Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold53
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: 4419549
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 41486 characters in sequence are not A, C, G, or T
File 22 of 28
Found at i:3314837 original size:13 final size:13
Alignment explanation
Indices: 3314819--3314845 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3314809 ACATACTGCT
3314819 TTGTATCGATACA
1 TTGTATCGATACA
3314832 TTGTATCGATACA
1 TTGTATCGATACA
3314845 T
1 T
3314846 ATTCATTGTA
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:3314842 original size:33 final size:32
Alignment explanation
Indices: 3314800--3314861 Score: 97
Period size: 33 Copynumber: 1.9 Consensus size: 32
3314790 CACACCCAAA
*
3314800 TGTATCGATACATACTGCTTTGTATCGATACAT
1 TGTATCGATACATA-TGCATTGTATCGATACAT
*
3314833 TGTATCGATACATATTCATTGTATCGATA
1 TGTATCGATACATATGCATTGTATCGATA
3314862 TACACTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATATGCATTGTATCGATACAT
Found at i:3314963 original size:20 final size:20
Alignment explanation
Indices: 3314911--3314963 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
3314901 AAACTCACAT
* * *
3314911 TGTATCGATGCATGAAGGAT
1 TGTATCGATACATGAAGAAA
* * *
3314931 TGTATCAAGACATGATGAAA
1 TGTATCGATACATGAAGAAA
3314951 TGTATCGATACAT
1 TGTATCGATACAT
3314964 TGAGCCCAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAA
Found at i:3316563 original size:12 final size:12
Alignment explanation
Indices: 3316546--3316580 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
3316536 AACCATTAAA
3316546 GATGATAAAGAT
1 GATGATAAAGAT
*
3316558 GATGATAATGAT
1 GATGATAAAGAT
*
3316570 GATGATGAAGA
1 GATGATAAAGA
3316581 AGTTGACTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.26
Consensus pattern (12 bp):
GATGATAAAGAT
Found at i:3317302 original size:13 final size:13
Alignment explanation
Indices: 3317284--3317310 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3317274 ACATTATGCT
3317284 TTGTATCGATACA
1 TTGTATCGATACA
3317297 TTGTATCGATACA
1 TTGTATCGATACA
3317310 T
1 T
3317311 GCACAATTGT
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:3317379 original size:81 final size:81
Alignment explanation
Indices: 3317244--3317408 Score: 312
Period size: 81 Copynumber: 2.0 Consensus size: 81
3317234 AAACCCTTGT
* *
3317244 ATGTATCGATACACATCCAGATGTATCGATACATTATGCTTTGTATCGATACATTGTATCGATAC
1 ATGTATCGATACACATCCAGATGTATCAATACATTATGCTTTGTATCGATACATTATATCGATAC
3317309 ATGCACAATTGTATCG
66 ATGCACAATTGTATCG
3317325 ATGTATCGATACACATCCAGATGTATCAATACATTATGCTTTGTATCGATACATTATATCGATAC
1 ATGTATCGATACACATCCAGATGTATCAATACATTATGCTTTGTATCGATACATTATATCGATAC
3317390 ATGCACAATTGTATCG
66 ATGCACAATTGTATCG
3317406 ATG
1 ATG
3317409 CATGAAACTG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (81 bp):
ATGTATCGATACACATCCAGATGTATCAATACATTATGCTTTGTATCGATACATTATATCGATAC
ATGCACAATTGTATCG
Found at i:3323906 original size:52 final size:53
Alignment explanation
Indices: 3323821--3323947 Score: 211
Period size: 52 Copynumber: 2.4 Consensus size: 53
3323811 ATATGAAAAG
* *
3323821 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGAT-ACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATAACATCTGGGCAAAT
*
3323873 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATA-ACATCTGGGCAAAT
3323927 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
3323948 AAGATCAATG
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
52 35 0.50
54 35 0.50
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (53 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATAACATCTGGGCAAAT
Found at i:3323958 original size:54 final size:54
Alignment explanation
Indices: 3323821--3323967 Score: 194
Period size: 54 Copynumber: 2.8 Consensus size: 54
3323811 ATATGAAAAG
* * *
3323821 TTGCTTGCATGTATCGATACATTTA-ATAGTGTATCGAT--ACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TAAGATAATGTATCGATACACATCTGGGCAAAT
***
3323873 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACACATCTGGGCAAAT
3323927 TTGCCTGCATGTATCGATACA-AAGATCAATGTATCGATACA
1 TTGCCTGCATGTATCGATACATAAGAT-AATGTATCGATACA
3323968 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
51 2 0.02
52 32 0.38
53 2 0.02
54 49 0.58
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (54 bp):
TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACACATCTGGGCAAAT
Found at i:3323971 original size:13 final size:13
Alignment explanation
Indices: 3323953--3323980 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3323943 ATACAAAGAT
3323953 CAATGTATCGATA
1 CAATGTATCGATA
3323966 CAATGTATCGATA
1 CAATGTATCGATA
3323979 CA
1 CA
3323981 TTTGAGTAAT
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:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3324058 original size:33 final size:33
Alignment explanation
Indices: 3324021--3324087 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3324011 AGTAGCTTAA
3324021 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3324054 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3324087 A
1 A
3324088 AATAGTAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3324061 original size:13 final size:13
Alignment explanation
Indices: 3324043--3324067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3324033 CAAAAAAATA
3324043 TGTATCGATACAT
1 TGTATCGATACAT
3324056 TGTATCGATACA
1 TGTATCGATACA
3324068 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3325133 original size:49 final size:48
Alignment explanation
Indices: 3324928--3325720 Score: 812
Period size: 49 Copynumber: 16.9 Consensus size: 48
3324918 AAGATGAGAA
* * * * * *
3324928 AAAAGATGTCAATGTGCTGATTCAAGGCTAGCTACATTGAACTTAAAGATGG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A--G
3324980 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA----G
* *
3325032 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTT--AG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
3325078 ---AGGTGCCAATGTGCTGATTCAAGTCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
*
3325123 AAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----
1 AA-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
3325168 -AAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* *
3325215 ATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTT--AG
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
3325262 ---AGGTGCCAATATGTTGATTCAAGGCCAACGATATTGGACTT----
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
3325303 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
*
3325350 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * * *
3325395 -AAAGGTGCCAATGTGCTGATTCAGGGCTAGCTACATTGGACTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
*
3325442 ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGG
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-G
*
3325492 TAAAA-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----
1 -AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
3325536 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTAAAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
3325583 ATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGG
1 A-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-G
** *
3325633 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
* * *
3325677 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTA
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
3325721 GAAGGGTTGC
Statistics
Matches: 635, Mismatches: 67, Indels: 86
0.81 0.09 0.11
Matches are distributed among these distances:
42 3 0.00
43 257 0.40
44 1 0.00
45 2 0.00
46 1 0.00
47 2 0.00
49 276 0.43
50 7 0.01
51 3 0.00
52 83 0.13
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (48 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
Found at i:3325177 original size:92 final size:91
Alignment explanation
Indices: 3324981--3325725 Score: 802
Period size: 92 Copynumber: 8.1 Consensus size: 91
3324971 TAAAGATGGA
* *
3324981 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGAAAATGTGCCAATA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA----GAAAAGGTGCCAATA
*
3325046 TGCTGATTCAAGGCCAGCTATATTGGGCTT
62 TGCTGATTCAAGGCCAGCTATATTGGACTT
* * * * *
3325076 AGAGGTGCCAATGTGCTGATTCAAGTCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAA-AAGGTGCCAATATGC
*
3325141 TGATTCAAGGCCAGCGATATTGGACTT
65 TGATTCAAGGCCAGCTATATTGGACTT
* * * * *
3325168 AAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-AAAGGTGCCAATATGC
*
3325233 TGATTCAAGGCCAGCTATATTGGGCTT
65 TGATTCAAGGCCAGCTATATTGGACTT
* * * *
3325260 AGAGGTGCCAATATGTTGATTCAAGGCCAACGATATTGGACTT-----AAAGGTGCCAATGTGCT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAAGGTGCCAATATGCT
* *
3325320 GATTCAAGGCCAGCTACATTGGGCTTAAAGAT
66 GATTCAAGGCCAGCTATATTGGAC-T-----T
*
3325352 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-----AAAGGTGCCAATGTGCT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAAGGTGCCAATATGCT
* * *
3325412 GATTCAGGGCTAGCTACATTGGACTTAAAGAT
66 GATTCAAGGCCAGCTATATTGGAC-T-----T
3325444 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTAAAA-GTGCCAATATG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-G-AAAAGGTGCCAATATG
*
3325508 CTGATTCAAGGCCAGCGATATTGGACTT
64 CTGATTCAAGGCCAGCTATATTGGACTT
* * * * * *
3325536 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-AAAGGTGCCAATATGC
*
3325601 TGATTCAAGGCCAGCGATATTGGACTT
65 TGATTCAAGGCCAGCTATATTGGACTT
3325628 AAAGGTGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-----AAAGGTGCCAA
1 --A----AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAAGGTGCCAA
* * *
3325688 TGTGCTGATTCAAGGCCAGCTACATTGGGCTT
60 TATGCTGATTCAAGGCCAGCTATATTGGACTT
3325720 AGAAGG
1 A-AAGG
3325726 GTTGCCACCG
Statistics
Matches: 579, Mismatches: 48, Indels: 54
0.85 0.07 0.08
Matches are distributed among these distances:
86 38 0.07
87 6 0.01
90 2 0.00
91 6 0.01
92 410 0.71
94 1 0.00
95 42 0.07
97 1 0.00
98 70 0.12
99 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (91 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAAAAGGTGCCAATATGCT
GATTCAAGGCCAGCTATATTGGACTT
Found at i:3325517 original size:141 final size:140
Alignment explanation
Indices: 3324981--3325720 Score: 918
Period size: 141 Copynumber: 5.3 Consensus size: 140
3324971 TAAAGATGGA
* *
3324981 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGAAAATGTGCCAATA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAA-GT---AAAGGTGCCAATA
* * *
3325046 TGCTGATTCAAGGCCAGCTATATTGGGCTT--A-G---AGGTGCCAATGTGCTGATTCAAGTCCA
62 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTAAAGGTGCCAATATGCTGATTCAAGGCCA
* *
3325105 GCTACATTGGACTT
127 GCGATATTGGACTT
* *
3325119 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T----TAAAGGTGCCAA
1 -----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTAAAGGTGCCAA
* * * * *
3325179 TGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGC
60 TATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTAAAGGTGCCAATATGCTGATTCAAGGC
* *
3325244 CAGCTATATTGGGCTT
125 CAGCGATATTGGACTT
* * * * * *
3325260 AGAGGTGCCAATATGTTGATTCAAGGCCAACGATATTGGAC-T----TAAAGGTGCCAATGTGCT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTAAAGGTGCCAATATGCT
* * *
3325320 GATTCAAGGCCAGCTACATTGGGCTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
66 GATTCAAGGCCAGCTATATTGGACTTAAAGGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
3325385 TATTGGACTT
131 TATTGGACTT
* * *
3325395 AAAGGTGCCAATGTGCTGATTCAGGGCTAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG-TAAAGGTGCCAATATGC
* *
3325460 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTAAAAGTGCCAATATGCTGATTCAAGGCCAGCG
65 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCG
3325525 ATATTGGACTT
130 ATATTGGACTT
* * * *
3325536 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG-TAAAGGTGCCAATATGC
* *
3325601 TGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATATGCTGATTCAAGGCCAGCG
65 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCG
3325666 ATATTGGACTT
130 ATATTGGACTT
* *
3325677 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
3325721 GAAGGGTTGC
Statistics
Matches: 544, Mismatches: 40, Indels: 28
0.89 0.07 0.05
Matches are distributed among these distances:
135 197 0.36
136 2 0.00
137 1 0.00
138 1 0.00
141 302 0.56
143 2 0.00
144 39 0.07
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (140 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGTAAAGGTGCCAATATGCT
GATTCAAGGCCAGCTATATTGGACTTAAAGGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGA
