Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2340
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: 37143
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:849 original size:114 final size:116
Alignment explanation
Indices: 634--866 Score: 434
Period size: 114 Copynumber: 2.0 Consensus size: 116
624 AATATTTATG
634 AGCTTTGCATACGTGTGACAGCCCTAATTTGACCTTAGTCGGAAAGTGGTTTCGAGACCACAAAA
1 AGCTTTGCATAC--GTGACAGCCCTAATTTGACCTTAGTCGGAAAGTGGTTTCGAGACCACAAAA
699 TCGAGTCGTAAAAAAAATAATTAATCGTCATATTTAATGCTTAATATATTTGA
64 TCGAGTCGTAAAAAAAATAATTAATCGTCATATTTAATGCTTAATATATTTGA
752 AGCTTTGCATA-GTGACAGCCCTAA-TTGACCTTAGTCGGAAAGTGGTTTCGAGACCACAAAATC
1 AGCTTTGCATACGTGACAGCCCTAATTTGACCTTAGTCGGAAAGTGGTTTCGAGACCACAAAATC
815 GAGTCGTAAAAAAAATAATTAATCGTCATATTTAATGCTTAATATATTTGA
66 GAGTCGTAAAAAAAATAATTAATCGTCATATTTAATGCTTAATATATTTGA
866 A
1 A
867 AGTGCATGTG
Statistics
Matches: 115, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
114 91 0.79
115 13 0.11
118 11 0.10
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (116 bp):
AGCTTTGCATACGTGACAGCCCTAATTTGACCTTAGTCGGAAAGTGGTTTCGAGACCACAAAATC
GAGTCGTAAAAAAAATAATTAATCGTCATATTTAATGCTTAATATATTTGA
Found at i:2812 original size:41 final size:41
Alignment explanation
Indices: 2755--2939 Score: 225
Period size: 41 Copynumber: 4.6 Consensus size: 41
2745 CGAGCTTGGG
*
2755 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAAT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
2796 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* * * *
2837 TTCGAAGGGATTTTGAGCCAGTG-TCATAACCGGACTTGGT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* * * * *
2877 TCCGAAGGGCCTTCGAGCCAGTGGCCTAAT--CCGAGCTTGGT
1 TTCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGT
*
2918 CTCGAAGGGC-TTTGAGCCAGTG
1 TTCGAAGGGCTTTTGAGCCAGTG
2940 TTAAGAATCG
Statistics
Matches: 126, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 42 0.33
41 80 0.63
43 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (41 bp):
TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
Found at i:2897 original size:81 final size:80
Alignment explanation
Indices: 2741--2940 Score: 215
Period size: 81 Copynumber: 2.5 Consensus size: 80
2731 TCGGGGTGTA
* * * *
2741 AATCCGAGCTTGGGTTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAATTTCGAAGGGC
1 AATCCGAACTTAGTTTCGAAGGG-TTTTGAGCCAGTG-TAATAACCGAACTTAATTCCGAAGGGC
* *
2806 TTTTGAGCCAGT-G-CT
64 CTTCGAGCCAGTGGCCT
* * **
2821 AATAACCGAACTTAGTTTCGAAGGGATTTTGAGCCAGTGTCATAACCGGACTTGGTTCCGAAGGG
1 AAT--CCGAACTTAGTTTCGAAGGG-TTTTGAGCCAGTGTAATAACCGAACTTAATTCCGAAGGG
2886 CCTTCGAGCCAGTGGCCT
63 CCTTCGAGCCAGTGGCCT
* * * *
2904 AATCCGAGCTTGGTCTCGAAGGGCTTTGAGCCAGTGT
1 AATCCGAACTTAGTTTCGAAGGGTTTTGAGCCAGTGT
2941 TAAGAATCGT
Statistics
Matches: 101, Mismatches: 15, Indels: 8
0.81 0.12 0.06
Matches are distributed among these distances:
80 16 0.16
81 49 0.49
82 31 0.31
83 5 0.05
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
AATCCGAACTTAGTTTCGAAGGGTTTTGAGCCAGTGTAATAACCGAACTTAATTCCGAAGGGCCT
TCGAGCCAGTGGCCT
Found at i:2966 original size:81 final size:76
Alignment explanation
Indices: 2741--2966 Score: 209
Period size: 81 Copynumber: 2.8 Consensus size: 76
2731 TCGGGGTGTA
* * *
2741 AATCCGAGCTTGGGTTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAATTTCGAAGGGC
1 AATCCGAGCTT-GGTTCGAAGGGC-TTTGAGCCAGTG-TAATAACCG-GCTTGATTCCGAAGGGC
* *
2806 TTTTGAGCCAGTGCT
62 CTTCGAGCCAGTGCT
* * * * *
2821 AATAACCGAACTTAGTTTCGAAGGGATTTTGAGCCAGTGTCATAACCGGACTTGGTTCCGAAGGG
1 AAT--CCGAGCTT-GGTTCGAAGGG-CTTTGAGCCAGTGTAATAACCGG-CTTGATTCCGAAGGG
2886 CCTTCGAGCCAGTGGCCT
61 CCTTCGAGCCAGT-G-CT
* * *
2904 AATCCGAGCTTGGTCTCGAAGGGCTTTGAGCCAGTGTTAAGAATCGTGCTTGATTCCAAAGGG
1 AATCCGAGCTTGGT-TCGAAGGGCTTTGAGCCAGTG-TAATAACCG-GCTTGATTCCGAAGGG
2967 TGGTTGTGCC
Statistics
Matches: 118, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
80 17 0.14
81 65 0.55
82 31 0.26
83 5 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (76 bp):
