Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397271.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_89.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4184555
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 83639 characters in sequence are not A, C, G, or T
File 10 of 11
Found at i:3543463 original size:74 final size:74
Alignment explanation
Indices: 3543356--3543497 Score: 248
Period size: 74 Copynumber: 1.9 Consensus size: 74
3543346 AAACTTATAT
** * *
3543356 TTATAAATATGTATTCATTAAATGATGGTCATTGAAATTTTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATTAAATGATGAACATTGAAATATTTTTTATTATAATTATTAATAAGAT
3543421 TTAAACCAA
66 TTAAACCAA
3543430 TTATAAATATGTATTCATTAAATGATGAACATTGAAATATTTTTTATTATAATTATTAATAAGAT
1 TTATAAATATGTATTCATTAAATGATGAACATTGAAATATTTTTTATTATAATTATTAATAAGAT
3543495 TTA
66 TTA
3543498 TTCCATTTAC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 64 1.00
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.46
Consensus pattern (74 bp):
TTATAAATATGTATTCATTAAATGATGAACATTGAAATATTTTTTATTATAATTATTAATAAGAT
TTAAACCAA
Found at i:3543512 original size:74 final size:74
Alignment explanation
Indices: 3543354--3543512 Score: 246
Period size: 74 Copynumber: 2.1 Consensus size: 74
3543344 TAAAACTTAT
** * *
3543354 ATTTATAAATATGTATTCATTAAATGATGGTCATTGAAATTTTTTTTATTATAATTATTAGTAAG
1 ATTTATAAATATGTATTCATTAAATGATGAACATTGAAATATTTTTTATTATAATTATTAATAAG
3543419 ATTTAAACC
66 ATTTAAACC
*
3543428 AATTATAAATATGTATTCATTAAATGATGAACATTGAAATATTTTTTATTATAATTATTAATAAG
1 ATTTATAAATATGTATTCATTAAATGATGAACATTGAAATATTTTTTATTATAATTATTAATAAG
**
3543493 ATTTATTCC
66 ATTTAAACC
*
3543502 ATTTACAAATA
1 ATTTATAAATA
3543513 AAAAATTTAA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.46
Consensus pattern (74 bp):
ATTTATAAATATGTATTCATTAAATGATGAACATTGAAATATTTTTTATTATAATTATTAATAAG
ATTTAAACC
Found at i:3543605 original size:13 final size:14
Alignment explanation
Indices: 3543580--3543624 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
3543570 TATTATATAA
3543580 TTTAAATATTAATAT
1 TTTAAA-ATTAATAT
3543595 TTT-AAATTAATTAT
1 TTTAAAATTAA-TAT
3543609 TTTAAAATTTAATAT
1 TTTAAAA-TTAATAT
3543624 T
1 T
3543625 AATATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.19
14 8 0.30
15 10 0.37
16 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAAAATTAATAT
Found at i:3543613 original size:22 final size:22
Alignment explanation
Indices: 3543588--3543646 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
3543578 AATTTAAATA
3543588 TTAATATTTTAA-ATTAATTATT
1 TTAATATTTTAATATTAA-TATT
*
3543610 TTAA-AATTTAATATTAATATT
1 TTAATATTTTAATATTAATATT
* *
3543631 TTTATTTTTTAATATT
1 TTAATATTTTAATATT
3543647 TTAAGTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTAATATTTTAATATTAATATT
Found at i:3545827 original size:44 final size:43
Alignment explanation
Indices: 3545716--3545847 Score: 153
Period size: 44 Copynumber: 3.0 Consensus size: 43
3545706 AGCTAAGTGT
* *
3545716 AACATAATCATGGGAA-GTGGAGACCTTCTT-AATCCACT-TCAC