TATTGGACTT
Found at i:3325794 original size:32 final size:34
Alignment explanation
Indices: 3325720--3325880 Score: 237
Period size: 32 Copynumber: 4.9 Consensus size: 34
3325710 CATTGGGCTT
*
3325720 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-AG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGAA
*
3325753 AGAATGGTTGCCACCGACTTGTGT-GGCTTTGAA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGAA
3325786 AGAA-GGTTGCCACCGACTTGTGT-GGCTTTGAA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGAA
3325818 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTG--
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGAA
* *
3325849 GGAAGGGTTGCCACTGACTTGTGTGGGCTTTG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTG
3325881 GGAAGGGAGA
Statistics
Matches: 121, Mismatches: 4, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
31 3 0.02
32 83 0.69
33 35 0.29
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (34 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTGAA
Found at i:3325941 original size:35 final size:36
Alignment explanation
Indices: 3325883--3325984 Score: 131
Period size: 34 Copynumber: 2.9 Consensus size: 36
3325873 GGGCTTTGGG
*
3325883 AAGGGAGAAAGA-TGCCACGGAGTTGTGGAC-TTAA
1 AAGGGAAAAAGAGTGCCACGGAGTTGTGGACTTTAA
* *
3325917 AAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAA
1 AAGGGAAAAAGAGTGCCACGGAGTTGTGGACTTTAA
* *
3325953 AA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTT
1 AAGGGAAAAAGAGTGCCACGGAGTTGTGGACTTT
3325985 GAAGAAAAGG
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
34 32 0.52
35 23 0.38
36 6 0.10
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (36 bp):
AAGGGAAAAAGAGTGCCACGGAGTTGTGGACTTTAA
Found at i:3326017 original size:32 final size:31
Alignment explanation
Indices: 3325890--3326119 Score: 180
Period size: 32 Copynumber: 7.2 Consensus size: 31
3325880 GGGAAGGGAG
* * **
3325890 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACTGAGTCGTGGACTTTGAA--G-A
* * * *
3325924 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAGA-TGCCACTGAGTCGTGGACTTT--GAAG-A
* * * *
3325959 AAAGGTGCCACGGAGTTGTGGGCTTTGAAGA
1 AAAGATGCCACTGAGTCGTGGACTTTGAAGA
*
3325990 AAAGGATGTCACTGAGTCGTGGACTTTG-AGA
1 AAA-GATGCCACTGAGTCGTGGACTTTGAAGA
3326021 CAAA-ATGCCACTGAGTCGTGGACTTTGAAGA
1 -AAAGATGCCACTGAGTCGTGGACTTTGAAGA
*
3326052 AAATGATGCCACTCAGTCGTGGACTTTG-AGA
1 AAA-GATGCCACTGAGTCGTGGACTTTGAAGA
* *
3326083 AGAGATTGCCACTGAGTCGTGGGCTTTG-AGA
1 AAAGA-TGCCACTGAGTCGTGGACTTTGAAGA
*
3326114 AGAGAT
1 AAAGAT
3326120 TTGAAGAATT
Statistics
Matches: 171, Mismatches: 16, Indels: 22
0.82 0.08 0.11
Matches are distributed among these distances:
30 28 0.16
31 43 0.25
32 47 0.27
34 25 0.15
35 25 0.15
37 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (31 bp):
AAAGATGCCACTGAGTCGTGGACTTTGAAGA
Found at i:3326047 original size:62 final size:63
Alignment explanation
Indices: 3325964--3326111 Score: 210
Period size: 62 Copynumber: 2.4 Consensus size: 63
3325954 AAGAAAAAGG
* * * *
3325964 TGCCACGGAGTTGTGGGCTTTGAAGAAAAGGATGTCACTGAGTCGTGGACTTTGAGACA-A-AA
1 TGCCACTGAGTCGTGGGCTTTGAAGAAAAGGATGCCACTCAGTCGTGGACTTTGAGA-AGAGAA
* * *
3326026 TGCCACTGAGTCGTGGACTTTGAAGAAAATGATGCCACTCAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGGCTTTGAAGAAAAGGATGCCACTCAGTCGTGGACTTTGAGAAGAGAA
3326089 TGCCACTGAGTCGTGGGCTTTGA
1 TGCCACTGAGTCGTGGGCTTTGA
3326112 GAAGAGATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
61 1 0.01
62 52 0.68
63 23 0.30
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (63 bp):
TGCCACTGAGTCGTGGGCTTTGAAGAAAAGGATGCCACTCAGTCGTGGACTTTGAGAAGAGAA
Found at i:3326120 original size:31 final size:30
Alignment explanation
Indices: 3325958--3326119 Score: 182
Period size: 32 Copynumber: 5.2 Consensus size: 30
3325948 TTTAAAAAGA
* * * *
3325958 AAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTG-AG
*
3325989 AAAAGGATGTCACTGAGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
3326020 ACAAA-ATGCCACTGAGTCGTGGACTTTGAAG
1 A-AAAGATGCCACTGAGTCGTGGACTTTG-AG
*
3326051 AAAATGATGCCACTCAGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
* *
3326082 AAGAGATTGCCACTGAGTCGTGGGCTTTGAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTGAG
*
3326113 AAGAGAT
1 AAAAGAT
3326120 TTGAAGAATT
Statistics
Matches: 115, Mismatches: 10, Indels: 13
0.83 0.07 0.09
Matches are distributed among these distances:
30 28 0.24
31 43 0.37
32 44 0.38
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.24
Consensus pattern (30 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAG
Found at i:3334331 original size:52 final size:53
Alignment explanation
Indices: 3334246--3334394 Score: 214
Period size: 54 Copynumber: 2.8 Consensus size: 53
3334236 ATATGAAAAG
* *
3334246 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATAC-ATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACAATCTGGGCAAAT
*
3334298 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACAAATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATAC-AATCTGGGCAAAT
*
3334352 TTGCCTGCATGTATCGATACA--AAGATCAATGTATCGATACAAT
1 TTGCCTGCATGTATCGATACATTTA-AT-AATGTATCGATACAAT
3334395 GTATCGATAC
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
52 37 0.42
53 5 0.06
54 46 0.52
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (53 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACAATCTGGGCAAAT
Found at i:3334368 original size:54 final size:52
Alignment explanation
Indices: 3334246--3334372 Score: 209
Period size: 52 Copynumber: 2.4 Consensus size: 52
3334236 ATATGAAAAG
* *
3334246 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
3334298 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACAAATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATAC--ATCTGGGCAAAT
3334352 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
3334373 AAGATCAATG
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
52 37 0.53
54 33 0.47
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:3334396 original size:13 final size:13
Alignment explanation
Indices: 3334378--3334405 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3334368 ATACAAAGAT
3334378 CAATGTATCGATA
1 CAATGTATCGATA
3334391 CAATGTATCGATA
1 CAATGTATCGATA
3334404 CA
1 CA
3334406 TTTGAGTAAT
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:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:3334483 original size:33 final size:33
Alignment explanation
Indices: 3334446--3334512 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3334436 AGTAGCTTAA
3334446 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
3334479 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
3334512 A
1 A
3334513 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3334486 original size:13 final size:13
Alignment explanation
Indices: 3334468--3334492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3334458 CAAAAAAATA
3334468 TGTATCGATACAT
1 TGTATCGATACAT
3334481 TGTATCGATACA
1 TGTATCGATACA
3334493 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3335824 original size:27 final size:27
Alignment explanation
Indices: 3335786--3335840 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
3335776 AAAAGACTGA
*
3335786 GTGATCGTCCAATTATAGGAACTAAAT
1 GTGATCATCCAATTATAGGAACTAAAT
3335813 GTGATCATCCAATTATAGGAACTAAAT
1 GTGATCATCCAATTATAGGAACTAAAT
3335840 G
1 G
3335841 GGTATTTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (27 bp):
GTGATCATCCAATTATAGGAACTAAAT
Found at i:3341539 original size:13 final size:13
Alignment explanation
Indices: 3341521--3341547 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3341511 ATAATGTTCT
3341521 TTGTATCGATACA
1 TTGTATCGATACA
3341534 TTGTATCGATACA
1 TTGTATCGATACA
3341547 T
1 T
3341548 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:3343369 original size:34 final size:34
Alignment explanation
Indices: 3343319--3343397 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 34
3343309 CAAAAACAGG
* *
3343319 GAGAAATTTTTGAAAATAAATTTTTATCAAGGGA
1 GAGAAAATTTTCAAAATAAATTTTTATCAAGGGA
*
3343353 GAGAAAATTTTCAAAATAAATTTTTATCAAGGGG
1 GAGAAAATTTTCAAAATAAATTTTTATCAAGGGA
3343387 GAGAAAATTTT
1 GAGAAAATTTT
3343398 TTAACAAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (34 bp):
GAGAAAATTTTCAAAATAAATTTTTATCAAGGGA
Found at i:3344029 original size:20 final size:19
Alignment explanation
Indices: 3343983--3344039 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
3343973 TTCTATCGAT
*
3343983 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
*
3344002 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
*
3344021 ACAATTGTATCAATACATG
1 AC-ATTGTATCGATACATG
3344040 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:3344107 original size:13 final size:13
Alignment explanation
Indices: 3344089--3344113 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3344079 CATGGCACAT
3344089 TGTATCGATACAA
1 TGTATCGATACAA
3344102 TGTATCGATACA
1 TGTATCGATACA
3344114 TAATGAATTG
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:3352045 original size:34 final size:35
Alignment explanation
Indices: 3352007--3352079 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
3351997 ATTTTCTACA
* *
3352007 TTTCAAAAAGCTTTTATATTC-TTTGTTGTTATTC
1 TTTCAAAAAGCATTTATATTCATTTGTTCTTATTC
** *
3352041 TTTCAAAGCGCATTTGTATTCATTTGTTCTTATTC
1 TTTCAAAAAGCATTTATATTCATTTGTTCTTATTC
3352076 TTTC
1 TTTC
3352080 CACAAACACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
34 17 0.52
35 16 0.48
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.55
Consensus pattern (35 bp):
TTTCAAAAAGCATTTATATTCATTTGTTCTTATTC
Found at i:3355614 original size:150 final size:147
Alignment explanation
Indices: 3355432--3355925 Score: 573
Period size: 148 Copynumber: 3.3 Consensus size: 147
3355422 GTGCCTGGAT
* * * * * *
3355432 ATCCTATAGGACTTGGAAAAGTAAAAGCGAACCTATGCTTAATACATACCTTCGGCATAGAAGCG
1 ATCCTAGAGGACTTGAAAAAGTAAAAGCGAACCTACGCCTAATACATACCTTCGACATAAAAGCG
*
3355497 ACCTGGTAGTTTCATAGGGCTAGTTTTTACGTGAAAAATGCTAAAAGGTCCCTAAGGTCTACTAT
66 ACCTGGTAGTTTCATAGGGCTAGTTTTTA-G-GAAAAATGCTAAAAGGTCCCTAAGGTCTACCAT
*
3355562 CAACTTAGAAATGCCCAGTG
129 CAACTTAGAAATGCTC-GTG
* * * *
3355582 ATCCTAGAGGACTTGAAAAAGTAAAAGTGAACCTACGCCTCATACATACCTTCGATAAAAAAGCG
1 ATCCTAGAGGACTTGAAAAAGTAAAAGCGAACCTACGCCTAATACATACCTTCGACATAAAAGCG
* * *
3355647 ACC-GAGTAATTTCATAGGGTTAGGTTTTT-GGAAAAATGCTAAAAGGTCTCTAAGGTCTACCAT
66 ACCTG-GTAGTTTCATAGGGCTA-GTTTTTAGGAAAAATGCTAAAAGGTCCCTAAGGTCTACCAT
* *
3355710 TAACTTAAAAATGCTCTGTG
129 CAACTTAGAAATGCTC-GTG
* * * * *
3355730 ATCTTAGAGGACTTGAAAAAGTAAAAACGAACTTACGCCTAATACATACCCTT-GCCATAAAAGT
1 ATCCTAGAGGACTTGAAAAAGTAAAAGCGAACCTACGCCTAATACATA-CCTTCGACATAAAAGC
* * * * * * *
3355794 GACCTGATAGTTTCATATGGCTAGGTTTCAGGGGAAAAATGATAAAAGATCATCCCTAAGGTCCA
65 GACCTGGTAGTTTCATAGGGCTAGTTTTTA--GGAAAAATGCTAAAAG---GTCCCTAAGGTCTA
3355859 CCATCAACTTAGAAATGCTCGATG
125 CCATCAACTTAGAAATGCTCG-TG
*
3355883 ATCCTAGAGGACTTGAAAAAGTAAAAGCAAACCTA-GCCTAATA
1 ATCCTAGAGGACTTGAAAAAGTAAAAGCGAACCTACGCCTAATA
3355926 TGTACTATTG
Statistics
Matches: 290, Mismatches: 43, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
147 4 0.01
148 114 0.39
149 7 0.02
150 88 0.30
151 6 0.02
152 9 0.03
153 62 0.21
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (147 bp):
ATCCTAGAGGACTTGAAAAAGTAAAAGCGAACCTACGCCTAATACATACCTTCGACATAAAAGCG
ACCTGGTAGTTTCATAGGGCTAGTTTTTAGGAAAAATGCTAAAAGGTCCCTAAGGTCTACCATCA
ACTTAGAAATGCTCGTG
Found at i:3357487 original size:14 final size:14
Alignment explanation
Indices: 3357468--3357501 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3357458 TCTCTATTTC
*
3357468 TTTTTTTCTTTTG-
1 TTTTTTTCCTTTGA
3357481 TTTTTTTCCTTTGA
1 TTTTTTTCCTTTGA
3357495 TTTTTTT
1 TTTTTTT
3357502 TTCATGCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.03, C:0.09, G:0.06, T:0.82
Consensus pattern (14 bp):
TTTTTTTCCTTTGA
Found at i:3358571 original size:14 final size:15
Alignment explanation
Indices: 3358552--3358582 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3358542 TTTTTCAATT
3358552 TTAAATATATTT-TA
1 TTAAATATATTTATA
3358566 TTAAATATATTTATA
1 TTAAATATATTTATA
3358581 TT
1 TT
3358583 TTAGTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTAAATATATTTATA
Found at i:3358580 original size:20 final size:20
Alignment explanation
Indices: 3358557--3358597 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
3358547 CAATTTTAAA
*
3358557 TATATTTTATTAAATATATT
1 TATATTTTAGTAAATATATT
3358577 TATATTTTAGTAAATATATT
