Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 20 of 185
Found at i:5665827 original size:73 final size:73
Alignment explanation
Indices: 5665750--5665888 Score: 165
Period size: 73 Copynumber: 1.9 Consensus size: 73
5665740 CTTATAAGAG
* * *
5665750 CCATAT-TCAAGAAGCTCATGCGAGCCA-ATAACGAGTAGCTCCGAAGAGCCATTAATCAGGAAG
1 CCATATATCAAGAAGCTCAAGCAAGCCACAT--CGAGAAGCTCCGAAGAGCCATTAATCAGGAAG
5665813 CTCCGGATAA
64 CTCCGGATAA
* * * * * *
5665823 CCATATATCAGGAAGTTCAAGCAAGCTACATCGGGAAGCTCTGGAGAGCCATTAATCAGGAAGCT
1 CCATATATCAAGAAGCTCAAGCAAGCCACATCGAGAAGCTCCGAAGAGCCATTAATCAGGAAGCT
5665888 C
66 C
5665889 ACAAAAAGCC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 37 0.67
74 16 0.29
75 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.19
Consensus pattern (73 bp):
CCATATATCAAGAAGCTCAAGCAAGCCACATCGAGAAGCTCCGAAGAGCCATTAATCAGGAAGCT
CCGGATAA
Found at i:5666982 original size:16 final size:13
Alignment explanation
Indices: 5666948--5666975 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5666938 TTTTATTTTA
5666948 TTATTTATCATCT
1 TTATTTATCATCT
5666961 TTATTTATCATCT
1 TTATTTATCATCT
5666974 TT
1 TT
5666976 CCAATTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (13 bp):
TTATTTATCATCT
Found at i:5684683 original size:21 final size:22
Alignment explanation
Indices: 5684654--5684694 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5684644 CCAAAACAGA
*
5684654 CTTTGAGCGGCGCTTTTTAGGC
1 CTTTGAGCGGCACTTTTTAGGC
5684676 CTTT-AGCGGCACTTTTTAG
1 CTTTGAGCGGCACTTTTTAG
5684695 CGCCGCTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.22, G:0.27, T:0.39
Consensus pattern (22 bp):
CTTTGAGCGGCACTTTTTAGGC
Found at i:5684787 original size:43 final size:43
Alignment explanation
Indices: 5684740--5684974 Score: 248
Period size: 43 Copynumber: 5.5 Consensus size: 43
5684730 GGAAAAAGCA
* *
5684740 CCGCTAAAGACCACAACCTTTAACGGCGCTTCTTCCACAAACG
1 CCGCTAAAGACCATAACCTTTAGCGGCGCTTCTTCCACAAACG
* *
5684783 CCGCTAAAGA-CAAAGACCTTTAGCGGCGCTTCTCCCACAAACG
1 CCGCTAAAGACCATA-ACCTTTAGCGGCGCTTCTTCCACAAACG
* * * * *
5684826 CCGCTATAGACCATGACCTTTCGCGACGCTT-TTATCACAAACG
1 CCGCTAAAGACCATAACCTTTAGCGGCGCTTCTT-CCACAAACG
*
5684869 CCGCTATAA-ACCATGACCTTTAGCGGCGCTT-TTCCCACAAACG
1 CCGCTA-AAGACCATAACCTTTAGCGGCGCTTCTT-CCACAAACG
* ** *
5684912 CCGCTAAAGAACA-AACCTTTAGCGGCGCTTCTAGCAAAAACG
1 CCGCTAAAGACCATAACCTTTAGCGGCGCTTCTTCCACAAACG
* *
5684954 CCGCTAAA-AACATAATCTTTA
1 CCGCTAAAGACCATAACCTTTA
5684975 AAAAAAATTA
Statistics
Matches: 164, Mismatches: 21, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.02
42 44 0.27
43 113 0.69
44 3 0.02
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.21
Consensus pattern (43 bp):
CCGCTAAAGACCATAACCTTTAGCGGCGCTTCTTCCACAAACG
Found at i:5686173 original size:3 final size:3
Alignment explanation
Indices: 5686165--5686192 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5686155 TACATCAATA
5686165 ACT ACT ACT ACT ACT ACT ACT ACT ACT A
1 ACT ACT ACT ACT ACT ACT ACT ACT ACT A
5686193 GAACGATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ACT
Found at i:5688544 original size:7 final size:7
Alignment explanation
Indices: 5688532--5688589 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
5688522 CTAATTAATT
5688532 TAAACCC
1 TAAACCC
5688539 TAAACCC
1 TAAACCC
5688546 T-AACCC
1 TAAACCC
5688552 --AACCC
1 TAAACCC
5688557 TTAAATCCC
1 -TAAA-CCC
**
5688566 TAAATTC
1 TAAACCC
5688573 TAAACCC
1 TAAACCC
*
5688580 CAAACCC
1 TAAACCC
5688587 TAA
1 TAA
5688590 CTCGACCCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
5 5 0.12
6 5 0.12
7 22 0.54
8 6 0.15
9 3 0.07
ACGTcount: A:0.41, C:0.40, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:5688577 original size:41 final size:41
Alignment explanation
Indices: 5688528--5688624 Score: 160
Period size: 41 Copynumber: 2.4 Consensus size: 41
5688518 AAAACTAATT
5688528 AATT-TAAACCCTAAACCCTAACCCAACCCTTAAATCCCTA
1 AATTCTAAACCCTAAACCCTAACCCAACCCTTAAATCCCTA
* * *
5688568 AATTCTAAACCCCAAACCCTAACTCGACCCTTAAATCCCTA
1 AATTCTAAACCCTAAACCCTAACCCAACCCTTAAATCCCTA
5688609 AATTCTAAACCCTAAA
1 AATTCTAAACCCTAAA
5688625 TAATTAACTC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 4 0.08
41 48 0.92
ACGTcount: A:0.40, C:0.36, G:0.01, T:0.23
Consensus pattern (41 bp):
AATTCTAAACCCTAAACCCTAACCCAACCCTTAAATCCCTA
Found at i:5688652 original size:21 final size:21
Alignment explanation
Indices: 5688628--5688687 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
5688618 CCCTAAATAA
* *
5688628 TTAACTCTTAACCCATAACTC
1 TTAACCCTTAACCCATAAATC
* *
5688649 TTAACCCTTAAACCTTAAATC
1 TTAACCCTTAACCCATAAATC
**
5688670 CCAACCCTTAACCCATAA
1 TTAACCCTTAACCCATAA
5688688 TCCCTAAATC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.37, C:0.35, G:0.00, T:0.28
Consensus pattern (21 bp):
TTAACCCTTAACCCATAAATC
Found at i:5688666 original size:14 final size:14
Alignment explanation
Indices: 5688629--5688655 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5688619 CCTAAATAAT
5688629 TAACTCTTAACCCA
1 TAACTCTTAACCCA
5688643 TAACTCTTAACCC
1 TAACTCTTAACCC
5688656 TTAAACCTTA
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:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (14 bp):
TAACTCTTAACCCA
Found at i:5688991 original size:8 final size:7
Alignment explanation
Indices: 5688953--5689080 Score: 64
Period size: 7 Copynumber: 18.1 Consensus size: 7
5688943 ACTAGTTAAT
5688953 CTAAACC
1 CTAAACC
5688960 CTAAACC
1 CTAAACC
*
5688967 ATAAA-C
1 CTAAACC
* *
5688973 TTAAACT
1 CTAAACC
5688980 CTAAAACC
1 CT-AAACC
5688988 CTAAACC
1 CTAAACC
* *
5688995 CTTAACA
1 CTAAACC
5689002 C-ATAACC
1 CTA-AACC
5689009 TCTAAACC
1 -CTAAACC
*
5689017 TTAAACC
1 CTAAACC
* *
5689024 C-CAGCC
1 CTAAACC
*
5689030 TTTAAACC
1 -CTAAACC
*
5689038 ATAAACC
1 CTAAACC
*
5689045 GTAAACC
1 CTAAACC
*
5689052 GTAAACC
1 CTAAACC
*
5689059 ATAAACC
1 CTAAACC
* *
5689066 ATAACCC
1 CTAAACC
5689073 CTAAACC
1 CTAAACC
5689080 C
1 C
5689081 ATAATCCACA
Statistics
Matches: 92, Mismatches: 22, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
6 8 0.09
7 69 0.75
8 14 0.15
9 1 0.01
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:5689022 original size:29 final size:28
Alignment explanation
Indices: 5688952--5689024 Score: 85
Period size: 29 Copynumber: 2.6 Consensus size: 28
5688942 CACTAGTTAA
*
5688952 TCTAAACCCTAAA-CCATAAACTTAAAC
1 TCTAAACCCTAAACCCATAAACATAAAC
* *
5688979 TCTAAAACCCTAAACCCTTAACACATAACC
1 TCT-AAACCCTAAACCCATAA-ACATAAAC
*
5689009 TCTAAACCTTAAACCC
1 TCTAAACCCTAAACCC
5689025 CAGCCTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 3 0.08
28 10 0.26
29 17 0.44
30 9 0.23
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (28 bp):
TCTAAACCCTAAACCCATAAACATAAAC
Found at i:5689049 original size:14 final size:14
Alignment explanation
Indices: 5689032--5689099 Score: 64
Period size: 14 Copynumber: 4.8 Consensus size: 14
5689022 CCCCAGCCTT
*
5689032 TAAACCATAAACCG
1 TAAACCATAAACCA
*
5689046 TAAACCGTAAACCA
1 TAAACCATAAACCA
* *
5689060 TAAACCATAACCCC
1 TAAACCATAAACCA
*
5689074 TAAACCCATAATCCA
1 TAAA-CCATAAACCA
* *
5689089 CAAACCTTAAA
1 TAAACCATAAA
5689100 ATGGTAACAC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
14 32 0.74
15 11 0.26
ACGTcount: A:0.49, C:0.32, G:0.03, T:0.16
Consensus pattern (14 bp):
TAAACCATAAACCA
Found at i:5689056 original size:21 final size:21
Alignment explanation
Indices: 5689032--5689099 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
5689022 CCCCAGCCTT
* *
5689032 TAAACCATAAACCGTAAACCG
1 TAAACCATAAACCATAAACCC
*
5689053 TAAACCATAAACCATAACCCC
1 TAAACCATAAACCATAAACCC
* * *
5689074 TAAACCCATAATCCACAAACCT
1 TAAA-CCATAAACCATAAACCC
5689096 TAAA
1 TAAA
5689100 ATGGTAACAC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 22 0.56
22 17 0.44
ACGTcount: A:0.49, C:0.32, G:0.03, T:0.16
Consensus pattern (21 bp):
TAAACCATAAACCATAAACCC
Found at i:5689099 original size:22 final size:21
Alignment explanation
Indices: 5688983--5689099 Score: 67
Period size: 21 Copynumber: 5.5 Consensus size: 21
5688973 TTAAACTCTA
* *
5688983 AAACCCTAAACCCTTAA-CAC
1 AAACCCTAAACCATAAACCAC
*
5689003 ATAACCTCTAAACCTTAAACC-C
1 A-AACC-CTAAACCATAAACCAC
* * * **
5689025 CAGCCTTTAAACCATAAACCGT
1 AAACC-CTAAACCATAAACCAC
* *
5689047 AAACCGTAAACCATAAACCAT
1 AAACCCTAAACCATAAACCAC
* *
5689068 AACCCCTAAACCCATAATCCAC
1 AAACCCTAAA-CCATAAACCAC
*
5689090 AAACCTTAAA
1 AAACCCTAAA
5689100 ATGGTAACAC
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.01
21 42 0.56
22 31 0.41
23 1 0.01
ACGTcount: A:0.44, C:0.35, G:0.03, T:0.18
Consensus pattern (21 bp):
AAACCCTAAACCATAAACCAC
Found at i:5689364 original size:40 final size:40
Alignment explanation
Indices: 5689312--5689388 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
5689302 TTAAATCCCT
*
5689312 GAGCATTAGCGGTGCTTTTTAAAAAACACCGCTAAAAATA
1 GAGCATTAGCGGTGCTTTATAAAAAACACCGCTAAAAATA
* * **
5689352 GAGCATTCGCGGTGCTTTATCAAAAACGTCGCTAAAA
1 GAGCATTAGCGGTGCTTTATAAAAAACACCGCTAAAA
5689389 GCCCTGAGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (40 bp):
