Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr4
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: 30015117
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1306243 characters in sequence are not A, C, G, or T
File 21 of 85
Found at i:6954164 original size:27 final size:27
Alignment explanation
Indices: 6954127--6954178 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
6954117 GTTTAAAGGC
6954127 TTAGAGTTTAGGGTTTATGGTTTAGTT
1 TTAGAGTTTAGGGTTTATGGTTTAGTT
* *
6954154 TTAGGGTTTAGTGTTTATGGTTTAG
1 TTAGAGTTTAGGGTTTATGGTTTAG
6954179 CTAAAAACAT
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:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (27 bp):
TTAGAGTTTAGGGTTTATGGTTTAGTT
Found at i:6954170 original size:20 final size:20
Alignment explanation
Indices: 6954110--6954163 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
6954100 AAAGTCTATA
* *
6954110 TTTTAGGGTTTAAAGGCTTAG
1 TTTTAGGGTTT-ATGGTTTAG
*
6954131 AGTTTAGGGTTTATGGTTTAG
1 -TTTTAGGGTTTATGGTTTAG
6954152 TTTTAGGGTTTA
1 TTTTAGGGTTTA
6954164 GTGTTTATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.39
21 7 0.25
22 10 0.36
ACGTcount: A:0.20, C:0.02, G:0.30, T:0.48
Consensus pattern (20 bp):
TTTTAGGGTTTATGGTTTAG
Found at i:6954380 original size:43 final size:42
Alignment explanation
Indices: 6954316--6954396 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 42
6954306 AAGGTTAATT
* *
6954316 AAGTTGAGCAATAGTAGCGTTTTTTTGCTCAAAATGCCATGAA
1 AAGTTGAACAATAGTAGCGTTTTTTTG-TCAAAACGCCATGAA
6954359 AAGTTGAACAATAGT-GACGTTTTTTTGTCAAAACGCCA
1 AAGTTGAACAATAGTAG-CGTTTTTTTGTCAAAACGCCA
6954397 CAAATATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
42 11 0.31
43 24 0.69
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (42 bp):
AAGTTGAACAATAGTAGCGTTTTTTTGTCAAAACGCCATGAA
Found at i:6954720 original size:16 final size:16
Alignment explanation
Indices: 6954699--6954734 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
6954689 CCGGCGGTCG
6954699 CTCTGTCACCCGCTTC
1 CTCTGTCACCCGCTTC
*
6954715 CTCTGTCGCCCGCTTC
1 CTCTGTCACCCGCTTC
6954731 CTCT
1 CTCT
6954735 ATTCACGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.50, G:0.14, T:0.33
Consensus pattern (16 bp):
CTCTGTCACCCGCTTC
Found at i:6955605 original size:7 final size:7
Alignment explanation
Indices: 6955593--6955628 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
6955583 CACTCATTAT
6955593 ATTTTAA
1 ATTTTAA
6955600 ATTTTAA
1 ATTTTAA
6955607 ATTTTAA
1 ATTTTAA
6955614 ATTTTAA
1 ATTTTAA
6955621 ATTTTAA
1 ATTTTAA
6955628 A
1 A
6955629 AATAATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTTTAA
Found at i:6955781 original size:9 final size:9
Alignment explanation
Indices: 6955769--6956042 Score: 199
Period size: 9 Copynumber: 30.4 Consensus size: 9
6955759 ATCATATCAA
6955769 AACTTACAT
1 AACTTACAT
6955778 AACTTACAT
1 AACTTACAT
*
6955787 AATTTACAT
1 AACTTACAT
6955796 AAC-T---T
1 AACTTACAT
6955801 AACTTACAT
1 AACTTACAT
*
6955810 AACTCACAT
1 AACTTACAT
*
6955819 AACATACAT
1 AACTTACAT
6955828 AACTTA-AT
1 AACTTACAT
*
6955836 AACTTATAT
1 AACTTACAT
*
6955845 ATATCATATCAT
1 A-A-CTTA-CAT
6955857 AACTTACAT
1 AACTTACAT
*
6955866 AACTCACAT
1 AACTTACAT
*
6955875 AACATACAT
1 AACTTACAT
6955884 AACTTA-AT
1 AACTTACAT
*
6955892 AACTTATAT
1 AACTTACAT
*
6955901 ATATCATATCAT
1 A-A-CTTA-CAT
6955913 AACTTACAT
1 AACTTACAT
*
6955922 AACTCACAT
1 AACTTACAT
*
6955931 AACATACAT
1 AACTTACAT
6955940 AACTTA-AT
1 AACTTACAT
*
6955948 AACTTATAT
1 AACTTACAT
*
6955957 ATATCATATCAT
1 A-A-CTTA-CAT
* *
6955969 AACTTTCAA
1 AACTTACAT
*
6955978 AACTCACAT
1 AACTTACAT
*
6955987 AACTCACAT
1 AACTTACAT
6955996 AACTTACAT
1 AACTTACAT
6956005 AA--TACAT
1 AACTTACAT
* *
6956012 AA-ATATAT
1 AACTTACAT
* *
6956020 ATCATATCAT
1 AACTTA-CAT
6956030 AACTTACAT
1 AACTTACAT
6956039 AACT
1 AACT
6956043 NNNNNNNNNN
Statistics
Matches: 212, Mismatches: 34, Indels: 38
0.75 0.12 0.13
Matches are distributed among these distances:
5 4 0.02
6 1 0.00
7 7 0.03
8 30 0.14
9 132 0.62
10 17 0.08
11 12 0.06
12 9 0.04
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (9 bp):
AACTTACAT
Found at i:6955803 original size:23 final size:23
Alignment explanation
Indices: 6955777--6955821 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
6955767 AAAACTTACA
* *
6955777 TAACTTACATAATTTACATAACT
1 TAACTTACATAACTCACATAACT
6955800 TAACTTACATAACTCACATAAC
1 TAACTTACATAACTCACATAAC
6955822 ATACATAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.33
Consensus pattern (23 bp):
TAACTTACATAACTCACATAACT
Found at i:6955810 original size:32 final size:32
Alignment explanation
Indices: 6955769--6955834 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
6955759 ATCATATCAA
* **
6955769 AACTTACATAACTTACATAATTTACATAACTT
1 AACTTACATAACTCACATAACATACATAACTT
6955801 AACTTACATAACTCACATAACATACATAACTT
1 AACTTACATAACTCACATAACATACATAACTT
6955833 AA
1 AA
6955835 TAACTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (32 bp):
AACTTACATAACTCACATAACATACATAACTT
Found at i:6955869 original size:56 final size:56
Alignment explanation
Indices: 6955800--6956042 Score: 398
Period size: 56 Copynumber: 4.2 Consensus size: 56
6955790 TTACATAACT
6955800 TAACTTACATAACTCACATAACATACATAACTTAATAACTTATATATATCATATCA
1 TAACTTACATAACTCACATAACATACATAACTTAATAACTTATATATATCATATCA
6955856 TAACTTACATAACTCACATAACATACATAACTTAATAACTTATATATATCATATCA
1 TAACTTACATAACTCACATAACATACATAACTTAATAACTTATATATATCATATCA
6955912 TAACTTACATAACTCACATAACATACATAACTTAATAACTTATATATATCATATCA
1 TAACTTACATAACTCACATAACATACATAACTTAATAACTTATATATATCATATCA
* * *
6955968 TAACTTTCAAAACTCACATAAC-TCACATAACTTACATAATACATAAATATATATCATATCA
1 TAACTTACATAACTCACATAACAT-ACATAACTTA-AT-A-AC-T-TATATATATCATATCA
6956029 TAACTTACATAACT
1 TAACTTACATAACT
6956043 NNNNNNNNNN
Statistics
Matches: 176, Mismatches: 5, Indels: 7
0.94 0.03 0.04
Matches are distributed among these distances:
55 1 0.01
56 142 0.81
57 2 0.01
58 1 0.01
59 2 0.01
60 1 0.01
61 27 0.15
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (56 bp):
TAACTTACATAACTCACATAACATACATAACTTAATAACTTATATATATCATATCA
Found at i:6961833 original size:20 final size:21
Alignment explanation
Indices: 6961808--6961847 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6961798 TGACAGGATG
6961808 TTGACTAGA-GTTGACCATCA
1 TTGACTAGATGTTGACCATCA
*
6961828 TTGACTGGATGTTGACCATC
1 TTGACTAGATGTTGACCATC
6961848 CATGTGGCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
TTGACTAGATGTTGACCATCA
Found at i:6963651 original size:21 final size:21
Alignment explanation
Indices: 6963621--6963660 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6963611 GCAGCTATAG
6963621 ATCATAACTTATAGCGGCGTT
1 ATCATAACTTATAGCGGCGTT
* *
6963642 ATCATGACTTTTAGCGGCG
1 ATCATAACTTATAGCGGCG
6963661 CTTTCCCCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
ATCATAACTTATAGCGGCGTT
Found at i:6963740 original size:42 final size:42
Alignment explanation
Indices: 6963671--6963766 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
6963661 CTTTCCCCAC
* * * * *
6963671 AAACGCCGCTATAGATCATGACTTTTAGC-GTCCTTTTTTTAT
1 AAACGCCGCTAAAGAACACGACCTTTAGCGGT-CTTTTTTTAA
*
6963713 AAACGCCGCTAAAGAACACGACCTTTAGCGGTGTTTTTTTAA
1 AAACGCCGCTAAAGAACACGACCTTTAGCGGTCTTTTTTTAA
*
6963755 AAACGCCACTAA
1 AAACGCCGCTAA
6963767 TTTTGACAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACACGACCTTTAGCGGTCTTTTTTTAA
Found at i:6964094 original size:22 final size:21
Alignment explanation
Indices: 6964050--6964121 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
6964040 TTCTACTCTG
* *
6964050 CTCTGCTTCCCTCACTGCAGC
1 CTCTGCTTCCCTCGCTGCTGC
*
6964071 CTCTGCTTCTCCTCGCTGTTGC
1 CTCTGCTTC-CCTCGCTGCTGC
*
6964093 CTCTACTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
*
6964114 ATCTGCTT
1 CTCTGCTT
6964122 TAAGTTGTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 26 0.60
22 17 0.40
ACGTcount: A:0.06, C:0.43, G:0.15, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCTGC
Found at i:6965379 original size:21 final size:21
Alignment explanation
Indices: 6965353--6965396 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
6965343 TGTCCCAAAT
6965353 TGATTGCGTTTTTTGCACGAA
1 TGATTGCGTTTTTTGCACGAA
*
6965374 TGATTGTGTTTTTTGCACGAA
1 TGATTGCGTTTTTTGCACGAA
6965395 TG
1 TG
6965397 TAGCAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.45
Consensus pattern (21 bp):
TGATTGCGTTTTTTGCACGAA
Found at i:6967449 original size:39 final size:39
Alignment explanation
Indices: 6967379--6967456 Score: 122
Period size: 41 Copynumber: 2.0 Consensus size: 39
6967369 ATTTGATGCA
6967379 TTAATATGACATTATTTTTAATTGTTAAATTTTTAAAATTT
1 TTAATATGACATTA-TTTTAATTGTTAAA-TTTTAAAATTT
*
6967420 TTAATATGACATTA-TTTAATTGTTCAATTTTAAAATT
1 TTAATATGACATTATTTTAATTGTTAAATTTTAAAATT
6967457 GAATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 10 0.28
39 12 0.33
41 14 0.39
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (39 bp):
TTAATATGACATTATTTTAATTGTTAAATTTTAAAATTT
Found at i:6967773 original size:7 final size:7
Alignment explanation
Indices: 6967758--6967843 Score: 127
Period size: 7 Copynumber: 12.0 Consensus size: 7
6967748 AGATCATAGG
6967758 CCCTAAA
1 CCCTAAA
*
6967765 CCTTAAA
1 CCCTAAA
6967772 CCCTAAA
1 CCCTAAA
*
6967779 CCTATAAAA
1 CC-CT-AAA
6967788 CCCTAAA
1 CCCTAAA
6967795 CCCTAAA
1 CCCTAAA
6967802 CCCTAAA
1 CCCTAAA
6967809 CCCTAAA
1 CCCTAAA
6967816 CCCTAAA