1 TATATTTTAGTAAATATATT
3358597 T
1 T
3358598 TAAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TATATTTTAGTAAATATATT
Found at i:3358610 original size:20 final size:18
Alignment explanation
Indices: 3358566--3358613 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
3358556 ATATATTTTA
*
3358566 TTAAATATATTTATATTT
1 TTAAATATATTTAAATTT
3358584 TAGTAAATATATTTTAAATATT
1 T--TAAATATA-TTTAAAT-TT
3358606 TTAAATAT
1 TTAAATAT
3358614 TAATTCGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
20 15 0.60
21 6 0.24
22 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
TTAAATATATTTAAATTT
Found at i:3391117 original size:23 final size:25
Alignment explanation
Indices: 3391091--3391141 Score: 88
Period size: 23 Copynumber: 2.1 Consensus size: 25
3391081 TATTGCATTA
3391091 ATATTAAAAAAATAAAA-AAAAA-T
1 ATATTAAAAAAATAAAACAAAAACT
3391114 ATATTAAAAAAATAAAACAAAAACT
1 ATATTAAAAAAATAAAACAAAAACT
3391139 ATA
1 ATA
3391142 AAGAAACTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 17 0.65
24 5 0.19
25 4 0.15
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (25 bp):
ATATTAAAAAAATAAAACAAAAACT
Found at i:3392569 original size:16 final size:15
Alignment explanation
Indices: 3392527--3392569 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
3392517 GTACATGCAA
3392527 TTTAGTATTACATTT
1 TTTAGTATTACATTT
*
3392542 TTTAATGTATTACGTGTT
1 TTT-A-GTATTACAT-TT
3392560 TTTAGTATTA
1 TTTAGTATTA
3392570 AATGCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 3 0.12
16 7 0.29
17 9 0.38
18 5 0.21
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.58
Consensus pattern (15 bp):
TTTAGTATTACATTT
Found at i:3404195 original size:24 final size:24
Alignment explanation
Indices: 3404168--3404213 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
3404158 AGGTTATTGC
3404168 ATTAATATTAAAAAAATAAAAAAA
1 ATTAATATTAAAAAAATAAAAAAA
3404192 ATTAATATTAAAAAAATAAAAA
1 ATTAATATTAAAAAAATAAAAA
3404214 CAAAACTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (24 bp):
ATTAATATTAAAAAAATAAAAAAA
Found at i:3405808 original size:22 final size:23
Alignment explanation
Indices: 3405775--3405818 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
3405765 ATGCTTCGGT
3405775 TGTGATTCTTGATGATGATATGA
1 TGTGATTCTTGATGATGATATGA
*
3405798 TGTGA-TCTTGATGATGCTATG
1 TGTGATTCTTGATGATGATATG
3405819 TTAGATTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.43
Consensus pattern (23 bp):
TGTGATTCTTGATGATGATATGA
Found at i:3408187 original size:138 final size:138
Alignment explanation
Indices: 3407938--3408348 Score: 576
Period size: 138 Copynumber: 3.0 Consensus size: 138
3407928 TTAATAGGTG
* * * *
3407938 ATTGATCACATCTAGTTCAAAAAGATCGGTGATGACTCTTTAACCTAG-TCATATCATATTTTTG
1 ATTGATCACATCTAGCTCAAAAAGATCGGTGATGACTCCTTAACCCAGCT-ATATCATA-TTTCG
*
3408002 -TACGAAAAGCTCAGACGAGCAATTTGTTTCGATGGTTGAGGCCTTATAATGATCAAAGTGTTAT
64 ATACGAAAAGCTCAGACGAGCAATTTGTTTCGATGGTTGAGGCCTTATAATGATTAAAGTGTTAT
3408066 CTGCTCTGAT
129 CTGCTCTGAT
* *
3408076 ATTGATCACATCAAGCTCAAAAAGATCGGTGATGAGTCCTTAACCCAGCTATATCATATTTCGAT
1 ATTGATCACATCTAGCTCAAAAAGATCGGTGATGACTCCTTAACCCAGCTATATCATATTTCGAT
* * * * * *
3408141 ATGAAAAGTTCAAACGAGCAATTTGCTTCGATGGTTGAGGCTTTATAATGATTAAAGTGCTATCT
66 ACGAAAAGCTCAGACGAGCAATTTGTTTCGATGGTTGAGGCCTTATAATGATTAAAGTGTTATCT
3408206 GCTCTGAT
131 GCTCTGAT
* * *
3408214 ATTGATCACATCTAGCTCAAAAATATCGGTGATGACTCCTTAACCCAACTGTATCATATTTC-AG
1 ATTGATCACATCTAGCTCAAAAAGATCGGTGATGACTCCTTAACCCAGCTATATCATATTTCGA-
* * * * *
3408278 TACAAAAAGCTCAGACAAGCAATTTGTTTTGATGGTTGAGGCCCTATAACGATTAAAGTGTTATC
65 TACGAAAAGCTCAGACGAGCAATTTGTTTCGATGGTTGAGGCCTTATAATGATTAAAGTGTTATC
*
3408343 TACTCT
130 TGCTCT
3408349 AATACGTCGG
Statistics
Matches: 240, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
137 5 0.02
138 234 0.98
139 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (138 bp):
ATTGATCACATCTAGCTCAAAAAGATCGGTGATGACTCCTTAACCCAGCTATATCATATTTCGAT
ACGAAAAGCTCAGACGAGCAATTTGTTTCGATGGTTGAGGCCTTATAATGATTAAAGTGTTATCT
GCTCTGAT
Found at i:3408838 original size:55 final size:55
Alignment explanation
Indices: 3408754--3408896 Score: 216
Period size: 55 Copynumber: 2.6 Consensus size: 55
3408744 TGGGGACGAA
3408754 TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAG
1 TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAG
* *
3408809 TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAG
1 TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAG
* * * *
3408864 TTGGTGGCACTTTTTACTCCTCAATGAGCAGGA
1 TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
3408897 TACACTTTAT
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 2 0.02
55 79 0.98
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (55 bp):
TTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAG
Found at i:3409655 original size:21 final size:21
Alignment explanation
Indices: 3409629--3409686 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
3409619 AAAAAATTTC
*
3409629 CAAATGTATCGATACATTTGTA
1 CAAATGTATCGATACA-TTCTA
*
3409651 -GAATGTATCGATACATTCTA
1 CAAATGTATCGATACATTCTA
3409671 CAAATGTATCGATACA
1 CAAATGTATCGATACA
3409687 GGGTCCCAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (21 bp):
CAAATGTATCGATACATTCTA
Found at i:3409746 original size:19 final size:19
Alignment explanation
Indices: 3409722--3409789 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
3409712 AATTCAACGA
3409722 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
3409741 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
3409756 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
3409773 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
3409790 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:3409760 original size:32 final size:32
Alignment explanation
Indices: 3409724--3409786 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3409714 TTCAACGATT
*
3409724 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3409756 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3409787 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3409761 original size:13 final size:13
Alignment explanation
Indices: 3409743--3409767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3409733 ACATAAGTTT
3409743 TGTATCGATACAA
1 TGTATCGATACAA
3409756 TGTATCGATACA
1 TGTATCGATACA
3409768 TAAGTATTGT
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:3409847 original size:13 final size:13
Alignment explanation
Indices: 3409829--3409854 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3409819 CATTTTTCTG
3409829 TGTATCGATACAT
1 TGTATCGATACAT
3409842 TGTATCGATACAT
1 TGTATCGATACAT
3409855 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3409851 original size:33 final size:33
Alignment explanation
Indices: 3409809--3409872 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
3409799 GCCAAGGAAA
***
3409809 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
3409842 TGTATCGATACATGGATCTTTGTATCGATAC
1 TGTATCGATACATGGATCTGTGTATCGATAC
3409873 GTTTGGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3412266 original size:51 final size:53
Alignment explanation
Indices: 3412204--3412545 Score: 208
Period size: 52 Copynumber: 6.5 Consensus size: 53
3412194 AGTTTATCAA
* * * *
3412204 TTCTCCATAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
3412255 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ATAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * * *** * * *
3412309 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAAC
1 TTCTTCATAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAAT
** ** * * *
3412362 CCCGTT-ATTTTCGAGGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAAT
1 TTC-TTCATAATC--GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * * *
3412416 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAATT
1 TTCTT-CATAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* *
3412469 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCGAT
1 TT-CTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
3412521 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCATAATCGGGGATACTCCAAC
3412546 CTCGTTATTT
Statistics
Matches: 221, Mismatches: 46, Indels: 47
0.70 0.15 0.15
Matches are distributed among these distances:
50 4 0.02
51 37 0.17
52 81 0.37
53 36 0.16
54 38 0.17
55 22 0.10
57 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (53 bp):
TTCTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:3412529 original size:104 final size:103
Alignment explanation
Indices: 3412212--3412544 Score: 291
Period size: 104 Copynumber: 3.2 Consensus size: 103
3412202 AATTCTCCAT
* * * *
3412212 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGATACT
1 AATCGGGGATACTCCAA-TCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
*
3412276 CTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCAC
65 CCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TTCAC
* * * ** * * * ** **
3412317 AATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA--CCCCGTTATTTTCGAGGG
1 AATCGGGGATACTCCAATCCGGTTTTATTTTC---AAAACACCAATTTTCC-TT-TAATC--GGG
* * *
3412379 GATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTTCCAC
59 GATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT-CAC
*
3412424 AATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAATCC-GGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
* *
3412489 CCAACTCCGATTTTATTTCCAAAAATACCGATTTTTCAC
65 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAC
*
3412528 AATCGAGGATACTCCAA
1 AATCGGGGATACTCCAA
3412545 CCTCGTTATT
Statistics
Matches: 174, Mismatches: 38, Indels: 33
0.71 0.16 0.13
Matches are distributed among these distances:
103 6 0.03
104 44 0.25
105 30 0.17
106 21 0.12
107 41 0.24
108 4 0.02
109 28 0.16
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (103 bp):
AATCGGGGATACTCCAATCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTC
CAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAC
Found at i:3424557 original size:17 final size:16
Alignment explanation
Indices: 3424535--3424612 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 16
3424525 CATTCTCTTC
*
3424535 AAAAAAAAAAGCAAAAA
1 AAAAAAAAAAAC-AAAA
3424552 AAAAAAACAAAACAAAA
1 AAAAAAA-AAAACAAAA
*
3424569 CAAAAAACAAAACAAAGA
1 -AAAAAAAAAAACAAA-A
3424587 AAAAGAGAGAAAAA-AAAA
1 AAAA-A-A-AAAAACAAAA
*
3424605 AAGAAAAA
1 AAAAAAAA
3424613 TCTACTTAAG
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
15 2 0.04
16 1 0.02
17 24 0.47
18 16 0.31
19 4 0.08
20 4 0.08
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAACAAAA
Found at i:3424590 original size:22 final size:21
Alignment explanation
Indices: 3424549--3424612 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
3424539 AAAAAAGCAA
3424549 AAAAAAAAAACAAA-ACAAAAC
1 AAAAAAAAAACAAAGA-AAAAC
*
3424570 AAAAAACAAAACAAAGAAAAAG
1 AAAAAA-AAAACAAAGAAAAAC
3424592 AGAGAAAAAAAA-AAAGAAAAA
1 A-A-AAAAAAAACAAAGAAAAA
3424613 TCTACTTAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
21 6 0.16
22 22 0.58
23 6 0.16
24 4 0.11
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACAAAGAAAAAC
Found at i:3424609 original size:12 final size:12
Alignment explanation
Indices: 3424535--3424612 Score: 68
Period size: 12 Copynumber: 6.3 Consensus size: 12
3424525 CATTCTCTTC
3424535 AAAAAAAAAAGCA
1 AAAAAAAAAAG-A
3424548 AAAAAAAAAA-A
1 AAAAAAAAAAGA
* * *
3424559 CAAAACAAAACA
1 AAAAAAAAAAGA
* *
3424571 AAAAACAAAACA
1 AAAAAAAAAAGA
*
3424583 AAGAAAAAGAGAGA
1 AA-AAAAA-AAAGA
3424597 AAAAAAAAAAGA
1 AAAAAAAAAAGA
3424609 AAAA
1 AAAA
3424613 TCTACTTAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
11 9 0.16
12 22 0.40
13 19 0.35
14 5 0.09
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:3425658 original size:55 final size:54
Alignment explanation
Indices: 3425575--3426376 Score: 995
Period size: 55 Copynumber: 14.4 Consensus size: 54
3425565 CTCCGTCCGC
*
3425575 TTTTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
3425629 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
3425684 TTTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
** *
3425739 CCTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACAGAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
3425793 TTTTCCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
*
3425848 TTTTCCAGTCCTCAGAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
** * *
3425903 CCTTCAGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACAC-----CTTTCAAAGCCCACACAAGTTGGTGGCA
