Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 7 of 138
Found at i:1826795 original size:11 final size:11
Alignment explanation
Indices: 1826764--1826795 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1826754 GCAATATCTG
*
1826764 ACAAATCTCAA
1 ACAAATCTCTA
1826775 ACAAATCTCTA
1 ACAAATCTCTA
1826786 ACAAATCTCT
1 ACAAATCTCT
1826796 TATGGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:1826999 original size:18 final size:19
Alignment explanation
Indices: 1826966--1827002 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1826956 ATCTTCAAAA
1826966 CTTGAACTCGAACTCTTCT
1 CTTGAACTCGAACTCTTCT
*
1826985 CTTGAA-TCGAGCTCTTCT
1 CTTGAACTCGAACTCTTCT
1827003 GGACTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.38
Consensus pattern (19 bp):
CTTGAACTCGAACTCTTCT
Found at i:1827111 original size:25 final size:25
Alignment explanation
Indices: 1827044--1827112 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
1827034 CACTTCCCAT
*
1827044 ATCTCGAACCGTCAACTC-TTCCAC
1 ATCTCGAACCTTCAACTCTTTCCAC
* **
1827068 GTCTCGAACCTTCGGCTCTTTCCAC
1 ATCTCGAACCTTCAACTCTTTCCAC
* *
1827093 ATCTTGAATCTTCAACTCTT
1 ATCTCGAACCTTCAACTCTT
1827113 CTTACGTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
24 14 0.40
25 21 0.60
ACGTcount: A:0.20, C:0.36, G:0.10, T:0.33
Consensus pattern (25 bp):
ATCTCGAACCTTCAACTCTTTCCAC
Found at i:1841029 original size:21 final size:21
Alignment explanation
Indices: 1840984--1841030 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1840974 GGAAAAATTC
*
1840984 TATATACACTTCATTTATTAT
1 TATATACACTTCACTTATTAT
1841005 TATATACA-TCTCACTT-TTAT
1 TATATACACT-TCACTTATTAT
1841025 ATATAT
1 -TATAT
1841031 CCCAAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATACACTTCACTTATTAT
Found at i:1842281 original size:23 final size:23
Alignment explanation
Indices: 1842255--1842311 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 23
1842245 TTGATTTGAC
1842255 TTAAAATAATAAAATATTATTTT
1 TTAAAATAATAAAATATTATTTT
*
1842278 TTAAAAAATATAAAATATTATTTT
1 TTAAAATA-ATAAAATATTATTTT
1842302 TTAAATATAA
1 TTAAA-ATAA
1842312 ATATATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 7 0.23
24 21 0.70
25 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTAAAATAATAAAATATTATTTT
Found at i:1842290 original size:24 final size:25
Alignment explanation
Indices: 1842257--1842306 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
1842247 GATTTGACTT
1842257 AAAATAATAAAATATTATTTTTTAA
1 AAAATAATAAAATATTATTTTTTAA
1842282 AAAAT-ATAAAATATTATTTTTTAA
1 AAAATAATAAAATATTATTTTTTAA
1842306 A
1 A
1842307 TATAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAATAATAAAATATTATTTTTTAA
Found at i:1842317 original size:22 final size:22
Alignment explanation
Indices: 1842255--1842347 Score: 84
Period size: 24 Copynumber: 4.1 Consensus size: 22
1842245 TTGATTTGAC
1842255 TTAAAATAATAAAATATTATTTT
1 TTAAAAT-ATAAAATATTATTTT
1842278 TTAAAAAATATAAAATATTATTTT
1 TT--AAAATATAAAATATTATTTT
**
1842302 TT-AAATAT-AAATATATATAAAT
1 TTAAAATATAAAATAT-TAT-TTT
* *
1842324 TTAAAATTTAAAA-ATAATTTT
1 TTAAAATATAAAATATTATTTT
1842345 TTA
1 TTA
1842348 TATAATATCG
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
20 6 0.10
21 13 0.22
22 5 0.09
23 9 0.16
24 20 0.34
25 5 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TTAAAATATAAAATATTATTTT
Found at i:1854895 original size:17 final size:18
Alignment explanation
Indices: 1854873--1854912 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1854863 ATTTTACAAA
1854873 TTAATAAAAATT-TAT-AT
1 TTAAT-AAAATTATATCAT
1854890 TTAATAAAATTATATCAT
1 TTAATAAAATTATATCAT
1854908 TTAAT
1 TTAAT
1854913 TATTAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 8 0.38
18 7 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATAAAATTATATCAT
Found at i:1854927 original size:24 final size:25
Alignment explanation
Indices: 1854879--1854946 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 25
1854869 CAAATTAATA
* *
1854879 AAAATTTATAT-TTAATAAAATTAT
1 AAAATTTACATATTAATAATATTAT
**
1854903 ATCATTTA-ATTATTAATAATA-TAT
1 AAAATTTACA-TATTAATAATATTAT
1854927 AAAATTTACATATTAATAAT
1 AAAATTTACATATTAATAAT
1854947 TTAATAATAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
23 1 0.03
24 26 0.72
25 9 0.25
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAATTTACATATTAATAATATTAT
Found at i:1854951 original size:32 final size:32
Alignment explanation
Indices: 1854893--1854958 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
1854883 TTTATATTTA
*
1854893 ATAAAATTATATCATTTAATTATTAATAATAT
1 ATAAAATTATATCATTTAATAATTAATAATAT
1854925 ATAAAATT-TA-CATATTAATAATTTAATAATAT
1 ATAAAATTATATCAT-TTAATAA-TTAATAATAT
1854957 AT
1 AT
1854959 CATGTAAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 3 0.10
31 8 0.26
32 20 0.65
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (32 bp):
ATAAAATTATATCATTTAATAATTAATAATAT
Found at i:1856098 original size:29 final size:30
Alignment explanation
Indices: 1856035--1856101 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 30
1856025 TTAATTTTAA
1856035 AAATAAAAAATAATTAATTTAATAAAATATC
1 AAAT-AAAAATAATTAATTTAATAAAATATC
*
1856066 AAATAAAAA-AATTAGTTATAACTAAAAT-T-
1 AAATAAAAATAATTAATT-TAA-TAAAATATC
1856095 AAATAAA
1 AAATAAA
1856102 TTATATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 14 0.42
30 9 0.27
31 10 0.30
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (30 bp):
AAATAAAAATAATTAATTTAATAAAATATC
Found at i:1857985 original size:18 final size:18
Alignment explanation
Indices: 1857945--1857987 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1857935 GCTAATAATT
1857945 TAAAATTTATAAACTAAA
1 TAAAATTTATAAACTAAA
* *
1857963 AAAAATTTAATCAA-TAAA
1 TAAAATTT-ATAAACTAAA
1857981 TAAAATT
1 TAAAATT
1857988 ATCTTATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATTTATAAACTAAA
Found at i:1864944 original size:9 final size:9
Alignment explanation
Indices: 1864930--1864959 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1864920 AATATTTTAT
1864930 TAATTAAAA
1 TAATTAAAA
1864939 TAATTAAAA
1 TAATTAAAA
1864948 TATATTAAAA
1 TA-ATTAAAA
1864958 TA
1 TA
1864960 TAAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:1864956 original size:10 final size:10
Alignment explanation
Indices: 1864932--1864961 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1864922 TATTTTATTA
1864932 ATTAAAATA-
1 ATTAAAATAT
1864941 ATTAAAATAT
1 ATTAAAATAT
1864951 ATTAAAATAT
1 ATTAAAATAT
1864961 A
1 A
1864962 AAAATTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:1865121 original size:66 final size:66
Alignment explanation
Indices: 1864979--1865109 Score: 244
Period size: 66 Copynumber: 2.0 Consensus size: 66
1864969 TATTAAACTC
* *
1864979 ACGAGTTATTCAAATTGAATATAAGAATGTTCGAATTTAATTTGATCGATAAGTAGAGTTATTCG
1 ACGAGTTATTCAAATTAAATATAAGAATGTTCGAATTCAATTTGATCGATAAGTAGAGTTATTCG
1865044 G
66 G
1865045 ACGAGTTATTCAAATTAAATATAAGAATGTTCGAATTCAATTTGATCGATAAGTAGAGTTATTCG
1 ACGAGTTATTCAAATTAAATATAAGAATGTTCGAATTCAATTTGATCGATAAGTAGAGTTATTCG
1865110 TCTTGGTTAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.36
Consensus pattern (66 bp):
ACGAGTTATTCAAATTAAATATAAGAATGTTCGAATTCAATTTGATCGATAAGTAGAGTTATTCG
G
Found at i:1865188 original size:52 final size:52
Alignment explanation
Indices: 1865126--1865230 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
1865116 TTATTCGACT
1865126 TGATTCGATAATAATTAAGTTAAATTTAAGTTTTATTCAAATAAAATTTGAA
1 TGATTCGATAATAATTAAGTTAAATTTAAGTTTTATTCAAATAAAATTTGAA
1865178 TGATTCGATAATAATTAAGTTAAATTTAAGTTTTATTCAAATAAAATTTGAA
1 TGATTCGATAATAATTAAGTTAAATTTAAGTTTTATTCAAATAAAATTTGAA
1865230 T
1 T
1865231 AAATCTACGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.43
Consensus pattern (52 bp):
TGATTCGATAATAATTAAGTTAAATTTAAGTTTTATTCAAATAAAATTTGAA
Found at i:1871737 original size:24 final size:24
Alignment explanation
Indices: 1871710--1871757 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1871700 TTTTATTTTG
1871710 TATAT-TTAAGTA-ATTTTTTATAAA
1 TATATATTAA-TATATTTTTT-TAAA
1871734 TATATATTAATATATTTTTTTAAA
1 TATATATTAATATATTTTTTTAAA
1871758 AAAATATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TATATATTAATATATTTTTTTAAA
