Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1559
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: 258979
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 3 of 3
Found at i:235678 original size:168 final size:168
Alignment explanation
Indices: 235469--236091 Score: 934
Period size: 168 Copynumber: 3.6 Consensus size: 168
235459 TGTTTACAAG
*
235469 TACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCCTACAAATACAA
1 TACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCCTACAAGTACAA
*
235534 GTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCCTATATTTACAAGTCTCCACCTC
66 GTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCCTACATTTACAAGTCTCCACCTC
*
235599 CACCACCACCATCACCACCTAAGCCACACCCCTATATT
131 CACCACCACCATCACCACCTAAGCCACACCCCTACATT
235637 TACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCCTACAAGTACAA
1 TACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCCTACAAGTACAA
*
235702 GTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCTACATTTACAAGTCTCCACCTC
66 GTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCCTACATTTACAAGTCTCCACCTC
235767 CACCACCACCATCACCACCTAAGCCACACCCCTACATT
131 CACCACCACCATCACCACCTAAGCCACACCCCTACATT
235805 TACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCACACCCACACCC
1 TACAAGTCTCCACCTCCACCACCACCATCACCACCTAAG------------CCACACCCACACCC
235870 CTACAAGTACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACACCCCTACA
54 CTACAAGTACAAGTCTCCACCACCACCACCACCATCACCACCTAAG------CCACACCCCTACA
** *
235935 AGTACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAGCCACACCCCTACATT
113 TTTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCTACATT
* **
235991 TACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAG------CCACACCCCTACATTTACAA
1 TACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCCTACAAGTACAA
* *
236050 GTCTCCACCTCCGCCACCACCATCACCACCTAAGCCACACCC
66 GTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCC
236092 ACACCCACAC
Statistics
Matches: 424, Mismatches: 13, Indels: 42
0.89 0.03 0.09
Matches are distributed among these distances:
162 8 0.02
168 253 0.60
180 59 0.14
186 104 0.25
ACGTcount: A:0.30, C:0.51, G:0.04, T:0.14
Consensus pattern (168 bp):
TACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCCTACAAGTACAA
GTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCCTACATTTACAAGTCTCCACCTC
CACCACCACCATCACCACCTAAGCCACACCCCTACATT
Found at i:235853 original size:6 final size:6
Alignment explanation
Indices: 235844--235869 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
235834 ACCACCTAAG
235844 CCACAC CCACAC CCACAC CCACAC CC
1 CCACAC CCACAC CCACAC CCACAC CC
235870 CTACAAGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (6 bp):
CCACAC
Found at i:235886 original size:240 final size:240
Alignment explanation
Indices: 235622--236223 Score: 1096
Period size: 240 Copynumber: 2.5 Consensus size: 240
235612 ACCACCTAAG
* ** *
235622 CCACACCCCTATATTTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACA
1 CCACACCCCTACAAATACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACA
235687 CCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCTACATTT
66 CCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCTACATTT
235752 ACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCTACATTTACAAGTCTCCA
131 ACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCTACATTTACAAGTCTCCA
235817 CCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCACAC
196 CCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCACAC
*
235862 CCACACCCCTACAAGTACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACA
1 CCACACCCCTACAAATACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACA
*
235927 CCCCTACAAGTACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAGCCACACCCCTACATTT
66 CCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCTACATTT
*
235992 ACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAGCCACACCCCTACATTTACAAGTCTCCA
