Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 7 of 130
Found at i:1830182 original size:30 final size:30
Alignment explanation
Indices: 1830146--1830206 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1830136 TCTTGAATTG
1830146 TCTGATTGATTCATTGCTTGTTATATGTTC
1 TCTGATTGATTCATTGCTTGTTATATGTTC
1830176 TCTGATTGATTCATTGCTTGTTATATGTTC
1 TCTGATTGATTCATTGCTTGTTATATGTTC
1830206 T
1 T
1830207 AGATATCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.54
Consensus pattern (30 bp):
TCTGATTGATTCATTGCTTGTTATATGTTC
Found at i:1838522 original size:12 final size:12
Alignment explanation
Indices: 1838505--1838532 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1838495 AATATTATAT
1838505 TTATATAATTAA
1 TTATATAATTAA
1838517 TTATATAATTAA
1 TTATATAATTAA
1838529 TTAT
1 TTAT
1838533 TATATCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTATATAATTAA
Found at i:1838969 original size:18 final size:18
Alignment explanation
Indices: 1838946--1839005 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 18
1838936 TATTTATAAG
1838946 ATATTTTTAATATAAATT
1 ATATTTTTAATATAAATT
1838964 ATATTTTAATTATATATAAATAT
1 ATA-TTT--TTA-ATATAAAT-T
1838987 AATATTTTT-AT-TAAATT
1 -ATATTTTTAATATAAATT
1839004 AT
1 AT
1839006 TATGTAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
16 2 0.06
17 1 0.03
18 8 0.22
19 5 0.14
21 5 0.14
22 8 0.22
23 4 0.11
24 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATATTTTTAATATAAATT
Found at i:1838999 original size:24 final size:22
Alignment explanation
Indices: 1838955--1838999 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
1838945 GATATTTTTA
1838955 ATATAAATTATATTTTAATTAT
1 ATATAAATTATATTTTAATTAT
*
1838977 ATATAAATATAATATTTTTATTA
1 ATATAAAT-T-ATATTTTAATTA
1839000 AATTATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 1 0.05
24 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATAAATTATATTTTAATTAT
Found at i:1839037 original size:24 final size:24
Alignment explanation
Indices: 1838977--1839037 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
1838967 TTTTAATTAT
* *
1838977 ATATAA-ATATAATATTTTTATTA
1 ATATAATATATAATAATTTTATGA
* *
1839000 A-ATTATTATGTAATAATTTTATGA
1 ATA-TAATATATAATAATTTTATGA
1839024 ATATAATATATAAT
1 ATATAATATATAAT
1839038 TAAATAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
22 1 0.03
23 3 0.10
24 24 0.83
25 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (24 bp):
ATATAATATATAATAATTTTATGA
Found at i:1841887 original size:28 final size:28
Alignment explanation
Indices: 1841856--1841912 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
1841846 GTACTTTAAC
*
1841856 TACTGTGAAAGCTACTATAAAGAAAACT
1 TACTGCGAAAGCTACTATAAAGAAAACT
*
1841884 TACTGCGAAAGCTATTATAAAGAAAACT
1 TACTGCGAAAGCTACTATAAAGAAAACT
1841912 T
1 T
1841913 GCCTGAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (28 bp):
TACTGCGAAAGCTACTATAAAGAAAACT
Found at i:1842384 original size:2 final size:2
Alignment explanation
Indices: 1842379--1842418 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1842369 ACCAAAGTTT
1842379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1842419 GGGTTCAGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1849082 original size:9 final size:10
Alignment explanation
Indices: 1849052--1849085 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1849042 ATAATTATTT
1849052 TATATTTAAA
1 TATATTTAAA
1849062 TATATTTAAA
1 TATATTTAAA
1849072 -ATATATTAAA
1 TATAT-TTAAA
1849082 TATA
1 TATA
1849086 ACATTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.18
10 15 0.68
11 3 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TATATTTAAA
Found at i:1851004 original size:30 final size:29
Alignment explanation
Indices: 1850929--1851015 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 29
1850919 ATTTGAATTA
*
1850929 TTTTATATTTTAAAATAAAATTTTA-TATCT
1 TTTTATA-TTT-AAATAAAATTTTATTTTCT
* * * *
1850959 TATTGTATCTAAATAAAATTTTATTTTTT
1 TTTTATATTTAAATAAAATTTTATTTTCT
1850988 GTTTTATATTTAAAT-AAATATTTATTTT
1 -TTTTATATTTAAATAAAAT-TTTATTTT
1851016 AAATAAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
28 13 0.28
29 9 0.20
30 24 0.52
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (29 bp):
TTTTATATTTAAATAAAATTTTATTTTCT
Found at i:1851092 original size:30 final size:29
Alignment explanation
Indices: 1851043--1851111 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 29
1851033 TATGGTAATG
* * *
1851043 ATTTATTTATGTAAAATTAAAGGTTAAAT
1 ATTTATTTAAGCAAAATTAAAGGTTAAAA
*
1851072 ATTTATTTAAGCATAAATTAAAGTTTAAAA
1 ATTTATTTAAGCA-AAATTAAAGGTTAAAA
1851102 ATTTATTTAA
1 ATTTATTTAA
1851112 ATGTAATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 11 0.31
30 24 0.69
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.45
Consensus pattern (29 bp):
ATTTATTTAAGCAAAATTAAAGGTTAAAA
Found at i:1862955 original size:23 final size:22
Alignment explanation
Indices: 1862911--1862951 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1862901 TTATTTTTAT
*
1862911 AAAAAATTATAATATAAAATTA
1 AAAAAATTATAACATAAAATTA
1862933 AAAAAATT-TAACATAAAAT
1 AAAAAATTATAACATAAAAT
1862952 ATTATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAATTATAACATAAAATTA
Found at i:1864010 original size:23 final size:24
Alignment explanation
Indices: 1863967--1864035 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 24
1863957 AATTATAATC
*
1863967 ATAATCAAGT-ATTACAT-ATTTAA
1 ATAATCAA-TAATTATATGATTTAA
*
1863990 ATAATCAATTAATT-TA-GATTTGA
1 ATAATCAA-TAATTATATGATTTAA
*
1864013 TTAATCAATAATTATATGATTTA
1 ATAATCAATAATTATATGATTTA
1864036 TTAATAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 5 0.14
23 24 0.65
24 8 0.22
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (24 bp):
ATAATCAATAATTATATGATTTAA
Found at i:1864038 original size:23 final size:23
Alignment explanation
Indices: 1863991--1864040 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1863981 CATATTTAAA
1863991 TAATCAATTAATTTAGATTTGAT
1 TAATCAATTAATTTAGATTTGAT
1864014 TAATCAA-TAATTATATGATTT-AT
1 TAATCAATTAATT-TA-GATTTGAT
1864037 TAAT
1 TAAT
1864041 AAAATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.20
23 15 0.60
24 5 0.20
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (23 bp):
TAATCAATTAATTTAGATTTGAT
Found at i:1872186 original size:2 final size:2
Alignment explanation
Indices: 1872179--1872205 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1872169 TTTCAGTTAC
1872179 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1872206 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1872210 original size:2 final size:2
Alignment explanation
Indices: 1872205--1872246 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1872195 ATATATATAT
1872205 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1872247 TGCTTTGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1873103 original size:152 final size:152
Alignment explanation
Indices: 1872827--1873105 Score: 350
Period size: 152 Copynumber: 1.8 Consensus size: 152
1872817 CGCACCTATC
* * * * *
1872827 ACACAATATTAAAATAGAGTTTTCTCTTGCTAATCATCAAAATACATCGTTAAAACCTTTAATAT
1 ACACAATATTAAAATAAAGCTTTCTCTTGCTAATCATCAAAATACACCGTTAAAACCTTGAATAG
* * * *
1872892 TATTAGCTTTGTATTTGAACACTGTGTAATGCTTGTGGCATAAGCACGAGCAGGTAAATTATTAA
66 TATTAGCTTTGTATTTGAACACTGTGCAATGCATGCGGCATAAGAACGAGCAGGTAAATTATTAA
1872957 AATCCCTTATACCACATGCATT
131 AATCCCTTATACCACATGCATT
* * * ** *
1872979 ACACAGTATTAAAATAAAGCTTTCTCTTGCTGATCATCAAAATACGCCG-TAGAGTCCTTGAATG
1 ACACAATATTAAAATAAAGCTTTCTCTTGCTAATCATCAAAATACACCGTTA-AAACCTTGAATA
*
1873043 GTATTAGCTCTT-TATTTGAACACTGTGCAATGCATGCGGTAT-AGAAGCGAGC-GAGTAAATTA
65 GTATTAGCT-TTGTATTTGAACACTGTGCAATGCATGCGGCATAAGAA-CGAGCAG-GTAAATTA
1873105 T
127 T
1873106 GCATATAAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
151 6 0.06
152 99 0.93
153 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (152 bp):
ACACAATATTAAAATAAAGCTTTCTCTTGCTAATCATCAAAATACACCGTTAAAACCTTGAATAG
