Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397273.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_239.1, 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: 3496717
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 46782 characters in sequence are not A, C, G, or T
File 6 of 9
Found at i:1786918 original size:16 final size:16
Alignment explanation
Indices: 1786897--1786929 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1786887 AATGATTGTA
1786897 AAGAAGGTTGTTTGAT
1 AAGAAGGTTGTTTGAT
1786913 AAGAAGGTTGTTTGAT
1 AAGAAGGTTGTTTGAT
1786929 A
1 A
1786930 GGGACGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (16 bp):
AAGAAGGTTGTTTGAT
Found at i:1789949 original size:22 final size:23
Alignment explanation
Indices: 1789921--1789967 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1789911 ATTTCTATGC
1789921 ATTACTA-CAAGAACTAAGCT-AA
1 ATTACTATCAA-AACTAAGCTCAA
*
1789943 ATTACTATCAAAATTAAGCTCAA
1 ATTACTATCAAAACTAAGCTCAA
1789966 AT
1 AT
1789968 AACTCTATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (23 bp):
ATTACTATCAAAACTAAGCTCAA
Found at i:1794010 original size:14 final size:14
Alignment explanation
Indices: 1793991--1794038 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
1793981 TTCTTGCATG
1793991 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
*
1794005 TTTCTTTTC-TCTC
1 TTTCTTTTCTTTTC
1794018 TTTCTTTCTCTTTTC
1 TTTCTTT-TCTTTTC
1794033 -TTCTTT
1 TTTCTTT
1794039 GTTATAGGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 10 0.33
14 17 0.57
15 3 0.10
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:1794036 original size:10 final size:10
Alignment explanation
Indices: 1793991--1794036 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
1793981 TTCTTGCATG
*
1793991 TTTCTTTTCT
1 TTTCTTCTCT
1794001 TTTCTT-TCT
1 TTTCTTCTCT
1794010 TTTC-TCTC-
1 TTTCTTCTCT
1794018 TTTCTTTCTCT
1 TTTC-TTCTCT
1794029 TTTCTTCT
1 TTTCTTCT
1794037 TTGTTATAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
8 5 0.16
9 9 0.28
10 14 0.44
11 4 0.12
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTCTTCTCT
Found at i:1796882 original size:68 final size:67
Alignment explanation
Indices: 1796785--1796913 Score: 161
Period size: 68 Copynumber: 1.9 Consensus size: 67
1796775 AAGATTATGT
* *
1796785 ATATGATGTAAATTCTATATAAAATATGAGGTGATTAAGTATA-CATGACAAATGCCATGAGATA
1 ATATGATGTAAATTCCATATAAAACATGAGGTGATTAAG-A-AGCATGACAAATGCCATGAGATA
1796849 ACAC
64 ACAC
* ** * **
1796853 ATATGATGTATATTCCATATACTACATGAGGTGATTGAGAAGCATGATGAATGCCATGAGA
1 ATATGATGTAAATTCCATATAAAACATGAGGTGATTAAGAAGCATGACAAATGCCATGAGA
1796914 GTGTATAGAT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
66 1 0.02
67 18 0.35
68 33 0.63
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (67 bp):
ATATGATGTAAATTCCATATAAAACATGAGGTGATTAAGAAGCATGACAAATGCCATGAGATAAC
AC
Found at i:1810659 original size:21 final size:20
Alignment explanation
Indices: 1810634--1810675 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1810624 AATTAATTAA
1810634 TTTAAATAAATCATATTCAAT
1 TTTAAATAAATCA-ATTCAAT
* *
1810655 TTTAAATTAATTAATTCAAT
1 TTTAAATAAATCAATTCAAT
1810675 T
1 T
1810676 CCGTAGGCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAAATAAATCAATTCAAT
Found at i:1814029 original size:2 final size:2
Alignment explanation
Indices: 1814018--1814052 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1814008 GTGGGTGTGG
*
1814018 TA TA -A TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1814053 GAACAAGATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1817375 original size:40 final size:40
Alignment explanation
Indices: 1817320--1817434 Score: 158
Period size: 40 Copynumber: 2.9 Consensus size: 40
1817310 ATGTATCGAT
*
1817320 ACATGTTCATCTGTTACCAAATGTATCGATACATCAAGAC
1 ACATGTTCATCTGTTACCAAATATATCGATACATCAAGAC
* * * * *
1817360 ACATGTTTATTTGTTACCAAATATATCGATACATTAGGAT
1 ACATGTTCATCTGTTACCAAATATATCGATACATCAAGAC
**
1817400 ACATGTTCATCTGTTACCAAATCCATCGATACATC
1 ACATGTTCATCTGTTACCAAATATATCGATACATC
1817435 CTCAAATGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (40 bp):
ACATGTTCATCTGTTACCAAATATATCGATACATCAAGAC
Found at i:1818527 original size:52 final size:49
Alignment explanation
Indices: 1818468--1818641 Score: 181
Period size: 52 Copynumber: 3.4 Consensus size: 49
1818458 TATTTTGATT
*
1818468 TTAAAATTTTAATTTAATTTTTAGAA-TTAAAATTATTATTTTTAATCTATAA
1 TTAAAATTTTAATTTAA-TTTTA-AATTTAAAATTATTA-TTATAATCTAT-A
* *
1818520 TTAAAATTTTAATTTTATTTTAAATTTAAATATTAATTATTATAATTTATA
1 TTAAAATTTTAATTTAATTTTAAATTTAAA-ATT-ATTATTATAATCTATA
*
1818571 TTAAAATTTTAATTTTAATTTTAAATTTAAAA-TATTACTTGTCATAGTCTATA
1 TTAAAATTTTAA-TTTAATTTTAAATTTAAAATTATTA--T-T-ATAATCTATA
* *
1818624 TTAAAGTTTTAGTTTAAT
1 TTAAAATTTTAATTTAAT
1818642 CTAGAGAAAG
Statistics
Matches: 106, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
49 4 0.04
50 3 0.03
51 25 0.24
52 52 0.49
53 22 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (49 bp):
TTAAAATTTTAATTTAATTTTAAATTTAAAATTATTATTATAATCTATA
Found at i:1818533 original size:6 final size:6
Alignment explanation
Indices: 1818524--1818600 Score: 57
Period size: 6 Copynumber: 12.3 Consensus size: 6
1818514 CTATAATTAA
* * * **
1818524 AATTTT AATTTT -ATTTT AAATTTA AATATT AATTATT ATAATTT ATATTAA
1 AATTTT AATTTT AATTTT -AATTTT AATTTT AATT-TT A-ATTTT A-ATTTT
*
1818575 AATTTT AATTTT AATTTT AAATTT AA
1 AATTTT AATTTT AATTTT AATTTT AA
1818601 AATATTACTT
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
5 5 0.09
6 35 0.62
7 14 0.25
8 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (6 bp):
AATTTT
Found at i:1822887 original size:13 final size:13
Alignment explanation
Indices: 1822869--1822893 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1822859 ATGATGGTTG
1822869 GATTTTTCAAAAT
1 GATTTTTCAAAAT
1822882 GATTTTTCAAAA
1 GATTTTTCAAAA
1822894 GTACTTTCAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
GATTTTTCAAAAT
Found at i:1832230 original size:27 final size:30
Alignment explanation
Indices: 1832164--1832231 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 30
1832154 TATCAATATA
1832164 TTTAATTTTTGTTGATTAATTTAGTGTTTAT
1 TTTAATTTTTGTT-ATTAATTTAGTGTTTAT
1832195 TTTAA-TTTTGTT-TTAA-TTAGT-TTT-T
1 TTTAATTTTTGTTATTAATTTAGTGTTTAT
1832220 CTTTAATTTTTG
1 -TTTAATTTTTG
1832232 GATTACTTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
25 1 0.03
26 8 0.23
27 10 0.29
28 4 0.11
30 7 0.20
31 5 0.14
ACGTcount: A:0.21, C:0.01, G:0.10, T:0.68
Consensus pattern (30 bp):
TTTAATTTTTGTTATTAATTTAGTGTTTAT
Found at i:1836426 original size:38 final size:39
Alignment explanation
Indices: 1836370--1836443 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
1836360 GATGTCACAG
*
1836370 GTCTTAGTGAGGTAAAAAA-CTCCACTAAG-TGAACACCA
1 GTCTTAGTGAGGTAAAAAATC-CCAATAAGTTGAACACCA
* *
1836408 GTCTTGGTGAGGTGAAAAATCCCAATAAGTTGAACA
1 GTCTTAGTGAGGTAAAAAATCCCAATAAGTTGAACA
1836444 ATGTCCAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 24 0.77
39 7 0.23
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (39 bp):
GTCTTAGTGAGGTAAAAAATCCCAATAAGTTGAACACCA
Found at i:1844234 original size:17 final size:18
Alignment explanation
Indices: 1844205--1844238 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1844195 AGGGATATAG
1844205 TATTTTTATTAAAATAAA
1 TATTTTTATTAAAATAAA
1844223 TATTTTTA-TAAAATAA
1 TATTTTTATTAAAATAA
1844239 GTCGAGAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTTTTATTAAAATAAA
Found at i:1846721 original size:73 final size:73
Alignment explanation
Indices: 1846576--1846770 Score: 291
Period size: 73 Copynumber: 2.7 Consensus size: 73
1846566 GTCCAGTTCA
* * * * *
1846576 AAGATAGAGAAGACTTAGTCGACTAAGAAGCATGGTTAGTCAATTAAGAGCTCACTGCCAGAAAC
1 AAGATAGAGATGACTTAATCGACTAAGAAGCAT-GTTAGTCAACTAAGAGCTCACTACCAAAAAC
1846641 TTCAGTTAC
65 TTCAGTTAC
* *
1846650 AAGATAGAGATGACTTAATCGATTAAGAAGCATGTTAGTCAACTAAGAGCTTACTACCAAAAACT
1 AAGATAGAGATGACTTAATCGACTAAGAAGCATGTTAGTCAACTAAGAGCTCACTACCAAAAACT
*
1846715 TTAGTTAC
66 TCAGTTAC
* *
1846723 AAGATAGAGATAACTTAATCGACTAATAAGCATGTTAGTCAACTAAGA
1 AAGATAGAGATGACTTAATCGACTAAGAAGCATGTTAGTCAACTAAGA
1846771 ACACTCTGTC
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
73 80 0.73
74 30 0.27
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.25
Consensus pattern (73 bp):
AAGATAGAGATGACTTAATCGACTAAGAAGCATGTTAGTCAACTAAGAGCTCACTACCAAAAACT
TCAGTTAC
Found at i:1852959 original size:18 final size:19
Alignment explanation
Indices: 1852918--1852960 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1852908 TCTTGAGGGG
1852918 TCATCTATTGATAGTTAAGT
1 TCATCTATTGATAG-TAAGT
*
1852938 TCATCTATTGATAG-ATGT
1 TCATCTATTGATAGTAAGT
1852956 TCATC
1 TCATC
1852961 CAACTTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.36
20 14 0.64
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (19 bp):
TCATCTATTGATAGTAAGT
Found at i:1865842 original size:32 final size:32
Alignment explanation
Indices: 1865791--1865862 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
1865781 CAATATTTGA
*
1865791 CCCCATTGCACCTTCGGCTAGCAATTTACAAT
1 CCCCATTGAACCTTCGGCTAGCAATTTACAAT
* *
1865823 CCCTATTGAACCTTGGGCTAGCAATTTACAAT
1 CCCCATTGAACCTTCGGCTAGCAATTTACAAT
1865855 CCCCATTG
1 CCCCATTG
1865863 CACATTAGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.32, G:0.14, T:0.29
Consensus pattern (32 bp):
