Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 131 of 161
Found at i:41032570 original size:3 final size:3
Alignment explanation
Indices: 41032562--41032609 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
41032552 GCATTCATCC
41032562 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41032610 AGAGCTGCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41032821 original size:4 final size:4
Alignment explanation
Indices: 41032812--41032849 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
41032802 TTTAAAACAC
41032812 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
41032850 ATTGCTTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:41033855 original size:40 final size:40
Alignment explanation
Indices: 41033801--41033911 Score: 136
Period size: 40 Copynumber: 2.8 Consensus size: 40
41033791 CGTTTGGATA
*
41033801 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAT-
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT-TG
** *
41033841 AAAAACGCCGCTAAAGGTCGAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
* * *
41033881 GAAAACGCAGCTAAAAAT-AAGCATTACCGGC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGC
41033912 TTTTTCCAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
39 12 0.20
40 48 0.80
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
Found at i:41034008 original size:41 final size:41
Alignment explanation
Indices: 41033963--41034206 Score: 346
Period size: 41 Copynumber: 6.0 Consensus size: 41
41033953 TGAGTTTTTG
* * * *
41033963 GGGCCTTTAGCAGCGTTTTTTCAA-AAACGCCGCTAATTCTC
1 GGGCCTTTAGCGGCG-TTTTTGAATAAGCGCCGCTAATGCTC
** *
41034004 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATTTTA
1 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
*
41034045 GGGCCTTTAGCGGTGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
* * *
41034086 AGGCCTTTAGCGGCGTTTTGGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
* *
41034127 GGGCCTTTAGTGGTGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
*
41034168 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGC
41034207 CCGCTTTTGA
Statistics
Matches: 181, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 7 0.04
41 174 0.96
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
Found at i:41034670 original size:14 final size:15
Alignment explanation
Indices: 41034642--41034674 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
41034632 AAGGTTTATA
41034642 GATTATGGAATTAGG
1 GATTATGGAATTAGG
41034657 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
41034671 GATT
1 GATT
41034675 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:41034912 original size:14 final size:14
Alignment explanation
Indices: 41034893--41034952 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
41034883 TAAATAAGAT
*
41034893 TTAGGGGTTAGTAG
1 TTAGGGGTTAGGAG
*
41034907 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAG
*
41034921 TTAGGGGTTA-AAGG
1 TTAGGGGTTAGGA-G
* *
41034935 TTAGAGGTTAAGAG
1 TTAGGGGTTAGGAG
41034949 TTAG
1 TTAG
41034953 TGATTTAGGG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
14 37 0.97
15 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.43, T:0.32
Consensus pattern (14 bp):
TTAGGGGTTAGGAG
Found at i:41034916 original size:7 final size:7
Alignment explanation
Indices: 41034893--41034944 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
41034883 TAAATAAGAT
41034893 TTAGGGG
1 TTAGGGG
**
41034900 TTAGTAG
1 TTAGGGG
41034907 TTAGGGG
1 TTAGGGG
41034914 TTAGGGG
1 TTAGGGG
41034921 TTAGGGG
1 TTAGGGG
**
41034928 TTAAAGG
1 TTAGGGG
*
41034935 TTAGAGG
1 TTAGGGG
41034942 TTA
1 TTA
41034945 AGAGTTAGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.23, C:0.00, G:0.44, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:41034930 original size:21 final size:21
Alignment explanation
Indices: 41034893--41034951 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
41034883 TAAATAAGAT
* **
41034893 TTAGGGGTTAGTAGTTAGGGG
1 TTAGGGGTTAGGAGTTAAAGG
*
41034914 TTAGGGGTTAGGGGTTAAAGG
1 TTAGGGGTTAGGAGTTAAAGG
* *
41034935 TTAGAGGTTAAGAGTTA
1 TTAGGGGTTAGGAGTTA
41034952 GTGATTTAGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.32
Consensus pattern (21 bp):
TTAGGGGTTAGGAGTTAAAGG
Found at i:41035448 original size:13 final size:13
Alignment explanation
Indices: 41035430--41035454 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41035420 ATAAATAAAT
41035430 AAATTAATGTAAC
1 AAATTAATGTAAC
41035443 AAATTAATGTAA
1 AAATTAATGTAA
41035455 AAGATTGACA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
AAATTAATGTAAC
Found at i:41037767 original size:25 final size:25
Alignment explanation
Indices: 41037738--41037785 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
41037728 CACGTATCTA
*
41037738 AAATTAAGTGTTTAAAAATTTTGCT
1 AAATTAAGTATTTAAAAATTTTGCT
41037763 AAATTAAGTATTTAAAAATTTTG
1 AAATTAAGTATTTAAAAATTTTG
41037786 AGCTTTGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (25 bp):
AAATTAAGTATTTAAAAATTTTGCT
Found at i:41038539 original size:77 final size:77
Alignment explanation
Indices: 41038410--41038563 Score: 290
Period size: 77 Copynumber: 2.0 Consensus size: 77
41038400 ATTCTTTAAA
*
41038410 TATCTTCATATGTACAGCTACTGCTTGAGTATGCTAACCTTTTTAATTTTTTGACTGGACATATT
1 TATCTTCATATGTACAGCTACTGCTTGAGTATGCTAACCTTTTTAATCTTTTGACTGGACATATT
*
41038475 CATTAGGAGACG
66 CATCAGGAGACG
41038487 TATCTTCATATGTACAGCTACTGCTTGAGTATGCTAACCTTTTTAATCTTTTGACTGGACATATT
1 TATCTTCATATGTACAGCTACTGCTTGAGTATGCTAACCTTTTTAATCTTTTGACTGGACATATT
41038552 CATCAGGAGACG
66 CATCAGGAGACG
41038564 CTAATCTTTA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (77 bp):
TATCTTCATATGTACAGCTACTGCTTGAGTATGCTAACCTTTTTAATCTTTTGACTGGACATATT
CATCAGGAGACG
Found at i:41039617 original size:43 final size:43
Alignment explanation
Indices: 41039557--41039647 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
41039547 CTTTGAGTTC
* * * *
41039557 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
*
41039599 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATATTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
41039642 ATTACC
1 ATTACC
41039648 TTGCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
Found at i:41039994 original size:43 final size:43
Alignment explanation
Indices: 41039922--41040125 Score: 247
Period size: 42 Copynumber: 4.8 Consensus size: 43
41039912 AAGATATATT
**
41039922 TTTAGCGGCGTTTGTGTTAAAAGCGCCGCTAAAGGTCTAT-TC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTATGTC
* * * * * *
41039964 TATAGTGGCGTTTGTGGGAAAAAGCACCGCTAAAGCTCAATATC
1 TTTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGGTCTATGTC
*
41040008 TTTAGCGGCGTTTGTGGG-GAAGCGCCGCTAAAGGTCT-TGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-GTC
* *
41040050 TTTAGTGGCGTTTGTGGG-AAAGCGCCGCTAAATGTC-ATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-GTC
41040092 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
41040126 TTAGCAACGC
Statistics
Matches: 138, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 86 0.62
43 33 0.24
44 18 0.13
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTATGTC
Found at i:41040042 original size:85 final size:82
Alignment explanation
Indices: 41039917--41040125 Score: 260
Period size: 86 Copynumber: 2.5 Consensus size: 82
41039907 TTTAAAAGAT
* **
41039917 ATATTTTTAGCGGCGTTTGTGTTAAAAGCGCCGCTAAAGGTCTAT-TCTATAGTGGCGTTTGTGG
1 ATATCTTTAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGTCT-TGTCTATAGTGGCGTTTGTGG
41039981 GAAAAAGCACCGCTAAA-GCTC
64 G--AAAGCACCGCTAAATG-TC
* *
41040002 AATATCTTTAGCGGCGTTTGTGGGGAAGCGCCGCTAAAGGTCTTGGTCTTTAGTGGCGTTTGTGG
1 -ATATCTTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTT-GTCTATAGTGGCGTTTGTGG
*
41040067 GAAAGCGCCGCTAAATGTC
64 GAAAGCACCGCTAAATGTC
*
41040086 ATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
1 AT-ATCTTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAG
41040126 TTAGCAACGC
Statistics
Matches: 110, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
83 2 0.02
84 36 0.33
85 33 0.30
86 39 0.35
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (82 bp):
ATATCTTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTGTCTATAGTGGCGTTTGTGGGA
AAGCACCGCTAAATGTC
Found at i:41042576 original size:12 final size:12
Alignment explanation
Indices: 41042561--41042602 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
41042551 TATAAGTCTT
41042561 TTTATAATTAAA
1 TTTATAATTAAA
41042573 TTTAT-A-TAAA
1 TTTATAATTAAA
41042583 TTTTTATAATTAAA
1 --TTTATAATTAAA
41042597 TTTATA
1 TTTATA
41042603 TATTGTTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 4 0.15
11 1 0.04
12 16 0.62
13 1 0.04
14 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTATAATTAAA
Found at i:41042586 original size:24 final size:24
Alignment explanation
Indices: 41042559--41042604 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
41042549 AATATAAGTC
41042559 TTTTTATAATTAAATTTATATAAA
1 TTTTTATAATTAAATTTATATAAA
41042583 TTTTTATAATTAAATTTATATA
1 TTTTTATAATTAAATTTATATA
41042605 TTGTTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTTATAATTAAATTTATATAAA
Found at i:41042596 original size:14 final size:14
Alignment explanation
Indices: 41042559--41042604 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
41042549 AATATAAGTC
41042559 TTTTTATAATTAAA
1 TTTTTATAATTAAA
41042573 --TTTAT-A-TAAA
1 TTTTTATAATTAAA
41042583 TTTTTATAATTAAA
1 TTTTTATAATTAAA
*
41042597 TTTATATA
1 TTTTTATA
41042605 TTGTTTGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
10 4 0.15
11 1 0.04
12 10 0.37
13 1 0.04
14 11 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTTATAATTAAA
Found at i:41044741 original size:17 final size:18
Alignment explanation
Indices: 41044719--41044755 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
41044709 TATATTTGGT
41044719 AAATAAAAAT-TAAAATA
1 AAATAAAAATCTAAAATA
*
41044736 AAATAAAAATCTAAATTA
1 AAATAAAAATCTAAAATA
41044754 AA
1 AA
41044756 TAATTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATAAAAATCTAAAATA
Found at i:41049468 original size:120 final size:120
Alignment explanation
Indices: 41049265--41049487 Score: 283
Period size: 120 Copynumber: 1.9 Consensus size: 120
41049255 GGACTTGAAT
*** * *
41049265 ATCTACAATTTTGGCACAAGAATCACCCCAAAAGGTGGTCTGAAGGTTTCGAAAAGTCAAGTCCA
1 ATCTACAATTTCAACACAAGAATCACCCCAAAAGGTGGTCAGAAGGTCTCGAAAAGTCAAGTCCA
**
41049330 ATTGACCCTTGTGAAACCCAAC-GATTAATCTTGAACTTTCGAAGAGGACTCGACG
66 ATTGACCCTTACGAAACCCAACAG-TTAATCTTGAACTTTCGAAGAGGACTCGACG
* * **
41049385 ATCTACAATTTCAACACAAGAATCACCCCAAAATGTGGTCAGATGGTCTC-AGGCAGTCAAG-CC
1 ATCTACAATTTCAACACAAGAATCACCCCAAAAGGTGGTCAGAAGGTCTCGA-AAAGTCAAGTCC
41049448 AAAGTT-ACCCTTACGAAACCCAACAGTTAATCTTGAACTT
65 -AA-TTGACCCTTACGAAACCCAACAGTTAATCTTGAACTT