TATTAGCTTTGTATTTGAACACTGTGCAATGCATGCGGCATAAGAACGAGCAGGTAAATTATTAA
AATCCCTTATACCACATGCATT
Found at i:1873304 original size:168 final size:168
Alignment explanation
Indices: 1872956--1873337 Score: 493
Period size: 168 Copynumber: 2.3 Consensus size: 168
1872946 TAAATTATTA
*
1872956 AAATCCCTTATACCACATGCATTACACAGTATTAAAATAAAGCTTTCTCTTGCTGATCATCAAAA
1 AAATCCCTTATACCACATGCATTGCACAGTATTAAAATAAAGCTTTCTCTTGCTGATCATCAAAA
* * * *
1873021 TACGCCGTAGAGTCCTTGAATGGTATTAGCTCTTTATTTGAACACTGTGCAATGCATGCGGTATA
66 TACGCCGCAGAATCCTTGAATGGTATTAGCTCTATATTTGAACACTGTGCAATGCATGCGGCATA
*
1873086 GAAGCGAGCGAGTAAATTATGCATATAAAACCTATTTT
131 GAAGCGAGCGAGTAAATTATGCATATAAAACCTACTTT
* * * *
1873124 GAATCCCTTATACCACATACACTGCACAGTATTAAAATAGATCGCTTTCTCTTGCT-ATCATCAA
1 AAATCCCTTATACCACATGCATTGCACAGTATTAAAATA-A-AGCTTTCTCTTGCTGATCATCAA
* ** * * * * *
1873188 AATATGTTGCAGAATTCTTGAATGGTATTAGCTCTATATTTGAATACTGTGTAATGCTTGTGGCA
64 AATACGCCGCAGAATCCTTGAATGGTATTAGCTCTATATTTGAACACTGTGCAATGCATGCGGCA
*
1873253 TA-AGAGTGAGC-AGGTAAATTAT-CATATAAAACCTACTTT
129 TAGA-AGCGAGCGA-GTAAATTATGCATATAAAACCTACTTT
* * * *
1873292 AAATCTCTTATACCACATGCATTGCACAATATTAAAAGAGAGCTTT
1 AAATCCCTTATACCACATGCATTGCACAGTATTAAAATAAAGCTTT
1873338 TTTCTTAGTT
Statistics
Matches: 183, Mismatches: 27, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
166 5 0.03
168 86 0.47
169 79 0.43
170 13 0.07
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (168 bp):
AAATCCCTTATACCACATGCATTGCACAGTATTAAAATAAAGCTTTCTCTTGCTGATCATCAAAA
TACGCCGCAGAATCCTTGAATGGTATTAGCTCTATATTTGAACACTGTGCAATGCATGCGGCATA
GAAGCGAGCGAGTAAATTATGCATATAAAACCTACTTT
Found at i:1874209 original size:2 final size:2
Alignment explanation
Indices: 1874202--1874231 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1874192 TTGATTCTTT
1874202 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1874232 AACATATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1876516 original size:168 final size:168
Alignment explanation
Indices: 1876307--1876824 Score: 582
Period size: 168 Copynumber: 3.1 Consensus size: 168
1876297 CACACCCTGC
* * * * * ** * **
1876307 ACACAATATTAAAATAGAGCTTTATCTTGCTAATTATCAAAATACGTCGCGGAATCTTTTAATAT
1 ACACAGTATTAAAATAAAGTTTTATCTTGCTGATCATCAAAATACGTCGTAGAATCTTTGAATGG
*
1876372 TATTAGCGT-TGTATTTGAACACTATGTAATGCTTGTGGCATAAGCACGAGCAAGTAAATTATGC
66 TATTAGC-TCTGTATTTGAACACTATGTAATGCTTGTGGCATAAGCATGAGCAAGTAAATTATGC
*
1876436 ATATAAAACCTGCTTTGAATCCCTTATACCACATGTGTT
130 ATATAAAACCTACTTTGAATCCCTTATACCACATGTGTT
* * * *
1876475 ACACAGTATTAAAATAAAGTTTTCTCTTGCTGATCATCAAAATATGTCGTAAAATCTTTGAGTGG
1 ACACAGTATTAAAATAAAGTTTTATCTTGCTGATCATCAAAATACGTCGTAGAATCTTTGAATGG
* * * * * *
1876540 TATTAGCTCTGTATTCGAACACTGTGCAATGCATGCGGCATAAGCATGA-CCAGATAAATTATGC
66 TATTAGCTCTGTATTTGAACACTATGTAATGCTTGTGGCATAAGCATGAGCAAG-TAAATTATGC
* * *
1876604 ATATAAAACCTACTTTGAATCCTTTATATCACATACACTG-T
130 ATATAAAACCTACTTTGAATCCCTTATACCACAT---GTGTT
* * * *
1876645 ATA-A-TATTAAAATAAAGTTTTATTTTTTGCTGATCATCAAAATACGTTGTAGAATCCTTGAAT
1 ACACAGTATTAAAATAAAGTTTTA--TCTTGCTGATCATCAAAATACGTCGTAGAATCTTTGAAT
* *
1876708 GGTATTAGCTCTGTATTTGAATACTATGTAATGCTTGTGGCATAAG-AGTGAGCAGGTAAATTAT
64 GGTATTAGCTCTGTATTTGAACACTATGTAATGCTTGTGGCATAAGCA-TGAGCAAGTAAATTAT
* * * **
1876772 -CGTATAAAACCTACTTTGAATCTCTTATACCACAAGCATT
128 GCATATAAAACCTACTTTGAATCCCTTATACCACATGTGTT
*
1876812 GCACAGTATTAAA
1 ACACAGTATTAAA
1876825 CTAGAGCTTT
Statistics
Matches: 287, Mismatches: 51, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
167 6 0.02
168 151 0.53
169 39 0.14
170 87 0.30
171 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (168 bp):
ACACAGTATTAAAATAAAGTTTTATCTTGCTGATCATCAAAATACGTCGTAGAATCTTTGAATGG
TATTAGCTCTGTATTTGAACACTATGTAATGCTTGTGGCATAAGCATGAGCAAGTAAATTATGCA
TATAAAACCTACTTTGAATCCCTTATACCACATGTGTT
Found at i:1878712 original size:41 final size:41
Alignment explanation
Indices: 1878667--1878749 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
1878657 TTAACTTTAG
* *
1878667 TCTTTAAATCTCATAATCAAGATAATAAAACAGATATAAGT
1 TCTTTAAATCTCAAAATCAAGAAAATAAAACAGATATAAGT
*
1878708 TCTTTAAATCTCAAAATCAAGAAAATAAAACAGATGTAAGT
1 TCTTTAAATCTCAAAATCAAGAAAATAAAACAGATATAAGT
1878749 T
1 T
1878750 AACTTTCCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.30
Consensus pattern (41 bp):
TCTTTAAATCTCAAAATCAAGAAAATAAAACAGATATAAGT
Found at i:1879466 original size:15 final size:16
Alignment explanation
Indices: 1879434--1879466 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1879424 TTTTTTTTTT
*
1879434 TTTTGCATCTTGTGAA
1 TTTTGCATCTTGTAAA
1879450 TTTTGCAT-TTGTAAA
1 TTTTGCATCTTGTAAA
1879465 TT
1 TT
1879467 AATTTTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.55
Consensus pattern (16 bp):
TTTTGCATCTTGTAAA
Found at i:1882671 original size:2 final size:2
Alignment explanation
Indices: 1882664--1882688 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1882654 CTTGATATTC
1882664 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1882689 GTACTTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1883566 original size:82 final size:82
Alignment explanation
Indices: 1883426--1883594 Score: 230
Period size: 82 Copynumber: 2.1 Consensus size: 82
1883416 AAACCTGCTC
* *
1883426 TGAATCCCTTATACCACATGCATTACACAGTATTAAAATAAAGCTTTCTCTTGCTGATCATCAAA
1 TGAATCCCTTATACCACATACACTACACAGTATTAAAATAAAGCTTTCTCTTGCTGATCATCAAA
*
1883491 ATACATCGTAGAATCCT
66 ATACATCGTAAAATCCT
* * ** * * *
1883508 TGAATCTCTTATACCACATACACTGCATGGTATTAAAATAGAGCTTTCTTTTGTTGATCATCAAA
1 TGAATCCCTTATACCACATACACTACACAGTATTAAAATAAAGCTTTCTCTTGCTGATCATCAAA
* *
1883573 ATACGTTGTAAAATCCT
66 ATACATCGTAAAATCCT
1883590 TGAAT
1 TGAAT
1883595 TGTATTAGCT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (82 bp):
TGAATCCCTTATACCACATACACTACACAGTATTAAAATAAAGCTTTCTCTTGCTGATCATCAAA
ATACATCGTAAAATCCT
Found at i:1886107 original size:2 final size:2
Alignment explanation
Indices: 1886100--1886134 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1886090 ATCGATATTG
* *
1886100 AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1886135 AACACATAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:1887270 original size:168 final size:168
Alignment explanation
Indices: 1886738--1887265 Score: 605
Period size: 168 Copynumber: 3.1 Consensus size: 168
1886728 CGCACCCAGC
* * * * **
1886738 ACACAATATTAAAATAGAGCTTTATCTTGCTAATCTTCAAAATACGTCGCAGAATTTTTTTAT-A
1 ACACAATATTAAAATAGAGCTTTTTCTTGCTGATCATCAAAATACGTCGTAGAATTTTTAAATGA
* * * * **
1886802 TTATTAGCTTTGTATTTAAACACTGTGTAATGCTTGTGGCATAAGCA-CAAGTAGGTAAATTATG
66 -TATTAACTCTGTATTTGAACACTGTGTAATGCTTGTGGCATAA-AAGTGAGTAGGTAAATTATG
* **
1886866 CATATAAAACCTACTTTAAATCCCTTATACCACATGCGTT
129 CATATAAAACCTACTTTGAATCCCTTATACCACATGCACT
** * * * * ** * *
1886906 ACACAGCATTAAAATAAAGCTTTCTCTTGCTGATTATCAAAATACGTTGTAGAATCCTTGAATGG
1 ACACAATATTAAAATAGAGCTTTTTCTTGCTGATCATCAAAATACGTCGTAGAATTTTTAAATGA
* * * * ** * * * *
1886971 TATTGACTCTGTATTTGAACATTGTGCAATGCATGCAGTATAAGAGTGAGCAGGTAAATTATGTA
66 TATTAACTCTGTATTTGAACACTGTGTAATGCTTGTGGCATAAAAGTGAGTAGGTAAATTATGCA
* *
1887036 TATAAAACCTACTTTGAATCCCTTACACCGCATGCACT
131 TATAAAACCTACTTTGAATCCCTTATACCACATGCACT
* *
1887074 GCACAATATTAAAATAGAGCTATTTT-TTTCTGATCATCAAAATACGTCGTAGAATTTTTAAATG
1 ACACAATATTAAAATAGAGCT-TTTTCTTGCTGATCATCAAAATACGTCGTAGAATTTTTAAATG
*
1887138 ATATTAACTCTGTATTTGAATACTGTGTAATGCTTGTGGCATAAAAGTGAGTAGGTAAATTAT-C
65 ATATTAACTCTGTATTTGAACACTGTGTAATGCTTGTGGCATAAAAGTGAGTAGGTAAATTATGC
* *
1887202 ATATTAAACCTACTTTGAATCTCTTATACCACATGCACT
130 ATATAAAACCTACTTTGAATCCCTTATACCACATGCACT
* *
1887241 ACACAGTATTAAAATAGAGTTTTTT
1 ACACAATATTAAAATAGAGCTTTTT
1887266 TTTTTTTTTT
Statistics
Matches: 293, Mismatches: 64, Indels: 8
0.80 0.18 0.02
Matches are distributed among these distances:
166 4 0.01
167 54 0.18
168 232 0.79
169 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (168 bp):
ACACAATATTAAAATAGAGCTTTTTCTTGCTGATCATCAAAATACGTCGTAGAATTTTTAAATGA
TATTAACTCTGTATTTGAACACTGTGTAATGCTTGTGGCATAAAAGTGAGTAGGTAAATTATGCA
TATAAAACCTACTTTGAATCCCTTATACCACATGCACT