CCCCATTGAACCTTCGGCTAGCAATTTACAAT
Found at i:1872037 original size:27 final size:25
Alignment explanation
Indices: 1871989--1872038 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
1871979 TTATGACCTA
* *
1871989 GCCACATATATCAACCCGTGGCCTT
1 GCCACATATATCAAACCATGGCCTT
1872014 GCCACATATATCACAAACCATGGCC
1 GCCACATATAT--CAAACCATGGCC
1872039 CCAGCCATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
27 10 0.48
ACGTcount: A:0.30, C:0.36, G:0.14, T:0.20
Consensus pattern (25 bp):
GCCACATATATCAAACCATGGCCTT
Found at i:1880667 original size:13 final size:14
Alignment explanation
Indices: 1880640--1880668 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1880630 AAAACCTTAG
1880640 CAAATTCCAAAATA
1 CAAATTCCAAAATA
1880654 CAAATTCC-AAATA
1 CAAATTCCAAAATA
1880667 CA
1 CA
1880669 TAACATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (14 bp):
CAAATTCCAAAATA
Found at i:1884423 original size:22 final size:22
Alignment explanation
Indices: 1884395--1884446 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
1884385 ATAACTTAAA
1884395 AATTTCTTTTAAAGTAAGAAAC
1 AATTTCTTTTAAAGTAAGAAAC
1884417 AATTTCTTTTAAAGTAAGAAAC
1 AATTTCTTTTAAAGTAAGAAAC
1884439 AATTTCTT
1 AATTTCTT
1884447 ACTCTTTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (22 bp):
AATTTCTTTTAAAGTAAGAAAC
Found at i:1884596 original size:76 final size:77
Alignment explanation
Indices: 1884417--1884629 Score: 293
Period size: 76 Copynumber: 2.8 Consensus size: 77
1884407 AGTAAGAAAC
* * * *
1884417 AATTTCTTTTAAAGTAAGAAACAATTTCTTACTCTTTATGAATCACACAAAAATTAAAATTCTAC
1 AATTACTTTTAAAGTAGGAAACAATTTCTTATTTTTTATGAATCAC-CAAAAATTAAAATTCTAC
*
1884482 CCTTAAGTTTAGG
65 CCTTAAGTTTAAG
** * *
1884495 AATTACTTTTAAAGTAGGAAACAATTTCTTATTTTTTATGAATCACCTGAAATTAAAGTTCTA-T
1 AATTACTTTTAAAGTAGGAAACAATTTCTTATTTTTTATGAATCACCAAAAATTAAAATTCTACC
* *
1884559 TTTAATTTTAAG
66 CTTAAGTTTAAG
* *
1884571 AATTACTTTTAAAATAGGAAACAATTTCTTATTTTTTATGAATCACCCAAAATTAAAAT
1 AATTACTTTTAAAGTAGGAAACAATTTCTTATTTTTTATGAATCACCAAAAATTAAAAT
1884630 AGGTGGTATT
Statistics
Matches: 120, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
76 64 0.53
77 14 0.12
78 42 0.35
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (77 bp):
AATTACTTTTAAAGTAGGAAACAATTTCTTATTTTTTATGAATCACCAAAAATTAAAATTCTACC
CTTAAGTTTAAG
Found at i:1897127 original size:16 final size:16
Alignment explanation
Indices: 1897106--1897145 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1897096 ATTTGGATTT
*
1897106 AATAAAAATATAAAAA
1 AATAAAAATACAAAAA
*
1897122 AATAAAAATCCAAAAA
1 AATAAAAATACAAAAA
1897138 AATAAAAA
1 AATAAAAA
1897146 CTTAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (16 bp):
AATAAAAATACAAAAA
Found at i:1923272 original size:11 final size:13
Alignment explanation
Indices: 1923254--1923289 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
1923244 CAGAGATTTT
1923254 GGAGGCAGCAAGA
1 GGAGGCAGCAAGA
1923267 -GA-GCAGCAA-A
1 GGAGGCAGCAAGA
1923277 GGAGGCAGCAAGA
1 GGAGGCAGCAAGA
1923290 AACTATTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
10 1 0.05
11 9 0.45
12 9 0.45
13 1 0.05
ACGTcount: A:0.42, C:0.17, G:0.42, T:0.00
Consensus pattern (13 bp):
GGAGGCAGCAAGA
Found at i:1927053 original size:21 final size:22
Alignment explanation
Indices: 1927024--1927067 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1927014 AAGTGATTAA
1927024 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
1927045 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1927067 T
1 T
1927068 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1942610 original size:13 final size:13
Alignment explanation
Indices: 1942592--1942617 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1942582 GGAATTTAAG
1942592 GGTATTTTAGGAA
1 GGTATTTTAGGAA
1942605 GGTATTTTAGGAA
1 GGTATTTTAGGAA
1942618 AGCTGACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (13 bp):
GGTATTTTAGGAA
Found at i:1942995 original size:73 final size:73
Alignment explanation
Indices: 1942879--1943018 Score: 176
Period size: 73 Copynumber: 1.9 Consensus size: 73
1942869 CAAGAGATAG
* ** * * *
1942879 TGTTAGTCGACTAAGAGCTTACTGTTAGAAACTGAGTTTAGAGACAGAAATGACTTAATCGACTA
1 TGTTAGCCGACTAAGAGCTTACTGCCAGAAACTGAGTTCAGAGACAGAAACGACTTAATCAACTA
1942944 AGAAGTTT
66 AGAAGTTT
* *
1942952 TGTTAGCCGACTAAGAGCTTATTGCCA-AAAGCT-AGGTTCAGAGACAGAGACGACTTAATCAAC
1 TGTTAGCCGACTAAGAGCTTACTGCCAGAAA-CTGA-GTTCAGAGACAGAAACGACTTAATCAAC
1943015 TAAG
64 TAAG
1943019 TGGCAATGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
72 4 0.07
73 53 0.93
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (73 bp):
TGTTAGCCGACTAAGAGCTTACTGCCAGAAACTGAGTTCAGAGACAGAAACGACTTAATCAACTA
AGAAGTTT
Found at i:1943101 original size:18 final size:18
Alignment explanation
Indices: 1943078--1943112 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1943068 TGCTAGAAGA
1943078 CAGAATCTATCTAACAGT
1 CAGAATCTATCTAACAGT
1943096 CAGAATCTATCTAACAG
1 CAGAATCTATCTAACAG
1943113 CGATCAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.11, T:0.26
Consensus pattern (18 bp):
CAGAATCTATCTAACAGT
Found at i:1946865 original size:17 final size:17
Alignment explanation
Indices: 1946843--1946878 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1946833 TTTACACCTT
*
1946843 AATGAACAAGGTACTTC
1 AATGAAAAAGGTACTTC
1946860 AATGAAAAAGGTACTTC
1 AATGAAAAAGGTACTTC
1946877 AA
1 AA
1946879 CTATTCCTTG
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:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (17 bp):
AATGAAAAAGGTACTTC
Found at i:1951859 original size:21 final size:19
Alignment explanation
Indices: 1951809--1951861 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
1951799 TGCAATTTGT
1951809 TTCAAATGTAGTGATACATG
1 TTCAAATGTA-TGATACATG
* *
1951829 CTCATGATGTATCGATACATG
1 TTCA-AATGTAT-GATACATG
1951850 TTCACAATGTAT
1 TTCA-AATGTAT
1951862 TGATGCAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (19 bp):
TTCAAATGTATGATACATG
Found at i:1952998 original size:80 final size:80
Alignment explanation
Indices: 1952880--1953109 Score: 259
Period size: 80 Copynumber: 2.9 Consensus size: 80
1952870 AGACTGTATC
* * * *
1952880 ATGCATGCCATGAGATGAATGTGTTAGGACAGTCATATACACTATGGA-CTAAACATTTGA-GTG
1 ATGCATGCCATGAGATGAATGTGTTGGGATAGTCATATACACTA-GAAGCTAAACATGT-ATGTG
1952943 ATTTATGAGGTTATGAA
64 ATTTATGAGGTTATGAA
** * * * *
1952960 ATGTGTGTCATGAGATGCATGTGTTGGGATAGTTATATACACTAGAAGCTAAGCATGTATGTGAT
1 ATGCATGCCATGAGATGAATGTGTTGGGATAGTCATATACACTAGAAGCTAAACATGTATGTGAT
1953025 TTATGAGGTTATGAA
66 TTATGAGGTTATGAA
* * * * * * *
1953040 ATGCATGCCATGAGATGTATGTGTTGAGATAATCATATACATTATAGGCTAAGCATG-ATGATGA
1 ATGCATGCCATGAGATGAATGTGTTGGGATAGTCATATACACTAGAAGCTAAACATGTATG-TGA
1953104 TTTATG
65 TTTATG
1953110 GAAATGTTAT
Statistics
Matches: 127, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
79 6 0.05
80 121 0.95
ACGTcount: A:0.32, C:0.10, G:0.25, T:0.33
Consensus pattern (80 bp):
ATGCATGCCATGAGATGAATGTGTTGGGATAGTCATATACACTAGAAGCTAAACATGTATGTGAT
TTATGAGGTTATGAA
Found at i:1960564 original size:22 final size:20
Alignment explanation
Indices: 1960536--1960591 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
1960526 TTTGACAAAC
**
1960536 ATGTATCGATACATGTTTCATA
1 ATGTATCGATACATG-GGC-TA
*
1960558 ATGTATCAATACATGGGCTA
1 ATGTATCGATACATGGGCTA
1960578 ATGTATCGATACAT
1 ATGTATCGATACAT
1960592 TTCGTCTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 15 0.50
21 1 0.03
22 14 0.47
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATGGGCTA
Found at i:1961468 original size:68 final size:68
Alignment explanation
Indices: 1961365--1961541 Score: 194
Period size: 68 Copynumber: 2.6 Consensus size: 68
1961355 TATGTATACG
* * ** * * * *
1961365 ATGTGAATTCTATATACCATACAAGATGATCAAGTATGCATCATGTATACTAT-AGGATGGTGTA
1 ATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATCATGTATACCATGAGAAT-GTGCA
1961429 TATA
65 TATA
* * * *
1961433 ATGTAAATTCCATATACCATATGAGGTGATTAAGTATGCATGATTTATGCCATGAGAATGTGCAT
1 ATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATCATGTATACCATGAGAATGTGCAT
*
1961498 ATG
66 ATA
* * *
1961501 ATGTATATTCCATATACTATATGAGATTATTAAGTATGCAT
1 ATGTAAATTCCATATACCATATGAGATGATTAAGTATGCAT
1961542 AATTAATGGT
Statistics
Matches: 91, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
68 87 0.96
69 4 0.04
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (68 bp):
ATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATCATGTATACCATGAGAATGTGCAT
ATA
Found at i:1961556 original size:68 final size:68
Alignment explanation
Indices: 1961425--1961681 Score: 309
Period size: 68 Copynumber: 3.8 Consensus size: 68
1961415 TATAGGATGG
* * * * * * * *
1961425 TGTATATAATGTAAATTCCATATACCATATGAGGTGATTAAGTATGCATGATTTATGCCATGAGA
1 TGTATATGATGTATATTCCATATACTACATGAGATGATTAAGTATGCATAATTAATGCTATGAGA
*
1961490 ATG
66 ATA
* * * *
1961493 TGCATATGATGTATATTCCATATACTATATGAGATTATTAAGTATGCATAATTAATGGTATGAGA
1 TGTATATGATGTATATTCCATATACTACATGAGATGATTAAGTATGCATAATTAATGCTATGAGA
1961558 ATA
66 ATA
* * * * * *
1961561 TGTGTATGACGTATATTCCATATACTACATGAGATGGTTAAGTTTGCATGATTAATGCTACGAGA
1 TGTATATGATGTATATTCCATATACTACATGAGATGATTAAGTATGCATAATTAATGCTATGAGA
1961626 ATA
66 ATA
* *
1961629 TGTATATGTTGTATATTCCGTATACTACATGAGATGATTAAGT-TAGCATAATT
1 TGTATATGATGTATATTCCATATACTACATGAGATGATTAAGTAT-GCATAATT
1961682 GCCATAAGAT
Statistics
