Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 23 of 208
Found at i:6601573 original size:16 final size:18
Alignment explanation
Indices: 6601534--6601567 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6601524 TAAGTTTATA
6601534 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
6601551 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
6601568 AATTTAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:6610084 original size:18 final size:19
Alignment explanation
Indices: 6610041--6610086 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
6610031 AATTAATTTA
* *
6610041 AACATATAAATAATTATTTC
1 AACA-ATAAACAATTATTCC
6610061 AA-AATAAACAA-TATTCC
1 AACAATAAACAATTATTCC
6610078 AACAATAAA
1 AACAATAAA
6610087 TTCATCAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 7 0.30
18 13 0.57
19 1 0.04
20 2 0.09
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (19 bp):
AACAATAAACAATTATTCC
Found at i:6611466 original size:41 final size:41
Alignment explanation
Indices: 6611394--6611488 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
6611384 CTTTCGGGGA
* *
6611394 TTTAGTGGCGTTTTTAGGTAAGCGCCGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGC
* * * *
6611435 TTTAGCGGCGTTTTTAAGTAATCGTCTCTAATGTTCAGGGC
1 TTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGC
6611476 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
6611489 ACCAGAAAGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.17, C:0.18, G:0.28, T:0.37
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATGCTCAGGGC
Found at i:6611675 original size:88 final size:90
Alignment explanation
Indices: 6611512--6611676 Score: 228
Period size: 88 Copynumber: 1.8 Consensus size: 90
6611502 GCAAAAAACC
** *
6611512 TAAGCCCAACGACGCCGTTTACCGAGATTTCGGGGATTTAGCGGTGTTTTCGGGAAAGCGCCGCT
1 TAAGCCCAACGAC-CCGTTTACCGAGATTTCGGGGATTTAGCGGTCATTTCGGGAAAGCGCCGCA
*
6611577 AGTGCTCAGGGACTTCGTGGCGTTTT
65 AATGCTCAGGGACTTCGTGGCGTTTT
* * *
6611603 TAAGCCCAAC-A-CCGTTTTCTGAGCTTTCGGGGATTTAGCGG-CATTTCGGAGAAAGCGCCGCA
1 TAAGCCCAACGACCCGTTTACCGAGATTTCGGGGATTTAGCGGTCATTTCGG-GAAAGCGCCGCA
6611665 AATGCTCAGGGA
65 AATGCTCAGGGA
6611677 TTTAGCGGCG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
87 6 0.09
88 49 0.74
90 1 0.02
91 10 0.15
ACGTcount: A:0.21, C:0.24, G:0.30, T:0.25
Consensus pattern (90 bp):
TAAGCCCAACGACCCGTTTACCGAGATTTCGGGGATTTAGCGGTCATTTCGGGAAAGCGCCGCAA
ATGCTCAGGGACTTCGTGGCGTTTT
Found at i:6611793 original size:73 final size:72
Alignment explanation
Indices: 6611673--6611855 Score: 240
Period size: 73 Copynumber: 2.5 Consensus size: 72
6611663 CAAATGCTCA
* * * **
6611673 GGGATTTAGCGGCGTTTCGGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACGATGCCGTTTTCTG
1 GGGATTTAGCGGCGTTTC-TAAAAAGCGCCGCTAATGAACCTAAGCCCAACGATGCCGTTTTCTG
6611738 AGCTTTTCC
65 AGC-TTTCC
* *
6611747 GGGATTTAGCAGCGTTTCTAAAAAACGCCGCTAATGAACCTAAGCCCAACGATGCCGTTTTCTGA
1 GGGATTTAGCGGCGTTTCTAAAAAGCGCCGCTAATGAACCTAAGCCCAACGATGCCGTTTTCTGA
*
6611812 GCTTTCG
66 GCTTTCC
* * *
6611819 GGGATTTAGCGGCATTTTTTGAAAAGCGCCGCTAATG
1 GGGATTTAGCGGC-GTTTCTAAAAAGCGCCGCTAATG
6611856 CTCAAGGATT
Statistics
Matches: 95, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
72 16 0.17
73 62 0.65
74 17 0.18
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (72 bp):
GGGATTTAGCGGCGTTTCTAAAAAGCGCCGCTAATGAACCTAAGCCCAACGATGCCGTTTTCTGA
GCTTTCC
Found at i:6612159 original size:38 final size:37
Alignment explanation
Indices: 6612103--6612195 Score: 105
Period size: 38 Copynumber: 2.5 Consensus size: 37
6612093 GGATTTAAGG
* ** *
6612103 TTTAGGGGTTAGGTGTTATGTTTTAAGGGTTAGGGGGA
1 TTTAGGGGTTAGGAGTTATACTTTAAGGGTTA-AGGGA
* *
6612141 TTTAGGGGTTAGGAGTTATACTTTAGGGGTTAATGGA
1 TTTAGGGGTTAGGAGTTATACTTTAAGGGTTAAGGGA
* *
6612178 TTTAGGGGTAAGGGGTTA
1 TTTAGGGGTTAGGAGTTA
6612196 GGGTTTATGG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 19 0.40
38 28 0.60
ACGTcount: A:0.22, C:0.01, G:0.40, T:0.38
Consensus pattern (37 bp):
TTTAGGGGTTAGGAGTTATACTTTAAGGGTTAAGGGA
Found at i:6612225 original size:29 final size:29
Alignment explanation
Indices: 6612162--6612227 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
6612152 GGAGTTATAC
6612162 TTTAGGGGTTAATGGATTTAGGGGTAAGGG
1 TTTA-GGGTTAATGGATTTAGGGGTAAGGG
* *
6612192 GTTAGGGTTTATGGATTT-GGGGTTTAA-GG
1 TTTAGGGTTAATGGATTTAGGGG--TAAGGG
6612221 TTTAGGG
1 TTTAGGG
6612228 CTTCAACGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.13
29 21 0.68
30 6 0.19
ACGTcount: A:0.20, C:0.00, G:0.42, T:0.38
Consensus pattern (29 bp):
TTTAGGGTTAATGGATTTAGGGGTAAGGG
Found at i:6615062 original size:18 final size:18
Alignment explanation
Indices: 6615036--6615165 Score: 113
Period size: 18 Copynumber: 6.9 Consensus size: 18
6615026 CATTACTTAC
6615036 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
*
6615053 ATTACATTACTTAAATAT
1 ATTACATTACTAAAATAT
6615071 ATTAC-TTACTAAAATGTAT
1 ATTACATTACTAAAA--TAT
*
6615090 AACTTACATTACTTAAATAT
1 -A-TTACATTACTAAAATAT
*
6615110 ATTACATTACTTAAAATTT
1 ATTACATTAC-TAAAATAT
* *
6615129 ATATATATATA-TATATATAT
1 AT-TACAT-TACTA-AAATAT
*
6615149 ATTACATTACTTAAATA
1 ATTACATTACTAAAATA
6615166 AAAATTAGCT
Statistics
Matches: 91, Mismatches: 11, Indels: 21
0.74 0.09 0.17
Matches are distributed among these distances:
17 13 0.14
18 31 0.34
19 19 0.21
20 14 0.15
21 6 0.07
22 8 0.09
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.44
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:6615080 original size:39 final size:41
Alignment explanation
Indices: 6615032--6615163 Score: 129
Period size: 39 Copynumber: 3.3 Consensus size: 41
6615022 ATTACATTAC
6615032 TTACATTACTTACTAAA-ATAT-A-TTACATTACTTAAATATA
1 TTACATTACTTA--AAATATATAACTTACATTACTTAAATATA
*
6615072 TTAC-TTAC-TAAAATGTATAACTTACATTACTTAAATATA
1 TTACATTACTTAAAATATATAACTTACATTACTTAAATATA
* * *
6615111 TTACATTACTTAAAATTTAT-A--TATATATA-TATATATATA
1 TTACATTACTTAAAATATATAACTTACAT-TACT-TAAATATA
6615150 TTACATTACTTAAA
1 TTACATTACTTAAA
6615164 TAAAAATTAG
Statistics
Matches: 81, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
36 3 0.04
37 3 0.04
38 8 0.10
39 49 0.60
40 9 0.11
41 9 0.11
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.44
Consensus pattern (41 bp):
TTACATTACTTAAAATATATAACTTACATTACTTAAATATA
Found at i:6615154 original size:57 final size:56
Alignment explanation
Indices: 6615036--6615165 Score: 153
Period size: 57 Copynumber: 2.3 Consensus size: 56
6615026 CATTACTTAC
* *
6615036 ATTAC-TTACTAAAATATATTACATTACTTAAATATATTACTTACTAAAATGTATA
1 ATTACATTACTTAAATATATTACATTACTTAAATATATTACTTACTAAAATATATA
6615091 ACTTACATTACTTAAATATATTACATTACTTAAA-AT-TTA-TATA-TATATATATATATA
1 A-TTACATTACTTAAATATATTACATTACTTAAATATATTACT-TACTA-A-A-ATATATA
6615148 TATTACATTACTTAAATA
1 -ATTACATTACTTAAATA
6615166 AAAATTAGCT
Statistics
Matches: 66, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
54 3 0.05
55 7 0.11
56 7 0.11
57 48 0.73
58 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.01, T:0.44
Consensus pattern (56 bp):
ATTACATTACTTAAATATATTACATTACTTAAATATATTACTTACTAAAATATATA
Found at i:6615750 original size:9 final size:9
Alignment explanation
Indices: 6615732--6616314 Score: 188
Period size: 9 Copynumber: 67.8 Consensus size: 9
6615722 TAATAAATAA
*
6615732 AACTTGCAT
1 AACTTACAT
6615741 AACTTACAT
1 AACTTACAT
*
6615750 AA-TAACATAAT
1 AACTTAC---AT
6615761 AACTTACAT
1 AACTTACAT
*
6615770 AA--TACAC
1 AACTTACAT
6615777 AACTTACAT
1 AACTTACAT
*
6615786 AACTTAAAT
1 AACTTACAT
6615795 AACTTACAT
1 AACTTACAT
*
6615804 -A-GTACAT
1 AACTTACAT
**
6615811 AACTTTGAT
1 AACTTACAT
*
6615820 AACTAACAT
1 AACTTACAT
* *
6615829 TA--TACAC
1 AACTTACAT
6615836 AACTTACAT
1 AACTTACAT
6615845 AACTTACAT
1 AACTTACAT
*
6615854 AACTTAAAT
1 AACTTACAT
6615863 AACTTACAT
1 AACTTACAT
6615872 AA--TACAT
1 AACTTACAT
6615879 AACTT-CGAT
1 AACTTAC-AT
*
6615888 AACTAACAT
1 AACTTACAT
* *
6615897 TA--TACAC
1 AACTTACAT
6615904 AACTTACAT
1 AACTTACAT
6615913 AA--TACAT
1 AACTTACAT
** *
6615920 TTCTTGCAT
1 AACTTACAT
6615929 AACTTACAT
1 AACTTACAT
* *
6615938 TA--TACAC
1 AACTTACAT
6615945 AACTTA-ATT
1 AACTTACA-T
*
6615954 AATATTATACAT
1 -A-ACT-TACAT
*
6615966 AACATACAT
1 AACTTACAT
6615975 AA--TACAT
1 AACTTACAT
6615982 AA--TACAT
1 AACTTACAT
*
6615989 AA--TACAC
1 AACTTACAT
6615996 AACTTA-ATT
1 AACTTACA-T
*
6616005 AATATTATACAT
1 -A-ACT-TACAT
6616017 AACTTACAT
1 AACTTACAT
*
6616026 -A-GTACAT
1 AACTTACAT
*
6616033 AACTAACAT
1 AACTTACAT
*
6616042 -A-GTACAT
1 AACTTACAT
*
6616049 AACATACAT
1 AACTTACAT
6616058 AA--TACAT
1 AACTTACAT
*
6616065 AA--TACAC
1 AACTTACAT
6616072 AACTTA-ATT
1 AACTTACA-T
*
6616081 AAAATTATACAT
1 --AACT-TACAT
*
6616093 AACATACA-
1 AACTTACAT
*
6616101 AA-ATACAT
1 AACTTACAT
6616109 AA--TACAT
1 AACTTACAT
6616116 AACTTACAT
1 AACTTACAT
*
6616125 AAATTACAT
1 AACTTACAT
*
6616134 AA--TACAC
1 AACTTACAT
6616141 AACTTA-ATT
1 AACTTACA-T
*
6616150 AATATTATACAT
1 -A-ACT-TACAT
6616162 AACTTA-ATT
1 AACTTACA-T
*
6616171 AATATTATACAT
1 -A-ACT-TACAT
*
6616183 AACATACAT
1 AACTTACAT
6616192 AA--TACAT
1 AACTTACAT
6616199 AACTTACAT
1 AACTTACAT
6616208 AACTTACAT
1 AACTTACAT
6616217 AACTTACAT
1 AACTTACAT
* *
6616226 -A-GTACAC
1 AACTTACAT
*
6616233 AACTAACAT
1 AACTTACAT
*
6616242 AA--TACAC
1 AACTTACAT
6616249 AACTTACAT
1 AACTTACAT
* *
6616258 AGCTTACAG
1 AACTTACAT
6616267 AA--TACAT
1 AACTTACAT
6616274 AACTTACAT
1 AACTTACAT
*
6616283 AACTTATAT
1 AACTTACAT
*
6616292 AA--TACAA
1 AACTTACAT
6616299 AACTTACAT
1 AACTTACAT
*
6616308 AATTTAC
1 AACTTAC
6616315 CTAATACATA
Statistics
Matches: 426, Mismatches: 80, Indels: 136
0.66 0.12 0.21
Matches are distributed among these distances:
7 123 0.29
8 21 0.05
9 227 0.53
10 13 0.03
11 19 0.04
12 18 0.04
13 5 0.01
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:6615789 original size:25 final size:25
Alignment explanation
Indices: 6615732--6615914 Score: 116
Period size: 25 Copynumber: 7.4 Consensus size: 25
