Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1135
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: 107926
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1436 original size:20 final size:20
Alignment explanation
Indices: 1391--1436 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1381 GTTAACAGAC
*
1391 CATGATTCATGCATTTTGAG
1 CATGTTTCATGCATTTTGAG
1411 CTATGTTTCATGCA-TTTGCAG
1 C-ATGTTTCATGCATTTTG-AG
1432 CATGT
1 CATGT
1437 CCAGCAGCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (20 bp):
CATGTTTCATGCATTTTGAG
Found at i:6796 original size:16 final size:16
Alignment explanation
Indices: 6775--6853 Score: 79
Period size: 16 Copynumber: 4.9 Consensus size: 16
6765 TCAACAACCT
*
6775 GAATCCGAACTGACCC
1 GAATCCGAAATGACCC
**
6791 GAATCCGAAATGACTT
1 GAATCCGAAATGACCC
* *
6807 GAACCCGAAATAACCC
1 GAATCCGAAATGACCC
6823 GAATCC-AGAATGACCC
1 GAATCCGA-AATGACCC
* *
6839 GAACCCAAAATGACC
1 GAATCCGAAATGACC
6854 TAAATAATTA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
15 1 0.02
16 49 0.96
17 1 0.02
ACGTcount: A:0.39, C:0.32, G:0.16, T:0.13
Consensus pattern (16 bp):
GAATCCGAAATGACCC
Found at i:7916 original size:16 final size:16
Alignment explanation
Indices: 7892--7950 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 16
7882 TAAACTCGAT
7892 TGACCCGAACCCAAAA
1 TGACCCGAACCCAAAA
* * *
7908 TGACTCGAATCCAAAG
1 TGACCCGAACCCAAAA
* * *
7924 TGATCCGAATCCGAAA
1 TGACCCGAACCCAAAA
7940 TGACCCGAACC
1 TGACCCGAACC
7951 TGAAAACGAC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.37, C:0.32, G:0.17, T:0.14
Consensus pattern (16 bp):
TGACCCGAACCCAAAA
Found at i:9998 original size:7 final size:7
Alignment explanation
Indices: 9988--10017 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
9978 AATTAAAAAA
9988 AAAAAGG
1 AAAAAGG
9995 -AAAAGG
1 AAAAAGG
10001 AAAAAGG
1 AAAAAGG
10008 AAAAAGG
1 AAAAAGG
10015 AAA
1 AAA
10018 CAGTAGCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:13569 original size:14 final size:14
Alignment explanation
Indices: 13552--13580 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13542 TTATTAAAAT
13552 AAAAAATGAAAAGA
1 AAAAAATGAAAAGA
13566 AAAAAATGAAAAGA
1 AAAAAATGAAAAGA
13580 A
1 A
13581 GGAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (14 bp):
AAAAAATGAAAAGA
Found at i:13957 original size:21 final size:19
Alignment explanation
Indices: 13907--13962 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
13897 TAAAATGTTT
*
13907 AATAATAAAAATTAAT-TAA
1 AATAA-AAAAATAAATATAA
*
13926 AACAAAAAAATAAATACTAA
1 AATAAAAAAATAAATA-TAA
13946 AATAAGAAAAATAAATA
1 AATAA-AAAAATAAATA
13963 AAATAATGTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 9 0.29
19 4 0.13
20 7 0.23
21 11 0.35
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAAAATAAATATAA
Found at i:13966 original size:18 final size:17
Alignment explanation
Indices: 13907--13968 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 17
13897 TAAAATGTTT
*
13907 AATAATAAAAATTAATTAA
1 AATAA-AAAAA-TAAATAA
*
13926 AACAAAAAAATAAATACTAA
1 AATAAAAAAAT-AA-A-TAA
13946 AATAAGAAAAATAAATAA
1 AATAA-AAAAATAAATAA
13964 AATAA
1 AATAA
13969 TGTCATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.03
18 15 0.42
19 5 0.14
20 9 0.25
21 6 0.17
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (17 bp):
AATAAAAAAATAAATAA
Found at i:23611 original size:32 final size:32
Alignment explanation
Indices: 23574--23649 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
23564 CATTTCATAG
*
23574 TGTATCGATACATCTGGGCAAATTTACCTGTA
1 TGTATCGATACATCTGGGCAAATTTACCTGCA
*
23606 TGTATCGATACATCTTGGCAAATTTACCTGCA
1 TGTATCGATACATCTGGGCAAATTTACCTGCA
23638 TGTATCGATACA
1 TGTATCGATACA
23650 AAGATCAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATCTGGGCAAATTTACCTGCA
Found at i:23771 original size:32 final size:32
Alignment explanation
Indices: 23730--23797 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
23720 TTCGTAACTG
23730 TACATTGTATCAATACAAAACTTATATATCGA
1 TACATTGTATCAATACAAAACTTATATATCGA
* *
23762 TACATTGTATCAATACAACACTTATGTATCGA
1 TACATTGTATCAATACAAAACTTATATATCGA
23794 TACA
1 TACA
23798 AATCGTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.41, C:0.18, G:0.07, T:0.34
Consensus pattern (32 bp):
TACATTGTATCAATACAAAACTTATATATCGA
Found at i:24549 original size:52 final size:52
Alignment explanation
Indices: 24447--25357 Score: 370
Period size: 49 Copynumber: 18.2 Consensus size: 52
24437 GGTATTGGGT
* * * *
24447 TTAAAGATGAGAAAAAGGATG-TCAATGTGCTGATTCACGGTCAGCGACATTAGAC
1 TTAAAGATGAG-AAAA--ATGCT-AATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * * **
24502 TTGAAGATGAGAAAAATGCTAATGTACTGATTCAAGGCCAACAACATTAGGTT
1 TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATT-GGAC
** * * *
24555 TTAAAGATGATG-AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGAC
1 TTAAAGATGA-GAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * * * * *
24607 TTAAAGATGAAGGTGAGAAAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGG
1 TTAAAGATG-A---GA-AAAA-TGCT--A-ATG------TGCTGATTCAAGGCCAGCAACATTGG
*
24672 GC
51 AC
* *
24674 TTAAAGATGAGAAAAAAGGATG-TCAATGTGCTGATTCAAGGCCAGCTACATTGAAC
1 TTAAAGATGAG--AAAA--ATGCT-AATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * * ** **
24730 TTGAATATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAATAACATTGGGT
1 TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* *
24782 TTAAAGATGAGAAAAAGGATG-TCAATGTGCTGATTCAAGGCCAGCTACATTGAAC
1 TTAAAGATGAG-AAAA--ATGCT-AATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * * * * *
24837 TTAAAGATG-GAAAAGGTGCCAATATACTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAA-ATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * *
24889 TT-AA-A-G-G-----TGCTAATGTGCTGATTCAAAGCCAGCTACATTAGAC
1 TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * * * *
24932 TTAAAGA--AG-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * *
24981 TT-AA-A-G-G-----TGCCAATGTGCTGATTCAAGGCCGGCTACATTGGAC
1 TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * *
25024 TTAAAGA--AG-AAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTAGAC
1 TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * *
25073 TT-AA-A-G-G-----TGCCAATGTGCTGATTCAGGGCCAGCTACATTGGAC
1 TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * * * *
25116 TTAAAGAT---AAAGGTG-TCGATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAAATGCT-AATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * * *
25165 TTAAAGAT--G-AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACTTTGGAC
1 TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* *
25214 TT-AA-A--AG-----TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * * * *
25257 TTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* *
25306 TT-AA-A-G-G-----TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
25349 TTAAAGATG
1 TTAAAGATG
25358 GAGGTGCCAA
Statistics
Matches: 689, Mismatches: 98, Indels: 147
0.74 0.10 0.16
Matches are distributed among these distances:
43 174 0.25
44 10 0.01
45 7 0.01
46 1 0.00
47 7 0.01
48 8 0.01
49 179 0.26
50 1 0.00
51 2 0.00
52 108 0.16
53 49 0.07
54 10 0.01
55 50 0.07
56 30 0.04
57 2 0.00
58 2 0.00
60 1 0.00
61 2 0.00
62 3 0.00
63 2 0.00
64 4 0.01
65 3 0.00
66 2 0.00
67 32 0.05
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.25
Consensus pattern (52 bp):
TTAAAGATGAGAAAAATGCTAATGTGCTGATTCAAGGCCAGCAACATTGGAC
Found at i:24679 original size:67 final size:68
Alignment explanation
Indices: 24557--24683 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
24547 ATTAGGTTTT
* * *
24557 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGGTG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGGTG
24622 AGA
66 AGA
* * * *
24625 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
24684 GAAAAAAGGA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGGTG
AGA
Found at i:24762 original size:228 final size:228
Alignment explanation
Indices: 24355--24845 Score: 679
Period size: 228 Copynumber: 2.1 Consensus size: 228
24345 CCACTGTGCA
* * * * *
24355 GATTCAAGGCCTGCCACACTGGACTTAAAGATGATGAGGATGAAGAGTGATAAAAGGACCAATAT
1 GATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGAGGATGAAAAGTGATAAAAGGACCAATAT
* * *
24420 GTTGATTCACGGCCAACGGTATTGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAC
66 GTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAA
* *
24485 GGTCAGCGACATTAGACTTGAAGATGAGAAAAATGCTAATGTACTGATTCAAGGCCAACAACATT
131 GGCCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTACTGATTCAAGGCCAACAACATT
*
24550 AGGTTTTAAAGATGATG-AAGG-TGCCAATATGCT
196 -GGGTTTAAAGATGA-GAAAGGATGCCAATATGCT
* *
24583 GATTCAAGGCCAGCAATATTGGACTTAAAGATGAAG-GTGA-GAAAAGTGATAAAGATG-CCAAT
1 GATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGAG-GATGAAAAGTGATAAA-AGGACCAAT
24645 ATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAAGGATGTCAATGTGCTGATT
64 ATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAG-AAAAAGGATGTCAATGTGCTGATT
* * * *
24710 CAAGGCCAGCTACATT-GAACTTGAATATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAATAA
128 CAAGGCCAGCGACATTAG-ACTTGAAGATGAGAAAAATGCCAATGTACTGATTCAAGGCCAACAA
* *
24774 CATTGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCT
192 CATTGGGTTTAAAGATGAG--AAAGGATGCCAATATGCT
* *
24813 GATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 GATTCAAGGCCAGCAACATTGGACTTAAAGATG
24846 GAAAAGGTGC
Statistics
Matches: 233, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
226 1 0.00
227 70 0.30
228 118 0.51
229 4 0.02
230 40 0.17
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (228 bp):
GATTCAAGGCCAGCAACATTGGACTTAAAGATGAAGAGGATGAAAAGTGATAAAAGGACCAATAT
GTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAA
GGCCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTACTGATTCAAGGCCAACAACATT
GGGTTTAAAGATGAGAAAGGATGCCAATATGCT
Found at i:24835 original size:107 final size:108
Alignment explanation
Indices: 24633--24894 Score: 366
Period size: 107 Copynumber: 2.4 Consensus size: 108
24623 GAAAAGTGAT
* * * *
24633 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAAGGATGTC
1 AAAGATGCCAATATGCTGATTCAAGGCCAACAACATTGGGCTTAAAGATGAGAAAAAAGGATGTC
* *
24698 AATGTGCTGATTCAAGGCCAGCTACATTGAACTTGAATATGAGA
66 AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-GA
* * *
24742 AAA-ATGCCAATGTGCTGATTCAAGGCCAATAACATTGGGTTTAAAGATGAG-AAAAAGGATGTC
1 AAAGATGCCAATATGCTGATTCAAGGCCAACAACATTGGGCTTAAAGATGAGAAAAAAGGATGTC
24805 AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
66 AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * * * *
24848 AAAGGTGCCAATATACTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 AAAGATGCCAATATGCTGATTCAAGGCCAACAACATTGGGCTTAAAG
24895 GTGCTAATGT
Statistics
Matches: 134, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
106 5 0.04
107 85 0.63
108 41 0.31
109 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (108 bp):
AAAGATGCCAATATGCTGATTCAAGGCCAACAACATTGGGCTTAAAGATGAGAAAAAAGGATGTC
AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:24910 original size:43 final size:43
Alignment explanation
Indices: 24848--25354 Score: 555
Period size: 43 Copynumber: 11.1 Consensus size: 43
24838 TAAAGATGGA
* * *
24848 AAAGGTGCCAATATACTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
24891 AAAGGTGCTAATGTGCTGATTCAAAGCCAGCTACATTAGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* *
24934 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 -----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
24983 AAAGGTGCCAATGTGCTGATTCAAGGCCGGCTACATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* *
25026 AAAGAAGAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTAGACTT
1 -----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
25075 AAAGGTGCCAATGTGCTGATTCAGGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
* * * *
25124 AAAGGTGTCGATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
* *
25167 AAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACTTTGGACTT
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
