Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000121.1 Hibiscus syriacus cultivar Beakdansim tig00000218_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: 2099483
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1498643 original size:22 final size:22
Alignment explanation
Indices: 1498613--1498668 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
1498603 GTTTAGTATT
1498613 CGTCCCGAAGGACCACTAGATA
1 CGTCCCGAAGGACCACTAGATA
* *
1498635 CGTCTCGAAGGACCACTGGATA
1 CGTCCCGAAGGACCACTAGATA
1498657 CGTCCCGAAGGA
1 CGTCCCGAAGGA
1498669 TTAATATACC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (22 bp):
CGTCCCGAAGGACCACTAGATA
Found at i:1499127 original size:2 final size:2
Alignment explanation
Indices: 1499120--1499154 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1499110 TACAAATTCC
1499120 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
1499155 CTAACTCATG
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:1499872 original size:64 final size:63
Alignment explanation
Indices: 1499771--1499933 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 63
1499761 TCCCTTGACG
* * * *
1499771 GGTGCATCGATGCACTACC-CATGTATCGGTGCATAAAT-CCTATTCGATGTT-TGTATTTTAAG
1 GGTGCATCGATGCACT-CCTTATGAATCGATGCATAAATGCC-ATTCGATGTTAT-TAATTTAA-
1499833 AA
62 AA
* *
1499835 GGTGCATCGATGCACTCCTTATGAATCGATGCATAAATGGCATTCGATGTTCAATTAATTTAAAT
1 GGTGCATCGATGCACTCCTTATGAATCGATGCATAAATGCCATTCGATGTT--ATTAATTTAAAA
*
1499900 GAGTGCATCGATGCACTCCTTATGCATCGATGCA
1 G-GTGCATCGATGCACTCCTTATGAATCGATGCA
1499934 CCTTCAACAA
Statistics
Matches: 86, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
63 2 0.02
64 42 0.49
65 3 0.03
66 38 0.44
67 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (63 bp):
GGTGCATCGATGCACTCCTTATGAATCGATGCATAAATGCCATTCGATGTTATTAATTTAAAA
Found at i:1502087 original size:18 final size:18
Alignment explanation
Indices: 1502064--1502106 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1502054 TTTTATACAG
1502064 GCACTTCCTGAGGTGTTC
1 GCACTTCCTGAGGTGTTC
1502082 GCACTTCCTGAGGTGTTC
1 GCACTTCCTGAGGTGTTC
*
1502100 GCTCTTC
1 GCACTTC
1502107 TCCCTGCCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.09, C:0.30, G:0.26, T:0.35
Consensus pattern (18 bp):
GCACTTCCTGAGGTGTTC
Found at i:1503123 original size:22 final size:22
Alignment explanation
Indices: 1503074--1503192 Score: 156
Period size: 22 Copynumber: 5.6 Consensus size: 22
1503064 GTTCAGTATT
*
1503074 CGTCCCGAATGACCACT--AT-
1 CGTCCCGAAGGACCACTAGATA
1503093 -GTCCCGAAGGACCACTAGATA
1 CGTCCCGAAGGACCACTAGATA
*
1503114 CGTCCTGAAGGACCACTAGATA
1 CGTCCCGAAGGACCACTAGATA
* *
1503136 CGTCCTGAAGGACCACTGGATA
1 CGTCCCGAAGGACCACTAGATA
*
1503158 CGTCCCGAAGGACCACTGGATA
1 CGTCCCGAAGGACCACTAGATA
*
1503180 TGTCCCGAAGGAC
1 CGTCCCGAAGGAC
1503193 TAATATACCC
Statistics
Matches: 91, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.16
20 2 0.02
22 74 0.81
ACGTcount: A:0.29, C:0.30, G:0.24, T:0.17
Consensus pattern (22 bp):
CGTCCCGAAGGACCACTAGATA
Found at i:1506238 original size:46 final size:46
Alignment explanation
Indices: 1506172--1506260 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
1506162 TATAAATGAT
1506172 ATATGAATATGCAATACGTGATACATGTGATATGATATGAAATGGC
1 ATATGAATATGCAATACGTGATACATGTGATATGATATGAAATGGC
* *
1506218 ATATGAATATGTAATTCGTGATACATGTGATATGATATGAAAT
1 ATATGAATATGCAATACGTGATACATGTGATATGATATGAAAT
1506261 ACATGGTTAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (46 bp):
ATATGAATATGCAATACGTGATACATGTGATATGATATGAAATGGC
Found at i:1512986 original size:46 final size:46
Alignment explanation
Indices: 1512916--1513022 Score: 182
Period size: 46 Copynumber: 2.4 Consensus size: 46
1512906 GAGATAAGCT
*
1512916 ATGTGA-AT-ATATGAAATAATATATGAATATGCAATACGTGATAC
1 ATGTGATATGATATGAAATAACATATGAATATGCAATACGTGATAC
*
1512960 ATGTGATATGATATGAAATAACATATGAATATGTAATACGTGATAC
1 ATGTGATATGATATGAAATAACATATGAATATGCAATACGTGATAC
1513006 ATGTGATATGATATGAA
1 ATGTGATATGATATGAA
1513023 TACATGGTTA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
44 6 0.10
45 2 0.03
46 51 0.86
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.33
Consensus pattern (46 bp):
ATGTGATATGATATGAAATAACATATGAATATGCAATACGTGATAC
Found at i:1513014 original size:23 final size:22
Alignment explanation
Indices: 1512942--1513016 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
1512932 TAATATATGA
1512942 ATATGCAATACGTGATACATGTG
1 ATATG-AATACGTGATACATGTG
* ** *
1512965 ATATG-ATATGAAATAACATATG
1 ATATGAATACGTGAT-ACATGTG
1512987 AATATGTAATACGTGATACATGTG
1 -ATATG-AATACGTGATACATGTG
1513011 ATATGA
1 ATATGA
1513017 TATGAATACA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
21 6 0.15
22 7 0.17
23 15 0.38
24 6 0.15
25 6 0.15
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (22 bp):
ATATGAATACGTGATACATGTG
Found at i:1513231 original size:38 final size:38
Alignment explanation
Indices: 1513175--1513270 Score: 138
Period size: 38 Copynumber: 2.5 Consensus size: 38
1513165 TATAAGACAT
* *
1513175 ATGATAGGTCCTACGGGACACAGATTACATCCTTCAGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCAGG
* * *
1513213 ATGACAGGTCCTTCGGGACACAGATGGCATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCAGG
*
1513251 ATGATAGGTCATTCGGGACA
1 ATGATAGGTCCTTCGGGACA
1513271 TTTATACGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCAGG
Found at i:1521146 original size:41 final size:42
Alignment explanation
Indices: 1521101--1521231 Score: 124
Period size: 41 Copynumber: 3.2 Consensus size: 42
1521091 AGTTCACGGT
*
1521101 GTTTGTAAACC-AACGCCGCCACATGCCAACTCTATTGCGGC
1 GTTTGTAAACCAAACGCCACCACATGCCAACTCTATTGCGGC
* * * *
1521142 GTTTGTAAACCAAACGCCACTATATTCCAACTCTATTGCGGT
1 GTTTGTAAACCAAACGCCACCACATGCCAACTCTATTGCGGC
* * * * * * *
1521184 GTTTACTAAA--AAATGCCACTACTTGACAAATCTATAGCGGC
1 GTTT-GTAAACCAAACGCCACCACATGCCAACTCTATTGCGGC
1521225 GTTTGTA
1 GTTTGTA
1521232 TAAAAACAAC
Statistics
Matches: 73, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 2 0.03
41 38 0.52
42 29 0.40
43 4 0.05
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (42 bp):
GTTTGTAAACCAAACGCCACCACATGCCAACTCTATTGCGGC
Found at i:1522820 original size:42 final size:39
Alignment explanation
Indices: 1522754--1522911 Score: 133
Period size: 42 Copynumber: 3.8 Consensus size: 39
1522744 TTGTTAAAAC
*
1522754 AACGCCACTAT-TGATTAACACTATTACGGCGTTTTAGGAATA
1 AACGCCACTATATG-TTAA-TCTATTACGGCGTTTT-GG-ATA
*
1522796 AACGCCACTATATGTGTAATCTATTGCGGCGTTTGTGGTATA
1 AACGCCACTATATGT-TAATCTATTACGGCGTTT-TGG-ATA
* * * *
1522838 AACACCGCTA-AT-TTACCGATTTATTACGGCGTTTTGGCTAA
1 AACGCCACTATATGTTA---ATCTATTACGGCGTTTTGGAT-A
*
1522879 AACGCCACTATATGTTAATCTATTGCGGCGTTT
1 AACGCCACTATATGTTAATCTATTACGGCGTTT
1522912 GTTATAAAAT
Statistics
Matches: 95, Mismatches: 12, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
39 2 0.02
40 16 0.17
41 14 0.15
42 54 0.57
43 9 0.09
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (39 bp):
AACGCCACTATATGTTAATCTATTACGGCGTTTTGGATA
Found at i:1527441 original size:38 final size:38
Alignment explanation
Indices: 1527390--1527464 Score: 89
Period size: 41 Copynumber: 1.9 Consensus size: 38
1527380 AACTTAATGT
*
1527390 TAAATTTTGAAT-GGATACTAAAATGAAATAAAAAAAC
1 TAAATTTTGAATGGGATACTAAAATAAAATAAAAAAAC
* *
1527427 TAAAGTTTTTAATGGCGGGTACTAAAATAAAATAAAAA
1 TAAA-TTTTGAAT-G-GGATACTAAAATAAAATAAAAA
1527465 CTAAACTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
37 4 0.13
38 7 0.23
41 20 0.65
ACGTcount: A:0.53, C:0.05, G:0.13, T:0.28
Consensus pattern (38 bp):
TAAATTTTGAATGGGATACTAAAATAAAATAAAAAAAC
Found at i:1532135 original size:17 final size:17
Alignment explanation
Indices: 1532115--1532150 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1532105 TGATCATGCC
1532115 AGTGTAAAGATCCTGCA
1 AGTGTAAAGATCCTGCA
*
1532132 AGTGTAAATATCCTGCA
1 AGTGTAAAGATCCTGCA
1532149 AG
1 AG
1532151 ATACAAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (17 bp):
AGTGTAAAGATCCTGCA
Found at i:1533008 original size:24 final size:25
Alignment explanation
Indices: 1532967--1533016 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1532957 ACCTAAGTGT
1532967 CGCGTAGAGATTTATCCCGAAGGAC
1 CGCGTAGAGATTTATCCCGAAGGAC
* *
1532992 CGCGTAGA-ATTTGTCCCGAATGAC
1 CGCGTAGAGATTTATCCCGAAGGAC
1533016 C
1 C
1533017 ACATATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (25 bp):
CGCGTAGAGATTTATCCCGAAGGAC
Found at i:1533247 original size:29 final size:30
Alignment explanation
Indices: 1533205--1533274 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
1533195 ACATAATTTA
* * *
1533205 TATCGCATAGACATAACA-TTCCATACCTT
1 TATCACATAAACATAACATTTCCATACATT
**
1533234 TATCACATAAACATTTCATTTTCCATACATT
1 TATCACATAAACATAACA-TTTCCATACATT
*
1533265 TATCCCATAA
1 TATCACATAA
1533275 TTCATATAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 14 0.42
31 19 0.58
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (30 bp):
TATCACATAAACATAACATTTCCATACATT
Found at i:1539817 original size:24 final size:25
Alignment explanation
Indices: 1539777--1539825 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
1539767 CATAAGTGAT
1539777 GCGTAGAGATTTATCCCGAAGGACC
1 GCGTAGAGATTTATCCCGAAGGACC
* *
1539802 GCGTAGA-ATTTGTCCCGAATGACC
1 GCGTAGAGATTTATCCCGAAGGACC
1539826 ACATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (25 bp):