131 ACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCTACATTTACAAGTCTCCA
*
236057 CCTCCGCCACCACCATCACCACCTAAGCCACACCCACACCCACAC
196 CCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCACAC
* *
236102 CCACACCCCTACAAATACAAGTCTCCACCGCCGCCACCACCATCACCACCTAAGCCACACCCACA
1 CCACACCCCTACAAATACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACA
* *
236167 CCCCTACAAATACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCC
66 CCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCC
236224 ACATCCACAC
Statistics
Matches: 349, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
240 349 1.00
ACGTcount: A:0.31, C:0.52, G:0.05, T:0.13
Consensus pattern (240 bp):
CCACACCCCTACAAATACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACA
CCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCTACATTT
ACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCTACATTTACAAGTCTCCA
CCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCACAC
Found at i:235900 original size:72 final size:68
Alignment explanation
Indices: 235790--236265 Score: 310
Period size: 60 Copynumber: 7.6 Consensus size: 68
235780 ACCACCTAAG
**
235790 CCACACCCCTACATTTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACA
1 CCACACCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACA--C-C-
235855 CCCACAC
62 CCCACAC
*
235862 CCACACCCCTACAAGTACAAGTCTCCACCACCACCACCACCATCACCACCTAAG--------CCA
1 CCACACCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCCA
235919 CAC
66 CAC
*
235922 CCACACCCCTACAAGTACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAGCCACA----C-
1 CCACACCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCCA
235982 C-C
66 CAC
* ** * * *
235984 CTACA--TTTACAAGT-C---TCCACCTCCGCCACCACCA---TCACCACCTAAGCCACA----C
1 CCACACCCCTACAAGTACAAGT-CTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCC
236036 -C-C
65 ACAC
* ** * * *
236038 CTACA--TTTACAAGT-C---TCCACCTCCGCCACCACCA---TCACCACCTAAGCCACACCCAC
1 CCACACCCCTACAAGTACAAGT-CTCCACCTCCACCACCACCATCACCACCTAAGCCACA--C-C
236094 ACCCACAC
62 -CCCACAC
* * *
236102 CCACACCCCTACAAATACAAGTCTCCACCGCCGCCACCACCATCACCACCTAAG--------CCA
1 CCACACCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCCA
236159 CAC
66 CAC
* *
236162 CCACACCCCTACAAATACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACA--CCCA
1 CCACACCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCCA
*
236225 CAT
66 CAC
* *
236228 CCACACCCCTACAAATACAAGTCTCCACCGCCACCACC
1 CCACACCCCTACAAGTACAAGTCTCCACCTCCACCACC
236266 TCCAGTTTAC
Statistics
Matches: 350, Mismatches: 23, Indels: 68
0.79 0.05 0.15
Matches are distributed among these distances:
54 71 0.20
56 1 0.00
57 13 0.04
59 1 0.00
60 123 0.35
62 6 0.02
63 2 0.01
64 6 0.02
66 48 0.14
67 1 0.00
69 14 0.04
70 1 0.00
72 63 0.18
ACGTcount: A:0.31, C:0.52, G:0.05, T:0.12
Consensus pattern (68 bp):
CCACACCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCCA
CAC
Found at i:236093 original size:6 final size:6
Alignment explanation
Indices: 236084--236109 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
236074 ACCACCTAAG
236084 CCACAC CCACAC CCACAC CCACAC CC
1 CCACAC CCACAC CCACAC CCACAC CC
236110 CTACAAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (6 bp):
CCACAC
Found at i:236175 original size:126 final size:123
Alignment explanation
Indices: 235622--236265 Score: 571
Period size: 126 Copynumber: 5.3 Consensus size: 123
235612 ACCACCTAAG
* ** * *
235622 CCACACCCCTATATTTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCAC-
1 CCACACCCCTACAAATACAAGTCTCCACCGCCGCCACCACCATCACCACCTAAGCCACACCC-CT
* *
235686 ACCCCTACAAGTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAG------------
65 ACCAC-AC-A-TACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACAC
** * *
235736 CCACACCCCTACATTTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCCT-
1 CCACACCCCTACAAATACAAGTCTCCACCGCCGCCACCACCATCACCACCTAAGCCACACCCCTA
** *
235800 --ACATTTACAAGTCTCCACCTCCACCACCACCATCACCACCTAAGCCACACCCACACCCACAC
