Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 80 of 310
Found at i:25603961 original size:7 final size:7
Alignment explanation
Indices: 25603949--25603984 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
25603939 TTATATGTAC
25603949 TAATAAA
1 TAATAAA
25603956 TAATAAA
1 TAATAAA
25603963 TAATAAAA
1 TAAT-AAA
*
25603971 TAATATA
1 TAATAAA
25603978 TAATAAA
1 TAATAAA
25603985 ATGAAGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TAATAAA
Found at i:25603973 original size:15 final size:15
Alignment explanation
Indices: 25603949--25603986 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
25603939 TTATATGTAC
25603949 TAAT-AAATAATAAA
1 TAATAAAATAATAAA
*
25603963 TAATAAAATAATATA
1 TAATAAAATAATAAA
25603978 TAATAAAAT
1 TAATAAAAT
25603987 GAAGATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAATAAAATAATAAA
Found at i:25604034 original size:29 final size:30
Alignment explanation
Indices: 25603962--25604035 Score: 73
Period size: 33 Copynumber: 2.4 Consensus size: 30
25603952 TAAATAATAA
*
25603962 ATAATA-AAATAATATATAATAAAATGAAG
1 ATAATATAAATAATATATAACAAAATGAAG
*
25603991 ATAATATAGGGAATAATATATAACAAAA-G-AT
1 ATAATATA---AATAATATATAACAAAATGAAG
25604022 ATAATATACAATAA
1 ATAATATA-AATAA
25604036 AATCTATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 11 0.29
30 1 0.03
31 9 0.24
32 1 0.03
33 16 0.42
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (30 bp):
ATAATATAAATAATATATAACAAAATGAAG
Found at i:25604049 original size:13 final size:13
Alignment explanation
Indices: 25604025--25604058 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
25604015 AAAAGATATA
25604025 ATATACAATAAAAT
1 ATATA-AATAAAAT
*
25604039 CTATAAATAAAAT
1 ATATAAATAAAAT
25604052 ATATAAA
1 ATATAAA
25604059 ATATAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (13 bp):
ATATAAATAAAAT
Found at i:25604068 original size:11 final size:11
Alignment explanation
Indices: 25604024--25604093 Score: 63
Period size: 11 Copynumber: 6.2 Consensus size: 11
25604014 CAAAAGATAT
25604024 AATATACAATAA
1 AATATA-AATAA
25604036 AATCTATAAATAA
1 AA--TATAAATAA
25604049 AATAT--ATAA
1 AATATAAATAA
25604058 AATATAAATAA
1 AATATAAATAA
*
25604069 CATGATAAATAA
1 AAT-ATAAATAA
* *
25604081 TACATAAATAA
1 AATATAAATAA
25604092 AA
1 AA
25604094 ATATTATATA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
9 9 0.18
11 18 0.37
12 11 0.22
13 7 0.14
14 4 0.08
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (11 bp):
AATATAAATAA
Found at i:25604102 original size:47 final size:51
Alignment explanation
Indices: 25604041--25604160 Score: 128
Period size: 49 Copynumber: 2.4 Consensus size: 51
25604031 AATAAAATCT
*
25604041 ATAAATAAAATATATAAAATATAAATAACATG-ATAAATAATA-CATAAATA
1 ATAAATAATATATATAAAATATAAATAACATGTATAAATAATATCATAAA-A
* * *
25604091 A-AAATATTATATATAATAAT-T---TTACATGTATAAATAATATTTATAAAA
1 ATAAATAATATATATAA-AATATAAATAACATGTATAAATAATA-TCATAAAA
25604139 ATAAATAATATATATAAAATAT
1 ATAAATAATATATATAAAATAT
25604161 TTAAAATAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
46 6 0.10
47 10 0.17
48 5 0.08
49 34 0.58
50 4 0.07
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.35
Consensus pattern (51 bp):
ATAAATAATATATATAAAATATAAATAACATGTATAAATAATATCATAAAA
Found at i:25604106 original size:15 final size:15
Alignment explanation
Indices: 25604088--25604201 Score: 63
Period size: 15 Copynumber: 7.4 Consensus size: 15
25604078 TAATACATAA
25604088 ATAAAAATATTATAT
1 ATAAAAATATTATAT
* * *
25604103 ATAATAATTTTACAT
1 ATAAAAATATTATAT
* * * *
25604118 GTATAAATAATATTT
1 ATAAAAATATTATAT
*
25604133 ATAAAAATAAATAATAT
1 ATAAAAAT--ATTATAT
*
25604150 ATATAAAATATT-TAAA
1 ATA-AAAATATTAT-AT
25604166 ATAAATAA-ATTATAT
1 ATAAA-AATATTATAT
*
25604181 AT-AAAATGTATATAT
1 ATAAAAATAT-TATAT
25604196 ATAAAA
1 ATAAAA
25604202 GGATTAAAAT
Statistics
Matches: 71, Mismatches: 19, Indels: 17
0.66 0.18 0.16
Matches are distributed among these distances:
13 2 0.03
14 3 0.04
15 42 0.59
16 12 0.17
17 7 0.10
18 5 0.07
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (15 bp):
ATAAAAATATTATAT
Found at i:25604142 original size:19 final size:19
Alignment explanation
Indices: 25604120--25604157 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
25604110 TTTTACATGT
*
25604120 ATAAATAATATTTATAAAA
1 ATAAATAATATATATAAAA
25604139 ATAAATAATATATATAAAA
1 ATAAATAATATATATAAAA
25604158 TATTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAATAATATATATAAAA
Found at i:25604175 original size:31 final size:28
Alignment explanation
Indices: 25604126--25604187 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 28
25604116 ATGTATAAAT
*
25604126 AATATTTATAAAAATAAATAATATATATAA
1 AATATTTAAAAAAATAAAT--TATATATAA
25604156 AATATTTAAAATAAATAAATTATATATAA
1 AATATTTAAAA-AAATAAATTATATATAA
25604185 AAT
1 AAT
25604188 GTATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 12 0.40
30 10 0.33
31 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AATATTTAAAAAAATAAATTATATATAA
Found at i:25604709 original size:232 final size:232
Alignment explanation
Indices: 25604303--25604767 Score: 921
Period size: 232 Copynumber: 2.0 Consensus size: 232
25604293 AGGGACTCAC
*
25604303 TCGACAATTTGACCCTAATCCCAAAACGACGTCGTCCCGAAATAGGCTTTATAATAGCAACTAGG
1 TCGACAATTTGACCCTAATCCCAAAACGACGTCGTCCCGAAATAGGCTTCATAATAGCAACTAGG
25604368 ACTAAATTGAGACGAAAATAAAAGGTCAGGGTCAAATTAAAATAAAATAAAATTTGAATTGAAAG
66 ACTAAATTGAGACGAAAATAAAAGGTCAGGGTCAAATTAAAATAAAATAAAATTTGAATTGAAAG
25604433 AAATTACAAATTCTGAAAATGTGGAAGGACCAATTGTGCAATTAGCCCTTTAAGCAAAAACACGC
131 AAATTACAAATTCTGAAAATGTGGAAGGACCAATTGTGCAATTAGCCCTTTAAGCAAAAACACGC
25604498 GGATCCTTCCCGGGTCACGGGTCAACATACGGGTCCT
196 GGATCCTTCCCGGGTCACGGGTCAACATACGGGTCCT
25604535 TCGACAATTTGACCCTAATCCCAAAACGACGTCGTCCCGAAATAGGCTTCATAATAGCAACTAGG
1 TCGACAATTTGACCCTAATCCCAAAACGACGTCGTCCCGAAATAGGCTTCATAATAGCAACTAGG
25604600 ACTAAATTGAGACGAAAATAAAAGGTCAGGGTCAAATTAAAATAAAATAAAATTTGAATTGAAAG
66 ACTAAATTGAGACGAAAATAAAAGGTCAGGGTCAAATTAAAATAAAATAAAATTTGAATTGAAAG
25604665 AAATTACAAATTCTGAAAATGTGGAAGGACCAATTGTGCAATTAGCCCTTTAAGCAAAAACACGC
131 AAATTACAAATTCTGAAAATGTGGAAGGACCAATTGTGCAATTAGCCCTTTAAGCAAAAACACGC
25604730 GGATCCTTCCCGGGTCACGGGTCAACATACGGGTCCT
196 GGATCCTTCCCGGGTCACGGGTCAACATACGGGTCCT
25604767 T
1 T
25604768 TATTTAAACG
Statistics
Matches: 232, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
232 232 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.23
Consensus pattern (232 bp):
TCGACAATTTGACCCTAATCCCAAAACGACGTCGTCCCGAAATAGGCTTCATAATAGCAACTAGG
ACTAAATTGAGACGAAAATAAAAGGTCAGGGTCAAATTAAAATAAAATAAAATTTGAATTGAAAG
AAATTACAAATTCTGAAAATGTGGAAGGACCAATTGTGCAATTAGCCCTTTAAGCAAAAACACGC
GGATCCTTCCCGGGTCACGGGTCAACATACGGGTCCT
Found at i:25605976 original size:90 final size:90
Alignment explanation
Indices: 25605862--25606178 Score: 456
Period size: 90 Copynumber: 3.5 Consensus size: 90
25605852 AATATTCTTA
* * * * *
25605862 ATCTTCTCCCTGTCAAATACAGAGATGCCAAATCTGTCATTTTCGATCTGCTTCGATGCAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACAC
* * *
25605927 AAGAATGTCAGATCTGTTATCTTTG
66 ACGAATGTCAGATCTGCTATCTTCG
* * *
25605952 ATTTGCTCCCCGTCTAATACAGAGACGTCAAACCTGTCATTTTCGATCTGCTTCGATGTAAACAC
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACAC
*
25606017 ACGAATGTCAGATCTACTATCTTCG
66 ACGAATGTCAGATCTGCTATCTTCG
*
25606042 ATCTGCTCCCCATCTAATACAGAGACGCCAAATCTGTCATCTTT-GATCTGCTTCGATGTAAACA
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCAT-TTTCGATCTGCTTCGATGTAAACA
* *
25606106 CACGAATTTTAGATCTGCTATCTTCG
65 CACGAATGTCAGATCTGCTATCTTCG
* * *
25606132 ATCTGCTTCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTCGAT
1 ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATTTTCGAT
25606179 TTGTTCCCTG
Statistics
Matches: 202, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
89 2 0.01
90 197 0.98
91 3 0.01
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (90 bp):
ATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATTTTCGATCTGCTTCGATGTAAACAC
ACGAATGTCAGATCTGCTATCTTCG
Found at i:25606084 original size:45 final size:44
Alignment explanation
Indices: 25605877--25606211 Score: 196
Period size: 45 Copynumber: 7.5 Consensus size: 44
25605867 CTCCCTGTCA
* * * * *
25605877 AATACAGAGATGCCAAATCTGTCATTTTCGATCTGCTTCGATGCA
1 AATACAGAGATGTCAAATCTGTCATCTTCGATCTGCTCCCAT-CT
* * * * * *
25605922 AACACA-AGAATGTCAGATCTGTTATCTTTGATTTGCTCCCCGTCT
1 AATACAGAG-ATGTCAAATCTGTCATCTTCGATCTGCT-CCCATCT
* * * * * *
25605967 AATACAGAGACGTCAAACCTGTCATTTTCGATCTGCTTCGATGT
1 AATACAGAGATGTCAAATCTGTCATCTTCGATCTGCTCCCATCT
* * *
25606011 AA-ACACACGAATGTCAGATCT-ACTATCTTCGATCTGCTCCCCATCT
1 AATACAGA-G-ATGTCAAATCTGTC-ATCTTCGATCTGCT-CCCATCT
* * * * * *
25606057 AATACAGAGACGCCAAATCTGTCATCTTTGATCTGCTTCGATGT
1 AATACAGAGATGTCAAATCTGTCATCTTCGATCTGCTCCCATCT
* * * * *
25606101 AA-ACACACGAATTTTAGATCTG-CTATCTTCGATCTGCTTCCCGTCT
1 AATACAGA-G-ATGTCAAATCTGTC-ATCTTCGATCTGC-TCCCATCT
* * * *
25606147 AATACAGAGATGCCAAATCTGTCATCTTCGATTTGTTCCC-TGT
1 AATACAGAGATGTCAAATCTGTCATCTTCGATCTGCTCCCATCT
*
25606190 CAATACAGAGATGGCAAATCTG
1 -AATACAGAGATGTCAAATCTG
25606212 CTATCTACAT
Statistics
Matches: 213, Mismatches: 61, Indels: 33
0.69 0.20 0.11
Matches are distributed among these distances:
43 10 0.05
44 41 0.19
45 134 0.63
46 20 0.09
47 8 0.04
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (44 bp):
AATACAGAGATGTCAAATCTGTCATCTTCGATCTGCTCCCATCT
Found at i:25617143 original size:43 final size:44
Alignment explanation
Indices: 25617087--25617174 Score: 110
