Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold256
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: 1244454
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 8 of 8
Found at i:1223439 original size:92 final size:92
Alignment explanation
Indices: 1223214--1223673 Score: 726
Period size: 92 Copynumber: 5.0 Consensus size: 92
1223204 AAAAAGATGT
* * * *
1223214 CAATGTGCTAATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAATATGCTGATT
*
1223279 CAAGGCCAGCTATATTGGACTTAAAAGTG-
63 CAAGGCCAGCTATATTGGACTTAAAGGTGC
*
1223308 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGATGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
*
1223373 GGCCAACTATATTGGACTTAAAGGTGC
66 GGCCAGCTATATTGGACTTAAAGGTGC
1223400 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATGCTGATTCA
* **
1223464 AGGCCAGCGATATTGGACTTGGAGGTGC
65 AGGCCAGCTATATTGGACTTAAAGGTGC
1223492 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
* * *
1223557 GGCCAACGATATTGGGCTTAAAGGTGC
66 GGCCAGCTATATTGGACTTAAAGGTGC
*
1223584 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
*
1223649 GGCCAGCTATATTGGGCTTAGAAGG
66 GGCCAGCTATATTGGACTTA-AAGG
1223674 GTTGCCACCG
Statistics
Matches: 343, Mismatches: 19, Indels: 9
0.92 0.05 0.02
Matches are distributed among these distances:
91 47 0.14
92 253 0.74
93 5 0.01
94 38 0.11
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAAGGTGC
Found at i:1223747 original size:32 final size:33
Alignment explanation
Indices: 1223668--1223904 Score: 401
Period size: 33 Copynumber: 7.2 Consensus size: 33
1223658 TATTGGGCTT
1223668 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
1223701 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1223734 AG-AGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1223765 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1223798 AAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1223831 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
*
1223865 AGAAGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1223898 A-AAGGGT
1 AGAAGGGT
1223905 GAAAGATGCC
Statistics
Matches: 193, Mismatches: 6, Indels: 11
0.92 0.03 0.05
Matches are distributed among these distances:
31 3 0.02
32 63 0.33
33 91 0.47
34 36 0.19
ACGTcount: A:0.19, C:0.18, G:0.35, T:0.28
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1223747 original size:65 final size:65
Alignment explanation
Indices: 1223661--1223904 Score: 397
Period size: 65 Copynumber: 3.8 Consensus size: 65
1223651 CCAGCTATAT
* *
1223661 TGGGC-TTAGA-AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTG
1223724 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTT-GAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTG
*
1223788 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCGACTTG
1 TGGGCTTTAG-AGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGG-TTGCCACCGACTTG
1223853 TG
64 TG
*
1223855 TGGGCTTTAGAGAAGGTTTGCCACCGACTTGTGTGGGCTTTAGA-AAGGGT
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGT
1223905 GAAAGATGCC
Statistics
Matches: 170, Mismatches: 5, Indels: 10
0.92 0.03 0.05
Matches are distributed among these distances:
63 5 0.03
64 37 0.22
65 58 0.34
66 15 0.09
67 55 0.32
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (65 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTGCCACCGACTTGTG
Found at i:1224034 original size:67 final size:66
Alignment explanation
Indices: 1223886--1224502 Score: 619
Period size: 67 Copynumber: 9.2 Consensus size: 66
1223876 CACCGACTTG
* ** * * * *
1223886 TGTGGGCTTTAGAAAGGGTGAAAGATGCCACGAAGTTGTGGAC-TTAAAAAGAACAAGGTGCCAC
1 TGTGGACTTTA-AAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCAC
1223950 GGAGT
62 GGAGT
* *
1223955 TGTGGGCTTTAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGA
1 TGTGGACTTTAAAAGGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGA
1224020 GT
65 GT
* * * *
1224022 CGTGGACTTTAAAAGGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCGAC
1 TGTGGACTTTAAAAGGG-AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCAC
1224087 GGAGT
62 GGAGT
* ** *
1224092 TGTGGACTTAAAAAAAGAAAAAGGTGCCACGAAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAG
1 TGTGGACTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAG
1224157 T
66 T
* * * *
1224158 CGTGGAC-TTAAAA-GGAACAGGGTGCCACGGAGTTTTGGGCTTTGAAAAGAAGGTGCCACGGAG
1 TGTGGACTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAG
1224221 T
66 T
* * * * *
1224222 CGTGGACTTTAAAAGGGAAAAAAAGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAGGTGCGAC
1 TGTGGACTTTAAAAGGG-AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCAC
1224287 GGAGT
62 GGAGT
**
1224292 TGTGGAC-TTAAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAG
1 TGTGGACTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAG
1224356 T
66 T
* *
1224357 TGTGGAC-TTAAAA-GGAACAAGGTGCCACGGAGTTGTGGACTTT-AAAAGGGAAAAAGAGTGCC
1 TGTGGACTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--G---AAG-GTGCC
1224419 ACGGAGT
60 ACGGAGT
* * * *
1224426 TGTGGGCTTTGAAAA--G---AAGGTGCCACGGAGTCGTGGACTTTAAGAAGGAAAAAGAGTGCC
1 TGTGGACTTT-AAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTT--GAA--AAGAAG-GTGCC
1224486 ACGGAGT
60 ACGGAGT
1224493 TGTGGACTTT
1 TGTGGACTTT
1224503 GATGCCACTG
Statistics
Matches: 474, Mismatches: 49, Indels: 52
0.82 0.09 0.09
Matches are distributed among these distances:
63 4 0.01
64 80 0.17
65 39 0.08
66 22 0.05
