Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_pilon, whole genome shotgun sequence
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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 51
Found at i:6024563 original size:15 final size:15
Alignment explanation
Indices: 6024539--6024574 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
6024529 TATGATAATT
*
6024539 AAGAAATGAAATGGA
1 AAGAATTGAAATGGA
6024554 AAGAATTGAAATGGA
1 AAGAATTGAAATGGA
*
6024569 TAGAAT
1 AAGAAT
6024575 AGTTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (15 bp):
AAGAATTGAAATGGA
Found at i:6024744 original size:22 final size:23
Alignment explanation
Indices: 6024716--6024786 Score: 65
Period size: 25 Copynumber: 3.0 Consensus size: 23
6024706 ATTTATAAGT
6024716 TGGTGATAATATAGGCG-TGAT-A
1 TGGTGATAATAT-GGCGATGATAA
*
6024738 TGGTGATGGAATATGGTGATGATAA
1 TGGTGAT--AATATGGCGATGATAA
*
6024763 TGGTGATAGACTATGGTGATGATA
1 TGGTGATA-A-TATGGCGATGATA
6024787 TAGGCGTGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
22 7 0.17
23 4 0.10
24 10 0.24
25 21 0.50
ACGTcount: A:0.31, C:0.03, G:0.34, T:0.32
Consensus pattern (23 bp):
TGGTGATAATATGGCGATGATAA
Found at i:6024753 original size:13 final size:13
Alignment explanation
Indices: 6024735--6024783 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
6024725 TATAGGCGTG
6024735 ATATGGTGATGGA
1 ATATGGTGATGGA
6024748 ATATGGTGAT-G-
1 ATATGGTGATGGA
*
6024759 ATAATGGTGATAGA
1 AT-ATGGTGATGGA
*
6024773 CTATGGTGATG
1 ATATGGTGATG
6024784 ATATAGGCGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 19 0.61
14 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.35, T:0.33
Consensus pattern (13 bp):
ATATGGTGATGGA
Found at i:6024777 original size:25 final size:25
Alignment explanation
Indices: 6024733--6024786 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
6024723 AATATAGGCG
*
6024733 TGAT-ATGGTGATGGAATATGGTGA
1 TGATAATGGTGATAGAATATGGTGA
*
6024757 TGATAATGGTGATAGACTATGGTGA
1 TGATAATGGTGATAGAATATGGTGA
6024782 TGATA
1 TGATA
6024787 TAGGCGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.31, C:0.02, G:0.33, T:0.33
Consensus pattern (25 bp):
TGATAATGGTGATAGAATATGGTGA
Found at i:6027109 original size:178 final size:178
Alignment explanation
Indices: 6026767--6027122 Score: 687
Period size: 177 Copynumber: 2.0 Consensus size: 178
6026757 TCAACATTAT
6026767 GATTTTGCTAAATCACTTTGAATAGGGAAATCATTTTGTTATGCAGTTCTTTAATTTATCGAACT
1 GATTTTGCTAAATCACTTTGAATAGGGAAATCATTTTGTTATGCAGTTCTTTAATTTATCGAACT
*
6026832 AATATACGAACTGGTTCTTCTTCATAAATCAAATTTGGTCGGATCTTAATTTCCTCTGATGCAAG
66 AATATACGAACTGGTTCTTCTTCATAAATCAAATCTGGTCGGATCTTAATTTCCTCTGATGCAAG
6026897 ACATGTGAATGATCCAATCGATACTTTCTAAGCTTCGACACATGAAAA
131 ACATGTGAATGATCCAATCGATACTTTCTAAGCTTCGACACATGAAAA
6026945 GATTTTGCT-AATCACTTTGAATAGGGAAATCATTTTGTTATGCAGTTCTTTAATTTATCGAACT
1 GATTTTGCTAAATCACTTTGAATAGGGAAATCATTTTGTTATGCAGTTCTTTAATTTATCGAACT
6027009 AATATACGAACTGGTTCTTCTTCATAAATCAAATCTGGTCGGATCTTAATTTCCTCTGATGCAAA
66 AATATACGAACTGGTTCTTCTTCATAAATCAAATCTGGTCGGATCTTAATTTCCTCTGATGC-AA
6027074 GACATGTGAATGATCCAATCGATACTTTCTAAGCTTCGACACATGAAAA
130 GACATGTGAATGATCCAATCGATACTTTCTAAGCTTCGACACATGAAAA
6027123 ACATTGTATA
Statistics
Matches: 176, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
177 116 0.66
178 60 0.34
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (178 bp):
GATTTTGCTAAATCACTTTGAATAGGGAAATCATTTTGTTATGCAGTTCTTTAATTTATCGAACT
AATATACGAACTGGTTCTTCTTCATAAATCAAATCTGGTCGGATCTTAATTTCCTCTGATGCAAG
ACATGTGAATGATCCAATCGATACTTTCTAAGCTTCGACACATGAAAA
Found at i:6030834 original size:45 final size:45
Alignment explanation
Indices: 6030783--6030984 Score: 370
Period size: 45 Copynumber: 4.5 Consensus size: 45
6030773 CAATTTAATC
*
6030783 CCATAAGCTTGTAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
6030828 CCATAAGCTCATAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
6030873 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
6030918 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTGCCA-TTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
6030962 CCATAAGCTCGTAAGCTTATTTT
1 CCATAAGCTCGTAAGCTTATTTT
6030985 CATACTTACC
Statistics
Matches: 153, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
44 28 0.18
45 125 0.82
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
Found at i:6032689 original size:20 final size:20
Alignment explanation
Indices: 6032664--6032703 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
6032654 ACCCACGTCT
6032664 GGTTTGGAGAAGAAGATGAG
1 GGTTTGGAGAAGAAGATGAG
6032684 GGTTTGGAGAAGAAGATGAG
1 GGTTTGGAGAAGAAGATGAG
6032704 CATGTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.45, T:0.20
Consensus pattern (20 bp):
GGTTTGGAGAAGAAGATGAG
Found at i:6034763 original size:24 final size:24
Alignment explanation
Indices: 6034736--6034809 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
6034726 GCTTGTAAGC
6034736 TTATTTTACCAACATACTTACCAT
1 TTATTTTACCAACATACTTACCAT
* ** *
6034760 TTA--TT-CCAA-A-AGCTCATAAGC
1 TTATTTTACCAACATA-CTTACCA-T
6034781 TTATTTTACCAACATACTTACCAT
1 TTATTTTACCAACATACTTACCAT
6034805 TTATT
1 TTATT
6034810 CCATAAGCTC
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
19 1 0.03
20 5 0.14
21 7 0.20
22 2 0.06
23 2 0.06
24 12 0.34
25 5 0.14
26 1 0.03
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.41
Consensus pattern (24 bp):
TTATTTTACCAACATACTTACCAT
Found at i:6034780 original size:45 final size:45
Alignment explanation
Indices: 6034707--6034921 Score: 342
Period size: 45 Copynumber: 4.8 Consensus size: 45
6034697 ATCAAAGTAT
* * *
6034707 TTACAATTTAATCCAATAAGCTTGTAAGCTTATTTTACCAACATAC
1 TTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAACATAC
* *
6034753 TTACCATTTATTCCAAAAGCTCATAAGCTTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAACATAC
*
6034798 TTACCATTTATTCCATAAGCTCGTAAGCTTATTGTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAACATAC
*
6034843 TTACCATTTTTTCCATAAGCTCGTAAGCTTATTTTACCAACATAC
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAACATAC
*
6034888 TTACCA-TTATTCCATAAGCTTGTAAGCTTATTTT
1 TTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
6034922 CATACTTACC
Statistics
Matches: 157, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
44 26 0.17
45 119 0.76
46 12 0.08
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAACATAC
Found at i:6035081 original size:40 final size:40
Alignment explanation
Indices: 6035002--6035082 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
6034992 ATTGGAGTCA
* * *
6035002 AATATTGCACCGAAGTGCTGAGGTCGAGCATTGCTCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGCATTACCCACCT
* *
6035042 AATAATGCACCGTAGTGCTGAGGTCG-GGATTTACCCACCT
1 AATAATGCACCGAAGTGCTGAGGTCGAGCA-TTACCCACCT
6035082 A
1 A
6035083 GTACACCGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 33 0.94
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAGGTCGAGCATTACCCACCT
Found at i:6043595 original size:45 final size:45
Alignment explanation
Indices: 6043544--6043733 Score: 353
Period size: 45 Copynumber: 4.2 Consensus size: 45
6043534 CAATTTAACC
*
6043544 CCATAAGCTTGTAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
6043589 CCATAAGCTCATAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
6043634 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
6043679 CCATAAGCTCGTAAACTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
6043724 CCATAAGCTC
1 CCATAAGCTC
6043734 ATAGTATAAC
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 141 1.00
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
Found at i:6045249 original size:13 final size:11
Alignment explanation
Indices: 6045208--6045292 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
6045198 ACAATCTGTC
6045208 CATCACCATTAT
1 CATCACCA-TAT
*
6045220 CA-CGCCTATAT
1 CATCACC-ATAT
6045231 CATCACCATAGT
1 CATCACCATA-T
6045243 CCATCACCATTAT
1 -CATCACCA-TAT
*
6045256 CA-CGCCTATAT
1 CATCACC-ATAT
6045267 CATCACCATATT
1 CATCACCATA-T
6045279 CCATCACCATAT
1 -CATCACCATAT