GCGTAGAGATTTATCCCGAAGGACC
Found at i:1540056 original size:29 final size:30
Alignment explanation
Indices: 1540014--1540083 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
1540004 ACATAATTTA
* *
1540014 TATCGCATAGACA-TAATATTCCATACCTT
1 TATCACATAAACATTAATATTCCATACCTT
* * *
1540043 TATCACATAAACATTTCATTTTTCATACCTT
1 TATCACATAAACA-TTAATATTCCATACCTT
*
1540074 TATCCCATAA
1 TATCACATAA
1540084 TTCATATAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 11 0.33
31 22 0.67
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (30 bp):
TATCACATAAACATTAATATTCCATACCTT
Found at i:1545204 original size:28 final size:26
Alignment explanation
Indices: 1545173--1545227 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
1545163 TTTTACTAAT
1545173 AATTTATTTTCACCGTTAAAATTTTATA
1 AATTTATTTT-ACC-TTAAAATTTTATA
**
1545201 AATTTATTTTTTCTTAAAATTTTATA
1 AATTTATTTTACCTTAAAATTTTATA
1545227 A
1 A
1545228 GTTCGTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.56
27 1 0.04
28 10 0.40
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (26 bp):
AATTTATTTTACCTTAAAATTTTATA
Found at i:1545236 original size:26 final size:26
Alignment explanation
Indices: 1545188--1545237 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1545178 ATTTTCACCG
*
1545188 TTAAAATTTTATAAATTTATTTTTTC
1 TTAAAATTTTATAAATTCATTTTTTC
* *
1545214 TTAAAATTTTATAAGTTCGTTTTT
1 TTAAAATTTTATAAATTCATTTTT
1545238 CATATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (26 bp):
TTAAAATTTTATAAATTCATTTTTTC
Found at i:1546792 original size:38 final size:39
Alignment explanation
Indices: 1546710--1546792 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 39
1546700 AACAAGTTGA
* *
1546710 AAAATATTTATATATTTTCTTTAAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAAATTGAAAATCAT
* *
1546750 -AAAATTTATATAATTTT-TTTTACAAAATTGAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAAATTGAAAATCAT
1546787 AAAAAT
1 AAAAAT
1546793 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
37 2 0.05
38 27 0.73
39 8 0.22
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.45
Consensus pattern (39 bp):
AAAAATTTATATATTTTCTTTAAAAAAATTGAAAATCAT
Found at i:1549425 original size:52 final size:52
Alignment explanation
Indices: 1549335--1549438 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 52
1549325 AGGCTCTTAG
* *
1549335 ATTGAATAAAATTTAATGCTGATGCTAACTCCTCATTTTTTTAAGTGATATA
1 ATTGAATAAAATTAAAGGCTGATGCTAACTCCTCATTTTTTTAAGTGATATA
* * * * *
1549387 ATTGAATAAAATTAAAGGGTGATGTTAATTCCTTATTTTTTTCAGTGATATA
1 ATTGAATAAAATTAAAGGCTGATGCTAACTCCTCATTTTTTTAAGTGATATA
1549439 TATATATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (52 bp):
ATTGAATAAAATTAAAGGCTGATGCTAACTCCTCATTTTTTTAAGTGATATA
Found at i:1552910 original size:19 final size:19
Alignment explanation
Indices: 1552888--1552924 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1552878 GGTTTATTTA
*
1552888 ATTTAACTCAAATAAATAT
1 ATTTAACTAAAATAAATAT
*
1552907 ATTTAATTAAAATAAATA
1 ATTTAACTAAAATAAATA
1552925 AAATTTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTAACTAAAATAAATAT
Found at i:1552928 original size:24 final size:24
Alignment explanation
Indices: 1552882--1552926 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1552872 TAATTTGGTT
* *
1552882 TATTTAATTTAACTCAAATAAATA
1 TATTTAATTAAAATCAAATAAATA
1552906 TATTTAATTAAAAT-AAATAAA
1 TATTTAATTAAAATCAAATAAA
1552927 ATTTAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (24 bp):
TATTTAATTAAAATCAAATAAATA
Found at i:1561113 original size:25 final size:25
Alignment explanation
Indices: 1561081--1561135 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
1561071 GATATGCAGA
1561081 AGATTCATATCAAAGACAACATAGC
1 AGATTCATATCAAAGACAACATAGC
* *
1561106 AGATTCATATGAAAGACAACATTGC
1 AGATTCATATCAAAGACAACATAGC
1561131 AGATT
1 AGATT
1561136 TCATGACGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (25 bp):
AGATTCATATCAAAGACAACATAGC
Found at i:1566972 original size:2 final size:2
Alignment explanation
Indices: 1566965--1567011 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1566955 GAAATTCAGA
1566965 AT AT AT AT AT AT 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 AT AT AT
1567007 AT AT A
1 AT AT A
1567012 GATAAAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1569244 original size:26 final size:26
Alignment explanation
Indices: 1569215--1569271 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
1569205 CGAATCATTC
1569215 CACAGGATTTGCATAGAAGAATTGGT
1 CACAGGATTTGCATAGAAGAATTGGT
1569241 CACAGGATTTGCATAGAAGAATTGGT
1 CACAGGATTTGCATAGAAGAATTGGT
1569267 CACAG
1 CACAG
1569272 TTTCCATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.35, C:0.14, G:0.26, T:0.25
Consensus pattern (26 bp):
CACAGGATTTGCATAGAAGAATTGGT
Found at i:1569849 original size:40 final size:40
Alignment explanation
Indices: 1569775--1569899 Score: 171
Period size: 40 Copynumber: 3.1 Consensus size: 40
1569765 TATTTTAGTG
* *
1569775 ACCAAAGATGAA-ATTCCCATGTGTACAAGTTTGGCCACCT
1 ACCAAAGATGAATTTTCCAATGTGTACAAG-TTGGCCACCT
* *
1569815 ACCAAAGATGAATTTTCCAATGCGTACAAGTTGGCCAACT
1 ACCAAAGATGAATTTTCCAATGTGTACAAGTTGGCCACCT
* * *
1569855 ACCAAAGATGAATTTTTCAATGTGTACAAGTTAGCCACCA
1 ACCAAAGATGAATTTTCCAATGTGTACAAGTTGGCCACCT
1569895 ACCAA
1 ACCAA
1569900 CTTATCAACT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
40 61 0.81
41 14 0.19
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (40 bp):
ACCAAAGATGAATTTTCCAATGTGTACAAGTTGGCCACCT
Found at i:1574577 original size:40 final size:40
Alignment explanation
Indices: 1574522--1574622 Score: 148
Period size: 40 Copynumber: 2.5 Consensus size: 40
1574512 TCCCATGTTC
1574522 ACAAGTTTGGCCACCTACCAAAGATGAATTTTCCAAAGTGT
1 ACAAG-TTGGCCACCTACCAAAGATGAATTTTCCAAAGTGT
* * *
1574563 ACAAGTTGGTCACCTACCAAAGATGAATTTTTCAATGTGT
1 ACAAGTTGGCCACCTACCAAAGATGAATTTTCCAAAGTGT
* *
1574603 ACAAGTTAGCCACCAACCAA
1 ACAAGTTGGCCACCTACCAA
1574623 CTTGTCAACT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
40 49 0.91
41 5 0.09
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.26
Consensus pattern (40 bp):
ACAAGTTGGCCACCTACCAAAGATGAATTTTCCAAAGTGT
Found at i:1581273 original size:41 final size:41
Alignment explanation
Indices: 1581211--1581570 Score: 228
Period size: 41 Copynumber: 8.7 Consensus size: 41
1581201 TAAAGAGTGG
**
1581211 ACTTTAGTGGC-TTTTTATACAAACGCCATTATAGACTCAT
1 ACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCAT
* *
1581251 ACTTTAGTGGCGTTTTTATACAAACGCCG-TAATAGGACACAT
1 ACTTTAGTGGCATTTTTATACAAACGCCGCT-ATA-GACTCAT
* * * * ** * *
1581293 A-TATAATGACATTTTT-TAAAAAACAACG-TAAGAGATTCAT
1 ACTTTAGTGGCATTTTTAT-ACAAACGCCGCT-ATAGACTCAT
* * * * * **
1581333 ACTTTAATGGCATTTTTTTAATAAATGCCGCAATTTA-TCAAT
1 ACTTTAGTGGCATTTTTAT-ACAAACGCCGCTATAGACTC-AT
* * * * * * *
1581375 ACATTAGGGGCGTTTGTATACAAACACCGCTAAAGACTCGT
1 ACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCAT
* * * *
1581416 ACTTTAATGGCATTTTTATACAAAAGTCGCTAAAGACTCAT
1 ACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCAT
* * * * * **
1581457 ATTTTAGTGACGTTTTTATACAAAAGTCGCTATAGACTTGT
1 ACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCAT
* *
1581498 ACTTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGT
1 ACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCAT
* * *
1581539 ACTTTAGTGTCGTTTGTGTCTACAAACGCCGC
1 ACTTTAGTGGCATTT-T-TATACAAACGCCGC
1581571 AAGTTTATAG
Statistics
Matches: 247, Mismatches: 62, Indels: 19
0.75 0.19 0.06
Matches are distributed among these distances:
40 19 0.08
41 180 0.73
42 35 0.14
43 13 0.05
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (41 bp):
ACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCAT
Found at i:1583476 original size:21 final size:21
Alignment explanation
Indices: 1583452--1583495 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1583442 TGATTTATTA
*
1583452 TTATGGATTTCAAGTTTCTTG
1 TTATGAATTTCAAGTTTCTTG
*
1583473 TTATGAATTTCAAGTTTGTTG
1 TTATGAATTTCAAGTTTCTTG
1583494 TT
1 TT
1583496 TTTTATGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.55
Consensus pattern (21 bp):
TTATGAATTTCAAGTTTCTTG
Found at i:1584066 original size:18 final size:17
Alignment explanation
Indices: 1584035--1584070 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1584025 ATTCTGATTG
*
1584035 ATTTTAATTTAATTTAA
1 ATTTTAATTAAATTTAA
1584052 ATTTTAAATTAAATTTAA
1 ATTTT-AATTAAATTTAA
1584070 A
1 A
1584071 CCATAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTAATTAAATTTAA
Found at i:1584103 original size:14 final size:13
Alignment explanation
Indices: 1584080--1584119 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
1584070 ACCATAATAT
1584080 TTAAAT-ATTAAA
1 TTAAATAATTAAA
*
1584092 TTAAATTAATTAAT
1 TTAAA-TAATTAAA
1584106 TTAAATAATTAAA
1 TTAAATAATTAAA
1584119 T
1 T
1584120 CCGAAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.21
13 9 0.38
14 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TTAAATAATTAAA
Found at i:1585737 original size:27 final size:28
Alignment explanation
Indices: 1585704--1585758 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
1585694 AAGAATGAAC
1585704 TTATAAAATTTTAAA-A-AAATAATAAAT
1 TTATAAAATTTTAAAGACAAA-AATAAAT
1585731 TTATAAAATTTTAAAGACAAAAATAAAT
1 TTATAAAATTTTAAAGACAAAAATAAAT
1585759 CAACAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 15 0.58
