Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 11 of 196
Found at i:3183588 original size:7 final size:7
Alignment explanation
Indices: 3183578--3183603 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3183568 TTGGGGTAGA
3183578 TGGGAGG
1 TGGGAGG
3183585 TGGGAGG
1 TGGGAGG
3183592 TGGGAGG
1 TGGGAGG
3183599 TGGGA
1 TGGGA
3183604 TGGGAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.69, T:0.15
Consensus pattern (7 bp):
TGGGAGG
Found at i:3183891 original size:9 final size:9
Alignment explanation
Indices: 3183877--3183913 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
3183867 TATAGTTTGA
3183877 TATTCGAAT
1 TATTCGAAT
3183886 TATTCGAAT
1 TATTCGAAT
*
3183895 TATTCGAGT
1 TATTCGAAT
3183904 TATTCGAAT
1 TATTCGAAT
3183913 T
1 T
3183914 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:3195493 original size:13 final size:13
Alignment explanation
Indices: 3195477--3195515 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3195467 TAGGGTCAAA
*
3195477 GTGTAGGTTGAGT
1 GTGTAGGTTGAGC
3195490 GTGTAGGTTGAGC
1 GTGTAGGTTGAGC
3195503 GTGTAGGTTGAGC
1 GTGTAGGTTGAGC
3195516 AATTGTGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.15, C:0.05, G:0.46, T:0.33
Consensus pattern (13 bp):
GTGTAGGTTGAGC
Found at i:3195773 original size:25 final size:25
Alignment explanation
Indices: 3195735--3195791 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
3195725 TTTTCTCATG
* *
3195735 TTCTCTTCTCCCTCTTTCATTTT-TT
1 TTCTCTTATCCCTCTCTC-TTTTCTT
*
3195760 TTCTCTTATTCCTCTCTCTTTTCTT
1 TTCTCTTATCCCTCTCTCTTTTCTT
*
3195785 TTTTCTT
1 TTCTCTT
3195792 TATCAGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 4 0.15
25 23 0.85
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.67
Consensus pattern (25 bp):
TTCTCTTATCCCTCTCTCTTTTCTT
Found at i:3199095 original size:38 final size:38
Alignment explanation
Indices: 3199048--3199142 Score: 127
Period size: 38 Copynumber: 2.5 Consensus size: 38
3199038 ATACAAAAAT
* * *
3199048 AGTAAACATGCTTAACATGTATTCAATTCAATAGTAGC
1 AGTAGACATGCTTAACATGTATTCAATTCAACAATAGC
* * *
3199086 AGTAGACATGTTTAACATGTATTCGATTTAACAATAGC
1 AGTAGACATGCTTAACATGTATTCAATTCAACAATAGC
*
3199124 AGTAGGCATGCTTAACATG
1 AGTAGACATGCTTAACATG
3199143 CAATTAGTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (38 bp):
AGTAGACATGCTTAACATGTATTCAATTCAACAATAGC
Found at i:3200830 original size:19 final size:19
Alignment explanation
Indices: 3200806--3200849 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
3200796 GAAAGAATAC
3200806 CTATTTTTTTATATAACAT
1 CTATTTTTTTATATAACAT
3200825 CTATTTTTTTATATAACAT
1 CTATTTTTTTATATAACAT
*
3200844 CAATTT
1 CTATTT
3200850 AGTAAGATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (19 bp):
CTATTTTTTTATATAACAT
Found at i:3206527 original size:31 final size:31
Alignment explanation
Indices: 3206492--3206555 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 31
3206482 ATATTAATAT
3206492 AATATTTA-AATTTATTATTATATTT-TTTGAA
1 AATATTTAGAATTT-TTA-TATATTTCTTTGAA
*
3206523 AATATTTATGTATTTTTATATATTTCTTTGAA
1 AATATTTA-GAATTTTTATATATTTCTTTGAA
3206555 A
1 A
3206556 TCTTTTAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 15 0.52
32 10 0.34
33 4 0.14
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.58
Consensus pattern (31 bp):
AATATTTAGAATTTTTATATATTTCTTTGAA
Found at i:3212890 original size:28 final size:28
Alignment explanation
Indices: 3212859--3212912 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
3212849 ATGTTAAAAG
*
3212859 AAATTTTCATTTTTTTTAAAAATTATAC
1 AAATTTTAATTTTTTTTAAAAATTATAC
*
3212887 AAATTTTAATTTTTTTTAAATATTAT
1 AAATTTTAATTTTTTTTAAAAATTAT
3212913 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (28 bp):
AAATTTTAATTTTTTTTAAAAATTATAC
Found at i:3215431 original size:15 final size:16
Alignment explanation
Indices: 3215411--3215451 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3215401 AAAATAAATT
3215411 ATTAAAAATT-TAAAA
1 ATTAAAAATTATAAAA
*
3215426 ATT-AAAATTATTAAA
1 ATTAAAAATTATAAAA
*
3215441 AGTAAAAATTA
1 ATTAAAAATTA
3215452 ATTCAATCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 6 0.27
15 9 0.41
16 7 0.32
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
ATTAAAAATTATAAAA
Found at i:3216724 original size:27 final size:27
Alignment explanation
Indices: 3216665--3216725 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
3216655 TAATACAAAG
* *
3216665 TAGTGGCGCCTATCTCAGAGGCGCCAA
1 TAGTGGTGCCTATCTCACAGGCGCCAA
* * *
3216692 TGGTGGTGCCTATCTGACAGGCGCCAT
1 TAGTGGTGCCTATCTCACAGGCGCCAA
3216719 TAGTGGT
1 TAGTGGT
3216726 ATCATGTTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.25
Consensus pattern (27 bp):
TAGTGGTGCCTATCTCACAGGCGCCAA
Found at i:3219827 original size:21 final size:21
Alignment explanation
Indices: 3219796--3220016 Score: 113
Period size: 21 Copynumber: 10.4 Consensus size: 21
3219786 AATTAATTAT
3219796 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
3219818 AAAAAATTACAATATTCAT--
1 AAAAAATTACAATATTCATAC
* * * *
3219837 ATAAAATTACAAAATTAATTAT
1 AAAAAATTACAATATTCA-TAC
3219859 AAAATAATTACAA-A--C--AC
1 AAAA-AATTACAATATTCATAC
* * * *
3219876 AAAAATTTATAACATAATCCTA-
1 AAAAAATTA-CA-ATATTCATAC
** * * * *
3219898 AATTACTAACAA-ATTAATTAT
1 AAAAAATTACAATATTCA-TAC
3219919 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
3219941 --AAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
3219960 AAAATTAAAAAATTACAATATTCATAC
1 ------AAAAAATTACAATATTCATAC
3219987 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
*
3220008 AAAATATTA
1 AAAAAATTA
3220017 ATCTAAAATT
Statistics
Matches: 153, Mismatches: 23, Indels: 47
0.69 0.10 0.21
Matches are distributed among these distances:
16 4 0.03
17 6 0.04
18 1 0.01
19 35 0.23
20 6 0.04
21 48 0.31
22 21 0.14
23 13 0.08
27 19 0.12
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:3219844 original size:19 final size:19
Alignment explanation
Indices: 3219801--3219863 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
3219791 ATTATAAAAT
*
3219801 AATTACAATATTCATACAAAA
1 AATTACAATATTCAT--ATAA
3219822 AATTACAATATTCATATAA
1 AATTACAATATTCATATAA
* *
3219841 AATTACAAAATTAATTATAA
1 AATTACAATATTCA-TATAA
3219861 AAT
1 AAT
3219864 AATTACAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.39
20 8 0.21
21 15 0.39
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
AATTACAATATTCATATAA
Found at i:3220009 original size:48 final size:47
Alignment explanation
Indices: 3219918--3220012 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 47
3219908 AAATTAATTA
3219918 TAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAAT
1 TAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAAT
3219965 TAAAA-AATTACAATATTCATACAAAAAATTACAATATTCATACAAAAT
1 TAAAATAATTACAATATTCATAC--AAAATTACAATATTCATACAAAAT
3220013 ATTAATCTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
46 17 0.37
47 5 0.11
48 24 0.52
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.31
Consensus pattern (47 bp):
TAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAAT
Found at i:3220091 original size:61 final size:62
Alignment explanation
Indices: 3219785--3220092 Score: 230
Period size: 61 Copynumber: 4.9 Consensus size: 62
3219775 ATTTGTCTAC
* * *
3219785 AAATTAATTATAAAATAATTACAATATTCATACAAAA-A--ATTACAATATTCATATAAAATTAC
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCCAA-A-AC-TAT-AAATTAC
3219847 A
62 A
* * *
3219848 AAATTAATTATAAAATAATTACAA-A--CACA-AAAATTTA-TAA--CATAA-TCCTAAATTACT
1 AAATTAATTATAAAATAATTACAATATTCATACAAAA--TACTAATCCAAAACT-ATAAATTAC-
3219905 AA
62 -A
* * *
3219907 CAAATTAATTATAAAATAATTACAATATTCATACAAAATTACAATATTCATACAAAATTAAAAAA
1 -AAATTAATTATAAAATAATTACAATATTCATACAAAA-TAC--TA---ATCCAAAACT-ATAAA
3219972 TTACA
58 TTACA
* * * * * *
3219977 ATATTCA-TACAAAA-AATTACAATATTCATACAAAATATTAATCTAAAATTATAAA-TACA
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATTACA
3220036 AAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCCAAAACTATAAA
1 AAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCCAAAACTATAAA
3220093 CACTAAACAT
Statistics
Matches: 199, Mismatches: 23, Indels: 48
0.74 0.09 0.18
Matches are distributed among these distances:
57 8 0.04
58 1 0.01
59 14 0.07
60 38 0.19
61 49 0.25
62 2 0.01
63 31 0.16
64 6 0.03
66 4 0.02
67 21 0.11
68 6 0.03
69 6 0.03
70 1 0.01
71 4 0.02
72 8 0.04
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (62 bp):
AAATTAATTATAAAATAATTACAATATTCATACAAAATACTAATCCAAAACTATAAATTACA
Found at i:3220114 original size:7 final size:7
Alignment explanation
Indices: 3220104--3220129 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3220094 ACTAAACATA
3220104 AATAATT
1 AATAATT
3220111 AATAATT
1 AATAATT
3220118 AATAATT
1 AATAATT
3220125 AATAA
1 AATAA
3220130 CAAAAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
AATAATT
Found at i:3221567 original size:3 final size:3
Alignment explanation
Indices: 3221537--3221593 Score: 60
Period size: 3 Copynumber: 18.7 Consensus size: 3
3221527 AAAATAAAAC
* * *
3221537 TAA TAA TATT TAA TAG TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