66 CCACACATACAAGTCTCCACCACCACCACCACCATCACCACCTAAG------CCACACCCACAC
* * *
235862 CCACACCCCTACAAGTACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCAC-
1 CCACACCCCTACAAATACAAGTCTCCACCGCCGCCACCACCATCACCACCTAAGCCACACCC-CT
* * *
235926 ACCCCTACAAGTACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAG------------
65 ACCAC-AC-A-TACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACAC
** *
235976 CCACACCCCTACATTTACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAGCCACACCCCT-
1 CCACACCCCTACAAATACAAGTCTCCACCGCCGCCACCACCATCACCACCTAAGCCACACCCCTA
** * *
236040 --ACATTTACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAGCCACACCCACACCCACAC
66 CCACACATACAAGTCTCCACCACCACCACCACCATCACCACCTAAG------CCACACCCACAC
236102 CCACACCCCTACAAATACAAGTCTCCACCGCCGCCACCACCATCACCACCTAAGCCACACCCAC-
1 CCACACCCCTACAAATACAAGTCTCCACCGCCGCCACCACCATCACCACCTAAGCCACACCC-CT
* *
236166 ACCCCTACAAATACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACAT
65 A--CC-ACACATACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACAC
*
236228 CCACACCCCTACAAATACAAGTCTCCACCGCCACCACC
1 CCACACCCCTACAAATACAAGTCTCCACCGCCGCCACC
236266 TCCAGTTTAC
Statistics
Matches: 451, Mismatches: 27, Indels: 92
0.79 0.05 0.16
Matches are distributed among these distances:
108 78 0.17
110 2 0.00
111 2 0.00
113 2 0.00
114 119 0.26
126 166 0.37
127 2 0.00
129 1 0.00
130 1 0.00
132 78 0.17
ACGTcount: A:0.31, C:0.52, G:0.05, T:0.13
Consensus pattern (123 bp):
CCACACCCCTACAAATACAAGTCTCCACCGCCGCCACCACCATCACCACCTAAGCCACACCCCTA
CCACACATACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACAC
Found at i:236226 original size:66 final size:66
Alignment explanation
Indices: 236030--236265 Score: 313
Period size: 60 Copynumber: 3.6 Consensus size: 66
236020 ACCACCTAAG
** * *
236030 CCACACCCCTACATTTACAAGTCTCCACCTCCGCCACCACCATCACCACCTAAGCCACACCCACA
1 CCACACCCCTACAAATACAAGTCTCCACCGCCACCACCACCATCACCACCTAAG------CCACA
236095 CCCACAC
60 CCCACAC
*
236102 CCACACCCCTACAAATACAAGTCTCCACCGCCGCCACCACCATCACCACCTAAG------CCACA
1 CCACACCCCTACAAATACAAGTCTCCACCGCCACCACCACCATCACCACCTAAGCCACACCCACA
236161 C
66 C
*
236162 CCACACCCCTACAAATACAAGTCTCCACCACCACCACCACCATCACCACCTAAGCCACACCCACA
1 CCACACCCCTACAAATACAAGTCTCCACCGCCACCACCACCATCACCACCTAAGCCACACCCACA
*
236227 T
66 C
236228 CCACACCCCTACAAATACAAGTCTCCACCGCCACCACC
1 CCACACCCCTACAAATACAAGTCTCCACCGCCACCACC
236266 TCCAGTTTAC
Statistics
Matches: 151, Mismatches: 7, Indels: 18
0.86 0.04 0.10
Matches are distributed among these distances:
60 58 0.38
66 42 0.28
72 51 0.34
ACGTcount: A:0.32, C:0.53, G:0.05, T:0.11
Consensus pattern (66 bp):
CCACACCCCTACAAATACAAGTCTCCACCGCCACCACCACCATCACCACCTAAGCCACACCCACA
C
Found at i:237409 original size:21 final size:21
Alignment explanation
Indices: 237365--237408 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
237355 TTGTAAATAT
**
237365 AATAAAAAATAGTAATTTAAA
1 AATAAAAAATAAAAATTTAAA
237386 AATAAAAAATAAAAATATTAAA
1 AATAAAAAATAAAAAT-TTAAA
237408 A
1 A
237409 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (21 bp):
AATAAAAAATAAAAATTTAAA
Found at i:238205 original size:16 final size:17
Alignment explanation
Indices: 238181--238213 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
238171 CTGGCTTTCC
*
238181 AACTTTCCC-TGATAGT
1 AACTATCCCATGATAGT
238197 AACTATCCCATGATAGT
1 AACTATCCCATGATAGT
238214 TGATTAAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (17 bp):
AACTATCCCATGATAGT
Found at i:240659 original size:28 final size:27
Alignment explanation
Indices: 240628--240682 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
240618 TTTTATTTAA
240628 AATTTAATTATAAAAATATTAATTTTTT
1 AATTTAATTATAAAAAT-TTAATTTTTT
** **
240656 AATTTTTTTATTTAAATTTAATTTTTT
1 AATTTAATTATAAAAATTTAATTTTTT
240683 TTTAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
AATTTAATTATAAAAATTTAATTTTTT
Found at i:240686 original size:17 final size:19
Alignment explanation
Indices: 240653--240692 Score: 66
Period size: 17 Copynumber: 2.2 Consensus size: 19