1 AACACAATCATGGGAATGTAGAGACCTT-TTCAATCCA-TATCAC
*
3545758 AACACAATCATGGGAATGTAAAGACCTTTTCAATCCATATCAC
1 AACACAATCATGGGAATGTAGAGACCTTTTCAATCCATATCAC
* * *
3545801 AACAGCAATCATGGAAATGTTGAGACCTTCTCAATCCATATTCAC
1 AACA-CAATCATGGGAATGTAGAGACCTTTTCAATCCATA-TCAC
3545846 AA
1 AA
3545848 TACTCATATG
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
42 18 0.23
43 23 0.29
44 31 0.40
45 6 0.08
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (43 bp):
AACACAATCATGGGAATGTAGAGACCTTTTCAATCCATATCAC
Found at i:3555045 original size:12 final size:12
Alignment explanation
Indices: 3555028--3555067 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
3555018 GGACTTCGTG
3555028 GTTTTAAGTTGA
1 GTTTTAAGTTGA
3555040 GTTTTAAGTTGA
1 GTTTTAAGTTGA
3555052 GTTTTAAGTTTGA
1 GTTTTAAG-TTGA
3555065 GTT
1 GTT
3555068 ATTATAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 20 0.74
13 7 0.26
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (12 bp):
GTTTTAAGTTGA
Found at i:3556948 original size:6 final size:6
Alignment explanation
Indices: 3556906--3556936 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
3556896 AATTGTGAAT
3556906 GAAAAA G-AAAA GAAAAA GAAAAA GAAAAA GA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GA
3556937 TCAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:3568879 original size:26 final size:26
Alignment explanation
Indices: 3568837--3568933 Score: 90
Period size: 26 Copynumber: 3.8 Consensus size: 26
3568827 TTAATTAAAA
* *
3568837 ATAATTTTACCACCAGAAGTGGATGG
1 ATAATTTTACCATCAGAAGTGGATAG
* ** * *
3568863 ATAATTTTATCATCAGAA-TTTAAAA
1 ATAATTTTACCATCAGAAGTGGATAG
*
3568888 ATTATTTTACCA-CTAGAAGTGGATAG
1 ATAATTTTACCATC-AGAAGTGGATAG
*
3568914 ATAATTTTACCATCAAAAGT
1 ATAATTTTACCATCAGAAGT
3568934 AGATGGATGT
Statistics
Matches: 53, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
24 1 0.02
25 16 0.30
26 35 0.66
27 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (26 bp):
ATAATTTTACCATCAGAAGTGGATAG
Found at i:3568895 original size:51 final size:51
Alignment explanation
Indices: 3568831--3568928 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
3568821 TTTATTTTAA
* *
3568831 TTAAAAATAATTTTACCACCAGAAGTGGATGGATAATTTTATCATCAGAAT
1 TTAAAAATAATTTTACCACCAGAAGTGGATAGATAATTTTACCATCAGAAT
* *
3568882 TTAAAAATTATTTTACCACTAGAAGTGGATAGATAATTTTACCATCA
1 TTAAAAATAATTTTACCACCAGAAGTGGATAGATAATTTTACCATCA
3568929 AAAGTAGATG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (51 bp):
TTAAAAATAATTTTACCACCAGAAGTGGATAGATAATTTTACCATCAGAAT
Found at i:3574817 original size:16 final size:17
Alignment explanation
Indices: 3574792--3574826 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3574782 AGAAGGTTGA
*
3574792 AGAGACAAGAG-AAAGG
1 AGAGAAAAGAGAAAAGG
3574808 AGAGAAAAGAGAAAAGG
1 AGAGAAAAGAGAAAAGG
3574825 AG
1 AG
3574827 TTGAAAGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.60, C:0.03, G:0.37, T:0.00
Consensus pattern (17 bp):
AGAGAAAAGAGAAAAGG
Found at i:3584610 original size:21 final size:21
Alignment explanation