3221583 TTA TCA TAA TA
1 TAA TAA TAA TA
3221594 CAAAAATAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 42 0.95
4 2 0.05
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:3223025 original size:27 final size:27
Alignment explanation
Indices: 3222994--3223048 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
3222984 CATTGGCGCT
* **
3222994 TCCCTATGAGGCACTGTTAATGGCACC
1 TCCCTATGAGACACAATTAATGGCACC
*
3223021 TCCCTATGAGACACAATTAGTGGCACC
1 TCCCTATGAGACACAATTAATGGCACC
3223048 T
1 T
3223049 ACCTGACAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.25
Consensus pattern (27 bp):
TCCCTATGAGACACAATTAATGGCACC
Found at i:3235943 original size:11 final size:11
Alignment explanation
Indices: 3235902--3235947 Score: 56
Period size: 12 Copynumber: 4.0 Consensus size: 11
3235892 TTCACGAACA
3235902 AACTCGTTTAT
1 AACTCGTTTAT
*
3235913 AAGCTTGTTTATT
1 AA-CTCGTTTA-T
3235926 AACTCGTTTAT
1 AACTCGTTTAT
*
3235937 GACTCGTTTAT
1 AACTCGTTTAT
3235948 TTATTAATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 13 0.43
12 14 0.47
13 3 0.10
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (11 bp):
AACTCGTTTAT
Found at i:3237433 original size:23 final size:22
Alignment explanation
Indices: 3237358--3237443 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
3237348 ATTTTGATTG
*
3237358 GCCTTCGTGGCGAATTCTGGTTA
1 GCCTTTGTGGCGAATTCT-GTTA
* *
3237381 GCCTTTGTGGCGAATTATGTTT
1 GCCTTTGTGGCGAATTCTGTTA
* * *
3237403 GACATTTGTGGCTAATTCTAATTA
1 G-CCTTTGTGGCGAATTCT-GTTA
*
3237427 GCCTTTGTGGCGTATTC
1 GCCTTTGTGGCGAATTC
3237444 AGTATGCTAC
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
22 4 0.08
23 43 0.86
24 3 0.06
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.41
Consensus pattern (22 bp):
GCCTTTGTGGCGAATTCTGTTA
Found at i:3237476 original size:48 final size:46
Alignment explanation
Indices: 3237364--3237477 Score: 115
Period size: 46 Copynumber: 2.4 Consensus size: 46
3237354 ATTGGCCTTC
* ** *
3237364 GTGGCGAATTCTGGTTAGCCTTTGTGGCGAATTATGTTTGACATTT
1 GTGGCTAATTCTAATTAGCCTTTGTGGCGAATTATGTATGACATTT
* *
3237410 GTGGCTAATTCTAATTAGCCTTTGTGGCGTATTCA-GTATGCTACCTTT
1 GTGGCTAATTCTAATTAGCCTTTGTGGCGAATT-ATGTATG--ACATTT
*
3237458 GTGGC-ATATTCTATTTAGCC
1 GTGGCTA-ATTCTAATTAGCC
3237478 CTTGATGCGT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
46 33 0.58
47 2 0.04
48 22 0.39
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.41
Consensus pattern (46 bp):
GTGGCTAATTCTAATTAGCCTTTGTGGCGAATTATGTATGACATTT
Found at i:3242261 original size:37 final size:38
Alignment explanation
Indices: 3242207--3242281 Score: 116
Period size: 37 Copynumber: 2.0 Consensus size: 38
3242197 CTGCATCAGG
* *
3242207 AGAAAATTGAGGAAAATTATACAAT-GAAGCACAAAAT
1 AGAAAATAGAGGAAAATTAGACAATGGAAGCACAAAAT
*
3242244 AGAAAATAGAGGGAAATTAGACAATGGAAGCACAAAAT
1 AGAAAATAGAGGAAAATTAGACAATGGAAGCACAAAAT
3242282 CAAGCAGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 22 0.65
38 12 0.35
ACGTcount: A:0.56, C:0.08, G:0.20, T:0.16
Consensus pattern (38 bp):
AGAAAATAGAGGAAAATTAGACAATGGAAGCACAAAAT
Found at i:3246019 original size:21 final size:21
Alignment explanation
Indices: 3245995--3246039 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3245985 TTTTTTATAC
*
3245995 TTATTATGTAAATTAATATTT
1 TTATTATGTAAATAAATATTT
* *
3246016 TTATTTTTTAAATAAATATTT
1 TTATTATGTAAATAAATATTT
3246037 TTA
1 TTA
3246040 AGTAATTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTATTATGTAAATAAATATTT
Found at i:3246931 original size:42 final size:39
Alignment explanation
Indices: 3246884--3247181 Score: 170
Period size: 42 Copynumber: 7.1 Consensus size: 39
3246874 GAGGTGAAGT
* *
3246884 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGAC
1 TGGTGGTGGTGG-GATAGAACTGGTGGTGGTGGGAA-GA-AC
* * *
3246926 GGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGAAC
1 TGGTGGTGG-TGGGATAGAACTGGTGGTGGTGG-GA-AGAAC
* * *
3246968 TGGTGGAGGTGGGA-AGGAGACGGGTGGTGGAGGGGACAGAAC
1 TGGTGGTGGTGGGATA-GA-ACTGGTGGTGG-TGGGA-AGAAC
* * *
3247010 TGGTGGAGGTGGGA-AGGAGACGGGTGGTGGAGGGGATAGAAC
1 TGGTGGTGGTGGGATA-GA-ACTGGTGGTGG-TGGGA-AGAAC
* * *
3247052 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGAAAGGAGAC
1 TGGTGGTGGTGG-GATAGAACTGGTGGTGGTGGGAA-GA-AC
* * * *
3247094 GGGTGGTGGAGGGGAGAGAACTGGTGGTGGTGGAGATTGAAC
1 TGGTGGTGG-TGGGATAGAACTGGTGGTGGTGG-GA-AGAAC
* * *
3247136 TGGTGGAGGTGGAGAGTAG-ACGGGTGGTGGAGGGGAGAGAAC
1 TGGTGGTGGTGG-GA-TAGAACTGGTGGTGG-TGGGA-AGAAC
3247178 TGGT
1 TGGT
3247182 TGAGGTGGTG
Statistics
Matches: 206, Mismatches: 34, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
40 2 0.01
41 13 0.06
42 170 0.83
43 21 0.10
ACGTcount: A:0.22, C:0.05, G:0.54, T:0.18
Consensus pattern (39 bp):
TGGTGGTGGTGGGATAGAACTGGTGGTGGTGGGAAGAAC
Found at i:3246951 original size:63 final size:63
Alignment explanation
Indices: 3246884--3247021 Score: 258
Period size: 63 Copynumber: 2.2 Consensus size: 63
3246874 GAGGTGAAGT
*
3246884 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAAC
1 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGACAGAAC
3246947 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGACAGAAC
1 TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGACAGAAC
*
3247010 TGGTGGAGGTGG
1 TGGTGGTGGTGG
3247022 GAAGGAGACG
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 73 1.00
ACGTcount: A:0.21, C:0.05, G:0.55, T:0.19
Consensus pattern (63 bp):
TGGTGGTGGTGGAGATTGAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGACAGAAC
Found at i:3247141 original size:105 final size:105
Alignment explanation
Indices: 3246901--3247126 Score: 425
Period size: 105 Copynumber: 2.2 Consensus size: 105
3246891 GGTGGAGATT
3246901 GAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGA
1 GAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGA
*
3246966 ACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGACA
66 ACTGGTGGAGGTGGAAAGGAGACGGGTGGTGGAGGGGACA
3247006 GAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGA
1 GAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGA
*
3247071 ACTGGTGGAGGTGGAAAGGAGACGGGTGGTGGAGGGGAGA
66 ACTGGTGGAGGTGGAAAGGAGACGGGTGGTGGAGGGGACA
*
3247111 GAACTGGTGGTGGTGG
1 GAACTGGTGGAGGTGG
3247127 AGATTGAACT
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 118 1.00
ACGTcount: A:0.23, C:0.05, G:0.55, T:0.17
Consensus pattern (105 bp):
GAACTGGTGGAGGTGGGAAGGAGACGGGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGA
ACTGGTGGAGGTGGAAAGGAGACGGGTGGTGGAGGGGACA
Found at i:3247163 original size:63 final size:63
Alignment explanation
Indices: 3246927--3247342 Score: 336
Period size: 63 Copynumber: 6.3 Consensus size: 63
3246917 GAAGGAGACG
* * * * * * * * *
3246927 GGTGGTGGAGGGGATAGAACTGGTGGTGGTGGAGATTGA-ACTGGTGGAGGTGGGAAG-GAGACG
1 GGTGGTGGTGGGGATTGAACTGGTGGAGGTGGAGA-GGAGACGGGTGGTGGAGGGGAGAGA-ACT
* ** *
3246990 GGTGGTGGAGGGGACAGAACTGGTGGAGGTGG-GAAGGAGACGGGTGGTGGAGGGGATAGAACT
1 GGTGGTGGTGGGGATTGAACTGGTGGAGGTGGAG-AGGAGACGGGTGGTGGAGGGGAGAGAACT
* *
3247053 GGTGGTGGTGGAGATTGAACTGGTGGAGGTGGAAAGGAGACGGGTGGTGGAGGGGAGAGAACT
1 GGTGGTGGTGGGGATTGAACTGGTGGAGGTGGAGAGGAGACGGGTGGTGGAGGGGAGAGAACT
* *
3247116 GGTGGTGGTGGAGATTGAACTGGTGGAGGTGGAGAGTAGACGGGTGGTGGAGGGGAGAGAACTGG
1 GGTGGTGGTGGGGATTGAACTGGTGGAGGTGGAGAGGAGACGGGTGGTGGAGGGGAGAGAAC---
3247181 TTGAGGT
63 ------T
* * *
3247188 GGTGGTGGTGGTGGTGATTGAACTGGTGGAGGTGGAGGGGAGCGAACTGGTTGTGGTGGTGGTGA
1 GGTGGTGGT-G-GG-GATTGAACTGGTGGAGGTGGAGAGGA--G-AC-GG--GTGGTGGAGGGGA
*
3247253 GTAG-ACG
57 G-AGAACT
* ** * *
3247260 GGTGGTGGAGGGGAGAGAACTGGTGGAGGTGGAGAGTAGACAGGTGGTGGAGGGGAGAGAACT
1 GGTGGTGGTGGGGATTGAACTGGTGGAGGTGGAGAGGAGACGGGTGGTGGAGGGGAGAGAACT
* * * *
3247323 TGTTGTGGTGGTGAGTGAAC
1 GGTGGTGGTGGGGATTGAAC
3247343 GGGAGGTTTT
Statistics
Matches: 292, Mismatches: 37, Indels: 48
0.77 0.10 0.13
Matches are distributed among these distances:
62 5 0.02
63 191 0.65
64 2 0.01
65 1 0.00
66 2 0.01
67 1 0.00
69 22 0.08
70 2 0.01
71 1 0.00
72 18 0.06
73 1 0.00
74 1 0.00
75 24 0.08
77 1 0.00
78 2 0.01
79 2 0.01
81 14 0.05
82 2 0.01
ACGTcount: A:0.21, C:0.05, G:0.54, T:0.19
Consensus pattern (63 bp):
GGTGGTGGTGGGGATTGAACTGGTGGAGGTGGAGAGGAGACGGGTGGTGGAGGGGAGAGAACT
Found at i:3247187 original size:42 final size:42
Alignment explanation
Indices: 3246964--3247189 Score: 191
Period size: 42 Copynumber: 5.4 Consensus size: 42
3246954 GGTGGAGATT
* *
3246964 GAACTGGTGGAGGTGG-GAAGGAGACGGGTGGTGGAGGGGACA
1 GAACTGGTGGAGGTGGAG-AGTAGACGGGTGGTGGAGGGGAGA
* *
3247006 GAACTGGTGGAGGTGG-GAAGGAGACGGGTGGTGGAGGGGATA
1 GAACTGGTGGAGGTGGAG-AGTAGACGGGTGGTGGAGGGGAGA
* * *
3247048 GAACTGGTGGTGGTGGAGA-TTGAAC---TGGTGGAGGTGGAAA
1 GAACTGGTGGAGGTGGAGAGTAG-ACGGGTGGTGGAGG-GGAGA
* * * **
3247088 GGAGACGGGTGGTGGAGG-GGAGAG-A-ACTGGTGGTGGTGGAGATT
1 -GA-AC---TGGTGGAGGTGGAGAGTAGACGGGTGGTGGAGGGGAGA
3247132 GAACTGGTGGAGGTGGAGAGTAGACGGGTGGTGGAGGGGAGA
1 GAACTGGTGGAGGTGGAGAGTAGACGGGTGGTGGAGGGGAGA
*
3247174 GAACTGGTTGAGGTGG
1 GAACTGGTGGAGGTGG
3247190 TGGTGGTGGT
Statistics
Matches: 152, Mismatches: 17, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
39 18 0.12