Period size: 43 Copynumber: 2.0 Consensus size: 44
25617077 TAATATATAT
** *
25617087 ATAATAATATTTCATGCAAATATAACTTAA-AAT-AATAACATAA
1 ATAATAATATTTCACACAAATATAA-TAAACAATAAATAACATAA
25617130 ATAATCAAT-TTTCACACAAATATAATAAACAATAAATAACATAA
1 ATAAT-AATATTTCACACAAATATAATAAACAATAAATAACATAA
25617174 A
1 A
25617175 AGTAAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
42 3 0.08
43 22 0.56
44 14 0.36
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.30
Consensus pattern (44 bp):
ATAATAATATTTCACACAAATATAATAAACAATAAATAACATAA
Found at i:25617422 original size:20 final size:19
Alignment explanation
Indices: 25617387--25617452 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
25617377 AACGATTAAT
25617387 ATATATATATATAAAACATA
1 ATATATATATA-AAAACATA
* *
25617407 CTATATGATATAAAAACTTA
1 ATATAT-ATATAAAAACATA
* *
25617427 ATATATTTATAAAAATAATA
1 ATATATATATAAAAA-CATA
25617447 ATATAT
1 ATATAT
25617453 TAAATAGGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 8 0.21
20 25 0.66
21 5 0.13
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (19 bp):
ATATATATATAAAAACATA
Found at i:25617584 original size:7 final size:7
Alignment explanation
Indices: 25617572--25617614 Score: 68
Period size: 7 Copynumber: 6.0 Consensus size: 7
25617562 TTATATGTAC
25617572 TAATAAA
1 TAATAAA
25617579 TAATAAA
1 TAATAAA
25617586 TAATAAA
1 TAATAAA
25617593 TAATAAAA
1 TAAT-AAA
*
25617601 TAATATA
1 TAATAAA
25617608 TAATAAA
1 TAATAAA
25617615 ATGAAGATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TAATAAA
Found at i:25617603 original size:15 final size:15
Alignment explanation
Indices: 25617572--25617616 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
25617562 TTATATGTAC
25617572 TAATAAATAAT-AAA
1 TAATAAATAATAAAA
25617586 TAATAAATAATAAAA
1 TAATAAATAATAAAA
*
25617601 TAATATATAATAAAA
1 TAATAAATAATAAAA
25617616 T
1 T
25617617 GAAGATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAATAAATAATAAAA
Found at i:25617604 original size:22 final size:21
Alignment explanation
Indices: 25617572--25617614 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
25617562 TTATATGTAC
25617572 TAATAAATAATAAATAATAAA
1 TAATAAATAATAAATAATAAA
*
25617593 TAATAAAATAATATATAATAAA
1 TAAT-AAATAATAAATAATAAA
25617615 ATGAAGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
TAATAAATAATAAATAATAAA
Found at i:25618086 original size:71 final size:64
Alignment explanation
Indices: 25617938--25618087 Score: 176
Period size: 71 Copynumber: 2.2 Consensus size: 64
25617928 ACTTTAACAA
* * *
25617938 TTCATGCAAATATAATATAGAAAATGATAAATAACGACATAAATTACATAATATACATTATCAT
1 TTCATGCAAATATAATATAGAAAATAATAAATAACAACATAAATTACATAATATACATAATCAT
* *
25618002 TTCATGCAGATATAATCATAGAAAATAATGAATATAACAATATAAATTACATAATATATATACAA
1 TTCATGCAAATATAAT-ATAGAAAATAAT-AA-ATAACAACATAAATTAC---ATA-ATATAC-A
25618067 TAAT-AT
58 TAATCAT
25618073 TTCATGCAAATATAA
1 TTCATGCAAATATAA
25618088 CTTAAAATAA
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
64 15 0.21
65 11 0.15
66 2 0.03
67 15 0.21
70 3 0.04
71 22 0.31
72 4 0.06
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.32
Consensus pattern (64 bp):
TTCATGCAAATATAATATAGAAAATAATAAATAACAACATAAATTACATAATATACATAATCAT
Found at i:25618399 original size:20 final size:19
Alignment explanation
Indices: 25618364--25618429 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
25618354 AACGATTAAT
25618364 ATATATATATATAAAACATA
1 ATATATATATA-AAAACATA
* *
25618384 CTATATGATATAAAAACTTA
1 ATATAT-ATATAAAAACATA
* *
25618404 ATATATTTATAAAAATAATA
1 ATATATATATAAAAA-CATA
25618424 ATATAT
1 ATATAT
25618430 TAAATAGGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 8 0.21
20 25 0.66
21 5 0.13
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (19 bp):
ATATATATATAAAAACATA
Found at i:25618561 original size:7 final size:7
Alignment explanation
Indices: 25618549--25618591 Score: 68
Period size: 7 Copynumber: 6.0 Consensus size: 7
25618539 TTATATGTAC
25618549 TAATAAA
1 TAATAAA
25618556 TAATAAA
1 TAATAAA
25618563 TAATAAA
1 TAATAAA
25618570 TAATAAAA
1 TAAT-AAA
*
25618578 TAATATA
1 TAATAAA
25618585 TAATAAA
1 TAATAAA
25618592 ATGAAGATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TAATAAA
Found at i:25618581 original size:22 final size:21
Alignment explanation
Indices: 25618549--25618591 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
25618539 TTATATGTAC
25618549 TAATAAATAATAAATAATAAA
1 TAATAAATAATAAATAATAAA
*
25618570 TAATAAAATAATATATAATAAA
1 TAAT-AAATAATAAATAATAAA
25618592 ATGAAGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
TAATAAATAATAAATAATAAA
Found at i:25618587 original size:19 final size:19
Alignment explanation
Indices: 25618561--25618717 Score: 54
Period size: 21 Copynumber: 7.7 Consensus size: 19
25618551 ATAAATAATA
25618561 AATA-ATAAATAATAAAAT
1 AATATATAAATAATAAAAT
* *
25618579 AATATATAATAAAATGAAGAT
1 AATATATAA-ATAAT-AAAAT
**
25618600 AATATAGGGAATAATATATAAT
1 AATATA-TAAATAATA-A-AAT
25618622 AAAATATATAATATATAATAAAAT
1 --AATATAT-A-A-ATAATAAAAT
* *
25618646 CTATATATAAAATCTATAAAAT
1 -AATATAT-AAAT-AATAAAAT
* *
25618668 -ATAAATAACATGAT-AAAT
1 AATATATAA-ATAATAAAAT
*
25618686 AATACATAAAT-A-AAAAT
1 AATATATAAATAATAAAAT
*
25618703 ATTATATATAATAAT
1 AATATATA-AATAAT
25618718 TTTACATGTA
Statistics
Matches: 105, Mismatches: 16, Indels: 34
0.68 0.10 0.22
Matches are distributed among these distances:
17 11 0.10
18 13 0.12
19 16 0.15
20 12 0.11
21 17 0.16
22 11 0.10
23 8 0.08
24 9 0.09
25 2 0.02
26 6 0.06
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (19 bp):
AATATATAAATAATAAAAT
Found at i:25618622 original size:7 final size:7
Alignment explanation
Indices: 25618610--25618715 Score: 55
Period size: 7 Copynumber: 15.9 Consensus size: 7
25618600 AATATAGGGA
25618610 ATAATAT
1 ATAATAT
25618617 ATAATA-
1 ATAATAT
25618623 A-AATAT
1 ATAATAT
25618629 ATAATAT
1 ATAATAT
25618636 ATAATA-
1 ATAATAT
*
25618642 A-AATCT
1 ATAATAT
25618648 AT-ATAT
1 ATAATAT
* *
25618654 AAAATCT
1 ATAATAT
*
25618661 ATAAAAT
1 ATAATAT
*
25618668 ATAAATAAC
1 AT-AAT-AT
* *
25618677 ATGATAA
1 ATAATAT
*
25618684 ATAATAC
1 ATAATAT
25618691 ATAA-AT
1 ATAATAT
*
25618697 A-AAAAT
1 ATAATAT
*
25618703 ATTATAT
1 ATAATAT
25618710 ATAATA
1 ATAATA
25618716 ATTTTACATG
Statistics
Matches: 73, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
5 9 0.12
6 13 0.18
7 44 0.60
8 4 0.05
9 3 0.04
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (7 bp):
ATAATAT
Found at i:25618630 original size:14 final size:15
Alignment explanation
Indices: 25618549--25618716 Score: 80
Period size: 15 Copynumber: 10.9 Consensus size: 15
25618539 TTATATGTAC
*
25618549 TAATAAATAAT-AAA
1 TAATATATAATAAAA
*
25618563 TAATAAATAATAAAA
1 TAATATATAATAAAA
25618578 TAATATATAATAAAA
1 TAATATATAATAAAA
* *
25618593 TGAAGATA-ATATAGGGAA
1 T-AATATATA-ATA--AAA
25618611 TAATATATAATAAAA
1 TAATATATAATAAAA
25618626 T-ATATAATATATAATAA
1 TAATAT-ATA-ATAA-AA
*
25618643 -AATCTATATATAAAA
1 TAATATATA-ATAAAA
* *
25618658 T-CTATAAAATATAAA
1 TAATATATAATA-AAA
* *
25618673 TAACATGATAA-ATAA
1 TAATAT-ATAATAAAA
*
25618688 TACATAAATAA-AAATA
1 TA-ATATATAATAAA-A
*
25618704 TTATATATAATAA
1 TAATATATAATAA
25618717 TTTTACATGT
Statistics
Matches: 119, Mismatches: 18, Indels: 32
0.70 0.11 0.19
Matches are distributed among these distances:
14 18 0.15
15 52 0.44
16 29 0.24
17 16 0.13
18 4 0.03
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (15 bp):
TAATATATAATAAAA
Found at i:25618657 original size:13 final size:14
Alignment explanation
Indices: 25618633--25618673 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
25618623 AAATATATAA
25618633 TATATAATAAAATC
1 TATATAATAAAATC
25618647 TATAT-ATAAAATC
1 TATATAATAAAATC
*
25618660 TATAAAATATAAAT
1 TATATAATA-AAAT
25618674 AACATGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 12 0.50
14 8 0.33
15 4 0.17
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (14 bp):
TATATAATAAAATC
Found at i:25618713 original size:15 final size:15
Alignment explanation
Indices: 25618695--25618808 Score: 63
Period size: 15 Copynumber: 7.4 Consensus size: 15
25618685 TAATACATAA
25618695 ATAAAAATATTATAT
1 ATAAAAATATTATAT
* * *
25618710 ATAATAATTTTACAT
1 ATAAAAATATTATAT
* * * *
25618725 GTATAAATAATATTT
1 ATAAAAATATTATAT
*
25618740 ATAAAAATAAATAATAT
1 ATAAAAAT--ATTATAT
*
25618757 ATATAAAATATT-TAAA
1 ATA-AAAATATTAT-AT
25618773 ATAAATAA-ATTATAT
1 ATAAA-AATATTATAT
*
25618788 AT-AAAATGTATATAT
1 ATAAAAATAT-TATAT
25618803 ATAAAA
1 ATAAAA
25618809 GGATTAAAAT
Statistics
Matches: 71, Mismatches: 19, Indels: 17
0.66 0.18 0.16
Matches are distributed among these distances:
13 2 0.03
14 3 0.04
15 42 0.59
16 12 0.17
17 7 0.10
18 5 0.07
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (15 bp):
ATAAAAATATTATAT
Found at i:25618749 original size:19 final size:19
Alignment explanation
Indices: 25618727--25618764 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
25618717 TTTTACATGT
*
25618727 ATAAATAATATTTATAAAA
1 ATAAATAATATATATAAAA
25618746 ATAAATAATATATATAAAA
1 ATAAATAATATATATAAAA
25618765 TATTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAAATAATATATATAAAA
Found at i:25618782 original size:31 final size:28
Alignment explanation
Indices: 25618733--25618794 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 28
25618723 ATGTATAAAT
*
25618733 AATATTTATAAAAATAAATAATATATATAA
1 AATATTTAAAAAAATAAAT--TATATATAA
25618763 AATATTTAAAATAAATAAATTATATATAA
1 AATATTTAAAA-AAATAAATTATATATAA
25618792 AAT