6615722 TAATAAATAA
*
6615732 AACTTGCATAACTTACATAATA-AC
1 AACTTACATAACTTACATAATACAC
6615756 -A--TA-ATAACTTACATAATACAC
1 AACTTACATAACTTACATAATACAC
*
6615777 AACTTACATAACTTAAATAACTTACA-
1 AACTTACATAACTTACATAA--TACAC
* * **
6615803 TA-GTACATAACTTTGATAACTA-AC
1 AACTTACATAACTTACATAA-TACAC
* * *
6615827 -ATTATACACAACTTACATAACTTACAT
1 AACT-TACATAACTTACATAA--TACAC
* *
6615854 AACTTAAATAACTTACATAATACAT
1 AACTTACATAACTTACATAATACAC
* *
6615879 AACTT-CGATAACTAACATTATACAC
1 AACTTAC-ATAACTTACATAATACAC
6615904 AACTTACATAA
1 AACTTACATAA
6615915 TACATTTCTT
Statistics
Matches: 124, Mismatches: 20, Indels: 29
0.72 0.12 0.17
Matches are distributed among these distances:
20 15 0.12
21 3 0.02
22 1 0.01
23 3 0.02
24 4 0.03
25 73 0.59
26 4 0.03
27 19 0.15
28 2 0.02
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.31
Consensus pattern (25 bp):
AACTTACATAACTTACATAATACAC
Found at i:6615801 original size:34 final size:34
Alignment explanation
Indices: 6615758--6616293 Score: 160
Period size: 34 Copynumber: 16.1 Consensus size: 34
6615748 ATAATAACAT
*
6615758 AATAACTTACATAATACACAACTTACATAACTTA
1 AATAACTTACATAATACATAACTTACATAACTTA
* **
6615792 AATAACTTACATAGTACATAACTTTGATAAC-TA
1 AATAACTTACATAATACATAACTTACATAACTTA
* *
6615825 ACATTA--TACACAACTTACATAACTTACATAACTTA
1 A-ATAACTTACATAA--TACATAACTTACATAACTTA
6615860 AATAACTTACATAATACATAACTT-CGATAAC-TA
1 AATAACTTACATAATACATAACTTAC-ATAACTTA
* * ** *
6615893 ACATTA--TACACAACTTACATAA--TACATTTCTTG
1 A-ATAACTTACATAA--TACATAACTTACATAACTTA
* * * *
6615926 CATAACTTACATTATACACAACTTA-ATTAATATTA
1 AATAACTTACATAATACATAACTTACA-TAA-CTTA
*
6615961 TACATAACATACATAATACATAA--TACATAA--TA
1 -A-ATAACTTACATAATACATAACTTACATAACTTA
* * *
6615993 CACAACTTA-AT--TA-AT-ATTATACATAACTTA
1 AATAACTTACATAATACATAACT-TACATAACTTA
* * * *
6616023 CAT-A-GTACATAACTAACAT-A-GTACATAACATA
1 AATAACTTACATAA-T-ACATAACTTACATAACTTA
* * ** *
6616055 CATAA--TACATAATACACAACTTAATTAAAATTA
1 AATAACTTACATAATACATAACTTACAT-AACTTA
* *
6616088 TACATAACATACAAAATACATAA--TACATAACTTA
1 -A-ATAACTTACATAATACATAACTTACATAACTTA
* * * *
6616122 CATAAATTACATAATACACAACTTA-ATTAATATTA
1 AATAACTTACATAATACATAACTTACA-TAA-CTTA
* *
6616157 TACATAACTTA-AT--TA-AT-ATTATACATAACATA
1 -A-ATAACTTACATAATACATAACT-TACATAACTTA
*
6616189 CATAA--TACATAACTTACATAACTTACATAACTTA
1 AATAACTTACATAA--TACATAACTTACATAACTTA
* * * *
6616223 CAT-A-GTACACAACTAACATAA--TACACAACTTA
1 AATAACTTACATAA-T-ACATAACTTACATAACTTA
* * *
6616255 CATAGCTTACAGAATACATAACTTACATAACTTA
1 AATAACTTACATAATACATAACTTACATAACTTA
*
6616289 TATAA
1 AATAA
6616294 TACAAAACTT
Statistics
Matches: 369, Mismatches: 72, Indels: 122
0.66 0.13 0.22
Matches are distributed among these distances:
25 1 0.00
26 2 0.01
27 2 0.01
28 11 0.03
29 7 0.02
30 17 0.05
31 2 0.01
32 89 0.24
33 28 0.08
34 143 0.39
35 22 0.06
36 9 0.02
37 36 0.10
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (34 bp):
AATAACTTACATAATACATAACTTACATAACTTA
Found at i:6615852 original size:68 final size:68
Alignment explanation
Indices: 6615772--6615949 Score: 261
Period size: 68 Copynumber: 2.6 Consensus size: 68
6615762 ACTTACATAA
* * *
6615772 TACACAACTTACATAACTTAAATAACTTACATAGTACATAACTTTGATAACTAACATTATACACA
1 TACATAACTTACATAACTTAAATAACTTACATAATACATAACTTCGATAACTAACATTATACACA
6615837 ACT
66 ACT
6615840 TACATAACTTACATAACTTAAATAACTTACATAATACATAACTTCGATAACTAACATTATACACA
1 TACATAACTTACATAACTTAAATAACTTACATAATACATAACTTCGATAACTAACATTATACACA
6615905 ACT
66 ACT
** ** * *
6615908 TACATAA--TACATTTCTTGCATAACTTACATTATACACAACTT
1 TACATAACTTACATAACTTAAATAACTTACATAATACATAACTT
6615950 AATTAATATT
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
66 29 0.29
68 72 0.71
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (68 bp):
TACATAACTTACATAACTTAAATAACTTACATAATACATAACTTCGATAACTAACATTATACACA
ACT
Found at i:6615858 original size:43 final size:43
Alignment explanation
Indices: 6615806--6615896 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
6615796 ACTTACATAG
** *
6615806 TACATAACTTTGATAACTAACATTATACACAACTTAC-ATAACT
1 TACATAACTTAAATAACTAACATAATACACAACTT-CGATAACT
* *
6615849 TACATAACTTAAATAACTTACATAATACATAACTTCGATAACT
1 TACATAACTTAAATAACTAACATAATACACAACTTCGATAACT
*
6615892 AACAT
1 TACAT
6615897 TATACACAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 40 0.98
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (43 bp):
TACATAACTTAAATAACTAACATAATACACAACTTCGATAACT
Found at i:6615882 original size:16 final size:16
Alignment explanation
Indices: 6615738--6616310 Score: 212
Period size: 16 Copynumber: 34.9 Consensus size: 16
6615728 ATAAAACTTG
6615738 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
6615755 CATAATAACTTACATAATA
1 C---ATAACTTACATAATA
*
6615774 CACAACTTACATAACTTA
1 CATAACTTACATAA--TA
* *
6615792 AATAACTTACATAGTA
1 CATAACTTACATAATA
**
6615808 CATAACTTTGATAACTAA
1 CATAACTTACATAA-T-A
* *
6615826 CATTA--TACACAACTTA
1 CATAACTTACATAA--TA
6615842 CATAACTTACATAACTTA
1 CATAACTTACATAA--TA
*
6615860 AATAACTTACATAATA
1 CATAACTTACATAATA
6615876 CATAACTT-CGAT-A-A
1 CATAACTTAC-ATAATA
*
6615890 C-T-A---ACATTATA
1 CATAACTTACATAATA
*
6615901 CACAACTTACATAATA
1 CATAACTTACATAATA
*
6615917 CAT---TT-C-T--TG
1 CATAACTTACATAATA
*
6615926 CATAACTTACATTATA
1 CATAACTTACATAATA
* *
6615942 CACAACTTAATTAATATTATA
1 CATAACTT-A--CATA--ATA
*
6615963 CATAACATACATAATA
1 CATAACTTACATAATA
6615979 CATAA--TACATAATA
1 CATAACTTACATAATA
* *
6615993 CACAACTTAATTAATATTATA
1 CATAACTT-A--CATA--ATA
*
6616014 CATAACTTACATAGTA
1 CATAACTTACATAATA
* *
6616030 CATAACTAACATAGTA
1 CATAACTTACATAATA
*
6616046 CATAACATACATAATA
1 CATAACTTACATAATA
*
6616062 CATAA--TACA-CA-A
1 CATAACTTACATAATA
* * *
6616074 CTTAA-TTAAAATTATA
1 CATAACTT-ACATAATA
* *
6616090 CATAACATACAAAATA
1 CATAACTTACATAATA
6616106 CATAA--TACATAACTTA
1 CATAACTTACATAA--TA
*
6616122 CATAAATTACATAATA
1 CATAACTTACATAATA
* *
6616138 CACAACTTAATTAATATTATA
1 CATAACTT-A--CATA--ATA
*
6616159 CATAACTTAATTAATATTATA
1 CATAACTT-A--CATA--ATA
*
6616180 CATAACATACATAATA
1 CATAACTTACATAATA
6616196 CATAACTTACATAACTTA
1 CATAACTTACATAA--TA
*
6616214 CATAACTTACATAGTA
1 CATAACTTACATAATA
* *
6616230 CACAACTAACATAATA
1 CATAACTTACATAATA
* *
6616246 CACAACTTACATAGCTTA
1 CATAACTTACATA--ATA
*
6616264 CAGAA--TACATAACTTA
1 CATAACTTACATAA--TA
*
6616280 CATAACTTATATAATA
1 CATAACTTACATAATA
*
6616296 CAAAACTTACATAAT
1 CATAACTTACATAAT
6616311 TTACCTAATA
Statistics
Matches: 430, Mismatches: 66, Indels: 121
0.70 0.11 0.20
Matches are distributed among these distances:
9 6 0.01
10 2 0.00
11 3 0.01
12 9 0.02
13 7 0.02
14 28 0.07
15 3 0.01
16 205 0.48
17 7 0.02
18 84 0.20
19 10 0.02
20 17 0.04
21 49 0.11
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:6615919 original size:41 final size:41
Alignment explanation
Indices: 6615863--6615950 Score: 133
Period size: 41 Copynumber: 2.1 Consensus size: 41
6615853 TAACTTAAAT
6615863 AACTTACATAATACATAACTT-CGATAACTAACATTATACAC
1 AACTTACATAATACATAACTTGC-ATAACTAACATTATACAC
** *
6615904 AACTTACATAATACATTTCTTGCATAACTTACATTATACAC
1 AACTTACATAATACATAACTTGCATAACTAACATTATACAC
6615945 AACTTA
1 AACTTA
6615951 ATTAATATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 42 0.98
42 1 0.02
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (41 bp):
AACTTACATAATACATAACTTGCATAACTAACATTATACAC
Found at i:6616042 original size:76 final size:74
Alignment explanation
Indices: 6615936--6616209 Score: 297
Period size: 76 Copynumber: 3.8 Consensus size: 74
6615926 CATAACTTAC
* *
6615936 ATTATACACAACTTA-AT-TA-ATATTATACATAACATACATAATACATAATACATAATACACAA
1 ATTATACATAACTTACATATACATAATA-ACATAACATACATAATACATAATACATAATACACAA
6615998 CTTAATTAAT
65 CTTAATTAAT
*
6616008 ATTATACATAACTTACATAGTACATAACTAACATAGTACATA-A-CATACATAATACATAATACA
1 ATTATACATAACTTACATA-TACATAA-TAACATA--ACATACATAATACATAATACATAATACA
*
6616071 CAACTTAATTAAA
62 CAACTTAATTAAT
* * *
6616084 ATTATACATAACATACAAAATACATAAT-ACATAACTTACAT-A-A-AT--TACATAATACACAA
1 ATTATACATAACTTAC-ATATACATAATAACATAACATACATAATACATAATACATAATACACAA
6616143 CTTAATTAAT
65 CTTAATTAAT
*
6616153 ATTATACATAACTTA-AT-TA-ATATTATACATAACATACATAATACATAACTTACATAA
1 ATTATACATAACTTACATATACATAATA-ACATAACATACATAATACATAA--TACATAA
6616210 CTTACATAAC
Statistics
Matches: 171, Mismatches: 12, Indels: 36
0.78 0.05 0.16
Matches are distributed among these distances:
65 4 0.02
66 2 0.01
67 13 0.08
68 1 0.01
69 38 0.22
70 2 0.01
71 2 0.01
72 19 0.11
73 4 0.02
74 12 0.07
75 3 0.02
76 61 0.36
77 5 0.03
78 5 0.03
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.32
Consensus pattern (74 bp):
ATTATACATAACTTACATATACATAATAACATAACATACATAATACATAATACATAATACACAAC
TTAATTAAT
Found at i:6616133 original size:25 final size:24
Alignment explanation
Indices: 6616028--6616325 Score: 169
Period size: 25 Copynumber: 12.6 Consensus size: 24
6616018 ACTTACATAG
* * *
6616028 TACATAACTAACATAGTACATAACA
1 TACATAAAT-ACATAATACATAACT
*
6616053 TACAT-AATACATAATACACAACT
1 TACATAAATACATAATACATAACT
* * *
6616076 TA-ATTAA-A-ATTATACATAACA
1 TACATAAATACATAATACATAACT
6616097 TACA-AAATACATAATACATAACT
1 TACATAAATACATAATACATAACT
*
6616120 TACATAAATTACATAATACACAACT
1 TACATAAA-TACATAATACATAACT
* *
6616145 TA-ATTAAT--ATTATACATAACT
1 TACATAAATACATAATACATAACT
* * *
6616166 TA-ATTAAT--ATTATACATAACA
1 TACATAAATACATAATACATAACT
6616187 TACAT-AATACATAACTTACATAACT
1 TACATAAATACATAA--TACATAACT
* * *
6616212 TACATAACTTACATAGTACACAACT
1 TACATAA-ATACATAATACATAACT
* * *
6616237 AACAT-AATACACAACTTACATAGCT
1 TACATAAATACATAA--TACATAACT
*
6616262 TACA-GAATACATAACTTACATAACT
1 TACATAAATACATAA--TACATAACT
* * *
6616287 TATAT-AATACAAAACTTACATAATT
1 TACATAAATACATAA--TACATAACT
*
6616312 TACCT-AATACATAA
1 TACATAAATACATAA
6616326 ATATATATCA
Statistics
Matches: 221, Mismatches: 35, Indels: 34
0.76 0.12 0.12
Matches are distributed among these distances:
21 50 0.23
22 7 0.03
23 40 0.18
24 10 0.05
25 107 0.48
26 1 0.00
27 6 0.03
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.30
