Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004117.1 Hibiscus syriacus cultivar Beakdansim tig00009009_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: 2456583
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 8 of 9
Found at i:1976998 original size:3 final size:3
Alignment explanation
Indices: 1976990--1977033 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1976980 TCTATTTTAT
1976990 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1977034 CCACACGGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1978365 original size:16 final size:18
Alignment explanation
Indices: 1978333--1978366 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1978323 TATTAATTTA
1978333 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1978351 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1978367 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1979040 original size:130 final size:130
Alignment explanation
Indices: 1978836--1979083 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
1978826 AATTTTCTTC
* * *
1978836 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACAGGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
1978901 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * * *
1978966 TAATTAGGTGGTGACAGGTGTCACCAATGACACGTGTCATGGTCATGTGCTAACACATGTCATAT
1 TAATTAGGTGGTGACAGGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
1979031 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1979084 TATATAAATA
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACAGGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1979532 original size:35 final size:35
Alignment explanation
Indices: 1979482--1979557 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
1979472 AATTGAATTT
* *
1979482 AATTGAATTATTTTGGAATTTAGGCTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGCTTTAGAATGA
* * *
1979517 AATTGAATTACTTTGGAAATTGGGGTTTATAATGA
1 AATTGAATTACTTTGGAAATTAGGCTTTAGAATGA
1979552 AATTGA
1 AATTGA
1979558 GGACTGTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.41
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGCTTTAGAATGA
Found at i:1979977 original size:2 final size:2
Alignment explanation
Indices: 1979970--1980019 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1979960 TTTGTACTCG
1979970 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1980012 AT AT AT AT
1 AT AT AT AT
1980020 TCTAAGAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1982800 original size:7 final size:7
Alignment explanation
Indices: 1982788--1982826 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
1982778 CCGACCCAAC
1982788 CCGTTGA
1 CCGTTGA
1982795 CCGTTGA
1 CCGTTGA
1982802 CCGTTGA
1 CCGTTGA
1982809 CCCGTTGA
1 -CCGTTGA
1982817 CCGTTGA
1 CCGTTGA
1982824 CCG
1 CCG
1982827 GCGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.13, C:0.33, G:0.28, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:1982815 original size:15 final size:15
Alignment explanation
Indices: 1982788--1982835 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 15
1982778 CCGACCCAAC
1982788 CCGTTGA-CCGTTGA
1 CCGTTGACCCGTTGA
1982802 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
1982817 CCGTTGACCGGCGTTGA
1 CCGTTGACC--CGTTGA
1982834 CC
1 CC
1982836 ATTGTTGACC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.23
15 16 0.52
17 8 0.26
ACGTcount: A:0.12, C:0.33, G:0.29, T:0.25
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:1986853 original size:13 final size:12
Alignment explanation
Indices: 1986835--1986883 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 12
1986825 TCATAACCCG
1986835 ACCCGACCCGTTT
1 ACCCGACCCG-TT
*
1986848 ACCCGACCAGTT
1 ACCCGACCCGTT
1986860 GACCCGACCCG--
1 -ACCCGACCCGTT
1986871 ACCCGACCCGTT
1 ACCCGACCCGTT
1986883 A
1 A
1986884 ACTCGACCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
10 10 0.32
12 3 0.10
13 18 0.58
ACGTcount: A:0.20, C:0.47, G:0.18, T:0.14
Consensus pattern (12 bp):
ACCCGACCCGTT
Found at i:1986877 original size:36 final size:36
Alignment explanation
Indices: 1986830--1986899 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
1986820 ACCGGTCATA
*
1986830 ACCCGACCCGACCCGTTTACCCGACCAGTTGACCCG
1 ACCCGACCCGACCCGTTAACCCGACCAGTTGACCCG
* *
1986866 ACCCGACCCGACCCGTTAACTCGACCTGTTGACC
1 ACCCGACCCGACCCGTTAACCCGACCAGTTGACC
1986900 GTTGACCACC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.20, C:0.46, G:0.19, T:0.16
Consensus pattern (36 bp):
ACCCGACCCGACCCGTTAACCCGACCAGTTGACCCG
Found at i:1986890 original size:23 final size:23
Alignment explanation
Indices: 1986848--1986891 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1986838 CGACCCGTTT
*
1986848 ACCCGACCAGTTGACCCGACCCG
1 ACCCGACCAGTTAACCCGACCCG
* *
1986871 ACCCGACCCGTTAACTCGACC
1 ACCCGACCAGTTAACCCGACC
1986892 TGTTGACCGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.48, G:0.18, T:0.11
Consensus pattern (23 bp):
ACCCGACCAGTTAACCCGACCCG
Found at i:1989356 original size:24 final size:24
Alignment explanation
Indices: 1989329--1989396 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
1989319 TTCGATTTGA
*
1989329 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATAG
* *
1989353 ATTCTGATATGATATTTGACATAG
1 ATTCTGATCTGATACTTGACATAG
1989377 ATTCTGATCTGATACTTGAC
1 ATTCTGATCTGATACTTGAC
1989397 CTGATTTATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATAG
Found at i:1993363 original size:17 final size:17
Alignment explanation
Indices: 1993341--1993378 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
1993331 CAAACTGTAA
1993341 TTATTATTTTATTCTA-T
1 TTATTATTTT-TTCTACT
1993358 TTATTATTTTTTCTACT
1 TTATTATTTTTTCTACT
1993375 TTAT
1 TTAT
1993379 CTTTATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTATTTTTTCTACT
Found at i:1998320 original size:37 final size:40
Alignment explanation
Indices: 1998269--1998352 Score: 129
Period size: 41 Copynumber: 2.1 Consensus size: 40
1998259 AAATTCTAAA
*
1998269 AATATAAACTTAAAG-A-T-AATCACACTACTATAGACAT
1 AATATAAACATAAAGAACTCAATCACACTACTATAGACAT
1998306 AATATAAACATAAAGATACTCAATCACACTACTATAGACAT
1 AATATAAACATAAAGA-ACTCAATCACACTACTATAGACAT
1998347 AATATA
1 AATATA
1998353 CTTATTTTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
37 14 0.33
39 1 0.02
40 1 0.02
41 26 0.62
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (40 bp):
AATATAAACATAAAGAACTCAATCACACTACTATAGACAT
Found at i:2001346 original size:12 final size:12
Alignment explanation
Indices: 2001316--2001348 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2001306 AATATACATG
2001316 ATCGATAT-AAT
1 ATCGATATGAAT
2001327 ATCGGATATGAAT
1 ATC-GATATGAAT
2001340 ATCGATATG
1 ATCGATATG
2001349 TTACTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.15
12 11 0.55
13 6 0.30
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (12 bp):
ATCGATATGAAT
Found at i:2003110 original size:2 final size:2
Alignment explanation
Indices: 2003103--2003133 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2003093 TCTTCCCTCC
2003103 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2003134 AGTTCGGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2004522 original size:29 final size:29
Alignment explanation
Indices: 2004479--2004561 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
2004469 CTCACCTAAC
2004479 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
2004509 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
2004538 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2004562 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:2009232 original size:29 final size:29
Alignment explanation
Indices: 2009189--2009271 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
2009179 CTCACCTAAC
2009189 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
2009219 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
2009248 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2009272 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:2013654 original size:14 final size:14
Alignment explanation
Indices: 2013633--2013662 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2013623 AACCCTGAAT
2013633 CCTAAACTCTAAAC
1 CCTAAACTCTAAAC
*
2013647 CCTAAACTTTAAAC
1 CCTAAACTCTAAAC
2013661 CC
1 CC