1 AAT
25618795 GTATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 12 0.40
30 10 0.33
31 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AATATTTAAAAAAATAAATTATATATAA
Found at i:25622180 original size:20 final size:18
Alignment explanation
Indices: 25622138--25622180 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
25622128 TTCTTTATCA
*
25622138 TCAATTATATAAATGCAT
1 TCAATTATATAAATCCAT
*
25622156 CCAATTATAATCAAATCCAT
1 TCAATTAT-AT-AAATCCAT
25622176 TCAAT
1 TCAAT
25622181 AACAATTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 7 0.35
19 2 0.10
20 11 0.55
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (18 bp):
TCAATTATATAAATCCAT
Found at i:25625621 original size:79 final size:81
Alignment explanation
Indices: 25625485--25625669 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
25625475 TTGAATGATG
* *
25625485 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
25625549 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
25625564 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
25625626 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
25625644 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
25625670 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:25625683 original size:40 final size:40
Alignment explanation
Indices: 25625486--25625669 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
25625476 TGAATGATGT
* * * *
25625486 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
25625526 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
25625566 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
25625604 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
25625645 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
25625670 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:25625691 original size:79 final size:79
Alignment explanation
Indices: 25625538--25625702 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
25625528 GGACTAAGAT
* * **
25625538 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
25625603 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
25625617 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
25625680 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
25625696 CCGAAGG
1 CCGAAGG
25625703 TACGTGGTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:25633578 original size:79 final size:81
Alignment explanation
Indices: 25633442--25633626 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
25633432 TTGAATGATG
*
25633442 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
25633506 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
25633521 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
25633583 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGATACTATA
* *
25633601 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
25633627 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.63
80 33 0.36
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGATACTATA
Found at i:25633640 original size:40 final size:40
Alignment explanation
Indices: 25633443--25633626 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
25633433 TGAATGATGT
* * * *
25633443 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
25633483 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
25633523 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
25633561 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
25633602 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
25633627 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:25633648 original size:79 final size:79
Alignment explanation
Indices: 25633495--25633659 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
25633485 GGACTAAGAT
* **
25633495 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
25633560 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
25633574 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
25633637 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
25633653 CCGAAGG
1 CCGAAGG
25633660 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:25636556 original size:19 final size:19
Alignment explanation
Indices: 25636532--25636570 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
25636522 ATGGCTAAGG
25636532 TATGTGATTTATTCAGGTA
1 TATGTGATTTATTCAGGTA
25636551 TATGTGATTTATTCAGGTA
1 TATGTGATTTATTCAGGTA
25636570 T
1 T
25636571 GGTCCATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.49
Consensus pattern (19 bp):
TATGTGATTTATTCAGGTA
Found at i:25638700 original size:12 final size:13
Alignment explanation
Indices: 25638683--25638714 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
25638673 TTTGATATTT
25638683 TGTGATGAG-TTG
1 TGTGATGAGTTTG
25638695 TGTGAT-AGTTTG
1 TGTGATGAGTTTG
25638707 TGTGATGA
1 TGTGATGA
25638715 ATGGAAGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 15 0.83
13 1 0.06
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.44
Consensus pattern (13 bp):
TGTGATGAGTTTG
Found at i:25641536 original size:93 final size:92
Alignment explanation
Indices: 25641337--25641625 Score: 301
Period size: 95 Copynumber: 3.1 Consensus size: 92
25641327 TTACATAAAA
* * * * * * *
25641337 TTTTTAATGAAATTAGTGAAGAAATTTATCACTTATTTATAAGCTCAATGTGAGATATAAGAGTG
1 TTTTTAATGAAAATAGTGAAGAAAGTAAT-ACTTATTTATAAGC-AAATGCGAG-CATGAGAGTG
* * * *
25641402 TTCTCTAGTCAATATTGGATTAAAATAAAC
63 TTCTCTAGCCAATGTAGGATTAAAATTAAC
* *
25641432 -TTTTAATGAAAATAGTGAAGAAAGTAATACTTATTTATTGAGCAAATGCGAGCATGAGAGAGTT
1 TTTTTAATGAAAATAGTGAAGAAAGTAATACTTATTTA-TAAGCAAATGCGAGCATGAGAGTGTT
* *
25641496 TTCTAGCCAATGTAAGATTAAAATTAAC
65 CTCTAGCCAATGTAGGATTAAAATTAAC
* * * * * * * *
25641524 TTTTTAATGAAAATAGTAAAAAAAAGCTAACACTTATTTAAAAAGCAAGTGCAAGCGTGGGAGTG
1 TTTTTAATGAAAATAGT-GAAGAAAG-TAATACTTATTT-ATAAGCAAATGCGAGCATGAGAGTG
25641589 TTCTCTAGCCAATGTAGGATTAAAATTAAC
63 TTCTCTAGCCAATGTAGGATTAAAATTAAC
25641619 TTTTTAA
1 TTTTTAA
25641626 GGGAGCAAAA
Statistics
Matches: 162, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
92 31 0.19
93 32 0.20
94 35 0.22
95 63 0.39
96 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (92 bp):
TTTTTAATGAAAATAGTGAAGAAAGTAATACTTATTTATAAGCAAATGCGAGCATGAGAGTGTTC
TCTAGCCAATGTAGGATTAAAATTAAC
Found at i:25642518 original size:19 final size:19
Alignment explanation
Indices: 25642475--25642511 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
25642465 TGAGCAAAAC
*
25642475 TCAATTTGATTCAAGTTAA
1 TCAATTTGAGTCAAGTTAA
25642494 TCAATTTGAGT-AAGTTAA
1 TCAATTTGAGTCAAGTTAA
25642512 GTTAATTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (19 bp):
TCAATTTGAGTCAAGTTAA
Found at i:25644245 original size:22 final size:24
Alignment explanation
Indices: 25644204--25644250 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
25644194 TAGTAATATA
25644204 AAAACATTAAAATTAATATTAAAT
1 AAAACATTAAAATTAATATTAAAT
* *
25644228 AAAA-ATT-AAATTATTATTTAAT
1 AAAACATTAAAATTAATATTAAAT
25644250 A
1 A
25644251 TAATATTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 14 0.67
23 3 0.14
24 4 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
AAAACATTAAAATTAATATTAAAT
Found at i:25649870 original size:30 final size:30
Alignment explanation
Indices: 25649824--25649947 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
25649814 TTTTATTATG
*
25649824 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
25649855 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
25649885 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
25649915 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
25649945 CCA
1 CCA
25649948 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:25649879 original size:15 final size:15
Alignment explanation
Indices: 25649834--25649941 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
25649824 CCAATATCTC
25649834 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
25649849 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
25649864 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
25649879 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
25649894 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
25649909 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
25649924 GATACCCATATCTTT
1 GATACCCATATCTTT
25649939 GAT
1 GAT
25649942 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:25654110 original size:30 final size:30
Alignment explanation
Indices: 25654064--25654157 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
25654054 TTTTATTATG
*
25654064 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
25654095 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
25654125 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
25654155 CCA
1 CCA
25654158 TAAATATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:25654119 original size:15 final size:15
Alignment explanation
Indices: 25654074--25654151 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
25654064 CCAATATCTC
25654074 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
25654089 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
25654104 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
25654119 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
25654134 GATACCCATATCTTT
1 GATACCCATATCTTT
25654149 GAT
1 GAT
25654152 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:25658265 original size:28 final size:29
Alignment explanation
Indices: 25658204--25658267 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