240643 ATATTAATTT
240653 TTTAATTTTTTTATTTAAA
1 TTTAATTTTTTTATTTAAA
240672 TTTAA-TTTTTT-TTTAAA
1 TTTAATTTTTTTATTTAAA
240689 TTTA
1 TTTA
240693 TTAAGCTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 10 0.48
18 6 0.29
19 5 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTAATTTTTTTATTTAAA
Found at i:242015 original size:25 final size:24
Alignment explanation
Indices: 241975--242045 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 24
241965 ATTAGTATAA
241975 AATTAATTTA-ATTTTATATATTTT
1 AATTAATTTATA-TTTATATATTTT
* * *
241999 TATGTAATTTATATTTATTTAATTT
1 AAT-TAATTTATATTTATATATTTT
242024 AATT-A-TTATATTT-TATATTTT
1 AATTAATTTATATTTATATATTTT
242045 A
1 A
242046 TTTATGTAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
21 7 0.18
22 8 0.21
23 1 0.03
24 3 0.08
25 19 0.49
26 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.63
Consensus pattern (24 bp):
AATTAATTTATATTTATATATTTT
Found at i:242043 original size:20 final size:19
Alignment explanation
Indices: 241980--242048 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
241970 TATAAAATTA
241980 ATTTAATTTTATATATTTTT
1 ATTTAATTTTATAT-TTTTT
*
242000 ATGTAA-TTTATATTTATTT
1 ATTTAATTTTATATTT-TTT
*
242019 AATTTAATTATTATATTTTAT
1 -ATTTAATT-TTATATTTTTT
*
242040 ATTTTATTT
1 ATTTAATTT
242049 ATGTAGATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.05
19 11 0.27
20 17 0.41
21 3 0.07
22 8 0.20
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (19 bp):
ATTTAATTTTATATTTTTT
Found at i:243659 original size:24 final size:25
Alignment explanation
Indices: 243630--243678 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
243620 TATTTTTAAA
*
243630 CAAAAATAATATGATATATT-AATTT
1 CAAAATTAATAT-ATATATTGAATTT
243655 CAAAATTAATATATATATTGAATT
1 CAAAATTAATATATATATTGAATT
243679 AAAAAATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (25 bp):
CAAAATTAATATATATATTGAATTT
Found at i:243684 original size:25 final size:25
Alignment explanation
Indices: 243631--243686 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
243621 ATTTTTAAAC
*
243631 AAAAA-TAATATGATATATTAATTT
1 AAAAATTAATATGATATATTAATTA
*
243655 CAAAATTAATAT-ATATATTGAATTA
1 AAAAATTAATATGATATATT-AATTA
243680 AAAAATT
1 AAAAATT
243687 TGTACAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (25 bp):
AAAAATTAATATGATATATTAATTA
Found at i:244238 original size:6 final size:7
Alignment explanation
Indices: 244221--244317 Score: 59
Period size: 6 Copynumber: 14.6 Consensus size: 7
244211 TCATATATTT
244221 TTATATA
1 TTATATA
244228 TTATA-A
1 TTATATA
244234 TTATAT-
1 TTATATA
*
244240 TTAAAATA
1 TT-ATATA
244248 TTATATA
1 TTATATA
244255 TT-TATA
1 TTATATA
*
244261 -TAAAT-
1 TTATATA
244266 TTAATATA
1 TT-ATATA
244274 TTA-ATAA
1 TTATAT-A
*
244281 TT-TATG
1 TTATATA
244287 TTATATA
1 TTATATA
*
244294 -TAAATA
1 TTATATA
244300 TTGATATA
1 TT-ATATA
244308 TT-TATA
1 TTATATA
244314 TTAT
1 TTAT
244318 TTTTAACATA
Statistics
Matches: 69, Mismatches: 8, Indels: 26
0.67 0.08 0.25
Matches are distributed among these distances:
5 1 0.01
6 30 0.43
7 28 0.41
8 10 0.14
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (7 bp):
TTATATA
Found at i:244264 original size:20 final size:20
Alignment explanation
Indices: 244225--244314 Score: 56
Period size: 20 Copynumber: 4.8 Consensus size: 20
244215 ATATTTTTAT
*
244225 ATATTATA-ATTATATTTAAA
1 ATATTATATATT-TATATAAA
244245 ATATTATATATTTATAT-AA
1 ATATTATATATTTATATAAA
*
244264 AT-TTA-ATA--TAT-TAAT
1 ATATTATATATTTATATAAA
*
244279 A-ATT-TAT-GTTATATATAA
1 ATATTATATATTTATATA-AA
244297 ATATTGATATATTTATAT
1 ATATT-ATATATTTATAT
244315 TATTTTTAAC
Statistics
Matches: 54, Mismatches: 4, Indels: 22
0.68 0.05 0.28
Matches are distributed among these distances:
14 1 0.02
15 9 0.17
16 3 0.06
17 5 0.09
18 5 0.09
19 7 0.13
20 12 0.22
21 6 0.11
22 6 0.11
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATATTATATATTTATATAAA
Found at i:244274 original size:35 final size:35
Alignment explanation