6045291 CA
1 CA
6045293 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:6045252 original size:36 final size:36
Alignment explanation
Indices: 6045205--6045309 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
6045195 GATACAATCT
6045205 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6045241 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
6045277 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6045310 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6049744 original size:13 final size:11
Alignment explanation
Indices: 6049703--6049787 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
6049693 ACAATCTGTC
6049703 CATCACCATTAT
1 CATCACCA-TAT
*
6049715 CA-CGCCTATAT
1 CATCACC-ATAT
6049726 CATCACCATAGT
1 CATCACCATA-T
6049738 CCATCACCATTAT
1 -CATCACCA-TAT
*
6049751 CA-CGCCTATAT
1 CATCACC-ATAT
6049762 CATCACCATATT
1 CATCACCATA-T
6049774 CCATCACCATAT
1 -CATCACCATAT
6049786 CA
1 CA
6049788 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:6049747 original size:36 final size:36
Alignment explanation
Indices: 6049700--6049804 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
6049690 GATACAATCT
6049700 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6049736 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
6049772 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6049805 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6060112 original size:13 final size:11
Alignment explanation
Indices: 6060071--6060155 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
6060061 ACAATCTGTC
6060071 CATCACCATTAT
1 CATCACCA-TAT
*
6060083 CA-CGCCTATAT
1 CATCACC-ATAT
6060094 CATCACCATAGT
1 CATCACCATA-T
6060106 CCATCACCATTAT
1 -CATCACCA-TAT
*
6060119 CA-CGCCTATAT
1 CATCACC-ATAT
6060130 CATCACCATATT
1 CATCACCATA-T
6060142 CCATCACCATAT
1 -CATCACCATAT
6060154 CA
1 CA
6060156 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:6060115 original size:36 final size:36
Alignment explanation
Indices: 6060068--6060172 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
6060058 GATACAATCT
6060068 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6060104 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
6060140 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6060173 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6064608 original size:13 final size:11
Alignment explanation
Indices: 6064567--6064651 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
6064557 ACAATCTGTC
6064567 CATCACCATTAT
1 CATCACCA-TAT
*
6064579 CA-CGCCTATAT
1 CATCACC-ATAT
6064590 CATCACCATAGT
1 CATCACCATA-T
6064602 CCATCACCATTAT
1 -CATCACCA-TAT
*
6064615 CA-CGCCTATAT
1 CATCACC-ATAT
6064626 CATCACCATATT
1 CATCACCATA-T
6064638 CCATCACCATAT
1 -CATCACCATAT
6064650 CA
1 CA
6064652 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:6064611 original size:36 final size:36
Alignment explanation
Indices: 6064564--6064668 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
6064554 GATACAATCT
6064564 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6064600 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
6064636 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6064669 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6065367 original size:15 final size:16
Alignment explanation
Indices: 6065347--6065383 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
6065337 CTTCCTGATG
6065347 ATGTATAA-AACATCC
1 ATGTATAATAACATCC
*
6065362 ATGTATAATATCATCC
1 ATGTATAATAACATCC
6065378 ATGTAT
1 ATGTAT
6065384 TGCACTCACC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (16 bp):
ATGTATAATAACATCC
Found at i:6073962 original size:45 final size:45
Alignment explanation
Indices: 6073911--6074112 Score: 361
Period size: 45 Copynumber: 4.5 Consensus size: 45
6073901 CAATTTAATC
*
6073911 CCATAAGCTTGTAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
*
6073956 CCATAAGCTCATAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
6074001 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
* *
6074046 CCATAAACTCGTAAGCTTATTTTACCAACATACTTGCCA-TTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
6074090 CCATAAGCTCGTAAGCTTATTTT
1 CCATAAGCTCGTAAGCTTATTTT
6074113 CATACTTACC
Statistics
Matches: 151, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
44 27 0.18
45 124 0.82
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
Found at i:6081302 original size:45 final size:45
Alignment explanation
Indices: 6081251--6081407 Score: 271
Period size: 45 Copynumber: 3.5 Consensus size: 45
6081241 CAATTTAATC
6081251 CCATAAGCTCATAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCATAAGCTTATTTTACCAACATACTTACCATTTATT
6081296 CCATAAGCTCATAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCATAAGCTTATTTTACCAACATACTTACCATTTATT
* * *
6081341 CCATAAGCTCGTAAGCTTATTTTACCAACAAACTTGCCA-TTATT
1 CCATAAGCTCATAAGCTTATTTTACCAACATACTTACCATTTATT
*
6081385 CCATAAGCTCGTAAGCTTATTTT
1 CCATAAGCTCATAAGCTTATTTT
6081408 CATACTTACC
Statistics
Matches: 109, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
44 28 0.26
45 81 0.74
ACGTcount: A:0.32, C:0.24, G:0.07, T:0.37
Consensus pattern (45 bp):
CCATAAGCTCATAAGCTTATTTTACCAACATACTTACCATTTATT
Found at i:6097386 original size:17 final size:15
Alignment explanation
Indices: 6097364--6097421 Score: 62
Period size: 17 Copynumber: 3.6 Consensus size: 15
6097354 AAATTGGAGT
6097364 ACAAAAAGAAAGAAAA
1 ACAAAAAG-AAGAAAA
6097380 GACAAAAAGAAGAAAA
1 -ACAAAAAGAAGAAAA
*
6097396 TTCAGAAAAGAAGAAAA
1 -ACA-AAAAGAAGAAAA
*
6097413 AGAAAAAGA
1 ACAAAAAGA
6097422 TTTCAAAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.17
16 10 0.28
17 20 0.56
ACGTcount: A:0.74, C:0.05, G:0.17, T:0.03
Consensus pattern (15 bp):
ACAAAAAGAAGAAAA
Found at i:6097412 original size:26 final size:26
Alignment explanation
Indices: 6097374--6097437 Score: 80
Period size: 25 Copynumber: 2.5 Consensus size: 26
6097364 ACAAAAAGAA
*
6097374 AGAAAAGACAAAAAGAAGAAA-A-TTC
1 AGAAAAGAGAAAAAGAA-AAAGATTTC
6097399 AGAAAAGAAGAAAAAGAAAAAGATTTC
1 AGAAAAG-AGAAAAAGAAAAAGATTTC
6097426 A-AAAAGAGAAAA
1 AGAAAAGAGAAAA
6097438 GCAAGCCAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 16 0.46
26 15 0.43
27 4 0.11
ACGTcount: A:0.70, C:0.05, G:0.17, T:0.08
Consensus pattern (26 bp):
AGAAAAGAGAAAAAGAAAAAGATTTC
Found at i:6100292 original size:23 final size:23
Alignment explanation
Indices: 6100264--6100384 Score: 65
Period size: 23 Copynumber: 5.1 Consensus size: 23
6100254 ACAATCTGTC
6100264 CATCACCATTATCA-CGCCTATAT
1 CATCACCATTATCATCGCC-ATAT
*
6100287 CATCACCA-TAGTCCATCTCCAT-T
1 CATCACCATTA-T-CATCGCCATAT
* *
6100310 -ATCACGCCTATATCATCACCATAGT
1 CATCAC-CAT-TATCATCGCCATA-T
*
6100335 CCATCACTATTATCA-CGCCTATAT
1 -CATCACCATTATCATCGCC-ATAT
*
6100359 CATCACCA-TATTCCATCACCATAT
1 CATCACCATTA-T-CATCGCCATAT
6100383 CA
1 CA
6100385 CGCCTATATT
Statistics
Matches: 76, Mismatches: 8, Indels: 27
0.68 0.07 0.24
Matches are distributed among these distances:
22 9 0.12
23 27 0.36
24 17 0.22
25 17 0.22
26 1 0.01
27 5 0.07
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.30
Consensus pattern (23 bp):
CATCACCATTATCATCGCCATAT
Found at i:6100309 original size:36 final size:36
Alignment explanation
Indices: 6100261--6100401 Score: 239
Period size: 36 Copynumber: 3.9 Consensus size: 36
6100251 GATACAATCT
6100261 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
6100297 GTCCATCTCCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
6100333 GTCCATCACTATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
6100369 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6100402 ACTTATAAAT
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.21
36 78 0.79
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6100341 original size:13 final size:11
Alignment explanation
Indices: 6100264--6100384 Score: 68
Period size: 11 Copynumber: 10.2 Consensus size: 11
6100254 ACAATCTGTC
6100264 CATCACCATTAT
1 CATCACCA-TAT
*
6100276 CA-CGCCTATAT
1 CATCACC-ATAT
6100287 CATCACCATAGT