25658194 AAGCCCCCTC
* *
25658204 CCAAAAAAAACCTAACCCCCCCCAAAAAAA
1 CCAAGAAAAACCTAA-CCCCCCAAAAAAAA
25658234 --AAGAAAAACCTAA-CCCCCAAAAAAAA
1 CCAAGAAAAACCTAACCCCCCAAAAAAAA
25658260 CCAAGAAA
1 CCAAGAAA
25658268 CCCTAGCGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
26 12 0.40
28 18 0.60
ACGTcount: A:0.61, C:0.33, G:0.03, T:0.03
Consensus pattern (29 bp):
CCAAGAAAAACCTAACCCCCCAAAAAAAA
Found at i:25658761 original size:33 final size:33
Alignment explanation
Indices: 25658724--25658813 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 33
25658714 GTTATATATT
* *
25658724 TCTTATGTATATATTCTTAAATATTATTATACA
1 TCTTATGTATATATTCTCAAATACTATTATACA
*
25658757 TCTTATGTATATATTCTCAAATACTATTATATA
1 TCTTATGTATATATTCTCAAATACTATTATACA
* * *
25658790 TACATATATATATATT-TAAAATAC
1 T-CTTATGTATATATTCTCAAATAC
25658814 CATATTGTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
33 38 0.76
34 12 0.24
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (33 bp):
TCTTATGTATATATTCTCAAATACTATTATACA
Found at i:25660520 original size:12 final size:12
Alignment explanation
Indices: 25660503--25660538 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
25660493 ATTCATTTGA
25660503 CATTCATGCATT
1 CATTCATGCATT
*
25660515 CATTCATGCATC
1 CATTCATGCATT
*
25660527 CATTCATTCATT
1 CATTCATGCATT
25660539 GCATATCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.42
Consensus pattern (12 bp):
CATTCATGCATT
Found at i:25660532 original size:16 final size:17
Alignment explanation
Indices: 25660511--25660542 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
25660501 GACATTCATG
25660511 CATTCATTCA-TGCATC
1 CATTCATTCATTGCATC
25660527 CATTCATTCATTGCAT
1 CATTCATTCATTGCAT
25660543 ATCCCATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.28, G:0.06, T:0.41
Consensus pattern (17 bp):
CATTCATTCATTGCATC
Found at i:25670690 original size:11 final size:11
Alignment explanation
Indices: 25670666--25670708 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
25670656 TTCTAATACG
*
25670666 TATATATATTA
1 TATATATTTTA
*
25670677 TATGTATTTTA
1 TATATATTTTA
* *
25670688 TATATATTATG
1 TATATATTTTA
25670699 TATATATTTT
1 TATATATTTT
25670709 TTAATGCCAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TATATATTTTA
Found at i:25674372 original size:127 final size:127
Alignment explanation
Indices: 25674210--25674508 Score: 445
Period size: 127 Copynumber: 2.4 Consensus size: 127
25674200 GTAATGATTG
* * * *
25674210 ATGTTTGGGAACTCGAGGAATTGTGCCCTACCGTGCTGGGTTTCGATTTCCCATTTGTTCAAAAT
1 ATGTTTGGAAATTCAAGGAATCGTGCCCTACCGTGCTGGGTTTCGATTTCCCATTTGTTCAAAAT
*
25674275 AATCGAATATTCCTTTAGAATTTCACTCGTGTTTCCCAAATTTTAAAACAAGACAATGTTCA
66 AATCGAATATTCCTTTAGAATTTCACTCGTGTTTCCCAAATTCTAAAACAAGACAATGTTCA
*** * *
25674337 ATGTTTGGAAATTTGGGGAATCGTGCCCTATCGTGCTGGGTTTCGATTTCCCGTTTGTTCAAAAT
1 ATGTTTGGAAATTCAAGGAATCGTGCCCTACCGTGCTGGGTTTCGATTTCCCATTTGTTCAAAAT
* * * * *
25674402 AATCGAATATTCCTTTTGAATTTCACTCGTGTTTTCTAAATTCTAAAGCAAGGCAATGTTCA
66 AATCGAATATTCCTTTAGAATTTCACTCGTGTTTCCCAAATTCTAAAACAAGACAATGTTCA
* *
25674464 ATGTTTGGAAATTCAAGGAATCGTGCCCTACCATGATGGGTTTCG
1 ATGTTTGGAAATTCAAGGAATCGTGCCCTACCGTGCTGGGTTTCG
25674509 GTTTTTCGTT
Statistics
Matches: 153, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
127 153 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (127 bp):
ATGTTTGGAAATTCAAGGAATCGTGCCCTACCGTGCTGGGTTTCGATTTCCCATTTGTTCAAAAT
AATCGAATATTCCTTTAGAATTTCACTCGTGTTTCCCAAATTCTAAAACAAGACAATGTTCA
Found at i:25677470 original size:47 final size:46
Alignment explanation
Indices: 25677387--25677501 Score: 140
Period size: 47 Copynumber: 2.5 Consensus size: 46
25677377 TAGCTCAGCC
* * * * *
25677387 ATGGTCTTACACGTATCACATATCACATTGATGCCATATCCCATAT
1 ATGGTCTTACACGAAGCACATATAACACTGATGCCATATCCCATAA
* *
25677433 ATGGTCTTACACAGAAGCACATATAATACTGATGCCATGTCCCATAA
1 ATGGTCTTACAC-GAAGCACATATAACACTGATGCCATATCCCATAA
*
25677480 ATGGTCTTATACGAAAGCACAT
1 ATGGTCTTACACG-AAGCACAT
25677502 TATCACATCA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
46 13 0.22
47 46 0.78
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (46 bp):
ATGGTCTTACACGAAGCACATATAACACTGATGCCATATCCCATAA
Found at i:25677521 original size:53 final size:50
Alignment explanation
Indices: 25677416--25677562 Score: 142
Period size: 47 Copynumber: 2.9 Consensus size: 50
25677406 ATATCACATT
* * *
25677416 GATGCCATATCCCATATATGGTCTTACAC-AGAAGCACATAT-A-AT-ACT
1 GATGCCATGTCCCATATATGGTCTTATACGA-AAGCACATATCACATCACC
*
25677463 GATGCCATGTCCCATAAATGGTCTTATACGAAAGCACATTATCACATCACACC
1 GATGCCATGTCCCATATATGGTCTTATACGAAAGCACA-TATCACAT--CACC
** **
25677516 GATGCCATAG-CCCAGCTATGGTCTTATACGGGAGCACATATCACATC
1 GATGCCAT-GTCCCATATATGGTCTTATACGAAAGCACATATCACATC
25677563 TTTTTTGTCA
Statistics
Matches: 83, Mismatches: 9, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
47 33 0.40
48 4 0.05
49 1 0.01
50 3 0.04
52 8 0.10
53 33 0.40
54 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (50 bp):
GATGCCATGTCCCATATATGGTCTTATACGAAAGCACATATCACATCACC
Found at i:25677559 original size:47 final size:47
Alignment explanation
Indices: 25677355--25677560 Score: 128
Period size: 47 Copynumber: 4.2 Consensus size: 47
25677345 TGTACATAGT
* * ** * *
25677355 CACATATCACACACCGAAGCCATAGCTCAGCCATGGTCTTACAC-GTAT
1 CACATAT--CACACCGATGCCATAGCCCAGATATGGTCTTACACGGAAG
** * * *
25677403 CACATATCACATTGATGCCATATCCCATATATGGTCTTACACAGAAG
1 CACATATCACACCGATGCCATAGCCCAGATATGGTCTTACACGGAAG
* * * * * * *
25677450 CACATATAATACTGATGCCAT-GTCCCATAAATGGTCTTATACGAAAG
1 CACATATCACACCGATGCCATAG-CCCAGATATGGTCTTACACGGAAG
* * *
25677497 CACATTATCACATCACACCGATGCCATAGCCCAGCTATGGTCTTATACGGGAG
1 CAC---AT---ATCACACCGATGCCATAGCCCAGATATGGTCTTACACGGAAG
25677550 CACATATCACA
1 CACATATCACA
25677561 TCTTTTTTGT
Statistics
Matches: 123, Mismatches: 26, Indels: 19
0.73 0.15 0.11
Matches are distributed among these distances:
46 27 0.22
47 49 0.40
48 7 0.06
50 4 0.03
53 35 0.28
54 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (47 bp):
CACATATCACACCGATGCCATAGCCCAGATATGGTCTTACACGGAAG
Found at i:25693070 original size:21 final size:21
Alignment explanation
Indices: 25693029--25693075 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
25693019 TATCAAGTAT
*
25693029 GTAAAAGAATTCATATTTATA
1 GTAAAAGAATTCATATATATA
*
25693050 GTAAAATAATT-ATATAATATA
1 GTAAAAGAATTCATAT-ATATA
25693071 -TAAAA
1 GTAAAA
25693076 ATATAAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (21 bp):
GTAAAAGAATTCATATATATA
Found at i:25697623 original size:21 final size:21
Alignment explanation
Indices: 25697582--25697628 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
25697572 TATCAAGTAT
*
25697582 GTAAAAGAATTCATATTTATA
1 GTAAAAGAATTCATATATATA
*
25697603 GTAAAATAATT-ATATAATATA
1 GTAAAAGAATTCATAT-ATATA
25697624 -TAAAA
1 GTAAAA
25697629 ATATAAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (21 bp):
GTAAAAGAATTCATATATATA
Found at i:25697829 original size:16 final size:16
Alignment explanation
Indices: 25697801--25697833 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25697791 AAATGATAAT
25697801 AATATATAGATAAAAA
1 AATATATAGATAAAAA
25697817 AATA-ATAGTATAAAAA
1 AATATATAG-ATAAAAA
25697833 A
1 A
25697834 TGACATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (16 bp):
AATATATAGATAAAAA
Found at i:25697948 original size:11 final size:11
Alignment explanation
Indices: 25697932--25697957 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
25697922 TACGAGTAAA
25697932 AATATAACAAT
1 AATATAACAAT
25697943 AATATAACAAT
1 AATATAACAAT
25697954 AATA
1 AATA
25697958 ATATAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (11 bp):
AATATAACAAT
Found at i:25697972 original size:16 final size:16
Alignment explanation
Indices: 25697951--25698039 Score: 63
Period size: 16 Copynumber: 5.1 Consensus size: 16
25697941 ATAATATAAC
25697951 AATAATAATATAAAAT
1 AATAATAATATAAAAT
*
25697967 AATAATAATTTGTGAAAAAT
1 AATAATAA--TAT--AAAAT
25697987 AATAAATAATAATACAAAT
1 AAT-AATAAT-ATA-AAAT
*
25698006 AATATATAATAGAATAAT
1 AATA-ATAATATAA-AAT
*
25698024 TAT-ATAATATAAAAT
1 AATAATAATATAAAAT
25698039 A
1 A
25698040 TAAAAATAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
15 3 0.05
16 16 0.28
17 1 0.02
18 11 0.19
19 13 0.22
20 9 0.16
21 5 0.09
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (16 bp):
AATAATAATATAAAAT
Found at i:25714369 original size:22 final size:23
Alignment explanation
Indices: 25714317--25714369 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
25714307 AATTCTCTTA
*
25714317 AAATTT-ATTAAATTATAAATTT
1 AAATTTAATAAAATTATAAATTT
* * *
25714339 ATATATAATAAAATTAT-ACTTT
1 AAATTTAATAAAATTATAAATTT
25714361 AAATTTAAT
1 AAATTTAAT
25714370 TTTTTTTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATTTAATAAAATTATAAATTT
Found at i:25714871 original size:28 final size:26
Alignment explanation
Indices: 25714840--25714899 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
25714830 GTATGTTATT
25714840 TAAATTATATAATAATATATAAAATAAA
1 TAAATTATATAATAATA-ATAAAA-AAA
* * *
25714868 TAAATAATATATTAATAATTAAAAAA
1 TAAATTATATAATAATAATAAAAAAA
25714894 TAAATT
1 TAAATT
25714900 GAACTTAGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 8 0.29
27 5 0.18
28 15 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAATTATATAATAATAATAAAAAAA
Found at i:25720317 original size:48 final size:48
Alignment explanation
Indices: 25720194--25720317 Score: 167
Period size: 48 Copynumber: 2.6 Consensus size: 48
25720184 ACATTATGAG
