Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1291
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: 8821
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Found at i:1852 original size:9 final size:9
Alignment explanation
Indices: 1824--1860 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
1814 TCCACCGCAC
1824 CCACCACAG
1 CCACCACAG
1833 CCA-C-CAG
1 CCACCACAG
1840 -CACCACAG
1 CCACCACAG
1848 CCACCACAG
1 CCACCACAG
1857 CCAC
1 CCAC
1861 TGCTATTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
6 2 0.08
7 4 0.16
8 4 0.16
9 15 0.60
ACGTcount: A:0.32, C:0.57, G:0.11, T:0.00
Consensus pattern (9 bp):
CCACCACAG
Found at i:1860 original size:15 final size:15
Alignment explanation
Indices: 1825--1853 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1815 CCACCGCACC
1825 CACCACAGCCACCAG
1 CACCACAGCCACCAG
1840 CACCACAGCCACCA
1 CACCACAGCCACCA
1854 CAGCCACTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.55, G:0.10, T:0.00
Consensus pattern (15 bp):
CACCACAGCCACCAG
Found at i:1874 original size:72 final size:72
Alignment explanation
Indices: 1768--2054 Score: 312
Period size: 72 Copynumber: 4.0 Consensus size: 72
1758 CTGCCACACC
* * * *
1768 CACCACAGCCGCCACAGCCACTGCTACTT-GCCATGCTTCCACAACCTCCACCGCACCCACCACA
1 CACCACAACCACCACAGCCACTGCTA-TTCACCATGCTTCCACAACCTCCACCACACCCACCACA
1832 GCCACCAG
65 GCCACCAG
* *
1840 CACCACAGCCACCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCGCCACACCCACCACAG
1 CACCACAACCACCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCACACCCACCACAG
*
1905 ---CCTG
66 CCACCAG
* * * * *
1909 CACCACAACCGCCACAACCACTGCTATTCACCATGCTTCCACAACCACCCCCGCACCCACCACCA
1 CACCACAACCACCACAGCCACTGCTATTCACCATGCTTCCACAACC-TCCAC-CACAC-CCACCA
* *
1974 CAACCACCTG
63 CAGCCACCAG
** * * * * * *
1984 CACCACAACCACCACAGCCACCACTCTTCACCATGTTTCCGCAGCCTGCACCACAACCACCACAG
1 CACCACAACCACCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCACACCCACCACAG
2049 CCACCA
66 CCACCA
2055 CTTTTTGTTG
Statistics
Matches: 181, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
69 46 0.25
70 3 0.02
71 6 0.03
72 79 0.44
73 3 0.02
74 2 0.01
75 42 0.23
ACGTcount: A:0.28, C:0.52, G:0.09, T:0.11
Consensus pattern (72 bp):
CACCACAACCACCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCACACCCACCACAG
CCACCAG
Found at i:1902 original size:21 final size:21
Alignment explanation
Indices: 1878--1927 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1868 CACCATGCTT
* *
1878 CCACAACCTCCGCCACACCCA
1 CCACAACCTCCACCACAACCA
* * *
1899 CCACAGCCTGCACCACAACCG
1 CCACAACCTCCACCACAACCA
1920 CCACAACC
1 CCACAACC
1928 ACTGCTATTC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.58, G:0.08, T:0.04
Consensus pattern (21 bp):
CCACAACCTCCACCACAACCA
Found at i:1950 original size:69 final size:70
Alignment explanation
Indices: 1768--1971 Score: 286
Period size: 69 Copynumber: 2.9 Consensus size: 70
1758 CTGCCACACC
*
1768 CACCACAGCCGCCACAGCCACTGCTACTT-GCCATGCTTCCACAACCTCCACCGCACCCACCACA
1 CACCACAGCCGCCACAGCCACTGCTA-TTCACCATGCTTCCACAACCTCCACCGCACCCACCACA