1 CATCACCATA-T
*
6100299 CCATCTCCATTAT
1 -CATCACCA-TAT
*
6100312 CA-CGCCTATAT
1 CATCACC-ATAT
6100323 CATCACCATAGT
1 CATCACCATA-T
*
6100335 CCATCACTATTAT
1 -CATCACCA-TAT
*
6100348 CA-CGCCTATAT
1 CATCACC-ATAT
6100359 CATCACCATATT
1 CATCACCATA-T
6100371 CCATCACCATAT
1 -CATCACCATAT
6100383 CA
1 CA
6100385 CGCCTATATT
Statistics
Matches: 86, Mismatches: 9, Indels: 29
0.69 0.07 0.23
Matches are distributed among these distances:
11 34 0.40
12 22 0.26
13 26 0.30
14 4 0.05
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.30
Consensus pattern (11 bp):
CATCACCATAT
Found at i:6100811 original size:12 final size:11
Alignment explanation
Indices: 6100794--6100829 Score: 54
Period size: 12 Copynumber: 3.1 Consensus size: 11
6100784 CAAAAAAGCA
6100794 AAAAGAAAGAAG
1 AAAAGAAA-AAG
6100806 AAAAGAAAAGAG
1 AAAAGAAAA-AG
6100818 AAAAGAAAAAG
1 AAAAGAAAAAG
6100829 A
1 A
6100830 CTCCTACATC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:6100816 original size:17 final size:17
Alignment explanation
Indices: 6100794--6100826 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6100784 CAAAAAAGCA
6100794 AAAAGA-AAGAAGAAAAG
1 AAAAGAGAA-AAGAAAAG
6100811 AAAAGAGAAAAGAAAA
1 AAAAGAGAAAAGAAAA
6100827 AGACTCCTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAAGAGAAAAGAAAAG
Found at i:6100885 original size:14 final size:15
Alignment explanation
Indices: 6100851--6100897 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
6100841 AATTTGGAGT
6100851 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
6100866 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
6100880 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
6100897 G
1 G
6100898 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:6105620 original size:2 final size:2
Alignment explanation
Indices: 6105604--6105639 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
6105594 TCATAATAAC
*
6105604 TA TA AA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6105640 GATAATAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6111455 original size:15 final size:15
Alignment explanation
Indices: 6111420--6111448 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6111410 GTGCTTCAAC
6111420 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
6111434 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
6111449 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:6111537 original size:12 final size:12
Alignment explanation
Indices: 6111520--6111549 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6111510 GATTTCTTTG
6111520 ACTTTGCACTTC
1 ACTTTGCACTTC
6111532 ACTTTGCACTTC
1 ACTTTGCACTTC
*
6111544 ATTTTG
1 ACTTTG
6111550 TATTTTTCTT
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:0.17, C:0.27, G:0.10, T:0.47
Consensus pattern (12 bp):
ACTTTGCACTTC
Found at i:6118710 original size:20 final size:19
Alignment explanation
Indices: 6118685--6118756 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
6118675 TTGGCTTTGC
6118685 TTTCTTTTTTTTGAAATTCT
1 TTTCTTTTTTTTG-AATTCT
*
6118705 TTTCTTTTTTTATGAATTTT
1 TTTCTTTTTTT-TGAATTCT
6118725 TCTTCTTCTTTTTT--A-TCT
1 T-TTCTT-TTTTTTGAATTCT
6118743 TTTCTTTCTTTTTG
1 TTTCTTT-TTTTTG
6118757 TACTCTAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
16 1 0.02
17 10 0.22
18 3 0.07
19 1 0.02
20 17 0.38
21 8 0.18
22 5 0.11
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTCTTTTTTTTGAATTCT
Found at i:6118715 original size:21 final size:20
Alignment explanation
Indices: 6118685--6118756 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 20
6118675 TTGGCTTTGC
6118685 TTTC-TTTTTTTTGAAATTCT
1 TTTCTTTTTTTTTG-AATTCT
* *
6118705 TTTCTTTTTTTATGAATTTT
1 TTTCTTTTTTTTTGAATTCT
*
6118725 TCTTCTTCTTTTTT--A-TCT
1 T-TTCTTTTTTTTTGAATTCT
*
6118743 TTTCTTTCTTTTTG
1 TTTCTTTTTTTTTG
6118757 TACTCTAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
17 10 0.24
18 3 0.07
19 1 0.02
20 10 0.24
21 18 0.43
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.74
Consensus pattern (20 bp):
TTTCTTTTTTTTTGAATTCT
Found at i:6121397 original size:18 final size:20
Alignment explanation
Indices: 6121376--6121417 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
6121366 AAAGCACTCA
*
6121376 AAAAGGAAAA-AGAAG-AAG
1 AAAAGGAAAATAAAAGAAAG
6121394 AAAA-GAAAATAAAAGAAAG
1 AAAAGGAAAATAAAAGAAAG
6121413 AAAAG
1 AAAAG
6121418 TTGGAAGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 5 0.25
18 8 0.40
19 7 0.35
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AAAAGGAAAATAAAAGAAAG
Found at i:6122690 original size:13 final size:11
Alignment explanation
Indices: 6122665--6122818 Score: 118
Period size: 11 Copynumber: 13.0 Consensus size: 11
6122655 ATTTATAAGT
*
6122665 TGGTGATAATA
1 TGGTGATGATA
6122676 TGGTGATGGAATA
1 TGGTGAT-G-ATA
6122689 TGGTGATGATA
1 TGGTGATGATA
*
6122700 TAGGCG-TGATAA
1 T-GGTGATGAT-A
6122712 TGGTGATGGACTA
1 TGGTGAT-GA-TA
6122725 TGGTGATGATA
1 TGGTGATGATA
6122736 TAGGTG-TGATAA
1 T-GGTGATGAT-A
6122748 TGGTGATGGAATA
1 TGGTGAT-G-ATA
6122761 TGGTGATGATA
1 TGGTGATGATA
*
6122772 TAGGCG-TGATAA
1 T-GGTGATGAT-A
6122784 TGGTGATGGACTA
1 TGGTGAT-GA-TA
6122797 TGGTGATGATA
1 TGGTGATGATA
6122808 TAGGTG-TGATA
1 T-GGTGATGATA
6122819 ATTATGATGG
Statistics
Matches: 120, Mismatches: 5, Indels: 36
0.75 0.03 0.22
Matches are distributed among these distances:
11 48 0.40
12 29 0.24
13 39 0.32
14 4 0.03
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:6122718 original size:23 final size:23
Alignment explanation
Indices: 6122688--6122791 Score: 83
Period size: 23 Copynumber: 4.4 Consensus size: 23
6122678 GTGATGGAAT
6122688 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
*
6122711 ATGGTGATGGACTAT-GGTGATGAT-
1 ATGGTGAT-GA-TATAGGCG-TGATA
*
6122735 ATAGGTG-TGATA-ATG-GTGATGGAA
1 AT-GGTGATGATATAGGCGTGAT---A
6122759 TATGGTGATGATATAGGCGTGATA
1 -ATGGTGATGATATAGGCGTGATA
6122783 ATGGTGATG
1 ATGGTGATG
6122792 GACTATGGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 26
0.69 0.03 0.28
Matches are distributed among these distances:
20 4 0.06
21 1 0.02
22 3 0.05
23 19 0.29
24 13 0.20
25 18 0.28
26 2 0.03
27 5 0.08
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.32
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:6122754 original size:72 final size:72
Alignment explanation
Indices: 6122675--6122829 Score: 292
Period size: 72 Copynumber: 2.2 Consensus size: 72
6122665 TGGTGATAAT
6122675 ATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGG
1 ATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGG
6122740 TGTGATA
66 TGTGATA
6122747 ATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGG
1 ATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGG
6122812 TGTGATA
66 TGTGATA
**
6122819 ATTATGATGGA
1 ATGGTGATGGA
6122830 CAGATTGTAT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 81 1.00
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.32
Consensus pattern (72 bp):
ATGGTGATGGAATATGGTGATGATATAGGCGTGATAATGGTGATGGACTATGGTGATGATATAGG
TGTGATA
Found at i:6122830 original size:36 final size:36
Alignment explanation
Indices: 6122675--6122830 Score: 258
Period size: 36 Copynumber: 4.3 Consensus size: 36
6122665 TGGTGATAAT
*
6122675 ATGGTGATGGAATATGGTGATGATATAGGCGTGATA
1 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
*
6122711 ATGGTGATGGACTATGGTGATGATATAGGTGTGATA
1 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
*
6122747 ATGGTGATGGAATATGGTGATGATATAGGCGTGATA
1 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
*
6122783 ATGGTGATGGACTATGGTGATGATATAGGTGTGATA
1 ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
**
6122819 ATTATGATGGAC
1 ATGGTGATGGAC
6122831 AGATTGTATC
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 112 1.00
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (36 bp):
ATGGTGATGGACTATGGTGATGATATAGGCGTGATA
Found at i:6127254 original size:13 final size:11
Alignment explanation
Indices: 6127236--6127380 Score: 100
Period size: 11 Copynumber: 12.2 Consensus size: 11
6127226 ATAGGCGTGC
