Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g01484.F2
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: 3761
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Found at i:1638 original size:15 final size:17
Alignment explanation
Indices: 1608--1639 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1598 TTATTTTTTT
1608 TTCTATGAATAAAATAA
1 TTCTATGAATAAAATAA
1625 TTCTAT-AA-AAAATAA
1 TTCTATGAATAAAATAA
1640 ATTTTCTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (17 bp):
TTCTATGAATAAAATAA
Found at i:1724 original size:45 final size:46
Alignment explanation
Indices: 1670--1887 Score: 167
Period size: 45 Copynumber: 4.5 Consensus size: 46
1660 TTTAAAGTTC
*
1670 AAATTTCATAACTTACATAA-TACATAAATATATATATCATATCAT
1 AAATGTCATAACTTACATAACTACATAAATATATATATCATATCAT
1715 AAATGTCATAACTTACATAACTTACAT-AA-ATATATATCATATCAT
1 AAATGTCATAACTTACATAAC-TACATAAATATATATATCATATCAT
* * * * * * *
1760 AACT-TATATAACTCACATAACATACATAACT-TACATAACTTATATAAAT
1 AAATGT-CATAACTTACATAAC-TACATAAATATATAT-A-TCATAT-CAT
*
1809 ATATATCAGATCATAACTTACATAACTTACATAATACATAAATATATATCATAACAT
1 A-A-AT--G-TCATAACTTACATAAC-TACAT-A-A-AT--ATATATATCATATCAT
1866 AAATGTCATAACTTACATAACT
1 AAATGTCATAACTTACATAACT
1888 TAATTATACT
Statistics
Matches: 135, Mismatches: 18, Indels: 34
0.72 0.10 0.18
Matches are distributed among these distances:
44 1 0.01
45 56 0.41
46 7 0.05
47 6 0.04
48 5 0.04
49 3 0.02
50 1 0.01
51 2 0.01
52 16 0.12
53 1 0.01
54 18 0.13
55 4 0.03
56 2 0.01
57 4 0.03
58 4 0.03
59 1 0.01
60 4 0.03
ACGTcount: A:0.48, C:0.16, G:0.01, T:0.34
Consensus pattern (46 bp):
AAATGTCATAACTTACATAACTACATAAATATATATATCATATCAT
Found at i:1733 original size:9 final size:9
Alignment explanation
Indices: 1721--1889 Score: 98
Period size: 9 Copynumber: 19.0 Consensus size: 9
1711 TCATAAATGT
1721 CATAACTTA
1 CATAACTTA
1730 CATAACTTA
1 CATAACTTA
*
1739 CATAA-ATA
1 CATAACTTA
* * *
1747 TATATCATA
1 CATAACTTA
1756 TCATAACTTA
1 -CATAACTTA
* *
1766 TATAACTCA
1 CATAACTTA
*
1775 CATAACATA
1 CATAACTTA
1784 CATAACTTA
1 CATAACTTA
1793 CATAACTTA
1 CATAACTTA
* *
1802 TATAA-ATA
1 CATAACTTA
* * **
1810 TATATCAGA
1 CATAACTTA
1819 TCATAACTTA
1 -CATAACTTA
1829 CATAACTTA
1 CATAACTTA
1838 CATAA--TA
1 CATAACTTA
*
1845 CATAA-ATA
1 CATAACTTA
* * *
1853 TATATCATAA
1 CATAAC-TTA
*
1863 CATAAATGT-
1 CATAACT-TA
1872 CATAACTTA
1 CATAACTTA
1881 CATAACTTA
1 CATAACTTA
1890 ATTATACTTA
Statistics
Matches: 122, Mismatches: 29, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
7 7 0.06
8 17 0.14
9 83 0.68
10 15 0.12
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:1760 original size:36 final size:36
Alignment explanation
Indices: 1720--1842 Score: 147
Period size: 36 Copynumber: 3.7 Consensus size: 36
1710 ATCATAAATG
1720 TCATAACTTACATAACTTACATAAATATATATCATA
1 TCATAACTTACATAACTTACATAAATATATATCATA
* *
1756 TCATAACTTATATAAC-T-C----ACATA-A-CATA
1 TCATAACTTACATAACTTACATAAATATATATCATA
* *
1784 -CATAACTTACATAACTTATATAAATATATATCAGA
1 TCATAACTTACATAACTTACATAAATATATATCATA
1819 TCATAACTTACATAACTTACATAA