40 10 0.07
41 4 0.03
42 94 0.62
43 3 0.02
44 7 0.05
45 16 0.11
ACGTcount: A:0.23, C:0.05, G:0.55, T:0.17
Consensus pattern (42 bp):
GAACTGGTGGAGGTGGAGAGTAGACGGGTGGTGGAGGGGAGA
Found at i:3247198 original size:33 final size:33
Alignment explanation
Indices: 3247158--3247222 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
3247148 AGAGTAGACG
*
3247158 GGTGGTGGAGGGGAGAGAACTGGTTGAGGTGGT
1 GGTGGTGGAGGGGAGAGAACTGGTGGAGGTGGT
* * **
3247191 GGTGGTGGTGGTGATTGAACTGGTGGAGGTGG
1 GGTGGTGGAGGGGAGAGAACTGGTGGAGGTGG
3247223 AGGGGAGCGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.15, C:0.03, G:0.57, T:0.25
Consensus pattern (33 bp):
GGTGGTGGAGGGGAGAGAACTGGTGGAGGTGGT
Found at i:3247234 original size:24 final size:23
Alignment explanation
Indices: 3247207--3247293 Score: 72
Period size: 24 Copynumber: 3.8 Consensus size: 23
3247197 GGTGGTGATT
3247207 GAACTGGTGGAGGTGGAGGGGAG
1 GAACTGGTGGAGGTGGAGGGGAG
* * * *
3247230 CGAACTGGTTGTGGTGGTGGTGAG
1 -GAACTGGTGGAGGTGGAGGGGAG
* *
3247254 TAGAC--G-GGTGGTGGAGGGGAG
1 GA-ACTGGTGGAGGTGGAGGGGAG
3247275 AGAACTGGTGGAGGTGGAG
1 -GAACTGGTGGAGGTGGAG
3247294 AGTAGACAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
21 14 0.29
22 2 0.04
23 2 0.04
24 30 0.62
ACGTcount: A:0.20, C:0.06, G:0.56, T:0.18
Consensus pattern (23 bp):
GAACTGGTGGAGGTGGAGGGGAG
Found at i:3247264 original size:42 final size:43
Alignment explanation
Indices: 3247218--3247340 Score: 160
Period size: 42 Copynumber: 2.8 Consensus size: 43
3247208 AACTGGTGGA
*
3247218 GGTGGAGGGGAGCGAACTGGTTGTGGTGGTGGTGAGTAGACGGGT
1 GGTGGAGGGGAGAGAACT-GTTGTGGTGGTGGTGAGTAGAC-GGT
* *
3247263 GGTGGAGGGGAGAGAACTG--GTGGAGGTGGAGAGTAGACAGGT
1 GGTGGAGGGGAGAGAACTGTTGTGGTGGTGGTGAGTAGAC-GGT
3247305 GGTGGAGGGGAGAGAACTTGTTGTGGTGGTGAGTGA
1 GGTGGAGGGGAGAGAAC-TGTTGTGGTGGTG-GTGA
3247341 ACGGGAGGTT
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
42 37 0.54
43 2 0.03
44 1 0.01
45 25 0.37
46 3 0.04
ACGTcount: A:0.20, C:0.05, G:0.54, T:0.20
Consensus pattern (43 bp):
GGTGGAGGGGAGAGAACTGTTGTGGTGGTGGTGAGTAGACGGT
Found at i:3247266 original size:21 final size:21
Alignment explanation
Indices: 3247240--3247309 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
3247230 CGAACTGGTT
* *
3247240 GTGGTGGTGGTGAGTAGACGG
1 GTGGTGGTGGAGAGTAGACAG
* * *
3247261 GTGGTGGAGGGGAG-AGAACTG
1 GTGGTGGTGGAGAGTAG-ACAG
*
3247282 GTGGAGGTGGAGAGTAGACAG
1 GTGGTGGTGGAGAGTAGACAG
3247303 GTGGTGG
1 GTGGTGG
3247310 AGGGGAGAGA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 2 0.05
21 35 0.90
22 2 0.05
ACGTcount: A:0.20, C:0.04, G:0.57, T:0.19
Consensus pattern (21 bp):
GTGGTGGTGGAGAGTAGACAG
Found at i:3247283 original size:18 final size:18
Alignment explanation
Indices: 3247262--3247322 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 18
3247252 AGTAGACGGG
3247262 TGGTGGAGGGGAGAGAAC
1 TGGTGGAGGGGAGAGAAC
3247280 TGGTGGAGGTGGAGAGTAGAC
1 TGGTGGAGG-GGAGAG-A-AC
3247301 AGGTGGTGGAGGGGAGAGAAC
1 ---TGGTGGAGGGGAGAGAAC
3247322 T
1 T
3247323 TGTTGTGGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
18 10 0.27
19 6 0.16
20 1 0.03
21 4 0.11
22 1 0.03
23 6 0.16
24 9 0.24
ACGTcount: A:0.26, C:0.05, G:0.54, T:0.15
Consensus pattern (18 bp):
TGGTGGAGGGGAGAGAAC
Found at i:3253751 original size:22 final size:22
Alignment explanation
Indices: 3253726--3253774 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
3253716 TGTGACGTCA
*
3253726 CGACGTCACACACATGTCATTG
1 CGACGTCACACACATGTCAATG
*
3253748 CGACGTCACACATATGTCAATG
1 CGACGTCACACACATGTCAATG
3253770 CGACG
1 CGACG
3253775 AGTTCCGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (22 bp):
CGACGTCACACACATGTCAATG
Found at i:3258875 original size:42 final size:42
Alignment explanation
Indices: 3258826--3259013 Score: 191
Period size: 42 Copynumber: 4.5 Consensus size: 42
3258816 GAATAGAATT
* *
3258826 TCGTAAGAGCTAAATGAAAACCCATAAGAGTTGAACAGAAGC
1 TCGTAAGAGCTAAATGAAAACTCATAAGAGTTAAACAGAAGC
* * * * **
3258868 TTGTAAGAGCTGAATGGAAACTCATATGAGTTAAATGGAAGC
1 TCGTAAGAGCTAAATGAAAACTCATAAGAGTTAAACAGAAGC
* * *
3258910 TCATAAGAGCTGAACAT--AAACTCATAAGAGCTGAACAGAAGC
1 TCGTAAGAGCT-AA-ATGAAAACTCATAAGAGTTAAACAGAAGC
** * * *
3258952 TCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAAGC
1 TCGTAAGAGCTAAATGAAAACTCATAAGAGTTAAACAGAAGC
*
3258994 TCGTAAGAGCTAAACGAAAA
1 TCGTAAGAGCTAAATGAAAA
3259014 GTAAAACATG
Statistics
Matches: 118, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 112 0.95
43 1 0.01
44 2 0.02
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (42 bp):
TCGTAAGAGCTAAATGAAAACTCATAAGAGTTAAACAGAAGC
Found at i:3258904 original size:63 final size:63
Alignment explanation
Indices: 3258830--3259012 Score: 197
Period size: 63 Copynumber: 2.9 Consensus size: 63
3258820 AGAATTTCGT
* * * ** *
3258830 AAGAGCTAAATGAAAACCCATAAGAGTTGAACAGAAGCTTGTAAGAGCTGAATGGAAACTCAT
1 AAGAGCTAAATGGAAACTCATAAGAGTTGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCAA
* * * * * * * *
3258893 ATGAGTTAAATGGAAGCTCATAAGAGCTGAACATAAACTCATAAGAGCTGAACAGAAGCTCAA
1 AAGAGCTAAATGGAAACTCATAAGAGTTGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCAA
* * * *
3258956 AAGAGCTAAACGGAAACTCATATGAGTTAAACAGAAGCTCGTAAGAGCTAAAC-GAAA
1 AAGAGCTAAATGGAAACTCATAAGAGTTGAACAGAAGCTCGTAAGAGCTGAACAGAAA
3259013 AGTAAAACAT
Statistics
Matches: 94, Mismatches: 26, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
62 3 0.03
63 91 0.97
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.18
Consensus pattern (63 bp):
AAGAGCTAAATGGAAACTCATAAGAGTTGAACAGAAGCTCGTAAGAGCTGAACAGAAACTCAA
Found at i:3258971 original size:84 final size:84
Alignment explanation
Indices: 3258843--3259004 Score: 234
Period size: 84 Copynumber: 1.9 Consensus size: 84
3258833 AGCTAAATGA
* *** * * **
3258843 AAACCCATAAGAGTTGAACAGAAGCTTGTAAGAGCTGAATGGAAACTCATATGAGTTAAATGGAA
1 AAACCCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
3258908 GCTCATAAGAGCTGAACAT
66 GCTCATAAGAGCTGAACAT
*
3258927 AAACTCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
1 AAACCCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
*
3258992 GCTCGTAAGAGCT
66 GCTCATAAGAGCT
3259005 AAACGAAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 68 1.00
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.19
Consensus pattern (84 bp):
AAACCCATAAGAGCTGAACAGAAGCTCAAAAGAGCTAAACGGAAACTCATATGAGTTAAACAGAA
GCTCATAAGAGCTGAACAT
Found at i:3258987 original size:21 final size:21
Alignment explanation
Indices: 3258829--3259009 Score: 119
Period size: 21 Copynumber: 8.6 Consensus size: 21
3258819 TAGAATTTCG
* * *
3258829 TAAGAGCTAAATGAAAACCCA
1 TAAGAGCTAAACGGAAACTCA
* * * * **
3258850 TAAGAGTTGAACAGAAGCTTG
1 TAAGAGCTAAACGGAAACTCA
* *
3258871 TAAGAGCTGAATGGAAACTCA
1 TAAGAGCTAAACGGAAACTCA
* * * *
3258892 TATGAGTTAAATGGAAGCTCA
1 TAAGAGCTAAACGGAAACTCA
* **
3258913 TAAGAGCTGAACATAAACTCA
1 TAAGAGCTAAACGGAAACTCA
* * *
3258934 TAAGAGCTGAACAGAAGCTCA
1 TAAGAGCTAAACGGAAACTCA
*
3258955 AAAGAGCTAAACGGAAACTCA
1 TAAGAGCTAAACGGAAACTCA
* * * * *
3258976 TATGAGTTAAACAGAAGCTCG
1 TAAGAGCTAAACGGAAACTCA
3258997 TAAGAGCTAAACG
1 TAAGAGCTAAACG
3259010 AAAAGTAAAA
Statistics
Matches: 119, Mismatches: 41, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 119 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (21 bp):
TAAGAGCTAAACGGAAACTCA
Found at i:3273396 original size:15 final size:15
Alignment explanation
Indices: 3273330--3273399 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
3273320 ATAGCAAGAA
* *
3273330 TTATATAAAATATTA
1 TTATATAATATATTT
*
3273345 CTACTATAA-ATATTT
1 TTA-TATAATATATTT
* * * *
3273360 ATATTTTATATTTTT
1 TTATATAATATATTT
3273375 GTTATATAATATATTT
1 -TTATATAATATATTT
3273391 TTATATAAT
1 TTATATAAT
3273400 TTGGTATTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
14 3 0.07
15 23 0.55
16 16 0.38
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (15 bp):
TTATATAATATATTT
Found at i:3274455 original size:18 final size:18
Alignment explanation
Indices: 3274432--3274474 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3274422 ACCCAATCCA
**
3274432 AACCCAAGTATTCAACCC
1 AACCCAAGTACGCAACCC
*
3274450 AACCCAATTACGCAACCC
1 AACCCAAGTACGCAACCC
3274468 AACCCAA
1 AACCCAA
3274475 TCATAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.42, G:0.05, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACGCAACCC
Found at i:3274589 original size:9 final size:9
Alignment explanation
Indices: 3274567--3274629 Score: 81
Period size: 9 Copynumber: 6.9 Consensus size: 9
3274557 ATTATGTAGT
*
3274567 GGTTCAATTT
1 GGTT-AATTC
3274577 GGTTAATTC
1 GGTTAATTC
3274586 GGTTAATTC
1 GGTTAATTC
* *
3274595 GGGTAATCC
1 GGTTAATTC
*
3274604 GATTAATTC
1 GGTTAATTC
3274613 GGTTAATTC
1 GGTTAATTC
3274622 GGTTAATT
1 GGTTAATT
3274630 TTTAACCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
9 42 0.91
10 4 0.09
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (9 bp):
GGTTAATTC
Found at i:3281903 original size:18 final size:20
Alignment explanation
Indices: 3281880--3281919 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
3281870 AATAGTAGGG