GAGCATTAGCGGTGCTTTATAAAAAACACCGCTAAAAATA
Found at i:5689442 original size:41 final size:41
Alignment explanation
Indices: 5689303--5689684 Score: 498
Period size: 41 Copynumber: 9.3 Consensus size: 41
5689293 TAAAATATTT
* * *** *
5689303 TAAATCCCTGAGCATTAGCGGTGCTTTTTAAAAAACACCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
** * * ** *
5689344 TAAA--AATAGAGCATTCGCGGTGCTTTATCAAAAACGTCGC
1 TAAAGCCCT-GAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
* *
5689384 TAAAAGCCCTGAGCATTAGCGACGCTATCCCAAAAACGCCGC
1 T-AAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
5689426 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
*
5689467 TAAAGCCCTGAGCATTAGCGGCGCTTCCCCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
* *
5689508 TAAAGCCCTAAGCATTAGCGGCGCTTTCCCAAAAACGCTGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
*
5689549 TAAAGCCCTGAGCATTAGCGGCGCTTCCCCAAAAACGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
** *
5689590 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAAAACAGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
* * * *
5689631 TAAAGCCCTGACCATTAGCGGCACTTTTCCAAAAATGCCGC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
5689672 TAAAGCCCTGAGC
1 TAAAGCCCTGAGC
5689685 TTTCTGGGAA
Statistics
Matches: 301, Mismatches: 36, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
39 1 0.00
40 28 0.09
41 245 0.81
42 26 0.09
43 1 0.00
ACGTcount: A:0.30, C:0.31, G:0.20, T:0.19
Consensus pattern (41 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCCCAAAAACGCCGC
Found at i:5689764 original size:40 final size:40
Alignment explanation
Indices: 5689696--5689804 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
5689686 TTCTGGGAAA
* *
5689696 CGCCACTAATGCTTG-TTTTTAGCTGCGTTTTTCATAAAG
1 CGCCACTAATGCTTGATTTTTAGCGGCGTTTTTCAAAAAG
* * *
5689735 CGCCACTAATACTCGATCTTTAGCGGCGTTTTTCAAAAAG
1 CGCCACTAATGCTTGATTTTTAGCGGCGTTTTTCAAAAAG
* *
5689775 CGCCGCTAATGCTTGATTTTTAGCGACGTT
1 CGCCACTAATGCTTGATTTTTAGCGGCGTT
5689805 ATTTATCCAA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
39 13 0.22
40 46 0.78
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (40 bp):
CGCCACTAATGCTTGATTTTTAGCGGCGTTTTTCAAAAAG
Found at i:5696033 original size:33 final size:32
Alignment explanation
Indices: 5695991--5696142 Score: 98
Period size: 33 Copynumber: 4.5 Consensus size: 32
5695981 ATATGGTGGG
5695991 ATCAGCACTTAGCAACCACCAATGAGTCGGGGA
1 ATCAGCACTTAGCAACCACCAATGA-TCGGGGA
*
5696024 ATCAGCACTTAGCAACC-CC--T--TGGGGGA
1 ATCAGCACTTAGCAACCACCAATGATCGGGGA
* * *
5696051 ATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGA
1 ATCAGCACTTAGCAA-CCAC--CA-A--T--GAT-CGG-GGA
* *
5696093 ATCAGCACTTAGTAACCACCAATGATTCGAGGA
1 ATCAGCACTTAGCAACCACCAATGA-TCGGGGA
*
5696126 ATCAGCACTTAGAAACC
1 ATCAGCACTTAGCAACC
5696143 CTTTTTATAT
Statistics
Matches: 94, Mismatches: 9, Indels: 32
0.70 0.07 0.24
Matches are distributed among these distances:
27 20 0.21
28 2 0.02
29 1 0.01
30 1 0.01
31 1 0.01
32 2 0.02
33 36 0.38
34 3 0.03
35 1 0.01
36 2 0.02
38 1 0.01
39 2 0.02
40 1 0.01
41 5 0.05
42 16 0.17
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (32 bp):
ATCAGCACTTAGCAACCACCAATGATCGGGGA
Found at i:5696127 original size:102 final size:102
Alignment explanation
Indices: 5695944--5696143 Score: 328
Period size: 102 Copynumber: 2.0 Consensus size: 102
5695934 CCAGTGATTC
* * * *
5695944 GGGGAATCAACACTTAGCAACCCCTTTCACATTTAAGATATGGTGGGATCAGCACTTAGCAACCA
1 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
* *
5696009 CCAATGAGTCGGGGAATCAGCACTTAGCAACCCCTTG
66 CCAATGAGTCGAGGAATCAGCACTTAGAAACCCCTTG
*
5696046 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGTAACCA
1 GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
*
5696111 CCAATGATTCGAGGAATCAGCACTTAGAAACCC
66 CCAATGAGTCGAGGAATCAGCACTTAGAAACCC
5696144 TTTTTATATT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 90 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.21
Consensus pattern (102 bp):
GGGGAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
CCAATGAGTCGAGGAATCAGCACTTAGAAACCCCTTG
Found at i:5697484 original size:28 final size:28
Alignment explanation
Indices: 5697403--5697484 Score: 94
Period size: 28 Copynumber: 2.9 Consensus size: 28
5697393 AAAATAGCCT
*
5697403 TGACGGATTTCCACTTATAATATAGTTC
1 TGACGGATTTCCACTTATAATATAGTCC
* * * *
5697431 TGACAGACTTCTA-TATATAAGATAGTCC
1 TGACGGATTTCCACT-TATAATATAGTCC
*
5697459 TGATGGATTTCCACTTATAATATAGT
1 TGACGGATTTCCACTTATAATATAGT
5697485 TCTAACGAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
27 1 0.02
28 40 0.95
29 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (28 bp):
TGACGGATTTCCACTTATAATATAGTCC
Found at i:5697527 original size:56 final size:54
Alignment explanation
Indices: 5697411--5697584 Score: 163
Period size: 56 Copynumber: 3.1 Consensus size: 54
5697401 CTTGACGGAT
* * * * *
5697411 TTCCACTTATAATATAGTTCTGACAGAC-TTCTATATATAAGATAGTCCTGATGGAT
1 TTCCACTTATAATATAGTTCTGACA-ACTTTCCAT-T-TAAGATAGTCCTAACGAAC
* *
5697467 TTCCACTTATAATATAGTTCTAACGAACTTTCGCATTTAAGATAGTCTTAACGAAC
1 TTCCACTTATAATATAGTTCTGAC-AACTTTC-CATTTAAGATAGTCCTAACGAAC
* * * *
5697523 TTCCACATATAAAATAG-TCTTGACAAATTTCAACATATAAGATAGTCCTAACGAAC
1 TTCCACTTATAATATAGTTC-TGACAACTTTC--CATTTAAGATAGTCCTAACGAAC
5697579 TTCCAC
1 TTCCAC
5697585 ATTTACAGTA
Statistics
Matches: 99, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
55 8 0.08
56 84 0.85
57 5 0.05
58 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.34
Consensus pattern (54 bp):
TTCCACTTATAATATAGTTCTGACAACTTTCCATTTAAGATAGTCCTAACGAAC
Found at i:5697539 original size:28 final size:28
Alignment explanation
Indices: 5697467--5697586 Score: 125
Period size: 28 Copynumber: 4.3 Consensus size: 28
5697457 CCTGATGGAT
* *
5697467 TTCCACTTATAATATAGT-TCTAACGAAC
1 TTCCACATATAAGATAGTCT-TAACGAAC
* * *
5697495 TTTCGCATTTAAGATAGTCTTAACGAAC
1 TTCCACATATAAGATAGTCTTAACGAAC
* * * *
5697523 TTCCACATATAAAATAGTCTTGACAAAT
1 TTCCACATATAAGATAGTCTTAACGAAC
* *
5697551 TTCAACATATAAGATAGTCCTAACGAAC
1 TTCCACATATAAGATAGTCTTAACGAAC
5697579 TTCCACAT
1 TTCCACAT
5697587 TTACAGTAAT
Statistics
Matches: 72, Mismatches: 19, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
28 71 0.99
29 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.33
Consensus pattern (28 bp):
TTCCACATATAAGATAGTCTTAACGAAC
Found at i:5702749 original size:13 final size:14
Alignment explanation
Indices: 5702731--5702759 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5702721 ATAATTTAAT
5702731 AATAAAT-AAACAA
1 AATAAATAAAACAA
5702744 AATAAATAAAACAA
1 AATAAATAAAACAA
5702758 AA
1 AA
5702760 ATCACATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (14 bp):
AATAAATAAAACAA
Found at i:5711905 original size:31 final size:32
Alignment explanation
Indices: 5711844--5711905 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
5711834 AATCATTTCA
** **
5711844 ACTCTTTTTCAAAAGGTTGATGGTTTAATTTG
1 ACTCTTTTTCAAAAGGTTGATAATCAAATTTG
5711876 ACTCTTTTT-AAAAGGTTGATAATCAAATTT
1 ACTCTTTTTCAAAAGGTTGATAATCAAATTT
5711906 AACTAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.45
Consensus pattern (32 bp):
ACTCTTTTTCAAAAGGTTGATAATCAAATTTG
Found at i:5720203 original size:27 final size:28
Alignment explanation
Indices: 5720149--5720209 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
5720139 ACACAATTTT
* *
5720149 AATTT-TTAATTTTAAAATTTGAATTTA
1 AATTTATTAATTTCAAAATTTGAACTTA
*
5720176 AATTTATTAATTTCAATATTT-AACTTA
1 AATTTATTAATTTCAAAATTTGAACTTA
*
5720203 AAGTTAT
1 AATTTAT
5720210 AAATCTCATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (28 bp):
AATTTATTAATTTCAAAATTTGAACTTA
Found at i:5721104 original size:20 final size:20
Alignment explanation
Indices: 5721081--5721118 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5721071 AAAACTTAAG
5721081 TATATTTTTAAA-ATTGTTCA
1 TATA-TTTTAAATATTGTTCA
5721101 TATATTTTAAATATTGTT
1 TATATTTTAAATATTGTT
5721119 TTATCAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (20 bp):
TATATTTTAAATATTGTTCA
Found at i:5721167 original size:17 final size:17
Alignment explanation
Indices: 5721124--5721167 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
5721114 TTGTTTTATC
* *
5721124 AATAATTTTATTTTACT
1 AATAATTTTATTTAAAT
*
5721141 -ATATTTTTATTTAAAT
1 AATAATTTTATTTAAAT
5721157 AATAATTTTAT
1 AATAATTTTAT
5721168 AAAACACGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
AATAATTTTATTTAAAT
Found at i:5721700 original size:15 final size:17
Alignment explanation
Indices: 5721666--5721702 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
5721656 TATCCTCTTA
5721666 ATTTACCTTAAATAATT
1 ATTTACCTTAAATAATT
*
5721683 ATTTA-CTTATAT-ATT
1 ATTTACCTTAAATAATT
5721698 ATTTA
1 ATTTA
5721703 TATAATTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 6 0.32
17 5 0.26
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTACCTTAAATAATT
Found at i:5721998 original size:20 final size:21
Alignment explanation