Consensus pattern (24 bp):
TACATAAATACATAATACATAACT
Found at i:6616157 original size:69 final size:67
Alignment explanation
Indices: 6616038--6616200 Score: 224
Period size: 69 Copynumber: 2.4 Consensus size: 67
6616028 TACATAACTA
*
6616038 ACATAGTACATAACATACATAATACATAATACACAACTTAATTAAAATTATACATAACATACAAA
1 ACATAATACATAACATACATAATACATAATACACAACTTAATTAAAATTATACATAACATACAAA
6616103 AT
66 AT
* * *
6616105 ACATAATACATAACTTACATAAATTACATAATACACAACTTAATTAATATTATACATAACTTA-A
1 ACATAATACATAACATACAT-AA-TACATAATACACAACTTAATTAAAATTATACATAACATACA
*
6616169 TTAAT
64 -AAAT
*
6616174 --ATTATACATAACATACATAATACATAA
1 ACATAATACATAACATACATAATACATAA
6616201 CTTACATAAC
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
65 7 0.08
66 2 0.02
67 34 0.40
68 3 0.03
69 40 0.47
ACGTcount: A:0.53, C:0.15, G:0.01, T:0.31
Consensus pattern (67 bp):
ACATAATACATAACATACATAATACATAATACACAACTTAATTAAAATTATACATAACATACAAA
AT
Found at i:6616182 original size:21 final size:21
Alignment explanation
Indices: 6616066--6616185 Score: 98
Period size: 21 Copynumber: 5.4 Consensus size: 21
6616056 ATAATACATA
* *
6616066 ATACACAACTTAATTAAAATT
1 ATACATAACTTAATTAATATT
* * *
6616087 ATACATAACATACA-AAATACATA
1 ATACATAACTTA-ATTAAT--ATT
* *
6616110 ATACATAACTTACATAAATTACATA
1 ATACATAACTTA-ATTAA-T--ATT
*
6616135 ATACACAACTTAATTAATATT
1 ATACATAACTTAATTAATATT
6616156 ATACATAACTTAATTAATATT
1 ATACATAACTTAATTAATATT
6616177 ATACATAAC
1 ATACATAAC
6616186 ATACATAATA
Statistics
Matches: 84, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
21 43 0.51
22 1 0.01
23 16 0.19
24 7 0.08
25 17 0.20
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (21 bp):
ATACATAACTTAATTAATATT
Found at i:6616190 original size:127 final size:128
Alignment explanation
Indices: 6615926--6616204 Score: 306
Period size: 127 Copynumber: 2.2 Consensus size: 128
6615916 ACATTTCTTG
* * * *
6615926 CATAACTTACATTATACACAACTTAATTAATATTATACATAACATACATAATACATAATACATAA
1 CATAACATACATAATACACAACTTAATTAAAATTATACATAACATACAAAATACATAATACATAA
* * *
6615991 TACACAACTTAATTAATATTATACATAACTTACATAGTACATAACTAACATAGTACATAACATA
66 TACACAACTAAATTAATA-TATACACAACTTACATAATACATAACTAACATAGTACATAACATA
6616055 CAT-A-ATACATAATACACAACTTAATTAAAATTATACATAACATACAAAATACATAATACATAA
1 CATAACATACATAATACACAACTTAATTAAAATTATACATAACATACAAAATACATAATACATAA
* * * * *
6616118 CT-TAC-A-TAAATTACATA-ATACACAACTTA-ATTAATA-TTATACATAACTTAATTA-ATAT
66 -TACACAACTAAATTA-ATATATACACAACTTACA-TAATACATA-AC-TAACAT-AGTACATAA
*
6616176 TATA
125 CATA
*
6616180 CATAACATACATAATACATAACTTA
1 CATAACATACATAATACACAACTTA
6616205 CATAACTTAC
Statistics
Matches: 128, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
123 3 0.02
124 17 0.13
125 20 0.16
126 8 0.06
127 75 0.59
128 2 0.02
129 3 0.02
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.32
Consensus pattern (128 bp):
CATAACATACATAATACACAACTTAATTAAAATTATACATAACATACAAAATACATAATACATAA
TACACAACTAAATTAATATATACACAACTTACATAATACATAACTAACATAGTACATAACATA
Found at i:6616194 original size:21 final size:21
Alignment explanation
Indices: 6616044--6616195 Score: 94
Period size: 21 Copynumber: 6.9 Consensus size: 21
6616034 ACTAACATAG
*
6616044 TACATAACATACATAATACATAA
1 TACATAACTTACATAAT--ATAA
* * *
6616067 TACACAACTTA-ATTAAAATTA
1 TACATAACTTACA-TAATATAA
* *
6616088 TACATAACATACAAAATACATAA
1 TACATAACTTACATAAT--ATAA
6616111 TACATAACTTACATAAATTACATAA
1 TACATAACTTACAT-AA-T--ATAA
* *
6616136 TACACAACTTA-ATTAATATTA
1 TACATAACTTACA-TAATATAA
*
6616157 TACATAACTTA-ATTAATATTA
1 TACATAACTTACA-TAATATAA
*
6616178 TACATAACATACATAATA
1 TACATAACTTACATAATA
6616196 CATAACTTAC
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
21 52 0.49
22 3 0.03
23 28 0.26
24 5 0.05
25 18 0.17
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (21 bp):
TACATAACTTACATAATATAA
Found at i:6621805 original size:21 final size:21
Alignment explanation
Indices: 6621781--6621832 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
6621771 GGCAACGAGG
*
6621781 GAAGCAGAGGCTATAGCAAGA
1 GAAGCAGAGGCTACAGCAAGA
* *
6621802 GAAGCAGAGGCTGCAGCGAGA
1 GAAGCAGAGGCTACAGCAAGA
6621823 GAAGCAGAGG
1 GAAGCAGAGG
6621833 TTCAAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.40, T:0.06
Consensus pattern (21 bp):
GAAGCAGAGGCTACAGCAAGA
Found at i:6622254 original size:42 final size:42
Alignment explanation
Indices: 6622176--6622486 Score: 378
Period size: 42 Copynumber: 7.4 Consensus size: 42
6622166 AATCCCAAAA
*
6622176 TTAGTGGCGTTTTTTA-TAAAAGCGCCGCTAAAGAACATCA-CTT
1 TTAGTGGCGTTTTTTACT--AAGCGCCGCTAAAGAACATGATC-T
* * *
6622219 TTAGTGGC-TATTTTTACAAAGAGCCGCTAAAGAACAGGATCT
1 TTAGTGGCGT-TTTTTACTAAGCGCCGCTAAAGAACATGATCT
* * **
6622261 TTAGAGGTGTCTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
1 TTAGTGGCGT-TTTTTACTAAGCGCCGCTAAAGAACATGATCT
6622304 TTAGTGGCGTTTTTTACTAAGCGCCGCTAAAGAACATGATCT
1 TTAGTGGCGTTTTTTACTAAGCGCCGCTAAAGAACATGATCT
* * * *
6622346 TTAGCGGCGTCTTTTT-TTAAGCGCTGCTAAAGAACACGATCT
1 TTAGTGGCGT-TTTTTACTAAGCGCCGCTAAAGAACATGATCT
* *
6622388 TTAGTGGCATTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
1 TTAGTGGCGTTTTTTACTAAGCGCCGCTAAAGAACATGATCT
* * *
6622430 TTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGACCT
1 TTAGTGGCGTTTTTTACTAAGCGCCGCTAAAGAACATGATCT
*
6622472 TTAGCGGCGTTTTTT
1 TTAGTGGCGTTTTTT
6622487 CTGTAAATGC
Statistics
Matches: 232, Mismatches: 30, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
41 5 0.02
42 171 0.74
43 56 0.24
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (42 bp):
TTAGTGGCGTTTTTTACTAAGCGCCGCTAAAGAACATGATCT
Found at i:6622454 original size:126 final size:126
Alignment explanation
Indices: 6622176--6622486 Score: 421
Period size: 126 Copynumber: 2.4 Consensus size: 126
6622166 AATCCCAAAA
* * *
6622176 TTAGTGGCGTTTTTTATAAAAGCGCCGCTAAAGAACATCACTTTTAGTGGC-TATTTTTACAAAG
1 TTAGTGGCGTTTTTTAT-TAAGCGCCGCTAAAGAACATGAC-TTTAGCGGCGT-TTTTTACAAAG
* ** *
6622240 AGCCGCTAAAGAACAGGATCTTTAGAGGTGTCTTTTTTTTAAGCGCCGCTAAAGAACATGATCT
63 AGCCGCTAAAGAACACGATCTTTAGAGGCATCTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
* ** *
6622304 TTAGTGGCGTTTTTTACTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTT-TTAAGC
1 TTAGTGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGA-CTTTAGCGGCGT-TTTTTACAAAGA
* *
6622368 GCTGCTAAAGAACACGATCTTTAGTGGCAT-TTTTTTCTAAGCGCCGCTAAAGAACATGATCT
64 GCCGCTAAAGAACACGATCTTTAGAGGCATCTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
*
6622430 TTAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTT
1 TTAGTGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGA-CTTTAGCGGCGTTTTTT
6622487 CTGTAAATGC
Statistics
Matches: 164, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
125 5 0.03
126 80 0.49
127 56 0.34
128 23 0.14
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (126 bp):
TTAGTGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGACTTTAGCGGCGTTTTTTACAAAGAGC
CGCTAAAGAACACGATCTTTAGAGGCATCTTTTTTCTAAGCGCCGCTAAAGAACATGATCT
Found at i:6625239 original size:18 final size:18
Alignment explanation
Indices: 6625218--6625274 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
6625208 AGGCCACATA
*
6625218 CAGAAGAGGTTATCGTGG
1 CAGAGGAGGTTATCGTGG
*
6625236 CAGAGGTGGTTATCGTGG
1 CAGAGGAGGTTATCGTGG
*
6625254 TAGAGGAGG---TCGTGG
1 CAGAGGAGGTTATCGTGG
6625269 CAGAGG
1 CAGAGG
6625275 TAGAAGTGCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 11 0.32
18 23 0.68
ACGTcount: A:0.23, C:0.11, G:0.46, T:0.21
Consensus pattern (18 bp):
CAGAGGAGGTTATCGTGG
Found at i:6628671 original size:18 final size:18
Alignment explanation
Indices: 6628617--6628663 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
6628607 CTGTTTTTGT
6628617 TATGATTTTCTGTTGAGA
1 TATGATTTTCTGTTGAGA
6628635 TATGA-TTTCTTGTTGAGA
1 TATGATTTTC-TGTTGAGA
6628653 TATGATTTTCT
1 TATGATTTTCT
6628664 ATTAAGATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.21, C:0.06, G:0.19, T:0.53
Consensus pattern (18 bp):
TATGATTTTCTGTTGAGA
Found at i:6632827 original size:18 final size:19
Alignment explanation
Indices: 6632804--6632847 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
6632794 AGCAACTTGA
*
6632804 GTTGAGCTTGCA-CTTTTG
1 GTTGAGCTTGCAGCTTTAG
6632822 GTTGAGCTTGCAGCTTTAG
1 GTTGAGCTTGCAGCTTTAG
6632841 G-TGAGCT
1 GTTGAGCT
6632848 CGCAAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.14, C:0.16, G:0.32, T:0.39
Consensus pattern (19 bp):
GTTGAGCTTGCAGCTTTAG
Found at i:6634239 original size:12 final size:12
Alignment explanation
Indices: 6634222--6634247 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6634212 TAAAACAGGC
6634222 TTTTAGCGGCGT
1 TTTTAGCGGCGT
6634234 TTTTAGCGGCGT
1 TTTTAGCGGCGT
6634246 TT
1 TT
6634248 GGATAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:6634547 original size:113 final size:114
Alignment explanation
Indices: 6634316--6634644 Score: 549
Period size: 113 Copynumber: 2.9 Consensus size: 114
6634306 AAAAAAAGCA
*
6634316 TTAGCGGCGTTTTT-GAGAAAGCGCCGC-AAAAAACCTAAGCCTAATGACGCCGTTTTCTGAGCT
1 TTAGCGGCGTTTTTGGA-AAAGCGCCGCAAAAAAACCTAAGCCTAACGACGCCGTTTTCTGAGCT
*
6634379 TTCAGAGATTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATGCCCAGGGCT
65 TTCAGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATGCCCAGGGCT
*
6634429 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCTAACGACGCCGTTTTCTGAACTT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCTAACGACGCCGTTTTCTGAGCTT
*
6634494 TCAGGGATTTAGTGGCGTTTTTGGTAAAGCGCCGCTAATG-CCAGGGCT
66 TCAGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATGCCCAGGGCT
*
6634542 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCTAACGACGCCGTTTTCTGAGCTT
* *
6634607 TCGGGGATTTAGCGGCGTTTTT-TTAAAAGCGCCGCTAA
66 TCAGGGATTTAGCGGCGTTTTTGGT-AAAGCGCCGCTAA
6634645 AAATATTTTA
Statistics
Matches: 204, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
112 1 0.00
113 128 0.63
114 75 0.37
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGGAAAAGCGCCGCAAAAAAACCTAAGCCTAACGACGCCGTTTTCTGAGCTT
