Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_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: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 23
Found at i:1937598 original size:19 final size:20
Alignment explanation
Indices: 1937551--1937598 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
1937541 TCTAAATCCT
*
1937551 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* * *
1937571 CTTTGAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
1937590 TTTTCAAAA
1 TTTTCAAAA
1937599 GAAAATCGTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:1938900 original size:20 final size:22
Alignment explanation
Indices: 1938875--1938934 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
1938865 CCGTTAGACA
1938875 GGGGGGAATCTGTTCCCCT-TGG
1 GGGGGGAATCTGTTCCCCTCT-G
* *
1938897 GGGGGGAATCAG-TACCCTCT-
1 GGGGGGAATCTGTTCCCCTCTG
*
1938917 GGGGGGAATCTGTACCCC
1 GGGGGGAATCTGTTCCCC
1938935 ATGGACATTC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 11 0.35
21 8 0.26
22 12 0.39
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.22
Consensus pattern (22 bp):
GGGGGGAATCTGTTCCCCTCTG
Found at i:1938919 original size:22 final size:22
Alignment explanation
Indices: 1938875--1938934 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 22
1938865 CCGTTAGACA
* *
1938875 GGGGGGAATCTGTTCCCCTTGG
1 GGGGGGAATCAGTACCCCTTGG
1938897 GGGGGGAATCAGTA-CCCTCT--
1 GGGGGGAATCAGTACCCCT-TGG
*
1938917 GGGGGGAATCTGTACCCC
1 GGGGGGAATCAGTACCCC
1938935 ATGGACATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 13 0.39
21 7 0.21
22 13 0.39
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.22
Consensus pattern (22 bp):
GGGGGGAATCAGTACCCCTTGG
Found at i:1941458 original size:18 final size:19
Alignment explanation
Indices: 1941426--1941461 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1941416 TCAAAATTTA
*
1941426 AAAACTATTAGAAAATAAT
1 AAAACTATTAAAAAATAAT
1941445 AAAA-TATTAAAAAATAA
1 AAAACTATTAAAAAATAA
1941462 AAATAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAACTATTAAAAAATAAT
Found at i:1942027 original size:6 final size:6
Alignment explanation
Indices: 1942016--1942051 Score: 51
Period size: 5 Copynumber: 6.5 Consensus size: 6
1942006 AAAGAACTTC
1942016 GGAAAG GGAAAG GG-AAG GG-AAG GG-AAG GGAAAG GGA
1 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGA
1942052 GAATCAAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 15 0.52
6 14 0.48
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (6 bp):
GGAAAG
Found at i:1942040 original size:16 final size:16
Alignment explanation
Indices: 1942019--1942051 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1942009 GAACTTCGGA
1942019 AAGGGAAAGGG-AAGGG
1 AAGGG-AAGGGAAAGGG
1942035 AAGGGAAGGGAAAGGG
1 AAGGGAAGGGAAAGGG
1942051 A
1 A
1942052 GAATCAAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (16 bp):
AAGGGAAGGGAAAGGG
Found at i:1942357 original size:3 final size:3
Alignment explanation
Indices: 1942349--1942391 Score: 77
Period size: 3 Copynumber: 14.0 Consensus size: 3
1942339 TCTAAGGTGT
1942349 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA
1942392 CGTTTTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1945029 original size:2 final size:2
Alignment explanation
Indices: 1945022--1945047 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1945012 ATTTTACCTA
1945022 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
1945048 TTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1946393 original size:22 final size:22
Alignment explanation
Indices: 1946362--1946423 Score: 115
Period size: 22 Copynumber: 2.8 Consensus size: 22
1946352 AACACTTAAT
*
1946362 ATATATAAATATTTTATTTGAA
1 ATATAAAAATATTTTATTTGAA
1946384 ATATAAAAATATTTTATTTGAA
1 ATATAAAAATATTTTATTTGAA
1946406 ATATAAAAATATTTTATT
1 ATATAAAAATATTTTATT
1946424 AATATATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (22 bp):
ATATAAAAATATTTTATTTGAA
Found at i:1952766 original size:2 final size:2
Alignment explanation
Indices: 1952759--1952788 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1952749 TGAATATGTT
1952759 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1952789 AATTGGGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1969383 original size:23 final size:22
Alignment explanation
Indices: 1969349--1969411 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
1969339 AATCTTACAT
1969349 GGCACTCTGGTGCATTTCTACGC
1 GGCACTC-GGTGCATTTCTACGC
* *
1969372 GGCACTACGGTGCAATTCTACGT
1 GGCACT-CGGTGCATTTCTACGC
*
1969395 GGCACTTTGGTGCATTT
1 GGCAC-TCGGTGCATTT
1969412 ATATGAGCTG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 32 0.94
24 2 0.06
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (22 bp):
GGCACTCGGTGCATTTCTACGC
Found at i:1978924 original size:35 final size:35
Alignment explanation
Indices: 1978883--1978953 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
1978873 AAGAAATAAG
*
1978883 TTTATGGGCCCTGCTTTTAATTTAGTTTATTAATA
1 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
1978918 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
1 TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
1978953 T
1 T
1978954 AGTTTTTAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (35 bp):
TTTATGGGCCCTGCTTTTAATTTAGTATATTAATA
Found at i:1982025 original size:4 final size:4
Alignment explanation
Indices: 1982016--1982040 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1982006 GGATATATAA
1982016 CTAG CTAG CTAG CTAG CTAG CTAG C
1 CTAG CTAG CTAG CTAG CTAG CTAG C
1982041 AAAACTAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (4 bp):
CTAG
Found at i:1986446 original size:25 final size:26
Alignment explanation
Indices: 1986408--1986459 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1986398 TTTTTTTGAT
*
1986408 TAAAAAATTAAATTTTTAATTTTAAA
1 TAAAAAATTAAATTTTTAATTTAAAA
* *
1986434 TAAAATATT-AATTTTTTATTTAAAA
1 TAAAAAATTAAATTTTTAATTTAAAA
1986459 T
1 T
1986460 TTAAATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TAAAAAATTAAATTTTTAATTTAAAA
Found at i:1988545 original size:71 final size:71
Alignment explanation
Indices: 1988448--1988593 Score: 213
Period size: 71 Copynumber: 2.1 Consensus size: 71
1988438 GAATTGTTAT
* *
1988448 TAAGCATCTCATCGTGATTAAATGACTGCTGTCTAATTTCATAGTTCAAACTGGGAGACATTTCA
1 TAAGCATCTCATCGTGATCAAATGACTGCTGTCTAATTTCATAGCTCAAACTGGGAGACATTTCA
1988513 GGAGTG
66 GGAGTG
* * * *
1988519 TAAGCAT-TACATCTTGATCAACTGACTGCTGTCTAATTTCATAGCTCAAACTGGGGGACATTTG
1 TAAGCATCT-CATCGTGATCAAATGACTGCTGTCTAATTTCATAGCTCAAACTGGGAGACATTTC
*
1988583 TGGAGTG
65 AGGAGTG
1988590 TAAG
1 TAAG
1988594 TAACGTCGGT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 1 0.01
71 66 0.99
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (71 bp):
TAAGCATCTCATCGTGATCAAATGACTGCTGTCTAATTTCATAGCTCAAACTGGGAGACATTTCA
GGAGTG
Found at i:1988688 original size:37 final size:37
Alignment explanation
Indices: 1988635--1988715 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
1988625 TGGCAATCAA
1988635 CTTTG-AAAAATATTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAAATATTTTTCAAAGTTTGGTAAATGTTT
*
1988671 CTTTGAAAAAATATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAATATTTTTCAAAGTTTGGTAAATGTTT
*
1988708 -GTTGAAAA
1 CTTTGAAAA
1988716 TAGGAATGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 12 0.29
37 30 0.71
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAAATATTTTTCAAAGTTTGGTAAATGTTT
Found at i:1992531 original size:46 final size:45
Alignment explanation
Indices: 1992422--1992531 Score: 139
Period size: 45 Copynumber: 2.4 Consensus size: 45
1992412 GAATAAATAT
* * * * * *
1992422 ATGCGAACTAGAAATCATGCAGTTAGGTTTATTTTTTGAGCATGT
1 ATGCGAATTAGAAATCATGCAGCTAGGTTTATTTTTCGAACAAGC
*
1992467 ATGCGAATTAGAAATCATGCGGCTAGGTTTATTTTCTCGAACAAGC
1 ATGCGAATTAGAAATCATGCAGCTAGGTTTATTTT-TCGAACAAGC
*
1992513 ATGCGAATTAGATATCATG
1 ATGCGAATTAGAAATCATG
1992532 TGGTTAGGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 32 0.57
46 24 0.43
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (45 bp):
ATGCGAATTAGAAATCATGCAGCTAGGTTTATTTTTCGAACAAGC
Found at i:1992904 original size:55 final size:55
Alignment explanation
Indices: 1992838--1992962 Score: 216
Period size: 55 Copynumber: 2.3 Consensus size: 55
1992828 AGGCGTTCAG
*
1992838 ATGATTCATGAAGAA-GAACATCCGATGAATGAAGAAATTTGAACCTGACTGAAGA
1 ATGATTCATGAAGAAGGAA-ATCCGATGAATGAAGAAATTTGAACCTGACTAAAGA
1992893 ATGATTCATGAAGAAGGAAATCCGATGAATGAAGAAATTTGAACCTGACTAAAGA
1 ATGATTCATGAAGAAGGAAATCCGATGAATGAAGAAATTTGAACCTGACTAAAGA
*
1992948 ACGATTCATGAAGAA
1 ATGATTCATGAAGAA
1992963 TGACAACCGA
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
55 64 0.96
56 3 0.04
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (55 bp):
ATGATTCATGAAGAAGGAAATCCGATGAATGAAGAAATTTGAACCTGACTAAAGA
Found at i:1993621 original size:72 final size:72
Alignment explanation
Indices: 1993504--1993653 Score: 282
Period size: 72 Copynumber: 2.1 Consensus size: 72
1993494 CCCTATTACA
*
1993504 CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATGTGATGATAGC
1 CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATATGATGATAGC
1993569 AAATGAT
66 AAATGAT
