Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold14
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: 2879421
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 64274 characters in sequence are not A, C, G, or T
File 12 of 17
Found at i:1918165 original size:13 final size:13
Alignment explanation
Indices: 1918147--1918174 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1918137 TTCTCATTAG
1918147 ATTTTTAAAATAT
1 ATTTTTAAAATAT
1918160 ATTTTTAAAATAT
1 ATTTTTAAAATAT
1918173 AT
1 AT
1918175 ACTTATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTTTAAAATAT
Found at i:1920869 original size:9 final size:9
Alignment explanation
Indices: 1920857--1920908 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
1920847 ATATAGAAAA
1920857 TTTTTTCTT
1 TTTTTTCTT
*
1920866 TTTTCTCTT
1 TTTTTTCTT
**
1920875 TTTCCTCTT
1 TTTTTTCTT
*
1920884 TCTTTTCTT
1 TTTTTTCTT
*
1920893 ATTTTTCTT
1 TTTTTTCTT
1920902 TCTTTTT
1 T-TTTTT
1920909 TTCATTAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
9 29 0.85
10 5 0.15
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:1920891 original size:20 final size:18
Alignment explanation
Indices: 1920858--1920907 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1920848 TATAGAAAAT
1920858 TTTTTCTTT-TTTCTCTT-
1 TTTTTCTTTCTTT-TCTTA
*
1920875 TTTCCTCTTTCTTTTCTTA
1 TTT-TTCTTTCTTTTCTTA
1920894 TTTTTCTTTCTTTT
1 TTTTTCTTTCTTTT
1920908 TTTCATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 3 0.11
18 19 0.68
19 6 0.21
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTCTTTCTTTTCTTA
Found at i:1921949 original size:11 final size:11
Alignment explanation
Indices: 1921927--1921958 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
1921917 TCCTTCATTC
1921927 TCTTTTTC-TT
1 TCTTTTTCTTT
1921937 TCTTTTTCTTT
1 TCTTTTTCTTT
1921948 TCTTTTT-TTT
1 TCTTTTTCTTT
1921958 T
1 T
1921959 TTCTCTCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TCTTTTTCTTT
Found at i:1924051 original size:21 final size:21
Alignment explanation
Indices: 1924012--1924050 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1924002 AAATTAATAA
*
1924012 ATAAATTAATTAATTAAAACT
1 ATAAAATAATTAATTAAAACT
1924033 ATAAAATAA-TAATTAAAA
1 ATAAAATAATTAATTAAAA
1924051 AGAAGTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAATAATTAATTAAAACT
Found at i:1924354 original size:2 final size:2
Alignment explanation
Indices: 1924347--1924373 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1924337 CTTAATTTTC
1924347 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1924374 CATAAAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1925006 original size:3 final size:3
Alignment explanation
Indices: 1924998--1925031 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1924988 TCATCTTTTC
1924998 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1925032 AACAAAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:1931467 original size:24 final size:24
Alignment explanation
Indices: 1931422--1931468 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1931412 ATGTAAATAT
*
1931422 AATATAAATATGAATTTGATTAAA
1 AATATAAATATGAATTTAATTAAA
* * *
1931446 AATATAAATTTTATTTTAATTAA
1 AATATAAATATGAATTTAATTAA
1931469 TTTATATTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (24 bp):
AATATAAATATGAATTTAATTAAA
Found at i:1931885 original size:18 final size:18
Alignment explanation
Indices: 1931843--1931891 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
1931833 AATTTAATAT
* *
1931843 ATTTATATAAATTTTTTA
1 ATTTAAATAAATTTTTAA
1931861 ATATTAAATAAATTTTTAA
1 AT-TTAAATAAATTTTTAA
*
1931880 ATTTAAACAAAT
1 ATTTAAATAAAT
1931892 AATTTATCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTAAATAAATTTTTAA
Found at i:1932845 original size:18 final size:18
Alignment explanation
Indices: 1932804--1932841 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1932794 TTACTTGCTC
1932804 TTTT-TTATTATAATTTA
1 TTTTATTATTATAATTTA
*
1932821 TTTTATTATTATCA-TTA
1 TTTTATTATTATAATTTA
1932838 TTTT
1 TTTT
1932842 TATTTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTATTATAATTTA
Found at i:1933893 original size:14 final size:15
Alignment explanation
Indices: 1933864--1933916 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
1933854 CGGTGAGATA
1933864 AAAAAATATTTAATT
1 AAAAAATATTTAATT
*
1933879 AAAATATATTT-ATT
1 AAAAAATATTTAATT
* **
1933893 ATAAAATAAATAATT
1 AAAAAATATTTAATT
1933908 AAAAAATAT
1 AAAAAATAT
1933917 ATTTTATTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
14 10 0.33
15 20 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAAATATTTAATT
Found at i:1933917 original size:31 final size:31
Alignment explanation
Indices: 1933861--1933920 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1933851 TGACGGTGAG
*
1933861 ATAAAAAAATATTTAATTAAAATATATTTATT
1 ATAAAAAAATAATTAA-TAAAATATATTTATT
1933893 ATAAAATAAATAATTAA-AAAATATATTT
1 ATAAAA-AAATAATTAATAAAATATATTT
1933921 TATTTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 11 0.42
32 6 0.23
33 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (31 bp):
ATAAAAAAATAATTAATAAAATATATTTATT
Found at i:1934037 original size:23 final size:24
Alignment explanation
Indices: 1934001--1934104 Score: 71
Period size: 23 Copynumber: 4.5 Consensus size: 24
1933991 TTATATTTAA
*
1934001 AAATAATTAAAA-TTATTTTGTATT
1 AAATAATTAAAATTTA-TTTATATT
1934025 AAATAA-TAAAATTTATTTATATT
1 AAATAATTAAAATTTATTTATATT
* * *
1934048 AAA-AATT-ATACTTATATTA-AAT
1 AAATAATTAAAATTTAT-TTATATT
* *
1934070 -AATTATTAAAATATTATTTGTATT
1 AAATAATTAAAAT-TTATTTATATT
1934094 AAA-AA-TAAAAT
1 AAATAATTAAAAT
1934105 AATAAAATAA
Statistics
Matches: 62, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
21 2 0.03
22 13 0.21
23 29 0.47
24 16 0.26
25 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (24 bp):
AAATAATTAAAATTTATTTATATT
Found at i:1934064 original size:18 final size:18
Alignment explanation
Indices: 1934032--1934075 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1934022 ATTAAATAAT
*
1934032 AAAATT-TATTTATATTA
1 AAAATTATACTTATATTA
1934049 AAAATTATACTTATATTA
1 AAAATTATACTTATATTA
1934067 AATAATTAT
1 AA-AATTAT
1934076 TAAAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 6 0.25
18 12 0.50
19 6 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AAAATTATACTTATATTA
Found at i:1934102 original size:6 final size:6
Alignment explanation
Indices: 1934093--1934133 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
1934083 TTATTTGTAT
* *
1934093 TAAAAA T-AAAA TAATAA -AATAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T
1934134 GAAAGTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
TAAAAA
Found at i:1934119 original size:68 final size:68
Alignment explanation
Indices: 1933991--1934121 Score: 153
Period size: 68 Copynumber: 1.9 Consensus size: 68
1933981 AAATTATTTT
* ** *
1933991 TTATATTTAAAAATAATTAAAATTATTTTGTATTAAATAATAAAATTTATTTATATTAAAAATTA
1 TTATATTTAAAAATAATTAAAATTATTTTGTATTAAATAATAAAATATATAAATAATAAAAATTA
1934056 TAC
66 TAC
*
1934059 TTATA-TTAAATAATTATTAAAA-TATTATTTGTATTAAA-AATAAAATA-ATAAAATAATAAAA
1 TTATATTTAAA-AATAATTAAAATTA-T-TTTGTATTAAATAATAAAATATAT-AAATAATAAAA
1934120 AT
62 AT
1934122 AAAAATAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
67 9 0.17
68 34 0.63
69 11 0.20
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (68 bp):
TTATATTTAAAAATAATTAAAATTATTTTGTATTAAATAATAAAATATATAAATAATAAAAATTA
TAC
Found at i:1934625 original size:22 final size:20
Alignment explanation
Indices: 1934590--1934637 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
1934580 TTAACGTTTT
* *
1934590 AAAATTTAATTAAAAAATTATA
1 AAAATTAAAATAAAAAA-TA-A
*
1934612 AAAATTAAAATAAATAATAA
1 AAAATTAAAATAAAAAATAA
1934632 AAAATT
1 AAAATT
1934638 GCTAAGTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 7 0.30
21 2 0.09
22 14 0.61
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATTAAAATAAAAAATAA
Found at i:1934726 original size:23 final size:23
Alignment explanation
Indices: 1934675--1934720 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1934665 AATTTAAAAA
*
1934675 ATAATTTTAATAAATAAAATAAT
1 ATAATTTTAAAAAATAAAATAAT
*
1934698 ATAATTTTAAAAAATATAATAAT
1 ATAATTTTAAAAAATAAAATAAT
1934721 GAAATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAATTTTAAAAAATAAAATAAT
Found at i:1934874 original size:35 final size:32
Alignment explanation
Indices: 1934834--1934901 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 32
1934824 TATATATTAT
1934834 AATAAATTATAAATAAAAATGTAAAATTTATATAA
1 AATAAATTATAAAT--AAAT-TAAAATTTATATAA
* *
1934869 AATAAATTATTAATATATTAAAATTTATATAA
1 AATAAATTATAAATAAATTAAAATTTATATAA
1934901 A
1 A
1934902 TATATAATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
32 15 0.48
33 3 0.10
35 13 0.42
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (32 bp):
AATAAATTATAAATAAATTAAAATTTATATAA
Found at i:1935427 original size:20 final size:20
Alignment explanation
Indices: 1935306--1935427 Score: 58
Period size: 20 Copynumber: 6.0 Consensus size: 20
1935296 AAATGATATA
1935306 AATATATAAATATATTAAAATT
1 AATATATAAA-ATA-TAAAATT
* *
1935328 --TATATAAAACA-AATTATT
1 AATATATAAAATATAA-AATT
* **
1935346 AATATATTAAAAT-TTATTTT
1 AATATA-TAAAATATAAAATT
* *
1935366 AATATATAATACT-TAAATTT
1 AATATATAA-AATATAAAATT
* *
1935386 AATTAAAATAAAA-ATAATATT
1 AA-T-ATATAAAATATAAAATT
1935407 AATATATAAAATATAAAATT
1 AATATATAAAATATAAAATT
1935427 A
1 A
1935428 CACAAAAAAT
Statistics
Matches: 76, Mismatches: 14, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
17 2 0.03
18 3 0.04
19 12 0.16
20 39 0.51
21 15 0.20
22 5 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATATAAAATATAAAATT
Found at i:1936690 original size:8 final size:7
Alignment explanation
Indices: 1936663--1936688 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1936653 AATATATCTT
1936663 TTTTTAA
1 TTTTTAA
1936670 TTTTTAA
1 TTTTTAA
1936677 TTTTTAA
1 TTTTTAA
1936684 TTTTT
1 TTTTT