67 133 0.28
68 49 0.10
69 82 0.17
70 59 0.12
71 4 0.01
72 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.20
Consensus pattern (66 bp):
TGTGGACTTTAAAAGGGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAG
T
Found at i:1224212 original size:200 final size:199
Alignment explanation
Indices: 1223906--1224501 Score: 812
Period size: 200 Copynumber: 3.0 Consensus size: 199
1223896 AGAAAGGGTG
* * * *
1223906 AAAGATGCCACGAAGTTGTGGAC-TTAAAAAGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAGGTGCCACGAAGTTGTGGGCTTTGAAAAG---AAGGTGCCACGGAGTTGTGGAC-TTAAAA-
* * *
1223970 GGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAA
61 GG-AACAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAA
1224035 AGGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCGACGGAGTTGTGGACT
125 AGGGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCGACGGAGTTGTGGACT
1224100 TAAAAAAAGAA
190 T-AAAAAAGAA
*
1224111 AAAGGTGCCACGAAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTAAAAGGAAC
1 AAAGGTGCCACGAAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAC
*
1224176 AGGGTGCCACGGAGTTTTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGGGAA
66 AGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGGGAA
*
1224241 AAAAAGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAGGTGCGACGGAGTTGTGGACTTAAAAA
131 AAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCGACGGAGTTGTGGACTTAAAAA
1224306 AGAA
196 AGAA
*
1224310 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAC
1 AAAGGTGCCACGAAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAC
* * * *
1224375 AAGGTGCCACGGAGTTGTGGACTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT---
66 AGGGTGCCACGGAGTTGTGGGCTTTGAAAA--G---AAG-GTGCCACGGAGTCGTGGACTTTAAA
* * * * *
1224436 ---GAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAGAAGGAAAAAGAGTGCCACGGAGTTGTGG
125 AGGGAAAA-AAAGTGCCACGGAGTTGTGGGCTTTAA-AAAGAAAAAG-GTGCGACGGAGTTGTGG
1224498 ACTT
187 ACTT
1224502 TGATGCCACT
Statistics
Matches: 358, Mismatches: 23, Indels: 24
0.88 0.06 0.06
Matches are distributed among these distances:
198 9 0.03
199 117 0.33
200 133 0.37
201 22 0.06
202 6 0.02
203 23 0.06
204 20 0.06
205 21 0.06
206 7 0.02
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (199 bp):
AAAGGTGCCACGAAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAC
AGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGGGAA
AAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCGACGGAGTTGTGGACTTAAAAA
AGAA
Found at i:1224515 original size:23 final size:23
Alignment explanation
Indices: 1224482--1224527 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1224472 GGAAAAAGAG
*
1224482 TGCCACGGAGTTGTGGACTTTGA
1 TGCCACGGAGTCGTGGACTTTGA
*
1224505 TGCCACTGAGTCGTGGACTTTGA
1 TGCCACGGAGTCGTGGACTTTGA
1224528 GACAAGATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (23 bp):
TGCCACGGAGTCGTGGACTTTGA
Found at i:1224603 original size:35 final size:36
Alignment explanation
Indices: 1224553--1224621 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
1224543 TGTCGTGGAC
*
1224553 TTAAAAGGAACAAAGAGAGCCACGGAGTTGTGGGAT
1 TTAAAAAGAACAAAGAGAGCCACGGAGTTGTGGGAT
* *
1224589 TTAAAAAGAA-AAAGAGTGCCATGGAGTTGTGGG
1 TTAAAAAGAACAAAGAGAGCCACGGAGTTGTGGG
1224622 CTTAAAAGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 21 0.70
36 9 0.30
ACGTcount: A:0.39, C:0.09, G:0.33, T:0.19
Consensus pattern (36 bp):
TTAAAAAGAACAAAGAGAGCCACGGAGTTGTGGGAT
Found at i:1224628 original size:27 final size:27
Alignment explanation
Indices: 1224598--1224773 Score: 104
Period size: 27 Copynumber: 6.0 Consensus size: 27
1224588 TTTAAAAAGA
* *
1224598 AAAAGAGTGCCATGGAGTTGTGGGCTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
1224625 AAAAGAGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
* *
1224652 AGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 -------AAAAGAGTGCCACGGAGTTGTGGACTT
**
1224686 AAAATG-GTGCCACAAAGTTGTGGACTT
1 AAAA-GAGTGCCACGGAGTTGTGGACTT
* * *
1224713 AGAAGGAAAAAGAGTGACACAGAGTTGTGGGCTT
1 -------AAAAGAGTGCCACGGAGTTGTGGACTT
*
1224747 AAAATG-GTGCCACAGAGTTGTGGACTT
1 AAAA-GAGTGCCACGGAGTTGTGGACTT
1224774 TGAAGGAAAA
Statistics
Matches: 121, Mismatches: 11, Indels: 34
0.73 0.07 0.20
Matches are distributed among these distances:
27 71 0.59
28 2 0.02
33 1 0.01
34 47 0.39
ACGTcount: A:0.32, C:0.12, G:0.33, T:0.22
Consensus pattern (27 bp):
AAAAGAGTGCCACGGAGTTGTGGACTT
Found at i:1224668 original size:34 final size:32
Alignment explanation
Indices: 1224594--1224899 Score: 181
Period size: 34 Copynumber: 10.0 Consensus size: 32
1224584 GGGATTTAAA
** *
1224594 AAGAAAAAGAGTGCCATGGAGTTGTGGGCTT-
1 AAGAAAAAGAGTGCCACAGAGTTGTGGACTTG
*
1224625 ----AAAAGAGTGCCACGGAGTTGTGGACTTAG
1 AAGAAAAAGAGTGCCACAGAGTTGTGGACTT-G
*
1224654 AAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT-
1 AA-GAAAAAGAGTGCCACAGAGTTGTGGACTTG
* *
1224686 ---AAAATG-GTGCCACAAAGTTGTGGACTTAG
1 AAGAAAAAGAGTGCCACAGAGTTGTGGACTT-G
* *
1224715 AAGGAAAAAGAGTGACACAGAGTTGTGGGCTT-
1 AA-GAAAAAGAGTGCCACAGAGTTGTGGACTTG
*
1224747 ---AAAATG-GTGCCACAGAGTTGTGGACTTTG
1 AAGAAAAAGAGTGCCACAGAGTTGTGGAC-TTG
* *
1224776 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTG
1 AA-GAAAAAGAGTGCCACAGAGTTGTGGAC-TTG
* * *
1224810 -AGACAAA-A-CGCCACTGAGTTGTGGACTTTG
1 AAGAAAAAGAGTGCCACAGAGTTGTGGAC-TTG
** *
1224840 AA-AAAAAG-GATGCCATTGAGTCGTGGACTTTG
1 AAGAAAAAGAG-TGCCACAGAGTTGTGGAC-TTG
* *
1224872 --GAAAAAGA-TGCCACTGAATTGTGGACTT