1 CCCTAAA
6967823 CCCTAAA
1 CCCTAAA
*
6967830 CCCTAAG
1 CCCTAAA
6967837 CCCTAAA
1 CCCTAAA
6967844 TTAACTACGA
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
7 64 0.90
8 2 0.03
9 5 0.07
ACGTcount: A:0.43, C:0.40, G:0.01, T:0.16
Consensus pattern (7 bp):
CCCTAAA
Found at i:6968037 original size:14 final size:13
Alignment explanation
Indices: 6968027--6968077 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
6968017 ATAAACCTTA
6968027 AACCCTTAACCCTT
1 AACCCTTAACCC-T
*
6968041 AACCCCTAACACCT
1 AACCCTTAAC-CCT
*
6968055 AAACCCTAAACCCT
1 -AACCCTTAACCCT
6968069 AACCCTTAA
1 AACCCTTAA
6968078 ATCATAATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 8 0.26
14 13 0.42
15 10 0.32
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (13 bp):
AACCCTTAACCCT
Found at i:6968078 original size:14 final size:14
Alignment explanation
Indices: 6968022--6968068 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
6968012 TAACTATAAA
6968022 CCTTAAACCCTTAAC
1 CCTTAAACCC-TAAC
*
6968037 CCTTAACCCCTAAC
1 CCTTAAACCCTAAC
6968051 ACC-TAAACCCTAAAC
1 -CCTTAAACCCT-AAC
6968066 CCT
1 CCT
6968069 AACCCTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (14 bp):
CCTTAAACCCTAAC
Found at i:6968155 original size:14 final size:14
Alignment explanation
Indices: 6968136--6968162 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6968126 AGAACATATA
6968136 TAAACTCTAAACCT
1 TAAACTCTAAACCT
6968150 TAAACTCTAAACC
1 TAAACTCTAAACC
6968163 CTGAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACTCTAAACCT
Found at i:6968218 original size:28 final size:28
Alignment explanation
Indices: 6968186--6968245 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
6968176 TATATATTTA
* ** *
6968186 TAAACTATAAACTCTAAACCCCAACCCT
1 TAAACAATAAACAATAAACCACAACCCT
*
6968214 TAAACAATAAACAATAAACCATAACCCT
1 TAAACAATAAACAATAAACCACAACCCT
6968242 TAAA
1 TAAA
6968246 TCCATAATCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (28 bp):
TAAACAATAAACAATAAACCACAACCCT
Found at i:6968449 original size:73 final size:73
Alignment explanation
Indices: 6968352--6968513 Score: 209
Period size: 76 Copynumber: 2.2 Consensus size: 73
6968342 TGCTTGACTA
* * **
6968352 TTGCGGCACTTTTTAAAAAACGCCACCAATGTCTCTAAAGCT-AAAGAAAAACGACATCGTTTGC
1 TTGCGGC-GTTTTTAAAAAACGCCACCAATGTCTCTAAAGCTAAAAAAAAAAAAACATCGTTTGC
6968416 TTAAAACTT
65 TTAAAACTT
* * *
6968425 TTGCGGCGTTTTTCAAAAAGCGCCACCAGTGTCTCTAAAGCTAAAAAAAAAAAAAAACGTCGTTT
1 TTGCGGCGTTTTT-AAAAAACGCCACCAATGTCTCTAAAGCT--AAAAAAAAAAAAACATCGTTT
6968490 GCTTAAAACTT
63 GCTTAAAACTT
*
6968501 TTGCGGCGCTTTT
1 TTGCGGCGTTTTT
6968514 GTGAAATCGC
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
72 5 0.06
73 33 0.43
76 39 0.51
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (73 bp):
TTGCGGCGTTTTTAAAAAACGCCACCAATGTCTCTAAAGCTAAAAAAAAAAAAACATCGTTTGCT
TAAAACTT
Found at i:6968566 original size:31 final size:31
Alignment explanation
Indices: 6968528--6968589 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
6968518 AATCGCCGCT
*
6968528 AATGCTTGACTTCTGCGGTGTTTTTCAAAGA
1 AATGCTTGACTTCTGCGATGTTTTTCAAAGA
6968559 AATGCTTGACTTCTGCGATGTTTTTCAAAGA
1 AATGCTTGACTTCTGCGATGTTTTTCAAAGA
6968590 GCGCCACTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (31 bp):
AATGCTTGACTTCTGCGATGTTTTTCAAAGA
Found at i:6968751 original size:24 final size:24
Alignment explanation
Indices: 6968724--6968776 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
6968714 GTCTCTAAAT
6968724 CTTAAGAA-AAAATGA-AGACGTTTG
1 CTTAA-AATAAAATGACA-ACGTTTG
*
6968748 CTTAAAATAAAATGACATCGTTTG
1 CTTAAAATAAAATGACAACGTTTG
6968772 CTTAA
1 CTTAA
6968777 CACTTTTGCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 2 0.08
24 23 0.88
25 1 0.04
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (24 bp):
CTTAAAATAAAATGACAACGTTTG
Found at i:6969091 original size:114 final size:113
Alignment explanation
Indices: 6968772--6969101 Score: 430
Period size: 115 Copynumber: 2.9 Consensus size: 113
6968762 ACATCGTTTG
* * *
6968772 CTTAACACTTTTGCGGCGCTTT-TGATAAAGCGCCGCTAATTCTTGAATATTTTGG-CGTTTCTA
1 CTTAACTCTTTTGCGGCGCTTTGTGAT--AGCGCCGCTAATGCTTG--TCTTTTGGACGTTTCTA
* *
6968835 GAAAAGCGCCACCAATGTCGCTAAAGCTCAACAAGAAAACGGCGTCGTTTGA
62 GAAAAGCGCCACCAATGTCGCTAAAGCTCAACAAAAAAACGGCGTCGTTTAA
* * *
6968887 CTTAACTTTTTTTGCGGCGCTTTGTGATAGTGCCGCTAATGCTTGTCTTTTGTAGCGTTTCTAGA
1 CTTAAC-TCTTTTGCGGCGCTTTGTGATAGCGCCGCTAATGCTTGTCTTTTGGA-CGTTTCTAGA
*
6968952 AAAGCACCACCAATGTCGCTAAAGCTCAACAAAAAAACGGCGTCGTTTAA
64 AAAGCGCCACCAATGTCGCTAAAGCTCAACAAAAAAACGGCGTCGTTTAA
* **
6969002 CTTAACTCTTTTGCGGCGCTTTGTGATAGCGCCGCTAATGCTTGTCTTTTGCGACGTTTTTTTAA
1 CTTAACTCTTTTGCGGCGCTTTGTGATAGCGCCGCTAATGCTTGTCTTTTG-GACGTTTCTAGAA
* * ** *
6969067 AAGCGCCACTAATATCTTTGAAGCTCAACAAAAAA
65 AAGCGCCACCAATGTCGCTAAAGCTCAACAAAAAA
6969102 TGACATTGTT
Statistics
Matches: 189, Mismatches: 21, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
113 6 0.03
114 80 0.42
115 85 0.45
116 14 0.07
117 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (113 bp):
CTTAACTCTTTTGCGGCGCTTTGTGATAGCGCCGCTAATGCTTGTCTTTTGGACGTTTCTAGAAA
AGCGCCACCAATGTCGCTAAAGCTCAACAAAAAAACGGCGTCGTTTAA
Found at i:6978272 original size:31 final size:31
Alignment explanation
Indices: 6978237--6978298 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
6978227 ACTCCTTTGG
6978237 CCCTCAACTTGCACACATTTACTGTTGCATA
1 CCCTCAACTTGCACACATTTACTGTTGCATA
6978268 CCCTCAACTTGCACACATTTACTGTTGCATA
1 CCCTCAACTTGCACACATTTACTGTTGCATA
6978299 TTCTTTCTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.32
Consensus pattern (31 bp):
CCCTCAACTTGCACACATTTACTGTTGCATA
Found at i:6979722 original size:7 final size:7
Alignment explanation
Indices: 6979712--6979738 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
6979702 AATTTGGTAT
6979712 TTTTAAA
1 TTTTAAA
6979719 TTTTAAA
1 TTTTAAA
6979726 TTTTAAA
1 TTTTAAA
6979733 TTTTAA
1 TTTTAA
6979739 GATTGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:7014979 original size:14 final size:12
Alignment explanation
Indices: 7014950--7015114 Score: 91
Period size: 12 Copynumber: 13.0 Consensus size: 12
7014940 GTTCATTTAA
*
7014950 TCATCAAGTCTT
1 TCATCAAGTTTT
7014962 TCATCAAGTGTTTT
1 TCATCAA--GTTTT
7014976 TCATCAAGTTTT
1 TCATCAAGTTTT
* *
7014988 TAATCAAGTCTT
1 TCATCAAGTTTT
**
7015000 TCATCAAGTCAT
1 TCATCAAGTTTT
*
7015012 TAATCAAGTTTT
1 TCATCAAGTTTT
*
7015024 TAATTACCAAGTTTTTT
1 TCA-T--CAAG--TTTT
* *
7015041 TTATTAAGTTTT
1 TCATCAAGTTTT
*
7015053 GCATCAAGTTCTT
1 TCATCAAGTT-TT
* *
7015066 T--TTAAGCTTT
1 TCATCAAGTTTT
7015076 TCATCAAGTCTTT
1 TCATCAAGT-TTT
*
7015089 TTATCAAGTGTTTT
1 TCATCAA--GTTTT
*
7015103 TAATCAAGTTTT
1 TCATCAAGTTTT
7015115 CAATCAAGCT
Statistics
Matches: 120, Mismatches: 20, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
10 3 0.03
11 5 0.04
12 64 0.53
13 12 0.10
14 23 0.19
15 6 0.05
16 1 0.01
17 6 0.05
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.49
Consensus pattern (12 bp):
TCATCAAGTTTT
Found at i:7015067 original size:26 final size:25
Alignment explanation
Indices: 7015031--7015097 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 25
7015021 TTTTAATTAC
*
7015031 CAAGTTTTTTTTATTAAGTTTTGCAT
1 CAAGTTCTTTTTATTAAGTTTT-CAT
7015057 CAAGTTC--TTT-TTAAGCTTTTCAT
1 CAAGTTCTTTTTATTAAG-TTTTCAT
*
7015080 CAAG-TCTTTTTATCAAGT
1 CAAGTTCTTTTTATTAAGT
7015098 GTTTTTAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
22 2 0.06
23 12 0.34
24 11 0.31
25 4 0.11
26 6 0.17
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.52
Consensus pattern (25 bp):
CAAGTTCTTTTTATTAAGTTTTCAT
Found at i:7015090 original size:22 final size:23
Alignment explanation
Indices: 7015044--7015091 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
7015034 GTTTTTTTTA
7015044 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTGCATCAAGTTCTTT
7015067 TTAAGCTTTT-CATCAAG-TCTTT
1 TTAAG-TTTTGCATCAAGTTCTTT
7015089 TTA
1 TTA
7015092 TCAAGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.33
23 12 0.50
24 4 0.17
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (23 bp):
TTAAGTTTTGCATCAAGTTCTTT
Found at i:7017635 original size:11 final size:13
Alignment explanation
Indices: 7017619--7017650 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
7017609 ATTTCACGGA
7017619 AAAATTTCA-T-G
1 AAAATTTCATTCG
7017630 AAAATTTCATTCG
1 AAAATTTCATTCG
7017643 AAAATTTC
1 AAAATTTC
7017651 GAGGTTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 1 0.05
13 9 0.47
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (13 bp):
AAAATTTCATTCG
Found at i:7018416 original size:33 final size:33
Alignment explanation
Indices: 7018378--7018496 Score: 114
Period size: 33 Copynumber: 3.4 Consensus size: 33
7018368 TCCCCTAAGG
*
7018378 GGTTGCTAAGTGCTGATTCCCCAAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
7018411 GGTTGCTAAGTGCTGATACCTCCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
7018453 GGTTGC-AAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
7018485 GGTTGCTAAGTG
1 GGTTGCTAAGTG
7018497 TTGAATCCAT
Statistics
Matches: 69, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
32 7 0.10
33 24 0.35
34 5 0.07
35 2 0.03
36 2 0.03
38 2 0.03
39 2 0.03
40 6 0.09
41 12 0.17
42 7 0.10
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:7018420 original size:102 final size:103
Alignment explanation
Indices: 7018244--7018473 Score: 315
Period size: 102 Copynumber: 2.3 Consensus size: 103
