Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold38
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: 2073527
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 14 of 15
Found at i:1879714 original size:3 final size:3
Alignment explanation
Indices: 1879672--1879703 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1879662 AAATACTAAA
1879672 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1879704 CCCAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1880237 original size:19 final size:18
Alignment explanation
Indices: 1880210--1880264 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 18
1880200 TTTATTAATT
1880210 AAATAATTATTTAAATAAA
1 AAAT-ATTATTTAAATAAA
1880229 ACAATATTAATTTAAATAAA
1 A-AATATT-ATTTAAATAAA
*
1880249 AAATATATTTTTAAAT
1 AAATAT-TATTTAAAT
1880265 TTAACTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATTATTTAAATAAA
Found at i:1880837 original size:2 final size:2
Alignment explanation
Indices: 1880825--1880864 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
1880815 TAAATATAAA
1880825 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1880865 CAAAGTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1881164 original size:17 final size:19
Alignment explanation
Indices: 1881144--1881182 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
1881134 CGGATCGAGT
1881144 TATTTAT-T-TTAAAATAA
1 TATTTATATGTTAAAATAA
1881161 TATTTATATGTTAAAATAA
1 TATTTATATGTTAAAATAA
1881180 TAT
1 TAT
1881183 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 1 0.05
19 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
TATTTATATGTTAAAATAA
Found at i:1881201 original size:21 final size:21
Alignment explanation
Indices: 1881144--1881195 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1881134 CGGATCGAGT
1881144 TATTTAT-T-TTAAAAT-A-A
1 TATTTATATGTTAAAATAATA
1881161 TATTTATATGTTAAAATAATA
1 TATTTATATGTTAAAATAATA
*
1881182 TATTTTTAT-TTAAA
1 TATTTATATGTTAAA
1881196 TTTAATTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.23
18 1 0.03
19 7 0.23
20 6 0.20
21 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTATATGTTAAAATAATA
Found at i:1881216 original size:21 final size:22
Alignment explanation
Indices: 1881192--1881236 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1881182 TATTTTTATT
1881192 TAAAT-TTAATTATAAAAT-ATA
1 TAAATATTAA-TATAAAATAATA
1881213 TAAATATTAATATAAAATAATA
1 TAAATATTAATATAAAATAATA
1881235 TA
1 TA
1881237 TTTTAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAATAATA
Found at i:1884456 original size:129 final size:130
Alignment explanation
Indices: 1884225--1884480 Score: 442
Period size: 129 Copynumber: 2.0 Consensus size: 130
1884215 TTCCCAAAGC
1884225 CATCTTTCATTTCACGACTATCCCACTCTCGCATACATGGGTGGTGAAAACCCTAGTCTCCATGG
1 CATCTTTCATTTCACGACTATCCCACTCTCGCATACATGGGTGGTGAAAACCCTAGTCTCCATGG
* * *
1884290 ATGTTTGATTATGTTTTTATGGTAGGGAAAATAAAACATTTTTAAATAATTCAAAACTAAAAGGA
66 ATGTTTGATTATGTTTTTATGGCAAGGAAAATAAAACATTTTTAAATAATTAAAAACTAAAAGGA
* * * *
1884355 CATCTTTCATTTCACGACTATCCCACTCTTGCATACATGGGTTGTG-ATATCCTAGTCTCCATGG
1 CATCTTTCATTTCACGACTATCCCACTCTCGCATACATGGGTGGTGAAAACCCTAGTCTCCATGG
1884419 ATGTTTGATTATGTTTTTATGGCAAGGAAAATAAAACATTTTTAAATAATTAAAAACTAAAA
66 ATGTTTGATTATGTTTTTATGGCAAGGAAAATAAAACATTTTTAAATAATTAAAAACTAAAA
1884481 AGAAAATGGA
Statistics
Matches: 119, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
129 75 0.63
130 44 0.37
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (130 bp):
CATCTTTCATTTCACGACTATCCCACTCTCGCATACATGGGTGGTGAAAACCCTAGTCTCCATGG
ATGTTTGATTATGTTTTTATGGCAAGGAAAATAAAACATTTTTAAATAATTAAAAACTAAAAGGA
Found at i:1884781 original size:4 final size:4
Alignment explanation
Indices: 1884772--1884810 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
1884762 AGAAAAGATG
*
1884772 GAAA GAAA G-AA -AAA GAGA GAAA GAAA GAAA GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
1884811 TTACGATCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 4 0.13
4 27 0.87
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:1884904 original size:3 final size:3
Alignment explanation
Indices: 1884896--1884926 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1884886 TGTATAATAC
1884896 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1884927 GTTTTAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1885847 original size:2 final size:2
Alignment explanation
Indices: 1885842--1885889 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1885832 ATATATGTAT
1885842 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1885884 AG AG AG
1 AG AG AG
1885890 GGGATTAACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1894723 original size:2 final size:2
Alignment explanation
Indices: 1894716--1894740 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1894706 ATGTGACGCA
1894716 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1894741 TGAAACAAGT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1894949 original size:3 final size:3
Alignment explanation
Indices: 1894941--1894968 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1894931 GAATCTCATG
1894941 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1894969 CCCTAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1897821 original size:18 final size:16
Alignment explanation
Indices: 1897782--1897825 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1897772 ATATTTAATA
1897782 TTATATAAATAAATTT
1 TTATATAAATAAATTT
* *
1897798 TGATATATAATAATTTAT
1 TTATATA-AATAAATT-T
1897816 TTATATAAAT
1 TTATATAAAT
1897826 TTTAAAATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 6 0.26
17 10 0.43
18 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTATATAAATAAATTT
Found at i:1898163 original size:16 final size:18
Alignment explanation
Indices: 1898144--1898181 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
1898134 TTTATTTTAA
1898144 TTTATTTTT-AAATT-TT
1 TTTATTTTTAAAATTATT
1898160 TTTATTTTTAAAATTATT
1 TTTATTTTTAAAATTATT
1898178 TTTA
1 TTTA
1898182 ATTACTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 5 0.25
18 6 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTTTAAAATTATT
Found at i:1898184 original size:27 final size:26
Alignment explanation
Indices: 1898129--1898182 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
1898119 TTCATTAATT
*
1898129 ATTTTTTTATTTTAATTTATTTTTAA
1 ATTTTTTTATTTTAAATTATTTTTAA
1898155 ATTTTTTTATTTTTAAAATTATTTTTAA
1 ATTTTTTTA-TTTT-AAATTATTTTTAA
1898183 TTACTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 9 0.36
27 4 0.16
28 12 0.48
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (26 bp):
ATTTTTTTATTTTAAATTATTTTTAA
Found at i:1898541 original size:19 final size:19
Alignment explanation
Indices: 1898519--1898567 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
1898509 ATATTAAAAA
*
1898519 TATTTTTTTATTTTTTATC
1 TATTTTTTTATTTTTAATC
*
1898538 TA-TTTTTTACATTTTAATC
1 TATTTTTTTA-TTTTTAATC
*
1898557 AATTTTTTTAT
1 TATTTTTTTAT
1898568 CGTTTAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 7 0.29
19 10 0.42
20 7 0.29
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTTTTATTTTTAATC
Found at i:1898824 original size:16 final size:16
Alignment explanation
Indices: 1898791--1898851 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 16