Found at i:1871739 original size:26 final size:25
Alignment explanation
Indices: 1871710--1871766 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
1871700 TTTTATTTTG
*
1871710 TATATTTAAGTA-A-TTTTTTATAAA
1 TATATTTAA-TATATTTTTTTAAAAA
1871734 TATATATTAATATATTTTTTTAAAAA
1 TATAT-TTAATATATTTTTTTAAAAA
*
1871760 AATATTT
1 TATATTT
1871767 TAATTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 7 0.25
25 7 0.25
26 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
TATATTTAATATATTTTTTTAAAAA
Found at i:1871783 original size:28 final size:31
Alignment explanation
Indices: 1871752--1871810 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
1871742 AATATATTTT
1871752 TTTAAAAAAAT-ATTT-TAAT-TTTAATAAA
1 TTTAAAAAAATAATTTATAATATTTAATAAA
* *
1871780 TTTAAAATAATAATTTATATTATTTAATAAA
1 TTTAAAAAAATAATTTATAATATTTAATAAA
1871811 AAAATTATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 10 0.38
29 4 0.15
30 3 0.12
31 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
TTTAAAAAAATAATTTATAATATTTAATAAA
Found at i:1873787 original size:12 final size:12
Alignment explanation
Indices: 1873772--1873803 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1873762 CATAACATTG
1873772 ATCATCTGTGAA
1 ATCATCTGTGAA
1873784 ATCATCTGTGAA
1 ATCATCTGTGAA
1873796 ATCATCTG
1 ATCATCTG
1873804 AGTATTCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (12 bp):
ATCATCTGTGAA
Found at i:1880914 original size:14 final size:14
Alignment explanation
Indices: 1880866--1880916 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
1880856 GTGAATTATT
*
1880866 ATTAGAAAAAATGATA
1 ATTA-AAAAAAT-TTA
1880882 ATTAAAAAAA-TTA
1 ATTAAAAAAATTTA
*
1880895 ATTTAAAAAAATTTT
1 A-TTAAAAAAATTTA
1880910 ATTAAAA
1 ATTAAAA
1880917 TATATAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 3 0.10
14 15 0.48
15 9 0.29
16 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (14 bp):
ATTAAAAAAATTTA
Found at i:1884461 original size:31 final size:31
Alignment explanation
Indices: 1884404--1884464 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1884394 AAGATGATTT
* *
1884404 TGGTATGATTTTGTGAAAATAGATAAAGATG
1 TGGTATGATTTTATGAAAATAAATAAAGATG
* *
1884435 TGGTGTGATTTTATGACAATAAATAAAGAT
1 TGGTATGATTTTATGAAAATAAATAAAGAT
1884465 TTTGCAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (31 bp):
TGGTATGATTTTATGAAAATAAATAAAGATG
Found at i:1893465 original size:11 final size:11
Alignment explanation
Indices: 1893442--1893470 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1893432 TTATTTAACA
1893442 TTTAAAA-AAT
1 TTTAAAATAAT
1893452 TTTAAAATAAT
1 TTTAAAATAAT
1893463 TTTAAAAT
1 TTTAAAAT
1893471 TATGAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TTTAAAATAAT
Found at i:1893507 original size:21 final size:22
Alignment explanation
Indices: 1893476--1893518 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1893466 AAAATTATGA
*
1893476 AATTATTTTTATGATAAATAAT
1 AATTATTTTTATGAAAAATAAT
*
1893498 AATT-TTTTTATTAAAAATAAT
1 AATTATTTTTATGAAAAATAAT
1893519 TAAAATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTATTTTTATGAAAAATAAT
Found at i:1893516 original size:18 final size:21
Alignment explanation
Indices: 1893476--1893520 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 21
1893466 AAAATTATGA
1893476 AATTATTTTTATGATAAATAAT
1 AATTATTTTTAT-ATAAATAAT
1893498 AATT-TTTTTAT-TAAA-AAT
1 AATTATTTTTATATAAATAAT
1893516 AATTA
1 AATTA
1893521 AAATAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 7 0.32
19 4 0.18
21 7 0.32
22 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AATTATTTTTATATAAATAAT
Found at i:1893986 original size:14 final size:15
Alignment explanation
Indices: 1893967--1894000 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1893957 ATTTTGATTT
*
1893967 ATATTTTTAA-ATAA
1 ATATTTTTAATAAAA
1893981 ATATTTTTAATAAAA
1 ATATTTTTAATAAAA
1893996 ATATT
1 ATATT
1894001 AATAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTTTTAATAAAA
Found at i:1894043 original size:6 final size:6
Alignment explanation
Indices: 1894032--1894062 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
1894022 TAAATATTGA
1894032 TTAAAT TTAAAT TTAAAT TTAAAT TATAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT
1894063 AATTTTCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:1894161 original size:36 final size:37
Alignment explanation
Indices: 1894111--1894181 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
1894101 TTAAATTCTG
* *
1894111 TTAATTTATATGTTTTAA-TTTTTTTAAAAAATTTTTA
1 TTAAATTATATGTTTAAAGTTTTTTT-AAAAATTTTTA
*
1894148 TTAAATTAT-TGTTTAAAGTTTTTTTTAAAATTTT
1 TTAAATTATATGTTTAAAGTTTTTTTAAAAATTTT
1894182 ACCTCGTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 15 0.50
37 15 0.50
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (37 bp):
TTAAATTATATGTTTAAAGTTTTTTTAAAAATTTTTA
Found at i:1894565 original size:66 final size:66
Alignment explanation
Indices: 1894490--1894661 Score: 245
Period size: 66 Copynumber: 2.6 Consensus size: 66
1894480 TTGGCTCACT
* * * * * * * *
1894490 ATTTTTTATACATTTACTAAAGGACAAAGGAGATTTAGGAATGTATGAGATTGACTTAGTATTCC
1 ATTTTTTATATAATTAATAAAGGAGAAAGGAGATTTAAGAATGGATGAGATTGACTCACTATTCC
1894555 A
66 A
* *
1894556 ATTTTTTATATAATTAATAAAGGAGAAAGGAGGTTTAAGAATGGATGAGATTGGCTCACTATTCC
1 ATTTTTTATATAATTAATAAAGGAGAAAGGAGATTTAAGAATGGATGAGATTGACTCACTATTCC
1894621 A
66 A
*
1894622 ATTTTTTATATAATTAATAAAGGAGAAGGGAGATTTAAGA
1 ATTTTTTATATAATTAATAAAGGAGAAAGGAGATTTAAGA
1894662 TTTTATATAA
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 94 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (66 bp):
ATTTTTTATATAATTAATAAAGGAGAAAGGAGATTTAAGAATGGATGAGATTGACTCACTATTCC
A
Found at i:1894674 original size:37 final size:37
Alignment explanation
Indices: 1894625--1894695 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
1894615 TATTCCAATT
*
1894625 TTTTATATAATTAATAAAGGAGAAGGGAGATTTAAGA
1 TTTTATATAATTAATAAAGGAGAAAGGAGATTTAAGA
*
1894662 TTTTATATAATTAATAAAGGAGAAAGGAGTTTTA
1 TTTTATATAATTAATAAAGGAGAAAGGAGATTTA
1894696 GGAATGTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.20, T:0.35
Consensus pattern (37 bp):
TTTTATATAATTAATAAAGGAGAAAGGAGATTTAAGA
Found at i:1894738 original size:103 final size:104
Alignment explanation
Indices: 1894559--1894763 Score: 331
Period size: 103 Copynumber: 2.0 Consensus size: 104
1894549 TATTCCAATT
*
1894559 TTTTATATAATTAATAAAGGAGAAAGGAGGTTTAAGAATGGATGAGATTGGCTCACTATTCCAAT
1 TTTTATATAATTAATAAAGGAGAAAGGAGGTTTAAGAATGGATGAGATTGGATCACTATTCCAAT
* * *
1894624 TTTTTATATAATTAAT-AAAGGAGAAGGGAGATTTAAGA
66 TGTTTATATAATTAATAAAAGGAAAAAGGAGATTTAAGA
* * *
1894662 TTTTATATAATTAATAAAGGAGAAAGGAGTTTTAGGAATGTATGAGATTGGATCACTATTCCAAT
1 TTTTATATAATTAATAAAGGAGAAAGGAGGTTTAAGAATGGATGAGATTGGATCACTATTCCAAT
1894727 TGTTTATATAATTAATAAAAAGGAAAAAGGAGATTTA
66 TGTTTATATAATTAAT-AAAAGGAAAAAGGAGATTTA
1894764 GGAATGCATG
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
103 76 0.82
105 17 0.18
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (104 bp):
TTTTATATAATTAATAAAGGAGAAAGGAGGTTTAAGAATGGATGAGATTGGATCACTATTCCAAT
TGTTTATATAATTAATAAAAGGAAAAAGGAGATTTAAGA
Found at i:1894891 original size:66 final size:66
Alignment explanation
Indices: 1894662--1895022 Score: 369
Period size: 66 Copynumber: 5.4 Consensus size: 66
1894652 AGATTTAAGA
* *
1894662 TTTTATATAATTAATAAAGGAGAAAGGAGTTTTAGGAATGTATGAGATTGGATCACTATTCCAAT
1 TTTTATATAATTAATAAAGGAGAAAGGAGGTTTAGGAATGTATGAGATTGGCTCACTATTCCAAT
1894727 T
66 T
* * * * *
1894728 GTTTATATAATTAATAAAAAGGAAAAAGGAGATTTAGGAATGCATGAGATTGGCTCACTATTCAA
1 TTTTATATAATTAAT--AAAGGAGAAAGGAGGTTTAGGAATGTATGAGATTGGCTCACTATTCCA
1894793 ATT
64 ATT
*
1894796 TTTTATATAATTAATAAAGGAGAAAGGAGGTTTAGGAATGTATGAGATTGGCTCATTATTCCAAT
1 TTTTATATAATTAATAAAGGAGAAAGGAGGTTTAGGAATGTATGAGATTGGCTCACTATTCCAAT
1894861 T
66 T
* * ** * * * *
1894862 TTTTATATAATTAATAAAGGAGAAGGGAGGTCTAATAGATCCATATAGAAATGTATGG--GATTG
1 TTTTATATAATTAATAAAGGAGAAAGGAGGTTTAGGA-AT--GTAT-GAGA--T-TGGCTCACT-
** *
1894925 GCTCACTATT
58 ATTC-CAATT
* * *
1894935 TTTTATATAATTAATAAAGGGGAAGGGAGGTCTAGGAATGTATGAGATTGGCTCAC---T---AT
1 TTTTATATAATTAATAAAGGAGAAAGGAGGTTTAGGAATGTATGAGATTGGCTCACTATTCCAAT
1894994 T
66 T