*
25216 AAAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
* *
25265 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
25308 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
25351 AAAG
1 AAAG
25355 ATGGAGGTGC
Statistics
Matches: 395, Mismatches: 39, Indels: 60
0.80 0.08 0.12
Matches are distributed among these distances:
43 197 0.50
44 4 0.01
45 1 0.00
47 1 0.00
48 4 0.01
49 188 0.48
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (43 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:24969 original size:49 final size:48
Alignment explanation
Indices: 24687--25385 Score: 712
Period size: 49 Copynumber: 14.6 Consensus size: 48
24677 AAGATGAGAA
* *
24687 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTGAATATG
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AA-A-G
** * **
24739 AGAAAAATGCCAATGTGCTGATTCAAGGCCA-ATAACATTGGGTTTAAAGATGAG
1 A-AAAGGTGCCAATGTGCTGATTCAAGGCCAGCT-ACATTGGACTT--A-A--AG
* *
24793 AAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 -AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AA-A--G
* * *
24847 AAAAGGTGCCAATATACTGATTCAAGGCCAGCTATATTGGACTT----
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* * *
24891 -AAAGGTGCTAATGTGCTGATTCAAAGCCAGCTACATTAGACTTAAAG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* *
24938 AAGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----
1 AA-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
24983 -AAAGGTGCCAATGTGCTGATTCAAGGCCGGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* *
25030 AAGAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTAGACTT----
1 AA-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
25075 -AAAGGTGCCAATGTGCTGATTCAGGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* * * *
25122 ATAAAGGTGTCGATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 A-AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* * *
25171 ATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACTTTGGACTT----
1 A-AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
25216 AAAA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* *
25263 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----
1 A-AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
25308 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
** *
25355 ATGGAGGTGCCAATATGCTGATTCAAGGCCA
1 A-AAAGGTGCCAATGTGCTGATTCAAGGCCA
25386 ACGATATTGG
Statistics
Matches: 544, Mismatches: 63, Indels: 83
0.79 0.09 0.12
Matches are distributed among these distances:
43 193 0.35
44 4 0.01
45 1 0.00
47 1 0.00
48 5 0.01
49 219 0.40
51 1 0.00
52 67 0.12
53 11 0.02
54 8 0.01
55 33 0.06
56 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (48 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
Found at i:24977 original size:92 final size:91
Alignment explanation
Indices: 24795--25354 Score: 672
Period size: 92 Copynumber: 6.0 Consensus size: 91
24785 AAGATGAGAA
* *
24795 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT-AA-A--GAAAAGGTGCCAAT
* *
24860 ATACTGATTCAAGGCCAGCTATATTGGACTT
61 ATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
24891 AAAGGTGCTAATGTGCTGATTCAAAGCCAGCTACATTAGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAA-AAGGTGCCAATATGC
*
24956 TGATTCAAGGCCAGCTATATTGGACTT
65 TGATTCAAGGCCAGCTACATTGGACTT
* * *
24983 AAAGGTGCCAATGTGCTGATTCAAGGCCGGCTACATTGGACTTAAAGAAGAAGGTGCTAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAA-AAGGTGCCAATATGC
*
25048 TGATTCAAGGCCAGCTACATTAGACTT
65 TGATTCAAGGCCAGCTACATTGGACTT
* * *
25075 AAAGGTGCCAATGTGCTGATTCAGGGCCAGCTACATTGGACTTAAAGATAAAGGTGTCGATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AAAGGTGCCAATATGC
*
25140 TGATTCAAGGCCAGCTATATTGGACTT
65 TGATTCAAGGCCAGCTACATTGGACTT
* *
25167 AAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACTTTGGACTT----AAAA-GTGCCAA
1 ----A--AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAGGTGCCAA
*
25227 TGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
60 TATGCTGATTCAAGGCCAGCTACATTGGAC-T-----T
* * *
25265 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-----AAAGGTGCCAATGTGCT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAGGTGCCAATATGCT
25325 GATTCAAGGCCAGCTACATTGGACTT
66 GATTCAAGGCCAGCTACATTGGACTT
25351 AAAG
1 AAAG
25355 ATGGAGGTGC
Statistics
Matches: 416, Mismatches: 33, Indels: 40
0.85 0.07 0.08
Matches are distributed among these distances:
86 5 0.01
91 7 0.02
92 315 0.76
93 6 0.01
94 4 0.01
95 33 0.08
96 6 0.01
98 40 0.10
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.26
Consensus pattern (91 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAGGTGCCAATATGCT
GATTCAAGGCCAGCTACATTGGACTT
Found at i:25402 original size:141 final size:141
Alignment explanation
Indices: 24804--25385 Score: 741
Period size: 141 Copynumber: 4.1 Consensus size: 141
24794 AAAAGGATGT
* *
24804 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATACTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT---AAAGGTGCCAATATGCTGATT
* * *
24869 CAAGGCCAGCTATATTGGACTT-A-AAGGTGCTAATGTGCTGATTCAAAGCCAGCTACATTAGAC
63 CAAGGCCAGCTATATTGGACTTAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
24932 TTAAAGAAGAAGGTGC
128 TTAAAG-AG-AGGTGC
* * *
24948 CAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* * * *
25007 GGCCGGCTACATTGGACTTAAAGAAGAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTAGA
66 GGCCAGCTATATTGGACTT----AAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
25072 CTT--A-A-AGGTGC
127 CTTAAAGAGAGGTGC
* * *
25083 CAATGTGCTGATTCAGGGCCAGCTACATTGGACTTAAAGATAAAGGTGTCGATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
* *
25148 GGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACTTTGGA
66 GGCCAGCTATATTGGACTT--A-A-GAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
25213 CTT-AA-A-A-GTGC
127 CTTAAAGAGAGGTGC
25224 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
25289 GGCCAGCTATATTGGACTT-A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
66 GGCCAGCTATATTGGACTTAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
25352 AAGATGGAGGTGC
131 AAGA--GAGGTGC
*
25365 CAATATGCTGATTCAAGGCCA
1 CAATGTGCTGATTCAAGGCCA
25386 ACGATATTGG
Statistics
Matches: 390, Mismatches: 27, Indels: 45
0.84 0.06 0.10
Matches are distributed among these distances:
135 115 0.29
136 3 0.01
137 3 0.01
138 1 0.00
139 3 0.01
140 3 0.01
141 228 0.58
142 3 0.01
143 1 0.00
144 30 0.08
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (141 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTAAGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
AAGAGAGGTGC
Found at i:25470 original size:34 final size:34
Alignment explanation
Indices: 25427--25734 Score: 208
Period size: 34 Copynumber: 9.5 Consensus size: 34
25417 ACCGGGACCA
*
25427 ACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCC
1 ACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCC
* *
25461 ACGGAGTTGTGGGCTT------AAAATG-GTGCC
1 ACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCC
* *
25488 ACGGAGTTGTAGACTTAAAAAGAAAAAGAGTGCC
1 ACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCC
* * *
25522 ACGGAGTGGTGGGCTTTAAAAAGAAAAAG-GATGCC
1 ACGGAGTTGTGGAC-TTAGAAAGAAAAAGAG-TGCC
*
25557 ACAGGA-TTGT-GAGCTTTGAAAG-----G-GTGCC
1 AC-GGAGTTGTGGA-CTTAGAAAGAAAAAGAGTGCC
* * * *
25585 ACGAAGTTGTGGATTTAGAAGGAAAAAAAGTGCC
1 ACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCC
* *
25619 ACGGAGTTGTGGGCTTTAAAAAGGAAAAAGA-TGCC
1 ACGGAGTTGTGGAC-TTAGAAA-GAAAAAGAGTGCC
* * * *
25654 ACAGAGTTGTGGGCTTTG-AA-AAGAA-AGTGCC
1 ACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCC
* *
25685 ACGGAGTCGTGGACTTTGAAAAGAAAAAG-GTGCC
1 ACGGAGTTGTGGACTTAG-AAAGAAAAAGAGTGCC
*
25719 ACGGAGTCGTGGACTT
1 ACGGAGTTGTGGACTT
25735 TGATGCCACT
Statistics
Matches: 217, Mismatches: 31, Indels: 52
0.72 0.10 0.17
Matches are distributed among these distances:
27 21 0.10
28 21 0.10
29 4 0.02
30 1 0.00
31 23 0.11
33 9 0.04
34 82 0.38
35 46 0.21
36 10 0.05
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (34 bp):
ACGGAGTTGTGGACTTAGAAAGAAAAAGAGTGCC
Found at i:25480 original size:27 final size:27
Alignment explanation
Indices: 25456--25507 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
25446 AGGAAAAAGA
* *
25456 GTGCCACGGAGTTGTGGGCTTAAAATG
1 GTGCCACGGAGTTGTAGACTTAAAATG
25483 GTGCCACGGAGTTGTAGACTTAAAA
1 GTGCCACGGAGTTGTAGACTTAAAA
25508 AGAAAAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (27 bp):
GTGCCACGGAGTTGTAGACTTAAAATG
Found at i:25522 original size:61 final size:62
Alignment explanation
Indices: 25427--25542 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 62
25417 ACCGGGACCA
* * * *
25427 ACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAATGGTGCC
1 ACGGAGTTGTAGACTTAAAAAGAAAAAGAGTGCCACGGAGTGGTGGGCTTTAAAATGGTGCC
25488 ACGGAGTTGTAGACTTAAAAAGAAAAAGAGTGCCACGGAGTGGTGGGCTTTAAAA
1 ACGGAGTTGTAGACTTAAAAAGAAAAAGAGTGCCACGGAGTGGTGGGCTTTAAAA
25543 AGAAAAAGGA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
61 44 0.88
62 6 0.12
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.21
Consensus pattern (62 bp):
ACGGAGTTGTAGACTTAAAAAGAAAAAGAGTGCCACGGAGTGGTGGGCTTTAAAATGGTGCC
Found at i:25548 original size:35 final size:35
Alignment explanation
Indices: 25483--25735 Score: 207
Period size: 35 Copynumber: 7.6 Consensus size: 35
25473 GCTTAAAATG
* *
25483 GTGCCACGGAGTTGTAGAC-TTAAAAAGAAAAAGA
1 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGA
*
25517 GTGCCACGGAGTGGTGGGCTTTAAAAAGAAAAAG-
1 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGA
* *
25551 GATGCCACAGGA-TTGTGAGCTTT-----G--AAAGG
1 G-TGCCAC-GGAGTTGTGGGCTTTAAAAAGAAAAAGA
* * * * *
25580 GTGCCACGAAGTTGT-GGATTTAGAAGGAAAAAAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGA
25614 GTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGA
1 GTGCCACGGAGTTGTGGGCTTTAAAAA-GAAAAAGA
* *
25650 -TGCCACAGAGTTGTGGGCTTTGAAAAG---AA-A
1 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGA
* * *
25680 GTGCCACGGAGTCGTGGACTTTGAAAAGAAAAAG-
1 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGA
* *
25714 GTGCCACGGAGTCGTGGACTTT
1 GTGCCACGGAGTTGTGGGCTTT
25736 GATGCCACTG
Statistics
Matches: 180, Mismatches: 20, Indels: 38
0.76 0.08 0.16
Matches are distributed among these distances:
27 6 0.03
28 14 0.08
29 1 0.01
30 2 0.01
31 26 0.14
32 1 0.01
34 59 0.33
35 61 0.34
36 10 0.06
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (35 bp):
GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGA
Found at i:25610 original size:97 final size:98
Alignment explanation
Indices: 25445--25735 Score: 344
Period size: 97 Copynumber: 3.0 Consensus size: 98
25435 GTGGACTTAG
* * * * *
25445 AAGGAAAAAGAGTGCCAC-GGAGTTGTGGGC-TTAAAATGGTGCCACGGAGTTGTAGACTTAAAA
1 AAGGAAAAAGA-TGCCACAGGAGTTGTGGGCTTTGAAAGGGTGCCACGGAGTTGTGGATTTAGAA
*
25508 AGAAAAAGAGTGCCACGGAGTGGTGGGCTTTAAA
65 AGAAAAAGAGTGCCACGGAGTCGTGGGCTTTAAA
* *
25542 AA-GAAAAAGGATGCCACAGGA-TTGTGAGCTTTGAAAGGGTGCCACGAAGTTGTGGATTTAGAA
1 AAGGAAAAA-GATGCCACAGGAGTTGTGGGCTTTGAAAGGGTGCCACGGAGTTGTGGATTTAGAA
* * *
25605 GGAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAA
65 AGAAAAAGAGTGCCACGGAGTCGTGGGCTTTAAA
* *
25639 AAGGAAAAAGATGCCACA-GAGTTGTGGGCTTTGAAAAGAAAGTGCCACGGAGTCGTGGACTTT-
1 AAGGAAAAAGATGCCACAGGAGTTGTGGGCTTTG-AAAG--GGTGCCACGGAGTTGTGGA-TTTA
*
25702 GAAAAGAAAAAG-GTGCCACGGAGTCGTGGACTTT
62 G-AAAGAAAAAGAGTGCCACGGAGTCGTGGGCTTT
25736 GATGCCACTG
Statistics
Matches: 166, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
96 21 0.13
97 87 0.52
98 10 0.06
100 37 0.22
101 11 0.07
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.20
Consensus pattern (98 bp):
AAGGAAAAAGATGCCACAGGAGTTGTGGGCTTTGAAAGGGTGCCACGGAGTTGTGGATTTAGAAA
GAAAAAGAGTGCCACGGAGTCGTGGGCTTTAAA
Found at i:25736 original size:65 final size:65
Alignment explanation
Indices: 25606--25737 Score: 185
Period size: 65 Copynumber: 2.0 Consensus size: 65
25596 GATTTAGAAG
* * * *
25606 GAAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAGATGCCACAGAGTTGTGGGCTTT