3281880 AAGG-AAAAA-GAAAAAAAA
1 AAGGAAAAAAGGAAAAAAAA
3281898 AAGGAAAAAAGGAAAAAAAA
1 AAGGAAAAAAGGAAAAAAAA
3281918 AA
1 AA
3281920 CCTATAGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.20
19 5 0.25
20 11 0.55
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (20 bp):
AAGGAAAAAAGGAAAAAAAA
Found at i:3282841 original size:22 final size:24
Alignment explanation
Indices: 3282789--3282842 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
3282779 TTTTTTGTGA
3282789 TTAAATTATTGCTATTAAATATGCT
1 TTAAATTATTGCTATTAAATAT-CT
* *
3282814 TGAAATTATTG-TATTATATAT-T
1 TTAAATTATTGCTATTAAATATCT
3282836 TTAAATT
1 TTAAATT
3282843 GAACTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 7 0.27
24 9 0.35
25 10 0.38
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (24 bp):
TTAAATTATTGCTATTAAATATCT
Found at i:3284122 original size:15 final size:13
Alignment explanation
Indices: 3284087--3284129 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
3284077 TATGAAGAAC
3284087 ATTTATATTTTTT
1 ATTTATATTTTTT
*
3284100 TTTCTATAATTTTGTT
1 ATT-TAT-ATTTT-TT
3284116 ATTTATATTTTTT
1 ATTTATATTTTTT
3284129 A
1 A
3284130 ATGTAATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 8 0.32
16 4 0.16
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (13 bp):
ATTTATATTTTTT
Found at i:3284567 original size:21 final size:21
Alignment explanation
Indices: 3284543--3284582 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3284533 GCGGAACTTC
*
3284543 TAAAAATTCTAAAAAAATAAT
1 TAAAAATTCAAAAAAAATAAT
*
3284564 TAAAAGTTCAAAAAAAATA
1 TAAAAATTCAAAAAAAATA
3284583 TAAAAAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (21 bp):
TAAAAATTCAAAAAAAATAAT
Found at i:3284589 original size:21 final size:20
Alignment explanation
Indices: 3284543--3284588 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
3284533 GCGGAACTTC
*
3284543 TAAAAATTCTAAAAAAATAA
1 TAAAAATTCAAAAAAAATAA
*
3284563 TTAAAAGTTCAAAAAAAAT-A
1 -TAAAAATTCAAAAAAAATAA
3284583 TAAAAA
1 TAAAAA
3284589 ACTTATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 5 0.23
20 1 0.05
21 16 0.73
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
TAAAAATTCAAAAAAAATAA
Found at i:3296411 original size:3 final size:3
Alignment explanation
Indices: 3296405--3296450 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
3296395 AAAGAAGATG
3296405 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3296451 CAAAGCTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3304151 original size:5 final size:5
Alignment explanation
Indices: 3304141--3304169 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
3304131 TCAACCAGCT
3304141 AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAA
3304170 AAGTGAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:3311044 original size:50 final size:50
Alignment explanation
Indices: 3310986--3311091 Score: 212
Period size: 50 Copynumber: 2.1 Consensus size: 50
3310976 TTCCATGAAT
3310986 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
1 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
3311036 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
1 TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
3311086 TTTACA
1 TTTACA
3311092 AAAGTTGTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (50 bp):
TTTACATCTTTTTAATTTTGTCCCTAAATCATAATTTCATCAAAATTCTC
Found at i:3317167 original size:24 final size:24
Alignment explanation
Indices: 3317135--3317181 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3317125 CTAAATTTAT
*
3317135 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
3317159 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
3317182 ATTTCCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:3321482 original size:10 final size:10
Alignment explanation
Indices: 3321421--3321474 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
3321411 AAAATTAGAA
*
3321421 AAAAAATTAT
1 AAAATATTAT
*
3321431 -AAAT-TTGT
1 AAAATATTAT
*
3321439 AAAATTTTAT
1 AAAATATTAT
*
3321449 AAAA-ATCAT
1 AAAATATTAT
3321458 AAAATATTAT
1 AAAATATTAT
3321468 AAAATAT
1 AAAATAT
3321475 ATAGAAATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 3 0.09
9 14 0.40
10 18 0.51
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
AAAATATTAT
Found at i:3322036 original size:16 final size:16
Alignment explanation
Indices: 3322015--3322046 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3322005 TTTTATAATA
3322015 TTTTTTACAATTTTAT
1 TTTTTTACAATTTTAT
*
3322031 TTTTTTACTATTTTAT
1 TTTTTTACAATTTTAT
3322047 AAAAAAATAA
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:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTACAATTTTAT
Found at i:3322132 original size:11 final size:11
Alignment explanation
Indices: 3322112--3322151 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
3322102 AAAAAAATTC
3322112 AATTTTTTTAT
1 AATTTTTTTAT
*
3322123 AATTTATTTAT
1 AATTTTTTTAT
*
3322134 GATTTTTTTAT
1 AATTTTTTTAT
3322145 AATTTTT
1 AATTTTT
3322152 GTGATTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (11 bp):
AATTTTTTTAT
Found at i:3322138 original size:22 final size:21
Alignment explanation
Indices: 3322113--3322221 Score: 77
Period size: 22 Copynumber: 5.3 Consensus size: 21
3322103 AAAAAATTCA
3322113 ATTTTTTTATAATTTATTTATG
1 ATTTTTTTATAATTT-TTTATG
*
3322135 ATTTTTTTATAA-TTTTTGTG
1 ATTTTTTTATAATTTTTTATG
*
3322155 ATTTTTATA-AATTTTTT-T-
1 ATTTTTTTATAATTTTTTATG
* * **
3322173 ATTTTATAATAAATTTTAAAT-
1 ATTTTTTTAT-AATTTTTTATG
*
3322194 ATTTTTTCTACAAATTTTTTAT-
1 ATTTTTT-TA-TAATTTTTTATG
3322216 ATTTTT
1 ATTTTT
3322222 AATATATTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.09
19 3 0.04
20 24 0.35
21 9 0.13
22 27 0.39
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (21 bp):
ATTTTTTTATAATTTTTTATG
Found at i:3322159 original size:18 final size:17
Alignment explanation
Indices: 3322138--3322182 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
3322128 ATTTATGATT
3322138 TTTTTATAATTTTTGTGA
1 TTTTTATAATTTTT-TGA
*
3322156 TTTTTATAAATTTTTTTA
1 TTTTTAT-AATTTTTTGA
3322174 -TTTTATAAT
1 TTTTTATAAT
3322183 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 3 0.12
17 6 0.24
18 9 0.36
19 7 0.28
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (17 bp):
TTTTTATAATTTTTTGA
Found at i:3322168 original size:10 final size:10
Alignment explanation
Indices: 3322138--3322267 Score: 54
Period size: 11 Copynumber: 12.9 Consensus size: 10
3322128 ATTTATGATT
3322138 TTTTTAT-AA
1 TTTTTATAAA
* *
3322147 TTTTTGT-GA
1 TTTTTATAAA
3322156 TTTTTATAAA
1 TTTTTATAAA
*
3322166 TTTTT-T-TA
1 TTTTTATAAA
3322174 TTTTATAATAAA
1 TTTT-T-ATAAA
* **
3322186 TTTTAAATATT
1 TTTT-TATAAA
*
3322197 TTTTCTACAAA
1 TTTT-TATAAA
*
3322208 TTTTT-TATA
1 TTTTTATAAA
*
3322217 TTTTTAATATA
1 TTTTT-ATAAA
** *
3322228 TTTCCATAAT
1 TTTTTATAAA
3322238 TTTTTATAAA
1 TTTTTATAAA
*
3322248 TTTTTAATAAT
1 TTTTT-ATAAA
3322259 TTTTTATAA
1 TTTTTATAA
3322268 CTTTATTGAT
Statistics
Matches: 89, Mismatches: 24, Indels: 15
0.70 0.19 0.12
Matches are distributed among these distances:
8 5 0.06
9 22 0.25
10 26 0.29
11 30 0.34
12 6 0.07
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:3322170 original size:11 final size:10
Alignment explanation
Indices: 3322115--3322267 Score: 75
Period size: 10 Copynumber: 15.0 Consensus size: 10
3322105 AAAATTCAAT
3322115 TTTTTTATAA
1 TTTTTTATAA
*
3322125 TTTATTTATGAT
1 TTT-TTTAT-AA
3322137 TTTTTTATAA
1 TTTTTTATAA
* *
3322147 -TTTTTGTGA
1 TTTTTTATAA
3322156 -TTTTTATAAA
1 TTTTTTAT-AA
3322166 TTTTTT-T-A
1 TTTTTTATAA
*
3322174 TTTTATAATAAA
1 TTTT-TTAT-AA
** *
3322186 TTTTAAATAT
1 TTTTTTATAA
*
3322196 TTTTTCTACAAA
1 TTTTT-TA-TAA
3322208 TTTTTTAT-A
1 TTTTTTATAA
*
3322217 TTTTTAAT-A
1 TTTTTTATAA
**
3322226 TATTTCCATAA
1 T-TTTTTATAA
3322237 TTTTTTATAAA
1 TTTTTTAT-AA
*
3322248 TTTTTAATAA
1 TTTTTTATAA
3322258 TTTTTTATAA
1 TTTTTTATAA
3322268 CTTTATTGAT
Statistics
Matches: 109, Mismatches: 21, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
8 5 0.05
9 24 0.22
10 33 0.30
11 32 0.29
12 15 0.14
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:3322226 original size:31 final size:31
Alignment explanation
Indices: 3322184--3322263 Score: 85
Period size: 31 Copynumber: 2.5 Consensus size: 31
3322174 TTTTATAATA
*
3322184 AATTTTAAATATTTTTTCTACA-AATTTTTTAT
1 AATTTTTAATATTTTTTC--CATAATTTTTTAT
*
3322216 -ATTTTTAATA-TATTTCCATAATTTTTTAT
1 AATTTTTAATATTTTTTCCATAATTTTTTAT
3322245 AAATTTTTAATAATTTTTT
1 -AATTTTTAAT-ATTTTTT
3322264 ATAACTTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
28 2 0.05
29 10 0.25
30 5 0.12
31 18 0.45
32 1 0.03
33 4 0.10
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (31 bp):
AATTTTTAATATTTTTTCCATAATTTTTTAT
Found at i:3322263 original size:42 final size:41
Alignment explanation
Indices: 3322156--3322264 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 41
3322146 ATTTTTGTGA
* * *
3322156 TTTTTATAAATTTTTTTATTTTATAATAAATTTTAAATATT
1 TTTTTATAAATTTTTATATTTTTTAATAAATTTTAAATAAT
* * **
3322197 TTTTCTACAAATTTTT-TATATTTTTAATATA-TTTCCATAAT