Indices: 3584589--3584628 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3584579 TGCGTTATGT
3584589 TTCA-AATGTAACGATACATG
1 TTCATAATGTAACGATACATG
* *
3584609 TTCATAATGTATCGGTACAT
1 TTCATAATGTAACGATACAT
3584629 ATGGTCATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (21 bp):
TTCATAATGTAACGATACATG
Found at i:3590172 original size:2 final size:2
Alignment explanation
Indices: 3590165--3590195 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3590155 ACAAACAGAG
3590165 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3590196 GTAAGAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3601491 original size:29 final size:28
Alignment explanation
Indices: 3601449--3601519 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 28
3601439 TTTCATGTTT
* *
3601449 TAAATTAAGACAAACATATTTTTTTGTC
1 TAAATTAACACAAACATATTTTCTTGTC
*
3601477 TAAATTAACACCAAACATGTTTTCTTGTC
1 TAAATTAACA-CAAACATATTTTCTTGTC
*
3601506 TAAATTAAGACAAA
1 TAAATTAACACAAA
3601520 TATGTTAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 13 0.34
29 25 0.66
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (28 bp):
TAAATTAACACAAACATATTTTCTTGTC
Found at i:3601524 original size:28 final size:28
Alignment explanation
Indices: 3601363--3601525 Score: 143
Period size: 28 Copynumber: 5.6 Consensus size: 28
3601353 TCTTATCTTT
3601363 AATTAAGACAAATAT-TTTATCTTGTCTA
1 AATTAAGACAAATATGTTT-TCTTGTCTA
* *
3601391 AATTGAGACAAATATGTTTTCTTATC-A
1 AATTAAGACAAATATGTTTTCTTGTCTA
* * *
3601418 AGATTAAGATAAAAAAATAT-TTTTCATGTTTTA
1 A-ATTAAG----ACAAATATGTTTTCTTG-TCTA
* * *
3601451 AATTAAGACAAACATATTTTTTTGTCTA
1 AATTAAGACAAATATGTTTTCTTGTCTA
* *
3601479 AATTAACACCAAACATGTTTTCTTGTCTA
1 AATTAAGA-CAAATATGTTTTCTTGTCTA
3601508 AATTAAGACAAATATGTT
1 AATTAAGACAAATATGTT
3601526 AAAGTTGCCA
Statistics
Matches: 108, Mismatches: 17, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
27 2 0.02
28 50 0.46
29 34 0.31
31 6 0.06
32 14 0.13
33 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (28 bp):
AATTAAGACAAATATGTTTTCTTGTCTA
Found at i:3606930 original size:21 final size:20
Alignment explanation
Indices: 3606896--3606940 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
3606886 ATAATTAGAT
3606896 ATTTTTATTAATTTAT-TTTA
1 ATTTTTATTAATTT-TCTTTA
*
3606916 ATTTTATATTTATTTTCTTTA
1 ATTTT-TATTAATTTTCTTTA
3606937 ATTT
1 ATTT
3606941 GGCCATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTTTATTAATTTTCTTTA
Found at i:3611029 original size:73 final size:74
Alignment explanation
Indices: 3610826--3611029 Score: 205
Period size: 73 Copynumber: 2.8 Consensus size: 74
3610816 CTAAAAGTGT
* ** * * *
3610826 GCTCTTAGTTGACTAACCATGCTTCTTAAACGATTAAGTCTTCTCTGTCTTGTAATAAAATTCTC
1 GCTCTTAGTTGGCTAACCATGCTTCTTAGTCAATTAAGTCTTCTCTGTCTTGCAATCAAATTCTC
3610891 TAGCAATGA
66 TAGCAATGA
* ** * * **
3610900 GCTCTTAGCTGGCTAATAATGCTTCTTAGTCAACTAAGTCTTCTCTATCTCACAATCAAATT-T-
1 GCTCTTAGTTGGCTAACCATGCTTCTTAGTCAATTAAGTCTTCTCTGTCTTGCAATCAAATTCTC
* **
3610963 TTGACTGTGA
66 TAG-CAATGA
* * * *
