Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1104
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: 28897
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:385 original size:17 final size:17
Alignment explanation
Indices: 351--383 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
341 AATTTTACTC
351 AAAATAAATATAAATTT
1 AAAATAAATATAAATTT
*
368 AAAATACATA-AAATTT
1 AAAATAAATATAAATTT
384 TAGATGTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAAATATAAATTT
Found at i:452 original size:25 final size:25
Alignment explanation
Indices: 424--471 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
414 AGAATTAGAG
* *
424 TAAAATAATAAAAATATAATTTTTT
1 TAAAAAAATAAAAATAAAATTTTTT
*
449 TAAAAAAATTAAAATAAAATTTT
1 TAAAAAAATAAAAATAAAATTTT
472 ATTATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TAAAAAAATAAAAATAAAATTTTTT
Found at i:642 original size:22 final size:21
Alignment explanation
Indices: 593--650 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
583 AGTTATTAGC
* *
593 ATATTAAATTCAAATATTTTAA
1 ATATTTAATT-AAATAATTTAA
*
615 ATATTTGAGTTAAATAATTTATA
1 ATATTT-AATTAAATAATTTA-A
638 A-ATTTAATTAAAT
1 ATATTTAATTAAAT
651 TTATATATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
21 7 0.23
22 18 0.60
23 5 0.17
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (21 bp):
ATATTTAATTAAATAATTTAA
Found at i:5923 original size:2 final size:2
Alignment explanation
Indices: 5916--5943 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5906 TTCTCCCTCC
5916 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5944 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5948 original size:2 final size:2
Alignment explanation
Indices: 5943--5967 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5933 TCTCTCTCTC
5943 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5968 GTAGAGCGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7110 original size:16 final size:18
Alignment explanation
Indices: 7091--7138 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
7081 ATAAAAATTT
7091 TATA-AAATATAAATAA-
1 TATATAAATATAAATAAC
*
7107 TATATAAA-ATAATTAAC
1 TATATAAATATAAATAAC
*
7124 AATATAAATATAAAT
1 TATATAAATATAAAT
7139 TAATTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 11 0.42
17 10 0.38
18 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TATATAAATATAAATAAC
Found at i:7139 original size:19 final size:18
Alignment explanation
Indices: 7095--7141 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
7085 AAATTTTATA
*
7095 AAATATAAA-TAATATAT
1 AAATATAAATTAAAATAT
7112 AAA-AT-AATTAACAATAT
1 AAATATAAATTAA-AATAT
7129 AAATATAAATTAA
1 AAATATAAATTAA
7142 TTATTATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
15 2 0.08
16 5 0.20
17 10 0.40
18 2 0.08
19 6 0.24
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATATAAATTAAAATAT
Found at i:7187 original size:20 final size:20
Alignment explanation
Indices: 7162--7203 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
7152 AATATTAATT
7162 TAAAAT-TAATTGATAATAAA
1 TAAAATATAATTGA-AATAAA
*
7182 TAAAATATAATTTAAATAAA
1 TAAAATATAATTGAAATAAA
7202 TA
1 TA
7204 TAAGATCACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TAAAATATAATTGAAATAAA
Found at i:8589 original size:2 final size:2
Alignment explanation
Indices: 8582--8607 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8572 GAGAAGAAGA
8582 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
8608 GGGGGGGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10153 original size:31 final size:31
Alignment explanation
Indices: 10112--10197 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
10102 ATTATTTATT
*
10112 TTAAACAAATTAAGATTTTATTTAAATATAAA
1 TTAAA-AAATTAAGATTTTATTTAAATAAAAA
* *
10144 TTAAAAAATTAAG-TATTCATTTAATTAAAAA