** * **
3425962 CCTTCAGTCCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCATC-CAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCA-CACAAGTTGGTGGCA
* * *
3426021 CCTTT-AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGA--C----ACCTTTCAAAGCCCACACAAGTTGGTGGCA
3426081 TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * * *
3426136 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCGCACATAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
3426191 CCTTTCAGTCCCCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
3426246 TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * *
3426301 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
3426356 CTTTTTACTCCTCAATGAGCA
1 -TTTTCAGTCCTCAAAGAGCA
3426377 AGATACACTT
Statistics
Matches: 671, Mismatches: 43, Indels: 67
0.86 0.06 0.09
Matches are distributed among these distances:
53 2 0.00
54 79 0.12
55 434 0.65
56 14 0.02
58 2 0.00
59 92 0.14
60 25 0.04
61 18 0.03
64 4 0.01
65 1 0.00
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (54 bp):
TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:3425848 original size:164 final size:162
Alignment explanation
Indices: 3425577--3426376 Score: 1041
Period size: 164 Copynumber: 4.8 Consensus size: 162
3425567 CCGTCCGCTT
* *
3425577 TTCAGTCCCCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
1 TTCAGTCCTCAAAGAGCAGGACACCTTT-AAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTC
* *
3425642 AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAGAGAGCAG
64 AAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAG
3425706 GACACCTCTTAAAGCCCACACAAGTTGGTGGCACC
128 GACACCTCTTAAAGCCCACACAAGTTGGTGGCACC
* *
3425741 TTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACAGAAGTTGGTGGCATTTTCCAGTCCTC
1 TTCAGTCCTCAAAGAGCAGGACACCTTT-AAAGCCCACACAAGTTGGTGGCACTTT-CAGTCCTC
* *
3425806 AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAGAGAGCAG
64 AAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAAAGAGCAG
3425870 GACACCTCTTAAAGCCCACACAAGTTGGTGGCACC
128 GACACCTCTTAAAGCCCACACAAGTTGGTGGCACC
* *
3425905 TTCAGTCCTCAAAGAGCGGGACACATTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCAGT
1 TTCAGTCCTCAAAGAGCAGGACAC-----C-TTTAAAGCCCACACAAGTTGGTGGCACTTTCAGT
* * *
3425970 CCTCAAAGAGCGGGATGCCTTTTCTTTTAAAGCCCATC-CAAGTTGGTGGCACCTTT-AGTCCTC
60 CCTCAAAGAGCAGGACGCC-TTTC----AAAGCCCA-CACAAGTTGGTGGCACTTTTCAGTCCTC
** * **
3426033 AAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATT
119 AAAGAGCAGGA--C---ACCTCTT-AAAGCCCACACAAGTTGGTGGCACC
3426083 TTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCT
1 TT-CAGTCCTCAAAGAGCAGGACACCT-TTAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCT
* * * *
3426148 CAAAGAGCAGGACGCCTTTCAAAGCGCACATAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAG
63 CAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAG
* **
3426213 GACACCTTTTAAAGCCCACACAAGTTGGTGGCATT
128 GACACCTCTTAAAGCCCACACAAGTTGGTGGCACC
3426248 TTCCAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCT
1 TT-CAGTCCTCAAAGAGCAGGACACCT-TTAAAGCCCACACAAGTTGGTGGCA-CTTTCAGTCCT
* * * *
3426313 CAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGCA
63 CAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCA
3426377 AGATACACTT
Statistics
Matches: 579, Mismatches: 33, Indels: 47
0.88 0.05 0.07
Matches are distributed among these distances:
164 185 0.32
165 146 0.25
166 5 0.01
168 20 0.03
169 31 0.05
170 27 0.05
171 17 0.03
172 17 0.03
173 22 0.04
174 35 0.06
175 24 0.04
177 4 0.01
178 25 0.04
179 21 0.04
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (162 bp):
TTCAGTCCTCAAAGAGCAGGACACCTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAA
AGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGAC
ACCTCTTAAAGCCCACACAAGTTGGTGGCACC
Found at i:3427225 original size:13 final size:13
Alignment explanation
Indices: 3427207--3427231 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3427197 ACATAAGTTT
3427207 TGTATCGATACAA
1 TGTATCGATACAA
3427220 TGTATCGATACA
1 TGTATCGATACA
3427232 TAATTAGCTA
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:3429719 original size:51 final size:53
Alignment explanation
Indices: 3429657--3429998 Score: 210
Period size: 52 Copynumber: 6.5 Consensus size: 53
3429647 AGTTTATCAA
* * * *
3429657 TTCTCCATAATCGGGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
*
3429708 TT-TTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ATAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * * * * * * *
3429762 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGAGGATACTCCAAC
1 TTCTTCATAATCGGGGATACTCCAACTCCGATTTTAT-TTCCA-AAAACACCAAT
** * * * *
3429815 CCCGTT-AT-TTCCGAGGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAAT
1 TTC-TTCATAAT-C--GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAAT
* * * *
3429869 TT-TTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAATT
1 TTCTT-CATAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-T
* *
3429922 TTCCTT--TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCGAT
1 TT-CTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
3429974 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCATAATCGGGGATACTCCAAC
3429999 CTCGTTATTT
Statistics
Matches: 221, Mismatches: 43, Indels: 53
0.70 0.14 0.17
Matches are distributed among these distances:
50 4 0.02
51 37 0.17
52 83 0.38
53 35 0.16
54 36 0.16
55 23 0.10
57 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (53 bp):
TTCTTCATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:3429797 original size:24 final size:26
Alignment explanation
Indices: 3429771--3429821 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
3429761 TTTCTTCACA
*
3429771 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGAGGATACTCCAACCCCGTTAA-C
3429798 ATCGAGGATACTCCAACCCCGTTA
1 ATCGAGGATACTCCAACCCCGTTA
3429822 TTTCCGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (26 bp):
ATCGAGGATACTCCAACCCCGTTAAC
Found at i:3429884 original size:107 final size:105
Alignment explanation
Indices: 3429720--3430112 Score: 332
Period size: 107 Copynumber: 3.7 Consensus size: 105
3429710 TTCTATAATC
*
3429720 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTA-TTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCC
3429785 AACCCCGTTAATCATCGAGGATACTCCAACCCCGTTATTTCCGA
63 AACCCCGTTAATCATCGAGGATACTCCAACCCCGTTA-TTCCGA
* * *
3429829 GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCCA
1 GGGGATACTCCAACTCCGATTTTATTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCCA
** * ** * * ** * *
3429893 ATCCTGGTTTTATTTTC-A--AAACGCCAATTTTCCTTTAAT-C--
64 A-CCCCG-TTAATCATCGAGGATACTCCAA--CCCCGTTATTCCGA
* * *
3429933 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCGATTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTA-TTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
* * *
3429998 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
65 CCCCGTTA-ATCATCGAGGATACTCCAACCCCGTTA-TTCCGA
* ** * * *** * * *
3430041 GGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAAC
1 GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
3430106 CCCGTTA
66 CCCGTTA
3430113 TTTTCGAAGG
Statistics
Matches: 224, Mismatches: 44, Indels: 34
0.74 0.15 0.11
Matches are distributed among these distances:
102 2 0.01
103 7 0.03
104 47 0.21
105 14 0.06
106 20 0.09
107 75 0.33
108 31 0.14
109 28 0.12
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (105 bp):
GGGGATACTCCAACTCCGATTTTATTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTAATCATCGAGGATACTCCAACCCCGTTATTCCGA
Found at i:3429982 original size:104 final size:103
Alignment explanation
Indices: 3429665--3429997 Score: 300
Period size: 104 Copynumber: 3.2 Consensus size: 103
3429655 AATTCTCCAT
* * * *
3429665 AATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTT-CTATAATCGGGGATACT
1 AATCGGGGATACTCCAA-TCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
*
3429729 CTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCAC
65 CCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TTCAC
* * * ** * * ** * *
3429770 AATCGGGGATACTCCAACCCCG-TTAATCATCGAGGATACTCCAA--CCCCGTTATTTCCGAGGG
1 AATCGGGGATACTCCAATCCGGTTTTATTTTC-A--AAACACCAATTTTCCTTTA-AT-C--GGG
* * *
3429832 GATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTTCCAC
59 GATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT-CAC
*
3429877 AATCGGGGATACTCCAATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGGGATACT
1 AATCGGGGATACTCCAATCC-GGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACT
* *
3429942 CCAACTCCGATTTTATTTCCAAAAATACCGATTTTTCAC
65 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAC
*
3429981 AATCGAGGATACTCCAA
1 AATCGGGGATACTCCAA
3429998 CCTCGTTATT
Statistics
Matches: 176, Mismatches: 36, Indels: 33
0.72 0.15 0.13
Matches are distributed among these distances:
103 6 0.03
104 45 0.26
105 32 0.18
106 19 0.11
107 38 0.22
108 8 0.05
109 28 0.16
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (103 bp):
AATCGGGGATACTCCAATCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTC
CAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAC
Found at i:3430018 original size:28 final size:28
Alignment explanation
Indices: 3429982--3430058 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
3429972 ATTTTTCACA
* * *
3429982 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
3430010 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
3430038 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
3430059 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:3430032 original size:212 final size:212
Alignment explanation
Indices: 3429660--3430065 Score: 620
Period size: 212 Copynumber: 1.9 Consensus size: 212
3429650 TTATCAATTC
* * *
3429660 TCCATAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
3429725 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * *
3429790 CGTTAATCATCGAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTATC
131 CGTTAATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
3429855 GCTAAAACACTAATTTT
196 GCTAAAACACTAATTTT
* * *
3429872 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGGGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
3429936 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCGATTT-TTCACAATCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * *
3429999 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
3430064 AT
193 AT
3430066 TCCCAAAATA
Statistics
Matches: 175, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
211 31 0.18
212 109 0.62
213 35 0.20
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (212 bp):
TCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:3431688 original size:133 final size:133
Alignment explanation
Indices: 3431440--3431699 Score: 326
Period size: 133 Copynumber: 2.0 Consensus size: 133
3431430 AGTTACTGAG
* * * *
3431440 TATATAACTATTTAATATTTAATTAATTTAAGTTCAAATTCTATATAATCAAGTTTATTTATTAG
1 TATATAACTATTTAATATTTAATTAACTCAAGTTCAAATTCTATATAACCAAGTTAATTTATTAG
* **
3431505 AATAATAATATGACTCATGTTCCTAAATGTTCCATGTTCAATTG-TTTTTTTTATATATTATTAT
66 AATAATAATATGACTCATGTTCCTAAATGTTCCAAGACCAATTGTTTTTTTTTA-ATATTATTAT
3431569 CTAA
130 CTAA
* * * *
3431573 TATATAACTATTTAATATTTATTTTACTCAAGTTCAAATTCTATATAACCACGTTAATTTATTGG
1 TATATAACTATTTAATATTTAATTAACTCAAGTTCAAATTCTATATAACCAAGTTAATTTATTAG
* * * * ** *
3431638 GAT-ATAGTGTGTCTCATGTTTTTAAATGTTCTAAGACCAATTGTTATTTTTTTAATATTATT
66 AATAATAATATGACTCATGTTCCTAAATGTTCCAAGACCAATTGTT-TTTTTTTAATATTATT
3431700 CTATATATTA
Statistics
Matches: 107, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
132 31 0.29
133 68 0.64
134 8 0.07
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.49
Consensus pattern (133 bp):
TATATAACTATTTAATATTTAATTAACTCAAGTTCAAATTCTATATAACCAAGTTAATTTATTAG
AATAATAATATGACTCATGTTCCTAAATGTTCCAAGACCAATTGTTTTTTTTTAATATTATTATC
TAA
Found at i:3432655 original size:20 final size:21
Alignment explanation
Indices: 3432608--3432659 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3432598 GAAAGGTGTA
3432608 TTTGGATGAAATGATGCATTG
1 TTTGGATGAAATGATGCATTG
* *
3432629 GTTGGATGAAA-GAATGCCTT-
1 TTTGGATGAAATG-ATGCATTG
3432649 TTTGGATGAAA
1 TTTGGATGAAA
3432660 AAAATGTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.35
Consensus pattern (21 bp):
TTTGGATGAAATGATGCATTG
Found at i:3433460 original size:21 final size:21
Alignment explanation
Indices: 3433436--3433475 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
3433426 CTAATGATGA
3433436 AATATTTTGAATTCAAAATAC
1 AATATTTTGAATTCAAAATAC
3433457 AATATTTTGAATTCAAAAT