Matches: 161, Mismatches: 27, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
67 1 0.01
68 160 0.99
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (68 bp):
TGTATATGATGTATATTCCATATACTACATGAGATGATTAAGTATGCATAATTAATGCTATGAGA
ATA
Found at i:1961895 original size:31 final size:31
Alignment explanation
Indices: 1961857--1961963 Score: 144
Period size: 31 Copynumber: 3.5 Consensus size: 31
1961847 ATCATAAAAT
*
1961857 GCCTAAGGTGCAATAGGGATATACGTTGCTA
1 GCCTAAGGTGCAATAGGGATATACGTTGCCA
*
1961888 GCCTAAGGTGCAAT-GGTGCTATACGTTGCCA
1 GCCTAAGGTGCAATAGG-GATATACGTTGCCA
* * *
1961919 ACCTAAGATGCAATAGGGTTATACGTTGCCA
1 GCCTAAGGTGCAATAGGGATATACGTTGCCA
*
1961950 GCCCAAGGTGCAAT
1 GCCTAAGGTGCAAT
1961964 TGGGTTGTAC
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
30 2 0.03
31 62 0.94
32 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (31 bp):
GCCTAAGGTGCAATAGGGATATACGTTGCCA
Found at i:1961969 original size:31 final size:31
Alignment explanation
Indices: 1961861--1961989 Score: 134
Period size: 31 Copynumber: 4.2 Consensus size: 31
1961851 TAAAATGCCT
* * * *
1961861 AAGGTGCAATAGGGATATACGTTGCTAGCCT
1 AAGGTGCAATAGGGTTATACGTTGCCAACCC
* *
1961892 AAGGTGCAAT-GGTGCTATACGTTGCCAACCT
1 AAGGTGCAATAGG-GTTATACGTTGCCAACCC
* *
1961923 AAGATGCAATAGGGTTATACGTTGCCAGCCC
1 AAGGTGCAATAGGGTTATACGTTGCCAACCC
* * * *
1961954 AAGGTGCAATTGGGTTGTACATTACCAACCC
1 AAGGTGCAATAGGGTTATACGTTGCCAACCC
1961985 AAGGT
1 AAGGT
1961990 TGATGGGGGT
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
30 2 0.02
31 79 0.95
32 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (31 bp):
AAGGTGCAATAGGGTTATACGTTGCCAACCC
Found at i:1961982 original size:62 final size:62
Alignment explanation
Indices: 1961858--1961983 Score: 164
Period size: 62 Copynumber: 2.0 Consensus size: 62
1961848 TCATAAAATG
* * * * *
1961858 CCTAAGGTGCAATAGGGATATACGTTGCTAGCCTAAGGTGCAATGGTGCTATACGTTGCCAA
1 CCTAAGATGCAATAGGGATATACGTTGCCAGCCCAAGGTGCAATGGTGCTATACATTACCAA
* * *
1961920 CCTAAGATGCAATAGGGTTATACGTTGCCAGCCCAAGGTGCAATTGG-GTTGTACATTACCAA
1 CCTAAGATGCAATAGGGATATACGTTGCCAGCCCAAGGTGCAA-TGGTGCTATACATTACCAA
1961982 CC
1 CC
1961984 CAAGGTTGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
62 52 0.95
63 3 0.05
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25
Consensus pattern (62 bp):
CCTAAGATGCAATAGGGATATACGTTGCCAGCCCAAGGTGCAATGGTGCTATACATTACCAA
Found at i:1970393 original size:8 final size:8
Alignment explanation
Indices: 1970376--1970405 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1970366 AAGTGAGAAA
*
1970376 AAAGGGAG
1 AAAGGAAG
1970384 AAAGGAAG
1 AAAGGAAG
1970392 AAAGGAAG
1 AAAGGAAG
1970400 AAAGGA
1 AAAGGA
1970406 GGAAGAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (8 bp):
AAAGGAAG
Found at i:1972564 original size:21 final size:22
Alignment explanation
Indices: 1972529--1972572 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1972519 CTCTTAAAGT
1972529 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
1972551 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
1972572 A
1 A
1972573 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:1977028 original size:21 final size:22
Alignment explanation
Indices: 1976993--1977036 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1976983 CTCTAAAAGT
1976993 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
1977015 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
1977036 A
1 A
1977037 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:1983882 original size:18 final size:19
Alignment explanation
Indices: 1983859--1983895 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1983849 CAAGTGGAGA
1983859 ATTTTA-GAATAAAATAAT
1 ATTTTATGAATAAAATAAT
*
1983877 ATTTTATTAATAAAATAAT
1 ATTTTATGAATAAAATAAT
1983896 TTAAAGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (19 bp):
ATTTTATGAATAAAATAAT
Found at i:1988812 original size:33 final size:34
Alignment explanation
Indices: 1988757--1988860 Score: 149
Period size: 33 Copynumber: 3.1 Consensus size: 34
1988747 GAAACCATGA
1988757 GTTATGGTTACTCTCATGAAAAGCCATTGTGAGG
1 GTTATGGTTACTCTCATGAAAAGCCATTGTGAGG
* *
1988791 GTTATGGTT-CTCCCATGAAAAGCCATTGTAAGG
1 GTTATGGTTACTCTCATGAAAAGCCATTGTGAGG
* *
1988824 GTTATGGTTGA-TCTCATAAAAACCCATTGTGAGG
1 GTTATGGTT-ACTCTCATGAAAAGCCATTGTGAGG
1988858 GTT
1 GTT
1988861 TAATGCTTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
33 31 0.50
34 31 0.50
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (34 bp):
GTTATGGTTACTCTCATGAAAAGCCATTGTGAGG
Found at i:1988859 original size:34 final size:33
Alignment explanation
Indices: 1988757--1988860 Score: 145
Period size: 34 Copynumber: 3.1 Consensus size: 33
1988747 GAAACCATGA
1988757 GTTATGGTTACTCTCATGAAAAGCCATTGTGAGG
1 GTTATGGTTA-TCTCATGAAAAGCCATTGTGAGG
* * *
1988791 GTTATGGTTCTCCCATGAAAAGCCATTGTAAGG
1 GTTATGGTTATCTCATGAAAAGCCATTGTGAGG
* *
1988824 GTTATGGTTGATCTCATAAAAACCCATTGTGAGG
1 GTTATGGTT-ATCTCATGAAAAGCCATTGTGAGG
1988858 GTT
1 GTT
1988861 TAATGCTTGA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 30 0.49
34 31 0.51
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (33 bp):
GTTATGGTTATCTCATGAAAAGCCATTGTGAGG
Found at i:1995267 original size:71 final size:71
Alignment explanation
Indices: 1995191--1995369 Score: 245
Period size: 71 Copynumber: 2.5 Consensus size: 71
1995181 AAACTTGAAG
* * *
1995191 ATTACATAACCATAGTTCACTATAAAGGAAGCATAGTCGACCCTGACAAGT-AAAAGGCA-AGAA
1 ATTACACAACCATAGTTGACTATAAAGGAAGCATAGTCGA-CCTAACAAGTCAAAAGGCAGA-AA
1995254 AAGTCAAC
64 AAGTCAAC
* * * *
1995262 ATTACACAATCATAGTTGACTATAAAGGAGGCATAATCGACCTAACAAGTCAAAAGTCAGAAAAA
1 ATTACACAACCATAGTTGACTATAAAGGAAGCATAGTCGACCTAACAAGTCAAAAGGCAGAAAAA
**
1995327 GTCATG
66 GTCAAC
1995333 ATTACACAACCATAGTTGACTATAAAGGAAGCATAGT
1 ATTACACAACCATAGTTGACTATAAAGGAAGCATAGT
1995370 TGACAATAGT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
70 9 0.10
71 84 0.89
72 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.21
Consensus pattern (71 bp):
ATTACACAACCATAGTTGACTATAAAGGAAGCATAGTCGACCTAACAAGTCAAAAGGCAGAAAAA
GTCAAC
Found at i:1996273 original size:450 final size:449
Alignment explanation
Indices: 1995432--1996313 Score: 1132
Period size: 450 Copynumber: 2.0 Consensus size: 449
1995422 CTAAAAAAAG
* * ** *
1995432 ATTATACTCAACTATGGAAGCCCTAATTGAGAAATTTTAAGAACATAGTTGACCCTAAGAGCTTT
1 ATTATACTCAACTATGGAAGCCCTAATTGAGAAATTTGAAAAACATAGTCAACCCTAAGAGCATT
* * ** * * ***
1995497 ATAGTAGACCATTAAGCTTTAGTAATGGTCATATTTGATTCCAACTTGTGTCTAACTACTCCAAA
66 ATAGTAGACCATCAAGCTTCAACAACGGTCATATTTGATTCAAACTTCCATCTAACTACTCCAAA
* * * * *
1995562 CTTTGTCATAGCTATAAATCAACGCATTCAAGGCATTTTGAAGTAATAGAAGACCTAAACCAAAG
131 CTTTGCCACAGCTATAAATCAACGCATTCAAGGCATTTTAAAGTAAAAGAAGACCTAAACCAAAA
* * *
1995627 CTTTAAACCCTAAAGAGACTACCCAAAAATTCATCTTCACTCTCTAGCATCTTTTTAGCCTTCCA
196 CTTCAAACCCTAAAGAGACTACCCAAAAATTCATATTCACTCTCTAGCATATTTTTAGCCTTCCA
* * *
1995692 CCAAGCTTATAAAGTTGAATCCTTACTTCTTTCAAGCCAATTTAATTCACTAACTACAAACAAGC
261 CCAAACTTACAAAGTTGAATCCTTACTTCATTCAAGCCAATTTAATTCACTAACTACAAACAAGC
* *
1995757 TAAAATCTCTAACGTCTAGCCTTTGTGAGGTAAATCTTTGCTAGTACTCCTTTGTACACACATCT
326 TAAAATCTCTAACATCCAGCCTTTGTGAGGTAAATCTTTGCTAGTACTCCTTTGTACACACATCT
* * *
1995822 TGTAAAGGTTCTAGCTTAACCTTAAAAAATTATCTTGTGAAGGTTATCGACCAGGGGAAA
391 TGTAAAGGTTCCAGATTAACCTTAAAAAACTATCTTGT-AAGGTTATCGACCAGGGGAAA
* * *
1995882 ATTATACTCGACTATGGAAGCCCTAATTGAGAAATTTGAAAAACATAGTCAACGCTAGGAGCATT
1 ATTATACTCAACTATGGAAGCCCTAATTGAGAAATTTGAAAAACATAGTCAACCCTAAGAGCATT
* *
1995947 GTAGTCA-ATCC-TCAAGCTTCAACAACGGTCGTATTTGATTCAAACTTCCATCTAAC-AGCTCC
66 ATAGT-AGA-CCATCAAGCTTCAACAACGGTCATATTTGATTCAAACTTCCATCTAACTA-CTCC
* * ** * *
1996009 AAACTTTGCCCCAGCTATAAAT-AGATGCATTTGAGGCATTTTAAAGTAAAAGAATG-CTTGAAC
128 AAACTTTGCCACAGCTATAAATCA-ACGCATTCAAGGCATTTTAAAGTAAAAGAA-GACCTAAAC
* * * *
1996072 CAAAACTTCAAACCCTAGAA-AGACTA-CTAAAAGTTCATATTCACTCTCTAGTATATTTTTAGT
191 CAAAACTTCAAACCCTA-AAGAGACTACCCAAAAATTCATATTCACTCTCTAGCATATTTTTAGC
* * *
1996135 CTTCCACGAAACTTACAAAGTTGAATCCTTACTTCATTCAAGCTAATTTTAATTCTCTAACTACA
255 CTTCCACCAAACTTACAAAGTTGAATCCTTACTTCATTCAAGCCAA-TTTAATTCACTAACTACA
** * *
1996200 CCCAAGCTAAAATCTC-AAGCATCCAGCCTTTGTGAGGTAAATCTTTGCTATTACTCTTTTGTAC
319 AACAAGCTAAAATCTCTAA-CATCCAGCCTTTGTGAGGTAAATCTTTGCTAGTACTCCTTTGTAC
* * *
1996264 ATACATCTTGTAAAGGTTCCAGATTAACTTTAAAAAGCTATCTTGTAAGG
383 ACACATCTTGTAAAGGTTCCAGATTAACCTTAAAAAACTATCTTGTAAGG
1996314 GTTAACGCTT
Statistics
Matches: 369, Mismatches: 55, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
449 80 0.22
450 283 0.77
451 6 0.02
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (449 bp):
ATTATACTCAACTATGGAAGCCCTAATTGAGAAATTTGAAAAACATAGTCAACCCTAAGAGCATT
ATAGTAGACCATCAAGCTTCAACAACGGTCATATTTGATTCAAACTTCCATCTAACTACTCCAAA
CTTTGCCACAGCTATAAATCAACGCATTCAAGGCATTTTAAAGTAAAAGAAGACCTAAACCAAAA
CTTCAAACCCTAAAGAGACTACCCAAAAATTCATATTCACTCTCTAGCATATTTTTAGCCTTCCA
CCAAACTTACAAAGTTGAATCCTTACTTCATTCAAGCCAATTTAATTCACTAACTACAAACAAGC
TAAAATCTCTAACATCCAGCCTTTGTGAGGTAAATCTTTGCTAGTACTCCTTTGTACACACATCT
TGTAAAGGTTCCAGATTAACCTTAAAAAACTATCTTGTAAGGTTATCGACCAGGGGAAA
Found at i:1998269 original size:21 final size:19
Alignment explanation
Indices: 1998243--1998283 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
1998233 AATTTAAAAC
1998243 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
1998264 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
1998283 A
1 A