Indices: 5721955--5721998 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5721945 TATGTTATTA
*
5721955 TTATTTGATTTCACTTTTTGG
1 TTATTTGATTTCACTATTTGG
5721976 TTATTT-ATTTCA-TATTTGTG
1 TTATTTGATTTCACTATTTG-G
5721996 TTA
1 TTA
5721999 GGTTAATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 10 0.48
21 6 0.29
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (21 bp):
TTATTTGATTTCACTATTTGG
Found at i:5726170 original size:24 final size:24
Alignment explanation
Indices: 5726125--5726170 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
5726115 TTTGAACTAA
* *
5726125 TATGCGAAACCTTATGTGAATAAG
1 TATGCGAAACCTTAAGTAAATAAG
5726149 TATGCGAAA-CTTAAAGTAAATA
1 TATGCGAAACCTT-AAGTAAATA
5726171 TGCATGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.28
Consensus pattern (24 bp):
TATGCGAAACCTTAAGTAAATAAG
Found at i:5729127 original size:11 final size:11
Alignment explanation
Indices: 5729113--5729167 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
5729103 AGATAAATAT
5729113 TATTTTATTAA
1 TATTTTATTAA
*
5729124 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
5729137 TATTTTATTAT
1 TATTTTATTAA
**
5729148 TATTTTATTGT
1 TATTTTATTAA
5729159 TATTTTATT
1 TATTTTATT
5729168 TAGTATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 25 0.66
12 6 0.16
13 7 0.18
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:5730826 original size:62 final size:65
Alignment explanation
Indices: 5730700--5730827 Score: 163
Period size: 63 Copynumber: 2.0 Consensus size: 65
5730690 TGAGCATCTC
* * * * *
5730700 GATCGGTATTTGATCCTGCATGTGTTGCGGACATACCGCAACTCTTTGTGAGCGTCCTGTTATAT
1 GATCGGTATTTGATCCTGCATGTATTGCGGACATACCACAACTCTTTATGAGCGTCCCGATATAT
* * *
5730765 GATCGGTA-TTGATCCTG-TTGTATTGTGGACATACCACAGCTC-TTATGAGCGTCCCGATATAT
1 GATCGGTATTTGATCCTGCATGTATTGCGGACATACCACAACTCTTTATGAGCGTCCCGATATAT
5730827 G
1 G
5730828 GCTCTTCATG
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
62 18 0.33
63 20 0.36
64 9 0.16
65 8 0.15
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.34
Consensus pattern (65 bp):
GATCGGTATTTGATCCTGCATGTATTGCGGACATACCACAACTCTTTATGAGCGTCCCGATATAT
Found at i:5730840 original size:26 final size:25
Alignment explanation
Indices: 5730803--5730851 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
5730793 ACATACCACA
5730803 GCTCTTATGAGCGTCCCGATATATG
1 GCTCTTATGAGCGTCCCGATATATG
*
5730828 GCTCTTCATGAGCTTCCCGATATA
1 GCTCTT-ATGAGCGTCCCGATATA
5730852 GCTCGCTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (25 bp):
GCTCTTATGAGCGTCCCGATATATG
Found at i:5753922 original size:18 final size:17
Alignment explanation
Indices: 5753894--5753928 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5753884 ATTATTAAGA
*
5753894 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
5753911 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
5753929 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:5753949 original size:120 final size:120
Alignment explanation
Indices: 5753803--5754185 Score: 757
Period size: 120 Copynumber: 3.2 Consensus size: 120
5753793 TTTTCAAGTT
*
5753803 ATATATTTAATAATTATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
5753868 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
5753923 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
5753988 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
5754043 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
1 ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
5754108 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
66 TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
5754163 ATATATTTAATAATAATTATGTT
1 ATATATTTAATAATAATTATGTT
5754186 TAAATATGAT
Statistics
Matches: 262, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 262 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
ATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATCATATATTATGATTTCAGTAAAT
TAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAA
Found at i:5754042 original size:18 final size:17
Alignment explanation
Indices: 5754014--5754048 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5754004 ATTATTAAGA
*
5754014 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
5754031 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
5754049 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:5754162 original size:18 final size:17
Alignment explanation
Indices: 5754134--5754168 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5754124 ATTATTAAGA
*
5754134 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
5754151 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
5754169 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:5754425 original size:16 final size:16
Alignment explanation
Indices: 5754404--5754471 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
5754394 GATTTGCTAT
5754404 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5754420 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
5754436 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
5754452 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5754468 TACA
1 TACA
5754472 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:5758357 original size:16 final size:17
Alignment explanation
Indices: 5758338--5758369 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5758328 TTATTAAATC
5758338 ATATATTTAA-ATTAAA
1 ATATATTTAATATTAAA
5758354 ATATATTTAATATTAA
1 ATATATTTAATATTAA
5758370 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATTTAATATTAAA
Found at i:5758448 original size:120 final size:120
Alignment explanation
Indices: 5758324--5758616 Score: 475
Period size: 120 Copynumber: 2.4 Consensus size: 120
5758314 AATTATTTTA
* * *
5758324 AATTTTATTAAATCATATATTTAAATTAAAATATATTTAATATTAATTAT-TTAAAATTT-TATT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT--AATTTATATT
*
5758387 TTATAGTATCATATATTAT-GATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTACAGTATCATATATTATAG-TTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* * *
5758444 AATTTTATTAAATTATATATTTTAATTATATTATATTTAATAATAATTATGTTATTTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
5758509 ACAGTATCATATATTATAGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATAGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
5758564 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
5758617 TAAATATGAT
Statistics
Matches: 161, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
119 4 0.02
120 154 0.96
121 3 0.02
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
ACAGTATCATATATTATAGTTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:5758476 original size:18 final size:17
Alignment explanation
Indices: 5758445--5758479 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5758435 ATTATTAAGA
5758445 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
*
5758462 ATTTTAATTATATTATAT
1 ATTTT-ATTAAATTATAT
5758480 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:5758569 original size:61 final size:61
Alignment explanation
Indices: 5758384--5758571 Score: 183
Period size: 61 Copynumber: 3.1 Consensus size: 61
5758374 TTAAAATTTT
5758384 ATTTTATAGTATCATATATTAT-GATTTGAGTAAATTCATATAAGAATATTAATTATTAAGA
1 ATTTTATAGTATCATATATTATAG-TTTGAGTAAATTCATATAAGAATATTAATTATTAAGA
* * * * * * * * * *
5758445 ATTTTATTA-AATTATATATTTTAATTAT-ATTATATTTA-ATAATAATTATGTTATT-TT-A-T
1 ATTTTA-TAGTATCATATATTATAGTT-TGAGTAAATTCATATAAGAA-TAT-TAATTATTAAGA
*
5758504 ATTTTACAGTATCATATATTATAGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGA
1 ATTTTATAGTATCATATATTATAGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGA
5758565 ATTTTAT
1 ATTTTAT
5758572 TAAATTATAT
Statistics
Matches: 94, Mismatches: 22, Indels: 22
0.68 0.16 0.16
Matches are distributed among these distances:
58 6 0.06
59 31 0.33
60 14 0.15
61 36 0.38
62 7 0.07
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (61 bp):
ATTTTATAGTATCATATATTATAGTTTGAGTAAATTCATATAAGAATATTAATTATTAAGA
Found at i:5758593 original size:18 final size:17
Alignment explanation
Indices: 5758565--5758599 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5758555 ATTATTAAGA
*
5758565 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
5758582 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
5758600 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:5758713 original size:147 final size:149
Alignment explanation
Indices: 5758553--5758827 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
5758543 ATAAGAATAT
*
5758553 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
5758618 AAATATGATTAAATTATTTATTATTGAT-ATTAATAATCTTATTAAAATTTAAATAA-AATAATT
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
5758681 TACCAAAACAAATTTCTGC
131 TACCAAAACAAATTTCTGC
5758700 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
*
5758765 AAATATGATTAAATTATTTATTTTTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
66 AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAA
5758828 CAATAATCAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 91 0.74
148 27 0.22
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTAAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAAATAATCTTATTAAAATTTAAATAACAATAATT
TACCAAAACAAATTTCTGC
Found at i:5758740 original size:18 final size:17
Alignment explanation
Indices: 5758712--5758746 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5758702 ATTATTAAGA
*
5758712 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
5758729 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
5758747 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:5758957 original size:44 final size:45
Alignment explanation
Indices: 5758908--5759002 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
5758898 TTACACCTCT
* *
5758908 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
5758952 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
5758997 ATTACA
1 ATTACA
5759003 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:5759002 original size:16 final size:16
Alignment explanation
Indices: 5758983--5759050 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
5758973 GATTTGCTAT
* *
5758983 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
5758999 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5759015 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
5759031 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
5759047 TACA
1 TACA
5759051 GCGAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:5763490 original size:22 final size:22
Alignment explanation
Indices: 5763462--5763505 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5763452 AAATAAGAAG
5763462 AAGAATAAACATCATATGCAAT
1 AAGAATAAACATCATATGCAAT
5763484 AAGAATAAACATCATATGCAAT
1 AAGAATAAACATCATATGCAAT
5763506 TTTATCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (22 bp):
AAGAATAAACATCATATGCAAT
Found at i:5767774 original size:44 final size:43
Alignment explanation
Indices: 5767719--5767859 Score: 165
Period size: 44 Copynumber: 3.2 Consensus size: 43
5767709 AGTTGTTAAA
*
5767719 TGGTAAGAAATGAACATGCATTATAATTGTTTGATTGGTTGTCT
1 TGGTAAGAAATGAACATGCATTATAATTGTTTGATTGATTGT-T
* * * *
5767763 TGGTAATAAATGAACACGCATTATAAATGTTTGGTTGATTGTT
1 TGGTAAGAAATGAACATGCATTATAATTGTTTGATTGATTGTT
* * * * *
5767806 TGGCAAGAAATGGACATGTAATATAATTGTCTTGGTTGATTGTT
1 TGGTAAGAAATGAACATGCATTATAATTGT-TTGATTGATTGTT
5767850 TAGGTAAGAA
1 T-GGTAAGAA
5767860 TTTCAATGGT
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
43 24 0.29
44 51 0.62
45 7 0.09
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.38
Consensus pattern (43 bp):
TGGTAAGAAATGAACATGCATTATAATTGTTTGATTGATTGTT
Found at i:5771800 original size:16 final size:16
Alignment explanation
Indices: 5771781--5771815 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5771771 ATATATTGTT
5771781 ATATTATATTATTATA
1 ATATTATATTATTATA
*
5771797 ATATTATATTATTGTA
1 ATATTATATTATTATA
5771813 ATA
1 ATA
5771816 ATAAAACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATATTATATTATTATA
Found at i:5785979 original size:418 final size:419
Alignment explanation
Indices: 5784991--5786037 Score: 1579
Period size: 421 Copynumber: 2.5 Consensus size: 419
5784981 TCTAACAGGT
* * *
5784991 ATAACCTTCACAAC-ACTCTATTATTTACTTGGGGCTAAGATAGAACCATTTCATAGGTTTTGTA
1 ATAACATTCACAACTA-TCTATTATTTACTT-GGGTTAAGATAGAACCATTTCATAGTTTTTGTA
* * ** * * *
5785055 GCCTAACTAAAACCTTCTAACTTTTCGAAGGCTTAACTAAAAACTTATTTAATTTTTATGGCTCA
64 GCTTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCA
* * * *
5785120 ATTAGTAATCCTCCGAATATGCAAATTGGTGATTTGTATAAACAAATGAAAAACCTCAAAAATGT
129 ATTAGTAATCCTCTGAATATACAAATTGGTGATTTGTGTAAA-AAATGAAAAACCTCTAAAATGT
* *
5785185 TTGAGTGTTTGCAAAGTCATATAGTAATTGGATTTTGGTGTAATTACTTGCATAATTACTCCAAT
193 ATGAGTGTTTGCAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGCATAATTACTCCAAT
*
5785250 TCTCAACCTCGCCTAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGGG
258 TCTCAACCTCGCCGAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGGG
5785315 ATCCACCAATTACACCCAAATTCAATTACTAAGTTGTTTTCCAAACATAGCCAAAAGGTTTTCCC
323 ATCCACCAATTACACCCAAATTCAATTACTAAGTTGTTTTCCAAACATAGCCAAAAGGTTTTCCC
* * *
5785380 AGTTCAGTAATTGGTATCTTTCAATAACAAGG
388 AGTTCACTAATTGGCATCTTTCAAGAACAAGG
* * *
5785412 TATAACTTTCACAACTCTTTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAG
1 -ATAACATTCACAACTATCTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAG
5785477 CTTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCAA
65 CTTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCAA
*
5785542 TTAGTAATCCT-TCGAATATACAAATTGGTGATATGTGTAAGAAAATGAAAAACCTCTAAAATGT
130 TTAGTAATCCTCT-GAATATACAAATTGGTGATTTGTGTAA-AAAATGAAAAACCTCTAAAATGT
* **
5785606 ATGAGTGTTTGGAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGTGTAATTACTCCAAT
193 ATGAGTGTTTGCAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGCATAATTACTCCAAT
* * * * *
5785671 TCTCACCCTCGTCGAAGAGTTGGAAAGTGTAATT-GGGTGCTTCAATTATACCCATTTTAATGTG
258 TCTCAACCTCGCCGAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGGG
* * *
5785735 ATCCACCAGTTACACCCAAATTCAATTACTAAGTTGCTTTT-CAAACATAGCCTAAAGGTTTTCT
323 ATCCACCAATTACACCCAAATTCAATTACTAAGTTG-TTTTCCAAACATAGCCAAAAGGTTTTCC
*
5785799 CAGTTCACTAATTGGCATCTTTCAAGGACAAGG
387 CAGTTCACTAATTGGCATCTTTCAAGAACAAGG
* *
5785832 -TAACATTCACAACTATCTATTATTTACTTGGGTTAAGGTAGAACCATTTCATAATTTTTGTAGC
1 ATAACATTCACAACTATCTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAGC
* *
5785896 TTAACTAGAACCTTGTAACTTTTCGAAGGCCCAACTAAAAA-TCTCTCTAGTTTTTATGGTTCAA
66 TTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACT-TCTCTAGTTTTTATGGCTCAA
*
5785960 TTAGTAATCCTCTGAATATACAAATTGGTGATTTGTGTAAAAAAATGAAAATCCTCTAAAATGTA
130 TTAGTAATCCTCTGAATATACAAATTGGTGATTTGTGT-AAAAAATGAAAAACCTCTAAAATGTA
*
5786025 -G-GTGTTTACAAAG
194 TGAGTGTTTGCAAAG
5786038 TTTAGCTTAT
Statistics
Matches: 572, Mismatches: 46, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
416 10 0.02
417 2 0.00
418 177 0.31
419 3 0.01
420 112 0.20
421 241 0.42
422 27 0.05
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (419 bp):
ATAACATTCACAACTATCTATTATTTACTTGGGTTAAGATAGAACCATTTCATAGTTTTTGTAGC
TTAACTAGAACCTTCTAACTTTTCGAAGGCCCAACTAAAAACTTCTCTAGTTTTTATGGCTCAAT
TAGTAATCCTCTGAATATACAAATTGGTGATTTGTGTAAAAAATGAAAAACCTCTAAAATGTATG
AGTGTTTGCAAAGCCATATAGTAATTGGATTTTGGTGTAATTACTTGCATAATTACTCCAATTCT
CAACCTCGCCGAAGAGTTGGAAAGTGTAATTGGGGTGCTTCAATTATACACAATTTAATGGGATC
CACCAATTACACCCAAATTCAATTACTAAGTTGTTTTCCAAACATAGCCAAAAGGTTTTCCCAGT
TCACTAATTGGCATCTTTCAAGAACAAGG
Found at i:5788432 original size:3 final size:3
Alignment explanation
Indices: 5788417--5788464 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
5788407 GCTGTTGTAA
* *
5788417 AAG AAG GAG AAG AAG AAG GAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
5788465 CAGAGTGTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5801057 original size:9 final size:9
Alignment explanation
Indices: 5801039--5801105 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
5801029 TTTGGTTAAA
*
5801039 AATTAACCG
1 AATTACCCG
5801048 AATTACCCG
1 AATTACCCG
* *
5801057 AATTAACTG
1 AATTACCCG
* *
5801066 AATTAACCA
1 AATTACCCG
5801075 AATTACCCG
1 AATTACCCG
*
5801084 AATTACCTG
1 AATTACCCG
5801093 AATTACCCG
1 AATTACCCG
5801102 AATT
1 AATT
5801106 GAATCACTAC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 49 1.00
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (9 bp):
AATTACCCG
Found at i:5801071 original size:27 final size:27
Alignment explanation
Indices: 5801039--5801105 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
5801029 TTTGGTTAAA
5801039 AATTAACCGAATTACCCGAATTAACTG
1 AATTAACCGAATTACCCGAATTAACTG
* *
5801066 AATTAACCAAATTACCCGAATTACCTG
1 AATTAACCGAATTACCCGAATTAACTG
*
5801093 AATTACCCGAATT
1 AATTAACCGAATT
5801106 GAATCACTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (27 bp):
AATTAACCGAATTACCCGAATTAACTG
Found at i:5801278 original size:18 final size:18
Alignment explanation
Indices: 5801255--5801294 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5801245 TTTATGATTA
5801255 GGTTGGGTTCGATAATTG
1 GGTTGGGTTCGATAATTG
* *
5801273 GGTTGGGTTGGATACTTG
1 GGTTGGGTTCGATAATTG
5801291 GGTT
1 GGTT
5801295 TGGATTGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.05, G:0.42, T:0.40
Consensus pattern (18 bp):
GGTTGGGTTCGATAATTG
Found at i:5801302 original size:19 final size:18
Alignment explanation
Indices: 5801255--5801302 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
5801245 TTTATGATTA
* *
5801255 GGTTGGGTTCGATAATTG
1 GGTTGGATTGGATAATTG
* *
5801273 GGTTGGGTTGGATACTTG
1 GGTTGGATTGGATAATTG
5801291 GGTTTGGATTGG
1 GG-TTGGATTGG
5801303 GTTTAGGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.12, C:0.04, G:0.44, T:0.40
Consensus pattern (18 bp):
GGTTGGATTGGATAATTG
Found at i:5803269 original size:24 final size:24
Alignment explanation
Indices: 5803219--5803271 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
5803209 CAAAGAATAG
* * * * *