28 8 0.31
29 3 0.12
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (28 bp):
TTATAAAATTTTAAAGACAAAAATAAAT
Found at i:1587879 original size:12 final size:12
Alignment explanation
Indices: 1587862--1587887 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1587852 GTAGACACTC
1587862 GACTTAATATTA
1 GACTTAATATTA
1587874 GACTTAATATTA
1 GACTTAATATTA
1587886 GA
1 GA
1587888 ATAGTAGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (12 bp):
GACTTAATATTA
Found at i:1588936 original size:22 final size:22
Alignment explanation
Indices: 1588891--1588960 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
1588881 ATAAGCATCA
* *
1588891 AATACAATAAATAATATT-TATT
1 AATA-AATTAATAATATTATTTT
1588913 AATAAATTAATAATATTATTTT
1 AATAAATTAATAATATTATTTT
1588935 AA-AATATTAAACTAAT-TTA-TTT
1 AATAA-ATT-AA-TAATATTATTTT
1588957 AATA
1 AATA
1588961 TTTATGTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 14 0.34
22 17 0.41
23 6 0.15
24 4 0.10
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (22 bp):
AATAAATTAATAATATTATTTT
Found at i:1588986 original size:14 final size:14
Alignment explanation
Indices: 1588969--1589056 Score: 63
Period size: 14 Copynumber: 6.2 Consensus size: 14
1588959 TATTTATGTC
1588969 AATATTATTATTAA
1 AATATTATTATTAA
*
1588983 AATATTA-TATCTAC
1 AATATTATTAT-TAA
* * *
1588997 AATTTTATAAATAAA
1 AATATTAT-TATTAA
*
1589012 AATATTATGATTAA
1 AATATTATTATTAA
*
1589026 TATATT-TTATTAA
1 AATATTATTATTAA
**
1589039 AATAAAATTATTATA
1 AATATTATTATTA-A
1589054 AAT
1 AAT
1589057 TATAGTAATT
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
13 12 0.21
14 30 0.54
15 12 0.21
16 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (14 bp):
AATATTATTATTAA
Found at i:1589455 original size:159 final size:156
Alignment explanation
Indices: 1589248--1589561 Score: 531
Period size: 159 Copynumber: 2.0 Consensus size: 156
1589238 CGTAAAATGG
1589248 CTTACGGAAAATCAGATGATAAGTCGTTTTCCAGAAAATATAAAGAAAATTCAATTGATCAGAAA
1 CTTACGGAAAATCAGATGATAAGTCGTTTTCCAGAAAATATAAAGAAAATTCAATTGATCAG-AA
1589313 AAATAAATTACATTAACCATCTG-TTTTCATTAACCAAACACTGAAAAATGAGAAAAAAATATTT
65 AAATAAATTACATTAACCATCTGTTTTTCATTAACCAAACACTGAAAAAT--GAAAAAAATA-TT
1589377 TTCAAAAAAAACAATTACAAGGAAACAAAA
127 TTCAAAAAAAACAATTACAAGGAAACAAAA
*
1589407 CTTACGGAAAATCAGATGATAAGTCGTTTTCCAGAAAATATAAAGAAAATTCAGTTGATCAGAAA
1 CTTACGGAAAATCAGATGATAAGTCGTTTTCCAGAAAATATAAAGAAAATTCAATTGATCAGAAA
* * * *
1589472 AATGAATTATATTAACCATTTGTTTTTCATTAACCAAACACTGAAAAATGAAAAAAATATTTTCC
66 AATAAATTACATTAACCATCTGTTTTTCATTAACCAAACACTGAAAAATGAAAAAAATATTTTCA
*
1589537 AAAAAAATAATTACAAGGAAACAAA
131 AAAAAAACAATTACAAGGAAACAAA
1589562 TAGACCCTTT
Statistics
Matches: 148, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
156 29 0.20
157 10 0.07
158 22 0.15
159 87 0.59
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (156 bp):
CTTACGGAAAATCAGATGATAAGTCGTTTTCCAGAAAATATAAAGAAAATTCAATTGATCAGAAA
AATAAATTACATTAACCATCTGTTTTTCATTAACCAAACACTGAAAAATGAAAAAAATATTTTCA
AAAAAAACAATTACAAGGAAACAAAA
Found at i:1603117 original size:23 final size:22
Alignment explanation
Indices: 1603091--1603154 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
1603081 CAGCTCATAT
1603091 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* * *
1603114 AATTGCACCGGAGTACCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
1603137 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
1603155 TATAATAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:1603295 original size:103 final size:103
Alignment explanation
Indices: 1603170--1603490 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
1603160 TAATGTCCAT
*
1603170 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1603235 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1603273 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1603338 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
1603376 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
1603441 GACCTCACACATGTTCCAAAGAATACATATATATCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
1603479 AAGGACCACATA
1 AAGGACCACATA
1603491 GACCCTCTAC
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 213 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1604058 original size:21 final size:21
Alignment explanation
Indices: 1604034--1604076 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1604024 TCATATTCGT
* *
1604034 TTGAGGGGGGATCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
* *
1604055 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGGACCGATTCCCC
1604076 T
1 T
1604077 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGGACCGATTCCCC
Found at i:1606238 original size:43 final size:43
Alignment explanation
Indices: 1606165--1606433 Score: 135
Period size: 43 Copynumber: 6.2 Consensus size: 43
1606155 TTTCAACAAA
** * *
1606165 AAAACGCCGCAATAGGT-TACAACATATAGCGGCGATTGT-TCA-
1 AAAACGCCGCAATAGGTAT-TGATATTTAGCGGCGATT-TATCAT
*
1606207 ACAAACGCCGCAAAAGGTATTGATATTTAGCGGCG-TTTATCATT
1 A-AAACGCCGCAATAGGTATTGATATTTAGCGGCGATTTATCA-T
* * ** *
1606251 AAAACGCCGCAATAGGTTTTGATATTTAACGGC-ATTTGGCAG
1 AAAACGCCGCAATAGGTATTGATATTTAGCGGCGATTTATCAT
* * * *
1606293 ACAAACGCCGCAATA-GTCGTTGATGTTTAGCGGCGTTTTCTTCA-
1 A-AAACGCCGCAATAGGT-ATTGATATTTAGCGGCGATTT-ATCAT
* ** * * * * *
1606337 AAAACGCCGCAGTAAATTTTTATTTTTACCGGCG-TTT-TCCT
1 AAAACGCCGCAATAGGTATTGATATTTAGCGGCGATTTATCAT
* * * *
1606378 AAAAACGCCGCAGAATATGTATTGAGATTTTGCGGCGTTTTTATCA-
1 -AAAACGCCGC--AATAGGTATTGATATTTAGCGGCG-ATTTATCAT
1606424 AAAACGCCGC
1 AAAACGCCGC
1606434 TAAATGTATG
Statistics
Matches: 175, Mismatches: 34, Indels: 33
0.72 0.14 0.14
Matches are distributed among these distances:
40 2 0.01
41 1 0.01
42 22 0.13
43 111 0.63
44 22 0.13
45 12 0.07
46 3 0.02
47 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (43 bp):
AAAACGCCGCAATAGGTATTGATATTTAGCGGCGATTTATCAT
Found at i:1606796 original size:21 final size:21
Alignment explanation
Indices: 1606772--1606825 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1606762 ATATATTACT
*
1606772 TCTCTCTGTTCTGCCGCTGCC
1 TCTCTCTGTGCTGCCGCTGCC
* *
1606793 TCTCGCTGTGCTGCCGCTGCT
1 TCTCTCTGTGCTGCCGCTGCC
*
1606814 TCTCTCTCTGCT
1 TCTCTCTGTGCT
1606826 TCCGTTGCTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.00, C:0.41, G:0.20, T:0.39
Consensus pattern (21 bp):
TCTCTCTGTGCTGCCGCTGCC
Found at i:1606834 original size:21 final size:21
Alignment explanation
Indices: 1606801--1606870 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
1606791 CCTCTCGCTG
* *
1606801 TGCTGCCGCTGCTTCTCTCTC
1 TGCTTCCGCTGCTGCTCTCTC
* **
1606822 TGCTTCCGTTGCTGCTCTAGC
1 TGCTTCCGCTGCTGCTCTCTC
1606843 TGCTTCCGCTGCTGCTCTCTC
1 TGCTTCCGCTGCTGCTCTCTC
*
1606864 TGTTTCC
1 TGCTTCC
1606871 CTTGCTTCAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.01, C:0.39, G:0.20, T:0.40
Consensus pattern (21 bp):
TGCTTCCGCTGCTGCTCTCTC
Found at i:1612517 original size:42 final size:42
Alignment explanation
Indices: 1612461--1612550 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 42
1612451 TATATCAGAA
* * *
1612461 TATTGCGGCGTTTTTAATAC-AAACGCCGCAAAGGAACTATTT
1 TATTGCGGCATTTTT-ATACAAAACGCCACAAAGGAACTATTC
* * *
1612503 TATTGCTGCATTTTTTTACGAAAACGCCACTAAGGAACTATTC
1 TATTGCGGCATTTTTATAC-AAAACGCCACAAAGGAACTATTC
1612546 TATTG
1 TATTG
1612551 AGGTGATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 3 0.08
42 13 0.32
43 24 0.60
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (42 bp):
TATTGCGGCATTTTTATACAAAACGCCACAAAGGAACTATTC
Found at i:1613276 original size:41 final size:41
Alignment explanation
Indices: 1613210--1613370 Score: 204
Period size: 41 Copynumber: 4.0 Consensus size: 41
1613200 CGTTTATACA
1613210 AAAAAACACCACTATTGATTA-CACTATT-CTGGCGTTTGTT
1 AAAAAACACCACTATTGATTATCACTATTGC-GGCGTTTGTT
*
1613250 AAAAAACGCCACTATTGATTATCACTATTGCGGCGTTT-TT
1 AAAAAACACCACTATTGATTATCACTATTGCGGCGTTTGTT
* * * * **
1613290 CTAAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCT
1 -AAAAAACACCACTATTGATTATCACTATTGCGGCGTTTGT-T
1613333 -AAAAACACCACTATTGATTATCACTATTGCGGCGTTTG
1 AAAAAACACCACTATTGATTATCACTATTGCGGCGTTTG
1613371 AGGAATAAAC
Statistics
Matches: 105, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
40 22 0.21
41 80 0.76
42 2 0.02
43 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (41 bp):
AAAAAACACCACTATTGATTATCACTATTGCGGCGTTTGTT
Found at i:1613328 original size:82 final size:81
Alignment explanation
Indices: 1613211--1613369 Score: 257
Period size: 82 Copynumber: 2.0 Consensus size: 81
1613201 GTTTATACAA
* *
1613211 AAAAACACCACTATTGATTACACTATTCTGGCGTTTGT-TAAAAAACGCCACTATTGATTATCAC
1 AAAAACACCACTATTGATTACACTATTATGGCGTTTGTCT-AAAAACACCACTATTGATTATCAC
1613275 TATTGCGGCGTTTTTCT
65 TATTGCGGCGTTTTTCT
* *
1613292 AAAAACGCCATTATTGATTAACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
1 AAAAACACCACTATTGATT-ACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCAC
1613357 TATTGCGGCGTTT
65 TATTGCGGCGTTT
1613370 GAGGAATAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
81 17 0.24
82 54 0.75
83 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (81 bp):
AAAAACACCACTATTGATTACACTATTATGGCGTTTGTCTAAAAACACCACTATTGATTATCACT
ATTGCGGCGTTTTTCT
Found at i:1613450 original size:42 final size:41
Alignment explanation
Indices: 1613399--1613550 Score: 130
