Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008488.1 Hibiscus syriacus cultivar Beakdansim tig00111330_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12876159
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 54 of 54
Found at i:12709050 original size:14 final size:14
Alignment explanation
Indices: 12709031--12709057 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12709021 CCTTAATAAC
12709031 AAATATTTATATTA
1 AAATATTTATATTA
12709045 AAATATTTATATT
1 AAATATTTATATT
12709058 TTTTTCTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATATTTATATTA
Found at i:12709284 original size:41 final size:42
Alignment explanation
Indices: 12709198--12709305 Score: 155
Period size: 41 Copynumber: 2.6 Consensus size: 42
12709188 ACTCTTTGTA
* * * *
12709198 TTTAATCGTAAAATCAATACACACTAGAGGACCTTTTTTATG
1 TTTAATAGTAAAATCAATACACATTAGAAGACCTTTCTTATG
12709240 TTTAATAGTAAAATCAATACACATTA-AAGACCTTTCTTATG
1 TTTAATAGTAAAATCAATACACATTAGAAGACCTTTCTTATG
* *
12709281 TTTAATGGTAAAATCGATACACATT
1 TTTAATAGTAAAATCAATACACATT
12709306 TAAGTTCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 36 0.60
42 24 0.40
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (42 bp):
TTTAATAGTAAAATCAATACACATTAGAAGACCTTTCTTATG
Found at i:12712378 original size:2 final size:2
Alignment explanation
Indices: 12712371--12712430 Score: 88
Period size: 2 Copynumber: 30.0 Consensus size: 2
12712361 AGAAATGAGG
12712371 GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GTA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA GA GA
12712413 GA GA GA -A GTA GA GA GA GA
1 GA GA GA GA G-A GA GA GA GA
12712431 ATAGTTGAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.04
2 48 0.89
3 4 0.07
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
GA
Found at i:12712396 original size:20 final size:20
Alignment explanation
Indices: 12712371--12712430 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
12712361 AGAAATGAGG
12712371 GAGAGAGAG-AG-AGAGAGA
1 GAGAGAGAGAAGTAGAGAGA
12712389 GAGAGAGAGAAGTAGAGAGA
1 GAGAGAGAGAAGTAGAGAGA
12712409 GAGAGAGAGAAGTAGAGAGA
1 GAGAGAGAGAAGTAGAGAGA
12712429 GA
1 GA
12712431 ATAGTTGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 9 0.22
19 2 0.05
20 29 0.73
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (20 bp):
GAGAGAGAGAAGTAGAGAGA
Found at i:12725115 original size:181 final size:178
Alignment explanation
Indices: 12724805--12725164 Score: 648
Period size: 181 Copynumber: 2.0 Consensus size: 178
12724795 CCTATCAATC
*
12724805 ATGAATCGGTTGATTAAAACTACCATGCCCTTGATAGCAATAGAAAATGCCAATATACATATATA
1 ATGAAACGGTTGATTAAAACTACCATGCCCTTGATAGCAATAGAAAATGCCAATATACATATATA
*
12724870 TCATCTGGCAATCAGAGTTAGCAGATAATATGTGAATGTATATGACTGTAGTCTGTATATTTATA
66 TCATCTAGCAATCAGAGTTAGCAGATAATATGTGAATGTATATGACTGTAGTCTGTATATTTATA
12724935 TAGTTTCAAGAAGGAAAAGAAGAACCTAAGCTGCAGACTACTATAATTTCA
131 TAGTTTCAAGAAGG--AA-AAGAACCTAAGCTGCAGACTACTATAATTTCA
12724986 ATGAAACGGTTGATTAAAACTACCATGCCCTTGATAGCAATAGAAAATGCCAATATACATATATA
1 ATGAAACGGTTGATTAAAACTACCATGCCCTTGATAGCAATAGAAAATGCCAATATACATATATA
* * *
12725051 TCATCTAGCCATCAGAGTTAGCAGATAATATGTGACTGTATATTACTGTAGTCTGTATATTTATA
66 TCATCTAGCAATCAGAGTTAGCAGATAATATGTGAATGTATATGACTGTAGTCTGTATATTTATA
12725116 TAGTTTCAAGAAGGAAAAGAACCTAAGCTGCAGACTACTATAATTTCA
131 TAGTTTCAAGAAGGAAAAGAACCTAAGCTGCAGACTACTATAATTTCA
12725164 A
1 A
12725165 AAAGCATGGA
Statistics
Matches: 174, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
178 33 0.19
179 2 0.01
181 139 0.80
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (178 bp):
ATGAAACGGTTGATTAAAACTACCATGCCCTTGATAGCAATAGAAAATGCCAATATACATATATA
TCATCTAGCAATCAGAGTTAGCAGATAATATGTGAATGTATATGACTGTAGTCTGTATATTTATA
TAGTTTCAAGAAGGAAAAGAACCTAAGCTGCAGACTACTATAATTTCA
Found at i:12730919 original size:21 final size:21
Alignment explanation
Indices: 12730893--12730942 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
12730883 TGTCGGCGAA
*
12730893 GAAGAGAAGGGTGGAAGTGAT
1 GAAGAGAAGGGCGGAAGTGAT
12730914 GAAGAGAAGGGCGGAAGTGAT
1 GAAGAGAAGGGCGGAAGTGAT
12730935 GAAGAGAA
1 GAAGAGAA
12730943 TCCGACAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.02, G:0.46, T:0.10
Consensus pattern (21 bp):
GAAGAGAAGGGCGGAAGTGAT
Found at i:12740570 original size:5 final size:5
Alignment explanation
Indices: 12740560--12740584 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12740550 GAGAAAGGTA
12740560 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
12740585 GCACTAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:12742609 original size:3 final size:3
Alignment explanation
Indices: 12742603--12742666 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
12742593 ACCCCCCAAG
12742603 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
12742651 TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT T
12742667 GTATAGTGGC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:12743608 original size:21 final size:20
Alignment explanation
Indices: 12743563--12743630 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
12743553 ACTGTGCAAG
*
12743563 AAGAAG-AAT-AATAAGAAT
1 AAGAAGAAATGAAGAAGAAT
*
12743581 AATAAGAAATGAAGAAGAAT
1 AAGAAGAAATGAAGAAGAAT
*
12743601 AAAGAAGAAA-GAAAGAAGGAAG
1 -AAGAAGAAATG-AAGAA-GAAT
12743623 AAGAAGAA
1 AAGAAGAA
12743631 GACCAGGGGG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 5 0.12
19 3 0.07
20 9 0.22
21 21 0.51
22 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.09
Consensus pattern (20 bp):
AAGAAGAAATGAAGAAGAAT
Found at i:12751326 original size:29 final size:30
Alignment explanation
Indices: 12751284--12751355 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
12751274 CCCGAAAGAC
*
12751284 CTATCTAGAGGTCACAAAG-ACCCCGGTAA
1 CTATCCAGAGGTCACAAAGAACCCCGGTAA
* *
12751313 CTATCCAGAGGTCATAAAGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCCCGGTAA
* *
12751343 CTGTCCATAGGTC
1 CTATCCAGAGGTC
12751356 CCGACGAACA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGGTAA
Found at i:12751379 original size:31 final size:31
Alignment explanation
Indices: 12751341--12751405 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
12751331 GAACCTCGGT
*
12751341 AACTGTCCATAGGTCCCGACGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
*
12751372 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
12751403 AAC
1 AAC
12751406 CCTCGACTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:12752037 original size:16 final size:16
Alignment explanation
Indices: 12752022--12752059 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12752012 AATCATATCA
12752022 ATAACACATAT-AATC
1 ATAACACATATAAATC
*
12752037 ATGCACACATATAAATC
1 AT-AACACATATAAATC
12752054 ATAACA
1 ATAACA
12752060 AACACATACC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
15 2 0.11
16 11 0.58
17 6 0.32
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.24
Consensus pattern (16 bp):
ATAACACATATAAATC
Found at i:12752475 original size:64 final size:63
Alignment explanation
Indices: 12752401--12752541 Score: 169
Period size: 64 Copynumber: 2.2 Consensus size: 63