1936689 TACTCAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:1936715 original size:18 final size:18
Alignment explanation
Indices: 1936694--1936728 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1936684 TTTTTTACTC
1936694 AAAATATTT-TTTAATTAT
1 AAAAT-TTTCTTTAATTAT
1936712 AAAATTTTCTTTAATTA
1 AAAATTTTCTTTAATTA
1936729 CTATTAAGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
AAAATTTTCTTTAATTAT
Found at i:1939114 original size:73 final size:73
Alignment explanation
Indices: 1938992--1939139 Score: 260
Period size: 73 Copynumber: 2.0 Consensus size: 73
1938982 CGTCTCGTAA
* *
1938992 AGATATTGGAACTTAACACTGACAATGAGATAGAAAAAATATGTGGAAATGCCTCATGTTTCATG
1 AGATATTGGAACTTAACACTGACAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
*
1939057 AAATTATG
66 AAATAATG
*
1939065 AGATATTGGAACTTAACACTGACAATGAGACAGGAAAAATATGTAGAAATGCCTCATGTTTCATG
1 AGATATTGGAACTTAACACTGACAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
1939130 AAATAATG
66 AAATAATG
1939138 AG
1 AG
1939140 GGAATTAACG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 71 1.00
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (73 bp):
AGATATTGGAACTTAACACTGACAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
AAATAATG
Found at i:1941572 original size:17 final size:17
Alignment explanation
Indices: 1941552--1941598 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
1941542 ATATATGTAA
1941552 AATATAAATATATATTT
1 AATATAAATATATATTT
* * *
1941569 AATATAAGTATGTGTTT
1 AATATAAATATATATTT
*
1941586 AATATTAATATAT
1 AATATAAATATAT
1941599 TTAAATTTTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
AATATAAATATATATTT
Found at i:1951892 original size:20 final size:20
Alignment explanation
Indices: 1951867--1951905 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1951857 CATTTCAAGC
1951867 ATGTATCAATACATTTACTT
1 ATGTATCAATACATTTACTT
*
1951887 ATGTATCAATATATTTACT
1 ATGTATCAATACATTTACT
1951906 ATTTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.13, G:0.05, T:0.46
Consensus pattern (20 bp):
ATGTATCAATACATTTACTT
Found at i:1957416 original size:60 final size:60
Alignment explanation
Indices: 1957312--1957536 Score: 231
Period size: 60 Copynumber: 3.8 Consensus size: 60
1957302 CTTCTAGACA
* * * *
1957312 ATTTCATTAAGTTTTGGTTTTGCCCAAGTCATTGTTTAGGTTTCTAGCTTCGTTTAAGCC
1 ATTTCATTGAGTCTTGGTTTTGCCCAAGTCATTATTTAGGTTTCTAGATTCGTTTAAGCC
* * * * * * *
1957372 ATTTAATTGAGT-TTCGGTTTCGCCCAAGACATTATTTAGCTTTCTAGTTTCATCCT-AGCC
1 ATTTCATTGAGTCTT-GGTTTTGCCCAAGTCATTATTTAGGTTTCTAGATTCGT-TTAAGCC
** * * * *
1957432 ATTTGGTTGAGTCTTGGTTTAGCCCAAGTCATTATTTAGGTTTTTAGATTTG-TCAAGACC
1 ATTTCATTGAGTCTTGGTTTTGCCCAAGTCATTATTTAGGTTTCTAGATTCGTTTAAG-CC
* *
1957492 ATTTCGTTGAGTCTTGGTTTTGCCCAAGTCATTGTTTAGGTTTCT
1 ATTTCATTGAGTCTTGGTTTTGCCCAAGTCATTATTTAGGTTTCT
1957537 GGTTTATCAA
Statistics
Matches: 136, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
59 4 0.03
60 129 0.95
61 3 0.02
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.45
Consensus pattern (60 bp):
ATTTCATTGAGTCTTGGTTTTGCCCAAGTCATTATTTAGGTTTCTAGATTCGTTTAAGCC
Found at i:1957581 original size:59 final size:59
Alignment explanation
Indices: 1957438--1957663 Score: 181
Period size: 59 Copynumber: 3.8 Consensus size: 59
1957428 AGCCATTTGG
* * * * *
1957438 TTGAGTCTTGGTTT-AGCCCAAGTCATTATTTAGGTTTTTAGATTTGTCAAGACCATTTCG
1 TTGACTCTTGGTTTCA-CCCAAGTCATTATTTAGGTTTTT-GGTTTATCAACACCATTTCA
* ** * *
1957498 TTGAGTCTTGGTTTTGCCCAAGTCATTGTTTAGGTTTCTGGTTTATCAACACCATTTCA
1 TTGACTCTTGGTTTCACCCAAGTCATTATTTAGGTTTTTGGTTTATCAACACCATTTCA
* ** * *
1957557 TTGACTTTTGGTTTCACTTAAGTCATTATTTA-GTTTTTGGTTTTATCCAA-GCCATTTTA
1 TTGACTCTTGGTTTCACCCAAGTCATTATTTAGGTTTTTGG-TTTAT-CAACACCATTTCA
* * * * * * *
1957616 TTGAGTCCTGATTTCGCCTAAGTCATT-TTGTAGGTTTTTAGTGTATCA
1 TTGACTCTTGGTTTCACCCAAGTCATTATT-TAGGTTTTTGGTTTATCA
1957664 TTTCATAGAA
Statistics
Matches: 136, Mismatches: 25, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
58 11 0.08
59 80 0.59
60 45 0.33
ACGTcount: A:0.20, C:0.15, G:0.18, T:0.46
Consensus pattern (59 bp):
TTGACTCTTGGTTTCACCCAAGTCATTATTTAGGTTTTTGGTTTATCAACACCATTTCA
Found at i:1957758 original size:59 final size:57
Alignment explanation
Indices: 1957689--1957800 Score: 152
Period size: 59 Copynumber: 1.9 Consensus size: 57
1957679 GTTTTGCCTA
* * * *
1957689 AGTCATTTTTAGATTTTTGGTTCTGTCTAGCCTATTTTTTTGAGTTTTAGTTTCATCCC
1 AGTCAATTTTAGATTTTTGGTTCTGCCAAGCC--TTTTTTTGAGCTTTAGTTTCATCCC
* *
1957748 AGTCAATTTTAGGTTTTTGGTTCTGCCAAGCCTTTTTTTGAGCTTTGGTTTCA
1 AGTCAATTTTAGATTTTTGGTTCTGCCAAGCCTTTTTTTGAGCTTTAGTTTCA
1957801 ACCACGTCAG
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 19 0.40
59 28 0.60
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.52
Consensus pattern (57 bp):
AGTCAATTTTAGATTTTTGGTTCTGCCAAGCCTTTTTTTGAGCTTTAGTTTCATCCC
Found at i:1957820 original size:57 final size:58
Alignment explanation
Indices: 1957689--1957824 Score: 159
Period size: 57 Copynumber: 2.3 Consensus size: 58
1957679 GTTTTGCCTA
* * * * * *
1957689 AGTCATTTTTAGATTTTTGGTTCTGTCTAGCCTATTTTTTTGAGTTTTAGTTTCATCCC
1 AGTCAATTTTAGGTTTTTGGTTCTGCCAAGCC-ATTTTTTTGAGCTTTAGTTTCAACCC
*
1957748 AGTCAATTTTAGGTTTTTGGTTCTGCCAAGCC-TTTTTTTGAGCTTTGGTTTCAA-CC
1 AGTCAATTTTAGGTTTTTGGTTCTGCCAAGCCATTTTTTTGAGCTTTAGTTTCAACCC
* *
1957804 ACGTCAGTTTTGGGTTTTTGG
1 A-GTCAATTTTAGGTTTTTGG
1957825 GCCCATCTAG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
56 3 0.04
57 36 0.54
59 28 0.42
ACGTcount: A:0.15, C:0.15, G:0.20, T:0.50
Consensus pattern (58 bp):
AGTCAATTTTAGGTTTTTGGTTCTGCCAAGCCATTTTTTTGAGCTTTAGTTTCAACCC
Found at i:1959051 original size:14 final size:14
Alignment explanation
Indices: 1959034--1959071 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1959024 ATACATGATT
1959034 TTTAATTTTTACAA
1 TTTAATTTTTACAA
1959048 TTTAATCTTTT-CAA
1 TTTAAT-TTTTACAA
1959062 -TTAATTTTTA
1 TTTAATTTTTA
1959072 TGGTATAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.18
13 5 0.23
14 9 0.41
15 4 0.18
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAATTTTTACAA
Found at i:1961965 original size:33 final size:32
Alignment explanation
Indices: 1961928--1962024 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 32
1961918 AAAGGTTTCG
*
1961928 CTTAGGTCACAACTTTAACTATCATGGTTTTGC
1 CTTA-GTCACATCTTTAACTATCATGGTTTTGC
* * * *
1961961 CTTAGTCAACTTTTTTAACTA--AAGGTTTCGC
1 CTTAGTC-ACATCTTTAACTATCATGGTTTTGC
* * *
1961992 CTTAGTCATATCATTGACTATCATGGTTTTGC
1 CTTAGTCACATCTTTAACTATCATGGTTTTGC
1962024 C
1 C
1962025 CTGGTCAGTC
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
30 8 0.16
31 15 0.31
32 12 0.24
33 14 0.29
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (32 bp):
CTTAGTCACATCTTTAACTATCATGGTTTTGC
Found at i:1962548 original size:33 final size:33
Alignment explanation
Indices: 1962490--1962554 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1962480 CACACCCAAA
*
1962490 TGTATCGATACAAATTGCTAAGTATCGATACAT
1 TGTATCGATACAAATTGCTAAGTATCAATACAT
**
1962523 TGTATCGATACAAATTGCTTTGTATCAATACA
1 TGTATCGATACAAATTGCTAAGTATCAATACA
1962555 CCATGAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAAATTGCTAAGTATCAATACAT
Found at i:1966437 original size:13 final size:13
Alignment explanation
Indices: 1966419--1966444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1966409 TACACCAAGT
1966419 ATGTATCGATACA
1 ATGTATCGATACA
1966432 ATGTATCGATACA
1 ATGTATCGATACA
1966445 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1966442 original size:32 final size:33
Alignment explanation
Indices: 1966401--1966464 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1966391 TAGCCAAACT
* **
1966401 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1966433 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1966465 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1966527 original size:20 final size:20
Alignment explanation
Indices: 1966499--1966536 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1966489 CTATATTTTC
1966499 AAATATGTATCGATACATAA
1 AAATATGTATCGATACATAA
*
1966519 AAATTTGTATCGATACAT
1 AAATATGTATCGATACAT
1966537 TTACACGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (20 bp):
AAATATGTATCGATACATAA
Found at i:1968696 original size:21 final size:21
Alignment explanation
Indices: 1968663--1968707 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1968653 TTGCAAGTTG
*
1968663 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1968685 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1968705 AAA
1 AAA
1968708 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1975201 original size:13 final size:13
Alignment explanation
Indices: 1975183--1975208 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1975173 TACACCAAGT
1975183 ATGTATCGATACA
1 ATGTATCGATACA
1975196 ATGTATCGATACA
1 ATGTATCGATACA
1975209 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1981114 original size:52 final size:52
Alignment explanation
Indices: 1980966--1981092 Score: 218
Period size: 52 Copynumber: 2.4 Consensus size: 52
1980956 CGAAATATGA
*
1980966 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* * *
1981018 AAATTTTCCTGTATGTATCGATACATTTCATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1981070 AAATTTGCCTGCATGTATCGATA
1 AAATTTGCCTGCATGTATCGATA
1981093 TAAAGATCAG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1981121 original size:13 final size:13
Alignment explanation
Indices: 1981103--1981127 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1981093 TAAAGATCAG
1981103 TGTATCGATACAA
1 TGTATCGATACAA
1981116 TGTATCGATACA
1 TGTATCGATACA
1981128 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1981190 original size:13 final size:13
Alignment explanation
Indices: 1981172--1981223 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
1981162 AGCTTCGTAG
1981172 CGATACATTGTAT
1 CGATACATTGTAT
1981185 CGATACAACACTTATGTAT
1 CGAT---ACA-TT--GTAT
1981204 CGATACATTGTAT
1 CGATACATTGTAT
1981217 CGATACA
1 CGATACA