Found at i:1888123 original size:2 final size:2
Alignment explanation
Indices: 1888116--1888153 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1888106 GTTTGACTCT
*
1888116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1888154 CGTGCGGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1890770 original size:18 final size:18
Alignment explanation
Indices: 1890743--1890778 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1890733 TCTAAATCAG
1890743 AGCCTCGGAGGTACTGCC
1 AGCCTCGGAGGTACTGCC
* *
1890761 AGCCTTGGAGGTATTGCC
1 AGCCTCGGAGGTACTGCC
1890779 GTGAGGAGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.28, G:0.33, T:0.22
Consensus pattern (18 bp):
AGCCTCGGAGGTACTGCC
Found at i:1904888 original size:22 final size:22
Alignment explanation
Indices: 1904861--1904914 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
1904851 ATTGAAATAT
1904861 TAAATTAAACATTTTAAAAATG
1 TAAATTAAACATTTTAAAAATG
1904883 TAAATTAAACATTTTAAAAATG
1 TAAATTAAACATTTTAAAAATG
*
1904905 TGAAAGTAAA
1 T-AAATTAAA
1904915 GTAATCCAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 23 0.77
23 7 0.23
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (22 bp):
TAAATTAAACATTTTAAAAATG
Found at i:1915765 original size:27 final size:27
Alignment explanation
Indices: 1915726--1915805 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 27
1915716 ATAAGCCCAA
* * *
1915726 CAACCCCAATGGCTCCTAGCCCTTCAT
1 CAACCCCAATGGCCCCAAGCCCATCAT
* *
1915753 CAACTCCACTGGCCCCAAGCCCATCAT
1 CAACCCCAATGGCCCCAAGCCCATCAT
** * *
1915780 CTGCCCCAATGGCACCAACCCCATCA
1 CAACCCCAATGGCCCCAAGCCCATCA
1915806 ATAAGTTCAC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.25, C:0.47, G:0.11, T:0.16
Consensus pattern (27 bp):
CAACCCCAATGGCCCCAAGCCCATCAT
Found at i:1917341 original size:27 final size:27
Alignment explanation
Indices: 1917310--1917364 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1917300 TTATATAAAA
*
1917310 TTATTTAAATAAAATTT-ATAAAATTTT
1 TTATTTAAA-AAAATTTAATAAAAATTT
*
1917337 TTATTTAAAATAATTTAATAAAAATTT
1 TTATTTAAAAAAATTTAATAAAAATTT
1917364 T
1 T
1917365 AAATTGATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TTATTTAAAAAAATTTAATAAAAATTT
Found at i:1919714 original size:2 final size:2
Alignment explanation
Indices: 1919707--1919738 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1919697 AGCCCCCTAT
1919707 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1919739 CTAAGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1924971 original size:280 final size:280
Alignment explanation
Indices: 1924470--1925313 Score: 1634
Period size: 280 Copynumber: 3.0 Consensus size: 280
1924460 TGAACACTCG
1924470 AACAGCAATTGTTCTGGTAAAATTTCATCATTCTTCATTTATTGAAAGAGTGAACGCTGATTAAC
1 AACAGCAATTGTTCTGGTAAAATTTCATCATTCTTCATTTATTGAAAGAGTGAACGCTGATTAAC
*
1924535 TCTTTTTGGGCTGTGAAAGCTGATTAGCTGAAACTCTAACTTTGACTCATCTAAAACATATTAAA
66 TCTTTTTGGGCTGTGAAAGCTGATTAGCTGAAACTCTAACTTTGCCTCATCTAAAACATATTAAA
*
1924600 AAACAAGAAAAAAATAATCTTTGACTTAGTCTGCCAACTGATATGTGCACCACTATGGTAATGTA
131 AAACAAGAAAAAAATAATCTTTGACTTAGTCTGCCAACTGATATGTGCACCACTATGGTAATCTA
1924665 AAGATTAACACTATTGACTTAGTCTATCTAGGCATGCGTATATAAAAAATAAAATATTAAATATT
196 AAGATTAACACTATTGACTTAGTCTATCTAGGCATGCGTATATAAAAAATAAAATATTAAATATT
1924730 TTAAAAATTCATGTGGATGA
261 TTAAAAATTCATGTGGATGA
1924750 AACAGCAATTGTTCTGGTAAAATTTCATCATTCTTCATTTATTGAAAGAGTGAACGCTGATTAAC
1 AACAGCAATTGTTCTGGTAAAATTTCATCATTCTTCATTTATTGAAAGAGTGAACGCTGATTAAC
1924815 TCTTTTTGGGCTGTGAAAGCTGATTAGCTGAAACTCTAACTTTGCCTCATCTAAAACATATTAAA
66 TCTTTTTGGGCTGTGAAAGCTGATTAGCTGAAACTCTAACTTTGCCTCATCTAAAACATATTAAA
*
1924880 AAACAAGAAAAAAATAATCTTTGACTTAGCCTGCCAACTGATATGTGCACCACTATGGTAATCTA
131 AAACAAGAAAAAAATAATCTTTGACTTAGTCTGCCAACTGATATGTGCACCACTATGGTAATCTA
* * *
1924945 AAGATTAACACTATTGGCTTAGTCTATCTAGGCATGCTTATATCAAAAATAAAATATTAAATATT
196 AAGATTAACACTATTGACTTAGTCTATCTAGGCATGCGTATATAAAAAATAAAATATTAAATATT
1925010 TTAAAAATTCATGTGGATGA
261 TTAAAAATTCATGTGGATGA
1925030 AACAGCAATTGTTCTGGTAAAATTTCATCATTCTTCATTTATTGAAAGAGTGAACGCTGATTAAC
1 AACAGCAATTGTTCTGGTAAAATTTCATCATTCTTCATTTATTGAAAGAGTGAACGCTGATTAAC
1925095 TCTTTTTGGGCTGTGAAAGCTGATTAGCTGAAACTCTAACTTTGCCTCATCTAAAACATATTAAA
66 TCTTTTTGGGCTGTGAAAGCTGATTAGCTGAAACTCTAACTTTGCCTCATCTAAAACATATTAAA
1925160 AAACAAGAAAAAAATAATCTTTGACTTAGTCTGCCAACTGATATGTGCACCACTATGGTAATCTA
131 AAACAAGAAAAAAATAATCTTTGACTTAGTCTGCCAACTGATATGTGCACCACTATGGTAATCTA
1925225 AAGATTAACACTATTGACTTAGTCTATCTAGGCATGCGTATATAAAAAATAAAATATTAAATATT
196 AAGATTAACACTATTGACTTAGTCTATCTAGGCATGCGTATATAAAAAATAAAATATTAAATATT
1925290 TTAAAAATTCATGTGGATGA
261 TTAAAAATTCATGTGGATGA
1925310 AACA
1 AACA
1925314 TGACATTTTA
Statistics
Matches: 554, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
280 554 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (280 bp):
AACAGCAATTGTTCTGGTAAAATTTCATCATTCTTCATTTATTGAAAGAGTGAACGCTGATTAAC
TCTTTTTGGGCTGTGAAAGCTGATTAGCTGAAACTCTAACTTTGCCTCATCTAAAACATATTAAA
AAACAAGAAAAAAATAATCTTTGACTTAGTCTGCCAACTGATATGTGCACCACTATGGTAATCTA
AAGATTAACACTATTGACTTAGTCTATCTAGGCATGCGTATATAAAAAATAAAATATTAAATATT
TTAAAAATTCATGTGGATGA
Found at i:1933061 original size:11 final size:11
Alignment explanation
Indices: 1933018--1933080 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
1933008 ATGAAAATAG
1933018 TATATTTTAAT
1 TATATTTTAAT
1933029 TATAATATTT-A-
1 TAT-AT-TTTAAT
*
1933040 TAAACTTTTAAT
1 TATA-TTTTAAT
*
1933052 TTTATTTTAA-
1 TATATTTTAAT
*
1933062 GATATTTTAAT
1 TATATTTTAAT
1933073 TATATTTT
1 TATATTTT
1933081 TACTACCAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
10 12 0.30
11 20 0.50
12 5 0.12
13 3 0.08
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (11 bp):
TATATTTTAAT
Found at i:1938264 original size:18 final size:20
Alignment explanation
Indices: 1938234--1938284 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1938224 TCGTATCTAT
1938234 ATTTTA-TATAAT-ATAAAA
1 ATTTTATTATAATAATAAAA
*
1938252 ATTTTATTA-AATAATATAA
1 ATTTTATTATAATAATAAAA
*
1938271 ATTATTATTTTAAT
1 ATT-TTATTATAAT
1938285 TATTTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 9 0.33
19 10 0.37
20 5 0.19
21 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTATTATAATAATAAAA
Found at i:1938327 original size:15 final size:16
Alignment explanation
Indices: 1938307--1938336 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1938297 TATATTTTTA
1938307 TTTTAAAAA-TATATT
1 TTTTAAAAATTATATT
1938322 TTTTAAAAATTATAT
1 TTTTAAAAATTATAT
1938337 AAATATGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAAAATTATATT
Found at i:1938445 original size:37 final size:36
Alignment explanation
Indices: 1938404--1938473 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
1938394 TTCACATTAA
*
1938404 TTAAATATCATAAAAATTAAATAATT-TAATATAATCG
1 TTAAATATAATAAAAATT--ATAATTATAATATAATCG
* *
1938441 TTAAATATAATTATAATTATAATTATAATATAA
1 TTAAATATAATAAAAATTATAATTATAATATAA
1938474 AAATTAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 6 0.21
36 8 0.28
37 15 0.52
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
TTAAATATAATAAAAATTATAATTATAATATAATCG
Found at i:1938461 original size:12 final size:11
Alignment explanation
Indices: 1938444--1938473 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
1938434 ATAATCGTTA
1938444 AATATAATTAT
1 AATATAATTAT
1938455 AATTATAATTAT
1 AA-TATAATTAT
1938467 AATATAA
1 AATATAA
1938474 AAATTAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
AATATAATTAT
Found at i:1938898 original size:20 final size:20
Alignment explanation
Indices: 1938873--1938917 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1938863 TATCCTTCAG
1938873 AAAATAATTAATT-ATAAATC
1 AAAATAA-TAATTAATAAATC
*
1938893 AAAATAATAATTAATAAATT
1 AAAATAATAATTAATAAATC
1938913 AAAAT
1 AAAAT
1938918 TCCAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATAATAATTAATAAATC
Found at i:1946366 original size:15 final size:15
Alignment explanation