12752391 TCTTTAACAT
* *
12752401 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCAT-TTTAAAGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTCATCTTTAAAGA
* * * * * *
12752464 GATGCATCGATGCACTCCTTATGCATCGATGCACCATTTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
12752528 GTGCATCGATGCAC
1 GTGCATCGATGCAC
12752542 ATTCAATGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
63 21 0.31
64 46 0.69
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCATCTTTAAAGA
Found at i:12754007 original size:29 final size:29
Alignment explanation
Indices: 12753959--12754031 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
12753949 GGCTGCTGGA
* * *
12753959 AACCGGTTTAACCAGTTTTCAACCGTTTCG
1 AACCGGTTTGACC-GGTTTCAACCGGTTCG
* *
12753989 -ATCGGTTCTGACCGGTTTCGACCGGTTCG
1 AACCGGTT-TGACCGGTTTCAACCGGTTCG
12754018 AACCGGTTTGACCG
1 AACCGGTTTGACCG
12754032 ATCTGAACCG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:12754008 original size:20 final size:20
Alignment explanation
Indices: 12753979--12754052 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
12753969 ACCAGTTTTC
*
12753979 AACC-GTTTCGATCGGTTCTG
1 AACCGGTTTCGACCGGTTC-G
12753999 -ACCGGTTTCGACCGGTTCG
1 AACCGGTTTCGACCGGTTCG
*
12754018 AACCGGTTT-GACC-GATCTG
1 AACCGGTTTCGACCGGTTC-G
*
12754037 AACCGATTT-GACCGGT
1 AACCGGTTTCGACCGGT
12754053 CTGACCCGAC
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.07
19 21 0.46
20 22 0.48
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (20 bp):
AACCGGTTTCGACCGGTTCG
Found at i:12754031 original size:9 final size:9
Alignment explanation
Indices: 12753991--12754058 Score: 55
Period size: 10 Copynumber: 7.1 Consensus size: 9
12753981 CCGTTTCGAT
12753991 CGGTTCTGAC
1 CGGTT-TGAC
12754001 CGGTTTCGAC
1 CGGTTT-GAC
*
12754011 CGGTTCGAAC
1 CGGTTTG-AC
12754021 CGGTTTGAC
1 CGGTTTGAC
* *
12754030 CGATCTGAAC
1 CGGTTTG-AC
*
12754040 CGATTTGAC
1 CGGTTTGAC
*
12754049 CGGTCTGAC
1 CGGTTTGAC
12754058 C
1 C
12754059 CGACCTGACC
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
9 19 0.40
10 29 0.60
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.26
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:12754039 original size:19 final size:19
Alignment explanation
Indices: 12753995--12754056 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
12753985 TTCGATCGGT
12753995 TCTG-ACCGGTTTCGACCGG
1 TCTGAACCGGTTT-GACCGG
*
12754014 T-TCGAACCGGTTTGACCGA
1 TCT-GAACCGGTTTGACCGG
*
12754033 TCTGAACCGATTTGACCGG
1 TCTGAACCGGTTTGACCGG
12754052 TCTGA
1 TCTGA
12754057 CCCGACCTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.03
19 27 0.73
20 9 0.24
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.27
Consensus pattern (19 bp):
TCTGAACCGGTTTGACCGG
Found at i:12754061 original size:19 final size:19
Alignment explanation
Indices: 12754024--12754078 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
12754014 TTCGAACCGG
* *
12754024 TTTGACCGATCTGAACCGA
1 TTTGACCGGTCTGACCCGA
12754043 TTTGACCGGTCTGACCCGA
1 TTTGACCGGTCTGACCCGA
**
12754062 CCTGACC-GT-TGACCCGA
1 TTTGACCGGTCTGACCCGA
12754079 CCCGACCGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 8 0.25
18 2 0.06
19 22 0.69
ACGTcount: A:0.20, C:0.33, G:0.24, T:0.24
Consensus pattern (19 bp):
TTTGACCGGTCTGACCCGA
Found at i:12754076 original size:17 final size:17
Alignment explanation
Indices: 12754054--12754092 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
12754044 TTGACCGGTC
*
12754054 TGACCCGACCTGACCGT
1 TGACCCGACCCGACCGT
12754071 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
12754088 TGACC
1 TGACC
12754093 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.44, G:0.23, T:0.15
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:12761296 original size:20 final size:21
Alignment explanation
Indices: 12761266--12761334 Score: 83
Period size: 20 Copynumber: 3.4 Consensus size: 21
12761256 AAAACGGTTT
*
12761266 AACCGGTTTTCAACCGGTTCTG
1 AACCGG-TTTCGACCGGTTCTG
*
12761288 -ACCGGTTTCGATCGGTTC-G
1 AACCGGTTTCGACCGGTTCTG
12761307 AACCGGTTT-GACCGG-TCTG
1 AACCGGTTTCGACCGGTTCTG
12761326 AACCGGTTT
1 AACCGGTTT
12761335 GATCGGTCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 2 0.05
19 16 0.38
20 19 0.45
21 5 0.12
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
AACCGGTTTCGACCGGTTCTG
Found at i:12761328 original size:19 final size:19
Alignment explanation
Indices: 12761278--12761345 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 19
12761268 CCGGTTTTCA
12761278 ACCGGTTCTG-ACCGGTTTCG
1 ACCGG-TCTGAACCGGTTT-G
*
12761298 ATCGGT-TCGAACCGGTTTG
1 ACCGGTCT-GAACCGGTTTG
12761317 ACCGGTCTGAACCGGTTTG
1 ACCGGTCTGAACCGGTTTG
*
12761336 ATCGGTCTGA
1 ACCGGTCTGA
12761346 CCCGACCGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 1 0.02
19 28 0.67
20 13 0.31
ACGTcount: A:0.15, C:0.25, G:0.31, T:0.29
Consensus pattern (19 bp):
ACCGGTCTGAACCGGTTTG
Found at i:12761341 original size:9 final size:9
Alignment explanation
Indices: 12761278--12761347 Score: 59
Period size: 10 Copynumber: 7.3 Consensus size: 9
12761268 CCGGTTTTCA
12761278 ACCGGTTCTG
1 ACCGGTT-TG
12761288 ACCGGTTTCG
1 ACCGGTTT-G
* *
12761298 ATCGGTTCG
1 ACCGGTTTG
12761307 AACCGGTTTG
1 -ACCGGTTTG
*
12761317 ACCGGTCTG
1 ACCGGTTTG
12761326 AACCGGTTTG
1 -ACCGGTTTG
* *
12761336 ATCGGTCTG
1 ACCGGTTTG
12761345 ACC
1 ACC
12761348 CGACCGACCC
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
9 19 0.40
10 29 0.60
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:12771798 original size:22 final size:22
Alignment explanation
Indices: 12771772--12771817 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12771762 AATTATATTA
*
12771772 AAAAATTCTAAAATTTAAAATTC
1 AAAAA-TCTAAAATATAAAATTC
* *
12771795 AAAAATCTATAATATATAATTC
1 AAAAATCTAAAATATAAAATTC
12771817 A
1 A
12771818 TACATATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.35
Consensus pattern (22 bp):
AAAAATCTAAAATATAAAATTC
Found at i:12771975 original size:23 final size:24
Alignment explanation
Indices: 12771932--12771976 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
12771922 ATACATATTT
*
12771932 TAAAAATAATTTAAAATATTAATG
1 TAAAAATAATTGAAAATATTAATG
12771956 TAAAAA-AATTGAAGAA-ATTAA
1 TAAAAATAATTGAA-AATATTAA
12771977 GAATTTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (24 bp):
TAAAAATAATTGAAAATATTAATG
Found at i:12772072 original size:13 final size:13
Alignment explanation
Indices: 12772054--12772079 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12772044 TGAGAATTAT
12772054 GAATAAAAAATAA
1 GAATAAAAAATAA
12772067 GAATAAAAAATAA
1 GAATAAAAAATAA
12772080 AAATTATATA
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
GAATAAAAAATAA
Found at i:12776495 original size:138 final size:138
Alignment explanation
Indices: 12776314--12776719 Score: 663
Period size: 138 Copynumber: 3.0 Consensus size: 138
12776304 AAATGCTTAT
* * *
12776314 TTTTCCTGATTTTAATGTACTCATATATGCCTCTCGCTTGATATTTTGAAATTATTTGAATTACC
1 TTTTCTTGATTTTAATGTACTCATATATGCCTCTCACTTGATATTTTCAAATTATTTGAATTACC
*
12776379 ATGGGAAATTTGGGGGGAACAGTATAGGAGATGCAAGGAAGTCTTACCACATGGGCTGGAAATCA