Period size: 42 Copynumber: 3.7 Consensus size: 41
1613389 ATGTGTAATA
*
1613399 TATTACGGCGTTTGTGGTATAAACGCCATGAATTTACCACTC
1 TATTGCGGCGTTTGTGGTATAAACGCCAT-AATTTACCACTC
* * * *
1613441 TATTGCGGCGTTT-TGGCT-CAATCGCCGCAAAATTTA-TACTC
1 TATTGCGGCGTTTGTGG-TATAAACG-C-CATAATTTACCACTC
* * *
1613482 TATTGTGGCGTTTGTGGTATAAACGCCGCTAATTTACCACCC
1 TATTGCGGCGTTTGTGGTATAAACGCC-ATAATTTACCACTC
* * * *
1613524 TATTGCGGCATTTTTTGTAAAAACGCC
1 TATTGCGGCGTTTGTGGTATAAACGCC
1613551 GCTATATGTC
Statistics
Matches: 86, Mismatches: 17, Indels: 14
0.74 0.15 0.12
Matches are distributed among these distances:
40 1 0.01
41 31 0.36
42 52 0.60
43 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (41 bp):
TATTGCGGCGTTTGTGGTATAAACGCCATAATTTACCACTC
Found at i:1613569 original size:42 final size:42
Alignment explanation
Indices: 1613478--1613597 Score: 125
Period size: 42 Copynumber: 2.9 Consensus size: 42
1613468 CAAAATTTAT
* * * * *
1613478 ACTCTATTGTGGCGTTTGTGGTATAAACGCCGCTAATTTACC
1 ACTCTATTGCGGCGTTTGTAGTAAAAACGCCGCTAATGTACA
* * * *
1613520 ACCCTATTGCGGCATTTTTTGTAAAAACGCCGCTATATGT-CA
1 ACTCTATTGCGGCGTTTGTAGTAAAAACGCCGCTA-ATGTACA
* *
1613562 ACTCTATTGCAGCGTTTGTACTAAAAACGCCGCTAA
1 ACTCTATTGCGGCGTTTGTAGTAAAAACGCCGCTAA
1613598 AGTATCAATT
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
41 1 0.02
42 59 0.94
43 3 0.05
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (42 bp):
ACTCTATTGCGGCGTTTGTAGTAAAAACGCCGCTAATGTACA
Found at i:1625745 original size:8 final size:8
Alignment explanation
Indices: 1625734--1625778 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
1625724 TTAAAATTTT
1625734 AAATATAA
1 AAATATAA
1625742 AAATATAA
1 AAATATAA
*
1625750 AAA-AT-T
1 AAATATAA
1625756 AAATATAA
1 AAATATAA
1625764 AAATATAA
1 AAATATAA
*
1625772 AATTATA
1 AAATATA
1625779 TGTATGTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 3 0.09
7 4 0.12
8 25 0.78
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (8 bp):
AAATATAA
Found at i:1625757 original size:22 final size:22
Alignment explanation
Indices: 1625732--1625773 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1625722 GTTTAAAATT
1625732 TTAAATATAAAAATATAAAAAA
1 TTAAATATAAAAATATAAAAAA
1625754 TTAAATATAAAAATATAAAA
1 TTAAATATAAAAATATAAAA
1625774 TTATATGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TTAAATATAAAAATATAAAAAA
Found at i:1626128 original size:15 final size:15
Alignment explanation
Indices: 1626110--1626168 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
1626100 TATTTTTCTT
*
1626110 ATTTTTTTATATTTA
1 ATTTTTTTAAATTTA
*
1626125 ATTTTTTGAAATTT-
1 ATTTTTTTAAATTTA
*
1626139 -TTATATTTTATATTTA
1 ATT-T-TTTTAAATTTA
1626155 ATTTTTTTAAATTT
1 ATTTTTTTAAATTT
1626169 TTTAAAAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
13 2 0.06
14 1 0.03
15 29 0.83
16 1 0.03
17 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
ATTTTTTTAAATTTA
Found at i:1626148 original size:30 final size:30
Alignment explanation
Indices: 1626114--1626170 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
1626104 TTTCTTATTT
1626114 TTTTATATTTAATTTTTTGAAATTTTTATA
1 TTTTATATTTAATTTTTTGAAATTTTTATA
*
1626144 TTTTATATTTAATTTTTTTAAATTTTT
1 TTTTATATTTAATTTTTTGAAATTTTT
1626171 TAAAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (30 bp):
TTTTATATTTAATTTTTTGAAATTTTTATA
Found at i:1626588 original size:10 final size:10
Alignment explanation
Indices: 1626556--1626590 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1626546 ATAACCTGAT
1626556 AATTTTAAAA
1 AATTTTAAAA
*
1626566 AATTTATATAA
1 AATTT-TAAAA
1626577 AATTTTAAAA
1 AATTTTAAAA
1626587 AATT
1 AATT
1626591 AAAATTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
AATTTTAAAA
Found at i:1637294 original size:12 final size:12
Alignment explanation
Indices: 1637279--1637303 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1637269 ATATTTTCGG
1637279 TAAAATATTATT
1 TAAAATATTATT
1637291 TAAAATATTATT
1 TAAAATATTATT
1637303 T
1 T
1637304 TTTTTATGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:1638146 original size:15 final size:15
Alignment explanation
Indices: 1638111--1638147 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1638101 AAACCATGTT
*
1638111 AAATAAAAAGGTAAT
1 AAATAAAAAGGTAAG
*
1638126 AGATAAAAAGGTAAG
1 AAATAAAAAGGTAAG
1638141 AAATAAA
1 AAATAAA
1638148 TAAATTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (15 bp):
AAATAAAAAGGTAAG
Found at i:1638280 original size:13 final size:13
Alignment explanation
Indices: 1638222--1638296 Score: 53
Period size: 13 Copynumber: 5.6 Consensus size: 13
1638212 AAATAGTAAG
*
1638222 TAAAATAAATATAA
1 TAAAATAAAGA-AA
1638236 -AAAATAAAGAAA
1 TAAAATAAAGAAA
* *
1638248 AAGAAGAAAAAGAAA
1 TA-AA-ATAAAGAAA
* *
1638263 AAAAATATAGAAA
1 TAAAATAAAGAAA
* *
1638276 TAAAACAAATAAA
1 TAAAATAAAGAAA
1638289 TAAAATAA
1 TAAAATAA
1638297 TAATAAAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
12 2 0.04
13 33 0.67
14 4 0.08
15 10 0.20
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.15
Consensus pattern (13 bp):
TAAAATAAAGAAA
Found at i:1638280 original size:54 final size:51
Alignment explanation
Indices: 1638222--1638345 Score: 126
Period size: 54 Copynumber: 2.3 Consensus size: 51
1638212 AAATAGTAAG
1638222 TAAAATAAATATAAAAAATAAAGA-AAAAGAAG-AAAAAGAAAAAAAATATAGAAA
1 TAAAA-AAATA-AAAAAATAAA-ATAAAA-AAGTAAAAAGAAAAAAAATATA-AAA
* * * *
1638276 TAAAACAAATAAATAAAATAATAATAAAAAAGTAAAAATAATATATATATAAAA
1 TAAAA-AAATAAA-AAAATAA-AATAAAAAAGTAAAAAGAAAAAAAATATAAAA
1638330 TAAAAAAATAAAAAAA
1 TAAAAAAATAAAAAAA
1638346 AGTAAATATA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
52 4 0.07
53 9 0.15
54 29 0.48
55 19 0.31
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.18
Consensus pattern (51 bp):
TAAAAAAATAAAAAAATAAAATAAAAAAGTAAAAAGAAAAAAAATATAAAA
Found at i:1638293 original size:28 final size:28
Alignment explanation
Indices: 1638232--1638307 Score: 68
Period size: 28 Copynumber: 2.7 Consensus size: 28
1638222 TAAAATAAAT
*
1638232 ATAAAAAATAAAGAAAAAGAAGAAAAAG
1 ATAAAAAATAAAGAAAAAGAACAAAAAG
* *
1638260 AAAAAAAATATAGAAATAA-AACAAATAA-
1 ATAAAAAATAAAGAAA-AAGAACAAA-AAG
1638288 ATAAAATAATAATA-AAAAAG
1 ATAAAA-AATAA-AGAAAAAG
1638308 TAAAAATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
28 26 0.68
29 11 0.29
30 1 0.03
ACGTcount: A:0.78, C:0.01, G:0.08, T:0.13
Consensus pattern (28 bp):
ATAAAAAATAAAGAAAAAGAACAAAAAG
Found at i:1638314 original size:25 final size:24
Alignment explanation
Indices: 1638275--1638342 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
1638265 AAATATAGAA
* *
1638275 ATAAAACAAATAAATAAAATA-AT
1 ATAAAATAAAAAAATAAAATATAT
*
1638298 AATAAAA-AAGTAAAAATAATATATAT
1 -ATAAAATAA--AAAAATAAAATATAT
1638324 ATAAAATAAAAAAATAAAA
1 ATAAAATAAAAAAATAAAA
1638343 AAAAGTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.05
24 15 0.41
25 16 0.43
26 4 0.11
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (24 bp):
ATAAAATAAAAAAATAAAATATAT
Found at i:1638331 original size:41 final size:43
Alignment explanation
Indices: 1638286--1638432 Score: 146
Period size: 41 Copynumber: 3.4 Consensus size: 43
1638276 TAAAACAAAT
*
1638286 AAATAAAATAATAATAAAAAAGTAAA-A-ATA-ATATATATATA
1 AAATAAAAAAATAA-AAAAAAGTAAATATATATATATATATATA
1638327 AAATAAAAAAATAAAAAAAAGTAAATATATATATATATATATA
1 AAATAAAAAAATAAAAAAAAGTAAATATATATATATATATATA
1638370 AAATTAATAAAACTGATAATAAAAAA-T-AATATAT-T-TATATATATA
1 AAA-TAA-AAAA---ATAA-AAAAAAGTAAATATATATATATATATATA
**
1638415 ATCTAAAAAAAATAAAAA
1 AAAT-AAAAAAATAAAAA
1638433 TATATACTAA
Statistics
Matches: 93, Mismatches: 3, Indels: 21
0.79 0.03 0.18
Matches are distributed among these distances:
40 14 0.15
41 18 0.19
42 3 0.03
43 14 0.15
44 8 0.09
45 17 0.18
46 1 0.01
47 7 0.08
48 5 0.05
49 6 0.06
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.29
Consensus pattern (43 bp):
AAATAAAAAAATAAAAAAAAGTAAATATATATATATATATATA
Found at i:1638336 original size:24 final size:22
Alignment explanation
Indices: 1638254--1638340 Score: 68
Period size: 24 Copynumber: 3.6 Consensus size: 22
1638244 GAAAAAGAAG
*
1638254 AAAAAGAAAAAA-AATATAGAAAT
1 AAAAA-AAAAAATAATATA-ATAT
* *
1638277 AAAACAAATAAATAAAATAATAAT
1 AAAA-AAAAAAATAATATAAT-AT
1638301 AAAAAAGTAAAAATAATATATATAT
1 AAAAAA--AAAAATAATATA-ATAT
1638326 AAAATAAAAAAATAA
1 AAAA-AAAAAAATAA
1638341 AAAAAAGTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
23 12 0.23
24 20 0.38
25 16 0.31
26 4 0.08
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (22 bp):
AAAAAAAAAAATAATATAATAT
Found at i:1638344 original size:31 final size:31
Alignment explanation
Indices: 1638273--1638357 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 31
1638263 AAAAATATAG
*
1638273 AAATAAAACAAA-TAAATAAAATAATAATAAAA
1 AAATAAAA-AAAGTAAAT-ATATAATAATAAAA
* *
1638305 AAGTAAAAATAA-TATATATATAA-AATAAAA
1 AAATAAAAA-AAGTAAATATATAATAATAAAA
1638335 AAATAAAAAAAAGTAAATATATA
1 AAAT-AAAAAAAGTAAATATATA
1638358 TATATATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 12 0.27
31 20 0.44
32 13 0.29
ACGTcount: A:0.74, C:0.01, G:0.02, T:0.22
Consensus pattern (31 bp):
AAATAAAAAAAGTAAATATATAATAATAAAA
Found at i:1638345 original size:9 final size:9
Alignment explanation
Indices: 1638222--1638351 Score: 66
Period size: 9 Copynumber: 13.4 Consensus size: 9
1638212 AAATAGTAAG
*
1638222 TAAAATAAA
1 TAAAAAAAA
*
1638231 TATAAAAAA