Indices: 1946346--1946375 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1946336 TGAAAACAGA
*
1946346 AAGAAAATATGGGCT
1 AAGAAAATATCGGCT
1946361 AAGAAAATATCGGCT
1 AAGAAAATATCGGCT
1946376 TTAAACCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.20
Consensus pattern (15 bp):
AAGAAAATATCGGCT
Found at i:1954419 original size:16 final size:16
Alignment explanation
Indices: 1954400--1954430 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1954390 ATTTTGTTTA
*
1954400 TAATTTTTAATAAAAG
1 TAATTATTAATAAAAG
1954416 TAATTATTAATAAAA
1 TAATTATTAATAAAA
1954431 TTTATTAATT
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:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAATTATTAATAAAAG
Found at i:1954437 original size:16 final size:17
Alignment explanation
Indices: 1954406--1954443 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1954396 TTTATAATTT
1954406 TTAATAAAAGTAATT-A
1 TTAATAAAAGTAATTAA
* *
1954422 TTAATAAAATTTATTAA
1 TTAATAAAAGTAATTAA
1954439 TTAAT
1 TTAAT
1954444 TAATGGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAATAAAAGTAATTAA
Found at i:1954557 original size:13 final size:14
Alignment explanation
Indices: 1954534--1954563 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1954524 AACATTGTTA
1954534 AAAATATTAAAATT
1 AAAATATTAAAATT
1954548 AAAA-ATTAAAATT
1 AAAATATTAAAATT
1954561 AAA
1 AAA
1954564 TAAAAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATTAAAATT
Found at i:1957883 original size:8 final size:8
Alignment explanation
Indices: 1957870--1957897 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1957860 AGTTATTTGC
1957870 AAAATAAA
1 AAAATAAA
1957878 AAAATAAA
1 AAAATAAA
1957886 AAAATAAA
1 AAAATAAA
1957894 AAAA
1 AAAA
1957898 ACCCAAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:1957950 original size:32 final size:32
Alignment explanation
Indices: 1957914--1958009 Score: 82
Period size: 32 Copynumber: 3.2 Consensus size: 32
1957904 ATGCATATAG
1957914 ATTTTAAAAGATTATGTGAGCTATGCTTTTAA
1 ATTTTAAAAGATTATGTGAGCTATGCTTTTAA
* * * *
1957946 ATTTTACCAA-A--A--TGA--TATAG-ATATAG
1 ATTTTA-AAAGATTATGTGAGCTAT-GCTTTTAA
1957972 ATTTTAAAAGATTATGTGAGCTATGCTTTTAA
1 ATTTTAAAAGATTATGTGAGCTATGCTTTTAA
1958004 ATTTTA
1 ATTTTA
1958010 CCCAAATGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 20
0.62 0.11 0.27
Matches are distributed among these distances:
25 2 0.04
26 13 0.28
27 1 0.02
28 4 0.09
30 4 0.09
31 1 0.02
32 19 0.41
33 2 0.04
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.43
Consensus pattern (32 bp):
ATTTTAAAAGATTATGTGAGCTATGCTTTTAA
Found at i:1957998 original size:58 final size:58
Alignment explanation
Indices: 1957908--1958025 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
1957898 ACCCAAATGC
1957908 ATATAGATTTTAAAAGATTATGTGAGCTATGCTTTTAAATTTTACCAAAATGATATAG
1 ATATAGATTTTAAAAGATTATGTGAGCTATGCTTTTAAATTTTACCAAAATGATATAG
*
1957966 ATATAGATTTTAAAAGATTATGTGAGCTATGCTTTTAAATTTTACCCAAATGATATAG
1 ATATAGATTTTAAAAGATTATGTGAGCTATGCTTTTAAATTTTACCAAAATGATATAG
1958024 AT
1 AT
1958026 TCTAAATGAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.40
Consensus pattern (58 bp):
ATATAGATTTTAAAAGATTATGTGAGCTATGCTTTTAAATTTTACCAAAATGATATAG
Found at i:1958932 original size:22 final size:22
Alignment explanation
Indices: 1958901--1958960 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
1958891 AACAGATTCA
*
1958901 AAAT-TTTTTATTTGTATTTAAT
1 AAATATTTTTATTT-AATTTAAT
*
1958923 -AATATTTTTAATTAATTTAAT
1 AAATATTTTTATTTAATTTAAT
1958944 AAATATAATTTTATTTA
1 AAATAT--TTTTATTTA
1958961 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 10 0.32
22 13 0.42
24 8 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AAATATTTTTATTTAATTTAAT
Found at i:1959288 original size:2 final size:2
Alignment explanation
Indices: 1959281--1959315 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1959271 TCGATCGAAC
1959281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1959316 ACTAGCATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1959401 original size:17 final size:18
Alignment explanation
Indices: 1959375--1959408 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1959365 TTATAAAAAC
*
1959375 ATTATTTTTTAA-TATAA
1 ATTATATTTTAACTATAA
1959392 ATTATATTTTAACTATA
1 ATTATATTTTAACTATA
1959409 TATAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATATTTTAACTATAA
Found at i:1960299 original size:2 final size:2
Alignment explanation
Indices: 1960292--1960326 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1960282 ATATCTTAAT
1960292 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1960327 CAAGAATGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1960633 original size:16 final size:16
Alignment explanation
Indices: 1960599--1960632 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1960589 TTCAATATAT
1960599 AAATTAAAAAAATTAA
1 AAATTAAAAAAATTAA
1960615 AAATT-AAAAAATTAA
1 AAATTAAAAAAATTAA
1960630 AAA
1 AAA
1960633 AAGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTAAAAAAATTAA
Found at i:1960634 original size:9 final size:8
Alignment explanation
Indices: 1960599--1960633 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
1960589 TTCAATATAT
1960599 AAATTAAAA
1 AAATT-AAA
1960608 AAATT-AA
1 AAATTAAA
1960615 AAATTAAA
1 AAATTAAA
1960623 AAATTAAA
1 AAATTAAA
1960631 AAA
1 AAA
1960634 AGAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.28
8 13 0.52
9 5 0.20
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAATTAAA
Found at i:1960650 original size:24 final size:24
Alignment explanation
Indices: 1960599--1960655 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
1960589 TTCAATATAT
* **
1960599 AAATTAAAAAAATTAAAAATTAAA
1 AAATTAAAAAAATGAAAAAAAAAA
1960623 AAATTAAAAAAA-GAAAAAAAAAA
1 AAATTAAAAAAATGAAAAAAAAAA
1960646 CAAATCTAAA
1 -AAAT-TAAA
1960656 TGTCACGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 8 0.29
24 16 0.57
25 4 0.14
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.18
Consensus pattern (24 bp):
AAATTAAAAAAATGAAAAAAAAAA
Found at i:1964632 original size:11 final size:12
Alignment explanation
Indices: 1964604--1964633 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1964594 GATGCACACA
1964604 TTTTATTAATTG
1 TTTTATTAATTG
1964616 TTTTATTAATT-
1 TTTTATTAATTG
1964627 TTTTATT
1 TTTTATT
1964634 TTGAATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTTATTAATTG
Found at i:1964822 original size:18 final size:19
Alignment explanation
Indices: 1964799--1964834 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1964789 TTTTCTTATT
*
1964799 TATATT-ATTATTTTTTAA
1 TATATTAATTAATTTTTAA
1964817 TATATTAATTAATTTTTA
1 TATATTAATTAATTTTTA
1964835 TTTATTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATTAATTAATTTTTAA
Found at i:1965513 original size:34 final size:35
Alignment explanation
Indices: 1965440--1965515 Score: 86
Period size: 35 Copynumber: 2.2 Consensus size: 35
1965430 ATAAAAGTAA
*
1965440 AAAAAAAAATTTCATTCATTCTTTTCCTTCAGCAG
1 AAAAAAAAATTTCATTCATTCTTTTCCTTCAGCAC
* *
1965475 AAAAAAAATTTTCATTTTCATT-TTTT-TTTCAGC-C
1 AAAAAAAAATTTCA--TTCATTCTTTTCCTTCAGCAC
1965509 AAAAAAA
1 AAAAAAA
1965516 TCGTCTGTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 7 0.19
35 19 0.53
36 4 0.11
37 6 0.17
ACGTcount: A:0.41, C:0.16, G:0.04, T:0.39
Consensus pattern (35 bp):
AAAAAAAAATTTCATTCATTCTTTTCCTTCAGCAC
Found at i:1965849 original size:19 final size:18
Alignment explanation
Indices: 1965815--1965863 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
1965805 AAAGAAATTT
1965815 TTTTTTATTCTAGAAACAC
1 TTTTTTATTCTAGAAA-AC
* *
1965834 TTTTTTATTTTGGAAAAC
1 TTTTTTATTCTAGAAAAC
*
1965852 TATTTTTTTTCT
1 T-TTTTTATTCT
1965864 CCGATTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.59
Consensus pattern (18 bp):
TTTTTTATTCTAGAAAAC
Found at i:1966622 original size:24 final size:24
Alignment explanation
Indices: 1966568--1966614 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
1966558 GAAGGATAAG
1966568 AAAAA-AAATAAGAAAGAAAAAAT