1 AAGAAAAAGAGTGCCACAGAGTTGTGGACTT
1224900 TTAGGACAAA
Statistics
Matches: 220, Mismatches: 28, Indels: 56
0.72 0.09 0.18
Matches are distributed among these distances:
27 61 0.28
28 12 0.05
29 2 0.01
30 38 0.17
31 8 0.04
32 24 0.11
33 11 0.05
34 64 0.29
ACGTcount: A:0.33, C:0.13, G:0.32, T:0.23
Consensus pattern (32 bp):
AAGAAAAAGAGTGCCACAGAGTTGTGGACTTG
Found at i:1224679 original size:61 final size:61
Alignment explanation
Indices: 1224309--1224807 Score: 416
Period size: 61 Copynumber: 8.0 Consensus size: 61
1224299 TTAAAAAAGA
* * * *
1224309 AAAAG-GTGCCACGGAGTTGTGGGCTTTGAA--AAGAAG-GTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
1224366 AAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGG
1 AAAA-G----A-GTGCCACGGAGTTGTGGAC-TTAGAA-GGAAAAAGAGTGCCACGGAGTTGTGG
1224431 GCTTT
58 GC-TT
* *
1224436 GAAAAGAAGGTGCCACGGAGTCGTGGACTTTAAGAAGGAAAAAGAGTGCCACGGAGTTGTGGACT
1 -AAAAG-A-GTGCCACGGAGTTGTGGAC-TT-AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCT
1224501 T
61 T
* * * * * * * *
1224502 ---TGA-TGCCACTGAGTCGTGGACTTTG-A-G-ACAAGA-TGCCAC-TATGTCGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGA-GTTGTGGGCTT
* * * * *
1224555 AAAAGGAACAAAGAGAGCCACGGAGTTGTGGGATTTAAAAAGAAAAAGAGTGCCATGGAGTTGTG
1 -------A-AAAGAGTGCCACGGAGTTGT-GGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTG
1224620 GGCTT
57 GGCTT
*
1224625 AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
** * *
1224686 AAAATG-GTGCCACAAAGTTGTGGACTTAGAAGGAAAAAGAGTGACACAGAGTTGTGGGCTT
1 AAAA-GAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* *
1224747 AAAATG-GTGCCACAGAGTTGTGGACTTTGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAA-GAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1224808 TGAGACAAAA
Statistics
Matches: 368, Mismatches: 39, Indels: 66
0.78 0.08 0.14
Matches are distributed among these distances:
52 1 0.00
53 16 0.04
54 5 0.01
55 1 0.00
56 1 0.00
57 5 0.01
58 3 0.01
59 17 0.05
61 149 0.40
62 21 0.06
63 1 0.00
64 20 0.05
65 15 0.04
66 7 0.02
67 52 0.14
68 9 0.02
69 23 0.06
70 17 0.05
71 5 0.01
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.21
Consensus pattern (61 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:1224829 original size:30 final size:31
Alignment explanation
Indices: 1224503--1225031 Score: 229
Period size: 30 Copynumber: 16.9 Consensus size: 31
1224493 TGTGGACTTT
* *
1224503 GATGCCACTGAGTCGTGGACTTTGAG-ACAA
1 GATGCCACTGAGTTGTGGACTTTGAGAAAAA
* **
1224533 GATGCCACT-ATGTCGTGGACTTAAAAGGAACAAA
1 GATGCCACTGA-GTTGTGGACTT-TGA-GAA-AAA
* * *
1224567 GAGAGCCACGGAGTTGTGGGA-TTTAAAAAGAAAAA
1 GA-TGCCACTGAGTTGT-GGACTTT---GAGAAAAA
* *
1224602 GAGTGCCA-TGGAGTTGTGGGC-TT-A-AAAGA
1 GA-TGCCACT-GAGTTGTGGACTTTGAGAAAAA
* *
1224631 G-TGCCACGGAGTTGTGGACTTAGAAGGAAAAA
1 GATGCCACTGAGTTGTGGACTTTG-A-GAAAAA
* * *
1224663 GAGTGCCACAGAGTTGTGGGC-TT---AAAAT
1 GA-TGCCACTGAGTTGTGGACTTTGAGAAAAA
* ** *
1224691 GGTGCCACAAAGTTGTGGACTTAGAAGGAAAAA
1 GATGCCACTGAGTTGTGGACTTTG-A-GAAAAA
* * * *
1224724 GAGTGACACAGAGTTGTGGGC-TT---AAAAT
1 GA-TGCCACTGAGTTGTGGACTTTGAGAAAAA
* *
1224752 GGTGCCACAGAGTTGTGGACTTTGAAGGAAAAA
1 GATGCCACTGAGTTGTGGACTTTG-A-GAAAAA
* * *
1224785 GAGTGCCACGGAGTTGTGGGCTTTGAGACAAA
1 GA-TGCCACTGAGTTGTGGACTTTGAGAAAAA
* *
1224817 -ACGCCACTGAGTTGTGGACTTTGAAAAAAA
1 GATGCCACTGAGTTGTGGACTTTGAGAAAAA
* *
1224847 GGATGCCATTGAGTCGTGGACTTTG-GAAAAA
1 -GATGCCACTGAGTTGTGGACTTTGAGAAAAA
* * *
1224878 GATGCCACTGAATTGTGGACTTTTAGGACAAA
1 GATGCCACTGAGTTGTGGACTTTGA-GAAAAA
* *
1224910 -ATGCCACTGAGTCGTGGGCTTTGAGAAGAAAAA
1 GATGCCACTGAGTTGTGGACTTT--G-AGAAAAA
* * ** *
1224943 GGTGCCACGGAGTCATGGACTTT-AGGACAAA
1 GATGCCACTGAGTTGTGGACTTTGA-GAAAAA
* * * *
1224974 -ATGCCACTGAATCGTGGGCTTTGAG-AAGA
1 GATGCCACTGAGTTGTGGACTTTGAGAAAAA
* *
1225003 GATTGCCACTGAGTCGTGGACTTTTAGAA
1 GA-TGCCACTGAGTTGTGGACTTTGAGAA
1225032 GGTATTTGAA
Statistics
Matches: 379, Mismatches: 72, Indels: 94
0.70 0.13 0.17
Matches are distributed among these distances:
27 47 0.12
28 14 0.04
29 8 0.02
30 86 0.23
31 53 0.14
32 37 0.10
33 19 0.05
34 78 0.21
35 28 0.07
36 7 0.02
37 2 0.01
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.23
Consensus pattern (31 bp):
GATGCCACTGAGTTGTGGACTTTGAGAAAAA
Found at i:1224845 original size:122 final size:121
Alignment explanation
Indices: 1224594--1224847 Score: 325
Period size: 122 Copynumber: 2.1 Consensus size: 121
1224584 GGGATTTAAA
* ** *
1224594 AAGAAAAAGAGTGCCATGGAGTTGTGGGCTTAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGA
1 AAGAAAAAGAGTGACACAGAGTTGTGGGCTTAAAAGAGTGCCACAGAGTTGTGGACTTAGAAGGA
***
1224659 AAAAGAGTGCCACAGAGTTGTGGGCTTAAAATGGTGCCACAAAGTTGTGGACTTAG
66 AAAAGAGTGCCACAGAGTTGTGGGCTTAAAATAACGCCACAAAGTTGTGGACTTAG
*
1224715 AAGGAAAAAGAGTGACACAGAGTTGTGGGCTTAAAATG-GTGCCACAGAGTTGTGGACTTTGAAG
1 AA-GAAAAAGAGTGACACAGAGTTGTGGGCTTAAAA-GAGTGCCACAGAGTTGTGGACTTAGAAG
* ** *
1224779 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAGACAA-AACGCCACTGAGTTGTGGACTTTG
64 GAAAAAGAGTGCCACAGAGTTGTGGGC-TT-A-A-AATAACGCCACAAAGTTGTGGACTTAG
1224840 AA-AAAAAG
1 AAGAAAAAG
1224848 GATGCCATTG
Statistics
Matches: 115, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
121 2 0.02
122 80 0.70
123 9 0.08
124 1 0.01
125 21 0.18
126 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (121 bp):
AAGAAAAAGAGTGACACAGAGTTGTGGGCTTAAAAGAGTGCCACAGAGTTGTGGACTTAGAAGGA
AAAAGAGTGCCACAGAGTTGTGGGCTTAAAATAACGCCACAAAGTTGTGGACTTAG