1993576 CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATATGATGATAGC
1 CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATATGATGATAGC
*
1993641 AACTGAT
66 AAATGAT
1993648 CAAGAA
1 CAAGAA
1993654 CCTGTTAGGG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (72 bp):
CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAGCCAATATGATGATAGC
AAATGAT
Found at i:1995676 original size:2 final size:2
Alignment explanation
Indices: 1995669--1995696 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1995659 GTATACCCAA
1995669 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
1995697 GTTTATACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1997189 original size:125 final size:125
Alignment explanation
Indices: 1996967--1997215 Score: 331
Period size: 125 Copynumber: 2.0 Consensus size: 125
1996957 TACCCACATT
* * * *
1996967 GGGGCATGACTAAACCCACATCATGTTGAGATGACAAGATTTGGACCAAGGAGTCATGAAGAATG
1 GGGGCACGACTAAACCCACATCATGTTGAGATGACAAGATTTAGACCAAGAAGGCATGAAGAATG
* * *
1997032 AGCCTTACAAATTAAGGTGATGGGGCATTTTGAAGGC-CTGTACCAGTATGAGATAATGTC
66 AGCATTACAAATTAAGGTGATGGGGCATTTTGAAGGCTCT-TACCAGAATAAGATAATGTC
* *
1997092 GGGGCACGACTGAACCCACATCATGTTGAGATGATAAGATTTAGACCAAGAAGGCATTGAA-AAT
1 GGGGCACGACTAAACCCACATCATGTTGAGATGACAAGATTTAGACCAAGAAGGCA-TGAAGAAT
* * * * * *
1997156 GAGCATTATAATTTGAGGTGTTTGGGCATTTTGAAGGCTCTTACCTGAATAAGATAATGT
65 GAGCATTACAAATTAAGGTGATGGGGCATTTTGAAGGCTCTTACCAGAATAAGATAATGT
1997216 TGCGGCATTA
Statistics
Matches: 107, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
125 101 0.94
126 6 0.06
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (125 bp):
GGGGCACGACTAAACCCACATCATGTTGAGATGACAAGATTTAGACCAAGAAGGCATGAAGAATG
AGCATTACAAATTAAGGTGATGGGGCATTTTGAAGGCTCTTACCAGAATAAGATAATGTC
Found at i:1998504 original size:36 final size:37
Alignment explanation
Indices: 1998419--1998513 Score: 129
Period size: 36 Copynumber: 2.6 Consensus size: 37
1998409 AAAGTCAAGT
* * *
1998419 CTTCACCAAAGAGTAGTGAAGCGAATCCATTTTGAGC
1 CTTCACCAAAGAGTAGTGAAGCGAAACCATCTTAAGC
* *
1998456 CTTGACCAAAGAGTAGTGAAG-TAAACCATCTTAAGC
1 CTTCACCAAAGAGTAGTGAAGCGAAACCATCTTAAGC
*
1998492 CTTCACCGAAGAGTAGTGAAGC
1 CTTCACCAAAGAGTAGTGAAGC
1998514 ATATCCTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 30 0.60
37 20 0.40
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (37 bp):
CTTCACCAAAGAGTAGTGAAGCGAAACCATCTTAAGC
Found at i:1998980 original size:54 final size:54
Alignment explanation
Indices: 1998918--1999133 Score: 360
Period size: 54 Copynumber: 4.0 Consensus size: 54
1998908 GTAGTAAAGT
*
1998918 AGAAGAAGATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
*
1998972 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1999026 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
* * * * *
1999080 AGAAGAAGATGTTTGAGTTCTATACTTCCTGAAAGTAAGAGGGAGCGAACCTGT
1 AGAAGAAGATGTTCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCTGT
1999134 TTATTGAAGA
Statistics
Matches: 153, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
54 132 0.86
55 21 0.14
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCTGTA
Found at i:1999193 original size:55 final size:55
Alignment explanation
Indices: 1999134--1999447 Score: 320
Period size: 55 Copynumber: 5.7 Consensus size: 55
1999124 GCGAACCTGT
* * * * *
1999134 TTATTGAAGATTGTTCGAGTCTTATACACTCTAAAGAAATAGAGACCAGACACAA
1 TTATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
* * *
1999189 TTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGCAATAGGGAGCAGACCCGA
1 TTATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
** * * *
1999244 TTACAGAAGATTATTCGAGT-TCTATACT-TCCTGAAAGAAAGAGGGAGC-GA-ACCTGT
1 TTATTGAAGATTGTTCGAGTCT-TATACTCT-CTG-AAGAAATAGGGAGCAGACA-C-GA
* *
1999300 TTAATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAGATAGGGGAGCAGACACGA
1 TTATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATA-GGGAGCAGACACGA
* *
1999356 TTATTGAAGATTGTTCGAGTCTCATACTCTCTGAA-AAATAGGGAGCAGACCCGA
1 TTATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
** *
1999410 TTA-CAAAGATTATTCGAGT-TATATACT-TCCTGAAGAAA
1 TTATTGAAGATTGTTCGAGTCT-TATACTCT-CTGAAGAAA
1999448 GATGGAGCTA
Statistics
Matches: 216, Mismatches: 30, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
52 2 0.01
53 23 0.11
54 21 0.10
55 85 0.39
56 79 0.37
57 5 0.02
58 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (55 bp):
TTATTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGA
Found at i:1999290 original size:166 final size:165
Alignment explanation
Indices: 1999094--1999460 Score: 594
Period size: 166 Copynumber: 2.2 Consensus size: 165
1999084 GAAGATGTTT
* *
1999094 GAGTTCTATACTTCCTGAAAGTAAGAGGGAGCGAACCTGTTTATTGAAGATTGTTCGAGTCTTAT
1 GAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCTGTTTAATGAAGATTGTTCGAGTCTTAT
1999159 ACACTCTAAAGAAATA-GAGACCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGA
66 ACACTCTAAAGAAATAGGAGACCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGA
*
1999223 AGCAATAGGGAGCAGACCCGATTACAGAAGATTATTC
131 A-AAATAGGGAGCAGACCCGATTACA-AAGATTATTC
1999260 GAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCTGTTTAATGAAGATTGTTCGAGTCTTAT
1 GAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCTGTTTAATGAAGATTGTTCGAGTCTTAT
* * * * * *
1999325 ACTCTCTGAAGAGATAGGGGAGCAGACACGATTATTGAAGATTGTTCGAGTCTCATACTCTCTGA
66 ACACTCTAAAGAAATAGGAGACCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGA
1999390 AAAATAGGGAGCAGACCCGATTACAAAGATTATTC
131 AAAATAGGGAGCAGACCCGATTACAAAGATTATTC
* * *
1999425 GAGTTATATACTTCCTG-AAGAAAGATGGAGCTAACC
1 GAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACC
1999461 CGTAGGTAAA
Statistics
Matches: 188, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
164 17 0.09
165 26 0.14
166 99 0.53
167 46 0.24
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (165 bp):
GAGTTCTATACTTCCTGAAAGAAAGAGGGAGCGAACCTGTTTAATGAAGATTGTTCGAGTCTTAT
ACACTCTAAAGAAATAGGAGACCAGACACAATTATTGAAGATTGTTCGAGTCTCATACTCTCTGA
AAAATAGGGAGCAGACCCGATTACAAAGATTATTC
Found at i:1999668 original size:53 final size:53
Alignment explanation
Indices: 1999583--1999687 Score: 149
Period size: 53 Copynumber: 2.0 Consensus size: 53
1999573 TCAAGTTTTA
*
1999583 AAGCATAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAG-GAAACCCGT
1 AAGCAAAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCG-AACCCGT
* * * *
1999636 AAGCAAAAGATTTTTTGAGTTTTACTCTCTGAAGCAAGAGGGAGCGAACCCG
1 AAGCAAAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG
1999688 CTAGTCGAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
53 45 0.98
54 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (53 bp):
AAGCAAAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGT
Found at i:1999915 original size:20 final size:20
Alignment explanation
Indices: 1999870--1999915 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
1999860 GACCAACAAA
*
1999870 ATCGCAATGCGATCGCTAAT
1 ATCGCAACGCGATCGCTAAT
* *
1999890 -TCGCAACGCGATCTCTATT
1 ATCGCAACGCGATCGCTAAT
1999909 ATCGCAA
1 ATCGCAA
1999916 ATTCGCGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATCGCTAAT
Found at i:2000049 original size:20 final size:20
Alignment explanation
Indices: 2000021--2000070 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2000011 AATTGGGAAA
*
2000021 ATCGTAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
2000041 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
2000061 ATCGCAATGC
1 ATCGCAATGC
2000071 AATAATACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:2000708 original size:19 final size:19
Alignment explanation
Indices: 2000686--2000831 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
2000676 GAAACCAAAA
*
2000686 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2000705 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2000724 TCGCGTTGCGATTTTC---
1 TCGCGTTGCGATTTTCATT
* **
2000740 T--CGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
2000757 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
2000771 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
2000790 TCTACGTTGCGATTCTCATT
1 TC-GCGTTGCGATTTTCATT
*
2000810 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
2000830 TC
1 TC
2000832 AACCAAAAGA
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
14 20 0.20
16 3 0.03
17 3 0.03
19 45 0.44
20 29 0.28
21 2 0.02
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2000756 original size:33 final size:33
Alignment explanation
Indices: 2000719--2000806 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
2000709 GTTGCGATTT
*
2000719 TCATTTCGCGTTGCGATTTTCTCGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
2000752 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
2000785 TCATTTCTACGTTGCGATTCTC
1 TCATTTC-GCGTTGCGATTCTC
2000807 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 38 0.75
34 13 0.25
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:2004411 original size:14 final size:14
Alignment explanation
Indices: 2004392--2004427 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2004382 ATTGTTTAAT
2004392 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
2004406 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
2004420 TGATTTGT
1 TGATTTGT