2013663 ACATCAGCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (14 bp):
CCTAAACTCTAAAC
Found at i:2018302 original size:16 final size:16
Alignment explanation
Indices: 2018264--2018307 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
2018254 CATTTTTAGT
*
2018264 TAACAATTTATTAATA
1 TAACAATTAATTAATA
**
2018280 TTTCAATTAATTAATA
1 TAACAATTAATTAATA
*
2018296 TAACAATAAATT
1 TAACAATTAATT
2018308 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAACAATTAATTAATA
Found at i:2023109 original size:2 final size:2
Alignment explanation
Indices: 2023102--2023137 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2023092 TATGCTAGAA
2023102 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2023138 TAGAAATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2023527 original size:31 final size:31
Alignment explanation
Indices: 2023491--2023550 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
2023481 AACTTAAAAG
*
2023491 AGTTTTGTAATACTGAAATTTAAATAATTTT
1 AGTTTTATAATACTGAAATTTAAATAATTTT
2023522 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTATAATACTGAAATTTAAATAATT
2023551 CATACAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (31 bp):
AGTTTTATAATACTGAAATTTAAATAATTTT
Found at i:2023601 original size:22 final size:22
Alignment explanation
Indices: 2023573--2023695 Score: 246
Period size: 22 Copynumber: 5.6 Consensus size: 22
2023563 ATAATAATTT
2023573 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2023595 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2023617 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2023639 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2023661 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2023683 TTTTAAAATAAAT
1 TTTTAAAATAAAT
2023696 TTTAAAATAG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 101 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:2023712 original size:11 final size:12
Alignment explanation
Indices: 2023682--2023721 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2023672 ATCAATCCAT
2023682 ATTTTAAAATAA
1 ATTTTAAAATAA
*
2023694 ATTTTAAAATAG
1 ATTTTAAAATAA
2023706 A-TTT-AAAT-A
1 ATTTTAAAATAA
2023715 ATTTTAA
1 ATTTTAA
2023722 TATTCTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 7 0.29
11 4 0.17
12 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:2023740 original size:10 final size:10
Alignment explanation
Indices: 2023727--2023757 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2023717 TTTAATATTC
*
2023727 TTTGAAGAGA
1 TTTGAAGACA
2023737 TTTGAAGACA
1 TTTGAAGACA
2023747 TTTGAAGACA
1 TTTGAAGACA
2023757 T
1 T
2023758 AAAACCATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (10 bp):
TTTGAAGACA
Found at i:2024060 original size:15 final size:15
Alignment explanation
Indices: 2024040--2024068 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2024030 TCCAGCTCCA
2024040 AACAAGAACAAGAAG
1 AACAAGAACAAGAAG
2024055 AACAAGAACAAGAA
1 AACAAGAACAAGAA
2024069 AGGTAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.14, G:0.17, T:0.00
Consensus pattern (15 bp):
AACAAGAACAAGAAG
Found at i:2027655 original size:22 final size:22
Alignment explanation
Indices: 2027616--2027658 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2027606 CCGAAATAAT
*
2027616 AATAAAAATATTATTTTAATTC
1 AATAAAAATATGATTTTAATTC
2027638 AATAAAAATAATGA-TTTAATT
1 AATAAAAAT-ATGATTTTAATT
2027659 GAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AATAAAAATATGATTTTAATTC
Found at i:2028671 original size:34 final size:34
Alignment explanation
Indices: 2028628--2028693 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
2028618 TATGACTCGC
2028628 TTTCCACGGCAATGACTTGATGAGAGAGTGTTTT
1 TTTCCACGGCAATGACTTGATGAGAGAGTGTTTT
2028662 TTTCCACGGCAATGACTTGATGAGAGAGTGTT
1 TTTCCACGGCAATGACTTGATGAGAGAGTGTT
2028694 ATCCCCTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.33
Consensus pattern (34 bp):
TTTCCACGGCAATGACTTGATGAGAGAGTGTTTT
Found at i:2034444 original size:3 final size:3
Alignment explanation
Indices: 2034436--2034463 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2034426 ATTTGATAGA
2034436 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
2034464 GATTGAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:2044925 original size:109 final size:109
Alignment explanation
Indices: 2044734--2044939 Score: 340
Period size: 109 Copynumber: 1.9 Consensus size: 109
2044724 TGATTTTGTA
* * * *
2044734 TGATAAATTCTATGTGTCGTTTTTGACTAATATAAATGGCTCAGCTAAGAAAAACATTTGGAACC
1 TGATAAATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCTAAGAAAAACATTAGGAACC
*
2044799 CCGTTCTGTTCCCCAAAGCAAAGACTATAGAAATGAATATATTT
66 CCATTCTGTTCCCCAAAGCAAAGACTATAGAAATGAATATATTT
*
2044843 TGATAGATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCTAAGAAAAACATTAGGAACC
1 TGATAAATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCTAAGAAAAACATTAGGAACC
* *
2044908 TCATTCTGTTCCCCAAAGCATAGACTATAGAA
66 CCATTCTGTTCCCCAAAGCAAAGACTATAGAA
2044940 TCTATTCTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 89 1.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (109 bp):
TGATAAATTCTATGTGCCGGTTTTGACTAATATAAATGGCCCAGCTAAGAAAAACATTAGGAACC
CCATTCTGTTCCCCAAAGCAAAGACTATAGAAATGAATATATTT
Found at i:2046498 original size:21 final size:20
Alignment explanation
Indices: 2046412--2046569 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
2046402 AAATGACCAA
**
2046412 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2046431 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2046451 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2046471 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
2046492 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
2046513 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2046533 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
2046554 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2046570 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2046562 original size:20 final size:20
Alignment explanation
Indices: 2046537--2046730 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
2046527 GATTTTCAAT
* *
2046537 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
2046557 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
2046577 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2046597 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
2046617 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
2046637 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2046657 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
2046677 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
2046698 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
2046718 AATCGCAACGCGA
1 AATCGCAACGCGA
2046731 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:2046582 original size:40 final size:39
Alignment explanation
Indices: 2046537--2046730 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 39
2046527 GATTTTCAAT
* ** *
2046537 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAAC-CATA
* * *
2046577 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
** * * *
2046617 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACCATA
* ** *
2046657 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAA-CCAT-A
2046698 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
2046731 TATTTAAAGC
Statistics
Matches: 128, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 94 0.73
41 33 0.26
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (39 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACCATA
Found at i:2046620 original size:60 final size:60
Alignment explanation
Indices: 2046537--2046729 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2046527 GATTTTCAAT
* ** * *
2046537 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
2046597 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
2046657 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
2046718 AATCGCAACGCG
1 AATCGCAACGCG
2046730 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:2047150 original size:33 final size:33
Alignment explanation
Indices: 2047111--2047181 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2047101 TTCACTTAGA
*
2047111 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2047144 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2047177 TTTCA