3610973 GCTTTTAGTTGGCTAACCATACTTTTTAGTCAATTAAGTATTCTCTGTCTTGCAATC
1 GCTCTTAGTTGGCTAACCATGCTTCTTAGTCAATTAAGTCTTCTCTGTCTTGCAATC
3611030 TACTTTATTC
Statistics
Matches: 102, Mismatches: 27, Indels: 3
0.77 0.20 0.02
Matches are distributed among these distances:
72 2 0.02
73 51 0.50
74 49 0.48
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (74 bp):
GCTCTTAGTTGGCTAACCATGCTTCTTAGTCAATTAAGTCTTCTCTGTCTTGCAATCAAATTCTC
TAGCAATGA
Found at i:3613371 original size:20 final size:20
Alignment explanation
Indices: 3613343--3613382 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3613333 CTTCAAGCAT
* * *
3613343 TATTCTCAATTATCGTCAAG
1 TATTATCAATCATCATCAAG
3613363 TATTATCAATCATCATCAAG
1 TATTATCAATCATCATCAAG
3613383 CATTCATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (20 bp):
TATTATCAATCATCATCAAG
Found at i:3618117 original size:72 final size:74
Alignment explanation
Indices: 3617945--3618122 Score: 200
Period size: 72 Copynumber: 2.4 Consensus size: 74
3617935 TCTTAGTTAA
* * *
3617945 CTAACCATGCTTATTAGTCAATTAAGTCTTCTTTACCTTATAATCAAATTCTCTAGCAGTGAGCT
1 CTAACCATACTTATTAGTCAATTAAGTCTTCTTTACCTCACAATCAAATTCTCTAGCAGTGAGCT
3618010 CTTAGCTGG
66 CTTAGCTGG
* * * * * * *
3618019 CTAACAATACTTCTTAGTCGACTAAGTCTT-TTCTATCTCACAATCAAATT-TTTA-CTGTGAGC
1 CTAACCATACTTATTAGTCAATTAAGTCTTCTT-TACCTCACAATCAAATTCTCTAGCAGTGAGC
* *
3618081 TTTTAGTTGG
65 TCTTAGCTGG
* *
3618091 TTAACCATACTTATTAGTCAATTAAGTATTCT
1 CTAACCATACTTATTAGTCAATTAAGTCTTCT
3618123 CTGTCTTCTA
Statistics
Matches: 84, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
72 39 0.46
73 6 0.07
74 39 0.46
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (74 bp):
CTAACCATACTTATTAGTCAATTAAGTCTTCTTTACCTCACAATCAAATTCTCTAGCAGTGAGCT
CTTAGCTGG
Found at i:3619464 original size:70 final size:70
Alignment explanation
Indices: 3619301--3619520 Score: 336
Period size: 70 Copynumber: 3.1 Consensus size: 70
3619291 AATATCATAA
* * * * *
3619301 AGCCCTAGTTGACTACAAAGGAAGCATAGTTGACCTTATTCTAAAAAGATCAAGAAAATCAAGCT
1 AGCCATAGTTGACTAC-AA-GAAGTATAGTTGACCTTGTTCCAAAAAGACCAAGAAAATCAAG-T
*
3619366 --CAAAAT
63 AGAAAAAT
*
3619372 AGCCATAGTTGACTACAAGAAGTATATTTGACCTTGTTCCAAAAAGACCAAGAAAATCAAGTAGA
1 AGCCATAGTTGACTACAAGAAGTATAGTTGACCTTGTTCCAAAAAGACCAAGAAAATCAAGTAGA
3619437 AAAAT
66 AAAAT
3619442 AGCCATAGTTGACTACAAGAAGTATAGTTGACCTTGTTCCAAAAAGACCAAGAAAATCAAGTAGA
1 AGCCATAGTTGACTACAAGAAGTATAGTTGACCTTGTTCCAAAAAGACCAAGAAAATCAAGTAGA
3619507 AAAAT
66 AAAAT
3619512 AGCCATAGT
1 AGCCATAGT
3619521 CACCTATAGA
Statistics
Matches: 139, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
68 1 0.01
69 38 0.27
70 85 0.61
71 15 0.11
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (70 bp):
AGCCATAGTTGACTACAAGAAGTATAGTTGACCTTGTTCCAAAAAGACCAAGAAAATCAAGTAGA
AAAAT
Found at i:3621877 original size:37 final size:37
Alignment explanation
Indices: 3621827--3621901 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3621817 TTCAAAAATC
3621827 ACCTCATTTAAAGTTCGGTAGAGAGTGTTATGATCGA
1 ACCTCATTTAAAGTTCGGTAGAGAGTGTTATGATCGA
3621864 ACCTCATTTAAAGTTCGGTAGAGAGTGTTATGATCGA