1898781 TTTAATTTGA
1898791 TAATAATTAAAAATAAT
1 TAATAATTAAAAA-AAT
*
1898808 TTATAATTAAAAAAAT
1 TAATAATTAAAAAAAT
* *
1898824 TAATGAGTAAAAAAA-
1 TAATAATTAAAAAAAT
*
1898839 TAA-AAATAAAAAA
1 TAATAATTAAAAAA
1898852 TAATGAGTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
14 8 0.21
15 3 0.08
16 15 0.39
17 12 0.32
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (16 bp):
TAATAATTAAAAAAAT
Found at i:1899584 original size:13 final size:14
Alignment explanation
Indices: 1899558--1899590 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1899548 AATTTAATTA
1899558 AATAAAAATATAAT
1 AATAAAAATATAAT
1899572 AATAAAAAT-TAAT
1 AATAAAAATATAAT
*
1899585 AGTAAA
1 AATAAA
1899591 TTAAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
AATAAAAATATAAT
Found at i:1900564 original size:19 final size:20
Alignment explanation
Indices: 1900508--1900571 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 20
1900498 ATAAATAATT
* * *
1900508 TATTTTATTATTTAAAATAA
1 TATTTTATTAATTAAATTTA
*
1900528 TATTTTATTAA-TATATTTA
1 TATTTTATTAATTAAATTTA
1900547 TATTTTA-TAATTAAATTTA
1 TATTTTATTAATTAAATTTA
*
1900566 AATTTT
1 TATTTT
1900572 TTATTATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 3 0.08
19 24 0.65
20 10 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTTATTAATTAAATTTA
Found at i:1902354 original size:3 final size:3
Alignment explanation
Indices: 1902348--1902377 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1902338 TTGGAAGTAG
1902348 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1902378 ATAAAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1904456 original size:28 final size:28
Alignment explanation
Indices: 1904424--1904478 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1904414 CGGATCGTCA
*
1904424 GCTTTCATTGTATAATATACATAATATC
1 GCTTTCATTATATAATATACATAATATC
*
1904452 GCTTTTATTATATAATATACATAATAT
1 GCTTTCATTATATAATATACATAATAT
1904479 TTTTATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (28 bp):
GCTTTCATTATATAATATACATAATATC
Found at i:1904962 original size:3 final size:3
Alignment explanation
Indices: 1904954--1904978 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1904944 ATGAGGGGCC
1904954 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1904979 TAACTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1905540 original size:54 final size:54
Alignment explanation
Indices: 1905458--1905564 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
1905448 AATAGATGAG
*
1905458 AAAACATGGATTTTGGATTTTTCATTTCTCACCATGGGATTTCTTATTCCTTTC
1 AAAACATGGATTTTGGATTTGTCATTTCTCACCATGGGATTTCTTATTCCTTTC
1905512 AAAACATGGATTTTGGATTTCGT-ATTTCTCACCATGGGATTTCTTATTCCTTT
1 AAAACATGGATTTTGGATTT-GTCATTTCTCACCATGGGATTTCTTATTCCTTT
1905565 TCACTACAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
54 50 0.98
55 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.46
Consensus pattern (54 bp):
AAAACATGGATTTTGGATTTGTCATTTCTCACCATGGGATTTCTTATTCCTTTC
Found at i:1906162 original size:20 final size:19
Alignment explanation
Indices: 1906129--1906174 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
1906119 GAGAGTTTTA
*
1906129 AAAATCATTTAAAAAAATT
1 AAAATAATTTAAAAAAATT
*
1906148 AAGATAATTTAAAAAAAATT
1 AAAATAATTT-AAAAAAATT
1906168 AAAATAA
1 AAAATAA
1906175 ATATAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATAATTTAAAAAAATT
Found at i:1906181 original size:21 final size:20
Alignment explanation
Indices: 1906139--1906181 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1906129 AAAATCATTT
* *
1906139 AAAAAAATTAAGATAATTTA
1 AAAAAAATTAAAATAATATA
1906159 AAAAAAATTAAAATAAATATA
1 AAAAAAATTAAAAT-AATATA
1906180 AA
1 AA
1906182 TAAATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAAAATTAAAATAATATA
Found at i:1906554 original size:16 final size:17
Alignment explanation
Indices: 1906533--1906570 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
1906523 TTTAGATTTA
1906533 TTTTAAATTTAAA-AAT
1 TTTTAAATTTAAATAAT
1906549 TTTTAAATTTAAATAAT
1 TTTTAAATTTAAATAAT
1906566 TTTTA
1 TTTTA
1906571 TTTAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTAAATTTAAATAAT
Found at i:1906575 original size:15 final size:15
Alignment explanation
Indices: 1906532--1906575 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1906522 ATTTAGATTT
*
1906532 ATTTTAAATTTAAAA
1 ATTTTTAATTTAAAA
1906547 ATTTTTAAATTTAAATA
1 ATTTTT-AATTTAAA-A
1906564 ATTTTT-ATTTAA
1 ATTTTTAATTTAA
1906576 TTTTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 11 0.42
16 8 0.31
17 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTTAATTTAAAA
Found at i:1906798 original size:14 final size:15
Alignment explanation
Indices: 1906772--1906802 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1906762 ACCGAATAGC
1906772 AAAATTATTAAAATT
1 AAAATTATTAAAATT
1906787 AAAATT-TTAAAATT
1 AAAATTATTAAAATT
1906801 AA
1 AA
1906803 TAAGTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTATTAAAATT
Found at i:1906828 original size:29 final size:29
Alignment explanation
Indices: 1906795--1906862 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
1906785 TTAAAATTTT
1906795 AAAATTAATAAGT-ATTTATATAAATATAA
1 AAAATTAATAA-TAATTTATATAAATATAA
* * *
1906824 AAAATATAA-AATAATTTATTTATATATTA
1 AAAAT-TAATAATAATTTATATAAATATAA
*
1906853 CAAATTAATA
1 AAAATTAATA
1906863 TATTATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
28 4 0.12
29 25 0.78
30 3 0.09
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (29 bp):
AAAATTAATAATAATTTATATAAATATAA
Found at i:1907783 original size:31 final size:31
Alignment explanation
Indices: 1907737--1907798 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1907727 TATTATATGA
1907737 ACTTACTTTTTATTATAGAGATTTAAAATTT
1 ACTTACTTTTTATTATAGAGATTTAAAATTT
1907768 ACTTA-TTTTTCATTATAGAGATTTAAAATTT
1 ACTTACTTTTT-ATTATAGAGATTTAAAATTT
1907799 GTAAAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (31 bp):
ACTTACTTTTTATTATAGAGATTTAAAATTT
Found at i:1908834 original size:15 final size:15
Alignment explanation
Indices: 1908814--1908852 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1908804 GGTTTTGGGC
*
1908814 TTTTTTTAATTCAAA
1 TTTTTTTAATTAAAA
*
1908829 TTTTTTAAATTAAAA
1 TTTTTTTAATTAAAA
*
1908844 ATTTTTTAA
1 TTTTTTTAA
1908853 AATTATTCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTTTAATTAAAA
Found at i:1909775 original size:18 final size:18
Alignment explanation
Indices: 1909754--1909788 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1909744 AAATGAATAT
1909754 AAAAAAATA-AAATATAA
1 AAAAAAATATAAATATAA
*
1909771 AAAAATATATAAATATAA
1 AAAAAAATATAAATATAA
1909789 TATAATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAAAATATAAATATAA
Found at i:1909795 original size:18 final size:17
Alignment explanation
Indices: 1909749--1909815 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 17
1909739 TGATTAAATG
*
1909749 AATATAA-AAAAAT-AA
1 AATATAATAAATATAAA
* *
1909764 AATATAAAAAAATATATA
1 AATAT-AATAAATATAAA
1909782 AATATAATATAATATAAA
1 AATATAATA-AATATAAA
*
1909800 AATATCATAAATATAA
1 AATATAATAAATATAA
1909816 TACAAAATCA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 5 0.12
16 2 0.05
17 15 0.35
18 21 0.49
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.28
Consensus pattern (17 bp):