1 TCATAACTTACATAACTTACATAA
1843 TACATAAATA
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
27 14 0.20
28 5 0.07
29 1 0.01
30 4 0.06
33 4 0.06
34 2 0.03
35 4 0.06
36 37 0.52
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (36 bp):
TCATAACTTACATAACTTACATAAATATATATCATA
Found at i:1779 original size:63 final size:63
Alignment explanation
Indices: 1721--1849 Score: 208
Period size: 63 Copynumber: 2.1 Consensus size: 63
1711 TCATAAATGT
* *
1721 CATAACTTACATAACTTACATAAATATATATCATATCATAACTTATATAACTCACATAACATA
1 CATAACTTACATAACTTACATAAATATATATCAGATCATAACTTACATAACTCACATAACATA
* *
1784 CATAACTTACATAACTTATATAAATATATATCAGATCATAACTTACATAACTTACAT-A-ATA
1 CATAACTTACATAACTTACATAAATATATATCAGATCATAACTTACATAACTCACATAACATA
1845 CATAA
1 CATAA
1850 ATATATATCA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
61 8 0.13
62 1 0.02
63 53 0.85
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.33
Consensus pattern (63 bp):
CATAACTTACATAACTTACATAAATATATATCAGATCATAACTTACATAACTCACATAACATA
Found at i:1798 original size:27 final size:26
Alignment explanation
Indices: 1676--1886 Score: 101
Period size: 27 Copynumber: 7.9 Consensus size: 26
1666 GTTCAAATTT
1676 CATAACTTACATAA-TACATAA-ATA
1 CATAACTTACATAACTACATAACATA
* * * * *
1700 TATATATCATATCATAAATGTCATAACTTA
1 CATA-A-CTTA-CATAACT-ACATAACATA
* * *
1730 CATAACTTACATAAATATATATCATA
1 CATAACTTACATAACTACATAACATA
*
1756 TCATAACTTATATAACTCACATAACATA
1 -CATAACTTACATAACT-ACATAACATA
*
1784 CATAACTTACATAACTTATATAA-ATA
1 CATAACTTACATAAC-TACATAACATA
* * ** *
1810 TATATCAGATCATAACTTACATAACTTA
1 CATAACTTA-CATAAC-TACATAACATA
* * *
1838 CATAA--TACATAAATATATATCATAA
1 CATAACTTACATAACTACATAACAT-A
*
1863 CATAAATGT-CATAACTTACATAAC
1 CATAACT-TACATAAC-TACATAAC
1887 TTAATTATAC
Statistics
Matches: 139, Mismatches: 32, Indels: 28
0.70 0.16 0.14
Matches are distributed among these distances:
24 10 0.07
25 12 0.09
26 18 0.13
27 63 0.45
28 25 0.18
29 6 0.04
30 5 0.04
ACGTcount: A:0.48, C:0.17, G:0.01, T:0.34
Consensus pattern (26 bp):
CATAACTTACATAACTACATAACATA
Found at i:1867 original size:43 final size:44
Alignment explanation
Indices: 1784--1887 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 44
1774 ACATAACATA
* * *
1784 CATAACTTACATAACTTATATAAATATATATCAGATCATAACT-T
1 CATAACTTACATAAC-TACATAAATATATATCAGAACATAAATGT
*
1828 ACATAACTTACATAA-TACATAAATATATATCATAACATAAATGT
1 -CATAACTTACATAACTACATAAATATATATCAGAACATAAATGT
1872 CATAACTTACATAACT
1 CATAACTTACATAACT
1888 TAATTATACT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
43 37 0.70
44 2 0.04
45 14 0.26
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (44 bp):
CATAACTTACATAACTACATAAATATATATCAGAACATAAATGT
Found at i:3566 original size:13 final size:15
Alignment explanation
Indices: 3532--3565 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
3522 ATGTTGTGCA
3532 AATAAACATAGAAAAT
1 AATAAACATA-AAAAT
3548 AATAAACATAAAATAT
1 AATAAACATAAAA-AT
3564 AA
1 AA
3566 AATTACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.21
Consensus pattern (15 bp):
AATAAACATAAAAAT
Done.