1 TTTCA
2047182 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2047321 original size:14 final size:14
Alignment explanation
Indices: 2047302--2047356 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2047292 AGAATGACTG
2047302 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2047316 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
2047335 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2047349 TCGCAACG
1 TCGCAACG
2047357 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2047339 original size:33 final size:33
Alignment explanation
Indices: 2047302--2047372 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2047292 AGAATGACTG
**
2047302 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2047335 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2047368 TCGCA
1 TCGCA
2047373 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:2047390 original size:19 final size:19
Alignment explanation
Indices: 2047368--2047465 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
2047358 GAAACCAAAA
*
2047368 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2047387 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2047401 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2047420 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
2047434 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
2047453 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2047466 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2047409 original size:14 final size:14
Alignment explanation
Indices: 2047390--2047479 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
2047380 TTTCATTTCG
2047390 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2047404 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2047423 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2047437 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2047454 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2047470 CGTTGCGATT
1 CGTTGCGATT
2047480 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2047415 original size:33 final size:33
Alignment explanation
Indices: 2047373--2047487 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
2047363 CAAAATCGCA
2047373 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2047406 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2047439 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2047472 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2047488 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2049392 original size:92 final size:93
Alignment explanation
Indices: 2049186--2049564 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
2049176 TAGATTGCTT
*
2049186 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2049251 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2049279 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2049343 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2049371 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2049435 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2049463 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2049528 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2049556 AGTAAATTT
1 AGTAAATTT
2049565 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2049416 original size:185 final size:185
Alignment explanation
Indices: 2049186--2049566 Score: 737
Period size: 185 Copynumber: 2.1 Consensus size: 185
2049176 TAGATTGCTT
2049186 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
2049251 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2049316 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2049371 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
2049436 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
2049501 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2049556 AGTAAATTTAT
1 AGTAAATTTAT
2049567 CCATTCAAGT
Statistics
Matches: 193, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 101 0.52
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATATAT
TTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2049648 original size:19 final size:19
Alignment explanation
Indices: 2049608--2049736 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2049598 TAGTTTACTT
* *
2049608 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2049628 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2049647 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2049666 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2049680 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2049699 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2049713 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2049732 TCGCA
1 TCGCA
2049737 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2049687 original size:33 final size:32
Alignment explanation
Indices: 2049644--2049736 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2049634 CGCGAAACCA
**
2049644 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2049676 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2049709 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2049737 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2049734 original size:52 final size:52
Alignment explanation
Indices: 2049608--2049736 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
2049598 TAGTTTACTT
**
2049608 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
2049660 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
2049713 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2049737 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2049754 original size:19 final size:19
Alignment explanation
Indices: 2049732--2049866 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2049722 GAAACCAAAA
*
2049732 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2049751 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2049767 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2049784 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2049800 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2049817 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2049836 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2049856 TCGTGTTGCGA
1 TCGCGTTGCGA
2049867 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2049773 original size:14 final size:14
Alignment explanation
Indices: 2049754--2049810 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2049744 TTTCATTTCG
2049754 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2049768 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2049785 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2049801 CGTTGCGATT
1 CGTTGCGATT
2049811 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2049779 original size:33 final size:33
Alignment explanation
Indices: 2049737--2049829 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2049727 CAAAATCGCA
*
2049737 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2049770 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2049803 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2049830 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2051782 original size:14 final size:14
Alignment explanation
Indices: 2051763--2051798 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2051753 ATTGTTTAAT
2051763 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2051777 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2051791 TGATTTGT
1 TGATTTGT
2051799 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2051973 original size:20 final size:19
Alignment explanation
Indices: 2051905--2051987 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
2051895 AAAAATGACT
2051905 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2051924 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2051938 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2051957 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2051977 ATCGCAATGCG
1 ATCGCAATGCG
2051988 TTTATAATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 21 0.38
20 19 0.34
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2052040 original size:19 final size:19
