Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1602
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: 27928
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:1815 original size:27 final size:28
Alignment explanation
Indices: 1731--1828 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
1721 CATGAGATTG
* * * *
1731 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
1760 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
1788 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
1815 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
1829 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:1839 original size:27 final size:27
Alignment explanation
Indices: 1759--1841 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
1749 TAAATTGTAC
* *
1759 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
1787 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
1814 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
1841 A
1 A
1842 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:1842 original size:29 final size:27
Alignment explanation
Indices: 1731--1842 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
1721 CATGAGATTG
** * *
1731 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
1760 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
1788 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
1815 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
1843 TTTGAATCAC
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:9880 original size:27 final size:28
Alignment explanation
Indices: 9796--9893 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
9786 CATGAGATTG
* * * *
9796 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
9825 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
9853 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
9880 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
9894 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:9904 original size:27 final size:27
Alignment explanation
Indices: 9824--9906 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
9814 TAAATTGTAC
* *
9824 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
9852 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
9879 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
9906 A
1 A
9907 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:9907 original size:29 final size:27
Alignment explanation
Indices: 9796--9907 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
9786 CATGAGATTG
** * *
9796 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
9825 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
9853 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
9880 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
9908 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:14728 original size:6 final size:6
Alignment explanation
Indices: 14719--14805 Score: 79
Period size: 6 Copynumber: 14.2 Consensus size: 6
14709 AATAAAATTG
* *
14719 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA ATTAA-AT AAATTA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A--AATAA AAATAA
* * *
14768 AATTAA ATAA-ATA AAATAA AAATAA GAATAA GAATAA A
1 AAATAA A-AATA-A AAATAA AAATAA AAATAA AAATAA A
14806 TAAAAAAAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
5 2 0.03
6 57 0.85
7 6 0.09
8 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (6 bp):
AAATAA
Found at i:14751 original size:44 final size:43
Alignment explanation
Indices: 14726--14813 Score: 53
Period size: 45 Copynumber: 2.0 Consensus size: 43
14716 TTGAAATAAA
*
14726 AATAAAAATAAAAAT-A-AAAATAAA-AATAAATTAAATAAATTA
1 AATAAAAATAAAAATAATAAAATAAATAA-AAA-TAAATAAATAA
* *
14768 AAT-TAAATAAATAA-AATAAAAATAAGAATAAGAATAAATAAA-AA
1 AATAAAAATAAA-AATAAT-AAAAT-A-AATAAAAATAAATAAATAA
14812 AA
1 AA
14814 GGAGGATTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 12
0.71 0.06 0.24
Matches are distributed among these distances:
41 7 0.19
42 6 0.17
44 8 0.22
45 9 0.25
46 4 0.11
47 2 0.06
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (43 bp):
AATAAAAATAAAAATAATAAAATAAATAAAAATAAATAAATAA
Found at i:14763 original size:9 final size:9
Alignment explanation
Indices: 14749--14787 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
14739 ATAAAAATAA
14749 AAATAAATT
1 AAATAAATT
14758 AAATAAATT
1 AAATAAATT
14767 AAATTAAA-T
1 AAA-TAAATT
*
14776 AAATAAAAT
1 AAATAAATT
14785 AAA
1 AAA
14788 AATAAGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.14
9 20 0.71
10 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAATAAATT
Found at i:14763 original size:50 final size:50
Alignment explanation
Indices: 14705--14813 Score: 131
Period size: 50 Copynumber: 2.2 Consensus size: 50
14695 TTCAAAAGAA
14705 AAAT-AATAAAATTGAAA-T-AA-AAATAAAAATAAAAATAAAAATAAAAAT
1 AAATAAATAAAATT-AAATTAAATAAAT-AAAATAAAAATAAAAATAAAAAT
* *
14753 AAATTAAAT-AAATTAAATTAAATAAATAAAATAAAAATAAGAATAAGAAT
1 AAA-TAAATAAAATTAAATTAAATAAATAAAATAAAAATAAAAATAAAAAT
14803 AAATAAA-AAAA
1 AAATAAATAAAA
14814 GGAGGATTCA
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
48 6 0.11
49 14 0.26
50 29 0.55
51 4 0.08
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (50 bp):
AAATAAATAAAATTAAATTAAATAAATAAAATAAAAATAAAAATAAAAAT
Found at i:14771 original size:14 final size:14
Alignment explanation
Indices: 14752--14784 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
14742 AAAATAAAAA
14752 TAAATTAAATAAAT
1 TAAATTAAATAAAT
14766 TAAATTAAATAAAT
1 TAAATTAAATAAAT
*
14780 AAAAT
1 TAAAT
14785 AAAAATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATTAAATAAAT
Found at i:22070 original size:26 final size:26
Alignment explanation
Indices: 22041--22100 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
22031 TCCCTTTGAA
* * *
22041 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
22067 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
22095 CCATTC
1 TCATTC
22101 TCAATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:22116 original size:28 final size:28
Alignment explanation
Indices: 22048--22126 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
22038 GAATCATTCG
*
22048 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTTGCACACTAAGTGCCATTCTCA
* *
22076 ATATCTCGCACACTAAGTGCCATTCTCA
1 ATATTTTGCACACTAAGTGCCATTCTCA
* * *
22104 ATATTTTGTACACTGAGTACCAT
1 ATATTTTGCACACTAAGTGCCAT
22127 ATGTGATTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (28 bp):
ATATTTTGCACACTAAGTGCCATTCTCA
Done.