Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 53 of 322
Found at i:16506194 original size:17 final size:17
Alignment explanation
Indices: 16506172--16506210 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
16506162 TTTTAAAATG
16506172 AAAACAAATT-AATCTAA
1 AAAAC-AATTGAATCTAA
*
16506189 AAAACAATTGAATCTTA
1 AAAACAATTGAATCTAA
16506206 AAAAC
1 AAAAC
16506211 TTAATGAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.62, C:0.13, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAACAATTGAATCTAA
Found at i:16510396 original size:40 final size:40
Alignment explanation
Indices: 16510319--16510616 Score: 440
Period size: 40 Copynumber: 7.5 Consensus size: 40
16510309 AAACCAAGTA
* *
16510319 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
16510358 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
16510398 CCTTCGGGACCTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
16510438 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
16510478 CCTTCGGGACCTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
16510518 CCTTCGAGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * **
16510558 CCTTCGGGACTTAGCCCAGA-ATTAGTCACTAACACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
16510598 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
16510617 TTATCATCCG
Statistics
Matches: 235, Mismatches: 21, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 15 0.06
40 220 0.94
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:16514176 original size:28 final size:26
Alignment explanation
Indices: 16514145--16514208 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
16514135 AATTACTTGA
* **
16514145 ATACCCCTATGTATGGAAAATTACTGTT
1 ATACCCCTA-G-ATGCAAAATTACCATT
* *
16514173 ATACCTCTAGGTGCAAAATTACCATT
1 ATACCCCTAGATGCAAAATTACCATT
16514199 ATACCCCTAG
1 ATACCCCTAG
16514209 GGTTACTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 21 0.70
27 1 0.03
28 8 0.27
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.31
Consensus pattern (26 bp):
ATACCCCTAGATGCAAAATTACCATT
Found at i:16514378 original size:28 final size:27
Alignment explanation
Indices: 16514313--16514398 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
16514303 AGGAAGTGTC
* *
16514313 CTGGTGGCTATGCCACAATTATCT-AAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
16514340 CTGGTGGCTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTAT
* *
16514368 CTGGTGACTCTGTCACATTATCTGT-T
1 CTGGTGGCTCTGCCACATTATCTGTAT
16514394 CTGGT
1 CTGGT
16514399 AGCCATGCTG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 6 0.11
27 31 0.58
28 16 0.30
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.37
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACATTATCTGTAT
Found at i:16515035 original size:56 final size:56
Alignment explanation
Indices: 16514949--16515124 Score: 352
Period size: 56 Copynumber: 3.1 Consensus size: 56
16514939 ACAAGGGATG
16514949 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
16515005 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
16515061 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
16515117 ATGGGCAA
1 ATGGGCAA
16515125 TAAACTAATA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 120 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:16524005 original size:40 final size:41
Alignment explanation
Indices: 16523946--16524090 Score: 206
Period size: 40 Copynumber: 3.6 Consensus size: 41
16523936 CATTTGAATG
* *
16523946 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGATT
*
16523986 TTATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGATT
* *
16524026 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGATT
* *
16524066 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
16524091 ATTGTGCTTG
Statistics
Matches: 96, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
40 93 0.97
41 3 0.03
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (41 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGATT
Found at i:16524109 original size:80 final size:80
Alignment explanation
Indices: 16523946--16524117 Score: 204
Period size: 80 Copynumber: 2.2 Consensus size: 80
16523936 CATTTGAATG
* * * * *
16523946 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
* *
16524011 TTTATGCGAGTTGAT
66 ATTATGCGAGTGGAT
* *
16524026 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGC
* ** *
16524090 AATTGTGCTTGTGGTT
65 AATTATGCGAGTGGAT
16524106 ATATCC-GGCTAA
1 ATATCCGGGCTAA
16524118 ATTCCGAAGA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 6 0.08
80 70 0.90
81 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
ATTATGCGAGTGGAT
Found at i:16532650 original size:8 final size:8
Alignment explanation
Indices: 16532637--16532669 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
16532627 CTAGATCAGC
16532637 AAAAGCCG
1 AAAAGCCG
16532645 AAAAGCC-
1 AAAAGCCG
16532652 AAAATGCCG
1 AAAA-GCCG
16532661 AAAAGCCG
1 AAAAGCCG
16532669 A
1 A
16532670 TATTTTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 4 0.17
8 15 0.65
9 4 0.17
ACGTcount: A:0.52, C:0.24, G:0.21, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:16540677 original size:3 final size:3
Alignment explanation
Indices: 16540669--16540704 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
16540659 CTGGAAATTG
16540669 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16540705 AAGAAAAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16540726 original size:7 final size:7
Alignment explanation
Indices: 16540716--16540742 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
16540706 AGAAAAAGGT
16540716 AAAACTG
1 AAAACTG
16540723 AAAACTG
1 AAAACTG
16540730 AAAACTG
1 AAAACTG
16540737 AAAACT
1 AAAACT
16540743 ACAAATTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (7 bp):
AAAACTG
Found at i:16541696 original size:18 final size:18
Alignment explanation
Indices: 16541652--16541696 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
16541642 TAGCAGAACT
*
16541652 CATAAAATAAGCAGTATG
1 CATAAAATAAGCAATATG
** *
16541670 CATGTAATAAGCAATTTG
1 CATAAAATAAGCAATATG
16541688 CATAAAATA
1 CATAAAATA
16541697 GGTAGATTAC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (18 bp):
CATAAAATAAGCAATATG
Found at i:16541790 original size:17 final size:16
Alignment explanation
Indices: 16541770--16541832 Score: 72
Period size: 17 Copynumber: 3.7 Consensus size: 16
16541760 CAAATAGCCG
*
16541770 TTCATACTATATAACAT
1 TTCATAC-ACATAACAT
*
16541787 TTCATAACACATAACAG
1 TTCAT-ACACATAACAT
16541804 TTCATACAACATAACAT
1 TTCATAC-ACATAACAT
16541821 TTCATACCACAT
1 TTCATA-CACAT
16541833 CAAAACTCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 2 0.05
17 35 0.88
18 3 0.08
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.32
Consensus pattern (16 bp):
TTCATACACATAACAT
Found at i:16541832 original size:34 final size:34
Alignment explanation
Indices: 16541753--16541832 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 34
16541743 GAGATAATAG
* * * * *
16541753 TTCATACCAAATAGCCGTTCATACTATATAACAT
1 TTCATACCACATAACAGTTCATACAACATAACAT
*
16541787 TTCATAACACATAACAGTTCATACAACATAACAT
1 TTCATACCACATAACAGTTCATACAACATAACAT
16541821 TTCATACCACAT
1 TTCATACCACAT
16541833 CAAAACTCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.30
Consensus pattern (34 bp):
TTCATACCACATAACAGTTCATACAACATAACAT
Found at i:16541843 original size:34 final size:34
Alignment explanation
Indices: 16541771--16541843 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
16541761 AAATAGCCGT
* * **
16541771 TCATACTATATAACATTTCATAACACATAACAGT
1 TCATACAACATAACATTTCATAACACATAACAAC
*
16541805 TCATACAACATAACATTTCATACCACATCAA-AAC
1 TCATACAACATAACATTTCATAACACAT-AACAAC
16541839 TCATA
1 TCATA
16541844 TATTTCAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
34 31 0.94
35 2 0.06
ACGTcount: A:0.45, C:0.25, G:0.01, T:0.29
Consensus pattern (34 bp):
TCATACAACATAACATTTCATAACACATAACAAC
Found at i:16542539 original size:36 final size:36
Alignment explanation
Indices: 16542459--16542546 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
16542449 ACACAATTTG
* * *
16542459 CAAATTAATACAGTTTGCCATATTAATACAAATCAC
1 CAAATTAACACAGTTCGCCATAATAATACAAATCAC
* * *
16542495 CAAATTAACACAGTTCGCCATAATAATATAATTCGC
1 CAAATTAACACAGTTCGCCATAATAATACAAATCAC
* *
16542531 CAAGTTAACACGGTTC
1 CAAATTAACACAGTTC
16542547 ACAATATAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (36 bp):
CAAATTAACACAGTTCGCCATAATAATACAAATCAC
Found at i:16542608 original size:17 final size:17
Alignment explanation
Indices: 16542582--16542624 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
16542572 ACACGGCATT
16542582 GTTTGCACATAAGTAAG
1 GTTTGCACATAAGTAAG
* *
16542599 GTTTGTACATAGGTAAG
1 GTTTGCACATAAGTAAG
*
16542616 GTTTACACA
1 GTTTGCACA
16542625 CAACATACAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (17 bp):
GTTTGCACATAAGTAAG
Found at i:16559290 original size:37 final size:37
Alignment explanation
Indices: 16559226--16559299 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
16559216 TTACAAGCCA
*
16559226 AAATCATTATAAGCCACATCTCATGGCTACAT-ACAAC
1 AAATCATTATAAGCCACATATCATGGCTA-ATCACAAC
16559263 AAATCATTATAAGCCA-ATAT-ATTTGGCTAATCACAAC
1 AAATCATTATAAGCCACATATCA--TGGCTAATCACAAC
16559300 GACATCGATC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
35 1 0.03
36 5 0.15
37 27 0.82
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (37 bp):
AAATCATTATAAGCCACATATCATGGCTAATCACAAC
Found at i:16561510 original size:27 final size:26
Alignment explanation
Indices: 16561456--16561542 Score: 68
Period size: 27 Copynumber: 3.3 Consensus size: 26
16561446 TTAGTTTACC
* * *
16561456 AAATTACTGAAATACCCCC-AATTGTA
1 AAATTAC-CAAATACCCCCGATTTATA
*
16561482 AAATTACCAAAGTACCCCCGGTTTATA
1 AAATTACCAAA-TACCCCCGATTTATA
* * *
16561509 AAACTACCCAAATATCCTCGATTTATA
1 AAATTA-CCAAATACCCCCGATTTATA
*
16561536 GAATTAC
1 AAATTAC
16561543 TGTTTTACCT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
25 3 0.06
