Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1581
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: 16408
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:407 original size:15 final size:15
Alignment explanation
Indices: 387--416 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
377 ACAACTTTAC
*
387 CTTTAAGCATAAAGA
1 CTTTAAGCACAAAGA
402 CTTTAAGCACAAAGA
1 CTTTAAGCACAAAGA
417 GGATGATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (15 bp):
CTTTAAGCACAAAGA
Found at i:3129 original size:26 final size:28
Alignment explanation
Indices: 3093--3148 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
3083 TTTTGATCGA
3093 AATTATTATTT-ATTTAA-TAAAATAAT
1 AATTATTATTTAATTTAATTAAAATAAT
* *
3119 AATTTTTATTTAAATTTAATTATAATAAT
1 AATTATTATTT-AATTTAATTAAAATAAT
3148 A
1 A
3149 TATAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.40
28 6 0.24
29 9 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AATTATTATTTAATTTAATTAAAATAAT
Found at i:3168 original size:37 final size:33
Alignment explanation
Indices: 3099--3173 Score: 80
Period size: 36 Copynumber: 2.2 Consensus size: 33
3089 TCGAAATTAT
*
3099 TATTTATTTAATAAAATAATAATTTTTATTTAA
1 TATTTATTTAATAAAATAAAAATTTTTATTTAA
*
3132 -ATTTAATTATAATAATATATAAAAATTATTTTTTTAA
1 TATTT-ATT-TAATAA-A-ATAAAAATT-TTTATTTAA
3169 TATTT
1 TATTT
3174 TTAACAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
32 4 0.12
33 3 0.09
34 6 0.18
35 1 0.03
36 8 0.24
37 8 0.24
38 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TATTTATTTAATAAAATAAAAATTTTTATTTAA
Found at i:5625 original size:2 final size:2
Alignment explanation
Indices: 5620--5649 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5610 ATACATACGT
5620 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5650 AAAGCCACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5958 original size:26 final size:27
Alignment explanation
Indices: 5937--5989 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
5927 ATAAATTTAA
5937 ATTTATTT-AATTTAATT-TAAATAAT
1 ATTTATTTAAATTTAATTATAAATAAT
*
5962 TTTTATTTAAATTTAATTATAAA-AAT
1 ATTTATTTAAATTTAATTATAAATAAT
5988 AT
1 AT
5990 ATAAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 13 0.54
27 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATTTATTTAAATTTAATTATAAATAAT
Found at i:5974 original size:21 final size:21
Alignment explanation
Indices: 5910--5977 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
5900 TATTAGTGTC
5910 ATTTAAATAAAATTTTTA--TAA
1 ATTTAAAT--AATTTTTATTTAA
5931 ATTTAAAT--TTATTTAATTT-A
1 ATTTAAATAATT-TTT-ATTTAA
5951 ATTTAAATAATTTTTATTTAA
1 ATTTAAATAATTTTTATTTAA
5972 ATTTAA
1 ATTTAA
5978 TTATAAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
17 2 0.05
18 3 0.08
19 1 0.03
20 13 0.32
21 19 0.47
22 2 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTAAATAATTTTTATTTAA
Found at i:6015 original size:38 final size:36
Alignment explanation
Indices: 5964--6043 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 36
5954 TAAATAATTT
* *
5964 TTATTTAA-A-TTTAATTATAAAAATATATAAAATAATA
1 TTATTTAATATTTTAA-AATAAAAA-ATAAAAAATAA-A
6001 TT-TTTAATATTTTAAAATAAAAAATAAAAAATAAA
1 TTATTTAATATTTTAAAATAAAAAATAAAAAATAAA
6036 TTATTTAA
1 TTATTTAA
6044 ATCAAAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
35 3 0.08
36 20 0.53
37 10 0.26
38 5 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (36 bp):
TTATTTAATATTTTAAAATAAAAAATAAAAAATAAA
Found at i:6183 original size:27 final size:27
Alignment explanation
Indices: 6125--6199 Score: 68
Period size: 27 Copynumber: 2.8 Consensus size: 27
6115 ATAATTAAAT
* * *