6127236 TATGGTGATGGAA
1 TATGGTGAT-G-A
6127249 TATGGTGATGA
1 TATGGTGATGA
*
6127260 TATAGGCG-TGA
1 TAT-GGTGATGA
6127271 TAATGGTGATGGA
1 T-ATGGTGAT-GA
6127284 CTATGGTGATGA
1 -TATGGTGATGA
*
6127296 TATAGGCG-TGA
1 TAT-GGTGATGA
6127307 TAATGGTGATGGAA
1 T-ATGGTGAT-G-A
6127321 TATGGTGATGA
1 TATGGTGATGA
*
6127332 TATAGGCG-TGA
1 TAT-GGTGATGA
6127343 TAATGGTGATGGA
1 T-ATGGTGAT-GA
6127356 CTATGGTGATGA
1 -TATGGTGATGA
6127368 TATAGGTG-TGA
1 TAT-GGTGATGA
6127379 TA
1 TA
6127381 ATTGTGATGG
Statistics
Matches: 110, Mismatches: 6, Indels: 34
0.73 0.04 0.23
Matches are distributed among these distances:
11 40 0.36
12 28 0.25
13 38 0.35
14 4 0.04
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (11 bp):
TATGGTGATGA
Found at i:6127280 original size:23 final size:23
Alignment explanation
Indices: 6127250--6127353 Score: 74
Period size: 23 Copynumber: 4.4 Consensus size: 23
6127240 GTGATGGAAT
6127250 ATGGTGATGATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
*
6127273 ATGGTGATGGACTAT-GGTGATGAT-
1 ATGGTGAT-GA-TATAGGCG-TGATA
* *
6127297 ATAGGCG-TGATA-ATG-GTGATGGAA
1 AT-GGTGATGATATAGGCGTGAT---A
6127321 TATGGTGATGATATAGGCGTGATA
1 -ATGGTGATGATATAGGCGTGATA
6127345 ATGGTGATG
1 ATGGTGATG
6127354 GACTATGGTG
Statistics
Matches: 63, Mismatches: 5, Indels: 26
0.67 0.05 0.28
Matches are distributed among these distances:
20 4 0.06
21 1 0.02
22 3 0.05
23 19 0.30
24 12 0.19
25 17 0.27
26 2 0.03
27 5 0.08
ACGTcount: A:0.29, C:0.04, G:0.37, T:0.31
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:6127289 original size:36 final size:36
Alignment explanation
Indices: 6127216--6127392 Score: 293
Period size: 36 Copynumber: 4.9 Consensus size: 36
6127206 ATTTATAAGT
* * *
6127216 TGGTGATAATATAGGCGTGCT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
6127251 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
6127287 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
6127323 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
* *
6127359 TGGTGATGATATAGGTGTGATAATTGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
6127393 AGATTGTATC
Statistics
Matches: 134, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 19 0.14
36 115 0.86
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:6143884 original size:33 final size:33
Alignment explanation
Indices: 6143804--6143908 Score: 97
Period size: 33 Copynumber: 3.1 Consensus size: 33
6143794 GATACAATCT
* *
6143804 TTCCATCACCATTATCACGCCTATATCATCA-CC
1 TTCCATCACCA-TATCACGCCAATAACATCATCC
6143837 ATATTCCATCACCATATCACGCCAATAACATCATCC
1 ---TTCCATCACCATATCACGCCAATAACATCATCC
* * * *
6143873 TTCCATTACCATTTCATCACCATTAA-ATCATCC
1 TTCCATCACCATATCA-CGCCAATAACATCATCC
6143906 TTC
1 TTC
6143909 ATTCATCAAC
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
33 24 0.39
34 7 0.11
35 17 0.28
36 13 0.21
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.31
Consensus pattern (33 bp):
TTCCATCACCATATCACGCCAATAACATCATCC
Found at i:6148300 original size:33 final size:33
Alignment explanation
Indices: 6148221--6148324 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
6148211 ATACAATCTG
* *
6148221 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
6148257 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
6148290 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
6148323 TC
1 TC
6148325 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:6150268 original size:25 final size:25
Alignment explanation
Indices: 6150234--6150295 Score: 124
Period size: 25 Copynumber: 2.5 Consensus size: 25
6150224 GATATTATAA
6150234 TTATGAATGCATTCTGCCACCTATT
1 TTATGAATGCATTCTGCCACCTATT
6150259 TTATGAATGCATTCTGCCACCTATT
1 TTATGAATGCATTCTGCCACCTATT
6150284 TTATGAATGCAT
1 TTATGAATGCAT
6150296 ATGCATTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (25 bp):
TTATGAATGCATTCTGCCACCTATT
Found at i:6161398 original size:19 final size:21
Alignment explanation
Indices: 6161374--6161425 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
6161364 CGGCTAACAA
*
6161374 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
6161393 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
6161414 CATGTATTTTCA
1 CATGTATTTTCA
6161426 AAGGGGTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:6165336 original size:19 final size:21
Alignment explanation
Indices: 6165312--6165363 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
6165302 CGGCCAAGAG
*
6165312 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
6165331 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
6165352 CATGTATTTTCA
1 CATGTATTTTCA
6165364 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:6196305 original size:36 final size:36
Alignment explanation
Indices: 6196258--6196362 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6196248 GATACAATCT
*
6196258 GTCCATCACCATTATCACGCCTATATCATCACCGTA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6196294 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
6196330 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6196363 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.37, G:0.06, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6197826 original size:10 final size:10
Alignment explanation
Indices: 6197805--6197867 Score: 69
Period size: 10 Copynumber: 6.5 Consensus size: 10
6197795 ATTTTTTTTT
6197805 CAAAAAAA--
1 CAAAAAAAGG
6197813 CAAAAAAAGG
1 CAAAAAAAGG
6197823 CAAAAAAAGG
1 CAAAAAAAGG
*
6197833 CAAAAAAA-A
1 CAAAAAAAGG
6197842 CAAAAAAAGAG
1 CAAAAAAAG-G
* *
6197853 CCAAAAAAGC
1 CAAAAAAAGG
6197863 CAAAA
1 CAAAA
6197868 TTTCAAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
8 8 0.17
9 8 0.17
10 22 0.48
11 8 0.17
ACGTcount: A:0.75, C:0.14, G:0.11, T:0.00
Consensus pattern (10 bp):
CAAAAAAAGG
Found at i:6197846 original size:29 final size:30
Alignment explanation
Indices: 6197806--6197867 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 30
6197796 TTTTTTTTTC
*
6197806 AAAAAAACAAAAAAAG-GCAAAAAAAGGCA
1 AAAAAAACAAAAAAAGAGCAAAAAAAGCCA
*
6197835 AAAAAAACAAAAAAAGAGCCAAAAAAGCCA
1 AAAAAAACAAAAAAAGAGCAAAAAAAGCCA
6197865 AAA
1 AAA
6197868 TTTCAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.76, C:0.13, G:0.11, T:0.00
Consensus pattern (30 bp):
AAAAAAACAAAAAAAGAGCAAAAAAAGCCA
Found at i:6207162 original size:19 final size:20
Alignment explanation
Indices: 6207105--6207154 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
6207095 ATGATGGGTT
*
6207105 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
6207124 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
6207144 TAAG-AATGAAA
1 TAAGTAATGAAA
6207155 TGAAATAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:6207996 original size:25 final size:27
Alignment explanation
Indices: 6207937--6207996 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 27
6207927 TTTTCTTGCT
6207937 TTCTTTT-TGAATTTCTTTTTCTTTTC
1 TTCTTTTCTGAATTTCTTTTTCTTTTC
*
6207963 TTCTATTCTG-ATTT-TTTTTCTTTT-
1 TTCTTTTCTGAATTTCTTTTTCTTTTC
6207987 TGTCTTTTCT
1 T-TCTTTTCT
6207997 TTCTTTTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 1 0.03
25 17 0.57
26 10 0.33
27 2 0.07
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.73
Consensus pattern (27 bp):
TTCTTTTCTGAATTTCTTTTTCTTTTC
Found at i:6209863 original size:19 final size:19
Alignment explanation
Indices: 6209836--6209885 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
6209826 ATGATGGGTT
6209836 TAAGAAATGAATAATAA-T-A
1 TAAG-AATGAA-AATAAGTAA
6209855 TAAGTAATGAAAATAAGTAA
1 TAAG-AATGAAAATAAGTAA
6209875 TAAGAATGAAA
1 TAAGAATGAAA
6209886 TGAAATAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 5 0.18
19 18 0.64
20 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.14, T:0.24
Consensus pattern (19 bp):
TAAGAATGAAAATAAGTAA
Found at i:6210347 original size:19 final size:21
Alignment explanation
Indices: 6210304--6210355 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
6210294 GAAACCCCTT
6210304 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