41049488 CCTATAGGGA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
119 3 0.03
120 82 0.93
121 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (120 bp):
ATCTACAATTTCAACACAAGAATCACCCCAAAAGGTGGTCAGAAGGTCTCGAAAAGTCAAGTCCA
ATTGACCCTTACGAAACCCAACAGTTAATCTTGAACTTTCGAAGAGGACTCGACG
Found at i:41050738 original size:157 final size:155
Alignment explanation
Indices: 41050453--41050755 Score: 428
Period size: 157 Copynumber: 1.9 Consensus size: 155
41050443 TGACTCCATA
* * * *
41050453 GCTAAATAATGTTGTAATTAATAGACGTAGGTTCAAGCCTTGATTATAAATTATTTGATCTCTAA
1 GCTAAATAATGTTGTAATTAATAGACGTAGGGTCAA-CCTTAATTACAAATTATTTGAGCTCTAA
** * *
41050518 TTTATATGTTTAATAAGTCCCTCTACTAGCTCGATATAACCTTGATGGTTTGCTTTAATTGATGA
65 TTTATATGTCCAATAAGTCCCTCCACTAGCTCGATATAACCTTGATGGTTTGCATTAATTGATGA
*
41050583 AATGAGAAATTGTGAATAACTCTATG
130 AATGAAAAATTGTGAATAACTCTATG
* *
41050609 GCTAAATAATGTTTTTATTAATAGACGTAGGGTCGGAA-CTTAATTACAAATTATTTGAGCTCTA
1 GCTAAATAATGTTGTAATTAATAGACGTAGGGTC--AACCTTAATTACAAATTATTTGAGCTCTA
* ** *
41050673 ACTTTATGTGTCCAATCGGTCCCTCCCCTAGCTCGATATAACCTTGATGGTTTGCATTAATTGAT
64 A-TTTATATGTCCAATAAGTCCCTCCACTAGCTCGATATAACCTTGATGGTTTGCATTAATTGAT
41050738 GAAATGAAAAATTGTGAA
128 GAAATGAAAAATTGTGAA
41050756 ACAATGAAGA
Statistics
Matches: 129, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
156 55 0.43
157 72 0.56
158 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (155 bp):
GCTAAATAATGTTGTAATTAATAGACGTAGGGTCAACCTTAATTACAAATTATTTGAGCTCTAAT
TTATATGTCCAATAAGTCCCTCCACTAGCTCGATATAACCTTGATGGTTTGCATTAATTGATGAA
ATGAAAAATTGTGAATAACTCTATG
Found at i:41053025 original size:12 final size:11
Alignment explanation
Indices: 41053008--41053042 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
41052998 AACAAATCCT
41053008 CTCTCATATTTC
1 CTCTCA-ATTTC
41053020 CTCTCAA-TTC
1 CTCTCAATTTC
41053030 CTCTCAATTTC
1 CTCTCAATTTC
41053041 CT
1 CT
41053043 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 6 0.27
12 6 0.27
ACGTcount: A:0.17, C:0.37, G:0.00, T:0.46
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:41054245 original size:7 final size:7
Alignment explanation
Indices: 41054235--41054259 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41054225 ATTCGATTGA
41054235 TATTTAG
1 TATTTAG
41054242 TATTTAG
1 TATTTAG
41054249 TATTTAG
1 TATTTAG
41054256 TATT
1 TATT
41054260 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:41055585 original size:29 final size:29
Alignment explanation
Indices: 41055546--41055773 Score: 270
Period size: 29 Copynumber: 8.3 Consensus size: 29
41055536 CACCTAACTT
*
41055546 AACCCTAAACCCTAACCTAAATTAATTAAA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
*
41055576 AACCCTAACCCTAACCTAATTTAATTTAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
41055605 AACCCTAACCCT-ACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
* *
41055633 AACCCTAACCCCTAACCTAAATTAATTACA
1 AACCCTAA-CCCTAACCTAATTTAATTAAA
*
41055663 AATCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
41055692 AACCCTAA-CC---CC----TTAACTTAAA
1 AACCCTAACCCTAACCTAATTTAA-TTAAA
*
41055714 AACCCTAACCTTAACCTAATTTAATT--A
1 AACCCTAACCCTAACCTAATTTAATTAAA
41055741 AA----AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
41055766 AACCCTAA
1 AACCCTAA
41055774 ACTAAGTTAA
Statistics
Matches: 170, Mismatches: 11, Indels: 35
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.02
22 13 0.08
23 20 0.12
25 5 0.03
26 2 0.01
27 3 0.02
28 25 0.15
29 67 0.39
30 31 0.18
ACGTcount: A:0.45, C:0.28, G:0.00, T:0.27
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:41055712 original size:22 final size:21
Alignment explanation
Indices: 41055683--41055723 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
41055673 CTAACCTAAT
41055683 TTAATTAAAAACCCTAACCCC
1 TTAATTAAAAACCCTAACCCC
41055704 TTAACTTAAAAACCCTAACC
1 TTAA-TTAAAAACCCTAACC
41055724 TTAACCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (21 bp):
TTAATTAAAAACCCTAACCCC
Found at i:41055773 original size:18 final size:20
Alignment explanation
Indices: 41055727--41055769 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 20
41055717 CCTAACCTTA
41055727 ACCTAATTTAATTAAAAACCC
1 ACCTAATTTAATTAAAAA-CC
41055748 TAACCTAATTTAATTAAAAACC
1 --ACCTAATTTAATTAAAAACC
41055770 CTAAACTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:41055925 original size:116 final size:116
Alignment explanation
Indices: 41055780--41056017 Score: 431
Period size: 116 Copynumber: 2.1 Consensus size: 116
41055770 CTAAACTAAG
* *
41055780 TTAACAATGTTACATTCACGTAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAA
1 TTAATAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAA
41055845 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
* *
41055896 TTAATAATTTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAATTAA
1 TTAATAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAA
*
41055961 TAATTTTATATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
66 TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
41056012 TTAATA
1 TTAATA
41056018 CAATTTATCA
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (116 bp):
TTAATAATGTTACATTCACATAATGTTAGATTTGGAAAAATGTTTTGACTGGTACTAACAAATAA
TAATTTTACATAATTTGATAATTTTACTAACCATTAATACAATTTTTTGAC
Found at i:41056034 original size:17 final size:18
Alignment explanation
Indices: 41055993--41056034 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
41055983 TTTACTAACC
* *
41055993 ATTAATACAATTTTTTGA
1 ATTAATACAATTTTATCA
*
41056011 CTTAATACAA-TTTATCA
1 ATTAATACAATTTTATCA
41056028 ATTAATA
1 ATTAATA
41056035 ATTTCACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (18 bp):
ATTAATACAATTTTATCA
Found at i:41059352 original size:126 final size:125
Alignment explanation
Indices: 41059048--41059413 Score: 497
Period size: 126 Copynumber: 2.9 Consensus size: 125
41059038 CCCAAACATG
* ** * * *
41059048 CTACTGTAGCAAAAGCGCGTCCACGAGGGCTTGATTTCACAAATTCTTCTCAAATAGAATCTTAC
1 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *
41059113 TAGAAGCGATTTTATATTATTTGCTCAAAAACATC--AAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
* *
41059171 CTACTGTAGCAAAAGCG-AGT-AACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGCGCA-TCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* * *
41059234 CTAGAAGCGATTTTGTACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTTCGTGAC
65 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAA-AATTATTTCTTACATGAC
*
41059296 CTACTATAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* ** ***
41059361 TAGAAGTGATTTTATACTATTTTATCAGAAACGTCAAATTGAAATTATTTCTT
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTT
41059414 CTAGGACCTA
Statistics
Matches: 213, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
122 68 0.32
123 18 0.08
124 5 0.02
125 44 0.21
126 78 0.37
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGAC
Found at i:41062715 original size:50 final size:50
Alignment explanation
Indices: 41062645--41063011 Score: 279
Period size: 50 Copynumber: 7.4 Consensus size: 50
41062635 GTTGCCTGTA
* * * *
41062645 GCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTG
1 GCTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
* * * ** * * * *
41062695 GCTTTAAACCGTTCCACTGCACCGCCTGGGAAATAAGATTCGCCGTTGTA
1 GCTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
* * * *
41062745 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCATTATG
1 GCTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
* * ** * * * *
41062795 ACTTCAATCTGTTTCACTGCACCGCCTGAGAAGTAAGATT-GTCGTTGTG
1 GCTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
* * * * * *
41062844 GCTTCAATCTTTTTAACTGGAATGTCAGGGAAGCAAGATTCGCCGTTGTG
1 GCTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
* * ** * * * * *
41062894 GCTTTAAACTGTTCCACTGCACCGCCTGGGAAATAAGATTCGCTGTTGTA
1 GCTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
* * * * * **
41062944 GCTTTAATCT-TTTAACTGCAATGTTGGGGAAGCAATATTTGCTATTGTG
1 GCTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
* *
41062993 GCTTCAATCTGTTCCACTG
1 GCTTTAATCTGTTTCACTG
41063012 TACTGCCTAG
Statistics
Matches: 235, Mismatches: 80, Indels: 4
0.74 0.25 0.01
Matches are distributed among these distances:
49 71 0.30
50 164 0.70
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (50 bp):
GCTTTAATCTGTTTCACTGCAATGTCGGGGAAGTAAGATTCGCCGTTGTG
Found at i:41062882 original size:99 final size:99
Alignment explanation
Indices: 41062641--41063011 Score: 503
Period size: 99 Copynumber: 3.7 Consensus size: 99
41062631 ATTCGTTGCC
* * *
41062641 TGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCGTTGTGGCTTTAAACCG
1 TGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTCAAACTG
41062706 TTCCACTGCACCGCCTGGGAAATAAGATTCGCCGT
66 TTCCACTGCACCGCCTGGGAAATAAGATTCG-CGT
* * * * *
41062741 TGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCGCCATTATGACTTCAATCTG
1 TGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTCAAACTG
* * *
41062806 TTTCACTGCACCGCCTGAGAAGTAAGATT-GTCGT
66 TTCCACTGCACCGCCTGGGAAATAAGATTCG-CGT
* * * * *
41062840 TGTGGCTTCAATCTTTTTAACTGGAATGTCAGGGAAGCAAGATTCGCCGTTGTGGCTTTAAACTG
1 TGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTCAAACTG
41062905 TTCCACTGCACCGCCTGGGAAATAAGATTCGCTGT
66 TTCCACTGCACCGCCTGGGAAATAAGATTCGC-GT
* * * * * *
41062940 TGTAGCTTTAATC-TTTTAACTGCAATGTTGGGGAAGCAATATTTGCTATTGTGGCTTCAATCTG
1 TGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTCAAACTG
41063004 TTCCACTG
66 TTCCACTG
41063012 TACTGCCTAG
Statistics
Matches: 233, Mismatches: 36, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
99 136 0.58
100 97 0.42
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (99 bp):
TGTAGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCGCCATTGTGGCTTCAAACTG
TTCCACTGCACCGCCTGGGAAATAAGATTCGCGT
Found at i:41063088 original size:44 final size:45
Alignment explanation
Indices: 41063033--41063120 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 45
41063023 ACGTAAGTTT
* *
41063033 TGCTATTCTCAGTCTGC-CT-CACTGCAACTTCAGGGGGATAAGACC
1 TGCTATTCTCAGTC--CACTCCACTGCAACCTCAGGGAGATAAGACC
*
41063078 TGCT-TTCTCAGTCCACTCCGCTGCAACCTCAGGGAGATAAGAC
1 TGCTATTCTCAGTCCACTCCACTGCAACCTCAGGGAGATAAGAC
41063121 TTGATGCGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
42 1 0.03
43 2 0.05
44 31 0.82
45 4 0.11
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.25
Consensus pattern (45 bp):
TGCTATTCTCAGTCCACTCCACTGCAACCTCAGGGAGATAAGACC
Found at i:41063482 original size:175 final size:176
Alignment explanation
Indices: 41063286--41063604 Score: 464
Period size: 175 Copynumber: 1.8 Consensus size: 176
41063276 TAGTACAGGA
*
41063286 AGGCAAGGCTAATGTCTTCGATCTACTTCACTGTCAGTACAGGAAAGCAAGAT-CTGCTATCTTT
1 AGGCAAGGCTAATGTCTTCGATCTACTTCACTGTCAGTACAAGAAAGCAAGATGC-GCTAT-TTT