66 ATGGGAAATTTGGGGGGAACAGTATAGGAGATGCAAGGAAGTCTTACCACATGGGCCGGAAATCA
12776444 CTTGATAC
131 CTTGATAC
*
12776452 TTTTCTTGATTTTAATGTACTCATATATGCCTCTCACTTGATATTTTCAAATTATTTGAATGACC
1 TTTTCTTGATTTTAATGTACTCATATATGCCTCTCACTTGATATTTTCAAATTATTTGAATTACC
*
12776517 ATGGGAAATTTGAGGGGAACAGTATAGGAGATGCAAGGAAGTCTTACCACATGGGCCGGAAATCA
66 ATGGGAAATTTGGGGGGAACAGTATAGGAGATGCAAGGAAGTCTTACCACATGGGCCGGAAATCA
*
12776582 CTTGATAT
131 CTTGATAC
** * *
12776590 TTTTCTTGATTTTAATGTACTTGTATATG-C-CTCACTTAATATTTTTAAATTATTTGAATTACC
1 TTTTCTTGATTTTAATGTACTCATATATGCCTCTCACTTGATATTTTCAAATTATTTGAATTACC
* * **
12776653 ATGGGAAATTTGGGGAGAACAGTATAGGAGATGCAAAGAAGTCTTACCACATGGGCCATAAATCA
66 ATGGGAAATTTGGGGGGAACAGTATAGGAGATGCAAGGAAGTCTTACCACATGGGCCGGAAATCA
12776718 CT
131 CT
12776720 AGGCTGAAAA
Statistics
Matches: 251, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
136 92 0.37
137 1 0.00
138 158 0.63
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (138 bp):
TTTTCTTGATTTTAATGTACTCATATATGCCTCTCACTTGATATTTTCAAATTATTTGAATTACC
ATGGGAAATTTGGGGGGAACAGTATAGGAGATGCAAGGAAGTCTTACCACATGGGCCGGAAATCA
CTTGATAC
Found at i:12779566 original size:103 final size:103
Alignment explanation
Indices: 12779387--12779594 Score: 337
Period size: 103 Copynumber: 2.0 Consensus size: 103
12779377 CCTGATGATA
* * *
12779387 TTTCTTTAGTATAACTTATTTTGATTGGTTTTTGTTTTGCTTTCAGCTATTAAGCACTGGTTTGC
1 TTTCTTTAGTATAACTTATATTGATTGGTTTTTGTTTTGCTATCAGCTATTAAGCACGGGTTTGC
12779452 TTAAATAAGTCCTCTTTTATTT-ATTTCCAGAACTGGAT
66 TTAAATAAGTCCTCTTTT-TTTGATTTCCAGAACTGGAT
* *
12779490 TTTCTTTAGTATAGCTTATATTGATTGGTTTTTGTTTTGCTATCAGCTATTGAGCACGGGTTTGC
1 TTTCTTTAGTATAACTTATATTGATTGGTTTTTGTTTTGCTATCAGCTATTAAGCACGGGTTTGC
* *
12779555 TTACATAAGTCCTCTTTTTTTGCTTTCCAGAACTGGAT
66 TTAAATAAGTCCTCTTTTTTTGATTTCCAGAACTGGAT
12779593 TT
1 TT
12779595 GAGGAGGATA
Statistics
Matches: 97, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
102 3 0.03
103 94 0.97
ACGTcount: A:0.20, C:0.14, G:0.16, T:0.50
Consensus pattern (103 bp):
TTTCTTTAGTATAACTTATATTGATTGGTTTTTGTTTTGCTATCAGCTATTAAGCACGGGTTTGC
TTAAATAAGTCCTCTTTTTTTGATTTCCAGAACTGGAT
Found at i:12780799 original size:21 final size:22
Alignment explanation
Indices: 12780773--12780816 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
12780763 TCAAAAGAAA
12780773 ATGTTTTG-ATGTTATAGTTTC
1 ATGTTTTGCATGTTATAGTTTC
12780794 ATGTTTTGCATGTTATAGTTTC
1 ATGTTTTGCATGTTATAGTTTC
12780816 A
1 A
12780817 AGATTTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.55
Consensus pattern (22 bp):
ATGTTTTGCATGTTATAGTTTC
Found at i:12782728 original size:29 final size:29
Alignment explanation
Indices: 12782705--12782920 Score: 125
Period size: 29 Copynumber: 7.5 Consensus size: 29
12782695 CAGGACATAT
*
12782705 ATATAATCCCATGCAGAATTAGGACGAGG
1 ATATAATCCCATGCAGAATTAGGACGAAG
* * * * *
12782734 ATATAATCCTATGCAGAATCATGACGGAT
1 ATATAATCCCATGCAGAATTAGGACGAAG
* * * * *
12782763 ATTTAATTCCATGTAAAACCTA-GACG-AG
1 ATATAATCCCATGCAGAA-TTAGGACGAAG
* * * *
12782791 ATATAATCCAATGCAGAATCACGACGAGG
1 ATATAATCCCATGCAGAATTAGGACGAAG
* * * * *
12782820 ATATAATCTCATGTAGAATCAGGATGAGG
1 ATATAATCCCATGCAGAATTAGGACGAAG
* * **
12782849 ATATAATCCCATGCAGAATCAAGACGGGG
1 ATATAATCCCATGCAGAATTAGGACGAAG
* * **
12782878 ATATAAT-CCATTCTAGAATCA-GAATAAG
1 ATATAATCCCATGC-AGAATTAGGACGAAG
*
12782906 ATATAATCTCATGCA
1 ATATAATCCCATGCA
12782921 AAATCAAGAC
Statistics
Matches: 143, Mismatches: 39, Indels: 11
0.74 0.20 0.06
Matches are distributed among these distances:
27 1 0.01
28 34 0.24
29 107 0.75
30 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (29 bp):
ATATAATCCCATGCAGAATTAGGACGAAG
Found at i:12782805 original size:57 final size:56
Alignment explanation
Indices: 12782725--12782885 Score: 166
Period size: 57 Copynumber: 2.8 Consensus size: 56
12782715 ATGCAGAATT
* *
12782725 AGGACGAGGATATAATCCTATGCAGAATCATGACGGATATTTAAT-TCCATGTAAAACC
1 AGGACGAGGATATAATCCAATGCAGAATCAAGACGGATA--TAATCT-CATGTAAAACC
* * *
12782783 TA-GACGA-GATATAATCCAATGCAGAATCACGACGAGGATATAATCTCATGTAGAATC
1 -AGGACGAGGATATAATCCAATGCAGAATCAAGAC--GGATATAATCTCATGTAAAACC
* *
12782840 AGGATGAGGATATAATCCCATGCAGAATCAAGACGGGGATATAATC
1 AGGACGAGGATATAATCCAATGCAGAATCAAGAC--GGATATAATC
12782886 CATTCTAGAA
Statistics
Matches: 89, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
56 1 0.01
57 41 0.46
58 41 0.46
59 6 0.07
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (56 bp):
AGGACGAGGATATAATCCAATGCAGAATCAAGACGGATATAATCTCATGTAAAACC
Found at i:12782861 original size:86 final size:84
Alignment explanation
Indices: 12782705--12782943 Score: 216
Period size: 86 Copynumber: 2.8 Consensus size: 84
12782695 CAGGACATAT
*
12782705 ATATAATCCCATGCAGAATTAGGACGAGGATATAATC-CTATGCAGAATCATGACGGATATTTAA
1 ATATAAT-CCATGCAGAATCA-GACGAGGATATAATCTC-ATGCAGAATCATGACGGATA-TTAA
* * *
12782769 TTCCATGTAAAACCTAGAC-GAG
62 TCCCATGCAAAACCAAGACGGAG
*
12782791 ATATAATCCAATGCAGAATCACGACGAGGATATAATCTCATGTAGAATCAGGATGA-GGATA-TA
1 ATATAATCC-ATGCAGAATCA-GACGAGGATATAATCTCATGCAGAATC---ATGACGGATATTA
* * *
12782854 ATCCCATGCAGAATCAAGACGGGG
61 ATCCCATGCAAAACCAAGACGGAG
* ** * * * *
12782878 ATATAATCCATTCTAGAATCAGAATAAGATATAATCTCATGCAAAATCAAGACGGGATATAAATC
1 ATATAATCCATGC-AGAATCAGACGAGGATATAATCTCATGCAGAATCATGAC-GGATATTAATC
12782943 C
64 C
12782944 ATACAGAACC
Statistics
Matches: 126, Mismatches: 17, Indels: 20
0.77 0.10 0.12
Matches are distributed among these distances:
83 3 0.02
85 7 0.06
86 88 0.70
87 19 0.15
88 5 0.04
89 4 0.03
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (84 bp):
ATATAATCCATGCAGAATCAGACGAGGATATAATCTCATGCAGAATCATGACGGATATTAATCCC
ATGCAAAACCAAGACGGAG
Found at i:12782908 original size:115 final size:114
Alignment explanation
Indices: 12782705--12782961 Score: 270
Period size: 115 Copynumber: 2.2 Consensus size: 114
12782695 CAGGACATAT
* * * * *
12782705 ATATAATCCCATGCAGAATTAGGACGAGGATATAATCCTATGCAGAATCATGACGGATATTTAAT
1 ATATAATCCCATGCAGAATCAGGACGAGGATATAATCCCATGCAGAATCAAGACGGAGATATAAT
* * * *
12782770 TCCATGTAAAACCTAGACGAGATATAATC-CAATGCAGAATCACGACGAGG
66 TCCATCTAAAACCTAGACAAGATATAATCTC-ATGCAAAATCAAGACG-GG
* * * *
12782820 ATATAATCTCATGTAGAATCAGGATGAGGATATAATCCCATGCAGAATCAAGACGGGGATATAA-
1 ATATAATCCCATGCAGAATCAGGACGAGGATATAATCCCATGCAGAATCAAGACGGAGATATAAT
* * *
12782884 TCCATTCTAGAATC-AGAATAAGATATAATCTCATGCAAAATCAAGACGGG
66 TCCA-TCTAAAACCTAG-ACAAGATATAATCTCATGCAAAATCAAGACGGG
* * *
12782934 ATATAAAT-CCATACAGAACCATGACGAG
1 ATAT-AATCCCATGCAGAATCAGGACGAG
12782962 ATTATGTTCT
Statistics
Matches: 116, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
114 26 0.22
115 89 0.77
116 1 0.01
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.23
Consensus pattern (114 bp):
ATATAATCCCATGCAGAATCAGGACGAGGATATAATCCCATGCAGAATCAAGACGGAGATATAAT
TCCATCTAAAACCTAGACAAGATATAATCTCATGCAAAATCAAGACGGG
Found at i:12782927 original size:57 final size:57
Alignment explanation
Indices: 12782789--12782945 Score: 194
Period size: 58 Copynumber: 2.7 Consensus size: 57
12782779 AACCTAGACG
* * * *
12782789 AGATATAATCCAATGCAGAATCACGACGAGGATATAATCTCA-TGTAGAATCAGGATGA