1894995 TTTTATATAATTAATAAAGGAGAAAGGA
1 TTTTATATAATTAATAAAGGAGAAAGGA
1895023 AGTGGACCAA
Statistics
Matches: 251, Mismatches: 31, Indels: 32
0.80 0.10 0.10
Matches are distributed among these distances:
60 29 0.12
64 1 0.00
66 96 0.38
67 3 0.01
68 61 0.24
69 6 0.02
70 6 0.02
71 3 0.01
72 5 0.02
73 41 0.16
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (66 bp):
TTTTATATAATTAATAAAGGAGAAAGGAGGTTTAGGAATGTATGAGATTGGCTCACTATTCCAAT
T
Found at i:1896595 original size:22 final size:23
Alignment explanation
Indices: 1896554--1896600 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1896544 TCAATCCAGT
* * *
1896554 TGAAGGTTTCAACTACATCCCAA
1 TGAAGGTCTCAACTAAATCCAAA
1896577 TGAAGGTCT-AACTAAATCCAAA
1 TGAAGGTCTCAACTAAATCCAAA
1896599 TG
1 TG
1896601 GCCTCTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (23 bp):
TGAAGGTCTCAACTAAATCCAAA
Found at i:1897687 original size:19 final size:19
Alignment explanation
Indices: 1897652--1897692 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1897642 CATAATTTTT
1897652 AAATAAAAAATCAAAATCA
1 AAATAAAAAATCAAAATCA
*
1897671 AAATCAAAAAAT-TAAATCA
1 AAAT-AAAAAATCAAAATCA
1897690 AAA
1 AAA
1897693 GAACATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (19 bp):
AAATAAAAAATCAAAATCA
Found at i:1898026 original size:14 final size:15
Alignment explanation
Indices: 1898007--1898040 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1897997 ATTTTGATTT
1898007 ATATTTTTAAAT-AA
1 ATATTTTTAAATAAA
*
1898021 ATATTTTTAATTAAA
1 ATATTTTTAAATAAA
1898036 ATATT
1 ATATT
1898041 AATAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTTTAAATAAA
Found at i:1898049 original size:27 final size:27
Alignment explanation
Indices: 1898019--1898070 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1898009 ATTTTTAAAT
1898019 AAATATTTTTAATT-AAAATATTAATAA
1 AAAT-TTTTTAATTCAAAATATTAATAA
**
1898046 AAATTTTTTCCTTCAAAATATTAAT
1 AAATTTTTTAATTCAAAATATTAAT
1898071 CAAATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (27 bp):
AAATTTTTTAATTCAAAATATTAATAA
Found at i:1898154 original size:12 final size:13
Alignment explanation
Indices: 1898137--1898166 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1898127 ATTTATCAAT
1898137 TTAAATT-TTTTA
1 TTAAATTATTTTA
1898149 TTAAATTATTTTA
1 TTAAATTATTTTA
1898162 TTAAA
1 TTAAA
1898167 AAATTTCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAAATTATTTTA
Found at i:1898431 original size:28 final size:28
Alignment explanation
Indices: 1898397--1898465 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
1898387 AAGTAATAAA
1898397 GCGAATGGAACTTATTGTGATTAAAAAG
1 GCGAATGGAACTTATTGTGATTAAAAAG
1898425 GCGAATGGAACTTATTGTGATTAAAAAG
1 GCGAATGGAACTTATTGTGATTAAAAAG
*
1898453 GCGAACGGAACTT
1 GCGAATGGAACTT
1898466 GAACTTGTAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (28 bp):
GCGAATGGAACTTATTGTGATTAAAAAG
Found at i:1918599 original size:2 final size:2
Alignment explanation
Indices: 1918577--1918621 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1918567 AATTTATTTA
* *
1918577 AT AT GT AT A- AT AT AA 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
1918618 AT AT
1 AT AT
1918622 GTAAAGGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1918972 original size:15 final size:15
Alignment explanation
Indices: 1918949--1919004 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
1918939 AAAATATCAT
*
1918949 AATTATAATTAAAAA
1 AATTTTAATTAAAAA
1918964 AATTTTAATT--AAA
1 AATTTTAATTAAAAA
*
1918977 AA-TTTATATTAAATA
1 AATTTTA-ATTAAAAA
1918992 AATTTT-ATTAAAA
1 AATTTTAATTAAAA
1919005 TTAATATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
12 4 0.12
13 8 0.24
14 6 0.18
15 13 0.38
16 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTTTAATTAAAAA
Found at i:1918980 original size:28 final size:27
Alignment explanation
Indices: 1918951--1919012 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
1918941 AATATCATAA
1918951 TTATAATTAAAAAAATTTTAATTAAAAAT
1 TTAT-ATTAAAAAAATTTT-ATTAAAAAT
*
1918980 TTATATTAAATAAATTTTATT-AAAAT
1 TTATATTAAAAAAATTTTATTAAAAAT
*
1919006 TAATATT
1 TTATATT
1919013 TAAATTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 11 0.35
27 3 0.10
28 13 0.42
29 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TTATATTAAAAAAATTTTATTAAAAAT
Found at i:1919005 original size:15 final size:13
Alignment explanation
Indices: 1918960--1919004 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
1918950 ATTATAATTA
1918960 AAAAAATTTTAATT
1 AAAAAATTTT-ATT
1918974 -AAAAATTTATATT
1 AAAAAATTT-TATT
1918987 AAATAAATTTTATT
1 AAA-AAATTTTATT
1919001 AAAA
1 AAAA
1919005 TTAATATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 12 0.43
14 10 0.36
15 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAAAATTTTATT
Found at i:1919014 original size:16 final size:14
Alignment explanation
Indices: 1918956--1919003 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
1918946 CATAATTATA
*
1918956 ATTAAAAAAATTTT
1 ATTAAATAAATTTT
1918970 AATT-AA-AAATTTAT
1 -ATTAAATAAATTT-T
1918984 ATTAAATAAATTTT
1 ATTAAATAAATTTT
1918998 ATTAAA
1 ATTAAA
1919004 ATTAATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 9 0.30
14 12 0.40
15 9 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAAATAAATTTT
Found at i:1919015 original size:27 final size:27
Alignment explanation
Indices: 1918949--1919017 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 27
1918939 AAAATATCAT
*
1918949 AATTATAATTAAAAAAATTTTAATTAAA
1 AATTAT-ATTAAATAAATTTTAATTAAA
1918977 AATTTATATTAAATAAATTTT-ATT-AA
1 AA-TTATATTAAATAAATTTTAATTAAA
1919003 AATTAATATTTAAAT
1 AATT-ATA-TTAAAT
1919018 TTAATCGGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 2 0.05
26 7 0.19
27 9 0.24
28 15 0.41
29 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
AATTATATTAAATAAATTTTAATTAAA
Found at i:1932757 original size:22 final size:22
Alignment explanation
Indices: 1932731--1932774 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1932721 TGTATATTTA
*
1932731 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1932753 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
1932775 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:1932974 original size:23 final size:25
Alignment explanation
Indices: 1932948--1933014 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 25
1932938 AAAATTTTCA
* *
1932948 GCCTTCATTGTTG-A-CTTTTTTAG
1 GCCTTCATTGTTGAATCCTGTTTAG
*
1932971 GCCTTCGTTGTTGAATCCTGTTTAG
1 GCCTTCATTGTTGAATCCTGTTTAG
**
1932996 GCCTTCATTGCCGAATCCT
1 GCCTTCATTGTTGAATCCT
1933015 TTCAAAGAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.33
24 1 0.03
25 23 0.64
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.43
Consensus pattern (25 bp):
GCCTTCATTGTTGAATCCTGTTTAG
Found at i:1936657 original size:22 final size:22
Alignment explanation
Indices: 1936631--1936674 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1936621 TGTATATTTA
* *
1936631 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCCAGAATTAAG
1936653 TATTTGTATCCCCAGAATTAAG
1 TATTTGTATCCCCAGAATTAAG
1936675 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (22 bp):
TATTTGTATCCCCAGAATTAAG
Found at i:1937209 original size:2 final size:2
Alignment explanation
Indices: 1937202--1937230 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1937192 ATTTTACAAT
1937202 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1937231 TTTCCCCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1941201 original size:146 final size:147
Alignment explanation
Indices: 1940937--1941229 Score: 473
Period size: 146 Copynumber: 2.0 Consensus size: 147
1940927 AGGATATGAG
* *
1940937 GTTTCCAGGTATTTTATTGGTATAAATTAAACTAGAAAATGACTTGAAGTCAACGAGGCGAGACA
1 GTTTCCAGGTATTTTATTGGTATAAATTAAACTACAAAAGGACTTGAAGTCAACGAGGCGAGACA
** *
1941002 GGTATAATTTCAATTTAAATTGTGTGTTCTACAATCAATCTTTTAATTTCTAGTTAAATATAATA
66 GCCATAATTTCAATTTAAATTATGTGTTCTACAATCAATCTTTTAATTTCTAGTTAAATATAATA
**
1941067 -TTGTTATGTTTAATTT
131 TTTGTTATACTTAATTT
*
1941083 GTTTCCAGGTATTTTATTTGTATAAATTAAACTACAAAAGGACTTGAAGTCAACGAGGCGAG-CG
1 GTTTCCAGGTATTTTATTGGTATAAATTAAACTACAAAAGGACTTGAAGTCAACGAGGCGAGAC-
* *
1941147 AGCCATAATTTCAATTTAAATTATGTTTTCTACAATCACTCTTTTAATTTCTAGTTAAATATAAT