1981224 ATTCGTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1982067 original size:49 final size:48
Alignment explanation
Indices: 1981974--1982349 Score: 283
Period size: 49 Copynumber: 7.9 Consensus size: 48
1981964 CAATATTAGA
** * ** * *
1981974 GCCAATACACTGATTCAAGGCCAACGATTTTGGACTTAAGGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATT-GATTTAAAGATGAAGGT
** * * *
1982023 TTCAATGTGCTGAATCAAGGCCAGCGACATTGATTTGAAAGATGACGAAGGC
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGATTT-AAAGAT---GAAGGT
* * *
1982075 GTCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATT-GATTTAAAGATGAAGGT
* * *
1982124 GCCAATGTGCTGATTCAAGGCCACCGACATTGGTCTTAAAGATG-AGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGAT-TTAAAGATGAAGGT
* *
1982172 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATT-GATTTAAAGATGAAGGT
* * * * * **
1982215 GCCAGTGTGCTGATTCAAGGCTAGCAACATTGGTCTTAAAGACAAAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATTGAT-TTAAAGATGAAGGT
* *
1982264 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGT
1 GCCAATATGCTGATTCAAGGCCAGCGACATT-GATTTAAAGATGAAGGT
*
1982307 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGATTTAGAAGA
1 GCCAATATGCTGATTCAAGGCCAGCGACATT-GATTTA-AAGA
1982350 AGACGCCACC
Statistics
Matches: 260, Mismatches: 46, Indels: 43
0.74 0.13 0.12
Matches are distributed among these distances:
42 1 0.00
43 71 0.27
44 1 0.00
45 1 0.00
47 1 0.00
48 40 0.15
49 102 0.39
50 1 0.00
52 38 0.15
53 4 0.02
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (48 bp):
GCCAATATGCTGATTCAAGGCCAGCGACATTGATTTAAAGATGAAGGT
Found at i:1982229 original size:43 final size:44
Alignment explanation
Indices: 1982077--1982340 Score: 280
Period size: 43 Copynumber: 5.7 Consensus size: 44
1982067 ACGAAGGCGT
* *
1982077 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTT--A-A--AAGGTGC
* *
1982126 CAATGTGCTGATTCAAGGCCACCGACATTGGTCTTAAAGATGAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A--AGGTGC
* *
1982174 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGGTGC
* * * *
1982217 CAGTGTGCTGATTCAAGGCTAGCAACATTGGTCTTAAAGACAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTT----A-AAAGGTGC
* *
1982266 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGGTGC
1982309 CAATGTGCTGATTCAAGGCCAGCGACATTGGA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGA
1982341 TTTAGAAGAA
Statistics
Matches: 185, Mismatches: 22, Indels: 22
0.81 0.10 0.10
Matches are distributed among these distances:
43 73 0.39
45 1 0.01
46 3 0.02
47 1 0.01
48 39 0.21
49 68 0.37
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.25
Consensus pattern (44 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAGGTGC
Found at i:1982300 original size:92 final size:91
Alignment explanation
Indices: 1982025--1982339 Score: 425
Period size: 92 Copynumber: 3.3 Consensus size: 91
1982015 ATGAAGGTTT
* * * *
1982025 CAATGTGCTGAATCAAGGCCAGCGACATTGAT-TTGAAAGATGACGAAGGCGTCAATATGCTGAT
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AAAGA--A--AAGGTGCCAATATGCTGAT
1982089 TCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGC
61 TCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
* **
1982126 CAATGTGCTGATTCAAGGCCACCGACATTGGTCTTAAAGATGAGGTGCCAATATGCTGATTCAAG
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAGGTGCCAATATGCTGATTCAAG
1982191 GCCAGCGATATTGGACTTAAAGGTGC
66 GCCAGCGATATTGGACTTAAAGGTGC
* * *
1982217 CAGTGTGCTGATTCAAGGCTAGCAACATTGGTCTTAAAGACAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-AAAGGTGCCAATATGCTGATTCAA
1982282 GGCCAGCGATATTGGACTTAAAGGTGC
65 GGCCAGCGATATTGGACTTAAAGGTGC
1982309 CAATGTGCTGATTCAAGGCCAGCGACATTGG
1 CAATGTGCTGATTCAAGGCCAGCGACATTGG
1982340 ATTTAGAAGA
Statistics
Matches: 196, Mismatches: 16, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
91 43 0.22
92 77 0.39
93 1 0.01
97 39 0.20
101 34 0.17
102 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (91 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAGGTGCCAATATGCTGATTCAAG
GCCAGCGATATTGGACTTAAAGGTGC
Found at i:1982378 original size:27 final size:28
Alignment explanation
Indices: 1982351--1982405 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1982341 TTTAGAAGAA
*
1982351 GACGCCACCAACTTGTGTGCTTTTGAAG
1 GACGCCACCAACTTGTGGGCTTTTGAAG
** *
1982379 GTTGCCACTAACTTGTGGGCTTTTGAA
1 GACGCCACCAACTTGTGGGCTTTTGAA
1982406 AATGGTGCCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (28 bp):
GACGCCACCAACTTGTGGGCTTTTGAAG
Found at i:1982459 original size:34 final size:34
Alignment explanation
Indices: 1982421--1982517 Score: 126
Period size: 35 Copynumber: 2.9 Consensus size: 34
1982411 TGCCATTGAC
*
1982421 TTGTGGGCTTAAAAGGAAAAAGAGTGCCACAGAG
1 TTGTGGGCTTAAAAAGAAAAAGAGTGCCACAGAG
* *
1982455 TTGTGGGCTTACAAAAGAAAATGAGTGCCACGGAG
1 TTGTGGGCTTA-AAAAGAAAAAGAGTGCCACAGAG
*
1982490 TTGTGGACTTAAAAA-AGAAAAG-GTGCCA
1 TTGTGGGCTTAAAAAGA-AAAAGAGTGCCA
1982518 ATATGCTGAC
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.12
34 19 0.34
35 30 0.54
ACGTcount: A:0.38, C:0.12, G:0.30, T:0.20
Consensus pattern (34 bp):
TTGTGGGCTTAAAAAGAAAAAGAGTGCCACAGAG
Found at i:1982482 original size:35 final size:33
Alignment explanation
Indices: 1982403--1982517 Score: 124
Period size: 35 Copynumber: 3.4 Consensus size: 33
1982393 GTGGGCTTTT
** * *
1982403 GAAAATGGTGCCATTGACTTGTGGGCTTAAAAG
1 GAAAATGGTGCCACAGAGTTGTGGGCTTAAAAA
*
1982436 GAAAAAGAGTGCCACAGAGTTGTGGGCTTACAAAA
1 GAAAATG-GTGCCACAGAGTTGTGGGCTTA-AAAA
* *
1982471 GAAAATGAGTGCCACGGAGTTGTGGACTTAAAAAA
1 GAAAATG-GTGCCACAGAGTTGTGGGCTT-AAAAA
1982506 GAAAA-GGTGCCA
1 GAAAATGGTGCCA
1982518 ATATGCTGAC
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
33 12 0.17
34 20 0.28
35 38 0.54
36 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.20
Consensus pattern (33 bp):
GAAAATGGTGCCACAGAGTTGTGGGCTTAAAAA
Found at i:1982599 original size:32 final size:34
Alignment explanation
Indices: 1982551--1982637 Score: 106
Period size: 32 Copynumber: 2.6 Consensus size: 34
1982541 TATTGGGCTT
* *
1982551 AAAGGTGTCACAGAGTTGTGGACTTAAAAA-G-A
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGGAA
* *
1982583 AAAGGTGCCACGGAGTTATGGGCTTAAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAAGGAA
* *
1982617 AAAGATGCCACGGACTTGTGG
1 AAAGGTGCCACGGAGTTGTGG
1982638 GCTTTTGAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
32 26 0.57
33 1 0.02
34 19 0.41
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.20
Consensus pattern (34 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAAGGAA
Found at i:1982626 original size:34 final size:32
Alignment explanation
Indices: 1982563--1982641 Score: 104
Period size: 34 Copynumber: 2.4 Consensus size: 32
1982553 AGGTGTCACA
* *
1982563 GAGTTGTGGACTTAAAAAGAAAAGGTGCCACG
1 GAGTTGTGGGCTTAAAAAGAAAAGATGCCACG
*
1982595 GAGTTATGGGCTTAAAAAGGAAAAAGATGCCACG
1 GAGTTGTGGGCTTAAAAA-G-AAAAGATGCCACG
*
1982629 GACTTGTGGGCTT
1 GAGTTGTGGGCTT
1982642 TTGAAGGTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 16 0.40
33 1 0.03
34 23 0.57
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.22
Consensus pattern (32 bp):
GAGTTGTGGGCTTAAAAAGAAAAGATGCCACG
Found at i:1982663 original size:28 final size:28
Alignment explanation
Indices: 1982620--1982705 Score: 111
Period size: 28 Copynumber: 3.0 Consensus size: 28
1982610 AAAGGAAAAA
*
1982620 GATGCCACGGACTTGTGGGCTTTTGAAG
1 GATGCCACTGACTTGTGGGCTTTTGAAG
* * *
1982648 GTTGCCACTGATTTGTGGGC-TTTGAAAAA
1 GATGCCACTGACTTGTGGGCTTTTG--AAG
1982677 GATGCCACTGACTTGTGGGCTTTTGAAG
1 GATGCCACTGACTTGTGGGCTTTTGAAG
1982705 G
1 G
1982706 GTGAGGAATG
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 4 0.08
28 20 0.42
29 20 0.42
30 4 0.08
ACGTcount: A:0.20, C:0.16, G:0.33, T:0.31
Consensus pattern (28 bp):
GATGCCACTGACTTGTGGGCTTTTGAAG
Found at i:1982692 original size:29 final size:29
Alignment explanation
Indices: 1982614--1982699 Score: 113
Period size: 29 Copynumber: 3.0 Consensus size: 29
1982604 GCTTAAAAAG
*
1982614 GAAAAAGATGCCACGGACTTGTGGGCTTTT
1 GAAAAAGATGCCACTGACTTGTGGGC-TTT
* * *
1982644 G--AAGGTTGCCACTGATTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
1982671 GAAAAAGATGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTT
1982700 TGAAGGGTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 4 0.09
28 19 0.40
29 23 0.49
30 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (29 bp):
GAAAAAGATGCCACTGACTTGTGGGCTTT
Found at i:1984142 original size:16 final size:16
Alignment explanation
Indices: 1984123--1984158 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
1984113 ATCCGGACCC
1984123 TTTTTG-TTGTTGTTT
1 TTTTTGTTTGTTGTTT
1984138 TTTTTGTTTGTTGTTT
1 TTTTTGTTTGTTGTTT
1984154 TTTTT
1 TTTTT
1984159 TTCTTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (16 bp):
TTTTTGTTTGTTGTTT
Found at i:1984149 original size:19 final size:18
Alignment explanation
Indices: 1984125--1984181 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
1984115 CCGGACCCTT
*
1984125 TTTGTTGTTGTTTTTTTTG
1 TTTGTTGTT-TTTTTTTTC
1984144 TTTGTTGTTTTTTTTTTC
1 TTTGTTGTTTTTTTTTTC
*
1984162 TTTTTTGTTTTTTTTCTTC
1 TTTGTTGTTTTTTTT-TTC
1984181 T
1 T
1984182 CTTTTTTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 22 0.63
19 13 0.37
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.82
Consensus pattern (18 bp):
TTTGTTGTTTTTTTTTTC
Found at i:1984172 original size:16 final size:17
Alignment explanation
Indices: 1984132--1984179 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
1984122 CTTTTTGTTG
*
1984132 TTGTTTTTTTTGTTTGT
1 TTGTTTTTTTTCTTTGT
*
1984149 TGTTTTTTTTTTCTTT-T
1 T-TGTTTTTTTTCTTTGT
1984166 TTGTTTTTTTTCTT
1 TTGTTTTTTTTCTT
1984180 CTCTTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 12 0.44
17 3 0.11
18 12 0.44
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.85
Consensus pattern (17 bp):
TTGTTTTTTTTCTTTGT
Found at i:1984192 original size:21 final size:20
Alignment explanation
Indices: 1984123--1984192 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 20