6210325 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
6210344 TGAAGATACATG
1 TGAAAATACATG
6210356 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:6213823 original size:19 final size:20
Alignment explanation
Indices: 6213766--6213815 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
6213756 ATGATGGGTT
*
6213766 TAAGAAATGAATAAT-AAT-A
1 TAAGTAATGAA-AATAAATAA
6213785 TAAGTAATGAAAATAAATAA
1 TAAGTAATGAAAATAAATAA
6213805 TAAG-AATGAAA
1 TAAGTAATGAAA
6213816 TGAAATAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
TAAGTAATGAAAATAAATAA
Found at i:6214277 original size:19 final size:21
Alignment explanation
Indices: 6214234--6214277 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
6214224 GAAACCTCTT
6214234 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
6214255 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
6214274 TGAA
1 TGAA
6214278 GATATATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.26
20 4 0.17
21 13 0.57
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.34
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:6219154 original size:13 final size:12
Alignment explanation
Indices: 6219135--6219220 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
6219125 ATATGGGCGT
6219135 GATATGGTGATG
1 GATATGGTGATG
6219147 GAATATGGTGAT-
1 G-ATATGGTGATG
*
6219159 GATATAGGCG-T-
1 GATAT-GGTGATG
6219170 GATAATGGTGATG
1 GAT-ATGGTGATG
6219183 GACTATGGTGAT-
1 GA-TATGGTGATG
*
6219195 GATATAGGCG-T-
1 GATAT-GGTGATG
6219206 GATAATGGTGATG
1 GAT-ATGGTGATG
6219219 GA
1 GA
6219221 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:6219190 original size:36 final size:36
Alignment explanation
Indices: 6219117--6219221 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
6219107 ATTTATAAGT
* * *
6219117 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
6219152 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
6219188 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
6219222 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:6221573 original size:19 final size:21
Alignment explanation
Indices: 6221530--6221581 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
6221520 GAAACCCCTT
6221530 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
6221551 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
6221570 TGAAGATACATG
1 TGAAAATACATG
6221582 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:6225667 original size:19 final size:21
Alignment explanation
Indices: 6225624--6225675 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
6225614 GAAACCCCTT
6225624 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
6225645 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
6225664 TGAAGATACATG
1 TGAAAATACATG
6225676 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:6228690 original size:17 final size:17
Alignment explanation
Indices: 6228668--6228702 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
6228658 TAAAGTTCTT
6228668 AAAAGAACTAACTCGAG
1 AAAAGAACTAACTCGAG
6228685 AAAAGAACTAACTCGAG
1 AAAAGAACTAACTCGAG
6228702 A
1 A
6228703 CCTTTCAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.17, G:0.17, T:0.11
Consensus pattern (17 bp):
AAAAGAACTAACTCGAG
Found at i:6231792 original size:13 final size:11
Alignment explanation
Indices: 6231749--6231833 Score: 57
Period size: 11 Copynumber: 7.2 Consensus size: 11
6231739 ACAATCTGTC
6231749 CATCACCATTAT
1 CATCACCA-TAT
*
6231761 CA-CGCCTATAT
1 CATCACC-ATAT
*
6231772 CTTCACCATAGT
1 CATCACCATA-T
6231784 CCATCACCATTAT
1 -CATCACCA-TAT
*
6231797 CA-CGCCTATAT
1 CATCACC-ATAT
6231808 CATCACCATATT
1 CATCACCATA-T
6231820 CCATCACCATAT
1 -CATCACCATAT
6231832 CA
1 CA
6231834 CGCCCATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
11 23 0.40
12 15 0.26
13 18 0.31
14 2 0.03
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:6231793 original size:36 final size:36
Alignment explanation
Indices: 6231746--6231850 Score: 160
Period size: 36 Copynumber: 2.9 Consensus size: 36
6231736 GATACAATCT
6231746 GTCCATCACCATTATCACGCCTATATCTTCACCATA
1 GTCCATCACCATTATCACGCCTATATCTTCACCATA
*
6231782 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCTTCACCATA
* *
6231818 TTCCATCACCA-TATCACGCCCATAT-TATCACCA
1 GTCCATCACCATTATCACGCCTATATCT-TCACCA
6231851 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCTTCACCATA
Found at i:6232317 original size:17 final size:17
Alignment explanation
Indices: 6232297--6232337 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
6232287 AAAAGAAAAG
6232297 AAGAAAATTCAAAGCAA
1 AAGAAAATTCAAAGCAA
6232314 AAGAAAATTCAAAGCAA
1 AAGAAAATTCAAAGCAA
6232331 AAGAAAA
1 AAGAAAA
6232338 AGTGAAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.68, C:0.10, G:0.12, T:0.10
Consensus pattern (17 bp):
AAGAAAATTCAAAGCAA
Found at i:6234162 original size:13 final size:11
Alignment explanation
Indices: 6234121--6234205 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
6234111 ACAATTTGTC
6234121 CATCACCATTAT
1 CATCACCA-TAT
*
6234133 CATGC-CTATAT
1 CAT-CACCATAT
6234144 CATCACCATAGT
1 CATCACCATA-T
6234156 CCATCACCATTAT
1 -CATCACCA-TAT
*
6234169 CA-CGCCTATAT
1 CATCACC-ATAT
6234180 CATCACCATATT
1 CATCACCATA-T
6234192 CCATCACCATAT
1 -CATCACCATAT
6234204 CA
1 CA
6234206 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.02
11 23 0.38
12 14 0.23
13 20 0.33
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:6234165 original size:36 final size:36
Alignment explanation
Indices: 6234118--6234222 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6234108 GATACAATTT
*
6234118 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6234154 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
6234190 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6234223 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6234701 original size:14 final size:15
Alignment explanation
Indices: 6234667--6234713 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
6234657 AATTTTGAGT
6234667 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
6234682 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
6234696 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
6234713 G
1 G
6234714 TGAAGCAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:6239873 original size:36 final size:36
Alignment explanation
Indices: 6239826--6239994 Score: 295
Period size: 36 Copynumber: 4.7 Consensus size: 36
6239816 GATACAATCT
6239826 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
6239862 GTCCATCACCATTATAACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
6239898 TTCCATCACCATTATCACGCCTATATCATTACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6239934 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
6239970 TTCCATCACCA-TATCACGCCTATAT
1 GTCCATCACCATTATCACGCCTATAT
6239995 TGTCACCAAC
Statistics
Matches: 126, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 14 0.11
36 112 0.89
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6239906 original size:13 final size:12
Alignment explanation
Indices: 6239887--6239983 Score: 53
Period size: 13 Copynumber: 8.0 Consensus size: 12
6239877 AACGCCTATA
6239887 TCATCACCATAT
1 TCATCACCATAT
6239899 TCCATCACC--AT
1 T-CATCACCATAT
*
6239910 T-ATCACGCCTAT
1 TCATCAC-CATAT
*
6239922 ATCATTACCATAGT
1 -TCATCACCATA-T
*
6239936 CCATCACC--AT
1 TCATCACCATAT
*
6239946 T-ATCACGCCTAT
1 TCATCAC-CATAT
6239958 ATCATCACCATAT
1 -TCATCACCATAT
6239971 TCCATCACCATAT
1 T-CATCACCATAT
6239984 CACGCCTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 25
0.68 0.06 0.26
Matches are distributed among these distances:
9 10 0.15
10 3 0.05
11 4 0.06
12 6 0.09
13 33 0.50
14 10 0.15
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.31
Consensus pattern (12 bp):
TCATCACCATAT
Found at i:6245095 original size:36 final size:36
Alignment explanation
Indices: 6245048--6245152 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6245038 GATACAATCT