65 AGCCATAATTTCAATTTAAATTATGTGTTCTACAATCAATCTTTTAATTTCTAGTTAAATATAAT
1941212 ATTTGTTATACTTAATTT
130 ATTTGTTATACTTAATTT
1941230 ATCTATTGAA
Statistics
Matches: 135, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
145 1 0.01
146 120 0.89
147 14 0.10
ACGTcount: A:0.34, C:0.11, G:0.14, T:0.41
Consensus pattern (147 bp):
GTTTCCAGGTATTTTATTGGTATAAATTAAACTACAAAAGGACTTGAAGTCAACGAGGCGAGACA
GCCATAATTTCAATTTAAATTATGTGTTCTACAATCAATCTTTTAATTTCTAGTTAAATATAATA
TTTGTTATACTTAATTT
Found at i:1952709 original size:25 final size:25
Alignment explanation
Indices: 1952676--1952726 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
1952666 AGTCTCACCC
*
1952676 TTTTCTTAAAAATCTA-TAGCCCTTT
1 TTTTCTTAAAAAT-TATTAACCCTTT
* *
1952701 TTTTTTTAACAATTATTAACCCTTT
1 TTTTCTTAAAAATTATTAACCCTTT
1952726 T
1 T
1952727 CAATATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.27, C:0.18, G:0.02, T:0.53
Consensus pattern (25 bp):
TTTTCTTAAAAATTATTAACCCTTT
Found at i:1952762 original size:21 final size:21
Alignment explanation
Indices: 1952738--1952777 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1952728 AATATATTAC
1952738 TACATTTAAT-CGTATAAATGA
1 TACA-TTAATACGTATAAATGA
*
1952759 TACATTAATATGTATAAAT
1 TACATTAATACGTATAAAT
1952778 TATTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
TACATTAATACGTATAAATGA
Found at i:1952766 original size:20 final size:22
Alignment explanation
Indices: 1952738--1952799 Score: 58
Period size: 23 Copynumber: 2.9 Consensus size: 22
1952728 AATATATTAC
1952738 TACATTTAAT-CGTATAAATGA
1 TACATTTAATACGTATAAATGA
* *
1952759 TACA-TTAATATGTATAAATTA
1 TACATTTAATACGTATAAATGA
*
1952780 TTTA-ATTTAATACGAATAAA
1 --TACATTTAATACGTATAAA
1952800 ATTTAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 5 0.15
21 13 0.39
22 1 0.03
23 14 0.42
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (22 bp):
TACATTTAATACGTATAAATGA
Found at i:1952941 original size:21 final size:19
Alignment explanation
Indices: 1952902--1952952 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 19
1952892 AATTTATGAG
*
1952902 TTTAATTAAATTTTTATAT
1 TTTAATAAAATTTTTATAT
1952921 TTTAATAAATATTTTTAATAT
1 TTTAATAAA-ATTTTT-ATAT
1952942 TTTAATTAAAA
1 TTTAA-TAAAA
1952953 AATTATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 8 0.29
20 6 0.21
21 10 0.36
22 4 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTAATAAAATTTTTATAT
Found at i:1952967 original size:26 final size:22
Alignment explanation
Indices: 1952912--1952965 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
1952902 TTTAATTAAA
*
1952912 TTTT-TATATTTTAATAAATAT
1 TTTTATATATTTTAATAAAAAT
1952933 TTTTA-ATATTTTAATTAAAAAAT
1 TTTTATATATTTTAA-T-AAAAAT
*
1952956 TATTATATAT
1 TTTTATATAT
1952966 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 13 0.48
22 1 0.04
23 9 0.33
24 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTATATATTTTAATAAAAAT
Found at i:1961583 original size:2 final size:2
Alignment explanation
Indices: 1961576--1961605 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1961566 CTCTGTTGCC
1961576 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
1961606 TGCTATATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1972303 original size:11 final size:11
Alignment explanation
Indices: 1972287--1972317 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1972277 TGGCGGAGGA
1972287 AGAGGAGAGAG
1 AGAGGAGAGAG
1972298 AGAGGAGAGAG
1 AGAGGAGAGAG
1972309 AGAGGAGAG
1 AGAGGAGAG
1972318 CCATTGAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (11 bp):
AGAGGAGAGAG
Found at i:1985510 original size:25 final size:23
Alignment explanation
Indices: 1985473--1985526 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
1985463 ATAAATAAAT
* *
1985473 CTTTTTATTTGATCAATTTTTT-TG
1 CTTTTGATTTGAT--ATTTTTTAAG
1985497 CTTTTGATCTTGATATTTTTTAAG
1 CTTTTGAT-TTGATATTTTTTAAG
1985521 CTTTTG
1 CTTTTG
1985527 TTCTATCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 7 0.27
24 14 0.54
25 5 0.19
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.63
Consensus pattern (23 bp):
CTTTTGATTTGATATTTTTTAAG
Found at i:1985625 original size:20 final size:22
Alignment explanation
Indices: 1985586--1985626 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1985576 AAAGCCATAT
*
1985586 TTTTTCTTTTTTATTATTTCTG
1 TTTTTCTTTTTTAATATTTCTG
1985608 TTTTT-TTTTTTAAT-TTTCT
1 TTTTTCTTTTTTAATATTTCT
1985627 AACAATGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.10, C:0.07, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTTCTTTTTTAATATTTCTG
Found at i:1986187 original size:25 final size:25
Alignment explanation
Indices: 1986159--1986225 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
1986149 TTTAATGTGA
*
1986159 AAAAAATATATAAATTATAAAGTATA
1 AAAAAATATATAAATTATAAA-TATT
* * *
1986185 AAAAAAT-TAAAAATTTTAGATATT
1 AAAAAATATATAAATTATAAATATT
1986209 AAAAAATATATATAATT
1 AAAAAATATATA-AATT
1986226 TTGAGACATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
24 10 0.29
25 13 0.38
26 11 0.32
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (25 bp):
AAAAAATATATAAATTATAAATATT
Found at i:1986226 original size:26 final size:25
Alignment explanation
Indices: 1986158--1986241 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 25
1986148 TTTTAATGTG
* *
1986158 AAAAAAATATATAAATTATAAAGTAT
1 AAAAAAATATATAAATTTTAGA-TAT
*
1986184 AAAAAAAT-TAAAAATTTTAGATAT
1 AAAAAAATATATAAATTTTAGATAT
* *
1986208 TAAAAAATATATATAATTTTGAGACAT
1 AAAAAAATATATA-AATTTT-AGATAT
1986235 AAAAAAA
1 AAAAAAA
1986242 GAAGGATAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
24 10 0.21
25 13 0.27
26 14 0.29
27 11 0.23
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (25 bp):
AAAAAAATATATAAATTTTAGATAT
Found at i:1986974 original size:35 final size:34
Alignment explanation
Indices: 1986892--1986976 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 34
1986882 CCTGGGGGTA
* *
1986892 CTAAAAGACACAAGAATCTTCTTTCTTTGATGTC
1 CTAAGAGAGACAAGAATCTTCTTTCTTTGATGTC
* * * *
1986926 CTAAGAGATACAAGAATCTTATTTTGTTTGATTTGC
1 CTAAGAGAGACAAGAATCTT-CTTTCTTTGATGT-C
*
1986962 CTGAG-GAGACAAGAA
1 CTAAGAGAGACAAGAA
1986977 AACTTTGAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 18 0.43
35 19 0.45
36 5 0.12
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (34 bp):
CTAAGAGAGACAAGAATCTTCTTTCTTTGATGTC
Found at i:1987973 original size:21 final size:22
Alignment explanation
Indices: 1987923--1987982 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
1987913 TACTTAGGTA
*
1987923 AAATTTTATATATATTAAGTGT
1 AAATTTTGTATATATTAAGTGT
**
1987945 AAAGTTTTGTATATATTGGGTG-
1 AAA-TTTTGTATATATTAAGTGT
1987967 AAATTTTGTATATATT
1 AAATTTTGTATATATT
1987983 TACTCAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.38
22 6 0.18
23 15 0.44
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (22 bp):
AAATTTTGTATATATTAAGTGT
Found at i:1989273 original size:24 final size:24
Alignment explanation
Indices: 1989241--1989292 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1989231 ATTTATTATT
* *
1989241 TTTTGTTATTTGGTTGAACATTTA
1 TTTTATTATTTGATTGAACATTTA
*
1989265 TTTTATTATTTGATTGGACATTTA
1 TTTTATTATTTGATTGAACATTTA
1989289 TTTT
1 TTTT
1989293 TAGCATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.21, C:0.04, G:0.13, T:0.62
Consensus pattern (24 bp):
TTTTATTATTTGATTGAACATTTA
Found at i:1991845 original size:26 final size:26
Alignment explanation
Indices: 1991796--1991846 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
1991786 TTAGATTGTA
* * *
1991796 TTTGAGTATTGCTCATTGATTTAGAG
1 TTTGAGTATTGCTCAATAACTTAGAG
*
1991822 TTTGTGTATTGCTCAATAACTTAGA
1 TTTGAGTATTGCTCAATAACTTAGA
1991847 CTTTATGAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (26 bp):
TTTGAGTATTGCTCAATAACTTAGAG
Found at i:2018485 original size:7 final size:7
Alignment explanation
Indices: 2018473--2018503 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2018463 TATTATTATT
2018473 AAATATA
1 AAATATA
2018480 AAATATA
1 AAATATA
2018487 AAATATA
1 AAATATA
*
2018494 AAATACA
1 AAATATA
2018501 AAA
1 AAA
2018504 AATATATCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (7 bp):
AAATATA