* * *
41063350 -AACCTACTCTACTGTAACCCAGTGAGGCAAGGCTAGTGTC-TCGATCTGCTTCGCTGTCAATGC
64 CAACCTACTCCACTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTCAATGC
*
41063413 AAGAAGGCGAGATCTGCTATCTTTAACCTGCCCCGCTGCAACCGAGTG
129 AAGAAGGCAAGATCTGCTATCTTTAACCTGCCCCGCTGCAACCGAGTG
* * * *
41063461 AGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAAGAAGGTAAGATGCGCTATTTTCA
1 AGGCAAGGCTAATGTCTTCGATCTACTTCACTGTCAGTACAAGAAAGCAAGATGCGCTATTTTCA
* * * ** *
41063526 ACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTGATGCAG
66 ACCTACTCCACTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTCAATGCAA
41063591 GAAGGCAAGATCTG
131 GAAGGCAAGATCTG
41063605 TAATTTTCAA
Statistics
Matches: 126, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
174 3 0.02
175 87 0.69
176 36 0.29
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (176 bp):
AGGCAAGGCTAATGTCTTCGATCTACTTCACTGTCAGTACAAGAAAGCAAGATGCGCTATTTTCA
ACCTACTCCACTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCGATCTGCTTCGCTGTCAATGCAA
GAAGGCAAGATCTGCTATCTTTAACCTGCCCCGCTGCAACCGAGTG
Found at i:41063529 original size:88 final size:88
Alignment explanation
Indices: 41063286--41063604 Score: 394
Period size: 88 Copynumber: 3.6 Consensus size: 88
41063276 TAGTACAGGA
* * * *
41063286 AGGCAAGGCTAATGTCTTCGATCTACTTCACTGTCAGTACAGGAAAGCAAGATCTGCTATCTTTA
1 AGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAAGAAGGCAAGATCTGCTATCTTTA
* ** *
41063351 ACCTACTCTACTGTAACCCAGTG
66 ACCTGCTCCGCTGCAACCCAGTG
* * * *
41063374 AGGCAAGGCTAGTGTC-TCGATCTGCTTCGCTGTCAATGCAAGAAGGCGAGATCTGCTATCTTTA
1 AGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAAGAAGGCAAGATCTGCTATCTTTA
* *
41063438 ACCTGCCCCGCTGCAACCGAGTG
66 ACCTGCTCCGCTGCAACCCAGTG
*
41063461 AGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAAGAAGGTAAGATGC-GCTAT-TTT
1 AGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAAGAAGGCAAGAT-CTGCTATCTTT
*
41063524 CAACCTGCTCCGCTGCAACCCAGGG
65 -AACCTGCTCCGCTGCAACCCAGTG
* * * * *
41063549 AGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGT-TGATGCAGGAAGGCAAGATCTG
1 AGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAG-TACAAGAAGGCAAGATCTG
41063605 TAATTTTCAA
Statistics
Matches: 198, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
87 79 0.40
88 118 0.60
89 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (88 bp):
AGGCAAGGCTAGTGTCTTCGATCTGCTTCACTGTCAGTACAAGAAGGCAAGATCTGCTATCTTTA
ACCTGCTCCGCTGCAACCCAGTG
Found at i:41063796 original size:44 final size:44
Alignment explanation
Indices: 41063743--41063844 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
41063733 CCTTTATTTT
* *
41063743 AATCCGCTCCACTGTAATCTCAGGGAAAT-AGAATTATTGGCTTC
1 AATCTGCTCCACTGTAACCTCAGGGAAATAAG-ATTATTGGCTTC
** * *
41063787 AATCTGCTCCGTTGTAACCTCAGGGAGATAAGATTTTTGGCTTC
1 AATCTGCTCCACTGTAACCTCAGGGAAATAAGATTATTGGCTTC
*
41063831 AATCTACTCCACTG
1 AATCTGCTCCACTG
41063845 CTGACCAGAG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
44 46 0.96
45 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGTAACCTCAGGGAAATAAGATTATTGGCTTC
Found at i:41066067 original size:29 final size:28
Alignment explanation
Indices: 41066019--41066113 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
41066009 TTTCCTTTCC
* * *
41066019 TTTTTTCTTTTTGCCATTTTCAATTTGAT
1 TTTTTTCTTTTT-TCTTTTTTAATTTGAT
* **
41066048 TTTTTTCTTTTTTCTTTTTTACTTTCTT
1 TTTTTTCTTTTTTCTTTTTTAATTTGAT
* *
41066076 TTTTGTTTTTTTTTCCGTTTTTTTATTTTGAT
1 TTTT-TTCTTTTTT-C--TTTTTTAATTTGAT
41066108 TTTTTT
1 TTTTTT
41066114 TATTTTTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
28 14 0.27
29 20 0.38
30 1 0.02
31 2 0.04
32 15 0.29
ACGTcount: A:0.07, C:0.11, G:0.05, T:0.77
Consensus pattern (28 bp):
TTTTTTCTTTTTTCTTTTTTAATTTGAT
Found at i:41066110 original size:23 final size:23
Alignment explanation
Indices: 41066084--41066135 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
41066074 TTTTTTGTTT
* *
41066084 TTTTTTCCGTTTTTTTATTTTGA
1 TTTTTTCCATTTTTTTATTTCGA
**
41066107 TTTTTTTTATTTTTTTATTTCGA
1 TTTTTTCCATTTTTTTATTTCGA
41066130 TTTTTT
1 TTTTTT
41066136 TTATTTTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.79
Consensus pattern (23 bp):
TTTTTTCCATTTTTTTATTTCGA
Found at i:41066134 original size:15 final size:15
Alignment explanation
Indices: 41066116--41066146 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41066106 ATTTTTTTTA
41066116 TTTTTTTATTTCGAT
1 TTTTTTTATTTCGAT
*
41066131 TTTTTTTATTTTGAT
1 TTTTTTTATTTCGAT
41066146 T
1 T
41066147 GGGAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.03, G:0.06, T:0.77
Consensus pattern (15 bp):
TTTTTTTATTTCGAT
Found at i:41066136 original size:23 final size:23
Alignment explanation
Indices: 41066093--41066142 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
41066083 TTTTTTTCCG
*
41066093 TTTTTTTATTTTGATTTTTTTTA
1 TTTTTTTATTTCGATTTTTTTTA
41066116 TTTTTTTATTTCGATTTTTTTTA
1 TTTTTTTATTTCGATTTTTTTTA
41066139 TTTT
1 TTTT
41066143 GATTGGGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.12, C:0.02, G:0.04, T:0.82
Consensus pattern (23 bp):
TTTTTTTATTTCGATTTTTTTTA
Found at i:41079024 original size:19 final size:19
Alignment explanation
Indices: 41079002--41079065 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
41078992 CATAACATTA
41079002 TAAAATTTATTAGAAATTG
1 TAAAATTTATTAGAAATTG
* * *
41079021 TAAAATATTA-TACATATTA
1 TAAAAT-TTATTAGAAATTG
*
41079040 TAATAAATTATTAGAAATTG
1 TAA-AATTTATTAGAAATTG
41079060 TAAAAT
1 TAAAAT
41079066 ATTGTAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 20 0.59
20 14 0.41
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (19 bp):
TAAAATTTATTAGAAATTG
Found at i:41079058 original size:39 final size:37
Alignment explanation
Indices: 41078985--41079068 Score: 123
Period size: 39 Copynumber: 2.2 Consensus size: 37
41078975 AAAAATAATA
* *
41078985 AAAATATCATAACATTATAAAATTTATTAGAAATTGT
1 AAAATATTATAACATTATAAAAATTATTAGAAATTGT
*
41079022 AAAATATTATACATATTATAATAAATTATTAGAAATTGT
1 AAAATATTATA-ACATTATAA-AAATTATTAGAAATTGT
41079061 AAAATATT
1 AAAATATT
41079069 GTAAAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
37 10 0.24
38 8 0.19
39 24 0.57
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (37 bp):
AAAATATTATAACATTATAAAAATTATTAGAAATTGT
Found at i:41079078 original size:21 final size:19
Alignment explanation
Indices: 41079054--41079101 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 19
41079044 AAATTATTAG
41079054 AAATTGTAAAATATTGTAAAA
1 AAATTGTAAAAT-TT-TAAAA
41079075 AAATAT-TAAAATTTTAAAA
1 AAAT-TGTAAAATTTTAAAA
41079094 AAATTGTA
1 AAATTGTA
41079102 GCACACCGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 1 0.04
19 11 0.44
20 2 0.08
21 10 0.40
22 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (19 bp):
AAATTGTAAAATTTTAAAA
Found at i:41079082 original size:30 final size:29
Alignment explanation
Indices: 41079034--41079093 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
41079024 AATATTATAC
* *
41079034 ATATTATAATAAATTATTAGAAATTGTAAA
1 ATATTATAAAAAAATATTA-AAATTGTAAA
* *
41079064 ATATTGTAAAAAAATATTAAAATTTTAAA
1 ATATTATAAAAAAATATTAAAATTGTAAA
41079093 A
1 A
41079094 AAATTGTAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (29 bp):
ATATTATAAAAAAATATTAAAATTGTAAA
Found at i:41079087 original size:39 final size:38
Alignment explanation
Indices: 41079002--41079087 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
41078992 CATAACATTA
* * *
41079002 TAAAATTTATTAGAAATTGTAAAATATTATACATATTAT
1 TAAAA-TTATTAGAAATTGTAAAATATTATAAAAAATAT
* *
41079041 AATAAATTATTAGAAATTGTAAAATATTGTAAAAAAATAT
1 TA-AAATTATTAGAAATTGTAAAATATTAT-AAAAAATAT
41079081 TAAAATT
1 TAAAATT
41079088 TTAAAAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
39 29 0.74
40 10 0.26
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.40
Consensus pattern (38 bp):
TAAAATTATTAGAAATTGTAAAATATTATAAAAAATAT
Found at i:41081284 original size:42 final size:42
Alignment explanation
Indices: 41081235--41081399 Score: 179
Period size: 42 Copynumber: 3.9 Consensus size: 42
41081225 CGCTTTAGAA
* * *
41081235 CCACACGGCCAGGGACATGGGCGTGTGCCCAGGCCATGTGAG
1 CCACACGGGCAAGGACATGGGCGTGTGCCCAAGCCATGTGAG
* * * * *
41081277 CTACACGGGCAAGGACATCGGCGTATG-CCTAGACCGTGTGAG
1 CCACACGGGCAAGGACATGGGCGTGTGCCCAAG-CCATGTGAG
* * **
41081319 CCACACTGGCAAGGACATGGGTGTGTGCCCAAGCTGTGTGAG
1 CCACACGGGCAAGGACATGGGCGTGTGCCCAAGCCATGTGAG
* * *
41081361 CCACACGGGCAAGGATATGGGTGTGTGTCCAAGCCATGT
1 CCACACGGGCAAGGACATGGGCGTGTGCCCAAGCCATGT
41081400 AACTCACTGT
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
41 3 0.03
42 94 0.93
43 4 0.04
ACGTcount: A:0.22, C:0.26, G:0.35, T:0.17
Consensus pattern (42 bp):
CCACACGGGCAAGGACATGGGCGTGTGCCCAAGCCATGTGAG
Found at i:41081357 original size:146 final size:146
Alignment explanation
Indices: 41081088--41081357 Score: 335
Period size: 146 Copynumber: 1.8 Consensus size: 146
41081078 GACTGTCGAC
* * *
41081088 ACCACACGGCCAGGGACATGGGCATGTGCCCAGGCTATGTGAGCCACACGGGTAAGGATATGGCG
1 ACCACACGGCCAGGGACATGGGCATGTGCCCAGGCCATGTGAGCCACACGGGCAAGGACATGGCG
* * * * * * *
41081153 TGTACCCAGGCCACGTGAGCCATACAGAAAAAGGACATTGACGTGTGTCCAGGTTGTGTAACTTA
66 TATACCCAGACCACGTGAGCCACACAGAAAAAGGACATGGACGTGTGCCCAAGCTGTGTAACTTA
41081218 CTGTTTACGCTTTAGA
131 CTGTTTACGCTTTAGA
* *
41081234 ACCACACGGCCAGGGACATGGGCGTGTGCCCAGGCCATGTGAGCTACACGGGCAAGGACATCGGC
1 ACCACACGGCCAGGGACATGGGCATGTGCCCAGGCCATGTGAGCCACACGGGCAAGGACAT-GGC
* * ** * ** **
41081299 GTATGCCTAGACCGTGTGAGCCACACTG-GCAAGGACATGGGTGTGTGCCCAAGCTGTGT
65 GTATACCCAGACCACGTGAGCCACACAGAAAAAGGACATGGACGTGTGCCCAAGCTGTGT
41081358 GAGCCACACG
Statistics
Matches: 102, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
146 79 0.77
147 23 0.23
ACGTcount: A:0.24, C:0.25, G:0.32, T:0.19
Consensus pattern (146 bp):
ACCACACGGCCAGGGACATGGGCATGTGCCCAGGCCATGTGAGCCACACGGGCAAGGACATGGCG
TATACCCAGACCACGTGAGCCACACAGAAAAAGGACATGGACGTGTGCCCAAGCTGTGTAACTTA
CTGTTTACGCTTTAGA
Found at i:41082456 original size:25 final size:25
Alignment explanation
Indices: 41082428--41082475 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41082418 TATTGCTCTA
*
41082428 CTCTGTTCCATCTTGTTCTGTTCTG
1 CTCTATTCCATCTTGTTCTGTTCTG
* *
41082453 CTCTATTCGATTTTGTTCTGTTC
1 CTCTATTCCATCTTGTTCTGTTC
41082476 GAATTACGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.06, C:0.25, G:0.15, T:0.54
Consensus pattern (25 bp):
CTCTATTCCATCTTGTTCTGTTCTG
Found at i:41083103 original size:23 final size:24
Alignment explanation
Indices: 41083077--41083125 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
41083067 GTATTTAGTT
*
41083077 AAAAATA-AAATAAATTTT-ATAA
1 AAAAATATAAAAAAATTTTAATAA
* *
41083099 AAAAATCTAAAAATATTTTAATAA
1 AAAAATATAAAAAAATTTTAATAA
41083123 AAA
1 AAA
41083126 TTGACTCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 6 0.27