* * * * *
25720194 AGCTAGTGTAACACATGTCTGGGACATACATCGGCCTCGAGATATATA
1 AGCTAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGAGATATACA
* *
25720242 AACCAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGAGATATACA
1 AGCTAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGAGATATACA
* *
25720290 AGCTAGTGTAAGACCTATCTAGGACATG
1 AGCTAGTGTAAGACATGTCTAGGACATG
25720318 GCATTAGCTT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (48 bp):
AGCTAGTGTAAGACATGTCTAGGACATGCATCAGCCTCGAGATATACA
Found at i:25726488 original size:46 final size:45
Alignment explanation
Indices: 25726436--25726607 Score: 195
Period size: 46 Copynumber: 3.7 Consensus size: 45
25726426 TCCGAGTTCT
*
25726436 GAACTCGTTGAGTTGAGTCCGAGTTCACTTACGAATGCGAATGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCGAA-GTCC
*** *
25726482 GAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-TCC
1 GAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-AA-T-GCGAAGTCC
* * *
25726529 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCGAA-GTCC
*
25726575 GAGCTCGTTGAGTTGAGTCCGAGTTCACTTATG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATG
25726608 GGCGGGTTAC
Statistics
Matches: 107, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 65 0.61
47 31 0.29
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGAATGCGAAGTCC
Found at i:25726529 original size:120 final size:120
Alignment explanation
Indices: 25726316--25726554 Score: 442
Period size: 120 Copynumber: 2.0 Consensus size: 120
25726306 TTGGGCATCC
* * *
25726316 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGGGTTGAGTC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTACGAATGCGAATGTCCGAACTCGTTGAGTTGAGTC
*
25726381 TGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCT
66 CGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCT
25726436 GAACTCGTTGAGTTGAGTCCGAGTTCACTTACGAATGCGAATGTCCGAACTCGTTGAGTTGAGTC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTACGAATGCGAATGTCCGAACTCGTTGAGTTGAGTC
25726501 CGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTC
66 CGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTC
25726555 ACTTATGGAT
Statistics
Matches: 115, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 115 1.00
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (120 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTACGAATGCGAATGTCCGAACTCGTTGAGTTGAGTC
CGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCT
Found at i:25734422 original size:40 final size:40
Alignment explanation
Indices: 25734376--25734466 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
25734366 TCGGTATCCT
*
25734376 ACACTTAGTACCTCA-TATAGCCGAAGCTATTACAATTCGC
1 ACACTTAGTACCT-ATTATAGCCGAAGCTATTACAAATCGC
* *
25734416 ACACTTAGT-GCTATTTATAGCCGAAGCTATTTCAAATCGC
1 ACACTTAGTACCTA-TTATAGCCGAAGCTATTACAAATCGC
25734456 ACACTTAGTAC
1 ACACTTAGTAC
25734467 TGAAAATAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
38 1 0.02
39 2 0.05
40 41 0.93
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (40 bp):
ACACTTAGTACCTATTATAGCCGAAGCTATTACAAATCGC
Found at i:25735498 original size:13 final size:13
Alignment explanation
Indices: 25735462--25735499 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
25735452 TCCAAACGAT
25735462 AAAATTATCACAC
1 AAAATTATCACAC
25735475 AAAACTT-TCACAC
1 AAAA-TTATCACAC
25735488 AAAATTATCACA
1 AAAATTATCACA
25735500 TATTGTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 19 0.83
14 2 0.09
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAATTATCACAC
Found at i:25739394 original size:175 final size:175
Alignment explanation
Indices: 25739103--25739452 Score: 700
Period size: 175 Copynumber: 2.0 Consensus size: 175
25739093 ATTGATAAAG
25739103 AGTTCAATTTGACATTTAGGACTAAATTGCAAAAGTTGCAAAATATGGGTTCTAGAAGAATTAAG
1 AGTTCAATTTGACATTTAGGACTAAATTGCAAAAGTTGCAAAATATGGGTTCTAGAAGAATTAAG
25739168 CATGAAATTGCCATGGATTATTAATTAGAGGTCCTTAAATAGAAATTTACCCAAATTTTATTTTT
66 CATGAAATTGCCATGGATTATTAATTAGAGGTCCTTAAATAGAAATTTACCCAAATTTTATTTTT
25739233 ATGGACAAAAATGGGCATGAATAGGAAAAATTTGAAAGAAAGGCC
131 ATGGACAAAAATGGGCATGAATAGGAAAAATTTGAAAGAAAGGCC
25739278 AGTTCAATTTGACATTTAGGACTAAATTGCAAAAGTTGCAAAATATGGGTTCTAGAAGAATTAAG
1 AGTTCAATTTGACATTTAGGACTAAATTGCAAAAGTTGCAAAATATGGGTTCTAGAAGAATTAAG
25739343 CATGAAATTGCCATGGATTATTAATTAGAGGTCCTTAAATAGAAATTTACCCAAATTTTATTTTT
66 CATGAAATTGCCATGGATTATTAATTAGAGGTCCTTAAATAGAAATTTACCCAAATTTTATTTTT
25739408 ATGGACAAAAATGGGCATGAATAGGAAAAATTTGAAAGAAAGGCC
131 ATGGACAAAAATGGGCATGAATAGGAAAAATTTGAAAGAAAGGCC
25739453 TCAAGGGCAT
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 175 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (175 bp):
AGTTCAATTTGACATTTAGGACTAAATTGCAAAAGTTGCAAAATATGGGTTCTAGAAGAATTAAG
CATGAAATTGCCATGGATTATTAATTAGAGGTCCTTAAATAGAAATTTACCCAAATTTTATTTTT
ATGGACAAAAATGGGCATGAATAGGAAAAATTTGAAAGAAAGGCC
Found at i:25752310 original size:11 final size:11
Alignment explanation
Indices: 25752289--25752313 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25752279 TTCATTTTCC
25752289 TTTAATTTTAG
1 TTTAATTTTAG
25752300 TTTAATTTTAG
1 TTTAATTTTAG
25752311 TTT
1 TTT
25752314 TTACAATTTT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTAATTTTAG
Found at i:25757232 original size:51 final size:48
Alignment explanation
Indices: 25757110--25757299 Score: 229
Period size: 49 Copynumber: 3.9 Consensus size: 48
25757100 GAACCTATCT
* * **
25757110 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTTTC
* * *
25757158 TGGTAC-AAGTAGTAGCCTACACTTAGTACTACACACGTGATCACAGTTTTC
1 -GGTACGCA-TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTTTC
*
25757209 AGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATTC
1 -GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCAATT-TTC
* *
25757259 GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACC
25757300 TCACAATAGT
Statistics
Matches: 121, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
48 1 0.01
49 75 0.62
50 5 0.04
51 39 0.32
52 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (48 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTTTC
Found at i:25757283 original size:100 final size:100
Alignment explanation
Indices: 25757110--25757297 Score: 324
Period size: 100 Copynumber: 1.9 Consensus size: 100
25757100 GAACCTATCT
25757110 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACAAGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACAAGTAGTAGCC
25757175 TACACTTAGTACTACACACGTGATCACAGTTTTCA
66 TACACTTAGTACTACACACGTGATCACAGTTTTCA
* * *
25757210 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTAT-TCGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCT-GGTACAAGTAGTAGC
*
25757274 CTGCACTTAGTACTACACACGTGA
65 CTACACTTAGTACTACACACGTGA
25757298 CCTCACAATA
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
99 1 0.01
100 82 0.99
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACAAGTAGTAGCC
TACACTTAGTACTACACACGTGATCACAGTTTTCA
Found at i:25759301 original size:15 final size:15
Alignment explanation
Indices: 25759251--25759309 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
25759241 AAAACCGAAT
25759251 AAAGAAATCCAAGATA
1 AAAGAAATCCAAGA-A
* *
25759267 GAA-AAA-CCCAGAA
1 AAAGAAATCCAAGAA
25759280 TAAAGAAATCCAAGAA
1 -AAAGAAATCCAAGAA
*
25759296 AAAGAAACCCAAGA
1 AAAGAAATCCAAGA
25759310 TACGATATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 1 0.03
14 7 0.20
15 19 0.54
16 8 0.23
ACGTcount: A:0.63, C:0.17, G:0.14, T:0.07
Consensus pattern (15 bp):
AAAGAAATCCAAGAA
Found at i:25759304 original size:30 final size:31
Alignment explanation
Indices: 25759230--25759306 Score: 106
Period size: 30 Copynumber: 2.5 Consensus size: 31
25759220 TTACGGAATA
*
25759230 AAGATAACAAGAAAACC-GAATAAAGAAATCC
1 AAGATAA-AAGAAACCCAGAATAAAGAAATCC
*
25759261 AAGATAGAA-AAACCCAGAATAAAGAAATCC
1 AAGATAAAAGAAACCCAGAATAAAGAAATCC
25759291 AAGA-AAAAGAAACCCA
1 AAGATAAAAGAAACCCA
25759307 AGATACGATA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 8 0.20
30 27 0.66
31 6 0.15
ACGTcount: A:0.62, C:0.17, G:0.13, T:0.08
Consensus pattern (31 bp):
AAGATAAAAGAAACCCAGAATAAAGAAATCC
Found at i:25762422 original size:51 final size:49
Alignment explanation
Indices: 25762295--25762489 Score: 221
Period size: 49 Copynumber: 3.9 Consensus size: 49
25762285 TAGCCGAACC
* *
25762295 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* * * * * *
25762344 AATCTGGTAC-AAGTAGTAGCCTACACTTAGTACTACACACGTGATCACAGT
1 TATCAGGTACGCA-TAGTAGCCTGCACTTAGTACTACACACGCGA-C-CAAT
* *
25762395 TTTCAGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* * * * *
25762444 TATCCGGTACACGTAGTAGCTTGCACTTAGTACTACACACGTGACC
1 TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACC
25762490 TCACAATAGT
Statistics
Matches: 121, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
49 79 0.65
50 2 0.02
51 38 0.31
52 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCAGGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
Found at i:25762473 original size:100 final size:100
Alignment explanation
Indices: 25762300--25762487 Score: 331
Period size: 100 Copynumber: 1.9 Consensus size: 100
25762290 GAACCTATCT
*
25762300 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCTGGTACAAGTAGTAGCC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACAAGTAGTAGCC
25762365 TACACTTAGTACTACACACGTGATCACAGTTTTCA
66 TACACTTAGTACTACACACGTGATCACAGTTTTCA
* * *
25762400 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCT
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACAAGTAGTAGCC
*
25762465 TGCACTTAGTACTACACACGTGA
66 TACACTTAGTACTACACACGTGA
25762488 CCTCACAATA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 83 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATAATCCGGTACAAGTAGTAGCC
TACACTTAGTACTACACACGTGATCACAGTTTTCA
Found at i:25769702 original size:16 final size:16
Alignment explanation
Indices: 25769677--25769707 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25769667 AAGAAAGAGG
*
25769677 TAAAATAAAAGAAAAA
1 TAAAAAAAAAGAAAAA
25769693 TAAAAAAAAAGAAAA
1 TAAAAAAAAAGAAAA
25769708 GAATGGCAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (16 bp):
TAAAAAAAAAGAAAAA
Found at i:25770939 original size:7 final size:7
Alignment explanation
Indices: 25770927--25770972 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
25770917 ATGCCCGTGT
25770927 CACAATA
1 CACAATA
25770934 CACAATA
1 CACAATA
25770941 CACAATA
1 CACAATA
25770948 CACAATA
1 CACAATA
25770955 CACAATA
1 CACAATA
25770962 CACAATA
1 CACAATA
25770969 CACA
1 CACA
25770973 TAAATAACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (7 bp):
CACAATA
Found at i:25780058 original size:40 final size:40
Alignment explanation
Indices: 25779998--25780181 Score: 221
Period size: 40 Copynumber: 4.6 Consensus size: 40
25779988 TATTCGAATG
*
25779998 ATATCCGGGCTAAG-TCCCGAAGGCTTTTATGCTAGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* * *
25780038 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAG-TGACT
* * * *
25780078 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
*
25780118 ATATCCGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTATGCTAGTGACT
* *
25780158 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
25780182 CTTGTGCAAG
Statistics
Matches: 123, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 119 0.97
41 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTATGCTAGTGACT
Found at i:25780131 original size:80 final size:80
Alignment explanation
Indices: 25779998--25780181 Score: 246
Period size: 80 Copynumber: 2.3 Consensus size: 80
25779988 TATTCGAATG
* * *
25779998 ATATCCGGGCTAAGTCCCGAAGGCTTTTATGCTAGTGACTATATCCGGACTAAGAT-CCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAG-TCCCGAAGGC
* *
25780062 ATTTGTGCGAGTTG-CT
65 ATTTATGCGAG-TGACC
* * *
25780078 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACTATATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
*
25780143 TTTATGCTAGTGACC
66 TTTATGCGAGTGACC
*
25780158 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
25780182 CTTGTGCAAG
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
79 3 0.03
80 88 0.97
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCTAGCGACTATATCCGGACTAAGTCCCGAAGGCA
TTTATGCGAGTGACC
Found at i:25791859 original size:40 final size:39
Alignment explanation
Indices: 25791828--25791982 Score: 202
Period size: 40 Copynumber: 3.9 Consensus size: 39
25791818 GGACTAAGAT
* *
25791828 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
25791868 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
25791908 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* *
25791948 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTT
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTT
25791983 GGTTCTTGTG
Statistics
Matches: 107, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
40 104 0.97
41 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:25796681 original size:13 final size:12
Alignment explanation
Indices: 25796652--25796681 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
25796642 TCCTGAGTTG
25796652 ATTTTTGTAGGA
1 ATTTTTGTAGGA
*
25796664 ATTTTTGTAGGC
1 ATTTTTGTAGGA
25796676 ATTTTT
1 ATTTTT
25796682 AACATAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.20, C:0.03, G:0.20, T:0.57
Consensus pattern (12 bp):
ATTTTTGTAGGA
Found at i:25797264 original size:19 final size:20
Alignment explanation
Indices: 25797240--25797285 Score: 85
Period size: 19 Copynumber: 2.4 Consensus size: 20
25797230 CATCCAAACA
25797240 CCAGAAAAGTAAATCA-TTT
1 CCAGAAAAGTAAATCATTTT
25797259 CCAGAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCATTTT
25797279 CCAGAAA
1 CCAGAAA
25797286 TCATTTTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (20 bp):
CCAGAAAAGTAAATCATTTT
Found at i:25797306 original size:14 final size:14
Alignment explanation
Indices: 25797269--25797299 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
25797259 CCAGAAAAGT
25797269 AAATCATTTTCCAG
1 AAATCATTTTCCAG
25797283 AAATCATTTTCCAG
1 AAATCATTTTCCAG
25797297 AAA
1 AAA
25797300 ATATTTTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:25800331 original size:16 final size:16
Alignment explanation
Indices: 25800289--25800331 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
25800279 TAATAAGAGT
25800289 TATTTTGTAGGAATTA
1 TATTTTGTAGGAATTA
25800305 TAATTTTGTAGGAATTA
1 T-ATTTTGTAGGAATTA
*
25800322 TATTTGGTAG
1 TATTTTGTAG
25800332 TTTCGACGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (16 bp):
TATTTTGTAGGAATTA
Found at i:25808910 original size:4 final size:4
Alignment explanation
Indices: 25808901--25808935 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
25808891 TATTTTTATT
25808901 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
25808936 TATTAAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:25812272 original size:39 final size:40
Alignment explanation
Indices: 25812227--25812411 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
25812217 GCTCCTCGTT
* * *
25812227 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
25812267 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
25812306 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
25812346 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
25812387 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
25812412 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:25812327 original size:40 final size:39
Alignment explanation
Indices: 25812194--25812411 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
25812184 AAATCACGTA
* * **
25812194 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
25812233 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
25812272 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
25812312 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
25812352 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
25812392 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
25812412 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:25817765 original size:227 final size:227
Alignment explanation
Indices: 25817370--25817825 Score: 804
Period size: 227 Copynumber: 2.0 Consensus size: 227
25817360 TCTGGTTATA
25817370 TCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTCCAGATGGTCTACCTCGAGC
1 TCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTCCAGATGGTCTACCTCGAGC
* * *
25817435 AGTGGTAGCACCCGGTTTCCCACTCTGATTTTCATTCTGTTCAAACAACCTCGGGCAATCTTTAA
66 AGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCAAACAACCTCGGGCAATCTTTAA
* *
25817500 TGAAGTGGTCCACTGATCCGCATTTGTAACAGGAGCGGTCAGGAAATCTACAACTCCCCGAATGC
131 TGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGAAATCTACAACTCCCCGAATGC
*
25817565 CATTTACCGCAATATCGACATTCCGTTCTGTC
196 CATTTACCGCAATATCGACATTCCGTTCTATC
* *
25817597 TCATCTCTAGATCCTCTCTGACCACCACTAGCATTGCCCGTATTTCCAGATGGTCTACCTCGAGC
1 TCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTCCAGATGGTCTACCTCGAGC
**
25817662 AGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCCGACAACCTCGGGCAATCTTTAA
66 AGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCAAACAACCTCGGGCAATCTTTAA
*
25817727 TGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGGAATCTACAACTCCCCGAATGC
131 TGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGAAATCTACAACTCCCCGAATGC
*
25817792 CATTTACCGCAATATCGACATTTCGTTCTATC
196 CATTTACCGCAATATCGACATTCCGTTCTATC
25817824 TC
1 TC
25817826 GACGTTCATT
Statistics
Matches: 217, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
227 217 1.00
ACGTcount: A:0.23, C:0.31, G:0.18, T:0.28
Consensus pattern (227 bp):
TCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTCCAGATGGTCTACCTCGAGC
AGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCAAACAACCTCGGGCAATCTTTAA
TGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGAAATCTACAACTCCCCGAATGC
CATTTACCGCAATATCGACATTCCGTTCTATC
Found at i:25820424 original size:40 final size:39
Alignment explanation
Indices: 25820326--25820588 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
25820316 TCCTCGTTCA
* * * *
25820326 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
25820365 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
25820404 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
25820444 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
25820484 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
25820524 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
25820565 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
25820589 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:25820548 original size:120 final size:119
Alignment explanation
Indices: 25820326--25820588 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
25820316 TCCTCGTTCA
* * *
25820326 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
25820391 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
25820444 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