1998284 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:2024017 original size:38 final size:37
Alignment explanation
Indices: 2023957--2024043 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 37
2023947 GGGTGTATTG
* *
2023957 TATTCTTGCCCCCACATTTGGCTATATTATCATGTGA
1 TATTCTTACCCCCACATCTGGCTATATTATCATGTGA
** *
2023994 TATTCTTACTCCCCACATCTGGCTATATTATTGTGTGG
1 TATTCTTAC-CCCCACATCTGGCTATATTATCATGTGA
2024032 TATTCTTACCCC
1 TATTCTTACCCC
2024044 TCATATTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
37 11 0.25
38 33 0.75
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (37 bp):
TATTCTTACCCCCACATCTGGCTATATTATCATGTGA
Found at i:2024558 original size:29 final size:29
Alignment explanation
Indices: 2024525--2024603 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 29
2024515 ATTTAAGAAA
*
2024525 ATTCAAATAAGTCCTTATACTTTTA-TTG
1 ATTCAAATAAGACCTTATACTTTTATTTG
* *
2024553 CATTCAATTAA-ACCTTTGTACTTTTATTTTG
1 -ATTCAAATAAGACC-TTATACTTTTA-TTTG
* *
2024584 AGTCAAATAAGCCCTTATAC
1 ATTCAAATAAGACCTTATAC
2024604 CTAATGATTG
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
28 2 0.05
29 19 0.49
30 13 0.33
31 5 0.13
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.43
Consensus pattern (29 bp):
ATTCAAATAAGACCTTATACTTTTATTTG
Found at i:2024703 original size:33 final size:33
Alignment explanation
Indices: 2024666--2024729 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
2024656 TGACATGACA
*
2024666 TGACATGATAAAATATTATAATTGATGATGATG
1 TGACATGATAAAATATCATAATTGATGATGATG
* * * *
2024699 TGACATGTTGACATGTCATAATTGATGATGA
1 TGACATGATAAAATATCATAATTGATGATGA
2024730 CATAATATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (33 bp):
TGACATGATAAAATATCATAATTGATGATGATG
Found at i:2025473 original size:35 final size:35
Alignment explanation
Indices: 2025434--2025500 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
2025424 ATAGAGGTTC
2025434 AAAAGCTGAAATTCATATAAAGTGAAGGTTAATTT
1 AAAAGCTGAAATTCATATAAAGTGAAGGTTAATTT
*
2025469 AAAAGTTGAAATTCATATAAAGTGAAGGTTAA
1 AAAAGCTGAAATTCATATAAAGTGAAGGTTAA
2025501 GTTATACTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.48, C:0.04, G:0.18, T:0.30
Consensus pattern (35 bp):
AAAAGCTGAAATTCATATAAAGTGAAGGTTAATTT
Found at i:2025489 original size:18 final size:17
Alignment explanation
Indices: 2025434--2025494 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
2025424 ATAGAGGTTC
2025434 AAAAGCTGAAATTCATAT
1 AAAAG-TGAAATTCATAT
* * *
2025452 -AAAGTGAAGGTTAATTT
1 AAAAGTGAA-ATTCATAT
2025469 AAAAGTTGAAATTCATAT
1 AAAAG-TGAAATTCATAT
2025487 -AAAGTGAA
1 AAAAGTGAA
2025495 GGTTAAGTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
16 8 0.24
17 13 0.38
18 9 0.26
19 4 0.12
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (17 bp):
AAAAGTGAAATTCATAT
Found at i:2027241 original size:73 final size:73
Alignment explanation
Indices: 2027133--2027271 Score: 215
Period size: 73 Copynumber: 1.9 Consensus size: 73
2027123 GAGAGACAGC
**
2027133 GTTAGTCGACTAAGAGCTTACTGTCAAAAACTGGGTTTAGAGATAGAAATGACTTAATCGACTAA
1 GTTAGTCGACTAAGAGCTTACTACCAAAAACTGGGTTTAGAGATAGAAATGACTTAATCGACTAA
2027198 GAAGTTTT
66 GAAGTTTT
* * * * *
2027206 GTTAGTCGACTAAGAGCTTTCTACCAGAAATTGGGTTTAGAGATAGAAGTGACTTAGTCGACTAA
1 GTTAGTCGACTAAGAGCTTACTACCAAAAACTGGGTTTAGAGATAGAAATGACTTAATCGACTAA
2027271 G
66 G
2027272 TGATAATATT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 59 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (73 bp):
GTTAGTCGACTAAGAGCTTACTACCAAAAACTGGGTTTAGAGATAGAAATGACTTAATCGACTAA
GAAGTTTT
Found at i:2027284 original size:73 final size:73
Alignment explanation
Indices: 2027134--2027295 Score: 200
Period size: 73 Copynumber: 2.2 Consensus size: 73
2027124 AGAGACAGCG
**
2027134 TTAGTCGACTAAGAGCTTACTGTCAAAAACTGGGTTTAGAGATAGAAATGACTTAATCGACTAAG
1 TTAGTCGACTAAGAGCTTACTACCAAAAACTGGGTTTAGAGATAGAAATGACTTAATCGACTAAG
** *
2027199 AAGTTTTG
66 AAGTAATA
* * * * *
2027207 TTAGTCGACTAAGAGCTTTCTACCAGAAATTGGGTTTAGAGATAGAAGTGACTTAGTCGACTAAG
1 TTAGTCGACTAAGAGCTTACTACCAAAAACTGGGTTTAGAGATAGAAATGACTTAATCGACTAAG
*
2027272 -TGATAATA
66 AAG-TAATA
*
2027280 TTAGTCGATTAAGAGC
1 TTAGTCGACTAAGAGC
2027296 ATTTTGTTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
72 1 0.01
73 75 0.99
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (73 bp):
TTAGTCGACTAAGAGCTTACTACCAAAAACTGGGTTTAGAGATAGAAATGACTTAATCGACTAAG
AAGTAATA
Found at i:2028813 original size:19 final size:19
Alignment explanation
Indices: 2028782--2028827 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
2028772 AAACTTAAAG
*
2028782 AAGAAGAAAA--AAAAGAT
1 AAGAAGAAAAGCAAAAGAA
2028799 AA-AAGAAAAGCAAAAGAA
1 AAGAAGAAAAGCAAAAGAA
2028817 AAGAAGAAAAG
1 AAGAAGAAAAG
2028828 TATTATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 7 0.28
17 2 0.08
18 8 0.32
19 8 0.32
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (19 bp):
AAGAAGAAAAGCAAAAGAA
Found at i:2035197 original size:73 final size:73
Alignment explanation
Indices: 2035095--2035272 Score: 196
Period size: 73 Copynumber: 2.4 Consensus size: 73
2035085 GAGCATTTAG
* * * * * ** *
2035095 TCGACCAAGAGACAGTGTTAGTCGACTAAGAGCTTACTGTCAGAAACTGGGTTCAGAGAAAAAAA
1 TCGACTAAGAGATAATGTTAGTCAACTAAGAGCATACTACCAGAAACTGAGTTCAGAGAAAAAAA
2035160 TGACTTAA
66 TGACTTAA
** * * * *
2035168 TCGACTAAGA-AGTTTTGTTAGTCAACTAAGATCATACTACCAGAAACTGAGTTCAGAGACAGAG
1 TCGACTAAGAGA-TAATGTTAGTCAACTAAGAGCATACTACCAGAAACTGAGTTCAGAGAAAAAA
*
2035232 ATGACTTAG
65 ATGACTTAA
*
2035241 TCGACTAAGTGATAATGTTAGTCAACTAAGAG
1 TCGACTAAGAGATAATGTTAGTCAACTAAGAG
2035273 TATTCTGTCT
Statistics
Matches: 85, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
72 1 0.01
73 83 0.98
74 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (73 bp):
TCGACTAAGAGATAATGTTAGTCAACTAAGAGCATACTACCAGAAACTGAGTTCAGAGAAAAAAA
TGACTTAA
Found at i:2038957 original size:80 final size:80
Alignment explanation
Indices: 2038875--2039264 Score: 536
Period size: 80 Copynumber: 4.9 Consensus size: 80
2038865 AGATTGTAAC
* * *
2038875 ATGTATGTCATGAGATGTATGTGTT-AGGCATA-TCATATACACTATGGG-TCAAGCATGTAAGT
1 ATGTATGCCATGAGATGTATATGTTGA-G-ATAGTCATATACACTATGGGCT-AAGCATGTAAAT
* ** *
2038937 GATTTATAAGTTTATGAC
63 GATTTATGAGGCTATGAA
2038955 ATGTATGCCATGAGATGTATATGTTGAGATAGTCATATACACTATGGGCTAAGCATGTAAATGAT
1 ATGTATGCCATGAGATGTATATGTTGAGATAGTCATATACACTATGGGCTAAGCATGTAAATGAT
2039020 TTATGAGGCTATGAA
66 TTATGAGGCTATGAA
* *
2039035 ATGTATGCCATGAGATGTATACGTTGAGATAGTCATATACATTATGGGCTAAGCATGTAAATGAT
1 ATGTATGCCATGAGATGTATATGTTGAGATAGTCATATACACTATGGGCTAAGCATGTAAATGAT
2039100 TTATGAGGCTATGAA
66 TTATGAGGCTATGAA
* *
2039115 ATGTATGCCATGAGATGTATACGTTGAGATAGTCATATACATTATGGGCTAAGCATGTAAATGAT
1 ATGTATGCCATGAGATGTATATGTTGAGATAGTCATATACACTATGGGCTAAGCATGTAAATGAT
* *
2039180 TTATGAGACTATAAA
66 TTATGAGGCTATGAA
* * * * * * *
2039195 ATGTATGTCATAAGATATATGTGTTGAGATAGTTATATACACTATGGGCTAAGTATG-ATGATGA
1 ATGTATGCCATGAGATGTATATGTTGAGATAGTCATATACACTATGGGCTAAGCATGTA-AATGA
2039259 TTTATG
65 TTTATG
2039265 GAGATGTTAT
Statistics
Matches: 286, Mismatches: 20, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
79 4 0.01
80 280 0.98
81 2 0.01
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (80 bp):
ATGTATGCCATGAGATGTATATGTTGAGATAGTCATATACACTATGGGCTAAGCATGTAAATGAT
TTATGAGGCTATGAA
Found at i:2046732 original size:102 final size:102
Alignment explanation
Indices: 2046579--2046784 Score: 376
Period size: 102 Copynumber: 2.0 Consensus size: 102
2046569 CATAAGGGCC
* *
2046579 AAATGTGGGGCGTTATACCACATAAATACCCAAGCCAAATGTGGAACTTCATACCACAAATGAAA
1 AAATGTGGGGCGTTATAACAAATAAATACCCAAGCCAAATGTGGAACTTCATACCACAAATGAAA
2046644 AAGGACCAAATGTAGGGTGTTATACCACACAATTTAT
66 AAGGACCAAATGTAGGGTGTTATACCACACAATTTAT
*
2046681 AAATGTGGGGCGTTATAACAAATAAATACCCAAGCCAAATGTGGAACTTCATACCACAAATGACA
1 AAATGTGGGGCGTTATAACAAATAAATACCCAAGCCAAATGTGGAACTTCATACCACAAATGAAA
*
2046746 AAGGACCAAATGTAGGGTGTTATACCACACACTTTAT
66 AAGGACCAAATGTAGGGTGTTATACCACACAATTTAT
2046783 AA
1 AA
2046785 TTATGATATT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 100 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.22
Consensus pattern (102 bp):
AAATGTGGGGCGTTATAACAAATAAATACCCAAGCCAAATGTGGAACTTCATACCACAAATGAAA
AAGGACCAAATGTAGGGTGTTATACCACACAATTTAT
Found at i:2049823 original size:30 final size:30
Alignment explanation
Indices: 2049788--2049882 Score: 84
Period size: 30 Copynumber: 3.2 Consensus size: 30
2049778 TTATTACTGG
*
2049788 TTATACCTCTAGAGAAAAGGTAGTTAAAGA
1 TTATACCTCTAGAGAAAAGATAGTTAAAGA
* * *
2049818 TTATACCT-TCATAGAAAAGATAGTTAATGT
1 TTATACCTCT-AGAGAAAAGATAGTTAAAGA
* * * * * *
2049848 TTATGCCTCTATAAAAAAGAAAGATAAAGG
1 TTATACCTCTAGAGAAAAGATAGTTAAAGA
2049878 TTATA
1 TTATA
2049883 TCTTTGTTGA
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
29 1 0.02
30 50 0.96
31 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (30 bp):
TTATACCTCTAGAGAAAAGATAGTTAAAGA
Found at i:2051385 original size:24 final size:23
Alignment explanation
Indices: 2051349--2051399 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
2051339 TTTTTTTATC
* *
2051349 TTTTTTAAAAATATAATAATA-A
1 TTTTTTAAAAATAAAAAAATATA
2051371 TTTTTTAAATTAATAAAAAAATATA
1 TTTTTTAAA--AATAAAAAAATATA
2051396 TTTT
1 TTTT
2051400 ATTCTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.38
24 10 0.42
25 5 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTTTAAAAATAAAAAAATATA
Found at i:2054977 original size:22 final size:21
Alignment explanation
Indices: 2054952--2054992 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2054942 AATCTGTCCC
2054952 AAAAACATAAATATAATTAACA
1 AAAAACATAAA-ATAATTAACA
*
2054974 AAAAACATAAAATGATTAA
1 AAAAACATAAAATAATTAA
2054993 AATATCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.22
Consensus pattern (21 bp):
AAAAACATAAAATAATTAACA
Found at i:2061188 original size:6 final size:6
Alignment explanation
Indices: 2061124--2061299 Score: 100
Period size: 6 Copynumber: 29.3 Consensus size: 6
2061114 TTCTGAGGAC
* * * * * * * *
2061124 AGGGAT TGGGAT CGAGAT AGGGAA AGAGAA AGGGAA AGGGAG AGGGAT
1 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT
* * * * * * * * *
2061172 CGTGAT CGGGAT AGGGAG AGGGAT CGGGAT CGTGAT CGGGAT AGGAAT
1 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT
* * * * * *
2061220 AGAGAT CGGGAT CGGGAT AGGGAT AGGAAC AGGGAT CGGGAT AGGGAT
1 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT
* * * * *
2061268 AAGGAT AGGAAC AGGGAT TGGGAT TGGGAT AG
1 AGGGAT AGGGAT AGGGAT AGGGAT AGGGAT AG
2061300 AGAAAGAGCC
Statistics
Matches: 130, Mismatches: 40, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 130 1.00
ACGTcount: A:0.32, C:0.06, G:0.46, T:0.15
Consensus pattern (6 bp):
AGGGAT
Found at i:2069573 original size:18 final size:18
Alignment explanation
Indices: 2069550--2069597 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
2069540 GTAATCATGC
2069550 TCATCTTTTAGCCTCCAA
1 TCATCTTTTAGCCTCCAA
2069568 TCATCTTTTAGCCTCCAA
1 TCATCTTTTAGCCTCCAA
2069586 TCATCTTTTAGC
1 TCATCTTTTAGC
2069598 TTACAAACGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.21, C:0.31, G:0.06, T:0.42
Consensus pattern (18 bp):
TCATCTTTTAGCCTCCAA
Found at i:2075624 original size:16 final size:16
Alignment explanation
Indices: 2075603--2075634 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2075593 GCAAAATTTA
2075603 GATTTTGATTCTTTTG
1 GATTTTGATTCTTTTG
*
2075619 GATTTTGATTTTTTTG
1 GATTTTGATTCTTTTG
2075635 ATATTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.03, G:0.19, T:0.66
Consensus pattern (16 bp):
GATTTTGATTCTTTTG
Found at i:2077000 original size:68 final size:68
Alignment explanation
Indices: 2076835--2077099 Score: 238
Period size: 68 Copynumber: 3.9 Consensus size: 68
2076825 GCATGTTGGT
* * * * * * *
2076835 ATGATGAATGCCATAAGATTATGTATACGATGTAAACTCCATGTACCA-GATGAGATGATCAAGT
1 ATGATTAATGCCATAAGAATATGTATATGATGTAAATTCCATATA-CATTATGAGATGATTAAGT
2076899 ATGC
65 ATGC
* * * * *
2076903 ATGATGT-ATACTAT-AGGATGGTGTATATGATGTAAATTCCATATACATTATGAGGTGATTAAG
1 ATGAT-TAATGCCATAAGAAT-ATGTATATGATGTAAATTCCATATACATTATGAGATGATTAAG
2076966 TATGC
64 TATGC
* * * * * *
2076971 ATGATTAATGCCATAAGAATATGTGTATGATGTATATTCCATATAC-TACATGAGATCATTGAGC
1 ATGATTAATGCCATAAGAATATGTATATGATGTAAATTCCATATACAT-TATGAGATGATTAAGT
*
2077035 AAGC
65 ATGC
* * * *
2077039 AT-A--AATGCCATGAGATTATGTATATGATGTAAATTCCATATACCTTATGAGATGAGTAAGT
1 ATGATTAATGCCATAAGAATATGTATATGATGTAAATTCCATATACATTATGAGATGATTAAGT
2077100 GTGTATGTGA
Statistics
Matches: 157, Mismatches: 33, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
65 47 0.30
66 1 0.01
67 8 0.05
68 97 0.62
69 4 0.03
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (68 bp):
ATGATTAATGCCATAAGAATATGTATATGATGTAAATTCCATATACATTATGAGATGATTAAGTA
TGC
Found at i:2079022 original size:20 final size:20
Alignment explanation
Indices: 2078973--2079012 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2078963 AGTTAAATTC
2078973 AGGGAAGAATTTTCCTTAAG
1 AGGGAAGAATTTTCCTTAAG
2078993 AGGGAAGAATTTTCCTTAAG
1 AGGGAAGAATTTTCCTTAAG
2079013 GGGTGAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (20 bp):
AGGGAAGAATTTTCCTTAAG
Found at i:2079382 original size:20 final size:20
Alignment explanation
Indices: 2079359--2079398 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2079349 GATAAATAAG
2079359 CAGATCTATCCATAGATGGC
1 CAGATCTATCCATAGATGGC
**
2079379 CAGATCTATTGATAGATGGC
1 CAGATCTATCCATAGATGGC
2079399 TCCCATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (20 bp):
CAGATCTATCCATAGATGGC
Found at i:2087009 original size:28 final size:28
Alignment explanation
Indices: 2086947--2087113 Score: 174
Period size: 29 Copynumber: 5.7 Consensus size: 28
2086937 TTAAGACAAC
*
2086947 TCTTGTCTTTAATTAAGACAAAAATAT-TTT
1 TCTTGTC-TAAATTAAGAC--AAATATGTTT
*
2086977 ATCTTGTCTAAATTGAGACAAATATGTTT
1 -TCTTGTCTAAATTAAGACAAATATGTTT
* * *
2087006 TCTTGTCTAGATTAAGGCAAAAATTATTTTT
1 TCTTGTCTAAATTAA-G-ACAAA-TATGTTT
* *
2087037 TTTTGTCTTAAATTAAGACAAATATATTT
1 TCTTGTC-TAAATTAAGACAAATATGTTT
*
2087066 TCTTGTCTAAATTAAGACCAAACATGTTT
1 TCTTGTCTAAATTAAGA-CAAATATGTTT
2087095 TCTTGTCTAAATTAAGACA
1 TCTTGTCTAAATTAAGACA
2087114 TGTTAAAGCT
Statistics
Matches: 117, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
28 31 0.26
29 42 0.36
30 17 0.15
31 20 0.17
32 7 0.06
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.43
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAATATGTTT
Found at i:2087067 original size:60 final size:58
Alignment explanation
Indices: 2086947--2087113 Score: 203
Period size: 60 Copynumber: 2.8 Consensus size: 58
2086937 TTAAGACAAC
* * *
2086947 TCTTGTCTTTAATTAAGACAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTT
1 TCTTGTC-TAAATTAAGACAAAAATATTTTATCTTGTCTAAATTAAGACAAATATATTT
* * * *
2087006 TCTTGTCTAGATTAAGGCAAAAATTATTTTTTTTTGTCTTAAATTAAGACAAATATATTT
1 TCTTGTCTAAATTAAGACAAAAA-TATTTTATCTTGTC-TAAATTAAGACAAATATATTT
* *
2087066 TCTTGTCTAAATTAAGACCAAACAT-GTTT-TCTTGTCTAAATTAAGACA
1 TCTTGTCTAAATTAAGA-CAAAAATATTTTATCTTGTCTAAATTAAGACA
2087114 TGTTAAAGCT
Statistics
Matches: 93, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
57 12 0.13
58 19 0.20
59 22 0.24
60 35 0.38
61 5 0.05
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.43
Consensus pattern (58 bp):
TCTTGTCTAAATTAAGACAAAAATATTTTATCTTGTCTAAATTAAGACAAATATATTT
Found at i:2091447 original size:17 final size:17
Alignment explanation
Indices: 2091422--2091455 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2091412 ATTAAACTCT
*
2091422 TTTACTTAAGTTTATAG
1 TTTAATTAAGTTTATAG
2091439 TTTAATTAAGTTTATAG
1 TTTAATTAAGTTTATAG
2091456 AAGTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (17 bp):
TTTAATTAAGTTTATAG
Found at i:2091464 original size:19 final size:17
Alignment explanation
Indices: 2091427--2091465 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2091417 ACTCTTTTAC
*
2091427 TTAAGTTTATAGTTTAA
1 TTAAGTTTATAGGTTAA
2091444 TTAAGTTTATAGAAGTTAA
1 TTAAGTTTATAG--GTTAA
2091463 TTA
1 TTA
2091466 CCTAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
19 7 0.37
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (17 bp):
TTAAGTTTATAGGTTAA
Found at i:2105036 original size:21 final size:21
Alignment explanation
Indices: 2105010--2105058 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
2105000 TCTATGACAC
2105010 AATCTATTGATAGATTCAAGG
1 AATCTATTGATAGATTCAAGG
* *
2105031 AATCTATTGATAGGTTCGAGG
1 AATCTATTGATAGATTCAAGG
2105052 AATCTAT
1 AATCTAT
2105059 CAATAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (21 bp):
AATCTATTGATAGATTCAAGG
Found at i:2106670 original size:21 final size:22
Alignment explanation
Indices: 2106645--2106688 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
2106635 AAGTGATTAA
2106645 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
*
2106666 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
2106688 T
1 T
2106689 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:2123003 original size:30 final size:28
Alignment explanation
Indices: 2122906--2123072 Score: 106
Period size: 29 Copynumber: 5.8 Consensus size: 28
2122896 CTTTAACATG
* * *
2122906 TTTGTCTTAGTTTAGACAGGAA-AACAT
1 TTTGTCTTAATTTAGACAAGAACAATAT
* * *
2122933 GTTTGGCCTTAATTTGGATAAGAA-AATAT
1 -TTT-GTCTTAATTTAGACAAGAACAATAT
*
2122962 ATTTGTATTAATTTAAGACAAGAACAATAT
1 -TTTGTCTTAATTT-AGACAAGAACAATAT
* * * *
2122992 TTTCATCTTAATCTAGA-AAGAAAAACAT
1 TTT-GTCTTAATTTAGACAAGAACAATAT
* *
2123020 ATTTGTCTCAATTTAGACAGGATACAATATT
1 -TTTGTCTTAATTTAGACAAGA-ACAATA-T
*
2123051 TTTGTCTTAATTAAAGACAAGA
1 TTTGTCTTAATT-TAGACAAGA
2123073 GTTGTCTTAA
Statistics
Matches: 105, Mismatches: 25, Indels: 15
0.72 0.17 0.10
Matches are distributed among these distances:
28 30 0.29
29 40 0.38
30 27 0.26
31 8 0.08
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (28 bp):
TTTGTCTTAATTTAGACAAGAACAATAT
Found at i:2139575 original size:13 final size:13
Alignment explanation
Indices: 2139559--2139602 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
2139549 TCCACCTGAG
*
2139559 AAGAGAAGGAAAA
1 AAGAGAAAGAAAA
2139572 AAGAGAAAGAAAA
1 AAGAGAAAGAAAA
*
2139585 GAGAGAAAAGAAGAA
1 AAGAG-AAAGAA-AA
2139600 AAG
1 AAG
2139603 GCTCGGTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 16 0.62
14 6 0.23
15 4 0.15
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (13 bp):
AAGAGAAAGAAAA
Found at i:2143108 original size:16 final size:16
Alignment explanation
Indices: 2143087--2143118 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2143077 GCAAAATTTA
2143087 GATTTTGATTCTTTTG
1 GATTTTGATTCTTTTG
*
2143103 GATTTTGATTTTTTTG
1 GATTTTGATTCTTTTG
2143119 ATATTTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.03, G:0.19, T:0.66
Consensus pattern (16 bp):
GATTTTGATTCTTTTG