1 AAAAATAAATAAGAAAGAAAAAAT
*
1966591 AAAAATAAATAA-AATGAAAAAAT
1 AAAAATAAATAAGAAAGAAAAAAT
1966614 A
1 A
1966615 TTAAATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (24 bp):
AAAAATAAATAAGAAAGAAAAAAT
Found at i:1966626 original size:3 final size:3
Alignment explanation
Indices: 1966618--1966655 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1966608 AAAAATATTA
1966618 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1966656 AATGATGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1972421 original size:21 final size:21
Alignment explanation
Indices: 1972370--1972422 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1972360 TTTTATTAAT
* *
1972370 AAAATGTTAAACTATTTTAAA
1 AAAATGTTGAACTATTTAAAA
* *
1972391 AAAATATTGAAGTATTTAAAA
1 AAAATGTTGAACTATTTAAAA
1972412 AAAATGTTGAA
1 AAAATGTTGAA
1972423 TTCTTAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (21 bp):
AAAATGTTGAACTATTTAAAA
Found at i:1982815 original size:20 final size:19
Alignment explanation
Indices: 1982785--1982846 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
1982775 ATGCTTTAGA
*
1982785 GGTTACAAAAATGTTATAAT
1 GGTTAAAAAAATGTTA-AAT
1982805 GGTTAAAAAAAACT-TTAAAT
1 GGTT-AAAAAAA-TGTTAAAT
*
1982825 -ATTAAAAAAATGTTACAAT
1 GGTTAAAAAAATGTTA-AAT
1982844 GGT
1 GGT
1982847 ACAATAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
17 1 0.03
18 10 0.29
19 5 0.15
20 8 0.24
21 9 0.26
22 1 0.03
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (19 bp):
GGTTAAAAAAATGTTAAAT
Found at i:1983018 original size:15 final size:17
Alignment explanation
Indices: 1982993--1983024 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1982983 ATAAGAGCAC
1982993 TTTACTTATAAT-TTAT
1 TTTACTTATAATATTAT
1983009 TTTA-TTATAATATTAT
1 TTTACTTATAATATTAT
1983025 AATTATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTACTTATAATATTAT
Found at i:1983040 original size:22 final size:23
Alignment explanation
Indices: 1982998--1983042 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1982988 AGCACTTTAC
* *
1982998 TTATAATTTATTTTATTATAATA
1 TTATAATTTATTTAATCATAATA
1983021 TTATAA-TTATTTAATCATAATA
1 TTATAATTTATTTAATCATAATA
1983043 AAAAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTATAATTTATTTAATCATAATA
Found at i:1988749 original size:16 final size:15
Alignment explanation
Indices: 1988729--1988776 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1988719 AAAAGGAAAA
1988729 TTAAATAAAACGAAT
1 TTAAATAAAACGAAT
** *
1988744 TATAAA-AAAATAAAA
1 T-TAAATAAAACGAAT
1988759 TTAAATAAAACGAAT
1 TTAAATAAAACGAAT
1988774 TTA
1 TTA
1988777 TTTGAGGTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (15 bp):
TTAAATAAAACGAAT
Found at i:2006073 original size:28 final size:29
Alignment explanation
Indices: 2006037--2006108 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
2006027 CAATGTAAAT
* *
2006037 TATTATTTTAGATAAATTA-AAATTAATA
1 TATTATTTTAGAAAAAATATAAATTAATA
* *
2006065 TATTTTTTTTGAAAAAATATAAATTAATA
1 TATTATTTTAGAAAAAATATAAATTAATA
2006094 TA-TA-TTTA-AAAAAAT
1 TATTATTTTAGAAAAAAT
2006109 TACTTAAACA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
26 7 0.19
27 3 0.08
28 16 0.43
29 11 0.30
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (29 bp):
TATTATTTTAGAAAAAATATAAATTAATA
Found at i:2011718 original size:17 final size:17
Alignment explanation
Indices: 2011686--2011736 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
2011676 ATATTAATAA
*
2011686 TTTAAATAATATAAATTT
1 TTTAAA-AAAATAAATTT
2011704 TTTAAAAAAATAAATTT
1 TTTAAAAAAATAAATTT
** *
2011721 AATAAATAAATAAATT
1 TTTAAAAAAATAAATT
2011737 ATCTTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 23 0.79
18 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TTTAAAAAAATAAATTT
Found at i:2018859 original size:16 final size:17
Alignment explanation
Indices: 2018835--2018868 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2018825 ATTTTATCTT
2018835 AATATATTTTTATATAA
1 AATATATTTTTATATAA
*
2018852 AATA-ATTTTTATTTAA
1 AATATATTTTTATATAA
2018868 A
1 A
2018869 TATCATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATATATTTTTATATAA
Found at i:2019858 original size:17 final size:16
Alignment explanation
Indices: 2019836--2019880 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
2019826 AATAAATTTT
2019836 TTTATTTTTTACTACAA
1 TTTATTTTTT-CTACAA
* *
2019853 TTTATTTTCTTTTACAT
1 TTTATTTT-TTCTACAA
2019870 TTTATTTTTTC
1 TTTATTTTTTC
2019881 AAACCAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTATTTTTTCTACAA
Found at i:2022150 original size:15 final size:16
Alignment explanation
Indices: 2022116--2022153 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2022106 CATTTTTTTG
*
2022116 TTTTTATATTAATATA
1 TTTTTATATGAATATA
*
2022132 TTTTTATATGAA-ATT
1 TTTTTATATGAATATA
2022147 TTTTTAT
1 TTTTTAT
2022154 CTAAATATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (16 bp):
TTTTTATATGAATATA
Found at i:2022304 original size:12 final size:12
Alignment explanation
Indices: 2022289--2022333 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
2022279 AATAGTATTA
2022289 TTATATATAAAT
1 TTATATATAAAT
*
2022301 TTATGTAT--AT
1 TTATATATAAAT
*
2022311 TTATAAATAAAT
1 TTATATATAAAT
2022323 TTATAT-TAAAT
1 TTATATATAAAT
2022334 CAAAATTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
10 8 0.30
11 5 0.19
12 14 0.52
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
TTATATATAAAT
Found at i:2022728 original size:26 final size:25
Alignment explanation
Indices: 2022699--2022758 Score: 84
Period size: 26 Copynumber: 2.4 Consensus size: 25
2022689 GTATTTCGAT
2022699 TTTAATTAAATTAATTCATAAATTGA
1 TTTAATTAAATTAATTCATAAATT-A
* *
2022725 TTTAATTTAATTAATTGATAAATTA
1 TTTAATTAAATTAATTCATAAATTA
*
2022750 TTAAATTAA
1 TTTAATTAA
2022759 TTCTTAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 8 0.27
26 22 0.73
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (25 bp):
TTTAATTAAATTAATTCATAAATTA
Found at i:2022980 original size:22 final size:22
Alignment explanation
Indices: 2022935--2022979 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2022925 TATTTAATTT
*
2022935 ATTTTAAATATGATAAATTAAA
1 ATTTTAAATATAATAAATTAAA
*
2022957 ATTTTAGAATATAATTAATTAAA
1 ATTTTA-AATATAATAAATTAAA
2022980 TATATTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
ATTTTAAATATAATAAATTAAA
Found at i:2023264 original size:10 final size:10
Alignment explanation
Indices: 2023251--2023276 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2023241 TTTTCTTTTT
2023251 TTTTTTTTAA
1 TTTTTTTTAA
2023261 TTTTTTTTAA
1 TTTTTTTTAA
2023271 TTTTTT
1 TTTTTT
2023277 AAATGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:2024891 original size:22 final size:21
Alignment explanation
Indices: 2024863--2024904 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2024853 TTTTTTATTT
* *
2024863 ATTAAATTTAACTCATTTTAAA
1 ATTAAATGTAACAC-TTTTAAA
2024885 ATTAAATGTAACACTTTTAA
1 ATTAAATGTAACACTTTTAA
2024905 CGTTTAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTAAATGTAACACTTTTAAA
Found at i:2025376 original size:23 final size:23
Alignment explanation
Indices: 2025341--2025391 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
2025331 GAAAATTGAA
2025341 AAAAATATATAAATATTAAAATTT
1 AAAAATATATAAATATT-AAATTT
* *
2025365 AAAATTAT-TAAATATTAATTTT
1 AAAAATATATAAATATTAAATTT
2025387 AAAAA
1 AAAAA
2025392 ATTGACATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 9 0.38
23 8 0.33
24 7 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAAATATATAAATATTAAATTT
Found at i:2025712 original size:22 final size:21
Alignment explanation
Indices: 2025684--2025724 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2025674 ATAAATTATT
*
2025684 ATTATAATTAAATAATTATAAC
1 ATTATAA-TAAAAAATTATAAC
2025706 ATTATAATAAAAAATTATA
1 ATTATAATAAAAAATTATA
2025725 GATAATATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTATAATAAAAAATTATAAC
Found at i:2025887 original size:1 final size:1
Alignment explanation