AATATAATAAATATAAA
Found at i:1909800 original size:27 final size:27
Alignment explanation
Indices: 1909750--1909830 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 27
1909740 GATTAAATGA
*
1909750 ATATAAA-AAAATAAAATATAAAAAAAT
1 ATATAAATATAATAAAATAT-AAAAAAT
*
1909777 ATATAAATATAATATAATAT-AAAAAT
1 ATATAAATATAATAAAATATAAAAAAT
*
1909803 ATCATAAATATAATACAAA-ATCAAAAAT
1 AT-ATAAATATAATA-AAATATAAAAAAT
1909831 GAACGTGTGG
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
26 8 0.17
27 21 0.45
28 18 0.38
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (27 bp):
ATATAAATATAATAAAATATAAAAAAT
Found at i:1912167 original size:36 final size:37
Alignment explanation
Indices: 1912097--1912175 Score: 101
Period size: 36 Copynumber: 2.1 Consensus size: 37
1912087 TAAAAAATAA
*
1912097 AAATATTTATTAATTTTAAATATAAAATAATAAAACAT
1 AAATATTTATTAATTTT-AATATAAAATAATAAAACAC
1912135 AAATA-TTATTAATTTT-ATCAT-AAATAAGTAAAACAC
1 AAATATTTATTAATTTTAAT-ATAAAATAA-TAAAACAC
1912171 AAATA
1 AAATA
1912176 ATAATATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
35 8 0.21
36 14 0.37
37 11 0.29
38 5 0.13
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (37 bp):
AAATATTTATTAATTTTAATATAAAATAATAAAACAC
Found at i:1912822 original size:17 final size:17
Alignment explanation
Indices: 1912800--1912835 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1912790 AATTAAACAC
1912800 TTTAAAAATTATAAATT
1 TTTAAAAATTATAAATT
* *
1912817 TTTAAAAGTTATTAATT
1 TTTAAAAATTATAAATT
1912834 TT
1 TT
1912836 GGATTTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAAAATTATAAATT
Found at i:1913695 original size:97 final size:97
Alignment explanation
Indices: 1913543--1913839 Score: 445
Period size: 98 Copynumber: 3.0 Consensus size: 97
1913533 ATGAATCCGT
*
1913543 CAACTCATCCCCAAATGCCCACATCAAGCAAGTCTTGGAACGTCCCTGGACTTTTATATAAAGTG
1 CAACTCATCCCCAAATGCTCACATC-AGCAAGTCTTGGAACGTCCCTGGACTTTTATATAAAGTG
*
1913608 GCTTCCCCTTCCAAAACAAAATCTTTAATCCAC
65 GCTTCCCCTTCCAAAACAAAATCATTAATCCAC
*
1913641 CAACACATCCCCAAATGCTCACATCAGCAAGTCTTGGAACGTCCCTGGACTTTTATATAAA-TGG
1 CAACTCATCCCCAAATGCTCACATCAGCAAGTCTTGGAACGTCCCTGGACTTTTATATAAAGTGG
* * *
1913705 CTTCCCCTTTCAAAAAAAAAAATCATTAATCTAC
66 CTTCCCC-TTC-CAAAACAAAATCATTAATCCAC
* * *
1913739 CAACTCATCCCTAAATGCTCACATCAGCAAGTC-TGGAATCGTCCCTGGACTTTTATATGAAGCG
1 CAACTCATCCCCAAATGCTCACATCAGCAAGTCTTGGAA-CGTCCCTGGACTTTTATATAAAGTG
*
1913803 GCTTCCCCTCCCAAAACAAAAATCATTAATCCAC
65 GCTTCCCCTTCCAAAAC-AAAATCATTAATCCAC
1913837 CAA
1 CAA
1913840 ATGCCCACAT
Statistics
Matches: 180, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
96 10 0.06
97 48 0.27
98 113 0.63
99 9 0.05
ACGTcount: A:0.33, C:0.30, G:0.11, T:0.25
Consensus pattern (97 bp):
CAACTCATCCCCAAATGCTCACATCAGCAAGTCTTGGAACGTCCCTGGACTTTTATATAAAGTGG
CTTCCCCTTCCAAAACAAAATCATTAATCCAC
Found at i:1915761 original size:11 final size:12
Alignment explanation
Indices: 1915747--1915796 Score: 61
Period size: 11 Copynumber: 4.4 Consensus size: 12
1915737 TATATATTTG
1915747 ATATATTAAA-A
1 ATATATTAAATA
*
1915758 ATATA-TAAATT
1 ATATATTAAATA
1915769 ATATATT-AATA
1 ATATATTAAATA
*
1915780 ATAAATTAAATA
1 ATATATTAAATA
1915792 ATATA
1 ATATA
1915797 ATTTCATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 4 0.12
11 19 0.59
12 9 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATATATTAAATA
Found at i:1915793 original size:15 final size:16
Alignment explanation
Indices: 1915751--1915796 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
1915741 TATTTGATAT
1915751 ATTAAA-AATATATAA
1 ATTAAATAATATATAA
1915766 ATTATATATTAATA-ATAA
1 ATTA-A-A-TAATATATAA
1915784 ATTAAATAATATA
1 ATTAAATAATATA
1915797 ATTTCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
15 9 0.35
16 3 0.12
17 2 0.08
18 8 0.31
19 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAAATAATATATAA
Found at i:1915810 original size:20 final size:19
Alignment explanation
Indices: 1915787--1915840 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
1915777 ATAATAAATT
*
1915787 AAATAATATAATTTCATTAA
1 AAATAATATAATTTCAAT-A
* * *
1915807 AAATAAATTTATTTTTAATA
1 AAAT-AATATAATTTCAATA
1915827 AAATAATATAATTT
1 AAATAATATAATTT
1915841 AATTTCCGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 8 0.30
20 9 0.33
21 10 0.37
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATAATATAATTTCAATA
Found at i:1916395 original size:9 final size:9
Alignment explanation
Indices: 1916379--1916428 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
1916369 CATTTGTGAT
1916379 AAAAATTTA
1 AAAAATTTA
*
1916388 ATAAATTTA
1 AAAAATTTA
1916397 AAAAA--TA
1 AAAAATTTA
1916404 AAATAA-TTA
1 AAA-AATTTA
*
1916413 AAAATTTTA
1 AAAAATTTA
1916422 AAAAATT
1 AAAAATT
1916429 ATTATAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
7 5 0.15
8 3 0.09
9 26 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAAAATTTA
Found at i:1916421 original size:25 final size:24
Alignment explanation
Indices: 1916377--1916427 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
1916367 TTCATTTGTG
*
1916377 ATAAAAATTTAATAAATTTAAAAA
1 ATAAAAAATTAATAAATTTAAAAA
1916401 ATAAAATAATTAA-AAATTTTAAAAA
1 ATAAAA-AATTAATAAA-TTTAAAAA
1916426 AT
1 AT
1916428 TATTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAAAAATTAATAAATTTAAAAA
Found at i:1916914 original size:2 final size:2
Alignment explanation
Indices: 1916909--1916936 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1916899 GTGTGTGTTA
1916909 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
1916937 GGGATTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1917497 original size:17 final size:19
Alignment explanation
Indices: 1917461--1917497 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1917451 ATCTCATTGC
*
1917461 AAAATATATGAAGAAGCAA
1 AAAATATATCAAGAAGCAA
1917480 AAAATA-ATCAAGAA-CAA
1 AAAATATATCAAGAAGCAA
1917497 A
1 A
1917498 TTCATGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.68, C:0.08, G:0.11, T:0.14
Consensus pattern (19 bp):
AAAATATATCAAGAAGCAA
Found at i:1922785 original size:3 final size:3
Alignment explanation
Indices: 1922777--1922802 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1922767 CACATGTTTA
1922777 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1922803 ATTCATTATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1923082 original size:22 final size:22
Alignment explanation
Indices: 1923061--1923101 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1923051 ATTATCAAAT
*
1923061 TTTAA-ATTTTATCACTAAAAA
1 TTTAATATTTTATCAATAAAAA
1923082 TTTAATATTTTATCAATAAA
1 TTTAATATTTTATCAATAAA
1923102 TTATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTAATATTTTATCAATAAAAA
Found at i:1924266 original size:18 final size:19
Alignment explanation
Indices: 1924245--1924282 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1924235 TATATAAATA
1924245 TTAATA-TTAATATATTTT
1 TTAATAGTTAATATATTTT
1924263 TTAATAGTTTAATATATTTT
1 TTAATAG-TTAATATATTTT
1924283 AAATAGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
TTAATAGTTAATATATTTT
Found at i:1924287 original size:19 final size:20
Alignment explanation
Indices: 1924251--1924289 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1924241 AATATTAATA
*
1924251 TTAATATATTTTTTAATAGT
1 TTAATATATTTTTAAATAGT
1924271 TTAATATA-TTTTAAATAGT