1 TAAAAAAAA
1638240 TAAAGAAAAA
1 TAAA-AAAAA
* *
1638250 GAAGAAAAA
1 TAAAAAAAA
*
1638259 GAAAAAAAA
1 TAAAAAAAA
* *
1638268 T-ATAGAAA
1 TAAAAAAAA
*
1638276 TAAAACAAA
1 TAAAAAAAA
1638285 TAAATAAAATAA
1 T-AA-AAAA-AA
1638297 TAATAAAAAA
1 TAA-AAAAAA
1638307 GTAAAAATAATA
1 -TAAAAA-AA-A
*
1638319 TATATATAAAA
1 TA-A-AAAAAA
1638330 T-AAAAAAA
1 TAAAAAAAA
1638338 TAAAAAAAA
1 TAAAAAAAA
1638347 GTAAA
1 -TAAA
1638352 TATATATATA
Statistics
Matches: 95, Mismatches: 14, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
8 12 0.13
9 37 0.39
10 18 0.19
11 19 0.20
12 7 0.07
13 2 0.02
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:1638412 original size:51 final size:50
Alignment explanation
Indices: 1638336--1638431 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 50
1638326 AAAATAAAAA
**
1638336 AATAAAAAAAAGTAAATATATATATATATATATAAAATTAATAAAACTGAT
1 AATAAAAAAAAGTAAATATATATATATA-ATATAAAAAAAATAAAACTGAT
* * *
1638387 AATAAAAAATAA-TATATTTATATATATAATCTAAAAAAAATAAAA
1 AATAAAAAA-AAGTAAATATATATATATAATATAAAAAAAATAAAA
1638432 ATATATACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
50 14 0.36
51 23 0.59
52 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (50 bp):
AATAAAAAAAAGTAAATATATATATATAATATAAAAAAAATAAAACTGAT
Found at i:1638483 original size:23 final size:22
Alignment explanation
Indices: 1638428--1638489 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
1638418 TAAAAAAAAT
1638428 AAAAATATATAC-T-AAAGTAAA
1 AAAAATAT-TACATAAAAGTAAA
*
1638449 AAAGAA-AATACATAAAATGTAAA
1 AAA-AATATTACATAAAA-GTAAA
1638472 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
1638490 AAAAAAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 7 0.21
23 14 0.42
24 4 0.12
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAAATATTACATAAAAGTAAA
Found at i:1638836 original size:37 final size:36
Alignment explanation
Indices: 1638788--1638889 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
1638778 ATAGTATAAC
1638788 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
* *
1638825 TTTATCATATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
1638859 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1638890 TAGGACAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
34 32 0.54
37 27 0.46
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1639741 original size:105 final size:105
Alignment explanation
Indices: 1639424--1640188 Score: 1069
Period size: 105 Copynumber: 7.3 Consensus size: 105
1639414 CATTGTTCCA
* * * * ** * * *
1639424 AGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
1639489 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
1639530 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* *
1639590 AACGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
1639630 AATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
* * *
1639695 AGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTATGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1639735 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1639800 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1639840 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1639905 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
1639945 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTG-TGACAGGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
*
1640009 AGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1640049 AGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAG
* * *
1640114 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1640155 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1640189 CGCAGATGGC
Statistics
Matches: 597, Mismatches: 50, Indels: 21
0.89 0.07 0.03
Matches are distributed among these distances:
99 1 0.00
100 79 0.13
101 1 0.00
102 4 0.01
103 4 0.01
104 101 0.17
105 305 0.51
106 77 0.13
107 4 0.01
109 21 0.04
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1640882 original size:68 final size:65
Alignment explanation
Indices: 1640792--1640949 Score: 208
Period size: 68 Copynumber: 2.4 Consensus size: 65
1640782 AAGATATCTG
* * **
1640792 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
1640857 TT
64 TT
* * * *
1640859 TGTGTTTCAAGAGTAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
1640924 T
65 T
*
1640925 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
1640950 ATAGACGAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 21 0.27
66 3 0.04
67 24 0.30
68 31 0.39
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:1640925 original size:67 final size:65
Alignment explanation
Indices: 1640792--1641185 Score: 238
Period size: 65 Copynumber: 5.8 Consensus size: 65
1640782 AAGATATCTG
* * * **
1640792 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
1640857 TT
64 TT
* * *
1640859 TGTGTTTCAAGAGTAATTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
1640924 T
65 T
* ** * *
1640925 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAATTTGTTTTAAGGGAAA-----T--A-A-A
** *
1640989 GACAAA-ACT
56 TTCAAAGATT
* * * * * *** * * *
1640998 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAATAAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * *
1641063 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGA-T-
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T-AA-ATTC
* *
1641126 AGACGAAAT
59 A-AAG-ATT
** *
1641135 TTGTTTCAAGAGAAACTGTCTCAAGATAGACAAAATTTGTTTCAAGGGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
1641186 CTGTCTCAAG
Statistics
Matches: 253, Mismatches: 52, Indels: 39
0.74 0.15 0.11
Matches are distributed among these distances:
64 5 0.02
65 80 0.32
66 8 0.03
67 24 0.09
68 31 0.12
70 2 0.01
71 3 0.01
72 55 0.22
73 40 0.16
74 5 0.02
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:1640976 original size:36 final size:35
Alignment explanation
Indices: 1640925--1641205 Score: 263
Period size: 36 Copynumber: 8.0 Consensus size: 35
1640915 TTCAAAGATT
* *
1640925 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
1640961 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
1640996 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
* * * **
1641034 TTGTTTCAA-ATAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGA-GAAAC-TGTCTCAAGAGAGACAAAA
*
1641063 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
1641098 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
*
1641135 TTGTTTCAAGAGAAACTGTCTCAAGATAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
1641170 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1641206 CTCTTCTAGT
Statistics
Matches: 203, Mismatches: 26, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 9 0.04
36 134 0.66
37 33 0.16
38 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:1641035 original size:138 final size:137
Alignment explanation
Indices: 1640876--1641186 Score: 426
Period size: 138 Copynumber: 2.3 Consensus size: 137
1640866 CAAGAGTAAT
* * *
1640876 TGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* *
1640941 TGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC
66 TGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCC
1641005 AAAAGAAAC
129 AAAAGAAAC
* *** * *
1641014 TGTCTCAAGGGAGACGAAATTTGTTTCAAATAAAACATATTCAAATATTTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
* * * * *
1641079 TGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTTCAA
66 TGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAA
*
1641144 GAGAAAC
131 AAGAAAC
**
1641151 TGTCTCAAGATAGACAAAATTTGTTTCAAGGGAAAC
1 TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAAC
1641187 TGTCTCAAGA
Statistics
Matches: 149, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
137 48 0.32
138 101 0.68
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (137 bp):
TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTTTGTTTCAAGGGAAAC
TGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAA
AAGAAAC
Found at i:1641143 original size:21 final size:21
Alignment explanation
Indices: 1641119--1641180 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1641109 GGAAACTGTC
1641119 TCAAGATAGACGAAATTTGTT
1 TCAAGATAGACGAAATTTGTT
* *
1641140 TC---A-AGA-GAAA-CTGTC
1 TCAAGATAGACGAAATTTGTT
*
1641155 TCAAGATAGACAAAATTTGTT
1 TCAAGATAGACGAAATTTGTT
1641176 TCAAG
1 TCAAG
1641181 GGAAACTGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 12
0.64 0.11 0.26
Matches are distributed among these distances:
15 5 0.17
16 4 0.13
17 3 0.10
18 2 0.07
19 3 0.10
20 3 0.10
21 10 0.33
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (21 bp):
TCAAGATAGACGAAATTTGTT
Found at i:1641711 original size:18 final size:18
Alignment explanation
Indices: 1641684--1641719 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1641674 TGTTGAATCC
* *
1641684 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
1641702 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1641720 TTGATGTTGA
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:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1642159 original size:22 final size:22
Alignment explanation
Indices: 1642133--1642187 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
1642123 TTGTGTTTGG
1642133 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1642155 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1642177 TCAAAGGTTTG