Indices: 244208--244311 Score: 97
Period size: 37 Copynumber: 2.9 Consensus size: 35
244198 GATATACTTT
* *
244208 ATTTCATATATTTTTATATATTATAATTATATTTAA-A
1 ATTT-ATATATTTATATAAATT-TAA-TATATTTAATA
244245 ATATTATATATTTATATAAATTTAATATA-TTAATA
1 AT-TTATATATTTATATAAATTTAATATATTTAATA
* * *
244280 ATTTATGT-TATATATAAATATTGATATATTTA
1 ATTTATATATTTATATAAAT-TTAATATATTTA
244312 TATTATTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
33 10 0.17
34 16 0.28
35 10 0.17
36 3 0.05
37 17 0.29
38 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (35 bp):
ATTTATATATTTATATAAATTTAATATATTTAATA
Found at i:244514 original size:2 final size:2
Alignment explanation
Indices: 244507--244538 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
244497 GCAATATGCA
244507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
244539 GTTTATAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:245697 original size:17 final size:18
Alignment explanation
Indices: 245675--245724 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
245665 GACCACAATA
245675 AAAATATTAA-A-AAAATT
1 AAAATATTAATATAAAA-T
245692 AAAATA-TAATATAAAAT
1 AAAATATTAATATAAAAT
245709 AAAATA-TAATATAAAA
1 AAAATATTAATATAAAA
245725 ATAATATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.10
17 24 0.77
18 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATTAATATAAAAT
Found at i:245702 original size:22 final size:22
Alignment explanation
Indices: 245677--245722 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
245667 CCACAATAAA
*
245677 AATATTAAAA-AAATTAAAATAT
1 AATA-TAAAATAAAATAAAATAT
*
245699 AATATAAAATAAAATATAATAT
1 AATATAAAATAAAATAAAATAT
245721 AA
1 AA
245723 AAATAATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (22 bp):
AATATAAAATAAAATAAAATAT
Found at i:245764 original size:17 final size:19
Alignment explanation
Indices: 245742--245783 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
245732 GAATTAGATA
245742 AAATAATAT-TAA-AATTT
1 AAATAATATATAATAATTT
*
245759 AAATAAATATATAATATTTT
1 AAAT-AATATATAATAATTT
245779 AAATA
1 AAATA
245784 TAATTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 5 0.24
19 4 0.19
20 8 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATAATATATAATAATTT
Found at i:245797 original size:13 final size:13
Alignment explanation
Indices: 245779--245818 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
245769 ATAATATTTT
245779 AAATATAATTATA
1 AAATATAATTATA
245792 AAATATAAATT-T-
1 AAATAT-AATTATA
245804 -AATATAATTATA
1 AAATATAATTATA
245816 AAA
1 AAA
245819 ATTAACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 4 0.17
11 6 0.26
13 9 0.39
14 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATATAATTATA
Found at i:245812 original size:24 final size:27
Alignment explanation
Indices: 245761--245818 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 27
245751 TAAAATTTAA
245761 ATAAATATATAATATTTTAAATATAATT
1 ATAAA-ATATAATATTTTAAATATAATT
245789 ATAAAATATAA-A-TTT-AATATAATT
1 ATAAAATATAATATTTTAAATATAATT
245813 ATAAAA
1 ATAAAA
245819 ATTAACAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 15 0.50
25 3 0.10
26 1 0.03
27 6 0.20
28 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATAAAATATAATATTTTAAATATAATT
Found at i:246075 original size:2 final size:2
Alignment explanation
Indices: 246068--246095 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
246058 AATTTTACAA
246068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
246096 GTTTTTCTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:246573 original size:34 final size:33
Alignment explanation
Indices: 246525--246745 Score: 248
Period size: 34 Copynumber: 6.5 Consensus size: 33
246515 TGGTAAAAAC
**
246525 CACCATTTAATCAACAATGACAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
246558 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
246592 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
246626 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * **
246660 CTCCCATTTAGTCAACAATGAAAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATG-GTAACCTACCAAAT
*
246694 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
246728 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
246746 TCTCCCACTT
Statistics
Matches: 159, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 23 0.14
34 130 0.82
35 6 0.04
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:246641 original size:68 final size:67
Alignment explanation
Indices: 246527--246745 Score: 278
Period size: 68 Copynumber: 3.2 Consensus size: 67
246517 GTAAAAACCA
* * * *
246527 CCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGAAAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
246592 CAC
65 CAC
* ** * *
246595 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGAAAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
246660 CTC
65 CAC
* * * *
246663 CCATTTAGTCAACAATGAAAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGAAAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
246728 CA-
65 CAC
246730 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
246746 TCTCCCACTT
Statistics
Matches: 130, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 112 0.86
69 1 0.01
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGAAAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:246704 original size:102 final size:101
Alignment explanation
Indices: 246525--246745 Score: 334
Period size: 102 Copynumber: 2.2 Consensus size: 101
246515 TGGTAAAAAC
** *
246525 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGAAAAACCACCAA
* *
246590 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** ** * *
246626 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGAAAAACCACCA
1 CAC-CATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGAAAAACCACCA
246691 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
246728 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
246746 TCTCCCACTT
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
101 16 0.15
102 90 0.85
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGAAAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:251171 original size:34 final size:33
Alignment explanation
Indices: 251118--251336 Score: 235
Period size: 34 Copynumber: 6.5 Consensus size: 33
251108 TGGTAAAAAA
* *
251118 CACCATTTAATCAATAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
* *
251151 CTACCATTTAGTCAACAATGGTAAGCC-ATCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
251185 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
251219 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
251253 CTCTCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 CAC-CATTTAATCAACAATGG-TAACCTACCAAAT
* *
251287 CACCCATTTAATCAACAATGATAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
251321 CACCATTTAATCAACA
1 CACCATTTAATCAACA
251337 CTTGTTAATT
Statistics
Matches: 158, Mismatches: 20, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
33 21 0.13
34 131 0.83
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:251234 original size:68 final size:67
Alignment explanation
Indices: 251120--251334 Score: 261
Period size: 68 Copynumber: 3.2 Consensus size: 67
251110 GTAAAAAACA
* * * *
251120 CCATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCATCAAAT
1 CCATTTAATCAATAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
251185 CAC
65 CAC
* * *
251188 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAATAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
251253 CTC
65 CAC
* * * * * * *
251256 TCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGATAAACTACCAAAT
1 CCATTTAATCAATAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
251321 CA-
65 CAC
251323 CCATTTAATCAA
1 CCATTTAATCAA
251335 CACTTGTTAA
Statistics
Matches: 125, Mismatches: 20, Indels: 5
0.83 0.13 0.03
Matches are distributed among these distances:
67 12 0.10
68 112 0.90
69 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (67 bp):
CCATTTAATCAATAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:251262 original size:102 final size:101
Alignment explanation
Indices: 251118--251336 Score: 314
Period size: 102 Copynumber: 2.2 Consensus size: 101
251108 TGGTAAAAAA
* * * *
251118 CACCATTTAATCAATAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCATCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* * *
251183 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGATAAACTACCAAAT
** * *
251219 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCT-CTCATTTAGTCAACAATGGCAAACCACC
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAGTCAACAATGGCAAACCACC
251283 AAATCACCCATTTAATCAACAATGATAAACTACCAAAT
64 AAATCACCCATTTAATCAACAATGATAAACTACCAAAT
251321 CACCATTTAATCAACA
1 CACCATTTAATCAACA
251337 CTTGTTAATT
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
101 15 0.15
102 88 0.85
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGATAAACTACCAAAT
Found at i:252860 original size:16 final size:16
Alignment explanation
Indices: 252841--252937 Score: 51
Period size: 16 Copynumber: 6.1 Consensus size: 16
252831 CGAATTATTG
252841 TTATAATTAATTTTAA
1 TTATAATTAATTTTAA
*
252857 TTATTATTTAA-TTTAA
1 TTA-TAATTAATTTTAA
* * * *
252873 TAAAAATTATTTTTTA
1 TTATAATTAATTTTAA
252889 TT-TAAATTTAATTTTAA
1 TTAT-AA-TTAATTTTAA
* *
252906 -AATATATTAATATTAA
1 TTATA-ATTAATTTTAA
252922 TATATAA--AATTTTAA
1 T-TATAATTAATTTTAA
252937 T
1 T
252938 ATTTTTAAAT
Statistics
Matches: 59, Mismatches: 14, Indels: 17
0.66 0.16 0.19
Matches are distributed among these distances:
15 12 0.20
16 27 0.46
17 17 0.29
18 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATAATTAATTTTAA
Found at i:252872 original size:22 final size:21
Alignment explanation
Indices: 252833--252901 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
252823 ACTTGACCCG
252833 AATTATTGTTATAA-TTAATTTT
1 AATTATT-TT-TAATTTAATTTT
***
252855 AATTATTATTTAATTTAATAAA
1 AATTATT-TTTAATTTAATTTT
* *
252877 AATTATTTTTTATTTAAATTT
1 AATTATTTTTAATTTAATTTT
252898 AATT
1 AATT
252902 TTAAAATATA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
21 16 0.43
22 21 0.57
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (21 bp):
AATTATTTTTAATTTAATTTT
Found at i:253626 original size:2 final size:2
Alignment explanation
Indices: 253619--253668 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
253609 CAGCTGACTT
253619 TA TA TA TA TA TA 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 TA TA TA TA TA TA
253661 TA TA TA TA
1 TA TA TA TA
253669 AAAACCCCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:253768 original size:3 final size:3
Alignment explanation
Indices: 253755--253801 Score: 76
Period size: 3 Copynumber: 15.3 Consensus size: 3
253745 CTATAAATTG
*
253755 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
253801 T
1 T
253802 TCCTAAGGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:253999 original size:20 final size:21
Alignment explanation
Indices: 253966--254008 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
253956 TTTTTAATCT
*
253966 ATAAATTAAAAATCGAATTAA
1 ATAAATTAAAAATCAAATTAA
253987 ATAAATT-AAAATCAAATTAA
1 ATAAATTAAAAATCAAATTAA
254007 AT
1 AT
254009 TTACTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (21 bp):
ATAAATTAAAAATCAAATTAA
Found at i:254016 original size:20 final size:20
Alignment explanation
Indices: 253974--254018 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
253964 CTATAAATTA
* *
253974 AAAATCGAATTAAATAAATT
1 AAAATCAAATTAAATAAACT
**
253994 AAAATCAAATTAAATTTACT
1 AAAATCAAATTAAATAAACT
254014 AAAAT
1 AAAAT
254019 TAAACTAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAATCAAATTAAATAAACT
Found at i:255150 original size:3 final size:3
Alignment explanation
Indices: 255142--255170 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
255132 TTTCTTATAT
255142 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
255171 TAAAGCTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Done.