7018234 ATTGAATATA
* * ****
7018244 AAGGGGGTTGCTAAGTACTGATT-CCCTCAAGGGGTTGCTAAGTGCTGATTTCCTGGTTCATTGG
1 AAGGGGGTTGCTAAGTGCTGATTCCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
* *
7018308 TGGTTGCTAAGTGCTGAGT-CCACCGTATTTTAAATTTG
66 TGGTTGCTAAGTGCTGA-TACCACCGTATCTTAAATGTG
* *
7018346 AAGGGGGTTGCTGAGTGCTAATTCCCCT-AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
1 AAGGGGGTTGCTAAGTGCTGATTCCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
*
7018410 TGGTTGCTAAGTGCTGATACCTCCGTATCTTAAATGTG
66 TGGTTGCTAAGTGCTGATACCACCGTATCTTAAATGTG
*
7018448 AAAGGGGTTGC-AAGTGCTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
7018474 GAATCATTGG
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
101 14 0.12
102 94 0.84
103 4 0.04
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (103 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
TGGTTGCTAAGTGCTGATACCACCGTATCTTAAATGTG
Found at i:7023261 original size:33 final size:33
Alignment explanation
Indices: 7023224--7023370 Score: 108
Period size: 33 Copynumber: 4.4 Consensus size: 33
7023214 TCCCCCAAGG
7023224 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
7023257 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
* *
7023299 GGTTGCTGAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
7023326 GGTTGCTAAGTGTTGATTCCCCGAATCATTGCT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
7023359 GGTTGCTAAGTG
1 GGTTGCTAAGTG
7023371 TTGAATCCAC
Statistics
Matches: 90, Mismatches: 9, Indels: 30
0.70 0.07 0.23
Matches are distributed among these distances:
27 20 0.22
28 2 0.02
31 2 0.02
32 1 0.01
33 33 0.37
34 3 0.03
35 1 0.01
37 2 0.02
38 2 0.02
39 1 0.01
41 2 0.02
42 21 0.23
ACGTcount: A:0.18, C:0.19, G:0.29, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:7023368 original size:102 final size:102
Alignment explanation
Indices: 7023192--7023381 Score: 317
Period size: 102 Copynumber: 1.9 Consensus size: 102
7023182 ATTGAATATA
* * *
7023192 AAGGGGGTTGCTAAGTGTTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGCT
*
7023257 GGTTGCTAAGTGCTGATTCCACCGTATTTTAAATGTG
66 GGTTGCTAAGTGCTGAATCCACCGTATTTTAAATGTG
* *
7023294 AAGGGGGTTGCTGAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCGAATCATTGCT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGCT
*
7023359 GGTTGCTAAGTGTTGAATCCACC
66 GGTTGCTAAGTGCTGAATCCACC
7023382 AATAACGGAT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 81 1.00
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.32
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGCT
GGTTGCTAAGTGCTGAATCCACCGTATTTTAAATGTG
Found at i:7030239 original size:50 final size:50
Alignment explanation
Indices: 7030120--7030368 Score: 282
Period size: 50 Copynumber: 4.8 Consensus size: 50
7030110 GATAATAACA
* *** *
7030120 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTCTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-GGGGACCTCTCATCTCGG
* * *
7030171 TGCCCATGCCATGCCCCAGACATGGTCTTACAGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
7030221 TGCCAATGCCATCTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
7030271 TGCCCATGCCATGTCCCAGACATGGTCTTAAAGGGGACACCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGG--ACCTC-TCATCTC--GG
* * *
7030326 ATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
7030369 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
50 89 0.53
51 29 0.17
52 5 0.03
53 6 0.04
54 4 0.02
55 2 0.01
56 32 0.19
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:7030306 original size:100 final size:104
Alignment explanation
Indices: 7030119--7030368 Score: 328
Period size: 100 Copynumber: 2.4 Consensus size: 104
7030109 TGATAATAAC
* *** *
7030119 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTCTCATGTCGGTGCCCATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATCTCGGTGCCCATGCCATG
* *
7030184 CCCCAGACATGGTCTTACAGGGG-ACCTC-TCATCT-TGG
65 CCCCAGACATGGTCTTAAAGGGGAACCTCATCATCTAAGG
* * *
7030221 -TGCCAATGCCATCTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGC
*
7030285 CCCAGACATGGTCTTAAAGGGGACACCTCATGATCTCAAGG
66 CCCAGACATGGTCTTAAAGGGGA-ACCTCATCATCT-AAGG
* *
7030326 ATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
7030369 TTACCCAAAT
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
100 46 0.36
101 31 0.24
102 5 0.04
103 5 0.04
105 2 0.02
106 39 0.30
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGC
CCCAGACATGGTCTTAAAGGGGAACCTCATCATCTAAGG
Found at i:7030740 original size:30 final size:30
Alignment explanation
Indices: 7030706--7030763 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
7030696 CCTTGACTCT
7030706 AACTTTTACAAAATTACGA-TTTTGCCCCTA
1 AACTTTTACAAAATTAC-ATTTTTGCCCCTA
* *
7030736 AACTTTTGCATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACATTTTTGCCCC
7030764 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACATTTTTGCCCCTA
Found at i:7031383 original size:18 final size:18
Alignment explanation
Indices: 7031360--7031396 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
7031350 TTCATAACAA
*
7031360 TTGGACACCTCTAGCATG
1 TTGGACACCTCTAACATG
7031378 TTGGACACCTCTAACATG
1 TTGGACACCTCTAACATG
7031396 T
1 T
7031397 AGAACTCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (18 bp):
TTGGACACCTCTAACATG
Found at i:7037837 original size:50 final size:51
Alignment explanation
Indices: 7037722--7037960 Score: 268
Period size: 50 Copynumber: 4.6 Consensus size: 51
7037712 GATAATAACA
* * * ***
7037722 TGCCAAAGCCATGTCCCAGACATGGTCTTCCATGGGGTGTTCTCATGC-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGGACCTCTCAT-CTCGG
*
7037773 TGCCCATGCCATGTCCCAGACATGGTCTTACA-GGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGGACCTCTCATCTCGG
* * *
7037823 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGGACCTCTCATCTCGG
* * * * *
7037873 TGCCCATGCCATGTCCCAGGCATGGTCTTACAGGGGGTCTCGCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGGAC-CTC-TCATCTC--GG
7037928 ATGCCAATGCCATGTCCCAGACATGGTCTTACA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACA
7037961 TGAGATCTCT
Statistics
Matches: 161, Mismatches: 20, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 88 0.55
51 33 0.20
52 2 0.01
53 6 0.04
55 1 0.01
56 30 0.19
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.24
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGGACCTCTCATCTCGG
Found at i:7037900 original size:100 final size:105
Alignment explanation
Indices: 7037721--7037962 Score: 316
Period size: 100 Copynumber: 2.3 Consensus size: 105
7037711 TGATAATAAC
* *** *
7037721 ATGCCAAAGCCATGTCCCAGACATGGTCTTCCATGGGGTGTTCTCATGCCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATGCCAGTGCCCATGCCATG
*
7037786 TCCCAGACATGGTCTTACA-GGGGAC-CTC-TCATCTC-GG
65 TCCCAGACATGGTCTTACAGGGGGACTCGCATCATCTCAGG
*
7037823 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-CTCAGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGC-CAGTGCCCATGCCATG
* * *
7037886 TCCCAGGCATGGTCTTACAGGGGGTCTCGCATGATCTCAAGG
65 TCCCAGACATGGTCTTACAGGGGGACTCGCATCATCTC-AGG
*
7037928 ATGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATG
7037963 AGATCTCTTT
Statistics
Matches: 122, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
99 1 0.01
100 42 0.34
101 36 0.30
102 2 0.02
103 6 0.05
105 2 0.02
106 33 0.27
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.24
Consensus pattern (105 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGCCAGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGGACTCGCATCATCTCAGG
Found at i:7038329 original size:30 final size:30
Alignment explanation
Indices: 7038295--7038352 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
7038285 CCTCGACTCT
7038295 AACTTTGACAAAATTACAATTTTGCCCCTA
1 AACTTTGACAAAATTACAATTTTGCCCCTA
* * *
7038325 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTGACAAAATTACAATTTTGCCCC
7038353 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTGCCCCTA
Found at i:7046736 original size:14 final size:12
Alignment explanation
Indices: 7046707--7046870 Score: 107
Period size: 12 Copynumber: 13.0 Consensus size: 12
7046697 GTTCATTTAA
*
7046707 TCATCAAGTCTT
1 TCATCAAGTTTT
7046719 TCATCAAGTGTTTT
1 TCATCAA--GTTTT
7046733 TCATCAAGTTTT
1 TCATCAAGTTTT
* *
7046745 TAATCAAGTCTT
1 TCATCAAGTTTT
**
7046757 TCATCAAGTCAT
1 TCATCAAGTTTT
*
7046769 TAATCAAGTTTT
1 TCATCAAGTTTT
*
7046781 TAATTACCAAGTTTTT
1 TCA-T--CAAG-TTTT
* *
7046797 TTATTAAGTTTT
1 TCATCAAGTTTT
*
7046809 GCATCAAGTTCTT
1 TCATCAAGTT-TT
* *
7046822 T--TTAAGCTTT
1 TCATCAAGTTTT
7046832 TCATCAAGTCTTT
1 TCATCAAGT-TTT
7046845 TCATTCAAGTGTTT
1 TCA-TCAAGT-TTT
*
7046859 TAATCAAGTTTT
1 TCATCAAGTTTT
7046871 CAAACAAGCT
Statistics
Matches: 121, Mismatches: 20, Indels: 22
0.74 0.12 0.13
Matches are distributed among these distances:
10 3 0.02
11 5 0.04
12 62 0.51
13 18 0.15
14 22 0.18
15 5 0.04
16 6 0.05
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (12 bp):
TCATCAAGTTTT
Found at i:7046836 original size:23 final size:22
Alignment explanation
Indices: 7046800--7046845 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
7046790 AGTTTTTTTA
7046800 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTGCATCAAG-TCTTT
7046823 TTAAGCTTTT-CATCAAGTCTTT
1 TTAAG-TTTTGCATCAAGTCTTT
7046845 T
1 T
7046846 CATTCAAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 12 0.55
24 4 0.18
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (22 bp):