1 TTAAAAAATTAAGAT-TTTATTTAAATAAAAA
* *
10175 TT-AAAAATTAATAGTTTATTTAA
1 TTAAAAAATTAAGATTTTATTTAA
10198 GTTTATGATT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
30 18 0.39
31 23 0.50
32 5 0.11
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.42
Consensus pattern (31 bp):
TTAAAAAATTAAGATTTTATTTAAATAAAAA
Found at i:23088 original size:30 final size:30
Alignment explanation
Indices: 23052--23113 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
23042 AAATATCTTA
*
23052 TTATTTATTTTATTATAA-AATAAAATTTTT
1 TTATTTATTATATTA-AATAATAAAATTTTT
*
23082 TTATTTATTATATTAAATTATTAAAATTTTT
1 TTATTTATTATATTAAA-TAATAAAATTTTT
23113 T
1 T
23114 AATAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 14 0.50
31 12 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TTATTTATTATATTAAATAATAAAATTTTT
Found at i:23179 original size:18 final size:16
Alignment explanation
Indices: 23156--23189 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
23146 TATTTTATCA
23156 CTTAAAATAATATAAAAT
1 CTTAAAA-AA-ATAAAAT
23174 CTTAAAAAAATAAAAT
1 CTTAAAAAAATAAAAT
23190 TGAAAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 2 0.12
18 7 0.44
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
CTTAAAAAAATAAAAT
Found at i:23713 original size:23 final size:23
Alignment explanation
Indices: 23687--23755 Score: 56
Period size: 23 Copynumber: 3.0 Consensus size: 23
23677 ATTTTTAAAT
23687 TTTTAAATAATTTATTATTTTTA
1 TTTTAAATAATTTATTATTTTTA
*
23710 TTTT-ACTAATTTA--ATTTTTAA
1 TTTTAAATAATTTATTATTTTT-A
* *
23731 TATAAACATAATTT-TTATTTATTA
1 TTTTAA-ATAATTTATTATTT-TTA
23755 T
1 T
23756 ATATGTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
20 6 0.17
21 3 0.08
22 9 0.25
23 10 0.28
24 6 0.17
25 2 0.06
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTAAATAATTTATTATTTTTA
Found at i:24095 original size:33 final size:31
Alignment explanation
Indices: 24058--24135 Score: 88
Period size: 33 Copynumber: 2.5 Consensus size: 31
24048 TTAAACAACG
* *
24058 TATATATATAAATATAATTATATTTAATATTA
1 TATATATATAAATATAATTA-ATATAATATGA
*
24090 TTATATAAATAAA-ATAATTAATATAATATGA
1 -TATATATATAAATATAATTAATATAATATGA
*
24121 TAT-GATATAAATATA
1 TATATATATAAATATA
24136 TATTTTAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 6 0.15
30 6 0.15
31 9 0.23
32 7 0.18
33 11 0.28
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (31 bp):
TATATATATAAATATAATTAATATAATATGA
Found at i:24182 original size:18 final size:17
Alignment explanation
Indices: 24141--24208 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 17
24131 ATATATATTT
24141 TAAAATTTATATAAA-A
1 TAAAATTTATATAAATA
*
24157 T-TAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
24172 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
24190 TAAAATATT-T-TAAATA
1 TAAAAT-TTATATAAATA
24206 TAA
1 TAA
24209 TTATAATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
13 3 0.07
14 5 0.12
15 4 0.09
16 10 0.23
17 8 0.19
18 10 0.23
19 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:24189 original size:20 final size:20
Alignment explanation
Indices: 24148--24191 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
24138 TTTTAAAATT
*
24148 TATATAAAATTAATTATTAA
1 TATATAAAATTAATTATAAA
*
24168 TATATCAAAATTTA-TATAAA
1 TATAT-AAAATTAATTATAAA
24188 TATA
1 TATA
24192 AAATATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TATATAAAATTAATTATAAA
Found at i:28855 original size:22 final size:22
Alignment explanation
Indices: 28829--28878 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
28819 TAAAAAATAT
*
28829 AATATATT-TTTAATATTATAAA
1 AATAT-TTATTTAATATGATAAA
* *
28851 AATATTTATTTTATATGATTAA
1 AATATTTATTTAATATGATAAA
28873 AATATT
1 AATATT
28879 AATATAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AATATTTATTTAATATGATAAA
Done.