Indices: 2025876--2025905 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2025866 TTTCCATTAT
*
2025876 CCCCACCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
2025906 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2032970 original size:13 final size:13
Alignment explanation
Indices: 2032952--2032978 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2032942 ACATATATGA
2032952 CTTTGAAATTGAC
1 CTTTGAAATTGAC
2032965 CTTTGAAATTGAC
1 CTTTGAAATTGAC
2032978 C
1 C
2032979 AAAAATTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (13 bp):
CTTTGAAATTGAC
Found at i:2034469 original size:16 final size:16
Alignment explanation
Indices: 2034450--2034496 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2034440 TCATTTTTTG
*
2034450 TTTTTATCTTAATATA
1 TTTTTATCTAAATATA
* *
2034466 TTTTTATATGAAA-ATT
1 TTTTTATCT-AAATATA
2034482 TTTTTATCTAAATAT
1 TTTTTATCTAAATAT
2034497 CATATGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.80
17 2 0.08
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTTATCTAAATATA
Found at i:2034640 original size:18 final size:18
Alignment explanation
Indices: 2034625--2034663 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2034615 ATAGTATTAT
*
2034625 TATATATAAATTTATTTA
1 TATATATAAATATATTTA
*
2034643 TATTTATAAATATATTTA
1 TATATATAAATATATTTA
2034661 TAT
1 TAT
2034664 TGAAAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATAAATATATTTA
Found at i:2034664 original size:18 final size:18
Alignment explanation
Indices: 2034629--2034664 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2034619 TATTATTATA
*
2034629 TATAAATTTATTTATATT
1 TATAAATATATTTATATT
2034647 TATAAATATATTTATATT
1 TATAAATATATTTATATT
2034665 GAAAAATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATAAATATATTTATATT
Found at i:2034671 original size:18 final size:18
Alignment explanation
Indices: 2034632--2034671 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2034622 TATTATATAT
* * *
2034632 AAATTTATTTATATTTAT
1 AAATATATTTATATTGAA
2034650 AAATATATTTATATTGAA
1 AAATATATTTATATTGAA
2034668 AAAT
1 AAAT
2034672 GAGAAAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AAATATATTTATATTGAA
Found at i:2037866 original size:15 final size:15
Alignment explanation
Indices: 2037809--2038172 Score: 77
Period size: 14 Copynumber: 24.7 Consensus size: 15
2037799 TAGAATCTTG
2037809 TTTTAGGGTTTTAAGA
1 TTTTAGGGTTTT-AGA
2037825 --TTAGGGTTTTGAGA
1 TTTTAGGGTTTT-AGA
2037839 TTTT-GGAGTTTTAGA
1 TTTTAGG-GTTTTAGA
*
2037854 TTTTAGGGCTTTAG-
1 TTTTAGGGTTTTAGA
* * *
2037868 -TTT-GAGTTTAAAGGG
1 TTTTAGGGTTT-TA-GA
* *
2037883 TTTTAGGGTTTAAAGGGT
1 TTTTAGGGTTT-TA--GA
* *
2037901 TTTTA-GG-CTTGGA
1 TTTTAGGGTTTTAGA
* *
2037914 TTTTATGG-TTTGGA
1 TTTTAGGGTTTTAGA
*
2037928 ATTTAGGGTTTT-GA
1 TTTTAGGGTTTTAGA
** *
2037942 TTTTAAAG-TTTAGG
1 TTTTAGGGTTTTAGA
* *
2037956 GTTTAGGGTTTCA-A
1 TTTTAGGGTTTTAGA
* * *
2037970 TTTTAAGATTTGA-A
1 TTTTAGGGTTTTAGA
* *
2037984 GTTCAGGGTTTT-GA
1 TTTTAGGGTTTTAGA
2037998 TTTTAGGG-TTTAGA
1 TTTTAGGGTTTTAGA
** *
2038012 -TTTAGATTTTTAGT
1 TTTTAGGGTTTTAGA
*
2038026 TTTTAGAG-TTTAGA
1 TTTTAGGGTTTTAGA
* *
2038040 TTTTAGGGTTTGAAGG
1 TTTTAGGGTTT-TAGA
* * * *
2038056 GTTTATGTTTTTAGT
1 TTTTAGGGTTTTAGA
*
2038071 TTTTATGGTTTTAAGGA
1 TTTTAGGGTTTT-A-GA
* *
2038088 -TTTAGAG-TTTAAA
1 TTTTAGGGTTTTAGA
* * *
2038101 TTTTATGGTTTGGAGG
1 TTTTAGGGTTT-TAGA
* **
2038117 GTTTAGATTTTTA-A
1 TTTTAGGGTTTTAGA
*
2038131 TTTTTAGGGTTTTAGG
1 -TTTTAGGGTTTTAGA
2038147 TATTTAGGG-TTTAGA
1 T-TTTAGGGTTTTAGA
*
2038162 TTTTAAGGTTT
1 TTTTAGGGTTT
2038173 GAAGTTTAAA
Statistics
Matches: 249, Mismatches: 70, Indels: 59
0.66 0.19 0.16
Matches are distributed among these distances:
12 4 0.02
13 22 0.09
14 95 0.38
15 66 0.27
16 44 0.18
17 11 0.04
18 7 0.03
ACGTcount: A:0.22, C:0.01, G:0.27, T:0.51
Consensus pattern (15 bp):
TTTTAGGGTTTTAGA
Found at i:2038024 original size:21 final size:21
Alignment explanation
Indices: 2037991--2038050 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
2037981 GAAGTTCAGG
*
2037991 GTTTTGATTTTAGGGTTTAGA
1 GTTTAGATTTTAGGGTTTAGA
**
2038012 -TTTAGATTTTTAGTTTTTAGA
1 GTTTAGA-TTTTAGGGTTTAGA
2038033 GTTTAGATTTTAGGGTTT
1 GTTTAGATTTTAGGGTTT
2038051 GAAGGGTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.16
21 21 0.66
22 6 0.19
ACGTcount: A:0.20, C:0.00, G:0.23, T:0.57
Consensus pattern (21 bp):
GTTTAGATTTTAGGGTTTAGA
Found at i:2038075 original size:31 final size:30
Alignment explanation
Indices: 2038034--2038201 Score: 101
Period size: 31 Copynumber: 5.6 Consensus size: 30
2038024 GTTTTTAGAG
*
2038034 TTTAGATTTTAGGGTTTGAAGGGTTTATGTT
1 TTTAAATTTTAGGGTTTGAAGGGTTTA-GTT
** * * * **
2038065 TTTAGTTTTTATGGTTTTAAGGATTTAGAG
1 TTTAAATTTTAGGGTTTGAAGGGTTTAGTT
* *
2038095 TTTAAATTTTATGGTTTGGAGGGTTTAGATT
1 TTTAAATTTTAGGGTTTGAAGGGTTTAG-TT
* * * **
2038126 TTTAATTTTTAGGGTTT-TAGGTATTTAGGG
1 TTTAAATTTTAGGGTTTGAAGG-GTTTAGTT
* * *
2038156 TTTAGATTTTAAGGTTTGAA--GTTTAAATT
1 TTTAAATTTTAGGGTTTGAAGGGTTT-AGTT
*
2038185 TTT-AATTTTAGAGTTTG
1 TTTAAATTTTAGGGTTTG
2038202 GAGTTTAGGG
Statistics
Matches: 103, Mismatches: 30, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
28 14 0.14
29 4 0.04
30 41 0.40
31 44 0.43
ACGTcount: A:0.23, C:0.00, G:0.24, T:0.53
Consensus pattern (30 bp):
TTTAAATTTTAGGGTTTGAAGGGTTTAGTT
Found at i:2038094 original size:61 final size:61
Alignment explanation
Indices: 2038019--2038193 Score: 216
Period size: 61 Copynumber: 2.9 Consensus size: 61
2038009 AGATTTAGAT
* * * *
2038019 TTTTA-GTTTTTAGAGTTTAGATTTTAGGGTTTGAAGGGTTTATG-TTTTTAGTTTTTATGG
1 TTTTAGGTATTTAGAGTTTAGATTTTAAGGTTTGAAGGGTTTA-GATTTTTAATTTTTAGGG
* * *
2038079 TTTTAAGG-ATTTAGAGTTTAAATTTTATGGTTTGGAGGGTTTAGATTTTTAATTTTTAGGG
1 TTTT-AGGTATTTAGAGTTTAGATTTTAAGGTTTGAAGGGTTTAGATTTTTAATTTTTAGGG
* *
2038140 TTTTAGGTATTTAGGGTTTAGATTTTAAGGTTTGAA--GTTTAAATTTTTAATTTT
1 TTTTAGGTATTTAGAGTTTAGATTTTAAGGTTTGAAGGGTTTAGATTTTTAATTTT
2038194 AGAGTTTGGA
Statistics
Matches: 100, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
59 17 0.17
60 8 0.08
61 74 0.74
62 1 0.01
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (61 bp):
TTTTAGGTATTTAGAGTTTAGATTTTAAGGTTTGAAGGGTTTAGATTTTTAATTTTTAGGG
Found at i:2038106 original size:30 final size:30
Alignment explanation
Indices: 2038027--2038230 Score: 125
Period size: 30 Copynumber: 6.9 Consensus size: 30
2038017 ATTTTTAGTT
*
2038027 TTTAGAGTTTAGATTTTAGGGTTTGAAGGG
1 TTTAGAGTTTAGATTTTAGGGTTTGAAGGA
** * * *
2038057 TTTATGTTTTTAGTTTTTATGGTTTTAAGGA
1 TTTA-GAGTTTAGATTTTAGGGTTTGAAGGA
* * * *
2038088 TTTAGAGTTTAAATTTTATGGTTTGGAGGG
1 TTTAGAGTTTAGATTTTAGGGTTTGAAGGA
* *
2038118 TTTAGATTTTTA-ATTTTTAGGGTTT-TAGGTA
1 TTTAGA-GTTTAGA-TTTTAGGGTTTGAAGG-A
* *
2038149 TTTAGGGTTTAGATTTTAAGGTTTGAA-G-
1 TTTAGAGTTTAGATTTTAGGGTTTGAAGGA
* * * *
2038177 TTTAAATTTTTA-ATTTTAGAGTTTGGA-G-
1 TTTAGA-GTTTAGATTTTAGGGTTTGAAGGA
* * *
2038205 TTTAGGGTTTCGATTATAGGGTTTGA
1 TTTAGAGTTTAGATTTTAGGGTTTGA
2038231 GGTTTATGGT
Statistics
Matches: 132, Mismatches: 34, Indels: 18
0.72 0.18 0.10
Matches are distributed among these distances:
27 3 0.02
28 32 0.24
29 4 0.03
30 48 0.36
31 45 0.34
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.51
Consensus pattern (30 bp):
TTTAGAGTTTAGATTTTAGGGTTTGAAGGA
Found at i:2038370 original size:3 final size:3
Alignment explanation
Indices: 2038364--2038408 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
2038354 TAATGAAAAT
*
2038364 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2038409 TAATAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2039779 original size:14 final size:13
Alignment explanation
Indices: 2039756--2039802 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
2039746 ATTAAACCAA
*
2039756 TATTAATATTTTAT
1 TATTATTATTTT-T
2039770 TATTATTATTTTT
1 TATTATTATTTTT
*
2039783 CTATTATAATTTTT
1 -TATTATTATTTTT
2039797 TATTAT
1 TATTAT
2039803 AATTATTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 7 0.23
14 23 0.77
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTATTTTT
Found at i:2039800 original size:13 final size:13
Alignment explanation
Indices: 2039763--2039806 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 13
2039753 CAATATTAAT
*
2039763 ATTTTATTATTATT
1 ATTTT-TTATTATA
2039777 ATTTTTCTATTATA
1 ATTTTT-TATTATA
2039791 ATTTTTTATTATA
1 ATTTTTTATTATA
2039804 ATT
1 ATT
2039807 ATTAATAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTTTATTATA
Found at i:2042459 original size:21 final size:22
Alignment explanation
Indices: 2042418--2042460 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2042408 TTTTTTATAC
2042418 AGAAATAAAAAATACAATCAAT
1 AGAAATAAAAAATACAATCAAT
* *
2042440 AGAAATAATAATTA-AATCAAT
1 AGAAATAAAAAATACAATCAAT
2042461 TTTTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.65, C:0.07, G:0.05, T:0.23
Consensus pattern (22 bp):
AGAAATAAAAAATACAATCAAT
Found at i:2042545 original size:11 final size:11
Alignment explanation
Indices: 2042516--2042576 Score: 56
Period size: 11 Copynumber: 5.8 Consensus size: 11
2042506 TAAAATTAAT
2042516 TTAAAATATTA
1 TTAAAATATTA
* *
2042527 TCATAATATTA
1 TTAAAATATTA
*
2042538 TTAAAATAATA
1 TTAAAATATTA
* *
2042549 TT--ATTAAT-
1 TTAAAATATTA
2042557 TTAAAATATTA
1 TTAAAATATTA
2042568 TTAAAATAT
1 TTAAAATAT
2042577 CATTGATATA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
8 2 0.05
9 5 0.13
10 4 0.10
11 28 0.72
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (11 bp):
TTAAAATATTA
Found at i:2042546 original size:14 final size:14
Alignment explanation
Indices: 2042529--2042575 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
2042519 AAATATTATC
2042529 ATAATATTATTAAA
1 ATAATATTATTAAA
2042543 ATAATATTATTAATTTA
1 ATAATATTATTAA---A
2042560 A-AATATTATTAAA
1 ATAATATTATTAAA
2042573 ATA
1 ATA
2042576 TCATTGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.07
14 14 0.48
16 11 0.38
17 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATAATATTATTAAA
Found at i:2043098 original size:21 final size:22
Alignment explanation
Indices: 2043074--2043118 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2043064 TTAATTAACT
* *
2043074 AAAATTTTAATTA-AAATTTAA
1 AAAACTTTAATTATAAAATTAA
2043095 AAAACTTTAATTATAAAATTAA
1 AAAACTTTAATTATAAAATTAA
2043117 AA
1 AA
2043119 CTAATGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAACTTTAATTATAAAATTAA
Found at i:2043504 original size:5 final size:5
Alignment explanation
Indices: 2043494--2043518 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2043484 CAACTCCTCA
2043494 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
2043519 TTATTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:2045747 original size:23 final size:22
Alignment explanation
Indices: 2045700--2045746 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
2045690 TTTTTAAATG
2045700 AAATTATAAATATTAAAATTTA
1 AAATTATAAATATTAAAATTTA
* *
2045722 AAATTATTGAATATT-AATTTTA
1 AAATTA-TAAATATTAAAATTTA
2045744 AAA
1 AAA
2045747 AATTTACATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTATAAATATTAAAATTTA
Found at i:2045806 original size:2 final size:2
Alignment explanation
Indices: 2045793--2045828 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2045783 CAATGTATTC
*
2045793 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2045829 TGCCAGAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2056531 original size:8 final size:8
Alignment explanation
Indices: 2056518--2056542 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2056508 GACAACTAAG
2056518 AATTTTAA
1 AATTTTAA
2056526 AATTTTAA
1 AATTTTAA
2056534 AATTTTAA
1 AATTTTAA
2056542 A
1 A
2056543 TTAAAATCTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:2057753 original size:18 final size:17
Alignment explanation
Indices: 2057730--2057763 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2057720 AAAATTTTAA
2057730 TTTTAATATTTATAATTT
1 TTTTAATATTTA-AATTT
*
2057748 TTTTAATTTTTAAATT
1 TTTTAATATTTAAATT
2057764 ATAAATTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAATATTTAAATTT
Found at i:2057765 original size:23 final size:24
Alignment explanation
Indices: 2057724--2057772 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
2057714 AATAATAAAA
*
2057724 TTTTAATTTTAATATTTATAATTT
1 TTTTAATTTTAATATTTATAAATT
2057748 TTTTAATTTTTAA-A-TTATAAATT
1 TTTTAA-TTTTAATATTTATAAATT
2057771 TT
1 TT
2057773 GGTAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 10 0.43
24 7 0.30
25 6 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (24 bp):
TTTTAATTTTAATATTTATAAATT
Found at i:2060321 original size:29 final size:29
Alignment explanation
Indices: 2060286--2060343 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2060276 ATGAGATAAA
*
2060286 TTTTCAATACTATAATACAAAATAAAAAT
1 TTTTCAATACTATAATACAAAAAAAAAAT
2060315 TTTTCAATACTATAATACAAAAAAAAAAT
1 TTTTCAATACTATAATACAAAAAAAAAAT
2060344 AGTACTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (29 bp):
TTTTCAATACTATAATACAAAAAAAAAAT
Found at i:2074351 original size:21 final size:21
Alignment explanation
Indices: 2074327--2074388 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
2074317 TAAATTACAA
2074327 TAAATAAATTTAAATAAATCT
1 TAAATAAATTTAAATAAATCT
* * *
2074348 TAAATGAATTTAAATGAATTT
1 TAAATAAATTTAAATAAATCT
*
2074369 TAAAATATAATTAAAATAAA
1 T-AAATA-AATTTAAATAAA
2074389 AGATAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 19 0.58
22 4 0.12
23 10 0.30
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (21 bp):
TAAATAAATTTAAATAAATCT
Found at i:2074352 original size:11 final size:10
Alignment explanation
Indices: 2074327--2074388 Score: 61
Period size: 11 Copynumber: 5.8 Consensus size: 10
2074317 TAAATTACAA
2074327 TAAATAAATT
1 TAAATAAATT
2074337 TAAATAAATCT
1 TAAATAAAT-T
*
2074348 TAAATGAATT
1 TAAATAAATT
*
2074358 TAAATGAATTT
1 TAAAT-AAATT
2074369 TAAAATATAATT
1 T-AAATA-AATT
*
2074381 AAAATAAA
1 TAAATAAA
2074389 AGATAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
10 17 0.40
11 19 0.44
12 7 0.16
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (10 bp):
TAAATAAATT
Found at i:2074460 original size:11 final size:11
Alignment explanation
Indices: 2074446--2074478 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
2074436 AAATAACGAA
2074446 TAAATGAATTT
1 TAAATGAATTT
*
2074457 TAAATAAATTT
1 TAAATGAATTT
2074468 TAAATGAATTT
1 TAAATGAATTT
2074479 ATTTACAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (11 bp):
TAAATGAATTT
Found at i:2081901 original size:40 final size:41
Alignment explanation
Indices: 2081836--2081915 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 41
2081826 ATTTTAGCAA
* *
2081836 AAATTTAAAATAATATATTTTTA-TTTA-ACATATTAATAT
1 AAATTTAAAATAACATATTTTTATTTTATACATATAAATAT
2081875 AAATTATAAAATAACAT-TTTTATATTTTATACATATAAATA
1 AAATT-TAAAATAACATATTTT-TATTTTATACATATAAATA
2081916 CAACACAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
39 9 0.26
40 12 0.34
41 4 0.11
42 10 0.29
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (41 bp):
AAATTTAAAATAACATATTTTTATTTTATACATATAAATAT
Found at i:2082667 original size:27 final size:27
Alignment explanation
Indices: 2082637--2082693 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 27
2082627 AATATTATTT
2082637 TTAAATATAAAATA-TAAAAATATAATA
1 TTAAATATAAAATATTAAAAA-ATAATA
*
2082664 TT-AA-ATAAATTATTAAAAAATAATA
1 TTAAATATAAAATATTAAAAAATAATA
2082689 -TAAAT
1 TTAAAT
2082694 GCTTGGGTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
24 1 0.04
25 15 0.58
26 8 0.31
27 2 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
TTAAATATAAAATATTAAAAAATAATA
Found at i:2084196 original size:47 final size:47
Alignment explanation
Indices: 2084124--2084217 Score: 134
Period size: 47 Copynumber: 2.0 Consensus size: 47
2084114 GTCTTGAGTA
* *
2084124 TTAAGATGATTGGCATTGATAGTTTTTGTCACTTAGTTTAGTTATTG
1 TTAAGATGATTGGCATTGATAGTTTTTGACACTAAGTTTAGTTATTG
* * * *
2084171 TTAAGTTGATTGTCATTGCTGGTTTTTGACACTAAGTTTAGTTATTG
1 TTAAGATGATTGGCATTGATAGTTTTTGACACTAAGTTTAGTTATTG