TCAGGGATTTAGCGGCGTTTTTGGTAAAGCGCCGCTAATGCCCAGGGCT
Found at i:6634910 original size:15 final size:15
Alignment explanation
Indices: 6634892--6634922 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6634882 CATATATTAA
6634892 GGTTTAGGGAGTATG
1 GGTTTAGGGAGTATG
*
6634907 GGTTTAGGGATTATG
1 GGTTTAGGGAGTATG
6634922 G
1 G
6634923 ATTAGGGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.35
Consensus pattern (15 bp):
GGTTTAGGGAGTATG
Found at i:6635229 original size:21 final size:20
Alignment explanation
Indices: 6635195--6635235 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
6635185 TTATGAATTA
*
6635195 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
6635215 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
6635236 AGGGGTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:6639309 original size:13 final size:13
Alignment explanation
Indices: 6639291--6639316 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6639281 TTATAAAATT
6639291 TTTACATTTTACA
1 TTTACATTTTACA
6639304 TTTACATTTTACA
1 TTTACATTTTACA
6639317 AAGCTTCAGC
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:0.00, T:0.54
Consensus pattern (13 bp):
TTTACATTTTACA
Found at i:6640182 original size:50 final size:50
Alignment explanation
Indices: 6640112--6640238 Score: 245
Period size: 50 Copynumber: 2.5 Consensus size: 50
6640102 CTAGATTGAG
6640112 GCTTATATGCAAAATGTGAGTTATGGATCTGGAGAAGGGAATGATAGGCT
1 GCTTATATGCAAAATGTGAGTTATGGATCTGGAGAAGGGAATGATAGGCT
6640162 GCTTATATGCAAAATGTGAGTTATGGATCTGGAGAAGGGAATGATAGGCT
1 GCTTATATGCAAAATGTGAGTTATGGATCTGGAGAAGGGAATGATAGGCT
*
6640212 GCTTCTATGCAAAATGTGAGTTATGGA
1 GCTTATATGCAAAATGTGAGTTATGGA
6640239 GTTGGTTTTC
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (50 bp):
GCTTATATGCAAAATGTGAGTTATGGATCTGGAGAAGGGAATGATAGGCT
Found at i:6641709 original size:43 final size:43
Alignment explanation
Indices: 6641659--6641887 Score: 244
Period size: 43 Copynumber: 5.3 Consensus size: 43
6641649 TTTTTTATGA
* * *
6641659 TCTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGGTCAGGT
1 TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
* * * * * * * **
6641702 TTTTTAGCGGCATTTGTGGGAAAAGCGTCGTTAAAGAACCTAA
1 TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
* * * * * *
6641745 CCTTTAGTGGCGTTTTTGGGAAAAGTGCCGCTAAAGGTCATGT
1 TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
* *
6641788 TCTTTAGCGGCGTTTGTGAAAAAAGCGTCGCTAAAGATCATGT
1 TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
* * *
6641831 TCTTTAGCGGTGTTTGTGG-AAAAGCGCTGCTAAAGATCATAT
1 TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
6641873 TCTTTAGCGGCGTTT
1 TCTTTAGCGGCGTTT
6641888 TTTCAAATAA
Statistics
Matches: 147, Mismatches: 39, Indels: 1
0.79 0.21 0.01
Matches are distributed among these distances:
42 34 0.23
43 113 0.77
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGATCATGT
Found at i:6641805 original size:86 final size:86
Alignment explanation
Indices: 6641660--6641887 Score: 278
Period size: 86 Copynumber: 2.7 Consensus size: 86
6641650 TTTTTATGAT
* * * * **
6641660 CTTTAGCGGCGTTTTTGGAAAAAGCGCCGCTAAAGGTCAGGTTTTTTAGCGGCATTTGTGGGAAA
1 CTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAAAAA
* *
6641725 AGCGTCGTTAAAGAACCTAAC
66 AGCGTCGCTAAAGAACATAAC
* *
6641746 CTTTAGTGGCGTTTTTGGGAAAAGTGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAAAAA
1 CTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAAAAA
* ***
6641811 AGCGTCGCTAAAGATCATGTT
66 AGCGTCGCTAAAGAACATAAC
* * * * *
6641832 CTTTAGCGGTGTTTGT-GGAAAAGCGCTGCTAAAGATCATATTCTTTAGCGGCGTTT
1 CTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTT
6641888 TTTCAAATAA
Statistics
Matches: 121, Mismatches: 21, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
85 36 0.30
86 85 0.70
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.32
Consensus pattern (86 bp):
CTTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGAAAAA
AGCGTCGCTAAAGAACATAAC
Found at i:6646863 original size:16 final size:16
Alignment explanation
Indices: 6646844--6646879 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6646834 CGGCTTGCAA
*
6646844 TTTGATAGGCTCACAC
1 TTTGACAGGCTCACAC
*
6646860 TTTGACAGGCTCGCAC
1 TTTGACAGGCTCACAC
6646876 TTTG
1 TTTG
6646880 CTTACTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.33
Consensus pattern (16 bp):
TTTGACAGGCTCACAC
Found at i:6647077 original size:25 final size:25
Alignment explanation
Indices: 6647034--6647081 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
6647024 ACCTTTTGAT
*
6647034 GAGCTCGCACCACTTGCTAAGCTCA
1 GAGCTCGCACCACTCGCTAAGCTCA
**
6647059 GAGCTCGCACTTCTCGCTAAGCT
1 GAGCTCGCACCACTCGCTAAGCT
6647082 TGTAGCTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (25 bp):
GAGCTCGCACCACTCGCTAAGCTCA
Found at i:6647106 original size:25 final size:27
Alignment explanation
Indices: 6647065--6647140 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 27
6647055 CTCAGAGCTC
* *
6647065 GCAC-TTCTCGCTAAGCTTGTAGCTTT
1 GCACATTCTTGCTGAGCTTGTAGCTTT
*
6647091 G-ACA-TCTTGCTGAGCTTGCAGC-TT
1 GCACATTCTTGCTGAGCTTGTAGCTTT
* * *
6647115 GCACATTTTTGCTGAGGTTATAGCTT
1 GCACATTCTTGCTGAGCTTGTAGCTT
6647141 ACACATTGGA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
24 3 0.08
25 20 0.51
26 15 0.38
27 1 0.03
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (27 bp):
GCACATTCTTGCTGAGCTTGTAGCTTT
Found at i:6648595 original size:56 final size:50
Alignment explanation
Indices: 6648525--6648761 Score: 210
Period size: 50 Copynumber: 4.6 Consensus size: 50
6648515 AATGAGATCC
* * *
6648525 CATGTAAAACCATGTCTGGGATATGGCATTGGTATCATTGAGATTATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGG---CATCGAG---ATGAGAGGTCT
* *
6648581 CATGTAAGAGCATGTCTGGGACATGGCGTTGGCATCGAGATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCT
** * * * * *
6648631 CCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCT
* * * * **
6648681 CATGTAAGACCATATCTGGGATATGGCGTTGGCAGTAC-A-A-GAAACATCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-T-CGAGATGAGAGGTCT
*
6648730 CATGTAAGACCATGTCTGGGACATGGCTTTGG
1 CATGTAAGACCATGTCTGGGACATGGCATTGG
6648762 AATGTTATTA
Statistics
Matches: 151, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
49 34 0.23
50 81 0.54
51 1 0.01
52 1 0.01
53 6 0.04
56 28 0.19
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGGTCT
Found at i:6648712 original size:100 final size:99
Alignment explanation
Indices: 6648569--6648756 Score: 245
Period size: 100 Copynumber: 1.9 Consensus size: 99
6648559 TCATTGAGAT
* * * * * **
6648569 TATGAGAGGTCTCATGTAAGAGCATGTCTGGGACATGGCGTTGGCA-T-CGAGATGAGAGGTCTC
1 TATGAGAAGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCAGTAC-A-A-GAAACATCTC
*
6648632 CCGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
63 ACGTAAGACCATGTCTGGGACATGGCATGGGCACCGA
* *
6648669 TATGAGAAGTCCCATGTAAGACCATATCTGGGATATGGCGTTGGCAGTACAAGAAACATCTCATG
1 TATGAGAAGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCAGTACAAGAAACATCTCACG
6648734 TAAGACCATGTCTGGGACATGGC
66 TAAGACCATGTCTGGGACATGGC
6648757 TTTGGAATGT
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
99 31 0.41
100 42 0.55
101 2 0.03
102 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (99 bp):
TATGAGAAGTCCCATGTAAGACCATATCTGGGACATGGCGTTGGCAGTACAAGAAACATCTCACG
TAAGACCATGTCTGGGACATGGCATGGGCACCGA
Found at i:6652720 original size:31 final size:31
Alignment explanation
Indices: 6652641--6652720 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
6652631 TTGATATATG
* * *
6652641 AACTTTAA-TTTGATGCAATTATACACATGA
1 AACTTTAATTTTGATTCAAATATACACATAA
* * * * *
6652671 AACTTTGATTGTGGTTCAAATGTATACATAA
1 AACTTTAATTTTGATTCAAATATACACATAA
6652702 AACTTTAATTTTGATTCAA
1 AACTTTAATTTTGATTCAA
6652721 TTATTTGCAC
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
30 7 0.18
31 31 0.82
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (31 bp):
AACTTTAATTTTGATTCAAATATACACATAA
Found at i:6660869 original size:29 final size:29
Alignment explanation
Indices: 6660837--6660895 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
6660827 CTACTAAGAC
6660837 ACTCAGGTTTTTCATATCATTCCTCAAAG
1 ACTCAGGTTTTTCATATCATTCCTCAAAG
6660866 ACTCAGGTTTTTCATATCATTCCTCAAAG
1 ACTCAGGTTTTTCATATCATTCCTCAAAG
6660895 A
1 A
6660896 ATATTAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (29 bp):
ACTCAGGTTTTTCATATCATTCCTCAAAG
Found at i:6662794 original size:12 final size:11
Alignment explanation
Indices: 6662766--6662795 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
6662756 TTTATTTTTT
6662766 TATTTTTAAAA
1 TATTTTTAAAA
6662777 TATTTTTAAAA
1 TATTTTTAAAA
6662788 TACTTTTT
1 TA-TTTTT
6662796 TATTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:6669790 original size:8 final size:8
Alignment explanation
Indices: 6669777--6669801 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6669767 TTCAGTTCAA
6669777 TTTCACTT
1 TTTCACTT
6669785 TTTCACTT
1 TTTCACTT
6669793 TTTCACTT
1 TTTCACTT
6669801 T
1 T
6669802 CAAATCACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTCACTT
Found at i:6669821 original size:45 final size:46
Alignment explanation
Indices: 6669756--6669842 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
6669746 ATAGGGTCTC
* * * *
6669756 CAAATTCACATTTCAGTTC-AATTTCACTTTTTCACTTTTTCACTTT
1 CAAATTCACAATTCAATTCAAAATTCACTTTTCCA-TTTTTCACTTT
6669802 CAAA-TCACAATTCAATTCAAAATTCACTTTTCCATTTTTCA
1 CAAATTCACAATTCAATTCAAAATTCACTTTTCCATTTTTCA
6669843 AGTCAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 19 0.53
46 17 0.47
ACGTcount: A:0.30, C:0.24, G:0.01, T:0.45
Consensus pattern (46 bp):
CAAATTCACAATTCAATTCAAAATTCACTTTTCCATTTTTCACTTT
Found at i:6669854 original size:39 final size:38
Alignment explanation
Indices: 6669786--6669860 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 38
6669776 ATTTCACTTT
*