TTAAGTTTTGCATCAAGTCTTT
Found at i:7051202 original size:40 final size:40
Alignment explanation
Indices: 7051145--7051239 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
7051135 CATTTGGATA
* * * *
7051145 GAAAACACCGCTGAAGATCGAGCATTAGCGGTGTTTTACT
1 GAAAACGCCGCTAAAGATCGAGCATTAACGGCGTTTTACT
* * *
7051185 TAAAACGCCGCTAAAGATCTAGCATTAACGGCGTTTTCCT
1 GAAAACGCCGCTAAAGATCGAGCATTAACGGCGTTTTACT
*
7051225 GAAAGCGCCGCTAAA
1 GAAAACGCCGCTAAA
7051240 AATAAGAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (40 bp):
GAAAACGCCGCTAAAGATCGAGCATTAACGGCGTTTTACT
Found at i:7051447 original size:41 final size:41
Alignment explanation
Indices: 7051320--7051457 Score: 168
Period size: 41 Copynumber: 3.4 Consensus size: 41
7051310 CTTTCGTTGA
* *
7051320 TTTAGCGGCGTTTTTGAAGAAGCGTCGCTAAAGCTTAGAGC
1 TTTAGCGGCATTTTTGAAGAAGCGTCGCTAATGCTTAGAGC
* * *
7051361 TTTAGCGGCATTTTTGAATAAGCGTCGCTAATGCTCAGAGG
1 TTTAGCGGCATTTTTGAAGAAGCGTCGCTAATGCTTAGAGC
* * ** * **
7051402 TTTAGTGGCATTTCTGAAGAAGCGTCGCTAATTATTGGATT
1 TTTAGCGGCATTTTTGAAGAAGCGTCGCTAATGCTTAGAGC
7051443 TTTAGCGGCATTTTT
1 TTTAGCGGCATTTTT
7051458 CCAAAAGTGC
Statistics
Matches: 81, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 81 1.00
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (41 bp):
TTTAGCGGCATTTTTGAAGAAGCGTCGCTAATGCTTAGAGC
Found at i:7051472 original size:82 final size:80
Alignment explanation
Indices: 7051320--7051497 Score: 196
Period size: 82 Copynumber: 2.2 Consensus size: 80
7051310 CTTTCGTTGA
* * * *
7051320 TTTAGCGGCGTTTTTGAAGAAGCGTCGCTAAAGCTTAGAGCTTTAGCGGCATTTTTGAATAAGCG
1 TTTAGCGGCATTTCTGAAGAAGCGTCGCTAAAGATTAGAGCTTTAGCGGCATTTTTCAATAAGCG
*
7051385 TCGCTAATGCTCAGAGG
66 CCGCTAATG-TCAG-GG
* ** * ** *
7051402 TTTAGTGGCATTTCTGAAGAAGCGTCGCTAATTATTGGATTTTTAGCGGCATTTTTCCAA-AAGT
1 TTTAGCGGCATTTCTGAAGAAGCGTCGCTAAAGATTAGAGCTTTAGCGGCATTTTT-CAATAAGC
7051466 GCCGCTAATGTCAGGG
65 GCCGCTAATGTCAGGG
*
7051482 TTTTAGCGGCGTTTCT
1 -TTTAGCGGCATTTCT
7051498 TTAAGAGCGC
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
80 2 0.03
81 17 0.21
82 59 0.74
83 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (80 bp):
TTTAGCGGCATTTCTGAAGAAGCGTCGCTAAAGATTAGAGCTTTAGCGGCATTTTTCAATAAGCG
CCGCTAATGTCAGGG
Found at i:7055070 original size:13 final size:13
Alignment explanation
Indices: 7055048--7055144 Score: 81
Period size: 13 Copynumber: 7.4 Consensus size: 13
7055038 AAGAAAAAGT
*
7055048 TTACTAAAATATA
1 TTACTCAAATATA
7055061 TTACTCAAATATA
1 TTACTCAAATATA
* *
7055074 TTACTTAAATACA
1 TTACTCAAATATA
7055087 TTACTTACTAAA-AT-
1 TTAC-T-C-AAATATA
* * *
7055101 TTACTTAATTACA
1 TTACTCAAATATA
*
7055114 TTACTTAAATATA
1 TTACTCAAATATA
*
7055127 TTACTCAAATACA
1 TTACTCAAATATA
7055140 TTACT
1 TTACT
7055145 TACTAAAATT
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
11 2 0.03
12 1 0.01
13 55 0.82
14 5 0.07
15 1 0.01
16 3 0.04
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
TTACTCAAATATA
Found at i:7055104 original size:27 final size:27
Alignment explanation
Indices: 7055074--7055156 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
7055064 CTCAAATATA
7055074 TTACTTAAATACATTACTTACTAAAAT
1 TTACTTAAATACATTACTTACTAAAAT
* *
7055101 TTACTTAATTACATTACTTA--AATAT
1 TTACTTAAATACATTACTTACTAAAAT
*
7055126 ATTACTCAAATACATTACTTACTAAAAT
1 -TTACTTAAATACATTACTTACTAAAAT
7055154 TTA
1 TTA
7055157 AGTATATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
25 4 0.08
26 18 0.38
27 22 0.46
28 4 0.08
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.42
Consensus pattern (27 bp):
TTACTTAAATACATTACTTACTAAAAT
Found at i:7055127 original size:53 final size:55
Alignment explanation
Indices: 7055042--7055271 Score: 202
Period size: 53 Copynumber: 4.1 Consensus size: 55
7055032 TTCAAAAAGA
* * * *
7055042 AAAAGTTTACTAAAATATATTACTCAAATATATTACTTAAATACATTAC-TTAC-T
1 AAAA-TTTACTTAATTACATTACTTAAATATATTACTTAAATACATTACATTACTT
*
7055096 AAAATTTACTTAATTACATTACTTAAATATATTACTCAAATACATTAC-TTAC-T
1 AAAATTTACTTAATTACATTACTTAAATATATTACTTAAATACATTACATTACTT
* * * *
7055149 AAAATTTAAGTATATATTACATTACTTACAT-TACTTACTAAAATATATTACATTACTT
1 AAAATTT-ACT-TA-ATTACATTACTTAAATATA-TTACTTAAATACATTACATTACTT
* * * * * * *
7055207 AAATATTTTACTTACTAAAATTTA-TTTAATACATTACTTAAATATATTACATAACTT
1 AAA-A-TTTACTTAATTACA-TTACTTAAATATATTACTTAAATACATTACATTACTT
7055264 AAAATTTA
1 AAAATTTA
7055272 TATATATATA
Statistics
Matches: 148, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
53 51 0.34
54 6 0.04
55 8 0.05
56 31 0.21
57 36 0.24
58 10 0.07
59 3 0.02
60 3 0.02
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (55 bp):
AAAATTTACTTAATTACATTACTTAAATATATTACTTAAATACATTACATTACTT
Found at i:7055204 original size:18 final size:18
Alignment explanation
Indices: 7055178--7055268 Score: 78
Period size: 18 Copynumber: 4.9 Consensus size: 18
7055168 CATTACTTAC
7055178 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
*
7055195 ATTACATTACTTAAATAT
1 ATTACATTACTAAAATAT
*
7055213 TTTAC-TTACTAAAATTTATTT
1 ATTACATTACTAAAA--TA--T
* *
7055234 AATACATTACTTAAATAT
1 ATTACATTACTAAAATAT
*
7055252 ATTACATAACTTAAAAT
1 ATTACATTAC-TAAAAT
7055269 TTATATATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
17 13 0.22
18 24 0.41
19 7 0.12
20 2 0.03
21 4 0.07
22 8 0.14
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:7055221 original size:22 final size:22
Alignment explanation
Indices: 7055170--7055221 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
7055160 ATATATTACA
7055170 TTACTTACATTACTTACTAAAAT
1 TTACTTACATTACTTAC-AAAAT
* *
7055193 ATA-TTACATTACTTA-AATATT
1 TTACTTACATTACTTACAA-AAT
7055214 TTACTTAC
1 TTACTTAC
7055222 TAAAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 2 0.08
21 4 0.17
22 16 0.67
23 2 0.08
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (22 bp):
TTACTTACATTACTTACAAAAT
Found at i:7055227 original size:17 final size:17
Alignment explanation
Indices: 7055178--7055232 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
7055168 CATTACTTAC
7055178 ATTACTTACTAAAATAT
1 ATTACTTACTAAAATAT
*
7055195 ATTACATTACTTAAATAT
1 ATTAC-TTACTAAAATAT
* *
7055213 TTTACTTACTAAAATTT
1 ATTACTTACTAAAATAT
7055230 ATT
1 ATT
7055233 TAATACATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 17 0.53
18 15 0.47
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTACTTACTAAAATAT
Found at i:7055240 original size:39 final size:38
Alignment explanation
Indices: 7055121--7055272 Score: 132
Period size: 39 Copynumber: 4.0 Consensus size: 38
7055111 ACATTACTTA
* * *
7055121 AATATATTACTCAAATACATTACTTACTAAAATTTAAGT
1 AATACATTACTTAAATACATTACTTACTAAAATTT-ATT
* **
7055160 -ATATATTACATTACTTACATTACTTACTAAAA--TA-T
1 AATACATTAC-TTAAATACATTACTTACTAAAATTTATT
* **
7055195 ATTACATTACTTAAATATTTTACTTACTAAAATTTATTT
1 AATACATTACTTAAATACATTACTTACTAAAATTTA-TT
* *
7055234 AATACATTACTTAAATATATTACATAACTTAAAATTTAT
1 AATACATTACTTAAATACATTAC-TTAC-TAAAATTTAT
7055273 ATATATATAT
Statistics
Matches: 93, Mismatches: 12, Indels: 15
0.77 0.10 0.12
Matches are distributed among these distances:
35 19 0.20
36 8 0.09
37 3 0.03
38 9 0.10
39 41 0.44
40 4 0.04
41 9 0.10
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.43
Consensus pattern (38 bp):
AATACATTACTTAAATACATTACTTACTAAAATTTATT
Found at i:7057252 original size:66 final size:66
Alignment explanation
Indices: 7057146--7057290 Score: 184
Period size: 66 Copynumber: 2.2 Consensus size: 66
7057136 AGCAAATTAC
* * *
7057146 ACAACTTAAAGCGGAGGCAGCATCGAGAGAAGCTGAGGTTCAAA-AAAGATATGAAGAACTCCAG
1 ACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAG-TATGAAGAACTCCAC
7057210 CT
65 CT
* * * * *
7057212 ACAACTTAAAGTAGATGTAGCAGCGAGAGAAGCTGAGGTTCAAAGGACGTATGAAGAACTCCACC
1 ACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCACC
7057277 T
66 T
* *
7057278 GCAGCTTAAAGCA
1 ACAACTTAAAGCA
7057291 TATGCGACAG
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
66 65 0.97
67 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.17
Consensus pattern (66 bp):
ACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCACC
T
Found at i:7057715 original size:43 final size:43
Alignment explanation
Indices: 7057645--7058082 Score: 537
Period size: 43 Copynumber: 10.3 Consensus size: 43
7057635 AAACTGCAGT
* * *
7057645 TAAAAGTCATGGTCTTTAGCGGCGCTTGTGGAAAAAGCGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * * * *
7057688 TAAAGGTCGTGGTCTATAGCAGCGCTTGTGGAAAAAGCACCGT
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
*
7057731 TAATGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * *
7057774 TAAAGGTCGTGGCCTATAGCGGCGTTTGTGGGAAAA-CGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * * * **
7057816 TAAAGGTCTTGGTCTATAACGGCATTTGTGGGAAAAGTACCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* *
7057859 TAAAGGTCGTGGTCTATAGCGGCGTTTGTAGG-GAAAGCGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGT-GGAAAAAGCGCCGC
**
7057902 TAAAGGTTGTGGTCTATAGCGGCGTTTGTGGAGAAAA-CGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGA-AAAAGCGCCGC
* * * *
7057945 TAAAGGTCATGGCCTATAGTGGCATTTGTGG-AAAAGTGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * *
7057987 TAAAAGTCATGGTCTATAGCGGCATTTGTCGG-AAAAGCGACGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGT-GGAAAAAGCGCCGC
*
7058030 TAAAGGTCATGGTCTATAGCTGCGTTTGT-GAAAAAGCGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
7058072 TAAAGGTCATG
1 TAAAGGTCATG