1 GAAAAAAAGTGCCACGGAGTCGTGGACTTTAAAAAGGAAAAAGATGCCACAGAGTCGTGGACTTT
* * *
25671 GAAAAGAAAGTGCCACGGAGTCGTGGACTTTGAAAA-GAAAAAGGTGCCACGGAGTCGTGGACTT
1 GAAAA-AAAGTGCCACGGAGTCGTGGACTTTAAAAAGGAAAAAGATGCCACAGAGTCGTGGACTT
25735 T
65 T
25736 GA
1 GA
25738 TGCCACTGAG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
65 32 0.54
66 27 0.46
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.20
Consensus pattern (65 bp):
GAAAAAAAGTGCCACGGAGTCGTGGACTTTAAAAAGGAAAAAGATGCCACAGAGTCGTGGACTTT
Found at i:25748 original size:23 final size:23
Alignment explanation
Indices: 25715--25758 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
25705 AAGAAAAAGG
25715 TGCCACGGAGTCGTGGACTTTGA
1 TGCCACGGAGTCGTGGACTTTGA
*
25738 TGCCACTGAGTCGTGGACTTT
1 TGCCACGGAGTCGTGGACTTT
25759 AAGACAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.32, T:0.30
Consensus pattern (23 bp):
TGCCACGGAGTCGTGGACTTTGA
Found at i:25772 original size:30 final size:29
Alignment explanation
Indices: 25736--25834 Score: 117
Period size: 30 Copynumber: 3.3 Consensus size: 29
25726 CGTGGACTTT
25736 GATGCCACTGAGTCGTGGACTTTAAGACAA
1 GATGCCACTGAGTCGTGGACTTT-AGACAA
* * *
25766 GATGCCACTAAGTCGTGGACTTTGGAAAGA
1 GATGCCACTGAGTCGTGGACTTTAGACA-A
* * *
25796 GATGCCACTGAATTGTGAACTTTGAGACAA
1 GATGCCACTGAGTCGTGGACTTT-AGACAA
25826 GATGCCACT
1 GATGCCACT
25835 AAGAAGGTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
29 3 0.05
30 52 0.90
31 3 0.05
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (29 bp):
GATGCCACTGAGTCGTGGACTTTAGACAA
Found at i:25789 original size:53 final size:55
Alignment explanation
Indices: 25681--25789 Score: 141
Period size: 53 Copynumber: 2.0 Consensus size: 55
25671 GAAAAGAAAG
* *
25681 TGCCACGGAGTCGTGGACTTTGAAAAGAAAAAGGTGCCACGGAGTCGTGGACTTTGA
1 TGCCACGGAGTCGTGGACTTT--AAAGAAAAAGATGCCACGAAGTCGTGGACTTTGA
* * *
25738 TGCCACTGAGTCGTGGACTTT-AAG-ACAAGATGCCACTAAGTCGTGGACTTTG
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGAAGTCGTGGACTTTG
25790 GAAAGAGATG
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
53 24 0.51
54 3 0.06
57 20 0.43
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (55 bp):
TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGAAGTCGTGGACTTTGA
Found at i:26779 original size:1 final size:1
Alignment explanation
Indices: 26775--26818 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
26765 TAAAAAGGGG
* * * *
26775 TTTTTTCTTTTTTTTTGTTTTTTTTTGTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
26819 GTGTTTGGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.02, G:0.07, T:0.91
Consensus pattern (1 bp):
T
Found at i:26790 original size:10 final size:10
Alignment explanation
Indices: 26775--26820 Score: 69
Period size: 10 Copynumber: 4.8 Consensus size: 10
26765 TAAAAAGGGG
*
26775 TTTTTTCTTT
1 TTTTTTGTTT
26785 TTTTTTGTTT
1 TTTTTTGTTT
26795 TTTTTTG--T
1 TTTTTTGTTT
26803 TTTTTTGTTT
1 TTTTTTGTTT
26813 TTTTTTGT
1 TTTTTTGT
26821 GTTTGGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
8 8 0.24
10 25 0.76
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:26798 original size:18 final size:18
Alignment explanation
Indices: 26774--26820 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
26764 GTAAAAAGGG
*
26774 GTTTTTTCTT-TTTTTTT
1 GTTTTTTTTTGTTTTTTT
26791 GTTTTTTTTTGTTTTTTT
1 GTTTTTTTTTGTTTTTTT
26809 GTTTTTTTTTGT
1 GTTTTTTTTTGT
26821 GTTTGGAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (18 bp):
GTTTTTTTTTGTTTTTTT
Found at i:27089 original size:9 final size:9
Alignment explanation
Indices: 27077--27116 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
27067 TTTCTGTGTT
27077 TTTTTTTTG
1 TTTTTTTTG
27086 -TTTTTTTG
1 TTTTTTTTG
*
27094 TTTTGTTTG
1 TTTTTTTTG
*
27103 TTTTTTTTC
1 TTTTTTTTG
27112 TTTTT
1 TTTTT
27117 GACTTTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 8 0.30
9 19 0.70
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:27091 original size:8 final size:8
Alignment explanation
Indices: 27078--27109 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
27068 TTCTGTGTTT
27078 TTTTTTTG
1 TTTTTTTG
27086 TTTTTTTG
1 TTTTTTTG
27094 TTTTGTTTG
1 TTTT-TTTG
27103 TTTTTTT
1 TTTTTTT
27110 TCTTTTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:27097 original size:17 final size:17
Alignment explanation
Indices: 27077--27109 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27067 TTTCTGTGTT
*
27077 TTTTTTTTGTTTTTTTG
1 TTTTGTTTGTTTTTTTG
27094 TTTTGTTTGTTTTTTT
1 TTTTGTTTGTTTTTTT
27110 TCTTTTTGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (17 bp):
TTTTGTTTGTTTTTTTG
Found at i:27123 original size:26 final size:26
Alignment explanation
Indices: 27073--27148 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 26
27063 CTTTTTTCTG
*
27073 TGTTT-TTTTTTTGTTTTTTTG--TTT
1 TGTTTGTTTTTTT-TCTTTTTGACTTT
27097 TGTTTGTTTTTTTTCTTTTTGACTTT
1 TGTTTGTTTTTTTTCTTTTTGACTTT
* * *
27123 TGTTTGTGTGTTTAC-TTTTGACTTT
1 TGTTTGTTTTTTTTCTTTTTGACTTT
27148 T
1 T
27149 CCATCATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
24 12 0.27
25 18 0.40
26 15 0.33
ACGTcount: A:0.04, C:0.05, G:0.14, T:0.76
Consensus pattern (26 bp):
TGTTTGTTTTTTTTCTTTTTGACTTT
Found at i:27147 original size:25 final size:26
Alignment explanation
Indices: 27094--27148 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
27084 TGTTTTTTTG
* * *
27094 TTTTGTTTGTTTTTTTTCTTTTTGAC
1 TTTTGTTTGTGTGTTTACTTTTTGAC
27120 TTTTGTTTGTGTGTTTAC-TTTTGAC
1 TTTTGTTTGTGTGTTTACTTTTTGAC
27145 TTTT
1 TTTT
27149 CCATCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.05, C:0.07, G:0.15, T:0.73
Consensus pattern (26 bp):
TTTTGTTTGTGTGTTTACTTTTTGAC
Found at i:30254 original size:13 final size:13
Alignment explanation
Indices: 30236--30260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30226 CATAAAGTGT
30236 TGTATCGATACAA
1 TGTATCGATACAA
30249 TGTATCGATACA
1 TGTATCGATACA
30261 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:30276 original size:32 final size:33
Alignment explanation
Indices: 30216--30292 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 33
