Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1099
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: 34123
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Found at i:5074 original size:39 final size:39
Alignment explanation
Indices: 4845--5067 Score: 245
Period size: 40 Copynumber: 5.6 Consensus size: 39
4835 TTGAATGATG
* * * *
4845 TCCGGGCTAAGTCGCCGAAGGC-TTTGTGCTAGTGACCATA
1 TCCGGGCTAAGT--CCGAAGGCATTTGTGCGAGTTACTAAA
* * *
4885 TCCGGACTAAGATCCGAAGGCATTTATACGAGTTACTAAA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
4925 TCTGGACTAAGATCCGAAGGTATTTGTGCGAGTTACT-AA
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
* *
4964 TCCGGGTTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
*
5003 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
*
5044 -CCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTG
5068 AACGAGTAGC
Statistics
Matches: 159, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
38 23 0.14
39 44 0.28
40 89 0.56
41 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:5089 original size:78 final size:78
Alignment explanation
Indices: 4852--5100 Score: 256
Period size: 78 Copynumber: 3.2 Consensus size: 78
4842 ATGTCCGGGC
* * * *
4852 TAAGTCGCCGAAGGC-TTTGTGCTAGTGACCATATCCGGACTAAGATCCGAAGGCATTT-ATACG
1 TAAGTC-CCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAG-TCCGAAGGCATTTGA-ACG
* *
4915 AGTTACTAAATCTGGAC
63 AGTTACTAAATCCGG-T
* * * **
4932 TAAGAT-CCGAAGGTATTTGTGCGAGTTACTA-ATCCGGGTTAAGCCCGAAGGCATTTGTGCGAG
1 TAAG-TCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGAACGAG
4995 TTACTAAATCCGGGT
65 TTACTAAATCC-GGT
* *
5010 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCGAAGGCATTTGAACGAG-
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGAACGAGT
*
5074 TAGCTATATCCGGT
66 TA-CTAAATCCGGT
* *
5088 TAAATTCCGAAGG
1 TAAGTCCCGAAGG
5101 TACGTGATTT
Statistics
Matches: 141, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
77 1 0.01
78 70 0.50
79 52 0.37
80 17 0.12
81 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (78 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCCGAAGGCATTTGAACGAGT
TACTAAATCCGGT
Found at i:5097 original size:39 final size:40
Alignment explanation
Indices: 4859--5100 Score: 196
Period size: 40 Copynumber: 6.2 Consensus size: 40
4849 GGCTAAGTCG
* * * **
4859 CCGAAGGC-TTTGTGCTAGTGACCATATCCGGACTAAGA-T
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAA-ATT
* * * * **
4898 CCGAAGGCATTTATACGAGTTACTAAATCTGGACTAAGA-T
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAA-ATT
* **
4938 CCGAAGGTATTTGTGCGAGTTACTA-ATCCGGGTT-AAGC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAATT
* * *
4976 CCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAATT
* *
5016 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCT--ATGT
1 CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAAT-T
**
5055 CCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATT
1 CCGAAGGCATTTGTGCGAGTTA-CTATATCCGGGTTAAATT
5094 CCGAAGG
1 CCGAAGG
5101 TACGTGATTT
Statistics
Matches: 169, Mismatches: 26, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
37 1 0.01
38 31 0.18
39 55 0.33
40 82 0.49
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGTTACTATATCCGGGTTAAATT
Found at i:12723 original size:40 final size:40
Alignment explanation
Indices: 12638--12868 Score: 265
Period size: 40 Copynumber: 5.8 Consensus size: 40
12628 TTGAATGATG
* * * * *
12638 TCCGGGCTAAGT-CCGAAGGC-TTTGTGCTAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
*
12676 TCCGGACTAAGAT-CCGAAGGCATTTGTACGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTACTAAA
* * * *
12716 TCTGGACTAAGAT-CCGAAGGTATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTACTAAA
* *
12756 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
*
12796 TCCGGGTTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTA-AA
* *