26 15 0.31
27 25 0.52
28 5 0.10
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.28
Consensus pattern (26 bp):
AAATTACCAAATACCCCCGATTTATA
Found at i:16561619 original size:27 final size:27
Alignment explanation
Indices: 16561584--16561713 Score: 138
Period size: 27 Copynumber: 4.8 Consensus size: 27
16561574 TTACCCTCGA
* * *
16561584 TTGTGAAATTACTAAAATACCCCTAGT
1 TTGTAAAATTACCAAAATACCCCTAAT
* *
16561611 TTGTAAAATTACCAAAATACCACTAGT
1 TTGTAAAATTACCAAAATACCCCTAAT
* *
16561638 TTGTGAAATTACCGAAATA-CCCTCAAT
1 TTGTAAAATTACCAAAATACCCCT-AAT
*
16561665 TTGTAAAATTACCAAAATACCCTTAAT
1 TTGTAAAATTACCAAAATACCCCTAAT
**
16561692 TTACAAAATTA-CAGAAATACCC
1 TTGTAAAATTACCA-AAATACCC
16561714 TTGACTTTCT
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
26 5 0.06
27 80 0.91
28 3 0.03
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (27 bp):
TTGTAAAATTACCAAAATACCCCTAAT
Found at i:16561701 original size:54 final size:54
Alignment explanation
Indices: 16561589--16561770 Score: 165
Period size: 54 Copynumber: 3.3 Consensus size: 54
16561579 CTCGATTGTG
* ***
16561589 AAATTACTA-AAATACCC-CTAGTTTGTAAAATTACCAAAATACCAC-TAGTTTGTG
1 AAATTAC-AGAAATACCCTC-AATTTGTAAAATTACCAAAATACC-CTTAGTTTACA
* *
16561643 AAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCTTAATTTACA
1 AAATTACAGAAATACCCTCAATTTGTAAAATTACCAAAATACCCTTAGTTTACA
* * * * * *
16561697 AAATTACAGAAATACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACA
1 AAATTACAGAAATACCC-TCAATTTGT-AAAATTACCA-AAATACCCTTAGTTTACA
*
16561753 AAATTACTGAAATACCCT
1 AAATTACAGAAATACCCT
16561771 TGGTTTTTAG
Statistics
Matches: 107, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
53 1 0.01
54 59 0.55
55 9 0.08
56 38 0.36
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (54 bp):
AAATTACAGAAATACCCTCAATTTGTAAAATTACCAAAATACCCTTAGTTTACA
Found at i:16561714 original size:27 final size:27
Alignment explanation
Indices: 16561643--16561771 Score: 118
Period size: 27 Copynumber: 4.7 Consensus size: 27
16561633 CTAGTTTGTG
* * **
16561643 AAATTACCGAAATACCCTCAATTTGTA
1 AAATTACAGAAATACCCTTAATTTACA
16561670 AAATTACCA-AAATACCCTTAATTTACA
1 AAATTA-CAGAAATACCCTTAATTTACA
*
16561697 AAATTACAGAAATACCCTTGACTTT-CTAA
1 AAATTACAGAAATACCCTT-AATTTAC--A
* * **
16561726 AAATTATAGAAATACCATTGGTTTACA
1 AAATTACAGAAATACCCTTAATTTACA
*
16561753 AAATTACTGAAATACCCTT
1 AAATTACAGAAATACCCTT
16561772 GGTTTTTAGA
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.02
27 55 0.65
28 8 0.10
29 19 0.23
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.31
Consensus pattern (27 bp):
AAATTACAGAAATACCCTTAATTTACA
Found at i:16561870 original size:27 final size:27
Alignment explanation
Indices: 16561817--16561894 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
16561807 AAATGACTAA
* *
16561817 AATACCCCTAATA-GGTAAAAAGGCCGT
1 AATACCCCT-ATAGGGTAAAATGACCGT
* *
16561844 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTATAGGGTAAAATGACCGT
*
16561871 AATACCCCTATATGGTAAAATGAC
1 AATACCCCTATAGGGTAAAATGAC
16561895 GAATATGCCA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 3 0.07
27 37 0.90
28 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (27 bp):
AATACCCCTATAGGGTAAAATGACCGT
Found at i:16562776 original size:24 final size:25
Alignment explanation
Indices: 16562705--16562774 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
16562695 AGGAAGTGCT
* * *
16562705 AAAAGGGCTATGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTATCA
16562730 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTATCA
*
16562755 AAAAAGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
16562775 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTATCA
Found at i:16563043 original size:31 final size:31
Alignment explanation
Indices: 16562994--16563076 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
16562984 CGCTTACAGT
16562994 AAAGGCTTCGG-CCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
16563024 AAAGGCTTCGGCCCAGTGATATCATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
16563055 AAAGGCTTCAGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
16563077 TCGAGACTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 15 0.31
31 34 0.69
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:16566197 original size:12 final size:12
Alignment explanation
Indices: 16566182--16566207 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16566172 GTAATGAACA
16566182 TTGGACATTTAT
1 TTGGACATTTAT
16566194 TTGGACATTTAT
1 TTGGACATTTAT
16566206 TT
1 TT
16566208 TGGTGATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (12 bp):
TTGGACATTTAT
Found at i:16569522 original size:15 final size:15
Alignment explanation
Indices: 16569498--16569535 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
16569488 TAAAACCTAA
*
16569498 AAATGAAATAGTATT
1 AAATGGAATAGTATT
16569513 AAATGGAATAGTATT
1 AAATGGAATAGTATT
16569528 AAATGGAA
1 AAATGGAA
16569536 GAAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (15 bp):
AAATGGAATAGTATT
Found at i:16573221 original size:46 final size:46
Alignment explanation
Indices: 16573120--16573208 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
16573110 TGTAACCCGC
* * *
16573120 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCACAT
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACGCTCACAT
* * *
16573166 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCA
1 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACGCTCA
16573209 ACCATCCTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (46 bp):
CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGACGCTCACAT
Found at i:16583051 original size:12 final size:12
Alignment explanation
Indices: 16583034--16583059 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16583024 GTAAGAACTA
16583034 TGTTGTTTTTAG
1 TGTTGTTTTTAG
16583046 TGTTGTTTTTAG
1 TGTTGTTTTTAG
16583058 TG
1 TG
16583060 ATGCTTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.27, T:0.65
Consensus pattern (12 bp):
TGTTGTTTTTAG
Found at i:16616279 original size:48 final size:48
Alignment explanation
Indices: 16616208--16616495 Score: 504
Period size: 48 Copynumber: 6.0 Consensus size: 48
16616198 CACAAGATAA
* *
16616208 AGATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATTTGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
16616256 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
16616304 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
* *
16616352 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGCGAAATATATATATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA-ATATGTATG
*
16616402 AGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATG
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
*
16616450 AGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTA
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTA
16616496 NNNNNNNNNN
Statistics
Matches: 231, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
48 184 0.80
49 4 0.02
50 43 0.19
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATG
Found at i:16616446 original size:98 final size:98
Alignment explanation
Indices: 16616208--16616492 Score: 502
Period size: 98 Copynumber: 2.9 Consensus size: 98
16616198 CACAAGATAA
* *
16616208 AGATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATTTGTATGAGATATGTATATGTGGT
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGT
*
16616273 AAAGCCGAATGGCTAATGTG-AA-ATATGTATG
66 AAAGCCGAATGGCTAATGTGAAATATATATATG
16616304 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGT
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGT
*
16616369 AAAGCCGAATGGCTAATGCGAAATATATATATG
66 AAAGCCGAATGGCTAATGTGAAATATATATATG
*
16616402 AGATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGT
1 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGT
*
16616467 AAAGCCGAATGGCTAGTGTGAAATAT
66 AAAGCCGAATGGCTAATGTGAAATAT
16616493 GTANNNNNNN
Statistics
Matches: 180, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
96 82 0.46
97 2 0.01
98 96 0.53
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (98 bp):
AGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGT
AAAGCCGAATGGCTAATGTGAAATATATATATG
Found at i:16616470 original size:146 final size:144
Alignment explanation
Indices: 16616208--16616495 Score: 513
Period size: 146 Copynumber: 2.0 Consensus size: 144
16616198 CACAAGATAA
* *
16616208 AGATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATTTGTATGAGATATGTATATGTGGT
1 AGATATGTATATGTGGTAAAGCCGAATGGATAATGCGAAATTTATATGAGATATGTATATGTGGT
16616273 AAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAAT
66 AAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAAT
16616338 GTGAAATATGTATG
131 GTGAAATATGTATG
*
16616352 AGATATGTATATGTGGTAAAGCCGAATGGCTAATGCGAAATATATATATGAGATATGTATATGTG
1 AGATATGTATATGTGGTAAAGCCGAATGGATAATGCGAAAT-T-TATATGAGATATGTATATGTG
*
16616417 GTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
64 GTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
*
16616482 GTGTGAAATATGTA
129 ATGTGAAATATGTA
16616496 NNNNNNNNNN
Statistics
Matches: 137, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
144 39 0.28
145 1 0.01
146 97 0.71
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (144 bp):
AGATATGTATATGTGGTAAAGCCGAATGGATAATGCGAAATTTATATGAGATATGTATATGTGGT
AAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAAT
GTGAAATATGTATG
Found at i:16619904 original size:33 final size:33
Alignment explanation
Indices: 16619823--16619889 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
16619813 TCAAACCAAG
16619823 AATTAAGAAGACATAATTTAGAACAAGAAACTA
1 AATTAAGAAGACATAATTTAGAACAAGAAACTA
16619856 AATTAAGAAGACATAATTTAGAACAAGAAACTA
1 AATTAAGAAGACATAATTTAGAACAAGAAACTA
16619889 A
1 A
16619890 GTATTTATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (33 bp):
AATTAAGAAGACATAATTTAGAACAAGAAACTA
Found at i:16626293 original size:14 final size:14
Alignment explanation