1 ACCTCATTTAAAGTTCGGTAGAGAGTGTTATGATCGA
3621901 A
1 A
3621902 ATTATGTGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (37 bp):
ACCTCATTTAAAGTTCGGTAGAGAGTGTTATGATCGA
Found at i:3628708 original size:20 final size:20
Alignment explanation
Indices: 3628683--3628720 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3628673 TTTTTAACAA
*
3628683 AGGAAATGAGAAAAAATCAT
1 AGGAAACGAGAAAAAATCAT
3628703 AGGAAACGAGAAAAAATC
1 AGGAAACGAGAAAAAATC
3628721 GAAGGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.08, G:0.21, T:0.11
Consensus pattern (20 bp):
AGGAAACGAGAAAAAATCAT
Found at i:3628726 original size:20 final size:19
Alignment explanation
Indices: 3628682--3628727 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
3628672 GTTTTTAACA
*
3628682 AAGGAAATGAGAAAAAATC
1 AAGGAAACGAGAAAAAATC
3628701 ATAGGAAACGAGAAAAAATC
1 A-AGGAAACGAGAAAAAATC
3628721 GAAGGAA
1 -AAGGAA
3628728 TTGAGGATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.61, C:0.07, G:0.24, T:0.09
Consensus pattern (19 bp):
AAGGAAACGAGAAAAAATC
Found at i:3633070 original size:21 final size:20
Alignment explanation
Indices: 3633027--3633074 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
3633017 CTCTTAAAGT
3633027 AATTTAAAATAAAACAACATAA
1 AATTT-AAATAAAACAACAT-A
* * *
3633049 AATTTAAGTAAAATAACTTA
1 AATTTAAATAAAACAACATA
3633069 AATTTA
1 AATTTA
3633075 TCACATAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 7 0.30
21 11 0.48
22 5 0.22
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (20 bp):
AATTTAAATAAAACAACATA
Found at i:3635537 original size:21 final size:20
Alignment explanation
Indices: 3635513--3635554 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
3635503 ATGTTTTATA
*
3635513 TATATATATATAGATGTATTT
1 TATATAAATATAGATG-ATTT
*
3635534 TATATAAATATATATGATTT
1 TATATAAATATAGATGATTT
3635554 T
1 T
3635555 GCTTTTCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
TATATAAATATAGATGATTT
Found at i:3635537 original size:23 final size:23
Alignment explanation
Indices: 3635503--3635547 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3635493 AAAGGTGTAA
*
3635503 ATGTTTTATATATATATATATAG
1 ATGTTTTATATATAAATATATAG
3635526 ATGTATTT-TATATAAATATATA
1 ATGT-TTTATATATAAATATATA
3635548 TGATTTTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (23 bp):
ATGTTTTATATATAAATATATAG
Found at i:3639698 original size:49 final size:49
Alignment explanation
Indices: 3639556--3639714 Score: 185
Period size: 49 Copynumber: 3.2 Consensus size: 49
3639546 GCTCCGGACA
* * * *
3639556 ATGATATGATATGAGATATGTATGTTCCATCCA-CAGATGATTCTGGACG
1 ATGATATGATGTGAGATATGTATGTTCCATCTATC-GATGATTTTAGACG
* * * * *
3639605 ATGATATAATGTGAGATATGTATGTTCCATTTGTGGATGGTTTTAGACG
1 ATGATATGATGTGAGATATGTATGTTCCATCTATCGATGATTTTAGACG
* ** *
3639654 ATGATATGATGTGAGATATGGATGTTCTGTCTATCGATGATTTTAGACA
1 ATGATATGATGTGAGATATGTATGTTCCATCTATCGATGATTTTAGACG
3639703 ATGATATGATGT
1 ATGATATGATGT
3639715 TGATTATGCA
Statistics
Matches: 91, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
