Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2969
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: 9814
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Found at i:1705 original size:39 final size:41
Alignment explanation
Indices: 1604--1787 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
1594 TTGAATGATG
* *
1604 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
1644 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
1684 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
1723 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
1762 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1788 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:1740 original size:79 final size:80
Alignment explanation
Indices: 1604--1787 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
1594 TTGAATGATG
*
1604 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
1668 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
1683 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
1745 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
1762 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1788 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:1810 original size:78 final size:79
Alignment explanation
Indices: 1657--1820 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
1647 GGACTAAGAT
* **
1657 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
1722 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
1736 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
1798 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
1814 CCGAAGG
1 CCGAAGG
1821 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:9620 original size:39 final size:41
Alignment explanation
Indices: 9520--9701 Score: 177
Period size: 39 Copynumber: 4.6 Consensus size: 41
9510 TTGAATGATG
* *
9520 TCCGGGCTAAGT-CCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
9559 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
9599 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* * *
9638 TCC-GGTTAAGTCCCGAAGGCAATTGTGCGAAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGATACTAATA
* *
9678 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
9702 GAACGAGTAC
Statistics
Matches: 122, Mismatches: 11, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
38 6 0.05
39 56 0.46
40 31 0.25
41 28 0.23
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:9675 original size:79 final size:77
Alignment explanation
Indices: 9520--9734 Score: 213
Period size: 79 Copynumber: 2.7 Consensus size: 77
9510 TTGAATGATG
* * * * * *
9520 TCCGGGCTAAGTCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTACTATATCCGG-TTAAG-TCCGAAGGCAATT
9584 GTGCGAGATACTA-A
63 GTGCGAGATACTATA
*
9598 TTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGTTAAGTCCCGAAGGCAATTG
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATATCCGGTTAAGT-CCGAAGGCAATTG
*
9663 TGCGAAGTTACTATA
64 TGCG-AGATACTATA
* * ** *
9678 ACCGGGCTATGTCCCGAAGGCA-TTGAACGAG-TACTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATATCCGGTT-AAGTCCGAAGG
9735 TACGTGATTT
Statistics
Matches: 116, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
77 1 0.01
78 40 0.34
79 57 0.49
80 18 0.16
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (77 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTATATCCGGTTAAGTCCGAAGGCAATTGTG
CGAGATACTATA
Found at i:9719 original size:78 final size:78
Alignment explanation
Indices: 9572--9734 Score: 197
Period size: 78 Copynumber: 2.1 Consensus size: 78
9562 GGACTAAGAT
* * **
9572 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
9637 ATCCGGTTAAGTC
66 ATCCGGTTAAATC
* *
9650 CCGAAGGCAATTGTGCGAAGTTACT-ATAACCGGGCTATGTCCCGAAGGCA-TTGAACGAG-TAC
1 CCGAAGGCAATTGTGCG-AGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTAC
* *
9712 TATATCCGGTTAAATT
63 TAAATCCGGTTAAATC
9728 CCGAAGG
1 CCGAAGG
9735 TACGTGATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 41 0.56
79 22 0.30
80 10 0.14
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (78 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGTTAAATC
Done.