Indices: 16626274--16626300 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16626264 ACAAATATTT
16626274 TCATATCATATCAA
1 TCATATCATATCAA
16626288 TCATATCATATCA
1 TCATATCATATCA
16626301 TTTTGAACAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (14 bp):
TCATATCATATCAA
Found at i:16645091 original size:29 final size:28
Alignment explanation
Indices: 16645055--16645132 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
16645045 TCATGAGATT
16645055 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
16645085 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
16645112 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
16645133 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:16645350 original size:174 final size:174
Alignment explanation
Indices: 16645085--16645412 Score: 620
Period size: 174 Copynumber: 1.9 Consensus size: 174
16645075 AAATTGTACA
16645085 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* *
16645150 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
16645215 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
16645259 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
16645324 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
16645389 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
16645413 ACCTTGAGTT
Statistics
Matches: 150, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 150 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:16653288 original size:39 final size:40
Alignment explanation
Indices: 16653193--16653415 Score: 273
Period size: 39 Copynumber: 5.7 Consensus size: 40
16653183 TTGAATGATG
*
16653193 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
16653231 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
16653272 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
16653311 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
16653350 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
16653389 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
16653416 AACGAGGAGC
Statistics
Matches: 166, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
39 93 0.56
40 61 0.37
41 11 0.07
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:16653379 original size:79 final size:81
Alignment explanation
Indices: 16653193--16653415 Score: 282
Period size: 79 Copynumber: 2.8 Consensus size: 81
16653183 TTGAATGATG
* * *
16653193 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATATCCGGGCTAAGACCCGAAGGCA
*
16653254 TTTGTGCGAGATACTAAT
64 TTTGTGCGAGATACTAAA
16653272 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
*
16653334 TGTGCGAGTTACTAAA
66 TGTGCGAGATACTAAA
* * * * *
16653350 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
16653414 TG
66 TG
16653416 AACGAGGAGC
Statistics
Matches: 128, Mismatches: 9, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
78 46 0.36
79 56 0.44
80 25 0.20
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:16653437 original size:79 final size:79
Alignment explanation
Indices: 16653193--16653448 Score: 224
Period size: 79 Copynumber: 3.3 Consensus size: 79
16653183 TTGAATGATG
* * * *
16653193 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** *
16653254 TTTGTGCGAGAT-ACTAAT
62 TTTGAACGAG-TGACTAAA
* *
16653272 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
** *
16653336 TGCGAGTTACTAAA
66 AACGAGTGACTAAA
* *
16653350 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATT
*
16653414 TGAACGAG-GAGCTATA
64 TGAACGAGTGA-CTAAA
* *
16653430 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
16653449 TACGTGATTT
Statistics
Matches: 153, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
77 1 0.01
78 45 0.29
79 70 0.46
80 36 0.24
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTGACTAAA
Found at i:16656279 original size:25 final size:26
Alignment explanation
Indices: 16656217--16656279 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
16656207 TATTTTCTCA
*
16656217 AAAATTTAAAAATTATTAATGATTAAAT
1 AAAA-TTAAAAATTA-TAATAATTAAAT
16656245 -AAATTGAAAAATTA-AATAATTAAAT
1 AAAATT-AAAAATTATAATAATTAAAT
16656270 AAAATTAAAA
1 AAAATTAAAA
16656280 TTTAGGAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
25 14 0.44
26 7 0.22
27 11 0.34
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (26 bp):
AAAATTAAAAATTATAATAATTAAAT
Found at i:16665475 original size:27 final size:27
Alignment explanation
Indices: 16665445--16665622 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
16665435 ATATTGAGTC
* * * *
16665445 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
16665472 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16665499 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
16665527 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
16665554 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
16665581 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16665608 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16665623 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:16665584 original size:82 final size:81
Alignment explanation
Indices: 16665466--16665621 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16665456 TGCTATATAA
* *
16665466 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16665531 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
16665548 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16665612 CACTTAGTGC
65 CACTTAGTGC
16665622 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:16673538 original size:27 final size:27
Alignment explanation
Indices: 16673508--16673685 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
16673498 ATATTGAGTC
* * * *
16673508 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
16673535 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16673562 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
16673590 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
16673617 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
16673644 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16673671 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16673686 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:16673647 original size:82 final size:81
Alignment explanation
Indices: 16673529--16673684 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16673519 TGCTATATAA
* *
16673529 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16673594 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
16673611 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16673675 CACTTAGTGC
65 CACTTAGTGC
16673685 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:16678211 original size:21 final size:21
Alignment explanation
Indices: 16678187--16678229 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
16678177 GGACCAAATC
16678187 GGAACAAAATAAAAA-TTTCAA
1 GGAA-AAAATAAAAATTTTCAA
**
16678208 GGAAAAGTTAAAAATTTTCAA
1 GGAAAAAATAAAAATTTTCAA
16678229 G
1 G
16678230 TCAGGGATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (21 bp):
GGAAAAAATAAAAATTTTCAA
Found at i:16684627 original size:2 final size:2
Alignment explanation
Indices: 16684620--16684656 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
16684610 GGTTGTTCTT
*
16684620 TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
16684657 GCCGTAATAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:16699948 original size:40 final size:40
Alignment explanation
Indices: 16699892--16700116 Score: 301
Period size: 40 Copynumber: 5.6 Consensus size: 40
16699882 CATTTGAATG
* *
16699892 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGA-T
* * *
16699932 TTATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGA-T
* *
16699972 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
*
16700012 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
** *
16700052 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
* *
16700092 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
16700117 ATTGTGCTTG
Statistics
Matches: 175, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 172 0.98
41 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGAT
Found at i:16700031 original size:80 final size:80
Alignment explanation
Indices: 16699892--16700143 Score: 330
Period size: 80 Copynumber: 3.2 Consensus size: 80
16699882 CATTTGAATG
* * * * *
16699892 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTTTATCCGGGCTAAGTCCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TATATCCGGGCTAAGACCCGAAGGC
*
16699956 ATTTATGCTAGTGATT
65 ATTTGTGCTAGTGATT
*
16699972 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCA
*
16700037 TTTGTGCGAGTTGA-T
66 TTTGTGCTAG-TGATT
* * * *
16700052 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCA
* * *
16700117 ATTGTGCTTGTGGTT
66 TTTGTGCTAGTGATT
16700132 ATATCC-GGCTAA
1 ATATCCGGGCTAA
16700144 ATTCCGAAGA
Statistics
Matches: 152, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
79 8 0.05
80 138 0.91
81 6 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGGCA
TTTGTGCTAGTGATT
Found at i:16700135 original size:120 final size:120
Alignment explanation
Indices: 16699892--16700143 Score: 312
Period size: 120 Copynumber: 2.1 Consensus size: 120
16699882 CATTTGAATG
* * * *
16699892 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCA
* * * * * * *
16699957 TTTATGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGAT
66 TTCATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGGAT
*
16700012 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGATTATATCCGGGCTAAGACCCGAAGGC
* * ** *
16700076 ATTCGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
65 ATTCATGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGGAT
16700132 ATATCC-GGCTAA
1 ATATCCGGGCTAA
16700144 ATTCCGAAGA
Statistics
Matches: 113, Mismatches: 17, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
119 6 0.05
120 102 0.90
121 5 0.04
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (120 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGATTATATCCGGGCTAAGACCCGAAGGCA
TTCATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGGAT
Found at i:16715054 original size:48 final size:48
Alignment explanation
Indices: 16714987--16715130 Score: 216
Period size: 48 Copynumber: 3.0 Consensus size: 48
16714977 GGGTTATGTC
* * *
16714987 TGATCCCATGTAAGACCATGTTTGGGACATGGAATTGGAATTGATATG
1 TGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCGATATG
* *
16715035 TGATCCCATGTAAGACCATGTTTGGGACATGGCAGTGGCATCGATATT
1 TGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCGATATG
* * *
16715083 TGATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCGATATG
1 TGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCGATATG
16715131 AGACATCGTG
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 86 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (48 bp):
TGATCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATCGATATG
Found at i:16715143 original size:48 final size:48
Alignment explanation
Indices: 16714988--16715150 Score: 175
Period size: 48 Copynumber: 3.4 Consensus size: 48
16714978 GGTTATGTCT
* * * * * * *
16714988 GATCCCATGTAAGACCATGTTTGGGACATGGAATTGGAATTGATATGT
1 GATCCCATGTAAGACCATATCTGGGACATGGCAGTGGCATCGATATGA
* * **
16715036 GATCCCATGTAAGACCATGTTTGGGACATGGCAGTGGCATCGATATTT
1 GATCCCATGTAAGACCATATCTGGGACATGGCAGTGGCATCGATATGA
* *
16715084 GATCCCATGTAAGACCATATCTGGGATATGGCATTGGCATCGATATGA
1 GATCCCATGTAAGACCATATCTGGGACATGGCAGTGGCATCGATATGA
* *
16715132 GA-CATCGTGTAAGACCATA
1 GATC-CCATGTAAGACCATA
16715151 GTTGCGGTAT
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 1 0.01
48 100 0.99
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (48 bp):
GATCCCATGTAAGACCATATCTGGGACATGGCAGTGGCATCGATATGA
Found at i:16718796 original size:22 final size:22
Alignment explanation
Indices: 16718771--16718817 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
16718761 GTGAATTTTA
16718771 ATGCTTT-ATTACTATT-ATGAGT
1 ATGCTTTGATTA-T-TTCATGAGT
16718793 ATGCTTTGATTATTTCATGAGT
1 ATGCTTTGATTATTTCATGAGT
16718815 ATG
1 ATG
16718818 TGATTGGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 2 0.09
22 17 0.74
23 4 0.17
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (22 bp):
ATGCTTTGATTATTTCATGAGT
Found at i:16718970 original size:21 final size:21
Alignment explanation
Indices: 16718941--16719015 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
16718931 CTAGGAACTA
*
16718941 TGTGATCTGAACTCATTGAGT
1 TGTGGTCTGAACTCATTGAGT
** *
16718962 TGTGGTCTGAGTTCA-TGATAT
1 TGTGGTCTGAACTCATTGA-GT
*
16718983 ATGTGG-CATCGAACTCATTGAGG
1 -TGTGGTC-T-GAACTCATTGAGT
16719006 TGTGGTCTGA
1 TGTGGTCTGA
16719016 GTTCATGATG
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
20 3 0.08
21 16 0.40
22 12 0.30
23 6 0.15
24 3 0.08
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.36
Consensus pattern (21 bp):
TGTGGTCTGAACTCATTGAGT
Found at i:16720498 original size:20 final size:20
Alignment explanation
Indices: 16720473--16720539 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
16720463 GATATGATAT
*
16720473 ACATGAT-TGATATGATATGC
1 ACATGATATG-TATGAAATGC
*
16720493 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
16720513 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
16720533 ACATGAT
1 ACATGAT
16720540 GTATTCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:16720618 original size:26 final size:26
Alignment explanation
Indices: 16720589--16720719 Score: 144
Period size: 26 Copynumber: 5.2 Consensus size: 26
16720579 GAGGAAGTGC
16720589 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* **
16720615 AAAAGGGCTTATGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* *
16720641 AAAAAGGCTTATGCCCAAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* * **
16720667 AAAATGGCTT-TGCCTCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
16720692 AAAAGGGCTT-GGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
16720715 AAAAG
1 AAAAG
16720720 AGGCAGGGCC
Statistics
Matches: 87, Mismatches: 18, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
23 5 0.06
24 3 0.03
25 26 0.30
26 53 0.61
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:16720668 original size:52 final size:51
Alignment explanation
Indices: 16720589--16720701 Score: 172
Period size: 52 Copynumber: 2.2 Consensus size: 51
16720579 GAGGAAGTGC
*
16720589 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAATTTACCG
1 AAAAGGGCTTATGCCCAAGTTTATTGAAAAGGGCTT-TGCCCCAATTTACCG
* * * *
16720641 AAAAAGGCTTATGCCCAAGTTTATTGAAAATGGCTTTGCCTCAGTTTACCG
1 AAAAGGGCTTATGCCCAAGTTTATTGAAAAGGGCTTTGCCCCAATTTACCG
16720692 AAAAGGGCTT
1 AAAAGGGCTT
16720702 GGCCCCAGTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
51 22 0.40
52 33 0.60
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATGCCCAAGTTTATTGAAAAGGGCTTTGCCCCAATTTACCG
Found at i:16734560 original size:15 final size:16
Alignment explanation
Indices: 16734540--16734569 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16734530 TTGTTACTGT
16734540 TTTAAACT-TTTAATC
1 TTTAAACTATTTAATC
16734555 TTTAAACTATTTAAT
1 TTTAAACTATTTAAT
16734570 TTGGGTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAACTATTTAATC
Found at i:16744353 original size:11 final size:11
Alignment explanation
Indices: 16744337--16744361 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16744327 ATATGATATT
16744337 TTATTATTTTA
1 TTATTATTTTA
16744348 TTATTATTTTA
1 TTATTATTTTA
16744359 TTA
1 TTA
16744362 GTATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:16748815 original size:11 final size:11
Alignment explanation
Indices: 16748799--16748823 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16748789 ATATGATATT
16748799 TTATTATTTTA
1 TTATTATTTTA
16748810 TTATTATTTTA
1 TTATTATTTTA
16748821 TTA
1 TTA
16748824 GTATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:16776805 original size:24 final size:26
Alignment explanation
Indices: 16776758--16776807 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
16776748 AGCCATGAAA
16776758 TCGCACACTTAGTGCTTAATATTTTCCT
1 TCGCACACTTAGTG--TAATATTTTCCT
16776786 TCGCACACTTAGTG-AA-ATTTTC
1 TCGCACACTTAGTGTAATATTTTC
16776808 ATGTCCATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.27
25 2 0.09
28 14 0.64
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.40
Consensus pattern (26 bp):
TCGCACACTTAGTGTAATATTTTCCT
Found at i:16778903 original size:20 final size:19
Alignment explanation
Indices: 16778859--16778913 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
16778849 AACACTAAGA
* *
16778859 ACCACTCCATTCACTTTCTT
1 ACCA-TCCATTTACTTACTT
16778879 ACCATTCCATTTACTTACTT
1 ACCA-TCCATTTACTTACTT
*
16778899 TCCATCTCATTTACT
1 ACCATC-CATTTACT
16778914 AATCATAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.22, C:0.35, G:0.00, T:0.44
Consensus pattern (19 bp):
ACCATCCATTTACTTACTT
Found at i:16779520 original size:87 final size:87
Alignment explanation
Indices: 16779429--16779602 Score: 303
Period size: 87 Copynumber: 2.0 Consensus size: 87
16779419 GAAACTTCCA
*
16779429 TTTCAACCTTTTCATAAAGGCATGACATAGTTTCTTTTGATCACTTGTCATGCATTTCCTTTACA
1 TTTCAACCTTTTCATAAAGACATGACATAGTTTCTTTTGATCACTTGTCATGCATTTCCTTTACA
*
16779494 TGCCCGTTAAACCGGTTAGAAT
66 CGCCCGTTAAACCGGTTAGAAT
* *
16779516 TTTCAACCTTTTCATAAATACATGACATAGTTTCTTTTGATCACTTGTCATTCATTTCCTTTACA
1 TTTCAACCTTTTCATAAAGACATGACATAGTTTCTTTTGATCACTTGTCATGCATTTCCTTTACA
*
16779581 CGCCCGTTAAACCGTTTAGAAT
66 CGCCCGTTAAACCGGTTAGAAT
16779603 ATCAGTGGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 82 1.00
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (87 bp):
TTTCAACCTTTTCATAAAGACATGACATAGTTTCTTTTGATCACTTGTCATGCATTTCCTTTACA
CGCCCGTTAAACCGGTTAGAAT
Found at i:16782177 original size:19 final size:18
Alignment explanation
Indices: 16782155--16782205 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
16782145 AACTAATTTT
16782155 TAATATTAATTTTTTAAGA
1 TAATATTAATTTTTTAA-A
16782174 TAAT-TTAATTATTTTTAAA
1 TAATATTAA-T-TTTTTAAA
16782193 T-ATATTAAATTTT
1 TAATATT-AATTTT
16782206 ATCCAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
18 9 0.32
19 10 0.36
20 9 0.32
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TAATATTAATTTTTTAAA
Found at i:16782203 original size:20 final size:20
Alignment explanation
Indices: 16782165--16782203 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16782155 TAATATTAAT
*
16782165 TTTTTAAGATAATTTAATTA
1 TTTTTAAGATAATTAAATTA
16782185 TTTTTAA-ATATATTAAATT
1 TTTTTAAGATA-ATTAAATT
16782204 TTATCCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTAAGATAATTAAATTA
Found at i:16782556 original size:20 final size:20
Alignment explanation
Indices: 16782509--16782556 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
16782499 ATAATAATAT
16782509 TAAAATA-TTAAACACATTA
1 TAAAATATTTAAACACATTA
* *
16782528 TATATTATTTATAA-ACATTA
1 TAAAATATTTA-AACACATTA
16782548 TAAAATATT
1 TAAAATATT
16782557 ATTTTAATAG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 5 0.22
20 16 0.70
21 2 0.09
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (20 bp):
TAAAATATTTAAACACATTA
Found at i:16783979 original size:48 final size:48
Alignment explanation
Indices: 16783905--16784131 Score: 236
Period size: 48 Copynumber: 4.9 Consensus size: 48
16783895 GGCTTATGTA
16783905 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
* * * * *
16783953 TGATCCCATGTAAGACCATATATGGGATATGGTC-TTAGCATCTATATG
1 TGATCCCATGTAAGACCATGTCTGGGACATGG-CATTGGCATCGATATG
** *
16784001 TGATTTCGTGTAAGACCATGTCTGGG--A---CA-TGGCATCGATATG
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
* * *
16784043 AGA-CATCATGTAAGACCATGTCTGGGACATGGCATTGACATCGATATG
1 TGATC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
* * * * *
16784091 TAATGCCATGTAAGACCATATCTGGGATACGGCATTGGCAT
1 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
16784132 TTTACTATGT
Statistics
Matches: 145, Mismatches: 24, Indels: 20
0.77 0.13 0.11
Matches are distributed among these distances:
42 34 0.23
44 1 0.01
46 1 0.01
47 2 0.01
48 106 0.73
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (48 bp):
TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
Found at i:16784090 original size:90 final size:92
Alignment explanation
Indices: 16783910--16784117 Score: 219
Period size: 90 Copynumber: 2.2 Consensus size: 92
16783900 ATGTATGATC
*
16783910 CCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATCCCATGTAAGACCATATA
1 CCATGTAAGACCATGTCTGGG--A--GCATTGGCATCGATATGAGATCCCATGTAAGACCATATA
* * * *
16783975 TGGGATATGGTCTTAGCATCTATATGTGATT
62 TGGGACATGGTCTTAGCATCGATATGTAATG
* * * * *
16784006 TCGTGTAAGACCATGTCTGGGA-CA-TGGCATCGATATGAGA-CATCATGTAAGACCATGTCTGG
1 CCATGTAAGACCATGTCTGGGAGCATTGGCATCGATATGAGATC-CCATGTAAGACCATATATGG
16784068 GACATGG-CATT-GACATCGATATGTAATG
65 GACATGGTC-TTAG-CATCGATATGTAATG
*
16784096 CCATGTAAGACCATATCTGGGA
1 CCATGTAAGACCATGTCTGGGA
16784118 TACGGCATTG
Statistics
Matches: 96, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
89 3 0.03
90 71 0.74
91 2 0.02
94 1 0.01
96 19 0.20
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (92 bp):
CCATGTAAGACCATGTCTGGGAGCATTGGCATCGATATGAGATCCCATGTAAGACCATATATGGG
ACATGGTCTTAGCATCGATATGTAATG
Found at i:16787629 original size:27 final size:27
Alignment explanation
Indices: 16787599--16787776 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
16787589 ATATTGAGTC
* * * *
16787599 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
16787626 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16787653 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
16787681 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
16787708 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
16787735 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16787762 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16787777 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:16787738 original size:82 final size:81
Alignment explanation
Indices: 16787620--16787775 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16787610 TGCTATATAA
* *
16787620 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16787685 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
16787702 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16787766 CACTTAGTGC
65 CACTTAGTGC
16787776 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:16795821 original size:27 final size:27
Alignment explanation
Indices: 16795791--16795968 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
16795781 ATATTGAGCC
* *
16795791 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
16795818 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
16795845 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
16795873 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
16795900 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
16795927 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
16795954 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16795969 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 25 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:16795930 original size:82 final size:81
Alignment explanation
Indices: 16795812--16795967 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
16795802 TGCTATATAA
* *
16795812 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16795877 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
16795894 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16795958 CACTTAGTGC
65 CACTTAGTGC
16795968 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:16803286 original size:48 final size:48
Alignment explanation
Indices: 16803210--16803342 Score: 151
Period size: 48 Copynumber: 2.8 Consensus size: 48
16803200 TAAGGTTATG
* * *
16803210 TGTGATCCCGTGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATATCTGGGACATGACATTGGCATCGATA
* * * *
16803258 TGTGATGCCATGTAAGACCATATTTGGGATATGACATTGGCATCTATA
1 TGTGATCCCATGTAAGACCATATCTGGGACATGACATTGGCATCGATA
* * * *
16803306 TGTGATTTCGA-GTAAAACCATGTCTGGGACATGACAT
1 TGTGA-TCCCATGTAAGACCATATCTGGGACATGACAT
16803343 CGATATGAGA
Statistics
Matches: 71, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
48 68 0.96
49 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATATCTGGGACATGACATTGGCATCGATA
Found at i:16805542 original size:23 final size:22
Alignment explanation
Indices: 16805494--16805544 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
16805484 TTTAATTATA
*
16805494 ATTAAAGAAAATATCATGTGTC
1 ATTAAAGAAAATATCACGTGTC
* * *
16805516 ATTAAAGAGAAGTGTCACGTGTT
1 ATTAAAGA-AAATATCACGTGTC
16805539 ATTAAA
1 ATTAAA
16805545 TTAAATCGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (22 bp):
ATTAAAGAAAATATCACGTGTC
Found at i:16805968 original size:29 final size:29
Alignment explanation
Indices: 16805912--16805969 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
16805902 TTAATCATAA
* * ***
16805912 TTATTGGATTAGGTTGATTTTTGTAAAAT
1 TTATTGGATTAAGTAGATTTTACAAAAAT
16805941 TTATTGGATTAAGTAGATTTTACAAAAAT
1 TTATTGGATTAAGTAGATTTTACAAAAAT
16805970 GCATTTAGCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (29 bp):
TTATTGGATTAAGTAGATTTTACAAAAAT
Found at i:16806489 original size:17 final size:16
Alignment explanation
Indices: 16806467--16806507 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
16806457 GTTTTGATGA
16806467 TATTTTTTAATT-ATT
1 TATTTTTTAATTAATT
*
16806482 TTTATTTTTAATTAATT
1 TAT-TTTTTAATTAATT
16806499 TATTTTTTA
1 TATTTTTTA
16806508 TTTTTAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 15 0.68
17 5 0.23
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTTTTAATTAATT
Found at i:16806508 original size:22 final size:20
Alignment explanation
Indices: 16806473--16806514 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
16806463 ATGATATTTT
16806473 TTAATTATTTTTATTTTTAA
1 TTAATTATTTTTATTTTTAA
16806493 TTAATTTATTTTTTATTTTTAA
1 TTAA-TTA-TTTTTATTTTTAA
16806515 ATCTTTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 3 0.15
22 13 0.65
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTAATTATTTTTATTTTTAA
Found at i:16806806 original size:142 final size:138
Alignment explanation
Indices: 16806584--16806906 Score: 361
Period size: 142 Copynumber: 2.3 Consensus size: 138
16806574 TATGTTTGTG
* * *
16806584 AAAA-TAATTAAAAATAAAAA-ATTGAAGCAATATGAAAT--AAAAAATACAAATGTGAGTAGTA
1 AAAATTAATTAAAAATAAAAAGATTGAAGCAATATGAAATAAAAAAAACACAAATATGAGGAGTA
** *
16806645 GAGGAACCGAACTCAAGACTTAAAGATATAATTACAACTATCTAACCATCTAA-TGGAAA-AACT
66 GAAAAACCAAACTCAAGACTTAAAGATATAATTACAACTATCTAACCATCTAACT--AAATAACT
*
16806708 AGTATGTTAAA
129 AATATGTT-AA
* * *
16806719 AAACATTAATTAAAAATTTAAAAAGTTTTAAGCAACATGAAATAAAAAAAACACAAATATGAGGA
1 AAA-ATTAATTAAAAA--TAAAAAGATTGAAGCAATATGAAATAAAAAAAACACAAATATGAGGA
* * * * ** *
16806784 GTAGAAAAATCAAACTCGAGACTTAAGGATGTAATTGTAATTATCTAACCATCTAACTAAATAAC
63 GTAGAAAAACCAAACTCAAGACTTAAAGATATAATTACAACTATCTAACCATCTAACTAAATAAC
16806849 TAATATGTTAA
128 TAATATGTTAA
* **
16806860 AAAATTAATTAAAAAATAAAAAGCTTGAAATAATATGAAATAAAAAA
1 AAAATTAATT-AAAAATAAAAAGATTGAAGCAATATGAAATAAAAAA
16806907 TACAAATGTG
Statistics
Matches: 156, Mismatches: 22, Indels: 16
0.80 0.11 0.08
Matches are distributed among these distances:
135 3 0.02
136 1 0.01
137 10 0.06
139 32 0.21
140 22 0.14
141 13 0.08
142 74 0.47
143 1 0.01
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (138 bp):
AAAATTAATTAAAAATAAAAAGATTGAAGCAATATGAAATAAAAAAAACACAAATATGAGGAGTA
GAAAAACCAAACTCAAGACTTAAAGATATAATTACAACTATCTAACCATCTAACTAAATAACTAA
TATGTTAA
Found at i:16818996 original size:89 final size:89
Alignment explanation
Indices: 16818827--16818996 Score: 227
Period size: 89 Copynumber: 1.9 Consensus size: 89
16818817 ATTCGTTTTC
** * * *
16818827 GATCTGTTTCCCTACTGCTTAGGGGGTTAAGATTCGTCAATCTTCAGCCTGTTACCCTACTGTTT
1 GATCTGTTTCCCTACTGCTTAGGGGAATAAGATTCGTAAATCCTCAGCCTGTTACCCTACTGCTT
* *
16818892 AAGGGTTTAAGGCTTGTCACCTTT
66 AAGGGGTTAAAGCTTGTCACCTTT
* *
16818916 GATCTGTTTCCCTACTGCTTAGGGTAATAAGA-TCTGTAAATCCTCAGCTTGTTACCCTACTGCT
1 GATCTGTTTCCCTACTGCTTAGGGGAATAAGATTC-GTAAATCCTCAGCCTGTTACCCTACTGCT
16818980 T-AGGGAGTTAAAGCTTG
65 TAAGGG-GTTAAAGCTTG
16818997 GTGGTCTGAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
88 6 0.09
89 64 0.91
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (89 bp):
GATCTGTTTCCCTACTGCTTAGGGGAATAAGATTCGTAAATCCTCAGCCTGTTACCCTACTGCTT
AAGGGGTTAAAGCTTGTCACCTTT
Found at i:16825485 original size:40 final size:40
Alignment explanation
Indices: 16825387--16825649 Score: 309
Period size: 40 Copynumber: 6.6 Consensus size: 40
16825377 TCCTCGTTCA
* * * ** *
16825387 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
16825426 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
16825466 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
16825506 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
16825546 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
16825586 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
16825626 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
16825650 CAGCATTCAA
Statistics
Matches: 199, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
39 37 0.19
40 154 0.77
41 8 0.04
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:16829699 original size:9 final size:9
Alignment explanation
Indices: 16829681--16829710 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16829671 TGCAATGCTG
16829681 ATGC-ATGA
1 ATGCGATGA
16829689 ATGCGATGA
1 ATGCGATGA
16829698 ATGCGATGA
1 ATGCGATGA
16829707 ATGC
1 ATGC
16829711 AAAAAAAGCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.23
Consensus pattern (9 bp):
ATGCGATGA
Found at i:16835798 original size:20 final size:20
Alignment explanation
Indices: 16835773--16835815 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
16835763 ATACAGATAC
16835773 CTAAAAACAATAATATGAAG
1 CTAAAAACAATAATATGAAG
16835793 CTAAAAACAATAATATGAAG
1 CTAAAAACAATAATATGAAG
16835813 CTA
1 CTA