25820509 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
25820565 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
25820589 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:25820597 original size:41 final size:41
Alignment explanation
Indices: 25820520--25820597 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
25820510 TTTGTATCTC
* * *
25820520 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
25820561 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
25820598 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:25827043 original size:41 final size:41
Alignment explanation
Indices: 25826986--25827070 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
25826976 AATGCCCAAA
25826986 CCACAAAATAGAAAAGTGAGTACTCACAATCCTATGACATG
1 CCACAAAATAGAAAAGTGAGTACTCACAATCCTATGACATG
*
25827027 CCACAAAATAGAAAAGTGAGTACTCACAGTCCTATGACATG
1 CCACAAAATAGAAAAGTGAGTACTCACAATCCTATGACATG
25827068 CCA
1 CCA
25827071 ACTATATCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.19
Consensus pattern (41 bp):
CCACAAAATAGAAAAGTGAGTACTCACAATCCTATGACATG
Found at i:25837954 original size:18 final size:18
Alignment explanation
Indices: 25837931--25837967 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
25837921 TTAAATTGTT
25837931 TTTTTATTATTATATGTG
1 TTTTTATTATTATATGTG
25837949 TTTTTATTATTATATGTG
1 TTTTTATTATTATATGTG
25837967 T
1 T
25837968 ATGGAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.68
Consensus pattern (18 bp):
TTTTTATTATTATATGTG
Found at i:25841054 original size:30 final size:30
Alignment explanation
Indices: 25841018--25841077 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
25841008 TCATGAATGG
25841018 AGCTTAACTCGACATTCCCTTATCTCCTCA
1 AGCTTAACTCGACATTCCCTTATCTCCTCA
25841048 AGCTTAACTCGACATTCCCTTATCTCCTCA
1 AGCTTAACTCGACATTCCCTTATCTCCTCA
25841078 TTCTGTCCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.37, G:0.07, T:0.33
Consensus pattern (30 bp):
AGCTTAACTCGACATTCCCTTATCTCCTCA
Found at i:25842679 original size:42 final size:43
Alignment explanation
Indices: 25842610--25842692 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 43
25842600 TTTTACATGT
*
25842610 AATCAAATACCGATGCCACTGTCCCAGACAGGGTCTTACACGA
1 AATCAAATACCGATGCCAATGTCCCAGACAGGGTCTTACACGA
*
25842653 AATCAAATA-CGATGCCAATGTCCCAGACATGGTCTTACAC
1 AATCAAATACCGATGCCAATGTCCCAGACAGGGTCTTACAC
25842693 ATAAATCATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 29 0.76
43 9 0.24
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (43 bp):
AATCAAATACCGATGCCAATGTCCCAGACAGGGTCTTACACGA
Found at i:25842699 original size:43 final size:42
Alignment explanation
Indices: 25842579--25842735 Score: 138
Period size: 43 Copynumber: 3.7 Consensus size: 42
25842569 AGCTCGTACA
* * * * *
25842579 ATGCTAATGTTCCAGACATGATTTTACA-TGTAATCAAATACCG
1 ATGCCAATGTCCCAGACATGGTCTTACACT-AAATCAAATA-CG
* * *
25842622 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAATACG
1 ATGCCAATGTCCCAGACATGGTCTTACACTAAATCAAATACG
*
25842664 ATGCCAATGTCCCAGACATGGTCTTACACATAAATCATAAGT-TG
1 ATGCCAATGTCCCAGACATGGTCTTACAC-TAAATCA-AA-TACG
* ** *
25842708 ATACCAATGTCGTAGACGTGGTCTTACA
1 ATGCCAATGTCCCAGACATGGTCTTACA
25842736 TGATAACACA
Statistics
Matches: 94, Mismatches: 16, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
42 29 0.31
43 37 0.39
44 27 0.29
45 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACTAAATCAAATACG
Found at i:25846978 original size:21 final size:22
Alignment explanation
Indices: 25846934--25846979 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
25846924 GGTCTCAGTG
* *
25846934 TTCACTTTGGTACATGAGTTTT
1 TTCAATTTGATACATGAGTTTT
* *
25846956 TTCAATTTGATACTTGATTTTT
1 TTCAATTTGATACATGAGTTTT
25846978 TT
1 TT
25846980 TGTCATGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.11, G:0.13, T:0.57
Consensus pattern (22 bp):
TTCAATTTGATACATGAGTTTT
Found at i:25856549 original size:10 final size:10
Alignment explanation
Indices: 25856522--25856557 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
25856512 AATGATAACA
25856522 AAACAACAAC
1 AAACAACAAC
*
25856532 ATAACAACAAT
1 A-AACAACAAC
25856543 AAACAACAAC
1 AAACAACAAC
25856553 AAACA
1 AAACA
25856558 GTAGTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.69, C:0.25, G:0.00, T:0.06
Consensus pattern (10 bp):
AAACAACAAC
Found at i:25873573 original size:30 final size:30
Alignment explanation
Indices: 25873539--25873604 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
25873529 CAAAGTTATA
* * *
25873539 ATTTATTCATTGAATTATTTAAAAATTTTT
1 ATTTAGTCACTGAATTACTTAAAAATTTTT
*
25873569 ATTTAAGTCACTGAATTACTTAAAAGTTTTT
1 ATTT-AGTCACTGAATTACTTAAAAATTTTT
25873600 ATTTA
1 ATTTA
25873605 AGTCCTTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (30 bp):
ATTTAGTCACTGAATTACTTAAAAATTTTT
Found at i:25873584 original size:31 final size:31
Alignment explanation
Indices: 25873549--25873608 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
25873539 ATTTATTCAT
*
25873549 TGAATTATTTAAAAATTTTTATTTAAGTCAC
1 TGAATTACTTAAAAATTTTTATTTAAGTCAC
*
25873580 TGAATTACTTAAAAGTTTTTATTTAAGTC
1 TGAATTACTTAAAAATTTTTATTTAAGTC
25873609 CTTAGTCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (31 bp):
TGAATTACTTAAAAATTTTTATTTAAGTCAC
Found at i:25875143 original size:16 final size:17
Alignment explanation
Indices: 25875117--25875153 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
25875107 TTTTTTTATT
25875117 TTTTGGATTTAAGGTTA
1 TTTTGGATTTAAGGTTA
*
25875134 TTTT-GATTTAGGGTTA
1 TTTTGGATTTAAGGTTA
25875150 TTTT
1 TTTT
25875154 AGGTTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.19, C:0.00, G:0.22, T:0.59
Consensus pattern (17 bp):
TTTTGGATTTAAGGTTA
Found at i:25875203 original size:28 final size:27
Alignment explanation
Indices: 25875123--25875204 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
25875113 TATTTTTTGG
* * *
25875123 ATTTAAGGTTATTTTGATTTAGG-GTTA
1 ATTT-AGGTTATTTCGATTTTGGTTTTA
* **
25875150 TTTTAGGTTATTTCGATTTTAATTTTA
1 ATTTAGGTTATTTCGATTTTGGTTTTA
25875177 ATTTAGGGTTATTTCGATTTTGGTTTTA
1 ATTTA-GGTTATTTCGATTTTGGTTTTA
25875205 TTTGTTATTA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
26 14 0.32
27 10 0.23
28 20 0.45
ACGTcount: A:0.22, C:0.02, G:0.18, T:0.57
Consensus pattern (27 bp):
ATTTAGGTTATTTCGATTTTGGTTTTA
Found at i:25875492 original size:62 final size:61
Alignment explanation
Indices: 25875392--25875524 Score: 212
Period size: 62 Copynumber: 2.2 Consensus size: 61
25875382 TTATTGTCTA
* *
25875392 TTATTGTCTGCCATGTGCATGAAAAAAATGGTTGTGTTTGTATTAAATTATTTTTGTATTGG
1 TTATTGTCTGCCATGTGCATGAAAAAAATGGTTATGTTTGTATTAAATTA-TTTTCTATTGG
* *
25875454 TTATTGTCTGCCATGTGCATGACAAAAATGGTTATGTTTGTATTAATTTATTTTCTATTGG
1 TTATTGTCTGCCATGTGCATGAAAAAAATGGTTATGTTTGTATTAAATTATTTTCTATTGG
*
25875515 TTATTATCTG
1 TTATTGTCTG
25875525 ACAGAAATGG
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
61 19 0.29
62 47 0.71
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.48
Consensus pattern (61 bp):
TTATTGTCTGCCATGTGCATGAAAAAAATGGTTATGTTTGTATTAAATTATTTTCTATTGG
Found at i:25877364 original size:17 final size:17
Alignment explanation
Indices: 25877332--25877363 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
25877322 TTAATATGCA
25877332 TGTAGTGACTATTTTTG
1 TGTAGTGACTATTTTTG
25877349 TGTA-TGACTATTTTT
1 TGTAGTGACTATTTTT
25877364 TAATATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.19, C:0.06, G:0.19, T:0.56
Consensus pattern (17 bp):
TGTAGTGACTATTTTTG
Found at i:25877391 original size:67 final size:67
Alignment explanation
Indices: 25877318--25877608 Score: 438
Period size: 67 Copynumber: 4.3 Consensus size: 67
25877308 TTAGTGAGTG
* * * ** * *
25877318 TTTTTTAATATGCATGTAGTGACTATTTTTGTGTATGACTATTTTTTAATATACATGTTGTTGAC
1 TTTTTTAATATGCATGCAGTGATTGTTGGTGTGTATAACTGTTTTTTAATATACATGTTGTTGAC
25877383 TA
66 TA
* * *
25877385 TTTTTTAATATGCATGCAGTGATTGTTGGTGTGTATGACTGTTTTTTAATATACATGCTATTGAC
1 TTTTTTAATATGCATGCAGTGATTGTTGGTGTGTATAACTGTTTTTTAATATACATGTTGTTGAC
25877450 TA
66 TA
25877452 TTTTTTAATATGCATGCAGTGATTGTTGGTGTGTATAACTGTTTTTTTAATATACATGTTGTTGA
1 TTTTTTAATATGCATGCAGTGATTGTTGGTGTGTATAACTG-TTTTTTAATATACATGTTGTTGA
25877517 CTA
65 CTA
*
25877520 TTTTTTAATAATATGCATGCAGTGATTGTTGGTGTGTATAAATGTTTATTTAATATACATGTTGT
1 -TTTTT--TAATATGCATGCAGTGATTGTTGGTGTGTATAACTGTTT-TTTAATATACATGTTGT
25877585 TGACTA
62 TGACTA
25877591 TTTTTTAATATGCATGCA
1 TTTTTTAATATGCATGCA
25877609 ATGAGTATTT
Statistics
Matches: 207, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
67 99 0.48
68 37 0.18
69 5 0.02
70 8 0.04
71 58 0.28
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (67 bp):
TTTTTTAATATGCATGCAGTGATTGTTGGTGTGTATAACTGTTTTTTAATATACATGTTGTTGAC
TA
Found at i:25885026 original size:12 final size:12
Alignment explanation
Indices: 25885011--25885042 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
25885001 GCAAAAGGAG
25885011 ATGCAAGAACAA
1 ATGCAAGAACAA
*
25885023 ATGCAAGAACAG
1 ATGCAAGAACAA
25885035 ATGCAAGA
1 ATGCAAGA
25885043 GAAAATGGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.22, T:0.09
Consensus pattern (12 bp):
ATGCAAGAACAA
Found at i:25885056 original size:26 final size:24
Alignment explanation
Indices: 25884994--25885042 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
25884984 GAAAGGTTGA
*
25884994 AACAAATGCAA-AAGGAGATGCAAG
1 AACAAATGCAAGAA-CAGATGCAAG
25885018 AACAAATGCAAGAACAGATGCAAG
1 AACAAATGCAAGAACAGATGCAAG
25885042 A
1 A