1 TTTT-TATAAATTTTTATAT-TTTTTAATAAATTTTAAATAAT
3322238 TTTTTATAAATTTTTAATAATTTTTTA
1 TTTTTATAAATTTTT-AT-ATTTTTTA
3322265 TAACTTTATT
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
40 10 0.18
41 18 0.32
42 26 0.46
43 2 0.04
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (41 bp):
TTTTTATAAATTTTTATATTTTTTAATAAATTTTAAATAAT
Found at i:3329734 original size:36 final size:36
Alignment explanation
Indices: 3329669--3329771 Score: 98
Period size: 36 Copynumber: 2.9 Consensus size: 36
3329659 GATTCTGGGT
* *
3329669 ATAGTCAGGATTTGCCCCTTGCCCAAAATTCTGCCC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
* * * *
3329705 ATAGCCAGGATTTGCCCCCTGTCCGAAATTTTGTCC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
* * * ** *
3329741 ATAACCAGAACTTGGTCCCTGCCCATAATTC
1 ATAGCCAGGATTTGCCCCCTGCCCAAAATTC
3329772 CCACCTTGTG
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 52 1.00
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (36 bp):
ATAGCCAGGATTTGCCCCCTGCCCAAAATTCTGCCC
Found at i:3330729 original size:2 final size:2
Alignment explanation
Indices: 3330722--3330754 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3330712 GAAGTTCATA
3330722 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3330755 TAAGAGGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3331940 original size:18 final size:18
Alignment explanation
Indices: 3331917--3331962 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
3331907 TGATTAAATG
*
3331917 ATATTTTTTATGC-ATTTT
1 ATATTTTTT-TACTATTTT
3331935 ATATTTTTTTACTATTTT
1 ATATTTTTTTACTATTTT
3331953 ATAATTTTTT
1 AT-ATTTTTT
3331963 CTAATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 7 0.28
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (18 bp):
ATATTTTTTTACTATTTT
Found at i:3331969 original size:18 final size:18
Alignment explanation
Indices: 3331930--3331974 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
3331920 TTTTTTATGC
*
3331930 ATTTTATATTTTTTTACT
1 ATTTTATAATTTTTTACT
3331948 ATTTTATAATTTTTT-CT
1 ATTTTATAATTTTTTACT
3331965 AATTTT-TAAT
1 -ATTTTATAAT
3331975 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTATAATTTTTTACT
Found at i:3331998 original size:28 final size:28
Alignment explanation
Indices: 3331948--3332011 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
3331938 TTTTTTTACT
3331948 ATTTTATAATTTTTTCTAATTTTTAATAA
1 ATTTTA-AATTTTTTCTAATTTTTAATAA
* *
3331977 ATTTTAAATATTTTT-TATTTTTTATTAA
1 ATTTTAAAT-TTTTTCTAATTTTTAATAA
*
3332005 AATTTAA
1 ATTTTAA
3332012 TAACTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 20 0.65
29 11 0.35
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTTTAAATTTTTTCTAATTTTTAATAA
Found at i:3337061 original size:43 final size:43
Alignment explanation
Indices: 3337011--3337096 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
3337001 TCATATTTCA
3337011 TTTCTCATCTCATAATCATTTCTCATATTTGT-CATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTT-TCCATTTCAATAT
* *
3337054 TTTCTCATCTCATATTCATTTCTCATCTTTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
3337097 CAATCACATA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 39 0.98
ACGTcount: A:0.23, C:0.23, G:0.01, T:0.52
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCATATTTTCCATTTCAATAT
Found at i:3347007 original size:19 final size:20
Alignment explanation
Indices: 3346985--3347026 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
3346975 TATTGCTTTC
*
3346985 TTGTTGTTTTTTT-ACTGTT
1 TTGTTGTTTTTTTCACTATT
3347004 TTGTTGTTTTTTTCACTATT
1 TTGTTGTTTTTTTCACTATT
3347024 TTG
1 TTG
3347027 CTACCTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.07, C:0.07, G:0.14, T:0.71
Consensus pattern (20 bp):
TTGTTGTTTTTTTCACTATT
Found at i:3347014 original size:20 final size:19
Alignment explanation
Indices: 3346985--3347026 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
3346975 TATTGCTTTC
* *
3346985 TTGTTGTTTTTTTACTGTT
1 TTGTTGTTTTTTCACTATT
3347004 TTGTTGTTTTTTTCACTATT
1 TTGTTG-TTTTTTCACTATT
3347024 TTG
1 TTG
3347027 CTACCTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.07, C:0.07, G:0.14, T:0.71
Consensus pattern (19 bp):
TTGTTGTTTTTTCACTATT
Found at i:3348402 original size:31 final size:31
Alignment explanation
Indices: 3348367--3348432 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
3348357 TATTCGAAGG
3348367 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
1 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
3348398 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
1 CAATTTAATCTTTTTATTTTTCTAAAAAAAC
3348429 CAAT
1 CAAT
3348433 AAAAATTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (31 bp):
CAATTTAATCTTTTTATTTTTCTAAAAAAAC
Found at i:3352310 original size:11 final size:11
Alignment explanation
Indices: 3352296--3352321 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
3352286 ATTTTTTTAA
3352296 TTTTAAAATAC
1 TTTTAAAATAC
3352307 TTTTAAAATAC
1 TTTTAAAATAC
3352318 TTTT
1 TTTT
3352322 TTTTAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:3352333 original size:10 final size:10
Alignment explanation
Indices: 3352318--3352380 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
3352308 TTTAAAATAC
3352318 TTTTTTTTAA
1 TTTTTTTTAA
3352328 TTTTTTTTAA
1 TTTTTTTTAA
3352338 ----TTTTAA
1 TTTTTTTTAA
3352344 TTTTTTTTAAAA
1 TTTTTTTT--AA
3352356 TACTTTTTTTAA
1 T--TTTTTTTAA
3352368 -TTTTTTTAA
1 TTTTTTTTAA
3352377 TTTT
1 TTTT
3352381 AAAATACTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 18
0.71 0.00 0.29
Matches are distributed among these distances:
6 6 0.14
9 9 0.20
10 17 0.39
12 5 0.11
14 7 0.16
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:3352343 original size:16 final size:16
Alignment explanation
Indices: 3352322--3352353 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3352312 AAATACTTTT
3352322 TTTTAATTTTTTTTAA
1 TTTTAATTTTTTTTAA
3352338 TTTTAATTTTTTTTAA
1 TTTTAATTTTTTTTAA
3352354 AATACTTTTT
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:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (16 bp):
TTTTAATTTTTTTTAA
Found at i:3352352 original size:41 final size:39
Alignment explanation
Indices: 3352271--3352391 Score: 156
Period size: 40 Copynumber: 3.0 Consensus size: 39
3352261 GCCCGAATAA
3352271 TAAATATA-TTTTTTT-ATTTTTTTAATTTTAAAATACTTT
1 TAAA-ATACTTTTTTTAATTTTTTTAATTTT-AAATACTTT
* **
3352310 TAAAATACTTTTTTTTAATTTTTTTTAATTTTAATTTTTTT
1 TAAAATAC-TTTTTTTAA-TTTTTTTAATTTTAAATACTTT
3352351 TAAAATACTTTTTTTAATTTTTTTAATTTTAAAATACTTT
1 TAAAATACTTTTTTTAATTTTTTTAATTTT-AAATACTTT
3352391 T
1 T
3352392 TTTAATTTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
38 3 0.04
39 17 0.24
40 23 0.32
41 15 0.21
42 13 0.18
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.65
Consensus pattern (39 bp):
TAAAATACTTTTTTTAATTTTTTTAATTTTAAATACTTT
Found at i:3352362 original size:29 final size:29
Alignment explanation
Indices: 3352329--3352407 Score: 115
Period size: 29 Copynumber: 2.7 Consensus size: 29
3352319 TTTTTTTAAT
3352329 TTTTTTTAATTTTAATTTTTTTTAAAATAC
1 TTTTTTTAATTTT-ATTTTTTTTAAAATAC
*
3352359 TTTTTTTAATTTT-TTTAATTTTAAAATAC
1 TTTTTTTAATTTTATTT-TTTTTAAAATAC
3352388 TTTTTTTAATTTTTATTTTT
1 TTTTTTTAA-TTTTATTTTT
3352408 AAAATAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
28 3 0.07
29 20 0.45
30 18 0.41
31 3 0.07
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.71
Consensus pattern (29 bp):
TTTTTTTAATTTTATTTTTTTTAAAATAC
Found at i:3352392 original size:41 final size:41
Alignment explanation
Indices: 3352271--3352392 Score: 164
Period size: 41 Copynumber: 3.0 Consensus size: 41
3352261 GCCCGAATAA
3352271 TAAATATA-TTTTTTT-ATTTTTTTAATTTTAAAATAC-TTT
1 TAAA-ATACTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
**
3352310 TAAAATACTTTTTTTTAATTTTTTTTAATTTT--AATTTTTTT
1 TAAAATAC-TTTTTTTAA-TTTTTTTAATTTTAAAATACTTTT
3352351 TAAAATACTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
1 TAAAATACTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
3352392 T
1 T
3352393 TTAATTTTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 12
0.82 0.05 0.14
Matches are distributed among these distances:
38 3 0.04
39 17 0.24
40 19 0.26
41 20 0.28
42 13 0.18
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (41 bp):
TAAAATACTTTTTTTAATTTTTTTAATTTTAAAATACTTTT
Found at i:3352420 original size:29 final size:28
Alignment explanation
Indices: 3352271--3352413 Score: 122
Period size: 27 Copynumber: 5.2 Consensus size: 28
3352261 GCCCGAATAA
* *
3352271 TAAATATA-TTTTTTTATTTTTTTAATTT
1 TAAA-ATACTTTTTTTAATTTTTTATTTT
** **
3352299 TAAAATAC-TTTTAAAATACTTT-TTTT
1 TAAAATACTTTTTTTAATTTTTTATTTT
*
3352325 T--AAT--TTTTTTTAATTTTAATTTTTTT
1 TAAAATACTTTTTTTAATTTT--TTATTTT
*
3352351 TAAAATACTTTTTTTAATTTTTTTAATTT
1 TAAAATACTTTTTTTAA-TTTTTTATTTT
3352380 TAAAATACTTTTTTTAA-TTTTTATTTT
1 TAAAATACTTTTTTTAATTTTTTATTTT
3352407 TAAAATA
1 TAAAATA
3352414 AATTTTTGGT
Statistics
Matches: 92, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
23 8 0.09
24 3 0.03
25 2 0.02
26 9 0.10
27 28 0.30
28 7 0.08
29 22 0.24
30 9 0.10
31 4 0.04