1 AATATTTTGAATTCAAAAT
3433476 GAACTAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (21 bp):
AATATTTTGAATTCAAAATAC
Found at i:3433666 original size:67 final size:67
Alignment explanation
Indices: 3433586--3433728 Score: 250
Period size: 67 Copynumber: 2.1 Consensus size: 67
3433576 ATGAGTATAG
* *
3433586 GAAGAAACTCCTACATATATCCGAGGAGTTCACTATTGAAAAGATACTAAGGCACTTGTGCATTG
1 GAAGAAACTCCTACATATATCCAAGGAGTTCACTATTGAAAAGATACTAAAGCACTTGTGCATTG
3433651 AA
66 AA
* *
3433653 TAAGAAACTCCTACATATGTCCAAGGAGTTCACTATTGAAAAGATACTAAAGCACTTGTGCATTG
1 GAAGAAACTCCTACATATATCCAAGGAGTTCACTATTGAAAAGATACTAAAGCACTTGTGCATTG
3433718 AA
66 AA
3433720 GAAGAAACT
1 GAAGAAACT
3433729 TGAAAGCACG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (67 bp):
GAAGAAACTCCTACATATATCCAAGGAGTTCACTATTGAAAAGATACTAAAGCACTTGTGCATTG
AA
Found at i:3438812 original size:14 final size:13
Alignment explanation
Indices: 3438790--3438824 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
3438780 AAATCTTCAC
*
3438790 TTTTTTTTTGTTT
1 TTTTTTTTTCTTT
3438803 TTTTTCTTTTCTTT
1 TTTTT-TTTTCTTT
3438817 TTTTTTTT
1 TTTTTTTT
3438825 ACAATTGCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:3448012 original size:22 final size:21
Alignment explanation
Indices: 3447962--3448020 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
3447952 AAAAGGTGTA
3447962 TTTGGATGAAATG-ATGCATTG
1 TTTGGATGAAA-GAATGCATTG
* *
3447983 GTTGGATGAAAGAATGCATTTT
1 TTTGGATGAAAGAATGCA-TTG
*
3448005 TTTGGATGAAAAAATG
1 TTTGGATGAAAGAATG
3448021 TAACTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 1 0.03
21 15 0.47
22 16 0.50
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (21 bp):
TTTGGATGAAAGAATGCATTG
Found at i:3448028 original size:22 final size:22
Alignment explanation
Indices: 3447984--3448028 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3447974 GATGCATTGG
* **
3447984 TTGGATGAAAGAATGCATTTTT
1 TTGGATGAAAAAATGCAACTTT
*
3448006 TTGGATGAAAAAATGTAACTTT
1 TTGGATGAAAAAATGCAACTTT
3448028 T
1 T
3448029 ATGACCAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (22 bp):
TTGGATGAAAAAATGCAACTTT
Found at i:3449437 original size:79 final size:79
Alignment explanation
Indices: 3449336--3449628 Score: 338
Period size: 79 Copynumber: 3.7 Consensus size: 79
3449326 TTGTTTTTAG
* * * * * *
3449336 AAATAATGGGGTTGGAGCATCCCTGATGGTGAAAAATTGATGTTTTAGAAATAAAATCGAGGTTG
1 AAATAACGGGGTTGGAGTATCCCTGATAGTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTT
* *
3449401 GAGTATCCCCTCAA
66 GAGTATCCTCTCGA
* * * *
3449415 AAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCAATGTTTTAGAAATAAAATCGGGGTTT
1 AAATAACGGGGTTGGAGTATCCCTGATAGTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTT
*
3449480 GAGTATCCTTTCGA
66 GAGTATCCTCTCGA
* * * * * *
3449494 AAATAACGGGGTTGAAGTATCCCTAATAATGGAAAATTGATGTTTTAAAAATAAAA-CTGGGGTT
1 AAATAACGGGGTTGGAGTATCCCTGATAGTGAAAAATCGATGTTTTAGAAATAAAATC-GGGGTT
*
3449558 TGAGTATCTTCTCGA
65 TGAGTATCCTCTCGA
* * * *
3449573 TAATAACAGGGTTGGAGTAT-CCTCGATAGTGGAAAATCGATATTTTAGAAATAAAA
1 AAATAACGGGGTTGGAGTATCCCT-GATAGTGAAAAATCGATGTTTTAGAAATAAAA
3449629 ACATCAATAA
Statistics
Matches: 181, Mismatches: 31, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
78 4 0.02
79 177 0.98
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.29
Consensus pattern (79 bp):
AAATAACGGGGTTGGAGTATCCCTGATAGTGAAAAATCGATGTTTTAGAAATAAAATCGGGGTTT
GAGTATCCTCTCGA
Found at i:3449585 original size:158 final size:158
Alignment explanation
Indices: 3449336--3449628 Score: 381
Period size: 158 Copynumber: 1.9 Consensus size: 158
3449326 TTGTTTTTAG
* * * ** *
3449336 AAATAATGGGGTTGGAGCATCCCTGATGGTGAAAAATTGATGTTTTAGAAATAAAATCGAGGTTG
1 AAATAACGGGGTTGAAGCATCCCTAATAATGAAAAATTGATGTTTTAAAAATAAAATCGAGGTTG
* * *
3449401 GAGTATCCCCTCAAAAATAACGGGGTTAGAGTATCCCCGATGGTGAAAAATCAATGTTTTAGAAA
66 GAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATAGTGAAAAATCAATATTTTAGAAA
3449466 TAAAATCGGGGTTTGAGTATCCTTTCGA
131 TAAAATCGGGGTTTGAGTATCCTTTCGA
* * *
3449494 AAATAACGGGGTTGAAGTATCCCTAATAATGGAAAATTGATGTTTTAAAAATAAAA-CTGGGGTT
1 AAATAACGGGGTTGAAGCATCCCTAATAATGAAAAATTGATGTTTTAAAAATAAAATC-GAGGTT
* ** * * * * * *
3449558 TGAGTATCTTCTCGATAATAACAGGGTTGGAGTATCCTCGATAGTGGAAAATCGATATTTTAGAA
65 GGAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATAGTGAAAAATCAATATTTTAGAA
3449623 ATAAAA
130 ATAAAA
3449629 ACATCAATAA
Statistics
Matches: 113, Mismatches: 21, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
157 1 0.01
158 112 0.99
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.29
Consensus pattern (158 bp):
AAATAACGGGGTTGAAGCATCCCTAATAATGAAAAATTGATGTTTTAAAAATAAAATCGAGGTTG
GAGTATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATAGTGAAAAATCAATATTTTAGAAA
TAAAATCGGGGTTTGAGTATCCTTTCGA
Found at i:3450124 original size:13 final size:13
Alignment explanation
Indices: 3450106--3450132 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3450096 ACATTATGCT
3450106 TTGTATCGATACA
1 TTGTATCGATACA
3450119 TTGTATCGATACA
1 TTGTATCGATACA
3450132 T
1 T
3450133 GTTAATTGTA
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:3450161 original size:20 final size:20
Alignment explanation
Indices: 3450118--3450192 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
3450108 GTATCGATAC
**
3450118 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
3450137 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
3450157 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
3450177 ATTGTATCGATACATG
1 ATTGTATCGATACATG
3450193 AGATTGGCAG
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
19 15 0.28
20 38 0.72
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:3450247 original size:20 final size:20
Alignment explanation
Indices: 3450222--3450274 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3450212 TACCACTGTT
*
3450222 TGTATCGATACATGGT-ACAA
1 TGTATCGATACATGATGA-AA
*
3450242 TGTATCGATACATGATGAAT
1 TGTATCGATACATGATGAAA
3450262 TGTATCGATACAT
1 TGTATCGATACAT
3450275 AGCTTGTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGATGAAA
Found at i:3458889 original size:19 final size:20
Alignment explanation
Indices: 3458865--3458914 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
3458855 ACATTATGCT
**
3458865 TTGTATCGATACAT-GTTAA
1 TTGTATCGATACATGGACAA
*
3458884 TTGTATCAATACATGGACAA
1 TTGTATCGATACATGGACAA
3458904 TTGTATCGATA
1 TTGTATCGATA
3458915 TATGAGATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:3458984 original size:13 final size:13
Alignment explanation
Indices: 3458963--3458993 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3458953 CGATACATGG
*
3458963 TACAATGTATCGA
1 TACATTGTATCGA
3458976 TACATTGTATCGA
1 TACATTGTATCGA
3458989 TACAT
1 TACAT
3458994 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:3458989 original size:33 final size:33
Alignment explanation
Indices: 3458947--3459013 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
3458937 CCACCACTGT
*
3458947 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
3458980 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
3459013 T
1 T
3459014 AGCTTGTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:3462081 original size:39 final size:39
Alignment explanation
Indices: 3462023--3462109 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
3462013 TAAATATATT
*
3462023 GATACATTTCCTTGATAGTATGCACGGTGGTTTTGTATC
1 GATACATTTCCTTGATAGTATACACGGTGGTTTTGTATC
* *
3462062 GATACATTTCCTTGGTAGTATACAGGGTGGTTTTGTATC
1 GATACATTTCCTTGATAGTATACACGGTGGTTTTGTATC
3462101 GATACATTT
1 GATACATTT
3462110 TAGGCATGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.22, C:0.14, G:0.23, T:0.41
Consensus pattern (39 bp):
GATACATTTCCTTGATAGTATACACGGTGGTTTTGTATC
Found at i:3462138 original size:13 final size:13
Alignment explanation
Indices: 3462116--3462176 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
3462106 ATTTTAGGCA
3462116 TGTATCGATACAT
1 TGTATCGATACAT
*
3462129 TGTATTGATACAT
1 TGTATCGATACAT
**
3462142 T-T-T--AGGCA-
1 TGTATCGATACAT
3462150 TGTATCGATACAT
1 TGTATCGATACAT
3462163 TGTATCGATACAT
1 TGTATCGATACAT
3462176 T
1 T
3462177 TACTGTTTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
8 1 0.03
9 4 0.11
10 1 0.03
11 1 0.03
12 4 0.11
13 27 0.71
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3462195 original size:34 final size:34
Alignment explanation
Indices: 3462094--3462177 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
3462084 CAGGGTGGTT
3462094 TTGTATCGATACATTTTAGGCATGTATCGATACA
1 TTGTATCGATACATTTTAGGCATGTATCGATACA
*
3462128 TTGTATTGATACATTTTAGGCATGTATCGATACA
1 TTGTATCGATACATTTTAGGCATGTATCGATACA
3462162 TTGTATCGATACATTT
1 TTGTATCGATACATTT
3462178 ACTGTTTGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.42
Consensus pattern (34 bp):
TTGTATCGATACATTTTAGGCATGTATCGATACA
Found at i:3463832 original size:154 final size:154
Alignment explanation
Indices: 3463594--3463894 Score: 367
Period size: 154 Copynumber: 2.0 Consensus size: 154
3463584 AACATATTCA
* * * *
3463594 TAAATGCACACATTTGGCATAAGAGTGACCTAGTGATTACCTAAGACTTGCTTTTAAAAAATTAC
1 TAAATGCACACATTGGGCATAAAAGTGACCTAGTGACTACCTAAGACTTGCTTCTAAAAAATTAC
** * * * *
3463659 CAAAATGCCCTTGGAGTATATGTTCGACGTAAAAGTATCTTAATAA-TTCTAAAGGACATGAAAA
66 CAAAATGCCCTTGGAGTATACCTTCAACGTAAAAGTATCCTAATAACCT-TAAAGGACACGAAAA
*
3463723 TGATAAGTAAAAGGATAACCTATCC
130 TGATAAGTAAAAAGATAACCTATCC
* * * * **
3463748 TAAATG-ACACCTTGGGCATAAAAGTGACCTAGTGACTA-TTAGGACTTGGTTCTAGGAAATCTT
1 TAAATGCACACATTGGGCATAAAAGTGACCTAGTGACTACCTAAGACTTGCTTCTA--AAAAATT
* *
3463811 ACCAAAATGCCCTTAGG-GTATACCTTCAACGTGAAAGTATCCTAGTAACCTTAAAGGACACGAA
64 ACCAAAATGCCCTT-GGAGTATACCTTCAACGTAAAAGTATCCTAATAACCTTAAAGGACACGAA
3463875 AATGATAAGTAAAAAGATAA
128 AATGATAAGTAAAAAGATAA
3463895 ACAAAGCAAC
Statistics
Matches: 124, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
152 12 0.10
153 28 0.23
154 81 0.65
155 3 0.02
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (154 bp):
TAAATGCACACATTGGGCATAAAAGTGACCTAGTGACTACCTAAGACTTGCTTCTAAAAAATTAC
CAAAATGCCCTTGGAGTATACCTTCAACGTAAAAGTATCCTAATAACCTTAAAGGACACGAAAAT
GATAAGTAAAAAGATAACCTATCC
Found at i:3465280 original size:152 final size:154
Alignment explanation
Indices: 3465086--3465369 Score: 412
Period size: 152 Copynumber: 1.9 Consensus size: 154
3465076 CCTAACAAGA
* * **
3465086 TAAAAAACCTAAAATATGTTTAATAAGGAATGAAACAATCCTCCTGTGGTACTAGGGACTCTCAG
1 TAAAAAACCCAAAATATGTTTAATAAGGAATGAAACAATCCTCCTATGCCACTAGGGACTCTCAG
* *
3465151 CCAAGCAAGGATACTCAAAG-AAAAATTTTGAACTT-TTCGCAAT-TGAGTCCTTAAAGTTTCTA
66 CCAAGCAAGGATACTCAAAGAAAAAATTTTGAACTTATTCGCAATAT-AATCCTTAAACTTTCTA
3465213 AAAATTTGTAAAAAGGTCCTTATGT
130 AAAATTTGTAAAAAGGTCCTTATGT
* * * * * *
3465238 TAAAAAACCCAAAATATGTTTAATAATGCATGAAATAGTCCTCTTATGCCACTAGGGACTCTCGG
1 TAAAAAACCCAAAATATGTTTAATAAGGAATGAAACAATCCTCCTATGCCACTAGGGACTCTCAG
* *
3465303 CCAAGCAAGGATACTCAAAGAAAAAATTTTGAACTTATTTGTAATATAATCCTTAAACTTTCTAA
66 CCAAGCAAGGATACTCAAAGAAAAAATTTTGAACTTATTCGCAATATAATCCTTAAACTTTCTAA
3465368 AA
131 AA
3465370 TTTCAAAATA
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
152 75 0.65
153 15 0.13
154 24 0.21
155 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.30
Consensus pattern (154 bp):
TAAAAAACCCAAAATATGTTTAATAAGGAATGAAACAATCCTCCTATGCCACTAGGGACTCTCAG
CCAAGCAAGGATACTCAAAGAAAAAATTTTGAACTTATTCGCAATATAATCCTTAAACTTTCTAA
AAATTTGTAAAAAGGTCCTTATGT
Found at i:3467442 original size:155 final size:154
Alignment explanation
Indices: 3467096--3467451 Score: 403
Period size: 154 Copynumber: 2.3 Consensus size: 154
3467086 AAACTCGATT
* * * * * * *
3467096 TAAAAAATTACGAAAATACCTCT-AGGAGGTACATTCGATGTAAAAGTGCTCAATACTTCTAAAA
1 TAAAAAATTATGAAAATACTTCTAAGG-GATACATTTGACGTAGAAGTGCTCAATACTCCTAAAA
* * *
3467160 GACTTGAAAAGGATTATAGATGCGATGAACCTATCATATATACCCACCGTTAGCATAAAGCGGAC
65 GACTTAAAAAGGATTATAGATGCGATGAAACTATCATAAATACCCACCGTTAGCATAAAGCGGAC
** *
3467225 CTGGTGACAACCTCGGACTTAGTTC
130 CCAGTGACAACCTAGGACTTAGTTC
* * **
3467250 TAAAAAATTATGAAAATATCTT-TAGGGGATACCTTTGACGTAGAAGTGCTTGATACTCCTAAAA
1 TAAAAAATTATGAAAATA-CTTCTAAGGGATACATTTGACGTAGAAGTGCTCAATACTCCTAAAA
* * * * * *
3467314 GACTTAAAAAGGATTATGGATGGGATGAAACTATCCTAAATACCCACC-TTTGATATTAAAGTGG
65 GACTTAAAAAGGATTATAGATGCGATGAAACTATCATAAATACCCACCGTTAG-CA-TAAAGCGG
* *
3467378 ACCCAGTGACAGCCTAGGACTTGGTTC
128 ACCCAGTGACAACCTAGGACTTAGTTC
* * *
3467405 TAGAAAATTATGAAAATACTTCTAAGGGATACTTTTGACATAGAAGT
1 TAAAAAATTATGAAAATACTTCTAAGGGATACATTTGACGTAGAAGT
3467452 ACCCAGTACC
Statistics
Matches: 168, Mismatches: 29, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