1984113 ATCCGGACCC
*
1984123 TTTTTGTTGTTGTTTTT-T-T
1 TTTTTGTT-TTTTTTTTCTCT
* *
1984142 TGTTTGTTGTTTTTTTTTTCT
1 TTTTTGTT-TTTTTTTTCTCT
1984163 TTTTTGTTTTTTTTCTTCTCT
1 TTTTTGTTTTTTTT-TTCTCT
1984184 TTTTTGTTT
1 TTTTTGTTT
1984193 GGAGGACACC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.34
20 7 0.16
21 22 0.50
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (20 bp):
TTTTTGTTTTTTTTTTCTCT
Found at i:1993674 original size:21 final size:21
Alignment explanation
Indices: 1993651--1993728 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
1993641 ATTTTTATCC
1993651 AAATGTATCGATACA-TTATA
1 AAATGTATCGATACATTTATA
*
1993671 CAAATGTATCGATACATTTGTA
1 -AAATGTATCGATACATTTATA
* * *
1993693 GAATGTATCAATACATTTGTA
1 AAATGTATCGATACATTTATA
*
1993714 GAATGTATCGATACA
1 AAATGTATCGATACA
1993729 AGGTCCCAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
21 48 0.92
22 4 0.08
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (21 bp):
AAATGTATCGATACATTTATA
Found at i:1993810 original size:19 final size:18
Alignment explanation
Indices: 1993786--1993848 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1993776 AAACAGAAAA
1993786 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1993805 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1993818 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1993837 TGTATCGATACA
1 TGTATCGATACA
1993849 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1993823 original size:13 final size:13
Alignment explanation
Indices: 1993805--1993829 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1993795 ACATAAGTGT
1993805 TGTATCGATACAA
1 TGTATCGATACAA
1993818 TGTATCGATACA
1 TGTATCGATACA
1993830 TAAGTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1993825 original size:32 final size:32
Alignment explanation
Indices: 1993784--1993856 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1993774 ACAAACAGAA
1993784 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
1993816 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
1993848 AATGTATCG
1 AATGTATCG
1993857 CTACGAAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:1993899 original size:21 final size:21
Alignment explanation
Indices: 1993873--1993915 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1993863 AGCTACTGCG
1993873 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
1993894 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
1993915 A
1 A
1993916 TATTGATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.28
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:1996342 original size:51 final size:51
Alignment explanation
Indices: 1996286--1996524 Score: 266
Period size: 52 Copynumber: 4.6 Consensus size: 51
1996276 TTAAGTTTCT
* * *
1996286 CAATTTTTCATAATTGGGGATACTCCAACCCTGGTTTTA-TTTCTAAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCTGATTTTATTTTC-AAAACAC
* * * *
1996337 TAATTTTCCACAATCGGGGATACTCCAACCCCGATTTTATTTTCGAAACAC
1 CAATTTTCCATAATCGGGGATACTCCAACCCTGATTTTATTTTCAAAACAC
* *
1996388 CAATTTTCCTTTAATCGAGGATACTCCAA-CCTCGATTTTATTTTCAAAACAC
1 CAATTTTCC-ATAATCGGGGATACTCCAACCCT-GATTTTATTTTCAAAACAC
* * * *
1996440 CAATTTTCCTTTAATCGGGGATACTCCAACTCTAATTTTATTTCCAAAAACAC
1 CAATTTTCC-ATAATCGGGGATACTCCAACCCTGATTTTATTTTC-AAAACAC
* * *
1996493 TAATTTTTTCACAATCGGGGATACTCCAACCC
1 CAA-TTTTCCATAATCGGGGATACTCCAACCC
1996525 CGTTAATCAT
Statistics
Matches: 160, Mismatches: 22, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
51 49 0.31
52 76 0.47
53 30 0.19
54 5 0.03
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (51 bp):
CAATTTTCCATAATCGGGGATACTCCAACCCTGATTTTATTTTCAAAACAC
Found at i:1996578 original size:28 final size:29
Alignment explanation
Indices: 1996509--1996580 Score: 105
Period size: 27 Copynumber: 2.6 Consensus size: 29
1996499 TTTCACAATC
1996509 GGGGATACTCCAACCCCGTTAATCATCGA
1 GGGGATACTCCAACCCCGTTAATCATCGA
**
1996538 --GGATACTCCAACCCCGTT-ATTGTCGA
1 GGGGATACTCCAACCCCGTTAATCATCGA
1996564 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
1996581 TGACTTTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 6 0.15
27 18 0.46
28 15 0.38
ACGTcount: A:0.25, C:0.33, G:0.21, T:0.21
Consensus pattern (29 bp):
GGGGATACTCCAACCCCGTTAATCATCGA
Found at i:1996624 original size:80 final size:79
Alignment explanation
Indices: 1996533--1996821 Score: 402
Period size: 79 Copynumber: 3.6 Consensus size: 79
1996523 CCCGTTAATC
* * *
1996533 ATCGAGGATACTCCAACCCCGTTATTGTCGAGGGGATACTCCAACCCCTGACTTTATTCCTAAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC-GGCTTTATTCCTAAAA
1996598 TATTGATTTCTCATA
65 TATTGATTTCTCATA
* *
1996613 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAGCCCCGGCTTTATTTCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
*
1996678 ATTAATTTCTCATA
66 ATTGATTTCTCATA
* * *
1996692 ATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTTTTATTTCC--AAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTA-TTCCTAAAA
* * *
1996755 TCATCGATTTTTTTCACA
65 T-ATTGA--TTTCTCATA
*
1996773 ATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
1996822 TTACCATCCC
Statistics
Matches: 187, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
78 4 0.02
79 82 0.44
80 48 0.26
81 53 0.28
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
ATTGATTTCTCATA
Found at i:1996836 original size:159 final size:158
Alignment explanation
Indices: 1996533--1996850 Score: 396
Period size: 160 Copynumber: 2.0 Consensus size: 158
1996523 CCCGTTAATC
*
1996533 ATCGAGGATACTCCAACCCCGTTATTGTCGAGGGGATACTCCAACCCCTGACTTTATTCCTAAAA
1 ATCGAGGATACTCCAACCCCGTTATTGCCGAGGGGATACTCCAACCCCTGACTTTATTCC-AAAA
* * * *
1996598 TATTGATTTCTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAGCCCCGG
65 TATCGATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGG
* * *
1996663 CTTTATTTCTAAAATATT-AATTTCTCATA
130 C-TTAATCCCAAAATATTAAATTTCTCATA
* **
1996692 ATCGGGGATACTCCAACCCCGTTATCT-CCGAGGGGATACTCCAACCCC-GGTTTTATTTCC-AA
1 ATCGAGGATACTCCAACCCCGTTAT-TGCCGAGGGGATACTCCAACCCCTGACTTTA-TTCCAAA
*
1996754 ATCATCGATTTTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACC
64 AT-ATCGA--TTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACC
*
1996819 CC-G-TTACCATCCCAAAATATTAAATTTTTCAT
126 CCGGCTTA--ATCCCAAAATATTAAATTTCTCAT
1996851 CGGAAAATAT
Statistics
Matches: 138, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
157 7 0.05
158 9 0.07
159 59 0.43
160 63 0.46
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.31
Consensus pattern (158 bp):
ATCGAGGATACTCCAACCCCGTTATTGCCGAGGGGATACTCCAACCCCTGACTTTATTCCAAAAT
ATCGATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGGC
TTAATCCCAAAATATTAAATTTCTCATA
Found at i:1996869 original size:160 final size:156
Alignment explanation
Indices: 1996539--1996841 Score: 373
Period size: 159 Copynumber: 1.9 Consensus size: 156
1996529 AATCATCGAG
* *
1996539 GATACTCCAACCCCGTTATTGTCGAGGGGATACTCCAACCCCTGACTTTATTCCTAAAATATTGA
1 GATACTCCAACCCCGTTATTGCCGAGGGGATACTCCAACCCCTGACTTTATTCC-AAAATATCGA
* * * *
1996604 TTTCTCATAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAGCCCCGGCTTTAT
65 TTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGGC-TTAA
* * *
1996669 TTCTAAAATATTAATTTCTCATAATCGGG
129 TCCCAAAATATTAATTTCT-ATAATCGGA
**
1996698 GATACTCCAACCCCGTTATCT-CCGAGGGGATACTCCAACCCC-GGTTTTATTTCC-AAATCATC
1 GATACTCCAACCCCGTTAT-TGCCGAGGGGATACTCCAACCCCTGACTTTA-TTCCAAAAT-ATC
*
1996760 GATTTTTTTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCC-G-T
63 GA--TTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGGCT
1996823 TACCATCCCAAAATATTAA
126 TA--ATCCCAAAATATTAA
1996842 ATTTTTCATC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
157 7 0.06
158 9 0.07
159 56 0.44
160 54 0.43
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (156 bp):
GATACTCCAACCCCGTTATTGCCGAGGGGATACTCCAACCCCTGACTTTATTCCAAAATATCGAT
TTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGGCTTAATC
CCAAAATATTAATTTCTATAATCGGA
Found at i:2009166 original size:6 final size:6
Alignment explanation
Indices: 2009155--2009237 Score: 104
Period size: 6 Copynumber: 14.5 Consensus size: 6
2009145 CTCTTCTAAA
* *
2009155 AAAAAC AAAAAC AAAAAC AAAAGC AAAAA- AAGAAGC AAAAA- AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AA-AAAC AAAAAC AAAAAC
2009202 AAAAAC AAAAA- AAAAAC AAAAA- AAAAAC -AAAAC AAA
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAA
2009238 GAAAAAGAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
5 22 0.33
6 43 0.64
7 2 0.03
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:2009176 original size:11 final size:11
Alignment explanation
Indices: 2009155--2009237 Score: 96
Period size: 11 Copynumber: 7.3 Consensus size: 11
2009145 CTCTTCTAAA
2009155 AAAAACAAAAAC
1 AAAAAC-AAAAC
2009167 AAAAACAAAAGC
1 AAAAACAAAA-C
2009179 AAAAA-AAGAAGC
1 AAAAACAA-AA-C
*
2009191 AAAAAAAAAAC
1 AAAAACAAAAC
*
2009202 AAAAACAAAAA
1 AAAAACAAAAC
*
2009213 AAAAACAAAAA
1 AAAAACAAAAC
2009224 AAAAACAAAAC
1 AAAAACAAAAC
2009235 AAA
1 AAA
2009238 GAAAAAGAGA
Statistics
Matches: 65, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
11 40 0.62
12 23 0.35
13 2 0.03
ACGTcount: A:0.84, C:0.12, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:2009252 original size:28 final size:27
Alignment explanation
Indices: 2009152--2009258 Score: 85
Period size: 28 Copynumber: 3.8 Consensus size: 27
2009142 ATTCTCTTCT
* *
2009152 AAAAAAAACA-AAAACAAAAACA-AAAGC
1 AAAAAAAAGAGAAAA-AAAAA-ACAAAAC
2009179 AAAA-AAAGAAGCAAAAAAAAAACAAAAAC
1 AAAAAAAAG-AG-AAAAAAAAAAC-AAAAC
* *
2009208 AAAAAAAAAACAAAAAAAAAACAAAAC
1 AAAAAAAAGAGAAAAAAAAAACAAAAC
2009235 AAAGAAAAAGAGAGAAAAGAAAAA
1 AAA-AAAAAGAGA-AAAA-AAAAA
2009259 GAACATGCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
26 3 0.05
27 14 0.22
28 23 0.35
29 17 0.26
30 8 0.12
ACGTcount: A:0.83, C:0.09, G:0.07, T:0.00
Consensus pattern (27 bp):
AAAAAAAAGAGAAAAAAAAAACAAAAC
Found at i:2009252 original size:29 final size:28
Alignment explanation
Indices: 2009162--2009258 Score: 99