7058083 ACCTTTAGCG
Statistics
Matches: 343, Mismatches: 45, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
41 5 0.01
42 92 0.27
43 241 0.70
44 5 0.01
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (43 bp):
TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
Found at i:7057896 original size:128 final size:128
Alignment explanation
Indices: 7057645--7058098 Score: 574
Period size: 128 Copynumber: 3.5 Consensus size: 128
7057635 AAACTGCAGT
* * * * * *
7057645 TAAAAGTCATGGTCTTTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGGTCGTGGTCTATAGCAG
1 TAAAGGTCGTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGG
** * * * *
7057710 CGCTTGTGGAAAAAGCACCGTTAATGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
66 CATTTGTGGGAAAAGTACCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGG-AAAAGCGCCGC
* * * *
7057774 TAAAGGTCGTGGCCTATAGCGGCGTTTGTGGGAAAA-CGCCGCTAAAGGTCTTGGTCTATAACGG
1 TAAAGGTCGTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGG
* *
7057838 CATTTGTGGGAAAAGTACCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTAGGGAAAGCGCCGC
66 CATTTGTGGGAAAAGTACCGCTAAAGGTCATGGTCTATAGCGGCGTTTGT-GGAAAAGCGCCGC
* * *
7057902 TAAAGGTTGTGGTCTATAGCGGCGTTTGTGGAGAAAA-CGCCGCTAAAGGTCATGGCCTATAGTG
1 TAAAGGTCGTGGTCTATAGCGGCGTTTGTGGA-AAAAGCGCCGCTAAAGGTCATGGTCTATAGCG
* * * *
7057966 GCATTTGT-GGAAAAGTGCCGCTAAAAGTCATGGTCTATAGCGGCATTTGTCGGAAAAGCGACGC
65 GCATTTGTGGGAAAAGTACCGCTAAAGGTCATGGTCTATAGCGGCGTTTGT-GGAAAAGCGCCGC
* * ** *
7058030 TAAAGGTCATGGTCTATAGCTGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCATGACCTTTAGCGG
1 TAAAGGTCGTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGG
7058094 CATTT
66 CATTT
7058099 ATTTATAAAA
Statistics
Matches: 285, Mismatches: 37, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
126 4 0.01
127 32 0.11
128 182 0.64
129 67 0.24
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (128 bp):
TAAAGGTCGTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGG
CATTTGTGGGAAAAGTACCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAGCGCCGC
Found at i:7057975 original size:171 final size:170
Alignment explanation
Indices: 7057645--7058082 Score: 576
Period size: 171 Copynumber: 2.6 Consensus size: 170
7057635 AAACTGCAGT
* * ** * *
7057645 TAAAAGTCATGGTCTTTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGGTCGTGGTCTATAGCAG
1 TAAAAGTCATGGTCTATAACGGCATTTGTGGGAAAAGCACCGCTAAAGGTCGTGGTCTATAGCAG
* * * *
7057710 CGCTTGTGGAAAAAGCACCGTTAATGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCT
66 CGTTTGTGG-AAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCT
* *
7057775 AAAGGTCGTGGCCTATAGCGGCGTTTGTGGGAAAA-CGCCGC
130 AAAGGTCATGGCCTATAGCGGCATTTGT-GGAAAAGCGCCGC
* * * *
7057816 TAAAGGTCTTGGTCTATAACGGCATTTGTGGGAAAAGTACCGCTAAAGGTCGTGGTCTATAGCGG
1 TAAAAGTCATGGTCTATAACGGCATTTGTGGGAAAAGCACCGCTAAAGGTCGTGGTCTATAGCAG
* **
7057881 CGTTTGTAGGGAAAGCGCCGCTAAAGGTTGTGGTCTATAGCGGCGTTTGTGGAGAAAA-CGCCGC
66 CGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGA-AAAAGCGCCGC
* *
7057945 TAAAGGTCATGGCCTATAGTGGCATTTGTGGAAAAGTGCCGC
129 TAAAGGTCATGGCCTATAGCGGCATTTGTGGAAAAGCGCCGC
* * * *
7057987 TAAAAGTCATGGTCTATAGCGGCATTTGTCGGAAAAGCGA-CGCTAAAGGTCATGGTCTATAGCT
1 TAAAAGTCATGGTCTATAACGGCATTTGTGGGAAAAGC-ACCGCTAAAGGTCGTGGTCTATAGCA
*
7058051 GCGTTTGTGAAAAAGCGCCGCTAAAGGTCATG
65 GCGTTTGTGGAAAAGCGCCGCTAAAGGTCATG
7058083 ACCTTTAGCG
Statistics
Matches: 231, Mismatches: 32, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
170 26 0.11
171 198 0.86
172 7 0.03
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (170 bp):
TAAAAGTCATGGTCTATAACGGCATTTGTGGGAAAAGCACCGCTAAAGGTCGTGGTCTATAGCAG
CGTTTGTGGAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTA
AAGGTCATGGCCTATAGCGGCATTTGTGGAAAAGCGCCGC
Found at i:7059520 original size:134 final size:134
Alignment explanation
Indices: 7059271--7059547 Score: 482
Period size: 134 Copynumber: 2.1 Consensus size: 134
7059261 GAGGTAGATT
* *
7059271 TATCAATAATTTAAGAAAGGTAATGATAATTTTTAACATTTTAAATTTTGGTCAAAAATAGAATG
1 TATCGATACTTTAAGAAAGGTAATGATAATTTTTAACATTTTAAATTTTGGTCAAAAATAGAATG
* *
7059336 CAAGTTTGGTATCATTTTTTTATGTGGTGTCGATACCATTTTGGGAAAATATCGATACCCTAAGG
66 CAAGTTTGGTATCATTTTTTTATGTGGTATCAATACCATTTTGGGAAAATATCGATACCCTAAGG
7059401 TCAA
131 TCAA
* * * *
7059405 TATCGATACTTTAAGAAAGGTACTGATAATTTTTGACATTTTAAATTTTGGTGAGAAATAGAATG
1 TATCGATACTTTAAGAAAGGTAATGATAATTTTTAACATTTTAAATTTTGGTCAAAAATAGAATG
7059470 CAAGTTTGGTATCATTTTTTTATGTGGTATCAATACCATTTTGGGAAAATATCGATACCCTAAGG
66 CAAGTTTGGTATCATTTTTTTATGTGGTATCAATACCATTTTGGGAAAATATCGATACCCTAAGG
7059535 TCAA
131 TCAA
7059539 TATCGATAC
1 TATCGATAC
7059548 CTACGTGATT
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
134 135 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (134 bp):
TATCGATACTTTAAGAAAGGTAATGATAATTTTTAACATTTTAAATTTTGGTCAAAAATAGAATG
CAAGTTTGGTATCATTTTTTTATGTGGTATCAATACCATTTTGGGAAAATATCGATACCCTAAGG
TCAA
Found at i:7059921 original size:174 final size:174
Alignment explanation
Indices: 7059630--7059978 Score: 565
Period size: 174 Copynumber: 2.0 Consensus size: 174
7059620 TGTACGCCTA
* *
7059630 GCATGATTTAATGATGATTAATGCATGTATGTCTTAAAACCTATGGAAATGCGAAGAATAACATG
1 GCATGATTTAATGATGATTAATGCATGTATGTCTTAAAACCTATGCAAATGCAAAGAATAACATG
* * * *
7059695 TGTCGACTTTAATAAAATGAACGTTGTAACGTATAAGTAGTGAGACGGTGGTGTGACATCTTTAT
66 TGTCAAATTTAATAAAATGAAAGTTGTAACGTACAAGTAGTGAGACGGTGGTGTGACATCTTTAT
*
7059760 ATTCGGGC-TTGACAACCAGCCCGGGTATAGGGTGTTACAAGGAT
131 ATTCGGGCTTTG-CAACCAGCCCGAGTATAGGGTGTTACAAGGAT
*
7059804 GCATGATTTAATGATGATTAATGCATGTATGTCTTAAAACCTGTGCAAATGCAAAGAATAACATG
1 GCATGATTTAATGATGATTAATGCATGTATGTCTTAAAACCTATGCAAATGCAAAGAATAACATG
*
7059869 TGTCAAATTTAATAAAATGAAAGTTGTAACGTACAAGTAGTGAGATGGTGGTGTGACATCTTTAT
66 TGTCAAATTTAATAAAATGAAAGTTGTAACGTACAAGTAGTGAGACGGTGGTGTGACATCTTTAT
** * *
7059934 ATTCGGGCTTTGTGACCAGGCCGAGTATAGGGTGTTATAAGGAT
131 ATTCGGGCTTTGCAACCAGCCCGAGTATAGGGTGTTACAAGGAT
7059978 G
1 G
7059979 AAAAGTCAAT
Statistics
Matches: 161, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
174 158 0.98
175 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.31
Consensus pattern (174 bp):
GCATGATTTAATGATGATTAATGCATGTATGTCTTAAAACCTATGCAAATGCAAAGAATAACATG
TGTCAAATTTAATAAAATGAAAGTTGTAACGTACAAGTAGTGAGACGGTGGTGTGACATCTTTAT
ATTCGGGCTTTGCAACCAGCCCGAGTATAGGGTGTTACAAGGAT
Found at i:7061713 original size:44 final size:44
Alignment explanation
Indices: 7061650--7061739 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
7061640 TCTCCAATTT
7061650 ACTAAGGGTCCAAATGAGGACTAGTATCAAAATTTTAAGGAGTG
1 ACTAAGGGTCCAAATGAGGACTAGTATCAAAATTTTAAGGAGTG
*
7061694 ACTAAGGGTCCAAATGAGGACTAGTATCAACATTTTAAGGAGTG
1 ACTAAGGGTCCAAATGAGGACTAGTATCAAAATTTTAAGGAGTG
7061738 AC
1 AC
7061740 CTTTAGGGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.24
Consensus pattern (44 bp):
ACTAAGGGTCCAAATGAGGACTAGTATCAAAATTTTAAGGAGTG
Found at i:7062909 original size:6 final size:6
Alignment explanation
Indices: 7062888--7062960 Score: 58
Period size: 6 Copynumber: 11.7 Consensus size: 6
7062878 ACTAACTTTA
* * * *
7062888 TTTAGT TTTATGT TTTATT TTTATT TGTACT TTTATT TTTATT ATTAGTT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-TT
*
7062938 GTTTTTAT TTTA-T TTTATT TTTA
1 -TTTAT-T TTTATT TTTATT TTTA
7062961 AGACTTATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
5 5 0.09
6 33 0.62
7 12 0.23
8 3 0.06
ACGTcount: A:0.18, C:0.01, G:0.07, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:7062951 original size:21 final size:23
Alignment explanation
Indices: 7062893--7062948 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
7062883 CTTTATTTAG
* *
7062893 TTTTATGTTTTATTTTTATTTGTA
1 TTTTAT-TTTTATTATTAGTTGTA
7062917 CTTTTATTTTTATTATTAGTTGT-
1 -TTTTATTTTTATTATTAGTTGTA
7062940 TTTTATTTT
1 TTTTATTTT
7062949 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.31
24 14 0.48
25 6 0.21
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTATTATTAGTTGTA
Found at i:7064679 original size:5 final size:5
Alignment explanation
Indices: 7064674--7064716 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
7064664 TGCTATAATT
* * * *
7064674 TGATT TGATA TGATA TGATA TGATA TGGTC TGATC TGATA TGA
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGA
7064717 AATACTACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (5 bp):
TGATA
Found at i:7067745 original size:21 final size:23
Alignment explanation
Indices: 7067715--7067765 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 23
7067705 ACATTAACAC
*
7067715 TTCAACACATTT-CCAAGCC-AA
1 TTCAAAACATTTACCAAGCCAAA
7067736 TTCAAAACATTTAAGCCAAGCCAAA
1 TTCAAAACATTT-A-CCAAGCCAAA
7067761 TTCAA
1 TTCAA
7067766 GTCTTATGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 11 0.44
24 7 0.28
25 7 0.28
ACGTcount: A:0.43, C:0.27, G:0.06, T:0.24
Consensus pattern (23 bp):
TTCAAAACATTTACCAAGCCAAA
Found at i:7070588 original size:98 final size:98
Alignment explanation
Indices: 7070419--7070610 Score: 350
Period size: 98 Copynumber: 2.0 Consensus size: 98
7070409 ATACAATAAA
7070419 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
7070484 CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
66 CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
*
7070517 ACTTTAAAAGAA-AGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTAT
1 ACTTTAAAAGAACA-TCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTAT
*