30206 TTCAACGATT
30216 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
30249 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
* *
30281 TATATCGCTACA
1 TGTATCGATACA
30293 AAGCTACTGC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 28 0.68
33 13 0.32
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:37808 original size:52 final size:52
Alignment explanation
Indices: 37730--37877 Score: 242
Period size: 52 Copynumber: 2.8 Consensus size: 52
37720 CGAAATATGA
*
37730 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
37782 AAATTTACCTGTATGTATCGAAACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
37834 AAATTTACCTGCATGTATCGATACATTTGAGTAATGTATCGATA
1 AAATTTACCTGCATGTATCGATACATTTCA-TAGTGTATCGATA
37878 TATTTTCTTA
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
52 76 0.86
53 12 0.14
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTACCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:37935 original size:19 final size:18
Alignment explanation
Indices: 37911--38007 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
37901 AACTGTATAT
37911 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
37930 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
37943 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
37962 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
37975 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
37994 TGTATCGATACAAA
1 TGTATCGATACAAA
38008 TCATTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 3 0.05
19 35 0.53
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:37948 original size:13 final size:13
Alignment explanation
Indices: 37930--37986 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
37920 ACAAAACTTA
37930 TGTATCGATACAT
1 TGTATCGATACAT
37943 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
37961 ATGTATCGATACAT
1 -TGTATCGATACAT
37975 TGTATCGATACA
1 TGTATCGATACA
37987 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:37950 original size:32 final size:32
Alignment explanation
Indices: 37909--38005 Score: 185
Period size: 32 Copynumber: 3.0 Consensus size: 32
37899 GTAACTGTAT
*
37909 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
37941 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
37973 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
38005 A
1 A
38006 AATCATTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:45482 original size:22 final size:23
Alignment explanation
Indices: 45454--45503 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
45444 AATTAAAACA
*
45454 CAAAATTAAACATC-AAAT-ACAT
1 CAAAATT-AACACCAAAATCACAT
45476 CAAAATTAACACCAAAATCACAT
1 CAAAATTAACACCAAAATCACAT
45499 CAAAA
1 CAAAA
45504 GATTACAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 5 0.20
22 11 0.44
23 9 0.36
ACGTcount: A:0.60, C:0.22, G:0.00, T:0.18
Consensus pattern (23 bp):
CAAAATTAACACCAAAATCACAT
Found at i:46726 original size:14 final size:14
Alignment explanation
Indices: 46700--46738 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
46690 AAATTATACC
46700 ATAAAAATT-AATT
1 ATAAAAATTAAATT
46713 A-AAAAGATTAAATT
1 ATAAAA-ATTAAATT
46727 ATAAAAATTAAA
1 ATAAAAATTAAA
46739 AATTATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.17
13 4 0.17
14 11 0.48
15 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
ATAAAAATTAAATT
Found at i:52588 original size:31 final size:31
Alignment explanation
Indices: 52551--52612 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
52541 TTATTTCGAG
*
52551 TTTAAATTATATTGAATTTAAAATTTTTTTA
1 TTTAAATTATATTAAATTTAAAATTTTTTTA
* * *
52582 TTTAAATTTTTTTAAATTTAAATTTTTTTTA
1 TTTAAATTATATTAAATTTAAAATTTTTTTA
52613 GATTCAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (31 bp):
TTTAAATTATATTAAATTTAAAATTTTTTTA
Found at i:52600 original size:16 final size:15
Alignment explanation
Indices: 52551--52610 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
52541 TTATTTCGAG
* *
52551 TTTAAATTATATTGAA
1 TTTAAATT-TTTTTAA
52567 TTTAAAATTTTTTT-A
1 TTT-AAATTTTTTTAA
52582 TTTAAATTTTTTTAAA
1 TTTAAATTTTTTT-AA
52598 TTTAAATTTTTTT
1 TTTAAATTTTTTT
52611 TAGATTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
14 10 0.26
15 4 0.10
16 20 0.51
17 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TTTAAATTTTTTTAA
Found at i:53115 original size:15 final size:14
Alignment explanation
Indices: 53097--53130 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
53087 AATATAAAAA
*
53097 ATATTAATAATTTTT
1 ATATTAAT-ATTTAT
53112 ATATTAATATTTAT
1 ATATTAATATTTAT
53126 ATATT
1 ATATT
53131 TTATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATATTAATATTTAT
Found at i:53591 original size:32 final size:32
Alignment explanation
Indices: 53555--53616 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
53545 ATTATTTCGA
*
53555 GTTTATATTATATTAAGTTAAAAATTTTTTGT
1 GTTTAAATTATATTAAGTTAAAAATTTTTTGT
* * * *
53587 GTTTAAATTTTTTTAAGTTTAAATTTTTTT
1 GTTTAAATTATATTAAGTTAAAAATTTTTT
53617 TAGATTTGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (32 bp):
GTTTAAATTATATTAAGTTAAAAATTTTTTGT
Found at i:53618 original size:17 final size:16
Alignment explanation
Indices: 53567--53616 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
53557 TTATATTATA
* *
53567 TTAAGTTAAAAATTTT
1 TTAAGTTTAAATTTTT
**
53583 TTGTGTTTAAATTTTT
1 TTAAGTTTAAATTTTT
53599 TTAAGTTTAAATTTTT
1 TTAAGTTTAAATTTTT
53615 TT
1 TT
53617 TAGATTTGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (16 bp):
TTAAGTTTAAATTTTT
Found at i:53694 original size:15 final size:16
Alignment explanation
Indices: 53653--53688 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
53643 TTTATTTGAG
* *
53653 TTTTAAAATTTAAGTT
1 TTTTCAAATTTAAATT
53669 TTTTCAAATTTAAATT
1 TTTTCAAATTTAAATT
53685 TTTT
1 TTTT
53689 TAATTTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTTCAAATTTAAATT
Found at i:54603 original size:16 final size:15
Alignment explanation
Indices: 54556--54620 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 15