1 TTAATATATTTTTAAATAGT
1924290 AATTCAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAATATATTTTTAAATAGT
Found at i:1924716 original size:23 final size:23
Alignment explanation
Indices: 1924670--1924756 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 23
1924660 GTGTTAAATT
* * *
1924670 TTAAATATAAATATAATAAATATA
1 TTAAATAT-ATTATATTAATTATA
*
1924694 TTAAATATTTTATATTAATTATA
1 TTAAATATATTATATTAATTATA
*
1924717 TTTAAATATATCATATTATATT-TA
1 -TTAAATATATTATATTA-ATTATA
1924741 TTAAATATATTATATT
1 TTAAATATATTATATT
1924757 TTAAATTAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
23 26 0.48
24 25 0.46
25 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAATATATTATATTAATTATA
Found at i:1925311 original size:27 final size:28
Alignment explanation
Indices: 1925267--1925323 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
1925257 GTTAAGTAAT
*
1925267 TTAAATTTT-AAAATTTAATAAAA-ATA
1 TTAAATTTTAAAAATTAAATAAAACATA
1925293 TTAAATTATTAAAAATTAAATAAAACATA
1 TTAAATT-TTAAAAATTAAATAAAACATA
1925322 TT
1 TT
1925324 TGTCAAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 7 0.26
27 2 0.07
28 13 0.48
29 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (28 bp):
TTAAATTTTAAAAATTAAATAAAACATA
Found at i:1927551 original size:10 final size:10
Alignment explanation
Indices: 1927522--1927558 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1927512 GAACAATCAA
1927522 AAAGAAAAAG
1 AAAGAAAAAG
*
1927532 --AGAAAGAG
1 AAAGAAAAAG
1927540 AAAGAAAAAG
1 AAAGAAAAAG
1927550 AAAGAAAAA
1 AAAGAAAAA
1927559 AAAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
8 7 0.30
10 16 0.70
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:1928828 original size:19 final size:19
Alignment explanation
Indices: 1928801--1928881 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
1928791 GTTTGATAAT
*
1928801 TTTTTAAAAATTTTATATA
1 TTTTAAAAAATTTTATATA
* *
1928820 TTTTAAAAATTTTTATGTA
1 TTTTAAAAAATTTTATATA
* *
1928839 TTGGT-----ATTTAATATA
1 TT-TTAAAAAATTTTATATA
*
1928854 TTTTAAAAAAATTTATATA
1 TTTTAAAAAATTTTATATA
1928873 TTTTAAAAA
1 TTTTAAAAA
1928882 TAATATTCTC
Statistics
Matches: 46, Mismatches: 10, Indels: 12
0.68 0.15 0.18
Matches are distributed among these distances:
14 1 0.02
15 9 0.20
19 35 0.76
20 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (19 bp):
TTTTAAAAAATTTTATATA
Found at i:1928869 original size:34 final size:34
Alignment explanation
Indices: 1928810--1928874 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
1928800 TTTTTTAAAA
* ** *
1928810 ATTTTATATATTTTAAAAATTTTTATGTATTGGT
1 ATTTAATATATTTTAAAAAAATTTATATATTGGT
1928844 ATTTAATATATTTTAAAAAAATTTATATATT
1 ATTTAATATATTTTAAAAAAATTTATATATT
1928875 TTAAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (34 bp):
ATTTAATATATTTTAAAAAAATTTATATATTGGT
Found at i:1929159 original size:2 final size:2
Alignment explanation
Indices: 1929154--1929182 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1929144 GAATATATGC
1929154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1929183 AATGAGTGTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1931806 original size:31 final size:31
Alignment explanation
Indices: 1931770--1931839 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
1931760 GAATTAAATC
*
1931770 AATTTAAATTA-TGTTAATATAAATTAATTTA
1 AATTTAAATTATTGTTAATATAAAAT-ATTTA
* *
1931801 AATTTAAATTATTTTTAATTTAAAATATTTA
1 AATTTAAATTATTGTTAATATAAAATATTTA
1931832 AATTTAAA
1 AATTTAAA
1931840 ACACTGACAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (31 bp):
AATTTAAATTATTGTTAATATAAAATATTTA
Found at i:1931814 original size:15 final size:15
Alignment explanation
Indices: 1931770--1931839 Score: 79
Period size: 16 Copynumber: 4.5 Consensus size: 15
1931760 GAATTAAATC
1931770 AATTTAAATTATGTT-
1 AATTTAAATTAT-TTA
*
1931785 AATATAAATTAATTTA
1 AATTTAAATT-ATTTA
*
1931801 AATTTAAATTATTTTT
1 AATTTAAATTA-TTTA
*
1931817 AATTTAAAATATTTA
1 AATTTAAATTATTTA
1931832 AATTTAAA
1 AATTTAAA
1931840 ACACTGACAC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
15 23 0.49
16 24 0.51
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (15 bp):
AATTTAAATTATTTA
Found at i:1932225 original size:14 final size:15
Alignment explanation
Indices: 1932189--1932233 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
1932179 AATTATAATA
*
1932189 AATATTTAATAATATT
1 AATATTT-ATAATTTT
*
1932205 GATATTTA-AATTTT
1 AATATTTATAATTTT
1932219 AATATTTATAATTTT
1 AATATTTATAATTTT
1932234 TTATGTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.48
15 7 0.28
16 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
AATATTTATAATTTT
Found at i:1932337 original size:21 final size:22
Alignment explanation
Indices: 1932296--1932340 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
1932286 TTAATTTCTT
*
1932296 AATTCAATTTAATTTGAAAAAA
1 AATTCAATTTAATTTAAAAAAA
*
1932318 AATTCAA-TTAA-TTAATAAAA
1 AATTCAATTTAATTTAAAAAAA
1932338 AAT
1 AAT
1932341 GATAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 4 0.19
22 7 0.33
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
AATTCAATTTAATTTAAAAAAA
Found at i:1932351 original size:61 final size:61
Alignment explanation
Indices: 1932267--1932382 Score: 189
Period size: 62 Copynumber: 1.9 Consensus size: 61
1932257 ATAGAGATTA
* *
1932267 AATTAATAAAACTGATAAATTAATTT-CTTAATTCAATTTAATTTGAAAAAAAATTCAATT
1 AATTAATAAAAATGATAAATTAATTTCCTTAATTCAATATAATTTGAAAAAAAATTCAATT
*
1932327 AATTAATAAAAAATGATAAATTAATTTCCTTAATTCAATATAATTTGACAAAAAAT
1 AATTAAT-AAAAATGATAAATTAATTTCCTTAATTCAATATAATTTGAAAAAAAAT
1932383 GAAAAACAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
60 7 0.14
61 18 0.35
62 26 0.51
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (61 bp):
AATTAATAAAAATGATAAATTAATTTCCTTAATTCAATATAATTTGAAAAAAAATTCAATT
Found at i:1933097 original size:2 final size:2
Alignment explanation
Indices: 1933085--1933122 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1933075 CTTTCTCTTC
*
1933085 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1933123 GAAAGAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1934403 original size:19 final size:19
Alignment explanation
Indices: 1934379--1934433 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
1934369 ATAATACTAG
1934379 AAAATAATAAAATATAATA
1 AAAATAATAAAATATAATA
*
1934398 AAAATATATTAAAAT-T-TTA
1 AAAATA-A-TAAAATATAATA
* *
1934417 AAAATTATATAATATAA
1 AAAATAATAAAATATAA
1934434 ATTATTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
17 5 0.18
18 2 0.07
19 13 0.46
20 2 0.07
21 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATAATAAAATATAATA
Found at i:1934427 original size:33 final size:33
Alignment explanation
Indices: 1934390--1934489 Score: 89
Period size: 33 Copynumber: 3.0 Consensus size: 33
1934380 AAATAATAAA
*
1934390 ATATAATAAAAATATATTAAAATTTTAAAAATT
1 ATATAATAAAAATATATTAAAATATTAAAAATT
* * **
1934423 ATATAATATAAAT-TATTAATATATTAAATTTT
1 ATATAATAAAAATATATTAAAATATTAAAAATT
* *
1934455 AAATAAATATAAAATAT-TTTAAATA-TAATAAATT
1 ATAT-AATA-AAAATATATTAAAATATTAA-AAATT
1934489 A
1 A
1934490 CATTAAAAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
32 18 0.35
33 19 0.37
34 14 0.27
35 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
ATATAATAAAAATATATTAAAATATTAAAAATT