Found at i:2019675 original size:29 final size:32
Alignment explanation
Indices: 2019634--2019701 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 32
2019624 GTTAATTTTT
2019634 AAAATAAACTTTA-AA-AATA-AAA-TAATATA
1 AAAATAAACTTTATAATAATACAAACTAATA-A
*
2019663 AAAATAAATTTTATAATAATACTAAACTAATAA
1 AAAATAAACTTTATAATAATAC-AAACTAATAA
2019696 AAAATA
1 AAAATA
2019702 TAGGAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 12 0.36
30 2 0.06
31 4 0.12
33 10 0.30
34 5 0.15
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.29
Consensus pattern (32 bp):
AAAATAAACTTTATAATAATACAAACTAATAA
Found at i:2019896 original size:20 final size:18
Alignment explanation
Indices: 2019852--2019899 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
2019842 TTTTTTTTTA
2019852 AAGTAATAAATAAAAATT
1 AAGTAATAAATAAAAATT
* * *
2019870 GATTAATATATTAAAAATAT
1 AAGTAATA-AATAAAAAT-T
2019890 AAGTAATAAA
1 AAGTAATAAA
2019900 AATGAGAAGA
Statistics
Matches: 22, Mismatches: 6, Indels: 3
0.71 0.19 0.10
Matches are distributed among these distances:
18 6 0.27
19 9 0.41
20 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
AAGTAATAAATAAAAATT
Found at i:2031954 original size:49 final size:50
Alignment explanation
Indices: 2031893--2033058 Score: 1182
Period size: 48 Copynumber: 24.0 Consensus size: 50
2031883 GTTTTGAGAA
* * * *
2031893 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTAAGAGGAG-CTTTTTT
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * *
2031942 AAGATGAAA-TTTTAAAGTTGTTGAGCCTCTGTTGAGAGAAGCCTTTTCC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* *
2031991 AAGAT-AAGATTTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAG-CTTTTCC
1 AAGATGAA-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * *
2032040 AA-ATGAAATTTTTAAACTTGTTGAGCCTCTGCTGAGATGAGCCATTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * ** *
2032089 AAGATG-GA-TTTTAAAGTTGTTAAGCCTCTATTGAAAGGAG-CTTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * * *
2032136 -AGATGAAATTTTTAAAATTGTTGAGCCTCTGCCGAGATGAGCCCTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* *
2032185 AAGA-GAAGA-TTTTAAAGTTATTGAGCCTCTCCTGAGAGGAGCCCTTTTT-
1 AAGATGAA-ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CCTTTTTC
* * * * *
2032234 AAAATG-GA-TTTTAAAGTTGTTAAGCCTCTGTTGAGAGAAG-CTTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * *
2032281 -AGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAACCCTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * *
2032330 AAGATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGTGAGGA-ACTTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * **
2032378 -A-A-G--A-TTTTAAAATTGTTAAGCCTCTATTGAGAGGAG-CTTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * *
2032421 AAGGTGAGAATTTTTAAAGTCGTTGAGCCTCTGCTGAGAAGAGCCATTTTTC
1 AAGATGA-AATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCC-TTTTTC
*
2032473 AA-ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CTTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * * * ** *
2032520 AAGATGAGAAATTTTAAAGCTGTTAAGCATCTATTGAGATGAGCCTTTTTC
1 AAGATGA-AATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * *
2032571 AAGATG--ATTTTTAAAGTTGTTGAGCCTCTACTAAAAGGAGCCTTTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCC-TTTTTC
* *
2032620 AAGGTAAAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTAT-
1 AAGAT-GAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTT-TC
* *
2032671 AAGATG--ATTTTTAAAGTTGTTAAGCCTCTACTGAG-GGAG-C-TTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
*
2032716 AAGATG-AATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * *
2032765 AAGATG-AATTTTTAAAGTCGTTGAGCCTCTGCTAAGAGGAACCCTTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGG-AGCCTTTTTC
* * * *
2032815 AA-ATGAGA-TTTTAAAGTTGTTAAGCCTCTACTGAGAAGAGCCCTTTTTC
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAG-CCTTTTTC
* * * * * *
2032864 AA-ATGAGA-TTTTAAA-TTCGTTAAGCCTCTACTAAAAGGAGCCCTTTTC
1 AAGATGAAATTTTTAAAGTT-GTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* * * *
2032912 AAGATGGGATTTTTTAAAGTTGTTGAGCCTCTACTGAGAGAAG-CTTTTTC
1 AAGAT-GAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* *
2032962 AAGATGAGAATTTTTAAAGTTGTTAAACCTCTGCTGAGAGGAGCCTTTTTC
1 AAGATGA-AATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
* *
2033013 AAGATG--ATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGAAGCATTTT
1 AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTT
2033059 CAAAAGAGAT
Statistics
Matches: 936, Mismatches: 129, Indels: 105
0.80 0.11 0.09
Matches are distributed among these distances:
43 34 0.04
44 2 0.00
45 10 0.01
46 45 0.05
47 26 0.03
48 285 0.30
49 270 0.29
50 157 0.17
51 63 0.07
52 44 0.05
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (50 bp):
AAGATGAAATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTTC
Found at i:2032053 original size:98 final size:99
Alignment explanation
Indices: 2031893--2033099 Score: 1216
Period size: 98 Copynumber: 12.4 Consensus size: 99
2031883 GTTTTGAGAA
* *
2031893 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTAAGAGGAGCTTTTTTAAGATGAAA-TTTTAA
1 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGAAATTTTTAA
* *
2031957 AGTTGTTGAGCCTCTGTTGAGAGAAGCCTTTTCC
66 AGTTGTTGAGCCTCTGCTGAGAGAAGCCTTTTTC
* * * *
2031991 AAGATAAGATTTTTAAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTCCAA-ATGAAATTTTTAA
1 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGAAATTTTTAA
* *
2032055 ACTTGTTGAGCCTCTGCTGAGATG-AGCCATTTTC
66 AGTTGTTGAGCCTCTGCTGAGA-GAAGCCTTTTTC
* * *
2032089 AAGATG-GA-TTTTAAAGTTGTTAAGCCTCTATTGAAAGGAGCTTTTTC-AGATGAAATTTTTAA
1 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGAAATTTTTAA
* * *
2032151 AATTGTTGAGCCTCTGCCGAGATG-AGCCCTTTTC
66 AGTTGTTGAGCCTCTGCTGAGA-GAAGCCTTTTTC
* * * *
2032185 AAGA-GAAGA-TTTTAAAGTTATTGAGCCTCTCCTGAGAGGAGCCCTTTTT-AAAATG-GA-TTT
1 AAGATG-AGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG--CTTTTTCAAGATGAAATTTT
* *
2032245 TAAAGTTGTTAAGCCTCTGTTGAGAGAAG-CTTTTTC
63 TAAAGTTGTTGAGCCTCTGCTGAGAGAAGCCTTTTTC
* * * *
2032281 -AGATGAGATTTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAACCCTTTTCAAGATGAGA-TTTTA
1 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGG-AGCTTTTTCAAGATGAAATTTTTA
*
2032344 AAGTTGTTGAGCCTCTGCTGTGAGGAA--CTTTTTC
65 AAGTTGTTGAGCCTCTGCTGAGA-GAAGCCTTTTTC
* * * *
2032378 ---A--AGA-TTTTAAAATTGTTAAGCCTCTATTGAGAGGAGCTTTTTCAAGGTGAGAATTTTTA
1 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGA-AATTTTTA
*
2032437 AAGTCGTTGAGCCTCTGCTGAGA-AGAGCCATTTTTC
65 AAGTTGTTGAGCCTCTGCTGAGAGA-AGCC-TTTTTC
* *
2032473 AA-ATGAGA-TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTTTTCAAGATGAGAAATTTTA
1 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGA-AATTTTTA
* * * **
2032536 AAGCTGTTAAGCATCTATTGAGATG-AGCCTTTTTC
65 AAGTTGTTGAGCCTCTGCTGAGA-GAAGCCTTTTTC
* * * *
2032571 AAGAT--GATTTTTAAAGTTGTTGAGCCTCTACTAAAAGGAGCCTTTTTTCAAGGTAAAAATTTT
1 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG-C-TTTTTCAAGAT-GAAATTTT
*
2032634 TAAAGTTGTTGAGCCTCTGCTGAGAGGAGCCTTTTAT-
63 TAAAGTTGTTGAGCCTCTGCTGAGAGAAGCCTTTT-TC
*
2032671 AAGAT--GATTTTTAAAGTTGTTAAGCCTCTACTGAG-GGAGC-TTTTCAAGATG-AATTTTTAA
1 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGAAATTTTTAA
* *
2032731 AGTTGTTGAGCCTCTGCTGAGAGGAGCCCTTTTC
66 AGTTGTTGAGCCTCTGCTGAGAGAAGCCTTTTTC
* * * * *
2032765 AAGATGA-ATTTTTAAAGTCGTTGAGCCTCTGCTAAGAGGAACCCTTTTTCAA-ATGAGA-TTTT
1 AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGG-A-GCTTTTTCAAGATGAAATTTTT
* *
2032827 AAAGTTGTTAAGCCTCTACTGAGA-AGAGCCCTTTTTC
64 AAAGTTGTTGAGCCTCTGCTGAGAGA-AG-CCTTTTTC
* * * * * *
2032864 AA-ATGAGA-TTTTAAA-TTCGTTAAGCCTCTACTAAAAGGAGCCCTTTTCAAGATGGGATTTTT
1 AAGATGAGATTTTTAAAGTT-GTTGAGCCTCTACTGAGAGGAG-CTTTTTCAAGAT-GAAATTTT
*
2032926 TAAAGTTGTTGAGCCTCTACTGAGAGAAG-CTTTTTC
63 TAAAGTTGTTGAGCCTCTGCTGAGAGAAGCCTTTTTC
* * *
2032962 AAGATGAGAATTTTTAAAGTTGTTAAACCTCTGCTGAGAGGAGCCTTTTTCAAGATG--ATTTTT
1 AAGATGAG-ATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAG-CTTTTTCAAGATGAAATTTTT
*
2033025 AAAGTTGTTGAGCCTCTGCTGAGAGAAG-CATTTTC
64 AAAGTTGTTGAGCCTCTGCTGAGAGAAGCCTTTTTC
* * * *
2033060 AA-AAGAGA-TTTTAAAGTTATCGAGCCT-TAAGTGAGAGGAG