25885043 GAAAATGGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.55, C:0.14, G:0.22, T:0.08
Consensus pattern (24 bp):
AACAAATGCAAGAACAGATGCAAG
Found at i:25893633 original size:134 final size:135
Alignment explanation
Indices: 25893237--25893642 Score: 478
Period size: 134 Copynumber: 3.0 Consensus size: 135
25893227 CTCCATGAGG
* * * * * *
25893237 TAGCAATGGAGCAGATCGAAGATGGTGAATCTTATCTTCTAGAGGTAGTAGGGGAGCAGATTTTA
1 TAGCAGTGGAGCAGATCGAAAATGGCGAATCTTATCTTCTCGAGGTAGCAAGGGAGCAGATTTTA
* * *
25893302 GCTACTAGCCTTATCTCCCTAAGGTAGCAAGGGAGTAGACTGAAGATTGTAGATCTTGTC-TCAT
66 GCCACTAGCCTTATCTCCCTAAGGTAGCAAGGGAGCAGACTGAAGATTGTAGATCTTGTCTTCTT
25893366 CGAGA
131 CGAGA
* ** * * ** *
25893371 AAATAGTGGAGTAAATCGAAAGCGGCGAATCTTATCTTCTCGAGGTATCAAGGGAGCAGATTTTA
1 TAGCAGTGGAGCAGATCGAAAATGGCGAATCTTATCTTCTCGAGGTAGCAAGGGAGCAGATTTTA
* * * *
25893436 GCCACTAGCCTTATCTCCCCAAAGTAGCAAGGGAGCAGATTGAAGATTGTAGATTTTGT-TTCTT
66 GCCACTAGCCTTATCTCCCTAAGGTAGCAAGGGAGCAGACTGAAGATTGTAGATCTTGTCTTCTT
25893500 CGAGA
131 CGAGA
* * * *
25893505 TAGCAGTGGGGCAGATAGAAAATGGCGAATCTTATCTTCTCGGGGCAGCAAGGGAGCAGATTTTA
1 TAGCAGTGGAGCAGATCGAAAATGGCGAATCTTATCTTCTCGAGGTAGCAAGGGAGCAGATTTTA
* * * * * * * *
25893570 GCCACCAGCCTTATCTCTCTGAGGTAGCAAAGGAGCAGGCTAAAGATCGTAG-TCTTATCTTCTT
66 GCCACTAGCCTTATCTCCCTAAGGTAGCAAGGGAGCAGACTGAAGATTGTAGATCTTGTCTTCTT
*
25893634 -GAGG
131 CGAGA
25893638 TAGCA
1 TAGCA
25893643 AGGGAGTAGA
Statistics
Matches: 224, Mismatches: 46, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
133 12 0.05
134 212 0.95
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (135 bp):
TAGCAGTGGAGCAGATCGAAAATGGCGAATCTTATCTTCTCGAGGTAGCAAGGGAGCAGATTTTA
GCCACTAGCCTTATCTCCCTAAGGTAGCAAGGGAGCAGACTGAAGATTGTAGATCTTGTCTTCTT
CGAGA
Found at i:25893660 original size:44 final size:46
Alignment explanation
Indices: 25893579--25893674 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 46
25893569 AGCCACCAGC
* *
25893579 CTTATC-TCTCTGAGGTAGCAAAGGAGCAGGCTAAAGATCGTAG-T
1 CTTATCTTCTCTGAGGTAGCAAAGGAGCAGACTAAAGATCGGAGAT
* * * * *
25893623 CTTATCTTCT-TGAGGTAGCAAGGGAGTAGATTGAAGATTGGAGAT
1 CTTATCTTCTCTGAGGTAGCAAAGGAGCAGACTAAAGATCGGAGAT
25893668 CTTATCT
1 CTTATCT
25893675 CCCTAGGTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
44 32 0.74
45 11 0.26
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (46 bp):
CTTATCTTCTCTGAGGTAGCAAAGGAGCAGACTAAAGATCGGAGAT
Found at i:25896037 original size:68 final size:68
Alignment explanation
Indices: 25895890--25896045 Score: 149
Period size: 68 Copynumber: 2.2 Consensus size: 68
25895880 AGCCGATTTG
* * * * *
25895890 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACATA
*
25895955 TATC
65 TATA
* *
25895959 TCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTACT
1 TCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTAC-
25896021 ATATAGTA
62 ATATA-TA
25896029 TCTCGTAGC-CTTCTTGT
1 TCTCGTAGCTC-TCTTGT
25896046 ACACATGATG
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
67 1 0.01
68 33 0.45
69 7 0.10
70 6 0.08
71 26 0.36
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.35
Consensus pattern (68 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACATAT
ATA
Found at i:25903556 original size:68 final size:68
Alignment explanation
Indices: 25903409--25903564 Score: 149
Period size: 68 Copynumber: 2.2 Consensus size: 68
25903399 AGCCGATTTG
* * * * *
25903409 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACATA
*
25903474 TATC
65 TATA
* *
25903478 TCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTACT
1 TCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTAC-
25903540 ATATAGTA
62 ATATA-TA
25903548 TCTCGTAGC-CTTCTTGT
1 TCTCGTAGCTC-TCTTGT
25903565 ACACATGATG
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
67 1 0.01
68 33 0.45
69 7 0.10
70 6 0.08
71 26 0.36
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.35
Consensus pattern (68 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACATAT
ATA
Found at i:25913763 original size:36 final size:36
Alignment explanation
Indices: 25913662--25913743 Score: 146
Period size: 36 Copynumber: 2.3 Consensus size: 36
25913652 GTTAGCCATG
25913662 TATACCAGCAGCCATATATAACAACATAAGCAACAA
1 TATACCAGCAGCCATATATAACAACATAAGCAACAA
* *
25913698 TATACCAGGAGCCATGTATAACAACATAAGCAACAA
1 TATACCAGCAGCCATATATAACAACATAAGCAACAA
25913734 TATACCAGCA
1 TATACCAGCA
25913744 ACAATATTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.48, C:0.24, G:0.11, T:0.17
Consensus pattern (36 bp):
TATACCAGCAGCCATATATAACAACATAAGCAACAA
Found at i:25920564 original size:79 final size:78
Alignment explanation
Indices: 25920462--25920685 Score: 281
Period size: 79 Copynumber: 2.8 Consensus size: 78
25920452 GCTCCTCGTT
* *
25920462 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
25920527 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
25920542 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
25920606 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
25920620 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
25920684 GA
63 GA
25920686 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
78 36 0.29
79 56 0.44
80 34 0.27
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:25920579 original size:39 final size:40
Alignment explanation
Indices: 25920462--25920685 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
25920452 GCTCCTCGTT
* *
25920462 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
25920502 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
25920542 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
25920581 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
25920620 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
25920661 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
25920686 CATCATTCAA
Statistics
Matches: 168, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 72 0.43
40 78 0.46
41 16 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:25928495 original size:79 final size:81
Alignment explanation
Indices: 25928393--25928577 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
25928383 GCTCCTCGTT
* *
25928393 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
25928456 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
25928473 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
25928537 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
25928553 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
25928578 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:25928577 original size:40 final size:40
Alignment explanation
Indices: 25928393--25928577 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
25928383 GCTCCTCGTT
* *
25928393 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
25928433 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
25928473 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
25928512 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
25928553 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
25928578 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:25931622 original size:3 final size:3
Alignment explanation
Indices: 25931614--25931658 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
25931604 ATGTTAAATT
25931614 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25931659 ATAAAACCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:25931701 original size:13 final size:12
Alignment explanation
Indices: 25931683--25931718 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
25931673 TGCAAACATT
25931683 AAGAAAGAAAAG
1 AAGAAAGAAAAG
25931695 AAAGAAAGAAAAG
1 -AAGAAAGAAAAG
25931708 AAGAAGAGAAA
1 AAGAA-AGAAA
25931719 GCTTACGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (12 bp):
AAGAAAGAAAAG
Found at i:25934137 original size:27 final size:27
Alignment explanation
Indices: 25934107--25934160 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
25934097 TCATACAACC
* *
25934107 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
25934134 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
25934161 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:25935943 original size:6 final size:6
Alignment explanation
Indices: 25935927--25935957 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
25935917 GTCATTTATA
*
25935927 TATATG GATATG TATATG TATATG TATATG T
1 TATATG TATATG TATATG TATATG TATATG T
25935958 TTGTGGTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (6 bp):
TATATG
Found at i:25937191 original size:41 final size:41
Alignment explanation
Indices: 25937134--25937218 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
25937124 TAGGAGTAGG
*
25937134 TGAATCACAACTACTTTTGCTACAGTACTTGCACCTACTTC
1 TGAATCACAACTACTTTTGCTACAGTACCTGCACCTACTTC
*
25937175 TGAATCACAACTACTTTTGCTATAGTACCTGCACCTACTTC
1 TGAATCACAACTACTTTTGCTACAGTACCTGCACCTACTTC
25937216 TGA
1 TGA
25937219 CGAGCTTCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.34
Consensus pattern (41 bp):
TGAATCACAACTACTTTTGCTACAGTACCTGCACCTACTTC
Found at i:25938271 original size:22 final size:22
Alignment explanation
Indices: 25938243--25938299 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
25938233 ATGCAAAGTC
25938243 ACACGCCCGTGTGGACTCAGGA
1 ACACGCCCGTGTGGACTCAGGA
25938265 ACACGCCCGTGTGGACTCAGGA
1 ACACGCCCGTGTGGACTCAGGA
25938287 ACACGCCCGTGTG
1 ACACGCCCGTGTG
25938300 CCTTCGACAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.21, C:0.33, G:0.32, T:0.14
Consensus pattern (22 bp):
ACACGCCCGTGTGGACTCAGGA
Done.