2004428 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:2004571 original size:14 final size:14
Alignment explanation
Indices: 2004552--2004608 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2004542 GCGAAATGAA
2004552 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2004566 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2004585 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2004599 AATCGCAACG
1 AATCGCAACG
2004609 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2004579 original size:33 final size:33
Alignment explanation
Indices: 2004534--2004623 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
2004524 AAAAAGTACT
*
2004534 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
2004567 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
2004600 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
2004624 GTTGCGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:2004593 original size:19 final size:19
Alignment explanation
Indices: 2004534--2004594 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
2004524 AAAAAGTACT
*
2004534 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
2004553 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
2004567 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
2004586 ATCGCAACG
1 ATCGCAACG
2004595 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:2004665 original size:33 final size:32
Alignment explanation
Indices: 2004623--2004748 Score: 166
Period size: 33 Copynumber: 3.9 Consensus size: 32
2004613 ATTAAATTCG
*
2004623 CGTTGCGATTTTCATTTCGCATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
2004656 CGTTGCGATTTT-ATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
* *
2004688 CGTTGTGATTTTCATTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
2004721 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
2004749 AGTAATTTCC
Statistics
Matches: 81, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
31 3 0.04
32 24 0.30
33 51 0.63
34 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:2004710 original size:65 final size:66
Alignment explanation
Indices: 2004616--2004747 Score: 221
Period size: 65 Copynumber: 2.0 Consensus size: 66
2004606 ACGCGAAATT
**
2004616 AAATTCGCGTTGCGATTTTCATTTCGCATTGTGATTCCCTCGTTGCGATTTT-ATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2004680 G
66 G
* *
2004681 AAATTCGCGTTGTGATTTTCATTTCGCATTGCAATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
2004746 G
66 G
2004747 A
1 A
2004748 TAGTAATTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
65 48 0.77
66 14 0.23
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (66 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCAATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:2007038 original size:12 final size:12
Alignment explanation
Indices: 2007021--2007045 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2007011 TCTTCGGGGA
2007021 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2007033 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2007045 C
1 C
2007046 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:2008090 original size:20 final size:20
Alignment explanation
Indices: 2008004--2008098 Score: 95
Period size: 20 Copynumber: 4.7 Consensus size: 20
2007994 GATTCTGTAT
*
2008004 TATCTCGTTGCGA-ACGTCAG
1 TATCGCGTTGCGATA-GTCAG
* *
2008024 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
2008044 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
2008065 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
2008085 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
2008099 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
19 3 0.05
20 42 0.68
21 15 0.24
22 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:2008112 original size:41 final size:41
Alignment explanation
Indices: 2008025--2008119 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
2008015 GAACGTCAGA
* * ** *
2008025 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
2008066 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
2008108 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
2008120 TTACTTATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:2008209 original size:21 final size:21
Alignment explanation
Indices: 2008169--2008209 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2008159 ACTGTAGACC
**
2008169 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
2008190 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
2008210 GCAAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:2014450 original size:3 final size:3
Alignment explanation
Indices: 2014444--2014518 Score: 107
Period size: 3 Copynumber: 25.0 Consensus size: 3
2014434 TTACCCATTT
* *
2014444 TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
2014492 TTA TTA -TA TGTA CTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA
2014519 AAAAATAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.94
4 2 0.03
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2015920 original size:15 final size:16
Alignment explanation
Indices: 2015881--2015927 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
2015871 TATAATAATA
2015881 ATAATTTATTTTTTAC
1 ATAATTTATTTTTTAC
*
2015897 ATAAATTA-TTTTTATC
1 ATAATTTATTTTTTA-C
2015913 AT-ATTTATTTATTTA
1 ATAATTTATTT-TTTA
2015928 TTTTTCAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.38
16 12 0.46
17 4 0.15
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (16 bp):
ATAATTTATTTTTTAC
Found at i:2016116 original size:23 final size:26
Alignment explanation
Indices: 2016084--2016133 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
2016074 CATTTTCTGA
*
2016084 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
2016107 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
2016133 T
1 T
2016134 TTTCTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:2019999 original size:15 final size:15
Alignment explanation
Indices: 2019979--2020010 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2019969 ATCAATACCT
2019979 TTTTGCATACATACA
1 TTTTGCATACATACA
*
2019994 TTTTGCATACATTCA
1 TTTTGCATACATACA
2020009 TT
1 TT
2020011 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATACA
Found at i:2023813 original size:18 final size:19
Alignment explanation
Indices: 2023785--2023821 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2023775 AGATGGCAAT
*
2023785 CATTCTTTACATTTTTTTA
1 CATTCTTTACATTTATTTA
2023804 CATT-TTTACATTTATTTA
1 CATTCTTTACATTTATTTA
2023822 TTTCATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (19 bp):
CATTCTTTACATTTATTTA
Found at i:2027347 original size:1 final size:1
Alignment explanation
Indices: 2027341--2027412 Score: 81
Period size: 1 Copynumber: 72.0 Consensus size: 1
2027331 ATGCTTGAAG
* * * * * * *
2027341 AAAAAAAAGAACAAAAAAGAAAAAAGAAAGAAAAAAAGAAAAAAAAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2027406 AAAAAAA
1 AAAAAAA
2027413 GGGGTCAAGA
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 57 1.00
ACGTcount: A:0.90, C:0.01, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:2027362 original size:19 final size:17
Alignment explanation
Indices: 2027338--2027413 Score: 107
Period size: 19 Copynumber: 4.2 Consensus size: 17
2027328 ATTATGCTTG
2027338 AAGAAAAAAAAGAACAAAA
1 AAGAAAAAAAA-AA-AAAA
2027357 AAGAAAAAAGAAAGAAAAA
1 AAGAAAAAA-AAA-AAAAA
2027376 AAGAAAAAAAAAAAAAAA
1 AAG-AAAAAAAAAAAAAA
2027394 AAGAAAAAAAAAAAAAA
1 AAGAAAAAAAAAAAAAA
2027411 AAG
1 AAG
2027414 GGGTCAAGAT
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
17 17 0.31
18 8 0.15
19 20 0.37
20 9 0.17
ACGTcount: A:0.88, C:0.01, G:0.11, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAAAAA
Found at i:2027365 original size:17 final size:15
Alignment explanation
Indices: 2027341--2027410 Score: 97
Period size: 15 Copynumber: 4.5 Consensus size: 15
2027331 ATGCTTGAAG
2027341 AAAAAAAAGAACAAAA
1 AAAAAAAAGAA-AAAA
2027357 AAGAAAAAAGAAAGAAA
1 AA-AAAAAAGAAA-AAA
*
2027374 AAAAGAAA-AAAAAA
1 AAAAAAAAGAAAAAA
2027388 AAAAAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
2027403 AAAAAAAA
1 AAAAAAAA
2027411 AAGGGGTCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
14 10 0.20
15 17 0.35
16 8 0.16
17 14 0.29
ACGTcount: A:0.90, C:0.01, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAA
Found at i:2027365 original size:18 final size:18
Alignment explanation
Indices: 2027341--2027413 Score: 103
Period size: 18 Copynumber: 3.9 Consensus size: 18
2027331 ATGCTTGAAG
2027341 AAAAAAAAGAACAAAAAAGA
1 AAAAAAAAG-A-AAAAAAGA
2027361 AAAAAGAAAGAAAAAAAGA
1 AAAAA-AAAGAAAAAAAGA
*
2027380 AAAAAAAAAAAAAAAAGA
1 AAAAAAAAGAAAAAAAGA
2027398 AAAAAAAA-AAAAAAAG
1 AAAAAAAAGAAAAAAAG
2027414 GGGTCAAGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
17 8 0.16
18 20 0.39
19 13 0.25
20 6 0.12
21 4 0.08
ACGTcount: A:0.89, C:0.01, G:0.10, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAAGA
Found at i:2027412 original size:26 final size:28
Alignment explanation
Indices: 2027338--2027413 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 28
2027328 ATTATGCTTG
2027338 AAGAAAAAAAAGAACAAAAAAGAAAAAAGA
1 AAGAAAAAAAA-AA-AAAAAAGAAAAAAGA
*