1 TCAAAGGTTTG
1642188 ATGGGATAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1642845 original size:12 final size:12
Alignment explanation
Indices: 1642830--1642893 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
1642820 TTCTTTTTGA
1642830 TTTTTGCTCTTT
1 TTTTTGCTCTTT
*
1642842 TTTTTGTTCTTGT
1 TTTTTGCTCTT-T
*
1642855 TTCTCTTTCTCTTT
1 TT-T-TTGCTCTTT
*
1642869 TTCTTTG-TTTTT
1 TT-TTTGCTCTTT
1642881 TTTTTGCT-TTT
1 TTTTTGCTCTTT
1642892 TT
1 TT
1642894 GCTTCTTTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
11 9 0.21
12 17 0.40
13 5 0.12
14 6 0.14
15 6 0.14
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (12 bp):
TTTTTGCTCTTT
Found at i:1642852 original size:28 final size:27
Alignment explanation
Indices: 1642816--1642883 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 27
1642806 CTTTTTGTCC
*
1642816 CTTT-TTCTTTTTGATTTTTGCTCTTTTT
1 CTTTGTTCTTTTT-ATCTTT-CTCTTTTT
*
1642844 -TTTGTTCTTGTTTCTCTTTCTCTTTTT
1 CTTTGTTCTT-TTTATCTTTCTCTTTTT
*
1642871 CTTTGTTTTTTTT
1 CTTTGTTCTTTTT
1642884 TTGCTTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 14 0.41
28 17 0.50
29 3 0.09
ACGTcount: A:0.01, C:0.15, G:0.07, T:0.76
Consensus pattern (27 bp):
CTTTGTTCTTTTTATCTTTCTCTTTTT
Found at i:1642906 original size:16 final size:16
Alignment explanation
Indices: 1642864--1642915 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
1642854 TTTCTCTTTC
*
1642864 TCTTTTTCTTTGTTT-T
1 TCTTTTGCTTT-TTTGT
*
1642880 TTTTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
1642897 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
1642912 TCTT
1 TCTT
1642916 GATTGGATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 8 0.26
16 17 0.55
17 6 0.19
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:1643706 original size:19 final size:20
Alignment explanation
Indices: 1643682--1643732 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1643672 AATGACCAAT
1643682 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
1643701 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1643721 AAAATCGCAACG
1 AAAATCGCAACG
1643733 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1643726 original size:20 final size:20
Alignment explanation
Indices: 1643682--1644039 Score: 200
Period size: 20 Copynumber: 17.6 Consensus size: 20
1643672 AATGACCAAT
* *
1643682 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1643701 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1643721 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1643741 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1643761 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1643782 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1643805 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
1643825 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1643845 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1643865 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1643885 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1643908 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
1643928 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1643948 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * * *
1643968 AGAATCACAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1643988 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
1644008 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
1644028 AAAATCGCAACG
1 AAAATCGCAACG
1644040 TTAAAAAGAA
Statistics
Matches: 280, Mismatches: 47, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.06
20 220 0.79
21 14 0.05
23 29 0.10
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1643918 original size:103 final size:103
Alignment explanation
Indices: 1643786--1644037 Score: 357
Period size: 103 Copynumber: 2.5 Consensus size: 103
1643776 GCTTCCAAGT
* * * *
1643786 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAATC
* *
1643851 GCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
66 GCAATGCGATTTATAGAATCACAATGCGATTGAGAGAA
*
1643889 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAATC
* *
1643954 GCAATGCGATTTATAGAATCACAATGCGATTTATAGAA
66 GCAATGCGATTTATAGAATCACAATGCGATTGAGAGAA
* * * * *
1643992 TCGCAATGCGA-TT-G-AGAGAATCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAA
1644038 CGTTAAAAAG
Statistics
Matches: 134, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
100 27 0.20
101 1 0.01
102 2 0.01
103 104 0.78
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (103 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTTATAGAATCACAATGCGATTGAGAGAA
Found at i:1643967 original size:123 final size:123
Alignment explanation
Indices: 1643807--1644029 Score: 410
Period size: 123 Copynumber: 1.8 Consensus size: 123
1643797 TTTAGAAGAA
* * *
1643807 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATCGCAATGCGATTTATAGAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCACAATGCGATTTATAGAATCG
*
1643872 CAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAG
66 CAATGCGATTGAGAGAATCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAG
1643930 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCACAATGCGATTTATAGAATCG
1 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCACAATGCGATTTATAGAATCG
1643995 CAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
66 CAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
1644030 AATCGCAACG
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 96 1.00
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (123 bp):
AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATCACAATGCGATTTATAGAATCG
CAATGCGATTGAGAGAATCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAG
Found at i:1644025 original size:40 final size:40
Alignment explanation
Indices: 1643807--1644037 Score: 291
Period size: 40 Copynumber: 5.7 Consensus size: 40
1643797 TTTAGAAGAA
* * *
1643807 AATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1643847 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
* * * *
1643887 AGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTTA-TAG--AATCGCAATGCGATTGAGAG
* * * * *
1643930 AATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
*
1643970 AATCACAATGCGATTTATAGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
* * *
1644010 AATCGCAACGCGATTTAGAAAATCGCAA
1 AATCGCAATGCGATTTATAGAATCGCAA
1644038 CGTTAAAAAG
Statistics
Matches: 163, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
40 127 0.78
41 2 0.01
42 2 0.01
43 32 0.20
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.23
Consensus pattern (40 bp):
AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAG
Found at i:1644049 original size:20 final size:20
Alignment explanation
Indices: 1644026--1644079 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1644016 AACGCGATTT
*
1644026 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
1644046 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
1644066 AGAAAATCGCAACG
1 AGAAAATCGCAACG
1644080 CGATCTTCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.19, G:0.19, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:1644226 original size:6 final size:6
Alignment explanation
Indices: 1644215--1644246 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1644205 GACACGTATT
1644215 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1644247 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1644949 original size:6 final size:6
Alignment explanation
Indices: 1644933--1644970 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1644923 TCTCGTCTCG
1644933 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1644971 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1645086 original size:20 final size:20
Alignment explanation
Indices: 1645042--1645169 Score: 184
Period size: 20 Copynumber: 6.4 Consensus size: 20
1645032 ATTTTCAACG
* * * *
1645042 TTGCAATTCTCTCAGTCGCG
1 TTGCGATTCTATCAATCGCA
* *
1645062 TTGCGACTCTCTCAATCGCA
1 TTGCGATTCTATCAATCGCA
* *
1645082 TTGCGATTATATAAATCGCA
1 TTGCGATTCTATCAATCGCA
1645102 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
1645122 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
1645142 TTGCGATTCTATCAATCGCA
1 TTGCGATTCTATCAATCGCA
1645162 TTGCGATT
1 TTGCGATT
1645170 TTCTTCTAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 98 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.35
Consensus pattern (20 bp):
TTGCGATTCTATCAATCGCA
Found at i:1645267 original size:20 final size:20
Alignment explanation
Indices: 1645057--1645313 Score: 117
Period size: 20 Copynumber: 12.8 Consensus size: 20
1645047 ATTCTCTCAG
* * *
1645057 TCGCGTTGCGACTCTCTCAA
1 TCGCGTTGCGATTTTCTAAA
* * *
1645077 TCGCATTGCGATTATATAAA
1 TCGCGTTGCGATTTTCTAAA
* * * *
1645097 TCGCATTGCGATTCTATCAA
1 TCGCGTTGCGATTTTCTAAA
* * * *
1645117 TCGCATTGCGATTCTATCAA
1 TCGCGTTGCGATTTTCTAAA
* * * *
1645137 TCGCATTGCGATTCTATCAA
1 TCGCGTTGCGATTTTCTAAA
*
1645157 TCGCATTGCGATTTTCTTCTAAA
1 TCGCGTTGCGA--TT-TTCTAAA
** ** *
1645180 TCGCGTTGCGAACTTGGAAGC
1 TCGCGTTGCGATTTTCTAA-A
*
1645201 TCGCGTTGCGATTTTCT--T
1 TCGCGTTGCGATTTTCTAAA
* ***
1645219 TTGACCGTTGCGATTTTCTTTT
1 TCG--CGTTGCGATTTTCTAAA
**
1645241 TAACGTTGCGATTTTCTAAA
1 TCGCGTTGCGATTTTCTAAA
* *
1645261 TCGCGTTGCGATTTT-GATA
1 TCGCGTTGCGATTTTCTAAA
* *
1645280 TCGCGTTGCGATTTT-GATA