6669786 TTCACTTTTTCACTTTCAAATCACAATTCAATTCAAAA
1 TTCACTTTTCCACTTTCAAATCACAATTCAATTCAAAA
* *
6669824 TTCACTTTTCCATTTTTCAAGTCA-ATATTCAATTCAA
1 TTCACTTTTCCA-CTTTCAAATCACA-ATTCAATTCAA
6669861 TGCCAAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 12 0.38
39 20 0.62
ACGTcount: A:0.33, C:0.23, G:0.01, T:0.43
Consensus pattern (38 bp):
TTCACTTTTCCACTTTCAAATCACAATTCAATTCAAAA
Found at i:6671081 original size:3 final size:3
Alignment explanation
Indices: 6671068--6671097 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6671058 TAACTATTTC
6671068 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6671098 ATATATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6673840 original size:18 final size:18
Alignment explanation
Indices: 6673817--6673856 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
6673807 CAGATCGATG
*
6673817 AGAATTGCAACCTGGATC
1 AGAATTGCAACCTAGATC
6673835 AGAATTGCAACCTAGATC
1 AGAATTGCAACCTAGATC
6673853 AGAA
1 AGAA
6673857 GGTAAAGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (18 bp):
AGAATTGCAACCTAGATC
Found at i:6679760 original size:27 final size:26
Alignment explanation
Indices: 6679715--6679765 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
6679705 AACATCGGAT
*
6679715 GGCTTGGGGGTAAGGCGAGTAAGGTA
1 GGCTTGGGGGTAAGACGAGTAAGGTA
*
6679741 GGCTTGGAGGGTGAGACGAGTAAGG
1 GGCTTGG-GGGTAAGACGAGTAAGG
6679766 AAGAATCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.24, C:0.08, G:0.51, T:0.18
Consensus pattern (26 bp):
GGCTTGGGGGTAAGACGAGTAAGGTA
Found at i:6681533 original size:23 final size:23
Alignment explanation
Indices: 6681507--6681627 Score: 99
Period size: 23 Copynumber: 5.3 Consensus size: 23
6681497 AATTTTATGG
6681507 ATTTGTTTGGCTAAATTGTAGGC
1 ATTTGTTTGGCTAAATTGTAGGC
* *
6681530 ATTTGTCTT-TC-ACAATTTTATGG-
1 ATTTGT-TTGGCTA-AATTGTA-GGC
*
6681553 ATTTGTTTGGCTAATTTGTAGGC
1 ATTTGTTTGGCTAAATTGTAGGC
* * *
6681576 ATTTGTCTT--CCATAATTTTAGGG
1 ATTTGT-TTGGCTA-AATTGTAGGC
*
6681599 ATTTGTTTGGCTAAATTGTGGGC
1 ATTTGTTTGGCTAAATTGTAGGC
6681622 ATTTGT
1 ATTTGT
6681628 CTTCCACAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
22 9 0.12
23 57 0.76
24 9 0.12
ACGTcount: A:0.20, C:0.10, G:0.22, T:0.48
Consensus pattern (23 bp):
ATTTGTTTGGCTAAATTGTAGGC
Found at i:6681557 original size:46 final size:46
Alignment explanation
Indices: 6681494--6681652 Score: 264
Period size: 46 Copynumber: 3.5 Consensus size: 46
6681484 AGTTACCTTT
*
6681494 CACAATTTTATGGATTTGTTTGGCTAAATTGTAGGCATTTGTCTTT
1 CACAATTTTATGGATTTGTTTGGCTAAATTGTAGGCATTTGTCTTC
*
6681540 CACAATTTTATGGATTTGTTTGGCTAATTTGTAGGCATTTGTCTTC
1 CACAATTTTATGGATTTGTTTGGCTAAATTGTAGGCATTTGTCTTC
* * *
6681586 CATAATTTTAGGGATTTGTTTGGCTAAATTGTGGGCATTTGTCTTC
1 CACAATTTTATGGATTTGTTTGGCTAAATTGTAGGCATTTGTCTTC
*
6681632 CACAATTTTAAGGATTTGTTT
1 CACAATTTTATGGATTTGTTT
6681653 CTATTTTATT
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 105 1.00
ACGTcount: A:0.21, C:0.11, G:0.20, T:0.47
Consensus pattern (46 bp):
CACAATTTTATGGATTTGTTTGGCTAAATTGTAGGCATTTGTCTTC
Found at i:6681648 original size:23 final size:23
Alignment explanation
Indices: 6681530--6681650 Score: 65
Period size: 23 Copynumber: 5.3 Consensus size: 23
6681520 AATTGTAGGC
* *
6681530 ATTTGTCTTTCACAATTTTATGG
1 ATTTGTCTTCCACAATTTTAAGG
* *
6681553 ATTTGT-TTGGC-TAATTTGT-AGG
1 ATTTGTCTT-CCACAATTT-TAAGG
* *
6681575 CATTTGTCTTCCATAATTTTAGGG
1 -ATTTGTCTTCCACAATTTTAAGG
* * *
6681599 ATTTGT-TTGGCTA-AATTGT-GGG
1 ATTTGTCTT--CCACAATTTTAAGG
6681621 CATTTGTCTTCCACAATTTTAAGG
1 -ATTTGTCTTCCACAATTTTAAGG
6681645 ATTTGT
1 ATTTGT
6681651 TTCTATTTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
22 16 0.21
23 44 0.58
24 16 0.21
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.48
Consensus pattern (23 bp):
ATTTGTCTTCCACAATTTTAAGG
Found at i:6685439 original size:14 final size:17
Alignment explanation
Indices: 6685420--6685457 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
6685410 ATTTATTTCT
6685420 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
6685434 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
6685451 TAATATA
1 TAATATA
6685458 CTTTACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:6685808 original size:22 final size:22
Alignment explanation
Indices: 6685780--6685932 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
6685770 TGTTGATAGT
*
6685780 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
6685802 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
6685824 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
6685846 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
6685868 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
6685890 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
6685912 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
6685933 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:6688516 original size:88 final size:89
Alignment explanation
Indices: 6688416--6688734 Score: 374
Period size: 88 Copynumber: 3.6 Consensus size: 89
6688406 ACAGATATTG
* * * * * * * *
6688416 GATTTGTCGCTTCAATCTGCTCCACTGCAACTTCAGGGAAACT-GGATTTG-TAGCTTCAATCTG
1 GATTTGTAGCTTCAATCTGCTCCACTACAACTTTAGAGAGA-TAAGATTCGCTATCTTCAATCTG
*
6688479 CTCCATTGCAACTTCAGGGAGATAA
65 CTCCACTGCAACTTCAGGGAGATAA
* * * **
6688504 GATTTTTAGCTTCAATTTGCTCTACTGTAACTTTAGAGAGATAAGATTCGCTATCTTCAATCTGC
1 GATTTGTAGCTTCAATCTGCTCCACTACAACTTTAGAGAGATAAGATTCGCTATCTTCAATCTGC
*
6688569 TCTACTGCAACTTCAGGGAGATAA
66 TCCACTGCAACTTCAGGGAGATAA
* **
6688593 GGTTTGTAGCTTCAATCTGCTCTTCTACAACTTTAGAGAGATAAGA-TCGCTATCTTCAATCTGC
1 GATTTGTAGCTTCAATCTGCTCCACTACAACTTTAGAGAGATAAGATTCGCTATCTTCAATCTGC
* * * * *
6688657 TGCACTACAAATTTAAGGAGATAA
66 TCCACTGCAACTTCAGGGAGATAA
* * *
6688681 GATTTGTAGCATCAATCTGCTCCACTACAACTTTAGAGAGATAATATTGGCTAT
1 GATTTGTAGCTTCAATCTGCTCCACTACAACTTTAGAGAGATAAGATTCGCTAT
6688735 GATGATTTCA
Statistics
Matches: 197, Mismatches: 31, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
87 1 0.01
88 115 0.58
89 81 0.41
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (89 bp):
GATTTGTAGCTTCAATCTGCTCCACTACAACTTTAGAGAGATAAGATTCGCTATCTTCAATCTGC
TCCACTGCAACTTCAGGGAGATAA
Found at i:6688678 original size:133 final size:133
Alignment explanation
Indices: 6688424--6688724 Score: 335
Period size: 133 Copynumber: 2.3 Consensus size: 133
6688414 TGGATTTGTC
* *
6688424 GCTTCAATCTGCTCCACTGCAACTTCAGGGA-A-ACTGGATTTGTAGCTTCAATCTGCTCCATTG
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA-AGGATTTGTAGCTTCAATCTGCTCCATTA
* *** * ** *
6688487 CAACTTCAGGGAGATAAGATTTTTAGCTTCAATTTGCTCTACTGTAACTTTAGAGAGATAAGATT
65 CAACTTCAGAGAGATAAGATCGCTAGCTTCAATCTGCTCTACTACAAATTTAGAGAGATAAGATT
6688552 CGCTA
130 CG-TA
* * *
6688557 TCTTCAATCTGCTCTACTGCAACTTCAGGGAGATAAGG-TTTGTAGCTTCAATCTGCT-CTTCTA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGATTTGTAGCTTCAATCTGCTCCAT-TA
* *
6688620 CAACTTTAGAGAGATAAGATCGCTATCTTCAATCTGCTGC-ACTACAAATTTA-AGGAGATAAGA
65 CAACTTCAGAGAGATAAGATCGCTAGCTTCAATCTGCT-CTACTACAAATTTAGA-GAGATAAGA
*
6688683 TTTGTA
128 TTCGTA
* * * *
6688689 GCATCAATCTGCTCCACTACAACTTTAGAGAGATAA
1 GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
6688725 TATTGGCTAT
Statistics
Matches: 141, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
132 35 0.25
133 101 0.72
134 4 0.03
135 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (133 bp):
GCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGATTTGTAGCTTCAATCTGCTCCATTAC
AACTTCAGAGAGATAAGATCGCTAGCTTCAATCTGCTCTACTACAAATTTAGAGAGATAAGATTC
GTA
Found at i:6688722 original size:44 final size:44
Alignment explanation
Indices: 6688416--6688724 Score: 309
Period size: 44 Copynumber: 7.0 Consensus size: 44
6688406 ACAGATATTG
* * * * *
6688416 GATTTGTCGCTTCAATCTGCTCCACTGCAACTTCAGGGAAACT-G
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGA-TAA
* * *
6688460 GATTTGTAGCTTCAATCTGCTCCATTGCAACTTCAGGGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
* * * *
6688504 GATTTTTAGCTTCAATTTGCTCTACTGTAACTTTAGAGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
* * * * *
6688548 GATTCGCTATCTTCAATCTGCTCTACTGCAACTTCAGGGAGATAA
1 GATTTG-TAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
* ** *
6688593 GGTTTGTAGCTTCAATCTGCTCTTCTACAACTTTAGAGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
* * * * *
6688637 GA-TCGCTATCTTCAATCTGCTGCACTACAAATTTA-AGGAGATAA
1 GATTTG-TAGCTTCAATCTGCTCCACTGCAACTTTAGA-GAGATAA
* *
6688681 GATTTGTAGCATCAATCTGCTCCACTACAACTTTAGAGAGATAA
1 GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
6688725 TATTGGCTAT
Statistics
Matches: 222, Mismatches: 37, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
43 4 0.02
44 178 0.80
45 40 0.18
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (44 bp):
GATTTGTAGCTTCAATCTGCTCCACTGCAACTTTAGAGAGATAA
Found at i:6702561 original size:12 final size:12
Alignment explanation
Indices: 6702543--6702572 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6702533 TAATAATAGC
6702543 ATAATATTAATA
1 ATAATATTAATA
*
6702555 TTAATATTAATA
1 ATAATATTAATA
6702567 ATAATA
1 ATAATA
6702573 ATCATATTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATAATATTAATA
Found at i:6702571 original size:18 final size:18
Alignment explanation
Indices: 6702544--6702591 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
6702534 AATAATAGCA
* *
6702544 TAATATTAATATTAATAT
1 TAATAATAATAATAATAT
*
6702562 TAATAATAATAATCATAT
1 TAATAATAATAATAATAT
*
6702580 TAGTAATAATAA
1 TAATAATAATAA
6702592 ATAAACGAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TAATAATAATAATAATAT
Found at i:6702816 original size:11 final size:11
Alignment explanation
Indices: 6702800--6702868 Score: 61
Period size: 12 Copynumber: 6.0 Consensus size: 11
6702790 TGTGTATAAC
* *
6702800 AATAAAGAAGT
1 AATAAATAAAT
6702811 AATAAATAAAT
1 AATAAATAAAT
6702822 AAATAAATAAAT
1 -AATAAATAAAT
6702834 AAATAAAT-AAT
1 -AATAAATAAAT
6702845 AATAAAATAGTAAT
1 AAT-AAATA--AAT