153 3 0.02
154 93 0.55
155 72 0.43
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (154 bp):
TAAAAAATTATGAAAATACTTCTAAGGGATACATTTGACGTAGAAGTGCTCAATACTCCTAAAAG
ACTTAAAAAGGATTATAGATGCGATGAAACTATCATAAATACCCACCGTTAGCATAAAGCGGACC
CAGTGACAACCTAGGACTTAGTTC
Found at i:3467466 original size:155 final size:154
Alignment explanation
Indices: 3467154--3467467 Score: 373
Period size: 155 Copynumber: 2.0 Consensus size: 154
3467144 CTCAATACTT
* * *
3467154 CTAAAAGACTTGAAAAGGATTATAGATGCGATGAACCTATCATATATACCCACCGTTAGCATAAA
1 CTAAAAGACTTAAAAAGGATTATAGATGCGATGAAACTATCATAAATACCCACCGTTAGCATAAA
** * *
3467219 GCGGACCTGGTGACAACCTCGGACTTAGTTCTAAAAAATTATGAAAATATCTTTAGGGGATACCT
66 GCGGACCCAGTGACAACCTAGGACTTAGTTCTAAAAAATTATGAAAATATCTTTAAGGGATACCT
* * ** *
3467284 TTGACGTAGAAGTGCTTGATACTC
131 TTGACATAGAAGTCCCAGATACCC
* * * * *
3467308 CTAAAAGACTTAAAAAGGATTATGGATGGGATGAAACTATCCTAAATACCCACC-TTTGATATTA
1 CTAAAAGACTTAAAAAGGATTATAGATGCGATGAAACTATCATAAATACCCACCGTTAG-CA-TA
* * * *
3467372 AAGTGGACCCAGTGACAGCCTAGGACTTGGTTCTAGAAAATTATGAAAATA-CTTCTAAGGGATA
64 AAGCGGACCCAGTGACAACCTAGGACTTAGTTCTAAAAAATTATGAAAATATCTT-TAAGGGATA
*
3467436 CTTTTGACATAGAAGTACCCAG-TACCC
128 CCTTTGACATAGAAGT-CCCAGATACCC
3467463 CTAAA
1 CTAAA
3467468 GGCCTCGAGA
Statistics
Matches: 134, Mismatches: 22, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
153 3 0.02
154 52 0.39
155 77 0.57
156 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (154 bp):
CTAAAAGACTTAAAAAGGATTATAGATGCGATGAAACTATCATAAATACCCACCGTTAGCATAAA
GCGGACCCAGTGACAACCTAGGACTTAGTTCTAAAAAATTATGAAAATATCTTTAAGGGATACCT
TTGACATAGAAGTCCCAGATACCC
Found at i:3469511 original size:167 final size:163
Alignment explanation
Indices: 3469219--3469726 Score: 495
Period size: 166 Copynumber: 3.0 Consensus size: 163
3469209 AATATATACT
** * * *
3469219 AAAAAAATTCAAAACTCAT-AAAATAAATTAAATTTCTCAAAACTAATTTAATGAGAGTTCAATG
1 AAAAAAATGAAAAACTCATGAAAATAAATGAAATTT-TCAAAACTAATTTAAT-AGAATTAAATG
** ** * * *
3469283 ACAATATCAGATGTATTATAAAAATTTTAAACCGAAGAAAATCTCCCTCAAAACATTTATGGGAT
64 ATGATATTTGATATATT-TAAAAATTTTAAACC-AAGAAAAACTCCCTCAAAACATTTATGGAAT
* *** * ***
3469348 AGAAAATTCAATTTTTTGGAAATAGAGGCATTTCAAGG
127 AGAAAACTCAATTTTTCAAAAACA-AAAAATTTCAAGG
* *
3469386 AAAAAAATGAAAAACTCATGAAAATAAATGAAAATTTCAAAACTAATTTAATATGAATTAAATTA
1 AAAAAAATGAAAAACTCATGAAAATAAATGAAATTTTCAAAACTAATTTAATA-GAATTAAATGA
* * * *
3469451 TGATATTTGATATATATTAAAAATTTTGAACCAAGAAAAACTCCCATGAAAACCTTTATGGAATT
65 TGATATTTGATATAT-TTAAAAATTTTAAACCAAGAAAAACTCCC-TCAAAACATTTATGGAATA
3469516 GAAAACTCAATTTTTCAAAAACAAAAAATTTCAAGG
128 GAAAACTCAATTTTTCAAAAACAAAAAATTTCAAGG
* * *
3469552 AAAAAAATGAAAAACTTATGAAAATAAATGAAATTTTCAAAACTGATTTAATACAAATTAAATGA
1 AAAAAAATGAAAAACTCATGAAAATAAATGAAATTTTCAAAACTAATTTAATA-GAATTAAATGA
* * **
3469617 TGATATTTGATGA-ATTTTAAAAATTATAAACCATGAAAAA-TCCCGTCAAAA-ATAATTACAGA
65 TGATATTTGAT-ATA-TTTAAAAATTTTAAACCAAGAAAAACTCCC-TCAAAACAT--TTATGGA
* * * *
3469679 GTAGAAAA-TCCAGTATTTCAAAAAGAAAGAGAATTTCAAGG
125 ATAGAAAACT-CAATTTTTCAAAAACAAA-A-AATTTCAAGG
3469720 AAAAAAA
1 AAAAAAA
3469727 GGTAAATTAA
Statistics
Matches: 285, Mismatches: 45, Indels: 21
0.81 0.13 0.06
Matches are distributed among these distances:
164 1 0.00
165 10 0.04
166 141 0.49
167 101 0.35
168 32 0.11
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (163 bp):
AAAAAAATGAAAAACTCATGAAAATAAATGAAATTTTCAAAACTAATTTAATAGAATTAAATGAT
GATATTTGATATATTTAAAAATTTTAAACCAAGAAAAACTCCCTCAAAACATTTATGGAATAGAA
AACTCAATTTTTCAAAAACAAAAAATTTCAAGG
Found at i:3469700 original size:166 final size:168
Alignment explanation
Indices: 3469219--3469928 Score: 472
Period size: 167 Copynumber: 4.3 Consensus size: 168
3469209 AATATATACT
** * * * * *
3469219 AAAAAAATTCAAAACTCAT-AAAATAAATTAAATTTCTCAAAACTAATTTAATGA-GAGTTCAAT
1 AAAAAAATGAAAAACTTATGAAAATAAATGAAATTT-TCAAAACTGATTTAAT-ATGAATTAAAT
* ** ** * * * * * ** *
3469282 GACAATATCAGATGTATTATAAAAATTTTAAACCGAAGAAAATCTCCC-TCAAAACATTTATGGG
64 AATGATATTTGATGAATTTTAAAAATTATAAACC-ATGAAAAACTCCCATCAAAACATTTACAGA
* * *** * * *
3469346 ATAGAAAATTCAATTTTTTGGAAATAGAG-GCATTTCAAGG
128 ATAGAAAACTCAATATTTCAAAAACAAAGAGAATTTCAAGG
* * * *
3469386 AAAAAAATGAAAAACTCATGAAAATAAATGAAAATTTCAAAACTAATTTAATATGAATTAAATTA
1 AAAAAAATGAAAAACTTATGAAAATAAATGAAATTTTCAAAACTGATTTAATATGAATTAAATAA
* * * * * * **
3469451 TGATATTTGAT-ATATATTAAAAATTTTGAACCAAGAAAAACTCCCATGAAAACCTTTATGGAAT
66 TGATATTTGATGA-ATTTTAAAAATTATAAACCATGAAAAACTCCCATCAAAACATTTACAGAAT
* *
3469515 TGAAAACTCAATTTTTCAAAAACAAA-A-AATTTCAAGG
130 AGAAAACTCAATATTTCAAAAACAAAGAGAATTTCAAGG
** *
3469552 AAAAAAATGAAAAACTTATGAAAATAAATGAAATTTTCAAAACTGATTTAATACAAATTAAATGA
1 AAAAAAATGAAAAACTTATGAAAATAAATGAAATTTTCAAAACTGATTTAATATGAATTAAATAA
* *
3469617 TGATATTTGATGAATTTTAAAAATTATAAACCATGAAAAA-TCCCGTCAAAA-ATAATTACAGAG
66 TGATATTTGATGAATTTTAAAAATTATAAACCATGAAAAACTCCCATCAAAACAT--TTACAGAA
* *
3469680 TAGAAAA-TCCAGTATTTCAAAAAGAAAGAGAATTTCAAGG
129 TAGAAAACT-CAATATTTCAAAAACAAAGAGAATTTCAAGG
** * * ** * * * *
3469720 AAAAAAA-GGTAAA-TTAATG-AAATAAACGGAATTTTTTGAAATTGATTTATTTTGAGTTAAAT
1 AAAAAAATGAAAAACTT-ATGAAAATAAA-TGAAATTTTCAAAACTGATTTAATATGAATTAAAT
* * * * **
3469782 AATAATCTTTGATGAATTTTAAAATTTATAAACTCATGAAAATCCTCCCAAAAAAAC-TTTAC-G
64 AATGATATTTGATGAATTTTAAAAATTATAAAC-CATGAAAA-ACTCCCATCAAAACATTTACAG
* ** * * *
3469845 AAGAAGAAAACTCTGTATTTTAAAAA-TAAGAAGAA-TTC---T
127 AA-TAGAAAACTCAATATTTCAAAAACAAAG-AGAATTTCAAGG
* * * *
3469884 AAAAAAATCAATAACTCATG-AAATAAAAGAAAATTTTCAAAACTG
1 AAAAAAATGAAAAACTTATGAAAATAAATG-AAATTTTCAAAACTG
3469929 CTTTGATGGA
Statistics
Matches: 437, Mismatches: 83, Indels: 48
0.77 0.15 0.08
Matches are distributed among these distances:
164 9 0.02
165 33 0.08
166 151 0.35
167 169 0.39
168 65 0.15
169 1 0.00
170 9 0.02
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (168 bp):
AAAAAAATGAAAAACTTATGAAAATAAATGAAATTTTCAAAACTGATTTAATATGAATTAAATAA
TGATATTTGATGAATTTTAAAAATTATAAACCATGAAAAACTCCCATCAAAACATTTACAGAATA
GAAAACTCAATATTTCAAAAACAAAGAGAATTTCAAGG
Found at i:3475164 original size:39 final size:39
Alignment explanation
Indices: 3475110--3475226 Score: 234
Period size: 39 Copynumber: 3.0 Consensus size: 39
3475100 ACCGAAAGTG
3475110 CTCTTCCTATCAACCTTACAACCACCAAAATCTGCGTCA
1 CTCTTCCTATCAACCTTACAACCACCAAAATCTGCGTCA
3475149 CTCTTCCTATCAACCTTACAACCACCAAAATCTGCGTCA
1 CTCTTCCTATCAACCTTACAACCACCAAAATCTGCGTCA
3475188 CTCTTCCTATCAACCTTACAACCACCAAAATCTGCGTCA
1 CTCTTCCTATCAACCTTACAACCACCAAAATCTGCGTCA
3475227 AAGTAAGCAT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.31, C:0.38, G:0.05, T:0.26
Consensus pattern (39 bp):
CTCTTCCTATCAACCTTACAACCACCAAAATCTGCGTCA
Found at i:3478346 original size:21 final size:21
Alignment explanation
Indices: 3478322--3478361 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3478312 TCTTCTTGCA
* *
3478322 ATTCACTCATTTTCTTTTCTG
1 ATTCAATCAATTTCTTTTCTG
*
3478343 ATTCAATTAATTTCTTTTC
1 ATTCAATCAATTTCTTTTC
3478362 AAGAATATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (21 bp):
ATTCAATCAATTTCTTTTCTG
Found at i:3480684 original size:21 final size:21
Alignment explanation
Indices: 3480658--3480710 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
3480648 GTCAACCTTG
*
3480658 TGTATCAATACCAATAGTACA
1 TGTATCGATACCAATAGTACA
3480679 TGTATCGATACCAATAGTACA
1 TGTATCGATACCAATAGTACA
3480700 TGTATCGATAC
1 TGTATCGATAC
3480711 ATCACGTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (21 bp):
TGTATCGATACCAATAGTACA
Found at i:3481045 original size:5 final size:5
Alignment explanation
Indices: 3481029--3481063 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
3481019 GAAACTAGTT
3481029 TAAAA TTAAAA TAAAA T-AAA TAAAA TAAAA TAAAA
1 TAAAA -TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
3481064 ATTCAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:3481051 original size:9 final size:10
Alignment explanation
Indices: 3481029--3481063 Score: 54
Period size: 9 Copynumber: 3.5 Consensus size: 10
3481019 GAAACTAGTT
3481029 TAAAATTAAAA
1 TAAAA-TAAAA
3481040 TAAAAT-AAA
1 TAAAATAAAA
3481049 TAAAATAAAA
1 TAAAATAAAA
3481059 TAAAA
1 TAAAA
3481064 ATTCAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.39
10 9 0.39
11 5 0.22
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:3481054 original size:14 final size:14
Alignment explanation
Indices: 3481035--3481062 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3481025 AGTTTAAAAT
3481035 TAAAATAAAATAAA
1 TAAAATAAAATAAA
3481049 TAAAATAAAATAAA
1 TAAAATAAAATAAA
3481063 AATTCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAATAAAATAAA
Found at i:3481073 original size:7 final size:6
Alignment explanation
Indices: 3481028--3481091 Score: 50
Period size: 5 Copynumber: 11.3 Consensus size: 6
3481018 TGAAACTAGT
*
3481028 TTAAAA TTAAAA -TAAAA -T-AAA -TAAAA -TAAAA TAAAAA TTCAAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TT-AAAA
*
3481072 TTAAAA -GAAAA TTAACAA TT
1 TTAAAA TTAAAA TTAA-AA TT
3481092 GACAATTATA
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
4 4 0.08
5 18 0.37
6 17 0.35
7 10 0.20
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.27
Consensus pattern (6 bp):
TTAAAA
Found at i:3481076 original size:19 final size:18
Alignment explanation
Indices: 3481029--3481082 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
3481019 GAAACTAGTT
3481029 TAAAATTAAAATAAAATAAA
1 TAAAATTAAAAT-AAA-AAA
*
3481049 TAAAA-TAAAATAAAAAT
1 TAAAATTAAAATAAAAAA
*
3481066 TCAAAATTAAAAGAAAA
1 T-AAAATTAAAATAAAA
3481083 TTAACAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 3 0.10
18 7 0.23
19 15 0.50
20 5 0.17
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (18 bp):
TAAAATTAAAATAAAAAA
Found at i:3482226 original size:16 final size:16
Alignment explanation
Indices: 3482205--3482236 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3482195 GTTGTAAAAT
3482205 CATGAAAAGTAAGACA
1 CATGAAAAGTAAGACA
3482221 CATGAAAAGTAAGACA
1 CATGAAAAGTAAGACA
3482237 TAAACGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.19, T:0.12
Consensus pattern (16 bp):
CATGAAAAGTAAGACA
Found at i:3482399 original size:66 final size:67
Alignment explanation
Indices: 3482329--3482462 Score: 148
Period size: 67 Copynumber: 2.0 Consensus size: 67
3482319 ACTAAGGGTG
* * *
3482329 ACTA-GGACAAAACCTAAGTC-GAAAAGGGGTTGAGTGGGGAGAAATC-GATAAAGTCAACTAAA
1 ACTAGGGACAAAA-CTAAGTCAAAAAAGGGGTTGAGTAGGG-CAAATCTGATAAAGTCAACTAAA
3482391 AGAA
64 AGAA
*** * * *
3482395 ACTAGGGTGGAAACTAAGTCAAAAAAGGTGTTGATTATGGCAAATCTGATAAAGTCAACTAAAAG
1 ACTAGGGACAAAACTAAGTCAAAAAAGGGGTTGAGTAGGGCAAATCTGATAAAGTCAACTAAAAG
3482460 AA
66 AA
3482462 A
1 A
3482463 AAAATTGTGG
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
66 16 0.29
67 40 0.71
ACGTcount: A:0.46, C:0.11, G:0.25, T:0.19
Consensus pattern (67 bp):
ACTAGGGACAAAACTAAGTCAAAAAAGGGGTTGAGTAGGGCAAATCTGATAAAGTCAACTAAAAG
AA
Found at i:3482455 original size:67 final size:67
Alignment explanation
Indices: 3482339--3482562 Score: 242
Period size: 68 Copynumber: 3.4 Consensus size: 67
3482329 ACTAGGACAA
* * * * **
3482339 AACCTAAGTC-GAAAAGGGGTTGAGTGGGGAGAAATC-GATAAAGTCAACTAAAAGAAACTAGGG
1 AACCTAAGTCAAAAAAGGTGTTGATTAGGGTCAAATCTGATAAAGTCAACTAAAAGAAA-TAGGG
3482402 TGG
65 TGG
* * * **
3482405 AAACTAAGTCAAAAAAGGTGTTGATTATGG-CAAATCTGATAAAGTCAACTAAAAGAAAAAAATT
1 AACCTAAGTCAAAAAAGGTGTTGATTAGGGTCAAATCTGATAAAGTCAACTAAAAG--AAATAGG
3482469 GTGG
64 GTGG
* * *
3482473 AACCTAAATCAAAAAAGGTGTTGATTAGGGTGAAAT-TGATAAAGTCAACTAAAAGAGATAGGGT
1 AACCTAAGTCAAAAAAGGTGTTGATTAGGGTCAAATCTGATAAAGTCAACTAAAAGAAATAGGGT
3482537 GG
66 GG
*
3482539 AACCTAAGTC-GAAAAGCGTGTTGA
1 AACCTAAGTCAAAAAAG-GTGTTGA
3482563 CCAGGACGAA
Statistics
Matches: 132, Mismatches: 20, Indels: 12
0.80 0.12 0.07
Matches are distributed among these distances:
65 5 0.04
66 37 0.28
67 32 0.24
68 51 0.39
69 7 0.05
ACGTcount: A:0.44, C:0.10, G:0.25, T:0.21
Consensus pattern (67 bp):
AACCTAAGTCAAAAAAGGTGTTGATTAGGGTCAAATCTGATAAAGTCAACTAAAAGAAATAGGGT
GG
Found at i:3482580 original size:66 final size:66
Alignment explanation
Indices: 3482339--3482594 Score: 234
Period size: 66 Copynumber: 3.8 Consensus size: 66
3482329 ACTAGGACAA
* * ** *
3482339 AACCTAAGTC-GAAAAGGGGTTGAGTGGGGA-GAAATCGATAAAGTCAACTAAAAGAAACTAGGG
1 AACCTAAGTCAAAAAAGGTGTTGA-TTAGGACGAAACCGATAAAGTCAACTAAAAGAAA-TAGGG
3482402 TGG
64 TGG
* * * *
3482405 AAACTAAGTCAAAAAAGGTGTTGATTATGG-C-AAATCTGATAAAGTCAACTAAAAGAAAAAAAT
1 AACCTAAGTCAAAAAAGGTGTTGATTA-GGACGAAA-CCGATAAAGTCAACTAAAAG--AAATAG
*
3482468 TGTGG
62 GGTGG
* ** ** *