5803219 AAAAGAATATATTTAAATTGTGTA
1 AAAAGAAAATAATTAAATAGGGAA
5803243 AAAAGAAAATAATTAAATAGGGAA
1 AAAAGAAAATAATTAAATAGGGAA
5803267 AAAAG
1 AAAAG
5803272 GGGAATCAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.15, T:0.25
Consensus pattern (24 bp):
AAAAGAAAATAATTAAATAGGGAA
Found at i:5806140 original size:22 final size:22
Alignment explanation
Indices: 5806102--5806145 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5806092 GGCCTCGAAG
*
5806102 ATCTAAACTAAACTTTGTCAAA
1 ATCTAAACTAAACTTTGCCAAA
* *
5806124 ATCTAAACTTAATTTTGCCAAA
1 ATCTAAACTAAACTTTGCCAAA
5806146 CAATCAGCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (22 bp):
ATCTAAACTAAACTTTGCCAAA
Found at i:5828629 original size:3 final size:3
Alignment explanation
Indices: 5828621--5828650 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5828611 TGAATTTAGG
5828621 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5828651 TCACATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5832389 original size:24 final size:24
Alignment explanation
Indices: 5832362--5832504 Score: 205
Period size: 24 Copynumber: 6.0 Consensus size: 24
5832352 TGGTACTCCA
* *
5832362 CCATCATCTGGAGGTGGTAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
* *
5832386 CCATCGTATGGAGGAGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
* *
5832410 CCATCGTATGGAGGAGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
* *
5832434 CCATCGTATGGAGGAGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
*
5832458 CCATCATACGGAGGTGGCAGTCCC
1 CCATCATATGGAGGTGGCAGTCCC
5832482 CCATCATATGGAGGTGGCAGTCC
1 CCATCATATGGAGGTGGCAGTCC
5832505 ACCAACTACT
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 111 1.00
ACGTcount: A:0.20, C:0.29, G:0.31, T:0.19
Consensus pattern (24 bp):
CCATCATATGGAGGTGGCAGTCCC
Found at i:5839430 original size:29 final size:29
Alignment explanation
Indices: 5839398--5839456 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5839388 TTAATAATAG
5839398 AAAATTAGCTATTAGGTTGGTTAAATGAT
1 AAAATTAGCTATTAGGTTGGTTAAATGAT
5839427 AAAATTAGCTATTAGGTTGGTTAAATGAT
1 AAAATTAGCTATTAGGTTGGTTAAATGAT
5839456 A
1 A
5839457 TATGTTGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.37
Consensus pattern (29 bp):
AAAATTAGCTATTAGGTTGGTTAAATGAT
Found at i:5840346 original size:14 final size:14
Alignment explanation
Indices: 5840329--5840356 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5840319 TATTAAATTG
5840329 TAGAACTAAAATGC
1 TAGAACTAAAATGC
5840343 TAGAACTAAAATGC
1 TAGAACTAAAATGC
5840357 CAAAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
TAGAACTAAAATGC
Found at i:5841442 original size:20 final size:18
Alignment explanation
Indices: 5841419--5841475 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
5841409 TTTAGTCATA
5841419 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATAT--T
*
5841439 TAATATATTTATT-AT-TT
1 TAATA-AATTATTAATATT
5841456 TAATAAATTATTTAATATT
1 TAATAAATTA-TTAATATT
5841475 T
1 T
5841476 TAATTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 4 0.13
17 8 0.26
18 2 0.06
19 4 0.13
20 7 0.23
21 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATAAATTATTAATATT
Found at i:5841451 original size:21 final size:20
Alignment explanation
Indices: 5841426--5841469 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
5841416 ATATAATAAA
*
5841426 TTATTAATATAATTAATATAT
1 TTATTAATATAATAAAT-TAT
* *
5841447 TTATTATTTTAATAAATTAT
1 TTATTAATATAATAAATTAT
5841467 TTA
1 TTA
5841470 ATATTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTAATATAATAAATTAT
Found at i:5841476 original size:20 final size:20
Alignment explanation
Indices: 5841419--5841479 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
5841409 TTTAGTCATA
5841419 TAATAAATTA-TTAATA---
1 TAATAAATTATTTAATATTT
* *
5841435 TAATTAATATATTTATTATTT
1 TAATAAAT-TATTTAATATTT
5841456 TAATAAATTATTTAATATTT
1 TAATAAATTATTTAATATTT
5841476 TAAT
1 TAAT
5841480 TTTATTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 7 0.19
17 2 0.06
18 5 0.14
20 15 0.42
21 7 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TAATAAATTATTTAATATTT
Found at i:5841499 original size:13 final size:14
Alignment explanation
Indices: 5841483--5841524 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
5841473 TTTTAATTTT
5841483 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
5841496 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
5841511 ATTTTAAATAATAT
1 ATTTT-AATAATAT
5841525 TCTTTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:5841509 original size:16 final size:16
Alignment explanation
Indices: 5841487--5841523 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
5841477 AATTTTATTT
5841487 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
5841504 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
5841519 TAATA
1 TAATA
5841524 TTCTTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:5844024 original size:44 final size:44
Alignment explanation
Indices: 5843970--5844304 Score: 145
Period size: 44 Copynumber: 7.3 Consensus size: 44
5843960 TATAGGAATT
* * * * *
5843970 GTAGTTTCAATCTACTCCGCTGCAATTTCAGGGAGATGAGATTC
1 GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTC
* *
5844014 GTAGCTTCAATCTGCTCCACTACAACTTCAGTGAGATAAGATTTGTAGC
1 GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGA--T-T--C
* * ** * * *
5844063 TTGTAGCTTTAATTTGTTCCACTGCAACTTCAGGGAAATAAGACTCGCTATG
1 --GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGA-----T-TC
* * * * * * *
5844115 GTAGATTTAATCCGAC-CCACTACAACTTAAGAGG-TATAGGATTT
1 GTAGCTTCAAT-CTACTCCACTACAACTTCAG-GGAGATAAGATTC
* * * * *
5844159 GTCA-TTTCAATCTGCTCCACTACAACTTTAGTGAGATAAGATTT
1 GT-AGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTC
* * * * *
5844203 GTAGCTTTAATCTACTCCACTGCAACTTCAGGAATATAAGATTT
1 GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTC
* * ** ** *
5844247 GTAGCTTCAATCTGCTTCACTGTAACTTCAAAGAGATAAGATTT
1 GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTC
* *
5844291 GTAGTTTTAATCTA
1 GTAGCTTCAATCTA
5844305 TGCTGCAACA
Statistics
Matches: 221, Mismatches: 54, Indels: 32
0.72 0.18 0.10
Matches are distributed among these distances:
43 4 0.02
44 145 0.66
45 2 0.01
46 1 0.00
47 1 0.00
49 1 0.00
50 28 0.13
51 37 0.17
54 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (44 bp):
GTAGCTTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTC
Found at i:5852623 original size:3 final size:3
Alignment explanation
Indices: 5852615--5852654 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5852605 ATTCCTTTTC
5852615 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5852655 ACTCACATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5852790 original size:31 final size:31
Alignment explanation
Indices: 5852725--5852790 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
5852715 TTTTTAACTA
* * *
5852725 AATTCGACCCTTAACATTTTAAAAGGAGTCG
1 AATTCGACCATCAACATTTTAAAAGAAGTCG
*
5852756 AATTCGACCATCAACATTTTATAAA-AAGTTG
1 AATTCGACCATCAACATTTTA-AAAGAAGTCG
5852787 AATT
1 AATT
5852791 TAACGAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (31 bp):
AATTCGACCATCAACATTTTAAAAGAAGTCG
Found at i:5853089 original size:14 final size:14
Alignment explanation
Indices: 5853072--5853098 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5853062 AAACAACTTC
5853072 TGGAAAATGAATTT
1 TGGAAAATGAATTT
5853086 TGGAAAATGAATT
1 TGGAAAATGAATT
5853099 GATTTTATGG
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:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (14 bp):
TGGAAAATGAATTT
Found at i:5853315 original size:17 final size:17
Alignment explanation
Indices: 5853278--5853329 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
5853268 AATCAAAATT
* *
5853278 TATTTTATGATAAGATAA
1 TATTTTATAATAA-TTAA
5853296 TATTTTATAATAATTAA
1 TATTTTATAATAATTAA
** *
5853313 TATAATATAATATTTAA
1 TATTTTATAATAATTAA
5853330 ACTTAATAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (17 bp):
TATTTTATAATAATTAA
Found at i:5853552 original size:16 final size:16
Alignment explanation
Indices: 5853531--5853561 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5853521 ATTTATATTA
5853531 ATTATATTAATAAATT
1 ATTATATTAATAAATT
*
5853547 ATTATATTACTAAAT
1 ATTATATTAATAAAT
5853562 ATAAATAATT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATATTAATAAATT
Found at i:5856670 original size:11 final size:11
Alignment explanation
Indices: 5856642--5856766 Score: 100
Period size: 11 Copynumber: 11.5 Consensus size: 11
5856632 ATTTTAAAAA
5856642 TTAAAAA-ATT
1 TTAAAAATATT
*
5856652 TAAAAAAAGTATT
1 T-TAAAAA-TATT
5856665 TTAAAAATATT
1 TTAAAAATATT
5856676 TTAAAAATATT
1 TTAAAAATATT
*
5856687 TT-AAAAT-TA
1 TTAAAAATATT
**
5856696 AAAAAAAGTATT
1 TTAAAAA-TATT
5856708 TTAAAAATATT
1 TTAAAAATATT
5856719 TT--AAA-ATT
1 TTAAAAATATT
* *
5856727 TTAAAAAAATA
1 TTAAAAATATT
**
5856738 AAAAAAAGTATT
1 TTAAAAA-TATT
5856750 TTAAAAATATT
1 TTAAAAATATT
5856761 TTAAAA
1 TTAAAA