Found at i:1934431 original size:38 final size:39
Alignment explanation
Indices: 1934379--1934471 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 39
1934369 ATAATACTAG
*
1934379 AAAATAATAAAATAT-AA-TAAAAATATATTAAAATTTTA
1 AAAATTATAAAATATAAATTAAAAATATATT-AAATTTTA
* **
1934417 AAAATTATATAATATAAATTATTAATATATTAAATTTTA
1 AAAATTATAAAATATAAATTAAAAATATATTAAATTTTA
*
1934456 AATAAATATAAAATAT
1 AA-AATTATAAAATAT
1934472 TTTAAATATA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 13 0.28
39 12 0.26
40 21 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (39 bp):
AAAATTATAAAATATAAATTAAAAATATATTAAATTTTA
Found at i:1934463 original size:20 final size:22
Alignment explanation
Indices: 1934400--1934489 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 22
1934390 ATATAATAAA
*
1934400 AATATATTAAAATTTTAAA-A-
1 AATATATTAATATTTTAAATAT
*
1934420 ATTATA-TAATA---TAAATTATT
1 AATATATTAATATTTTAAA-TA-T
1934440 AATATATTAA-ATTTTAAATA-
1 AATATATTAATATTTTAAATAT
*
1934460 AATATA-AAATATTTTAAATAT
1 AATATATTAATATTTTAAATAT
*
1934481 AATAAATTA
1 AATATATTA
1934490 CATTAAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 20
0.67 0.08 0.25
Matches are distributed among these distances:
16 4 0.08
18 1 0.02
19 6 0.11
20 27 0.51
21 8 0.15
22 3 0.06
23 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AATATATTAATATTTTAAATAT
Found at i:1935770 original size:22 final size:22
Alignment explanation
Indices: 1935746--1935787 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
1935736 TTTTTTAACA
1935746 AAAAAATTA-AAAT-TTAAAAT
1 AAAAAATTATAAATATTAAAAT
1935766 AAAAAATTATAAATATTAAAAT
1 AAAAAATTATAAATATTAAAAT
1935788 TTAAACTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 4 0.20
22 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAAAATTATAAATATTAAAAT
Found at i:1939191 original size:13 final size:13
Alignment explanation
Indices: 1939175--1939211 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1939165 ATTTTTTAAA
1939175 AATATTTATTTTT
1 AATATTTATTTTT
*
1939188 AATATTTATATTT
1 AATATTTATTTTT
*
1939201 AATATATATTT
1 AATATTTATTT
1939212 AAATATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AATATTTATTTTT
Found at i:1939520 original size:13 final size:13
Alignment explanation
Indices: 1939502--1939539 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1939492 ATTTATAAAT
*
1939502 ATATTTTTATTTA
1 ATATTTATATTTA
1939515 ATATTTATATTTA
1 ATATTTATATTTA
1939528 ATA--TATATTTA
1 ATATTTATATTTA
1939539 A
1 A
1939540 ATATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 9 0.38
13 15 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATATTTATATTTA
Found at i:1940440 original size:23 final size:25
Alignment explanation
Indices: 1940414--1940461 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1940404 ATAAATTTTT
*
1940414 AAATAAT-AA-ATTAAAGTTTAAAA
1 AAATAATAAATATTAAAATTTAAAA
*
1940437 AAATTATAAATATTAAAATTTAAAA
1 AAATAATAAATATTAAAATTTAAAA
1940462 TTTAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 2 0.10
25 13 0.62
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
AAATAATAAATATTAAAATTTAAAA
Found at i:1940950 original size:2 final size:2
Alignment explanation
Indices: 1940943--1940972 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1940933 TAAAAATGAG
1940943 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
1940973 TGTGATCTCG
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:1941639 original size:24 final size:25
Alignment explanation
Indices: 1941612--1941663 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
1941602 ATATATTGTA
*
1941612 TTATATT-TATTATTTATATTAT-TT
1 TTATATTATATT-TTTATATAATATT
1941636 TTATATTATATTTTTATATAATATT
1 TTATATTATATTTTTATATAATATT
1941661 TTA
1 TTA
1941664 AATAAAATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (25 bp):
TTATATTATATTTTTATATAATATT
Found at i:1941640 original size:11 final size:12
Alignment explanation
Indices: 1941612--1941654 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 12
1941602 ATATATTGTA
1941612 TTATATTTATTAT
1 TTATATTTATT-T
1941625 TTATA-TTATTT
1 TTATATTTATTT
1941636 TTATATTATATTT
1 TTATATT-TATTT
1941649 TTATAT
1 TTATAT
1941655 AATATTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.21
12 6 0.21
13 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTATATTTATTT
Found at i:1941644 original size:16 final size:16
Alignment explanation
Indices: 1941603--1941647 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
1941593 TGTATTAAAA
*
1941603 TATATTGTATTATATT
1 TATATTATATTATATT
*
1941619 TATTATTTATATTATTTT
1 TA-TA-TTATATTATATT
1941637 TATATTATATT
1 TATATTATATT
1941648 TTTATATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 9 0.36
17 4 0.16
18 12 0.48
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
TATATTATATTATATT
Found at i:1941659 original size:13 final size:13
Alignment explanation
Indices: 1941626--1941662 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1941616 ATTTATTATT
*
1941626 TATATTATTTTTA
1 TATAATATTTTTA
*
1941639 TATTATATTTTTA
1 TATAATATTTTTA
1941652 TATAATATTTT
1 TATAATATTTT
1941663 AAATAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATAATATTTTTA
Found at i:1942053 original size:5 final size:5
Alignment explanation
Indices: 1942043--1942104 Score: 62
Period size: 5 Copynumber: 13.2 Consensus size: 5
1942033 AGTATTTTTA
* *
1942043 TATAT TATATT TATAT T-TAA AATAT TATA- TAT-T TATA- TA-AT TATAT
1 TATAT TATA-T TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1942089 TATAT TATAT TATAT T
1 TATAT TATAT TATAT T
1942105 TTAAAATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
3 1 0.02
4 12 0.26
5 29 0.62
6 5 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:1943397 original size:8 final size:8
Alignment explanation
Indices: 1943386--1943546 Score: 54
Period size: 8 Copynumber: 19.6 Consensus size: 8
1943376 TAGATTTAGC
1943386 TATTTATA
1 TATTTATA
1943394 TATTTAGT-
1 TATTTA-TA
1943402 TATTTATA
1 TATTTATA
1943410 TATTTATA
1 TATTTATA
1943418 TTATATT-TA
1 -TAT-TTATA
*
1943427 -ATTTTTTA
1 TA-TTTATA
1943435 TATTATAATAA
1 TATT-T-AT-A
1943446 TATTTA-A
1 TATTTATA
*
1943453 T-TTATTTA
1 TATT-TATA
1943461 TATTTATA
1 TATTTATA
1943469 T-TTATATA
1 TATT-TATA
*
1943477 AATTT-TAA
1 TATTTAT-A
1943485 TATTT-TAA
1 TATTTAT-A
*
1943493 TAATTCATA
1 T-ATTTATA
*
1943502 T-TATATA
1 TATTTATA
* *
1943509 AATTTTAAAA
1 TA-TTT-ATA
1943519 TATTTATA
1 TATTTATA
1943527 TATTTA-A
1 TATTTATA
*
1943534 TATTTTTA
1 TATTTATA
1943542 TATTT
1 TATTT
1943547 TAATTATTTT
Statistics
Matches: 117, Mismatches: 14, Indels: 44
0.67 0.08 0.25
Matches are distributed among these distances:
6 2 0.02
7 20 0.17
8 59 0.50
9 23 0.20
10 8 0.07
11 5 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (8 bp):
TATTTATA
Found at i:1943398 original size:16 final size:16
Alignment explanation
Indices: 1943379--1943415 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1943369 TTTTGAATAG
1943379 ATTTAGCTATTTATAT
1 ATTTAGCTATTTATAT
*
1943395 ATTTAGTTATTTATAT
1 ATTTAGCTATTTATAT
1943411 ATTTA
1 ATTTA
1943416 TATTATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
ATTTAGCTATTTATAT
Found at i:1943419 original size:6 final size:6
Alignment explanation
Indices: 1943386--1943475 Score: 59
Period size: 6 Copynumber: 15.5 Consensus size: 6
1943376 TAGATTTAGC
* *