2027368 AAGAAAAAAAGAAAAAAAA-AAAAAA-A
1 AAGAAAAAAAAAAAAAAAAGAAAAAAGA
2027394 AAGAAAAAAAAAAAAAAAAG
1 AAGAAAAAAAAAAAAAAAAG
2027414 GGGTCAAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
26 19 0.44
27 6 0.14
28 6 0.14
29 2 0.05
30 10 0.23
ACGTcount: A:0.88, C:0.01, G:0.11, T:0.00
Consensus pattern (28 bp):
AAGAAAAAAAAAAAAAAAAGAAAAAAGA
Found at i:2028940 original size:115 final size:115
Alignment explanation
Indices: 2028683--2028919 Score: 388
Period size: 115 Copynumber: 2.1 Consensus size: 115
2028673 TTGGAGCAAG
* *
2028683 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTAT
1 TGAATCTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* * * *
2028748 CTGATCTGGTTTGGTATGAACCCCAAAAACCAATTATTGGATTTAAAAGA
66 CTGATCTGGTTCGGTAGGAACCACAAAAACCAATTATTGGAATTAAAAGA
*
2028798 TGAATGTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 TGAATCTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
2028863 CTGATCTGGTTCGGTAGGAACCAC-AGAACCAATTATTGGAATTAAAAGA
66 CTGATCTGGTTCGGTAGGAACCACAAAAACCAATTATTGGAATTAAAAGA
2028912 TGAA-CTGC
1 TGAATCTGC
2028920 ATGATCGTCT
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
113 3 0.03
114 27 0.23
115 85 0.74
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (115 bp):
TGAATCTGCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTCGGTAGGAACCACAAAAACCAATTATTGGAATTAAAAGA
Found at i:2029711 original size:24 final size:23
Alignment explanation
Indices: 2029667--2029712 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2029657 AGTTCATAAT
*
2029667 AAGAAGAATTCATCTGAAGAAGG
1 AAGAAGAATTCATATGAAGAAGG
2029690 AAGAAGAAATTCATAATG-AGAAG
1 AAGAAG-AATTCAT-ATGAAGAAG
2029713 AATTTGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 12 0.60
25 2 0.10
ACGTcount: A:0.52, C:0.07, G:0.24, T:0.17
Consensus pattern (23 bp):
AAGAAGAATTCATATGAAGAAGG
Found at i:2029864 original size:113 final size:113
Alignment explanation
Indices: 2029618--2030159 Score: 593
Period size: 113 Copynumber: 4.8 Consensus size: 113
2029608 TAGCAAAGAT
* * * *
2029618 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATAAGAAGAATTCATCTG
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTA
2029683 AAGAAGGAAGAAGAAA-TTCATAATGAGAAGAATTTGTTCAACCTTTT-C
65 AAGAAGGAAGAA-AAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
2029731 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAA
* * * *
2029796 AGAAGGCAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGT
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * ** * * **** * * *
2029844 TTAAATTCATCATTCAATGGATCAGCATTACCAGTTCGAGTTCATAATAAGAAGAACTCATATGA
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAA
* * *
2029909 AGAAGGAAGGAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * * * * *
2029957 TTAAATTCATCATTTGATGGATTAACATTGCCAG-GTAGAGTTTATAATGAGAAGAACTCGTC-A
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTA
** * *
2030020 TTTGAA-GAAGAAGAAA-TTCATAATGAGAAGAATTTGTCCAACTTTTTGC
65 -AAGAAGGAAGAA-AAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
2030069 TCAAAACCATCACTTGATAGATCAGCTTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCT--
1 TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAA
*
2030131 -GAA-GAAGAAGAAGTTCATAATGAGAAGAA
66 AGAAGGAAGAAAAAGTTCATAATGAGAAGAA
2030160 CTCATCTGAA
Statistics
Matches: 363, Mismatches: 58, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
107 2 0.01
108 25 0.07
111 25 0.07
112 126 0.35
113 185 0.51
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTAA
AGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:2030042 original size:225 final size:223
Alignment explanation
Indices: 2029656--2030159 Score: 612
Period size: 225 Copynumber: 2.3 Consensus size: 223
2029646 TTCCAGAAAA
* *
2029656 AAGTTCATAATAAGAAGAATTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAG-AGAAGTTCATAATGAGAAGAATTTGTT
* * *
2029721 CAACCTTTTCTCAAATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGA
65 CAACCTTTTCTCAAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGA
* * * * **
2029786 ACTCATCTAAAGAAGGCAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTAAATT
130 ACTCATCTAAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTCCAACTTTTTGCTCAAAAC
* *
2029851 CATCA-TTCAATGGATCAGCATTACCAGTTCG
195 CATCACTT-AATAGATCAGCATTACCAG--AG
*
2029882 -AGTTCATAATAAGAAGAACTCATATGAAGAAGGAAGGAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAA-GAGAAGTTCATAATGAGAAGAATTTGTT
* * * * * *
2029946 CAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAG-GTAGAGTTTATAATGAGAA
65 CAACCTTTT-CTCAAATCCATCATTTGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAA
* ** *
2030010 GAACTCGTC-ATTTGAA-GAAGAAGAAA-TTCATAATGAGAAGAATTTGTCCAACTTTTTGCTCA
128 GAACTCATCTA-AAGAAGGAAGAA-AAAGTTCATAATGAGAAGAACTTGTCCAACTTTTTGCTCA
* * *
2030072 AAACCATCACTTGATAGATCAGCTTTTCCAGAG
191 AAACCATCACTTAATAGATCAGCATTACCAGAG
*
2030105 AAGTTCATAATGAGAAGAACTCATCTGAAGAA-G-A-AGAAGTTCATAATGAGAAGAA
1 AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAAGTTCATAATGAGAAGAA
2030160 CTCATCTGAA
Statistics
Matches: 242, Mismatches: 29, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
220 21 0.09
222 1 0.00
223 2 0.01
224 29 0.12
225 129 0.53
226 60 0.25
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (223 bp):
AAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTCTCAAATCCATCATTTGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTAAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTGTCCAACTTTTTGCTCAAAACC
ATCACTTAATAGATCAGCATTACCAGAG
Found at i:2030147 original size:36 final size:36
Alignment explanation
Indices: 2030103--2030194 Score: 166
Period size: 36 Copynumber: 2.6 Consensus size: 36
2030093 GCTTTTCCAG
2030103 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
1 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
2030139 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
1 AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
* *
2030175 AAAAGTTCACAATGAGAAGA
1 AGAAGTTCATAATGAGAAGA
2030195 GCTTATTCAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.18
Consensus pattern (36 bp):
AGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
Found at i:2030158 original size:17 final size:17
Alignment explanation
Indices: 2030103--2030159 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
2030093 GCTTTTCCAG
2030103 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
*
2030120 AGAA-CTCATCTGAA-GAAGA
1 AGAAGTTCA--T-AATG-AGA
2030139 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
2030156 AGAA
1 AGAA
2030160 CTCATCTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
16 3 0.09
17 13 0.41
18 4 0.12
19 9 0.28
20 3 0.09
ACGTcount: A:0.49, C:0.09, G:0.23, T:0.19
Consensus pattern (17 bp):
AGAAGTTCATAATGAGA
Found at i:2030323 original size:160 final size:160
Alignment explanation
Indices: 2030096--2030478 Score: 686
Period size: 160 Copynumber: 2.4 Consensus size: 160
2030086 TAGATCAGCT
*
2030096 TTTCCAG-AGAAGTTCATAATGAGAAGAACTCATCTG-A--AG-AAGAAGAAGTTCATAATGAGA
1 TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGA
2030156 AGAACTCATCTGAAGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCATAATTCT
66 AGAACTCATCTGAAGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCATAATTCT
2030221 ATCACAGAAGCAGATAGATTAGCAACAACA
131 ATCACAGAAGCAGATAGATTAGCAACAACA
*
2030251 TTTCCAGAAAAAGTTCATAATGAGAAGAATTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGA
2030316 AGAACTCATCTGAAGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCATAATTCT
66 AGAACTCATCTGAAGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCATAATTCT
* *
2030381 ATCACAGAAGCAGATAGATTAGCAGCAACC
131 ATCACAGAAGCAGATAGATTAGCAACAACA
*
2030411 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGA
2030476 AGA
66 AGA
2030479 GCTTATTCAA
Statistics
Matches: 217, Mismatches: 6, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
155 7 0.03
156 27 0.12
157 1 0.00
159 2 0.01
160 180 0.83
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (160 bp):
TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGA
AGAACTCATCTGAAGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCAACCTTTTGCATAATTCT
ATCACAGAAGCAGATAGATTAGCAACAACA
Found at i:2030342 original size:36 final size:39
Alignment explanation
Indices: 2030256--2030354 Score: 141
Period size: 40 Copynumber: 2.6 Consensus size: 39
2030246 CAACATTTCC
*
2030256 AGAAAAAGTTCATAATGAGAAGAATTCATCTGAAGGAGAA
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAA-GAGAA
*
2030296 AGAAGAAGTTCATAATGAGAAGAACTCATCTG-A-AG-A
1 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAA
*
2030332 AGAAAAAGTTCACAATGAGAAGA
1 AGAAAAAGTTCATAATGAGAAGA
2030355 GCTTATTCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
36 22 0.40
37 2 0.04
39 1 0.02
40 30 0.55
ACGTcount: A:0.51, C:0.09, G:0.22, T:0.18
Consensus pattern (39 bp):
AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGAA
Found at i:2030491 original size:124 final size:119
Alignment explanation
Indices: 2030301--2030576 Score: 362
Period size: 124 Copynumber: 2.3 Consensus size: 119
2030291 GAGAAAGAAG
2030301 AAGTTCATAATGAGAAGAACTCATCTG-A-AGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCA
* * * * *