5856767 TTAAAATAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
8 5 0.06
9 4 0.04
10 13 0.14
11 46 0.51
12 18 0.20
13 4 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:5856672 original size:43 final size:42
Alignment explanation
Indices: 5856631--5856783 Score: 222
Period size: 42 Copynumber: 3.7 Consensus size: 42
5856621 ACCAAAAATT
*
5856631 TATTTTAAAA-ATTAAAAAATTTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATATTAAAAAATTAAAAAAAAGTATTTTAAAAA
**
5856672 TATTTTAAAAATATTTTAAAATTAAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATATTAAAAAATTAAAAAAAAGTATTTTAAAAA
* *
5856715 TATTTTAAAATTTTAAAAAAATAAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATATTAAAAAATTAAAAAAAAGTATTTTAAAAA
5856757 TATTTT-AAA-ATTAAAATAATTAAAAAA
1 TATTTTAAAATATTAAAA-AATTAAAAAA
5856784 TAAATATATT
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
40 6 0.06
41 18 0.18
42 42 0.42
43 34 0.34
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (42 bp):
TATTTTAAAATATTAAAAAATTAAAAAAAAGTATTTTAAAAA
Found at i:5856710 original size:32 final size:32
Alignment explanation
Indices: 5856667--5856737 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
5856657 AAAGTATTTT
5856667 AAAAATATTTTAAAAATATTTTAAAA-TTAAA
1 AAAAATATTTTAAAAATATTTTAAAATTTAAA
*
5856698 AAAAAGTATTTTAAAAATATTTTAAAATTTTAA
1 AAAAA-TATTTTAAAAATATTTTAAAATTTAAA
5856731 AAAAATA
1 AAAAATA
5856738 AAAAAAAGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 5 0.14
32 23 0.62
33 9 0.24
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (32 bp):
AAAAATATTTTAAAAATATTTTAAAATTTAAA
Found at i:5856772 original size:16 final size:16
Alignment explanation
Indices: 5856753--5856795 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5856743 AAGTATTTTA
* *
5856753 AAAATATTTTAAAATT
1 AAAATATTTAAAAAAT
*
5856769 AAAATAATTAAAAAAT
1 AAAATATTTAAAAAAT
5856785 AAATATATTTA
1 AAA-ATATTTA
5856796 GCCCGGGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAATATTTAAAAAAT
Found at i:5862405 original size:16 final size:17
Alignment explanation
Indices: 5862384--5862427 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
5862374 AATAAAACTA
5862384 ATAATAATTAAT-AATG
1 ATAATAATTAATAAATG
5862400 ATAATAA-TAATAAATG
1 ATAATAATTAATAAATG
5862416 ATAATACATTAA
1 ATAATA-ATTAA
5862428 AATAATTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.16
16 17 0.68
17 1 0.04
18 3 0.12
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (17 bp):
ATAATAATTAATAAATG
Found at i:5863224 original size:14 final size:14
Alignment explanation
Indices: 5863205--5863231 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5863195 ATGTAAAAGA
5863205 TAAAATAAAATAAG
1 TAAAATAAAATAAG
5863219 TAAAATAAAATAA
1 TAAAATAAAATAA
5863232 ACAAGCAGAA
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:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
TAAAATAAAATAAG
Found at i:5864376 original size:46 final size:45
Alignment explanation
Indices: 5864326--5864436 Score: 136
Period size: 45 Copynumber: 2.4 Consensus size: 45
5864316 AAAAAATTAC
* *
5864326 AATATATAATATATAAATAAAAAGTTAAAATTTATAAATTTATG-AA
1 AATATATAATATATAAA-AAAAACTAAAAATTTATAAATTT-TGAAA
5864372 AATATATAA-ATATATAAAAAAACTAAAAATTTATAAATTTTGTAAA
1 AATATATAATATATA-AAAAAAACTAAAAATTTATAAATTTTG-AAA
*
5864418 AAAATATAAATATATAAAA
1 AATATAT-AATATATAAAA
5864437 GAATTAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
44 2 0.04
45 26 0.46
46 19 0.33
47 5 0.09
48 5 0.09
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (45 bp):
AATATATAATATATAAAAAAAACTAAAAATTTATAAATTTTGAAA
Found at i:5864379 original size:18 final size:18
Alignment explanation
Indices: 5864352--5864408 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
5864342 ATAAAAAGTT
* *
5864352 AAAATTTATAAATTTATG
1 AAAATATATAAATTTATA
*
5864370 AAAATATATAAATATATA
1 AAAATATATAAATTTATA
* *
5864388 AAAAAACTAAAAATTTATA
1 AAAATA-TATAAATTTATA
5864407 AA
1 AA
5864409 TTTTGTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 20 0.62
19 12 0.38
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAATATATAAATTTATA
Found at i:5864400 original size:27 final size:27
Alignment explanation
Indices: 5864370--5864435 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
5864360 TAAATTTATG
5864370 AAAATATATAAA-TATATAAAAAAACTA
1 AAAATATATAAATTATATAAAAAAA-TA
* * *
5864397 AAAATTTATAAATTTTGTAAAAAAATA
1 AAAATATATAAATTATATAAAAAAATA
*
5864424 TAAATATATAAA
1 AAAATATATAAA
5864436 AGAATTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
27 23 0.70
28 10 0.30
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (27 bp):
AAAATATATAAATTATATAAAAAAATA
Found at i:5864445 original size:46 final size:45
Alignment explanation
Indices: 5864326--5864447 Score: 149
Period size: 46 Copynumber: 2.6 Consensus size: 45
5864316 AAAAAATTAC
5864326 AATATATAATATATAAATAAAAAGTT-AAAATTTATAAATTTATGAAAA
1 AATATA-AATATAT-AA-AAAAA-TTAAAAATTTATAAATTTATGAAAA
* *
5864374 TATATAAATATATAAAAAAACTAAAAATTTATAAATTT-TGTAAAAA
1 AATATAAATATATAAAAAAATTAAAAATTTATAAATTTATG--AAAA
*
5864420 AATATAAATATATAAAAGAATTAAAAAT
1 AATATAAATATATAAAAAAATTAAAAAT
5864448 CTCATATATA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
44 3 0.05
45 20 0.30
46 31 0.47
47 7 0.11
48 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (45 bp):
AATATAAATATATAAAAAAATTAAAAATTTATAAATTTATGAAAA
Found at i:5868349 original size:27 final size:25
Alignment explanation
Indices: 5868319--5868371 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
5868309 CCCCACGTGG
*
5868319 TAAAATGACTGTGATGCCCCTATGTTA
1 TAAAATGACTAT-ATG-CCCTATGTTA
*
5868346 TAAAATGACTATATGCTCTATGTTA
1 TAAAATGACTATATGCCCTATGTTA
5868371 T
1 T
5868372 GTATAACTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 11 0.46
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (25 bp):
TAAAATGACTATATGCCCTATGTTA
Found at i:5873269 original size:13 final size:15
Alignment explanation
Indices: 5873239--5873270 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5873229 ATATTTCATG
5873239 CATTTCATCAATAAT
1 CATTTCATCAATAAT
5873254 CATTTCAT-AA-AAT
1 CATTTCATCAATAAT
5873267 CATT
1 CATT
5873271 ATTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 2 0.12
15 8 0.47
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.41
Consensus pattern (15 bp):
CATTTCATCAATAAT
Found at i:5873794 original size:6 final size:6
Alignment explanation
Indices: 5873762--5873802 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
5873752 CACACTAGTA
* *
5873762 AACAGT AATCAGT AACGGT AGCAGT AACAGT AACAGT AACA
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACA
5873803 ATATTCAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (6 bp):
AACAGT
Found at i:5873904 original size:44 final size:45
Alignment explanation
Indices: 5873783--5873966 Score: 212
Period size: 45 Copynumber: 4.1 Consensus size: 45
5873773 GTAACGGTAG
* * *
5873783 CAGTAACAGTAACAGTAACAATATTCAACACATAAAGTG-CTGAAC
1 CAGTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCT-AAT
* * * *
5873828 CTGTAATAGTAACGGTAACAATATTCGACACACAAAGTGCCTAGT
1 CAGTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCTAAT
* * *
5873873 CGGTAACAGTAAC-GTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCTAAT
* * * *
5873917 CAGTAACAGTAACAGTAACAGTAGTCGGCACA-TAAGTGCCTAAT
1 CAGTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCTAAT
5873961 CAGTAA
1 CAGTAA
5873967 GCCGGCAAAT
Statistics
Matches: 120, Mismatches: 17, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
44 56 0.47
45 62 0.52
46 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCTAAT
Found at i:5873931 original size:39 final size:39
Alignment explanation
Indices: 5873835--5873933 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 39
5873825 AACCTGTAAT
* * * *
5873835 AGTAACGGTAACAATATTCGACACACAAAGTGCCTAGTC
1 AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
*
5873874 GGTAACAGTAACGTAACAGTATTCGACACACAAAGTGCCGAATC
1 AGTAAC----A-GTAACAGTATTCGACACACAAAGTGCCGAATC
5873918 AGTAACAGTAACAGTA
1 AGTAACAGTAACAGTA
5873934 ACAGTAGTCG
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
39 14 0.29
40 1 0.02
44 34 0.69
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (39 bp):
AGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATC
Found at i:5888691 original size:21 final size:21
Alignment explanation
Indices: 5888665--5888707 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5888655 GGTTCGCTGT
*
5888665 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
5888686 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
5888707 A
1 A
5888708 ATAGAGGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:5888707 original size:16 final size:16
Alignment explanation
Indices: 5888688--5888720 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5888678 TGTATTGGAT
*
5888688 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
5888704 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
5888720 T
1 T
5888721 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:5888765 original size:45 final size:44