Found at i:2144441 original size:68 final size:67
Alignment explanation
Indices: 2144362--2144619 Score: 304
Period size: 68 Copynumber: 3.8 Consensus size: 67
2144352 GGTATGATAA
*
2144362 ATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATCAAGTATGCATGA
1 ATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATGA
2144427 TGT
66 T-T
* * * *
2144430 ATACTATAAGATTGTGTATATGATGTAAATTCCATATACCATATGAGGTGATTAAGTATGCATGA
1 ATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATGA
2144495 TT
66 TT
* * * * * * * * * *
2144497 AATGCCATGAGATTAAGTATATAATGTATATTCTATATACTACATGAGATGATTGAGCAAGCATG
1 -ATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATG
*
2144562 ATAA
65 AT-T
* * *
2144566 ATGCCATGAGAATATGTATATGATG--AATTCCATATACCATATGAGATGAGTAAG
1 ATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAG
2144620 CATGTATATG
Statistics
Matches: 159, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
66 23 0.14
67 1 0.01
68 135 0.85
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.33
Consensus pattern (67 bp):
ATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTATGCATGA
TT
Found at i:2154055 original size:3 final size:3
Alignment explanation
Indices: 2154047--2154083 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2154037 TTCAGTAAGC
2154047 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
2154084 CACTACTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:2181159 original size:16 final size:16
Alignment explanation
Indices: 2181138--2181170 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2181128 TACTTATTTA
2181138 TCCTTTTT-CTCTTCTC
1 TCCTTTTTGCTC-TCTC
2181154 TCCTTTTTGCTCTCTC
1 TCCTTTTTGCTCTCTC
2181170 T
1 T
2181171 TCACTCCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.00, C:0.36, G:0.03, T:0.61
Consensus pattern (16 bp):
TCCTTTTTGCTCTCTC
Found at i:2181170 original size:21 final size:21
Alignment explanation
Indices: 2181145--2181197 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2181135 TTATCCTTTT
* * *
2181145 TCTCTTCTCTCCTTTTTGCTC
1 TCTCTTCACTCCCTTCTGCTC
2181166 TCTCTTCACTCCCTTCTGCTC
1 TCTCTTCACTCCCTTCTGCTC
2181187 TCTCTTCACTC
1 TCTCTTCACTC
2181198 TTCGGCTACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.04, C:0.43, G:0.04, T:0.49
Consensus pattern (21 bp):
TCTCTTCACTCCCTTCTGCTC
Found at i:2181799 original size:175 final size:175
Alignment explanation
Indices: 2181501--2181848 Score: 556
Period size: 175 Copynumber: 2.0 Consensus size: 175
2181491 AGATTGTTGC
* * **
2181501 TGGTATTTTGGTTGTCCATAGTGTTGATTCGTGATTGTTGTTTATATTTTGGGAATAATGTGTTG
1 TGGTATTTTGGTTGTCAATAGTGTTGATTCATGATTGTTGTTTATATTTTGGGAATAATGCATTG
* *
2181566 ATTCATGGTTGGATTGATTGATTGCTAGTCTTTTGTATTAATTCTAGTTGTATATGTGATTCACT
66 ATTCATGGTTGAATTGATTGATTGCTAGTCTTTTGTATTAATTCTAGTTGTATATGTGATTAACT
2181631 GTTGCTGGTATTTTAATTAGGAATAATGTGTTGGTTCATGGATTT
131 GTTGCTGGTATTTTAATTAGGAATAATGTGTTGGTTCATGGATTT
* * *
2181676 TGGTATTTTGGTTGTTGAAT-GTGTTGATTCATGGTTGTTGTTTATATTTTGGGAGTAATGCATT
1 TGGTATTTTGGTTG-TCAATAGTGTTGATTCATGATTGTTGTTTATATTTTGGGAATAATGCATT
*
2181740 GATTCATGGTTGAATTGATTGATTGCTAG-CATTTTGTATTAATTCTAGTTGTTTATGTGATTAA
65 GATTCATGGTTGAATTGATTGATTGCTAGTC-TTTTGTATTAATTCTAGTTGTATATGTGATTAA
* *
2181804 TTGTTGCTGGTATTTTAATTGGGAATAATGTGTTGGTTCATGGAT
129 CTGTTGCTGGTATTTTAATTAGGAATAATGTGTTGGTTCATGGAT
2181849 GCTGGTAGCT
Statistics
Matches: 159, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
174 1 0.01
175 155 0.97
176 3 0.02
ACGTcount: A:0.20, C:0.05, G:0.25, T:0.49
Consensus pattern (175 bp):
TGGTATTTTGGTTGTCAATAGTGTTGATTCATGATTGTTGTTTATATTTTGGGAATAATGCATTG
ATTCATGGTTGAATTGATTGATTGCTAGTCTTTTGTATTAATTCTAGTTGTATATGTGATTAACT
GTTGCTGGTATTTTAATTAGGAATAATGTGTTGGTTCATGGATTT
Found at i:2182142 original size:24 final size:24
Alignment explanation
Indices: 2182096--2182151 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
2182086 AAAAATTGTT
* * *
2182096 TTAGTAATTAAGGAATTAGTTAAA
1 TTAGTAATTAAGAAATAAATTAAA
*
2182120 TTAGTTATTAAGAAATAAATTAAA
1 TTAGTAATTAAGAAATAAATTAAA
*
2182144 TAAGTAAT
1 TTAGTAAT
2182152 ATTAGATAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (24 bp):
TTAGTAATTAAGAAATAAATTAAA
Found at i:2188769 original size:15 final size:16
Alignment explanation
Indices: 2188735--2188772 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
2188725 GAAAATAAAA
2188735 CTTTCCATTTTAAGAT
1 CTTTCCATTTTAAGAT
*
2188751 -TTTCCATTTTAA-TT
1 CTTTCCATTTTAAGAT
2188765 CTTTCCAT
1 CTTTCCAT
2188773 AATTAAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.95
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.55
Consensus pattern (16 bp):
CTTTCCATTTTAAGAT
Found at i:2189219 original size:184 final size:184
Alignment explanation
Indices: 2188870--2189220 Score: 501
Period size: 184 Copynumber: 1.9 Consensus size: 184
2188860 TGAGAACATG
* *
2188870 GATTAGTTTCCTAAATTGTATCTTATTTAGGTTACCTAAATGGTGACTTAACAAATTTTGAAAAC
1 GATTAGTTTCCTAAATTGTATCTTATTTAAGTTACCTAAATGGCGACTTAACAAATTTTGAAAAC
2188935 TTCTAATCAAACCAAAATTTTAAGGAAAGTTCAATGCTATCACAAAACTTTAGAAATTTCCTTTA
66 TTCTAATCAAACCAAAATTTTAAGGAAAGTTCAATGCTATCACAAAACTTTAGAAATTTCCTTTA
** * **
2189000 AAATTGGAAACTATTTCCTATGAATTTTTCAAATTAACTAACATTTATAATATT
131 AAATACGAAACTATTTCCTAGGAATTTCCCAAATTAACTAACATTTATAATATT
*
2189054 GATTAGTTTCCTAAATTGTATCTTGTTTAAGTTACCTAAATGGCGACTTAACAAATTTT-AGAAA
1 GATTAGTTTCCTAAATTGTATCTTATTTAAGTTACCTAAATGGCGACTTAACAAATTTTGA-AAA
* ** * * * *
2189118 CTTTTTGTGAAACTAAAATTTTAAGGAAAGTTTAATGCTATCACATAACTTTA-AGAATTT-CTT
65 CTTCTAATCAAACCAAAATTTTAAGGAAAGTTCAATGCTATCACAAAACTTTAGA-AATTTCCTT
* *
2189181 TAAAAGTACGAAATTATTTCTTAGGAATTTCCCAAATTAA
129 TAAAA-TACGAAACTATTTCCTAGGAATTTCCCAAATTAA
2189221 AATGCTTTCT
Statistics
Matches: 147, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
183 10 0.07
184 137 0.93
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.39
Consensus pattern (184 bp):
GATTAGTTTCCTAAATTGTATCTTATTTAAGTTACCTAAATGGCGACTTAACAAATTTTGAAAAC
TTCTAATCAAACCAAAATTTTAAGGAAAGTTCAATGCTATCACAAAACTTTAGAAATTTCCTTTA
AAATACGAAACTATTTCCTAGGAATTTCCCAAATTAACTAACATTTATAATATT
Found at i:2190362 original size:24 final size:24
Alignment explanation
Indices: 2190335--2190414 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 24
2190325 GTGGTCGCAA
**
2190335 CCACGTATATCACTTATGGCCTAG
1 CCACGTATATCACCCATGGCCTAG
* * *
2190359 CCACATATATCAACCCGTGGCCTTG
1 CCACGTATATC-ACCCATGGCCTAG
2190384 CCACGTATATCACAAACCATGGCCCTAG
1 CCACGTATATCAC---CCATGG-CCTAG
2190412 CCA
1 CCA
2190415 TGTCTAATAG
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 12 0.28
25 19 0.44
27 5 0.12
28 7 0.16
ACGTcount: A:0.28, C:0.35, G:0.15, T:0.23
Consensus pattern (24 bp):
CCACGTATATCACCCATGGCCTAG
Found at i:2192123 original size:21 final size:23
Alignment explanation
Indices: 2192072--2192123 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 23
2192062 GTTTCCTTTT
2192072 ATTTCATTTGCATTACATTTCAC
1 ATTTCATTTGCATTACATTTCAC
* * *
2192095 ATGT-ATTT-TATTGCATTTCAC
1 ATTTCATTTGCATTACATTTCAC
2192116 -TTTCATTT
1 ATTTCATTT
2192124 CCTTTTAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 15 0.62
22 4 0.17
23 3 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (23 bp):
ATTTCATTTGCATTACATTTCAC
Found at i:2201921 original size:18 final size:18
Alignment explanation
Indices: 2201908--2201950 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
2201898 TGATCTCTGA
2201908 AATG-TTCTCAATCTTCG
1 AATGCTTCTCAATCTTCG
*
2201925 AATGCTTCTCAATCTTCA
1 AATGCTTCTCAATCTTCG
2201943 AATGCTTC
1 AATGCTTC
2201951 CAAATGAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (18 bp):
AATGCTTCTCAATCTTCG
Found at i:2203780 original size:36 final size:38
Alignment explanation
Indices: 2203679--2203780 Score: 104
Period size: 36 Copynumber: 2.7 Consensus size: 38
2203669 NNNNNNNNNN
**
2203679 TATTATAAAGAGCACTATCCGAGGA-TAATAAATTGTGTGC
1 TATTATAAAGAGCACCCTCCGAGGATTAATAAA---TGTGC
* *
2203719 TATTTTAAAGAGCAGCCCT-CAAGGATTAAT-AA-GTGC
1 TATTATAAAGAGCA-CCCTCCGAGGATTAATAAATGTGC
2203755 TATTATAAAGAGCACCCTCCGAGGAT
1 TATTATAAAGAGCACCCTCCGAGGAT
2203781 AACAAANNNN
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
35 4 0.08
36 23 0.43
40 20 0.38
41 6 0.11
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (38 bp):
TATTATAAAGAGCACCCTCCGAGGATTAATAAATGTGC
Found at i:2204644 original size:23 final size:23
Alignment explanation
Indices: 2204617--2204661 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2204607 AAAAAGGAGA
2204617 ATCCTACTTAATTAAGGAATGCT
1 ATCCTACTTAATTAAGGAATGCT
*
2204640 ATCCTAGTTAATTAAGGAATGC
1 ATCCTACTTAATTAAGGAATGC
2204662 AATACCAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (23 bp):
ATCCTACTTAATTAAGGAATGCT
Found at i:2205612 original size:18 final size:19
Alignment explanation
Indices: 2205562--2205612 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
2205552 CATTCATTCG
*
2205562 GAAGCATTT-AAAGATTGA
1 GAAGCATTTCAGAGATTGA
2205580 GAAGCA-TTC-GTAGATTGA
1 GAAGCATTTCAG-AGATTGA
2205598 G-AGCATTTCAGAGAT
1 GAAGCATTTCAGAGAT
2205613 CAAGAAGAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
17 6 0.21
18 21 0.75
19 1 0.04
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.27
Consensus pattern (19 bp):
GAAGCATTTCAGAGATTGA
Found at i:2207625 original size:33 final size:33
Alignment explanation
Indices: 2207519--2207627 Score: 80
Period size: 33 Copynumber: 3.2 Consensus size: 33