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (28 bp):
TAAAATACTTTTTTTAATTTTTTATTTT
Found at i:3352622 original size:29 final size:30
Alignment explanation
Indices: 3352584--3352640 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
3352574 AGTGGGAGGG
* *
3352584 GAGGAGAGTAAAAGTTTTGGGGGAAAGTGA
1 GAGGAGAGTAAAAGTATTAGGGGAAAGTGA
3352614 GAGG-GAGTAAAAGTATTAGGGGAAAGT
1 GAGGAGAGTAAAAGTATTAGGGGAAAGT
3352641 AAAAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.42, T:0.19
Consensus pattern (30 bp):
GAGGAGAGTAAAAGTATTAGGGGAAAGTGA
Found at i:3355669 original size:17 final size:16
Alignment explanation
Indices: 3355637--3355678 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
3355627 AAAAATGATA
3355637 ATTTAATTTTTAATTT
1 ATTTAATTTTTAATTT
*
3355653 ATTTAACTTTTTTATTT
1 ATTTAA-TTTTTAATTT
*
3355670 AATTAATTT
1 ATTTAATTT
3355679 AATAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
ATTTAATTTTTAATTT
Found at i:3359416 original size:12 final size:11
Alignment explanation
Indices: 3359399--3359446 Score: 51
Period size: 12 Copynumber: 4.1 Consensus size: 11
3359389 GGATGCAAAG
3359399 GAAGAAGATGCA
1 GAAGAAGATG-A
*
3359411 GAAGAAGAAGTA
1 GAAGAAGATG-A
*
3359423 GAAGAAGACGA
1 GAAGAAGATGA
3359434 CGAAGAAGATGA
1 -GAAGAAGATGA
3359446 G
1 G
3359447 TACGAGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
11 2 0.06
12 29 0.94
ACGTcount: A:0.52, C:0.06, G:0.35, T:0.06
Consensus pattern (11 bp):
GAAGAAGATGA
Found at i:3360443 original size:16 final size:18
Alignment explanation
Indices: 3360422--3360458 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3360412 ATATTATCTT
3360422 AAAA-TTAAAA-ATATAA
1 AAAATTTAAAACATATAA
*
3360438 AAAATTTAAAACATTTAA
1 AAAATTTAAAACATATAA
3360456 AAA
1 AAA
3360459 CACATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 6 0.33
18 8 0.44
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAATTTAAAACATATAA
Found at i:3361078 original size:21 final size:21
Alignment explanation
Indices: 3361033--3361078 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 21
3361023 AATTTCCTTT
3361033 TAATAATAAAAAAATATTTTG
1 TAATAATAAAAAAATATTTTG
**
3361054 ---TAATAGGAAAATATTTTG
1 TAATAATAAAAAAATATTTTG
3361072 TAATAAT
1 TAATAAT
3361079 CAATTGCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 6
0.71 0.07 0.21
Matches are distributed among these distances:
18 16 0.80
21 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (21 bp):
TAATAATAAAAAAATATTTTG
Found at i:3361744 original size:14 final size:13
Alignment explanation
Indices: 3361718--3361756 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
3361708 ATAATATATG
3361718 AAAAATATTATTT
1 AAAAATATTATTT
3361731 AAAAATATTAATTT
1 AAAAATATT-ATTT
3361745 ATAAAAT-TTATT
1 A-AAAATATTATT
3361757 ATTAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 7 0.29
15 5 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAAAATATTATTT
Found at i:3361903 original size:15 final size:15
Alignment explanation
Indices: 3361857--3361905 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
3361847 TGTATGTTTA
3361857 ATAATATTGAAAATT
1 ATAATATTGAAAATT
* *
3361872 AT--T-TTTAAAA-A
1 ATAATATTGAAAATT
3361883 ATAATATTGAAAATT
1 ATAATATTGAAAATT
3361898 ATAATATT
1 ATAATATT
3361906 TTATTAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
11 2 0.08
12 6 0.23
13 2 0.08
14 6 0.23
15 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (15 bp):
ATAATATTGAAAATT
Found at i:3376655 original size:32 final size:32
Alignment explanation
Indices: 3376607--3376668 Score: 108
Period size: 32 Copynumber: 1.9 Consensus size: 32
3376597 TCAACATAAA
3376607 AATTAATGATGTTAATGTTGTTAATAAAAAGG
1 AATTAATGATGTTAATGTTGTTAATAAAAAGG
3376639 AATTAAATGATG-TAATGTTGTTAATAAAAA
1 AATT-AATGATGTTAATGTTGTTAATAAAAA
3376669 AGAGTATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (32 bp):
AATTAATGATGTTAATGTTGTTAATAAAAAGG
Found at i:3378216 original size:32 final size:32
Alignment explanation
Indices: 3378173--3378244 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
3378163 AGTTGTCCTG
*
3378173 TGATAG-CAAAACTGCTATTAACATTTGAGTT
1 TGATAGACAAAACTGCCATTAACATTTGAGTT
3378204 TGATAGACAAAACTGCCATTAACATTTGAGTT
1 TGATAGACAAAACTGCCATTAACATTTGAGTT
3378236 TGATAGACA
1 TGATAGACA
3378245 CTTTATCAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 6 0.15
32 33 0.85
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (32 bp):
TGATAGACAAAACTGCCATTAACATTTGAGTT
Found at i:3381840 original size:16 final size:16
Alignment explanation
Indices: 3381818--3381893 Score: 84
Period size: 16 Copynumber: 4.8 Consensus size: 16
3381808 CAAAAATTTT
3381818 TTAAAAATATTTTAAAA
1 TTAAAAA-ATTTTAAAA
*
3381835 TTAAAAAAATTTAAAA
1 TTAAAAAATTTTAAAA
**
3381851 --AAAGTATTTTAAAA
1 TTAAAAAATTTTAAAA
3381865 TTAAAAAATTTTAAAA
1 TTAAAAAATTTTAAAA
* *
3381881 ATAAAAAAATTTA
1 TTAAAAAATTTTA
3381894 TTATATTCGG
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
14 11 0.22
16 31 0.63
17 7 0.14
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (16 bp):
TTAAAAAATTTTAAAA
Found at i:3381845 original size:30 final size:29
Alignment explanation
Indices: 3381809--3381883 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
3381799 AAATTAAAAC
*
3381809 AAAAATTTTTTAAAAATATTTTAAAATTA
1 AAAAAATTTTTAAAAATATTTTAAAATTA
**
3381838 AAAAAATTTAAAAAAAGTATTTTAAAATT-
1 AAAAAATTTTTAAAAA-TATTTTAAAATTA
3381867 AAAAAA-TTTTAAAAATA
1 AAAAAATTTTTAAAAATA
3381884 AAAAAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 2 0.05
28 7 0.17
29 19 0.47
30 12 0.30
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (29 bp):
AAAAAATTTTTAAAAATATTTTAAAATTA
Found at i:3381852 original size:29 final size:30
Alignment explanation
Indices: 3381820--3381881 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
3381810 AAAATTTTTT
3381820 AAAAA-TATTTTAAAATTAAAAAAATTTAA
1 AAAAAGTATTTTAAAATTAAAAAAATTTAA
*
3381849 AAAAAGTATTTTAAAATTAAAAAATTTTAA
1 AAAAAGTATTTTAAAATTAAAAAAATTTAA
3381879 AAA
1 AAA
3381882 TAAAAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (30 bp):
AAAAAGTATTTTAAAATTAAAAAAATTTAA
Found at i:3386662 original size:174 final size:175
Alignment explanation
Indices: 3386361--3386708 Score: 486
Period size: 174 Copynumber: 2.0 Consensus size: 175
3386351 CTTCAAGCAA
* * * *
3386361 GGAACAAAATAAAAGCATAAAGTGACCATACAGAATGTTTCCATTTAAAACGACCATCACAGCAA
1 GGAACAAAACAAAAGCATAAAGTGACCATACAGAATGTTTCCATCTAAAACAACCATCACAGAAA
* *
3386426 ACCGCAGTAACATCATCAGAAAGACTGAATATTTCAAGGCCAATAACCCCAAACAATGTGATGCT
66 AACGCAGTAACATCATAAGAAAGACTGAATATTTCAAGGCCAATAACCCCAAACAATGTGATGCT
* * *
3386491 TACTATATTTTCAACATTGTGGGAGCCCTAAATCCTCACCACAAT
131 TACTACAATTTCAACATTGTGGGAACCCTAAATCCTCACCACAAT
*
3386536 GGAACAAAACAAAAGCATGAATGTGACCATACAGAATGTTTCCA-CTAAAA-AACCATCACAGAA
1 GGAACAAAACAAAAGCAT-AAAGTGACCATACAGAATGTTTCCATCTAAAACAACCATCACAGAA
* * * ** **
3386599 AAATGCAGTGACATCATAAGGAAGACTGAATATTTCAAGGCCAA-AATTTCCAAACCGTGTGATG
65 AAACGCAGTAACATCATAAGAAAGACTGAATATTTCAAGGCCAATAA-CCCCAAACAATGTGATG
* *
3386663 CTTACTACAATTTCAACATTGTGGGAACCTTAGATCCTCACCACAA
129 CTTACTACAATTTCAACATTGTGGGAACCCTAAATCCTCACCACAA
3386709 CGGACATGCA
Statistics
Matches: 152, Mismatches: 19, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
173 2 0.01
174 104 0.68
175 22 0.14
176 24 0.16
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (175 bp):
GGAACAAAACAAAAGCATAAAGTGACCATACAGAATGTTTCCATCTAAAACAACCATCACAGAAA
AACGCAGTAACATCATAAGAAAGACTGAATATTTCAAGGCCAATAACCCCAAACAATGTGATGCT
TACTACAATTTCAACATTGTGGGAACCCTAAATCCTCACCACAAT
Found at i:3402330 original size:45 final size:44
Alignment explanation
Indices: 3402243--3402397 Score: 161
Period size: 45 Copynumber: 3.5 Consensus size: 44
3402233 TACATGGTGG
* * *
3402243 ATCAGCACATAGCACAACCCTTATAGTCAATAGTACTCGGTGAA
1 ATCAGCACATAGCACCACCTTTATACTCAATAGTACTCGGTGAA
*
3402287 ATCAGCACATAGCAACCACCTTTATACTCAATGGTAC-CAGGTGAA
1 ATCAGCACATAGC-ACCACCTTTATACTCAATAGTACTC-GGTGAA
** * * *
3402332 ATCAGCACATAGCCACCACCTTTATTTTCATTAATA-TCGGGTGGA
1 ATCAGCACATAG-CACCACCTTTATACTCAATAGTACTC-GGTGAA
*
3402377 ATCAGCACATAGGATCCACCT
1 ATCAGCACATAGCA-CCACCT
3402398 ATATTTCCAA
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
44 15 0.16
45 78 0.83
46 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (44 bp):
ATCAGCACATAGCACCACCTTTATACTCAATAGTACTCGGTGAA
Found at i:3403936 original size:14 final size:15
Alignment explanation
Indices: 3403906--3403939 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3403896 TAAATTTCTT
*
3403906 TTTAACTATTGAAAA
1 TTTAACTATTCAAAA
3403921 TTTAACT-TTCAAAA
1 TTTAACTATTCAAAA
3403935 TTTAA
1 TTTAA
3403940 AATCAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (15 bp):
TTTAACTATTCAAAA
Found at i:3408224 original size:22 final size:23
Alignment explanation
Indices: 3408197--3408347 Score: 128
Period size: 25 Copynumber: 6.3 Consensus size: 23
3408187 CACTAATGAA
* *
3408197 CAGAGAGCACTAAAGTGCTATA-
1 CAGAGAGCACCAACGTGCTATAT
** *
3408219 CAGAGAGCA-CAGGTGTGCTA-AA
1 CAGAGAGCACCA-ACGTGCTATAT
** *
3408241 CAGAGAGCACTGACGTGCTAAAAT
1 CAGAGAGCACCAACGTGCT-ATAT