2084218 GATAAATAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.22, C:0.07, G:0.21, T:0.49
Consensus pattern (47 bp):
TTAAGATGATTGGCATTGATAGTTTTTGACACTAAGTTTAGTTATTG
Found at i:2086993 original size:20 final size:20
Alignment explanation
Indices: 2086968--2087008 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2086958 AAGTAAGACA
*
2086968 GCAATTTCCAGAATCTACAG
1 GCAATTTCCACAATCTACAG
2086988 GCAATTTCCACAATCTACAG
1 GCAATTTCCACAATCTACAG
2087008 G
1 G
2087009 GATTTATGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (20 bp):
GCAATTTCCACAATCTACAG
Found at i:2089591 original size:18 final size:17
Alignment explanation
Indices: 2089568--2089606 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
2089558 TAGATTTTAA
*
2089568 AATTAATAAATTACATTT
1 AATTAATAAAATA-ATTT
2089586 AATTAATAAAATAATTT
1 AATTAATAAAATAATTT
2089603 AATT
1 AATT
2089607 TTAGATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTAATAAAATAATTT
Found at i:2108639 original size:25 final size:24
Alignment explanation
Indices: 2108582--2108649 Score: 64
Period size: 26 Copynumber: 2.7 Consensus size: 24
2108572 GAATGAGTAT
* *
2108582 TAAATTTTTTATTTTTTTAATATA
1 TAAATTTTTTATATTATTAATATA
*
2108606 TAAGTATTTTTTATATTATTAATATG
1 TAA--ATTTTTTATATTATTAATATA
* *
2108632 TCAAATTTATTAAATTAT
1 T-AAATTTTTTATATTAT
2108650 AAATGAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 3 0.08
25 12 0.33
26 19 0.53
27 2 0.06
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (24 bp):
TAAATTTTTTATATTATTAATATA
Found at i:2108751 original size:19 final size:20
Alignment explanation
Indices: 2108723--2108774 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
2108713 TTTTCATTCG
2108723 TATA-TATTTATATT-AATC
1 TATATTATTTATATTAAATC
*
2108741 -ATGTCTATTTAT-TTAAATC
1 TATAT-TATTTATATTAAATC
2108760 TATATTATTTATATT
1 TATATTATTTATATT
2108775 TATTTGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 2 0.07
18 2 0.07
19 18 0.67
20 5 0.19
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (20 bp):
TATATTATTTATATTAAATC
Found at i:2113149 original size:36 final size:35
Alignment explanation
Indices: 2113108--2113185 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
2113098 ATTTTAATAT
*
2113108 TATAATATATATT-ATTTTATATTTATCATATTTATA
1 TATAATATATATTAATTTTA-AATTAT-ATATTTATA
* *
2113144 TATAAT-TTTATTAATTTTAAATTATATATTTTTA
1 TATAATATATATTAATTTTAAATTATATATTTATA
*
2113178 TATTATAT
1 TATAATAT
2113186 TATCACATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 13 0.36
35 11 0.31
36 12 0.33
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (35 bp):
TATAATATATATTAATTTTAAATTATATATTTATA
Found at i:2113182 original size:15 final size:15
Alignment explanation
Indices: 2113107--2113185 Score: 50
Period size: 15 Copynumber: 4.7 Consensus size: 15
2113097 AATTTTAATA
*
2113107 TTATAATATATATTATT
1 TTATATTATATA-T-TT
2113124 TTATATTTATCATATTT
1 TTATA-TTAT-ATATTT
* *
2113141 ATATATAATTTTATTAATT
1 -T-TAT-ATTATA-TATTT
*
2113160 TTAAATTATATATTT
1 TTATATTATATATTT
2113175 TTATATTATAT
1 TTATATTATAT
2113186 TATCACATTA
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
15 14 0.29
16 5 0.10
17 9 0.18
18 7 0.14
19 13 0.27
20 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATTATATATTT
Found at i:2116360 original size:34 final size:34
Alignment explanation
Indices: 2116317--2116389 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
2116307 TCAACTTGAC
2116317 CATCAAGGGCTTTTCCAAATA-GTACCTCCTAGAA
1 CATCAAGGGCTTTTCCAAA-AGGTACCTCCTAGAA
*
2116351 CATCAAGGGCTTTTCTAAAAGGTACCTCCTAGAA
1 CATCAAGGGCTTTTCCAAAAGGTACCTCCTAGAA
2116385 -ATCAA
1 CATCAA
2116390 TCATATCAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
33 6 0.16
34 31 0.84
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (34 bp):
CATCAAGGGCTTTTCCAAAAGGTACCTCCTAGAA
Found at i:2124649 original size:24 final size:23
Alignment explanation
Indices: 2124612--2124663 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
2124602 TTTATATAAG
* *
2124612 ATATATTATTAGTATATAAATATT
1 ATATATTATCAGTAAAT-AATATT
*
2124636 ATATATTGTCAGTAAATAATATT
1 ATATATTATCAGTAAATAATATT
*
2124659 TTATA
1 ATATA
2124664 AAAAATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (23 bp):
ATATATTATCAGTAAATAATATT
Found at i:2124783 original size:16 final size:18
Alignment explanation
Indices: 2124743--2124783 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
2124733 TATTTTATAT
2124743 TATTATATAATTGATTGA
1 TATTATATAATTGATTGA
* *
2124761 TAATATATAA-T-ATTTA
1 TATTATATAATTGATTGA
2124777 TATTATA
1 TATTATA
2124784 ACATTTCATC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 10 0.50
17 1 0.05
18 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
TATTATATAATTGATTGA
Found at i:2131732 original size:26 final size:26
Alignment explanation
Indices: 2131692--2131742 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2131682 ATAATTGATC
* * * *
2131692 AAAATTATTATAATATTTATTTTATT
1 AAAATTATGAAAATACTTATCTTATT
2131718 AAAATTATGAAAATACTTATCTTAT
1 AAAATTATGAAAATACTTATCTTAT
2131743 CATAATTAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (26 bp):
AAAATTATGAAAATACTTATCTTATT
Found at i:2131995 original size:128 final size:125
Alignment explanation
Indices: 2131842--2132162 Score: 359
Period size: 128 Copynumber: 2.6 Consensus size: 125
2131832 TTTTATTTAA
*
2131842 AAATTATTATAATACTTCTATTAAATTACATATTAAATTTTAAAATAACATAAAATTAATTAGC-
1 AAATTACTATAATAC-TCTATTAAATTACATATTAAATTTTAAAATAACATAAAATTAATTA-CA
* * * * *
2131906 TATTAAATTATTAGAAT-CCCTTACCATTGCTTCATAGAAATTTGACATATAGTATTTTGTTTG
64 TATTAAATTACTAAAATACCCTTACAATTGCTTCATA-AAAATTGACATATAGCATTTT-TTTG
* * *
2131969 AAATTTACTATAATATCTCTATTAAATTACATATTAAAATTTAATATAATATAAAATTAATTACA
1 AAA-TTACTATAATA-CTCTATTAAATTACATATTAAATTTTAAAATAACATAAAATTAATTACA
* * * * * *
2132034 TATTAAATTACTAAAATACCCTTATAATTGCTTTATAAAAATTGACATGTGGCATTTTATAG
64 TATTAAATTACTAAAATACCCTTACAATTGCTTCATAAAAATTGACATATAGCATTTTTTTG
* * *
2132096 AAATTAC-ATAATACCCCTATTAAATTACATATTAAA--TT--AATTACATAAAACTTAACTACA
1 AAATTACTATAATA-CTCTATTAAATTACATATTAAATTTTAAAATAACATAAAA-TTAATTACA
2132156 TATTAAA
64 TATTAAA
2132163 AACTTATAAT
Statistics
Matches: 168, Mismatches: 21, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
121 9 0.05
122 15 0.09
123 2 0.01
125 27 0.16
126 4 0.02
127 9 0.05
128 85 0.51
129 17 0.10
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (125 bp):
AAATTACTATAATACTCTATTAAATTACATATTAAATTTTAAAATAACATAAAATTAATTACATA
TTAAATTACTAAAATACCCTTACAATTGCTTCATAAAAATTGACATATAGCATTTTTTTG
Found at i:2132036 original size:16 final size:16
Alignment explanation
Indices: 2131993--2132043 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
2131983 ATCTCTATTA
2131993 AATTACATATTAAAATTT
1 AATTACATA-TAAAA-TT
2132011 AATATA-ATATAAAATT
1 AAT-TACATATAAAATT
*
2132027 AATTACATATTAAATT
1 AATTACATATAAAATT
2132043 A
1 A
2132044 CTAAAATACC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
17 5 0.17
18 6 0.20
19 2 0.07
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (16 bp):
AATTACATATAAAATT
Found at i:2132139 original size:16 final size:17
Alignment explanation
Indices: 2132118--2132162 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
2132108 ACCCCTATTA
2132118 AATTACATATTAAA-TT
1 AATTACATATTAAACTT
2132134 AATTACATA--AAACTT
1 AATTACATATTAAACTT
*
2132149 AACTACATATTAAA
1 AATTACATATTAAA
2132163 AACTTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 10 0.40
16 9 0.36
17 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTACATATTAAACTT
Found at i:2132193 original size:15 final size:18
Alignment explanation
Indices: 2132159--2132194 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 18
2132149 AACTACATAT
2132159 TAAAAACTTATAATAAAA
1 TAAAAACTTATAATAAAA
2132177 TAAAAA-TTA-AA-AAAA
1 TAAAAACTTATAATAAAA
2132192 TAA
1 TAA
2132195 TGTGGTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.39
16 2 0.11
17 3 0.17
18 6 0.33
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAAACTTATAATAAAA
Done.