1 AGATATAATCC-ATGCAGAATCAAGACGGGGATATAATC-CATTCTAGAATCAGAATGA
*
12782847 GGATATAATCCCATGCAGAATCAAGACGGGGATATAATCCATTCTAGAATCAGAAT-A
1 AGATATAAT-CCATGCAGAATCAAGACGGGGATATAATCCATTCTAGAATCAGAATGA
*
12782904 AGATATAATCTCATGCAAAATCAAGAC-GGGATATAAATCCAT
1 AGATATAATC-CATGCAGAATCAAGACGGGGATAT-AATCCAT
12782946 ACAGAACCAT
Statistics
Matches: 88, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
56 8 0.09
57 33 0.38
58 45 0.51
59 2 0.02
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (57 bp):
AGATATAATCCATGCAGAATCAAGACGGGGATATAATCCATTCTAGAATCAGAATGA
Found at i:12784714 original size:24 final size:24
Alignment explanation
Indices: 12784681--12784746 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
12784671 CATGATTTTT
*
12784681 TTTTTC-AAAAATATTTTTTCATA
1 TTTTTCTAAAAATATTTTTGCATA
12784704 TTTTTCTAAAAATCA-TTTTGCATA
1 TTTTTCTAAAAAT-ATTTTTGCATA
* *
12784728 TTTATTTTAAACATATTTT
1 TTT-TTCTAAAAATATTTT
12784747 CAGAATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 6 0.17
24 18 0.50
25 12 0.33
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTTCTAAAAATATTTTTGCATA
Found at i:12785149 original size:4 final size:4
Alignment explanation
Indices: 12785140--12785174 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
12785130 CATTCTTCAA
*
12785140 ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
12785175 TATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAC
Found at i:12785179 original size:4 final size:4
Alignment explanation
Indices: 12785148--12785195 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
12785138 AAATACATAC
* * * * *
12785148 ATAT ATAC ATAC ATAC ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
12785196 TTTAAACACA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (4 bp):
ATAT
Found at i:12785195 original size:8 final size:8
Alignment explanation
Indices: 12785144--12785194 Score: 66
Period size: 8 Copynumber: 6.4 Consensus size: 8
12785134 CTTCAAATAC
12785144 ATACATAT
1 ATACATAT
*
12785152 ATACATAC
1 ATACATAT
*
12785160 ATACATAC
1 ATACATAT
12785168 ATACATAT
1 ATACATAT
*
12785176 ATATATAT
1 ATACATAT
*
12785184 ATATATAT
1 ATACATAT
12785192 ATA
1 ATA
12785195 TTTTAAACAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (8 bp):
ATACATAT
Found at i:12785195 original size:12 final size:12
Alignment explanation
Indices: 12785140--12785190 Score: 75
Period size: 12 Copynumber: 4.2 Consensus size: 12
12785130 CATTCTTCAA
12785140 ATACATACATAT
1 ATACATACATAT
*
12785152 ATACATACATAC
1 ATACATACATAT
12785164 ATACATACATAT
1 ATACATACATAT
* *
12785176 ATATATATATAT
1 ATACATACATAT
12785188 ATA
1 ATA
12785191 TATATTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (12 bp):
ATACATACATAT
Found at i:12785646 original size:54 final size:54
Alignment explanation
Indices: 12785582--12785760 Score: 277
Period size: 54 Copynumber: 3.3 Consensus size: 54
12785572 TGTGGTTTTT
* * *
12785582 CACACATAGTGCCGATACAGTATTTCACAAACTCATTATGAATTACATGGGTTG
1 CACACATAGTGCCAATACAGTAATTCACAAACTCATTATGAATTACGTGGGTTG
* *
12785636 CACACATAGTGCCAATACTGTAATTCACAAACTCATTATGAATTACGTGAGTTG
1 CACACATAGTGCCAATACAGTAATTCACAAACTCATTATGAATTACGTGGGTTG
* * * *
12785690 TACACATAGTACCAATACGGTAATTCATAAACTCATTATGAATTACGTGGGTTG
1 CACACATAGTGCCAATACAGTAATTCACAAACTCATTATGAATTACGTGGGTTG
12785744 CACACATAGTGCCAATA
1 CACACATAGTGCCAATA
12785761 TCATGTAAAA
Statistics
Matches: 113, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 113 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (54 bp):
CACACATAGTGCCAATACAGTAATTCACAAACTCATTATGAATTACGTGGGTTG
Found at i:12786196 original size:21 final size:20
Alignment explanation
Indices: 12786159--12786221 Score: 92
Period size: 21 Copynumber: 3.1 Consensus size: 20
12786149 CCATTAGACA
12786159 GGGGGAAT-TGGTACCCCCTG
1 GGGGGAATCT-GTACCCCCTG
*
12786179 GGGGGAATCTGTTCCCCCTTG
1 GGGGGAATCTGTACCCCC-TG
12786200 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
12786220 GG
1 GG
12786222 CAATCTGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.49
21 20 0.51
ACGTcount: A:0.13, C:0.27, G:0.38, T:0.22
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:12790079 original size:22 final size:21
Alignment explanation
Indices: 12790054--12790094 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12790044 ATTCAAAGAG
*
12790054 GGGAACCGATTCCCCTGCTATA
1 GGGAACCGA-TACCCTGCTATA
*
12790076 GGGAATCGATACCCTGCTA
1 GGGAACCGATACCCTGCTA
12790095 CAGTGCTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTATA
Found at i:12791875 original size:20 final size:20
Alignment explanation
Indices: 12791850--12791888 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12791840 TTTTTCATTT
12791850 AGGGGGAATC-GATACCCCCC
1 AGGGGGAATCTG-TACCCCCC
12791870 AGGGGGAATCTGTACCCCC
1 AGGGGGAATCTGTACCCCC
12791889 TGCGTAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.13
Consensus pattern (20 bp):
AGGGGGAATCTGTACCCCCC
Found at i:12793216 original size:64 final size:63
Alignment explanation
Indices: 12793134--12793291 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 63
12793124 TTTAAGGTGC
* * * * *
12793134 ATCGATGCACATGCAGTGCATCGATGTAT-TAATTTAAAAAGAAAACATCGAATAGGATTTATGA
1 ATCGATGCATAAGGAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTATGA
* * * *
12793198 ATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTATGC
1 ATCGATGCATAAGGAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTATGA
*
12793262 ATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 ATCGATGCATAAG-G-AGTGCATCGATGCAT
12793292 ACCTCCATTA
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
63 1 0.01
64 57 0.71
65 21 0.26
66 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (63 bp):
ATCGATGCATAAGGAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTATGA
Found at i:12793977 original size:103 final size:103
Alignment explanation
Indices: 12793752--12793969 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
12793742 GTAGAGGGTC
* *
12793752 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
12793817 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
12793855 TATGTGGTCTTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
12793920 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
12793958 TATGTGGTCCTT
1 TATGTGGTCCTT
12793970 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:12794048 original size:23 final size:23
Alignment explanation
Indices: 12793986--12794048 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
12793976 ATTATTATAT
12793986 GGCACTACAG-TGCAATTCTACGC
1 GGCACT-CAGATGCAATTCTACGC
* * * *
12794009 GGCACTCCGGTGTAATTCTACGT
1 GGCACTCAGATGCAATTCTACGC
*
12794032 GGCACTTAGATGCAATT
1 GGCACTCAGATGCAATT
12794049 ATATGAGTTG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
22 2 0.06
23 30 0.94
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (23 bp):
GGCACTCAGATGCAATTCTACGC
Found at i:12800203 original size:64 final size:63
Alignment explanation
Indices: 12800116--12800273 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 63
12800106 TTGTTTAAGG
* * * * *