Period size: 30 Copynumber: 3.4 Consensus size: 28
2009152 AAAAAAAACA
2009162 AAAACAAAAACAAAAGC-AAAAAAAGAAG
1 AAAACAAAAACAAAA-CAAAAAAAAGAAG
* *
2009190 CAAAAAAAAAACAAAAACAAAAAAAA-AAC
1 -AAAACAAAAAC-AAAACAAAAAAAAGAAG
*
2009219 AAAAAAAAAACAAAACAAAGAAAAAGAGAG
1 AAAACAAAAACAAAACAAA-AAAAAGA-AG
*
2009249 AAAAGAAAAA
1 AAAACAAAAA
2009259 GAACATGCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
27 8 0.14
28 16 0.27
29 14 0.24
30 21 0.36
ACGTcount: A:0.82, C:0.09, G:0.08, T:0.00
Consensus pattern (28 bp):
AAAACAAAAACAAAACAAAAAAAAGAAG
Found at i:2009258 original size:1 final size:1
Alignment explanation
Indices: 2009152--2009243 Score: 58
Period size: 1 Copynumber: 92.0 Consensus size: 1
2009142 ATTCTCTTCT
* * * ** * ** * *
2009152 AAAAAAAACAAAAACAAAAACAAAAGCAAAAAAAGAAGCAAAAAAAAAACAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
2009217 ACAAAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
2009244 GAGAGAAAAG
Statistics
Matches: 65, Mismatches: 26, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:2010398 original size:55 final size:55
Alignment explanation
Indices: 2010314--2010564 Score: 360
Period size: 55 Copynumber: 4.5 Consensus size: 55
2010304 CCTCCTTTCG
* * *
2010314 CCTTTTTGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
2010369 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCCCACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
2010430 -CTTCCTAGTCCTCAAATAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTT-TTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
2010485 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAATCCCACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
2010540 CCTTTTAGTCCTCAAAGAGCAGGAC
1 CCTTTTAGTCCTCAAAGAGCAGGAC
2010565 ACTCTCTCTT
Statistics
Matches: 176, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
55 123 0.70
56 3 0.02
60 3 0.02
61 47 0.27
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (55 bp):
CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:2010578 original size:116 final size:113
Alignment explanation
Indices: 2010314--2010563 Score: 350
Period size: 116 Copynumber: 2.2 Consensus size: 113
2010304 CCTCCTTTCG
*
2010314 CCTTTTTGTCCTCAAAGAGCAGGAT-GCCTTTT-AAAGCCCACACAAGCTGGTGGCACCTTTTAG
1 CCTTTTAGTCCTCAAAGAGCAGGATCGCCTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAG
*
2010377 TCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCCCACAAGTTGGTGGCA
66 TCCTCAAAGAGCAGGACG----C-CCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
2010430 -CTTCCTAGTCCTCAAATAGCAGGA-CGCC-TTTCAAAGCCCACACAAGTTGGTGGCACCTTTTA
1 CCTT-TTAGTCCTCAAAGAGCAGGATCGCCTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTA
*
2010492 GTCCTCAAAGAGCAGGACG-CCTTTTAAATCCCACACAAGTTGGTGGCA
65 GTCCTCAAAGAGCAGGACGCCCTTTTAAAGCCCACACAAGTTGGTGGCA
2010540 CCTTTTAGTCCTCAAAGAGCAGGA
1 CCTTTTAGTCCTCAAAGAGCAGGA
2010564 CACTCTCTCT
Statistics
Matches: 122, Mismatches: 8, Indels: 14
0.85 0.06 0.10
Matches are distributed among these distances:
110 45 0.37
111 3 0.02
115 6 0.05
116 68 0.56
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (113 bp):
CCTTTTAGTCCTCAAAGAGCAGGATCGCCTTTTCAAAGCCCACACAAGCTGGTGGCACCTTTTAG
TCCTCAAAGAGCAGGACGCCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:2010670 original size:94 final size:94
Alignment explanation
Indices: 2010483--2010656 Score: 269
Period size: 94 Copynumber: 1.9 Consensus size: 94
2010473 AAGTTGGTGG
* * * ** * * *
2010483 CACCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTAAATCCCACACAAGTTGGTGGCACCTTTTAG
1 CACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAACCCCACACAAGCCGATGGAAACTTTTAG
2010548 TCCTCAAAGAGCAGGACACTCTCTCTTTT
66 TCCTCAAAGAGCAGGACACTCTCTCTTTT
2010577 CACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAACCCCACACAAGCCGAT-GAAACTTTTAG
1 CACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAACCCCACACAAGCCGATGGAAACTTTTAG
2010641 TCCTCAAAGAGCAGGA
66 TCCTCAAAGAGCAGGA
2010657 TGCCTCCTCC
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 25 0.35
94 47 0.65
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (94 bp):
CACCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAACCCCACACAAGCCGATGGAAACTTTTAG
TCCTCAAAGAGCAGGACACTCTCTCTTTT
Found at i:2010914 original size:43 final size:43
Alignment explanation
Indices: 2010817--2010980 Score: 144
Period size: 42 Copynumber: 3.8 Consensus size: 43
2010807 GCACTTTGTA
* *
2010817 GTCCTCAAAGAGCA-AGACTCATTTTATTTTCCTCTTTCTTTT
1 GTCCTCAAAGAGCAGAGACACATTTCATTTTCCTCTTTCTTTT
* *
2010859 GTCCTCAAAGAGCAGA-ACACATTTCGTTTT-CTTTTTCTCCTTT
1 GTCCTCAAAGAGCAGAGACACATTTCATTTTCCTCTTTCT--TTT
* * *
2010902 GTCCTCAAAGAGCAG-GACGC-TCTT-AATTTCCTTCTTTTCCCTTCTA
1 GTCCTCAAAGAGCAGAGACACAT-TTCATTTTCC-TC-TTT--CTT-TT
2010948 GTCCTCAAAGAGCA-AGACACATTTCATTTTCCT
1 GTCCTCAAAGAGCAGAGACACATTTCATTTTCCT
2010981 TTTTTTCTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 24
0.73 0.08 0.18
Matches are distributed among these distances:
41 7 0.07
42 29 0.30
43 25 0.26
44 1 0.01
45 4 0.04
46 22 0.23
47 9 0.09
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.39
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGAGACACATTTCATTTTCCTCTTTCTTTT
Found at i:2011802 original size:19 final size:19
Alignment explanation
Indices: 2011778--2011827 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
2011768 AAATAGAAAA
2011778 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
2011797 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
*
2011816 TTTATCGATACA
1 TGTATCGATACA
2011828 ATATATCGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:2011878 original size:21 final size:21
Alignment explanation
Indices: 2011852--2011893 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2011842 AGCTACTGCC
*
2011852 AAGGAAATGTATCGATACATT
1 AAGGAAATATATCGATACATT
2011873 AAGGAAATATATCGATACATT
1 AAGGAAATATATCGATACATT
2011894 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (21 bp):
AAGGAAATATATCGATACATT
Found at i:2014336 original size:51 final size:51
Alignment explanation
Indices: 2014271--2014510 Score: 320
Period size: 52 Copynumber: 4.6 Consensus size: 51
2014261 TAAGTTTCTC
*
2014271 AATTTTTCATAATCGGGGATACTCCAACCTCGATTTTA-TTTCTAAAACACT
1 AATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACT
* *
2014322 AATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACT
1 AATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACT
* * * * *
2014373 AATTTTCCTTTAATCCGGGATACTCCAACCCCGGTTTTATTTTCAAAACACC
1 AATTTTTC-ATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACT
* * *
2014425 AATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACT
1 AATTTTTC-ATAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACT
*
2014478 AATTTTTTCACAATCGGGGATACTCCAACCCCG
1 AA-TTTTTCATAATCGGGGATACTCCAACCCCG
2014511 TTAATCATCG
Statistics
Matches: 169, Mismatches: 16, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
51 50 0.30
52 84 0.50
53 30 0.18
54 5 0.03
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.35
Consensus pattern (51 bp):
AATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACT
Found at i:2014579 original size:79 final size:77
Alignment explanation
Indices: 2014489--2014776 Score: 339
Period size: 79 Copynumber: 3.6 Consensus size: 77
2014479 ATTTTTTCAC
*
2014489 AATCGGGGATACTCCAACCCCGTTAATCATCGA-GGATACTCCAACCCCTGACTTTATTCCTAAA
1 AATCGGGGATACTCCAACCCCGTT-ATC-TCGAGGGATACTCCAACCCC-GGCTTTATTCCTAAA
2014553 ATATTGATTTCTCAT
63 ATATTGATTTCTCAT
* * *
2014568 AATCGGGGATACTCTAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTTCTAAAA
1 AATCGGGGATACTCCAACCCCGTTA-TCTCGA-GGGATACTCCAACCCCGGCTTTATTCCTAAAA
*
2014633 TATTAATTTCTCAT
64 TATTGATTTCTCAT
*
2014647 AATCGGGGATACTCCAACCCCGTTATCTCCGAGGGGATACTCCAACCCCGGTTTTATTTCC--AA
1 AATCGGGGATACTCCAACCCCGTTATCT-CGA-GGGATACTCCAACCCCGGCTTTA-TTCCTAAA
* * *
2014710 ATCATCGATTTTTTTCAC
63 AT-ATTGA--TTTCTCAT
* *
2014728 AATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCC
1 AATCGGGGATACTCCAACCCCGTTA-TCTCGA-GGGATACTCCAACCCC
2014777 ATTACCATCT
Statistics
Matches: 185, Mismatches: 15, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
78 11 0.06
79 104 0.56
80 18 0.10
81 50 0.27
82 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (77 bp):
AATCGGGGATACTCCAACCCCGTTATCTCGAGGGATACTCCAACCCCGGCTTTATTCCTAAAATA
TTGATTTCTCAT
Found at i:2014749 original size:160 final size:159
Alignment explanation
Indices: 2014440--2014776 Score: 425
Period size: 160 Copynumber: 2.1 Consensus size: 159
2014430 TCCTTTAATC
* * *
2014440 GGGGATACTCCAACTCCGATTTTATTTTCAAAAACACTAATTTTTTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGACTTTATTTTCAAAAACACTAATTTTCTCACAATCGGGGATACTCCA
* *
2014505 ACCCCGTTAATCATCGAGGATACTCCAACCCCTGACTTTATTCCTAAAATATTGATTTCTCATAA
66 ACCCCGTTAATCATCGAGGATACTCCAACCCCTGACTTTATTCC-AAAATATCGATTTCTCACAA
* *
2014570 TCGGGGATACTCTAACCCCGTTATTTTCGA
130 TCGGGGATACTCCAACCCCGTTATTTTCAA
* * * * *
2014600 GGGGATACTCCAACCCCGGCTTTA-TTTCTAAAATATTAA-TTTCTCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGACTTTATTTTCAAAAACACTAATTTTCTCACAATCGGGGATACTCCA
** *
2014663 ACCCCGTT-ATC-TCCGAGGGGATACTCCAACCCC-GGTTTTATTTCC-AAATCATCGATTTTTT
66 ACCCCGTTAATCAT-CGA--GGATACTCCAACCCCTGACTTTA-TTCCAAAAT-ATCGA--TTTC
2014724 TCACAATCGGGGATACTCCAACCCCGTTATTTTCAA
124 TCACAATCGGGGATACTCCAACCCCGTTATTTTCAA
2014760 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
2014777 ATTACCATCT
Statistics
Matches: 155, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
156 1 0.01
157 10 0.06
158 39 0.25
159 31 0.20
160 74 0.48
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (159 bp):
GGGGATACTCCAACCCCGACTTTATTTTCAAAAACACTAATTTTCTCACAATCGGGGATACTCCA
ACCCCGTTAATCATCGAGGATACTCCAACCCCTGACTTTATTCCAAAATATCGATTTCTCACAAT
CGGGGATACTCCAACCCCGTTATTTTCAA
Found at i:2014804 original size:81 final size:79
Alignment explanation
Indices: 2014440--2014806 Score: 327
Period size: 79 Copynumber: 4.6 Consensus size: 79