Found at i:1224885 original size:62 final size:63
Alignment explanation
Indices: 1224594--1225026 Score: 234
Period size: 61 Copynumber: 7.0 Consensus size: 63
1224584 GGGATTTAAA
* * * * * * *
1224594 AAGAAAAAGAGTGCCATGGAGTTGTGGGC-TT-A-AAAGAGTGCCACGGAGTTGTGGACTTAG
1 AAGAAAAAGAGTGCCACGGAGTCGTGGACTTTGAGAAAAAATGCCACTGAGTTGTGGACTTTG
* * * *** ** *
1224654 AAGGAAAAAGAGTGCCACAGAGTTGTGGGC-TT-A-AAATGGTGCCACAAAGTTGTGGACTTAG
1 AA-GAAAAAGAGTGCCACGGAGTCGTGGACTTTGAGAAAAAATGCCACTGAGTTGTGGACTTTG
* * * * *** *
1224715 AAGGAAAAAGAGTGACACAGAGTTGTGGGC-TT-A-AAATGGTGCCACAGAGTTGTGGACTTTG
1 AA-GAAAAAGAGTGCCACGGAGTCGTGGACTTTGAGAAAAAATGCCACTGAGTTGTGGACTTTG
* * * *
1224776 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAGACAAAACGCCACTGAGTTGTGGACTTTG
1 AA-GAAAAAGAGTGCCACGGAGTCGTGGACTTTGAGAAAAAATGCCACTGAGTTGTGGACTTTG
** * *
1224840 AA-AAAAAG-GATGCCATTGAGTCGTGGACTTTG-GAAAAAGATGCCACTGAATTGTGGACTTTT
1 AAGAAAAAGAG-TGCCACGGAGTCGTGGACTTTGAGAAAAA-ATGCCACTGAGTTGTGGACTTTG
* * * * * **
1224902 AGGACAAA-A-TGCCACTGAGTCGTGGGCTTTGAGAAGAAAAAGGTGCCACGGAGTCATGGACTT
1 AAGAAAAAGAGTGCCACGGAGTCGTGGACTTTGAG-A-AAAAA--TGCCACTGAGTTGTGGACTT
1224965 T-
62 TG
* * * * * * * *
1224966 AGGACAAA-A-TGCCACTGAATCGTGGGCTTTGAGAAGAGATTGCCACTGAGTCGTGGACTTT
1 AAGAAAAAGAGTGCCACGGAGTCGTGGACTTTGAGAA-AAAATGCCACTGAGTTGTGGACTTT
1225027 TAGAAGGTAT
Statistics
Matches: 321, Mismatches: 38, Indels: 27
0.83 0.10 0.07
Matches are distributed among these distances:
60 2 0.01
61 183 0.57
62 49 0.15
63 10 0.03
64 60 0.19
65 17 0.05
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (63 bp):
AAGAAAAAGAGTGCCACGGAGTCGTGGACTTTGAGAAAAAATGCCACTGAGTTGTGGACTTTG
Found at i:1224978 original size:95 final size:95
Alignment explanation
Indices: 1224747--1225032 Score: 312
Period size: 95 Copynumber: 3.0 Consensus size: 95
1224737 TTGTGGGCTT
* * * *
1224747 AAAATGGTGCCACAGAGTTGTGGACTTTGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA-
1 AAAAAGGTGCCACAGAGTCGTGGACTTT--AGGAAAAAGA-TGCCACTGAATTGTGGGCTTTGAG
* *
1224811 GACAAAACGCCACTGAGTTGTGGACTTT-GAA-
63 GACAAAATGCCACTGAGTCGTGGACTTTAGAAG
** * *
1224842 AAAAAGGATGCCATTGAGTCGTGGACTTT-GGAAAAAGATGCCACTGAATTGTGGACTTTTAGGA
1 AAAAAGG-TGCCACAGAGTCGTGGACTTTAGGAAAAAGATGCCACTGAATTGTGGGCTTTGAGGA
*
1224906 CAAAATGCCACTGAGTCGTGGGCTTTGAGAAG
65 CAAAATGCCACTGAGTCGTGGACTTT-AGAAG
* * * * * *
1224938 AAAAAGGTGCCACGGAGTCATGGACTTTAGGACAAA-ATGCCACTGAATCGTGGGCTTTGAGAAG
1 AAAAAGGTGCCACAGAGTCGTGGACTTTAGGAAAAAGATGCCACTGAATTGTGGGCTTTGAGGAC
* *
1225002 AGATTGCCACTGAGTCGTGGACTTTTAGAAG
66 AAAATGCCACTGAGTCGTGGAC-TTTAGAAG
1225033 GTATTTGAAG
Statistics
Matches: 161, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
92 19 0.12
93 34 0.21
95 74 0.46
96 34 0.21
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (95 bp):
AAAAAGGTGCCACAGAGTCGTGGACTTTAGGAAAAAGATGCCACTGAATTGTGGGCTTTGAGGAC
AAAATGCCACTGAGTCGTGGACTTTAGAAG
Found at i:1226005 original size:17 final size:17
Alignment explanation
Indices: 1225985--1226018 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1225975 TCTTCTTCTT
*
1225985 TTTTTTTTCCTTTTTTG
1 TTTTGTTTCCTTTTTTG
*
1226002 TTTTGTTTCTTTTTTTG
1 TTTTGTTTCCTTTTTTG
1226019 GAAAAGAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (17 bp):
TTTTGTTTCCTTTTTTG
Found at i:1226014 original size:22 final size:22
Alignment explanation
Indices: 1225967--1226014 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1225957 GAAAAGGGGT
*
1225967 TTTTCCTTTCTTCTTCTTTTTT
1 TTTTCCTTTCTTCTTCTTTTTC
* *
1225989 TTTTCCTTTTTTGTT-TTGTTTC
1 TTTTCCTTTCTTCTTCTT-TTTC
1226011 TTTT
1 TTTT
1226015 TTTGGAAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.00, C:0.17, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTTCCTTTCTTCTTCTTTTTC
Found at i:1227945 original size:79 final size:79
Alignment explanation
Indices: 1227813--1228032 Score: 289
Period size: 79 Copynumber: 2.8 Consensus size: 79
1227803 TCATCTCGGA
* * * * *
1227813 GATACTCCAACCCCGGTTTTATTTTCAAAACATCAATTTTTCATAATCGGGGATACTCCAATCTC
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTC
* * *
1227878 GTTATTTTCGAGGG
66 GTCACTTTCGAGAG
* * * * **
1227892 GATACCCCTACCCCGATTTTATTCCCAAAACACCAATTTTTAACAATTTGGGATACTCCAACCTC
1 GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTC
1227957 GTCACTTTCGAGAG
66 GTCACTTTCGAGAG
*
1227971 GATACTCCAACCCC-AGTTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
1 GATACTCCAACCCCGA-TTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
1228033 TCCGATATTA
Statistics
Matches: 119, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
78 1 0.01
79 118 0.99
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (79 bp):
GATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCGGGGATACTCCAACCTC
GTCACTTTCGAGAG
Found at i:1228046 original size:51 final size:50
Alignment explanation
Indices: 1227970--1228085 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 50
1227960 ACTTTCGAGA
* * *
1227970 GGATACTCCAACCCCAGTTTTATTTCTAAAACACCAATTTTTCACAATCGG
1 GGATACTCCAACCCGA-TATTATTTCCAAAACACCAATTTTTCACAATCGG
*
1228021 GGATACTCCAACTCCGATATTATTTCCAAAACATCAATTTTTCACAATCGG
1 GGATACTCCAAC-CCGATATTATTTCCAAAACACCAATTTTTCACAATCGG
1228072 GGATACTCCAACCC
1 GGATACTCCAACCC
1228086 CGTTATTTCA
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
50 2 0.03
51 55 0.92
52 3 0.05
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.29
Consensus pattern (50 bp):
GGATACTCCAACCCGATATTATTTCCAAAACACCAATTTTTCACAATCGG