12800116 TGCATCGATGCACATGCAATGCATCGATGTAT-TAATTTAAAAAGAAAAAAACGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGTATCCAA-TTAAAAA-AAAAAAACGAATAGGATTTA
* * * * *
12800180 TGCATCGATGCATAAGGAGTGCATCGATGTATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGTAT-CCAATTAAAAAAAAAAAACGAATAGGATTTA
*
12800244 TGCATCGATGCAT-GGTGTAGTGCATCGATG
1 TGCATCGATGCATAAG-G-AGTGCATCGATG
12800274 CATACCTCCA
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
63 1 0.01
64 59 0.75
65 18 0.23
66 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGTATCCAATTAAAAAAAAAAAACGAATAGGATTTA
Found at i:12800916 original size:103 final size:103
Alignment explanation
Indices: 12800737--12800951 Score: 394
Period size: 103 Copynumber: 2.1 Consensus size: 103
12800727 GTAGAGGGTC
*
12800737 TATGTGGTCCTTCGGGACATATATGTACTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTACTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
12800802 TTGATCCTTGGCATATGTATATGATCCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATCCTTAAGGAATGA
* *
12800840 TATGTGGTCATTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTACTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
12800905 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATCCTTAAGGAATGA
12800943 TATGTGGTC
1 TATGTGGTC
12800952 CTTATGGTGG
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.25, C:0.13, G:0.26, T:0.36
Consensus pattern (103 bp):
TATGTGGTCATTCGGGACATATATGTACTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATCCTTAAGGAATGA
Found at i:12800993 original size:23 final size:23
Alignment explanation
Indices: 12800960--12801011 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
12800950 TCCTTATGGT
12800960 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
12800983 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
12801006 GGCACT
1 GGCACT
12801012 TAGGTACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.31, G:0.27, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:12801021 original size:23 final size:23
Alignment explanation
Indices: 12800958--12801022 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
12800948 GGTCCTTATG
12800958 GTGGCAC-TACGGTGCAATTCTAC
1 GTGGCACTTA-GGTGCAATTCTAC
* **
12800981 GCGGCACTCCGGTGCAATTCTAC
1 GTGGCACTTAGGTGCAATTCTAC
*
12801004 GTGGCACTTAGGTACAATT
1 GTGGCACTTAGGTGCAATT
12801023 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GTGGCACTTAGGTGCAATTCTAC
Found at i:12801987 original size:20 final size:20
Alignment explanation
Indices: 12801962--12802009 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
12801952 CTCATGTTGT
12801962 TTCCTTTATTTAATTTTTCA
1 TTCCTTTATTTAATTTTTCA
*
12801982 TTCCTTTATTTAATTTTTCC
1 TTCCTTTATTTAATTTTTCA
12802002 TTCCTTTA
1 TTCCTTTA
12802010 GTTTTTCCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.65
Consensus pattern (20 bp):
TTCCTTTATTTAATTTTTCA
Found at i:12802001 original size:16 final size:16
Alignment explanation
Indices: 12801961--12802017 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
12801951 TCTCATGTTG
12801961 TTTCCTTTATTTAATTTT
1 TTTCCTTTATTTAA--TT
12801979 TCATTCCTTTATTTAATT
1 T--TTCCTTTATTTAATT
** *
12801997 TTTCCTTCCTTTAGTT
1 TTTCCTTTATTTAATT
12802013 TTTCC
1 TTTCC
12802018 ACTAACTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 17 0.50
18 4 0.12
20 13 0.38
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTCCTTTATTTAATT
Found at i:12803705 original size:16 final size:18
Alignment explanation
Indices: 12803670--12803706 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
12803660 TTTACATTCC
12803670 TTTCATATCATTTATACT
1 TTTCATATCATTTATACT
*
12803688 TTTCAT-TC-TTTATCCT
1 TTTCATATCATTTATACT
12803704 TTT
1 TTT
12803707 AACTTTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 2 0.11
18 6 0.33
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCATATCATTTATACT
Found at i:12805576 original size:18 final size:18
Alignment explanation
Indices: 12805533--12805576 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
12805523 TCCAATCAAA
*
12805533 AACGTATTTATGAACAGT
1 AACGTATGTATGAACAGT
**
12805551 AAAATATGTATGAACAGT
1 AACGTATGTATGAACAGT
*
12805569 ACCGTATG
1 AACGTATG
12805577 AACAGTGATG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (18 bp):
AACGTATGTATGAACAGT
Found at i:12806414 original size:24 final size:24
Alignment explanation
Indices: 12806387--12806452 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
12806377 AGCTCATTTA
12806387 AATTTGCACCGTAGTGCCACGTAG
1 AATTTGCACCGTAGTGCCACGTAG
* * *
12806411 AATTTGCACCGAAGTGCCGCGTAT
1 AATTTGCACCGTAGTGCCACGTAG
* *
12806435 AAATT-CACCGTATTGCCA
1 AATTTGCACCGTAGTGCCA
12806453 TATAAGATTG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
23 10 0.29
24 25 0.71
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (24 bp):
AATTTGCACCGTAGTGCCACGTAG
Found at i:12808737 original size:29 final size:28
Alignment explanation
Indices: 12808695--12808816 Score: 129
Period size: 29 Copynumber: 4.2 Consensus size: 28
12808685 AAAATGGAAA
* **
12808695 CAGGATAGCGATATAATCCCATATAGAGC
1 CAGGAT-GAGATATAATCCCATATAGAAT
* *
12808724 CAGGATAGAGATATAATCGCATA-CGAAAT
1 CAGGAT-GAGATATAATCCCATATAG-AAT
* *
12808753 CAGGATGAGGATATAATCCCATACAAAAT
1 CAGGATGA-GATATAATCCCATATAGAAT
*
12808782 CAGGATGAGATATAATCCCACATAGAAT
1 CAGGATGAGATATAATCCCATATAGAAT
12808810 CAGGATG
1 CAGGATG
12808817 TGTAACACCC
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
28 27 0.34
29 52 0.66
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (28 bp):
CAGGATGAGATATAATCCCATATAGAAT
Found at i:12808768 original size:58 final size:56
Alignment explanation
Indices: 12808691--12808798 Score: 146
Period size: 58 Copynumber: 1.9 Consensus size: 56
12808681 TTCAAAAATG
* * *
12808691 GAAACAGGATAGCGATATAATCCCATATAGAGCCAGGATAGAGATATAATCGCATAC
1 GAAACAGGATAGCGATATAATCCCATACAAAACCAGGAT-GAGATATAATCGCATAC
*
12808748 GAAATCAGGATGAG-GATATAATCCCATACAAAATCAGGATGAGATATAATC
1 GAAA-CAGGAT-AGCGATATAATCCCATACAAAACCAGGATGAGATATAATC
12808799 CCACATAGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
57 15 0.33
58 28 0.62
59 2 0.04
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (56 bp):
GAAACAGGATAGCGATATAATCCCATACAAAACCAGGATGAGATATAATCGCATAC
Found at i:12810461 original size:15 final size:15
Alignment explanation
Indices: 12810441--12810470 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12810431 ATACCTCCCT
*
12810441 TATGGTATCGGTACC
1 TATGGTATCGATACC
12810456 TATGGTATCGATACC
1 TATGGTATCGATACC
12810471 ACCTTCCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (15 bp):
TATGGTATCGATACC
Found at i:12811433 original size:29 final size:28
Alignment explanation
Indices: 12811276--12811429 Score: 168
Period size: 29 Copynumber: 5.4 Consensus size: 28
12811266 AAGGATGTTA
12811276 CAGGACGAGATATAATCCCATACAGAAT
1 CAGGACGAGATATAATCCCATACAGAAT
* * *
12811304 TAGGACGAGGATACAATCCCATGCAGAAT
1 CAGGACGA-GATATAATCCCATACAGAAT
* * *
12811333 CATGACAGTGATATAATCCCATTCAGAAT
1 CAGGAC-GAGATATAATCCCATACAGAAT
*
12811362 CAGGACG-GATTATAATCTCATACAGAAT
1 CAGGACGAGA-TATAATCCCATACAGAAT
* *
12811390 CAGGATGCG-GATATAATCTCATGCAGAAT