6125 TTAAATAAAAATAAT-ATTTT-TATTA
1 TTAAATAATAATAATAATTTTAAATAA
6150 TTAAAATAATAATAATAATTTTAAATAA
1 TT-AAATAATAATAATAATTTTAAATAA
6178 TTAAATTATATAA-AA-AATTTTA
1 TTAAA-TA-ATAATAATAATTTTA
6200 TTAAAATTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 2 0.05
26 12 0.29
27 15 0.36
28 9 0.21
29 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TTAAATAATAATAATAATTTTAAATAA
Found at i:11513 original size:50 final size:50
Alignment explanation
Indices: 11380--11635 Score: 378
Period size: 50 Copynumber: 5.2 Consensus size: 50
11370 AGTTGTTATC
* *
11380 ATTGTTGACTA-TCATTCACCAA-CTTGTGACAATAG-AGAGAGGTGACCATA
1 ATTGTTGACAATTC-TTCACCAACCTT-TGACAATAGAAG-GAGGTGGCCATA
** *
11430 ATTGTTGATGA-TCTTCACCAACCTTTGACAATAGAAGGAGGTGGTCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
11479 ATTGTTGACAATTCTTCACCAACCTTTGACAATAG-AGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
*
11528 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
* *
11578 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGATGGCCATA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
11628 ATTGTTGA
1 ATTGTTGA
11636 ACTCTAAGTT
Statistics
Matches: 191, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
49 83 0.43
50 108 0.57
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (50 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
Found at i:11551 original size:99 final size:98
Alignment explanation
Indices: 11380--11635 Score: 408
Period size: 99 Copynumber: 2.6 Consensus size: 98
11370 AGTTGTTATC
* * *
11380 ATTGTTGACTA-TCATTCACCAA-CTTGTGACAATAGAGAGAGGTGACCATAATTGTTGATGATC
1 ATTGTTGACAATTC-TTCACCAACCTT-TGACAATAGAG-GAGGTGGCCATAATTGTTGACGATC
*
11443 TTCACCAACCTTTGACAATAGAAGGAGGTGGTCATA
63 TTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
11479 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGAGGTGGCCATAATTGTTGACGATTCTT
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGAGGTGGCCATAATTGTTGACGA-TCTT
11544 CACCAACCTTTGACAATAGAAGGAGGTGGCCATA
65 CACCAACCTTTGACAATAGAAGGAGGTGGCCATA
*
11578 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGGAGATGGCCATAATTGTTGA
1 ATTGTTGACAATTCTTCACCAACCTTTGACAATAGA-GGAGGTGGCCATAATTGTTGA
11636 ACTCTAAGTT
Statistics
Matches: 148, Mismatches: 5, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
98 21 0.14
99 102 0.69
100 25 0.17
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (98 bp):
ATTGTTGACAATTCTTCACCAACCTTTGACAATAGAGGAGGTGGCCATAATTGTTGACGATCTTC
ACCAACCTTTGACAATAGAAGGAGGTGGCCATA
Found at i:16174 original size:49 final size:49
Alignment explanation
Indices: 16042--16296 Score: 419
Period size: 49 Copynumber: 5.2 Consensus size: 49
16032 AGTTGTTGTC
16042 ATTGTTGAC-TATCATTCACCAACCTTTGACAATAG-AGAGAGGTGGCCATA
1 ATTGTTGACAT-TC-TTCACCAACCTTTGACAATAGAAG-GAGGTGGCCATA
16092 ATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
1 ATTGTTGAC-ATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
*
16142 ATTGTTGACATTCTTCACCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
16191 ATTGTTGACGATTCTTCACCAACCTTTGAC-ATAGAAGGAGGTGGCCATA
1 ATTGTTGAC-ATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
*
16240 ATTGTTGACATTCTTC-CCAACCTTTGACAATAGAGGGAGGTGGCCATA
1 ATTGTTGACATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
16288 ATTGTTGAC
1 ATTGTTGAC
16297 CTAAGTATAT
Statistics
Matches: 197, Mismatches: 3, Indels: 12
0.93 0.01 0.06
Matches are distributed among these distances:
47 12 0.06
48 34 0.17
49 75 0.38
50 71 0.36
51 4 0.02
52 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (49 bp):
ATTGTTGACATTCTTCACCAACCTTTGACAATAGAAGGAGGTGGCCATA
Done.