATCAAAGGAC-TTTAATGTCATTTAATGCAT
** * * **
21452 TTTGATATCATTT-AGGCTATTTTTCATGATCTAAGGACTTTTATGTAATTTTAT
65 TTTGATATCATTTAAATC-ATTTTCCATGATATAAGGACTTAGATGTAATTTTAT
21506 GAATAATGGG
Statistics
Matches: 238, Mismatches: 48, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
172 2 0.01
173 68 0.29
174 143 0.60
175 25 0.11
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (174 bp):
ATGAATTTTGATGCCATTTAGGTCATTTTCCATGATCAAAGGACTTTAATGTCATTTAATGCATT
TTGATATCATTTAAATCATTTTCCATGATATAAGGACTTAGATGTAATTTTATAAATTTTGATGT
CATCTAAATCATTTACCATGATCTAGAGACTAGTGTACAATCTC
Done.