3482473 AACCTAAATCAAAAAAGGTGTTGATTAGGGTGAAATTGATAAAGTCAACTAAAAGAGATAGGGTG
1 AACCTAAGTCAAAAAAGGTGTTGATTAGGACGAAACCGATAAAGTCAACTAAAAGAAATAGGGTG
3482538 G
66 G
* ** *
3482539 AACCTAAGTC-GAAAAGCGTGTTGACCAGGACGAAACCGATAAAGCCAACTAAAAGA
1 AACCTAAGTCAAAAAAG-GTGTTGATTAGGACGAAACCGATAAAGTCAACTAAAAGA
3482595 TATAAAAGCG
Statistics
Matches: 154, Mismatches: 27, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
65 5 0.03
66 61 0.40
67 33 0.21
68 49 0.32
69 6 0.04
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.19
Consensus pattern (66 bp):
AACCTAAGTCAAAAAAGGTGTTGATTAGGACGAAACCGATAAAGTCAACTAAAAGAAATAGGGTG
G
Found at i:3482580 original size:134 final size:135
Alignment explanation
Indices: 3482350--3482594 Score: 327
Period size: 134 Copynumber: 1.8 Consensus size: 135
3482340 ACCTAAGTCG
*
3482350 AAAAGGGGTTGAGTGGGGAGAAATCGATAAAGTCAACTAAAAGAAACTAGGGTGGAAACTAAGTC
1 AAAAGGGGTTGAGTAGGGAGAAATCGATAAAGTCAACTAAAAGAAACTAGGGTGGAAACTAAGTC
** * *
3482415 AAAAAAGGTGTTGATTATGGCAAATCTGATAAAGTCAACTAAAAGAAAAAAATTGTGGAACCTAA
66 AAAAAAGGTGTTGACCATGGCAAATCCGATAAAGCCAACTAAAAGAAAAAAATTGTGGAACCTAA
3482480 ATCAA
131 ATCAA
* * * * * *
3482485 AAAAGGTGTTGATTAGGGTGAAATTGATAAAGTCAACTAAAAGAGA-TAGGGTGGAACCTAAGTC
1 AAAAGGGGTTGAGTAGGGAGAAATCGATAAAGTCAACTAAAAGAAACTAGGGTGGAAACTAAGTC
*
3482549 -GAAAAGCGTGTTGACCA-GGACGAAA-CCGATAAAGCCAACTAAAAGA
66 AAAAAAG-GTGTTGACCATGG-C-AAATCCGATAAAGCCAACTAAAAGA
3482595 TATAAAAGCG
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
133 7 0.07
134 45 0.47
135 43 0.45
ACGTcount: A:0.45, C:0.11, G:0.25, T:0.19
Consensus pattern (135 bp):
AAAAGGGGTTGAGTAGGGAGAAATCGATAAAGTCAACTAAAAGAAACTAGGGTGGAAACTAAGTC
AAAAAAGGTGTTGACCATGGCAAATCCGATAAAGCCAACTAAAAGAAAAAAATTGTGGAACCTAA
ATCAA
Found at i:3482775 original size:81 final size:82
Alignment explanation
Indices: 3482657--3482863 Score: 204
Period size: 81 Copynumber: 2.5 Consensus size: 82
3482647 CGATAAAGCT
* * * * * *
3482657 AACAAGTTAAGGGTGTTGACCAAGGAAAAATCGATAAAGTCAATAAGGTAGAATGGTTGG-CTAG
1 AACAAGTTAAGGGGGTTGACCAAGGAAAAACCGATAAAGTCAACAAGGTAGAAGGGCTGGTC-AA
3482721 GGTAAAACCAATAAAACC
65 GGTAAAACCAATAAAACC
* * * *
3482739 AACAAGTT-GGGGGGTTGACTAAGGCAAAACCGATAAAGTCAACAAGTTAGAAGGGCTGGTCAAG
1 AACAAGTTAAGGGGGTTGACCAAGGAAAAACCGATAAAGTCAACAAGGTAGAAGGGCTGGTCAAG
* *
3482803 GTGAAACCAATAAAGCC
66 GTAAAACCAATAAAACC
* * * * ** *
3482820 AATAGGTTAAATGGGG-TGAACAAGGTGAAACCAATAAAGTCAAC
1 AACAAGTT-AAGGGGGTTGACCAAGGAAAAACCGATAAAGTCAAC
3482864 TCATTAGAGG
Statistics
Matches: 101, Mismatches: 21, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
81 65 0.64
82 32 0.32
83 4 0.04
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.18
Consensus pattern (82 bp):
AACAAGTTAAGGGGGTTGACCAAGGAAAAACCGATAAAGTCAACAAGGTAGAAGGGCTGGTCAAG
GTAAAACCAATAAAACC
Found at i:3482816 original size:41 final size:41
Alignment explanation
Indices: 3482765--3482863 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 41
3482755 GACTAAGGCA
* **
3482765 AAACCGATAAAGTCAACAAGTTAGAA-GGGCTGGTCAAGGTG
1 AAACCAATAAAGTCAACAAGTTA-AATGGGCTGAACAAGGTG
* * * *
3482806 AAACCAATAAAGCCAATAGGTTAAATGGGGTGAACAAGGTG
1 AAACCAATAAAGTCAACAAGTTAAATGGGCTGAACAAGGTG
3482847 AAACCAATAAAGTCAAC
1 AAACCAATAAAGTCAAC
3482864 TCATTAGAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
40 2 0.04
41 46 0.96
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.16
Consensus pattern (41 bp):
AAACCAATAAAGTCAACAAGTTAAATGGGCTGAACAAGGTG
Found at i:3482954 original size:41 final size:41
Alignment explanation
Indices: 3482847--3483478 Score: 252
Period size: 41 Copynumber: 15.6 Consensus size: 41
3482837 GAACAAGGTG
** * *
3482847 AAACCAATAAAGTCAACTC-ATTAGAGGGGTTGGCTAGGGCGA
1 AAACCAATAAAGTCAAC-CAATTAGAAAGGTTGACAAGGGC-A
** * *
3482889 AAA-TGATACAAG-CAACAAAGTAGAAAGGTTGACAAGGGCA
1 AAACCAATA-AAGTCAACCAATTAGAAAGGTTGACAAGGGCA
* * * *
3482929 AAACCAATAAAGTTAACCAAATAGAAAGGTTGGCAAAGGCA
1 AAACCAATAAAGTCAACCAATTAGAAAGGTTGACAAGGGCA
* * *
3482970 AAACCAATAAAGCCAA-CAGGTTA-AAGGGGTTGACTAAGGTG--
1 AAACCAATAAAGTCAACCA-ATTAGAA-AGGTTGAC-AAGG-GCA
* * * * * *
3483011 AAACTAATACAGTCAACCAATTAAAAAGGTTGGCTAGGGCG
1 AAACCAATAAAGTCAACCAATTAGAAAGGTTGACAAGGGCA
* * *
3483052 AAACCGATAAAGTCAACAAATTAG-AAGGTTGACTAGGGCA
1 AAACCAATAAAGTCAACCAATTAGAAAGGTTGACAAGGGCA
* * * *
3483092 AAACCGATAAAGCCAACCAATTAGAAGGGTTGGCTAA-GGCA
1 AAACCAATAAAGTCAACCAATTAGAAAGGTTGAC-AAGGGCA
* * * * * *
3483133 AAATCGATAAAGTCAACTAATTAGAGAGGTT-AGCACGGGTA
1 AAACCAATAAAGTCAACCAATTAGAAAGGTTGA-CAAGGGCA
* * * * *
3483174 AAACTAATAAAGCCAA-CAAGTTA-AAGGGTTAAC-CGAGGCA
1 AAACCAATAAAGTCAACCAA-TTAGAAAGGTTGACAAG-GGCA
* * * ** * * *
3483214 AAACTAATAAAATCAACTAATTAGAGGGGTTGGCTAGGGAA
1 AAACCAATAAAGTCAACCAATTAGAAAGGTTGACAAGGGCA
** *
3483255 AAACTGATAAAG-CTAA-CAAGTT--AAAGG--GATAA-GGCA
1 AAACCAATAAAGTC-AACCAA-TTAGAAAGGTTGACAAGGGCA
** * * * *
3483291 AAACTGATAAAATCAACCAATTAGAAGGGCTG-CCAGGGCA
1 AAACCAATAAAGTCAACCAATTAGAAAGGTTGACAAGGGCA
* * * * * * * *
3483331 AAATCGAGAAAGCCAA-TAAGTGAAAAAGGTTGACCAGGGCA
1 AAACCAATAAAGTCAACCAA-TTAGAAAGGTTGACAAGGGCA
* * *
3483372 AAACCAATAAAGTCAACAAATTA-AAGAGGTCGGCCAA-GGCA
1 AAACCAATAAAGTCAACCAATTAGAA-AGGT-TGACAAGGGCA
* * * * * *
3483413 AAACCGATAAAGCCAA-TAGATCAGAAGGGTTGACTAGGGCA
1 AAACCAATAAAGTCAACCA-ATTAGAAAGGTTGACAAGGGCA
** *
3483454 AAACTGATTAAGTCAACCAATTAGA
1 AAACCAATAAAGTCAACCAATTAGA
3483479 GGGCTTGGCC
Statistics
Matches: 440, Mismatches: 110, Indels: 81
0.70 0.17 0.13
Matches are distributed among these distances:
36 18 0.04
37 6 0.01
38 4 0.01
39 9 0.02
40 112 0.25
41 267 0.61
42 23 0.05
43 1 0.00
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.17
Consensus pattern (41 bp):
AAACCAATAAAGTCAACCAATTAGAAAGGTTGACAAGGGCA
Found at i:3483125 original size:81 final size:82
Alignment explanation
Indices: 3482683--3483716 Score: 479
Period size: 82 Copynumber: 12.7 Consensus size: 82
3482673 TGACCAAGGA
* * * * * * * * ** *
3482683 AAAATCGATAAAGTCAATAAGGTAGAATGGTTGGCTAGGGTAAAACCAATAAAACCAACAAGTT-
1 AAAACCGATAAAGCCAACAAGTTAGAAGGGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTA
* * *
3482747 GGGGGGTTGACTAAGGC
66 GAGAGGTTGACTAGGGC
* * * * * * * **
3482764 AAAACCGATAAAGTCAACAAGTTAGAAGGGCTGGTCAAGGTG--AAACCAATAAAGCCAATAGGT
1 AAAACCGATAAAGCCAACAAGTTAGAAGGG-TTGACTAGG-GCAAAACCGATAAAGTCAACAAAT
* * *
3482827 TAAATG-GGGTGAACAAGGTG-
64 TAGA-GAGGTTG-ACTAGG-GC
* * * * * *
3482847 -AAACCAATAAAGTCAACTCA-TTAGAGGGGTTGGCTAGGGCGAAAA-TGATACAAG-CAACAAA
1 AAAACCGATAAAGCCAAC-AAGTTAGAAGGGTTGACTAGGGC-AAAACCGATA-AAGTCAACAAA
* * *
3482908 GTAGAAAGGTTGACAAGGGC
63 TTAGAGAGGTTGACTAGGGC
* ** * * * * * * * **
3482928 AAAACCAATAAAGTTAACCAA-ATAGAAAGGTTGGCAAAGGCAAAACCAATAAAGCCAACAGGTT
1 AAAACCGATAAAGCCAA-CAAGTTAGAAGGGTTGACTAGGGCAAAACCGATAAAGTCAACAAATT
* * * *
3482992 AAAGGGGTTGACTAAGGT
65 AGAGAGGTTGACTAGGGC
* ** * * * * * *
3483010 GAAACTAATACAGTCAACCAA-TTAAAAAGGTTGGCTAGGGCGAAACCGATAAAGTCAACAAATT
1 AAAACCGATAAAGCCAA-CAAGTTAGAAGGGTTGACTAGGGCAAAACCGATAAAGTCAACAAATT
3483074 AGA-AGGTTGACTAGGGC
65 AGAGAGGTTGACTAGGGC
* * * *
3483091 AAAACCGATAAAGCCAACCAA-TTAGAAGGGTTGGCTAAGGCAAAATCGATAAAGTCAACTAATT
1 AAAACCGATAAAGCCAA-CAAGTTAGAAGGGTTGACTAGGGCAAAACCGATAAAGTCAACAAATT
*
3483155 AGAGAGGTT-AGC-ACGGGT
65 AGAGAGGTTGA-CTA-GGGC
** * * ** * *
3483173 AAAACTAATAAAGCCAACAAGTTA-AAGGGTTAAC-CGAGGCAAAACTAATAAAATCAACTAATT
1 AAAACCGATAAAGCCAACAAGTTAGAAGGGTTGACTAG-GGCAAAACCGATAAAGTCAACAAATT
* * *
3483236 AGAGGGGTTGGCTAGGGA
65 AGAGAGGTTGACTAGGGC
* * * * * *
3483254 AAAACTGATAAAGCTAACAAGTTA-AA-GG--GA-TAAGGCAAAACTGATAAAATCAACCAATTA
1 AAAACCGATAAAGCCAACAAGTTAGAAGGGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTA
* *
3483314 GA-AGGGCTG-CCAGGGC
66 GAGA-GGTTGACTAGGGC
* * * * * * * *
3483330 AAAATCGAGAAAGCCAATAAGTGAAAAAGGTTGACCAGGGCAAAACCAATAAAGTCAACAAATTA
1 AAAACCGATAAAGCCAACAAGTTAGAAGGGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTA
* * * * *
3483395 AAGAGGTCGGCCAAGGC
66 GAGAGGTTGACTAGGGC
* * * * *
3483412 AAAACCGATAAAGCCAA-TAGATCAGAAGGGTTGACTAGGGCAAAACTGATTAAGTCAACCAATT
1 AAAACCGATAAAGCCAACAAG-TTAGAAGGGTTGACTAGGGCAAAACCGATAAAGTCAACAAATT
* * *
3483476 AGAG-GGCTTGGCCAGGGT
65 AGAGAGG-TTGACTAGGGC
* * * * * * * *
3483494 GAAACCGATAAAGCCATCAAATTTA-AGGGGTTGACTAGGGCGAAATCGATAAACTCAACAAGTT
1 AAAACCGATAAAGCCAAC-AAGTTAGAAGGGTTGACTAGGGCAAAACCGATAAAGTCAACAAATT
* * *
3483558 AGAGGGGTT-AGCTTGGGT
65 AGAGAGGTTGA-CTAGGGC
* * ** * *
3483576 AAAATCGATAAAGCCAACAAGTTTGGGGGGTTGACTAGGGCAAAACCAATAAAGTCAACCAATTA
1 AAAACCGATAAAGCCAACAAGTTAGAAGGGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTA
** * *
3483641 GAGAGGTTGGTTAAGAC
66 GAGAGGTTGACTAGGGC
* * * * * * * *
3483658 GAAACCAATAAAGCCAATAAGAT-GGAGAGGTTGACCAAGGCAAAACCAATAAAGTCAAC
1 AAAACCGATAAAGCCAACAAGTTAGAAG-GGTTGACTAGGGCAAAACCGATAAAGTCAAC
3483717 TGATTAGTGT
Statistics
Matches: 736, Mismatches: 175, Indels: 83
0.74 0.18 0.08
Matches are distributed among these distances:
76 23 0.03
77 33 0.04
78 3 0.00
80 6 0.01
81 241 0.33
82 410 0.56
83 18 0.02
84 2 0.00
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.17
Consensus pattern (82 bp):
AAAACCGATAAAGCCAACAAGTTAGAAGGGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTA
GAGAGGTTGACTAGGGC
Found at i:3483445 original size:82 final size:82
Alignment explanation
Indices: 3483038--3483716 Score: 490
Period size: 82 Copynumber: 8.4 Consensus size: 82
3483028 CAATTAAAAA
* * * *
3483038 GGTTGGCTAGGGCGAAACCGATAAAGTCAACAAATTAGA-AGGTTGACTAGGGCAAAACCGATAA
1 GGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTAGAGAGGTTGGCCAGGGCAAAACCGATAA
3483102 AGCCAACCAA-TTAGAAG
66 AGCCAA-CAAGTTAGAAG
* * * * * * **
3483119 GGTTGGCTAAGGCAAAATCGATAAAGTCAACTAATTAGAGAGGTTAG-CACGGGTAAAACTAATA
1 GGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTAGAGAGGTTGGCCA-GGGCAAAACCGATA
3483183 AAGCCAACAAGTTA-AAG
65 AAGCCAACAAGTTAGAAG
* * ** * * * * * *
3483200 GGTTAAC-CGAGGCAAAACTAATAAAATCAACTAATTAGAGGGGTTGGCTAGGGAAAAACTGATA
1 GGTTGACTAG-GGCAAAACCGATAAAGTCAACAAATTAGAGAGGTTGGCCAGGGCAAAACCGATA
*
3483264 AAGCTAACAAGTTA-AA-
65 AAGCCAACAAGTTAGAAG
* * * * * * *
3483280 GG--GA-TAAGGCAAAACTGATAAAATCAACCAATTAGA-AGGGCT-GCCAGGGCAAAATCGAGA
1 GGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTAGAGA-GGTTGGCCAGGGCAAAACCGATA
* * * *
3483340 AAGCCAATAAGTGAAAAA
65 AAGCCAACAAGTTAGAAG
* * * * *
3483358 GGTTGACCAGGGCAAAACCAATAAAGTCAACAAATTAAAGAGGTCGGCCAAGGCAAAACCGATAA
1 GGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTAGAGAGGTTGGCCAGGGCAAAACCGATAA
* *
3483423 AGCCAA-TAGATCAGAAG
66 AGCCAACAAG-TTAGAAG
* * * **
3483440 GGTTGACTAGGGCAAAACTGATTAAGTCAACCAATTAGAG-GGCTTGGCCAGGGTGAAACCGATA
1 GGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTAGAGAGG-TTGGCCAGGGCAAAACCGATA
* * *
3483504 AAGCCATCAAATTTA-AGG
65 AAGCCAAC-AAGTTAGAAG
* * * * * * ** * *
3483522 GGTTGACTAGGGCGAAATCGATAAACTCAACAAGTTAGAGGGGTTAGCTTGGGTAAAATCGATAA
1 GGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTAGAGAGGTTGGCCAGGGCAAAACCGATAA
* **
3483587 AGCCAACAAGTTTGGGG
66 AGCCAACAAGTTAGAAG
* * ** * * * *
3483604 GGTTGACTAGGGCAAAACCAATAAAGTCAACCAATTAGAGAGGTTGGTTAAGACGAAACCAATAA
1 GGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTAGAGAGGTTGGCCAGGGCAAAACCGATAA
* * *
3483669 AGCCAATAAGAT-GGAG
66 AGCCAACAAGTTAGAAG
* * *
3483685 AGGTTGACCAAGGCAAAACCAATAAAGTCAAC
1 -GGTTGACTAGGGCAAAACCGATAAAGTCAAC
3483717 TGATTAGTGT
Statistics
Matches: 470, Mismatches: 107, Indels: 41
0.76 0.17 0.07
Matches are distributed among these distances:
76 24 0.05
77 32 0.07
78 3 0.01
80 4 0.01
81 143 0.30
82 259 0.55
83 4 0.01
84 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.17
Consensus pattern (82 bp):
GGTTGACTAGGGCAAAACCGATAAAGTCAACAAATTAGAGAGGTTGGCCAGGGCAAAACCGATAA
AGCCAACAAGTTAGAAG
Found at i:3483564 original size:41 final size:40
Alignment explanation
Indices: 3482847--3483649 Score: 239
Period size: 41 Copynumber: 19.8 Consensus size: 40
3482837 GAACAAGGTG
* * * *
3482847 AAACCAATAAAGTCAACTCATTAGAGGGGTTGGCTAGGGCGA
1 AAACCGATAAACTCAAC-AATTAGAGGGGTTGACTAGGGC-A
* * * ** *
3482889 AAA-TGATACAA-GCAACAAAGTAGAAAGGTTGACAAGGGCA
1 AAACCGATA-AACTCAAC-AATTAGAGGGGTTGACTAGGGCA
* * * * ** * * *
3482929 AAACCAATAAAGTTAACCAAATAGAAAGGTTGGCAAAGGCA
1 AAACCGATAAACTCAA-CAATTAGAGGGGTTGACTAGGGCA
* * * * **
3482970 AAACCAATAAAGC-CAACAGGTTAAAGGGGTTGACTAAGGTG
1 AAACCGATAAA-CTCAACA-ATTAGAGGGGTTGACTAGGGCA
** * * * ** * *
3483011 AAACTAATACAGTCAACCAATTAAAAAGGTTGGCTAGGGCG
1 AAACCGATAAACTCAA-CAATTAGAGGGGTTGACTAGGGCA
* *
3483052 AAACCGATAAAGTCAACAAATTAGA-AGGTTGACTAGGGCA
1 AAACCGATAAACTCAAC-AATTAGAGGGGTTGACTAGGGCA
* * *
3483092 AAACCGATAAAGC-CAACCAATTAGAAGGGTTGGCTAAGGCA