23 9 0.41
24 7 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAAAATATAAAAAAATTTTAATAA
Found at i:41091305 original size:36 final size:36
Alignment explanation
Indices: 41091265--41091470 Score: 146
Period size: 36 Copynumber: 5.7 Consensus size: 36
41091255 TGCCCAACAT
* * *
41091265 TGGTCAGTATAACTGACAAATAAGTGCACCCTGCAC
1 TGGTCGGTATAACTGAAAAATAAGTGCGCCCTGCAC
* * * *** *
41091301 TGGTCGGTA-AAATCGAAAAATAAATGTGCCCCATAT
1 TGGTCGGTATAACT-GAAAAATAAGTGCGCCCTGCAC
* * * *
41091337 TGGTTGGTATAACTGATAAATAAGTGTGCCCTGCGC
1 TGGTCGGTATAACTGAAAAATAAGTGCGCCCTGCAC
* * * * *
41091373 TGGTCGATAAAACTGAAAAATGAGTGTGCCCAGCAC
1 TGGTCGGTATAACTGAAAAATAAGTGCGCCCTGCAC
* * * *
41091409 TAGTCGGTATAAC-CAACAAATAAGTGCGTCCTGCGC
1 TGGTCGGTATAACTGAA-AAATAAGTGCGCCCTGCAC
* * *
41091445 TGGTCGGTAAAATTGAAAAATGAGTG
1 TGGTCGGTATAACTGAAAAATAAGTG
41091471 TTCAAAACCA
Statistics
Matches: 126, Mismatches: 40, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
35 5 0.04
36 116 0.92
37 5 0.04
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (36 bp):
TGGTCGGTATAACTGAAAAATAAGTGCGCCCTGCAC
Found at i:41091329 original size:72 final size:72
Alignment explanation
Indices: 41091217--41091471 Score: 269
Period size: 72 Copynumber: 3.5 Consensus size: 72
41091207 AATAACAAAT
* * * * *
41091217 TGCACCCTCCACTGGCCGATAAAATTGACAAATGAGTGTGCCCAACATTGGTCAGTATAACTGAC
1 TGCACCCTGCACTGGTCGATAAAATCGAAAAATGAGTGTGCCCAACATTGGTCGGTATAACTGAC
41091282 AAATAAG
66 AAATAAG
* * * * * * *
41091289 TGCACCCTGCACTGGTCGGTAAAATCGAAAAATAAATGTGCCCCATATTGGTTGGTATAACTGAT
1 TGCACCCTGCACTGGTCGATAAAATCGAAAAATGAGTGTGCCCAACATTGGTCGGTATAACTGAC
41091354 AAATAAG
66 AAATAAG
** * * * * **
41091361 TGTGCCCTGCGCTGGTCGATAAAA-CTGAAAAATGAGTGTGCCCAGCACTAGTCGGTATAACCAA
1 TGCACCCTGCACTGGTCGATAAAATC-GAAAAATGAGTGTGCCCAACATTGGTCGGTATAACTGA
41091425 CAAATAAG
65 CAAATAAG
** * * *
41091433 TGCGTCCTGCGCTGGTCGGTAAAATTGAAAAATGAGTGT
1 TGCACCCTGCACTGGTCGATAAAATCGAAAAATGAGTGT
41091472 TCAAAACCAA
Statistics
Matches: 150, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
71 1 0.01
72 149 0.99
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (72 bp):
TGCACCCTGCACTGGTCGATAAAATCGAAAAATGAGTGTGCCCAACATTGGTCGGTATAACTGAC
AAATAAG
Found at i:41095293 original size:46 final size:45
Alignment explanation
Indices: 41095243--41095600 Score: 423
Period size: 46 Copynumber: 8.3 Consensus size: 45
41095233 TGACAAGTGG
** * *
41095243 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGGTAGCTT-AGCTACACTTATCTGATCAAGTGAC
*
41095289 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAA
1 AAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGAC
*
41095335 AAAGTGAT-A-----AG--T-GCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAC
*
41095371 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAA
1 AAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTGAC
41095417 AAAGTGATAA---GT-GC-TA--T--ACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAC
* *
41095453 AAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAG
1 AAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAAGTGAC
41095499 AAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAAGTGAC
* * *
41095545 AAAGTGATAAGTGGTAGCCTGGCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAC
41095589 -AAGTGATAAGTG
1 AAAGTGATAAGTG
41095601 ATCATATGTA
Statistics
Matches: 274, Mismatches: 17, Indels: 45
0.82 0.05 0.13
Matches are distributed among these distances:
36 58 0.21
37 2 0.01
38 1 0.00
39 1 0.00
40 5 0.02
41 1 0.00
42 6 0.02
43 14 0.05
44 6 0.02
45 21 0.08
46 157 0.57
47 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (45 bp):
AAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAC
Found at i:41095352 original size:36 final size:36
Alignment explanation
Indices: 41095311--41095465 Score: 184
Period size: 36 Copynumber: 4.0 Consensus size: 36
41095301 GGTAGCTTTA
41095311 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
41095347 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
41095392 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
41095429 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
41095465 G
1 G
41095466 TTAGCCTTAG
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
36 65 0.63
37 2 0.02
40 2 0.02
42 2 0.02
45 2 0.02
46 30 0.29
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:41095407 original size:82 final size:82
Alignment explanation
Indices: 41095265--41095600 Score: 471
Period size: 82 Copynumber: 4.0 Consensus size: 82
41095255 AATAGCTTCG
*
41095265 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
41095330 GTGAAAAAGTGATAAGT
66 GTGAAAAAGTGATAAGT
*
41095347 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
41095412 GTGAAAAAGTGATAAGT
66 GTGAAAAAGTGATAAGT
* * *
41095429 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
*
41095494 GTGAGAAAGTGATAAGTGGTAGCCTT
66 GTGAAAAAGTGAT-A-----AG---T
* *
41095520 AGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTGGCTACACTTATCTGATC-
1 -GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCA
* *
41095583 AG-GGACAAGTGATAAGT
65 AGTGAAAAAGTGATAAGT
41095600 G
1 G
41095601 ATCATATGTA
Statistics
Matches: 230, Mismatches: 14, Indels: 23
0.86 0.05 0.09
Matches are distributed among these distances:
79 1 0.00
80 1 0.00
82 153 0.67
83 3 0.01
88 3 0.01
89 8 0.03
90 2 0.01
91 19 0.08
92 40 0.17
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (82 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
GTGAAAAAGTGATAAGT
Found at i:41095409 original size:128 final size:126
Alignment explanation
Indices: 41095243--41095600 Score: 412
Period size: 128 Copynumber: 2.8 Consensus size: 126
41095233 TGACAAGTGG
** ** *
41095243 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCT
1 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGC-
41095308 TTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGAC
65 -TAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGAC
*
41095371 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAA---GT-GCT
1 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCT
*
41095432 A--T--ACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCA
66 AGCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T-GCTACACTTATCTGATCA
* *
41095493 AGTGAG
121 AGAGAC
*
41095499 AAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCC
1 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAG-C
* * *
41095564 TGGCTACACTTATCTGATC-AG-GGACAAGTGATAAGTG
65 TAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTG
41095601 ATCATATGTA
Statistics
Matches: 196, Mismatches: 15, Indels: 41
0.78 0.06 0.16
Matches are distributed among these distances:
118 26 0.13
119 1 0.01
120 1 0.01
122 2 0.01
124 4 0.02
125 3 0.02
126 1 0.01
127 1 0.01
128 126 0.64
129 2 0.01
131 2 0.01
132 1 0.01
133 2 0.01
134 1 0.01
135 9 0.05
136 2 0.01
137 12 0.06
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (126 bp):
AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCT
AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTACACTTATCTGATCAAGAGAC
Found at i:41111830 original size:24 final size:26
Alignment explanation
Indices: 41111784--41111832 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
41111774 CGAGTTTGTT
41111784 TGTTCTTGTAAATACTTTATTCTTTGC
1 TGTTCTTG-AAATACTTTATTCTTTGC
41111811 TGTTCTTG-AATACTTT-TTCTTT
1 TGTTCTTGAAATACTTTATTCTTT
41111833 TCAAGACACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.27
25 8 0.36
27 8 0.36
ACGTcount: A:0.16, C:0.14, G:0.10, T:0.59
Consensus pattern (26 bp):
TGTTCTTGAAATACTTTATTCTTTGC
Found at i:41112985 original size:44 final size:44
Alignment explanation
Indices: 41112935--41113318 Score: 222
Period size: 44 Copynumber: 8.8 Consensus size: 44
41112925 GATCGCATCT
*
41112935 AGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACT-AAGTAAACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG-AAACA
* **
41112979 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAAGA-AACA
* * ** *
41113024 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG-AAACA
* * * * * *
41113069 A-TCCTATCTCCCTGAAGTTACAGTGGAGCGGA-TTAA-AACCTT
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAAC-A
* * * * * * * * *
41113111 GGATCTTATCTCTCTGAAGTTGTAG-AGAACAGA-T--CGCATCT
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAACA
*
41113152 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACT-AAGTAAACA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG-AAACA
* * **
41113196 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAAACTGAAGATGGC-
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAAGA-AACA
* * ** *
41113240 AGATCTTATCTCCCTGAAGATGCAGTGGAGCAGATTAAAGCCGATA
1 AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG-AAACA
* *
41113286 A-TCTTATCTCCCTAAAGTTGCAGTGGAGTAGAC
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
41113319 CCAAGAAATA
Statistics
Matches: 264, Mismatches: 52, Indels: 48
0.73 0.14 0.13
Matches are distributed among these distances:
40 21 0.08
41 8 0.03
42 3 0.01
43 16 0.06
44 137 0.52
45 72 0.27
46 7 0.03
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGAAACA
Found at i:41113024 original size:217 final size:217
Alignment explanation
Indices: 41112632--41113313 Score: 1105
Period size: 217 Copynumber: 3.1 Consensus size: 217
41112622 TCGGTGGCCA
* * *
41112632 ATAATCATATCTCCCTTAAGTTGCAGTGGAGCAGATTAAAACCTTGGATCTTACCTCTCTGAAGT
1 ATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTACCTCTCTGAAGT
* * * *
41112697 TGCAAAGAGCAAATCGCATCTAGTCTTATCTCCCTAAAATTGCAGTGGAGCAGACTAAGTAAACA
66 TGCAAAAAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
* * *
41112762 ATTCTTATCCTCCTGAAGTTGCAGTGAGACAGACTGAAGATGGCAAATCTTATATCCCTGAAGTT
131 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
* *
41112827 GCAGTAGAGCAGATTAAAGCTG
196 GCAGTGGAGCAGATTAAAGCCG
* *
41112849 ATAATCCTATTTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTACCTCTCTAAAGT
1 ATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTACCTCTCTGAAGT
* * *
41112914 TACAAAAAGCTGATCGCATCTAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
66 TGCAAAAAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
41112979 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
131 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
41113044 GCAGTGGAGCAGATTAAAGCCG
196 GCAGTGGAGCAGATTAAAGCCG
* * *
41113066 ATAATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTGAAGT
1 ATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTACCTCTCTGAAGT
* * *
41113131 TGTAGAGAA-CAGATCGCATCTAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAAC
66 TGCA-AAAAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAAC
* * *
41113195 AAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAAACTGAAGATGGCAGATCTTATCTCCCTGAAGA
