Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1320
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: 29536
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:3199 original size:22 final size:22
Alignment explanation
Indices: 3157--3201 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3147 TAAGTTTAGG
*
3157 GTATAAAAATAGTTCCGAATAT
1 GTATAAAAATAGTTCCCAATAT
*
3179 GTATACAAATA-TTCTCCAATAT
1 GTATAAAAATAGTTC-CCAATAT
3201 G
1 G
3202 GTATTGAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.33
Consensus pattern (22 bp):
GTATAAAAATAGTTCCCAATAT
Found at i:8865 original size:43 final size:43
Alignment explanation
Indices: 8807--8904 Score: 133
Period size: 43 Copynumber: 2.3 Consensus size: 43
8797 AAGATCAAGA
* * ** *
8807 CTTTTAGCGGCGTTTGTGATAAAAGCGCCGCTAAAAGTCATGG
1 CTTTTAACGGCGTTTGTGAGAAAAGCAACACTAAAAGTCATGG
*
8850 CTTTTAACGGTGTTTGTGAGAAAAGCAACACTAAAAGTCATGG
1 CTTTTAACGGCGTTTGTGAGAAAAGCAACACTAAAAGTCATGG
*
8893 CTTTTAGCGGCG
1 CTTTTAACGGCG
8905 CATTTTTTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (43 bp):
CTTTTAACGGCGTTTGTGAGAAAAGCAACACTAAAAGTCATGG
Found at i:9774 original size:13 final size:14
Alignment explanation
Indices: 9748--9776 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
9738 ACTAATGATG
9748 AATTAAACCATTAT
1 AATTAAACCATTAT
9762 AATTAAA-CATTAT
1 AATTAAACCATTAT
9775 AA
1 AA
9777 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:14882 original size:9 final size:9
Alignment explanation
Indices: 14868--14949 Score: 76
Period size: 9 Copynumber: 9.1 Consensus size: 9
14858 TATGTATTAC
*
14868 GTAAGTTAA
1 GTAAGTTAT
*
14877 GTAAGTTTT
1 GTAAGTTAT
14886 GTAAGTTAT
1 GTAAGTTAT
14895 GTAAGTTAT
1 GTAAGTTAT
* *
14904 GTTA-TGAT
1 GTAAGTTAT
* *
14912 ATACATTTAT
1 GTA-AGTTAT
*
14922 GTAAGGTAT
1 GTAAGTTAT
14931 GTAAGTTAT
1 GTAAGTTAT
*
14940 GTAACTTAT
1 GTAAGTTAT
14949 G
1 G
14950 ATATGATATA
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
8 4 0.07
9 49 0.84
10 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:14969 original size:13 final size:13
Alignment explanation
Indices: 14951--14980 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
14941 TAACTTATGA
14951 TATGATATATATT
1 TATGATATATATT
14964 TATGATATATATT
1 TATGATATATATT
14977 TATG
1 TATG
14981 TATTACGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (13 bp):
TATGATATATATT
Found at i:15418 original size:3 final size:3
Alignment explanation
Indices: 15405--15438 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
15395 ATACTCGAAT
15405 CAA CAAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA C-AA CAA CAA CAA CAA CAA CAA CAA CAA CAA
15439 TAATAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:17977 original size:16 final size:16
Alignment explanation
Indices: 17956--17988 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17946 TTGAGTGCTG