16835816 TTAATAATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.21
Consensus pattern (20 bp):
CTAAAAACAATAATATGAAG
Found at i:16835950 original size:22 final size:22
Alignment explanation
Indices: 16835925--16835967 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16835915 TATATATATA
*
16835925 TATAACTACATATATAAATGTG
1 TATAACTACATATAAAAATGTG
**
16835947 TATATGTACATATAAAAATGT
1 TATAACTACATATAAAAATGT
16835968 ACACTAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (22 bp):
TATAACTACATATAAAAATGTG
Found at i:16838823 original size:18 final size:19
Alignment explanation
Indices: 16838777--16838824 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
16838767 ATTAAGTATA
* *
16838777 TATATTATTATATACATATG
1 TATATTATT-TGTACAAATG
16838797 TATATTATTTGTACAAATG
1 TATATTATTTGTACAAATG
16838816 TA-ATTATTT
1 TATATTATTT
16838825 TTACCATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 7 0.27
19 10 0.38
20 9 0.35
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (19 bp):
TATATTATTTGTACAAATG
Found at i:16848140 original size:29 final size:28
Alignment explanation
Indices: 16848071--16848179 Score: 94
Period size: 28 Copynumber: 3.9 Consensus size: 28
16848061 CACGACCATG
* * *
16848071 TGCCCCTATTTTTCAGATTTTATAGTTT
1 TGCCCCTTTTTTTTAGATTTTATAATTT
** *
16848099 TGCCTATTATTTTTAGATTTTATAATTT
1 TGCCCCTTTTTTTTAGATTTTATAATTT
* *
16848127 TGCCCCCTTTTTTTAGAATTTTACAATTT
1 TGCCCCTTTTTTTTAG-ATTTTATAATTT
* * *
16848156 TG-ACCTTATTTTTCAAATTTTATA
1 TGCCCCTT-TTTTTTAGATTTTATA
16848180 GCTTTACCTA
Statistics
Matches: 63, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
28 44 0.70
29 19 0.30
ACGTcount: A:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (28 bp):
TGCCCCTTTTTTTTAGATTTTATAATTT
Found at i:16848828 original size:18 final size:18
Alignment explanation
Indices: 16848805--16848841 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16848795 TTTTATTACT
16848805 AGTGGTTTATCCACAACG
1 AGTGGTTTATCCACAACG
* *
16848823 AGTGGTTTTTCTACAACG
1 AGTGGTTTATCCACAACG
16848841 A
1 A
16848842 TAAGTGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (18 bp):
AGTGGTTTATCCACAACG
Found at i:16852809 original size:18 final size:17
Alignment explanation
Indices: 16852769--16852809 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
16852759 CATGCAGTAT
*
16852769 GGGTTCACACATGGCAT
1 GGGTTCACACATGGCAG
*
16852786 GGGTTCACACATAGGTAG
1 GGGTTCACACAT-GGCAG
16852804 GGGTTC
1 GGGTTC
16852810 TCATATGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (17 bp):
GGGTTCACACATGGCAG
Found at i:16854331 original size:13 final size:14
Alignment explanation
Indices: 16854305--16854342 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
16854295 ACATATATAG
16854305 ATAT-CAGAATCAA
1 ATATACAGAATCAA
16854318 ATATACAGAA-CAA
1 ATATACAGAATCAA
*
16854331 ATATACATAATC
1 ATATACAGAATC
16854343 CTACCCTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.55, C:0.16, G:0.05, T:0.24
Consensus pattern (14 bp):
ATATACAGAATCAA
Found at i:16860400 original size:40 final size:40
Alignment explanation
Indices: 16860356--16860476 Score: 127
Period size: 40 Copynumber: 3.0 Consensus size: 40
16860346 TGCTCCAATA
* * *
16860356 TATTTATTTGGCTTTGTGCCAAGCACGCTTTGTGCCGGTG
1 TATTTATTAGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTG
* * * * *
16860396 TATTTA-TCGAGCATTATGCCTAGCAGGATTTGTGTCGGTG
1 TATTTATTAG-GCTTTGTGCCTAGCAGGCTTTGTGCCGGTG
* * *
16860436 TGTTTATCAGGCTTTGTGCCTAGCAGGCTTTGTGCCAGTG
1 TATTTATTAGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTG
16860476 T
1 T
16860477 TGTCAATCAG
Statistics
Matches: 64, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
39 2 0.03
40 61 0.95
41 1 0.02
ACGTcount: A:0.15, C:0.18, G:0.28, T:0.39
Consensus pattern (40 bp):
TATTTATTAGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTG
Found at i:16867520 original size:27 final size:28
Alignment explanation
Indices: 16867490--16867555 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
16867480 GGGCATAATC
16867490 GTCATTTTACCATATA-GGGGTATTACG
1 GTCATTTTACCATATAGGGGGTATTACG
*
16867517 GTCATTTTACCCTATAGGGGGTATTACG
1 GTCATTTTACCATATAGGGGGTATTACG
* *
16867545 ATTATTTTACC
1 GTCATTTTACC
16867556 TATTCTGGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (28 bp):
GTCATTTTACCATATAGGGGGTATTACG
Found at i:16868929 original size:11 final size:11
Alignment explanation
Indices: 16868913--16868939 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
16868903 TTTCCCCCTT
16868913 ACTAAATCGGC
1 ACTAAATCGGC
16868924 ACTAAATCGGC
1 ACTAAATCGGC
16868935 ACTAA
1 ACTAA
16868940 GTCAAAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.26, G:0.15, T:0.19
Consensus pattern (11 bp):
ACTAAATCGGC
Found at i:16875831 original size:39 final size:39
Alignment explanation
Indices: 16875616--16875838 Score: 218
Period size: 40 Copynumber: 5.6 Consensus size: 39
16875606 TTGAATGCTG
* * * * *
16875616 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
16875656 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
16875695 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
16875736 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* *
16875776 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGCTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
16875815 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
16875839 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
39 38 0.24
40 104 0.67
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:16875858 original size:79 final size:80
Alignment explanation
Indices: 16875696--16875873 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
16875686 AGATACAAAT
* * * *
16875696 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
16875761 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
16875776 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGCTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
16875840 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
16875855 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
16875874 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:16883611 original size:40 final size:39
Alignment explanation
Indices: 16883580--16883789 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
16883570 GGACTAAGAT
* *
16883580 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
16883620 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
16883660 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
16883700 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
16883740 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
16883779 CCGAAGGCATT
1 CCGAAGGCATT
16883790 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:16883743 original size:120 final size:120
Alignment explanation
Indices: 16883527--16883789 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
16883517 TTGAATGCTG
* *
16883527 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
16883591 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
16883647 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
16883710 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
16883766 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
16883790 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:16883809 original size:79 final size:80
Alignment explanation
Indices: 16883528--16883824 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
16883518 TGAATGCTGT
* ** * * * **
16883528 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
16883591 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
16883608 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
16883672 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
16883688 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
16883752 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
16883767 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
16883825 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:16886140 original size:25 final size:25
Alignment explanation
Indices: 16886111--16886166 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
16886101 GGAAGCTCAT
16886111 AAGAGCCTATATCAGAACGCTCACG
1 AAGAGCCTATATCAGAACGCTCACG
*
16886136 AAGAGCCTATATCAGGACGCTCACG
1 AAGAGCCTATATCAGAACGCTCACG
16886161 AAGAGC
1 AAGAGC
16886167 TGCGTTTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (25 bp):
AAGAGCCTATATCAGAACGCTCACG
Found at i:16888425 original size:24 final size:24
Alignment explanation
Indices: 16888393--16888447 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
16888383 AAATAAGTCA
16888393 ACTCACTTTGTGATGACTCACAGG
1 ACTCACTTTGTGATGACTCACAGG
16888417 ACTCACTTTGTGATGACTCACAGG
1 ACTCACTTTGTGATGACTCACAGG
*
16888441 ACACACT
1 ACTCACT
16888448 CTTTAGACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (24 bp):
ACTCACTTTGTGATGACTCACAGG
Found at i:16890616 original size:80 final size:80
Alignment explanation
Indices: 16890531--16890691 Score: 277
Period size: 80 Copynumber: 2.0 Consensus size: 80
16890521 GGAGCTTTTA
* *
16890531 TAAAAAACGCCGCAAATGCTTAACCTTTAGCGGTATTTTTGTAAAAGCGCCGCTAATAATTTCAA
1 TAAAAAACGCCGCAAATGCTTAACCTTTAGCGGCATTTTTATAAAAGCGCCGCTAATAATTTCAA
16890596 CAAGACGCAGTCGTT
66 CAAGACGCAGTCGTT
* * *
16890611 TAAAAAGCGCCGCTAATGCTTAACCTTTAGCGGCGTTTTTATAAAAGCGCCGCTAATAATTTCAA
1 TAAAAAACGCCGCAAATGCTTAACCTTTAGCGGCATTTTTATAAAAGCGCCGCTAATAATTTCAA
16890676 CAAGACGCAGTCGTT
66 CAAGACGCAGTCGTT
16890691 T
1 T
16890692 CCTTTCGGCC
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (80 bp):
TAAAAAACGCCGCAAATGCTTAACCTTTAGCGGCATTTTTATAAAAGCGCCGCTAATAATTTCAA
CAAGACGCAGTCGTT
Found at i:16890617 original size:40 final size:41
Alignment explanation
Indices: 16890572--16890691 Score: 126
Period size: 40 Copynumber: 3.0 Consensus size: 41
16890562 GGTATTTTTG
16890572 TAAAAGCGCCGCTAATAATTTCAACAAGACGCAGTCGTTTA
1 TAAAAGCGCCGCTAATAATTTCAACAAGACGCAGTCGTTTA
** * *
16890613 -AAAAGCGCCGCTAAT-GCTT-AACCTTTAG-CGGC-GT-TTTTA