6702859 AAT-AATAAAT
1 AATAAATAAAT
6702869 GCACAAAAGA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
10 6 0.12
11 16 0.31
12 23 0.45
14 6 0.12
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:6702820 original size:4 final size:4
Alignment explanation
Indices: 6702811--6702843 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
6702801 ATAAAGAAGT
6702811 AATA AATA AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA AATA A
6702844 TAATAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:6702999 original size:8 final size:8
Alignment explanation
Indices: 6702979--6703083 Score: 60
Period size: 8 Copynumber: 13.8 Consensus size: 8
6702969 AGAATTAAAA
6702979 TAAA-AAG
1 TAAATAAG
6702986 TAAATAAG
1 TAAATAAG
*
6702994 TGAATAA-
1 TAAATAAG
* *
6703001 TATATAAA
1 TAAATAAG
6703009 TAAATAAG
1 TAAATAAG
**
6703017 TAAATGGG
1 TAAATAAG
*
6703025 TAAATAAA
1 TAAATAAG
*
6703033 TGAATAAAG
1 TAAAT-AAG
6703042 T-AA-AAG
1 TAAATAAG
*
6703048 -GAAT-AG
1 TAAATAAG
* *
6703054 TGAATAAA
1 TAAATAAG
*
6703062 TATATAAG
1 TAAATAAG
6703070 TAAATAAG
1 TAAATAAG
6703078 TAAATA
1 TAAATA
6703084 GATGAATAAA
Statistics
Matches: 74, Mismatches: 17, Indels: 13
0.71 0.16 0.12
Matches are distributed among these distances:
6 7 0.09
7 13 0.18
8 51 0.69
9 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (8 bp):
TAAATAAG
Found at i:6703981 original size:2 final size:2
Alignment explanation
Indices: 6703974--6704000 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6703964 ACCCTTCCCT
6703974 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6704001 GTTTATTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6709517 original size:20 final size:20
Alignment explanation
Indices: 6709492--6709531 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6709482 TGCATACAGC
6709492 TTGTATGCATACTGCAGCAA
1 TTGTATGCATACTGCAGCAA
**
6709512 TTGTATGCATGTTGCAGCAA
1 TTGTATGCATACTGCAGCAA
6709532 CATATTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (20 bp):
TTGTATGCATACTGCAGCAA
Found at i:6709577 original size:21 final size:20
Alignment explanation
Indices: 6709544--6709586 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
6709534 TATTTTCTGT
* * *
6709544 TTTAGTTGCAATGTATTTAG
1 TTTAGTTGAAATGAACTTAG
6709564 TTTAGTTGAAAATGAACTTAG
1 TTTAGTTG-AAATGAACTTAG
6709585 TT
1 TT
6709587 GTTGTTGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.47
Consensus pattern (20 bp):
TTTAGTTGAAATGAACTTAG
Found at i:6723077 original size:29 final size:28
Alignment explanation
Indices: 6723035--6723094 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
6723025 AATGGCCAAC
* *
6723035 CATGTTGCTGTTATGTTTTTGTTAAAGTG
1 CATGTTGCTATTATGATTTTGTT-AAGTG
*
6723064 CATGTTGCTATTATGATTTTGTTGAGTG
1 CATGTTGCTATTATGATTTTGTTAAGTG
6723092 CAT
1 CAT
6723095 ACAGCATGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.18, C:0.08, G:0.23, T:0.50
Consensus pattern (28 bp):
CATGTTGCTATTATGATTTTGTTAAGTG
Found at i:6724529 original size:23 final size:22
Alignment explanation
Indices: 6724468--6724548 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
6724458 GATCTGCAAA
* *
6724468 GCCTTAGTGGCATATTTTGTGAG
1 GCCTT-GTGGCATATTTTGTAAT
* **
6724491 GCTTGTGTGGTGTATTTTGTAAT
1 GCCT-TGTGGCATATTTTGTAAT
**
6724514 GCCTATGTGGCATATTCAGTAAT
1 GCCT-TGTGGCATATTTTGTAAT
6724537 GCCTTCGTGGCA
1 GCCTT-GTGGCA
6724549 AAAATCTAGT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 1 0.02
23 43 0.96
24 1 0.02
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (22 bp):
GCCTTGTGGCATATTTTGTAAT
Found at i:6725866 original size:31 final size:31
Alignment explanation
Indices: 6725826--6726032 Score: 138
Period size: 31 Copynumber: 6.7 Consensus size: 31
6725816 CAACAATATC
* *
6725826 TATATTCATATACGAATCAAATTCGGAAATG
1 TATAATCATATACAAATCAAATTCGGAAATG
* *
6725857 TATAATCATATACAAATC-AATTTGGCAATG
1 TATAATCATATACAAATCAAATTCGGAAATG
* * ** * **
6725887 AATAACCATATATGAATCAAGTTTAGAAATG
1 TATAATCATATACAAATCAAATTCGGAAATG
* *
6725918 TATAATCATATACAAATCAAATTC-TACATTG
1 TATAATCATATACAAATCAAATTCGGA-AATG
* * * *
6725949 TATAACCATATACGAAT-TAATTCGGCAACT-
1 TATAATCATATACAAATCAAATTCGG-AAATG
** *
6725979 TATCTTCATATACAAATCAATTTC-GACAATG
1 TATAATCATATACAAATCAAATTCGGA-AATG
* *
6726010 TATAA-CTATAAACAATTCAAATT
1 TATAATC-ATATACAAATCAAATT
6726033 TAGCAATATA
Statistics
Matches: 132, Mismatches: 36, Indels: 16
0.72 0.20 0.09
Matches are distributed among these distances:
29 1 0.01
30 47 0.36
31 83 0.63
32 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (31 bp):
TATAATCATATACAAATCAAATTCGGAAATG
Found at i:6725906 original size:61 final size:61
Alignment explanation
Indices: 6725832--6726032 Score: 212
Period size: 61 Copynumber: 3.3 Consensus size: 61
6725822 TATCTATATT
* *
6725832 CATATACGAATCAAATTCGGAAATGTATAATCATATACAAATCAATTTGGCAATGAATAAC
1 CATATACGAATCAAATTCGGAAATGTATAATCATATACAAATCAATTTGACAATGTATAAC
* * ** *
6725893 CATATATGAATCAAGTTTAGAAATGTATAATCATATACAAATCAAATTCT-ACATTGTATAAC
1 CATATACGAATCAAATTCGGAAATGTATAATCATATACAAATC-AATT-TGACAATGTATAAC
* * **
6725955 CATATACGAAT-TAATTCGGCAACT-TATCTTCATATACAAATCAATTTCGACAATGTATAAC
1 CATATACGAATCAAATTCGG-AAATGTATAATCATATACAAATCAATTT-GACAATGTATAAC
* *
6726016 TATAAAC-AATTCAAATT
1 CATATACGAA-TCAAATT
6726033 TAGCAATATA
Statistics
Matches: 114, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
59 1 0.01
60 6 0.05
61 76 0.67
62 30 0.26
63 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.32
Consensus pattern (61 bp):
CATATACGAATCAAATTCGGAAATGTATAATCATATACAAATCAATTTGACAATGTATAAC
Found at i:6726048 original size:26 final size:25
Alignment explanation
Indices: 6726019--6726069 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
6726009 GTATAACTAT
*
6726019 AAACAATTCAAATTTAGCAATATATA
1 AAACAA-TCAAATTCAGCAATATATA
*
6726045 AAACAATCAAATTCGGCAATATATA
1 AAACAATCAAATTCAGCAATATATA
6726070 TATCTATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.53, C:0.14, G:0.06, T:0.27
Consensus pattern (25 bp):
AAACAATCAAATTCAGCAATATATA
Found at i:6726599 original size:25 final size:25
Alignment explanation
Indices: 6726570--6726621 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
6726560 AAAATTGGTA
*
6726570 AGACATTTTCCATT-TTTCTCTAAGC
1 AGACATTTTCCATTCTCT-TCTAAGC
6726595 AGACATTTTCCATTCTCTTCTAAGC
1 AGACATTTTCCATTCTCTTCTAAGC
6726620 AG
1 AG
6726622 CATACATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
AGACATTTTCCATTCTCTTCTAAGC
Found at i:6729083 original size:8 final size:10
Alignment explanation
Indices: 6729063--6729093 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
6729053 AAAAACAATT
6729063 TATTAATATA
1 TATTAATATA
6729073 TATTAATATA
1 TATTAATATA
6729083 TATTAATATA
1 TATTAATATA
6729093 T
1 T
6729094 GTAAAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TATTAATATA
Found at i:6729146 original size:32 final size:32
Alignment explanation
Indices: 6729110--6729196 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
6729100 ACAACTTTTT
* * *
6729110 CAGAAAATATTTTCAGGAAATCTGCCAAACAG
1 CAGAAAATATTTTCAGCAAATCTACCAAACAC
* *
6729142 CAGAAAATATTTTACA-CAGATTTACCAAACAC
1 CAGAAAATATTTT-CAGCAAATCTACCAAACAC
*
6729174 CAGAAAATATTTTCGAGTAAATC
1 CAGAAAATATTTTC-AGCAAATC
6729197 ATTTTACAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
31 1 0.02
32 38 0.86
33 5 0.11
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.25
Consensus pattern (32 bp):
CAGAAAATATTTTCAGCAAATCTACCAAACAC
Found at i:6729214 original size:20 final size:20
Alignment explanation
Indices: 6729189--6729228 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6729179 AATATTTTCG
*
6729189 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
6729209 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
6729229 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:6729231 original size:34 final size:35
Alignment explanation
Indices: 6729177--6729243 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
6729167 CAAACACCAG
* *
6729177 AAAATATTTTCGAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
6729212 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
6729244 CATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:6729235 original size:14 final size:14
Alignment explanation
Indices: 6729212--6729251 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
6729202 ACAGAAAAGT
*
6729212 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
6729226 AAATCATTTTACGG
1 AAAACATTTTACAG
6729240 AAAACATTTTAC
1 AAAACATTTTAC
6729252 TGCCAATCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:6733220 original size:14 final size:14
Alignment explanation
Indices: 6733201--6733229 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6733191 CAACACCTTA
6733201 AGCAATCCTTGTTG
1 AGCAATCCTTGTTG
6733215 AGCAATCCTTGTTG
1 AGCAATCCTTGTTG
6733229 A
1 A
6733230 ACCAATATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (14 bp):
AGCAATCCTTGTTG
Found at i:6733843 original size:23 final size:23
Alignment explanation
Indices: 6733817--6733864 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
6733807 CTCCTTCAAG
*
6733817 TTAATAGCCACATTTCATAAGAC
1 TTAATAGCCACATTTAATAAGAC
6733840 TTAATAGCCACATTTAATAAGAC
1 TTAATAGCCACATTTAATAAGAC
6733863 TT
1 TT
6733865 GCCAATTGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (23 bp):
TTAATAGCCACATTTAATAAGAC
Found at i:6735411 original size:14 final size:14
Alignment explanation
Indices: 6735392--6735419 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6735382 CTGAAATTGT
6735392 TGTTAAAATCATTA
1 TGTTAAAATCATTA
6735406 TGTTAAAATCATTA
1 TGTTAAAATCATTA
6735420 AAAATGTTGA
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:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TGTTAAAATCATTA
Found at i:6741621 original size:39 final size:39
Alignment explanation
Indices: 6741555--6741634 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
6741545 GGAGTTAAGC