17956 AGCATTAACAACAGAA
1 AGCATTAACAACAGAA
*
17972 AGCATTAACAATAGAA
1 AGCATTAACAACAGAA
17988 A
1 A
17989 TCTGCGTTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (16 bp):
AGCATTAACAACAGAA
Found at i:18516 original size:83 final size:84
Alignment explanation
Indices: 18351--18557 Score: 213
Period size: 83 Copynumber: 2.5 Consensus size: 84
18341 ATAATTCAGT
* * * * * *
18351 TTTTTTGCGGTGTTTCTAAGATAGCGCCACTAATTCCTAC-ACCGCGCCACATAAAACGATGTAG
1 TTTTTAGCGGCGTTTATAAGATAGCGCCACTAAATCC-ACTACCGCGCCAAATAAAACGACGTAG
* ****
18415 TTTTCATTCGGTTTCTCATA
65 TTTCCATAAAATTTCTCATA
*
18435 TTTTTAGCGGCGTTTATAAGATAGCGCCACTAAATCCACTACC-CGCGAAATAAAACGACG-ACG
1 TTTTTAGCGGCGTTTATAAGATAGCGCCACTAAATCCACTACCGCGCCAAATAAAACGACGTA-G
18498 TTTCCATAAAATTTCTCATA
65 TTTCCATAAAATTTCTCATA
* * * ** *
18518 CTTTTAGTGGCGTTTATGACCTAGCGCCACTAACTCCACT
1 TTTTTAGCGGCGTTTATAAGATAGCGCCACTAAATCCACT
18558 GGCCTTCCAA
Statistics
Matches: 103, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
82 1 0.01
83 66 0.64
84 36 0.35
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (84 bp):
TTTTTAGCGGCGTTTATAAGATAGCGCCACTAAATCCACTACCGCGCCAAATAAAACGACGTAGT
TTCCATAAAATTTCTCATA
Found at i:18841 original size:14 final size:14
Alignment explanation
Indices: 18822--18947 Score: 95
Period size: 14 Copynumber: 9.1 Consensus size: 14
18812 CTCAATACCT
*
18822 TAAACCCTATAAAC
1 TAAACCCTATAACC
18836 TAAACCCTA-AACC
1 TAAACCCTATAACC
* * *
18849 CAATACCCAATACCC
1 TAA-ACCCTATAACC
18864 TAAACCCTATAGA-C
1 TAAACCCTATA-ACC
18878 TAAACCCTA-AACCC
1 TAAACCCTATAA-CC
*
18892 TAAACCCAAT-ACC
1 TAAACCCTATAACC
18905 ATAAACCCTATAGA-C
1 -TAAACCCTATA-ACC
18920 TAAACCCTA-AACC
1 TAAACCCTATAACC
*
18933 CAATACCCTA-AACC
1 TAA-ACCCTATAACC
18947 T
1 T
18948 TATAAACTAA
Statistics
Matches: 90, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
12 2 0.02
13 12 0.13
14 69 0.77
15 6 0.07
16 1 0.01
ACGTcount: A:0.44, C:0.37, G:0.02, T:0.17
Consensus pattern (14 bp):
TAAACCCTATAACC
Found at i:18855 original size:35 final size:35
Alignment explanation
Indices: 18806--18958 Score: 126
Period size: 35 Copynumber: 3.9 Consensus size: 35
18796 AACCAATAGA
18806 CTAAACCTCAATACCTTAAACCCTATAAACTAAACC
1 CTAAACC-CAATACCTTAAACCCTATAAACTAAACC
*
18842 CTAAACCCAATACCCAATACCCTAAACCCTATAGACTAAACCCTAAACC
1 CTAAACCCAATA-CC--T----TAAACCCTAT--A--AAC---TAAACC
* *
18891 CTAAACCCAATACCATAAACCCTATAGACTAAACC
1 CTAAACCCAATACCTTAAACCCTATAAACTAAACC
* *
18926 CTAAACCCAATACCCTAAACCTTATAAACTAAA
1 CTAAACCCAATACCTTAAACCCTATAAACTAAA
18959 TTTCAAACCA
Statistics
Matches: 96, Mismatches: 7, Indels: 29
0.73 0.05 0.22
Matches are distributed among these distances:
35 41 0.43
36 9 0.09
38 2 0.02
40 1 0.01
42 20 0.21
44 1 0.01
46 2 0.02
48 2 0.02
49 18 0.19
ACGTcount: A:0.45, C:0.35, G:0.01, T:0.19
Consensus pattern (35 bp):