6245048 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6245084 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
6245120 TTCTATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6245153 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6248322 original size:24 final size:24
Alignment explanation
Indices: 6248294--6248348 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
6248284 TGATGCCAAG
6248294 TCACGCCTAAGTTGCTGTTCATCT
1 TCACGCCTAAGTTGCTGTTCATCT
*
6248318 TCACGCCTAAGTTGTTGTTCATCT
1 TCACGCCTAAGTTGCTGTTCATCT
6248342 TCACGCC
1 TCACGCC
6248349 ATGGAGGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.31, G:0.16, T:0.36
Consensus pattern (24 bp):
TCACGCCTAAGTTGCTGTTCATCT
Found at i:6248955 original size:36 final size:36
Alignment explanation
Indices: 6248908--6249012 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6248898 GATACAATCT
6248908 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6248944 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
6248980 TTCTATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6249013 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6252184 original size:24 final size:24
Alignment explanation
Indices: 6252156--6252210 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
6252146 TGATGCCAAG
6252156 TCACGCCTAAGTTGCTGTTCATCT
1 TCACGCCTAAGTTGCTGTTCATCT
*
6252180 TCACGCCTAAGTTGTTGTTCATCT
1 TCACGCCTAAGTTGCTGTTCATCT
6252204 TCACGCC
1 TCACGCC
6252211 ATGGAGGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.31, G:0.16, T:0.36
Consensus pattern (24 bp):
TCACGCCTAAGTTGCTGTTCATCT
Found at i:6252817 original size:36 final size:36
Alignment explanation
Indices: 6252770--6252874 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6252760 GATACAATCT
6252770 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6252806 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
6252842 TTCTATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6252875 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6256044 original size:24 final size:24
Alignment explanation
Indices: 6256016--6256070 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
6256006 TGATGCCAAG
6256016 TCACGCCTAAGTTGCTGTTCATCT
1 TCACGCCTAAGTTGCTGTTCATCT
*
6256040 TCACGCCTAAGTTGTTGTTCATCT
1 TCACGCCTAAGTTGCTGTTCATCT
6256064 TCACGCC
1 TCACGCC
6256071 ATGGAGGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.31, G:0.16, T:0.36
Consensus pattern (24 bp):
TCACGCCTAAGTTGCTGTTCATCT
Found at i:6256674 original size:36 final size:36
Alignment explanation
Indices: 6256627--6256731 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6256617 GATACAATCT
6256627 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6256663 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
6256699 TTCTATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6256732 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6259901 original size:24 final size:24
Alignment explanation
Indices: 6259873--6259927 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
6259863 TGATGCCAAG
6259873 TCACGCCTAAGTTGTTGTTCATCT
1 TCACGCCTAAGTTGTTGTTCATCT
6259897 TCACGCCTAAGTTGTTGTTCATCT
1 TCACGCCTAAGTTGTTGTTCATCT
6259921 TCACGCC
1 TCACGCC
6259928 ATGGAGGAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.16, T:0.38
Consensus pattern (24 bp):
TCACGCCTAAGTTGTTGTTCATCT
Found at i:6260534 original size:36 final size:36
Alignment explanation
Indices: 6260487--6260591 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6260477 GATACAATCT
6260487 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6260523 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
6260559 TTCTATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6260592 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6263758 original size:24 final size:24
Alignment explanation
Indices: 6263730--6263784 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
6263720 TGATGCCAAG
6263730 TCACGCCTAAGTTGCTGTTCATCT
1 TCACGCCTAAGTTGCTGTTCATCT
*
6263754 TCACGCCTAAGTTGTTGTTCATCT
1 TCACGCCTAAGTTGCTGTTCATCT
6263778 TCACGCC
1 TCACGCC
6263785 ATGGAGGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.31, G:0.16, T:0.36
Consensus pattern (24 bp):
TCACGCCTAAGTTGCTGTTCATCT
Found at i:6264391 original size:36 final size:36
Alignment explanation
Indices: 6264344--6264448 Score: 167
Period size: 36 Copynumber: 2.9 Consensus size: 36
6264334 GATACAATCT
6264344 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6264380 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
6264416 TTCTATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6264449 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6267612 original size:24 final size:24
Alignment explanation
Indices: 6267584--6267638 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
6267574 TGATGCCAAG
6267584 TCACGCCTAAGTTGCTGTTCATCT
1 TCACGCCTAAGTTGCTGTTCATCT
*
6267608 TCACGCCTAAGTTGTTGTTCATCT
1 TCACGCCTAAGTTGCTGTTCATCT
6267632 TCACGCC
1 TCACGCC
6267639 ATGGAGGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.31, G:0.16, T:0.36
Consensus pattern (24 bp):
TCACGCCTAAGTTGCTGTTCATCT
Found at i:6268239 original size:13 final size:11
Alignment explanation
Indices: 6268198--6268282 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
6268188 ATAATATGTC
6268198 CATCACCATTAT
1 CATCACCA-TAT
*
6268210 CA-CGCCTATAT
1 CATCACC-ATAT
6268221 CATCACCATAGT
1 CATCACCATA-T
6268233 CCATCACCATTAT
1 -CATCACCA-TAT
*
6268246 CA-CGCCTATAT
1 CATCACC-ATAT
6268257 CATCACCATATT
1 CATCACCATA-T
6268269 CCATCACCATAT
1 -CATCACCATAT
6268281 CA
1 CA
6268283 CGCCCATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:6268242 original size:36 final size:36
Alignment explanation
Indices: 6268195--6268299 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
6268185 GATATAATAT
6268195 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6268231 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
6268267 TTCCATCACCA-TATCACGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6268300 ACTTATAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.30, C:0.37, G:0.05, T:0.28
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6272109 original size:13 final size:11
Alignment explanation
Indices: 6272087--6272169 Score: 71
Period size: 11 Copynumber: 7.1 Consensus size: 11
6272077 TATCACGCCT
6272087 ATATCATCACC
1 ATATCATCACC
6272098 ATAGTCCATCACC
1 ATA-T-CATCACC
*
6272111 ATTATCA-CGCC
1 A-TATCATCACC
6272122 TATATCATCACC
1 -ATATCATCACC
6272134 ATATTCCATCACC
1 ATA-T-CATCACC
6272147 ATATCATGC-CC
1 ATATCAT-CACC
*
6272158 ATATTATCACC
1 ATATCATCACC
6272169 A
1 A
6272170 ACTTATAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
10 1 0.02
11 28 0.47
12 10 0.17
13 19 0.32
14 2 0.03
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:6272117 original size:36 final size:36
Alignment explanation
Indices: 6272065--6272169 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
6272055 GATACAATCT
*
6272065 GTCCGTCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
6272101 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * * *
6272137 TTCCATCACCA-TATCATGCCCATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
6272170 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 19 0.30
36 45 0.70
ACGTcount: A:0.30, C:0.36, G:0.06, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:6272159 original size:24 final size:22
Alignment explanation
Indices: 6272070--6272169 Score: 64
Period size: 24 Copynumber: 4.3 Consensus size: 22
6272060 AATCTGTCCG
* *
6272070 TCACCATTATCA-CGCCTATATCA
1 TCACCA-TATCATCACC-ATATTA
6272093 TCACCATAGTCCATCACC--ATTA
1 TCACCATA-T-CATCACCATATTA
6272115 TCACGCCTATATCATCACCATATTCCA
1 TCA--CC-ATATCATCACCATATT--A
6272142 TCACCATATCATGC-CCATATTA
1 TCACCATATCAT-CACCATATTA
6272164 TCACCA
1 TCACCA
6272170 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 23
0.72 0.02 0.26
Matches are distributed among these distances:
22 15 0.23
23 14 0.22
24 19 0.30
25 12 0.19
27 4 0.06
ACGTcount: A:0.31, C:0.36, G:0.04, T:0.29