130 AAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGT
41113260 TGCAGTGGAGCAGATTAAAGCCG
195 TGCAGTGGAGCAGATTAAAGCCG
*
41113283 ATAATCTTATCTCCCTAAAGTTGCAGTGGAG
1 ATAATCCTATCTCCCTAAAGTTGCAGTGGAG
41113314 TAGACCCAAG
Statistics
Matches: 430, Mismatches: 34, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
217 427 0.99
218 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (217 bp):
ATAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTACCTCTCTGAAGT
TGCAAAAAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACA
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTT
GCAGTGGAGCAGATTAAAGCCG
Found at i:41119144 original size:12 final size:13
Alignment explanation
Indices: 41119116--41119146 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
41119106 ACATATCTTT
41119116 CAATTTAAAACTC
1 CAATTTAAAACTC
41119129 CAATTTAAAA-TC
1 CAATTTAAAACTC
41119141 CAATTT
1 CAATTT
41119147 CACTATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.35
Consensus pattern (13 bp):
CAATTTAAAACTC
Found at i:41131293 original size:50 final size:52
Alignment explanation
Indices: 41131226--41131332 Score: 148
Period size: 50 Copynumber: 2.1 Consensus size: 52
41131216 AAAATATAAG
* *
41131226 AAATATATAAATCATAAAACTTCAAAAAAAT-TAATGTATATATATAAATTGA
1 AAATATATAAATCATAAAA-TTCAAAAAAATATAAAGAATATATATAAATTGA
* *
41131278 AAATATA-AAAT-ATAAAATTGAAATAAATATAAAGAATATATATAAATTGA
1 AAATATATAAATCATAAAATTCAAAAAAATATAAAGAATATATATAAATTGA
41131328 AAATA
1 AAATA
41131333 AAATAACAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
49 9 0.18
50 30 0.60
51 4 0.08
52 7 0.14
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (52 bp):
AAATATATAAATCATAAAATTCAAAAAAATATAAAGAATATATATAAATTGA
Found at i:41131333 original size:24 final size:23
Alignment explanation
Indices: 41131263--41131335 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 23
41131253 AAATTAATGT
*
41131263 ATATATATAAATTGAAAATATAA
1 ATATATATAAATTGAAAATAAAA
41131286 A-ATATA-AAATTGAAATAAATATAAAGA
1 ATATATATAAATTG----AAA-ATAAA-A
41131313 ATATATATAAATTGAAAATAAAA
1 ATATATATAAATTGAAAATAAAA
41131336 TAACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 16
0.71 0.02 0.28
Matches are distributed among these distances:
21 6 0.15
22 5 0.12
23 2 0.05
24 5 0.12
25 6 0.15
26 4 0.10
27 2 0.05
28 5 0.12
29 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (23 bp):
ATATATATAAATTGAAAATAAAA
Found at i:41131646 original size:23 final size:23
Alignment explanation
Indices: 41131615--41131663 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
41131605 GACTATCTTT
*
41131615 TTTGTATATTTTTTTA-ATTTTA
1 TTTGTATATATTTTTAGATTTTA
41131637 TTTGTTATATATTTTTAGATTTTA
1 TTTG-TATATATTTTTAGATTTTA
41131661 TTT
1 TTT
41131664 TTAAAAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.17
23 11 0.46
24 9 0.38
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (23 bp):
TTTGTATATATTTTTAGATTTTA
Found at i:41133320 original size:29 final size:31
Alignment explanation
Indices: 41133273--41133340 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
41133263 TTGATAATTT
*
41133273 AGAATTTAGTTATTATAC-TTTT-ACTTCCA
1 AGAATTTAGTTATTATACTTTTTAAATTCCA
*
41133302 AGAATTTAGTT-TCTTTACTTTTTAAATTCCA
1 AGAATTTAGTTAT-TATACTTTTTAAATTCCA
41133333 A-AATTTAG
1 AGAATTTAG
41133341 GTTCAACTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 15 0.44
30 11 0.32
31 7 0.21
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (31 bp):
AGAATTTAGTTATTATACTTTTTAAATTCCA
Found at i:41137292 original size:16 final size:16
Alignment explanation
Indices: 41137245--41137296 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
41137235 TTCGCTGTAT
* *
41137245 TGGAATAGAGGCATAA
1 TGGAATAGAGACGTAA
41137261 TGGAATAGAGACGTAA
1 TGGAATAGAGACGTAA
* **
41137277 TGGGATAGAGGTGTAA
1 TGGAATAGAGACGTAA
41137293 TGGA
1 TGGA
41137297 TTATGCTTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.37, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGACGTAA
Found at i:41138016 original size:14 final size:15
Alignment explanation
Indices: 41137967--41138018 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
41137957 ATAAAATATA
41137967 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
41137982 TATTAAATATATTAT
1 AATTAAATATATTAT
41137997 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
41138010 AATTTAATA
1 AATTAAATA
41138019 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:41138068 original size:61 final size:60
Alignment explanation
Indices: 41138003--41138194 Score: 157
Period size: 61 Copynumber: 3.2 Consensus size: 60
41137993 TTATAATTAA
**
41138003 AATATATAATTTAATAAAATTCTTAATAATTAA-TATTCTTATATGAATTTACCCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAA-TAATTATTCTTATAT-AATTTACTAAAATCAT
* * * * * * *
41138064 AATATATGATGCT-ATAAAATATAAATTAA-CATAATTATTATTAGGTAT-ATTGTAATTAAA--
1 AATATATAAT-TTAATAAAAT-T--CTTAATAATAATTATTCTTA--TATAATT-TACTAAAATC
41138124 A-
59 AT
41138125 AATATATAATTTAATAAAATTCTTAAT-ATAATTATTCTTATATTAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATAATTATTCTTATA-TAATTTACTAAAATCAT
41138185 AATATATAAT
1 AATATATAAT
41138195 AATATAAAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
56 2 0.02
57 7 0.07
58 19 0.19
59 1 0.01
60 12 0.12
61 32 0.31
62 6 0.06
63 11 0.11
64 9 0.09
65 3 0.03
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATAATAATTATTCTTATATAATTTACTAAAATCAT
Found at i:41138226 original size:121 final size:120
Alignment explanation
Indices: 41137942--41138207 Score: 374
Period size: 120 Copynumber: 2.2 Consensus size: 120
41137932 TCTTGATTGG
* * *
41137942 ATAATATATGATACTATAAAATATAAATTAACATAATTATTATTAAATATATTATAATTAAAATA
1 ATAATATATAATAATATAAAAAATAAATTAACATAATTATTATTAAATATATTATAATTAAAATA
*
41138007 TATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACCCAAATC
66 TATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACCAAAATC
* ** * ** *
41138062 ATAATATATGATGCTATAAAATATAAATTAACATAATTATTATTAGGTATATTGTAATTAAAAAA
1 ATAATATATAATAATATAAAAAATAAATTAACATAATTATTATTAAATATATTATAATT--AAAA
* *
41138127 TATATAATTTAATAAAATTCTTAAT-A-TAATTATTCTTATATTAATTTACTAAAATC
64 TATATAATTTAATAAAATTCTTAATAATTAA-TATTCTTATATGAATTTACCAAAATC
41138183 ATAATATATAATAATATAAAAAATA
1 ATAATATATAATAATATAAAAAATA
41138208 TTTAATCTCA
Statistics
Matches: 132, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
120 58 0.44
121 45 0.34
122 29 0.22
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (120 bp):
ATAATATATAATAATATAAAAAATAAATTAACATAATTATTATTAAATATATTATAATTAAAATA
TATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACCAAAATC
Found at i:41138610 original size:77 final size:77
Alignment explanation
Indices: 41138483--41138644 Score: 315
Period size: 77 Copynumber: 2.1 Consensus size: 77
41138473 ATTTTTTGTC
*
41138483 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATCTTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATATTTGAACTTGAAATATATAAAATT
41138548 TTATTGACATAA
66 TTATTGACATAA
41138560 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATATTTGAACTTGAAATATATAAAATT
1 CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATATTTGAACTTGAAATATATAAAATT
41138625 TTATTGACATAA
66 TTATTGACATAA
41138637 CACTTTAA
1 CACTTTAA
41138645 GATTATCTCA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 84 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.41
Consensus pattern (77 bp):
CACTTTAATAATTGAACTTGACAATTAGATATATTTTAATATTTGAACTTGAAATATATAAAATT
TTATTGACATAA
Found at i:41142311 original size:20 final size:21
Alignment explanation
Indices: 41142286--41142325 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
41142276 CAATGAACTA
41142286 AGCCC-AATTAAGCC-AACCCC
1 AGCCCAAATT-AGCCTAACCCC
41142306 AGCCCAAATTAGCCTAACCC
1 AGCCCAAATTAGCCTAACCC
41142326 AAACCCGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.35, C:0.42, G:0.10, T:0.12
Consensus pattern (21 bp):
AGCCCAAATTAGCCTAACCCC
Found at i:41143589 original size:16 final size:17
Alignment explanation
Indices: 41143552--41143594 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
41143542 TATTTTAAAC
41143552 CTTTATATATAATATAT
1 CTTTATATATAATATAT
*
41143569 GTTTATATAT-ATATCA-
1 CTTTATATATAATAT-AT
41143585 CTTTATATAT
1 CTTTATATAT
41143595 GTTATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (17 bp):
CTTTATATATAATATAT
Found at i:41143631 original size:16 final size:18
Alignment explanation
Indices: 41143598--41143634 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
41143588 TATATATGTT
*
41143598 ATTTTAAAATTTTGTTTA
1 ATTTTAAAATTGTGTTTA
41143616 ATTTT-AAATTGT-TTTA
1 ATTTTAAAATTGTGTTTA
41143632 ATT
1 ATT
41143635 CCAATTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATTTTAAAATTGTGTTTA
Found at i:41143732 original size:26 final size:26
Alignment explanation
Indices: 41143703--41143763 Score: 95
Period size: 26 Copynumber: 2.3 Consensus size: 26
41143693 ATAAGACTAA
* *
41143703 TTATTTTAAGTTACTTTATATATTAT
1 TTATTTTAAGTTACTTTACATATTAC
*
41143729 TTATTTTAAGTTATTTTACATATTAC
1 TTATTTTAAGTTACTTTACATATTAC
41143755 TTATTTTAA
1 TTATTTTAA
41143764 AATTAACCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (26 bp):
TTATTTTAAGTTACTTTACATATTAC
Found at i:41145199 original size:28 final size:29
Alignment explanation
Indices: 41145126--41145205 Score: 81
Period size: 28 Copynumber: 2.7 Consensus size: 29
41145116 TTAATATAAC
* *
41145126 ATTTGGTATATGAACTTGACACTTTTTCCTA
1 ATTTGGTACATAAACTTGACAC--TTTCCTA
* ** *
41145157 ATTTAGTACCCAAACTTGACAC-TTCTTA
1 ATTTGGTACATAAACTTGACACTTTCCTA
41145185 ATTTGGTACATAAACTTGACA
1 ATTTGGTACATAAACTTGACA
41145206 ATTTTTTAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
28 23 0.57
31 17 0.43
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (29 bp):
ATTTGGTACATAAACTTGACACTTTCCTA
Found at i:41145802 original size:59 final size:60
Alignment explanation
Indices: 41145691--41145804 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 60
41145681 ATTGAACCTA
*
41145691 AAAAATAGCTTAGGTACCAAACTAGGGGAAAAATACCAAGTTCAAGTACCAAATTGGGCCT
1 AAAAATAGCTTAGGTACCAAACTA-GGGAAAAATACCAAGTTAAAGTACCAAATTGGGCCT
* * **
41145752 AAAAA-AGTTTAGGTACCAAATTA-GGAAAAAGTGTCAAGTTAAAGTACCAAATT
1 AAAAATAGCTTAGGTACCAAACTAGGGAAAAA-TACCAAGTTAAAGTACCAAATT
41145805 TGACAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 7 0.15
59 19 0.40
60 16 0.34
61 5 0.11
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.22
Consensus pattern (60 bp):
AAAAATAGCTTAGGTACCAAACTAGGGAAAAATACCAAGTTAAAGTACCAAATTGGGCCT
Found at i:41145819 original size:60 final size:59
Alignment explanation
Indices: 41145690--41145816 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 59
41145680 AATTGAACCT
* * * *
41145690 AAAAAATAGCTTAGGTACCAAACTAGGGGAAAAATACCAAGTTCAAGTACCAAATTGGGC