2030364 ACCTTTTGCATAATTCTATCACAGAAGCAGATAGATTAGCAGCAACCTTTCCA-GAGA
66 ACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACAGCAACC---CCACGA-A
* *
2030421 AAGTTCATAATGAGAAGAACTCATCTGAAGGAGAAAGAAGAAGTTCATAATGAGAAGAGCTTATT
1 AAGTTCATAATGAGAAGAACTCATCTGAA-GAG-AAGAAAAAGTTCACAATGAGAAGAGCTTATT
* * * * *
2030486 CAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCATCCCCACGAA
64 CAACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACAGCAACCCCACGAA
2030542 AAGTTCATAATGAGAAGAACTCATCTGAAGA-AAGA
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGA
2030577 GAAGAATTTA
Statistics
Matches: 139, Mismatches: 12, Indels: 12
0.85 0.07 0.07
Matches are distributed among these distances:
118 4 0.03
120 29 0.21
121 34 0.24
122 2 0.01
123 2 0.01
124 68 0.49
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (119 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAGAAGAAAAAGTTCACAATGAGAAGAGCTTATTCA
ACCTTTTGAATAACTCTATCACAGAAGCAAATAGATCAACAGCAACCCCACGAA
Found at i:2030727 original size:3 final size:3
Alignment explanation
Indices: 2030721--2030785 Score: 103
Period size: 3 Copynumber: 21.0 Consensus size: 3
2030711 TTACCCATTT
*
2030721 TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
2030770 TATA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA
2030786 AAAATAATTA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 52 0.88
4 7 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2032399 original size:23 final size:26
Alignment explanation
Indices: 2032367--2032416 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 26
2032357 CCTTTTCTGA
*
2032367 TATTTCTAAATA-A-ATAAA-TATTT
1 TATTTATAAATATATATAAATTATTT
2032390 TATTTATAAATATATATAAATTATTT
1 TATTTATAAATATATATAAATTATTT
2032416 T
1 T
2032417 TTTCTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
25 5 0.22
26 6 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTTATAAATATATATAAATTATTT
Found at i:2040923 original size:29 final size:29
Alignment explanation
Indices: 2040890--2040969 Score: 115
Period size: 29 Copynumber: 2.8 Consensus size: 29
2040880 GTTCAACTAT
* *
2040890 TGTTGGATATCTAGGCGTCTTCATTGCTA
1 TGTTGGATATCTAGGCGTCTTCAATGCAA
2040919 TGTTGGATATCTAGGCGTCTTCAATGCAA
1 TGTTGGATATCTAGGCGTCTTCAATGCAA
** *
2040948 ACTTGGATATGTAGGCGTCTTC
1 TGTTGGATATCTAGGCGTCTTC
2040970 CATGAAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (29 bp):
TGTTGGATATCTAGGCGTCTTCAATGCAA
Found at i:2041509 original size:16 final size:16
Alignment explanation
Indices: 2041488--2041519 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2041478 TTGATATTTA
2041488 ATGATTTAATAATGAT
1 ATGATTTAATAATGAT
*
2041504 ATGATTTAGTAATGAT
1 ATGATTTAATAATGAT
2041520 TTACTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (16 bp):
ATGATTTAATAATGAT
Found at i:2041633 original size:11 final size:11
Alignment explanation
Indices: 2041559--2041633 Score: 53
Period size: 11 Copynumber: 6.2 Consensus size: 11
2041549 TATTAATATT
2041559 TAATGATTTGATA
1 TAATGATTT-A-A
*
2041572 TAAATGATTTAG
1 T-AATGATTTAA
2041584 TAATGATTTAAAA
1 TAATGATTT--AA
2041597 TAATGAAATTGTAA
1 TAATG--ATT-TAA
*
2041611 TAATTA-TTAA
1 TAATGATTTAA
2041621 TAATGATTTAA
1 TAATGATTTAA
2041632 TA
1 TA
2041634 TTATTACTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
10 8 0.16
11 15 0.29
12 2 0.04
13 8 0.16
14 14 0.27
15 3 0.06
16 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:2042535 original size:13 final size:13
Alignment explanation
Indices: 2042517--2042562 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
2042507 ATCTACACAA
2042517 AATAATTATTAGT
1 AATAATTATTAGT
2042530 AATAATTATTA--
1 AATAATTATTAGT
*
2042541 AATCATTATTAGT
1 AATAATTATTAGT
*
2042554 AATTATTAT
1 AATAATTAT
2042563 AATTTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 10 0.34
13 19 0.66
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (13 bp):
AATAATTATTAGT
Found at i:2042574 original size:24 final size:24
Alignment explanation
Indices: 2042516--2042562 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2042506 AATCTACACA
2042516 AAATAATTATTAGTAATAATTATT
1 AAATAATTATTAGTAATAATTATT
* *
2042540 AAATCATTATTAGTAATTATTAT
1 AAATAATTATTAGTAATAATTAT
2042563 AATTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (24 bp):
AAATAATTATTAGTAATAATTATT
Found at i:2042655 original size:15 final size:14
Alignment explanation
Indices: 2042610--2042661 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
2042600 ATCAAATCAT
* *
2042610 TAAAT-ATTAATAA
1 TAAATCATTATTAC
*
2042623 TAAAACATTATTAC
1 TAAATCATTATTAC
*
2042637 TAAATCATTCATTAT
1 TAAATCATT-ATTAC
2042652 TAAATCATTA
1 TAAATCATTA
2042662 AATATCAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 4 0.12
14 15 0.47
15 13 0.41
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATCATTATTAC
Found at i:2042659 original size:64 final size:64
Alignment explanation
Indices: 2042581--2042709 Score: 174
Period size: 64 Copynumber: 2.0 Consensus size: 64
2042571 TATTTCGAAA
* *
2042581 TCATTACTAAATCATT-TATATCAAATCATTAAATATTAATAA-TA-AAACATTATTACTAAATC
1 TCATTACTAAATCATTAAATATCAAATCATTAAATA--AATAATTAGAAA-ATCATTACTAAATC
2042643 AT
63 AT
* *
2042645 TCATTATTAAATCATTAAATATCAAATTATTAAATAAATAATTAGAAAATCATTACTAAATCAT
1 TCATTACTAAATCATTAAATATCAAATCATTAAATAAATAATTAGAAAATCATTACTAAATCAT
2042709 T
1 T
2042710 ACTAATCATG
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
63 5 0.09
64 33 0.57
65 20 0.34
ACGTcount: A:0.50, C:0.11, G:0.01, T:0.39
Consensus pattern (64 bp):
TCATTACTAAATCATTAAATATCAAATCATTAAATAAATAATTAGAAAATCATTACTAAATCAT
Found at i:2042671 original size:15 final size:15
Alignment explanation
Indices: 2042638--2042680 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2042628 CATTATTACT
* * *
2042638 AAATCATTCATTATT
1 AAATCATTAAATATC
2042653 AAATCATTAAATATC
1 AAATCATTAAATATC
*
2042668 AAATTATTAAATA
1 AAATCATTAAATA
2042681 AATAATTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:2042696 original size:102 final size:100
Alignment explanation
Indices: 2042589--2042773 Score: 225
Period size: 102 Copynumber: 1.8 Consensus size: 100
2042579 AATCATTACT
*
2042589 AAATCATTTATATCAAATCATTA-AAT-ATTAA-TAATAAAACATTATTACTAAATCAT-TCATT
1 AAATCA-TTA-AT-AAATCATTACAATCATGAATTAATAAAA-ATTATTACT--ATCATATCATT
*
2042650 ATTAAATCATTAAATATCAAATTATTAAATAAATAATTAGA
60 ACTAAATCATTAAATATCAAATTATTAAATAAATAATTAGA
* *
2042691 AAATCATTACTAAATCATTACTAATCATGAATTTAATAATAATTATTACTATCATATCATTACTA
1 AAATCATTAATAAATCATTAC-AATCATGAA-TTAATAAAAATTATTACTATCATATCATTACTA
*
2042756 AATCATTAAATATTAAAT
64 AATCATTAAATATCAAAT
2042774 CATTGCTAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
99 9 0.12
100 1 0.01
101 11 0.15
102 35 0.49
103 9 0.12
104 7 0.10
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.39
Consensus pattern (100 bp):
AAATCATTAATAAATCATTACAATCATGAATTAATAAAAATTATTACTATCATATCATTACTAAA
TCATTAAATATCAAATTATTAAATAAATAATTAGA
Found at i:2043343 original size:16 final size:16
Alignment explanation
Indices: 2043317--2043350 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2043307 TTGTTTTGTT
2043317 AAATGATGC-TTTATA
1 AAATGATGCTTTTATA
2043332 AAATGTATGCTTTTATA
1 AAATG-ATGCTTTTATA
2043349 AA
1 AA
2043351 TTTCCTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 4 0.24
17 8 0.47
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (16 bp):
AAATGATGCTTTTATA
Found at i:2044117 original size:29 final size:29
Alignment explanation
Indices: 2044043--2044120 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
2044033 TCAACTATTG
* * * **
2044043 TTGGATATCTAGGCGTATTCATTGCTATG
1 TTGGATATCTAGGCGTCTTCAATGCAAAC
2044072 TTGGATATCTAGGCGTCTTCAATGCAAAC
1 TTGGATATCTAGGCGTCTTCAATGCAAAC
*
2044101 TTGGATATGTAGGCGTCTTC
1 TTGGATATCTAGGCGTCTTC
2044121 CATGAAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (29 bp):
TTGGATATCTAGGCGTCTTCAATGCAAAC
Found at i:2044838 original size:24 final size:24
Alignment explanation
Indices: 2044781--2044826 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2044771 AATCTACACA
2044781 AAATAATTA-TAGTAATAATTATT
1 AAATAATTATTAGTAATAATTATT
* *
2044804 AAATCATTATTAGTAATTATTAT
1 AAATAATTATTAGTAATAATTAT
2044827 AATTTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATAATTATTAGTAATAATTATT
Found at i:2044923 original size:16 final size:16
Alignment explanation
Indices: 2044902--2044933 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2044892 ATTATTACTA
2044902 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
2044918 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
2044934 TAAATATCAA
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:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:2044941 original size:21 final size:21
Alignment explanation
Indices: 2044916--2044981 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
2044906 TTACTAAATC
2044916 ATATCATTACTAAATCATTAA
1 ATATCATTACTAAATCATTAA
* *
2044937 ATATCAAATTTAAATAAATAATTAA
1 ATATC--A-TT-ACTAAATCATTAA
*
2044962 AAATCATTACTAAATCATTA
1 ATATCATTACTAAATCATTA
2044982 CTAATCATGA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
21 15 0.42
22 2 0.06
23 2 0.06
24 2 0.06
25 15 0.42
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (21 bp):
ATATCATTACTAAATCATTAA