1 AAACCGATAAA-CTCAA-CAATTAGAGGGGTTGACTAGGGCA
* * * *
3483133 AAATCGATAAAGTCAACTAATTAGAGAGGTT-AGC-ACGGGTA
1 AAACCGATAAACTCAAC-AATTAGAGGGGTTGA-CTA-GGGCA
** * * *
3483174 AAACTAATAAAGC-CAACAAGTTA-AAGGGTTAAC-CGAGGCA
1 AAACCGATAAA-CTCAACAA-TTAGAGGGGTTGACTAG-GGCA
** * * *
3483214 AAACTAATAAAATCAACTAATTAGAGGGGTTGGCTAGGGAA
1 AAACCGATAAACTCAAC-AATTAGAGGGGTTGACTAGGGCA
* * *
3483255 AAACTGATAAAGCT-AACAAGTTA-A-AGG--GA-TAAGGCA
1 AAACCGATAAA-CTCAACAA-TTAGAGGGGTTGACTAGGGCA
* * * * *
3483291 AAACTGATAAAATCAACCAATTAGAAGGGCTG-CCAGGGCA
1 AAACCGATAAACTCAA-CAATTAGAGGGGTTGACTAGGGCA
* * * * * ** *
3483331 AAATCGAGAAAGC-CAATAAGTGAAAAAGGTTGACCAGGGCA
1 AAACCGATAAA-CTCAACAA-TTAGAGGGGTTGACTAGGGCA
* * * * * * * *
3483372 AAACCAATAAAGTCAACAAATTAAAGAGGTCGGCCAAGGCA
1 AAACCGATAAACTCAAC-AATTAGAGGGGTTGACTAGGGCA
* * *
3483413 AAACCGATAAAGC-CAATAGATCAGAAGGGTTGACTAGGGCA
1 AAACCGATAAA-CTCAACA-ATTAGAGGGGTTGACTAGGGCA
* * * * * * **
3483454 AAACTGATTAAGTCAACCAATTAGAGGGCTTGGCCAGGGTG
1 AAACCGATAAACTCAA-CAATTAGAGGGGTTGACTAGGGCA
* *
3483495 AAACCGATAAAGCCATCAA-ATTTA-AGGGGTTGACTAGGGCG
1 AAACCGATAAA--C-TCAACAATTAGAGGGGTTGACTAGGGCA
* * *
3483536 AAATCGATAAACTCAACAAGTTAGAGGGGTT-AGCTTGGGTA
1 AAACCGATAAACTCAACAA-TTAGAGGGGTTGA-CTAGGGCA
* * *
3483577 AAATCGATAAAGC-CAACAAGTTTGGGGGGTTGACTAGGGCA
1 AAACCGATAAA-CTCAACAA-TTAGAGGGGTTGACTAGGGCA
* * *
3483618 AAACCAATAAAGTCAACCAATTAGAGAGGTTG
1 AAACCGATAAACTCAA-CAATTAGAGGGGTTG
3483650 GTTAAGACGA
Statistics
Matches: 566, Mismatches: 142, Indels: 107
0.69 0.17 0.13
Matches are distributed among these distances:
35 1 0.00
36 21 0.04
37 5 0.01
38 6 0.01
39 7 0.01
40 107 0.19
41 393 0.69
42 22 0.04
44 4 0.01
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.17
Consensus pattern (40 bp):
AAACCGATAAACTCAACAATTAGAGGGGTTGACTAGGGCA
Found at i:3484338 original size:76 final size:77
Alignment explanation
Indices: 3484258--3484600 Score: 372
Period size: 77 Copynumber: 4.5 Consensus size: 77
3484248 ACATAATAAG
* * * * * * * * *
3484258 GAATATATGGTTTCTAAAATTTTTATCAACAGTCGAAACAAAATGATAA-AAGGTTAATGGA-AA
1 GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTGATAACAA-CTTAAAGAAGAA
3484321 GGAACATGATAGA
65 GGAACATGATAGA
* *
3484334 GAATATGTGATTTCTAAAATTTTCATTAATAGCCAAAACAAACTGATAACAACTTAAAGAAGAAG
1 GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTGATAACAACTTAAAGAAGAAG
3484399 GAACATGATAGA
66 GAACATGATAGA
* *
3484411 GAATATGTGATTTCTAAAATTTTCATTAATAGCCAAAACAAACTGATAACAACTTAAAGAAGAAG
1 GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTGATAACAACTTAAAGAAGAAG
*
3484476 GAGCATGAT-GA
66 GAACATGATAGA
* * * * * **
3484487 GGAATATGTTATTTCTAAAGTTTTTATCAACAGCTAAAACAAACTAATAACATGTTGAAAG-A-A
1 -GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTGATAACAACTT-AAAGAAGA
* *
3484550 AGGAACATGATGGG
64 AGGAACATGATAGA
* * * * *
3484564 GAATATGCGGTTTCAAAAATTTCCATCAACAGTCAAA
1 GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAA
3484601 TAATTTAATA
Statistics
Matches: 230, Mismatches: 32, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
76 88 0.38
77 138 0.60
78 4 0.02
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (77 bp):
GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTGATAACAACTTAAAGAAGAAG
GAACATGATAGA
Found at i:3484431 original size:153 final size:153
Alignment explanation
Indices: 3484258--3484600 Score: 388
Period size: 153 Copynumber: 2.2 Consensus size: 153
3484248 ACATAATAAG
* * * * * *
3484258 GAATATATGGTTTCTAAAATTTTTATCAACAGTCGAAACAAAATGATAA-AAGGTTAATGGA-AA
1 GAATATGTGGTTTCTAAAATTTTCATCAACAGTCAAAACAAAATGATAACAA-CTTAAAGAAGAA
* * *
3484321 GGAACATGAT-AGAGAATATGTGATTTCTAAAATTTTCATTAATAGCCAAAACAAACTGATAACA
65 GGAACATGATGAG-GAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTAATAACA
3484385 ACTT-AAAGAAGAAGGAACATGATAGA
129 ACTTGAAAG-A-AAGGAACATGATAGA
* * * * *
3484411 GAATATGTGATTTCTAAAATTTTCATTAATAGCCAAAACAAACTGATAACAACTTAAAGAAGAAG
1 GAATATGTGGTTTCTAAAATTTTCATCAACAGTCAAAACAAAATGATAACAACTTAAAGAAGAAG
* * * * * **
3484476 GAGCATGATGAGGAATATGTTATTTCTAAAGTTTTTATCAACAGCTAAAACAAACTAATAACATG
66 GAACATGATGAGGAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTAATAACAAC
* *
3484541 TTGAAAGAAAGGAACATGATGGG
131 TTGAAAGAAAGGAACATGATAGA
* * *
3484564 GAATATGCGGTTTCAAAAATTTCCATCAACAGTCAAA
1 GAATATGTGGTTTCTAAAATTTTCATCAACAGTCAAA
3484601 TAATTTAATA
Statistics
Matches: 156, Mismatches: 30, Indels: 8
0.80 0.15 0.04
Matches are distributed among these distances:
153 90 0.58
154 60 0.38
155 6 0.04
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.27
Consensus pattern (153 bp):
GAATATGTGGTTTCTAAAATTTTCATCAACAGTCAAAACAAAATGATAACAACTTAAAGAAGAAG
GAACATGATGAGGAATATGTGATTTCTAAAATTTTCATCAACAGCCAAAACAAACTAATAACAAC
TTGAAAGAAAGGAACATGATAGA
Found at i:3485833 original size:21 final size:22
Alignment explanation
Indices: 3485808--3485855 Score: 73
Period size: 20 Copynumber: 2.2 Consensus size: 22
3485798 AGGAAGCTAG
3485808 AGTTTTTTAAATTTT-AAAATT
1 AGTTTTTTAAATTTTAAAAATT
3485829 AG-TTTTTAAATTTTAAAAATT
1 AGTTTTTTAAATTTTAAAAATT
3485850 ACGTTT
1 A-GTTT
3485856 CGCACTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.50
21 9 0.38
22 1 0.04
23 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (22 bp):
AGTTTTTTAAATTTTAAAAATT
Found at i:3486733 original size:15 final size:16
Alignment explanation
Indices: 3486706--3486736 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3486696 TCCAAATATT
3486706 TTTCTTGTTTCTTTTC
1 TTTCTTGTTTCTTTTC
3486722 TTTCTT-TTTCTTTTC
1 TTTCTTGTTTCTTTTC
3486737 AATTTGCTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTCTTGTTTCTTTTC
Found at i:3487104 original size:32 final size:30
Alignment explanation
Indices: 3487028--3487111 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 30
3487018 TTTGTTTCTA
* * *
3487028 TTGTTTTTTTTCTTCCTTTTCCGTTTTGTT
1 TTGTTTTTTTTCTTTCTTTTCCGTTCTGCT
*
3487058 TTGATTTTTCTTTCTTTCTTTTTCGATTGCTGCT
1 TTG-TTTTT-TTTCTTTCTTTTCCG-TT-CTGCT
3487092 TTGTTTTTTTTCTTT-TTTTC
1 TTGTTTTTTTTCTTTCTTTTC
3487112 TTTTCTTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 3 0.07
31 9 0.20
32 20 0.44
33 7 0.16
34 6 0.13
ACGTcount: A:0.02, C:0.15, G:0.10, T:0.73
Consensus pattern (30 bp):
TTGTTTTTTTTCTTTCTTTTCCGTTCTGCT
Found at i:3487115 original size:13 final size:12
Alignment explanation
Indices: 3487090--3487124 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3487080 TCGATTGCTG
3487090 CTTTGTTTTTTTT
1 CTTT-TTTTTTTT
3487103 CTTTTTTTCTTTT
1 CTTTTTTT-TTTT
3487116 CTTTTTTTT
1 CTTTTTTTT
3487125 GCTATTTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (12 bp):
CTTTTTTTTTTT
Found at i:3487164 original size:23 final size:22
Alignment explanation
Indices: 3487091--3487166 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 22
3487081 CGATTGCTGC
* *
3487091 TTTGTTTTTTTTCTTTTTTTCT
1 TTTGTTTTTTTTCTTATTTTAT
* *
3487113 TTTCTTTTTTTTGC-TATTTCGAT
1 TTTGTTTTTTTT-CTTATTT-TAT
3487136 TCTTGTTTTTTTTCTTATTATTAT
1 T-TTGTTTTTTTTCTTATT-TTAT
3487160 TTTGTTT
1 TTTGTTT
3487167 CTATTTTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
22 15 0.35
23 10 0.23
24 17 0.40
25 1 0.02
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.78
Consensus pattern (22 bp):
TTTGTTTTTTTTCTTATTTTAT
Found at i:3487511 original size:30 final size:30
Alignment explanation
Indices: 3487475--3487532 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
3487465 TCTTTGCTGC
3487475 TTTTTGTCTTCATTACAGA-ATCTTGATTCG
1 TTTTTGTCTTCATTACA-ACATCTTGATTCG
*
3487505 TTTTTGTCTTCATTGCAACATCTTGATT
1 TTTTTGTCTTCATTACAACATCTTGATT
3487533 GCTTTAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.19, C:0.17, G:0.12, T:0.52
Consensus pattern (30 bp):
TTTTTGTCTTCATTACAACATCTTGATTCG
Found at i:3487773 original size:19 final size:19
Alignment explanation
Indices: 3487732--3487839 Score: 68
Period size: 19 Copynumber: 5.7 Consensus size: 19
3487722 TATTTTTTGA
*
3487732 AATGCATGAAAT--AAAGC
1 AATGCATGAAATGCAATGC
3487749 -ATGCATGAAATGCAATGC
1 AATGCATGAAATGCAATGC
*
3487767 AATGCATGAAATGAACTTATGGC
1 AATGCATGAAATG--C-AAT-GC
* *
3487790 GTGAA-ACATGAAA-G-AAAGC
1 ---AATGCATGAAATGCAATGC
3487809 -ATGCATGAAATGCAATGC
1 AATGCATGAAATGCAATGC
3487827 AATGCATGAAATG
1 AATGCATGAAATG
3487840 AACATATGCA
Statistics
Matches: 70, Mismatches: 7, Indels: 26
0.68 0.07 0.25
Matches are distributed among these distances:
15 1 0.01
16 18 0.26
17 1 0.01
18 8 0.11
19 26 0.37
20 1 0.01
21 1 0.01
22 2 0.03
23 2 0.03
24 1 0.01
25 7 0.10
26 2 0.03
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.20
Consensus pattern (19 bp):
AATGCATGAAATGCAATGC
Found at i:3488006 original size:9 final size:10
Alignment explanation
Indices: 3487981--3488021 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
3487971 TAATTATCAC
3487981 TATTTTTATA
1 TATTTTTATA
*
3487991 TATTTTTATT
1 TATTTTTATA
3488001 TA-TTTTATA
1 TATTTTTATA
*
3488010 T-TTTATATA
1 TATTTTTATA
3488019 TAT
1 TAT
3488022 ATATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 14 0.54
10 12 0.46
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TATTTTTATA
Found at i:3488792 original size:60 final size:59
Alignment explanation
Indices: 3488649--3488876 Score: 181
Period size: 61 Copynumber: 3.8 Consensus size: 59
3488639 GAAACTACAA
* * * * ** ** *
3488649 AATGACTTGGGCAAAACCAAGAATCAAAGAAATGGACTGGATGAAACCAAAAACCTAAAAC
1 AATGACTTGGCCAAAACCAAGACTCAATGAAATGGCCTAAAT-AAAATAGAAACC-AAAAC
*** * *
3488710 AATGACTTGGGTGAAACAAAGACTTAATGAAATGGCCTAAATAAAATGAGAAACCAAAAC
1 AATGACTTGGCCAAAACCAAGACTCAATGAAATGGCCTAAATAAAAT-AGAAACCAAAAC
** * *
3488770 AATGACTTGGCCAAAACCAAGACTCAACT-AAATAACCTAAATGAAACTAGAAACCTAAAC
1 AATGACTTGGCCAAAACCAAGACTCAA-TGAAATGGCCTAAAT-AAAATAGAAACCAAAAC
** * *
3488830 AATGA-TTATTCCACAAACCAAGATTCAATGAAATGGCCTATATAAAA
1 AATGACTT-GGCCA-AAACCAAGACTCAATGAAATGGCCTAAATAAAA
3488877 CCAAAAATCG
Statistics
Matches: 133, Mismatches: 28, Indels: 13
0.76 0.16 0.07
Matches are distributed among these distances:
59 2 0.02
60 64 0.48
61 67 0.50
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (59 bp):
AATGACTTGGCCAAAACCAAGACTCAATGAAATGGCCTAAATAAAATAGAAACCAAAAC
Found at i:3489545 original size:44 final size:43
Alignment explanation
Indices: 3489491--3489628 Score: 115
Period size: 44 Copynumber: 3.1 Consensus size: 43
3489481 TAGATGTGCG
*
3489491 TGAAACGATGCAAATGCAAGCATCAATAAAATGACAAATGCATA
1 TGAAATGATGCAAATGCAAGCATCAATAAAATG-CAAATGCATA
* *
3489535 TGAAATGATGCAAATACCAATGTCATC--TAAAATGCAAAT--ATGCG
1 TGAAATGATGCAAAT-GCAA-G-CATCAATAAAATGCAAATGCAT--A
* *
3489579 TGAAAT-ATTGCAACTGTAAGCATCAATAAAATGGCAAATGCATA
1 TGAAATGA-TGCAAATGCAAGCATCAATAAAAT-GCAAATGCATA
*
3489623 TAAAAT
1 TGAAAT
3489629 TACACAAATG
Statistics
Matches: 75, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
41 4 0.05
42 3 0.04
43 9 0.12
44 42 0.56
45 10 0.13
46 3 0.04
47 4 0.05
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.23
Consensus pattern (43 bp):
TGAAATGATGCAAATGCAAGCATCAATAAAATGCAAATGCATA
Found at i:3491325 original size:20 final size:20
Alignment explanation
Indices: 3491255--3491326 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
3491245 GTTAGGCACA
* *
3491255 ATGTATCGATAC-TTTTCACT
1 ATGTATCGATACAATGTC-CT
* *
3491275 ATGTATCGATACAATGATACA
1 ATGTATCGATACAATG-TCCT
*
3491296 ATGTACCGATACAATGTCCT
1 ATGTATCGATACAATGTCCT
3491316 ATGTATCGATA
1 ATGTATCGATA
3491327 TAAACAGTGG
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 24 0.57
21 17 0.40
22 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATGTCCT
Found at i:3491416 original size:13 final size:13
Alignment explanation
Indices: 3491398--3491424 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3491388 TATAATGAAC
3491398 ATGTATCGATACA
1 ATGTATCGATACA
3491411 ATGTATCGATACA
1 ATGTATCGATACA
3491424 A
1 A
3491425 AGCAATATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3492099 original size:21 final size:22
Alignment explanation
Indices: 3492058--3492101 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3492048 AAAAATATAA
* *
3492058 CTCCCCTTTAATTAAACATTTT
1 CTCCCCCTTAATTAAAAATTTT
3492080 CTCCCCCTTAA-TAAAAATTTT
1 CTCCCCCTTAATTAAAAATTTT
3492101 C
1 C
3492102 CCTTTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCCCCCTTAATTAAAAATTTT
Found at i:3492343 original size:16 final size:17
Alignment explanation
Indices: 3492316--3492348 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3492306 GTAGATAATA
*
3492316 GCAAGAAAAACATTCAT
1 GCAAGAAAAACAGTCAT
3492333 GCAAG-AAAACAGTCAT
1 GCAAGAAAAACAGTCAT
3492349 AATTTCATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (17 bp):
GCAAGAAAAACAGTCAT
Done.