1832 GCCACCAG
65 G-C-CCAG
* * *
1840 CACCACAGCCACCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCGCCACACCCACCACAG
1 CACCACAGCCGCCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCACAG
*
1905 -CCTG
66 CCCAG
* * * *
1909 CACCACAACCGCCACAACCACTGCTATTCACCATGCTTCCACAACCACCCCCGCACCCACCAC
1 CACCACAGCCGCCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCAC
1972 CACAACCACC
Statistics
Matches: 120, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
69 60 0.50
71 2 0.02
72 58 0.48
ACGTcount: A:0.26, C:0.52, G:0.10, T:0.12
Consensus pattern (70 bp):
CACCACAGCCGCCACAGCCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCACAG
CCCAG
Found at i:1998 original size:69 final size:68
Alignment explanation
Indices: 1785--1998 Score: 182
Period size: 69 Copynumber: 3.1 Consensus size: 68
1775 GCCGCCACAG
* * * *
1785 CCACTGCTACTT-GCCATGCTTCCACAACCTCCACCGCACCCACCACAGCCACCAGCACCACAGC
1 CCACTGCTA-TTCACCATGCTTCCACAACCTCCACCGCACCCA-C-CA-CCACAACCACCGCA-C
*
1849 CACCA-CA
61 CACAACCA
* * *** * *
1856 GCCACTGCTATTCACCATGCTTCCACAACCTCCGCCACACCCACCA-CAGCCTGCACCACAACCG
1 -CCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCACCA-CAACCACCGC-ACCA
* *
1920 CCACAA
63 CAACCA
* *
1926 CCACTGCTATTCACCATGCTTCCACAACCACCCCCGCACCCACCACCACAACCACCTGCACCACA
1 CCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCACCACAACCACC-GCACCACA
1991 ACCA
65 ACCA
1995 CCAC
1 CCAC
1999 AGCCACCACT
Statistics
Matches: 120, Mismatches: 16, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
68 2 0.02
69 72 0.60
70 7 0.06
71 3 0.03
72 36 0.30
ACGTcount: A:0.28, C:0.52, G:0.08, T:0.12
Consensus pattern (68 bp):
CCACTGCTATTCACCATGCTTCCACAACCTCCACCGCACCCACCACCACAACCACCGCACCACAA
CCA
Found at i:2055 original size:75 final size:75
Alignment explanation
Indices: 1798--2046 Score: 219
Period size: 75 Copynumber: 3.4 Consensus size: 75
1788 CTGCTACTTG
* * * * * *
1798 CCATGCTTCCACAACCTCCACCGC-A-C-CCACCACAGCCACCAGCACCACAGCCACCACAGCCA
1 CCATGCTTCCACAACCACCACCACAACCACCACCACAACCACCTGCACCACAACCACCACAACCA
**
1860 CTGCTATTCA
66 CCACTATTCA
* * * *
1870 CCATGCTTCCACAACCTCCGCCAC-A-C-CCACCAC-A--GCCTGCACCACAACCGCCACAACCA
1 CCATGCTTCCACAACCACCACCACAACCACCACCACAACCACCTGCACCACAACCACCACAACCA
**
1929 CTGCTATTCA
66 CCACTATTCA
* * * *
1939 CCATGCTTCCACAACCACCCCCGCACCCACCACCACAACCACCTGCACCACAACCACCACAGCCA
1 CCATGCTTCCACAACCACCACCACAACCACCACCACAACCACCTGCACCACAACCACCACAACCA
*
2004 CCACTCTTCA
66 CCACTATTCA
* * * **
2014 CCATGTTTCCGCAGCCTGCACCACAACCACCAC
1 CCATGCTTCCACAACCACCACCACAACCACCAC
2047 AGCCACCACT
Statistics
Matches: 145, Mismatches: 26, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
69 51 0.35
71 1 0.01
72 38 0.26
73 1 0.01
75 54 0.37
ACGTcount: A:0.28, C:0.52, G:0.08, T:0.12
Consensus pattern (75 bp):
CCATGCTTCCACAACCACCACCACAACCACCACCACAACCACCTGCACCACAACCACCACAACCA
CCACTATTCA
Found at i:7476 original size:14 final size:14
Alignment explanation
Indices: 7454--7529 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
7444 TATTTGATGT
*
7454 TAAATAATATAATA