Alignment explanation
Indices: 5888699--5888793 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
5888689 GGATTAGAGG
* *
5888699 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
5888744 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
5888788 TGTAAT
1 TGTAAT
5888794 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:5888976 original size:18 final size:17
Alignment explanation
Indices: 5888955--5888989 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5888945 TTATTATTTA
*
5888955 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5888973 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5888990 GGTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5888983 original size:28 final size:27
Alignment explanation
Indices: 5888913--5888985 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
5888903 TTTATTATCA
*
5888913 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
5888941 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
5888968 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
5888986 AAATGGTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:5889102 original size:144 final size:147
Alignment explanation
Indices: 5888874--5889144 Score: 458
Period size: 144 Copynumber: 1.9 Consensus size: 147
5888864 ATGATTATTG
*
5888874 TTATTGTTATTTGAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
* *
5888939 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATGGTTAATAATTTGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTTGC
5889004 AAAAATTTGTTTTGGTAAA
129 AAAAATTTGTTTTGGTAAA
*
5889023 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
*
5889085 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATT
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATT
5889145 AATATTCTTA
Statistics
Matches: 117, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
144 89 0.76
145 1 0.01
148 22 0.19
149 5 0.04
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATGCTTAATAATTTGCAA
AAATTTGTTTTGGTAAA
Found at i:5889120 original size:18 final size:17
Alignment explanation
Indices: 5889099--5889133 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5889089 TTATTATTAA
*
5889099 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
5889117 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
5889134 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:5891480 original size:23 final size:23
Alignment explanation
Indices: 5891454--5891508 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
5891444 CAACCAAAAA
5891454 TGGAGTTAGACCTGGGTCAACTC
1 TGGAGTTAGACCTGGGTCAACTC
5891477 TGGAGTTAGACCTGGGTCAACTC
1 TGGAGTTAGACCTGGGTCAACTC
5891500 TGGAGTTAG
1 TGGAGTTAG
5891509 CCGAGGCCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.27
Consensus pattern (23 bp):
TGGAGTTAGACCTGGGTCAACTC
Found at i:5893000 original size:22 final size:22
Alignment explanation
Indices: 5892958--5893000 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5892948 ATTAACTACA
**
5892958 CATATCTCCAAAATATCTGCAG
1 CATATCTCCAAAATAAATGCAG
5892980 CATATCCTCC-AAATAAATGCA
1 CATAT-CTCCAAAATAAATGCA
5893001 TGATTTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.26
Consensus pattern (22 bp):
CATATCTCCAAAATAAATGCAG
Found at i:5894010 original size:12 final size:12
Alignment explanation
Indices: 5893993--5894020 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5893983 GTGATTAAGG
5893993 ACATTAATAGTA
1 ACATTAATAGTA
5894005 ACATTAATAGTA
1 ACATTAATAGTA
5894017 ACAT
1 ACAT
5894021 CATGGCTAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (12 bp):
ACATTAATAGTA
Found at i:5894887 original size:31 final size:31
Alignment explanation
Indices: 5894849--5894928 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
5894839 CATGGTTGAT
*
5894849 TTAGCAGCAAAAATCAATAGAAGGTACCATC
1 TTAGCAGCAAAAACCAATAGAAGGTACCATC
5894880 TTAGCAGCAAAAACCAATAGAAGGTACCATC
1 TTAGCAGCAAAAACCAATAGAAGGTACCATC
*
5894911 TTAGCTGCAAAAACCAAT
1 TTAGCAGCAAAAACCAAT
5894929 TAAAATCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (31 bp):
TTAGCAGCAAAAACCAATAGAAGGTACCATC
Found at i:5895936 original size:83 final size:83
Alignment explanation
Indices: 5895830--5896258 Score: 687
Period size: 83 Copynumber: 5.2 Consensus size: 83
5895820 ATTTGGAGAT
*
5895830 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTGTATTC
1 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
*
5895895 TTTGTGGCGTTTATTGAC
66 TTTGCGGCGTTTATTGAC
* *
5895913 AAAATGCCACTAATATTTAATTCGTCAATGAAACGGCGTCGTTTTGTTCAATTTTTATTATATTC
1 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
*
5895978 TTTGCAGCGTTTATTGAC
66 TTTGCGGCGTTTATTGAC
* * *
5895996 AAAACGCCACTAATATTTAATTCTTCAATGAAATGGCGCCGTTTTGTTCAATTTTTATTATTTTC
1 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
5896061 TTTGCGGCGTTTATTGAC
66 TTTGCGGCGTTTATTGAC
* * *
5896079 AAAACGCCACTAATATTTAATTTGTCAATGAAACGGCACCGTTTTGTTCAATTTTTATTATATTA
1 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
*
5896144 TTTGCGGTGTTTATTGAC
66 TTTGCGGCGTTTATTGAC
* * * * * *
5896162 AAAATGCCACTAATATTTAATTCATCAATGAAACAGCGCTGTTTTATTCAATTTTTATTATTTTC
1 AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
*
5896227 TTTACGGCGTTTATTGAC
66 TTTGCGGCGTTTATTGAC
5896245 AAAACGCCACTAAT
1 AAAACGCCACTAAT
5896259 TATTCACTTT
Statistics
Matches: 316, Mismatches: 30, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 316 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.41
Consensus pattern (83 bp):
AAAACGCCACTAATATTTAATTCGTCAATGAAACGGCGCCGTTTTGTTCAATTTTTATTATATTC
TTTGCGGCGTTTATTGAC
Found at i:5896754 original size:20 final size:21
Alignment explanation
Indices: 5896715--5896762 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
5896705 ATCTGTAACA
* *
5896715 CTAAATCCTAAATCCTAAACC
1 CTAAACCCTAAATCCAAAACC
5896736 CTAAACCCT-AATCCAAAACC
1 CTAAACCCTAAATCCAAAACC
*
5896756 CAAAACC
1 CTAAACC
5896763 ATGCATTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.46, C:0.38, G:0.00, T:0.17
Consensus pattern (21 bp):
CTAAACCCTAAATCCAAAACC
Found at i:5896900 original size:14 final size:14
Alignment explanation
Indices: 5896883--5896924 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
5896873 CATTAAAACA
5896883 TAAACCCTAAACCT
1 TAAACCCTAAACCT
*
5896897 TAAA-CCTCAAACCC
1 TAAACCCT-AAACCT
*
5896911 CAAACCCTAAACCT
1 TAAACCCTAAACCT
5896925 ACACTATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 3 0.13
14 17 0.74
15 3 0.13
ACGTcount: A:0.43, C:0.40, G:0.00, T:0.17
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:5896908 original size:21 final size:21
Alignment explanation
Indices: 5896884--5896924 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5896874 ATTAAAACAT
* *
5896884 AAACCCTAAACCTTAAACCTC
1 AAACCCCAAACCCTAAACCTC
5896905 AAACCCCAAACCCTAAACCT
1 AAACCCCAAACCCTAAACCT
5896925 ACACTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (21 bp):
AAACCCCAAACCCTAAACCTC
Found at i:5897119 original size:42 final size:41
Alignment explanation
Indices: 5897056--5897251 Score: 152
Period size: 41 Copynumber: 4.8 Consensus size: 41
5897046 GCCTCCGAGC
*
5897056 ATTAGCGGCGCTTTCT-AAAAACACCGCTAAAGCCTAGAGA
1 ATTAGCGGCGCTTTCTAAAAAACACCGCTAAAGCCCAGAGA
* * *
5897096 ATTAGCGGCGCTTTCTAAAAAA-ACGTGCTAAAACCCAAAGCA
1 ATTAGCGGCGCTTTCTAAAAAACAC-CGCTAAAGCCCAGAG-A
* * *
5897138 A-TAGCGGCACTTTCTTCAAAAACGA-CGCTAATGCCCAGA-A
1 ATTAGCGGCGCTTTC-TAAAAAAC-ACCGCTAAAGCCCAGAGA
* * * ** *
5897178 CATTAGCGGCGCTTTCTAGAAAACGCCGCTAAATCCCTCAGT
1 -ATTAGCGGCGCTTTCTAAAAAACACCGCTAAAGCCCAGAGA
* * *
5897220 ATTAGCGACGC-TTCTTCAAAAACGCCGCTAAA
1 ATTAGCGGCGCTTTC-TAAAAAACACCGCTAAA
5897252 TCCCCCAACA
Statistics
Matches: 123, Mismatches: 22, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
40 22 0.18
41 70 0.57
42 30 0.24
44 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCTAAAAAACACCGCTAAAGCCCAGAGA
Found at i:5897127 original size:83 final size:83
Alignment explanation
Indices: 5897053--5897273 Score: 211
Period size: 83 Copynumber: 2.7 Consensus size: 83
5897043 AAAGCCTCCG
* * *
5897053 AGCATTAGCGGCGCTTTC-T-AAAAAC-ACCGCTAAAGCCTAGAGA-ATTAGCGGCGCTTTCTAA
1 AGCAATAGCGGCACTTTCTTCAAAAACGA-CGCTAAAGCCCAGA-ACATTAGCGGCGCTTTCTAA
5897114 AAAAACGTGCTAAAACCCAA
64 AAAAACGTGCTAAAACCCAA
* *
5897134 AGCAATAGCGGCACTTTCTTCAAAAACGACGCTAATGCCCAGAACATTAGCGGCGCTTTCT-AGA
1 AGCAATAGCGGCACTTTCTTCAAAAACGACGCTAAAGCCCAGAACATTAGCGGCGCTTTCTAAAA
* * **
5897198 AAACGCCGCTAAATCCCTC
66 AAACG-TGCTAAAACCCAA
* * * * * * ** *
5897217 AGTATTAGCGACGC-TTCTTCAAAAACGCCGCTAAATCCCCCAACATTAGCGACGCTT
1 AGCAATAGCGGCACTTTCTTCAAAAACGACGCTAAAGCCCAGAACATTAGCGGCGCTT
5897274 CTTCAAAAAC
Statistics
Matches: 116, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
81 16 0.14
82 46 0.40
83 53 0.46
84 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.21
Consensus pattern (83 bp):
AGCAATAGCGGCACTTTCTTCAAAAACGACGCTAAAGCCCAGAACATTAGCGGCGCTTTCTAAAA
AAACGTGCTAAAACCCAA
Found at i:5897252 original size:41 final size:41