2014430 TCCTTTAATC
* * * * *
2014440 GGGGATACTCCAACTCCGATTTTATTTTCAAAAACACTAATTTTTTCACAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCG-TTCTA-TTTCCAAAATATTAATTTTTTCACAATCGGGGATACTCCA
* *
2014505 ACCCCGTTA--ATCATC
64 ACCCCGTTATTTTCA-A
* * * *
2014520 GAGGATACTCCAACCCCTGACTT-TA-TTCCTAAAATATTGA-TTTCTCATAATCGGGGATACTC
1 GGGGATACTCCAACCCC-G--TTCTATTTCC-AAAATATTAATTTTTTCACAATCGGGGATACTC
* *
2014582 TAACCCCGTTATTTTCGA
62 CAACCCCGTTATTTTCAA
* * *
2014600 GGGGATACTCCAACCCCGGCTT-TATTTCTAAAATATTAA-TTTCTCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCC-G-TTCTATTTCCAAAATATTAATTTTTTCACAATCGGGGATACTCCA
* * *
2014663 ACCCCGTTATCTCCGA
64 ACCCCGTTATTTTCAA
* * *
2014679 GGGGATACTCCAACCCCGGTTTTATTTCC-AAATCATCGATTTTTTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACCCC-GTTCTATTTCCAAAAT-AT-TAATTTTTTCACAATCGGGGATACTCC
2014743 AACCCCGTTATTTTCAA
63 AACCCCGTTATTTTCAA
* * * *
2014760 GGGGATACTCCAACCCCATTACCATCTCCAAAATATTAAATTTTTCA
1 GGGGATACTCCAACCCCGTT-CTATTTCCAAAATATTAATTTTTTCA
2014807 TCGGAAAATA
Statistics
Matches: 240, Mismatches: 35, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
78 6 0.03
79 111 0.46
80 53 0.22
81 64 0.27
82 6 0.03
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGTTCTATTTCCAAAATATTAATTTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCAA
Found at i:2020396 original size:32 final size:32
Alignment explanation
Indices: 2020359--2020435 Score: 154
Period size: 32 Copynumber: 2.4 Consensus size: 32
2020349 CATTTCATAG
2020359 TGTATCGATACATATGGGCAAATTTGCCTGTA
1 TGTATCGATACATATGGGCAAATTTGCCTGTA
2020391 TGTATCGATACATATGGGCAAATTTGCCTGTA
1 TGTATCGATACATATGGGCAAATTTGCCTGTA
2020423 TGTATCGATACAT
1 TGTATCGATACAT
2020436 TTCATAGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATATGGGCAAATTTGCCTGTA
Found at i:2020467 original size:84 final size:84
Alignment explanation
Indices: 2020326--2020486 Score: 295
Period size: 84 Copynumber: 1.9 Consensus size: 84
2020316 CGAAATATGA
*
2020326 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATATGGGCAAATTTGCCTGTA
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATATGGGCAAATTTGCCTGCA
2020391 TGTATCGATACATATGGGC
66 TGTATCGATACATATGGGC
* *
2020410 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAATTTGCCTGCA
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATATGGGCAAATTTGCCTGCA
2020475 TGTATCGATACA
66 TGTATCGATACA
2020487 ATGTATCGAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 74 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (84 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATATGGGCAAATTTGCCTGCA
TGTATCGATACATATGGGC
Found at i:2020492 original size:13 final size:13
Alignment explanation
Indices: 2020474--2020532 Score: 67
Period size: 13 Copynumber: 5.0 Consensus size: 13
2020464 ATTTGCCTGC
2020474 ATGTATCGATACA
1 ATGTATCGATACA
2020487 ATGTATCGATACA
1 ATGTATCGATACA
2020500 A---A--GAT-CA
1 ATGTATCGATACA
*
2020507 GTGTATCGATACA
1 ATGTATCGATACA
2020520 ATGTATCGATACA
1 ATGTATCGATACA
2020533 TTTGAGTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
7 2 0.05
8 3 0.08
10 2 0.05
12 3 0.08
13 28 0.74
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2020622 original size:13 final size:13
Alignment explanation
Indices: 2020604--2020628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2020594 ACAACACTTA
2020604 TGTATCGATACAT
1 TGTATCGATACAT
2020617 TGTATCGATACA
1 TGTATCGATACA
2020629 ACTCGTTGAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2023511 original size:131 final size:130
Alignment explanation
Indices: 2023349--2023709 Score: 356
Period size: 131 Copynumber: 2.7 Consensus size: 130
2023339 TATAGTTTTG
* * *
2023349 TCCTGGCCAACCTTTTTTCGACTTAGGTTTTGCCTTAGTCACCCGTAGTTGGTTTGTATGGTTTC
1 TCCTGGCCAACCTTTTTTCAACTTAAGTTTTGCCTTAGTCACCC-TAGTTGGTTCGTATGGTTTC
* *
2023414 ATCCTAGCCAACTCTTTTTTGACTTAGGTTCCACCTTAGTCACC-TTTAG-TTGTTTGTATGGTT
65 ATCCTAGCCAA-TCTTTTTTGACTTAGGTT-CACCTTAGTCACCATTAAGTTTGTTCGTATGGTT
2023477 TCA
128 TCA
* * * * *
2023480 TCCTGACCAA-CTCTTTTTCAATTTAAGTTTTGCCTTGGTCACCCTAAGTTGCTTCATATGGTTT
1 TCCTGGCCAACCT-TTTTTCAACTTAAGTTTTGCCTTAGTCACCCT-AGTTGGTTCGTATGGTTT
* * ** *
2023544 CAT-CTCGACCAAATCCTTTTCT-ACTTAGGTTTTCCTTGGTCACCATTAAGTTTGTTCGTATGG
64 CATCCTAG-CC-AAT-CTTTTTTGACTTAGGTTCACCTTAGTCACCATTAAGTTTGTTCGTATGG
2023607 TTTCA
126 TTTCA
* * * ** * * *
2023612 TCTTGGCCAACCTTTTTTCAACTT-AGATTCTACCTTAGTCACCAAAGTTGGTTCGCATAGTTTT
1 TCCTGGCCAACCTTTTTTCAACTTAAG-TTTTGCCTTAGTCACCCTAGTTGGTTCGTATGGTTTC
* * *
2023676 ATCCCAGCCAATCCTTTTAGACTTAGGTTTCACC
65 ATCCTAGCCAATCTTTTTTGACTTAGG-TTCACC
2023710 CTAATCTACC
Statistics
Matches: 183, Mismatches: 35, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
129 4 0.02
130 26 0.14
131 94 0.51
132 57 0.31
133 2 0.01
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.42
Consensus pattern (130 bp):
TCCTGGCCAACCTTTTTTCAACTTAAGTTTTGCCTTAGTCACCCTAGTTGGTTCGTATGGTTTCA
TCCTAGCCAATCTTTTTTGACTTAGGTTCACCTTAGTCACCATTAAGTTTGTTCGTATGGTTTCA
Found at i:2023607 original size:197 final size:197
Alignment explanation
Indices: 2023260--2023654 Score: 458
Period size: 197 Copynumber: 2.0 Consensus size: 197
2023250 TTGGTTACCC
* * ** * *
2023260 TTAGTTGTTTGTATGGCTTCGTCCTGACCAACCCTTTTTTTTTACTTAGGTTTTGCCATGGTCAG
1 TTAGTTGTTTGTATGGCTTCATCCTGACCAA-CCTCTTTTTCAACTTAAGTTTTGCCATGGTCAC
* * ** *
2023325 CCTTAGTTGGTTCATATAGTTTTGTCCTGGCCAACCTTTTTTCGACTTAGGTTTTGCCTTAGTCA
65 CCTAAGTTGCTTCATATAGTTTCATCCTGACCAACC-TTTTTCGACTTAGGTTTTGCCTTAGTCA
* * * *
2023390 CCCGTAGTTGGTTTGTATGGTTTCATCCTAGCCAACTCTTTTTT-GACTTAGGTTCCACCTTAGT
129 CCAGTAGTTGGTTCGTATGGTTTCATCCTAGCCAAC-CTTTTTTCAACTTAGATTCCACCTTAGT
2023454 CACCT
193 CACCT
* * *
2023459 TTAGTTGTTTGTATGGTTTCATCCTGACCAA-CTCTTTTTCAATTTAAGTTTTGCCTTGGTCACC
1 TTAGTTGTTTGTATGGCTTCATCCTGACCAACCTCTTTTTCAACTTAAGTTTTGCCATGGTCACC
* * *
2023523 CTAAGTTGCTTCATATGGTTTCAT-CTCGACCAAATCC-TTTTCTACTTAGGTTTT-CCTTGGTC
66 CTAAGTTGCTTCATATAGTTTCATCCT-GACC-AA-CCTTTTTCGACTTAGGTTTTGCCTTAGTC
* * * * *
2023585 ACCATTAAGTTTGTTCGTATGGTTTCATCTTGGCCAACCTTTTTTCAACTTAGATTCTACCTTAG
128 ACCAGT-AGTTGGTTCGTATGGTTTCATCCTAGCCAACCTTTTTTCAACTTAGATTCCACCTTAG
2023650 TCACC
192 TCACC
2023655 AAAGTTGGTT
Statistics
Matches: 165, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
196 20 0.12
197 112 0.68
198 2 0.01
199 31 0.19
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.44
Consensus pattern (197 bp):
TTAGTTGTTTGTATGGCTTCATCCTGACCAACCTCTTTTTCAACTTAAGTTTTGCCATGGTCACC
CTAAGTTGCTTCATATAGTTTCATCCTGACCAACCTTTTTCGACTTAGGTTTTGCCTTAGTCACC
AGTAGTTGGTTCGTATGGTTTCATCCTAGCCAACCTTTTTTCAACTTAGATTCCACCTTAGTCAC
CT
Found at i:2023630 original size:66 final size:64
Alignment explanation
Indices: 2023234--2023637 Score: 300
Period size: 66 Copynumber: 6.1 Consensus size: 64
2023224 TTGTCTTAAC
* * * * * * *
2023234 CAACTCAGATTTTACCTTGGTTACCCTTAGTTGTTTGTATGGCTTCGTCCTGACCAACCCTTTTT
1 CAACTTAGGTTTTGCCTTGGTCA-CCTTAGTTGTTCGTATGGTTTCATCCTGACCAA-CC-TTTT
2023299 TT
63 TT
** * * * ** *
2023301 TTACTTAGGTTTTGCCATGGTCAGCCTTAGTTGGTTCATATAGTTTTGTCCTGGCCAACCTTTTT
1 CAACTTAGGTTTTGCCTTGGTCA-CCTTAGTT-GTTCGTATGGTTTCATCCTGACCAACCTTTTT
2023366 T
64 T
* * * *
2023367 CGACTTAGGTTTTGCCTTAGTCACCCGTAGTTGGTTTGTATGGTTTCATCCT-AGCCAACTCTTT
1 CAACTTAGGTTTTGCCTTGGTCA-CCTTAGTT-GTTCGTATGGTTTCATCCTGA-CCAAC-CTTT
2023431 TTT
62 TTT
* *** * *
2023434 -GACTTAGGTTCCACCTTAGTCACCTTTAGTTGTTTGTATGGTTTCATCCTGACCAA-CTCTTTT
1 CAACTTAGGTTTTGCCTTGGTCACC-TTAGTTGTTCGTATGGTTTCATCCTGACCAACCT-TTTT
2023497 T
64 T
* * * *
2023498 CAATTTAAGTTTTGCCTTGGTCACCCTAAGTTGCTTCATATGGTTTCAT-CTCGACCAAATCC--
1 CAACTTAGGTTTTGCCTTGGTCA-CCTTAGTTG-TTCGTATGGTTTCATCCT-GACC-AA-CCTT
2023560 TTTT
61 TTTT
* * *
2023564 CTACTTAGGTTTT-CCTTGGTCACCATTAAGTTTGTTCGTATGGTTTCATCTTGGCCAACCTTTT
1 CAACTTAGGTTTTGCCTTGGTCACC-TT-AG-TTGTTCGTATGGTTTCATCCTGACCAACCTTTT
2023628 TT
63 TT
2023630 CAACTTAG
1 CAACTTAG
2023638 ATTCTACCTT
Statistics
Matches: 270, Mismatches: 48, Indels: 39
0.76 0.13 0.11
Matches are distributed among these distances:
63 2 0.01
64 9 0.03
65 60 0.22
66 140 0.52
67 39 0.14
68 19 0.07
69 1 0.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (64 bp):
CAACTTAGGTTTTGCCTTGGTCACCTTAGTTGTTCGTATGGTTTCATCCTGACCAACCTTTTTT
Found at i:2028314 original size:32 final size:32
Alignment explanation
Indices: 2028273--2028336 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2028263 AGAATTTTAA
2028273 ATAAATTTAAACTCAATCAACTCTATCTCTAT
1 ATAAATTTAAACTCAATCAACTCTATCTCTAT
* * * *
2028305 ATAAGTTTAAACTCTATTAACTCTATTTCTAT
1 ATAAATTTAAACTCAATCAACTCTATCTCTAT
2028337 GGAATTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.42
Consensus pattern (32 bp):
ATAAATTTAAACTCAATCAACTCTATCTCTAT
Found at i:2030860 original size:73 final size:73
Alignment explanation
Indices: 2030738--2030879 Score: 257
Period size: 73 Copynumber: 1.9 Consensus size: 73
2030728 CGTCTCGTAA
* *
2030738 AGATATTGGAACTTAACACTGACAATGAGATAGAAAAAATATGTGGAAATGCCTCATGTTTCATG
1 AGATATTGGAACTTAACACTGACAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
2030803 AAATTATG
66 AAATTATG
*
2030811 AGATATTGGAACTTAACACTGACAATGAGACAGGAAAAATATGTAGAAATGCCTCATGTTTCATG
1 AGATATTGGAACTTAACACTGACAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
2030876 AAAT
66 AAAT
2030880 AGTGAGGGAA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 66 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (73 bp):
AGATATTGGAACTTAACACTGACAATGAGACAGAAAAAATATGTAGAAATGCCTCATGTTTCATG
AAATTATG
Found at i:2032359 original size:12 final size:12
Alignment explanation
Indices: 2032342--2032368 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2032332 GCTCATCTGC
2032342 TGGCCAGATATG
1 TGGCCAGATATG
2032354 TGGCCAGATATG
1 TGGCCAGATATG
2032366 TGG
1 TGG
2032369 TTAGGCCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.37, T:0.26
Consensus pattern (12 bp):
TGGCCAGATATG
Found at i:2035549 original size:18 final size:18
Alignment explanation
Indices: 2035526--2035561 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2035516 TGCAAGTTTC