3408265 CAGAGAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACCAACGTGCTA-TA-T
*
3408290 TAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCT-AT-AT
3408315 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCT-AT-AT
3408340 CAGAGAGC
1 CAGAGAGC
3408348 GCGCTAAAGT
Statistics
Matches: 107, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
21 2 0.02
22 29 0.27
23 2 0.02
24 19 0.18
25 53 0.50
26 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.25, T:0.16
Consensus pattern (23 bp):
CAGAGAGCACCAACGTGCTATAT
Found at i:3408298 original size:25 final size:25
Alignment explanation
Indices: 3408241--3408347 Score: 162
Period size: 25 Copynumber: 4.3 Consensus size: 25
3408231 GTGTGCTAAA
**
3408241 CAGAGAGCACTGACGTGCTAA-AAT
1 CAGAGAGCACCAACGTGCTAATAAT
* *
3408265 CAGAGAGCACCAACGTGCTAGTAGT
1 CAGAGAGCACCAACGTGCTAATAAT
*
3408290 TAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
3408315 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
3408340 CAGAGAGC
1 CAGAGAGC
3408348 GCGCTAAAGT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
24 18 0.24
25 56 0.76
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.16
Consensus pattern (25 bp):
CAGAGAGCACCAACGTGCTAATAAT
Found at i:3409352 original size:16 final size:16
Alignment explanation
Indices: 3409331--3409367 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
3409321 GTTTTATCTA
3409331 TATAATAATATAATAT
1 TATAATAATATAATAT
3409347 TATAATAATATAATAT
1 TATAATAATATAATAT
*
3409363 AATAA
1 TATAA
3409368 CTTACTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TATAATAATATAATAT
Found at i:3409367 original size:8 final size:8
Alignment explanation
Indices: 3409330--3409361 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3409320 TGTTTTATCT
3409330 ATATAATA
1 ATATAATA
3409338 ATATAATA
1 ATATAATA
*
3409346 TTATAATA
1 ATATAATA
3409354 ATATAATA
1 ATATAATA
3409362 TAATAACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAATA
Found at i:3411425 original size:25 final size:25
Alignment explanation
Indices: 3411362--3411425 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
3411352 TTTTAATTTA
* *
3411362 ATTAGATTCATTTTATGATAGAATT
1 ATTAAATTCATTTTATGATAAAATT
* *
3411387 ATTTACTATC-TTTT-TGATAAAAATT
1 ATTAAAT-TCATTTTATGAT-AAAATT
3411412 ATTAAATTCATTTT
1 ATTAAATTCATTTT
3411426 CATAATTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
24 6 0.20
25 22 0.73
26 2 0.07
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (25 bp):
ATTAAATTCATTTTATGATAAAATT
Found at i:3413746 original size:13 final size:13
Alignment explanation
Indices: 3413728--3413753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3413718 TAACCAGTTT
3413728 GATGAGCATATTC
1 GATGAGCATATTC
3413741 GATGAGCATATTC
1 GATGAGCATATTC
3413754 ACTTCTATTT
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:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (13 bp):
GATGAGCATATTC
Found at i:3413776 original size:5 final size:6
Alignment explanation
Indices: 3413759--3413783 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3413749 TATTCACTTC
3413759 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
3413784 CCACTACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:3424824 original size:21 final size:22
Alignment explanation
Indices: 3424787--3424827 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3424777 TTTGTTTTGA
3424787 TTTTTAAGTTCTCTTTATTTAC
1 TTTTTAAGTTCTCTTTATTTAC
*
3424809 TTTTTAAGTT-TTTTTATTT
1 TTTTTAAGTTCTCTTTATTT
3424828 GTCCTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (22 bp):
TTTTTAAGTTCTCTTTATTTAC
Found at i:3424967 original size:21 final size:21
Alignment explanation
Indices: 3424923--3424998 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
3424913 TAAATATATT
* **
3424923 TTTTAAAAATTATTTTTTTTAA
1 TTTTAAATATTA-TTTTTAAAA
3424945 TTTTAAATATTATTTTTAAAA
1 TTTTAAATATTATTTTTAAAA
**
3424966 TTTTAAATATGCTTTTTAATAA
1 TTTTAAATATTATTTTTAA-AA
* *
3424988 TATAAAATATT
1 TTTTAAATATT
3424999 TAAAATATAT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
21 24 0.53
22 21 0.47
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (21 bp):
TTTTAAATATTATTTTTAAAA
Found at i:3424995 original size:22 final size:21
Alignment explanation
Indices: 3424957--3424997 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3424947 TTAAATATTA
* *
3424957 TTTTTAAAATTTTAAATATGC
1 TTTTTAAAATATAAAATATGC
3424978 TTTTTAATAATATAAAATAT
1 TTTTTAA-AATATAAAATAT
3424998 TTAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TTTTTAAAATATAAAATATGC
Found at i:3425087 original size:31 final size:31
Alignment explanation
Indices: 3425046--3425107 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
3425036 TTATTATTTG
3425046 TTTTATAATATTTTAAATGTATATTTTAAATT
1 TTTTATAATATTTTAAATGTA-ATTTTAAATT
** *
3425078 TTTTA-AATATTTTTTATTTAATTTTAAATT
1 TTTTATAATATTTTAAATGTAATTTTAAATT
3425108 ATTGATTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 10 0.37
31 12 0.44
32 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (31 bp):
TTTTATAATATTTTAAATGTAATTTTAAATT
Found at i:3425143 original size:20 final size:19
Alignment explanation
Indices: 3425120--3425164 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3425110 TGATTGGAAA
* *
3425120 AAAAAATGATTTATTTGTT
1 AAAAAAGGATTTATTTATT
*
3425139 GAAAACAGGATTTATTTATT
1 -AAAAAAGGATTTATTTATT
3425159 AAAAAA
1 AAAAAA
3425165 AATTGTAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (19 bp):
AAAAAAGGATTTATTTATT
Found at i:3425207 original size:22 final size:20
Alignment explanation
Indices: 3425181--3425235 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
3425171 AACTTTTTTT
3425181 AAAATATATATTAAAAAAGGTA
1 AAAATATATATTAAAAAA--TA
* ** *
3425203 AAAATTTATATTTGAAAATT
1 AAAATATATATTAAAAAATA
3425223 AAAATATATATTA
1 AAAATATATATTA
3425236 TAATTAGTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 12 0.44
22 15 0.56
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAATATATATTAAAAAATA
Found at i:3428814 original size:16 final size:15
Alignment explanation
Indices: 3428793--3428834 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
3428783 TATCTTTAAA
3428793 AATAATTTAAAAAAGT
1 AATAATTTAAAAAA-T
3428809 AATAATTTAAAAAAT
1 AATAATTTAAAAAAT
*
3428824 TAT-ATTTAAAA
1 AATAATTTAAAA
3428835 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 8 0.32
15 3 0.12
16 14 0.56
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (15 bp):
AATAATTTAAAAAAT
Found at i:3428961 original size:7 final size:7
Alignment explanation
Indices: 3428949--3429043 Score: 61
Period size: 7 Copynumber: 13.6 Consensus size: 7
3428939 AAATAATTAT
3428949 ATTTAAA
1 ATTTAAA
3428956 ATTTAAA
1 ATTTAAA
** *
3428963 AAATAAT
1 ATTTAAA
3428970 ATTT-AA
1 ATTTAAA
3428976 ATTTAAA
1 ATTTAAA
* *
3428983 ATAT-AT
1 ATTTAAA
3428989 ATTTAAA
1 ATTTAAA
3428996 ATTTAAA
1 ATTTAAA
* *
3429003 ATATAAT
1 ATTTAAA
3429010 ATTATAAA
1 ATT-TAAA
3429018 CCATTTAAA
1 --ATTTAAA
*
3429027 ATAT-AA
1 ATTTAAA
*
3429033 ATTTCAA
1 ATTTAAA
3429040 ATTT
1 ATTT
3429044 TATAAAACCA
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
6 14 0.21
7 42 0.64
8 3 0.05
9 4 0.06
10 3 0.05
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (7 bp):
ATTTAAA
Found at i:3428979 original size:20 final size:20
Alignment explanation
Indices: 3428922--3429017 Score: 95
Period size: 20 Copynumber: 4.5 Consensus size: 20
3428912 ATATATTTTA
3428922 AATATTTTATAATATTAAAATAAT
1 AATA-TTTA-AAT-TTAAAA-AAT
*
3428946 TATATTTAAAATTTAAAAAAT
1 AATATTT-AAATTTAAAAAAT
*
3428967 AATATTTAAATTTAAAATAT
1 AATATTTAAATTTAAAAAAT
*
3428987 -ATATTTAAAATTTAAAATAT
1 AATATTT-AAATTTAAAAAAT
3429007 AATATTATAAA
1 AATATT-TAAA
3429018 CCATTTAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.09
20 25 0.38
21 17 0.26
22 7 0.11
23 6 0.09
24 4 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTAAATTTAAAAAAT
Found at i:3428998 original size:40 final size:40
Alignment explanation
Indices: 3428922--3429043 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
3428912 ATATATTTTA
3428922 AATATTTTATAATATTAAAATAATTATATTTAAAATTTAAAAAAT
1 AATA-TTTA-AAT-TTAAAAT-A-TATATTTAAAATTTAAAAAAT
*
3428967 AATATTTAAATTTAAAATATATATTTAAAATTTAAAATAT
1 AATATTTAAATTTAAAATATATATTTAAAATTTAAAAAAT
* *
3429007 AATATTATAAACCATTTAAAATATAAATTTCAAATTT
1 AATATT-T-AA--ATTTAAAATATATATTTAAAATTT
3429044 TATAAAACCA
Statistics
Matches: 70, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
40 26 0.37
41 2 0.03
42 9 0.13
43 3 0.04
44 26 0.37
45 4 0.06
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (40 bp):
AATATTTAAATTTAAAATATATATTTAAAATTTAAAAAAT
Found at i:3429024 original size:64 final size:62
Alignment explanation
Indices: 3428923--3429043 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 62
3428913 TATATTTTAA
* *
3428923 ATATTTTATAATATTAAAATAATTATATTTAAAATTTAAAAAATAATATTT-AAATTTAAAAT
1 ATATTTTAAAATATTAAAATAATAATATTTAAAATTTAAAAAATAA-ATTTCAAATTTAAAAT
*
3428985 ATATATTTAAAAT-TTAAAAT-ATAATATTATAAACCATTTAAAATATAAATTTCAAATTT
1 ATAT-TTTAAAATATTAAAATAATAATATT-TAAA--ATTTAAAAAATAAATTTCAAATTT