1 AAGATGAGATTTTTAAAGTTGTTGAGCCTCT-ACTGAGAGGAG
2033100 TATTTTTTAT
Statistics
Matches: 939, Mismatches: 114, Indels: 115
0.80 0.10 0.10
Matches are distributed among these distances:
91 14 0.01
92 28 0.03
93 30 0.03
94 47 0.05
95 69 0.07
96 134 0.14
97 116 0.12
98 237 0.25
99 116 0.12
100 106 0.11
101 40 0.04
102 2 0.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.36
Consensus pattern (99 bp):
AAGATGAGATTTTTAAAGTTGTTGAGCCTCTACTGAGAGGAGCTTTTTCAAGATGAAATTTTTAA
AGTTGTTGAGCCTCTGCTGAGAGAAGCCTTTTTC
Found at i:2033296 original size:18 final size:18
Alignment explanation
Indices: 2033263--2033302 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
2033253 GAAATACAAA
*
2033263 AAAATACCAAATAATA-T
1 AAAATACCAAAAAATATT
2033280 AAAATACCAAAAAAATATT
1 AAAATACC-AAAAAATATT
2033299 AAAA
1 AAAA
2033303 AATAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 7 0.35
19 5 0.25
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATACCAAAAAATATT
Found at i:2033306 original size:28 final size:27
Alignment explanation
Indices: 2033246--2033311 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
2033236 TATTAAATAT
*
2033246 AAAATATGAAATACAAAAAAATACCAA
1 AAAATATAAAATACAAAAAAATACCAA
* **
2033273 ATAATATAAAATACCAAAAAAATATTAA
1 AAAATATAAAATA-CAAAAAAATACCAA
*
2033301 AAAATAGAAAA
1 AAAATATAAAA
2033312 ATATGAGGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.71, C:0.08, G:0.03, T:0.18
Consensus pattern (27 bp):
AAAATATAAAATACAAAAAAATACCAA
Found at i:2038981 original size:2 final size:2
Alignment explanation
Indices: 2038974--2039008 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2038964 TTAATACACT
*
2038974 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2039009 TATCATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2039672 original size:12 final size:13
Alignment explanation
Indices: 2039647--2039676 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2039637 TTATTGATGA
2039647 TAATTAAGATATT
1 TAATTAAGATATT
2039660 TAATTAA-ATATT
1 TAATTAAGATATT
2039672 TAATT
1 TAATT
2039677 TATTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TAATTAAGATATT
Found at i:2041024 original size:23 final size:23
Alignment explanation
Indices: 2040980--2041024 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2040970 TAAAGCTCTC
*
2040980 TGGGATTCAAATCTCAGCTTTTT
1 TGGGATTCAAATCTCAGATTTTT
* * *
2041003 TGGGATTGAGATCTCATATTTT
1 TGGGATTCAAATCTCAGATTTT
2041025 CAATGTTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (23 bp):
TGGGATTCAAATCTCAGATTTTT
Found at i:2041271 original size:16 final size:16
Alignment explanation
Indices: 2041252--2041283 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2041242 TAAAAGCTTA
*
2041252 ATGAAAATAATTTGGT
1 ATGAAAATAACTTGGT
2041268 ATGAAAATAACTTGGT
1 ATGAAAATAACTTGGT
2041284 GAATTCAATT
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:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (16 bp):
ATGAAAATAACTTGGT
Found at i:2042364 original size:465 final size:466
Alignment explanation
Indices: 2041444--2042378 Score: 1577
Period size: 465 Copynumber: 2.0 Consensus size: 466
2041434 AAAACAATAA
2041444 TTTTGTATGGATGATGTTATGAATACGAACACCATTTTCTCTTTTTTTTTGTTGAAAATTTGGAA
1 TTTTGTATGGATGATGTTATGAATACGAACACCATTTTCTCTTTTTTTTTGTTGAAAATTTGGAA
* * * *
2041509 TGCTTATCTAAACAGAGGCTTGACAAGTTTTGAAAATTTAAAGGTTCCTTTAAGTGTCATAAGGT
66 TGCTTATCTAAACAAAGACTTGACAAGTTTTGAAAATTTAAAGGTTCATCTAAGTGTCATAAGGT
* *
2041574 ATAAATTTGTAAACCTATAGTTAGACACAAACTAAAGAATCACCACTAATATTTTTTATTTAAAT
131 ATAAATCTGTAAACCTATAGTTAGACACAAACTAAAGAATCACCACTAATATTTCTTATTTAAAT
* * *
2041639 GTGATTGATCACCTAATGAATCTGTCATTTCAAGGAGCTCTTAAGCTTGACTAAGGATCCCTAAA
196 GTGATTGATCACCTAATGAATCTATCATTTCAAGGAGCTCTTAAGCTTAACTAAGGACCCCTAAA
* * *
2041704 AAATAGGTTTTGATTTTCAAAATAGAACTATATTCAGTAGTTCGATTACATGTAAAGAAGGTTAT
261 AAATAAGTTATGATTTTCAAAATAGAACTAGATTCAGTAGTTCGATTACATGTAAAGAAGGTTAT
*
2041769 AACACTCCCACAACTCTCATCCTAAGATGGTACCATTTAATTTTAAATTATCCTAACAATCATCT
326 AACACTCCCACAACTCCCATCCTAAGATGGTACCATTTAATTTTAAATTATCCTAACAATCATCT
* *
2041834 TAGTTCTAATGGTTTTTATTTTAATGTTTAAATATTAAAAATAATTTTTAAGACTTTTTCATCAA
391 TAGTTCTAATGGTTTTTATTTTAATGTTTAAATATTAAAAATAATTTTTAAGACTTCTCCATCAA
2041899 TCTGGTAGAAT
456 TCTGGTAGAAT
*
2041910 TTTTGTCTGGATGATGTTATGAATACGAACACCATTTTCTC-TTTTTTTTGTTGAAAATTTGGAA
1 TTTTGTATGGATGATGTTATGAATACGAACACCATTTTCTCTTTTTTTTTGTTGAAAATTTGGAA
* * * * * *
2041974 TGCTTCTCTAAACAAAGACTTGACAATTTTTGAAATTTTAAAGTTTCATCTAAGTGTTATAATGT
66 TGCTTATCTAAACAAAGACTTGACAAGTTTTGAAAATTTAAAGGTTCATCTAAGTGTCATAAGGT
*
2042039 ATAAATCTGTAAACCTATAGTTAGACACAAACTAAAGAATCACCACTAATCTTTCTTATTTAAAT
131 ATAAATCTGTAAACCTATAGTTAGACACAAACTAAAGAATCACCACTAATATTTCTTATTTAAAT
*
2042104 GTGATTGATCACCTAATGAATCTATCATTTCAATGAGCTCTTAAGCTTAACTAAGGACCCCTAAA
196 GTGATTGATCACCTAATGAATCTATCATTTCAAGGAGCTCTTAAGCTTAACTAAGGACCCCTAAA
* * **
2042169 AAATAAGTTATGATTTTCTAAATAGAACTAGATTTAGTAGTTCGATTACATGTGGAGAAGGTTAT
261 AAATAAGTTATGATTTTCAAAATAGAACTAGATTCAGTAGTTCGATTACATGTAAAGAAGGTTAT
* *
2042234 AACAC-CCTCATAACTCCCATCCTAAGATGGTACCATTTAATTTTAAATTATCTTAACAATCATC
326 AACACTCC-CACAACTCCCATCCTAAGATGGTACCATTTAATTTTAAATTATCCTAACAATCATC
2042298 TTAGTTCTAATGGTTTTTATTTTAATGTTTAAATATTAAAAATAATTTTTAAGACTTCTCCATCA
390 TTAGTTCTAATGGTTTTTATTTTAATGTTTAAATATTAAAAATAATTTTTAAGACTTCTCCATCA
2042363 ATCTGGTAGAAT
455 ATCTGGTAGAAT
2042375 TTTT
1 TTTT
2042379 AAAAATACTT
Statistics
Matches: 438, Mismatches: 30, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
464 2 0.00
465 396 0.90
466 40 0.09
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (466 bp):
TTTTGTATGGATGATGTTATGAATACGAACACCATTTTCTCTTTTTTTTTGTTGAAAATTTGGAA
TGCTTATCTAAACAAAGACTTGACAAGTTTTGAAAATTTAAAGGTTCATCTAAGTGTCATAAGGT
ATAAATCTGTAAACCTATAGTTAGACACAAACTAAAGAATCACCACTAATATTTCTTATTTAAAT
GTGATTGATCACCTAATGAATCTATCATTTCAAGGAGCTCTTAAGCTTAACTAAGGACCCCTAAA
AAATAAGTTATGATTTTCAAAATAGAACTAGATTCAGTAGTTCGATTACATGTAAAGAAGGTTAT
AACACTCCCACAACTCCCATCCTAAGATGGTACCATTTAATTTTAAATTATCCTAACAATCATCT
TAGTTCTAATGGTTTTTATTTTAATGTTTAAATATTAAAAATAATTTTTAAGACTTCTCCATCAA
TCTGGTAGAAT
Found at i:2042986 original size:13 final size:13
Alignment explanation
Indices: 2042965--2043006 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
2042955 GCTTATGTAT
*
2042965 TTTTATTATCATTA
1 TTTT-TTATAATTA
2042979 TTTTTTATAATTA
1 TTTTTTATAATTA
2042992 -TTTTTATAATT-
1 TTTTTTATAATTA
2043003 TTTT
1 TTTT
2043007 CTAATTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 14 0.54
13 8 0.31
14 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTATAATTA
Found at i:2043105 original size:4 final size:4
Alignment explanation
Indices: 2043063--2043110 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
2043053 TAAGTGATAA
* *
2043063 AAAT AAGT AAAT AAAC AAAT AAACT AAACT AAA- AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAA-T AAA-T AAAT AAAT AAAT AAAT AAA
2043111 ATTGAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 3 0.08
4 26 0.68
5 9 0.24
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:2045565 original size:17 final size:17
Alignment explanation
Indices: 2045540--2045582 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2045530 CATTTTTTTC
*
2045540 ATTTTTTTAGGCATAAT
1 ATTTTTTTAAGCATAAT
* *
2045557 ATTTCTTTAAGCATAGT
1 ATTTTTTTAAGCATAAT
2045574 ATTTTTTTA
1 ATTTTTTTA
2045583 CTACATTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.56
Consensus pattern (17 bp):
ATTTTTTTAAGCATAAT
Found at i:2056355 original size:3 final size:3
Alignment explanation
Indices: 2056349--2056389 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2056339 TTGTTGTGAA
2056349 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2056390 CATCATCATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2058431 original size:2 final size:2
Alignment explanation
Indices: 2058415--2058450 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2058405 AATAAGTGTC
* *
2058415 TA TA TA AA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2058451 AAGTGTCCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2064952 original size:51 final size:51
Alignment explanation
Indices: 2064882--2064981 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
