Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold996
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: 23607
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.33
Found at i:362 original size:18 final size:17
Alignment explanation
Indices: 329--367 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
319 AAATATAAAC
*
329 AATAAATGATACATATG
1 AATAAATGATAAATATG
*
346 AATAAATTGATAAATATT
1 AATAAA-TGATAAATATG
364 AATA
1 AATA
368 TATTTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (17 bp):
AATAAATGATAAATATG
Found at i:12477 original size:52 final size:52
Alignment explanation
Indices: 12396--12516 Score: 188
Period size: 52 Copynumber: 2.3 Consensus size: 52
12386 GAAAATTTAT
*
12396 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* * * * *
12448 TTGCATATATCGATATATTTTATAATGTATCGATACATCTTGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
12500 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
12517 AAGATCAGTG
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:12529 original size:52 final size:51
Alignment explanation
Indices: 12396--12536 Score: 176
Period size: 52 Copynumber: 2.7 Consensus size: 51
12386 GAAAATTTAT
12396 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* * * * * *
12448 TTGCATATATCGATATATTTTATAATGTATCGATACATCTTGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
12500 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
12537 ATGTATTGAT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
51 2 0.03
52 73 0.97
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:12631 original size:13 final size:13
Alignment explanation
Indices: 12613--12637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12603 CAAAAAAATA
12613 TGTATCGATACAT
1 TGTATCGATACAT
12626 TGTATCGATACA
1 TGTATCGATACA
12638 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12633 original size:33 final size:33
Alignment explanation
Indices: 12591--12657 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
12581 AGTAGCTTAA
12591 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
12624 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
12657 A
1 A
12658 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:13558 original size:55 final size:52
Alignment explanation
Indices: 13458--13889 Score: 365
Period size: 49 Copynumber: 8.7 Consensus size: 52
13448 GAAAAGTGAT
* * * * * * **
13458 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-A
* *
13512 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
13565 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
13608 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
13658 --AGGTGCCAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* **
13706 -AAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGAT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
13754 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-ATGGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
13803 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
13853 -AAGGTGCCAATATGCTAATTCAGGGCCAGCTATATTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTG
13890 GGCTTAGAAG
Statistics
Matches: 324, Mismatches: 38, Indels: 37
0.81 0.10 0.09
Matches are distributed among these distances:
43 38 0.12
44 1 0.00
46 3 0.01
47 1 0.00
48 44 0.14
49 153 0.47
51 3 0.01
52 34 0.10
53 6 0.02
54 5 0.02
55 36 0.11
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:13729 original size:49 final size:49
Alignment explanation
Indices: 13521--13895 Score: 485
Period size: 49 Copynumber: 7.7 Consensus size: 49
13511 AAAAGGATGT
* *
13521 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
*
13573 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
13616 CAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGTG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
13664 CAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
13713 CAATATGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
13762 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
13811 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
13860 CAATATGCTAATTCAGGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
13896 GAAGGGTTGC
Statistics
Matches: 282, Mismatches: 34, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
43 39 0.14
48 45 0.16
49 166 0.59
52 32 0.11
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:13795 original size:98 final size:98
Alignment explanation
Indices: 13455--13895 Score: 545
Period size: 98 Copynumber: 4.5 Consensus size: 98
13445 TGAGAAAAGT
* * * * * *
13455 GATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG-TG
* * *
13520 TCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
60 CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
13559 GATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCA
1 GAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCA
* *
13618 ATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAA
63 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * * * *
13654 GGT-GAGGTGCCAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
13718 TGCTGAGTCAAGGCCAGCTACATTGGTCTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* *
13751 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
13816 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * * *
13849 GATGAAGGTGCCAATATGCTAATTCAGGGCCAGCTATATTGGGCTTA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
13896 GAAGGGTTGC
Statistics
Matches: 298, Mismatches: 29, Indels: 26
0.84 0.08 0.07
Matches are distributed among these distances:
91 39 0.13
95 41 0.14
96 4 0.01
97 43 0.14
98 130 0.44
103 1 0.00
104 3 0.01
107 37 0.12
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (98 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
Found at i:13855 original size:147 final size:142
Alignment explanation
Indices: 13521--13895 Score: 538
Period size: 147 Copynumber: 2.6 Consensus size: 142
13511 AAAAGGATGT
*
13521 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
* *
13586 CAAGGCCAGCTATATTGGAC-T-TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGAC
63 CAAGGCCAGCTATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC
13649 TTAAAGGTGAGGTGC
128 TTAAAGGTGAGGTGC
* * *
13664 CAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGAGTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
* * *
13729 GGCCAGCTACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
66 GGCCAGCTATATTGGACTT----ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGA
*
13794 CTTAATGGTGAAGGTGC
127 CTTAAAGGTG-AGGTGC
* * *
13811 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTAATTCAG
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
13876 GGCCAGCTATATTGGGCTTA
66 GGCCAGCTATATTGGACTTA
13896 GAAGGGTTGC
Statistics
Matches: 207, Mismatches: 18, Indels: 14
0.87 0.08 0.06
Matches are distributed among these distances:
140 37 0.18
141 1 0.00
142 1 0.00
143 39 0.19
146 47 0.23
147 82 0.40
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (142 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
AAGGTGAGGTGC
Done.