Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold636
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: 11114
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Found at i:1718 original size:40 final size:39
Alignment explanation
Indices: 1634--1817 Score: 219
Period size: 39 Copynumber: 4.6 Consensus size: 39
1624 TTGAATGATG
* * * *
1634 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
1674 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
1714 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
1753 TCCGGGTTAAGTCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTA-AA
*
1793 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
1818 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
39 69 0.55
40 48 0.38
41 8 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:1835 original size:79 final size:78
Alignment explanation
Indices: 1635--1850 Score: 215
Period size: 79 Copynumber: 2.7 Consensus size: 78
1625 TGAATGATGT
** * * * **
1635 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTTACTATATCCGGGTTAAG-TCCGAAGGCATTT
*
1699 GTGCGAGATACTAATT
63 GTGCGAGATACTAATA
** *
1715 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTGTG
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTATATCCGGGTTAAGTCCGAAGGCATTTGTG
*
1780 CGAGTTACT-ATAA
66 CGAGATACTAAT-A
* *
1793 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATTCCGAAGG
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTATATCCGGGTT-AAGTCCGAAGG
1851 TACGTGATTT
Statistics
Matches: 118, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.02
78 39 0.33
79 60 0.51
80 17 0.14
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTATATCCGGGTTAAGTCCGAAGGCATTTGTG
CGAGATACTAATA
Found at i:9725 original size:39 final size:39
Alignment explanation
Indices: 9643--9842 Score: 203
Period size: 39 Copynumber: 5.1 Consensus size: 39
9633 TTGAATGATG
* *
9643 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTA-AGTGACCATA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGA-T-ACTATA
*
9682 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAT-
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTATA
* * *
9721 TCC-GGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTATA
* * *
9759 TCCGGGTTAAGCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTATA
* * **
9798 ACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGATA-CTATA
9838 TCCGG
1 TCCGG
9843 TTAAATTCCG
Statistics
Matches: 138, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
37 24 0.17
38 9 0.07
39 56 0.41
40 39 0.28
41 9 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTATA
Found at i:9842 original size:79 final size:75
Alignment explanation
Indices: 9695--9846 Score: 198
Period size: 76 Copynumber: 2.0 Consensus size: 75
9685 GGACTAAGAT
* **
9695 CCGAAGGCATTTGTGCGAGATACTATTCCGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGAAGGCATTTGTGCGAGATACTATACCGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAAT
9760 CCGGGTTAAGC
66 CC-GGTTAAGC
* *
9771 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCT
1 CCGAAGGCATTTGTGCGAGATACTAT-ACC-GGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CT
*
9835 ATATCCGGTTAA
62 AAATCCGGTTAA
9847 ATTCCGAAGG
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
76 25 0.38
77 2 0.03
78 14 0.21
79 25 0.38
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (75 bp):
CCGAAGGCATTTGTGCGAGATACTATACCGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAAAT
CCGGTTAAGC
Found at i:9854 original size:79 final size:76
Alignment explanation
Indices: 9689--9856 Score: 196
Period size: 79 Copynumber: 2.2 Consensus size: 76
9679 ATATCCGGAC
* **
9689 TAAGATCCGAAGGCATTTGTGCGAGATACTATTCCGGCTAAGCCCGAAGGCATTTGTGCGAGTTA
1 TAAG-TCCGAAGGCATTTGTGCGAGATACTATACCGGCTAAGCCCGAAGGCATTTGAACGAGTTA
9754 CTAAATCCGGGT
65 CTAAATCCGGGT
* * *
9766 TAAGCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-
1 TAAGTCCGAAGGCATTTGTGCGAGATACTAT-ACC-GGCTAAG-CCCGAAGGCATTTGAACGAGT
*
9830 TAGCTATATCC-GGT
63 TA-CTAAATCCGGGT
*
9844 TAAATTCCGAAGG
1 T-AAGTCCGAAGG
9857 TACGTGATTT
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
76 25 0.32
77 6 0.08
78 12 0.16
79 34 0.44
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (76 bp):
TAAGTCCGAAGGCATTTGTGCGAGATACTATACCGGCTAAGCCCGAAGGCATTTGAACGAGTTAC
TAAATCCGGGT
Done.