2064872 TATTTATTAA
* * *
2064882 AACTAATTTTAAGATTATCTCGACTCTTTGATGAAATC-TCAAAATTTTATT
1 AACTAATTTCAAGATTATCTCGA-TCTTCGATGAAATCTTAAAAATTTTATT
* *
2064933 AACTAATTTC-AGAATTATCTTGATCTTCGGTGAAATCTTAAAAATTTTA
1 AACTAATTTCAAG-ATTATCTCGATCTTCGATGAAATCTTAAAAATTTTA
2064982 AATAGATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 14 0.33
51 28 0.67
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (51 bp):
AACTAATTTCAAGATTATCTCGATCTTCGATGAAATCTTAAAAATTTTATT
Found at i:2066407 original size:23 final size:23
Alignment explanation
Indices: 2066377--2066422 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2066367 ATAAAGCTCA
2066377 TTGGGATTCAAATCCCAGATTTT
1 TTGGGATTCAAATCCCAGATTTT
* * *
2066400 TTGGGATTGAGATCTCAGATTTT
1 TTGGGATTCAAATCCCAGATTTT
2066423 CAAAGTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.41
Consensus pattern (23 bp):
TTGGGATTCAAATCCCAGATTTT
Found at i:2066632 original size:3 final size:3
Alignment explanation
Indices: 2066624--2066673 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
2066614 AAAAGAAATG
*
2066624 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2066672 AT
1 AT
2066674 TTAAAAGCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2066706 original size:16 final size:16
Alignment explanation
Indices: 2066685--2066716 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2066675 TAAAAGCTTA
*
2066685 ATGAAAATAATTTGGT
1 ATGAAAATAACTTGGT
2066701 ATGAAAATAACTTGGT
1 ATGAAAATAACTTGGT
2066717 GAATTCAATT
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:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (16 bp):
ATGAAAATAACTTGGT
Found at i:2067948 original size:13 final size:13
Alignment explanation
Indices: 2067927--2067969 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
2067917 GTTTATGTAT
*
2067927 TTTTATTATCATTA
1 TTTT-TTATAATTA
2067941 TTTTTTATAATTA
1 TTTTTTATAATTA
2067954 -TTTTTATAATT-
1 TTTTTTATAATTA
2067965 TTTTT
1 TTTTT
2067970 CTAATTTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 15 0.56
13 8 0.30
14 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTATAATTA
Found at i:2067959 original size:12 final size:12
Alignment explanation
Indices: 2067932--2067975 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
2067922 TGTATTTTTA
*
2067932 TTATCATTATTTT
1 TTATAATTA-TTT
2067945 TTATAATTATTT
1 TTATAATTATTT
2067957 TTATAATT-TTT
1 TTATAATTATTT
*
2067968 TTCTAATT
1 TTATAATT
2067976 TTCCTAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 10 0.34
12 11 0.38
13 8 0.28
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATAATTATTT
Found at i:2067968 original size:11 final size:11
Alignment explanation
Indices: 2067941--2067977 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
2067931 ATTATCATTA
2067941 TTTTTTATAAT
1 TTTTTTATAAT
2067952 TATTTTTATAAT
1 T-TTTTTATAAT
*
2067964 TTTTTTCTAAT
1 TTTTTTATAAT
2067975 TTT
1 TTT
2067978 CCTAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTTTATAAT
Found at i:2069503 original size:36 final size:36
Alignment explanation
Indices: 2069458--2069534 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
2069448 TCATAAAATT
* *
2069458 AAAAGCTCTTCTAACCAGAA-ACTATGAAACTTTGAA
1 AAAAACTCTTCTAACCA-AATACTATGAAACTTTAAA
* *
2069494 AAAAACTCTTCTAACCAAATGCTATGACACTTTAAA
1 AAAAACTCTTCTAACCAAATACTATGAAACTTTAAA
2069530 AAAAA
1 AAAAA
2069535 TTTCTCTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 2 0.06
36 34 0.94
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (36 bp):
AAAAACTCTTCTAACCAAATACTATGAAACTTTAAA
Found at i:2070523 original size:17 final size:17
Alignment explanation
Indices: 2070498--2070540 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
2070488 CTTTTTTTTC
*
2070498 ATTTTTTTAGGCATAAT
1 ATTTTTTTAAGCATAAT
* *
2070515 ATTTCTTTAAGCATAGT
1 ATTTTTTTAAGCATAAT
2070532 ATTTTTTTA
1 ATTTTTTTA
2070541 CTACATCAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.56
Consensus pattern (17 bp):
ATTTTTTTAAGCATAAT
Found at i:2084962 original size:3 final size:3
Alignment explanation
Indices: 2084956--2085014 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
2084946 TTGTTGTGAA
2084956 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2085004 ATT ATT ATT AT
1 ATT ATT ATT AT
2085015 CATATTCTAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2085896 original size:5 final size:5
Alignment explanation
Indices: 2085886--2085936 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
2085876 ATTTCTCAAA
** *
2085886 AAAAT AAAAT -AAAT AATAAT ATCAT AAAAT -AAAT AAAAC AAAAT AAAAT
1 AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
2085935 AA
1 AA
2085937 TCAAATCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 8 0.22
5 25 0.68
6 4 0.11
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:2085946 original size:19 final size:19
Alignment explanation
Indices: 2085886--2085936 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
2085876 ATTTCTCAAA
*
2085886 AAAATAAAATAAATAATAAT
1 AAAATAAAATAAATAA-AAC
**
2085906 ATCATAAAATAAATAAAAC
1 AAAATAAAATAAATAAAAC
2085925 AAAATAAAATAA
1 AAAATAAAATAA
2085937 TCAAATCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAATAAAATAAATAAAAC
Found at i:2086781 original size:3 final size:3
Alignment explanation
Indices: 2086775--2086800 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2086765 AAATGAAAAT
2086775 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2086801 TTAAAAGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2086957 original size:2 final size:2
Alignment explanation
Indices: 2086941--2086984 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
2086931 AATAAGTGTT
* *
2086941 TA TA TA AA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2086983 TA
1 TA
2086985 AAAAGTGTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:2088850 original size:1 final size:1
Alignment explanation
Indices: 2088844--2088869 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2088834 GCCCATTTTC
2088844 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2088870 CAATGCATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2095224 original size:2 final size:2
Alignment explanation
Indices: 2095217--2095241 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2095207 AACGAATTAA
2095217 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2095242 CCTGGACACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2101913 original size:2 final size:2
Alignment explanation
Indices: 2101906--2101930 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2101896 GATGATTGTT
2101906 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2101931 GTGCATACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2102265 original size:45 final size:45
Alignment explanation
Indices: 2102201--2102291 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
2102191 ATCTTTGAAA
2102201 ATGATTGATTATCCTTCATGCCAATTAAATCATTCTAGAGTGAGC
1 ATGATTGATTATCCTTCATGCCAATTAAATCATTCTAGAGTGAGC
2102246 ATGATTGATTATCCTTCATGCCAATTAAATCATTCTAGAGTGAGC
1 ATGATTGATTATCCTTCATGCCAATTAAATCATTCTAGAGTGAGC
2102291 A
1 A
2102292 AATCTTAGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (45 bp):
ATGATTGATTATCCTTCATGCCAATTAAATCATTCTAGAGTGAGC
Found at i:2104791 original size:20 final size:20
Alignment explanation
Indices: 2104768--2104812 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2104758 TCAAAAAGTA
*
2104768 AAAAAAAAATTTAAAATTTT
1 AAAAAAAAATTTAAAATATT
* *
2104788 AAAAAAAAGTTTTAAATATT
1 AAAAAAAAATTTAAAATATT
2104808 AAAAA
1 AAAAA
2104813 TATATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (20 bp):
AAAAAAAAATTTAAAATATT
Found at i:2105326 original size:23 final size:25
Alignment explanation
Indices: 2105299--2105344 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
2105289 CAATAAAAAA
*
2105299 TTTTAAAATTATTA-A-AAATTATT
1 TTTTAAAATAATTATATAAATTATT
2105322 TTTTAAAATAATTATATAAATTA
1 TTTTAAAATAATTATATAAATTA
2105345 ATTAAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 1 0.05
25 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTAAAATAATTATATAAATTATT
Found at i:2107974 original size:21 final size:21