Found at i:2044987 original size:21 final size:20
Alignment explanation
Indices: 2044895--2044989 Score: 54
Period size: 21 Copynumber: 4.5 Consensus size: 20
2044885 ATAAAACATT
2044895 ATTACTAATCATTACTAAATC
1 ATTA-TAATCATTACTAAATC
2044916 ---AT-ATCATTACTAAATC
1 ATTATAATCATTACTAAATC
* * *
2044932 ATTAAATATCAAATTTAAATAAATA
1 ATTATA-ATC--A-TT-ACTAAATC
*
2044957 ATTAAAAATCATTACTAAATC
1 ATT-ATAATCATTACTAAATC
2044978 ATTACTAATCAT
1 ATTA-TAATCAT
2044990 GAATTTAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 22
0.67 0.07 0.26
Matches are distributed among these distances:
16 14 0.25
17 1 0.02
18 1 0.02
19 1 0.02
20 1 0.02
21 18 0.32
22 2 0.04
23 2 0.04
24 2 0.04
25 12 0.21
26 3 0.05
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (20 bp):
ATTATAATCATTACTAAATC
Found at i:2046296 original size:29 final size:29
Alignment explanation
Indices: 2046262--2046341 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
2046252 CTTCAACTAT
* * *
2046262 TGTTGGATATCTAGGCATCTTCATTGCTA
1 TGTTGGATATCTAGGCGTCTTCAATGCAA
2046291 TGTTGGATATCTAGGCGTCTTCAATGCAA
1 TGTTGGATATCTAGGCGTCTTCAATGCAA
** *
2046320 ACTTGGATATGTAGGCGTCTTC
1 TGTTGGATATCTAGGCGTCTTC
2046342 CATGAAAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (29 bp):
TGTTGGATATCTAGGCGTCTTCAATGCAA
Found at i:2047032 original size:24 final size:24
Alignment explanation
Indices: 2047000--2047046 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2046990 AATCTACACA
*
2047000 AAATAATTATTAGTAATAATTATT
1 AAATAATTAGTAGTAATAATTATT
* *
2047024 AAATCATTAGTAGTAATTATTAT
1 AAATAATTAGTAGTAATAATTAT
2047047 AATTTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (24 bp):
AAATAATTAGTAGTAATAATTATT
Found at i:2047089 original size:25 final size:25
Alignment explanation
Indices: 2047061--2047199 Score: 96
Period size: 25 Copynumber: 5.7 Consensus size: 25
2047051 TAATTATTTG
2047061 AAATCATTACTAAATCATATATATC
1 AAATCATTACTAAATCATATATATC
* *
2047086 AAATCATTA--AATATTA-ATA-ATA
1 AAATCATTACTAA-ATCATATATATC
* * *
2047108 AAATTATTACT-AATCATTACAAATC
1 AAATCATTACTAAATCA-TATATATC
* *
2047133 ATATCATTACTAAATCATTAAATATC
1 AAATCATTACTAAATCA-TATATATC
* * *
2047159 AAATTATTAAATAAAT-A-AT-TATA
1 AAATCATT-ACTAAATCATATATATC
2047182 AAATCATTACTAAATCAT
1 AAATCATTACTAAATCAT
2047200 TACTAATCAT
Statistics
Matches: 87, Mismatches: 17, Indels: 21
0.70 0.14 0.17
Matches are distributed among these distances:
22 19 0.22
23 17 0.20
24 6 0.07
25 20 0.23
26 19 0.22
27 6 0.07
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.37
Consensus pattern (25 bp):
AAATCATTACTAAATCATATATATC
Found at i:2047138 original size:15 final size:16
Alignment explanation
Indices: 2047120--2047150 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2047110 ATTATTACTA
2047120 ATCATTAC-AAATCAT
1 ATCATTACTAAATCAT
2047135 ATCATTACTAAATCAT
1 ATCATTACTAAATCAT
2047151 TAAATATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (16 bp):
ATCATTACTAAATCAT
Found at i:2048784 original size:21 final size:22
Alignment explanation
Indices: 2048708--2048782 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
2048698 GAGGGTATAT
* *
2048708 TAGTCATTCGAGACGTATCCAA
1 TAGTCCTTCGAGACGTATCCAG
2048730 TAGTCCTTCGAGACGTATCCAG
1 TAGTCCTTCGAGACGTATCCAG
* *
2048752 TGGTCCTTCGGGACGTATCCAG
1 TAGTCCTTCGAGACGTATCCAG
2048774 T-GTCCTTCG
1 TAGTCCTTCG
2048783 GGTTGTATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
21 8 0.16
22 41 0.84
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (22 bp):
TAGTCCTTCGAGACGTATCCAG
Found at i:2048790 original size:21 final size:22
Alignment explanation
Indices: 2048714--2048807 Score: 100
Period size: 22 Copynumber: 4.3 Consensus size: 22
2048704 ATATTAGTCA
* * *
2048714 TTCGAGACGTATCCAATAGTCC
1 TTCGGGACGTATCCAGTGGTCC
*
2048736 TTCGAGACGTATCCAGTGGTCC
1 TTCGGGACGTATCCAGTGGTCC
2048758 TTCGGGACGTATCCAGT-GTCC
1 TTCGGGACGTATCCAGTGGTCC
** ** *
2048779 TTCGGGTTGTATATAGTGGTCA
1 TTCGGGACGTATCCAGTGGTCC
2048801 TTCGGGA
1 TTCGGGA
2048808 GAAATACTGA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 17 0.27
22 45 0.73
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (22 bp):
TTCGGGACGTATCCAGTGGTCC
Found at i:2048797 original size:43 final size:44
Alignment explanation
Indices: 2048710--2048807 Score: 117
Period size: 43 Copynumber: 2.2 Consensus size: 44
2048700 GGGTATATTA
* *
2048710 GTCATTCGAGACGTATCCAATAGTCCTTCGAGACGTATCCAGTG
1 GTCATTCGGGACGTATCCAATAGTCCTTCGAGACGTATACAGTG
* * * ** *
2048754 GTCCTTCGGGACGTATCCAGT-GTCCTTCGGGTTGTATATAGTG
1 GTCATTCGGGACGTATCCAATAGTCCTTCGAGACGTATACAGTG
2048797 GTCATTCGGGA
1 GTCATTCGGGA
2048808 GAAATACTGA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
43 27 0.60
44 18 0.40
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (44 bp):
GTCATTCGGGACGTATCCAATAGTCCTTCGAGACGTATACAGTG
Found at i:2055648 original size:22 final size:22
Alignment explanation
Indices: 2055623--2055718 Score: 101
Period size: 22 Copynumber: 4.5 Consensus size: 22
2055613 GGGTATATTA
*
2055623 GTCCTTCGGGACGTATCTAATG
1 GTCCTTCGGGACGTATCTAGTG
* *
2055645 GTCCTTCGTGACGTATCCAGTG
1 GTCCTTCGGGACGTATCTAGTG
* * * *
2055667 ATCCTTCAGGACATATATAGTG
1 GTCCTTCGGGACGTATCTAGTG
2055689 GTCCTTCGGGAC--A--TAGTG
1 GTCCTTCGGGACGTATCTAGTG
2055707 GTCCTTCGGGAC
1 GTCCTTCGGGAC
2055719 AAATACTGAA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
18 17 0.27
20 1 0.02
22 45 0.71
ACGTcount: A:0.19, C:0.24, G:0.27, T:0.30
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCTAGTG
Found at i:2055706 original size:18 final size:18
Alignment explanation
Indices: 2055683--2055719 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2055673 CAGGACATAT
2055683 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
2055701 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
2055719 A
1 A
2055720 AATACTGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (18 bp):
ATAGTGGTCCTTCGGGAC
Found at i:2056369 original size:14 final size:13
Alignment explanation
Indices: 2056349--2056399 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
2056339 GGGTGTTACA
2056349 AATCATTACTATC
1 AATCATTACTATC
2056362 ATATCATTACTA--
1 A-ATCATTACTATC
*
2056374 AATCATTAAATATC
1 AATCATT-ACTATC
2056388 AAATCATTACTA
1 -AATCATTACTA
2056400 AATCATACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
11 6 0.19
12 4 0.13
13 1 0.03
14 13 0.42
15 7 0.23
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (13 bp):
AATCATTACTATC
Found at i:2056393 original size:26 final size:25
Alignment explanation
Indices: 2056344--2056405 Score: 90
Period size: 26 Copynumber: 2.5 Consensus size: 25
2056334 GTTAGGGGTG
* *
2056344 TTAC-AAATCATTACTATCATATCA
1 TTACTAAATCATTAATATCAAATCA
2056368 TTACTAAATCATTAAATATCAAATCA
1 TTACTAAATCATT-AATATCAAATCA
2056394 TTACTAAATCAT
1 TTACTAAATCAT
2056406 ACTCGTACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 4 0.12
25 8 0.24
26 22 0.65
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.37
Consensus pattern (25 bp):
TTACTAAATCATTAATATCAAATCA
Found at i:2062972 original size:20 final size:21
Alignment explanation
Indices: 2062920--2063047 Score: 83
Period size: 20 Copynumber: 6.3 Consensus size: 21
2062910 TTCGCAATTC
2062920 AATTTCGAATTCGCAACAC-G
1 AATTTCGAATTCGCAACACAG
**
2062940 AAAGTC-AATTTCGCAACACAG
1 AATTTCGAA-TTCGCAACACAG
* *
2062961 -TTTTCGAATTCGTAACACAG
1 AATTTCGAATTCGCAACACAG
* *
2062981 AATTTGGAATTCGC-ACATAG
1 AATTTCGAATTCGCAACACAG
* * *
2063001 AA-GTCGAATTCCCAACTC-G
1 AATTTCGAATTCGCAACACAG
2063020 AATTT-GACAATTTCGCAACAC-G
1 AATTTCG--AA-TTCGCAACACAG
2063042 AATTTC
1 AATTTC
2063048 TTTTTAGCAA
Statistics
Matches: 80, Mismatches: 18, Indels: 17
0.70 0.16 0.15
Matches are distributed among these distances:
19 14 0.17
20 37 0.46
21 15 0.19
22 14 0.17
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (21 bp):
AATTTCGAATTCGCAACACAG
Found at i:2062990 original size:21 final size:20
Alignment explanation
Indices: 2062908--2062995 Score: 65
Period size: 20 Copynumber: 4.4 Consensus size: 20
2062898 ATAACCAATT
**
2062908 AATTCGCAATTCA-ATTTCG
1 AATTCGCAACACAGATTTCG
**
2062927 AATTCGCAACAC-GAAAGTC-
1 AATTCGCAACACAG-ATTTCG
*
2062946 AATTTCGCAACACAGTTTTCG
1 AA-TTCGCAACACAGATTTCG
* *
2062967 AATTCGTAACACAGAATTTGG
1 AATTCGCAACACAG-ATTTCG
2062988 AATTCGCA
1 AATTCGCA
2062996 CATAGAAGTC
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
19 12 0.23
20 26 0.50
21 14 0.27
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (20 bp):
AATTCGCAACACAGATTTCG
Found at i:2063094 original size:20 final size:20
Alignment explanation
Indices: 2063071--2063158 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 20
2063061 GATATTTAAA
2063071 TTCGCAACACGAGTTTCATT
1 TTCGCAACACGAGTTTCATT
* * *
2063091 TTCGCAACTCGA-TTTTATAA
1 TTCGCAACACGAGTTTCAT-T
* *
2063111 TTCGCAA-AGCGAGTTTTAAT
1 TTCGCAACA-CGAGTTTCATT
* * * *
2063131 TTCTCAACATGAATTTCGTT
1 TTCGCAACACGAGTTTCATT
2063151 TTCGCAAC
1 TTCGCAAC
2063159 TCTAATTTAG
Statistics
Matches: 51, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
19 5 0.10
20 40 0.78
21 6 0.12
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (20 bp):
TTCGCAACACGAGTTTCATT
Found at i:2063118 original size:60 final size:60
Alignment explanation