7070581 TCCTTTAGAATCCCAAACTCGGAATATTTC
65 TCCTTTAGAATCCCAAACTCAGAATATTTC
7070611 AAAAAATCTT
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
97 1 0.01
98 90 0.99
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
Found at i:7084677 original size:28 final size:25
Alignment explanation
Indices: 7084635--7084729 Score: 68
Period size: 28 Copynumber: 3.6 Consensus size: 25
7084625 ATATTAATTG
7084635 AAAAAAATATAATATGTACATATATAT
1 AAAAAAATATAATA--TACATATATAT
*
7084662 AAAAAAATAATTATATACATATATAGATT
1 AAAAAAAT-ATAATATACATATAT--A-T
**
7084691 ATAAAAACGATAAT-TACATATATA-
1 A-AAAAAATATAATATACATATATAT
*
7084715 CAAAAAATGATAATA
1 AAAAAAAT-ATAATA
7084730 ATTAAATTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
23 5 0.09
24 5 0.09
26 10 0.19
27 8 0.15
28 15 0.28
29 6 0.11
30 5 0.09
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (25 bp):
AAAAAAATATAATATACATATATAT
Found at i:7084680 original size:26 final size:27
Alignment explanation
Indices: 7084635--7084686 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
7084625 ATATTAATTG
*
7084635 AAAAAAATATAATATGTACATATATAT
1 AAAAAAATATAATATATACATATATAT
*
7084662 AAAAAAATA-ATTATATACATATATA
1 AAAAAAATATAATATATACATATATA
7084687 GATTATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (27 bp):
AAAAAAATATAATATATACATATATAT
Found at i:7093983 original size:21 final size:21
Alignment explanation
Indices: 7093959--7094006 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
7093949 GTGTGTGGAG
*
7093959 TAGCCACACAGGTATATGGGA
1 TAGCCACACAGGCATATGGGA
* * *
7093980 TAGCCATACGGGCATGTGGGA
1 TAGCCACACAGGCATATGGGA
7094001 TAGCCA
1 TAGCCA
7094007 AACGGCCATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.31, T:0.19
Consensus pattern (21 bp):
TAGCCACACAGGCATATGGGA
Found at i:7094011 original size:21 final size:21
Alignment explanation
Indices: 7093975--7094017 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
7093965 CACAGGTATA
* *
7093975 TGGGATAGCCATACGGGCATG
1 TGGGATAGCCAAACGGCCATG
7093996 TGGGATAGCCAAACGGCCATG
1 TGGGATAGCCAAACGGCCATG
7094017 T
1 T
7094018 CCTTGAGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.35, T:0.19
Consensus pattern (21 bp):
TGGGATAGCCAAACGGCCATG
Found at i:7095579 original size:18 final size:18
Alignment explanation
Indices: 7095556--7095602 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
7095546 CACAAAGTTA
7095556 CGAGCTCACTCAAGACTG
1 CGAGCTCACTCAAGACTG
* * *
7095574 CGAGCTCTC-CAATAGTG
1 CGAGCTCACTCAAGACTG
7095591 CGAGCTCA-TCAA
1 CGAGCTCACTCAA
7095603 AGCTACAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
CGAGCTCACTCAAGACTG
Found at i:7100659 original size:108 final size:108
Alignment explanation
Indices: 7100469--7100679 Score: 316
Period size: 108 Copynumber: 1.9 Consensus size: 108
7100459 TGCCGAAATG
*
7100469 AGAAAGGTGCATATTGGCCAATTATTTCTAACCTTCCTCGTGTGAGGATAAATTATGATGACATC
1 AGAAAGCTGCATATTGGCCAATTATTTCTAACCTTCCTC-TGTGAGGATAAATTATGATGACATC
*
7100534 CTCTGAACAAGAACAAGCAGATTGCATTTCTAGATGGATAGCAA
65 CTCTGAACAAGAACAAGCAGATTGCATTCCTAGATGGATAGCAA
* * * *
7100578 AGAAAGCTGCATATTGGCCTATTATTTCTCACCTTCACT-TGTGAGGATAAGTTATGTTGACATC
1 AGAAAGCTGCATATTGGCCAATTATTTCTAACCTTC-CTCTGTGAGGATAAATTATGATGACATC
* * *
7100642 TTCTGAACAAGCACAAGCGGATTGCATTCCTAGATGGA
65 CTCTGAACAAGAACAAGCAGATTGCATTCCTAGATGGA
7100680 CAGCGAAAAC
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 57 0.62
109 33 0.36
110 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (108 bp):
AGAAAGCTGCATATTGGCCAATTATTTCTAACCTTCCTCTGTGAGGATAAATTATGATGACATCC
TCTGAACAAGAACAAGCAGATTGCATTCCTAGATGGATAGCAA
Found at i:7103671 original size:19 final size:20
Alignment explanation
Indices: 7103647--7103685 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
7103637 AGAAAAAGAA
7103647 CGAAAAGTAT-AAAAGATGG
1 CGAAAAGTATAAAAAGATGG
7103666 CGAAAAGTATAAAAAGATGG
1 CGAAAAGTATAAAAAGATGG
7103686 AGATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.54, C:0.05, G:0.26, T:0.15
Consensus pattern (20 bp):
CGAAAAGTATAAAAAGATGG
Found at i:7103822 original size:13 final size:13
Alignment explanation
Indices: 7103804--7103831 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7103794 AAAAAAGTCT
7103804 ATTTATAGGTTAA
1 ATTTATAGGTTAA
7103817 ATTTATAGGTTAA
1 ATTTATAGGTTAA
7103830 AT
1 AT
7103832 AATAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.46
Consensus pattern (13 bp):
ATTTATAGGTTAA
Found at i:7105048 original size:23 final size:23
Alignment explanation
Indices: 7105014--7105064 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
7105004 CCATGTGCCA
*
7105014 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
7105037 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
7105060 AGTAA
1 TGTAA
7105065 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:7105447 original size:2 final size:2
Alignment explanation
Indices: 7105440--7105468 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7105430 ATGGTCAAAT
7105440 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
7105469 ATTCTAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7116594 original size:54 final size:54
Alignment explanation
Indices: 7116512--7116614 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
7116502 AACCTTATTT
* * *
7116512 CAAAAAACACCATTGTTCAAGAGGAAGCTACTGTTCAGGGGGAAACTATAGTTC
1 CAAAAAACACCATTATTCAAGAGGAAGCTACTGCTCAAGGGGAAACTATAGTTC
*
7116566 CAAAAAACACCATTATTCAATG-GGAAGCTACTGCTCAAGGGGAGACTAT
1 CAAAAAACACCATTATTCAA-GAGGAAGCTACTGCTCAAGGGGAAACTAT
7116615 TATTTAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 43 0.98
55 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (54 bp):
CAAAAAACACCATTATTCAAGAGGAAGCTACTGCTCAAGGGGAAACTATAGTTC
Found at i:7119556 original size:5 final size:5
Alignment explanation
Indices: 7119546--7119605 Score: 111
Period size: 5 Copynumber: 12.0 Consensus size: 5
7119536 ATGTTTTAAA
*
7119546 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TGTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
7119596 TATAT TATAT
1 TATAT TATAT
7119606 AAGTAAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 53 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:7120709 original size:21 final size:21
Alignment explanation
Indices: 7120660--7120744 Score: 100
Period size: 21 Copynumber: 4.0 Consensus size: 21
7120650 GGCTTTGCCG
*
7120660 ATCAGGCACTTTATGTATCGT
1 ATCAGGCACTTTATGTGTCGT
7120681 ACATCAGGCACTTTATGTGTCGT
1 --ATCAGGCACTTTATGTGTCGT
* **
7120704 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
*
7120725 TTCAGGCAC-TTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
7120745 TTACTGATCA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
20 9 0.16
21 26 0.47
23 20 0.36
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:7123374 original size:15 final size:15
Alignment explanation
Indices: 7123349--7123396 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
7123339 AAGGTTGTAG
* *
7123349 TAATAATAATAATGA
1 TAATGATAATAATAA
*
7123364 TGATGATAATAATAA
1 TAATGATAATAATAA
*
7123379 TAATGATAATAATTA
1 TAATGATAATAATAA
7123394 TAA
1 TAA
7123397 AAAAAACAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (15 bp):
TAATGATAATAATAA
Found at i:7123416 original size:3 final size:3
Alignment explanation
Indices: 7123349--7123396 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
7123339 AAGGTTGTAG
* * * * *
7123349 TAA TAA TAA TAA TGA TGA TGA TAA TAA TAA TAA TGA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
7123397 AAAAAACAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:7127568 original size:15 final size:15
Alignment explanation
Indices: 7127548--7127584 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
7127538 TTTACAATTT
7127548 CAATTTCAATTCGTC
1 CAATTTCAATTCGTC
7127563 CAATTTCAATTCGTC
1 CAATTTCAATTCGTC
7127578 CATATTT
1 CA-ATTT
7127585 TTAATTCTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.43
Consensus pattern (15 bp):
CAATTTCAATTCGTC
Found at i:7127924 original size:27 final size:27
Alignment explanation
Indices: 7127871--7127925 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
7127861 TATGTGCTAA
* * *
7127871 GAATCTTCCTCTTCTGTTGAGTTACCC
1 GAATCTTCCTCTTCTGGTAAGTAACCC
*
7127898 GAATCTTCCTCTTTTGGTAAGTAACCC
1 GAATCTTCCTCTTCTGGTAAGTAACCC
7127925 G
1 G
7127926 TAATGATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.38
Consensus pattern (27 bp):
GAATCTTCCTCTTCTGGTAAGTAACCC
Found at i:7130235 original size:18 final size:18
Alignment explanation
Indices: 7130214--7130271 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
7130204 TAAGTAAATA
7130214 AAAC-AAAGTAAATAAAAG
1 AAACTAAAG-AAATAAAAG
7130232 AAACTAAAGAAATAAAAG
1 AAACTAAAGAAATAAAAG
* *
7130250 AAACTAAAGAAGTATAAG
1 AAACTAAAGAAATAAAAG
7130268 AAAC
1 AAAC
7130272 AAAACAACAG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 33 0.89
19 4 0.11
ACGTcount: A:0.69, C:0.07, G:0.12, T:0.12
Consensus pattern (18 bp):
AAACTAAAGAAATAAAAG
Found at i:7130242 original size:9 final size:9
Alignment explanation
Indices: 7130228--7130260 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
7130218 AAAGTAAATA
7130228 AAAGAAACT
1 AAAGAAACT
7130237 AAAGAAA-T
1 AAAGAAACT
7130245 AAAAGAAACT
1 -AAAGAAACT
7130255 AAAGAA
1 AAAGAA
7130261 GTATAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.73, C:0.06, G:0.12, T:0.09
Consensus pattern (9 bp):
AAAGAAACT
