Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3801
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: 29861
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:7229 original size:40 final size:40
Alignment explanation
Indices: 7169--7385 Score: 343
Period size: 40 Copynumber: 5.5 Consensus size: 40
7159 CGGATGATAA
7169 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-AT
*
7210 -CGGACTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
7249 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
7289 CC-GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
7328 CCGGGCTAAATCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
*
7368 CC-GGCTAATTCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
7386 TACTTGGTTT
Statistics
Matches: 166, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
39 57 0.34
40 109 0.66
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:7332 original size:79 final size:79
Alignment explanation
Indices: 7165--7385 Score: 365
Period size: 79 Copynumber: 2.8 Consensus size: 79
7155 TATTCGGATG
7165 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAAT-CGGACTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-ATCCGG-CTAAGTCCCGAAGGC
7229 ATTTGTGCGAGTTACT
64 ATTTGTGCGAGTTACT
*
7245 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAGGCAT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAGGCAT
7310 TTGTGCGAGTTACT
66 TTGTGCGAGTTACT
* * *
7324 ATAACCGGGCTAAATCCCGAAGGCATTTGAGCGAG-TAGCTATATCCGGCTAATTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCCGGCTAAGTCCCGAAGG
7386 TACTTGGTTT
Statistics
Matches: 134, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
78 2 0.01
79 88 0.66
80 44 0.33
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGCTAAGTCCCGAAGGCAT
TTGTGCGAGTTACT
Found at i:11597 original size:40 final size:40
Alignment explanation
Indices: 11542--11763 Score: 358
Period size: 40 Copynumber: 5.6 Consensus size: 40
11532 TATTCGGATG
11542 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
11582 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
*
11622 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
11662 ATATCCAGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* *
11702 ATAACCGGGCTAAATCCCGAAGGCATTTGAGCGAG-TAGCT
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
* *
11742 ATATCC-GGCTAATTCCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGG
11764 TACTTGGTTT
Statistics
Matches: 173, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
39 17 0.10
40 156 0.90
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:14944 original size:55 final size:53
Alignment explanation
Indices: 14836--15029 Score: 203
Period size: 55 Copynumber: 3.6 Consensus size: 53
14826 ATTAGGGTTT
* * * * *
14836 AAGGATACCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATAG-CATTGATAA-G-TTCATAAGGC
* *
14891 AAGGAAATCATGTAAGACCATGTCAAGACATAGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATAGCATTGATAAGTT-C-ATAAGGC
* * * * * *
14946 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATAGCATTGATAAGTTCATAAGGC
14999 AAGGATACCATGTAAGACCATGTCAAGACAT
1 AAGGATACCATGTAAGACCATGTCAAGACAT
15030 GACAATGGTA
Statistics
Matches: 116, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
52 6 0.05
53 32 0.28
54 8 0.07
55 66 0.57
56 4 0.03
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.22
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATAGCATTGATAAGTTCATAAGGC
Found at i:15042 original size:108 final size:110
Alignment explanation
Indices: 14843--15043 Score: 302
Period size: 108 Copynumber: 1.8 Consensus size: 110
14833 TTTAAGGATA
*
14843 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGA
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
*
14908 CCATGTCAAGACATAGCATTGATAAGTTACTATAAGGCAAAGGTC
66 CCATGTCAAGACATAGCAATGATAAGTTACTATAAGGCAAAGGTC
* * *
14953 CCATGTAAGACCATGCCAAGGCATGG-CATTGGTGA-G-TTCATAAGGCAAGGATACCATGTAAG
1 CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAG
*
15015 ACCATGTCAAGACAT-GACAATGGTAAGTT
65 ACCATGTCAAGACATAG-CAATGATAAGTT
15044 TCAAAAGGAT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
107 4 0.05
108 46 0.55
109 7 0.08
110 26 0.31
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.22
Consensus pattern (110 bp):
CCATGTAAGACCATGCCAAGGCATGGAAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGA
CCATGTCAAGACATAGCAATGATAAGTTACTATAAGGCAAAGGTC
Found at i:19936 original size:46 final size:45
Alignment explanation
Indices: 19869--20040 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 45
19859 AACCCGCCCC
*
19869 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCATTCGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGGCATT-GCATCCA
* *
19915 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGG--G-C-A-TTGCATCCA
* * * * *
19963 TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCA
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGGCA-TTGCATCCA
*
20008 TAGGTGAACTCAGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCAGACTCAACTCAACGAGTTCGG
20041 ATGCTCAACC
Statistics
Matches: 104, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 1 0.01
46 57 0.55
47 27 0.26
48 3 0.03
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCAGACTCAACTCAACGAGTTCGGGCATTGCATCCA
Found at i:19982 original size:93 final size:93
Alignment explanation
Indices: 19874--20044 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
19864 GCCCCTAAGT
* * *
19874 GAACTCAGACTCAACTCAACGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
19939 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
19967 GAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAGGTGAACTCAGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
20032 CGAGTTCGGATGC
66 CGAGTTCGGATGC
20045 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:27530 original size:93 final size:93
Alignment explanation
Indices: 27423--27593 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
27413 GCCCCTAAGT
* *
27423 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27488 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
27516 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
27581 CGAGTTCGGATGC
66 CGAGTTCGGATGC
27594 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:27590 original size:46 final size:46
Alignment explanation
Indices: 27418--27590 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
27408 AACCCGCCCC
* * *
27418 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
27464 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
27512 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
27557 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
27591 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:28043 original size:30 final size:30
Alignment explanation
Indices: 28009--28068 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
27999 ATTTAATACG
28009 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
28039 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
28069 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Done.