Indices: 2063054--2063197 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 60
2063044 TTTCTTTTTA
* * * *
2063054 GCAAATCGATATTTAAATTCGCAACACGAGTTTCATTTTCGCAACTCGATTTTATAATTC
1 GCAAAGCGATATTTAAATTCGCAACACGAATTTCATTTTCGCAACTCGAATTTAGAATTC
* * * * * *
2063114 GCAAAGCGAGT-TTTAATTTCTCAACATGAATTTCGTTTTCGCAACTCTAATTTAGAATTT
1 GCAAAGCGA-TATTTAAATTCGCAACACGAATTTCATTTTCGCAACTCGAATTTAGAATTC
*
2063174 GCAACGCGA-ATTTAAAATTCGCAA
1 GCAAAGCGATATTT-AAATTCGCAA
2063198 ATTAGTTTTT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
59 3 0.04
60 64 0.94
61 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (60 bp):
GCAAAGCGATATTTAAATTCGCAACACGAATTTCATTTTCGCAACTCGAATTTAGAATTC
Found at i:2063124 original size:40 final size:39
Alignment explanation
Indices: 2063013--2063126 Score: 122
Period size: 40 Copynumber: 2.8 Consensus size: 39
2063003 GTCGAATTCC
* * *
2063013 CAACTCGAATTTGACAATTTCGCAACACGAATTTCTTTTTAG
1 CAACTCG-ATTTTA-AA-TTCGCAACACGAGTTTCATTTTAG
* *
2063055 CAAATCGATATTTAAATTCGCAACACGAGTTTCATTTTCG
1 CAACTCGAT-TTTAAATTCGCAACACGAGTTTCATTTTAG
2063095 CAACTCGATTTTATAATTCGCAA-AGCGAGTTT
1 CAACTCGATTTTA-AATTCGCAACA-CGAGTTT
2063127 TAATTTCTCA
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.08
40 45 0.71
41 4 0.06
42 9 0.14
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (39 bp):
CAACTCGATTTTAAATTCGCAACACGAGTTTCATTTTAG
Found at i:2063177 original size:20 final size:20
Alignment explanation
Indices: 2063151--2063197 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2063141 GAATTTCGTT
* * *
2063151 TTCGCAACTCTAATTTAGAA
1 TTCGCAACGCGAATTTAAAA
*
2063171 TTTGCAACGCGAATTTAAAA
1 TTCGCAACGCGAATTTAAAA
2063191 TTCGCAA
1 TTCGCAA
2063198 ATTAGTTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (20 bp):
TTCGCAACGCGAATTTAAAA
Found at i:2063469 original size:20 final size:20
Alignment explanation
Indices: 2063427--2063471 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2063417 GGAAAATCAT
*
2063427 TTTCATAGATAATTAGATAA
1 TTTCATAGATAATTAGACAA
*
2063447 TTTCATAGATAGATTA-ACCA
1 TTTCATAGATA-ATTAGACAA
2063467 TTTCA
1 TTTCA
2063472 CTTAGATTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTCATAGATAATTAGACAA
Found at i:2063649 original size:34 final size:34
Alignment explanation
Indices: 2063606--2063670 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
2063596 GAATTCAAAA
* * *
2063606 TTCGAGTTGCGAATTTCATTTTCGAGTTGCGGTT
1 TTCGAGTTGCGAATTTAAGTTTCGAATTGCGGTT
*
2063640 TTCGTGTTGCGAATTTAAGTTTCGAATTGCG
1 TTCGAGTTGCGAATTTAAGTTTCGAATTGCG
2063671 AATTCGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (34 bp):
TTCGAGTTGCGAATTTAAGTTTCGAATTGCGGTT
Found at i:2063673 original size:54 final size:54
Alignment explanation
Indices: 2063586--2063690 Score: 149
Period size: 54 Copynumber: 1.9 Consensus size: 54
2063576 GTTTTTTGAA
*
2063586 TTCGAGTTGCGAATTCAAAATTCGAGTTGCGAATTTC-ATTTTCGAGTTGCGGTT
1 TTCGAGTTGCGAATTCAAAATTCGAATTGCGAA-TTCGATTTTCGAGTTGCGGTT
* * **
2063640 TTCGTGTTGCGAATTTAAGTTTCGAATTGCGAATTCGATTTTCGAGTTGCG
1 TTCGAGTTGCGAATTCAAAATTCGAATTGCGAATTCGATTTTCGAGTTGCG
2063691 AATTTGATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
53 3 0.07
54 42 0.93
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.40
Consensus pattern (54 bp):
TTCGAGTTGCGAATTCAAAATTCGAATTGCGAATTCGATTTTCGAGTTGCGGTT
Found at i:2063699 original size:20 final size:20
Alignment explanation
Indices: 2063586--2063702 Score: 102
Period size: 20 Copynumber: 6.2 Consensus size: 20
2063576 GTTTTTTGAA
** **
2063586 TTCGAGTTGCGAATTCAAAA
1 TTCGAGTTGCGAATTTGATT
*
2063606 TTCGAGTTGCGAATTTCATT
1 TTCGAGTTGCGAATTTGATT
2063626 TTCGAGTTGCG-----G-TT
1 TTCGAGTTGCGAATTTGATT
* * *
2063640 TTCGTGTTGCGAATTTAAGT
1 TTCGAGTTGCGAATTTGATT
* *
2063660 TTCGAATTGCGAATTCGATT
1 TTCGAGTTGCGAATTTGATT
2063680 TTCGAGTTGCGAATTTGATT
1 TTCGAGTTGCGAATTTGATT
2063700 TTC
1 TTC
2063703 TTGAAAATTT
Statistics
Matches: 76, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
14 12 0.16
20 64 0.84
ACGTcount: A:0.21, C:0.14, G:0.23, T:0.42
Consensus pattern (20 bp):
TTCGAGTTGCGAATTTGATT
Found at i:2065099 original size:42 final size:42
Alignment explanation
Indices: 2065039--2065207 Score: 259
Period size: 42 Copynumber: 4.0 Consensus size: 42
2065029 CCCTATTTTT
*
2065039 TCATCGAGTCGATCCTCCACTTCGACACTGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACTGAGATCCATCACC
* *
2065081 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCTATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACTGAGATCCATCACC
*
2065123 TCATCGAGTCGATTCTCCACTTCGACTCTGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACTGAGATCCATCACC
* * * *
2065165 TCATCGAG-AGATTCTACACCTCGACACAGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACTGAGATCCATCACC
2065206 TC
1 TC
2065208 TAGCCAACTC
Statistics
Matches: 116, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
41 30 0.26
42 86 0.74
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (42 bp):
TCATCGAGTCGATTCTCCACTTCGACACTGAGATCCATCACC
Found at i:2065205 original size:21 final size:20
Alignment explanation
Indices: 2065152--2065207 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
2065142 CTTCGACTCT
*
2065152 GAGATCCATCACCTCATCGA
1 GAGATCCATCACCTCATCCA
*
2065172 GAGATTC-TACACCTCGA-CACA
1 GAGATCCAT-CACCTC-ATC-CA
2065193 GAGATCCATCACCTC
1 GAGATCCATCACCTC
2065208 TAGCCAACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 1 0.03
20 13 0.45
21 14 0.48
22 1 0.03
ACGTcount: A:0.30, C:0.36, G:0.14, T:0.20
Consensus pattern (20 bp):
GAGATCCATCACCTCATCCA
Found at i:2065245 original size:21 final size:21
Alignment explanation
Indices: 2065172--2065245 Score: 50
Period size: 21 Copynumber: 3.7 Consensus size: 21
2065162 ACCTCATCGA
* *
2065172 GAGATTCTACACCTCGACACA
1 GAGACTCTACACCTCGACACC
* * *
2065193 GAGA-TCCATCACCTCTA-GCC
1 GAGACTCTA-CACCTCGACACC
2065213 -A-ACTCTACACCTCGACACC
1 GAGACTCTACACCTCGACACC
2065232 GAGA-TCTATCACCT
1 GAGACTCTA-CACCT
2065246 ATTCCATCAC
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
18 8 0.20
19 6 0.15
20 9 0.22
21 17 0.43
ACGTcount: A:0.30, C:0.38, G:0.12, T:0.20
Consensus pattern (21 bp):
GAGACTCTACACCTCGACACC
Found at i:2065384 original size:21 final size:21
Alignment explanation
Indices: 2065345--2065492 Score: 97
Period size: 21 Copynumber: 7.1 Consensus size: 21
2065335 ACCTCCACGG
* *
2065345 GATGAGTTA-GTGTTTTACGT
1 GATGAGGTAGGTGCTTTACGT
*
2065365 GATGAGGTCGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
*
2065386 GATGA--TAATGGTGCATTACGT
1 GATGAGGT-A-GGTGCTTTACGT
* * *
2065407 GGTGAGGTAGCTGCTTTATGT
1 GATGAGGTAGGTGCTTTACGT
* ** *
2065428 GATAACAATA-GTGCTTTACAT
1 GATGA-GGTAGGTGCTTTACGT
* * *
2065449 GGTGAGGTAGCTGATTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
2065470 GATGAGGTATGTGCTCTACGT
1 GATGAGGTAGGTGCTTTACGT
2065491 GA
1 GA
2065493 GATTGTTTCA
Statistics
Matches: 93, Mismatches: 28, Indels: 13
0.69 0.21 0.10
Matches are distributed among these distances:
19 1 0.01
20 9 0.10
21 79 0.85
22 3 0.03
23 1 0.01
ACGTcount: A:0.22, C:0.11, G:0.32, T:0.35
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACGT
Found at i:2065406 original size:42 final size:42
Alignment explanation
Indices: 2065359--2065474 Score: 142
Period size: 42 Copynumber: 2.8 Consensus size: 42
2065349 AGTTAGTGTT
* * * * *
2065359 TTACGTGATGAGGTCGGTGCTTTACGTGATGATAATGGTGCA
1 TTACGTGGTGAGGTAGCTGCTTTACGTGATGACAATAGTGCA
* * *
2065401 TTACGTGGTGAGGTAGCTGCTTTATGTGATAACAATAGTGCT
1 TTACGTGGTGAGGTAGCTGCTTTACGTGATGACAATAGTGCA
* *
2065443 TTACATGGTGAGGTAGCTGATTTACGTGATGA
1 TTACGTGGTGAGGTAGCTGCTTTACGTGATGA
2065475 GGTATGTGCT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.34
Consensus pattern (42 bp):
TTACGTGGTGAGGTAGCTGCTTTACGTGATGACAATAGTGCA
Found at i:2065847 original size:21 final size:20
Alignment explanation
Indices: 2065821--2065952 Score: 106
Period size: 21 Copynumber: 6.3 Consensus size: 20
2065811 AGAAGAAGCT
2065821 GATCCACCTACCATTGTTCAG
1 GATCCACCT-CCATTGTTCAG
*
2065842 GATCCACTTCCCATTGTTCAG
1 GATCCACCT-CCATTGTTCAG
*
2065863 GATCTACCTCCAATTGTTCAG
1 GATCCACCTCC-ATTGTTCAG
* * *
2065884 GATTCACCTCTCATCGTTCAA
1 GATCCACCTC-CATTGTTCAG
* *
2065905 GAGGCC-CCTCCCATCGTTCAG
1 GA-TCCACCT-CCATTGTTCAG
* *
2065926 GATCCACCCCTCATCGTTCA-
1 GATCCACCTC-CATTGTTCAG
2065946 GATCCAC
1 GATCCAC
2065953 ATTCTATACT
Statistics
Matches: 92, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
20 12 0.13
21 77 0.84
22 3 0.03
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.28
Consensus pattern (20 bp):
GATCCACCTCCATTGTTCAG
Found at i:2065903 original size:42 final size:42
Alignment explanation
Indices: 2065825--2065946 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
2065815 GAAGCTGATC
* * * *
2065825 CACCTACC-ATTGTTCAGGATCCACTTCCCATTGTTCAGGA-T
1 CACCT-CCAATTGTTCAGGATCCACCTCTCATCGTTCAGGAGG
* *
2065866 CTACCTCCAATTGTTCAGGATTCACCTCTCATCGTTCAAGAGG
1 C-ACCTCCAATTGTTCAGGATCCACCTCTCATCGTTCAGGAGG
* * * *
2065909 CCCCTCCCATCGTTCAGGATCCACCCCTCATCGTTCAG
1 CACCTCCAATTGTTCAGGATCCACCTCTCATCGTTCAG
2065947 ATCCACATTC
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
41 3 0.05
42 62 0.94
43 1 0.02
ACGTcount: A:0.20, C:0.36, G:0.15, T:0.29
Consensus pattern (42 bp):
CACCTCCAATTGTTCAGGATCCACCTCTCATCGTTCAGGAGG