Alignment explanation
Indices: 2052016--2052289 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
2052006 GATTATCTCG
2052016 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2052035 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2052054 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2052068 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2052087 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2052106 TTGCGATTTCCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2052125 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2052144 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2052163 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2052177 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2052196 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2052215 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2052229 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2052249 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2052263 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2052282 TTGCGATT
1 TTGCGATT
2052290 GTATTTTCCG
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 29 0.13
16 24 0.11
17 21 0.09
18 3 0.01
19 137 0.61
20 12 0.05
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2052056 original size:52 final size:52
Alignment explanation
Indices: 2051994--2052261 Score: 455
Period size: 52 Copynumber: 5.0 Consensus size: 52
2051984 TGCGTTTATA
*
2051994 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2052046 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2052098 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA-TT-C-TCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
2052155 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2052207 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
2052260 AT
1 AT
2052262 GTTGGGATTT
Statistics
Matches: 207, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
52 131 0.63
53 19 0.09
54 5 0.02
55 6 0.03
56 2 0.01
57 44 0.21
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2052145 original size:109 final size:105
Alignment explanation
Indices: 2051994--2052261 Score: 459
Period size: 109 Copynumber: 2.5 Consensus size: 105
2051984 TGCGTTTATA
2051994 ATTTCGCATTGCGATT-ATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
*
2052058 GATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
66 GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2052098 ATTTCGCATTGCGATTTCCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 ATTTCGCATTGCGA-TT-CATCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
2052163 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
62 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2052207 ATTTCGCATTGCGATTC-TCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1 ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
2052262 GTTGGGATTT
Statistics
Matches: 155, Mismatches: 3, Indels: 11
0.92 0.02 0.07
Matches are distributed among these distances:
104 29 0.19
105 19 0.12
106 4 0.03
107 6 0.04
108 2 0.01
109 95 0.61
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (105 bp):
ATTTCGCATTGCGATTCATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGC
GATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2054588 original size:12 final size:12
Alignment explanation
Indices: 2054571--2054595 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2054561 TCTTCGGGGA
2054571 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2054583 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2054595 C
1 C
2054596 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2054804 original size:24 final size:24
Alignment explanation
Indices: 2054770--2054816 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2054760 CTGAAACATC
2054770 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2054794 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2054817 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2055521 original size:20 final size:20
Alignment explanation
Indices: 2055493--2055882 Score: 457
Period size: 20 Copynumber: 19.4 Consensus size: 20
2055483 AAATTTCAGT
* * * *
2055493 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2055513 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2055533 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2055553 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2055573 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2055593 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2055613 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2055633 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2055653 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2055673 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2055693 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
2055713 GTTGCGATTTTATGTATTA-TC
1 GTTGCGA-TTTACGGA-TACGC
2055734 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2055754 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2055774 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2055794 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2055814 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2055834 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2055854 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2055874 GTTGCGATT
1 GTTGCGATT
2055883 ATTGAAAATC
Statistics
Matches: 323, Mismatches: 36, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
19 7 0.02
20 295 0.91
21 19 0.06
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2064367 original size:27 final size:26
Alignment explanation
Indices: 2064320--2064374 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
2064310 ATGATTACAT
*
2064320 AATATCATATATATAACAATATATATA
1 AATATAATATATATAACAATA-ATATA
*
2064347 AATATAATAT-TATTAATAATAATATA
1 AATATAATATATA-TAACAATAATATA
2064373 AA
1 AA
2064375 CCCAAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (26 bp):
AATATAATATATATAACAATAATATA
Found at i:2064755 original size:37 final size:37
Alignment explanation
Indices: 2064661--2064822 Score: 191
Period size: 37 Copynumber: 4.4 Consensus size: 37
2064651 ATCAGACTCG
* * * *
2064661 AGATTTATTTGCTTCGCTACTGTTCCTTGAAGGC-TA
1 AGATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
* *
2064697 AGATTGATTTGTTTCAATACTCTTCCGTGAAGGCTTA
1 AGATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
* * * * *
2064734 AGATCGACTTACTTCACTACTCTTTCATGAAGGCTTA
1 AGATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
* *
2064771 AGATTGATTTGCTTCACTACTTTTTCGTGAAGGCTTA
1 AGATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
*
2064808 ATATTGATTTGCTTC
1 AGATTGATTTGCTTC
2064823 GAAGGTCAGA
Statistics
Matches: 106, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
36 28 0.26
37 78 0.74
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (37 bp):
AGATTGATTTGCTTCACTACTCTTCCGTGAAGGCTTA
Found at i:2066081 original size:15 final size:15
Alignment explanation
Indices: 2066047--2066094 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
2066037 TTGAACCCCC
*
2066047 TTTTATTCTTTTTCTTT
1 TTTTATT-TTTTT-ATT
*
2066064 TTTCTTTTTTTTTATT
1 TTT-TATTTTTTTATT
2066080 TTTTATTTTTTTATT
1 TTTTATTTTTTTATT
2066095 CAAACAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 11 0.41
16 5 0.19
17 8 0.30
18 3 0.11
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTATTTTTTTATT
Found at i:2066081 original size:17 final size:17
Alignment explanation
Indices: 2066055--2066091 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2066045 CCTTTTATTC
* *
2066055 TTTTTCTTTTTTCTTTT
1 TTTTTATTTTTTATTTT
2066072 TTTTTATTTTTTATTTT
1 TTTTTATTTTTTATTTT
2066089 TTT
1 TTT
2066092 ATTCAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.05, C:0.05, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTTATTTTTTATTTT
Found at i:2066092 original size:8 final size:8
Alignment explanation
Indices: 2066047--2066094 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
2066037 TTGAACCCCC
2066047 TTTTATTCT
1 TTTTATT-T
*
2066056 TTTTCTTT
1 TTTTATTT
*
2066064 TTTCTTTTT
1 TTT-TATTT
2066073 TTTTA-TT
1 TTTTATTT
2066080 TTTTATTT
1 TTTTATTT
2066088 TTTTATT
1 TTTTATT