1 AAAAAAAAGTTTAGGTACCAAACTA-GGGAAAAATACCAAGTTAAAGTACCAAATTGGAC
** * ** *
41145750 CTAAAAAAGTTTAGGTACCAAATTA-GGAAAAAGTGTCAAGTTAAAGTACCAAATTTGAC
1 AAAAAAAAGTTTAGGTACCAAACTAGGGAAAAA-TACCAAGTTAAAGTACCAAATTGGAC
41145809 AAAAAAAA
1 AAAAAAAA
41145817 AGTGTAACGA
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
58 7 0.13
59 27 0.50
60 20 0.37
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.20
Consensus pattern (59 bp):
AAAAAAAAGTTTAGGTACCAAACTAGGGAAAAATACCAAGTTAAAGTACCAAATTGGAC
Found at i:41146241 original size:20 final size:19
Alignment explanation
Indices: 41146197--41146241 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
41146187 CAAATAAATA
* *
41146197 AAAAAGAAAAAGGAAATAG
1 AAAAAGAAAAAAGAAACAG
41146216 AAAAAGAAAGAAAGAAACAG
1 AAAAAGAAA-AAAGAAACAG
*
41146236 AGAAAG
1 AAAAAG
41146242 TCAAACAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAAAAGAAACAG
Found at i:41146272 original size:21 final size:21
Alignment explanation
Indices: 41146214--41146272 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
41146204 AAAAGGAAAT
41146214 AGAAAAAGAAAGAAAGAAACAG
1 AGAAAAAGAAAGAAA-AAACAG
*** * * *
41146236 AGAAAGTCAAACAAAACACGG
1 AGAAAAAGAAAGAAAAAACAG
41146257 AGAAAAAGAAAGAAAA
1 AGAAAAAGAAAGAAAA
41146273 GAAAGAAGGA
Statistics
Matches: 27, Mismatches: 10, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
21 16 0.59
22 11 0.41
ACGTcount: A:0.69, C:0.08, G:0.20, T:0.02
Consensus pattern (21 bp):
AGAAAAAGAAAGAAAAAACAG
Found at i:41147225 original size:40 final size:39
Alignment explanation
Indices: 41147102--41147236 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 39
41147092 GACTTCGAGT
* *
41147102 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAA-TTATTACTTCGGATT-ATC
* * * * *
41147143 CGATGAGGCACTGAGTGCCAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAATTATTACTTCGGATTATC
* * *
41147180 TGATGAGACACTAGGTGTCAACTTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAA-TTATTACTTCGGATTATC
*
41147220 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
41147237 CCAAACTGGT
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
37 17 0.23
38 10 0.14
39 2 0.03
40 26 0.36
41 18 0.25
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAATTATTACTTCGGATTATC
Found at i:41159114 original size:126 final size:125
Alignment explanation
Indices: 41158902--41159280 Score: 537
Period size: 125 Copynumber: 3.0 Consensus size: 125
41158892 TTTAGGGTTT
* * * *
41158902 TAGGTC-CTAGAATAAATAATTTTGAGTTGACGTTTCTGATCAAATAGTATAAAATTGCTTCTAA
1 TAGGTCAC-AGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* *
41158966 CAGGATGCTATTTGAGAAGAATTTATAAAATCGCACCCTCGTGGACGCGCTTTTGCTACAG
65 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAG
*** * *
41159027 TAGGTCACAGAAGAAATAATTATTTTTTTGACGTTTTTGAGCAAATAGTATAAAATCGCTTGTAG
1 TAGGTCACAGAAGAAATAATT-TTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAG
* *
41159092 CAGGATGCTATTTGAGAAGAATTTGTGATATCGCACCCTCGTGGACGCGCTTTTGCTACAA
65 CAGGATGCTATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAG
* * * *
41159153 CAGGTCCCGGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTGTAAAATCGCTTCTAGC
1 TAGGTCACAGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * *
41159218 AGGATGCTATTTGAGAAGAATTTGTGAAATCG-AGTCGTCGTGGACGCGATTTTGCTACAG
66 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCA-CCCTCGTGGACGCGCTTTTGCTACAG
41159278 TAG
1 TAG
41159281 CATGTTTGGG
Statistics
Matches: 223, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
124 1 0.00
125 111 0.50
126 111 0.50
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (125 bp):
TAGGTCACAGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AGGATGCTATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAG
Found at i:41159241 original size:125 final size:125
Alignment explanation
Indices: 41158910--41159276 Score: 529
Period size: 126 Copynumber: 2.9 Consensus size: 125
41158900 TTTAGGTCCT
* * * *
41158910 AGAATAAATAATTTTGAGTTGACGTTTCTGATCAAATAGTATAAAATTGCTTCTAACAGGATGCT
1 AGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
* * **
41158975 ATTTGAGAAGAATTTATAAAATCGCACCCTCGTGGACGCGCTTTTGCTACAGTAGGTCAC
66 ATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAACAGGTCAC
*** * *
41159035 AGAAGAAATAATTATTTTTTTGACGTTTTTGAGCAAATAGTATAAAATCGCTTGTAGCAGGATGC
1 AGAAGAAATAATT-TTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGC
* *
41159100 TATTTGAGAAGAATTTGTGATATCGCACCCTCGTGGACGCGCTTTTGCTACAACAGGTCCC
65 TATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAACAGGTCAC
* *
41159161 GGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTGTAAAATCGCTTCTAGCAGGATGCT
1 AGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
* * *
41159226 ATTTGAGAAGAATTTGTGAAATCG-AGTCGTCGTGGACGCGATTTTGCTACA
66 ATTTGAGAAGAATTTGTGAAATCGCA-CCCTCGTGGACGCGCTTTTGCTACA
41159277 GTAGCATGTT
Statistics
Matches: 214, Mismatches: 26, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
124 1 0.00
125 103 0.48
126 110 0.51
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (125 bp):
AGAAGAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCT
ATTTGAGAAGAATTTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTACAACAGGTCAC
Found at i:41162507 original size:116 final size:116
Alignment explanation
Indices: 41162303--41162527 Score: 337
Period size: 116 Copynumber: 1.9 Consensus size: 116
41162293 ATTATTTGAT
* *
41162303 AATTGTATTAATTGTTACTAAAATTATCAAATAGTATAAATTTATTAATTGTTAGTACCAGTCAA
1 AATTGTATTAATGGTTACTAAAACTATCAAATAGTATAAATTTATTAATTGTTAGTACCAGTCAA
*
41162368 AACATTTTACCAAATCTAACATTATATGAATGTAAAATTATTAAGTCAAAA
66 AACATTTTACCAAATCTAACATTACATGAATGTAAAATTATTAAGTCAAAA
* *
41162419 AATTGTGTTAATGGTTAGTAAAACTATCAAATTATGTA-AAA-TTATTAATTGTTAGTACCAGTC
1 AATTGTATTAATGGTTACTAAAACTATCAAA-TA-GTATAAATTTATTAATTGTTAGTACCAGTC
* * * *
41162482 AAAACATTTTTCCAAATCTAACATTACGTGAATGTAATATTGTTAA
64 AAAACATTTTACCAAATCTAACATTACATGAATGTAAAATTATTAA
41162528 CTTAGTTTAG
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
116 90 0.92
117 5 0.05
118 3 0.03
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (116 bp):
AATTGTATTAATGGTTACTAAAACTATCAAATAGTATAAATTTATTAATTGTTAGTACCAGTCAA
AACATTTTACCAAATCTAACATTACATGAATGTAAAATTATTAAGTCAAAA
Found at i:41162564 original size:23 final size:23
Alignment explanation
Indices: 41162529--41162587 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
41162519 TATTGTTAAC
* * *
41162529 TTAGTTTAGGGTTTTTAAATAAT
1 TTAGGTTAGGGTTTTGAAATAAA
* *
41162552 TTAGGTTAAGGTTTTGAATTAAA
1 TTAGGTTAGGGTTTTGAAATAAA
41162575 TTAGGTTAGGGTT
1 TTAGGTTAGGGTT
41162588 AGTGTCTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (23 bp):
TTAGGTTAGGGTTTTGAAATAAA
Found at i:41162600 original size:29 final size:29
Alignment explanation
Indices: 41162555--41162797 Score: 198
Period size: 29 Copynumber: 8.3 Consensus size: 29
41162545 AAATAATTTA
* *
41162555 GGTTAAGGTTTTGAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
41162584 GGTTAGTGTCTTTAATTAAATTAAGATTAG
1 GGTTAGGGTTTTTAATTAAATT-AGGTTAG
*
41162614 AGTTTTTAGGGTTTTTAATTAAATTAGGTTAG
1 -G--GTTAGGGTTTTTAATTAAATTAGGTTAG
* *
41162646 GGTTAGGGTATTTAATT--A--GGGTTTA-
1 GGTTAGGGTTTTTAATTAAATTAGG-TTAG
41162671 GGTTAGGGTTTTTAATTAAATTAGGATTAG
1 GGTTAGGGTTTTTAATTAAATTAGG-TTAG
41162701 GGTTTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG---TTAGGGTTTTTAATTAAATTAGGTTAG
* ** *
41162733 GGTTAGAGTTTTTAATTAAGGTA-TTTA-
1 GGTTAGGGTTTTTAATTAAATTAGGTTAG
* * *
41162760 -ATTA-GGTTTTTGAATTAATTTAAGTTAG
1 GGTTAGGGTTTTT-AATTAAATTAGGTTAG
41162788 GGTTAGGGTT
1 GGTTAGGGTT
41162798 AGGGTTAGGG
Statistics
Matches: 171, Mismatches: 25, Indels: 35
0.74 0.11 0.15
Matches are distributed among these distances:
25 24 0.14
26 14 0.08
27 5 0.03
28 3 0.02
29 58 0.34
30 12 0.07
31 2 0.01
32 12 0.07
33 41 0.24
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.46
Consensus pattern (29 bp):
GGTTAGGGTTTTTAATTAAATTAGGTTAG
Found at i:41162707 original size:25 final size:23
Alignment explanation
Indices: 41162619--41162708 Score: 81
Period size: 24 Copynumber: 3.5 Consensus size: 23
41162609 ATTAGAGTTT
41162619 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
**
41162642 TTAGGGTTAGGGTATTTAATTAGGGTTTAGG
1 TTAGGG-T----T-TTTAATTA--AATTAGG
41162673 TTAGGGTTTTTAATTAAATTAGG
1 TTAGGGTTTTTAATTAAATTAGG
41162696 ATTAGGGTTTTTA
1 -TTAGGGTTTTTA
41162709 GGGTTTTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
23 11 0.20
24 13 0.24
25 8 0.15
26 1 0.02
28 1 0.02
29 8 0.15
30 1 0.02
31 11 0.20
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (23 bp):
TTAGGGTTTTTAATTAAATTAGG
Found at i:41162754 original size:25 final size:25
Alignment explanation
Indices: 41162619--41162708 Score: 85
Period size: 25 Copynumber: 3.5 Consensus size: 25
41162609 ATTAGAGTTT
41162619 TTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATT--A--AGGTTAGGG
* *
41162648 TTAGGGTATTTAATTAGGGTTTA-GG
1 TTAGGGTTTTTAATTAAGG-TTAGGG
* *
41162673 TTAGGGTTTTTAATTAA-ATTAGGA
1 TTAGGGTTTTTAATTAAGGTTAGGG
41162697 TTAGGGTTTTTA
1 TTAGGGTTTTTA
41162709 GGGTTTTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
23 3 0.06
24 13 0.25
25 19 0.36
26 3 0.06
27 1 0.02
29 14 0.26
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.47
Consensus pattern (25 bp):
TTAGGGTTTTTAATTAAGGTTAGGG
Found at i:41162768 original size:87 final size:87
Alignment explanation
Indices: 41162533--41162791 Score: 289
Period size: 87 Copynumber: 3.0 Consensus size: 87
41162523 GTTAACTTAG
* * * * * * * *
41162533 TTTAGGGTTTTTAAATAATTTAGGTTAAGGTTTTGA--ATTAAATTAGG--TTAGGGTTAGTGTC
1 TTTAGGGTTTTTAATTAAATTAGGTT-AGGGTTAGAGTATTTAATTAGGATTTA-GATTAGGGTT
*
41162594 TTTAATTAAATTAAGATTAGAGTT
64 TTTAATTAAATTAAGATTAGGGTT
* * *
41162618 TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTATTTAATTAGGGTTTAGGTTAGGGTTTT
1 TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGAGTATTTAATTAGGATTTAGATTAGGGTTTT
*
41162683 TAATTAAATTAGGATTAGGGTT
66 TAATTAAATTAAGATTAGGGTT
*
41162705 TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAGGTATTTA-ATTA-GGTT
1 TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGAGTATTTAATT-AGG-ATTTAGATTAGGGTT
*
41162768 TTTGAATTAATTTAAG-TTAGGGTT
64 TTT-AATTAAATTAAGATTAGGGTT
41162792 AGGGTTAGGG
Statistics
Matches: 151, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
84 6 0.04
85 24 0.16
86 10 0.07
87 88 0.58
88 19 0.13
89 4 0.03
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (87 bp):
TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGAGTATTTAATTAGGATTTAGATTAGGGTTTT
TAATTAAATTAAGATTAGGGTT
Found at i:41162794 original size:6 final size:6
Alignment explanation
Indices: 41162783--41162809 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41162773 ATTAATTTAA
41162783 GTTAGG GTTAGG GTTAGG GTTAGG GTT