Found at i:2071575 original size:40 final size:41
Alignment explanation
Indices: 2071531--2071610 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 41
2071521 CAAAAATCGA
* *
2071531 GTTACGAAA-ATGAAATTCCTGTTGCG-AAAATGAAACTCGC
1 GTTACGAAATA-GAAAATCCTGTTGCGAAAAAGGAAACTCGC
* *
2071571 GTTACGAATTAGAAAATCTTGTTGCGAAAAAGGAAACTCG
1 GTTACGAAATAGAAAATCCTGTTGCGAAAAAGGAAACTCG
2071611 TGTTGTGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 21 0.62
41 13 0.38
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (41 bp):
GTTACGAAATAGAAAATCCTGTTGCGAAAAAGGAAACTCGC
Found at i:2071578 original size:20 final size:20
Alignment explanation
Indices: 2071531--2071578 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2071521 CAAAAATCGA
*
2071531 GTTACGAAAATGAAATTCCT
1 GTTACGAAAATGAAACTCCT
*
2071551 GTTGCGAAAATGAAACTCGC-
1 GTTACGAAAATGAAACTC-CT
2071571 GTTACGAA
1 GTTACGAA
2071579 TTAGAAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (20 bp):
GTTACGAAAATGAAACTCCT
Found at i:2071714 original size:21 final size:21
Alignment explanation
Indices: 2071689--2071729 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2071679 ATTCGACTTC
2071689 TGTGTTGCAAATTCTAAATTA
1 TGTGTTGCAAATTCTAAATTA
* *
2071710 TGTGTTGCGAATTTTAAATT
1 TGTGTTGCAAATTCTAAATT
2071730 CGAGTTGCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.46
Consensus pattern (21 bp):
TGTGTTGCAAATTCTAAATTA
Found at i:2071760 original size:20 final size:20
Alignment explanation
Indices: 2071711--2071782 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
2071701 TCTAAATTAT
* *
2071711 GTGTTGCGAATTTTAAATTC
1 GTGTTACGAATTTGAAATTC
* *
2071731 GAGTTGCGAATTTAGAAATT-
1 GTGTTACGAATTT-GAAATTC
* *
2071751 GTGTTACGAAATTGAAGTTC
1 GTGTTACGAATTTGAAATTC
2071771 GTGTTACGAATT
1 GTGTTACGAATT
2071783 CGTTGGTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 5 0.12
20 33 0.77
21 5 0.12
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (20 bp):
GTGTTACGAATTTGAAATTC
Found at i:2075110 original size:7 final size:7
Alignment explanation
Indices: 2075098--2075126 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2075088 TTGGGTCACT
2075098 CAAATTC
1 CAAATTC
2075105 CAAATTC
1 CAAATTC
2075112 CAAATTC
1 CAAATTC
2075119 CAAATTC
1 CAAATTC
2075126 C
1 C
2075127 TTTCCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (7 bp):
CAAATTC
Found at i:2076918 original size:28 final size:28
Alignment explanation
Indices: 2076883--2076936 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
2076873 TAAAATTATC
* *
2076883 TTTTATTTTTGTTTTAACTTATTAAATA
1 TTTTATTTTGGTCTTAACTTATTAAATA
*
2076911 TTTTATTTTGGTCTTAATTTATTAAA
1 TTTTATTTTGGTCTTAACTTATTAAA
2076937 AAAAATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.63
Consensus pattern (28 bp):
TTTTATTTTGGTCTTAACTTATTAAATA
Found at i:2077233 original size:28 final size:28
Alignment explanation
Indices: 2077168--2077334 Score: 176
Period size: 28 Copynumber: 6.1 Consensus size: 28
2077158 AGATATTTTG
*
2077168 ATATATTTTTAAAAGTTAAAATAATAATAAA
1 ATATATTTTT--AA-TTTAAATAATAATAAA
2077199 ATATATTTTTAATTTAAAATAA-AATAAA
1 ATATATTTTTAATTT-AAATAATAATAAA
2077227 ATATATTTTTAATTTAAATAA-AAT-AA
1 ATATATTTTTAATTTAAATAATAATAAA
2077253 A-ATATTTTTAA-TTAAATAA-AAT-AA
1 ATATATTTTTAATTTAAATAATAATAAA
*
2077277 A-ATA-TTTT-ATTTAATTAATAATAAA
1 ATATATTTTTAATTTAAATAATAATAAA
*
2077302 AAATATTTTT-ATATTAAATTAATAATAAA
1 ATATATTTTTAAT-TTAAA-TAATAATAAA
2077331 ATAT
1 ATAT
2077335 TTAAATATAT
Statistics
Matches: 124, Mismatches: 4, Indels: 18
0.85 0.03 0.12
Matches are distributed among these distances:
22 1 0.01
23 11 0.09
24 20 0.16
25 13 0.10
26 6 0.05
27 15 0.12
28 27 0.22
29 21 0.17
31 10 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.44
Consensus pattern (28 bp):
ATATATTTTTAATTTAAATAATAATAAA
Found at i:2077342 original size:27 final size:26
Alignment explanation
Indices: 2077186--2077342 Score: 132
Period size: 24 Copynumber: 6.0 Consensus size: 26
2077176 TTAAAAGTTA
2077186 AAATAATAATAAAATATATTTTTAAT-TT
1 AAATAA-AATAAAA-ATA-TTTTAATATT
2077214 AAAATAAAATAAAATATATTTTTAAT-TT
1 -AAATAAAATAAAA-ATA-TTTTAATATT
*
2077242 AAATAAAAT-AAAATATTTTTA-ATT
1 AAATAAAATAAAAATATTTTAATATT
2077266 AAATAAAAT-AAAATATTTT-AT-TT
1 AAATAAAATAAAAATATTTTAATATT
* *
2077289 AATTAATAATAAAAAATATTTTTATATT
1 AAATAA-AAT-AAAAATATTTTAATATT
*
2077317 AAATTAATAAT-AAAATATTTAAATAT
1 AAA-TAA-AATAAAAATATTTTAATAT
2077343 ATTTCAAGTT
Statistics
Matches: 115, Mismatches: 5, Indels: 18
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.07
24 29 0.25
25 3 0.03
26 13 0.11
27 24 0.21
28 25 0.22
29 13 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AAATAAAATAAAAATATTTTAATATT
Found at i:2077345 original size:29 final size:25
Alignment explanation
Indices: 2077186--2077336 Score: 141
Period size: 27 Copynumber: 5.7 Consensus size: 25
2077176 TTAAAAGTTA
2077186 AAATAATAATAAAATATATTTT-TAATTT
1 AAATAA-AATAAAATAT-TTTTAT-A-TT
2077214 AAAATAAAATAAAATATATTTT-TAATTT
1 -AAATAAAATAAAATAT-TTTTAT-A-TT
2077242 AAATAAAATAAAATATTTTTA-ATT
1 AAATAAAATAAAATATTTTTATATT
2077266 AAATAAAATAAAATA-TTTTAT-TT
1 AAATAAAATAAAATATTTTTATATT
*
2077289 AATTAATAATAAAAAATATTTTTATATT
1 AAATAA-AAT--AAAATATTTTTATATT
2077317 AAATTAATAATAAAATATTT
1 AAA-TAA-AATAAAATATTT
2077337 AAATATATTT
Statistics
Matches: 112, Mismatches: 2, Indels: 18
0.85 0.02 0.14
Matches are distributed among these distances:
23 12 0.11
24 20 0.18
25 1 0.01
26 10 0.09
27 31 0.28
28 25 0.22
29 13 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATAAAATAAAATATTTTTATATT
Found at i:2078454 original size:3 final size:3
Alignment explanation
Indices: 2078446--2078475 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2078436 ATTCAAATGT
2078446 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2078476 ATCTAGATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2093940 original size:24 final size:23
Alignment explanation
Indices: 2093908--2093958 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
2093898 AAACAAACGT
*
2093908 TAAATGAACATATTCA-TGAACATA
1 TAAACGAACATATT-AGTGAACA-A
*
2093932 TAAACGAACATGTTAGTGAACAA
1 TAAACGAACATATTAGTGAACAA
2093955 TAAA
1 TAAA
2093959 TAAATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (23 bp):
TAAACGAACATATTAGTGAACAA
Found at i:2097758 original size:22 final size:22
Alignment explanation
Indices: 2097714--2097758 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2097704 TTTTTTGTTC
*
2097714 AACCTAAAATATTATAATGTTT
1 AACCTAAAATATTATAATCTTT
*
2097736 AACCTAAAA-AGTTATGATCTTT
1 AACCTAAAATA-TTATAATCTTT
2097758 A
1 A
2097759 TAACATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (22 bp):
AACCTAAAATATTATAATCTTT
Found at i:2099400 original size:5 final size:6
Alignment explanation
Indices: 2099369--2099430 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
2099359 AATAAGAGAT
2099369 AATATA AATATA AATATA AATAT- AATA-A AATA-A AATACTAA TAATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATA-T-A -AATATA
* *
2099417 TATATA TATATA AA
1 AATATA AATATA AA
2099431 ATTATATGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
5 13 0.27
6 29 0.59
7 1 0.02
8 2 0.04
9 4 0.08
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:2099410 original size:16 final size:16
Alignment explanation
Indices: 2099369--2099432 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 16
2099359 AATAAGAGAT
2099369 AATATAAATATAAATATA
1 AATAT-AATA-AAATATA
2099387 AATATAATAAAATA-A
1 AATATAATAAAATATA
*
2099402 AATACTAATAATATATA
1 AATA-TAATAAAATATA
*
2099419 TATATATATAAAAT
1 AATATA-ATAAAAT
2099433 TATATGTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
15 5 0.12
16 16 0.40
17 14 0.35
18 5 0.12
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AATATAATAAAATATA
Found at i:2099411 original size:21 final size:23
Alignment explanation
Indices: 2099370--2099430 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 23
2099360 ATAAGAGATA
2099370 ATATAAATATAAATATAAATATA
1 ATATAAATATAAATATAAATATA
2099393 ATA-AAATA-AAATACTAATAATATA
1 ATATAAATATAAATA-T-A-AATATA
*
2099417 TATATATATATAAA
1 -ATATAAATATAAA
2099431 ATTATATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 5 0.16
22 6 0.19
23 4 0.13
24 6 0.19
25 3 0.10
26 4 0.13
27 3 0.10
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
ATATAAATATAAATATAAATATA
Found at i:2099513 original size:70 final size:71
Alignment explanation
Indices: 2099428--2099596 Score: 211
Period size: 70 Copynumber: 2.4 Consensus size: 71
2099418 ATATATATAT
* * *
2099428 AAAATTATATGTTATATGTTTTCAAACGTACTTTAAAAACTATATA-T-TAT-ATTGTCAAAACC
1 AAAACTATATATTATATGTTTTCAAAAGTACTTTAAAAACTATATACTATATGATTGTCAAAACC
2099490 GTTTTAAA
66 G-TTT-AA
* * * * *
2099498 AAAACTATATATTATACGTTTTCAAAATTACTTTAAAAACTATATACTATATGTTTTTCAAAACT
1 AAAACTATATATTATATGTTTTCAAAAGTACTTTAAAAACTATATACTATATGATTGTCAAAACC
*
2099563 GTTTCA
66 GTTTAA
2099569 AAAACTATATA-TATATGTTTTCAAAAGT
1 AAAACTATATATTATATGTTTTCAAAAGT
2099597 TATATTTGAC
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
70 56 0.66
71 13 0.15
72 6 0.07
73 10 0.12
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.41
Consensus pattern (71 bp):
AAAACTATATATTATATGTTTTCAAAAGTACTTTAAAAACTATATACTATATGATTGTCAAAACC
GTTTAA
Done.