2035526 GAGGAAGTTGTGCTAATG
1 GAGGAAGTTGTGCTAATG
*
2035544 GAGGAAGTTGTGTTAATG
1 GAGGAAGTTGTGCTAATG
2035562 TGCACACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.39, T:0.31
Consensus pattern (18 bp):
GAGGAAGTTGTGCTAATG
Found at i:2035840 original size:6 final size:6
Alignment explanation
Indices: 2035831--2035858 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2035821 AACATTTATT
2035831 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
2035859 TATCGAGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:2039969 original size:581 final size:583
Alignment explanation
Indices: 2038903--2039971 Score: 1471
Period size: 581 Copynumber: 1.8 Consensus size: 583
2038893 TCAATCAAGG
* * * *
2038903 AAATTTAAGCTAAGTACAAAATCGTAATCATCCAAAAGGATTACCTCAATGGTTTTTTTACCATT
1 AAATTTAAGCCAAGCACAAAATCATAATCATCCAAAAAGATTACCTCAATGGTTTTTTTACCATT
* * * * * *
2038968 CTAGTCTCCCAATTGTAAGTCCACTTTTTTTGCCACACTTATAGTTGGGACTTCTTTTAAGTTAA
66 CCAATCTCCAAATTGTAAGTCCACTTTTTTTACCACACCTATAGTTGGGACCTCTTTTAAGTTAA
* * * **
2039033 CTATTTTGATCCACTCGATTGTCTTTTCAATTTTAAGATCAAGCTTTTTAGTGATTTTCTCGGAT
131 CTATTTTGATCCACTCGATTGTCTCTTCAACTTTAAGATCAAGCTTTTTAGTGACTTTCTCAAAT
* * *
2039098 ATAAATAAGTCCGCAGCTTTTGTGCCAACTAGAGCACTTATTTTTTTTGTTTGCAATCCTAATGT
196 ATAAATAAGTCCGAAGCTTTTGTGCCAACTAAAGCACTTATTTTTTTTGCTTGCAATCCTAATGT
*
2039163 CCACGAAACATTAGCCCTTTCTACTTTTGATACATTTTTGTTTTAATAAAATTTAGTATAATAGA
261 CCACGAAACATTAGCCCTTTCTACTTTTGACACATTTTTGTTTTAATAAAATTTAGTATAATAGA
* * * *
2039228 ACTAAGCTTTAGAGTATCATTTATCCTCTTAGTCAATGACAGGTAGCTTGGCTCATTGTAGGCAG
326 ACCAAGCTTCAGAGTATCATTTATCCTCTTAGTCAATGACAGATAGCTTGGCTCATTGGAGGCAG
* * * * *
2039293 TCTAACATCTTAGTCTTCGCATAATTGAGTATAATAGAACTAAGCTTTAGAGTCTCATTTTTTGG
391 TCTAACATCTTAATCTTCGCAGAATTGAGTATAATAGAACTAAGCTTTAGAATCTCATTCTTTGA
* *
2039358 CTCATCCTCTTCCTTACTAATGGTAGATAGCTTAGTTTTTTTGGCTCATAATTGAGTATAATAGA
456 CTCATCCTCCTCCTTACTAATGGCAGATAGCTTAGTTTTTTTGGCTCATAATTGAGTATAATAGA
2039423 ACTCGTCTTTTGATACATACGTAATCAGCAAAAGGAACAAAGCGTGTAATAATCCGATGAAGA
521 ACTCGTCTTTTGATACATACGTAATCAGCAAAAGGAACAAAGCGTGTAATAATCCGATGAAGA
* * *
2039486 AAATTTAAGCCAAGCACAAAGTCATAATCATCCAAAAAGATTACCTTAATGGTTTTTTTGCCATT
1 AAATTTAAGCCAAGCACAAAATCATAATCATCCAAAAAGATTACCTCAATGGTTTTTTTACCATT
* * *
2039551 CCAATCTCCAAATTGTAGGTCCA-TGTTTTTTACCACACCTATAGTTGGGACCT-TTTTGAGTTT
66 CCAATCTCCAAATTGTAAGTCCACT-TTTTTTACCACACCTATAGTTGGGACCTCTTTTAAGTTA
* * * * * * * *
2039614 ATTGTTTTGATCTACTTGGTTGTCTCTTCAACTTTGAGATCAAGCTTTTTGGTGACTTTCTTAAA
130 ACTATTTTGATCCACTCGATTGTCTCTTCAACTTTAAGATCAAGCTTTTTAGTGACTTTCTCAAA
* * ** *
2039679 TATAAATAAGTTCGAAGCTTTTGTGTCAACTAAAGCACTTATTTTTTTTGCTTGTGATCTTAATG
195 TATAAATAAGTCCGAAGCTTTTGTGCCAACTAAAGCACTTATTTTTTTTGCTTGCAATCCTAATG
* * * * * * * * * *
2039744 TCTATG-AACATTAGCCTTTTTTACTTTTGACACCTTTTTGTTTTAGTAGAATTTATTGTAATTG
260 TCCACGAAACATTAGCCCTTTCTACTTTTGACACATTTTTGTTTTAATAAAATTTAGTATAATAG
* *
2039808 AACCAAGCTTCAGAGTATCATTTATCCTCTTAGTCAATGACAGATAGTTTGGCTCGTTGCGA-GC
325 AACCAAGCTTCAGAGTATCATTTATCCTCTTAGTCAATGACAGATAGCTTGGCTCATTG-GAGGC
** * *
2039872 AGTCTCGCATCTTAATCTTTGCAGAATTGAGTATAATAGAACTAAGCTTTAGAATCTTATTCTTT
389 AGTCTAACATCTTAATCTTCGCAGAATTGAGTATAATAGAACTAAGCTTTAGAATCTCATTCTTT
* ** *
2039937 GACTCATTCTCCTCCTTGTTGATGGCAGATAGCTT
454 GACTCATCCTCCTCCTTACTAATGGCAGATAGCTT
2039972 GGCTCTTTGT
Statistics
Matches: 415, Mismatches: 69, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
581 190 0.46
582 123 0.30
583 102 0.25
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (583 bp):
AAATTTAAGCCAAGCACAAAATCATAATCATCCAAAAAGATTACCTCAATGGTTTTTTTACCATT
CCAATCTCCAAATTGTAAGTCCACTTTTTTTACCACACCTATAGTTGGGACCTCTTTTAAGTTAA
CTATTTTGATCCACTCGATTGTCTCTTCAACTTTAAGATCAAGCTTTTTAGTGACTTTCTCAAAT
ATAAATAAGTCCGAAGCTTTTGTGCCAACTAAAGCACTTATTTTTTTTGCTTGCAATCCTAATGT
CCACGAAACATTAGCCCTTTCTACTTTTGACACATTTTTGTTTTAATAAAATTTAGTATAATAGA
ACCAAGCTTCAGAGTATCATTTATCCTCTTAGTCAATGACAGATAGCTTGGCTCATTGGAGGCAG
TCTAACATCTTAATCTTCGCAGAATTGAGTATAATAGAACTAAGCTTTAGAATCTCATTCTTTGA
CTCATCCTCCTCCTTACTAATGGCAGATAGCTTAGTTTTTTTGGCTCATAATTGAGTATAATAGA
ACTCGTCTTTTGATACATACGTAATCAGCAAAAGGAACAAAGCGTGTAATAATCCGATGAAGA
Found at i:2040257 original size:21 final size:21
Alignment explanation
Indices: 2040231--2040286 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2040221 TTTTTGTCCA
*
2040231 AATGTATCGATACATTTTTAG
1 AATGTATCGATACATTTCTAG
2040252 AATGTATCGATACATTTCTAG
1 AATGTATCGATACATTTCTAG
2040273 AATGTATCGATACA
1 AATGTATCGATACA
2040287 AGGTCTCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (21 bp):
AATGTATCGATACATTTCTAG
Found at i:2040373 original size:19 final size:19
Alignment explanation
Indices: 2040345--2040407 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
2040335 AAACAGTAAC
*
2040345 TGTATTGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
2040364 TGTATAGATAC--AA----
1 TGTATCGATACATAAGTGT
2040377 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
2040396 TGTATCGATACA
1 TGTATCGATACA
2040408 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.37
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:2040387 original size:32 final size:32
Alignment explanation
Indices: 2040345--2040420 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
2040335 AAACAGTAAC
*
2040345 TGTATTGATACATAAGTGTTGTATAGATACAA
1 TGTATCGATACATAAGTGTTGTATAGATACAA
*
2040377 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATAGATACAA
*
2040409 TGTATCGCTACA
1 TGTATCGATACA
2040421 AAGCTACTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATAGATACAA
Found at i:2040462 original size:20 final size:20
Alignment explanation
Indices: 2040437--2040491 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
2040427 CTGTCAAGGA
2040437 AATGTATCGATACATTACTC
1 AATGTATCGATACATTACTC
*
2040457 AATGTATCGATACATTATTC
1 AATGTATCGATACATTACTC
2040477 AATGTATCGATACAT
1 AATGTATCGATACAT
2040492 GCAGGCAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTACTC
Found at i:2047427 original size:228 final size:228
Alignment explanation
Indices: 2046836--2047517 Score: 1262
Period size: 227 Copynumber: 3.0 Consensus size: 228
2046826 AAGGGTATTT
*
2046836 TGGTCATTTTAAAGTATTTTTAATATTCCTCCTATCATCCAGACA-GGTGTAGAAAATATTAAAA
1 TGGTCATTTTAAAATATTTTTAATATTCCTCCTATCATCCAGA-AGGGTGTAGAAAATATTAAAA
2046900 CTTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATTAATTTTGAAAAGTTTAGGGGCTTAA
65 CTTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATTAATTTTGAAAAGTTTAGGGGCTTAA
2046965 TTATAATTTTTCTCTTTTAAGTTATCTTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATT
130 TTATAATTTTTCTCTTTTAAGTTATCTTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATT
2047030 -TTTTTTTATCATTTTAAAGTCCTTTAAGGTTAC
195 ATTTTTTTATCATTTTAAAGTCCTTTAAGGTTAC
*
2047063 TGGTCATTTTAAAATATTTTTAATATTCCTCCTATCATCCAGAAGGGTGTAGAAAACATTAAAAC
1 TGGTCATTTTAAAATATTTTTAATATTCCTCCTATCATCCAGAAGGGTGTAGAAAATATTAAAAC
*
2047128 GTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATTAATTTTGAAAAGTTTAGGGGCTTAAT
66 TTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATTAATTTTGAAAAGTTTAGGGGCTTAAT
*
2047193 TATAATTTTTCTCTTTTAAGTTATCGTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATTA
131 TATAATTTTTCTCTTTTAAGTTATCTTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATTA
* *
2047258 TTTTTTTATTATTTTAAAGTCTTTTAAGGTTAC
196 TTTTTTTATCATTTTAAAGTCCTTTAAGGTTAC
*
2047291 TGGTCA-TTTAAAATATTTTTAATATTCCTTCTATCATCCAGAAGGGTGTAGAAAATATTAAAAC
1 TGGTCATTTTAAAATATTTTTAATATTCCTCCTATCATCCAGAAGGGTGTAGAAAATATTAAAAC
2047355 TTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATTAAATTTTGAAAAGTTTAGGGGCTTAA
66 TTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATT-AATTTTGAAAAGTTTAGGGGCTTAA
2047420 TTATAATTTTTCTCTTTTAAGTTATCTTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATT
130 TTATAATTTTTCTCTTTTAAGTTATCTTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATT
2047485 ATTTTTTTATCATTTTAAAGTCCTTTAAGGTTA
195 ATTTTTTTATCATTTTAAAGTCCTTTAAGGTTA
2047518 TTGTGACACT
Statistics
Matches: 440, Mismatches: 12, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
226 1 0.00
227 282 0.64
228 157 0.36
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.48
Consensus pattern (228 bp):
TGGTCATTTTAAAATATTTTTAATATTCCTCCTATCATCCAGAAGGGTGTAGAAAATATTAAAAC
TTTTTATATTCTTTCATTTTTCCGTTAGGTTGTGAAATTAATTTTGAAAAGTTTAGGGGCTTAAT
TATAATTTTTCTCTTTTAAGTTATCTTTGATGTTTTTGAATTCTCTATTTAGGGTGAAATAATTA
TTTTTTTATCATTTTAAAGTCCTTTAAGGTTAC
Found at i:2049980 original size:13 final size:13
Alignment explanation
Indices: 2049962--2049987 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2049952 TACACAAAGT
2049962 ATGTATCGATACA
1 ATGTATCGATACA
2049975 ATGTATCGATACA
1 ATGTATCGATACA
2049988 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2050147 original size:49 final size:47
Alignment explanation
Indices: 2050090--2050511 Score: 418
Period size: 43 Copynumber: 8.8 Consensus size: 47
2050080 ATGTGAACAC
* *
2050090 CTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TTT
* *
2050139 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C---
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTT
* * *
2050182 CTTTAAGACCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT--T
*
2050231 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C---
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTT
* *
2050274 CTTTAAGTCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTT--T
*
2050323 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C---
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTT
* *
2050366 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT---T
* * *
2050418 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-CC----T-T--T
* * *
2050473 CTTTAAGCCCAATATAGTTGGCCGTGAATCAGCACATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
2050512 ATATCCTTTT
Statistics
Matches: 318, Mismatches: 30, Indels: 44
0.81 0.08 0.11
Matches are distributed among these distances:
43 116 0.36
44 3 0.01