Found at i:7130417 original size:18 final size:18
Alignment explanation
Indices: 7130390--7130433 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
7130380 ATAAATAAAA
7130390 TAAAGTAAGTAAAAGAAAC
1 TAAAG-AAGTAAAAGAAAC
7130409 TAAAGAAGTAAAAGAAAC
1 TAAAGAAGTAAAAGAAAC
*
7130427 AAAAGAA
1 TAAAGAA
7130434 CAGCAGAAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.68, C:0.05, G:0.16, T:0.11
Consensus pattern (18 bp):
TAAAGAAGTAAAAGAAAC
Found at i:7131689 original size:18 final size:18
Alignment explanation
Indices: 7131666--7131701 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
7131656 GACACTGGGT
7131666 GTCATACTGTTACTTCGG
1 GTCATACTGTTACTTCGG
7131684 GTCATACTGTTACTTCGG
1 GTCATACTGTTACTTCGG
7131702 ATAGATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (18 bp):
GTCATACTGTTACTTCGG
Found at i:7132547 original size:27 final size:27
Alignment explanation
Indices: 7132517--7132569 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
7132507 ATGCATGAAT
*
7132517 GATTTATTAAAGGTAAAATAGTGGTAA
1 GATTTAATAAAGGTAAAATAGTGGTAA
* *
7132544 GATTTAATGATGGTAAAATAGTGGTA
1 GATTTAATAAAGGTAAAATAGTGGTA
7132570 TATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.34
Consensus pattern (27 bp):
GATTTAATAAAGGTAAAATAGTGGTAA
Found at i:7132575 original size:2 final size:2
Alignment explanation
Indices: 7132568--7132596 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7132558 AAAATAGTGG
7132568 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7132597 GATGTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7140647 original size:140 final size:138
Alignment explanation
Indices: 7140497--7140814 Score: 507
Period size: 139 Copynumber: 2.3 Consensus size: 138
7140487 ATTTTTTTAT
* *
7140497 TTTA-AATTTAAAAATTATAATGTATTAATAATA-TT-ATTACTTAATGAGACTTAGATTGCATT
1 TTTACAATTTAAAAATT-TAAT-TA-AAATAATACTTAAGTACTTAATGA-ACTTAGATTGCATT
7140559 TTTAGTAAAATTTACAAATATAATTTTTTGTATTAAAGACTGTTTTTATTTAATAGATTAAAATT
62 TTTAGTAAAATTTACAAATATAATTTTTTGTATTAAAGACTGTTTTTATTTAATAGATTAAAATT
7140624 AATATATTTTCA
127 AATATATTTTCA
* *
7140636 TTTACAATTTAAACATTTTATTAAAATAATATCTTAAGTACTTAATGAACTTAGATTGCATTTTT
1 TTTACAATTTAAAAATTTAATTAAAATAATA-CTTAAGTACTTAATGAACTTAGATTGCATTTTT
7140701 AGTAAAATTTACAAATATAATTTTTTGTATTAAAGACTGTTTTTATTTAATAGATTAAAATTAAT
65 AGTAAAATTTACAAATATAATTTTTTGTATTAAAGACTGTTTTTATTTAATAGATTAAAATTAAT
7140766 ATATTTTCA
130 ATATTTTCA
* *
7140775 TTTACAATTTAAACATTTTATTAAAATAATATCTTAAGTA
1 TTTACAATTTAAAAATTTAATTAAAATAATA-CTTAAGTA
7140815 AAAAAAATAT
Statistics
Matches: 171, Mismatches: 4, Indels: 8
0.93 0.02 0.04
Matches are distributed among these distances:
137 7 0.04
138 2 0.01
139 140 0.82
140 22 0.13
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (138 bp):
TTTACAATTTAAAAATTTAATTAAAATAATACTTAAGTACTTAATGAACTTAGATTGCATTTTTA
GTAAAATTTACAAATATAATTTTTTGTATTAAAGACTGTTTTTATTTAATAGATTAAAATTAATA
TATTTTCA
Found at i:7140711 original size:139 final size:140
Alignment explanation
Indices: 7140534--7140814 Score: 555
Period size: 139 Copynumber: 2.0 Consensus size: 140
7140524 ATAATATTAT
7140534 TACTTAATGAGACTTAGATTGCATTTTTAGTAAAATTTACAAATATAATTTTTTGTATTAAAGAC
1 TACTTAATGAGACTTAGATTGCATTTTTAGTAAAATTTACAAATATAATTTTTTGTATTAAAGAC
7140599 TGTTTTTATTTAATAGATTAAAATTAATATATTTTCATTTACAATTTAAACATTTTATTAAAATA
66 TGTTTTTATTTAATAGATTAAAATTAATATATTTTCATTTACAATTTAAACATTTTATTAAAATA
7140664 ATATCTTAAG
131 ATATCTTAAG
7140674 TACTTAATGA-ACTTAGATTGCATTTTTAGTAAAATTTACAAATATAATTTTTTGTATTAAAGAC
1 TACTTAATGAGACTTAGATTGCATTTTTAGTAAAATTTACAAATATAATTTTTTGTATTAAAGAC
7140738 TGTTTTTATTTAATAGATTAAAATTAATATATTTTCATTTACAATTTAAACATTTTATTAAAATA
66 TGTTTTTATTTAATAGATTAAAATTAATATATTTTCATTTACAATTTAAACATTTTATTAAAATA
7140803 ATATCTTAAG
131 ATATCTTAAG
7140813 TA
1 TA
7140815 AAAAAAATAT
Statistics
Matches: 141, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
139 131 0.93
140 10 0.07
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (140 bp):
TACTTAATGAGACTTAGATTGCATTTTTAGTAAAATTTACAAATATAATTTTTTGTATTAAAGAC
TGTTTTTATTTAATAGATTAAAATTAATATATTTTCATTTACAATTTAAACATTTTATTAAAATA
ATATCTTAAG
Found at i:7151199 original size:16 final size:16
Alignment explanation
Indices: 7151178--7151211 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7151168 TACTTAAAAG
7151178 TTAAAACTAATTGTTA
1 TTAAAACTAATTGTTA
* *
7151194 TTAAAATTCATTGTTA
1 TTAAAACTAATTGTTA
7151210 TT
1 TT
7151212 GAATTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
TTAAAACTAATTGTTA
Found at i:7151313 original size:25 final size:25
Alignment explanation
Indices: 7151283--7151330 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
7151273 AAGATTACTT
7151283 ATTTGAATTTAATTACAAACAATTA
1 ATTTGAATTTAATTACAAACAATTA
7151308 ATTTGAATTTAATTACAAACAAT
1 ATTTGAATTTAATTACAAACAAT
7151331 CAAATCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (25 bp):
ATTTGAATTTAATTACAAACAATTA
Found at i:7151409 original size:8 final size:8
Alignment explanation
Indices: 7151396--7151428 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
7151386 ATTTAATTAC
7151396 TTTTAACT
1 TTTTAACT
7151404 TTTTAACT
1 TTTTAACT
7151412 TTTTAACT
1 TTTTAACT
7151420 TTTTAACT
1 TTTTAACT
7151428 T
1 T
7151429 AAATATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTAACT
Found at i:7153341 original size:17 final size:17
Alignment explanation
Indices: 7153284--7153350 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
7153274 ACAAATATCT
7153284 GAAATTATACATCAAATGA
1 GAAATTATACATCAAA--A
* * * *
7153303 AAAATAATCCAACCAAAA
1 GAAATTATAC-ATCAAAA
*
7153321 GAAATTATACATCAAAC
1 GAAATTATACATCAAAA
7153338 GAAATTATACATC
1 GAAATTATACATC
7153351 TACTGTTTGT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
17 18 0.47
18 8 0.21
19 7 0.18
20 5 0.13
ACGTcount: A:0.55, C:0.16, G:0.06, T:0.22
Consensus pattern (17 bp):
GAAATTATACATCAAAA
Found at i:7153523 original size:8 final size:8
Alignment explanation
Indices: 7153512--7153551 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
7153502 AAGCACTGTC
7153512 GAGTCGTG
1 GAGTCGTG
7153520 GAGTCGTG
1 GAGTCGTG
7153528 GAGTCGT-
1 GAGTCGTG
7153535 G-GTCGTG
1 GAGTCGTG
7153542 GAGTCGTG
1 GAGTCGTG
7153550 GA
1 GA
7153552 TTGGTGGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 5 0.17
7 2 0.07
8 23 0.77
ACGTcount: A:0.12, C:0.12, G:0.50, T:0.25
Consensus pattern (8 bp):
GAGTCGTG
Found at i:7153541 original size:14 final size:14
Alignment explanation
Indices: 7153512--7153550 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 14
7153502 AAGCACTGTC
7153512 GAGTCGTGGAGTCGTG
1 GAGTCGT-G-GTCGTG
7153528 GAGTCGTGGTCGTG
1 GAGTCGTGGTCGTG
7153542 GAGTCGTGG
1 GAGTCGTGG
7153551 ATTGGTGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 15 0.65
15 1 0.04
16 7 0.30
ACGTcount: A:0.10, C:0.13, G:0.51, T:0.26
Consensus pattern (14 bp):
GAGTCGTGGTCGTG
Found at i:7153564 original size:22 final size:22
Alignment explanation
Indices: 7153516--7153573 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
7153506 ACTGTCGAGT
* *
7153516 CGTGGAGTCGTGGAGTCGTGGT
1 CGTGGAGTCGTGGATTCGTGGA
*
7153538 CGTGGAGTCGTGGATTGGTGGA
1 CGTGGAGTCGTGGATTCGTGGA
*
7153560 GGTGGAG--GTGGATT
1 CGTGGAGTCGTGGATT
7153574 TCCGATTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.22
22 25 0.78
ACGTcount: A:0.12, C:0.09, G:0.52, T:0.28
Consensus pattern (22 bp):
CGTGGAGTCGTGGATTCGTGGA
Found at i:7154534 original size:27 final size:27
Alignment explanation
Indices: 7154495--7154570 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
7154485 TAGTATTGGC
*
7154495 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
* *
7154522 GCCTATCTAGGAGGCGCCAACGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
7154549 GCCTATCTGGGAGGCGCCAATG
1 GCCTATCTGGGAGGCGCCAATG
7154571 CTCTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.17, C:0.24, G:0.38, T:0.21
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:7154611 original size:19 final size:19
Alignment explanation
Indices: 7154587--7154627 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
7154577 TTTTTTCGGG
*
7154587 TTTAGGGTTATGTTATAAA
1 TTTAGGATTATGTTATAAA
7154606 TTTAGGATTATGTTATAAA
1 TTTAGGATTATGTTATAAA
7154625 TTT
1 TTT
7154628 TTGTGTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (19 bp):
TTTAGGATTATGTTATAAA
Found at i:7158399 original size:5 final size:5
Alignment explanation
Indices: 7158382--7158432 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
7158372 AAAATTATGG
* * *
7158382 GGCCC GAGCCC GGCCC GGCCC GGCCC GGCTCA GGGCC GGGCC -GCCC GGCCC
1 GGCCC G-GCCC GGCCC GGCCC GGCCC GGC-CC GGCCC GGCCC GGCCC GGCCC
7158433 ATGGACAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 3 0.08
5 28 0.72
6 8 0.21
ACGTcount: A:0.04, C:0.53, G:0.41, T:0.02
Consensus pattern (5 bp):
GGCCC
Found at i:7158681 original size:18 final size:19
Alignment explanation
Indices: 7158655--7158691 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
7158645 GATAAATTAT
*
7158655 ATTAGTAAAAATAT-TTTA
1 ATTAATAAAAATATATTTA
7158673 ATTAATAAAAATATATTTA
1 ATTAATAAAAATATATTTA
7158692 TAGGGATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTAATAAAAATATATTTA
Found at i:7163787 original size:9 final size:9
Alignment explanation
Indices: 7163773--7163822 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
7163763 TTTTTTCATA
7163773 AAAAATTAT
1 AAAAATTAT
*
7163782 AAAAATTCT
1 AAAAATTAT
*
7163791 AATAATTAT
1 AAAAATTAT