Alignment explanation
Indices: 5897149--5897298 Score: 171
Period size: 41 Copynumber: 3.6 Consensus size: 41
5897139 TAGCGGCACT
* ** *
5897149 TTCTTCAAAAACGACGCT-AATGCCCAGAACATTAGCGGCGC
1 TTCTTCAAAAACGCCGCTAAAT-CCCCCAACATTAGCGACGC
* **
5897190 -T-TTCTAGAAAACGCCGCTAAATCCCTCAGTATTAGCGACGC
1 TTCTTC-A-AAAACGCCGCTAAATCCCCCAACATTAGCGACGC
5897231 TTCTTCAAAAACGCCGCTAAATCCCCCAACATTAGCGACGC
1 TTCTTCAAAAACGCCGCTAAATCCCCCAACATTAGCGACGC
*
5897272 TTCTTCAAAAACGCAGCTAAAGTCCCC
1 TTCTTCAAAAACGCCGCTAAA-TCCCC
5897299 AAAGCCTCAG
Statistics
Matches: 93, Mismatches: 10, Indels: 11
0.82 0.09 0.10
Matches are distributed among these distances:
39 3 0.03
40 2 0.02
41 75 0.81
42 10 0.11
43 3 0.03
ACGTcount: A:0.31, C:0.32, G:0.15, T:0.21
Consensus pattern (41 bp):
TTCTTCAAAAACGCCGCTAAATCCCCCAACATTAGCGACGC
Found at i:5897262 original size:82 final size:83
Alignment explanation
Indices: 5897096--5897292 Score: 204
Period size: 82 Copynumber: 2.4 Consensus size: 83
5897086 AGCCTAGAGA
* *
5897096 ATTAGCGGCGCTTTCTAAAAAAACGTGCTAAAACCCAAAGCAATAGCGGCACTTTCTTCAAAAAC
1 ATTAGCGGCGCTTTCTAAAAAAACGCGCTAAAACCCAAAGCAATAGCGACACTTTCTTCAAAAAC
*
5897161 GACGCTAATGCCCAGAAC
66 GACGCTAATGCCCACAAC
* * ** * * *
5897179 ATTAGCGGCGCTTTCT-AGAAAACGCCGCTAAATCCCTCAGTATTAGCGACGC-TTCTTCAAAAA
1 ATTAGCGGCGCTTTCTAAAAAAACG-CGCTAAAACCCAAAGCAATAGCGACACTTTCTTCAAAAA
* *
5897242 CGCCGCTAAAT-CCCCCAAC
65 CGACGCT-AATGCCCACAAC
* **
5897261 ATTAGCGACGC-TTCTTCAAAAACGCAGCTAAA
1 ATTAGCGGCGCTTTCTAAAAAAACGC-GCTAAA
5897293 GTCCCCAAAG
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
81 5 0.05
82 52 0.55
83 38 0.40
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (83 bp):
ATTAGCGGCGCTTTCTAAAAAAACGCGCTAAAACCCAAAGCAATAGCGACACTTTCTTCAAAAAC
GACGCTAATGCCCACAAC
Found at i:5897442 original size:41 final size:39
Alignment explanation
Indices: 5897350--5897425 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 39
5897340 GCTTCCTTAT
5897350 AAACGCCGCTAATGCTCAATTTTTAGCGGCGTTTTTCAA
1 AAACGCCGCTAATGCTCAATTTTTAGCGGCGTTTTTCAA
*
5897389 AAAGCGCCGCTAATGCTCGATTTTTAGCGGCGTTTTT
1 AAA-CGCCGCTAATGCTCAATTTTTAGCGGCGTTTTT
5897426 TGTCCAAACG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 3 0.09
40 32 0.91
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (39 bp):
AAACGCCGCTAATGCTCAATTTTTAGCGGCGTTTTTCAA
Found at i:5899894 original size:25 final size:25
Alignment explanation
Indices: 5899848--5899895 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
5899838 TTTATGGAAT
* *
5899848 TTATTTTGAATGAGAAATTGTATTC
1 TTATTATGAATGAGAAAGTGTATTC
5899873 TTATTATGAATTGA-AAAGTGTAT
1 TTATTATGAA-TGAGAAAGTGTAT
5899896 GTATAGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.85
26 3 0.15
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (25 bp):
TTATTATGAATGAGAAAGTGTATTC
Found at i:5900618 original size:60 final size:60
Alignment explanation
Indices: 5900552--5900673 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
5900542 CAAATGCAAA
5900552 GTTAAATTCTTGATATGCTTACTAAACTTTCATGAGCTTAACACGTTTCTTTTCAAACGC
1 GTTAAATTCTTGATATGCTTACTAAACTTTCATGAGCTTAACACGTTTCTTTTCAAACGC
5900612 GTTAAATTCTTGATATGCTTACTAAACTTTCATGAGCTTAACACGTTTCTTTTCAAACGC
1 GTTAAATTCTTGATATGCTTACTAAACTTTCATGAGCTTAACACGTTTCTTTTCAAACGC
5900672 GT
1 GT
5900674 GAGGGCTTGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (60 bp):
GTTAAATTCTTGATATGCTTACTAAACTTTCATGAGCTTAACACGTTTCTTTTCAAACGC
Found at i:5913958 original size:104 final size:105
Alignment explanation
Indices: 5913778--5914045 Score: 441
Period size: 104 Copynumber: 2.6 Consensus size: 105
5913768 TAACCGTTAT
* ** *
5913778 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCATCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
5913843 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
5913882 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
5913947 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
5913987 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
5914046 TTATATACAA
Statistics
Matches: 153, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
104 81 0.53
105 71 0.46
106 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:5914414 original size:30 final size:30
Alignment explanation
Indices: 5914380--5914437 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
5914370 CCACCCAACT
5914380 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
*** * *
5914410 TTTTGCGTAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
5914438 GCTCGGAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:5916589 original size:20 final size:20
Alignment explanation
Indices: 5916557--5916617 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
5916547 TTTAATATTA
*
5916557 AATTCATTTAATATTAAATT
1 AATTAATTTAATATTAAATT
* *
5916577 GATT-ATCTTAATATTGAATTT
1 AATTAAT-TTAATATT-AAATT
5916598 AATTAATTTAATATTAAATT
1 AATTAATTTAATATTAAATT
5916618 TAATCTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.06
20 15 0.44
21 15 0.44
22 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
AATTAATTTAATATTAAATT
Found at i:5916608 original size:21 final size:20
Alignment explanation
Indices: 5916557--5916626 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
5916547 TTTAATATTA
* *
5916557 AATTCATTTAATATTAAATT
1 AATTAATTTAATATTAATTT
*
5916577 GATT-ATCTTAATATTGAATTT
1 AATTAAT-TTAATATT-AATTT
5916598 AATTAATTTAATATTAAATTT
1 AATTAATTTAATATT-AATTT
5916619 AATCTAAT
1 AAT-TAAT
5916627 ATTTATCTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
19 2 0.05
20 11 0.26
21 23 0.55
22 6 0.14
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (20 bp):
AATTAATTTAATATTAATTT
Found at i:5916617 original size:16 final size:16
Alignment explanation
Indices: 5916546--5916664 Score: 67
Period size: 16 Copynumber: 7.8 Consensus size: 16
5916536 ATTTTAATAG
*
5916546 ATTTAATATTAAATTC
1 ATTTAATATTAAATTA
*
5916562 ATTTAATATTAAATTG
1 ATTTAATATTAAATTA
*
5916578 A-TT-ATCTT-AA-T-
1 ATTTAATATTAAATTA
*
5916589 ATTGAAT-TT-AATTA
1 ATTTAATATTAAATTA
5916603 ATTTAATATTAAATTTA
1 ATTTAATATTAAA-TTA
* ** *
5916620 ATCTAATATTTATCTTG
1 ATTTAATA-TTAAATTA
*
5916637 A--TAAGTATTATATTA
1 ATTTAA-TATTAAATTA
5916652 ATTTAATATTAAA
1 ATTTAATATTAAA
5916665 ATGATTAAGT
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
11 1 0.01
12 6 0.07
13 5 0.06
14 10 0.12
15 14 0.17
16 26 0.32
17 16 0.20
18 3 0.04
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
ATTTAATATTAAATTA
Found at i:5916785 original size:13 final size:13
Alignment explanation
Indices: 5916753--5916801 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
5916743 TTGAATTCAA
**
5916753 GAGAAAATTGTAGA
1 GAGAAAATTGT-TT
*
5916767 GAGAAAATTTTTT
1 GAGAAAATTGTTT
5916780 GAGAAAATTGTTT
1 GAGAAAATTGTTT
*
5916793 CAGAAAATT
1 GAGAAAATT
5916802 CTCTGAGATA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 20 0.67
14 10 0.33
ACGTcount: A:0.45, C:0.02, G:0.20, T:0.33
Consensus pattern (13 bp):
GAGAAAATTGTTT
Found at i:5918058 original size:31 final size:31
Alignment explanation
Indices: 5918006--5918077 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
5917996 TAACAGCTTA
*
5918006 GTGACTTAAATAAAGCATTTTGAATAGTTTG
1 GTGACTTAAATAAAACATTTTGAATAGTTTG
*
5918037 GTGATTTAAATGAAAAC-TTTTGAATAGTTTG
1 GTGACTTAAAT-AAAACATTTTGAATAGTTTG
5918068 GTGAC-TAAAT
1 GTGACTTAAAT
5918078 TGTAACATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 5 0.14
31 28 0.76
32 4 0.11
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (31 bp):
GTGACTTAAATAAAACATTTTGAATAGTTTG
Found at i:5924221 original size:11 final size:11
Alignment explanation
Indices: 5924205--5924248 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
5924195 GGAGGGTTTT
5924205 TTATAAAAATA
1 TTATAAAAATA
5924216 TTATAAAAATA
1 TTATAAAAATA
5924227 --ATAAAAAT-
1 TTATAAAAATA
5924235 TTACT-AAAATA
1 TTA-TAAAAATA
5924246 TTA
1 TTA
5924249 CAATTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 8 0.28
10 6 0.21
11 15 0.52
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
TTATAAAAATA
Found at i:5924292 original size:28 final size:28
Alignment explanation
Indices: 5924233--5924328 Score: 153
Period size: 27 Copynumber: 3.5 Consensus size: 28
5924223 AATAATAAAA
*
5924233 ATTTACTAAAATATTACAA-TTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
5924260 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
5924288 ATTTACCAAAATATATA-AAC-TTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTT
5924315 ATTTACCAAAATAT
1 ATTTACCAAAATAT
5924329 ATAAAAAAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
27 39 0.59
28 25 0.38
29 2 0.03
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:5924605 original size:19 final size:21
Alignment explanation
Indices: 5924567--5924605 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
5924557 AATAATTGAT
*
5924567 TATATTATTGTTATTATTTTG
1 TATATTATTGTTAATATTTTG
5924588 TATATT-TTG-TAATATTTT
1 TATATTATTGTTAATATTTT
5924606 TTGTTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TATATTATTGTTAATATTTTG
Done.