54546 TTAAGTCAGA
*
54556 TTAAGTTTAAATTATC
1 TTAAGTTTAAATT-TT
* *
54572 TCATGTTT-AATATTT
1 TTAAGTTTAAAT-TTT
54587 TTAATGTTTAAATTTTT
1 TTAA-GTTTAAA-TTTT
*
54604 TTAAATTTAAATTTT
1 TTAAGTTTAAATTTT
54619 TT
1 TT
54621 TTAAATTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
15 12 0.31
16 17 0.44
17 9 0.23
18 1 0.03
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (15 bp):
TTAAGTTTAAATTTT
Found at i:54606 original size:17 final size:17
Alignment explanation
Indices: 54574--54621 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
54564 AAATTATCTC
*
54574 ATGTTT-AATATTTTTA
1 ATGTTTAAATTTTTTTA
54590 ATGTTTAAATTTTTTTA
1 ATGTTTAAATTTTTTTA
*
54607 A-ATTTAAATTTTTTT
1 ATGTTTAAATTTTTTT
54622 TAAATTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 19 0.66
17 10 0.34
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
ATGTTTAAATTTTTTTA
Found at i:54621 original size:16 final size:17
Alignment explanation
Indices: 54593--54628 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
54583 ATTTTTAATG
54593 TTTAAA-TTTTTTTAAA
1 TTTAAATTTTTTTTAAA
54609 TTTAAATTTTTTTTAAA
1 TTTAAATTTTTTTTAAA
54626 TTT
1 TTT
54629 GAATATATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAAATTTTTTTTAAA
Found at i:55163 original size:15 final size:16
Alignment explanation
Indices: 55143--55180 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
55133 ATATTTATAT
55143 ATTAAATTAAAATT-A
1 ATTAAATTAAAATTAA
*
55158 ATTAAA-TAAATTTAA
1 ATTAAATTAAAATTAA
55173 ATTAAATT
1 ATTAAATT
55181 GAATCAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 6 0.30
15 13 0.65
16 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAAATTAAAATTAA
Found at i:55180 original size:20 final size:19
Alignment explanation
Indices: 55145--55192 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
55135 ATTTATATAT
*
55145 TAAATTAAAATTAATTAAA
1 TAAATTTAAATTAATTAAA
*
55164 TAAATTTAAATTAAATTGAA
1 TAAATTTAAATT-AATTAAA
*
55184 TCAATTTAA
1 TAAATTTAA
55193 TATATTCAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAATTTAAATTAATTAAA
Found at i:55720 original size:34 final size:34
Alignment explanation
Indices: 55676--55825 Score: 171
Period size: 34 Copynumber: 4.4 Consensus size: 34
55666 AAAAACCACA
* *
55676 ATTTAATCAACAATGGCAACCTATCAAATCTACC
1 ATTTAATCAACAATGGTAACCTACCAAATCTACC
*
55710 ATTTAGTCAACAATGGTAAGCC-ACCAAATC-ACCC
1 ATTTAATCAACAATGGTAA-CCTACCAAATCTA-CC
* * *
55744 ATTTAATCAATAATGGTAAGCTACCAAAT-TTCTC
1 ATTTAATCAACAATGGTAACCTACCAAATCTAC-C
* *
55778 ATTTAATCAACAATGGTAAGCTACCAAATCTCCC
1 ATTTAATCAACAATGGTAACCTACCAAATCTACC
*
55812 ATTTAGTCAACAAT
1 ATTTAATCAACAAT
55826 TCTCCCACTT
Statistics
Matches: 100, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
33 3 0.03
34 93 0.93
35 4 0.04
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (34 bp):
ATTTAATCAACAATGGTAACCTACCAAATCTACC
Found at i:55788 original size:68 final size:68
Alignment explanation
Indices: 55676--55825 Score: 203
Period size: 68 Copynumber: 2.2 Consensus size: 68
55666 AAAAACCACA
* *
55676 ATTTAATCAACAATGGCAACCTATCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATCA
1 ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGGTAAGCCACCAAATCA
55741 CCC
66 CCC
* * * * *
55744 ATTTAATCAATAATGGTAAGCTACCAAAT-TTCTCATTTAATCAACAATGGTAAGCTACCAAATC
1 ATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAATCAACAATGGTAAGCCACCAAATC
*
55808 TCCC
65 ACCC
*
55812 ATTTAGTCAACAAT
1 ATTTAATCAACAAT
55826 TCTCCCACTT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 2 0.03
68 69 0.97
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (68 bp):
ATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGGTAAGCCACCAAATCA
CCC
Found at i:60278 original size:34 final size:34
Alignment explanation
Indices: 60231--60381 Score: 164
Period size: 34 Copynumber: 4.4 Consensus size: 34
60221 GGTAAAAACC
* *
60231 ACCATTTAATCAACAATGGCAACCTATCAAATCT
1 ACCATTTAATCAACAATGGTAACCTACCAAATCT
*
60265 ACCATTTAGTCAACAATGGTAAGCC-ACCAAATC-
1 ACCATTTAATCAACAATGGTAA-CCTACCAAATCT
* *
60298 ACCAATTTAATCAATAATGGTAAGCTACCAAAT-T
1 ACC-ATTTAATCAACAATGGTAACCTACCAAATCT
* * *
60332 TCTCATTTAATCAACAATGGTAAGCTACTAAATCT
1 AC-CATTTAATCAACAATGGTAACCTACCAAATCT
* *
60367 CCCATTTAGTCAACA
1 ACCATTTAATCAACA
60382 CCCATTGTGA
Statistics
Matches: 100, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
33 4 0.04
34 91 0.91
35 5 0.05
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.28
Consensus pattern (34 bp):
ACCATTTAATCAACAATGGTAACCTACCAAATCT
Found at i:61525 original size:18 final size:18
Alignment explanation
Indices: 61502--61543 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
61492 CACCAAAACG
*
61502 ATATAAAATTAATTTGTT
1 ATATAAAATAAATTTGTT
61520 ATATAAAATAAATTTGTT
1 ATATAAAATAAATTTGTT
*
61538 ACATAA
1 ATATAA
61544 TTGCTTATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (18 bp):
ATATAAAATAAATTTGTT
Found at i:63980 original size:2 final size:2
Alignment explanation
Indices: 63973--64023 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
63963 TGCACTTCAC
* *
63973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TG TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64014 TA TA TA TA TA
1 TA TA TA TA TA
64024 AAAGCGAAGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:65615 original size:2 final size:2
Alignment explanation
Indices: 65608--65638 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
65598 GTTTACTATC
65608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
65639 CATTATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66731 original size:2 final size:2
Alignment explanation
Indices: 66724--66768 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
66714 AGTATGACAA
66724 AT AT AT AT AT 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 AT AT AT AT AT
66766 AT A
1 AT A
66769 ATTGCTCTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67459 original size:7 final size:8
Alignment explanation
Indices: 67438--67468 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