7163800 -AAAATTAAT
1 AAAAATT-AT
7163809 AAAAACTTAT
1 AAAAA-TTAT
7163819 AAAA
1 AAAA
7163823 GAGTCATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 5 0.15
9 17 0.50
10 10 0.29
11 2 0.06
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:7170811 original size:20 final size:20
Alignment explanation
Indices: 7170776--7170813 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7170766 GCTAACAAAA
**
7170776 TAGTCACTCAGGTTTCAATT
1 TAGTCACTCAACTTTCAATT
7170796 TAGTCACTCAACTTTCAA
1 TAGTCACTCAACTTTCAA
7170814 AAATGACAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.37
Consensus pattern (20 bp):
TAGTCACTCAACTTTCAATT
Found at i:7171910 original size:3 final size:3
Alignment explanation
Indices: 7171902--7171961 Score: 111
Period size: 3 Copynumber: 20.0 Consensus size: 3
7171892 TTATAGGATC
*
7171902 TCT TCT TCT TCT TCT TCT TCT TAT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
7171950 TCT TCT TCT TCT
1 TCT TCT TCT TCT
7171962 GTTATTTGGG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:7172052 original size:21 final size:21
Alignment explanation
Indices: 7172026--7172067 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
7172016 ATCTAACGTG
* *
7172026 GCTAGTTAATTGGCCATGTCA
1 GCTAGTTAACTGGCCACGTCA
7172047 GCTAGTTAACTGGCCACGTCA
1 GCTAGTTAACTGGCCACGTCA
7172068 CCTGTCCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
GCTAGTTAACTGGCCACGTCA
Found at i:7172261 original size:10 final size:10
Alignment explanation
Indices: 7172242--7172298 Score: 64
Period size: 10 Copynumber: 5.6 Consensus size: 10
7172232 TAATTTACCC
7172242 AAAAATTTATT
1 AAAAA-TTATT
7172253 AAAAATTA-T
1 AAAAATTATT
7172262 AAAACATTATT
1 AAAA-ATTATT
*
7172273 TAAAATT-TGT
1 AAAAATTAT-T
7172283 AAAAATTATT
1 AAAAATTATT
7172293 AAAAAT
1 AAAAAT
7172299 AGTAAATAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
9 6 0.15
10 24 0.60
11 10 0.25
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
AAAAATTATT
Found at i:7172271 original size:20 final size:19
Alignment explanation
Indices: 7172242--7172330 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 19
7172232 TAATTTACCC
7172242 AAAAATTTATTAAAAATTAT
1 AAAAA-TTATTAAAAATTAT
* *
7172262 AAAACATTATTTAAAATTTGT
1 AAAA-ATTA-TTAAAAATTAT
7172283 AAAAATTATTAAAAA-TAGT
1 AAAAATTATTAAAAATTA-T
* * *
7172302 AAATAGTTGTTAAAAATTGT
1 AAA-AATTATTAAAAATTAT
7172322 AAATAATTA
1 AAA-AATTA
7172331 ACAAATTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
18 1 0.02
19 10 0.18
20 29 0.53
21 15 0.27
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (19 bp):
AAAAATTATTAAAAATTAT
Found at i:7172304 original size:9 final size:10
Alignment explanation
Indices: 7172242--7172330 Score: 51
Period size: 10 Copynumber: 8.8 Consensus size: 10
7172232 TAATTTACCC
*
7172242 AAAAATTTATT
1 AAAAA-TTAGT
7172253 AAAAATTA-T
1 AAAAATTAGT
*
7172262 AAAACATTATT
1 AAAA-ATTAGT
* *
7172273 TAAAATTTGT
1 AAAAATTAGT
*
7172283 AAAAATTATT
1 AAAAATTAGT
7172293 AAAAA-TAGT
1 AAAAATTAGT
*
7172302 AAATAGTT-GTT
1 AAA-AATTAG-T
7172313 AAAAATT-GT
1 AAAAATTAGT
7172322 AAATAATTA
1 AAA-AATTA
7172331 ACAAATTAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
9 15 0.24
10 33 0.53
11 14 0.23
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (10 bp):
AAAAATTAGT
Found at i:7177645 original size:20 final size:20
Alignment explanation
Indices: 7177622--7177746 Score: 69
Period size: 20 Copynumber: 6.3 Consensus size: 20
7177612 ATGCCACAAT
*
7177622 AATTTTCAAAATTTTTATTA
1 AATTTTCAAAATTTTTAATA
7177642 AA-TTTCAAAAGTTTTTAATA
1 AATTTTCAAAA-TTTTTAATA
* * * *
7177662 ATTTTTTACAATTATTAATA
1 AATTTTCAAAATTTTTAATA
** * *
7177682 TTGTTTTTAAAATTTTTATTA
1 -AATTTTCAAAATTTTTAATA
*
7177703 ATTTTTC--AATTATTTAA-A
1 AATTTTCAAAATT-TTTAATA
* * * *
7177721 TATTTTTATAATTTTAAATA
1 AATTTTCAAAATTTTTAATA
7177741 AATTTT
1 AATTTT
7177747 GTTGCTGATT
Statistics
Matches: 79, Mismatches: 19, Indels: 14
0.71 0.17 0.12
Matches are distributed among these distances:
18 9 0.11
19 16 0.20
20 33 0.42
21 21 0.27
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (20 bp):
AATTTTCAAAATTTTTAATA
Found at i:7177664 original size:19 final size:18
Alignment explanation
Indices: 7177619--7177665 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
7177609 TAAATGCCAC
7177619 AATAATTTTCAAAATTTTT
1 AATAA-TTTCAAAATTTTT
*
7177638 ATTAAATTTCAAAAGTTTTT
1 AAT-AATTTCAAAA-TTTTT
7177658 AATAATTT
1 AATAATTT
7177666 TTTACAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (18 bp):
AATAATTTCAAAATTTTT
Found at i:7177690 original size:21 final size:20
Alignment explanation
Indices: 7177656--7177708 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
7177646 TCAAAAGTTT
*
7177656 TTAATAATTTTTTACAATTA
1 TTAATAATTTTTTAAAATTA
* *
7177676 TTAATATTGTTTTTAAAATTT
1 TTAATAAT-TTTTTAAAATTA
*
7177697 TTATTAATTTTT
1 TTAATAATTTTT
7177709 CAATTATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TTAATAATTTTTTAAAATTA
Found at i:7177745 original size:28 final size:28
Alignment explanation
Indices: 7177687--7177741 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
7177677 TAATATTGTT
* *
7177687 TTTAAAATTTTTATTAATTTTTCAATTA
1 TTTAAAATTTTTATTAATTTTTAAATAA
7177715 TTTAAATATTTTTA-TAA-TTTTAAATAA
1 TTTAAA-ATTTTTATTAATTTTTAAATAA
7177742 ATTTTGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.33
28 9 0.38
29 7 0.29
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
TTTAAAATTTTTATTAATTTTTAAATAA
Found at i:7177745 original size:39 final size:40
Alignment explanation
Indices: 7177654--7177746 Score: 102
Period size: 40 Copynumber: 2.4 Consensus size: 40
7177644 TTTCAAAAGT
* *
7177654 TTTTAATAATTTTTTACAATTATTAATATTGTTTTTAAAA
1 TTTTAATAAATTTTTACAATTATTAATATTATTTTTAAAA
* * *
7177694 TTTTTATTAATTTTT-CAATTATTTAA-A-TATTTTTATAA
1 TTTTAATAAATTTTTACAATTA-TTAATATTATTTTTAAAA
7177732 TTTTAAATAAATTTT
1 TTTT-AATAAATTTT
7177747 GTTGCTGATT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
38 13 0.30
39 15 0.34
40 16 0.36
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (40 bp):
TTTTAATAAATTTTTACAATTATTAATATTATTTTTAAAA
Found at i:7179603 original size:19 final size:18
Alignment explanation
Indices: 7179571--7179608 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
7179561 CCGGATTTAG
7179571 TTTATAATTAATTTTAAAT
1 TTTATAATTAA-TTTAAAT
7179590 TTTATAA-TATATTTAAAT
1 TTTATAATTA-ATTTAAAT
7179608 T
1 T
7179609 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTATAATTAATTTAAAT
Found at i:7180141 original size:22 final size:22
Alignment explanation
Indices: 7180085--7180143 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
7180075 CTAGTCATTT
7180085 TATATTTT--AAATATATTTTA
1 TATATTTTAAAAATATATTTTA
**
7180105 TA-ATTAAAAATAATATATTTTA
1 TATATTTTAAA-AATATATTTTA
7180127 TATATTTTAAAAATATA
1 TATATTTTAAAAATATA
7180144 CAATTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 3 0.10
20 2 0.06
21 1 0.03
22 19 0.61
23 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTTTAAAAATATATTTTA
Found at i:7180149 original size:25 final size:26
Alignment explanation
Indices: 7180108--7180165 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
7180098 TATTTTATAA
* *
7180108 TTAAAAATAATATATTTTATATA-TT
1 TTAAAAATAATAAATTTTATAGAGTT
*
7180133 TTAAAAAT-ATACAATTTTTTAGAGTT
1 TTAAAAATAATA-AATTTTATAGAGTT
7180159 TTAAAAA
1 TTAAAAA
7180166 ACAAAATACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 3 0.11
25 16 0.57
26 9 0.32
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (26 bp):
TTAAAAATAATAAATTTTATAGAGTT
Found at i:7181003 original size:23 final size:23
Alignment explanation
Indices: 7180960--7181006 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
7180950 CATTTATCTA
*
7180960 TTTTTGAATTTTTTATCTATTTT
1 TTTTTGAATTTTCTATCTATTTT
* *
7180983 TTTTTGAATTTTCTGTTTATTTT
1 TTTTTGAATTTTCTATCTATTTT
7181006 T
1 T
7181007 AGATTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (23 bp):
TTTTTGAATTTTCTATCTATTTT
Found at i:7189835 original size:25 final size:25
Alignment explanation
Indices: 7189758--7189843 Score: 118
Period size: 26 Copynumber: 3.3 Consensus size: 25
7189748 AACTTTCTTG
* *
7189758 AAATTTTATCAGGGCTAAAATCGTTA
1 AAATTTTATC-GGGGTAAAATCGTCA
7189784 AAATTTTATCGGGGTTAAAATCGTCA
1 AAATTTTATCGGGG-TAAAATCGTCA
*
7189810 AAATTTTATCGGGGTAAAATCATCAA
1 AAATTTTATCGGGGTAAAATCGTC-A
7189836 AAATTTTA
1 AAATTTTA
7189844 CTAGAGTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
25 12 0.22
26 43 0.78
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (25 bp):
AAATTTTATCGGGGTAAAATCGTCA
Found at i:7191427 original size:25 final size:26
Alignment explanation
Indices: 7191392--7191440 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
7191382 TGTACATCAG
*
7191392 AATAATATCTTTAGA-AATTTTTTAA
1 AATAATATCTTCAGAGAATTTTTTAA
*
7191417 AATAATCTCTTCAGAGAATTTTTT
1 AATAATATCTTCAGAGAATTTTTT
7191441 CTATACAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (26 bp):
AATAATATCTTCAGAGAATTTTTTAA
Found at i:7200433 original size:20 final size:22
Alignment explanation
Indices: 7200396--7200436 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
7200386 CGGTCAAATT
7200396 TTTTAATAAATACTAAAAATTTA
1 TTTTAATAAATAC-AAAAATTTA
7200419 TTTTAA-AAATA-AAAAATT
1 TTTTAATAAATACAAAAATT
7200437 AAAAAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
22 5 0.28
23 6 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTTAATAAATACAAAAATTTA
Done.