49 91 1.00
ACGTcount: A:0.29, C:0.09, G:0.25, T:0.38
Consensus pattern (49 bp):
ATGATATGATGTGAGATATGTATGTTCCATCTATCGATGATTTTAGACG
Found at i:3639728 original size:49 final size:49
Alignment explanation
Indices: 3639552--3639736 Score: 167
Period size: 49 Copynumber: 3.8 Consensus size: 49
3639542 GATGGCTCCG
* * ** * * *
3639552 GACAATGATATGATATGAGATATGTATGTTCCATCCA-CAGATGATTCTG
1 GACAATGATATGATGTGAGATATGCATGTTCTGTCTATC-GATGATTTTA
* * * ** * * * *
3639601 GACGATGATATAATGTGAGATATGTATGTTCCATTTGTGGATGGTTTTA
1 GACAATGATATGATGTGAGATATGCATGTTCTGTCTATCGATGATTTTA
* *
3639650 GACGATGATATGATGTGAGATATGGATGTTCTGTCTATCGATGATTTTA
1 GACAATGATATGATGTGAGATATGCATGTTCTGTCTATCGATGATTTTA
*
3639699 GACAATGATATGATGTTGA-TTATGCATGTTCTGTCTAT
1 GACAATGATATGATG-TGAGATATGCATGTTCTGTCTAT
3639737 GGAAGAATTT
Statistics
Matches: 113, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
49 110 0.97
50 3 0.03
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (49 bp):
GACAATGATATGATGTGAGATATGCATGTTCTGTCTATCGATGATTTTA
Found at i:3645472 original size:20 final size:22
Alignment explanation
Indices: 3645449--3645489 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3645439 TATTTAAACT
3645449 TATAATAC-T-AAATATAAATC
1 TATAATACATAAAATATAAATC
*
3645469 TATAATGCATAAAATATAAAT
1 TATAATACATAAAATATAAAT
3645490 AGTTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.34
Consensus pattern (22 bp):
TATAATACATAAAATATAAATC
Found at i:3649190 original size:19 final size:20
Alignment explanation
Indices: 3649153--3649191 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
3649143 TCTTTTCTGA
*
3649153 TCTTCTTTTTCCCGGAAACT
1 TCTTCTTTTTCCCGCAAACT
*
3649173 TCTTC-TTTTCCCTCAAACT
1 TCTTCTTTTTCCCGCAAACT
3649192 CCCCCTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.15, C:0.33, G:0.05, T:0.46
Consensus pattern (20 bp):
TCTTCTTTTTCCCGCAAACT
Found at i:3650929 original size:2 final size:2
Alignment explanation
Indices: 3650922--3650949 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3650912 GTTTGTACAT
3650922 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3650950 AAATATTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3654956 original size:24 final size:24
Alignment explanation
Indices: 3654929--3654979 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 24
3654919 TTAAATTGGA
3654929 TTTTTTAA-AAAAT-ATTATATTAT
1 TTTTTTAATAAAATAATTAT-TTAT
3654952 TTTTTTAATAAAATAAATTATTTAT
1 TTTTTTAATAAAAT-AATTATTTAT
3654977 TTT
1 TTT
3654980 ATGGATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 8 0.32
24 5 0.20
25 7 0.28
26 5 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTTTTAATAAAATAATTATTTAT
Found at i:3656493 original size:2 final size:2
Alignment explanation
Indices: 3656428--3656479 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3656418 GATGGTACAC
3656428 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3656470 AG AG AG AG AG
1 AG AG AG AG AG
3656480 GATCCTAGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3662925 original size:21 final size:20