1 TCGCGTTGCGATTTTCTAAA
1645299 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
1645314 ATTGGTCATT
Statistics
Matches: 198, Mismatches: 31, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
18 2 0.01
19 36 0.18
20 129 0.65
21 13 0.07
22 4 0.02
23 14 0.07
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCTAAA
Found at i:1645284 original size:19 final size:19
Alignment explanation
Indices: 1645244--1645313 Score: 113
Period size: 19 Copynumber: 3.6 Consensus size: 19
1645234 TTCTTTTTAA
* *
1645244 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTT-GATATCG
1645264 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGATATCG
1645283 CGTTGCGATTTTGATATCG
1 CGTTGCGATTTTGATATCG
1645302 CGTTGCGATTTT
1 CGTTGCGATTTT
1645314 ATTGGTCATT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
19 36 0.75
20 12 0.25
ACGTcount: A:0.16, C:0.17, G:0.24, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTGATATCG
Found at i:1648353 original size:15 final size:15
Alignment explanation
Indices: 1648335--1648364 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1648325 AAAACCATGT
*
1648335 TAGATAAAAATGTAA
1 TAGATAAAAAGGTAA
1648350 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
1648365 GAAATAAATA
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:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:1648519 original size:29 final size:29
Alignment explanation
Indices: 1648449--1648542 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
1648439 ATAGTAAGTA
*
1648449 AAATAAATATAAAAAATAAAGAAAAAGAAG
1 AAATAAATA-AAAAAATAAAGAAAAAGAAC
* *
1648479 AAA-AAGAAAAAAAAATATAGAAATAA-AAC
1 AAATAA-ATAAAAAAATAAAGAAA-AAGAAC
*
1648508 AAATAAATAAAATAATAATA-AAAAAGTAA-
1 AAATAAATAAAAAAATAA-AGAAAAAG-AAC
1648537 AAATAA
1 AAATAA
1648543 TATATATATA
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
28 2 0.04
29 38 0.73
30 12 0.23
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (29 bp):
AAATAAATAAAAAAATAAAGAAAAAGAAC
Found at i:1648527 original size:24 final size:24
Alignment explanation
Indices: 1648490--1648568 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 24
1648480 AAAAGAAAAA
*
1648490 AAAATATAGAAATAAAACAAATAAAT
1 AAAATATA-TAATAAAA-AAATAAAT
*
1648516 AAAATA-ATAATAAAAAAGTAAA-
1 AAAATATATAATAAAAAAATAAAT
*
1648538 AATAATATATATATAAAATAAAAAAAT
1 AA-AATATATA-ATAAAA-AAATAAAT
1648565 AAAA
1 AAAA
1648569 AAAGTAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
22 2 0.05
23 10 0.23
24 10 0.23
25 7 0.16
26 13 0.30
27 2 0.05
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.22
Consensus pattern (24 bp):
AAAATATATAATAAAAAAATAAAT
Found at i:1648540 original size:25 final size:24
Alignment explanation
Indices: 1648501--1648568 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 24
1648491 AAATATAGAA
* *
1648501 ATAAAACAAATAAATAAAATA-AT
1 ATAAAATAAAAAAATAAAATATAT
*
1648524 AATAAAA-AAGTAAAAATAATATATAT
1 -ATAAAATAA--AAAAATAAAATATAT
1648550 ATAAAATAAAAAAATAAAA
1 ATAAAATAAAAAAATAAAA
1648569 AAAGTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 2 0.05
24 15 0.41
25 16 0.43
26 4 0.11
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (24 bp):
ATAAAATAAAAAAATAAAATATAT
Found at i:1648541 original size:38 final size:39
Alignment explanation
Indices: 1648499--1648586 Score: 92
Period size: 39 Copynumber: 2.3 Consensus size: 39
1648489 AAAAATATAG
*
1648499 AAATAA-A-ACAAAT-AAATAAAATAATAATAAAAAAGTAA
1 AAATAATATACAAATAAAATAAAAAAAT-A-AAAAAAGTAA
* *
1648537 AAATAATATATATATAAAATAAAAAAATAAAAAAAGTAA
1 AAATAATATACAAATAAAATAAAAAAATAAAAAAAGTAA
*
1648576 ATATATATATA
1 AAATA-ATATA
1648587 TATAAATTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
38 6 0.14
39 15 0.36
40 10 0.24
41 11 0.26
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (39 bp):
AAATAATATACAAATAAAATAAAAAAATAAAAAAAGTAA
Found at i:1648560 original size:30 final size:31
Alignment explanation
Indices: 1648499--1648601 Score: 95
Period size: 30 Copynumber: 3.3 Consensus size: 31
1648489 AAAAATATAG
*
1648499 AAATAAAACAAA-TAAATAAAATAATAATAAAA
1 AAATAAAA-AAAGTAAAT-ATATAATAATAAAA
* *
1648531 AAGTAAAAATAA-TATATATATAA-AATAAAA
1 AAATAAAAA-AAGTAAATATATAATAATAAAA
*
1648561 AAATAAAAAAAGTAAATATATATATATATAAAT
1 AAATAAAAAAAGTAAATATATA-ATA-ATAAAA
*
1648594 TAATAAAA
1 AAATAAAA
1648602 CTGATAATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
29 2 0.03
30 24 0.41
31 7 0.12
32 14 0.24
33 12 0.20
ACGTcount: A:0.72, C:0.01, G:0.02, T:0.25
Consensus pattern (31 bp):
AAATAAAAAAAGTAAATATATAATAATAAAA
Found at i:1648571 original size:9 final size:9
Alignment explanation
Indices: 1648447--1648576 Score: 59
Period size: 9 Copynumber: 13.4 Consensus size: 9
1648437 AAATAGTAAG
*
1648447 TAAAATAAA
1 TAAAAAAAA
*
1648456 TATAAAAAA
1 TAAAAAAAA
1648465 TAAAGAAAAA
1 TAAA-AAAAA
*
1648475 GAAGAAAAAGA
1 TAA-AAAAA-A
1648486 -AAAAAAAA
1 TAAAAAAAA
* *
1648494 T-ATAGAAA
1 TAAAAAAAA
*
1648502 TAAAACAAA
1 TAAAAAAAA
1648511 TAAATAAAATAA
1 T-AA-AAAA-AA
1648523 TAATAAAAAA
1 TAA-AAAAAA
1648533 GTAAAAATAATA
1 -TAAAAA-AA-A
*
1648545 TATATATAAAA
1 TA-A-AAAAAA
1648556 T-AAAAAAA
1 TAAAAAAAA
*
1648564 TAAAAAAAG
1 TAAAAAAAA
1648573 TAAA
1 TAAA
1648577 TATATATATA
Statistics
Matches: 95, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
8 13 0.14
9 32 0.34
10 20 0.21
11 21 0.22
12 7 0.07
13 2 0.02
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:1648587 original size:38 final size:38
Alignment explanation
Indices: 1648512--1648652 Score: 129
Period size: 44 Copynumber: 3.4 Consensus size: 38
1648502 TAAAACAAAT
* *
1648512 AAATAAAATAATAATAAAAAAGTAAAAATAATATATATATA
1 AAATAAAAAAAT-A-AAAAAAGTAAATAT-ATATATATATA
1648553 AAATAAAAAAATAAAAAAAGTAAATATATATATATATA
1 AAATAAAAAAATAAAAAAAGTAAATATATATATATATA
* * *
1648591 AATTAATAAAACTGATAATAAAAAATAATATATTTATATATATA
1 AAATAA-AAAA---ATAA-AAAAAGTAA-ATATATATATATATA
**
1648635 ATCTAAAAAAAATAAAAA
1 AAAT-AAAAAAATAAAAA
1648653 TATATACTAA
Statistics
Matches: 86, Mismatches: 7, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
38 16 0.19
39 17 0.20
40 4 0.05
41 15 0.17
42 4 0.05
43 8 0.09
44 20 0.23
45 2 0.02
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.28
Consensus pattern (38 bp):
AAATAAAAAAATAAAAAAAGTAAATATATATATATATA
Found at i:1648703 original size:23 final size:22
Alignment explanation
Indices: 1648648--1648709 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
1648638 TAAAAAAAAT
1648648 AAAAATATATAC-T-AAAGTAAA
1 AAAAATAT-TACATAAAAGTAAA
*
1648669 AAAGAA-AATACATAAAATGTAAA
1 AAA-AATATTACATAAAA-GTAAA
1648692 AAAAATATTACATGAAAA
1 AAAAATATTACAT-AAAA
1648710 AAAAAAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
20 3 0.09
21 5 0.15
22 7 0.21
23 14 0.42
24 4 0.12
ACGTcount: A:0.68, C:0.05, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAAATATTACATAAAAGTAAA
Found at i:1649057 original size:37 final size:36
Alignment explanation
Indices: 1649014--1649115 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
1649004 ATAGTATAAC
1649014 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
1649051 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
*
1649085 TCTATCATATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1649116 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
34 32 0.53
37 28 0.47
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1659412 original size:20 final size:20
Alignment explanation
Indices: 1659371--1659414 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1659361 ATAGAGATGA
*
1659371 AATAAAAATAAATAATAAAT
1 AATAAAAATAAATAAGAAAT
*
1659391 AATAATAATAAA-AAGAAGAT
1 AATAAAAATAAATAAGAA-AT
1659411 AATA
1 AATA
1659415 TTATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (20 bp):
AATAAAAATAAATAAGAAAT
Found at i:1659423 original size:2 final size:2
Alignment explanation
Indices: 1659412--1659493 Score: 157
Period size: 2 Copynumber: 41.5 Consensus size: 2
1659402 AAAGAAGATA
1659412 AT AT -T AT AT AT 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 AT AT AT
1659453 AT AT AT 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 AT AT AT A
1659494 GGATACTAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 78 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1659712 original size:16 final size:16
Alignment explanation
Indices: 1659681--1659715 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1659671 TATATATAAA
1659681 TAAAATAAAACAAAAT
1 TAAAATAAAACAAAAT
1659697 TAAAA-AAAACACAAAT
1 TAAAATAAAACA-AAAT
1659713 TAA
1 TAA
1659716 CTTTATCGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (16 bp):
TAAAATAAAACAAAAT
Found at i:1668242 original size:14 final size:14
Alignment explanation
Indices: 1668223--1668250 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1668213 TTTGTCTGAT
1668223 GATTCTCCAGTAGC
1 GATTCTCCAGTAGC
1668237 GATTCTCCAGTAGC
1 GATTCTCCAGTAGC
1668251 ACAAACCTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (14 bp):
GATTCTCCAGTAGC
Found at i:1673581 original size:24 final size:24
Alignment explanation
Indices: 1673554--1673606 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1673544 AATAGAGATG
1673554 AAATAA-AAATAAAAAAATAATAAT
1 AAATAATAAA-AAAAAAATAATAAT
* *
1673578 AAATAATAAAAAAAAGATAATAGT
1 AAATAATAAAAAAAAAATAATAAT
1673602 AAATA
1 AAATA
1673607 TATATAGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (24 bp):