2066095 CAAACAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
7 7 0.21
8 14 0.41
9 13 0.38
ACGTcount: A:0.08, C:0.06, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTATTT
Found at i:2072963 original size:12 final size:12
Alignment explanation
Indices: 2072938--2073007 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
2072928 GCGGAGATAT
* *
2072938 CAGAAATCAAAA
1 CAGAATTCAGAA
2072950 CAGAATTCAGAA
1 CAGAATTCAGAA
*
2072962 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* * *
2072974 CAAAATCCAGAT
1 CAGAATTCAGAA
2072986 CAGAAATT-AGAA
1 CAG-AATTCAGAA
2072998 CAGAATTCAG
1 CAGAATTCAG
2073008 GTTATGTATC
Statistics
Matches: 44, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
11 6 0.14
12 33 0.75
13 5 0.11
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:2072970 original size:24 final size:24
Alignment explanation
Indices: 2072938--2073007 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
2072928 GCGGAGATAT
2072938 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAAAACAGAATTCAGAA
* * * * *
2072962 CAGATATCATAACAAAATCCAGAT
1 CAGAAATCAAAACAGAATTCAGAA
* *
2072986 CAGAAATTAGAACAGAATTCAG
1 CAGAAATCAAAACAGAATTCAG
2073008 GTTATGTATC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.17, G:0.13, T:0.17
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATTCAGAA
Found at i:2075574 original size:13 final size:13
Alignment explanation
Indices: 2075512--2075575 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
2075502 GTCAACGGTC
* *
2075512 AACGGGTCGGATC
1 AACGGGTCGGGTA
*
2075525 AACGGGTCGAGTCA
1 AACGGGTCGGGT-A
*
2075539 AA-GGGTCGGGTC
1 AACGGGTCGGGTA
*
2075551 AACAGGTCGGGTA
1 AACGGGTCGGGTA
2075564 AACGGGTCGGGT
1 AACGGGTCGGGT
2075576 CGAGTTATGA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 2 0.05
13 37 0.90
14 2 0.05
ACGTcount: A:0.23, C:0.19, G:0.42, T:0.16
Consensus pattern (13 bp):
AACGGGTCGGGTA
Found at i:2075574 original size:26 final size:27
Alignment explanation
Indices: 2075512--2075576 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 27
2075502 GTCAACGGTC
* *
2075512 AACGGGTCGGATCAACGGGTCGAGTCA
1 AACGGGTCGGGTCAACAGGTCGAGTCA
*
2075539 AA-GGGTCGGGTCAACAGGTCGGGT-A
1 AACGGGTCGGGTCAACAGGTCGAGTCA
2075564 AACGGGTCGGGTC
1 AACGGGTCGGGTC
2075577 GAGTTATGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.09
26 29 0.85
27 2 0.06
ACGTcount: A:0.23, C:0.20, G:0.42, T:0.15
Consensus pattern (27 bp):
AACGGGTCGGGTCAACAGGTCGAGTCA
Found at i:2087328 original size:25 final size:26
Alignment explanation
Indices: 2087282--2087334 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
2087272 TTTTTTAGTT
*
2087282 AAAATATATTAAATTATAAGATAGATA
1 AAAATATATTAAA-TATAAGATAAATA
*
2087309 AAAATATATTAAA-ATTAGATAAATA
1 AAAATATATTAAATATAAGATAAATA
2087334 A
1 A
2087335 TCATACTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 11 0.46
27 13 0.54
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (26 bp):
AAAATATATTAAATATAAGATAAATA
Found at i:2088183 original size:41 final size:41
Alignment explanation
Indices: 2088121--2088204 Score: 150
Period size: 41 Copynumber: 2.0 Consensus size: 41
2088111 AAATTAAAAA
* *
2088121 TAAATACAATAACCTTTAATTTAAAAGTTTTTATAATCCCG
1 TAAATAAAATAACCTTCAATTTAAAAGTTTTTATAATCCCG
2088162 TAAATAAAATAACCTTCAATTTAAAAGTTTTTATAATCCCG
1 TAAATAAAATAACCTTCAATTTAAAAGTTTTTATAATCCCG
2088203 TA
1 TA
2088205 GAACGCAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (41 bp):
TAAATAAAATAACCTTCAATTTAAAAGTTTTTATAATCCCG
Found at i:2088937 original size:62 final size:62
Alignment explanation
Indices: 2088868--2088992 Score: 187
Period size: 62 Copynumber: 2.0 Consensus size: 62
2088858 TAAATAACTC
* ** ** *
2088868 TATTACATTTAAGTACATTATTAAAGCGTGATGAGTCATTAAGTTTACCTGAGAAGTTGTTT
1 TATTACATTTAAATACATTATTAAAGCACGATGAGTCATTAAGCATACCTGAGAAATTGTTT
*
2088930 TATTACATTTAAATACATTATTAAAGCACGATGAGTCATTAAGCATGCCTGAGAAATTGTTT
1 TATTACATTTAAATACATTATTAAAGCACGATGAGTCATTAAGCATACCTGAGAAATTGTTT
2088992 T
1 T
2088993 CTCCGACGGT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.38
Consensus pattern (62 bp):
TATTACATTTAAATACATTATTAAAGCACGATGAGTCATTAAGCATACCTGAGAAATTGTTT
Found at i:2091777 original size:13 final size:13
Alignment explanation
Indices: 2091759--2091784 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2091749 ATAGTTGTTA
2091759 CAAAAGAGATTAT
1 CAAAAGAGATTAT
2091772 CAAAAGAGATTAT
1 CAAAAGAGATTAT
2091785 ACCTTTAAAG
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:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
CAAAAGAGATTAT
Found at i:2095857 original size:29 final size:29
Alignment explanation
Indices: 2095815--2095871 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
2095805 TTTTCACCTA
2095815 ACTAAATTAATGTAAGCAATGACATCAAT
1 ACTAAATTAATGTAAGCAATGACATCAAT
*
2095844 ACTAAATTGATGTAAGCAATGACATCAA
1 ACTAAATTAATGTAAGCAATGACATCAA
2095872 ATTAATTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.26
Consensus pattern (29 bp):
ACTAAATTAATGTAAGCAATGACATCAAT
Found at i:2098742 original size:29 final size:29
Alignment explanation
Indices: 2098700--2098756 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
2098690 TTTTCACCTA
2098700 ACTAAATTGATGTAAGCAATGACATCAAT
1 ACTAAATTGATGTAAGCAATGACATCAAT
2098729 ACTAAATTGATGTAAGCAATGACATCAA
1 ACTAAATTGATGTAAGCAATGACATCAA
2098757 ATTAATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (29 bp):
ACTAAATTGATGTAAGCAATGACATCAAT
Found at i:2100092 original size:3 final size:3
Alignment explanation
Indices: 2100084--2100109 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2100074 CTAGAATTTT
2100084 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
2100110 TAAGAGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:2103645 original size:13 final size:13
Alignment explanation
Indices: 2103627--2103652 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2103617 ATAGTTGTTA
2103627 CAAAAGAGATTAT
1 CAAAAGAGATTAT
2103640 CAAAAGAGATTAT
1 CAAAAGAGATTAT
2103653 ACCTTTAAAG
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:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (13 bp):
CAAAAGAGATTAT
Found at i:2106420 original size:23 final size:23
Alignment explanation
Indices: 2106377--2106421 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
2106367 TGAATCGAGA
2106377 AAAAAATCAATATAACTTTTTAAC
1 AAAAAATCAATATAAC-TTTTAAC
*
2106401 AAAAACTCACATATAA-TTTTA
1 AAAAAATCA-ATATAACTTTTA
2106422 TTTTTTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 8 0.42
25 6 0.32
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (23 bp):
AAAAAATCAATATAACTTTTAAC
Found at i:2115311 original size:18 final size:18
Alignment explanation
Indices: 2115288--2115322 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2115278 GAACAAAAAG
2115288 AACTTAAACAA-ACCAAAC
1 AACTTAAA-AATACCAAAC
2115306 AACTTAAAAATACCAAA
1 AACTTAAAAATACCAAA
2115323 AAGAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.14
Consensus pattern (18 bp):
AACTTAAAAATACCAAAC
Found at i:2120101 original size:20 final size:22
Alignment explanation
Indices: 2120062--2120114 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
2120052 AATATATATC
2120062 ATTATATTTT-TTCAATTAAA-
1 ATTATATTTTATTCAATTAAAG
*
2120082 ATTATATTTTATTTAA-TAAAG
1 ATTATATTTTATTCAATTAAAG
2120103 ATTGA-ATTTTAT
1 ATT-ATATTTTAT
2120115 ATATGTCGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 14 0.48
21 14 0.48
22 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTATATTTTATTCAATTAAAG
Found at i:2125855 original size:17 final size:18
Alignment explanation
Indices: 2125823--2125860 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
2125813 AAAGAAAAGG
2125823 AAAAGAAAATAAAATAAC
1 AAAAGAAAATAAAATAAC
2125841 AAAAGAAAA-AAAATAAC
1 AAAAGAAAATAAAATAAC
2125858 AAA
1 AAA
2125861 CCAAAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.82, C:0.05, G:0.05, T:0.08
Consensus pattern (18 bp):
AAAAGAAAATAAAATAAC
Found at i:2125866 original size:17 final size:17
Alignment explanation
Indices: 2125823--2125867 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2125813 AAAGAAAAGG
*
2125823 AAAAGAAAATAAAATAAC
1 AAAACAAAA-AAAATAAC
*
2125841 AAAAGAAAAAAAATAAC
1 AAAACAAAAAAAATAAC
*
2125858 AAACCAAAAA
1 AAAACAAAAA
2125868 TCAGAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.80, C:0.09, G:0.04, T:0.07