12837 -CCGGGCTATGTCCCGAAGGCATTTGAACGAGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGT
12869 AGCTATATCC
Statistics
Matches: 172, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
38 10 0.06
39 10 0.06
40 150 0.87
41 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTAAA
Found at i:12875 original size:40 final size:40
Alignment explanation
Indices: 12689--12894 Score: 217
Period size: 40 Copynumber: 5.2 Consensus size: 40
12679 GGACTAAGAT
* **
12689 CCGAAGGCATTTGTACGAGTTACTA-AATCTGGACTAAGAT-
1 CCGAAGGCATTTGTACGAGTTACTATAA-CCGGGTTAAG-TC
* *
12729 CCGAAGGTATTTGTGCGAGTTACTA-AATCCGGGTTAAGTC
1 CCGAAGGCATTTGTACGAGTTACTATAA-CCGGGTTAAGTC
*
12769 CCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGTTAAGTC
1 CCGAAGGCATTTGTACGAGTTACTATAA-CCGGGTTAAGTC
* *
12809 CCGAAGGCATTTGTACGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGTACGAGTTACTATAACCGGGTTAAGTC
* * * *
12849 CCGAAGGCATTTGAACGAG-TAGCTATATCC-GGTTAAATT
1 CCGAAGGCATTTGTACGAGTTA-CTATAACCGGGTTAAGTC
12888 CCGAAGG
1 CCGAAGG
12895 TACGTGATTT
Statistics
Matches: 148, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
39 15 0.10
40 131 0.89
41 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTACGAGTTACTATAACCGGGTTAAGTC
Found at i:12879 original size:120 final size:118
Alignment explanation
Indices: 12638--12894 Score: 281
Period size: 120 Copynumber: 2.2 Consensus size: 118
12628 TTGAATGATG
* * *
12638 TCCGGGCTAAGTCCGAAGGCTTTGTGCTAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGT
1 TCCGGGTTAAGTCCGAAGGCTTTGTGCGAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGT
* * **
12703 ACGAGTTACTAAATCTGGACTAAGATCCGAAGGTATTTGTGCGAGTTACTAAA
66 ACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAA
* * **
12756 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGTTAAGT-CCGAAGGC-TTTGTGCGAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
* * *
12820 TGTACGAGTTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAG-TAGCTATA
63 TGTACGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTTA-CTAAA
*
12876 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTT-AAGTCCGAAGG
12895 TACGTGATTT
Statistics
Matches: 117, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
118 11 0.09
119 23 0.20
120 81 0.69
121 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (118 bp):
TCCGGGTTAAGTCCGAAGGCTTTGTGCGAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTGT
ACGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAA
Found at i:28694 original size:45 final size:46
Alignment explanation
Indices: 28618--28704 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
28608 GGGACTTAGC
28618 CCGGAATTAGATATCTCGCACAAATGCCTTCGGATCTTAGTCTAGT
1 CCGGAATTAGATATCTCGCACAAATGCCTTCGGATCTTAGTCTAGT
*
28664 CCGGATTTAG-TAT-TCGCACACAATGCCTTCGGATCTTAGTC
1 CCGGAATTAGATATCTCGCACA-AATGCCTTCGGATCTTAGTC
28705 CGTGTTAGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
44 7 0.18
45 23 0.59
46 9 0.23
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (46 bp):
CCGGAATTAGATATCTCGCACAAATGCCTTCGGATCTTAGTCTAGT
Found at i:28706 original size:40 final size:40
Alignment explanation
Indices: 28519--28695 Score: 186
Period size: 40 Copynumber: 4.3 Consensus size: 40
28509 GCTCCTCGTT
*
28519 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAATTCGCA
* *
28559 CAAATGCCTTCGGGACTTAACCCGGA-TTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
*
28598 CAAAT-CCTTCGGGACTTAGCCCGGAATTAG-ATATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-AT-TCGCA
28638 CAAATGCCTTC-GGATCTTAGTCTAGTCCGGATTTAGT-ATTCGCA
1 CAAATGCCTTCGGGA-CTTAG-C----CCGGATTTAGTAATTCGCA
28682 CACAATGCCTTCGG
1 CA-AATGCCTTCGG
28696 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 6, Indels: 22
0.81 0.04 0.15
Matches are distributed among these distances:
38 20 0.17
39 21 0.18
40 37 0.32
41 10 0.09
42 1 0.01
44 7 0.06
45 11 0.09
46 10 0.09
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATTCGCA
Done.