1 CAGGA--CGAGATATAATCCCATACAGAAT
12811419 CAGGACGAGAT
1 CAGGACGAGAT
12811430 TATACCCTCT
Statistics
Matches: 108, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.04
28 32 0.30
29 67 0.62
30 5 0.05
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (28 bp):
CAGGACGAGATATAATCCCATACAGAAT
Found at i:12813882 original size:21 final size:21
Alignment explanation
Indices: 12813856--12813908 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
12813846 GTACATTGCT
12813856 GCAATATTTATTTTTATATTA
1 GCAATATTTATTTTTATATTA
12813877 GCAATATTTATTTTTATATTA
1 GCAATATTTATTTTTATATTA
* *
12813898 ACCATATTTAT
1 GCAATATTTAT
12813909 AATATATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.55
Consensus pattern (21 bp):
GCAATATTTATTTTTATATTA
Found at i:12813926 original size:16 final size:16
Alignment explanation
Indices: 12813905--12813943 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
12813895 TTAACCATAT
12813905 TTATAATATATTTAAA
1 TTATAATATATTTAAA
*
12813921 TTATAATATATTTAAT
1 TTATAATATATTTAAA
12813937 TTATAAT
1 TTATAAT
12813944 TAATAATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATAATATATTTAAA
Found at i:12815556 original size:24 final size:24
Alignment explanation
Indices: 12815451--12815558 Score: 78
Period size: 24 Copynumber: 4.5 Consensus size: 24
12815441 AACGGAGATA
* *
12815451 TCAGAAATCAAAATAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* * *
12815474 AACAGATATCAGAACAGAA-TCCAG
1 -TCAGAAATCAGAACAGAATTCAAG
* * *
12815498 ATTAGAAATCATAACAGAATTGAAG
1 -TCAGAAATCAGAACAGAATTCAAG
* *
12815523 TCATG-TATCAGAACATAATTCAAG
1 TCA-GAAATCAGAACAGAATTCAAG
12815547 TCAGAAATCAGA
1 TCAGAAATCAGA
12815559 TAAAATATTT
Statistics
Matches: 64, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
23 3 0.05
24 57 0.89
25 4 0.06
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.21
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:12818721 original size:350 final size:348
Alignment explanation
Indices: 12818086--12818786 Score: 1302
Period size: 350 Copynumber: 2.0 Consensus size: 348
12818076 AGTGGCGGCG
12818086 CATGGGCCCACTTCCGGCAGCCTATAAATCACGTAAAAATTTCTAAAAATTATTTTAAGGCATTT
1 CATGGGCCCACTTCCGGCAGCCTATAAATCACGTAAAAATTTCTAAAAATTATTTTAAGGCATTT
12818151 TAAGATACTTACCAAGCTCGGTTCACAATTTTGAATGGCGGAGAGCTCAATAAATCGGAAACTTT
66 TAAGATACTTACCAAGCTCGGTTCACAATTTTGAATGGCGGAGAGCTCAATAAATCGGAAACTTT
12818216 GATCGCTTCACCTCCTCACGCGCCGCCGCCGATACTTGGATCATTGGATCATTGGATCGTCGTGA
131 GATCGCTTCACCTCCTCACGCGCCGCCGCCGATACTTGGATCATTGGATCATTGGATCGTCGTGA
12818281 ATCGACGAAAAACCAACTGAAATCGATTTATTACCGACGATACTTCCGACTGAAATTAACGACGA
196 ATCGACGAAAAACCAACTGAAATCGATTTATTACCGACGATACTTCCGACTGAAATTAACGACGA
12818346 ACAACGACGATTCATGAAGAAAGGTTTGAGGGGTTTTGTTCCTCGGTCGACAACG-A-A-TGGTG
261 ACAACGACGATTCATGAAGAAAGGTTTGAGGGGTTTTGTTCCTCGGTCGACAACGAACAGTGGTG
12818408 GTTTCGATTCG-TGATCGGAGGT
326 GTTTCGATTCGTTGATCGGAGGT
12818430 CATGGGCCCACTTCCGGCAGCCTATAAATCACGTAAAAATTTCTAAAAATTATTTTAAGGCATTT
1 CATGGGCCCACTTCCGGCAGCCTATAAATCACGTAAAAATTTCTAAAAATTATTTTAAGGCATTT
12818495 TAAGATACTTACCAAGCTCGGTTCACAATTTTGAATGGCGGAGAGCTCAATTTCAATAAATCGGA
66 TAAGATACTTACCAAGCTCGGTTCACAATTTTGAATGGCGGAGAG--C----TCAATAAATCGGA
12818560 AACTTTGATCGCTTCACCTCCTCACGCGCCGCCGCCGATACTTGGATCATTGGATCATTGGATCG
125 AACTTTGATCGCTTCACCTCCTCACGCGCCGCCGCCGATACTTGGATCATTGGATCATTGGATCG
12818625 TCGTGAATCGACGAAAAACCAACTGAAATCGATTTATTACCGACGATACTTCCGACTGAAATTAA
190 TCGTGAATCGACGAAAAACCAACTGAAATCGATTTATTACCGACGATACTTCCGACTGAAATTAA
12818690 CGACGAACAACGACGATTCATGAAGAAAGGTTTGAGGGGTTTTGTTCCTCGGTCGACAACGAACA
255 CGACGAACAACGACGATTCATGAAGAAAGGTTTGAGGGGTTTTGTTCCTCGGTCGACAACGAACA
12818755 TGGTGGTGGTTTCGATTCGTTGATCGGAGGT
320 --GTGGTGGTTTCGATTCGTTGATCGGAGGT
12818786 C
1 C
12818787 GGACGGCGAG
Statistics
Matches: 345, Mismatches: 0, Indels: 12
0.97 0.00 0.03
Matches are distributed among these distances:
344 110 0.32
346 1 0.00
350 204 0.59
351 1 0.00
352 1 0.00
355 16 0.05
356 12 0.03
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (348 bp):
CATGGGCCCACTTCCGGCAGCCTATAAATCACGTAAAAATTTCTAAAAATTATTTTAAGGCATTT
TAAGATACTTACCAAGCTCGGTTCACAATTTTGAATGGCGGAGAGCTCAATAAATCGGAAACTTT
GATCGCTTCACCTCCTCACGCGCCGCCGCCGATACTTGGATCATTGGATCATTGGATCGTCGTGA
ATCGACGAAAAACCAACTGAAATCGATTTATTACCGACGATACTTCCGACTGAAATTAACGACGA
ACAACGACGATTCATGAAGAAAGGTTTGAGGGGTTTTGTTCCTCGGTCGACAACGAACAGTGGTG
GTTTCGATTCGTTGATCGGAGGT
Found at i:12823184 original size:32 final size:32
Alignment explanation
Indices: 12823143--12823208 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
12823133 TCAAGAGATT
12823143 GTGGAAATCAAATCGAAATTAACAACTATTCA
1 GTGGAAATCAAATCGAAATTAACAACTATTCA
12823175 GTGGAAATCAAATCGAAATTAACAACTATTCA
1 GTGGAAATCAAATCGAAATTAACAACTATTCA
12823207 GT
1 GT
12823209 TTGATGAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (32 bp):
GTGGAAATCAAATCGAAATTAACAACTATTCA
Found at i:12825611 original size:64 final size:64
Alignment explanation
Indices: 12825540--12825662 Score: 212
Period size: 64 Copynumber: 1.9 Consensus size: 64
12825530 TGCAAGGAGT
* *
12825540 CTTCAGTTGAAGACTCTAAGACTAGACTACTATACGTTTTTAACCTTC-AGAAGATTCCATTGCA
1 CTTCAGTTGAAGACTCCAAGACTAGACTACTATACGTCTTTAACCTTCGA-AAGATTCCATTGCA
12825604 CTTCAGTTGAAGACTCCAAGACTAGACTACTATACGTCTTTAACCTTCGAAAGATTCCA
1 CTTCAGTTGAAGACTCCAAGACTAGACTACTATACGTCTTTAACCTTCGAAAGATTCCA
12825663 AGAGTGCAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
64 55 0.98
65 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (64 bp):
CTTCAGTTGAAGACTCCAAGACTAGACTACTATACGTCTTTAACCTTCGAAAGATTCCATTGCA
Found at i:12826084 original size:21 final size:21
Alignment explanation
Indices: 12826059--12826098 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12826049 TAGTTCCATC
*
12826059 ATTAAAATAGAATCACGAGTG
1 ATTAAAATAGAACCACGAGTG
12826080 ATTAAAATAGAACCACGAG
1 ATTAAAATAGAACCACGAG
12826099 AACATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.17, T:0.20
Consensus pattern (21 bp):
ATTAAAATAGAACCACGAGTG
Found at i:12830070 original size:21 final size:21
Alignment explanation
Indices: 12830045--12830087 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12830035 CGTCTGACTT
12830045 CCGATCGACGAACCAAAACCA
1 CCGATCGACGAACCAAAACCA
12830066 CCGATCGACGAACCAAAACCA
1 CCGATCGACGAACCAAAACCA
12830087 C
1 C
12830088 TATCGTGTTC
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:0.42, C:0.40, G:0.14, T:0.05
Consensus pattern (21 bp):
CCGATCGACGAACCAAAACCA
Found at i:12833178 original size:24 final size:24
Alignment explanation
Indices: 12833122--12833190 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 24
12833112 AAATTACCTG
* * *
12833122 AATTCTGTTCTGATATCCGATCTG
1 AATTCTGTTATGATATCTGATCTA
*
12833146 GATTCTGTTATGATATCTGATCTA
1 AATTCTGTTATGATATCTGATCTA
* * *
12833170 AATTTTGTTTTGATTTCTGAT
1 AATTCTGTTATGATATCTGAT
12833191 ATCTCTGTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.22, C:0.13, G:0.16, T:0.49
Consensus pattern (24 bp):
AATTCTGTTATGATATCTGATCTA
Found at i:12837050 original size:28 final size:29
Alignment explanation
Indices: 12836969--12837095 Score: 157