48 3 0.01
49 116 0.36
52 37 0.12
53 2 0.01
55 40 0.13
56 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (47 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTT
Found at i:2050244 original size:92 final size:92
Alignment explanation
Indices: 2050087--2050465 Score: 632
Period size: 92 Copynumber: 4.1 Consensus size: 92
2050077 CCTATGTGAA
* **
2050087 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAACATATTGGCACCTTTTTCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
*
2050152 GTAGCTGGCCTTGACTCAGCACATTGG
66 GTAGCTGGCCTTGAATCAGCACATTGG
* *
2050179 CACCTTTAAGACCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
2050244 GTAGCTGGCCTTGAATCAGCACATTGG
66 GTAGCTGGCCTTGAATCAGCACATTGG
*
2050271 CACCTTTAAGTCTAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
2050336 GTAGCTGGCCTTGAATCAGCACATTGG
66 GTAGCTGGCCTTGAATCAGCACATTGG
* *
2050363 CACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTC
1 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCC
*
2050428 AATGTAGCTGGCCTTGAATCAGCACATTGA
63 AATGTAGCTGGCCTTGAATCAGCACATTGG
2050458 CATCCTTT
1 CA-CCTTT
2050466 TTCTCATCTT
Statistics
Matches: 270, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
92 220 0.81
94 2 0.01
95 43 0.16
96 5 0.02
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (92 bp):
CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAAT
GTAGCTGGCCTTGAATCAGCACATTGG
Found at i:2050444 original size:52 final size:55
Alignment explanation
Indices: 2050366--2050542 Score: 243
Period size: 55 Copynumber: 3.3 Consensus size: 55
2050356 ACATTGGCAC
* * * *
2050366 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
** *
2050418 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * *
2050473 CTTTAAGCCCAATATAGTTGGCCGTGAATCAGCACATTGATATCCTTTTTCTCAT
1 CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
2050528 CTTTAAGCCCAATAT
1 CTTTAAGCCCAATAT
2050543 CGTTGGCTGT
Statistics
Matches: 111, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
52 37 0.33
53 2 0.02
54 5 0.05
55 67 0.60
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (55 bp):
CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:2051425 original size:20 final size:20
Alignment explanation
Indices: 2051381--2051438 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2051371 ATTTCAACGA
***
2051381 TTTGTATCGATACATAAAGT
1 TTTGTATCGATACATATTTT
*
2051401 GTTGTATCGATACATATTTT
1 TTTGTATCGATACATATTTT
2051421 TTTGTATCGATACA-ATTT
1 TTTGTATCGATACATATTT
2051439 AAGCTACTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
TTTGTATCGATACATATTTT
Found at i:2051495 original size:13 final size:13
Alignment explanation
Indices: 2051477--2051504 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2051467 ATTACTCAAA
2051477 TGTATCGATACAC
1 TGTATCGATACAC
2051490 TGTATCGATACAC
1 TGTATCGATACAC
2051503 TG
1 TG
2051505 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:2060100 original size:13 final size:13
Alignment explanation
Indices: 2060082--2060107 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2060072 TACACAAAGT
2060082 ATGTATCGATACA
1 ATGTATCGATACA
2060095 ATGTATCGATACA
1 ATGTATCGATACA
2060108 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2060105 original size:32 final size:33
Alignment explanation
Indices: 2060064--2060127 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2060054 TAGCCAAACT
**
2060064 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
2060096 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
2060128 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:2060628 original size:34 final size:35
Alignment explanation
Indices: 2060565--2060631 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
2060555 CTAAGTGATT
2060565 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
2060601 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
2060632 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:2062335 original size:20 final size:17
Alignment explanation
Indices: 2062294--2062345 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 17
2062284 TTTTACCTAG
2062294 ATGTATCGATACATTAA
1 ATGTATCGATACATTAA
*
2062311 ATGTATCAATACATGTATGA
1 ATGTATCGATACAT-TA--A
2062331 ATGTATCGATACATT
1 ATGTATCGATACATT
2062346 CTTTCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 1 0.03
20 14 0.47
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (17 bp):
ATGTATCGATACATTAA
Found at i:2066353 original size:21 final size:21
Alignment explanation
Indices: 2066327--2066382 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
2066317 TGCAATGGAT
*
2066327 AATGTATCGATATAAACAGTA
1 AATGTATCGATACAAACAGTA
*
2066348 AATGTATCGATACAAATAGTA
1 AATGTATCGATACAAACAGTA
2066369 AATGTATCGATACA
1 AATGTATCGATACA
2066383 TTTACTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACAAACAGTA
Found at i:2079126 original size:2 final size:2
Alignment explanation
Indices: 2079105--2079144 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2079095 TTCTTTGACA
* * *
2079105 AT AT AT AC AT AC AT AC 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
2079145 TTCTGATAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2081787 original size:9 final size:9
Alignment explanation
Indices: 2081775--2081813 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2081765 TTAATTGAAA
2081775 AAATTAATT
1 AAATTAATT
2081784 AAATTAAATT
1 AAATT-AATT
*
2081794 TAATTAATT
1 AAATTAATT
*
2081803 TAATTAATT
1 AAATTAATT
2081812 AA
1 AA
2081814 GTCTAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AAATTAATT
Found at i:2081992 original size:23 final size:23
Alignment explanation
Indices: 2081961--2082022 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
2081951 TAAATCTATT
*
2081961 TAAATCTAAATTAAAAG-TTCATC
1 TAAAACTAAATTAAAAGCTT-ATC
* *
2081984 TAAACCTAAATTAAAAGCTTATT
1 TAAAACTAAATTAAAAGCTTATC
*
2082007 TAAAATTAAATTAAAA
1 TAAAACTAAATTAAAA
2082023 ACCTAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 32 0.94
24 2 0.06
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (23 bp):
TAAAACTAAATTAAAAGCTTATC
Found at i:2082032 original size:23 final size:23
Alignment explanation
Indices: 2081990--2082034 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2081980 CATCTAAACC
* * *
2081990 TAAATTAAAAGCTTATTTAAAAT
1 TAAATTAAAAACCTAATTAAAAT
2082013 TAAATTAAAAACCTAATTAAAA
1 TAAATTAAAAACCTAATTAAAA
2082035 CAAAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
TAAATTAAAAACCTAATTAAAAT
Found at i:2082052 original size:29 final size:30
Alignment explanation
Indices: 2082019--2082077 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
2082009 AAATTAAATT
2082019 AAAAACCTAATTAAAACAAAAAAAA-ATAAC
1 AAAAA-CTAATTAAAACAAAAAAAATATAAC
* *
2082049 AAAAACTATTTAAAATAAAAAAAATATAA
1 AAAAACTAATTAAAACAAAAAAAATATAA
2082078 ATTGAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (30 bp):
AAAAACTAATTAAAACAAAAAAAATATAAC
Found at i:2082070 original size:30 final size:30
Alignment explanation
Indices: 2082019--2082077 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2082009 AAATTAAATT
*
2082019 AAAAACCTAATTAAAACAAAAAAAAATAAC
1 AAAAACCTAATTAAAAAAAAAAAAAATAAC
* *
2082049 AAAAA-CTATTTAAAATAAAAAAAATATAA
1 AAAAACCTAATTAAAA-AAAAAAAAAATAA
2082078 ATTGAACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (30 bp):
AAAAACCTAATTAAAAAAAAAAAAAATAAC
Found at i:2082383 original size:2 final size:2
Alignment explanation
Indices: 2082376--2082403 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2082366 ATAGAAGATT
2082376 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
2082404 CACTAACTTC
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
Found at i:2082722 original size:20 final size:20
Alignment explanation
Indices: 2082699--2082743 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2082689 AGTTAAATAT
*
2082699 ATATTTTTATTAATAATTTA
1 ATATTTTTAATAATAATTTA
* * *
2082719 ATATATTTAATATTTATTTA
1 ATATTTTTAATAATAATTTA
2082739 ATATT
1 ATATT
2082744 AAATATTTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTTTAATAATAATTTA
Found at i:2082728 original size:17 final size:17
Alignment explanation
Indices: 2082708--2082769 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
2082698 TATATTTTTA
2082708 TTAATAATTTAATATAT
1 TTAATAATTTAATATAT
*
2082725 TTAAT-ATTTATTTAATAT
1 TTAATAATTTA-AT-ATAT
* * *
2082743 TAAATATTTTAAAATAT
1 TTAATAATTTAATATAT
2082760 TTAA-AATTTA
1 TTAATAATTTA
2082770 TTTAAATAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
16 10 0.29
17 13 0.37
18 8 0.23
19 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATAATTTAATATAT
Found at i:2082748 original size:18 final size:18
Alignment explanation
Indices: 2082721--2082793 Score: 64
Period size: 18 Copynumber: 4.1 Consensus size: 18
2082711 ATAATTTAAT
*
2082721 ATATTTAATATTTATTTA
1 ATATTAAATATTTATTTA
**
2082739 ATATTAAATATTT-TAAA
1 ATATTAAATATTTATTTA
2082756 ATATTTAAA-ATTTATTTA
1 ATA-TTAAATATTTATTTA
2082774 A-A-TAAATTATTTAATTTA
1 ATATTAAA-TATTT-ATTTA
2082792 AT
1 AT
2082794 TGATTGAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
15 4 0.09
17 14 0.32
18 26 0.59
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTAAATATTTATTTA
Found at i:2082748 original size:27 final size:26
Alignment explanation
Indices: 2082704--2082754 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
2082694 AATATATATT
*
2082704 TTTATTAATAATTTAATATATTTAATA
1 TTTATTAATAATTAAATAT-TTTAATA
2082731 TTTATTTAAT-ATTAAATATTTTAA
1 TTTA-TTAATAATTAAATATTTTAA
2082755 AATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 5 0.23
27 12 0.55
28 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTATTAATAATTAAATATTTTAATA
Found at i:2084838 original size:3 final size:3
Alignment explanation
Indices: 2084830--2084861 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2084820 GTTTCCCATT
2084830 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2084862 TCTGATGATT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Done.