Consensus pattern (17 bp):
AAAACAAAAAAAATAAC
Found at i:2126542 original size:59 final size:59
Alignment explanation
Indices: 2126479--2126613 Score: 148
Period size: 59 Copynumber: 2.3 Consensus size: 59
2126469 AAAAATATGA
* * * *
2126479 ATAGTCGGATGACAATTTTGTAACTTTTAATAGTC-TATGACTCAACAAAATAACGCTCT
1 ATAGTCAGAGGACAATTTTATAA-TTTTAATAGTCGAATGACTCAACAAAATAACGCTCT
* * * *
2126538 ATAGTTAGAGGACTATTTTATAATTTTAATAGTCGAATGACTCAGCAAAATAACAC-CT
1 ATAGTCAGAGGACAATTTTATAATTTTAATAGTCGAATGACTCAACAAAATAACGCTCT
* * *
2126596 ATAATTAGAGGACCATTT
1 ATAGTCAGAGGACAATTT
2126614 GTACACTTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
58 29 0.45
59 36 0.55
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (59 bp):
ATAGTCAGAGGACAATTTTATAATTTTAATAGTCGAATGACTCAACAAAATAACGCTCT
Found at i:2126565 original size:58 final size:59
Alignment explanation
Indices: 2126493--2126613 Score: 165
Period size: 58 Copynumber: 2.1 Consensus size: 59
2126483 TCGGATGACA
* * * * *
2126493 ATTTTGTAACTTTTAATAGTC-TATGACTCAACAAAATAACGCTCTATAGTTAGAGGACT
1 ATTTTATAACTTTTAATAGTCGAATGACTCAACAAAATAACAC-CTATAATTAGAGGACC
*
2126552 ATTTTATAA-TTTTAATAGTCGAATGACTCAGCAAAATAACACCTATAATTAGAGGACC
1 ATTTTATAACTTTTAATAGTCGAATGACTCAACAAAATAACACCTATAATTAGAGGACC
2126610 ATTT
1 ATTT
2126614 GTACACTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 29 0.53
59 26 0.47
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (59 bp):
ATTTTATAACTTTTAATAGTCGAATGACTCAACAAAATAACACCTATAATTAGAGGACC
Found at i:2128570 original size:15 final size:14
Alignment explanation
Indices: 2128545--2128586 Score: 75
Period size: 15 Copynumber: 2.9 Consensus size: 14
2128535 ATCTCTCTAT
2128545 TATATATAGTATGG
1 TATATATAGTATGG
2128559 TATATCATAGTATGG
1 TATAT-ATAGTATGG
2128574 TATATATAGTATG
1 TATATATAGTATG
2128587 ACTCTATGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.43
Consensus pattern (14 bp):
TATATATAGTATGG
Found at i:2129306 original size:22 final size:23
Alignment explanation
Indices: 2129281--2129336 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
2129271 CAAACGACTG
2129281 GAAAACGTATCA-AAAGACAGAA
1 GAAAACGTATCATAAAGACAGAA
* *
2129303 GAAAACGTATCATAAAGGCAGAT
1 GAAAACGTATCATAAAGACAGAA
2129326 GAAAACGTATC
1 GAAAACGTATC
2129337 GAATAATAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.52, C:0.14, G:0.20, T:0.14
Consensus pattern (23 bp):
GAAAACGTATCATAAAGACAGAA
Found at i:2136044 original size:63 final size:63
Alignment explanation
Indices: 2135945--2136072 Score: 256
Period size: 63 Copynumber: 2.0 Consensus size: 63
2135935 TGAACCGAGC
2135945 TTTGTAAGTATCTCGAAATCACTCAAAATAATTTTTAGAAATTTTTCCGGGATTTTATCACTG
1 TTTGTAAGTATCTCGAAATCACTCAAAATAATTTTTAGAAATTTTTCCGGGATTTTATCACTG
2136008 TTTGTAAGTATCTCGAAATCACTCAAAATAATTTTTAGAAATTTTTCCGGGATTTTATCACTG
1 TTTGTAAGTATCTCGAAATCACTCAAAATAATTTTTAGAAATTTTTCCGGGATTTTATCACTG
2136071 TT
1 TT
2136073 GCGCCCCCAC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (63 bp):
TTTGTAAGTATCTCGAAATCACTCAAAATAATTTTTAGAAATTTTTCCGGGATTTTATCACTG
Found at i:2136185 original size:13 final size:13
Alignment explanation
Indices: 2136167--2136259 Score: 65
Period size: 13 Copynumber: 7.3 Consensus size: 13
2136157 GTCACAATCC
2136167 GACCCGACCCGTT
1 GACCCGACCCGTT
2136180 GACCCGACCC---
1 GACCCGACCCGTT
2136190 GACCCGTTTACCC---
1 GACCCG---ACCCGTT
2136203 GACCCGACCCGTT
1 GACCCGACCCGTT
2136216 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
2136229 GACCAG-CCCCTT
1 GACCCGACCCGTT
*
2136241 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
2136256 GACC
1 GACC
2136260 GTTGACCGGA
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
10 10 0.15
12 9 0.13
13 38 0.57
14 1 0.01
15 9 0.13
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2136188 original size:18 final size:18
Alignment explanation
Indices: 2136165--2136226 Score: 115
Period size: 18 Copynumber: 3.4 Consensus size: 18
2136155 CGGTCACAAT
2136165 CCGACCCGACCCGTTGAC
1 CCGACCCGACCCGTTGAC
*
2136183 CCGACCCGACCCGTTTAC
1 CCGACCCGACCCGTTGAC
2136201 CCGACCCGACCCGTTGAC
1 CCGACCCGACCCGTTGAC
2136219 CCGACCCG
1 CCGACCCG
2136227 TTGACCAGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.16, C:0.52, G:0.21, T:0.11
Consensus pattern (18 bp):
CCGACCCGACCCGTTGAC
Found at i:2137539 original size:84 final size:84
Alignment explanation
Indices: 2137398--2137565 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
2137388 CTTAACTCGA
2137398 TTAAGTACGGATTTAATTGTTAAGATCCCGACTTAGTGCAGGAAAATTCATGATATTCCGTTTGT
1 TTAAGTACGGATTTAATTGTTAAGATCCCGACTTAGTGCAGGAAAATTCATGATATTCCGTTTGT
2137463 AAAATCTGAGAAGGCACTT
66 AAAATCTGAGAAGGCACTT
2137482 TTAAGTACGGATTTAATTGTTAAGATCCCGACTTAGTGCAGGAAAATTCATGATATTCCGTTTGT
1 TTAAGTACGGATTTAATTGTTAAGATCCCGACTTAGTGCAGGAAAATTCATGATATTCCGTTTGT
2137547 AAAATCTGAGAAGGCACTT
66 AAAATCTGAGAAGGCACTT
2137566 GACCCGAAAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (84 bp):
TTAAGTACGGATTTAATTGTTAAGATCCCGACTTAGTGCAGGAAAATTCATGATATTCCGTTTGT
AAAATCTGAGAAGGCACTT
Found at i:2138876 original size:23 final size:24
Alignment explanation
Indices: 2138850--2138939 Score: 103
Period size: 23 Copynumber: 3.8 Consensus size: 24
2138840 TCAAATTTGA
*
2138850 ATTCTGTTATGATA-TTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
2138873 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
2138896 ATTCTGATCTGATACATGACCTGA
1 ATTCTGATATGATACTTGACCTGG
*
2138920 ATTATGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
2138940 TTGAATTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
23 34 0.60
24 23 0.40
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:2138927 original size:24 final size:24
Alignment explanation
Indices: 2138859--2138949 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 24
2138849 AATTCTGTTA
* *
2138859 TGATA-TTGACCTGGATTCTGATC
1 TGATACTTGACCTGAATTATGATC
* * *
2138882 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACCTGAATTATGATC
* *
2138905 TGATACATGACCTGAATTATGATA
1 TGATACTTGACCTGAATTATGATC
*
2138929 TGATACTTGACTTGAATTATG
1 TGATACTTGACCTGAATTATG
2138950 TTTTATTGGG
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 27 0.46
24 32 0.54
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (24 bp):
TGATACTTGACCTGAATTATGATC
Found at i:2139046 original size:33 final size:35
Alignment explanation
Indices: 2138979--2139051 Score: 105
Period size: 33 Copynumber: 2.1 Consensus size: 35
2138969 TGGAGGAAGA
* *
2138979 TTACTTGGAGGCTCCTTGGCTGTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTTCGCTGTGTGCTCAGGGCC
*
2139014 TTACTTGCAGGCTCC-TCGCTTTG-GCTCAGGGCC
1 TTACTTGCAGGCTCCTTCGCTGTGTGCTCAGGGCC
2139047 TTACT
1 TTACT
2139052 GTTCGTGACG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 15 0.43
34 6 0.17
35 14 0.40
ACGTcount: A:0.10, C:0.29, G:0.29, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTTCGCTGTGTGCTCAGGGCC
Found at i:2141021 original size:13 final size:13
Alignment explanation
Indices: 2141003--2141095 Score: 65
Period size: 13 Copynumber: 7.3 Consensus size: 13
2140993 GTCACAATCC
2141003 GACCCGACCCGTT
1 GACCCGACCCGTT
2141016 GACCCGACCC---
1 GACCCGACCCGTT
2141026 GACCCGTTTACCC---
1 GACCCG---ACCCGTT
2141039 GACCCGACCCGTT
1 GACCCGACCCGTT
2141052 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
2141065 GACCAG-CCCCTT
1 GACCCGACCCGTT
*
2141077 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
2141092 GACC
1 GACC
2141096 GTTGACCGGA
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
10 10 0.15
12 9 0.13
13 38 0.57
14 1 0.01
15 9 0.13
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2141024 original size:18 final size:18
Alignment explanation
Indices: 2141001--2141062 Score: 115
Period size: 18 Copynumber: 3.4 Consensus size: 18
2140991 CGGTCACAAT
2141001 CCGACCCGACCCGTTGAC
1 CCGACCCGACCCGTTGAC
*
2141019 CCGACCCGACCCGTTTAC
1 CCGACCCGACCCGTTGAC
2141037 CCGACCCGACCCGTTGAC
1 CCGACCCGACCCGTTGAC
2141055 CCGACCCG
1 CCGACCCG
2141063 TTGACCAGCC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.16, C:0.52, G:0.21, T:0.11
Consensus pattern (18 bp):
CCGACCCGACCCGTTGAC
Found at i:2143597 original size:23 final size:24
Alignment explanation
Indices: 2143571--2143660 Score: 103
Period size: 23 Copynumber: 3.8 Consensus size: 24
2143561 TCAAATTTGA
*
2143571 ATTCTGTTATGATA-TTGACCTGG