1943386 TATTTA TATATT- TAGTTA T-TTATA TATTTA TA-TTA TATTTA -ATTTTT
1 TATTTA TAT-TTA TATTTA TATT-TA TATTTA TATTTA TATTTA TA-TTTA
* *
1943433 TATATTA TAATAA TATTTA -A-TT- TATTTA TATTTA TATTTA TAT
1 TAT-TTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TAT
1943476 AAATTTTAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 22
0.68 0.08 0.23
Matches are distributed among these distances:
4 3 0.05
5 12 0.18
6 41 0.63
7 9 0.14
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (6 bp):
TATTTA
Found at i:1943448 original size:25 final size:25
Alignment explanation
Indices: 1943393--1943469 Score: 93
Period size: 25 Copynumber: 3.0 Consensus size: 25
1943383 AGCTATTTAT
* *
1943393 ATATTTAGTTATTTATATATTTATATT
1 ATATTTAATT-TTT-TATATTTATATA
1943420 ATATTTAATTTTTTATA-TTATAATA
1 ATATTTAATTTTTTATATTTAT-ATA
1943445 ATATTTAATTTATTTATATTTATAT
1 ATATTTAATTT-TTTATATTTATAT
1943470 TTATATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 4 0.09
25 17 0.38
26 11 0.24
27 13 0.29
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (25 bp):
ATATTTAATTTTTTATATTTATATA
Found at i:1943484 original size:32 final size:31
Alignment explanation
Indices: 1943431--1943527 Score: 99
Period size: 32 Copynumber: 3.0 Consensus size: 31
1943421 TATTTAATTT
1943431 TTTATATTATA-ATAATATTTAATTTATTTATA
1 TTTATATTATATA-AAT-TTTAATTTATTTATA
*
1943463 TTTATATTTATATAAATTTTAATATT-TTAATAA
1 TTTATA-TTATATAAATTTTAAT-TTATTTAT-A
* **
1943496 TTCATATTATATAAATTTTAAAATATTTATA
1 TTTATATTATATAAATTTTAATTTATTTATA
1943527 T
1 T
1943528 ATTTAATATT
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
31 3 0.05
32 35 0.64
33 16 0.29
34 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (31 bp):
TTTATATTATATAAATTTTAATTTATTTATA
Found at i:1943497 original size:17 final size:16
Alignment explanation
Indices: 1943466--1943558 Score: 59
Period size: 17 Copynumber: 5.6 Consensus size: 16
1943456 ATTTATATTT
1943466 ATATTTATATAAATTTTA
1 ATATTT-TAT-AATTTTA
*
1943484 ATATTTTAATAA--TTC
1 ATATTTT-ATAATTTTA
*
1943499 ATATTATATAAATTTTA
1 ATATTTTAT-AATTTTA
*
1943516 AAATATTTAT-ATATTTA
1 ATAT-TTTATAAT-TTTA
1943533 ATATTTT-TATATTTTA
1 ATATTTTATA-ATTTTA
1943549 ATTATTTTAT
1 A-TATTTTAT
1943559 TCGTATCATA
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 2 0.03
15 11 0.19
16 10 0.17
17 23 0.39
18 13 0.22
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTTATAATTTTA
Found at i:1943556 original size:9 final size:8
Alignment explanation
Indices: 1943404--1943557 Score: 61
Period size: 8 Copynumber: 18.5 Consensus size: 8
1943394 TATTTAGTTA
1943404 TTTATATAT
1 TTTA-ATAT
*
1943413 TTATATTAT
1 TT-TAATAT
1943422 ATTTAAT-T
1 -TTTAATAT
*
1943430 TTTTATAT
1 TTTAATAT
*
1943438 TATAATAAT
1 TTTAAT-AT
1943447 ATTTAAT-T
1 -TTTAATAT
*
1943455 TATTTATA-
1 T-TTAATAT
1943463 TTT-ATAT
1 TTTAATAT
*
1943470 TTATATAAAT
1 TT-TA-ATAT
1943480 TTTAATAT
1 TTTAATAT
1943488 TTTAATA-
1 TTTAATAT
* *
1943495 ATTCATAT
1 TTTAATAT
1943503 TATATAA-AT
1 T-T-TAATAT
*
1943512 TTTAAAAT
1 TTTAATAT
1943520 ATTT-ATAT
1 -TTTAATAT
1943528 ATTTAATAT
1 -TTTAATAT
*
1943537 TTTTATAT
1 TTTAATAT
1943545 TTTAATTAT
1 TTTAA-TAT
1943554 TTTA
1 TTTA
1943558 TTCGTATCAT
Statistics
Matches: 111, Mismatches: 16, Indels: 36
0.68 0.10 0.22
Matches are distributed among these distances:
6 3 0.03
7 18 0.16
8 44 0.40
9 30 0.27
10 16 0.14
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (8 bp):
TTTAATAT
Found at i:1946141 original size:24 final size:24
Alignment explanation
Indices: 1946114--1946165 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1946104 GGGAAAAAAA
* * * *
1946114 AAATATTTGAATTTTAAATTTATT
1 AAATATTTAAATTTAAAAATAATT
1946138 AAATATTTAAATTTAAAAATAATT
1 AAATATTTAAATTTAAAAATAATT
1946162 AAAT
1 AAAT
1946166 TAATTAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
AAATATTTAAATTTAAAAATAATT
Found at i:1946146 original size:17 final size:17
Alignment explanation
Indices: 1946127--1946186 Score: 68
Period size: 16 Copynumber: 3.5 Consensus size: 17
1946117 TATTTGAATT
*
1946127 TTAAATTTATTAAATAT
1 TTAAATTTATTAAATAA
*
1946144 TTAAATTTA-AAAATAA
1 TTAAATTTATTAAATAA
* *
1946160 TTAAATTAATTAATTAAA
1 TTAAATTTATTAAAT-AA
1946178 TTAAATTTA
1 TTAAATTTA
1946187 AATAAAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
16 13 0.37
17 12 0.34
18 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTAAATTTATTAAATAA
Found at i:1946172 original size:33 final size:34
Alignment explanation
Indices: 1946127--1946196 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
1946117 TATTTGAATT
* *
1946127 TTAAATTTATTAAAT-ATTTAAATTTAAA-AATAA
1 TTAAATTAATTAAATAAATTAAATTTAAATAA-AA
*
1946160 TTAAATTAATTAATTAAATTAAATTTAAATAAAA
1 TTAAATTAATTAAATAAATTAAATTTAAATAAAA
1946194 TTA
1 TTA
1946197 TTTTTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
33 13 0.41
34 17 0.53
35 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
TTAAATTAATTAAATAAATTAAATTTAAATAAAA
Found at i:1946175 original size:13 final size:13
Alignment explanation
Indices: 1946157--1946181 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1946147 AATTTAAAAA
1946157 TAATTAAATTAAT
1 TAATTAAATTAAT
1946170 TAATTAAATTAA
1 TAATTAAATTAA
1946182 ATTTAAATAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:1948224 original size:24 final size:25
Alignment explanation
Indices: 1948197--1948246 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1948187 TAGTGGTTAG
1948197 TAAAACTTTTATCTAAT-CATTATT
1 TAAAACTTTTATCTAATACATTATT
* * *
1948221 TAAAATTTTTATTTAATATATTATT
1 TAAAACTTTTATCTAATACATTATT
1948246 T
1 T
1948247 TTATTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (25 bp):
TAAAACTTTTATCTAATACATTATT
Found at i:1949161 original size:27 final size:26
Alignment explanation
Indices: 1949140--1949218 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 26
1949130 TTTTATATTT
1949140 TTTTATATTTTAATTATATTTAAAATA
1 TTTTATA-TTTAATTATATTTAAAATA
1949167 TTTTATATTTAATTAAATAAATATTAAAATA
1 TTTTATATTTAATT--AT--AT-TTAAAATA
1949198 TTTATATATTTATATTATATT
1 TTT-TATATTTA-ATTATATT
1949219 ATTTTTTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
26 7 0.16
27 7 0.16
28 3 0.07
29 2 0.04
30 2 0.04
31 13 0.29
32 8 0.18
33 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTATATTTAATTATATTTAAAATA
Found at i:1949182 original size:20 final size:20
Alignment explanation
Indices: 1949144--1949183 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1949134 ATATTTTTTT
*
1949144 ATATTTTAATTATATTTAAA
1 ATATTTTAATTATAATTAAA
1949164 ATATTTTATATT-TAATTAAA
1 ATATTTTA-ATTATAATTAAA
1949184 TAAATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTTTAATTATAATTAAA
Found at i:1949206 original size:16 final size:16
Alignment explanation
Indices: 1949153--1949207 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
1949143 TATATTTTAA
1949153 TTATAT-TTAAAATAT
1 TTATATATTAAAATAT
* * *
1949168 TT-TATATTTAATTAA
1 TTATATATTAAAATAT
* *
1949183 ATAAATATTAAAATAT
1 TTATATATTAAAATAT
1949199 TTATATATT
1 TTATATATT
1949208 TATATTATAT
Statistics
Matches: 28, Mismatches: 10, Indels: 3
0.68 0.24 0.07
Matches are distributed among these distances:
14 3 0.11
15 9 0.32
16 16 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATATATTAAAATAT
Found at i:1949664 original size:64 final size:63
Alignment explanation