Found at i:1228103 original size:28 final size:29
Alignment explanation
Indices: 1228067--1228143 Score: 104
Period size: 28 Copynumber: 2.7 Consensus size: 29
1228057 ATTTTTCACA
1228067 ATCGGGGATACTCCAACCCCGTTA-TTTC
1 ATCGGGGATACTCCAACCCCGTTATTTTC
*
1228095 ATCGGGGATACTCCAACCCCATTATTTTC
1 ATCGGGGATACTCCAACCCCGTTATTTTC
* * *
1228124 A-AGGAGATACTCTAACCCCG
1 ATCGGGGATACTCCAACCCCG
1228144 ACTTTATTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 38 0.88
29 5 0.12
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTATTTTC
Found at i:1228105 original size:158 final size:158
Alignment explanation
Indices: 1227941--1228272 Score: 400
Period size: 158 Copynumber: 2.1 Consensus size: 158
1227931 TTAACAATTT
* * * * *
1227941 GGGATACTCCAACCTCGTCACTTTCGA-GAGGATACTCCAACCCC-AGTTTTATTTCTAAAACAC
1 GGGATACTCCAACCCCATCACTTTCAAGGA-GATACTCCAACCCCGA-CTTTATTTCCAAAACAC
* * * *
1228004 CAATTTTTCACAATCGGGGATACTCCAACTCCGATATTATTTCCAAAACATCAATTTTTCACAAT
64 CAATTTCTCACAATCGGGGATACTCCAACCCCGACATTATTTCCAAAACATCAACTTTTCACAAT
*
1228069 CGGGGATACTCCAACCCCGTTATTTCAT-CG
129 CGGGGATACTCCAACCCCGTTATTT-ATGAG
* * * * ***
1228099 GGGATACTCCAACCCCATTATTTTCAAGGAGATACTCTAACCCCGACTTTATTTCCAAAATATTG
1 GGGATACTCCAACCCCATCACTTTCAAGGAGATACTCCAACCCCGACTTTATTTCCAAAACACCA
* * * * * *
1228164 ATTTCTCACAATCGGGGATACTGCAACCCCGGCCTTATTTCTAAAGCATCGACTTTTCACAATCG
66 ATTTCTCACAATCGGGGATACTCCAACCCCGACATTATTTCCAAAACATCAACTTTTCACAATCG
*
1228229 GGGATACTCCAACCCCGTTATTTTTGAG
131 GGGATACTCCAACCCCGTTATTTATGAG
1228257 GGGATACTCCAACCCC
1 GGGATACTCCAACCCC
1228273 GATTTTATTT
Statistics
Matches: 147, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
157 1 0.01
158 143 0.97
159 3 0.02
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (158 bp):
GGGATACTCCAACCCCATCACTTTCAAGGAGATACTCCAACCCCGACTTTATTTCCAAAACACCA
ATTTCTCACAATCGGGGATACTCCAACCCCGACATTATTTCCAAAACATCAACTTTTCACAATCG
GGGATACTCCAACCCCGTTATTTATGAG
Found at i:1228192 original size:51 final size:50
Alignment explanation
Indices: 1228129--1228245 Score: 137
Period size: 51 Copynumber: 2.3 Consensus size: 50
1228119 TTTTCAAGGA
* * *
1228129 GATACTCTAACCCCGACTTTATTTCCAAAATATTGA-TTTCTCACAATCGGG
1 GATACTC-AACCCCGACCTTATTTCCAAAACATCGACTTT-TCACAATCGGG
* * *
1228180 GATACTGCAACCCCGGCCTTATTTCTAAAGCATCGACTTTTCACAATCGGG
1 GATACT-CAACCCCGACCTTATTTCCAAAACATCGACTTTTCACAATCGGG
1228231 GATACTCCAACCCCG
1 GATACT-CAACCCCG
1228246 TTATTTTTGA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 53 0.93
52 4 0.07
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (50 bp):
GATACTCAACCCCGACCTTATTTCCAAAACATCGACTTTTCACAATCGGG
Found at i:1228260 original size:79 final size:79
Alignment explanation
Indices: 1228177--1228378 Score: 210
Period size: 79 Copynumber: 2.6 Consensus size: 79
1228167 TCTCACAATC
* * * * * *
1228177 GGGGATACTGCAACCCCGGCCTTA-TTTCTAAAGCATCGACTTTTC-ACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGACCTTATTTTC-AAAACACCGA-TTTTCTACAATCAGGCATACTCCA
* *
1228240 ACCCCGTTATTTTTGA
64 ACCCCATTATTTTCGA
** * *
1228256 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCGATTTTCTATAATCAGGCATACTCCAAC
1 GGGGATACTCCAACCCCGACCTTATTTTCAAAACACCGATTTTCTACAATCAGGCATACTCCAAC
*
1228321 CCTATTATTTTCGA
66 CCCATTATTTTCGA
* ** * *
1228335 GGGGATACTCCAACCCCAATTTTATTTCCAAAACATCGATTTTC
1 GGGGATACTCCAACCCCGACCTTATTTTCAAAACACCGATTTTC
1228379 CATAATCGAT
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
78 5 0.05
79 95 0.91
80 4 0.04
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGACCTTATTTTCAAAACACCGATTTTCTACAATCAGGCATACTCCAAC
CCCATTATTTTCGA
Found at i:1228384 original size:79 final size:79
Alignment explanation
Indices: 1228198--1228402 Score: 243
Period size: 79 Copynumber: 2.6 Consensus size: 79
1228188 AACCCCGGCC
* * * * * * *
1228198 TTATTTCTAAAGCATCGACTTTT-CACAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGAT
1 TTATTTCCAAAACATCGA-TTTTCCATAATCAGGCATACTCCAACCCCATTATTTTCGAGGGGAT
*
1228262 ACTCCAACCCCGATT
65 ACTCCAACCCCAATT
* * * * *
1228277 TTATTTTCAAAATACCGATTTTCTATAATCAGGCATACTCCAACCCTATTATTTTCGAGGGGATA
1 TTATTTCCAAAACATCGATTTTCCATAATCAGGCATACTCCAACCCCATTATTTTCGAGGGGATA
1228342 CTCCAACCCCAATT
66 CTCCAACCCCAATT
* *
1228356 TTATTTCCAAAACATCGATTTTCCATAATCGATG-ATACTCTAACCCC
1 TTATTTCCAAAACATCGATTTTCCATAATC-AGGCATACTCCAACCCC
1228403 GATTTTATTT
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
78 4 0.04
79 98 0.94
80 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (79 bp):
TTATTTCCAAAACATCGATTTTCCATAATCAGGCATACTCCAACCCCATTATTTTCGAGGGGATA
CTCCAACCCCAATT
Found at i:1228401 original size:51 final size:51
Alignment explanation
Indices: 1228337--1228448 Score: 161
Period size: 51 Copynumber: 2.2 Consensus size: 51
1228327 ATTTTCGAGG
* *
1228337 GGATACTCCAACCCCAATTTTATTTCCAAAACATCGATTTTCCATAATCGA
1 GGATACTCTAACCCCAATTTTATTTCCAAAACACCGATTTTCCATAATCGA
* * * * *
1228388 TGATACTCTAACCCCGATTTTATTTCCAGAACACCGATTTTTCATAATCGG
1 GGATACTCTAACCCCAATTTTATTTCCAAAACACCGATTTTCCATAATCGA
1228439 GGATACTCTA
1 GGATACTCTA
1228449 GCATCGTTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
GGATACTCTAACCCCAATTTTATTTCCAAAACACCGATTTTCCATAATCGA
Found at i:1233115 original size:43 final size:43
Alignment explanation
Indices: 1233060--1233570 Score: 511
Period size: 43 Copynumber: 11.7 Consensus size: 43
1233050 ATTTCCTTCT
*
1233060 TTTTC-CCTTTTGTCCTCAAAGAGTAGGACGCACTTTATTTTCC
1 TTTTCTCC-TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC
*