AATCCGAGCTTGGTTCGAAGGGCTTTGAGCCAGTGTAATAACCGGCTTGATTCCGAAGGGCCTTC
GAGCCAGTGCT
Found at i:4829 original size:48 final size:48
Alignment explanation
Indices: 4687--4869 Score: 164
Period size: 48 Copynumber: 3.9 Consensus size: 48
4677 AACATAGTAA
* *
4687 GATGCCAATGCCATATCCCAGATATGGTCTTACATGGGATCACAAATC
1 GATGCCAATGCCATATCCCAAATATGGTCTTACATGGGATCACATATC
* * * * * * * *
4735 GAAGTCGATAGCCA-A--GCTAA-A--GTCTTACACGATG-TCTCATATC
1 GATGCCAAT-GCCATATCCCAAATATGGTCTTACATG-GGATCACATATC
*
4778 GATGCCAATGCCATATCCCAAATATGGTCTTACATGGGATCACATGTC
1 GATGCCAATGCCATATCCCAAATATGGTCTTACATGGGATCACATATC
* * * *
4826 GATGCCAATGCCATGTCCCAGACATGGTCTTGCATGGGATCACA
1 GATGCCAATGCCATATCCCAAATATGGTCTTACATGGGATCACA
4870 CATAACTCTA
Statistics
Matches: 103, Mismatches: 23, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
42 4 0.04
43 23 0.22
44 1 0.01
45 4 0.04
46 3 0.03
47 1 0.01
48 63 0.61
49 4 0.04
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (48 bp):
GATGCCAATGCCATATCCCAAATATGGTCTTACATGGGATCACATATC
Found at i:6773 original size:58 final size:58
Alignment explanation
Indices: 6661--6779 Score: 175
Period size: 58 Copynumber: 2.1 Consensus size: 58
6651 GAACTCCATG
* *
6661 AATCTGATTTTCTCTGAGTTTGGTCCAATCCAAAAGTGTTTGGAACTTACGCCCACAC
1 AATCTGATTTTCTCTGAGTTTGGTCCAATCCAAAAGCGTTCGGAACTTACGCCCACAC
* * * * *
6719 AATCTGATTTTCTCTGAGTTTGGTCCAATCCAAATGCGTTCGGCATTTATGCCCATAC
1 AATCTGATTTTCTCTGAGTTTGGTCCAATCCAAAAGCGTTCGGAACTTACGCCCACAC
6777 AAT
1 AAT
6780 GCCTTGTAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (58 bp):
AATCTGATTTTCTCTGAGTTTGGTCCAATCCAAAAGCGTTCGGAACTTACGCCCACAC
Found at i:17538 original size:15 final size:14
Alignment explanation
Indices: 17518--17580 Score: 54
Period size: 15 Copynumber: 4.3 Consensus size: 14
17508 GAGAAACCTA
17518 AAATAAAGAAATCC
1 AAATAAAGAAATCC
*
17532 AACATAAATAAATCCC
1 AA-ATAAAGAAAT-CC
* *
17548 AAATAGAGAAGTCC
1 AAATAAAGAAATCC
* *
17562 AATATAAGGAAATCA
1 AA-ATAAAGAAATCC
17577 AAAT
1 AAAT
17581 TACAATACCG
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
14 8 0.21
15 26 0.68
16 4 0.11
ACGTcount: A:0.59, C:0.14, G:0.10, T:0.17
Consensus pattern (14 bp):
AAATAAAGAAATCC
Found at i:17575 original size:30 final size:30
Alignment explanation
Indices: 17518--17575 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
17508 GAGAAACCTA
*
17518 AAATAAAGAAATCCAACATAAATAAATCCC
1 AAATAAAGAAATCCAACATAAAGAAATCCC
* * * *
17548 AAATAGAGAAGTCCAATATAAGGAAATC
1 AAATAAAGAAATCCAACATAAAGAAATC
17576 AAAATTACAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.57, C:0.16, G:0.10, T:0.17
Consensus pattern (30 bp):
AAATAAAGAAATCCAACATAAAGAAATCCC
Found at i:19248 original size:18 final size:19
Alignment explanation
Indices: 19215--19250 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19205 TTAAATTTAG
*
19215 TAAATTAATTGAATTATGT
1 TAAATTAAATGAATTATGT
19234 TAAATTAAATG-ATTATG
1 TAAATTAAATGAATTATG
19251 CTGCCAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (19 bp):
TAAATTAAATGAATTATGT
Found at i:19733 original size:64 final size:64
Alignment explanation
Indices: 19654--19837 Score: 187
Period size: 67 Copynumber: 2.8 Consensus size: 64
19644 AGACATTATG
* *
19654 ATGTAGCTAGGTCGCATGGTTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGTTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
19718 ATGTAGCTAGGTCGCATGCGTGGCT-CCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGA
1 ATGTAGCTAGGTCGCATG-GTTGATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGA
19782 TAA
62 TAA
* * * *
19785 AT-TGGCTAGGTCACATGGGTGATACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGTTGATACT-ATGTGTACACCATGTAG-ACAAGAGAGC
19838 CGAACTATAT
Statistics
Matches: 97, Mismatches: 16, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 21 0.22
65 7 0.07
66 16 0.16
67 33 0.34
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGTTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Done.