2207509 ATAACTTTAG
* *
2207519 GAATTTCTTTTAAAGTAGGAAACTATTTCCTAT
1 GAATTTCTTTTAAAGTAGAAAATTATTTCCTAT
* * * * *
2207552 GAA-TT-TTTCAAATTAAAATAATATCATCAATT-TTAG
1 GAATTTCTTTTAAAGTAGAA-AAT-T-AT---TTCCTAT
2207588 GAATTTCTTTTAAAGTAGAAAATTATTTCCTAT
1 GAATTTCTTTTAAAGTAGAAAATTATTTCCTAT
2207621 GAATTTC
1 GAATTTC
2207628 CCAAATTAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 18
0.65 0.14 0.21
Matches are distributed among these distances:
31 9 0.16
32 6 0.11
33 13 0.24
34 2 0.04
35 2 0.04
36 6 0.11
37 7 0.13
38 10 0.18
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (33 bp):
GAATTTCTTTTAAAGTAGAAAATTATTTCCTAT
Found at i:2207625 original size:69 final size:69
Alignment explanation
Indices: 2207514--2207684 Score: 227
Period size: 69 Copynumber: 2.5 Consensus size: 69
2207504 NTCACATAAC
* **
2207514 TTTAGGAATTTCTTTTAAAGTAGGAAACTATTTCCTATGAATTTTTCAAATTAAAATAATATCAT
1 TTTAGGAATTTCTTTTAAAGTAGAAAACTATTTCCTATGAATTTCCCAAATTAAAATAATATCAT
2207579 CAAT
66 CAAT
* ** *
2207583 TTTAGGAATTTCTTTTAAAGTAGAAAATTATTTCCTATGAATTTCCCAAATTAAAATGCTATCTT
1 TTTAGGAATTTCTTTTAAAGTAGAAAACTATTTCCTATGAATTTCCCAAATTAAAATAATATCAT
*
2207648 TAAT
66 CAAT
* * *
2207652 TTT-GAAAATTTCTTTTAAAGTAGGAAACAATTT
1 TTTAG-GAATTTCTTTTAAAGTAGAAAACTATTT
2207685 TATATTTTTT
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
68 1 0.01
69 88 0.99
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (69 bp):
TTTAGGAATTTCTTTTAAAGTAGAAAACTATTTCCTATGAATTTCCCAAATTAAAATAATATCAT
CAAT
Found at i:2210941 original size:10 final size:10
Alignment explanation
Indices: 2210926--2210951 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2210916 CCATTTAATT
2210926 GATGGCTAGA
1 GATGGCTAGA
2210936 GATGGCTAGA
1 GATGGCTAGA
2210946 GATGGC
1 GATGGC
2210952 CACATAATTC
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:0.27, C:0.12, G:0.42, T:0.19
Consensus pattern (10 bp):
GATGGCTAGA
Found at i:2213137 original size:28 final size:26
Alignment explanation
Indices: 2213076--2213146 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 26
2213066 TAATTTTTAA
*
2213076 TTATAATTACTTATTTTTAGTTGTTT
1 TTATAATTACTTATTTTTAGTAGTTT
2213102 TTATAATTAACTTATTTTTAGTGAGTTAT
1 TTATAATT-ACTTATTTTTAGT-AGTT-T
2213131 TT-TAATT--TTATTTTTA
1 TTATAATTACTTATTTTTA
2213147 TTTACTTTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 9 0.22
26 8 0.20
27 13 0.32
28 8 0.20
29 3 0.07
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (26 bp):
TTATAATTACTTATTTTTAGTAGTTT
Found at i:2215210 original size:17 final size:17
Alignment explanation
Indices: 2215184--2215217 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2215174 ATTAGGTAGA
2215184 AATTTACTTTTTCTTCC
1 AATTTACTTTTTCTTCC
*
2215201 AATTTTCTTTTTCTTCC
1 AATTTACTTTTTCTTCC
2215218 TTTAAGCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.24, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTACTTTTTCTTCC
Found at i:2217181 original size:20 final size:19
Alignment explanation
Indices: 2217140--2217181 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2217130 CTTCAATTAG
* *
2217140 TAGTTTTCCTTTAATTGGT
1 TAGTTTTCCTTTAACTGAT
2217159 TAGTTCTTCCTTTAACTGAT
1 TAGTT-TTCCTTTAACTGAT
2217179 TAG
1 TAG
2217182 GACTTCTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.52
Consensus pattern (19 bp):
TAGTTTTCCTTTAACTGAT
Found at i:2217187 original size:20 final size:20
Alignment explanation
Indices: 2217145--2217192 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
2217135 ATTAGTAGTT
* * **
2217145 TTCCTTTAATTGGTTAGTTC
1 TTCCTTTAACTGATTAGGAC
2217165 TTCCTTTAACTGATTAGGAC
1 TTCCTTTAACTGATTAGGAC
2217185 TTCTCTTT
1 TTC-CTTT
2217193 CTCCAACTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.17, C:0.19, G:0.12, T:0.52
Consensus pattern (20 bp):
TTCCTTTAACTGATTAGGAC
Found at i:2226804 original size:15 final size:17
Alignment explanation
Indices: 2226774--2226808 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
2226764 TATTTTATGT
2226774 TAATATTATAAAAATTA
1 TAATATTATAAAAATTA
2226791 TAAT-TTAT-AAAATTA
1 TAATATTATAAAAATTA
2226806 TAA
1 TAA
2226809 AATTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 4 0.22
17 4 0.22
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAATATTATAAAAATTA
Found at i:2227235 original size:143 final size:132
Alignment explanation
Indices: 2227022--2227290 Score: 324
Period size: 143 Copynumber: 2.0 Consensus size: 132
2227012 CAGCTGCCAT
* * * * *
2227022 GCTCCATCTTTTTTCTTTTCTTCCCAGCGGCCCAGCCACAGCCATGCCCTACCTTGTCGCCCCAT
1 GCTCCATCTTCTTTCTTTTCTCCCCAGCGGCCCAACCACAGCCATGCCCCACCTTGTCACCCCAT
* * *
2227087 CCCCAACTACCACACTCCATCTTCTTTTTTTTTCTCCTCAACGGCCCAACCATAGCCACGCCCNN
66 CCCCAACTACCACACTCCATCTTC-TTTCTTTTCTCCTCAACAGCCCAACCACAGCCACGCCC--
2227152 NNNNNNNNACCAC
128 --------ACCAC
* * *
2227165 GCTCCATCTTCTTTCTTTTCTCCCCAGTGGCCCAACCACAAG-CATGCCCCGCCTTGTCACCCTA
1 GCTCCATCTTCTTTCTTTTCTCCCCAGCGGCCCAACCAC-AGCCATGCCCCACCTTGTCACCCCA
2227229 TCCCCAACTACCACACTCCATCTTCTTTCTTTTCTCCTCAACAGCCCAACCACAGCCACGCC
65 TCCCCAACTACCACACTCCATCTTCTTTCTTTTCTCCTCAACAGCCCAACCACAGCCACGCC
2227291 TTGCCCTGTC
Statistics
Matches: 114, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
142 34 0.30
143 78 0.68
144 2 0.02
ACGTcount: A:0.17, C:0.44, G:0.09, T:0.26
Consensus pattern (132 bp):
GCTCCATCTTCTTTCTTTTCTCCCCAGCGGCCCAACCACAGCCATGCCCCACCTTGTCACCCCAT
CCCCAACTACCACACTCCATCTTCTTTCTTTTCTCCTCAACAGCCCAACCACAGCCACGCCCACC
AC
Found at i:2227309 original size:78 final size:78
Alignment explanation
Indices: 2227160--2227344 Score: 228
Period size: 78 Copynumber: 2.4 Consensus size: 78
2227150 NNNNNNNNNN
* *** * *
2227160 ACCACGCTCCATCTTCTTTCTTTTCTCCCCAGTGGCCCAACCACAAGCATGCCCCGCCTTGTCAC
1 ACCACACTCCATCTTCTTTCTTTTCTCCCCAACAGCCCAACCACAAGCACGCCCCGCCCTGTCAC
2227225 CCTATCCCCAACT
66 CCTATCCCCAACT
* ** *
2227238 ACCACACTCCATCTTCTTTCTTTTCTCCTCAACAGCCCAACCAC-AGCCACGCCTTGCCCTGTCG
1 ACCACACTCCATCTTCTTTCTTTTCTCCCCAACAGCCCAACCACAAG-CACGCCCCGCCCTGTCA
* * *
2227302 CCTTATCCCTAGCT
65 CCCTATCCCCAACT
*
2227316 GCCACACTCCATCTTCTTTCTTTTCTCCC
1 ACCACACTCCATCTTCTTTCTTTTCTCCC
2227345 TAGAAGCCTA
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
77 2 0.02
78 89 0.98
ACGTcount: A:0.17, C:0.45, G:0.09, T:0.29
Consensus pattern (78 bp):
ACCACACTCCATCTTCTTTCTTTTCTCCCCAACAGCCCAACCACAAGCACGCCCCGCCCTGTCAC
CCTATCCCCAACT
Found at i:2230241 original size:14 final size:14
Alignment explanation
Indices: 2230182--2230281 Score: 52
Period size: 14 Copynumber: 7.4 Consensus size: 14
2230172 GAATATATGC
*
2230182 GTTTACTTATTTAA
1 GTTTAGTTATTTAA
2230196 GTTTATGTTATTT--
1 GTTTA-GTTATTTAA
*
2230209 GTTTAGATT-TTTGTA
1 GTTTAG-TTATTT-AA
2230224 -TTTAGTTATTTAA
1 GTTTAGTTATTTAA
*
2230237 GTTTATGTT-GTT-A
1 GTTTA-GTTATTTAA
* **
2230250 -TTTAGATATTTTT
1 GTTTAGTTATTTAA
*
2230263 GTATAGTTATTTAA
1 GTTTAGTTATTTAA
2230277 GTTTA
1 GTTTA
2230282 TATCGTTTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 22
0.66 0.11 0.23
Matches are distributed among these distances:
11 2 0.03
12 10 0.16
13 11 0.17
14 32 0.50
15 9 0.14
ACGTcount: A:0.24, C:0.01, G:0.14, T:0.61
Consensus pattern (14 bp):
GTTTAGTTATTTAA
Found at i:2230251 original size:18 final size:20
Alignment explanation
Indices: 2230188--2230282 Score: 72
Period size: 22 Copynumber: 4.7 Consensus size: 20
2230178 ATGCGTTTAC
*
2230188 TTATTTAAGTTTATGT-TAT
1 TTATTTAAGTTTATGTATAG
* *
2230207 TTGTTT-AGATTTTTGTATTTAG
1 TTATTTAAG-TTTATGTA--TAG
2230229 TTATTTAAGTTTATGT-T-G
1 TTATTTAAGTTTATGTATAG
* *
2230247 TTATTTAGATATTTTTGTATAG
1 TTATTTA-A-GTTTATGTATAG
2230269 TTATTTAAGTTTAT
1 TTATTTAAGTTTAT
2230283 ATCGTTTTAT
Statistics
Matches: 58, Mismatches: 9, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
18 10 0.17
19 13 0.22
20 10 0.17
21 2 0.03
22 21 0.36
23 2 0.03
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (20 bp):
TTATTTAAGTTTATGTATAG
Found at i:2230270 original size:40 final size:39
Alignment explanation
Indices: 2230188--2230325 Score: 138
Period size: 40 Copynumber: 3.4 Consensus size: 39
2230178 ATGCGTTTAC
*
2230188 TTATTTAAGTTTATGTTATTTGTTTAG--ATTTTTGTATTTAG
1 TTATTTAAGTTTATGTT-GTT-TTTAGATATTTTTGTA--TAG
2230229 TTATTTAAGTTTATGTTGTTATTTAGATATTTTTGTATAG
1 TTATTTAAGTTTATGTTGTT-TTTAGATATTTTTGTATAG
* * * *
2230269 TTATTTAAGTTTATATCGTTTTATGGATATTTGTT-TTTAG
1 TTATTTAAGTTTATGTTGTTTT-TAGATATTT-TTGTATAG
*
2230309 TTATTTAATTTTATGTT
1 TTATTTAAGTTTATGTT
2230326 TAAGATATTT
Statistics
Matches: 84, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
39 2 0.02
40 54 0.64
41 19 0.23
42 9 0.11
ACGTcount: A:0.23, C:0.01, G:0.14, T:0.62
Consensus pattern (39 bp):
TTATTTAAGTTTATGTTGTTTTTAGATATTTTTGTATAG
Found at i:2240724 original size:2 final size:2
Alignment explanation
Indices: 2240678--2240707 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
2240668 CGTATTTCAC
2240678 AT AT AT CAT 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 A
2240708 GATAACTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2241841 original size:21 final size:22
Alignment explanation
Indices: 2241812--2241855 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2241802 AAGTGATTAA
2241812 TTTAAGTTATTTTA-ATTAAAT
1 TTTAAGTTATTTTATATTAAAT
* *
2241833 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATATTAAAT
2241855 T
1 T
2241856 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATATTAAAT
Found at i:2248042 original size:20 final size:20
Alignment explanation
Indices: 2247998--2248043 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2247988 CTTCAAGCAT
* *
2247998 CATTCTCAATTATCATCAAG
1 CATTATCAATCATCATCAAG
* *
2248018 TATTATCAATCATCATCATG
1 CATTATCAATCATCATCAAG
2248038 CATTAT
1 CATTAT
2248044 TTATTCTCAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (20 bp):
CATTATCAATCATCATCAAG
Found at i:2257251 original size:20 final size:20
Alignment explanation
Indices: 2257222--2257270 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
2257212 CAATCAGATT
*
2257222 AACAAATTCAAGCATTGATG
1 AACAATTTCAAGCATTGATG
2257242 AACAATTTCAAGCATTGATG
1 AACAATTTCAAGCATTGATG
2257262 AACAATTTC
1 AACAATTTC
2257271 TCATATTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (20 bp):
AACAATTTCAAGCATTGATG
Found at i:2261894 original size:17 final size:16
Alignment explanation
Indices: 2261847--2261894 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
2261837 TTAAATTTTG
* *
2261847 AAAAATAATATTATAT
1 AAAATTAATATTAAAT
*
2261863 ATAATTATATATTAAAT
1 AAAATTA-ATATTAAAT
2261880 AAAATTAATACTTAA
1 AAAATTAATA-TTAA
2261895 TTACTTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 8 0.31
17 18 0.69
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATTAATATTAAAT
Found at i:2266026 original size:29 final size:29
Alignment explanation
Indices: 2265973--2266047 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 29
2265963 TAATAGCTTT
* *
2265973 AACATGTTTA-TCTTAATTTATACAAAAA
1 AACATGTTTAGTCTTAATTGAGACAAAAA
*
2266001 AACATGTTTAGTCTTAATTGAGACAAGAA
1 AACATGTTTAGTCTTAATTGAGACAAAAA
* *
2266030 AATATATTT-GTCTTAATT
1 AACATGTTTAGTCTTAATT
2266048 TAAGATAAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 19 0.46
29 22 0.54
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.40
Consensus pattern (29 bp):
AACATGTTTAGTCTTAATTGAGACAAAAA
Found at i:2266064 original size:28 final size:29
Alignment explanation
Indices: 2265999--2266138 Score: 101
Period size: 28 Copynumber: 4.8 Consensus size: 29
2265989 TTTATACAAA
* * * *
2265999 AAAACATGTTTAGTCTTAATTGAGACAAG
1 AAAACATATTTTGTCTTAATTAAGATAAG
*
2266028 AAAATATA-TTTGTCTTAATTTAAGATAAG
1 AAAACATATTTTGTCTTAA-TTAAGATAAG
* ** *
2266057 AAAA-ATATTTTTTGCCTTAATCCAGATAAA
1 AAAACATA--TTTTGTCTTAATTAAGATAAG
*
2266087 AAAACATA-TTTGTCTTAAATT-AGTTAAG
1 AAAACATATTTTGTCTT-AATTAAGATAAG
2266115 ATAAA-ATATTTTTGTCTTAATTAA
1 A-AAACATA-TTTTGTCTTAATTAA
2266139 AGACAAGAGT
Statistics
Matches: 88, Mismatches: 13, Indels: 19
0.73 0.11 0.16
Matches are distributed among these distances:
28 28 0.32
29 28 0.32
30 20 0.23
31 12 0.14
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (29 bp):
AAAACATATTTTGTCTTAATTAAGATAAG
Found at i:2266064 original size:30 final size:29
Alignment explanation
Indices: 2266011--2266138 Score: 118
Period size: 30 Copynumber: 4.4 Consensus size: 29
2266001 AACATGTTTA
* *
2266011 GTCTTAATTGAGACAAG-AAAATATATTT
1 GTCTTAATTAAGATAAGAAAAATATATTT
*
2266039 GTCTTAATTTAAGATAAGAAAAATATTTTTT
1 GTCTTAA-TTAAGATAAGAAAAATA-TATTT
* ** *
2266070 GCCTTAATCCAGATAA-AAAAACATATTT
1 GTCTTAATTAAGATAAGAAAAATATATTT
* *
2266098 GTCTTAAATT-AGTTAAGATAAAATATTTTT
1 GTCTT-AATTAAGATAAGA-AAAATATATTT
2266128 GTCTTAATTAA
1 GTCTTAATTAA
2266139 AGACAAGAGT
Statistics
Matches: 80, Mismatches: 13, Indels: 12
0.76 0.12 0.11
Matches are distributed among these distances:
28 20 0.25
29 22 0.28
30 28 0.35
31 10 0.12
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (29 bp):
GTCTTAATTAAGATAAGAAAAATATATTT
Found at i:2266076 original size:59 final size:58
Alignment explanation
Indices: 2266013--2266146 Score: 153
Period size: 59 Copynumber: 2.3 Consensus size: 58
2266003 CATGTTTAGT
* * *
2266013 CTTAATTGAGACAAGAAAATATATTTGTCTTAATTTAAGATAAGA-AAAATATTTTTTGC
1 CTTAATTAAGACAAGAAAACATATTTGTCTTAAATT-AGATAAGATAAAATA-TTTTTGC
** * * * *
2266072 CTTAATCCAGATAAAAAAACATATTTGTCTTAAATTAGTTAAGATAAAATATTTTTGT
1 CTTAATTAAGACAAGAAAACATATTTGTCTTAAATTAGATAAGATAAAATATTTTTGC
2266130 CTTAATTAAAGACAAGA
1 CTTAATT-AAGACAAGA
2266147 GTAGTCTTAA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
58 19 0.31
59 42 0.69
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (58 bp):
CTTAATTAAGACAAGAAAACATATTTGTCTTAAATTAGATAAGATAAAATATTTTTGC
Found at i:2267633 original size:16 final size:16
Alignment explanation
Indices: 2267612--2267642 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2267602 CGTAACTGTT
2267612 TAAATTTGAAATAATC
1 TAAATTTGAAATAATC
*
2267628 TAAATTTTAAATAAT
1 TAAATTTGAAATAAT
2267643 TCCGTCTCAA
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:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATTTGAAATAATC
Found at i:2282719 original size:42 final size:45
Alignment explanation
Indices: 2282653--2282736 Score: 138
Period size: 43 Copynumber: 1.9 Consensus size: 45
2282643 CCTATTTTTT
2282653 TTAAAAAAATATATAATAATAGTAAT-TTT-AAATTAATAAAAAA
1 TTAAAAAAATATATAATAATAGTAATCTTTAAAATTAATAAAAAA
*
2282696 TTAATAAAATATAT-ATAATAGTAATCTTTAAAATTAATAAA
1 TTAAAAAAATATATAATAATAGTAATCTTTAAAATTAATAAA
2282737 GAGTAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
42 11 0.29
43 16 0.42
44 11 0.29
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (45 bp):
TTAAAAAAATATATAATAATAGTAATCTTTAAAATTAATAAAAAA
Found at i:2292697 original size:20 final size:20
Alignment explanation
Indices: 2292672--2292728 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
2292662 TATATTTTCT
2292672 TCATGTATCGATACATGGGG
1 TCATGTATCGATACATGGGG
*
2292692 TCATGTATCGATACATGTGG
1 TCATGTATCGATACATGGGG
* *
2292712 TCCTGTATCAATACATG
1 TCATGTATCGATACATG
2292729 AGCCTCTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
TCATGTATCGATACATGGGG
Found at i:2298647 original size:21 final size:21
Alignment explanation
Indices: 2298621--2298675 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2298611 TGTTCATGCA
2298621 ATTCATGACAAGGACTGATAC
1 ATTCATGACAAGGACTGATAC
* * * *
2298642 ATTCATAACAAAGATTGATGC
1 ATTCATGACAAGGACTGATAC
*
2298663 ATTTATGACAAGG
1 ATTCATGACAAGG
2298676 GTCGATGCCT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (21 bp):
ATTCATGACAAGGACTGATAC
Found at i:2302328 original size:21 final size:21
Alignment explanation
Indices: 2302299--2302353 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
2302289 GTGGTCTTAA
2302299 TTAAGGCAAGAGTTGTCTTTAT
1 TTAA-GCAAGAGTTGTCTTTAT
2302321 TTAAGCAAGAGTTGTCTTTAT
1 TTAAGCAAGAGTTGTCTTTAT
2302342 TTAAGCAAGAGT
1 TTAAGCAAGAGT
2302354 ATATGTGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 29 0.88
22 4 0.12
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (21 bp):
TTAAGCAAGAGTTGTCTTTAT
Found at i:2303448 original size:31 final size:32
Alignment explanation
Indices: 2303413--2303472 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
2303403 ATGACACTTG
2303413 GAAAA-GTGGGACTCAATTTATGATTATGATT
1 GAAAAGGTGGGACTCAATTTATGATTATGATT
** **
2303444 GAAAAGGTGGGTGTTGATTTATGATTATG
1 GAAAAGGTGGGACTCAATTTATGATTATG
2303473 TTTGGATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 5 0.21
32 19 0.79
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.37
Consensus pattern (32 bp):
GAAAAGGTGGGACTCAATTTATGATTATGATT
Found at i:2312308 original size:20 final size:20
Alignment explanation
Indices: 2312283--2312328 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2312273 TACATAAGTT
2312283 CATACAACACATTATGCCTA
1 CATACAACACATTATGCCTA
*
2312303 CATACAGCACATTATGCCTA
1 CATACAACACATTATGCCTA
2312323 CATACA
1 CATACA
2312329 TAACCACAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.30, G:0.07, T:0.24
Consensus pattern (20 bp):
CATACAACACATTATGCCTA
Found at i:2322616 original size:49 final size:49
Alignment explanation
Indices: 2322563--2322678 Score: 135
Period size: 49 Copynumber: 2.4 Consensus size: 49
2322553 GTGTTGAGGA
*
2322563 ATATGTTCCATCCGTGGATGATTCTAG-ACGATGATATGATGTGAGGTAT
1 ATATGTTCCATCCGTGGATGATT-TAGAACGATGATATGATGTGAGATAT
* ** * *
2322612 ATATGTTTCATTTGTGGATGATTTCGAATGATGATATGATGTGAGATAT
1 ATATGTTCCATCCGTGGATGATTTAGAACGATGATATGATGTGAGATAT
* * *
2322661 GTATGCTCCGTCCGTGGA
1 ATATGTTCCATCCGTGGA
2322679 AGAACTCCAA
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
48 2 0.04
49 52 0.96
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (49 bp):
ATATGTTCCATCCGTGGATGATTTAGAACGATGATATGATGTGAGATAT
Found at i:2328403 original size:22 final size:20
Alignment explanation
Indices: 2328346--2328403 Score: 53
Period size: 22 Copynumber: 2.8 Consensus size: 20
2328336 TCATGTGATT
* *
2328346 ACATGTATTGATACATAAGC
1 ACATGTATCGATACATAAGA
* *
2328366 ATATGTATCGACACATACAAGA
1 ACATGTATCGATACAT--AAGA
*
2328388 ACATGTATGGATACAT
1 ACATGTATCGATACAT
2328404 CATACAATGT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (20 bp):
ACATGTATCGATACATAAGA
Found at i:2332435 original size:29 final size:28
Alignment explanation
Indices: 2332370--2332435 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
2332360 CTTTCATAGC
* *
2332370 ATACTCATTTAAGAGCCAACATATGCACC
1 ATAC-CATTCAAGAGCCAACATATGCACA
** *
2332399 ATTTCATTCAAGGGCCAAACATATGCACA
1 ATACCATTCAAGAGCC-AACATATGCACA
2332428 ATACCATT
1 ATACCATT
2332436 TAAGTCTTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
28 10 0.34
29 19 0.66
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.26
Consensus pattern (28 bp):
ATACCATTCAAGAGCCAACATATGCACA
Done.