1233103 TTTTCTCCTTTGTCCTCAAAGAACAGGA--CA-TGTTCCATTCCCTT-C
1 TTTTCTCCTTTGTCCTCAAAGAGCAGGACGCACT-TT--ATT---TTCC
* * * *
1233148 TTTTCTCATTTTGTCCTCAAAAAGCAGGACGCACTTCATTTTCT
1 TTTTCTC-CTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC
* * *
1233192 TTTTTTCCCTTTTGTCCTCAAAGAGCAGGACGAACTTTATTTTTC
1 TTTTCT-CC-TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC
*
1233237 TTTTCTCCTTTGTCCTCAAAGAGCATGACGCACTTTATTTTCC
1 TTTTCTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC
* * *
1233280 TTTTCTCTTTTGTCCTCAAAGAGCAGGACACACTTCA-TTTCC
1 TTTTCTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC
* * *
1233322 TTCTTTTCCCTTTTGTCCTTAAAGAGCATGACGCACTTTATTTTCC
1 TT-TTCT-CC-TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC
* * *
1233368 TTTTCTCCTTTGTCTTCAAATAGCAGGACGCACTTTATTTTTC
1 TTTTCTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC
* * *
1233411 TTTTCTCCTTTGTCCTCAAAGAGCAGGACACGCTTCATTTT-C
1 TTTTCTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC
* *
1233453 TTATTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTTC
1 TT-TTCT-CC-TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC
* * * *
1233499 TTTT-TCTTTTGTCCTCAAAGAGCATGATGCA-TTTCGTTTTCC
1 TTTTCTCCTTTGTCCTCAAAGAGCAGGACGCACTTT-ATTTTCC
* *
1233541 TTTTGTTCTTTTGTCCTCGAAA-AGCAGGAC
1 TTTT-CTCCTTTGTCCTC-AAAGAGCAGGAC
1233571 ATACTCTTTT
Statistics
Matches: 392, Mismatches: 50, Indels: 51
0.80 0.10 0.10
Matches are distributed among these distances:
40 1 0.00
41 7 0.02
42 41 0.10
43 166 0.42
44 33 0.08
45 107 0.27
46 33 0.08
48 3 0.01
49 1 0.00
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.42
Consensus pattern (43 bp):
TTTTCTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCC
Found at i:1233277 original size:88 final size:87
Alignment explanation
Indices: 1233060--1233570 Score: 531
Period size: 88 Copynumber: 5.8 Consensus size: 87
1233050 ATTTCCTTCT
* * *
1233060 TTTTC-CCTTTTGTCCTCAAAGAGTAGGACGCACTTTATTTTCCTTTTCTCC-TTTGTCCTCAAA
1 TTTTCTCC-TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCTTTTTTTCCTTTTGTCCTCAAA
* ** * *
1233123 GAACAGGAC-ATGTTCCATTCCCTTC
65 GAGCAGGACGAACTT-TATT--TTTC
* * *
1233148 TTTTCTCATTTTGTCCTCAAAAAGCAGGACGCACTTCATTTTCTTTTTTTCCCTTTTGTCCTCAA
1 TTTTCTC-CTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCTTTTTTT-CCTTTTGTCCTCAA
1233213 AGAGCAGGACGAACTTTATTTTTC
64 AGAGCAGGACGAACTTTATTTTTC
* * *
1233237 TTTTCTCCTTTGTCCTCAAAGAGCATGACGCACTTTATTTTCCTTTTCT-CTTTTGTCCTCAAAG
1 TTTTCTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCTTTTTTTCCTTTTGTCCTCAAAG
*
1233301 AGCAGGAC-ACACTTCATTTCCTTC
66 AGCAGGACGA-ACTTTATTT--TTC
* * * * *
1233325 TTTTC-CCTTTTGTCCTTAAAGAGCATGACGCACTTTATTTTCCTTTTCTCC-TTTGTCTTCAAA
1 TTTTCTCC-TTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCTTTTTTTCCTTTTGTCCTCAAA
* *
1233388 TAGCAGGACGCACTTTATTTTTC
65 GAGCAGGACGAACTTTATTTTTC
* * * *
1233411 TTTTCTCCTTTGTCCTCAAAGAGCAGGACACGCTTCATTTTCTTATTTTCCCTTTTGTCCTCAAA
1 TTTTCTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCTT-TTTTTCCTTTTGTCCTCAAA
*
1233476 GAGCAGGACGCACTTTATTTTTC
65 GAGCAGGACGAACTTTATTTTTC
* * * * *
1233499 TTTT-TCTTTTGTCCTCAAAGAGCATGATGCA-TTTCGTTTTCCTTTTGTT-CTTTTGTCCTCGA
1 TTTTCTCCTTTGTCCTCAAAGAGCAGGACGCACTTT-ATTTT-CTTTTTTTCCTTTTGTCCTC-A
1233561 AA-AGCAGGAC
63 AAGAGCAGGAC
1233571 ATACTCTTTT
Statistics
Matches: 364, Mismatches: 42, Indels: 36
0.82 0.10 0.08
Matches are distributed among these distances:
85 1 0.00
86 90 0.25
87 41 0.11
88 156 0.43
89 48 0.13
90 2 0.01
91 23 0.06
92 3 0.01
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.42
Consensus pattern (87 bp):
TTTTCTCCTTTGTCCTCAAAGAGCAGGACGCACTTTATTTTCTTTTTTTCCTTTTGTCCTCAAAG
AGCAGGACGAACTTTATTTTTC
Found at i:1233360 original size:131 final size:131
Alignment explanation
Indices: 1233032--1233571 Score: 691
Period size: 131 Copynumber: 4.1 Consensus size: 131
1233022 AGGGAATCCC
* *
1233032 AAGAGCATGACACA-TTCCATTTCCTTCTTTTTCCCTTTTGTCCTCAAAGAGTAGGACGCACTTT
1 AAGAGCAGGACACACTT-CATTTCCTTC-TTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTT
*
1233096 ATTTTCCTTTTCTCCTTTGTCCTCAAAGAACAGGA--CATGTTCCATTCCCTT-CTTTTCTCATT
64 ATTTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACGCAT-TT-CATT---TTCCTTTTCTC-TT
1233158 TTGTCCTCA
123 TTGTCCTCA
* * * * *
1233167 AAAAGCAGGACGCACTTCATTTTCTTTTTTTCCCTTTTGTCCTCAAAGAGCAGGACGAACTTTAT
1 AAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTTAT
* *
1233232 TTTTCTTTTCTCCTTTGTCCTCAAAGAGCATGACGCACTTT-ATTTTCCTTTTCTCTTTTGTCCT
66 TTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACGCA-TTTCATTTTCCTTTTCTCTTTTGTCCT
1233296 CA
130 CA
* *
1233298 AAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTTGTCCTTAAAGAGCATGACGCACTTTAT
1 AAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTTAT
* * * *
1233363 TTTCCTTTTCTCCTTTGTCTTCAAATAGCAGGACGCACTTT-ATTTTTCTTTTCTCCTTTGTCCT
66 TTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACGCA-TTTCATTTTCCTTTTCTCTTTTGTCCT
1233427 CA
130 CA
* * *
1233429 AAGAGCAGGACACGCTTCATTTTCTTATTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTTAT
1 AAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTTAT
* * * * * *
1233494 TTTTCTTTT-TCTTTTGTCCTCAAAGAGCATGATGCATTTCGTTTTCCTTTTGTTCTTTTGTCCT
66 TTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACGCATTTCATTTTCCTTTT-CTCTTTTGTCCT
1233558 CGA
130 C-A
1233561 AA-AGCAGGACA
1 AAGAGCAGGACA
1233572 TACTCTTTTT
Statistics