Alignment explanation
Indices: 3662884--3662927 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3662874 GTAAAAATTG
**
3662884 ATTATTAATTAATTACTAGA
1 ATTATTAATTAATTAAAAGA
*
3662904 ATTATTAATCTTATTAAAAGA
1 ATTATTAAT-TAATTAAAAGA
3662925 ATT
1 ATT
3662928 TAGTCACATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
ATTATTAATTAATTAAAAGA
Found at i:3663755 original size:12 final size:12
Alignment explanation
Indices: 3663740--3663764 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3663730 ACATAATAAT
3663740 AAAAATAACAAC
1 AAAAATAACAAC
3663752 AAAAATAACAAC
1 AAAAATAACAAC
3663764 A
1 A
3663765 TACTCAATCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAATAACAAC
Found at i:3664209 original size:15 final size:15
Alignment explanation
Indices: 3664189--3664218 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3664179 GAAAGAAGGA
3664189 GAAGGAGAAATGCCC
1 GAAGGAGAAATGCCC
3664204 GAAGGAGAAATGCCC
1 GAAGGAGAAATGCCC
3664219 AAAAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.33, T:0.07
Consensus pattern (15 bp):
GAAGGAGAAATGCCC
Found at i:3665150 original size:31 final size:31
Alignment explanation
Indices: 3665112--3665188 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
3665102 TCGTAAGGAG
*
3665112 TAAATTGAACAAAATTATAG-AGTATAGGGAC
1 TAAATTGAACAAAATT-TAGTAGTACAGGGAC
* **
3665143 TAAATTGAATAAACCTTAGTAGTACAGGGAC
1 TAAATTGAACAAAATTTAGTAGTACAGGGAC
3665174 TAAATTGAACAAAAT
1 TAAATTGAACAAAAT
3665189 CTATCATACA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 3 0.08
31 35 0.92
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (31 bp):
TAAATTGAACAAAATTTAGTAGTACAGGGAC
Found at i:3672035 original size:73 final size:73
Alignment explanation
Indices: 3671958--3672112 Score: 184
Period size: 73 Copynumber: 2.1 Consensus size: 73
3671948 GTGTTAGTTG
* * * *
3671958 ACTAAGAGCTTACTACCAAAAATTGAGTTTAAAGACAGAAACGACTTAATTGACTAAGAAGTATT
1 ACTAAGAGCTTACTACCAAAAATTGAGTTCAAAGACAGAAACGACTTAATCGACTAAGAAGCAAT
3672023 GTTAGCCA
66 GTTAGCCA
* * * * * * * *
3672031 ACTAAGAGCTTATTGCCAGATATTGGGTTCAGAGACATAAACGACTTAATCGACTAAGTAGCAAT
1 ACTAAGAGCTTACTACCAAAAATTGAGTTCAAAGACAGAAACGACTTAATCGACTAAGAAGCAAT
* *
3672096 GTTAGTCG
66 GTTAGCCA
3672104 ACTAAGAGC
1 ACTAAGAGC
3672113 ATTCTATCTG
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (73 bp):
ACTAAGAGCTTACTACCAAAAATTGAGTTCAAAGACAGAAACGACTTAATCGACTAAGAAGCAAT
GTTAGCCA
Found at i:3674382 original size:11 final size:11
Alignment explanation
Indices: 3674366--3674390 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3674356 TTTTTTAGAA
3674366 TTAGGAATGAT
1 TTAGGAATGAT
3674377 TTAGGAATGAT
1 TTAGGAATGAT
3674388 TTA
1 TTA
3674391 TACTAATGAA
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:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (11 bp):
TTAGGAATGAT
Found at i:3678448 original size:60 final size:60
Alignment explanation
Indices: 3678355--3678475 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
3678345 TAATTGATAA
* * ** * *