Period size: 30 Copynumber: 4.3 Consensus size: 29
12836959 AATAATTACT
* *
12836969 AAAATAGCACCTTTTTCGAATTAAATTCTC
1 AAAATAGCA-CTTTTTCAAATTAAATTCCC
*
12836999 AAAATGGCACCTTTTTCAAATTAAATTCCC
1 AAAATAGCA-CTTTTTCAAATTAAATTCCC
*
12837029 AATATAGCACTTTTTC-AATTAAATTCCC
1 AAAATAGCACTTTTTCAAATTAAATTCCC
* * * *
12837057 AAAATATCACCTTTTCAAATTAATTTCTC
1 AAAATAGCACTTTTTCAAATTAAATTCCC
12837086 AAAATAGCAC
1 AAAATAGCAC
12837096 CCATTTCGAA
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 25 0.29
29 26 0.31
30 34 0.40
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAATAGCACTTTTTCAAATTAAATTCCC
Found at i:12837070 original size:29 final size:30
Alignment explanation
Indices: 12836940--12837119 Score: 183
Period size: 29 Copynumber: 6.2 Consensus size: 30
12836930 CCATTTTACA
* * *
12836940 AAAATAGCACCCTTTTT-AAAAT-AATTACT
1 AAAATAGCA-CCTTTTTCAAATTAAATTCCC
* *
12836969 AAAATAGCACCTTTTTCGAATTAAATTCTC
1 AAAATAGCACCTTTTTCAAATTAAATTCCC
*
12836999 AAAATGGCACCTTTTTCAAATTAAATTCCC
1 AAAATAGCACCTTTTTCAAATTAAATTCCC
*
12837029 AATATAGCA-CTTTTTC-AATTAAATTCCC
1 AAAATAGCACCTTTTTCAAATTAAATTCCC
* * *
12837057 AAAATATCACC-TTTTCAAATTAATTTCTC
1 AAAATAGCACCTTTTTCAAATTAAATTCCC
** * *
12837086 AAAATAGCACCCATTTCGAATT-AATTCCT
1 AAAATAGCACCTTTTTCAAATTAAATTCCC
12837115 AAAAT
1 AAAAT
12837120 GTCACCCGAT
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
28 31 0.25
29 49 0.39
30 46 0.37
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (30 bp):
AAAATAGCACCTTTTTCAAATTAAATTCCC
Found at i:12837112 original size:58 final size:59
Alignment explanation
Indices: 12836940--12837119 Score: 206
Period size: 58 Copynumber: 3.1 Consensus size: 59
12836930 CCATTTTACA
* * * *
12836940 AAAATAGCACCCTTTTTAAAATAATTACT-AAAATAGCACCTTTTTCGAATTAAATTCTC
1 AAAATAGCA-CCTTTTCAAATTAATTTCTCAAAATAGCACCTTTTTCGAATTAAATTCCC
* * * *
12836999 AAAATGGCACCTTTTTCAAATTAAATTCCCAATATAGCA-CTTTTTC-AATTAAATTCCC
1 AAAATAGCACC-TTTTCAAATTAATTTCTCAAAATAGCACCTTTTTCGAATTAAATTCCC
* ** *
12837057 AAAATATCACCTTTTCAAATTAATTTCTCAAAATAGCACCCATTTCGAATT-AATTCCT
1 AAAATAGCACCTTTTCAAATTAATTTCTCAAAATAGCACCTTTTTCGAATTAAATTCCC
12837115 AAAAT
1 AAAAT
12837120 GTCACCCGAT
Statistics
Matches: 101, Mismatches: 16, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
57 24 0.24
58 38 0.38
59 31 0.31
60 8 0.08
ACGTcount: A:0.39, C:0.21, G:0.04, T:0.36
Consensus pattern (59 bp):
AAAATAGCACCTTTTCAAATTAATTTCTCAAAATAGCACCTTTTTCGAATTAAATTCCC
Found at i:12837155 original size:17 final size:17
Alignment explanation
Indices: 12837133--12837169 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12837123 ACCCGATCAA
12837133 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
*
12837150 CGGTCAACGTGTCGGGT
1 CGGTCAACGGGTCGGGT
12837167 CGG
1 CGG
12837170 AACCGGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.24, G:0.46, T:0.19
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Found at i:12844287 original size:30 final size:30
Alignment explanation
Indices: 12844253--12844381 Score: 154
Period size: 30 Copynumber: 4.3 Consensus size: 30
12844243 AATAATTACT
* * *
12844253 AAAATAGCACCTTTTTCTAATTAAATTTCT
1 AAAATAGCACCTTTTTCGAATTAAATTCCC
* *
12844283 AAAATTGAACC-TTTTCGAATTAAATTCCC
1 AAAATAGCACCTTTTTCGAATTAAATTCCC
*
12844312 AATATAGCACCTTTTTCGAATTAAATTCCC
1 AAAATAGCACCTTTTTCGAATTAAATTCCC
** *
12844342 AAAATAG-ATTTTTTTTCAAATTAAATTCCC
1 AAAATAGCA-CCTTTTTCGAATTAAATTCCC
12844372 AAAATAGCAC
1 AAAATAGCAC
12844382 TCATATAGAA
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
29 24 0.29
30 58 0.70
31 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAATAGCACCTTTTTCGAATTAAATTCCC
Found at i:12844325 original size:59 final size:60
Alignment explanation
Indices: 12844253--12844381 Score: 170
Period size: 59 Copynumber: 2.2 Consensus size: 60
12844243 AATAATTACT
* * * * *
12844253 AAAATAGCACCTTTTTCTAATTAAATTTCTAAAATTGA-ACCTTTTCGAATTAAATTCCC
1 AAAATAGCACCTTTTTCGAATTAAATTCCCAAAATAGATACCTTTTCAAATTAAATTCCC
* ***
12844312 AATATAGCACCTTTTTCGAATTAAATTCCCAAAATAGATTTTTTTTCAAATTAAATTCCC
1 AAAATAGCACCTTTTTCGAATTAAATTCCCAAAATAGATACCTTTTCAAATTAAATTCCC
12844372 AAAATAGCAC
1 AAAATAGCAC
12844382 TCATATAGAA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
59 33 0.56
60 26 0.44
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (60 bp):
AAAATAGCACCTTTTTCGAATTAAATTCCCAAAATAGATACCTTTTCAAATTAAATTCCC
Found at i:12844393 original size:60 final size:59
Alignment explanation
Indices: 12844294--12844405 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 59
12844284 AAATTGAACC
* * * * *
12844294 TTTTCGAATTAAATTCCCAATATAGCACCTTTTTCGAATTAAATTCCCAAAATAGATTTT
1 TTTTCAAATTAAATTCCCAAAATAGCACCTATATAGAATT-AATTCCCAAAATAGATTTT
12844354 TTTTCAAATTAAATTCCCAAAATAGCA-CTCATATAGAATTAATTCCCAAAAT
1 TTTTCAAATTAAATTCCCAAAATAGCACCT-ATATAGAATTAATTCCCAAAAT
12844406 GTCACCCCGG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
59 14 0.30
60 32 0.70
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (59 bp):
TTTTCAAATTAAATTCCCAAAATAGCACCTATATAGAATTAATTCCCAAAATAGATTTT
Found at i:12844394 original size:30 final size:30
Alignment explanation
Indices: 12844253--12844405 Score: 111
Period size: 30 Copynumber: 5.2 Consensus size: 30
12844243 AATAATTACT
** * *
12844253 AAAATAGCAC-CTTTTTCTAATTAAATTTCT
1 AAAATAGCACTC-TTTTAGAATTAAATTCCC
* * *
12844283 AAAATTGAAC-CTTTTCGAATTAAATTCCC
1 AAAATAGCACTCTTTTAGAATTAAATTCCC
* *
12844312 AATATAGCAC-CTTTTTCGAATTAAATTCCC
1 AAAATAGCACTC-TTTTAGAATTAAATTCCC
* *
12844342 AAAATAG-ATTTTTTTTCA-AATTAAATTCCC
1 AAAATAGCA-CTCTTTT-AGAATTAAATTCCC
* *
12844372 AAAATAGCACTCATATAGAATT-AATTCCC
1 AAAATAGCACTCTTTTAGAATTAAATTCCC
12844401 AAAAT
1 AAAAT
12844406 GTCACCCCGG
Statistics
Matches: 101, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
29 37 0.37
30 63 0.62
31 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (30 bp):
AAAATAGCACTCTTTTAGAATTAAATTCCC
Found at i:12844442 original size:17 final size:17
Alignment explanation
Indices: 12844420--12844455 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12844410 CCCCGGTCAA
12844420 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
12844437 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
12844454 CG
1 CG
12844456 AATTAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.25, G:0.47, T:0.17
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Found at i:12844981 original size:18 final size:18
Alignment explanation
Indices: 12844958--12844994 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
12844948 TGGTATGAAA
*
12844958 CCAGAATCAATTTGCACG
1 CCAGAATCAATTTCCACG
12844976 CCAGAATCAATTTCCACG
1 CCAGAATCAATTTCCACG
12844994 C
1 C
12844995 ATATAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.22
Consensus pattern (18 bp):
CCAGAATCAATTTCCACG
Found at i:12845633 original size:28 final size:28
Alignment explanation
Indices: 12845573--12845633 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
12845563 AGAGGATAAC
**
12845573 GAAAAAATAAAAAGAGAGAAGAAATCGA
1 GAAAAAATAAAAAGAGAGAAGAAAAAGA
* *
12845601 GAAAAAATAAAAAATAGAGCAGAAAAAGA
1 GAAAAAAT-AAAAAGAGAGAAGAAAAAGA