Consensus pattern (22 bp):
TCACCATATCATCACCATATTA
Found at i:6280856 original size:22 final size:19
Alignment explanation
Indices: 6280828--6280873 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
6280818 GTGATACAAC
*
6280828 AAAAAAAGCAACAAGAAAGAAG
1 AAAAAAA-CAAAAAG-AA-AAG
6280850 AAAAAAACAAAAAGAAAAG
1 AAAAAAACAAAAAGAAAAG
6280869 AAAAA
1 AAAAA
6280874 GACTCATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 2 0.09
21 6 0.26
22 7 0.30
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAGAAAAG
Found at i:6296386 original size:10 final size:10
Alignment explanation
Indices: 6296373--6296428 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
6296363 TTTTTTGAAA
6296373 TTTTGGCTTTT
1 TTTTGG-TTTT
*
6296384 TTTTGTTTTT
1 TTTTGGTTTT
*
6296394 TTTTGCCTTTT
1 TTTTG-GTTTT
6296405 TTTT-GTTTT
1 TTTTGGTTTT
*
6296414 TTTTTGTTTT
1 TTTTGGTTTT
6296424 TTTTG
1 TTTTG
6296429 AAAAAAATAG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
9 8 0.21
10 18 0.46
11 13 0.33
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.82
Consensus pattern (10 bp):
TTTTGGTTTT
Found at i:6296397 original size:21 final size:21
Alignment explanation
Indices: 6296373--6296428 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
6296363 TTTTTTGAAA
6296373 TTTTGGCTTTTTTTTGTTTTT
1 TTTTGGCTTTTTTTTGTTTTT
*
6296394 TTTTGCCTTTTTTTTGTTTTT
1 TTTTGGCTTTTTTTTGTTTTT
6296415 TTTT-G-TTTTTTTTG
1 TTTTGGCTTTTTTTTG
6296429 AAAAAAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.27
21 24 0.73
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.82
Consensus pattern (21 bp):
TTTTGGCTTTTTTTTGTTTTT
Found at i:6296636 original size:50 final size:50
Alignment explanation
Indices: 6296561--6296657 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
6296551 GAACAAGCAA
* * *
6296561 GATAATATGGCTCTATCGAGCCCTCCTAGTCGCAATGAAAAGGCAAACAC
1 GATAATATGGCTCTAACCAACCCTCCTAGTCGCAATGAAAAGGCAAACAC
*
6296611 GATAATATGGCTCTAACCAACCCTCCTAGTCGCGATGAAAAGGCAAA
1 GATAATATGGCTCTAACCAACCCTCCTAGTCGCAATGAAAAGGCAAA
6296658 TTGGAGTGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (50 bp):
GATAATATGGCTCTAACCAACCCTCCTAGTCGCAATGAAAAGGCAAACAC
Found at i:6306871 original size:23 final size:25
Alignment explanation
Indices: 6306845--6306899 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
6306835 AAATCCAGCA
6306845 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACTCAAAGAGG
* *
6306868 AAGAAATTGAAAGCACTCAAAGAGG
1 AAGAAAATCAAAGCACTCAAAGAGG
6306893 AAGAAAA
1 AAGAAAA
6306900 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 1 0.04
25 7 0.26
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGG
Found at i:6313840 original size:18 final size:18
Alignment explanation
Indices: 6313819--6313859 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6313809 TTTTTTGAAA
*
6313819 TTTTAGCTTTTTTGGCTT
1 TTTTAGCTTTTTTGCCTT
* *
6313837 TTTTTGTTTTTTTGCCTT
1 TTTTAGCTTTTTTGCCTT
6313855 TTTTA
1 TTTTA
6313860 TTGTTTTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.10, G:0.12, T:0.73
Consensus pattern (18 bp):
TTTTAGCTTTTTTGCCTT
Found at i:6313846 original size:8 final size:8
Alignment explanation
Indices: 6313835--6313877 Score: 50
Period size: 8 Copynumber: 4.9 Consensus size: 8
6313825 CTTTTTTGGC
6313835 TTTTTTTG
1 TTTTTTTG
6313843 TTTTTTTG
1 TTTTTTTG
6313851 CCTTTTTTATTG
1 ---TTTTT-TTG
6313863 TTTTTTTG
1 TTTTTTTG
6313871 TTTTTTT
1 TTTTTTT
6313878 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 18 0.58
9 5 0.16
11 5 0.16
12 3 0.10
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:6313858 original size:20 final size:18
Alignment explanation
Indices: 6313835--6313879 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
6313825 CTTTTTTGGC
6313835 TTTTTTTGTTTTTTTGCCTT
1 TTTTTTTGTTTTTTTG--TT
*
6313855 TTTTATTGTTTTTTTGTT
1 TTTTTTTGTTTTTTTGTT
6313873 TTTTTTT
1 TTTTTTT
6313880 TAAAAATAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.84
Consensus pattern (18 bp):
TTTTTTTGTTTTTTTGTT
Found at i:6317417 original size:22 final size:23
Alignment explanation
Indices: 6317373--6317418 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
6317363 AAATCCAGCA
6317373 AAGAAAATCAAAGCACTCTAAAG
1 AAGAAAATCAAAGCACTCTAAAG
* *
6317396 AAGAAATTGAAAGCACTC-AAAG
1 AAGAAAATCAAAGCACTCTAAAG
6317418 A
1 A
6317419 GGAAGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.13
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCTAAAG
Found at i:6321703 original size:23 final size:25
Alignment explanation
Indices: 6321677--6321731 Score: 78
Period size: 23 Copynumber: 2.3 Consensus size: 25
6321667 AAATCCAGCA
6321677 AAGAAAATCAAAGCACTCAAA-A-G
1 AAGAAAATCAAAGCACTCAAAGAGG
* *
6321700 AAGAAATTGAAAGCACTCAAAGAGG
1 AAGAAAATCAAAGCACTCAAAGAGG
6321725 AAGAAAA
1 AAGAAAA
6321732 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 19 0.70
24 1 0.04
25 7 0.26
ACGTcount: A:0.60, C:0.13, G:0.18, T:0.09
Consensus pattern (25 bp):
AAGAAAATCAAAGCACTCAAAGAGG
Found at i:6331875 original size:15 final size:16
Alignment explanation
Indices: 6331844--6331880 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
6331834 TTTGATTATC
6331844 TTATTTCATCTTCTGT
1 TTATTTCATCTTCTGT
*
6331860 TTATTT-ATCTTTTGT
1 TTATTTCATCTTCTGT
6331875 TTATTT
1 TTATTT
6331881 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTCTGT
Found at i:6332246 original size:8 final size:8
Alignment explanation
Indices: 6332233--6332295 Score: 69
Period size: 8 Copynumber: 8.0 Consensus size: 8
6332223 TTTTTATTTT
6332233 CAAAAAAA
1 CAAAAAAA
6332241 CAAAAAAA
1 CAAAAAAA
6332249 C-AAAAAA
1 CAAAAAAA
6332256 CAAAAAAA
1 CAAAAAAA
6332264 GGC-AAAAAA
1 --CAAAAAAA
**
6332273 -AAAAAGG
1 CAAAAAAA
6332280 CAAAAAAA
1 CAAAAAAA
6332288 CAAAAAAA
1 CAAAAAAA
6332296 GAGCCAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
7 11 0.24
8 28 0.61
9 6 0.13
10 1 0.02
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:6332273 original size:13 final size:14
Alignment explanation
Indices: 6332252--6332292 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
6332242 AAAAAAACAA
6332252 AAAACAAAAAAAGGC
1 AAAA-AAAAAAAGGC
6332267 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
6332281 AAAAAAACAAAA
1 AAAAAAA-AAAA
6332293 AAAGAGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:6332313 original size:20 final size:20
Alignment explanation
Indices: 6332269--6332306 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6332259 AAAAAGGCAA
*
6332269 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
6332289 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
6332307 GCCAAAATTT
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:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:6339509 original size:23 final size:23
Alignment explanation
Indices: 6339410--6339513 Score: 65
Period size: 23 Copynumber: 4.4 Consensus size: 23
6339400 GTGATGGCCT
*
6339410 ATGGTGATTATATAGGCGTGATA
1 ATGGTGATGATATAGGCGTGATA
*
6339433 ATGGTGATGGA-ATATGGTGGTGAT-
1 ATGGTGAT-GATATA-GG-CGTGATA
* *
6339457 ATAGGCG-TGATA-ATG-GTGATGGA
1 AT-GGTGATGATATAGGCGTGAT--A
6339480 CTATGGTGATGATATAGGCGTGATA
1 --ATGGTGATGATATAGGCGTGATA
6339505 ATGGTGATG
1 ATGGTGATG
6339514 GACAGATTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 26
0.66 0.06 0.28
Matches are distributed among these distances:
20 5 0.08
22 1 0.02
23 23 0.37
24 10 0.16
25 16 0.26
26 2 0.03
27 5 0.08
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.32
Consensus pattern (23 bp):
ATGGTGATGATATAGGCGTGATA
Found at i:6339516 original size:36 final size:36
Alignment explanation
Indices: 6339348--6339516 Score: 286
Period size: 36 Copynumber: 4.7 Consensus size: 36
6339338 GTTGGTGACA
*
6339348 ATATAGGCGTGAT-ATGGTGATGGAATATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
* *
6339383 ATATAGGCGTGATAATGGTGATGGCCTATGGTGATT
1 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
* *
6339419 ATATAGGCGTGATAATGGTGATGGAATATGGTGGTG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