Matches: 359, Mismatches: 38, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
129 3 0.01
130 31 0.09
131 219 0.61
132 11 0.03
134 69 0.19
135 19 0.05
136 6 0.02
137 1 0.00
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.42
Consensus pattern (131 bp):
AAGAGCAGGACACACTTCATTTCCTTCTTTTCCCTTTTGTCCTCAAAGAGCAGGACGCACTTTAT
TTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACGCATTTCATTTTCCTTTTCTCTTTTGTCCTC
A
Found at i:1234275 original size:13 final size:13
Alignment explanation
Indices: 1234254--1234283 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1234244 ATACGTTGTT
*
1234254 CATTGTATCGATA
1 CATTATATCGATA
1234267 CATTATATCGATA
1 CATTATATCGATA
1234280 CATT
1 CATT
1234284 CAGGCATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:1236718 original size:79 final size:79
Alignment explanation
Indices: 1236582--1236800 Score: 300
Period size: 79 Copynumber: 2.8 Consensus size: 79
1236572 TTTTCATCTC
*
1236582 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACA-TCAATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACT-AATTTTTCACAATCGGGGATACTCCAA
1236646 TCC-CGT-TATTTCCGA
65 -CCTCGTCT-TTTCCGA
** * * *
1236661 GGGGATACTCCAACCCCGACTTTATTCCCAAAACACTAATTTTTCACAATTGAGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
*
1236726 CTCGTCTTTTTCGA
66 CTCGTCTTTTCCGA
* * *
1236740 AGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTC
1236801 TAACTCCGAT
Statistics
Matches: 122, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
78 2 0.02
79 118 0.97
80 2 0.02
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTTCACAATCGGGGATACTCCAAC
CTCGTCTTTTCCGA
Found at i:1236814 original size:51 final size:51
Alignment explanation
Indices: 1236741--1236856 Score: 196
Period size: 51 Copynumber: 2.3 Consensus size: 51
1236731 CTTTTTCGAA
* *
1236741 GGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCG
* *
1236792 GGGATACTCTAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCG
1236843 GGGATACTCCAACC
1 GGGATACTCCAACC
1236857 TCGTTATTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTTCACAATCG
Found at i:1236867 original size:31 final size:28
Alignment explanation
Indices: 1236839--1236914 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 28
1236829 ATTTTTCACA
* *
1236839 ATCGGGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCATTATTTC
1236867 ATCGGGGATACTCCAACCCCATTATTT-
1 ATCGGGGATACTCCAACCCCATTATTTC
1236894 -TCGAGGAGATACTCCAACCCC
1 ATCG-GG-GATACTCCAACCCC
1236915 GGCTTTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 3 0.07
27 2 0.05
28 39 0.89
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCATTATTTC
Found at i:1237070 original size:79 final size:79
Alignment explanation
Indices: 1236941--1237165 Score: 233
Period size: 79 Copynumber: 2.8 Consensus size: 79
1236931 TGACAATCGG
* *** *
1236941 GGATACTCCAACCCTGGCCTTA-TTTCTAAAACATCGACTTTTC-ATAATCAGGGATACTCCAAC
1 GGATACTCCAACCCCGATTTTATTTTC-AAAACACCGA-TTTTCTATAATCAGGGATACTCCAAC
* *
1237004 CCCATTATTT-TCGAGG
64 CCCATAATTTCT-GAGA
* * *
1237020 GGATACTCCAACCCCGATTTTATTTTCAAAATACTGATTTTCTATAATCAGAGATACTCCAACCC
1 GGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAACCC
*
1237085 TATAATTTCTGAGA
66 CATAATTTCTGAGA
* ** * *
1237099 GGCTACTTTAACCCCGATTTTATTTTCAGAACACCGATTTT-TCATAATCGGGGAATACTCCAAC
1 GGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCT-ATAATCAGGG-ATACTCCAAC
1237163 CCC
64 CCC
1237166 GATTTTATTT
Statistics
Matches: 121, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
78 6 0.05
79 98 0.81
80 17 0.14
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (79 bp):
GGATACTCCAACCCCGATTTTATTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAACCC
CATAATTTCTGAGA
Found at i:1237217 original size:51 final size:52
Alignment explanation
Indices: 1237108--1237209 Score: 170
Period size: 52 Copynumber: 2.0 Consensus size: 52
1237098 AGGCTACTTT
* * *
1237108 AACCCCGATTTTATTTTCAGAACACCGATTTTTCATAATCGGGGAATACTCC
1 AACCCCGATTTTATTTCCAGAATACCGATTTTCCATAATCGGGGAATACTCC
1237160 AACCCCGATTTTATTTCCAGAATACCGATTTTCCATAATCGGGG-ATACTC
1 AACCCCGATTTTATTTCCAGAATACCGATTTTCCATAATCGGGGAATACTC
1237210 TAGCCCCGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 6 0.13
52 41 0.87
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.32
Consensus pattern (52 bp):
AACCCCGATTTTATTTCCAGAATACCGATTTTCCATAATCGGGGAATACTCC
Found at i:1237243 original size:52 final size:52
Alignment explanation
Indices: 1237108--1237243 Score: 114
Period size: 52 Copynumber: 2.6 Consensus size: 52
1237098 AGGCTACTTT
* * * * ** *
1237108 AACCCCGATTTTATTTTCAGAACACCGATTTTTCATAATCGGGGAATACTCC
1 AACCCCGATTTTATCTCCAAAATACAAATTTTCCATAATCGGGGAATACTCC
* * ** *
1237160 AACCCCGATTTTATTTCCAGAATACCGATTTTCCATAATCGGGG-ATACTCT
1 AACCCCGATTTTATCTCCAAAATACAAATTTTCCATAATCGGGGAATACTCC
* *
1237211 AGCCCCG-TTGTTATCTCCAAAATATTAAATTTT
1 AACCCCGATT-TTATCTCCAAAATA-CAAATTTT
1237244 TCGTCGAGAG
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
50 2 0.03
51 24 0.33
52 46 0.64
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (52 bp):
AACCCCGATTTTATCTCCAAAATACAAATTTTCCATAATCGGGGAATACTCC
Found at i:1238789 original size:7 final size:7
Alignment explanation
Indices: 1238777--1238807 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1238767 ATGGTATTTT
1238777 TTTTTCA
1 TTTTTCA
1238784 TTTTTCA
1 TTTTTCA
1238791 TTTTTCA
1 TTTTTCA
1238798 TTTTTCA
1 TTTTTCA
1238805 TTT
1 TTT