1 ATTCTGATATGATACTTGACCTGG
* *
2143594 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACTTGACCTGG
* * *
2143617 ATTCTGATCTGATACATGACCTGA
1 ATTCTGATATGATACTTGACCTGG
*
2143641 ATTATGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
2143661 TTGAATTATG
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
23 34 0.60
24 23 0.40
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTGG
Found at i:2143648 original size:24 final size:24
Alignment explanation
Indices: 2143580--2143670 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 24
2143570 AATTCTGTTA
* *
2143580 TGATA-TTGACCTGGATTCTGATC
1 TGATACTTGACCTGAATTATGATC
* * *
2143603 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACCTGAATTATGATC
* *
2143626 TGATACATGACCTGAATTATGATA
1 TGATACTTGACCTGAATTATGATC
*
2143650 TGATACTTGACTTGAATTATG
1 TGATACTTGACCTGAATTATG
2143671 TTTTATTGGG
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 27 0.46
24 32 0.54
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (24 bp):
TGATACTTGACCTGAATTATGATC
Found at i:2143747 original size:35 final size:35
Alignment explanation
Indices: 2143700--2143774 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
2143690 TGGAGGAAGA
* *
2143700 TTACTTGGAGGCTCCTTGGCTGTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
*
2143735 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
2143770 TTACT
1 TTACT
2143775 GTTCGTGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.09, C:0.28, G:0.29, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
Found at i:2149785 original size:20 final size:18
Alignment explanation
Indices: 2149753--2149794 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
2149743 CTATGGAAGA
2149753 AAAAGAGGAGAGAGAAAG
1 AAAAGAGGAGAGAGAAAG
*
2149771 AAAAGAGAGAGGAGAGGAAG
1 AAAAGAG-GA-GAGAGAAAG
2149791 AAAA
1 AAAA
2149795 TAACATGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 2 0.10
20 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (18 bp):
AAAAGAGGAGAGAGAAAG
Found at i:2161281 original size:29 final size:29
Alignment explanation
Indices: 2161248--2161308 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
2161238 GAAAAATAAA
2161248 ATAAAAGAAAAGGAATGCCACAATCAGGG
1 ATAAAAGAAAAGGAATGCCACAATCAGGG
2161277 ATAAAAGAAAAGGAATGCCACAATCAGGG
1 ATAAAAGAAAAGGAATGCCACAATCAGGG
2161306 ATA
1 ATA
2161309 TGCTGTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.52, C:0.13, G:0.23, T:0.11
Consensus pattern (29 bp):
ATAAAAGAAAAGGAATGCCACAATCAGGG
Found at i:2163968 original size:17 final size:17
Alignment explanation
Indices: 2163946--2163980 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2163936 TTGACCGGTC
2163946 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2163963 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
2163980 T
1 T
2163981 TACCGTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:2163985 original size:7 final size:7
Alignment explanation
Indices: 2163974--2164004 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2163964 GACCCGACCC
2163974 GACCGTT
1 GACCGTT
*
2163981 TACCGTT
1 GACCGTT
2163988 GACCGTT
1 GACCGTT
2163995 GACCGTT
1 GACCGTT
2164002 GAC
1 GAC
2164005 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.29, G:0.26, T:0.29
Consensus pattern (7 bp):
GACCGTT
Found at i:2168220 original size:178 final size:176
Alignment explanation
Indices: 2167978--2168440 Score: 782
Period size: 176 Copynumber: 2.6 Consensus size: 176
2167968 TAATGGTAAG
* *
2167978 TATATGTTTCAGGTCCCATTCCTCCCGTTGTTGGAAACCTGACATCCCTCACACACATTCTTCTT
1 TATATGTTTCAGGTCCAATTCCTCCCGTTATTGGAAACCTGACATCCCTCACACACATTCTTCTT
*
2168043 TCCCATAACGAGTTGACAGGTACAATTCCATCTCCCTCTCTTCTTTTCCATACACTTTTCTTTCT
66 TCCCATAACGAGTTGACAGGTACAATTCCATCTCCCTCTCTTCTTTTCCATACAATTTTCTTTC-
*
2168108 TTTTTTCTTTTAAGTGTAAAAGACAGATAGCTTATAACGGTAAGTATA
130 -TTTTTCTTTTAAATGTAAAAGACAGATAGCTTATAACGGTAAGTATA
* *
2168156 TATATGTTTCAGGTCCAATTCCTCCCGTTATTGGAAACCTGACATCCCTCAGACACAATCTTCTT
1 TATATGTTTCAGGTCCAATTCCTCCCGTTATTGGAAACCTGACATCCCTCACACACATTCTTCTT
* * *
2168221 TCCCATAACAAGTTGACAGGTACAATTCCATCTCCCTCTCCTCTTTTCCATTCAATTTTCTTTCT
66 TCCCATAACGAGTTGACAGGTACAATTCCATCTCCCTCTCTTCTTTTCCATACAATTTTCTTTCT
2168286 TTTTCTTTTAAATGTAAAAGACAGATAGCTTATAACGGTAAGTATA
131 TTTTCTTTTAAATGTAAAAGACAGATAGCTTATAACGGTAAGTATA
2168332 TATATGTTTCAGGTCCAATTCCTCCCGTTATTGGAAACCTGACATCCCTCACACACATTCTTCTT
1 TATATGTTTCAGGTCCAATTCCTCCCGTTATTGGAAACCTGACATCCCTCACACACATTCTTCTT
* * * * *
2168397 TGCCATAACGAATTGACAAGTACAATTCCTTCTCCCTGTCTTCT
66 TCCCATAACGAGTTGACAGGTACAATTCCATCTCCCTCTCTTCT
2168441 CATTTTTGTT
Statistics
Matches: 267, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
176 146 0.55
178 121 0.45
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (176 bp):
TATATGTTTCAGGTCCAATTCCTCCCGTTATTGGAAACCTGACATCCCTCACACACATTCTTCTT
TCCCATAACGAGTTGACAGGTACAATTCCATCTCCCTCTCTTCTTTTCCATACAATTTTCTTTCT
TTTTCTTTTAAATGTAAAAGACAGATAGCTTATAACGGTAAGTATA
Found at i:2181786 original size:16 final size:16
Alignment explanation
Indices: 2181765--2181796 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2181755 ACGGCACTAC
2181765 AGACGCATACATTCAT
1 AGACGCATACATTCAT
2181781 AGACGCATACATTCAT
1 AGACGCATACATTCAT
2181797 GACATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (16 bp):
AGACGCATACATTCAT
Found at i:2190594 original size:24 final size:24
Alignment explanation
Indices: 2190567--2190666 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
2190557 GATATCAAAA
*
2190567 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
2190591 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
2190615 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
2190639 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
2190663 ATCA
1 ATCA
2190667 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:2190666 original size:48 final size:48
Alignment explanation
Indices: 2190560--2190668 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
2190550 AAACGGAGAT
* * * * *
2190560 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
2190608 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
2190656 ATCAGAAATCAGA
1 ATCAGAAATCAGA
2190669 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:2191812 original size:17 final size:17
Alignment explanation
Indices: 2191790--2191824 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2191780 CTTCCATCCG
*
2191790 ATCTTATTATTTAATTC
1 ATCTTATCATTTAATTC
*
2191807 ATCTTATCATTTACTTC
1 ATCTTATCATTTAATTC
2191824 A
1 A
2191825 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (17 bp):
ATCTTATCATTTAATTC
Found at i:2193093 original size:10 final size:9
Alignment explanation
Indices: 2193080--2193134 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 9
2193070 GTCAAAGTTT
2193080 TGGTCAACAG
1 TGGTCAAC-G
2193090 TGGTCAACG
1 TGGTCAACG
2193099 TGGGTCAAC-
1 T-GGTCAACG
2193108 -GGTCAAC-
1 TGGTCAACG
2193115 -GGTCAACG
1 TGGTCAACG
2193123 -GGTCAACG
1 TGGTCAACG
2193131 -GGTC
1 TGGTC
2193135 GGGTCAACGG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
7 14 0.33
8 12 0.28
9 2 0.05
10 15 0.35
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (9 bp):
TGGTCAACG
Found at i:2193113 original size:7 final size:7
Alignment explanation
Indices: 2193101--2193131 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
2193091 GGTCAACGTG
2193101 GGTCAAC
1 GGTCAAC
2193108 GGTCAAC
1 GGTCAAC
2193115 GGTCAAC
1 GGTCAAC
2193122 GGGTCAAC
1 -GGTCAAC
2193130 GG
1 GG
2193132 GTCGGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:2193128 original size:8 final size:8
Alignment explanation
Indices: 2193081--2193147 Score: 63
Period size: 8 Copynumber: 8.5 Consensus size: 8
2193071 TCAAAGTTTT
2193081 GGTCAACAG
1 GGTCAAC-G
2193090 TGGTCAACGTG
1 -GGTCAAC--G
2193101 GGTCAAC-
1 GGTCAACG
2193108 GGTCAAC-
1 GGTCAACG
2193115 GGTCAACG
1 GGTCAACG
2193123 GGTCAACG
1 GGTCAACG
2193131 GGT---CG
1 GGTCAACG
2193136 GGTCAACG
1 GGTCAACG
2193144 GGTC
1 GGTC
2193148 GGGTCGGGTC
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
5 5 0.10
7 14 0.27
8 17 0.33
10 14 0.27
11 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:2193139 original size:13 final size:13
Alignment explanation
Indices: 2193121--2193196 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