1 GTTAGG GTTAGG GTTAGG GTTAGG GTT
41162810 TTTAATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.48, T:0.37
Consensus pattern (6 bp):
GTTAGG
Found at i:41162840 original size:42 final size:42
Alignment explanation
Indices: 41162794--41162940 Score: 224
Period size: 42 Copynumber: 3.4 Consensus size: 42
41162784 TTAGGGTTAG
41162794 GGTTAGGGTTAGGGTTTTTAATTAGGGTTTTGAATTAATTTA
1 GGTTAGGGTTAGGGTTTTTAATTAGGGTTTTGAATTAATTTA
41162836 GGTTAGGGTTAGGGTTTTTAATTAGGG-TTTGAATTAATTTAGGTTA
1 GGTTAGGGTTAGGGTTTTTAATTAGGGTTTTGAATTAA--T---TTA
41162882 GGGTTAGGGTTAGGGTTTTTAATTAGGGTTTTGAATTAATTTA
1 -GGTTAGGGTTAGGGTTTTTAATTAGGGTTTTGAATTAATTTA
*
41162925 GGTTATGGTTAGGGTT
1 GGTTAGGGTTAGGGTT
41162941 ACGGTTAGGG
Statistics
Matches: 97, Mismatches: 1, Indels: 14
0.87 0.01 0.12
Matches are distributed among these distances:
41 10 0.10
42 42 0.43
43 4 0.04
46 4 0.04
47 27 0.28
48 10 0.10
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (42 bp):
GGTTAGGGTTAGGGTTTTTAATTAGGGTTTTGAATTAATTTA
Found at i:41162871 original size:54 final size:55
Alignment explanation
Indices: 41162710--41163087 Score: 417
Period size: 55 Copynumber: 7.1 Consensus size: 55
41162700 GGGTTTTTAG
* * *
41162710 GGTTTTT-AATTAAATTAGGTTAGGGTTAGAGTTTTTAATTAAGGTATTTAATTA
1 GGTTTTTGAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAGGGTATTTAATTA
* **** *
41162764 GGTTTTTGAATTAATTTAAGTTAGGGTTAGGG-TTAGGGTTAGGGTTTTTAATTA
1 GGTTTTTGAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAGGGTATTTAATTA
* *
41162818 GGGTTTTGAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAGGGT-TTGAATTA
1 GGTTTTTGAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAGGGTATTTAATTA
* * * *
41162872 --ATTTAG-GTT-A---GGGTTAGGGTTAGGGTTTTTAATTAGGGT-TTTGAATTA
1 GGTTTTTGAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAGGGTATTT-AATTA
* * * *
41162920 --ATTTAG-GTT-ATGGTTAGGGTTACGGTTAGGGTTTTTAATTAGGGTATTTAATTA
1 GGTTTTTGAATTAAT--TTA-GGTTAGGGTTAGGGTTTTTAATTAGGGTATTTAATTA
41162974 GGTTTTTGAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAGGGTATTTAATTA
1 GGTTTTTGAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAGGGTATTTAATTA
* * *
41163029 GGTTTTTGAATTAATTTAGGTTAAGGTTAGGGTATTTAATTAGGGCATTTAATTA
1 GGTTTTTGAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAGGGTATTTAATTA
41163084 GGTT
1 GGTT
41163088 AGAGTTTTTA
Statistics
Matches: 280, Mismatches: 30, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
47 30 0.11
48 15 0.05
50 1 0.00
51 2 0.01
52 4 0.01
54 92 0.33
55 125 0.45
56 7 0.03
57 2 0.01
58 2 0.01
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.47
Consensus pattern (55 bp):
GGTTTTTGAATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAGGGTATTTAATTA
Found at i:41162949 original size:41 final size:41
Alignment explanation
Indices: 41162815--41162960 Score: 150
Period size: 41 Copynumber: 3.4 Consensus size: 41
41162805 GGGTTTTTAA
****
41162815 TTAGGGTTTTGAATTAATTTAGGTTAGGGTTAGGGTTTTTAA
1 TTAGGGTTTTGAATTAATTTAGGTTAGGGTTAGGG-TTACGG
*
41162857 TTAGGG-TTTGAATTAATTTAGGTTAGGGTTAGGGTTAGGG
1 TTAGGGTTTTGAATTAATTTAGGTTAGGGTTAGGGTTACGG
*
41162897 TTTTTAATTAGGGTTTTGAATTAATTTAGGTTATGGTTAGGGTTACGG
1 -------TTAGGGTTTTGAATTAATTTAGGTTAGGGTTAGGGTTACGG
*
41162945 TTAGGGTTTTTAATTA
1 TTAGGGTTTTGAATTA
41162961 GGGTATTTAA
Statistics
Matches: 89, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
40 2 0.02
41 43 0.48
42 6 0.07
47 6 0.07
48 32 0.36
ACGTcount: A:0.23, C:0.01, G:0.29, T:0.47
Consensus pattern (41 bp):
TTAGGGTTTTGAATTAATTTAGGTTAGGGTTAGGGTTACGG
Found at i:41162960 original size:89 final size:90
Alignment explanation
Indices: 41162774--41162960 Score: 279
Period size: 89 Copynumber: 2.1 Consensus size: 90
41162764 GGTTTTTGAA
41162774 TTAATTTAAGTTAGGGTTAGGGTTAGGGTTAGGGTTTTTAATTAGGGTTTTGAATTAATTTAGGT
1 TTAA-TTAAGTTAGGGTTAGGGTTAGGGTTAGGGTTTTTAATTAGGGTTTTGAATTAATTTAGGT
**
41162839 TAGGGTTAGGGTTTTTAATTAGGGTT
65 TAGGGTTAGGGTTTACAATTAGGGTT
* *
41162865 TGAATTAATTTA-GGTTAGGGTTAGGGTTAGGGTTTTTAATTAGGGTTTTGAATTAATTTAGGTT
1 TTAATTAAGTTAGGGTTAGGGTTAGGGTTAGGGTTTTTAATTAGGGTTTTGAATTAATTTAGGTT
* **
41162929 ATGGTTAGGG-TTACGGTTAGGGTTT
66 AGGGTTAGGGTTTACAATTAGGG-TT
41162954 TTAATTA
1 TTAATTA
41162961 GGGTATTTAA
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
88 8 0.09
89 69 0.79
90 7 0.08
91 3 0.03
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.46
Consensus pattern (90 bp):
TTAATTAAGTTAGGGTTAGGGTTAGGGTTAGGGTTTTTAATTAGGGTTTTGAATTAATTTAGGTT
AGGGTTAGGGTTTACAATTAGGGTT
Found at i:41163073 original size:13 final size:13
Alignment explanation
Indices: 41162945--41163085 Score: 70
Period size: 13 Copynumber: 10.4 Consensus size: 13
41162935 AGGGTTACGG
*
41162945 TTAGGGTTTTTAA
1 TTAGGGTATTTAA
41162958 TTAGGGTATTTAA
1 TTAGGGTATTTAA
*
41162971 TTA-GGTTTTTGAA
1 TTAGGGTATTT-AA
*** * *
41162984 TTAATTTAGGTTAGGG
1 TTAGGGTA-TTTA--A
*
41163000 TTAGGGTTTTTAA
1 TTAGGGTATTTAA
41163013 TTAGGGTATTTAA
1 TTAGGGTATTTAA
*
41163026 TTA-GGTTTTTGAA
1 TTAGGGTATTT-AA
*** *
41163039 TTAATTTAGGTTAA
1 TTAGGGTA-TTTAA
41163053 GGTTAGGGTATTTAA
1 --TTAGGGTATTTAA
*
41163068 TTAGGGCATTTAA
1 TTAGGGTATTTAA
41163081 TTAGG
1 TTAGG
41163086 TTAGAGTTTT
Statistics
Matches: 94, Mismatches: 24, Indels: 20
0.68 0.17 0.14
Matches are distributed among these distances:
12 12 0.13
13 57 0.61
14 5 0.05
15 11 0.12
16 9 0.10
ACGTcount: A:0.27, C:0.01, G:0.25, T:0.48
Consensus pattern (13 bp):
TTAGGGTATTTAA
Found at i:41163127 original size:25 final size:25
Alignment explanation
Indices: 41163093--41163210 Score: 122
Period size: 25 Copynumber: 4.9 Consensus size: 25
41163083 AGGTTAGAGT
41163093 TTTTATTACATCAAATAAATTTCTA
1 TTTTATTACATCAAATAAATTTCTA
* *
41163118 TTTTACTACATCAAAT-AATATC-A
1 TTTTATTACATCAAATAAATTTCTA
** *
41163141 --AAATAAC-TCGAAA-AAATTTCTA
1 TTTTATTACATC-AAATAAATTTCTA
*
41163163 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAATTTCTA
41163188 TTTTATTACATCAAATAATATTT
1 TTTTATTACATCAAATAA-ATTT
41163211 AAATACGGCA
Statistics
Matches: 73, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.03
21 11 0.15
22 1 0.01
23 1 0.01
24 12 0.16
25 43 0.59
26 3 0.04
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (25 bp):
TTTTATTACATCAAATAAATTTCTA
Found at i:41163454 original size:18 final size:18
Alignment explanation
Indices: 41163431--41163465 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41163421 CGGAAAAGGA
*
41163431 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
41163449 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
41163466 AAATGCACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:41164119 original size:7 final size:7
Alignment explanation
Indices: 41164109--41164140 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
41164099 TTATATACAT
41164109 AATACTA
1 AATACTA
41164116 AATACTA
1 AATACTA
41164123 AATACTA
1 AATACTA
41164130 AATACTA
1 AATACTA
41164137 AATA
1 AATA
41164141 TCAATCGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:41165339 original size:51 final size:51
Alignment explanation
Indices: 41165283--41165399 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 51
41165273 TTTTAAAAAT
* * * *
41165283 GGAAATTTAGAGAAAATTGAAATTAAATATG-GATTTGAAATAATTTTAGAA
1 GGAAATTGAGAGAAAATTAAAATGAAATATGAG-TTTGAAAGAATTTTAGAA
* *
41165334 GGAAATTGAGAGGAAATTAAAATGAAATATGAGTTTGAGAGAATTTTAGAA
1 GGAAATTGAGAGAAAATTAAAATGAAATATGAGTTTGAAAGAATTTTAGAA
41165385 GGAAATTGAGAGAAA
1 GGAAATTGAGAGAAA
41165400 TTTGGAAAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 57 0.98
52 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.28
Consensus pattern (51 bp):
GGAAATTGAGAGAAAATTAAAATGAAATATGAGTTTGAAAGAATTTTAGAA
Found at i:41165396 original size:22 final size:22
Alignment explanation
Indices: 41165368--41165423 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
41165358 AAATATGAGT
*
41165368 TTGAGAGAATTTTAGAAGGAAA
1 TTGAGAGAATTTTAGAAAGAAA
* *
41165390 TTGAGAGAAATTTGGAAAGAAA
1 TTGAGAGAATTTTAGAAAGAAA
41165412 TTGAGAGGAATT
1 TTGAGA-GAATT
41165424 GAGAGGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 25 0.86
23 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTAGAAAGAAA
Found at i:41165401 original size:10 final size:10
Alignment explanation
Indices: 41165386--41165433 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
41165376 ATTTTAGAAG
41165386 GAAATTGAGA
1 GAAATTGAGA
*
41165396 GAAATTTGGAAA
1 GAAA-TT-GAGA
41165408 GAAATTGAGA
1 GAAATTGAGA
*
41165418 GGAATTGAGA
1 GAAATTGAGA
41165428 GGAAAT
1 -GAAAT
41165434 ATTAGAGAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
10 16 0.52
11 8 0.26
12 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (10 bp):
GAAATTGAGA
Found at i:41165412 original size:51 final size:51
Alignment explanation
Indices: 41165283--41165417 Score: 161
Period size: 51 Copynumber: 2.6 Consensus size: 51
41165273 TTTTAAAAAT
* * *
41165283 GGAAATTTAGAGAAAATTGAAATTAAATATG-GATTTGAAATAATTTTAGAA
1 GGAAATTGAGAG-AAATTGAAATGAAATATGAGATTTGAAAGAATTTTAGAA
* *
41165334 GGAAATTGAGAGGAAATTAAAATGAAATATGAG-TTTGAGAGAATTTTAGAA
1 GGAAATTGAGA-GAAATTGAAATGAAATATGAGATTTGAAAGAATTTTAGAA
41165385 GGAAATTGAGAGAAATTTGGAAA-GAAAT-TGAGA
1 GGAAATTGAGAGAAA-TT-GAAATGAAATATGAGA
41165418 GGAATTGAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
50 8 0.11
51 60 0.82
52 5 0.07
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (51 bp):
GGAAATTGAGAGAAATTGAAATGAAATATGAGATTTGAAAGAATTTTAGAA
Found at i:41166207 original size:37 final size:37
Alignment explanation
Indices: 41166139--41166209 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
41166129 TTTTATTTTT
*
41166139 ATTAAATTATATTTAATAATAATTATATTAAAATATG
1 ATTAAATTATATTTAATAATAATCATATTAAAATATG
* * * *
41166176 ATTAAATTATTTTTTATAATAATCCTGTTAAAAT
1 ATTAAATTATATTTAATAATAATCATATTAAAAT
41166210 TTAATAACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (37 bp):
ATTAAATTATATTTAATAATAATCATATTAAAATATG
Found at i:41166369 original size:23 final size:22
Alignment explanation
Indices: 41166339--41166386 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
41166329 AACATGATAA
*
41166339 TACTATTACAGTTCTATTCCAT
1 TACTATTACAATTCTATTCCAT
* *
41166361 TACTGATTACAATTTTATTCTAT
1 TACT-ATTACAATTCTATTCCAT
41166384 TAC
1 TAC
41166387 AGCGAACCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.48
Consensus pattern (22 bp):
TACTATTACAATTCTATTCCAT
Found at i:41178072 original size:15 final size:16
Alignment explanation
Indices: 41178052--41178083 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
41178042 CGTTTTAAGT
41178052 TTATAATA-TTTTATA
1 TTATAATATTTTTATA
41178067 TTATAATATTTTTATA
1 TTATAATATTTTTATA
41178083 T
1 T
41178084 ATTATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTATAATATTTTTATA
Found at i:41178095 original size:18 final size:17
Alignment explanation
