Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1711
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: 31578
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:5824 original size:28 final size:27
Alignment explanation
Indices: 5761--5912 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
5751 ATATTAAGTC
* * *
5761 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
5788 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
5816 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
5843 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
5871 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
5898 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
5913 GCACAATTTA
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:5845 original size:55 final size:55
Alignment explanation
Indices: 5761--5912 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
5751 ATATTAAGTC
* * *
5761 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
5816 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
5871 CGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCT
5913 GCACAATTTA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:11521 original size:25 final size:25
Alignment explanation
Indices: 11493--11599 Score: 117
Period size: 25 Copynumber: 4.3 Consensus size: 25
11483 ATGCTTTCAT
*
11493 GAGCTGTAAATCGGGAAGCTCATAC
1 GAGCTGTAAATCGAGAAGCTCATAC
**
11518 GAGCTACAAATC-AGGAAGCTCATAC
1 GAGCTGTAAATCGA-GAAGCTCATAC
* * *
11543 AAGCTGTAAATTGAAAAGCTCATAC
1 GAGCTGTAAATCGAGAAGCTCATAC
* *
11568 GACCTGCAAATCGAGAAGCTCATAC
1 GAGCTGTAAATCGAGAAGCTCATAC
*
11593 AAGCTGT
1 GAGCTGT
11600 GGTGTATCCA
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
25 63 0.98
26 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.20
Consensus pattern (25 bp):
GAGCTGTAAATCGAGAAGCTCATAC
Found at i:11548 original size:50 final size:50
Alignment explanation
Indices: 11494--11599 Score: 151
Period size: 50 Copynumber: 2.1 Consensus size: 50
11484 TGCTTTCATG
** *
11494 AGCTGTAAATCGGGAAGCTCATACGAGCTACAAATC-AGGAAGCTCATACA
1 AGCTGTAAATCGAAAAGCTCATACGACCTACAAATCGA-GAAGCTCATACA
* *
11544 AGCTGTAAATTGAAAAGCTCATACGACCTGCAAATCGAGAAGCTCATACA
1 AGCTGTAAATCGAAAAGCTCATACGACCTACAAATCGAGAAGCTCATACA
11594 AGCTGT
1 AGCTGT
11600 GGTGTATCCA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
50 49 0.98
51 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.20
Consensus pattern (50 bp):
AGCTGTAAATCGAAAAGCTCATACGACCTACAAATCGAGAAGCTCATACA
Found at i:21008 original size:46 final size:44
Alignment explanation
Indices: 20955--21124 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 44
20945 AACCCGCCCC
*
20955 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TT-GTATCCA
* * * *
21001 TAAGTGAACTCGGACTCAAATCAATGAGTTCGGATGCCTAGT-TACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-CTTGTATCCA
* * * *
21047 TTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTGCATCCA
1 -TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTGTATCCA
21092 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
21125 ATGCTCAACC
Statistics
Matches: 102, Mismatches: 15, Indels: 15
0.77 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 31 0.30
46 59 0.58
47 4 0.04
48 2 0.02
49 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (44 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTGTATCCA
Found at i:21121 original size:91 final size:92
Alignment explanation
Indices: 20960--21128 Score: 277
Period size: 91 Copynumber: 1.8 Consensus size: 92
20950 GCCCCTAAGT
* * *
20960 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGTATCCATAAGTGAACTCGGACTCAAATCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAAATCAA
*
21025 TGAGTTCGGATGCCTAGTTACATTCAC
66 CGAGTTCGGATGCCTAGTTACATTCAC
* *
21052 GAACTCGGACTCAACTCAACGAGTTCGGACATT-GCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAAATCAA
21116 CGAGTTCGGATGC
66 CGAGTTCGGATGC
21129 TCAACCATCC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
91 41 0.58
92 30 0.42
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAAATCAA
CGAGTTCGGATGCCTAGTTACATTCAC
Found at i:21582 original size:30 final size:30
Alignment explanation
Indices: 21548--21607 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
21538 ATTTAATACG
21548 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
21578 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
21608 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
Found at i:28617 original size:45 final size:46
Alignment explanation
Indices: 28502--28626 Score: 157
Period size: 45 Copynumber: 2.7 Consensus size: 46
28492 AACCCGCCCC
* *
28502 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA-GCATAGATACAT
* * * *
28549 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGA-CATTGCATCCA-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATAG-ATACAT
28593 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28627 TGCTCAACCA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
44 5 0.07
45 32 0.47
46 29 0.43
47 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGAGCATAGATACAT
Found at i:29066 original size:30 final size:30
Alignment explanation
Indices: 29032--29091 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
29022 ATTTAATACG
29032 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
29062 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
29092 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.