67428 AAAATAACTC
*
67438 TTTTATTA
1 TTTTTTTA
67446 TTTTTTTA
1 TTTTTTTA
67454 TTTTTTTA
1 TTTTTTTA
67462 TTTTTTT
1 TTTTTTT
67469 CAAAAGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTA
Found at i:70492 original size:13 final size:13
Alignment explanation
Indices: 70474--70500 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
70464 ATATTATGCT
70474 TTGTATCGATACA
1 TTGTATCGATACA
70487 TTGTATCGATACA
1 TTGTATCGATACA
70500 T
1 T
70501 GCATAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:70578 original size:20 final size:20
Alignment explanation
Indices: 70553--70623 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
70543 CCACTGTTTA
*
70553 TATCGATACATGGCATATTG
1 TATCGATACATGGCAAATTG
*
70573 TATCGATACATGGCACATTG
1 TATCGATACATGGCAAATTG
**
70593 TATCGATACATGATAAATTG
1 TATCGATACATGGCAAATTG
*
70613 TATCTATACAT
1 TATCGATACAT
70624 TGGTTCAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGCAAATTG
Found at i:72571 original size:31 final size:31
Alignment explanation
Indices: 72536--72600 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
72526 AATCAGAAGT
72536 AAATTCAAATTCCTATACTTTTGAAGAATTA
1 AAATTCAAATTCCTATACTTTTGAAGAATTA
72567 AAATTCAAATTCCTATACTTTTGAAGAATTA
1 AAATTCAAATTCCTATACTTTTGAAGAATTA
72598 AAA
1 AAA
72601 GATGCTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (31 bp):
AAATTCAAATTCCTATACTTTTGAAGAATTA
Found at i:77453 original size:13 final size:13
Alignment explanation
Indices: 77435--77459 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77425 TACAGTGGTC
77435 ATGTATCGATACA
1 ATGTATCGATACA
77448 ATGTATCGATAC
1 ATGTATCGATAC
77460 TGTGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:77477 original size:33 final size:32
Alignment explanation
Indices: 77418--77480 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
77408 ATCTTTGTAA
*
77418 GTATCGATACAGTGGTCATGTATCGATACAAT
1 GTATCGATACAGTGATCATGTATCGATACAAT
* *
77450 GTATCGATACTGTGCATTATGTATCGATACA
1 GTATCGATACAGTG-ATCATGTATCGATACA
77481 TCTGAAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (32 bp):
GTATCGATACAGTGATCATGTATCGATACAAT
Found at i:78926 original size:18 final size:17
Alignment explanation
Indices: 78899--78932 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
78889 TGTGTGGCTT
*
78899 TGTTTTGAGGAACTCGAA
1 TGTTTCGAGGAA-TCGAA
78917 TGTTTCGAGGAATCGA
1 TGTTTCGAGGAATCGA
78933 GCCCTCTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.12, G:0.29, T:0.32
Consensus pattern (17 bp):
TGTTTCGAGGAATCGAA
Found at i:80135 original size:8 final size:8
Alignment explanation
Indices: 80117--80153 Score: 65
Period size: 8 Copynumber: 4.5 Consensus size: 8
80107 ATTTCAACAT
80117 CAAACATCA
1 CAAA-ATCA
80126 CAAAATCA
1 CAAAATCA
80134 CAAAATCA
1 CAAAATCA
80142 CAAAATCA
1 CAAAATCA
80150 CAAA
1 CAAA
80154 GTTTAATCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 24 0.86
9 4 0.14
ACGTcount: A:0.62, C:0.27, G:0.00, T:0.11
Consensus pattern (8 bp):
CAAAATCA
Found at i:86107 original size:21 final size:20
Alignment explanation
Indices: 86078--86131 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
86068 TTACAAGCCA
*
86078 ATGTGTCGATACAAT-TTGGT
1 ATGTATCGATACAATCTT-GT
86098 CATGTATCGATAC-ATCTTGT
1 -ATGTATCGATACAATCTTGT
86118 ATGTATCGATACAA
1 ATGTATCGATACAA
86132 ACAGTTAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATCTTGT
Found at i:86755 original size:13 final size:13
Alignment explanation
Indices: 86737--86763 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
86727 ACAATGTTCT
86737 TTGTATCGATACA
1 TTGTATCGATACA
86750 TTGTATCGATACA
1 TTGTATCGATACA
86763 T
1 T
86764 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:89222 original size:20 final size:19
Alignment explanation
Indices: 89199--89271 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
89189 CACATCCAAA
*
89199 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
89219 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
89238 TGTATCGATACATGCACAAT
1 TGTATCGATACATGTTC-AT
89258 TGTATCGATACATG
1 TGTATCGATACATG
89272 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 17 0.35
20 30 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:95648 original size:38 final size:38
Alignment explanation
Indices: 95604--95679 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
95594 GTAGGTTTCG
95604 ATTTAATAAGTTTTAAATATCTTACATATTTATGAGAT
1 ATTTAATAAGTTTTAAATATCTTACATATTTATGAGAT
* *
95642 ATTTAATAAGTTTTAAATATCTTATATATTTGTGAGAT
1 ATTTAATAAGTTTTAAATATCTTACATATTTATGAGAT
95680 TCATCTTTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (38 bp):
ATTTAATAAGTTTTAAATATCTTACATATTTATGAGAT
Found at i:96792 original size:15 final size:16
Alignment explanation
Indices: 96767--96797 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
96757 TAAAAAATTG
96767 GTAGAAGAGAGAAAAA
1 GTAGAAGAGAGAAAAA
96783 GTAG-AGAGAGAAAAA
1 GTAGAAGAGAGAAAAA
96798 ATTTACCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.06
Consensus pattern (16 bp):
GTAGAAGAGAGAAAAA
Found at i:98962 original size:5 final size:5
Alignment explanation
Indices: 98952--98979 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
98942 CATCATATTG
98952 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
98980 GACTAGTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:105978 original size:75 final size:75
Alignment explanation
Indices: 105855--106003 Score: 298
Period size: 75 Copynumber: 2.0 Consensus size: 75
105845 CTCTATCAGG
105855 GTGCAGAGTATTAAGTAAGGTCTCACTAAAAGAAAATTATAACAAATGAGCACAGAAAAGAGTGA
1 GTGCAGAGTATTAAGTAAGGTCTCACTAAAAGAAAATTATAACAAATGAGCACAGAAAAGAGTGA
105920 ACAATTCTTT
66 ACAATTCTTT
105930 GTGCAGAGTATTAAGTAAGGTCTCACTAAAAGAAAATTATAACAAATGAGCACAGAAAAGAGTGA
1 GTGCAGAGTATTAAGTAAGGTCTCACTAAAAGAAAATTATAACAAATGAGCACAGAAAAGAGTGA
105995 ACAATTCTT
66 ACAATTCTT
106004 AGTATAGATG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (75 bp):
GTGCAGAGTATTAAGTAAGGTCTCACTAAAAGAAAATTATAACAAATGAGCACAGAAAAGAGTGA
ACAATTCTTT
Done.