CTAAACCCAATACCTTAAACCCTATAAACTAAACC
Found at i:18861 original size:42 final size:42
Alignment explanation
Indices: 18814--18949 Score: 213
Period size: 42 Copynumber: 3.2 Consensus size: 42
18804 GACTAAACCT
*
18814 CAATACCTTAAACCCTATAAACTAAACCCTAAACCCAATACC
1 CAATACCTTAAACCCTATAGACTAAACCCTAAACCCAATACC
*
18856 CAATACCCTAAACCCTATAGACTAAACCCTAAACCCTAA-ACC
1 CAATACCTTAAACCCTATAGACTAAACCCTAAACCC-AATACC
*
18898 CAATACCATAAACCCTATAGACTAAACCCTAAACCCAATACC
1 CAATACCTTAAACCCTATAGACTAAACCCTAAACCCAATACC
18940 CTAA-ACCTTA
1 C-AATACCTTA
18950 TAAACTAAAT
Statistics
Matches: 87, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
41 2 0.02
42 81 0.93
43 4 0.05
ACGTcount: A:0.44, C:0.36, G:0.01, T:0.18
Consensus pattern (42 bp):
CAATACCTTAAACCCTATAGACTAAACCCTAAACCCAATACC
Found at i:18967 original size:35 final size:35
Alignment explanation
Indices: 18893--19000 Score: 123
Period size: 35 Copynumber: 3.1 Consensus size: 35
18883 CCTAAACCCT
* * * **
18893 AAACCCAATACCATAAACCCTATAGACTAAA-CCC
1 AAACCCAATACCCTAAACCTTATAAACTAAATTTC
18927 TAAACCCAATACCCTAAACCTTATAAACTAAATTTC
1 -AAACCCAATACCCTAAACCTTATAAACTAAATTTC
* *
18963 AAA-CCAATACCCTAAACCTTA-AACCTAAATTTT
1 AAACCCAATACCCTAAACCTTATAAACTAAATTTC
18996 AAACC
1 AAACC
19001 TTAACCCCTA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
33 13 0.20
34 19 0.30
35 31 0.48
36 1 0.02
ACGTcount: A:0.46, C:0.31, G:0.01, T:0.22
Consensus pattern (35 bp):
AAACCCAATACCCTAAACCTTATAAACTAAATTTC
Found at i:19459 original size:22 final size:22
Alignment explanation
Indices: 19431--19484 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
19421 AAAATTTATT
*
19431 TTTAAGATTTTAGGGTTTAT-G
1 TTTAAGAGTTTAGGGTTTATAG
19452 ATTTAAGAGTTTAGGGTTTATAG
1 -TTTAAGAGTTTAGGGTTTATAG
19475 TTTAAG-GTTT
1 TTTAAGAGTTT
19485 GAGATTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.13
22 25 0.83
23 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (22 bp):
TTTAAGAGTTTAGGGTTTATAG
Found at i:19478 original size:14 final size:14
Alignment explanation
Indices: 19459--19506 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
19449 ATGATTTAAG
*
19459 AGTTTAGGGTTTAT
1 AGTTTAAGGTTTAT
*
19473 AGTTTAAGGTTT-G
1 AGTTTAAGGTTTAT
*
19486 AGATTTAAGGTCTAT
1 AG-TTTAAGGTTTAT
19501 AGTTTA
1 AGTTTA
19507 TGGGTTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 2 0.07
14 24 0.86
15 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (14 bp):
AGTTTAAGGTTTAT
Found at i:23308 original size:22 final size:22
Alignment explanation
Indices: 23266--23310 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
23256 TAAGTTTAGG
*
23266 GTATAAAAATAGTTCCGAATAT
1 GTATAAAAATAGTTCCCAATAT
*
23288 GTATACAAATA-TTCTCCAATAT
1 GTATAAAAATAGTTC-CCAATAT
23310 G
1 G
23311 GTATTGAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.33
Consensus pattern (22 bp):
GTATAAAAATAGTTCCCAATAT
Done.