3429044 TATAAAACCA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
61 7 0.14
62 15 0.29
63 11 0.22
64 18 0.35
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (62 bp):
ATATTTTAAAATATTAAAATAATAATATTTAAAATTTAAAAAATAAATTTCAAATTTAAAAT
Found at i:3435809 original size:29 final size:28
Alignment explanation
Indices: 3435776--3435983 Score: 166
Period size: 29 Copynumber: 7.2 Consensus size: 28
3435766 TGTATACAAC
*
3435776 CCCTAGAATCATGCGAGCCTATGTGTGAA
1 CCCTAGAA-CATGCGAGCCTATGTGCGAA
* ** *
3435805 CCCTAGGAACATACGAGCCTACATGTGAA
1 CCCTA-GAACATGCGAGCCTATGTGCGAA
*
3435834 CCCTAGGTACATGCGAGCCTATGTGCGAA
1 CCCTA-GAACATGCGAGCCTATGTGCGAA
* * *
3435863 CCCTAGGTACATGCGAACCTATATGCGAA
1 CCCTA-GAACATGCGAGCCTATGTGCGAA
* * * * **
3435892 TCCTAGGAACATGTGAACTTATGTGTAAA
1 CCCTA-GAACATGCGAGCCTATGTGCGAA
**
3435921 CCCTAAGAACATGCGAATCTATGTGCGAA
1 CCCT-AGAACATGCGAGCCTATGTGCGAA
* * *
3435950 CTCTAGGAACATGCGAGCCTA-ATGCGAT
1 CCCTA-GAACATGCGAGCCTATGTGCGAA
3435978 CCCTAG
1 CCCTAG
3435984 TTGCATGTAA
Statistics
Matches: 147, Mismatches: 29, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
27 1 0.01
28 10 0.07
29 132 0.90
30 4 0.03
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (28 bp):
CCCTAGAACATGCGAGCCTATGTGCGAA
Found at i:3435847 original size:58 final size:58
Alignment explanation
Indices: 3435776--3435970 Score: 230
Period size: 58 Copynumber: 3.4 Consensus size: 58
3435766 TGTATACAAC
* * * *
3435776 CCCTA-GAATCATGCGAGCCTATGTGTGAACCCTAGGAACATACGAGCCTACATGTGAA
1 CCCTAGGAA-CATGCGAGCCTATGTGTGAACCCTAGGAACATGCGAACCTATATGCGAA
* * *
3435834 CCCTAGGTACATGCGAGCCTATGTGCGAACCCTAGGTACATGCGAACCTATATGCGAA
1 CCCTAGGAACATGCGAGCCTATGTGTGAACCCTAGGAACATGCGAACCTATATGCGAA
* * * * * * * *
3435892 TCCTAGGAACATGTGAACTTATGTGTAAACCCTAAGAACATGCGAATCTATGTGCGAA
1 CCCTAGGAACATGCGAGCCTATGTGTGAACCCTAGGAACATGCGAACCTATATGCGAA
*
3435950 CTCTAGGAACATGCGAGCCTA
1 CCCTAGGAACATGCGAGCCTA
3435971 ATGCGATCCC
Statistics
Matches: 113, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
58 111 0.98
59 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (58 bp):
CCCTAGGAACATGCGAGCCTATGTGTGAACCCTAGGAACATGCGAACCTATATGCGAA
Found at i:3435877 original size:87 final size:87
Alignment explanation
Indices: 3435776--3435983 Score: 231
Period size: 87 Copynumber: 2.4 Consensus size: 87
3435766 TGTATACAAC
* * * * *
3435776 CCCTA-GAATCATGCGAGCCTATGTGTGAACCCTAGGAACATACGAGCCTACATGTGAACCCTAG
1 CCCTAGGAA-CATGCGAGCCTATATGCGAACCCTAGGAACATACGAACCTACATGTAAACCCTAA
* *
3435840 GTACATGCGAGCCTATGTGCGAA
65 GAACATGCGAACCTATGTGCGAA
* * * ** * **
3435863 CCCTAGGTACATGCGAACCTATATGCGAATCCTAGGAACATGTGAACTTATGTGTAAACCCTAAG
1 CCCTAGGAACATGCGAGCCTATATGCGAACCCTAGGAACATACGAACCTACATGTAAACCCTAAG
*
3435928 AACATGCGAATCTATGTGCGAA
66 AACATGCGAACCTATGTGCGAA
* *
3435950 CTCTAGGAACATGCGAGCCTA-ATGCGATCCCTAG
1 CCCTAGGAACATGCGAGCCTATATGCGAACCCTAG
3435984 TTGCATGTAA
Statistics
Matches: 99, Mismatches: 21, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
86 11 0.11
87 86 0.87
88 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (87 bp):
CCCTAGGAACATGCGAGCCTATATGCGAACCCTAGGAACATACGAACCTACATGTAAACCCTAAG
AACATGCGAACCTATGTGCGAA
Found at i:3435879 original size:17 final size:17
Alignment explanation
Indices: 3435824--3435881 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 17
3435814 CATACGAGCC
*
3435824 TACATGTGAACCCTAGG
1 TACATGCGAACCCTAGG
*
3435841 TACATGCG-AGCCTA--
1 TACATGCGAACCCTAGG
*
3435855 T--GTGCGAACCCTAGG
1 TACATGCGAACCCTAGG
3435870 TACATGCGAACC
1 TACATGCGAACC
3435882 TATATGCGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
12 4 0.13
13 5 0.16
14 1 0.03
15 1 0.03
16 5 0.16
17 15 0.48
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.21
Consensus pattern (17 bp):
TACATGCGAACCCTAGG
Found at i:3436016 original size:34 final size:35
Alignment explanation
Indices: 3435971--3436048 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 35
3435961 TGCGAGCCTA
* * * *
3435971 ATGCGATCCCTAGTTGCATGTAAGCATATATG-CC
1 ATGCGAACCCTAGGTACATGCAAGCATATATGACC
* *
3436005 ATGCGAACCCTAGGTACATGCAAGCCTATATGATC
1 ATGCGAACCCTAGGTACATGCAAGCATATATGACC
3436040 ATGCGAACC
1 ATGCGAACC
3436049 TGTAAACATG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 27 0.73
35 10 0.27
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (35 bp):
ATGCGAACCCTAGGTACATGCAAGCATATATGACC
Found at i:3454396 original size:2 final size:2
Alignment explanation
Indices: 3454391--3454424 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3454381 AAAAAAACAC
3454391 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3454425 GAGTTTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3457015 original size:68 final size:68
Alignment explanation
Indices: 3456943--3457086 Score: 288
Period size: 68 Copynumber: 2.1 Consensus size: 68
3456933 GCTCTAATTC
3456943 TAAAAAATTCAATAAATTCAACCCTCAATATTTACAAAATATGTCAATTTAGTCCTAACTCTAAA
1 TAAAAAATTCAATAAATTCAACCCTCAATATTTACAAAATATGTCAATTTAGTCCTAACTCTAAA
3457008 AAT
66 AAT
3457011 TAAAAAATTCAATAAATTCAACCCTCAATATTTACAAAATATGTCAATTTAGTCCTAACTCTAAA
1 TAAAAAATTCAATAAATTCAACCCTCAATATTTACAAAATATGTCAATTTAGTCCTAACTCTAAA
3457076 AAT
66 AAT
3457079 TAAAAAAT
1 TAAAAAAT
3457087 ATATGTATTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 76 1.00
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.32
Consensus pattern (68 bp):
TAAAAAATTCAATAAATTCAACCCTCAATATTTACAAAATATGTCAATTTAGTCCTAACTCTAAA
AAT
Found at i:3459669 original size:36 final size:35
Alignment explanation
Indices: 3459623--3459726 Score: 93
Period size: 36 Copynumber: 2.9 Consensus size: 35
3459613 CAACGGTGCA
* *
3459623 CATTTTTTACGCTTTATATTGCCAACGGAT-GGTGTG
1 CATTTCTTACG-TTTATATTGCCAACGAATGGGT-TG
* *
3459659 CATTTCTTACGTTTCATATTACCAATGAATGGGTTG
1 CATTTCTTACGTTT-ATATTGCCAACGAATGGGTTG
* * * *
3459695 CATCTCTCACATTTTATATTGCCAATGAATGG
1 CATTTCTTAC-GTTTATATTGCCAACGAATGG
3459727 CTTGAACTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
35 3 0.05
36 48 0.84
37 6 0.11
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.40
Consensus pattern (35 bp):
CATTTCTTACGTTTATATTGCCAACGAATGGGTTG
Found at i:3462503 original size:44 final size:44
Alignment explanation
Indices: 3462425--3462515 Score: 119
Period size: 44 Copynumber: 2.1 Consensus size: 44
3462415 GTAGGTCAAA
* *
3462425 TAATATCAAAATAACCTACACTAATCAGAATTTAAGTGGGTAAC
1 TAATATCAAAATAACCTACACTAATCAGAATTTAAGTGAGAAAC
* * ** *
3462469 TAATATTAAAATAACTTACACTAATTTGAGTTTAAGTGAGAAAC
1 TAATATCAAAATAACCTACACTAATCAGAATTTAAGTGAGAAAC
3462513 TAA
1 TAA
3462516 AAATAGAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (44 bp):
TAATATCAAAATAACCTACACTAATCAGAATTTAAGTGAGAAAC
Found at i:3474221 original size:18 final size:18
Alignment explanation
Indices: 3474198--3474271 Score: 80
Period size: 18 Copynumber: 4.0 Consensus size: 18
3474188 AAAAAATTAT
3474198 TTTAAAAATATTTTAAAA
1 TTTAAAAATATTTTAAAA
*
3474216 TTTAAAAA-AATTTAAAGTA
1 TTTAAAAATATTTTAAA--A
3474235 TTTTAAAAATATTTTTAAAA
1 -TTTAAAAATA-TTTTAAAA
*
3474255 -TTAAAAAAATTTTAAAA
1 TTTAAAAATATTTTAAAA
3474272 AAGTATTTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
17 15 0.31
18 16 0.33
19 1 0.02
20 9 0.19
21 1 0.02
22 6 0.12
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (18 bp):
TTTAAAAATATTTTAAAA
Found at i:3474249 original size:11 final size:11
Alignment explanation
Indices: 3474189--3474294 Score: 70
Period size: 11 Copynumber: 10.3 Consensus size: 11
3474179 ACAAAAATAA
3474189 AAAAATTATTTT
1 AAAAA-TATTTT
3474201 AAAAATATTTT
1 AAAAATATTTT
3474212 --AAA-A-TTT
1 AAAAATATTTT
*
3474219 AAAAA-AATTT
1 AAAAATATTTT
*
3474229 -AAAGTATTTT
1 AAAAATATTTT
3474239 AAAAATATTTT
1 AAAAATATTTT
*
3474250 -TAAA-A--TT
1 AAAAATATTTT
*
3474257 AAAAAAATTTT
1 AAAAATATTTT
3474268 AAAAAAGTATTTT
1 -AAAAA-TATTTT
*
3474281 AAAAGTATTTT
1 AAAAATATTTT
3474292 AAA
1 AAA
3474295 TTTTAAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 23
0.72 0.07 0.22
Matches are distributed among these distances:
7 5 0.07
8 4 0.05
9 12 0.16
10 10 0.13
11 26 0.34
12 14 0.18
13 5 0.07
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:3474314 original size:42 final size:42
Alignment explanation
Indices: 3474229--3474314 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
3474219 AAAAAAATTT
***
3474229 AAAGTATTTTAAAAATATTTTTAAAATTAAAAAAATTTTAAA
1 AAAGTATTTTAAAAATATTTTTAAAATTAAAAAAATAAAAAA
* *
3474271 AAAGTATTTTAAAAGTA-TTTTAAATTTTAAAAAAATAAAAAA
1 AAAGTATTTTAAAAATATTTTTAAA-ATTAAAAAAATAAAAAA
3474313 AA
1 AA
3474315 TTATTGTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
41 7 0.18
42 31 0.82
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (42 bp):
AAAGTATTTTAAAAATATTTTTAAAATTAAAAAAATAAAAAA
Found at i:3474341 original size:10 final size:10
Alignment explanation
Indices: 3474326--3474354 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3474316 TATTGTATTC
3474326 GGGCCGGGCT
1 GGGCCGGGCT
3474336 GGGCCGGGCT
1 GGGCCGGGCT
3474346 GGGCCGGGC
1 GGGCCGGGC
3474355 CCGGGCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (10 bp):
GGGCCGGGCT
Done.