1 TAAAAGCGCCGCTAATAATTTCAA-C--AAGAC-GCAGTCGTTTA
16890652 TAAAAGCGCCGCTAATAATTTCAACAAGACGCAGTCGTTT
1 TAAAAGCGCCGCTAATAATTTCAACAAGACGCAGTCGTTT
16890692 CCTTTCGGCC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
38 2 0.03
39 11 0.18
40 36 0.59
41 10 0.16
42 2 0.03
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (41 bp):
TAAAAGCGCCGCTAATAATTTCAACAAGACGCAGTCGTTTA
Found at i:16891387 original size:15 final size:15
Alignment explanation
Indices: 16891352--16891394 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16891342 TTAGTCGGTA
16891352 AAGG-TTAAGGGTTTT
1 AAGGATTAAGGG-TTT
* *
16891367 ATGGATTATGGGTTT
1 AAGGATTAAGGGTTT
16891382 AAGGATTAAGGGT
1 AAGGATTAAGGGT
16891395 CATGGGTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.28, C:0.00, G:0.35, T:0.37
Consensus pattern (15 bp):
AAGGATTAAGGGTTT
Found at i:16891490 original size:7 final size:7
Alignment explanation
Indices: 16891478--16891613 Score: 67
Period size: 7 Copynumber: 18.7 Consensus size: 7
16891468 ATGAGAGAGG
16891478 GGTTTAT
1 GGTTTAT
16891485 GGTTTAT
1 GGTTTAT
*
16891492 GAGTTAAT
1 G-GTTTAT
* *
16891500 GTTTTAA
1 GGTTTAT
*
16891507 GGTTTAAA
1 GGTTT-AT
*
16891515 GATTT-T
1 GGTTTAT
16891521 GGTTTAT
1 GGTTTAT
*
16891528 GGTTTAA
1 GGTTTAT
* *
16891535 GGGTTAG
1 GGTTTAT
*
16891542 GGTTTAA
1 GGTTTAT
*
16891549 GGTTTAG
1 GGTTTAT
*
16891556 GGGTTAGT
1 GGTTTA-T
* * *
16891564 AGATTAG
1 GGTTTAT
*
16891571 GGTTTAG
1 GGTTTAT
16891578 GGTTTTAT
1 GG-TTTAT
16891586 GGTTTTAT
1 GG-TTTAT
16891594 GGTTTAT
1 GGTTTAT
*
16891601 GTATTTAT
1 G-GTTTAT
16891609 GGTTT
1 GGTTT
16891614 GGGGTTTAAA
Statistics
Matches: 99, Mismatches: 24, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
6 4 0.04
7 59 0.60
8 36 0.36
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (7 bp):
GGTTTAT
Found at i:16891923 original size:26 final size:27
Alignment explanation
Indices: 16891850--16891924 Score: 109
Period size: 26 Copynumber: 2.9 Consensus size: 27
16891840 AATAATTTAA
*
16891850 AATTTTAAAGATTTCAAA-TTTAGAAT
1 AATTTTCAAGATTTCAAATTTTAGAAT
*
16891876 AAATTTCAAGATTTCAAATTTTA-AAT
1 AATTTTCAAGATTTCAAATTTTAGAAT
*
16891902 AATTTTCAATATTTCAAATTTTA
1 AATTTTCAAGATTTCAAATTTTA
16891925 TCTAATTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 40 0.91
27 4 0.09
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (27 bp):
AATTTTCAAGATTTCAAATTTTAGAAT
Found at i:16892070 original size:18 final size:17
Alignment explanation
Indices: 16892039--16892073 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16892029 TAGTTGATTG
*
16892039 TTTTTTAATTTATATTA
1 TTTTTAAATTTATATTA
16892056 TTTTTAAATTATATATTA
1 TTTTTAAATT-TATATTA
16892074 AATAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTAAATTTATATTA
Found at i:16896301 original size:9 final size:9
Alignment explanation
Indices: 16896287--16896364 Score: 84
Period size: 9 Copynumber: 8.3 Consensus size: 9
16896277 CTTAAATGAA
16896287 TTACATAAC
1 TTACATAAC
16896296 TTACATAAC
1 TTACATAAC
* *
16896305 TCATATAAC
1 TTACATAAC
*
16896314 TTACATAAT
1 TTACATAAC
16896323 TTACATAAC
1 TTACATAAC
*
16896332 TCACATAAC
1 TTACATAAC
*
16896341 GTACATAACAAC
1 TTACAT---AAC
16896353 TTACATAAC
1 TTACATAAC
16896362 TTA
1 TTA
16896365 ACTAATACAT
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
9 48 0.86
12 8 0.14
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (9 bp):
TTACATAAC
Found at i:16896326 original size:27 final size:27
Alignment explanation
Indices: 16896287--16896349 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
16896277 CTTAAATGAA
*
16896287 TTACATAACTTACATAACTCATATAAC
1 TTACATAACTTACATAACTCACATAAC
*
16896314 TTACATAATTTACATAACTCACATAAC
1 TTACATAACTTACATAACTCACATAAC
*
16896341 GTACATAAC
1 TTACATAAC
16896350 AACTTACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.44, C:0.22, G:0.02, T:0.32
Consensus pattern (27 bp):
TTACATAACTTACATAACTCACATAAC
Found at i:16901947 original size:21 final size:21
Alignment explanation
Indices: 16901903--16901948 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
16901893 AACTTAGAGT
** *
16901903 GGAGGCAGCAGCGCTAGAGGC
1 GGAGGCAGCAGCGAGAGAGCC
*
16901924 GGAGGCAGCAGCGAGGGAGCC
1 GGAGGCAGCAGCGAGAGAGCC
16901945 GGAG
1 GGAG
16901949 CAGAACAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.52, T:0.02
Consensus pattern (21 bp):
GGAGGCAGCAGCGAGAGAGCC
Found at i:16905929 original size:425 final size:426
Alignment explanation
Indices: 16905127--16905981 Score: 1460
Period size: 425 Copynumber: 2.0 Consensus size: 426
16905117 GACTTTGTAA
*
16905127 AAGCCAAAAATAGGAAAATCTTTTTTAATTTATTTTTGATTTTATATTAAATTAGTTTAGGCTAA
1 AAGCCAAAAATAGGAAAATATTTTTTAATTTATTTTTGATTTTATATTAAATTAGTTTAGGCTAA
*
16905192 ATTTAGTAAACCCCATGTATATAAATAGGGGCTTTATGTTCTTAGGAAATCATCCATTACTTTTG
66 ATTTAGTAAACCCCATGTATATAAATAGGGGCTTTATGTTCTTAGGAAATCATCAATTACTTTTG
*
16905257 TATTCCTACTTCAATTTAGAATTGAATTATTCTCCCTGATCCTATTTCCATTTGGAATTGAATTA
131 TATTCCTACTTCAATTTAGAATTGAATTATTCTCCCTGATCCTATTTCCAATTGGAATTGAATTA
* *
16905322 TTTTCTTTTCTCTTTCAATTTGATGTGGGAATTTTGTTCATTTCATTTCAATTTCTTTTTTCTTT
196 TTTTCTTTTCTCTTTCAATTTGACGTGGGAATTTTGTTCATTTCATTTCAATTTCTTTCTTCTTT
* * *
16905387 TTTAATTCGTGCAATTGCTTTCCAAGCCCTTTTATTCCCTAATCTCTTCCATTACCATACAAATT
261 CTAAATTCGTCCAATTGCTTTCCAAGCCCTTTTATTCCCTAATCTCTTCCATTACCATACAAATT
*
16905452 CAATCACCTTCCACAACTTACAAGCATGAATAAATTCCTACTTCACTAAATTTCA-TAGCTTTAG
326 CAATCACCTTCCACAACTTACAAGCATGAATAAATTCATACTTCACTAAATTTCATTAGCTTTAG
*
16905516 TCCGGTGTTCTTTCCGGTTGGGAATCGTAAGATAAG
391 GCCGGTGTTCTTTCCGGTTGGGAATCGTAAGATAAG
*
16905552 AAGCCAAAAATAGGAAAATATTTTTTATTTTATTTTTGATTTTATATTAAATTAGTTTAGGCTAA
1 AAGCCAAAAATAGGAAAATATTTTTTAATTTATTTTTGATTTTATATTAAATTAGTTTAGGCTAA
16905617 ATTTAGTAAACCCCATGTATATAAATAGGGGCTTTATGTTCTTAGGAAATCATCAATTACTTTTG
66 ATTTAGTAAACCCCATGTATATAAATAGGGGCTTTATGTTCTTAGGAAATCATCAATTACTTTTG
* * ** *
16905682 TATTCCTACTTCAATTTAGAATTGGATTATTCTCTCTTTTCCTATTTCCAATTGGACTTGAATTA
131 TATTCCTACTTCAATTTAGAATTGAATTATTCTCCCTGATCCTATTTCCAATTGGAATTGAATTA
*
16905747 TTTTCTTTTCTCTTTCAATTTGACGTGGGAATTTTGTTCATTTCATTTCGATTTCTTTCTTCTTT
196 TTTTCTTTTCTCTTTCAATTTGACGTGGGAATTTTGTTCATTTCATTTCAATTTCTTTCTTCTTT
16905812 CTAAATTCGTCCAATTGCTTTCCAAGCCCTTTTATTCCCTAATCTCTTCCATTACCATACAAATT
261 CTAAATTCGTCCAATTGCTTTCCAAGCCCTTTTATTCCCTAATCTCTTCCATTACCATACAAATT
* * *
16905877 CAATCACCTTCCACAGCTTACAAGCATGAATAAATTCATGCTTCATTAAATTTCATCTTAGCTTT
326 CAATCACCTTCCACAACTTACAAGCATGAATAAATTCATACTTCACTAAATTTCA--TTAGCTTT
* * * * *
16905942 AGGCCGTTGTTCTTTTCGGTTTGGAATTGTGAGATAAG
389 AGGCCGGTGTTCTTTCCGGTTGGGAATCGTAAGATAAG
16905980 AA
1 AA
16905982 TTCGTGCTAC
Statistics
Matches: 402, Mismatches: 25, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
425 361 0.90
428 41 0.10
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.43
Consensus pattern (426 bp):
AAGCCAAAAATAGGAAAATATTTTTTAATTTATTTTTGATTTTATATTAAATTAGTTTAGGCTAA
ATTTAGTAAACCCCATGTATATAAATAGGGGCTTTATGTTCTTAGGAAATCATCAATTACTTTTG
TATTCCTACTTCAATTTAGAATTGAATTATTCTCCCTGATCCTATTTCCAATTGGAATTGAATTA
TTTTCTTTTCTCTTTCAATTTGACGTGGGAATTTTGTTCATTTCATTTCAATTTCTTTCTTCTTT
CTAAATTCGTCCAATTGCTTTCCAAGCCCTTTTATTCCCTAATCTCTTCCATTACCATACAAATT
CAATCACCTTCCACAACTTACAAGCATGAATAAATTCATACTTCACTAAATTTCATTAGCTTTAG
GCCGGTGTTCTTTCCGGTTGGGAATCGTAAGATAAG
Found at i:16908371 original size:49 final size:50
Alignment explanation
Indices: 16908299--16908431 Score: 153
Period size: 50 Copynumber: 2.7 Consensus size: 50
16908289 CTAGTACGCA
* * * ** * *
16908299 TAGTAGCCTGAACTTATTACTACACATGCGACC-AA-TTTTTCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCT-GATACACG
* *
16908348 TAGTAGCTTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACG
*
16908398 CAGTAGCCTGCACTTAGTACTACACATGTGACCT
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCT
16908432 CACAATAGAT
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
49 28 0.40
50 40 0.57
51 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACG
Found at i:16917082 original size:50 final size:50
Alignment explanation
Indices: 16916969--16917101 Score: 180
Period size: 50 Copynumber: 2.7 Consensus size: 50
16916959 CTAGTACGCA
* * ** * *
16916969 TAGTAGCCTGCACTTATTACTACACATGCGACC-AATTATTCGGTGCACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATTCGATACACG
16917018 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCA-TCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATTC-GATACACG
*
16917068 TAGTAGCCTGCACTTAGTACTACACACGTGACCT
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCT
16917102 CACAATAGAT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
49 33 0.44
50 42 0.56
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATTCGATACACG
Found at i:16923001 original size:37 final size:37
Alignment explanation
Indices: 16922951--16923021 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
16922941 AATAAAGACG
*
16922951 GCTTGAACTGAGTAACTGGGATAGGGTGATTGGTACT
1 GCTTGAACTGAGTAACCGGGATAGGGTGATTGGTACT
16922988 GCTTGAACTGAGTAACCGGGATAGGGTGATTGGT
1 GCTTGAACTGAGTAACCGGGATAGGGTGATTGGT
16923022 TTGTCATCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.24, C:0.11, G:0.37, T:0.28
Consensus pattern (37 bp):
GCTTGAACTGAGTAACCGGGATAGGGTGATTGGTACT
Found at i:16933852 original size:611 final size:611
Alignment explanation
Indices: 16932686--16933909 Score: 2250
Period size: 611 Copynumber: 2.0 Consensus size: 611
16932676 TAAGGCTATA
*
16932686 TACCAAGCCATTTTACCACCCTTTTATGCACACACCTACACAACACAACATAGCACCAATTTATG
1 TACCAAGCCATTTTACCACCCTTTTATGCACACACCTACACAACACAACATAGCACCAATTCATG
*
16932751 CATATATATACAACCAAATCAGCCACAACAAATACATCAACACCACATTCACATGTTACCATCTA
66 CATATATATACAACCAAATCAGCCACAACAAATACATCAACACCACATTCACATGTTACCAACTA
16932816 ACATACATAAACATTACATACACATCAACTCAAATTATGTAAATTTCCAATCCATGAAAGACATC
131 ACATACATAAACATTACATACACATCAACTCAAATTATGTAAATTTCCAATCCATGAAAGACATC
*
16932881 ATTATCTAAATTACTTATACCAATAGTAGACAATTTCAAATGGCCTTATACAGAATGAACTTTCA
196 ATCATCTAAATTACTTATACCAATAGTAGACAATTTCAAATGGCCTTATACAGAATGAACTTTCA
*