6339455 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
6339491 ATATAGGCGTGATAATGGTGATGGAC
1 ATATAGGCGTGATAATGGTGATGGAC
6339517 AGATTGTATC
Statistics
Matches: 124, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
35 13 0.10
36 111 0.90
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (36 bp):
ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
Found at i:6352895 original size:22 final size:23
Alignment explanation
Indices: 6352859--6352902 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
6352849 TTTTTTTCCT
6352859 TTTTCAGTGCTTTCAATTTCTTC
1 TTTTCAGTGCTTTCAATTTCTTC
*
6352882 TTTTGAGTGC-TTCAATTTCTT
1 TTTTCAGTGCTTTCAATTTCTT
6352903 TGCTGATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.14, C:0.18, G:0.11, T:0.57
Consensus pattern (23 bp):
TTTTCAGTGCTTTCAATTTCTTC
Found at i:6354697 original size:15 final size:15
Alignment explanation
Indices: 6354677--6354711 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
6354667 TCAAGCAAGT
6354677 TTGTGAAGACCGAGA
1 TTGTGAAGACCGAGA
6354692 TTGTGAAGACCGAGA
1 TTGTGAAGACCGAGA
6354707 TTGTG
1 TTGTG
6354712 CTTCATAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (15 bp):
TTGTGAAGACCGAGA
Found at i:6354853 original size:19 final size:20
Alignment explanation
Indices: 6354829--6354868 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
6354819 TATCCTTTCT
6354829 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
6354848 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
6354868 T
1 T
6354869 ATTATTACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:6355169 original size:8 final size:8
Alignment explanation
Indices: 6355158--6355182 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6355148 GAGAAAAATC
6355158 AGAAAAGA
1 AGAAAAGA
6355166 AGAAAAGA
1 AGAAAAGA
6355174 AGAAAAGA
1 AGAAAAGA
6355182 A
1 A
6355183 AAGAAAAATA
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:6355180 original size:35 final size:35
Alignment explanation
Indices: 6355124--6355195 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
6355114 TTGGAGTGCA
*
6355124 AAAAGAAAGAAAAAGACAAAAGAAGAGAAAAATCAG
1 AAAAGAAAGAAAAAGACAAAAGAAAAGAAAAAT-AG
*
6355160 AAAAG-AAG-AAAAGAAGAAAAGAAAAGAAAAATAG
1 AAAAGAAAGAAAAAG-ACAAAAGAAAAGAAAAATAG
6355194 AA
1 AA
6355196 GTTCAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 9 0.27
35 19 0.58
36 5 0.15
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (35 bp):
AAAAGAAAGAAAAAGACAAAAGAAAAGAAAAATAG
Found at i:6355181 original size:13 final size:12
Alignment explanation
Indices: 6355123--6355195 Score: 51
Period size: 13 Copynumber: 5.7 Consensus size: 12
6355113 ATTGGAGTGC
6355123 AAAAAG-AAAGA
1 AAAAAGAAAAGA
*
6355134 AAAAGACAAAAGA
1 AAAA-AGAAAAGA
*
6355147 AGAGAAA-AATCAGA
1 A-A-AAAGAA-AAGA
6355161 AAAGAAGAAAAGA
1 AAA-AAGAAAAGA
6355174 AGAAAAGAAAAGA
1 A-AAAAGAAAAGA
6355187 AAAATAGAA
1 AAAA-AGAA
6355196 GTTCAAAAAG
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
11 4 0.08
12 5 0.10
13 29 0.58
14 10 0.20
15 2 0.04
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:6355190 original size:27 final size:26
Alignment explanation
Indices: 6355124--6355190 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 26
6355114 TTGGAGTGCA
6355124 AAAAG-AAAGAAAAAGACAAAAGAAG
1 AAAAGAAAAGAAAAAGACAAAAGAAG
* *
6355149 AGAAA-AATCAG-AAAAGAAGAAAAGAAG
1 A-AAAGAA-AAGAAAAAG-ACAAAAGAAG
6355176 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
6355191 TAGAAGTTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
25 1 0.03
26 14 0.42
27 18 0.55
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.01
Consensus pattern (26 bp):
AAAAGAAAAGAAAAAGACAAAAGAAG
Found at i:6364098 original size:11 final size:11
Alignment explanation
Indices: 6364082--6364141 Score: 77
Period size: 11 Copynumber: 5.5 Consensus size: 11
6364072 TTGCTATTTT
6364082 AAAAAAAACAA
1 AAAAAAAACAA
6364093 AAAAAAAAC-A
1 AAAAAAAACAA
**
6364103 AAAAAATGCAA
1 AAAAAAAACAA
*
6364114 AAAAAAAGGCAA
1 AAAAAAA-ACAA
6364126 AAAAAAAACAA
1 AAAAAAAACAA
6364137 AAAAA
1 AAAAA
6364142 GCAAAATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 8 0.19
11 24 0.56
12 11 0.26
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.02
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:6364127 original size:33 final size:30
Alignment explanation
Indices: 6364082--6364147 Score: 105
Period size: 33 Copynumber: 2.1 Consensus size: 30
6364072 TTGCTATTTT
6364082 AAAAAAAACAAAAAAAAAACAAAAAAATGCA
1 AAAAAAAACAAAAAAAAAACAAAAAAA-GCA
6364113 AAAAAAAAGGCAAAAAAAAAACAAAAAAAGCA
1 AAAAAAAA--CAAAAAAAAAACAAAAAAAGCA
6364145 AAA
1 AAA
6364148 TTTTCAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
31 8 0.24
32 6 0.18
33 19 0.58
ACGTcount: A:0.83, C:0.09, G:0.06, T:0.02
Consensus pattern (30 bp):
AAAAAAAACAAAAAAAAAACAAAAAAAGCA
Found at i:6368809 original size:1 final size:1
Alignment explanation
Indices: 6368803--6368863 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
6368793 TTTGCTATTT
* * * * *** *
6368803 AAAAAAAAACAAAAAAAAACAAAAAAAAGACAAAAAAAAGGCAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6368864 GCCAAAATTT
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:6368869 original size:11 final size:11
Alignment explanation
Indices: 6368803--6368870 Score: 95
Period size: 11 Copynumber: 6.4 Consensus size: 11
6368793 TTTGCTATTT
6368803 AAAAAAAA-AC
1 AAAAAAAAGAC
6368813 AAAAAAAA-AC
1 AAAAAAAAGAC
6368823 AAAAAAAAGAC
1 AAAAAAAAGAC
*
6368834 AAAAAAAAGGC
1 AAAAAAAAGAC
*
6368845 AAAAAAAAAAC
1 AAAAAAAAGAC
*
6368856 AAAAAAAAGCC
1 AAAAAAAAGAC
6368867 AAAA
1 AAAA
6368871 TTTCAAACGA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
10 18 0.35
11 34 0.65
ACGTcount: A:0.84, C:0.10, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAC
Found at i:6368870 original size:10 final size:10
Alignment explanation
Indices: 6368803--6368863 Score: 86
Period size: 10 Copynumber: 5.8 Consensus size: 10
6368793 TTTGCTATTT
6368803 AAAAAAAAAC
1 AAAAAAAAAC
6368813 AAAAAAAAAC
1 AAAAAAAAAC
6368823 AAAAAAAAGAC
1 AAAAAAAA-AC
*
6368834 AAAAAAAAGGC
1 AAAAAAAA-AC
6368845 AAAAAAAAAAC
1 -AAAAAAAAAC
6368856 AAAAAAAA
1 AAAAAAAA
6368864 GCCAAAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
10 26 0.55
11 13 0.28
12 8 0.17
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:6373459 original size:13 final size:13
Alignment explanation
Indices: 6373441--6373474 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
6373431 GATGATGGTC
6373441 TTGATGAAGGATG
1 TTGATGAAGGATG
*
6373454 TTGATGATGGATG
1 TTGATGAAGGATG
*
6373467 ATGATGAA
1 TTGATGAA
6373475 ATGGCAATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:6378846 original size:11 final size:13
Alignment explanation
Indices: 6378814--6378843 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
6378804 TGGCCAAAGA
6378814 TGAAAAGGTATGT
1 TGAAAAGGTATGT
6378827 TGAAAAGGTATG-
1 TGAAAAGGTATGT
6378839 TGAAA
1 TGAAA
6378844 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:6384106 original size:22 final size:20
Alignment explanation
Indices: 6384081--6384120 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6384071 ATGTTTGTTT
6384081 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
6384103 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
6384121 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:6385475 original size:13 final size:13
Alignment explanation
Indices: 6385453--6385482 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
6385443 ACTAAACACC
6385453 TTTC-ACATACCT
1 TTTCAACATACCT
6385465 TTTCAACATACCT
1 TTTCAACATACCT
6385478 TTTCA
1 TTTCA
6385483 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:6389659 original size:22 final size:20
Alignment explanation
Indices: 6389634--6389673 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
6389624 ATGTTTGTTT
6389634 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
6389656 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
6389674 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Done.