* *
6741555 TACAAGTTGGCCAATGAAAAGGTAAGAAAGACTTCGAGG
1 TACAAGTTGGCCAATGAAAAAGCAAGAAAGACTTCGAGG
* *
6741594 TACAGGTTGGCCTATGAAAAAGCAAGAAAGACTTCGAGG
1 TACAAGTTGGCCAATGAAAAAGCAAGAAAGACTTCGAGG
6741633 TA
1 TA
6741635 ATTTATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.19
Consensus pattern (39 bp):
TACAAGTTGGCCAATGAAAAAGCAAGAAAGACTTCGAGG
Found at i:6741985 original size:20 final size:19
Alignment explanation
Indices: 6741962--6742006 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
6741952 TTTATTATTA
6741962 TTTAACATTTTATATAAATT
1 TTTAA-ATTTTATATAAATT
* *
6741982 TTTAGAATTTTATGTAATTT
1 TTTA-AATTTTATATAAATT
6742002 TTTAA
1 TTTAA
6742007 TTTAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 20 0.91
21 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTAAATTTTATATAAATT
Found at i:6742009 original size:18 final size:20
Alignment explanation
Indices: 6741968--6742005 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6741958 ATTATTTAAC
6741968 ATTTTATATAAATTTTTAGA
1 ATTTTATATAAATTTTTAGA
* *
6741988 ATTTTATGTAATTTTTTA
1 ATTTTATATAAATTTTTA
6742006 ATTTAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTTTATATAAATTTTTAGA
Found at i:6742565 original size:21 final size:21
Alignment explanation
Indices: 6742528--6742576 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
6742518 TCCAAGCTTC
6742528 TTCCATTTTCCTCTATC-TCTT
1 TTCC-TTTTCCTCTATCGTCTT
*
6742549 TTCCTTTTCCTTTTATCGTTCTT
1 TTCCTTTTCC-TCTATCG-TCTT
6742572 TTCCT
1 TTCCT
6742577 CTTATTCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.25
21 9 0.38
23 9 0.38
ACGTcount: A:0.06, C:0.31, G:0.02, T:0.61
Consensus pattern (21 bp):
TTCCTTTTCCTCTATCGTCTT
Found at i:6743751 original size:24 final size:24
Alignment explanation
Indices: 6743724--6743781 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
6743714 GGGTTGGATC
*
6743724 TGATTATGTATATGAATATGCATT
1 TGATTATGTATATAAATATGCATT
* *
6743748 TGATTTTGTATCTAAATATGCATT
1 TGATTATGTATATAAATATGCATT
* *
6743772 CGATTCTGTA
1 TGATTATGTA
6743782 CTTGAACTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.47
Consensus pattern (24 bp):
TGATTATGTATATAAATATGCATT
Found at i:6745614 original size:20 final size:19
Alignment explanation
Indices: 6745569--6745607 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 19
6745559 AATATTACAA
6745569 AAATAAAAAAAATCTAAAG
1 AAATAAAAAAAATCTAAAG
6745588 AATATAAAAAAGAATCTAAA
1 AA-ATAAAAAA-AATCTAAA
6745608 ATAATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 8 0.44
21 8 0.44
ACGTcount: A:0.72, C:0.05, G:0.05, T:0.18
Consensus pattern (19 bp):
AAATAAAAAAAATCTAAAG
Found at i:6750028 original size:46 final size:45
Alignment explanation
Indices: 6749877--6750033 Score: 264
Period size: 45 Copynumber: 3.5 Consensus size: 45
6749867 TACATATGAT
*
6749877 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
6749920 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
**
6749965 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAATCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
6750011 CACTTATCACTTTGTCACTTGAT
1 CACTTATCACTTTGTCACTTGAT
6750034 TAGAAGTACT
Statistics
Matches: 108, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
43 10 0.09
44 5 0.05
45 65 0.60
46 28 0.26
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (45 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTAC
Found at i:6755808 original size:53 final size:53
Alignment explanation
Indices: 6755724--6755828 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 53
6755714 GAGATTCAAG
* *
6755724 TTAATAGCTACATTTAATAAAGCTTGACAATTGGAAGACGGTAATAATAATTT
1 TTAATAGCCACATTTAATAAAGCTTGACAATTGGAAGACGGTAATAAAAATTT
** * * *
6755777 TTAATAGCCACATTTAATACGGTTTGGCAATTGGAAGATGGTAATAAAAATT
1 TTAATAGCCACATTTAATAAAGCTTGACAATTGGAAGACGGTAATAAAAATT
6755829 GTTGCCACGA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (53 bp):
TTAATAGCCACATTTAATAAAGCTTGACAATTGGAAGACGGTAATAAAAATTT
Found at i:6756039 original size:15 final size:16
Alignment explanation
Indices: 6756014--6756043 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6756004 TTAGATTAGT
6756014 TTTTATTTTAAAATAA
1 TTTTATTTTAAAATAA
6756030 TTTT-TTTTAAAATA
1 TTTTATTTTAAAATA
6756044 TAATACACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTATTTTAAAATAA
Found at i:6756177 original size:36 final size:40
Alignment explanation
Indices: 6756117--6756203 Score: 119
Period size: 38 Copynumber: 2.2 Consensus size: 40
6756107 TAAAAAGTAT
* *
6756117 TTATATTAAAAAACACTACCATAAATATAAT-ATTTTTTA
1 TTATATTAAAAAACACTACAATAAATATAATAATATTTTA
6756156 TTATATTAAAAAA-AC-A-AATAAATATAATAAATATTTTA
1 TTATATTAAAAAACACTACAATAAATATAAT-AATATTTTA
6756194 TTATATTAAA
1 TTATATTAAA
6756204 TATAATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
36 11 0.25
37 1 0.02
38 19 0.43
39 13 0.30
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (40 bp):
TTATATTAAAAAACACTACAATAAATATAATAATATTTTA
Found at i:6756361 original size:21 final size:21
Alignment explanation
Indices: 6756335--6756375 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6756325 TTATTTAACA
*
6756335 TTTATAA-TTAATATAATATTT
1 TTTATAACATAATAT-ATATTT
6756356 TTTATAACATAATATATATT
1 TTTATAACATAATATATATT
6756376 CGGGCCAGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTATAACATAATATATATTT
Found at i:6756626 original size:12 final size:12
Alignment explanation
Indices: 6756611--6756653 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
6756601 CCTTAACAAA
6756611 ATTTTTAAAATT
1 ATTTTTAAAATT
*
6756623 ATTTTCAAAATT
1 ATTTTTAAAATT
6756635 ACTTTTTTAAAAATT
1 A--TTTTT-AAAATT
6756650 ATTT
1 ATTT
6756654 GGTTTGTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 12 0.46
13 3 0.12
14 4 0.15
15 7 0.27
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTTTAAAATT
Found at i:6758414 original size:4 final size:4
Alignment explanation
Indices: 6758407--6758436 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
6758397 TTGTATGATT
*
6758407 TTTA TTTA CTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
6758437 ACAGGCTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:6765290 original size:27 final size:27
Alignment explanation
Indices: 6765252--6765304 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
6765242 TTCATATGTA
6765252 TTTCCTTTTACATCTTACAAAGCAATG
1 TTTCCTTTTACATCTTACAAAGCAATG
6765279 TTTCCTTTTACATCTTACAAAGCAAT
1 TTTCCTTTTACATCTTACAAAGCAAT
6765305 AAATTGTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.42
Consensus pattern (27 bp):
TTTCCTTTTACATCTTACAAAGCAATG
Found at i:6765429 original size:16 final size:18
Alignment explanation
Indices: 6765397--6765429 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
6765387 TTCATCCTAA
6765397 AATTATATATGAAATTAT
1 AATTATATATGAAATTAT
6765415 AATTAT-TAT-AAATTA
1 AATTATATATGAAATTA
6765430 ACTTATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
AATTATATATGAAATTAT
Found at i:6772140 original size:13 final size:13
Alignment explanation
Indices: 6772122--6772146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6772112 ATTTTAATAC
6772122 TATAAAATTGTTG
1 TATAAAATTGTTG
6772135 TATAAAATTGTT
1 TATAAAATTGTT
6772147 TAGATGTTAT
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:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TATAAAATTGTTG
Found at i:6775205 original size:26 final size:26
Alignment explanation
Indices: 6775176--6775226 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
6775166 TAAGCTTTCC
6775176 AATGTGCAAGCTGCAACCTCAGCAAA
1 AATGTGCAAGCTGCAACCTCAGCAAA
* *
6775202 AATGTGCAAGTTGCAAGCTCAGCAA
1 AATGTGCAAGCTGCAACCTCAGCAA
6775227 GATGTCAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.18
Consensus pattern (26 bp):
AATGTGCAAGCTGCAACCTCAGCAAA
Found at i:6775269 original size:25 final size:25
Alignment explanation
Indices: 6775241--6775288 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
6775231 TCAAAGCTGC
* *
6775241 GAGCTTAGCGAGAAGTGCGAGCTAT
1 GAGCTCAGCAAGAAGTGCGAGCTAT
**
6775266 GAGCTCAGCAAGTGGTGCGAGCT
1 GAGCTCAGCAAGAAGTGCGAGCT
6775289 CATCAAAAGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.19, G:0.38, T:0.19
Consensus pattern (25 bp):
GAGCTCAGCAAGAAGTGCGAGCTAT
Found at i:6775289 original size:18 final size:18
Alignment explanation
Indices: 6775266--6775305 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6775256 TGCGAGCTAT
**
6775266 GAGCTCAGCAAGTGGTGC
1 GAGCTCAGCAAAAGGTGC
*
6775284 GAGCTCATCAAAAGGTGC
1 GAGCTCAGCAAAAGGTGC
6775302 GAGC
1 GAGC
6775306 CCTGTATAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.35, T:0.15
Consensus pattern (18 bp):
GAGCTCAGCAAAAGGTGC
Found at i:6775487 original size:16 final size:16
Alignment explanation
Indices: 6775444--6775488 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
6775434 AGACAGTAAG
*
6775444 CAAAATGCAAGCCTGT
1 CAAAATGCAAGCCTAT
* *
6775460 CAAAGTGTAAGCCTAT
1 CAAAATGCAAGCCTAT
*
6775476 CAAATTGCAAGCC
1 CAAAATGCAAGCC
6775489 GAAGTGGCGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (16 bp):
CAAAATGCAAGCCTAT
Found at i:6775544 original size:44 final size:44
Alignment explanation
Indices: 6775481--6775573 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
6775471 CCTATCAAAT
*
6775481 TGCAAGCCGAAGTGGCGGAC-AGTCTAAATGCAAACTTGAATGGG
1 TGCAAACCGAAGTGGCGGACGA-TCTAAATGCAAACTTGAATGGG
* ** *
6775525 TGCAAACCGGAGTGGCGGACGATCTAAATGCAAGTTTGAGTGGG
1 TGCAAACCGAAGTGGCGGACGATCTAAATGCAAACTTGAATGGG
6775569 TGCAA
1 TGCAA
6775574 GCCAAAATGG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 42 0.98
45 1 0.02
ACGTcount: A:0.30, C:0.17, G:0.33, T:0.19
Consensus pattern (44 bp):
TGCAAACCGAAGTGGCGGACGATCTAAATGCAAACTTGAATGGG
Found at i:6776903 original size:11 final size:11
Alignment explanation
Indices: 6776889--6776913 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6776879 ATATTAAGCC
6776889 AATATTAAAAT
1 AATATTAAAAT
6776900 AATATTAAAAT
1 AATATTAAAAT