2193111 CAACGGTCAA
2193121 CGGGTCAACGGGT
1 CGGGTCAACGGGT
2193134 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
2193152 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
2193165 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
2193178 CGGGTAAACGGGT
1 CGGGTCAACGGGT
2193191 CGGGTC
1 CGGGTC
2193197 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2193152 original size:18 final size:18
Alignment explanation
Indices: 2193115--2193170 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
2193105 AACGGTCAAC
2193115 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
2193136 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
2193154 GGTCAACTGGTCGGGTC
1 GGTCAACGGGTCGGGTC
2193171 AACTGGTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 23 0.68
21 11 0.32
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:2193159 original size:31 final size:31
Alignment explanation
Indices: 2193121--2193182 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
2193111 CAACGGTCAA
2193121 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
* *
2193152 CGGGTCAACTGGTCGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
2193183 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:2195327 original size:24 final size:24
Alignment explanation
Indices: 2195300--2195399 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
2195290 GATATCAAAA
*
2195300 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
2195324 ATCATAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* *
2195348 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
2195372 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
2195396 ATCA
1 ATCA
2195400 GATAAAATAT
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 54 0.93
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:2195399 original size:48 final size:48
Alignment explanation
Indices: 2195293--2195401 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
2195283 AAACGGAGAT
* * * * *
2195293 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
2195341 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
2195389 ATCAGAAATCAGA
1 ATCAGAAATCAGA
2195402 TAAAATATTC
Statistics
Matches: 47, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:2196521 original size:18 final size:18
Alignment explanation
Indices: 2196500--2196535 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2196490 CTTCCATCCG
*
2196500 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
2196518 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
2196536 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:2197799 original size:10 final size:9
Alignment explanation
Indices: 2197786--2197840 Score: 50
Period size: 10 Copynumber: 6.6 Consensus size: 9
2197776 GTCAAAGTTT
2197786 TGGTCAACAG
1 TGGTCAAC-G
2197796 TGGTCAACG
1 TGGTCAACG
2197805 TGGGTCAAC-
1 T-GGTCAACG
2197814 -GGTCAAC-
1 TGGTCAACG
2197821 -GGTCAACG
1 TGGTCAACG
2197829 -GGTCAACG
1 TGGTCAACG
2197837 -GGTC
1 TGGTC
2197841 GGGTCAACGG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
7 14 0.33
8 12 0.28
9 2 0.05
10 15 0.35
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (9 bp):
TGGTCAACG
Found at i:2197819 original size:7 final size:7
Alignment explanation
Indices: 2197807--2197837 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
2197797 GGTCAACGTG
2197807 GGTCAAC
1 GGTCAAC
2197814 GGTCAAC
1 GGTCAAC
2197821 GGTCAAC
1 GGTCAAC
2197828 GGGTCAAC
1 -GGTCAAC
2197836 GG
1 GG
2197838 GTCGGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:2197834 original size:8 final size:8
Alignment explanation
Indices: 2197787--2197853 Score: 63
Period size: 8 Copynumber: 8.5 Consensus size: 8
2197777 TCAAAGTTTT
2197787 GGTCAACAG
1 GGTCAAC-G
2197796 TGGTCAACGTG
1 -GGTCAAC--G
2197807 GGTCAAC-
1 GGTCAACG
2197814 GGTCAAC-
1 GGTCAACG
2197821 GGTCAACG
1 GGTCAACG
2197829 GGTCAACG
1 GGTCAACG
2197837 GGT---CG
1 GGTCAACG
2197842 GGTCAACG
1 GGTCAACG
2197850 GGTC
1 GGTC
2197854 GGGTCGGGTC
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
5 5 0.10
7 14 0.27
8 17 0.33
10 14 0.27
11 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:2197845 original size:13 final size:13
Alignment explanation
Indices: 2197827--2197902 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
2197817 CAACGGTCAA
2197827 CGGGTCAACGGGT
1 CGGGTCAACGGGT
2197840 CGGGTCAACGGGTCGGGT
1 CGGGTCAA-----CGGGT
*
2197858 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
2197871 CGGGTCAACTGGT
1 CGGGTCAACGGGT
*
2197884 CGGGTAAACGGGT
1 CGGGTCAACGGGT
2197897 CGGGTC
1 CGGGTC
2197903 GGGTCGGGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
18 13 0.24
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2197858 original size:18 final size:18
Alignment explanation
Indices: 2197821--2197876 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 18
2197811 AACGGTCAAC
2197821 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
2197842 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
2197860 GGTCAACTGGTCGGGTC
1 GGTCAACGGGTCGGGTC
2197877 AACTGGTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 23 0.68
21 11 0.32
ACGTcount: A:0.14, C:0.23, G:0.45, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:2197865 original size:31 final size:31
Alignment explanation
Indices: 2197827--2197888 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
2197817 CAACGGTCAA
2197827 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
* *
2197858 CGGGTCAACTGGTCGGGTCAACTGGTCGGGT
1 CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
2197889 AAACGGGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.13, C:0.23, G:0.45, T:0.19
Consensus pattern (31 bp):
CGGGTCAACGGGTCGGGTCAACGGGTCGGGT
Found at i:2201316 original size:31 final size:31
Alignment explanation
Indices: 2201281--2201382 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 31
2201271 AGACTCTGGC
*
2201281 AGGTTTAGTCGATGCTGGTAATTCCTTGTAT
1 AGGTTCAGTCGATGCTGGTAATTCCTTGTAT
* * *
2201312 AGGTTCA-AC-ACTGACTGGTAATTCCTATCTCTGGT
1 AGGTTCAGTCGA-TG-CTGGTAATTCC--T-TGT-AT
* *
2201347 AGGTTCAGTTGTTGCTGGTAATTCCTTGTAT
1 AGGTTCAGTCGATGCTGGTAATTCCTTGTAT
2201378 AGGTT
1 AGGTT
2201383 TAGCACCGAC
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
29 1 0.02
30 3 0.06
31 23 0.43
32 2 0.04
33 2 0.04
34 2 0.04
35 19 0.35
36 2 0.04
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.40
Consensus pattern (31 bp):
AGGTTCAGTCGATGCTGGTAATTCCTTGTAT
Found at i:2201380 original size:66 final size:66
Alignment explanation
Indices: 2201274--2201403 Score: 197
Period size: 66 Copynumber: 2.0 Consensus size: 66
2201264 GGTGTGAAGA
* *
2201274 CTCTGGCAGGTTTAGTCGATGCTGGTAATTCCTTGTATAGGTTCAACACTGACTGGTAATTCCTA
1 CTCTGGCAGGTTCAGTCGATGCTGGTAATTCCTTGTATAGGTTCAACACCGACTGGTAATTCCTA
2201339 T
66 T
* * * * *
2201340 CTCTGGTAGGTTCAGTTGTTGCTGGTAATTCCTTGTATAGGTTTAGCACCGACTGGTAATTCCT
1 CTCTGGCAGGTTCAGTCGATGCTGGTAATTCCTTGTATAGGTTCAACACCGACTGGTAATTCCT
2201404 TATGGACCTA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (66 bp):
CTCTGGCAGGTTCAGTCGATGCTGGTAATTCCTTGTATAGGTTCAACACCGACTGGTAATTCCTA
T
Found at i:2202309 original size:131 final size:134
Alignment explanation
Indices: 2202153--2202416 Score: 462
Period size: 131 Copynumber: 2.0 Consensus size: 134
2202143 TGAAATGTTA
2202153 ACAAATTTGAGGACTAATGTAGAATGATAGTCATAGTTTAGTGATAAAATTGAAATGTGTTAAAA
1 ACAAATTTGAGGACTAATGTAGAATGATAGTCATAGTTTAGTGATAAAATTGAAATGTGTTAAAA
2202218 TTTAGGGACTAATTTAAGGACATGTGATGCAA-T-T-TTAAATTTTACAAATAGTTTATATTAAA
66 TTTAGGGACTAATTTAAGGACATGTGATGCAATTATATTAAATTTTACAAATAGTTTATATTAAA
2202280 TTTT
131 TTTT
*
2202284 ACAAATTTGAGGACTAATGTAGAATGATAGTCATAGTTTAGTGATGAAATTGAAATGTGTTAAAA
1 ACAAATTTGAGGACTAATGTAGAATGATAGTCATAGTTTAGTGATAAAATTGAAATGTGTTAAAA
2202349 TTTAGGGACTAATTTAAGGACATGTGATGCAATTAACTCAATTAAATTTTACAAATAGTTTATAT
66 TTTAGGGACTAATTTAAGGACATGTGATGCAATT-A-T--ATTAAATTTTACAAATAGTTTATAT
2202414 TAA
127 TAA
2202417 TTACTTCAAA
Statistics
Matches: 125, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
131 96 0.77
132 1 0.01
135 1 0.01
138 27 0.22
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (134 bp):
ACAAATTTGAGGACTAATGTAGAATGATAGTCATAGTTTAGTGATAAAATTGAAATGTGTTAAAA
TTTAGGGACTAATTTAAGGACATGTGATGCAATTATATTAAATTTTACAAATAGTTTATATTAAA
TTTT
Done.