1238808 CTTTGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:1239153 original size:26 final size:25
Alignment explanation
Indices: 1239101--1239154 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
1239091 TTTTAACTAA
* * *
1239101 TTATTATATAAATTTATAAATTTAT
1 TTATTATATAAATGTATAAAATAAT
1239126 TTATTATATTAAATGTATAAAATAAT
1 TTATTATA-TAAATGTATAAAATAAT
1239152 TTA
1 TTA
1239155 AAACTTTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTATTATATAAATGTATAAAATAAT
Found at i:1239195 original size:20 final size:21
Alignment explanation
Indices: 1239142--1239198 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
1239132 TATTAAATGT
1239142 ATAAAATAATTTAAAACTTTTAC
1 ATAAAATAA-TTAAAA-TTTTAC
1239165 ATAAAAT--TTAAAATTTTA-
1 ATAAAATAATTAAAATTTTAC
1239183 ATAAAATAATTAAAAT
1 ATAAAATAATTAAAAT
1239199 AATATAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
18 7 0.22
19 5 0.16
20 13 0.41
23 7 0.22
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAAATAATTAAAATTTTAC
Found at i:1241891 original size:13 final size:14
Alignment explanation
Indices: 1241873--1241911 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1241863 TTTTATTTTT
*
1241873 AAAATAAAGATT-A
1 AAAATAAAAATTAA
1241886 AAAATAAAAATTAA
1 AAAATAAAAATTAA
1241900 AAAATAAAAATT
1 AAAATAAAAATT
1241912 CATGAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAATAAAAATTAA
Found at i:1242026 original size:5 final size:6
Alignment explanation
Indices: 1241983--1242025 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
1241973 TGATTGAAAA
*
1241983 AAATTT AAAATTT AAATTT AAATTT GAATTT -AATTT -AATTT AA
1 AAATTT -AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AA
1242026 TAACTCGAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
5 10 0.29
6 18 0.53
7 6 0.18
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:1242110 original size:48 final size:48
Alignment explanation
Indices: 1242049--1242156 Score: 109
Period size: 49 Copynumber: 2.2 Consensus size: 48
1242039 TATTTAAAAA
* *
1242049 ATAA-TAAATATTAA-AAAT-T-TTATTTATATTTTAATATTTATATATTTT
1 ATAATTAAA-ATTAACAAATATATTATTTA-A-TTAAATATATA-ATATTTT
1242097 ATAATTAAAATTAACTAAATATATTATTTAATTAAATATATAATATTTT
1 ATAATTAAAATTAAC-AAATATATTATTTAATTAAATATATAATATTTT
1242146 A-AATTTAAAAT
1 ATAA-TTAAAAT
1242157 ATTATATTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
48 11 0.21
49 19 0.37
50 13 0.25
51 2 0.04
52 7 0.13
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (48 bp):
ATAATTAAAATTAACAAATATATTATTTAATTAAATATATAATATTTT
Found at i:1242150 original size:21 final size:21
Alignment explanation
Indices: 1242104--1242165 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
1242094 TTTATAATTA
* *
1242104 AAATTAACTAAATATATTATT
1 AAATTAAATATATATATTATT
*
1242125 TAATTAAATATATAATATT-TT
1 AAATTAAATATAT-ATATTATT
1242146 AAATTTAAA-ATATTATATTA
1 AAA-TTAAATATA-TATATTA
1242166 ATATTTTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 22 0.67
22 11 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTAAATATATATATTATT
Found at i:1242194 original size:27 final size:24
Alignment explanation
Indices: 1242126--1242194 Score: 61
Period size: 27 Copynumber: 2.7 Consensus size: 24
1242116 TATATTATTT
1242126 AATTAAA--TATATAATATTTTAA
1 AATTAAATTTATATAATATTTTAA
*
1242148 ATTTAAAATATTATATTAATATTTTACTTA
1 AATT-AAAT-TTATA-TAATATTTTA---A
1242178 AATTAAATTTATATAAT
1 AATTAAATTTATATAAT
1242195 TGGACAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
22 3 0.08
23 3 0.08
26 4 0.11
27 14 0.38
28 5 0.14
29 4 0.11
30 4 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTAAATTTATATAATATTTTAA
Found at i:1242830 original size:8 final size:8
Alignment explanation
Indices: 1242819--1242861 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
1242809 TATAAAAATA
1242819 AAATTTTT
1 AAATTTTT
*
1242827 AAATTTAT
1 AAATTTTT
1242835 AAATATTTAT
1 AAAT-TTT-T
1242845 AAATTTTTT
1 AAA-TTTTT
1242854 AAATTTTT
1 AAATTTTT
1242862 TACTAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 16 0.53
9 6 0.20
10 7 0.23
11 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
AAATTTTT
Found at i:1242861 original size:10 final size:9
Alignment explanation
Indices: 1242817--1242863 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
1242807 AGTATAAAAA
*
1242817 TAAAATTTT
1 TAAATTTTT
*
1242826 TAAA-TTTA
1 TAAATTTTT
*
1242834 TAAATATTTA
1 TAAAT-TTTT
1242844 TAAATTTTT
1 TAAATTTTT
1242853 TAAATTTTT
1 TAAATTTTT
1242862 TA
1 TA
1242864 CTAAATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 7 0.21
9 18 0.53
10 9 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TAAATTTTT
Found at i:1243946 original size:16 final size:16
Alignment explanation
Indices: 1243925--1243955 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1243915 TTAATGTTCT
*
1243925 TATTTTTATTTTTATG
1 TATTTTTAATTTTATG
1243941 TATTTTTAATTTTAT
1 TATTTTTAATTTTAT
1243956 TTAAAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TATTTTTAATTTTATG
Found at i:1244071 original size:16 final size:16
Alignment explanation
Indices: 1244024--1244074 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 16
1244014 TTTTTAGTAA
*
1244024 TAAAAT-TTTTAAAATT
1 TAAAATATTATAAAA-T
1244040 TAAAAATATTAAATAAAAT
1 T-AAAATATT--ATAAAAT
1244059 TAAAATATTATAAAAT
1 TAAAATATTATAAAAT
1244075 CATAAAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
16 8 0.27
17 5 0.17
18 10 0.33
19 2 0.07
20 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAATATTATAAAAT
Done.