1 TAAAAAATATAATA
7468 TAAAAAATA-AAT-
1 TAAAAAATATAATA
* *
7480 T-TAAAAT-TGATA
1 TAAAAAATATAATA
*
7492 TAAAAAATATAAAAA
1 TAAAAAATAT-AATA
7507 TAAAAAA-ATAAATA
1 TAAAAAATAT-AATA
7521 TATAAAAAT
1 TA-AAAAAT
7530 TTATATAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
11 7 0.15
12 2 0.04
13 8 0.17
14 17 0.35
15 14 0.29
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (14 bp):
TAAAAAATATAATA
Found at i:7519 original size:20 final size:20
Alignment explanation
Indices: 7464--7527 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
7454 TAAATAATAT
*
7464 AATATAAAAAATAAATTTAAA
1 AATA-AAAAAATAAATATAAA
* * *
7485 ATTGATATAAA-AAATATAAA
1 AAT-AAAAAAATAAATATAAA
7505 AATAAAAAAATAAATATATAA
1 AATAAAAAAATAAATATA-AA
7526 AA
1 AA
7528 ATTTATATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 5 0.15
20 17 0.52
21 10 0.30
22 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
AATAAAAAAATAAATATAAA
Found at i:7731 original size:24 final size:25
Alignment explanation
Indices: 7704--7750 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
7694 AGTTAAATTA
*
7704 TATTTAATA-ATTTAAAAATATTTT
1 TATTTAATATAATTAAAAATATTTT
*
7728 TATTTAATATAATTATAAATATT
1 TATTTAATATAATTAAAAATATT
7751 AATATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTTAATATAATTAAAAATATTTT
Found at i:8234 original size:17 final size:17
Alignment explanation
Indices: 8214--8252 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
8204 GAATATATAA
8214 ATATATATTTTATAAAT
1 ATATATATTTTATAAAT
* * *
8231 ATATTTATTTTTTAATT
1 ATATATATTTTATAAAT
8248 ATATA
1 ATATA
8253 AAGATCATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATATTTTATAAAT
Found at i:8294 original size:17 final size:16
Alignment explanation
Indices: 8267--8298 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
8257 TCATATTTTT
8267 AATATTTATATTTAAA
1 AATATTTATATTTAAA
8283 AATATATTATATTTAA
1 AATAT-TTATATTTAA
8299 TATTTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATATTTATATTTAAA
Found at i:8320 original size:24 final size:22
Alignment explanation
Indices: 8264--8320 Score: 53
Period size: 24 Copynumber: 2.4 Consensus size: 22
8254 AGATCATATT
8264 TTTAATATTTATATTTAAAAATA
1 TTTAA-ATTTATATTTAAAAATA
*
8287 TATTATATTTAATATTTTGAAAAA-A
1 T-TTAAATTT-ATA-TTT-AAAAATA
8312 TTTAAATTT
1 TTTAAATTT
8321 CATAAATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 5 0.18
24 13 0.46
25 5 0.18
26 5 0.18
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTAAATTTATATTTAAAAATA
Found at i:8540 original size:27 final size:26
Alignment explanation
Indices: 8504--8571 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 26
8494 AGGTTAATAA
8504 TTTATATTATATA-AATT-TTAATATAT
1 TTTATATTATATATAATTATTAAT-T-T
*
8530 TTATATATTATTATATATTTATTAATTT
1 TT-TATATTA-TATATAATTATTAATTT
8558 TTTATATTATATAT
1 TTTATATTATATAT
8572 TATATTTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
26 7 0.19
27 14 0.38
28 7 0.19
29 4 0.11
30 5 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTATATTATATATAATTATTAATTT
Done.