AAATAATAAAAAAAAAATAATAAT
Found at i:1673583 original size:10 final size:9
Alignment explanation
Indices: 1673555--1673589 Score: 54
Period size: 10 Copynumber: 3.9 Consensus size: 9
1673545 ATAGAGATGA
1673555 AATAAAAAT
1 AATAAAAAT
1673564 AA-AAAAAT
1 AATAAAAAT
1673572 AATAATAAAT
1 AATAA-AAAT
1673582 AATAAAAA
1 AATAAAAA
1673590 AAAGATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.33
9 7 0.29
10 9 0.38
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AATAAAAAT
Found at i:1673587 original size:21 final size:20
Alignment explanation
Indices: 1673555--1673599 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1673545 ATAGAGATGA
1673555 AATAAAAATAAAAAAATA-AT
1 AATAAAAATAAAAAAA-AGAT
1673575 AATAAATAATAAAAAAAAGAT
1 AATAAA-AATAAAAAAAAGAT
1673596 AATA
1 AATA
1673600 GTAAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (20 bp):
AATAAAAATAAAAAAAAGAT
Found at i:1675402 original size:15 final size:15
Alignment explanation
Indices: 1675382--1675410 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1675372 GAAGACTAAC
1675382 TTTATTTTAATTTAT
1 TTTATTTTAATTTAT
1675397 TTTATTTTAATTTA
1 TTTATTTTAATTTA
1675411 ACAAATACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTTAATTTAT
Found at i:1676446 original size:60 final size:60
Alignment explanation
Indices: 1676347--1676507 Score: 182
Period size: 60 Copynumber: 2.7 Consensus size: 60
1676337 CCATATAATC
* * * * * *
1676347 ATTCAAAAGTTTGGGGACCAATATAAAATGAG-GACCATAGTTTGGGGA-GGAATTTGGAAT
1 ATTCAAAAGTTTGGAGACCAATTTAGAATGAGAG-TCATAGTTTAGGGATGAAATTT-GAAT
* *
1676407 GTTTAAAAGTTTGGAGACCAATTTAGAATGAGAGTCATAGTTTAGGGATGAAATTTGAAT
1 ATTCAAAAGTTTGGAGACCAATTTAGAATGAGAGTCATAGTTTAGGGATGAAATTTGAAT
* * * *
1676467 ATTCAAAAGTTTAGAGATCAATTTAGAATGATAATCATAGT
1 ATTCAAAAGTTTGGAGACCAATTTAGAATGAGAGTCATAGT
1676508 CCATTATCGT
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
60 78 0.92
61 7 0.08
ACGTcount: A:0.39, C:0.07, G:0.24, T:0.31
Consensus pattern (60 bp):
ATTCAAAAGTTTGGAGACCAATTTAGAATGAGAGTCATAGTTTAGGGATGAAATTTGAAT
Found at i:1677624 original size:30 final size:30
Alignment explanation
Indices: 1677588--1677647 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1677578 TCTTAATTTT
*
1677588 AATTTTAATTATTAGTATAAGAAGAAGCAA
1 AATTTTAATTATTAGTAGAAGAAGAAGCAA
1677618 AATTTTAATTATTAGTAGAAGAAGAAGCAA
1 AATTTTAATTATTAGTAGAAGAAGAAGCAA
1677648 TATAAAGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.32
Consensus pattern (30 bp):
AATTTTAATTATTAGTAGAAGAAGAAGCAA
Found at i:1678749 original size:1 final size:1
Alignment explanation
Indices: 1678743--1678767 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1678733 TGGCAAGTGC
1678743 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1678768 GGGGGGGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1683812 original size:20 final size:20
Alignment explanation
Indices: 1683787--1683855 Score: 129
Period size: 20 Copynumber: 3.5 Consensus size: 20
1683777 AATCCTATTC
1683787 CTGGTAATCTTTTATTTCCA
1 CTGGTAATCTTTTATTTCCA
1683807 CTGGTAATCTTTTATTTCCA
1 CTGGTAATCTTTTATTTCCA
1683827 CTGGTAATCTTTTATTTCCA
1 CTGGTAATCTTTTATTTCCA
*
1683847 CTGATAATC
1 CTGGTAATC
1683856 CTACATTCCG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.48
Consensus pattern (20 bp):
CTGGTAATCTTTTATTTCCA
Found at i:1684711 original size:30 final size:31
Alignment explanation
Indices: 1684654--1684712 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
1684644 GTTTCTAAAA
*
1684654 TATCATTTTATATAAATTAAAATATTATAAT
1 TATCATTTTATATAAATTAAAAAATTATAAT
*
1684685 TATC-TTTTATAT-ATTTAAGAAAATTATA
1 TATCATTTTATATAAATTAA-AAAATTATA
1684713 GTCATAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.20
30 16 0.64
31 4 0.16
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (31 bp):
TATCATTTTATATAAATTAAAAAATTATAAT
Found at i:1684795 original size:14 final size:15
Alignment explanation
Indices: 1684767--1684829 Score: 58
Period size: 14 Copynumber: 4.2 Consensus size: 15
1684757 AAAATATAAC
* *
1684767 TTATTCATTTGTATT
1 TTATACATTTATATT
1684782 TT-TACATTTATATT
1 TTATACATTTATATT
**
1684796 TTAATA-AAATATATT
1 TT-ATACATTTATATT
1684811 TTATACATTTAATATT
1 TTATACATTT-ATATT
1684827 TTA
1 TTA
1684830 AAAATATTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
14 15 0.39
15 13 0.34
16 10 0.26
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.59
Consensus pattern (15 bp):
TTATACATTTATATT
Found at i:1685052 original size:19 final size:19
Alignment explanation
Indices: 1685013--1685058 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1685003 TAATAATGAG
*
1685013 TAATATTAATTTATATATT
1 TAATATTAATATATATATT
1685032 TAATATTAATATA-ATACTT
1 TAATATTAATATATATA-TT
*
1685051 TAGTATTA
1 TAATATTA
1685059 TGCTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATATTAATATATATATT
Found at i:1688991 original size:18 final size:18
Alignment explanation
Indices: 1688965--1689017 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1688955 AGGGATTATC
*
1688965 AGTGATCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1688983 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
**
1689001 AGTGGTTATTCGGGACA
1 AGTGGTCCTTCGGGACA
1689018 AATATTCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1701433 original size:17 final size:17
Alignment explanation
Indices: 1701411--1701503 Score: 91
Period size: 17 Copynumber: 5.5 Consensus size: 17
1701401 ATTGTAAAAC
1701411 ATCTGATATCTGTAAAT
1 ATCTGATATCTGTAAAT
* *
1701428 ATCTGATAACTAT-AAT
1 ATCTGATATCTGTAAAT
1701444 CATCTGATATCTGTAAAT
1 -ATCTGATATCTGTAAAT
* * **
1701462 ATATGGTAAATGT-AAT
1 ATCTGATATCTGTAAAT
*
1701478 AATCTTATATCTGTAAAT
1 -ATCTGATATCTGTAAAT
1701496 ATCTGATA
1 ATCTGATA
1701504 ACTGAAAATC
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
16 6 0.10
17 46 0.79
18 6 0.10
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (17 bp):
ATCTGATATCTGTAAAT
Found at i:1701453 original size:34 final size:34
Alignment explanation
Indices: 1701410--1701521 Score: 143
Period size: 34 Copynumber: 3.3 Consensus size: 34
1701400 TATTGTAAAA
1701410 CATCTGATATCTGTAAATATCTGATAACTATAAT
1 CATCTGATATCTGTAAATATCTGATAACTATAAT
* * * *
1701444 CATCTGATATCTGTAAATATATGGTAAATGTAAT
1 CATCTGATATCTGTAAATATCTGATAACTATAAT
* * *
1701478 AATCTTATATCTGTAAATATCTGATAACTGAAAAT
1 CATCTGATATCTGTAAATATCTGATAACT-ATAAT
*
1701513 CATATGATA
1 CATCTGATA
1701522 AATGTAAACA
Statistics
Matches: 63, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
34 54 0.86
35 9 0.14
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.38
Consensus pattern (34 bp):
CATCTGATATCTGTAAATATCTGATAACTATAAT
Found at i:1701512 original size:17 final size:17
Alignment explanation
Indices: 1701406--1701522 Score: 67
Period size: 17 Copynumber: 6.8 Consensus size: 17
1701396 TGATTATTGT
* *
1701406 AAAACATCTGATATCTG
1 AAAATATCTGATAACTG
*
1701423 TAAATATCTGATAACT-
1 AAAATATCTGATAACTG
* *
1701439 ATAATCATCTGATATCTG
1 AAAAT-ATCTGATAACTG
* * * *
1701457 TAAATATATGGTAAATG
1 AAAATATCTGATAACTG
* * *
1701474 -TAATAATCTTATATCTG
1 AAAAT-ATCTGATAACTG
*
1701491 TAAATATCTGATAACTG
1 AAAATATCTGATAACTG
*
1701508 AAAATCATATGATAA
1 AAAAT-ATCTGATAA
1701523 ATGTAAACAT
Statistics
Matches: 72, Mismatches: 23, Indels: 9
0.69 0.22 0.09
Matches are distributed among these distances:
16 6 0.08
17 52 0.72
18 14 0.19
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (17 bp):
AAAATATCTGATAACTG
Found at i:1702330 original size:3 final size:3
Alignment explanation
Indices: 1702298--1702365 Score: 70
Period size: 3 Copynumber: 23.3 Consensus size: 3
1702288 ACTTAAAAAA
* * *
1702298 TAT TA- TAT TGT TAT TAT AAT AAT TACT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
*
1702343 TAT TAT T-T TA- TAT TAT AAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1702366 TTGTGGGCCA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1702337 original size:25 final size:23
Alignment explanation
Indices: 1702298--1702361 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
1702288 ACTTAAAAAA
*
1702298 TATTA-TATTGTTATTATAATAAT
1 TATTATTATTATTATTATAAT-AT
1702321 TACTTATTATTATTATTAT--TAT
1 TA-TTATTATTATTATTATAATAT
1702343 TATTATT-TTA-TATTATAAT
1 TATTATTATTATTATTATAAT
1702362 TATTTTGTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
19 6 0.17
20 3 0.08
21 6 0.17
22 4 0.11
23 3 0.08
24 3 0.08
25 11 0.31
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTATTATTATTATTATAATAT
Found at i:1704457 original size:6 final size:6
Alignment explanation
Indices: 1704443--1704596 Score: 62
Period size: 6 Copynumber: 24.0 Consensus size: 6
1704433 TATATATATA
* * *
1704443 TATTATT TATTTT TATTTT TATTTT TATTTT CT-TTTT TATTTA TATATA
1 TATT-TT TATTTT TATTTT TATTTT TATTTT -TATTTT TATTTT TATTTT
* *
1704492 TATTTTT TATTACCTT AATTTT T-TTCTT TTTTATT TATTTT CTATTTT
1 TA-TTTT TATT---TT TATTTT TATT-TT TATT-TT TATTTT -TATTTT
** * * * * *
1704540 TAATAACCT TATTAT TATTCTT TATTGT TATTGT TATTGT TA-TTT TATTAT
1 T-AT--TTT TATTTT TATT-TT TATTTT TATTTT TATTTT TATTTT TATTTT
1704591 TATTTT
1 TATTTT
1704597 ATTATTTTCA
Statistics
Matches: 116, Mismatches: 17, Indels: 29
0.72 0.10 0.18
Matches are distributed among these distances:
5 7 0.06
6 71 0.61
7 29 0.25
8 2 0.02
9 7 0.06
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (6 bp):
TATTTT
Done.