Indices: 1949553--1949686 Score: 169
Period size: 64 Copynumber: 2.1 Consensus size: 63
1949543 GAAAGAGTAG
** **
1949553 CATAATTATATGAAAGTGACACCACAAAACATTTGTATGAATTTTTTTTCGGTACAAAAAAAAT
1 CATAATTATATGAAAGTGACACCACAAAACATTTGTACAAAAATTTTTTCGGTA-AAAAAAAAT
* * * * *
1949617 CATAATTATATGAAAGTGGCACCATAAAATATTTGTACAAAAATTTTTTTGGTATAAAAAAAT
1 CATAATTATATGAAAGTGACACCACAAAACATTTGTACAAAAATTTTTTCGGTAAAAAAAAAT
*
1949680 CACAATT
1 CATAATT
1949687 TGAAAATAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
63 14 0.23
64 46 0.77
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (63 bp):
CATAATTATATGAAAGTGACACCACAAAACATTTGTACAAAAATTTTTTCGGTAAAAAAAAAT
Found at i:1951091 original size:19 final size:21
Alignment explanation
Indices: 1951040--1951092 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1951030 ATATTTTATT
1951040 TAAA-TTTAATTATAAAATATA
1 TAAATTTTAA-TATAAAATATA
*
1951061 TAAATATTAATATAAAA-ATA
1 TAAATTTTAATATAAAATATA
*
1951081 -ATATTTTAATAT
1 TAAATTTTAATAT
1951093 TTTTTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 10 0.36
20 3 0.11
21 11 0.39
22 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAATTTTAATATAAAATATA
Found at i:1951774 original size:33 final size:32
Alignment explanation
Indices: 1951724--1951791 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1951714 AAAATATAAT
* *
1951724 AAAATATATATTAATATATTAATATTTATATA
1 AAAATAAATATTAATATATTAAAATTTATATA
1951756 AAAATAAATTATTAATATATTAAAATTTATATA
1 AAAATAAA-TATTAATATATTAAAATTTATATA
1951789 AAA
1 AAA
1951792 TATTATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 7 0.21
33 26 0.79
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AAAATAAATATTAATATATTAAAATTTATATA
Found at i:1952447 original size:10 final size:10
Alignment explanation
Indices: 1952417--1952456 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
1952407 AAATATAATT
1952417 AAAA-TAAAA
1 AAAATTAAAA
1952426 AAAATCTAAAA
1 AAAAT-TAAAA
1952437 AAGAATTAAAA
1 AA-AATTAAAA
1952448 AAAATTAAA
1 AAAATTAAA
1952457 GGGGAAATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.14
10 7 0.25
11 14 0.50
12 3 0.11
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:1963536 original size:3 final size:3
Alignment explanation
Indices: 1963523--1963570 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
1963513 GCTCAAATTC
* * *
1963523 ATT AAT ATT ATT ATT AGT ATC 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
1963571 TTGTTTGGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1964074 original size:15 final size:16
Alignment explanation
Indices: 1964054--1964088 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1964044 TATTTCAAGC
1964054 ATAATA-AAACAAAAA
1 ATAATACAAACAAAAA
*
1964069 ATAATACAAACAAAAT
1 ATAATACAAACAAAAA
1964085 ATAA
1 ATAA
1964089 ATATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (16 bp):
ATAATACAAACAAAAA
Found at i:1964106 original size:28 final size:26
Alignment explanation
Indices: 1964028--1964106 Score: 61
Period size: 26 Copynumber: 2.9 Consensus size: 26
1964018 ATATAAATAT
* * *
1964028 AATACAAATATAAAATTATTTCAAGCAT
1 AATA-AAATATAAAAATA-TTCAAACAA
* *
1964056 AATAAAACA-AAAAATAATACAAACAA
1 AATAAAATATAAAAAT-ATTCAAACAA
1964082 AATATAAATATAAAAATATCTCAAA
1 AATA-AAATATAAAAATAT-TCAAA
1964107 TTTTATATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
26 15 0.38
27 11 0.28
28 14 0.35
ACGTcount: A:0.65, C:0.10, G:0.01, T:0.24
Consensus pattern (26 bp):
AATAAAATATAAAAATATTCAAACAA
Found at i:1964202 original size:18 final size:18
Alignment explanation
Indices: 1964163--1964203 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1964153 TAACATTCAT
*
1964163 TTAAACTCAATTATATCT
1 TTAAACTCAATTATATCA
1964181 TTAAACTCAATTATGA-CA
1 TTAAACTCAATTAT-ATCA
1964199 TTAAA
1 TTAAA
1964204 ATATATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (18 bp):
TTAAACTCAATTATATCA
Found at i:1964594 original size:25 final size:24
Alignment explanation
Indices: 1964566--1964617 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1964556 ACAATATTAG
* *
1964566 ACATGACATGAAAAAAATAATTAAA
1 ACATGACACG-AAAAAATAATAAAA
*
1964591 ACATGATACGAAAAAATAATAAAA
1 ACATGACACGAAAAAATAATAAAA
1964615 ACA
1 ACA
1964618 AGACGAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.65, C:0.10, G:0.08, T:0.17
Consensus pattern (24 bp):
ACATGACACGAAAAAATAATAAAA
Found at i:1969938 original size:19 final size:18
Alignment explanation
Indices: 1969914--1969949 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1969904 TAATTCAGAC
1969914 TATTATTTATTAATTAAAA
1 TATTATTT-TTAATTAAAA
*
1969933 TATTATTTTTATTTAAA
1 TATTATTTTTAATTAAA
1969950 TTTAATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATTTTTAATTAAAA
Found at i:1970373 original size:20 final size:20
Alignment explanation
Indices: 1970320--1970376 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
1970310 AATCAATATC
*
1970320 ATTTTATATTATATATTTAT
1 ATTTTATATTATATATTAAT
** *
1970340 A-TAAATTTTAATATATTAAT
1 ATTTTATATT-ATATATTAAT
1970360 ATTTTATATTATATATT
1 ATTTTATATTATATATT
1970377 TTTTAATATA
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 5 0.18
20 18 0.64
21 5 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTATATTATATATTAAT
Found at i:1970396 original size:40 final size:38
Alignment explanation
Indices: 1970320--1970416 Score: 101
Period size: 40 Copynumber: 2.5 Consensus size: 38
1970310 AATCAATATC
* *
1970320 ATTTTATATTATATATTTATATAAATTTTAATATATTAAT
1 ATTTTATATTATATATTTATATAAATATCAATATATT--T
*
1970360 ATTTTATATTATATATTT-TTTAATATAATCAA-ATATTT
1 ATTTTATATTATATATTTATATAA-AT-ATCAATATATTT
*
1970398 ATATTATATTATAT-TTTAT
1 ATTTTATATTATATATTTAT
1970417 GATATATTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
37 3 0.06
38 15 0.30
39 4 0.08
40 25 0.50
41 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (38 bp):
ATTTTATATTATATATTTATATAAATATCAATATATTT
Found at i:1970437 original size:33 final size:31
Alignment explanation
Indices: 1970331--1970437 Score: 108
Period size: 33 Copynumber: 3.3 Consensus size: 31
1970321 TTTTATATTA
**
1970331 TATATTTATATAAATTTTAATATATTAATATTT
1 TATA-TTATATATTTTTTAATATATTAA-ATTT
*
1970364 TATATTATATATTTTTTAATATAATCAAATATT
1 TATATTATATATTTTTTAATAT-ATTAAAT-TT
*
1970397 TATATTATATTATATTTTATGATATATTAAATTT
1 TATATTATA-TAT-TTTT-TAATATATTAAATTT
1970431 TA-ATTAT
1 TATATTAT
1970438 TTTTTCGAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
32 18 0.28
33 24 0.38
34 7 0.11
35 10 0.16
36 5 0.08
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (31 bp):
TATATTATATATTTTTTAATATATTAAATTT
Found at i:1971312 original size:2 final size:2
Alignment explanation
Indices: 1971305--1971348 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1971295 GGAGTTTAAA
1971305 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1971347 AG
1 AG
1971349 TTACCGGGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1973752 original size:23 final size:23
Alignment explanation
Indices: 1973722--1973797 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 23
1973712 TCTAAAGAAC
1973722 TCTTGTTAGTTTTTTTTGGACAG
1 TCTTGTTAGTTTTTTTTGGACAG
* *** *
1973745 TCTTGTTAG---TCTAAAGA-AC
1 TCTTGTTAGTTTTTTTTGGACAG
1973764 TCTTGTTAGTTTTTTTTGGACAG
1 TCTTGTTAGTTTTTTTTGGACAG
1973787 TCTTGTTAGTT
1 TCTTGTTAGTT
1973798 CATAATGACA