16932946 ACCAATATAAGCCAACATATTTGGCCAAATCAATTAAGACACATAACAAAATAACCAAGTCCCCT
261 ACCAATATAAGCCAACACATTTGGCCAAATCAATTAAGACACATAACAAAATAACCAAGTCCCCT
*
16933011 ATACATGCCATAACTCAAAAATGTTGAAATGATTGGTACCAAAATAATTGTTGATAGTGTGAGTG
326 ATACATGCCATAACTCAAAAATGTTGAAATCATTGGTACCAAAATAATTGTTGATAGTGTGAGTG
* *
16933076 GATCTCCGACAGTCTCCGATCCCCAAGCTAGCTTGGTAACGCTATAAAACAAAGGAAAGAAAGGG
391 GATCTCCGACAGTCTCCGATCCCCAAGCTAGCTTAGTAACACTATAAAACAAAGGAAAGAAAGGG
*
16933141 GAGCAAGCTTTACCACTTAGTAAGTTCCTATGCAAATAATAGGTATTATAATCACACATTAAACG
456 GAGCAAGCTTTACCACTTAGTAAGTTCCTATGCAAATAATAGGTATTATAATCACACATTAAACA
*
16933206 TACAATTAGCATGATAAAAATCTTTAGCAAGGGTTCATCACTTATCGAGTTCATTACGTATGAGT
521 TACAATTAGCATGATAAAAATCTTTAGCAAGGGTTCATCACTTATCGAGCTCATTACGTATGAGT
*
16933271 TTTACGTACATACCTGTACCAACTCG
586 TTTACGTACATACCTATACCAACTCG
*
16933297 TACCAAGCCATTTTACCACCCTTTTATGCACACACCTACACAACACAACATATCACCAATTCATG
1 TACCAAGCCATTTTACCACCCTTTTATGCACACACCTACACAACACAACATAGCACCAATTCATG
16933362 CATATATATACAACCAAATCAGCCACAACAAATACATCAACACCACATTCACATGTTACCAACTA
66 CATATATATACAACCAAATCAGCCACAACAAATACATCAACACCACATTCACATGTTACCAACTA
*
16933427 ACATACATAAACATTACATACACATCAGCTCAAATTATGTAAATTTCCAATCCATGAAAGACATC
131 ACATACATAAACATTACATACACATCAACTCAAATTATGTAAATTTCCAATCCATGAAAGACATC
*
16933492 ATCATCTAAATTACTTATACCAATAGTAGCCAATTTCAAATGGCCTTATACAGAATGAACTTTCA
196 ATCATCTAAATTACTTATACCAATAGTAGACAATTTCAAATGGCCTTATACAGAATGAACTTTCA
*
16933557 ACCAATATAAGTCAACACATTTGGCCAAATCAATTAAGACACATAACAAAATAACCAAGTCCCCT
261 ACCAATATAAGCCAACACATTTGGCCAAATCAATTAAGACACATAACAAAATAACCAAGTCCCCT
16933622 ATACATGCCATAACTCAAAAATGTTGAAATCATTGGTACCAAAATAATTGTTGATAGTGTGAGTG
326 ATACATGCCATAACTCAAAAATGTTGAAATCATTGGTACCAAAATAATTGTTGATAGTGTGAGTG
* * * *
16933687 GATCTCTGACAGTCTCCGATCCCCGAGCTAGCTTAGTGACACTATAAAACAAAGGAAAGAAATGG
391 GATCTCCGACAGTCTCCGATCCCCAAGCTAGCTTAGTAACACTATAAAACAAAGGAAAGAAAGGG
* *
16933752 GAGTAAGCTTTACCGCTTAGTAAGTTCCTATGCAAATAATAGGTATTATAATCACACATTAAACA
456 GAGCAAGCTTTACCACTTAGTAAGTTCCTATGCAAATAATAGGTATTATAATCACACATTAAACA
* *
16933817 TACAATTAGCATGATAAAAATCTTTAGCGAGGGTTCATCACTTATTGAGCTCATTACGTATGAGT
521 TACAATTAGCATGATAAAAATCTTTAGCAAGGGTTCATCACTTATCGAGCTCATTACGTATGAGT
16933882 TTTACGTACATACCTATACCAACTCG
586 TTTACGTACATACCTATACCAACTCG
16933908 TA
1 TA
16933910 ACATAGCACA
Statistics
Matches: 591, Mismatches: 22, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
611 591 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (611 bp):
TACCAAGCCATTTTACCACCCTTTTATGCACACACCTACACAACACAACATAGCACCAATTCATG
CATATATATACAACCAAATCAGCCACAACAAATACATCAACACCACATTCACATGTTACCAACTA
ACATACATAAACATTACATACACATCAACTCAAATTATGTAAATTTCCAATCCATGAAAGACATC
ATCATCTAAATTACTTATACCAATAGTAGACAATTTCAAATGGCCTTATACAGAATGAACTTTCA
ACCAATATAAGCCAACACATTTGGCCAAATCAATTAAGACACATAACAAAATAACCAAGTCCCCT
ATACATGCCATAACTCAAAAATGTTGAAATCATTGGTACCAAAATAATTGTTGATAGTGTGAGTG
GATCTCCGACAGTCTCCGATCCCCAAGCTAGCTTAGTAACACTATAAAACAAAGGAAAGAAAGGG
GAGCAAGCTTTACCACTTAGTAAGTTCCTATGCAAATAATAGGTATTATAATCACACATTAAACA
TACAATTAGCATGATAAAAATCTTTAGCAAGGGTTCATCACTTATCGAGCTCATTACGTATGAGT
TTTACGTACATACCTATACCAACTCG
Found at i:16934121 original size:41 final size:41
Alignment explanation
Indices: 16934064--16934164 Score: 202
Period size: 41 Copynumber: 2.5 Consensus size: 41
16934054 ATTCATGGGT
16934064 CTGCTCACACAAGCTGTCAGTCAAGACGTACCTACATAGTA
1 CTGCTCACACAAGCTGTCAGTCAAGACGTACCTACATAGTA
16934105 CTGCTCACACAAGCTGTCAGTCAAGACGTACCTACATAGTA
1 CTGCTCACACAAGCTGTCAGTCAAGACGTACCTACATAGTA
16934146 CTGCTCACACAAGCTGTCA
1 CTGCTCACACAAGCTGTCA
16934165 AGTATTCGTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (41 bp):
CTGCTCACACAAGCTGTCAGTCAAGACGTACCTACATAGTA
Found at i:16935879 original size:25 final size:25
Alignment explanation
Indices: 16935851--16935938 Score: 115
Period size: 25 Copynumber: 3.5 Consensus size: 25
16935841 CATGCAATAC
**
16935851 GCCACAAAAACTTTACTGATAACTT
1 GCCACAAAGGCTTTACTGATAACTT
* *
16935876 GCCACAAAGGCTTTAATGATAA-TCC
1 GCCACAAAGGCTTTACTGATAACT-T
*
16935901 GCCACAAAGGCTTTACAGATAACTT
1 GCCACAAAGGCTTTACTGATAACTT
16935926 GCCACAAAGGCTT
1 GCCACAAAGGCTT
16935939 GGTTTGATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
24 1 0.02
25 52 0.96
26 1 0.02
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (25 bp):
GCCACAAAGGCTTTACTGATAACTT
Found at i:16938340 original size:16 final size:16
Alignment explanation
Indices: 16938319--16938349 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16938309 CTATGCATGC
*
16938319 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
16938335 AAAATACAAAAGACA
1 AAAATACAAAAGACA
16938350 CAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:16939079 original size:67 final size:67
Alignment explanation
Indices: 16938971--16939096 Score: 216
Period size: 67 Copynumber: 1.9 Consensus size: 67
16938961 CAATTACAGG
* * *
16938971 TAGTTTACTATTGTTTCAATCGCATGATACCCCCGATCAGGGCATTCCACTCATACCCTTCTACT
1 TAGTTTACTATTATTTCAATCGCACGATACCCCCGAGCAGGGCATTCCACTCATACCCTTCTACT
16939036 CT
66 CT
*
16939038 TAGTTTACTATTATTTCAATCGCACGATACCCCCGAGCAGGGCATTCCATTCATACCCT
1 TAGTTTACTATTATTTCAATCGCACGATACCCCCGAGCAGGGCATTCCACTCATACCCT
16939097 ACTGTTCTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 55 1.00
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.33
Consensus pattern (67 bp):
TAGTTTACTATTATTTCAATCGCACGATACCCCCGAGCAGGGCATTCCACTCATACCCTTCTACT
CT
Found at i:16943247 original size:17 final size:16
Alignment explanation
Indices: 16943227--16943259 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
16943217 TCAAGTGGGG
16943227 ATTTTATTTGTTATTTT
1 ATTTTATTT-TTATTTT
16943244 ATTTTATTTTTATTTT
1 ATTTTATTTTTATTTT
16943260 CTTTCCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (16 bp):
ATTTTATTTTTATTTT
Found at i:16943736 original size:38 final size:38
Alignment explanation
Indices: 16943693--16943781 Score: 151
Period size: 38 Copynumber: 2.3 Consensus size: 38
16943683 AGTGTGGTTA
*
16943693 TGTGGGCCACACGGGTGTGTGGGTTCTAGGACATGCCG
1 TGTGGGCCACACGGGTGTATGGGTTCTAGGACATGCCG
*
16943731 TGTGGGCCACACGGGTGTATGGGTTCTAGGACATGTCG
1 TGTGGGCCACACGGGTGTATGGGTTCTAGGACATGCCG
*
16943769 TGTGGGACACACG
1 TGTGGGCCACACG
16943782 AGTGATGTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.16, C:0.20, G:0.40, T:0.24
Consensus pattern (38 bp):
TGTGGGCCACACGGGTGTATGGGTTCTAGGACATGCCG
Found at i:16943774 original size:21 final size:21
Alignment explanation
Indices: 16943709--16943774 Score: 50
Period size: 21 Copynumber: 3.3 Consensus size: 21
16943699 CCACACGGGT
*
16943709 GTGTGGGTTCTAGGACATGCC
1 GTGTGGGTTCTAGGACATGTC
* * **
16943730 GTGTGGG--CCA-CACGGGT-
1 GTGTGGGTTCTAGGACATGTC
*
16943747 GTATGGGTTCTAGGACATGTC
1 GTGTGGGTTCTAGGACATGTC
16943768 GTGTGGG
1 GTGTGGG
16943775 ACACACGAGT
Statistics
Matches: 30, Mismatches: 11, Indels: 8
0.61 0.22 0.16
Matches are distributed among these distances:
17 6 0.20
18 3 0.10
19 4 0.13
20 4 0.13
21 13 0.43
ACGTcount: A:0.14, C:0.17, G:0.42, T:0.27
Consensus pattern (21 bp):
GTGTGGGTTCTAGGACATGTC
Found at i:16947111 original size:49 final size:49
Alignment explanation
Indices: 16946995--16947127 Score: 157
Period size: 47 Copynumber: 2.8 Consensus size: 49
16946985 TAGGATATAA
* * *
16946995 TGCCGATGCCATGTCCTAGATATGGTCTTACACT-AGCTCTCACGTTAAG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGA-CTCCCACGTTAAG
* **
16947044 T--CGATGCCATGTCTCAGACATGGTCTTACACTGACTCCCAC-TATCCG
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCCCACGT-TAAG
*
16947091 TGCCGATGCCATGTCCCAGACATGGTCTTATACTGAC
1 TGCCGATGCCATGTCCCAGACATGGTCTTACACTGAC
16947128 ACATCATGAA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
46 1 0.01
47 37 0.51
48 1 0.01
49 33 0.46
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.29
Consensus pattern (49 bp):
TGCCGATGCCATGTCCCAGACATGGTCTTACACTGACTCCCACGTTAAG
Found at i:16955406 original size:112 final size:112
Alignment explanation
Indices: 16955221--16955549 Score: 622
Period size: 112 Copynumber: 2.9 Consensus size: 112
16955211 CACGGTCGTA
* *
16955221 TCTCTACCTGTGTGTTTACTACCATGCATTCTGACTTAAAAATTTTCAGGTGCAGGGGACACACG
1 TCTCTACCCGTGTGTTTACTACCATGCATTCTGACTTAAAAATTTTCAGGTGCAGGGGACACACA
* *
16955286 GCCATACCACACGCCCATGGGGTATCCGTGTGTCACACACAGCCGTG
66 GCCGTACCACACGCCCATAGGGTATCCGTGTGTCACACACAGCCGTG
16955333 TCTCTACCCGTGTGTTTACTACCATGCATTCTGACTTAAAAATTTTCAGGTGCAGGGGACACACA
1 TCTCTACCCGTGTGTTTACTACCATGCATTCTGACTTAAAAATTTTCAGGTGCAGGGGACACACA
16955398 GCCGTACCACACGCCCATAGGGTATCCGTGTGTCACACACAGCCGTG
66 GCCGTACCACACGCCCATAGGGTATCCGTGTGTCACACACAGCCGTG
16955445 TCTCTACCCGTGTGTTTACTACCATGCATTCTGACTTAAAAATTTTCAGGTGCAGGGGACACACA
1 TCTCTACCCGTGTGTTTACTACCATGCATTCTGACTTAAAAATTTTCAGGTGCAGGGGACACACA
16955510 GCCGTACCACACGCCCATAGGGTATCCGTGTGTCACACAC
66 GCCGTACCACACGCCCATAGGGTATCCGTGTGTCACACAC
16955550 GGCCTAGACA
Statistics
Matches: 213, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 213 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (112 bp):
TCTCTACCCGTGTGTTTACTACCATGCATTCTGACTTAAAAATTTTCAGGTGCAGGGGACACACA
GCCGTACCACACGCCCATAGGGTATCCGTGTGTCACACACAGCCGTG
Found at i:16957417 original size:46 final size:46
Alignment explanation
Indices: 16957247--16957416 Score: 154
Period size: 46 Copynumber: 3.7 Consensus size: 46
16957237 TGTAACACGC
* ** *
16957247 CCATAAGTGAACTCGAACTCAACTCAACAAGCTCGGGTGTTCTCAT
1 CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGACGTTCACAT
* *
16957293 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGAATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGAACTCAACTCAACGAGCTCG---GAC--GTTCACAT
* * *
16957343 -C-TCA-CGAACTCGAACTCAACTCAACGAG-TCCGGACGTTCGCAT
1 CCATAAGTGAACTCGAACTCAACTCAACGAGCT-CGGACGTTCACAT
16957386 CCATAAGTGAACTC-AGACTCAACTCAACGAG
1 CCATAAGTGAACTCGA-ACTCAACTCAACGAG
16957417 TTCAGATGCC
Statistics
Matches: 101, Mismatches: 12, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 3 0.03
45 3 0.03
46 55 0.54
47 24 0.24
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGAACTCAACTCAACGAGCTCGGACGTTCACAT
Done.