12845630 -AAAA
1 GAAAA
12845634 CGACAAATAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.43
29 16 0.57
ACGTcount: A:0.72, C:0.03, G:0.18, T:0.07
Consensus pattern (28 bp):
GAAAAAATAAAAAGAGAGAAGAAAAAGA
Found at i:12846425 original size:25 final size:25
Alignment explanation
Indices: 12846396--12846448 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
12846386 TCATCTGTTT
* *
12846396 TTTATTGTTATATTAATATTTTTTA
1 TTTATTATTATATTAATATTTATTA
* *
12846421 TTTATTATTATTTTCATATTTATTA
1 TTTATTATTATATTAATATTTATTA
12846446 TTT
1 TTT
12846449 TTTCTTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (25 bp):
TTTATTATTATATTAATATTTATTA
Found at i:12846442 original size:18 final size:18
Alignment explanation
Indices: 12846406--12846452 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
12846396 TTTATTGTTA
* *
12846406 TATTAATATTTT-TTATT
1 TATTATTATTTTCATATT
12846423 TATTATTATTTTCATATT
1 TATTATTATTTTCATATT
12846441 TATTATT-TTTTC
1 TATTATTATTTTC
12846453 TTTTAATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTATTATTTTCATATT
Found at i:12846457 original size:15 final size:15
Alignment explanation
Indices: 12846412--12846523 Score: 50
Period size: 17 Copynumber: 6.9 Consensus size: 15
12846402 GTTATATTAA
*
12846412 TATTTTTT-ATTTAT
1 TATTTTTTCTTTTAT
12846426 TATTATTTTCATATTTAT
1 TATT-TTTTC-T-TTTAT
12846444 TATTTTTTCTTTTAATCT
1 TATTTTTTCTTTT-A--T
*
12846462 TTTTTTGTTCTTTT-T
1 TATTTT-TTCTTTTAT
*
12846477 TGATTTGTTTTATTTTAT
1 T-A-TT-TTTTCTTTTAT
* *
12846495 CTTTTTTTATCTATTAT
1 -TATTTTT-TCTTTTAT
12846512 T-TTTTTTCTTTT
1 TATTTTTTCTTTT
12846524 CCCTTTGATT
Statistics
Matches: 76, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
14 9 0.12
15 14 0.18
16 6 0.08
17 21 0.28
18 18 0.24
19 8 0.11
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (15 bp):
TATTTTTTCTTTTAT
Found at i:12847977 original size:23 final size:23
Alignment explanation
Indices: 12847951--12848027 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
12847941 TAGTCCAATT
12847951 TTCCAAATTCGCGTTGCGATTTA
1 TTCCAAATTCGCGTTGCGATTTA
*
12847974 TTCCAAATT--TGTTGCGA--TA
1 TTCCAAATTCGCGTTGCGATTTA
* *
12847993 GTCCAAGTTCGCGTTGCGATTTA
1 TTCCAAATTCGCGTTGCGATTTA
12848016 TTCCAAATTCGC
1 TTCCAAATTCGC
12848028 TGCGATAGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 9 0.20
21 14 0.32
23 21 0.48
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (23 bp):
TTCCAAATTCGCGTTGCGATTTA
Found at i:12847987 original size:21 final size:21
Alignment explanation
Indices: 12847951--12848033 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
12847941 TAGTCCAATT
12847951 TTCCAAATTCGCGTTGCGATTTA
1 TTCCAAATT--CGTTGCGATTTA
*
12847974 TTCCAAATTTGTTGCGA--TA
1 TTCCAAATTCGTTGCGATTTA
* *
12847993 GTCCAAGTTCGCGTTGCGATTTA
1 TTCCAAATT--CGTTGCGATTTA
*
12848016 TTCCAAATTCGCTGCGAT
1 TTCCAAATTCGTTGCGAT
12848034 AGTCCAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
19 9 0.18
21 22 0.45
23 18 0.37
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (21 bp):
TTCCAAATTCGTTGCGATTTA
Found at i:12848004 original size:42 final size:42
Alignment explanation
Indices: 12847952--12848046 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
12847942 AGTCCAATTT
* *
12847952 TCCAAATTCGCGTTGCGATTTATTCCAAATTTGTTGCGATAG
1 TCCAAATTCGCGTTGCGATTTATTCCAAATTCGCTGCGATAG
*
12847994 TCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCTGCGATAG
1 TCCAAATTCGCGTTGCGATTTATTCCAAATTCGCTGCGATAG
*
12848036 TCCAAAATCGC
1 TCCAAATTCGC
12848047 AACGACTGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (42 bp):
TCCAAATTCGCGTTGCGATTTATTCCAAATTCGCTGCGATAG
Found at i:12848970 original size:19 final size:19
Alignment explanation
Indices: 12848946--12849035 Score: 99
Period size: 19 Copynumber: 4.5 Consensus size: 19
12848936 AATCGCAACG
*
12848946 CGAACTTCGACTATCGCAA
1 CGAACTTGGACTATCGCAA
12848965 CGAACTTGGACTATCGCAA
1 CGAACTTGGACTATCGCAA
* * *
12848984 TGAATTTGGAATAAATCGCAA
1 CGAACTTGGACT--ATCGCAA
12849005 CGCGAACTTGGACTATCGCAA
1 --CGAACTTGGACTATCGCAA
*
12849026 CGAATTTGGA
1 CGAACTTGGA
12849036 AAATCGCATT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
19 36 0.61
21 14 0.24
23 9 0.15
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.23
Consensus pattern (19 bp):
CGAACTTGGACTATCGCAA
Found at i:12849004 original size:61 final size:61
Alignment explanation
Indices: 12848909--12849035 Score: 200
Period size: 61 Copynumber: 2.1 Consensus size: 61
12848899 CGTTGCAATT
*
12848909 TTGGACTATTACAACGAATTTAGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
1 TTGGACTATCACAACGAATTTAGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
* * * * *
12848970 TTGGACTATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAAT
1 TTGGACTATCACAACGAATTTAGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
12849031 TTGGA
1 TTGGA
12849036 AAATCGCATT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (61 bp):
TTGGACTATCACAACGAATTTAGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAAC
Found at i:12849022 original size:42 final size:38
Alignment explanation
Indices: 12848958--12849043 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 38
12848948 AACTTCGACT
*
12848958 ATCGCAACGAACTTGGACTATCGCAATGAATTTGGAATAA
1 ATCGCAACGAACTTGGACTATCGCAACGAATTTGG-A-AA
12848998 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAA--CGAACTTGGACTATCGCAACGAATTTGGAAA
12849038 ATCGCA
1 ATCGCA
12849044 TTGCGATAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
40 15 0.35
41 1 0.02
42 27 0.63
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (38 bp):
ATCGCAACGAACTTGGACTATCGCAACGAATTTGGAAA
Found at i:12849041 original size:19 final size:19
Alignment explanation
Indices: 12848935--12849043 Score: 74
Period size: 19 Copynumber: 5.4 Consensus size: 19
12848925 AATTTAGAAT
*
12848935 AAATCGCAACGCGAACTTCGA
1 AAATCGCAA--CGAACTTGGA
**
12848956 CTATCGCAACGAACTTGGA
1 AAATCGCAACGAACTTGGA
** * *
12848975 CTATCGCAATGAATTTGGAA
1 AAATCGCAACGAACTTGG-A
12848995 TAAATCGCAACGCGAACTTGGA
1 -AAATCGCAA--CGAACTTGGA
** *
12849017 CTATCGCAACGAATTTGGA
1 AAATCGCAACGAACTTGGA
12849036 AAATCGCA
1 AAATCGCA
12849044 TTGCGATAGT
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
19 40 0.57
20 1 0.01
21 21 0.30
22 1 0.01
23 7 0.10
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (19 bp):
AAATCGCAACGAACTTGGA
Found at i:12849068 original size:21 final size:21
Alignment explanation
Indices: 12849039--12849091 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12849029 ATTTGGAAAA
*
12849039 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
* *
12849060 TCGCGTTGCGATAGTTGATGT
1 TCGCGTTGCGATAGTCGAAGT
12849081 TCGCGTTGCGA
1 TCGCGTTGCGA
12849092 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:12875896 original size:2 final size:2
Alignment explanation
Indices: 12875889--12875938 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
12875879 TTCATCCCAA
12875889 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12875930 AT AT AT AT A
1 AT AT AT AT A
12875939 AATACGAGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.