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
19 10 0.26
20 4 0.10
22 4 0.10
23 21 0.54
ACGTcount: A:0.17, C:0.11, G:0.20, T:0.53
Consensus pattern (23 bp):
TCTTGTTAGTTTTTTTTGGACAG
Found at i:1973758 original size:42 final size:42
Alignment explanation
Indices: 1973712--1973796 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
1973702 TAGATAATGC
1973712 TCTAAAGAACTCTTGTTAGTTTTTTTTGGACAGTCTTGTTAG
1 TCTAAAGAACTCTTGTTAGTTTTTTTTGGACAGTCTTGTTAG
1973754 TCTAAAGAACTCTTGTTAGTTTTTTTTGGACAGTCTTGTTAG
1 TCTAAAGAACTCTTGTTAGTTTTTTTTGGACAGTCTTGTTAG
1973796 T
1 T
1973797 TCATAATGAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (42 bp):
TCTAAAGAACTCTTGTTAGTTTTTTTTGGACAGTCTTGTTAG
Found at i:1977186 original size:5 final size:5
Alignment explanation
Indices: 1977176--1977204 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1977166 TGAAAGGGGC
1977176 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1977205 TGAAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:1978024 original size:9 final size:9
Alignment explanation
Indices: 1978006--1978059 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 9
1977996 ATTTATATAG
*
1978006 TATTTGTAT
1 TATTTTTAT
1978015 TATTTTTAT
1 TATTTTTAT
1978024 TATTTTTATAT
1 TA-TTTT-TAT
1978035 TATATTTTAAT
1 TAT-TTTT-AT
1978046 TATTTTTAT
1 TATTTTTAT
1978055 ATATT
1 -TATT
1978060 ATATTTTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
9 12 0.31
10 14 0.36
11 13 0.33
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (9 bp):
TATTTTTAT
Found at i:1978040 original size:22 final size:22
Alignment explanation
Indices: 1978015--1978084 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 22
1978005 GTATTTGTAT
1978015 TATTTTTATTATTTTTATATTA
1 TATTTTTATTATTTTTATATTA
*
1978037 TATTTTAATTATTTTTATATATTA
1 TATTTTTATTA-TTTT-TATATTA
* *
1978061 TATTTTTATCATATTTAATATTA
1 TATTTTTATTAT-TTTTATATTA
1978084 T
1 T
1978085 TAAATCTAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 10 0.24
23 12 0.29
24 19 0.46
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTTATTATTTTTATATTA
Found at i:1978041 original size:31 final size:32
Alignment explanation
Indices: 1977991--1978059 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
1977981 TTAAAATAAT
*
1977991 TATATATTTATATAGTATTTGT-ATTATTTTTA
1 TATATTTTTATATAGTATTT-TAATTATTTTTA
1978023 T-TATTTTTATATTA-TATTTTAATTATTTTTA
1 TATATTTTTATA-TAGTATTTTAATTATTTTTA
1978054 TATATT
1 TATATT
1978060 ATATTTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
30 1 0.03
31 25 0.76
32 7 0.21
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (32 bp):
TATATTTTTATATAGTATTTTAATTATTTTTA
Found at i:1978076 original size:11 final size:11
Alignment explanation
Indices: 1977989--1978076 Score: 65
Period size: 11 Copynumber: 7.8 Consensus size: 11
1977979 TTTTAAAATA
*
1977989 ATTATATATTT
1 ATTATATTTTT
*
1978000 ATATAGTATTTGT
1 AT-TA-TATTTTT
1978013 A-T-TATTTTT
1 ATTATATTTTT
1978022 ATTAT-TTTTAT
1 ATTATATTTT-T
*
1978033 ATTATATTTTA
1 ATTATATTTTT
*
1978044 ATTATTTTTATAT
1 ATTATATTT-T-T
1978057 ATTATATTTTT
1 ATTATATTTTT
*
1978068 ATCATATTT
1 ATTATATTT
1978077 AATATTATTA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
9 7 0.11
10 5 0.08
11 27 0.44
12 8 0.13
13 14 0.23
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (11 bp):
ATTATATTTTT
Found at i:1978081 original size:18 final size:17
Alignment explanation
Indices: 1978034--1978082 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
1978024 TATTTTTATA
1978034 TTATAT-TTTAATTATTT
1 TTATATATTTAA-TATTT
1978051 TTATATA-TT-ATATTT
1 TTATATATTTAATATTT
1978066 TTATCATATTTAATATT
1 TTAT-ATATTTAATATT
1978083 ATTAAATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 9 0.32
16 4 0.14
17 10 0.36
18 5 0.18
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATATTTAATATTT
Found at i:1978344 original size:2 final size:2
Alignment explanation
Indices: 1978337--1978362 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1978327 TGAAAGTTTC
1978337 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
1978363 TCAATTATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1978866 original size:14 final size:14
Alignment explanation
Indices: 1978844--1978878 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
1978834 AGATTTAAAA
1978844 TTAATTTT-AATTT
1 TTAATTTTAAATTT
1978857 TTATATTTTAAATTT
1 TTA-ATTTTAAATTT
1978872 TTAATTT
1 TTAATTT
1978879 AATGAAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 9 0.45
15 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTAATTTTAAATTT
Found at i:1979009 original size:19 final size:19
Alignment explanation
Indices: 1978977--1979024 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1978967 AATAAAATTT
* *
1978977 ATTAATTATATTATAAATTA
1 ATTATTTATTTTATAAA-TA
*
1978997 ATT-TTTATTTTATATATA
1 ATTATTTATTTTATAAATA
1979015 ATTATTTATT
1 ATTATTTATT
1979025 AATGCATTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.21
19 16 0.67
20 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTATTTATTTTATAAATA
Found at i:1980315 original size:4 final size:4
Alignment explanation
Indices: 1980306--1980332 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1980296 TGTTTTTATT
1980306 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1980333 TTAAGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1989422 original size:2 final size:2
Alignment explanation
Indices: 1989417--1989442 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1989407 ATATATATAT
1989417 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1989443 TTAGGAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1992426 original size:12 final size:12
Alignment explanation
Indices: 1992405--1992435 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1992395 CCTTTTAATC
*
1992405 TTATAACTATTT
1 TTATATCTATTT
1992417 TTATATCTATTT
1 TTATATCTATTT
1992429 TTATATC
1 TTATATC
1992436 AAGTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATATCTATTT
Found at i:1998315 original size:7 final size:7
Alignment explanation
Indices: 1998279--1998328 Score: 57
Period size: 7 Copynumber: 6.9 Consensus size: 7
1998269 ATAAAGTATT
1998279 TATTTAA
1 TATTTAA
*
1998286 T-TTATTA
1 TATT-TAA
1998293 TATTTAA
1 TATTTAA
1998300 TAAATTTAA
1 T--ATTTAA
1998309 TATTTAA
1 TATTTAA
1998316 TATTTAA
1 TATTTAA
1998323 TATTTA
1 TATTTA
1998329 TAATTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 2 0.05
7 26 0.70
8 2 0.05
9 7 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TATTTAA
Found at i:1998334 original size:14 final size:14
Alignment explanation
Indices: 1998292--1998334 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
1998282 TTAATTTATT
1998292 ATATTTAATAAATTTA
1 ATATTT-AT-AATTTA
1998308 ATATTTA-ATATTTA
1 ATATTTATA-ATTTA
1998322 ATATTTATAATTT
1 ATATTTATAATTT
1998335 TTTCTCGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.04
14 16 0.64
15 2 0.08
16 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATATTTATAATTTA
Found at i:1998738 original size:2 final size:2
Alignment explanation
Indices: 1998731--1998758 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1998721 TTTTCTATGT
1998731 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
1998759 CACACCTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.