Indices: 41178053--41178095 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
41178043 GTTTTAAGTT
*
41178053 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
41178070 TA-ATATTTTTATATATTA
1 TATA-ATTTTT-TATATTA
41178088 TATAATTT
1 TATAATTT
41178096 AGAACACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 1 0.05
17 7 0.32
18 13 0.59
19 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:41180216 original size:33 final size:34
Alignment explanation
Indices: 41180179--41180251 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 34
41180169 TTTGTACCCC
*
41180179 TTTTGAAAGAACTCTATGAGAGTTAGGG-TTTGT
1 TTTTGAAAGAACTCTATGAGAGTTAGGGTTTTAT
*****
41180212 TTTTGAGTTTGCTCTATGAGAGTTAGGGTTTTAT
1 TTTTGAAAGAACTCTATGAGAGTTAGGGTTTTAT
41180246 TTTTGA
1 TTTTGA
41180252 GGTTTGTGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 23 0.70
34 10 0.30
ACGTcount: A:0.22, C:0.05, G:0.26, T:0.47
Consensus pattern (34 bp):
TTTTGAAAGAACTCTATGAGAGTTAGGGTTTTAT
Found at i:41183282 original size:22 final size:22
Alignment explanation
Indices: 41183257--41183308 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
41183247 GGCCCAAACA
*
41183257 GCCTCTAAAACGCATGGGATGG
1 GCCTATAAAACGCATGGGATGG
41183279 GCCTATAAAACGCATGGGATGG
1 GCCTATAAAACGCATGGGATGG
41183301 GCCTATAA
1 GCCTATAA
41183309 CTGTGCGCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (22 bp):
GCCTATAAAACGCATGGGATGG
Found at i:41187545 original size:11 final size:11
Alignment explanation
Indices: 41187531--41187607 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
41187521 ATAAATATGG
41187531 ATTTGAGAGAA
1 ATTTGAGAGAA
*
41187542 ATTTTGA-AGGA
1 A-TTTGAGAGAA
*
41187553 GTTTGAGAGCAA
1 ATTTGAGAG-AA
41187565 A-TTGAGAGGAA
1 ATTTGAGA-GAA
41187576 ATTT-AGAAGAA
1 ATTTGAG-AGAA
41187587 A-TTGAGAGGAA
1 ATTTGAGA-GAA
41187598 ATTTGAGAGA
1 ATTTGAGAGA
41187608 GGATTAGTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
10 8 0.15
11 29 0.55
12 16 0.30
ACGTcount: A:0.43, C:0.01, G:0.30, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:41187570 original size:33 final size:33
Alignment explanation
Indices: 41187531--41187607 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
41187521 ATAAATATGG
* **
41187531 ATTTGAGAGAAATTTTGAAGGAGTTTGAGAGCAA
1 ATTTGAGAGAAATTTAGAA-GAAATTGAGAGCAA
*
41187565 A-TTGAGAGGAAATTTAGAAGAAATTGAGAGGAA
1 ATTTGAGA-GAAATTTAGAAGAAATTGAGAGCAA
41187598 ATTTGAGAGA
1 ATTTGAGAGA
41187608 GGATTAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 20 0.54
34 17 0.46
ACGTcount: A:0.43, C:0.01, G:0.30, T:0.26
Consensus pattern (33 bp):
ATTTGAGAGAAATTTAGAAGAAATTGAGAGCAA
Found at i:41187574 original size:22 final size:22
Alignment explanation
Indices: 41187531--41187607 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
41187521 ATAAATATGG
41187531 ATTTGAGAGAAATTTTGA-AGG-A
1 ATTTGAGAGAAA--TTGAGAGGAA
*
41187553 GTTTGAGAGCAAATTGAGAGGAA
1 ATTTGAGAG-AAATTGAGAGGAA
41187576 ATTT-AGAAGAAATTGAGAGGAA
1 ATTTGAG-AGAAATTGAGAGGAA
41187598 ATTTGAGAGA
1 ATTTGAGAGA
41187608 GGATTAGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.08
22 33 0.69
23 11 0.23
ACGTcount: A:0.43, C:0.01, G:0.30, T:0.26
Consensus pattern (22 bp):
ATTTGAGAGAAATTGAGAGGAA
Found at i:41198531 original size:17 final size:18
Alignment explanation
Indices: 41198511--41198546 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
41198501 ATTAATAACT
41198511 ATTATTA-AGTGATAATA
1 ATTATTATAGTGATAATA
*
41198528 ATTATTATATTGATAATA
1 ATTATTATAGTGATAATA
41198546 A
1 A
41198547 AAATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (18 bp):
ATTATTATAGTGATAATA
Found at i:41198545 original size:38 final size:37
Alignment explanation
Indices: 41198494--41198571 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 37
41198484 TACTAATACT
* *
41198494 TTATATTATTAAT-AACTATTATTAAGTGATAATAATTA
1 TTATATTATTAATAAAATATTATTAA-T-AAAATAATTA
41198532 TTATATTGA-TAATAAAAATATTATTAATAAAATAATTA
1 TTATATT-ATTAAT-AAAATATTATTAATAAAATAATTA
41198570 TT
1 TT
41198572 TTACTAATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
38 22 0.63
39 2 0.06
40 11 0.31
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (37 bp):
TTATATTATTAATAAAATATTATTAATAAAATAATTA
Found at i:41199534 original size:23 final size:23
Alignment explanation
Indices: 41199504--41199548 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
41199494 TTATTAAATA
* * *
41199504 TTAAAAAATATAATATAAATATT
1 TTAAAAAAAATAAAAAAAATATT
41199527 TTAAAAAAAATAAAAAAAATAT
1 TTAAAAAAAATAAAAAAAATAT
41199549 GGGCGGAGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
TTAAAAAAAATAAAAAAAATATT
Found at i:41201051 original size:22 final size:22
Alignment explanation
Indices: 41201011--41201052 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41201001 CTCATGCTAA
* *
41201011 TTTATTAATCTATATAAATTCC
1 TTTATTAATATATAGAAATTCC
*
41201033 TTTATTAATATATGGAAATT
1 TTTATTAATATATAGAAATT
41201053 AGGAATAAAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (22 bp):
TTTATTAATATATAGAAATTCC
Found at i:41201109 original size:12 final size:11
Alignment explanation
Indices: 41201089--41201119 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
41201079 CTTCATTATT
41201089 TTTTAAATTTA
1 TTTTAAATTTA
41201100 TTTTATAATTTA
1 TTTTA-AATTTA
41201112 TTTTAAAT
1 TTTTAAAT
41201120 AATGATATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:41204420 original size:27 final size:27
Alignment explanation
Indices: 41204366--41204418 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
41204356 TTAAGATGAC
* *
41204366 TATATAAAATTTTCAATAAATAAAAAT
1 TATATAAAATTATAAATAAATAAAAAT
*
41204393 TATATAAAATTAATAAATAGATAAAA
1 TATATAAAATT-ATAAATAAATAAAA
41204419 TTTTAGGTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (27 bp):
TATATAAAATTATAAATAAATAAAAAT
Found at i:41207474 original size:3 final size:3
Alignment explanation
Indices: 41207466--41207505 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
41207456 CTCCATTTCC
41207466 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
41207506 TTGTTAACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:41207917 original size:29 final size:29
Alignment explanation
Indices: 41207884--41207947 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
41207874 AGAAGAAGTA
* *
41207884 TAAAAATATTGCGCCATTTACTCAAAAAT
1 TAAAAATATTGAGCCATTTACTAAAAAAT
* *
41207913 TAAAAGTATTGAGCCATTTATTAAAAAAT
1 TAAAAATATTGAGCCATTTACTAAAAAAT
*
41207942 TGAAAA
1 TAAAAA
41207948 GGAAGGTCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.31
Consensus pattern (29 bp):
TAAAAATATTGAGCCATTTACTAAAAAAT
Found at i:41208506 original size:6 final size:6
Alignment explanation
Indices: 41208452--41208497 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
41208442 TTCCGATTTT
41208452 GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GCCA
1 GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GCCAAA GCCA
41208498 GCCATAGCCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.48, C:0.35, G:0.17, T:0.00
Consensus pattern (6 bp):
GCCAAA
Found at i:41214388 original size:21 final size:21
Alignment explanation
Indices: 41214364--41214406 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
41214354 TAGACAACAC
41214364 ATGGAATATGGATAACATGCA
1 ATGGAATATGGATAACATGCA
41214385 ATGGAATATGGATAACATGCA
1 ATGGAATATGGATAACATGCA
41214406 A
1 A
41214407 GATTTGTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.23
Consensus pattern (21 bp):
ATGGAATATGGATAACATGCA
Found at i:41217353 original size:14 final size:13
Alignment explanation
Indices: 41217334--41217364 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
41217324 TTCTTTCCCT
41217334 TTTCTTTCTTTTTC
1 TTTCTTTC-TTTTC
41217348 TTTCTTTCTTTTC
1 TTTCTTTCTTTTC
41217361 TTTC
1 TTTC
41217365 AAATTTTGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTTTCTTTTC
Found at i:41221522 original size:41 final size:39
Alignment explanation
Indices: 41221407--41221540 Score: 114
Period size: 41 Copynumber: 3.4 Consensus size: 39
41221397 ACCAGTTTGG
* * * * *
41221407 CACCCAATGCCTCATTGAATAATTCGAAGTAATAATTTGA
1 CACCCAGTG-CTCATCGAATAATCCGAAGTAGTAAATTGA
* * *
41221447 CACCTAGTGTCTCATC-AACTAAACCG-A--AGTAAATTGG
1 CACCCAGTG-CTCATCGAA-TAATCCGAAGTAGTAAATTGA
41221484 CACCCAGTGCGTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGC-TCATCGAA-TAATCCGAAGTAGTAAATTGA
41221525 CACCCAGTGTCTCATC
1 CACCCAGTG-CTCATC
41221541 AAATCAAAGT
Statistics
Matches: 74, Mismatches: 13, Indels: 13
0.74 0.13 0.13
Matches are distributed among these distances:
36 1 0.01
37 20 0.27
38 8 0.11
39 4 0.05
40 17 0.23
41 23 0.31
42 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCTCATCGAATAATCCGAAGTAGTAAATTGA
Found at i:41222035 original size:225 final size:225
Alignment explanation
Indices: 41221644--41222095 Score: 904
Period size: 225 Copynumber: 2.0 Consensus size: 225
41221634 CACTTTTCAA
41221644 ATACAACCAATATTCATTTCAATTCAAATAATCAATATATTCAATATATATATCAACTCAATCAA
1 ATACAACCAATATTCATTTCAATTCAAATAATCAATATATTCAATATATATATCAACTCAATCAA
41221709 TATAAATTTAATAAATTCATCATATACTAAATCAATCCATTTCAGTTGCAAAACACAATAATTCT
66 TATAAATTTAATAAATTCATCATATACTAAATCAATCCATTTCAGTTGCAAAACACAATAATTCT
41221774 CACCTCAACACTTACCGTATACATTAAATTGAATTAGAACAATTAACAACTAAATTCAGATTATA
131 CACCTCAACACTTACCGTATACATTAAATTGAATTAGAACAATTAACAACTAAATTCAGATTATA
41221839 GAAATACAAACCGAAAATTTCAAGCTATTC
196 GAAATACAAACCGAAAATTTCAAGCTATTC
41221869 ATACAACCAATATTCATTTCAATTCAAATAATCAATATATTCAATATATATATCAACTCAATCAA
1 ATACAACCAATATTCATTTCAATTCAAATAATCAATATATTCAATATATATATCAACTCAATCAA
41221934 TATAAATTTAATAAATTCATCATATACTAAATCAATCCATTTCAGTTGCAAAACACAATAATTCT
66 TATAAATTTAATAAATTCATCATATACTAAATCAATCCATTTCAGTTGCAAAACACAATAATTCT
41221999 CACCTCAACACTTACCGTATACATTAAATTGAATTAGAACAATTAACAACTAAATTCAGATTATA
131 CACCTCAACACTTACCGTATACATTAAATTGAATTAGAACAATTAACAACTAAATTCAGATTATA
41222064 GAAATACAAACCGAAAATTTCAAGCTATTC
196 GAAATACAAACCGAAAATTTCAAGCTATTC
41222094 AT
1 AT
41222096 CGTCGACTTT
Statistics
Matches: 227, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
225 227 1.00
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.32
Consensus pattern (225 bp):
ATACAACCAATATTCATTTCAATTCAAATAATCAATATATTCAATATATATATCAACTCAATCAA
TATAAATTTAATAAATTCATCATATACTAAATCAATCCATTTCAGTTGCAAAACACAATAATTCT
CACCTCAACACTTACCGTATACATTAAATTGAATTAGAACAATTAACAACTAAATTCAGATTATA
GAAATACAAACCGAAAATTTCAAGCTATTC
Found at i:41222286 original size:20 final size:20
Alignment explanation
Indices: 41222261--41222298 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41222251 TTAAACCAAG
* *
41222261 ACTAATTTTATTTTTTCACA
1 ACTAATTCTATATTTTCACA
41222281 ACTAATTCTATATTTTCA
1 ACTAATTCTATATTTTCA
41222299 TTCAATTTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (20 bp):
ACTAATTCTATATTTTCACA
Done.