Alignment explanation
Indices: 2107930--2107975 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2107920 TTTGTCATAT
* *
2107930 TTTAATATTTATTTATATTCA
1 TTTAAGATTTATTTATATTAA
2107951 TTTAAGATTTATTTAT-TTAAA
1 TTTAAGATTTATTTATATT-AA
2107972 TTTA
1 TTTA
2107976 TTTGATAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTAAGATTTATTTATATTAA
Found at i:2108652 original size:24 final size:24
Alignment explanation
Indices: 2108600--2108653 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2108590 ATTTAATTGG
* *
2108600 TTTAT-TGTATATAAATATATTTA
1 TTTATATGTATATAAATACATATA
* *
2108623 TATATATGTTTATAAATACATATA
1 TTTATATGTATATAAATACATATA
2108647 TTTATAT
1 TTTATAT
2108654 ATATTCGTGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
TTTATATGTATATAAATACATATA
Found at i:2109610 original size:20 final size:22
Alignment explanation
Indices: 2109571--2109611 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
2109561 TAAATTTATA
2109571 TAAATATATATAAATAAAAATT
1 TAAATATATATAAATAAAAATT
*
2109593 TAAATA-AT-TAATTAAAAAT
1 TAAATATATATAAATAAAAAT
2109612 AAAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATATATATAAATAAAAATT
Found at i:2109611 original size:26 final size:26
Alignment explanation
Indices: 2109556--2109629 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
2109546 TTTTTAATAT
* * *
2109556 AAATATAAATTTATATAAATATATAT
1 AAATAAAAATTTAAATAAATATATAA
*
2109582 AAATAAAAATTTAAATAATTA-ATTAA
1 AAATAAAAATTTAAATAAATATA-TAA
* * *
2109608 AAATAAAATTTTTAATATATAT
1 AAATAAAAATTTAAATAAATAT
2109630 CAAGTCAGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATAAAAATTTAAATAAATATATAA
Found at i:2127378 original size:24 final size:24
Alignment explanation
Indices: 2127342--2127417 Score: 64
Period size: 29 Copynumber: 3.0 Consensus size: 24
2127332 TGATTAAATT
*
2127342 AAAATTATTATTTATAAATAATATA
1 AAAATTA-AATTTATAAATAATATA
*
2127367 AAAATTAAATTTATATGAATTATAATA
1 AAAATTAAATTTATA--AATAAT-ATA
*
2127394 AAATGATTAAATTTA-AAAAAATAT
1 AAA--ATTAAATTTATAAATAATAT
2127418 TGAGAAATAC
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
24 7 0.17
25 9 0.21
26 9 0.21
27 6 0.14
28 1 0.02
29 10 0.24
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (24 bp):
AAAATTAAATTTATAAATAATATA
Found at i:2128393 original size:25 final size:25
Alignment explanation
Indices: 2128344--2128393 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
2128334 ATAAATTTTT
* *
2128344 ATAAATATATATTAATATATTTTTA
1 ATAAAAATATATTAATATATATTTA
2128369 ATAAAAATATATTAAT-TATAATTTA
1 ATAAAAATATATTAATATAT-ATTTA
2128394 TATTATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
ATAAAAATATATTAATATATATTTA
Found at i:2129444 original size:17 final size:16
Alignment explanation
Indices: 2129398--2129444 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2129388 AGATGTTACT
2129398 GGGGGAGAA-AGGAAA
1 GGGGGAGAAGAGGAAA
2129413 GGGTGGA-AAGAAGGAAA
1 GGG-GGAGAAG-AGGAAA
2129430 GGGGGAGGAAGAGGA
1 GGGGGA-GAAGAGGA
2129445 GGGATAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.19
16 6 0.22
17 13 0.48
18 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.55, T:0.02
Consensus pattern (16 bp):
GGGGGAGAAGAGGAAA
Found at i:2136427 original size:17 final size:17
Alignment explanation
Indices: 2136394--2136426 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2136384 AAAATTTTAA
2136394 AAATAATATATTTATAT
1 AAATAATATATTTATAT
2136411 AAAT-ATATA-TTATAT
1 AAATAATATATTTATAT
2136426 A
1 A
2136427 TTAATTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATAATATATTTATAT
Found at i:2140107 original size:18 final size:19
Alignment explanation
Indices: 2140084--2140120 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2140074 ATAATTTATG
2140084 TATTTATA-TAATATAAAA
1 TATTTATATTAATATAAAA
2140102 TATTTATATTAATATAAAA
1 TATTTATATTAATATAAAA
2140121 ATATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTTATATTAATATAAAA
Found at i:2140194 original size:11 final size:11
Alignment explanation
Indices: 2140180--2140223 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
2140170 AAATTTTCAA
2140180 TTATATTATTT
1 TTATATTATTT
*
2140191 TTATATATTTTAT
1 TTATAT-TATT-T
2140204 TTATATTATTT
1 TTATATTATTT
2140215 TTATATTAT
1 TTATATTAT
2140224 ATTATGGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTATATTATTT
Found at i:2140197 original size:13 final size:13
Alignment explanation
Indices: 2140181--2140220 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
2140171 AATTTTCAAT
2140181 TATATTATTTTTA
1 TATATTATTTTTA
*
2140194 TATATT-TTATT-
1 TATATTATTTTTA
2140205 TATATTATTTTTA
1 TATATTATTTTTA
2140218 TAT
1 TAT
2140221 TATATTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 6 0.26
12 8 0.35
13 9 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATATTATTTTTA
Found at i:2140203 original size:15 final size:14
Alignment explanation
Indices: 2140179--2140228 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
2140169 AAAATTTTCA
* *
2140179 ATTATATTATTTTT
1 ATTATTTTATTTAT
2140193 ATATATTTTATTTAT
1 AT-TATTTTATTTAT
2140208 ATTATTTTTATATTAT
1 ATTA-TTTTAT-TTAT
2140224 ATTAT
1 ATTAT
2140229 GGTATGGTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 4 0.13
15 19 0.61
16 8 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTATTTTATTTAT
Found at i:2140225 original size:16 final size:15
Alignment explanation
Indices: 2140190--2140228 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
2140180 TTATATTATT
2140190 TTTATA-TA-TTTTA
1 TTTATATTATTTTTA
2140203 TTTATATTATTTTTA
1 TTTATATTATTTTTA
2140218 TATTATATTAT
1 T-TTATATTAT
2140229 GGTATGGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 2 0.09
15 6 0.26
16 9 0.39
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATATTATTTTTA
Found at i:2140319 original size:16 final size:16
Alignment explanation
Indices: 2140298--2140329 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2140288 GGACATTCAG
2140298 CTTCCCACGAATCCAA
1 CTTCCCACGAATCCAA
2140314 CTTCCCACGAATCCAA
1 CTTCCCACGAATCCAA
2140330 AACAATGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.44, G:0.06, T:0.19
Consensus pattern (16 bp):
CTTCCCACGAATCCAA
Found at i:2148757 original size:2 final size:2
Alignment explanation
Indices: 2148750--2148787 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2148740 TTGACAACAT
2148750 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2148788 GCCCCACTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2150784 original size:2 final size:2
Alignment explanation
Indices: 2150777--2150810 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2150767 AACAAATTGC
2150777 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
2150811 GCATGCTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2151866 original size:39 final size:39
Alignment explanation
Indices: 2151823--2151900 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
2151813 CCATCTTTGG
*
2151823 TTTACAATGCTGAAATGAAAGTCAAGGCCTAGACGACTT
1 TTTACAATGCTGAAATGAAAGTAAAGGCCTAGACGACTT
* * *
2151862 TTTACGATGTTGAAATGCAAGTAAAGGCCTAGACGACTT
1 TTTACAATGCTGAAATGAAAGTAAAGGCCTAGACGACTT
2151901 AGGATGTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (39 bp):
TTTACAATGCTGAAATGAAAGTAAAGGCCTAGACGACTT
Found at i:2153335 original size:32 final size:33
Alignment explanation
Indices: 2153299--2153377 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 33
2153289 ATTATTTATT
*
2153299 AATTTTTAATTATTTATA-T-TATTTTAATATA
1 AATTTTTAATTATTTATAGTAAATTTTAATATA
*
2153330 AAATTTTAATATATTTA-AGTAAATTTTAATATA
1 AATTTTTAAT-TATTTATAGTAAATTTTAATATA
2153363 AATTTTT-ATT-TTTAT
1 AATTTTTAATTATTTAT
2153378 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
30 4 0.10
31 11 0.27
32 9 0.22
33 17 0.41
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (33 bp):
AATTTTTAATTATTTATAGTAAATTTTAATATA
Found at i:2153567 original size:7 final size:8
Alignment explanation
Indices: 2153547--2153578 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
2153537 TTTTAAATCG
2153547 ATTTTTTA
1 ATTTTTTA
2153555 ATTTTTTA
1 ATTTTTTA
2153563 ATTTTTTAA
1 ATTTTTT-A
2153572 ATTTTTT
1 ATTTTTT
2153579 TCTCACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTTTA
Done.