6776911 AAT
1 AAT
6776914 GAATTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:6783051 original size:30 final size:29
Alignment explanation
Indices: 6783015--6783074 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
6783005 TAACGCAAGG
*
6783015 GATGAATTTATCGTTGAAAGATAATTGGTT
1 GATGAATTTATCGTTG-AAGATAATTAGTT
*
6783045 GATGAATTTATCGTTGAGGATAATTAGTT
1 GATGAATTTATCGTTGAAGATAATTAGTT
6783074 G
1 G
6783075 TGGCAACGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.32, C:0.03, G:0.25, T:0.40
Consensus pattern (29 bp):
GATGAATTTATCGTTGAAGATAATTAGTT
Found at i:6788281 original size:13 final size:13
Alignment explanation
Indices: 6788263--6788288 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6788253 CATAATCATA
6788263 ATCTCTAAAAAAT
1 ATCTCTAAAAAAT
6788276 ATCTCTAAAAAAT
1 ATCTCTAAAAAAT
6788289 CTGAAACAAA
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
ATCTCTAAAAAAT
Found at i:6797060 original size:32 final size:32
Alignment explanation
Indices: 6797018--6797082 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 32
6797008 TTTTGTTAGG
*
6797018 TTATTAATTTTGTTA-GT-TTCTGTTTACATTT
1 TTATTAATTTT-TTATGTAATCTGTTTACATTT
6797049 TTATGTAATTTTTTATGTAATCTGTTTACATTT
1 TTAT-TAATTTTTTATGTAATCTGTTTACATTT
6797082 T
1 T
6797083 GAAACTGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 7 0.23
32 9 0.30
33 14 0.47
ACGTcount: A:0.22, C:0.06, G:0.09, T:0.63
Consensus pattern (32 bp):
TTATTAATTTTTTATGTAATCTGTTTACATTT
Found at i:6800727 original size:11 final size:11
Alignment explanation
Indices: 6800711--6800735 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6800701 AAACAACTTA
6800711 TAATGTCTAGG
1 TAATGTCTAGG
6800722 TAATGTCTAGG
1 TAATGTCTAGG
6800733 TAA
1 TAA
6800736 AGTATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (11 bp):
TAATGTCTAGG
Found at i:6802216 original size:46 final size:46
Alignment explanation
Indices: 6802146--6802307 Score: 249
Period size: 46 Copynumber: 3.6 Consensus size: 46
6802136 TTTGAGTACT
*
6802146 TCTGATC-AGTGGCAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
6802191 TCTGATCAAGTGACAAAGCGGTAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
6802237 TCTGATCAAGTGACAAAGTGATAAATGGTAGCCTTAGCTGCACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
6802283 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
6802308 ATCATACGTA
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
44 11 0.10
45 12 0.11
46 84 0.79
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:6803112 original size:28 final size:28
Alignment explanation
Indices: 6803072--6803140 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
6803062 AAATTGCAAA
6803072 ATAAAAAAA--ATTATAATTTTATTTAC
1 ATAAAAAAACCATTATAATTTTATTTAC
6803098 ATAAAAAAACCATTATAATTTTATTTAC
1 ATAAAAAAACCATTATAATTTTATTTAC
6803126 ATAAAAAAACCATTA
1 ATAAAAAAACCATTA
6803141 AATATGAGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 9 0.22
28 32 0.78
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (28 bp):
ATAAAAAAACCATTATAATTTTATTTAC
Found at i:6803477 original size:6 final size:6
Alignment explanation
Indices: 6803461--6803507 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
6803451 AGAATGTAGT
* *
6803461 TCTGTC TCTGGC ACTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGG
1 TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGG
6803508 TGCATGATGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.02, C:0.32, G:0.32, T:0.34
Consensus pattern (6 bp):
TCTGGC
Found at i:6807392 original size:14 final size:13
Alignment explanation
Indices: 6807366--6807416 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
6807356 GTTTATTTGA
6807366 AATATAATAATAT
1 AATATAATAATAT
6807379 AATATAATTAATAT
1 AATATAA-TAATAT
* *
6807393 AAT-TTACAATAT
1 AATATAATAATAT
*
6807405 AATAAAATAATA
1 AATATAATAATA
6807417 ATATACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:6808415 original size:38 final size:38
Alignment explanation
Indices: 6808364--6808481 Score: 213
Period size: 38 Copynumber: 3.2 Consensus size: 38
6808354 AAAAAGTCAG
*
6808364 TTATAATTAAACTTTTAATAAAATTATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
6808402 TTATAATTAAACTTTTAATAAAATGATTTTTAA-TTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
6808439 TT-TAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
6808476 TTATAA
1 TTATAA
6808482 ACTTTATATG
Statistics
Matches: 77, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
36 30 0.39
37 12 0.16
38 35 0.45
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:6808446 original size:36 final size:36
Alignment explanation
Indices: 6808367--6808486 Score: 199
Period size: 36 Copynumber: 3.3 Consensus size: 36
6808357 AAGTCAGTTA
*
6808367 TAATTAAACTTTTAATAAAATTATTTTTAATTTTTTT
1 TAATTAAACTTTTAATAAAATGATTTTTAA-TTTTTT
6808404 ATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
1 -TAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
6808441 TAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
1 TAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
6808477 T-A-TAAACTTT
1 TAATTAAACTTT
6808487 ATATGTTAAA
Statistics
Matches: 81, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
34 8 0.10
35 1 0.01
36 37 0.46
37 6 0.07
38 29 0.36
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (36 bp):
TAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
Found at i:6808729 original size:49 final size:50
Alignment explanation
Indices: 6808627--6808756 Score: 190
Period size: 49 Copynumber: 2.6 Consensus size: 50
6808617 TTATAAAACG
6808627 TTACAATATTCATACAAAAAATTACAATATTACAATATTCATACAAAAAAAA
1 TTACAATATTCATAC--AAAATTACAATATTACAATATTCATACAAAAAAAA
** * * *
6808679 TTGTAATATTCATATAAATTTATAATATTACAATATTCATAC-AAAAAAA
1 TTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAAA
6808728 TTACAATATTCATACAAAATTACAATATT
1 TTACAATATTCATACAAAATTACAATATT
6808757 CATACAAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
49 31 0.46
50 25 0.37
52 12 0.18
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.35
Consensus pattern (50 bp):
TTACAATATTCATACAAAATTACAATATTACAATATTCATACAAAAAAAA
Found at i:6808748 original size:19 final size:19
Alignment explanation
Indices: 6808705--6808869 Score: 115
Period size: 19 Copynumber: 8.2 Consensus size: 19
6808695 AATTTATAAT
6808705 ATTACAATATTCATACAAAAAA
1 ATTACAATATTCATAC---AAA
6808727 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
6808746 ATTACAATATTCATACAAA
1 ATTACAATATTCATACAAA
* * *
6808765 A-TACTA-ATCCAAAACTATAA
1 ATTACAATATTC-ATAC-A-AA
*
6808785 A-TACAAATTTAATT-ATAAAATA
1 ATTAC-AA--T-ATTCATACAA-A
6808807 ATTACAATATTCATA-AAA
1 ATTACAATATTCATACAAA
6808825 ATTTACAATATTCATACAAAAAA
1 A-TTACAATATTCATAC---AAA
*
6808848 ATTAGAATATTCATACAAA
1 ATTACAATATTCATACAAA
6808867 ATT
1 ATT
6808870 CTAATCCAAA
Statistics
Matches: 119, Mismatches: 8, Indels: 35
0.73 0.05 0.22
Matches are distributed among these distances:
17 3 0.03
18 9 0.08
19 49 0.41
20 10 0.08
21 2 0.02
22 35 0.29
23 9 0.08
25 2 0.02
ACGTcount: A:0.55, C:0.13, G:0.01, T:0.32
Consensus pattern (19 bp):
ATTACAATATTCATACAAA
Found at i:6808856 original size:22 final size:22
Alignment explanation
Indices: 6808801--6808867 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
6808791 ATTTAATTAT
*
6808801 AAAATAATTACAATATTCAT--
1 AAAAAAATTACAATATTCATAC
*
6808821 -AAAAATTTACAATATTCATAC
1 AAAAAAATTACAATATTCATAC
*
6808842 AAAAAAATTAGAATATTCATAC
1 AAAAAAATTACAATATTCATAC
6808864 AAAA
1 AAAA
6808868 TTCTAATCCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 17 0.43
22 23 0.57
ACGTcount: A:0.58, C:0.10, G:0.01, T:0.30
Consensus pattern (22 bp):
AAAAAAATTACAATATTCATAC
Found at i:6808910 original size:102 final size:99
Alignment explanation
Indices: 6808695--6808912 Score: 260
Period size: 102 Copynumber: 2.1 Consensus size: 99
6808685 TATTCATATA
6808695 AATTTATAATATTACAATATTCATACAAAAAAATTACAATATTCATACAAAATTACAATATTCAT
1 AATTTAT-A-ATTACAATATTCAT--AAAAAAATTACAATATTCATACAAAATTACAATATTCAT
* *
6808760 ACAAAATACTAATCCAAAACTATAAATACAAATTTAAT
62 ACAAAATACTAATCCAAAACTATAAACACAAATATAAT
* ** * *
6808798 TATAAAATAATTACAATATTCAT-AAAAATTTACAATATTCATACAAAAAAATTAGAATATTCAT
1 AAT-TTATAATTACAATATTCATAAAAAAATTACAATATTCATAC---AAAATTACAATATTCAT
*
6808862 ACAAAATTCTAATCC-AAACTATAAACACTAAATATAGAT
62 ACAAAATACTAATCCAAAACTATAAACAC-AAATATA-AT
6808901 AATTTATAATTA
1 AATTTATAATTA
6808913 ATAATTAATA
Statistics
Matches: 98, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
99 20 0.20
101 12 0.12
102 57 0.58
103 7 0.07
104 2 0.02
ACGTcount: A:0.54, C:0.12, G:0.01, T:0.33
Consensus pattern (99 bp):
AATTTATAATTACAATATTCATAAAAAAATTACAATATTCATACAAAATTACAATATTCATACAA
AATACTAATCCAAAACTATAAACACAAATATAAT
Found at i:6809031 original size:3 final size:3
Alignment explanation
Indices: 6809025--6809057 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
6809015 TTTTTTTTCT
*
6809025 TTC TTC TTC TTC TTC -TA TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
6809058 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 26 0.96
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:6809047 original size:14 final size:14
Alignment explanation
Indices: 6809028--6809054 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6809018 TTTTTCTTTC
6809028 TTCTTCTTCTTCTA
1 TTCTTCTTCTTCTA
6809042 TTCTTCTTCTTCT
1 TTCTTCTTCTTCT
6809055 TCTNNNNNNN
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.67
Consensus pattern (14 bp):
TTCTTCTTCTTCTA
Found at i:6809047 original size:17 final size:16
Alignment explanation
Indices: 6809021--6809057 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 16
6809011 CCTTTTTTTT
6809021 TTCTTTCTTCTTCTTC
1 TTCTTTCTTCTTCTTC
6809037 TTCTATTCTTCTTCTTC
1 TTCT-TTCTTCTTCTTC
6809054 TTCT
1 TTCT
6809058 NNNNNNNNNN
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.68
Consensus pattern (16 bp):
TTCTTTCTTCTTCTTC
Done.