3678355 TAAAAGGGGACTTGAAGCCGTGACTCATATTTGGTGACGTGGGGAGTTTCCACGAGTAGG
1 TAAAAGGGGACCTGAAACCCCGACTCATATTTGGTGACGTGGGGAATTACCACGAGTAGG
* ** *
3678415 TAAAAGGGGACCTGAAACCCCGACTTATATTTGGTGGTGTTGGGAATTACCACGAGTAGG
1 TAAAAGGGGACCTGAAACCCCGACTCATATTTGGTGACGTGGGGAATTACCACGAGTAGG
3678475 T
1 T
3678476 GTTGATGTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (60 bp):
TAAAAGGGGACCTGAAACCCCGACTCATATTTGGTGACGTGGGGAATTACCACGAGTAGG
Found at i:3679994 original size:17 final size:17
Alignment explanation
Indices: 3679965--3679997 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3679955 TTTTTGATAA
3679965 AATAAAACTTCTTATTG
1 AATAAAACTTCTTATTG
3679982 AATAATAAC-TCTTATT
1 AATAA-AACTTCTTATT
3679998 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (17 bp):
AATAAAACTTCTTATTG
Found at i:3680273 original size:28 final size:28
Alignment explanation
Indices: 3680139--3680308 Score: 142
Period size: 29 Copynumber: 5.8 Consensus size: 28
3680129 TAAGATAACA
* *
3680139 CTTGTCTATAATTAAGACAAAAAAATTTGAT
1 CTTGTCTA-AATTAAGACAAACATATTT--T
* * *
3680170 CTTGTCTAAATTGAGACAAATATGTTTT
1 CTTGTCTAAATTAAGACAAACATATTTT
* * * ** *
3680198 CCTATTTGGATTAAGACAAAATATATTATT
1 CTTGTCTAAATTAAGAC-AAACATATT-TT
*
3680228 TTTGTCTTAAATTAAGACAAACATATTTT
1 CTTGTC-TAAATTAAGACAAACATATTTT
* *
3680257 CTTGTCTAAATTAAGACCGAACATGTTTT
1 CTTGTCTAAATTAAGA-CAAACATATTTT
*
3680286 CTTGTCTAAACTAAGACAAACAT
1 CTTGTCTAAATTAAGACAAACAT
3680309 GTTAAAGCTT
Statistics
Matches: 112, Mismatches: 23, Indels: 11
0.77 0.16 0.08
Matches are distributed among these distances:
28 28 0.25
29 40 0.36
30 27 0.24
31 17 0.15
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (28 bp):
CTTGTCTAAATTAAGACAAACATATTTT
Found at i:3681704 original size:21 final size:23
Alignment explanation
Indices: 3681678--3681719 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
3681668 ACCATGAAGG
3681678 TGAAACTGAAAA-A-GAAAAACT
1 TGAAACTGAAAACATGAAAAACT
3681699 TGAAACTGAAAACATGAAAAA
1 TGAAACTGAAAACATGAAAAA
3681720 GGAAAATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
22 1 0.05
23 6 0.32
ACGTcount: A:0.62, C:0.10, G:0.14, T:0.14
Consensus pattern (23 bp):
TGAAACTGAAAACATGAAAAACT
Found at i:3684426 original size:21 final size:21
Alignment explanation
Indices: 3684401--3684476 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
3684391 TTTCATAGAG
*
3684401 TCTTGACACTTGGATTCAAAA
1 TCTTGACACTTGGTTTCAAAA
*
3684422 TCTTGACACTTGGTTTGAAAA
1 TCTTGACACTTGGTTTCAAAA
* *
3684443 TCTTGATACTTGGTTTCAAAG
1 TCTTGACACTTGGTTTCAAAA
*
3684464 TCTTGATACTTGG
1 TCTTGACACTTGG
3684477 CACAATGTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.39
Consensus pattern (21 bp):
TCTTGACACTTGGTTTCAAAA
Found at i:3685035 original size:28 final size:28
Alignment explanation
Indices: 3685004--3685070 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
3684994 GTTTTACCAA
* *
3685004 ATCCTTGAAAAAGGTAAGGTTTTGCTTG
1 ATCCTTGAAAAAGCTAAGGTTTTGCCTG
3685032 ATCCTTGAAAAAGCTAAGGTTTTGCCTG
1 ATCCTTGAAAAAGCTAAGGTTTTGCCTG
**
3685060 ATTTTTGAAAA
1 ATCCTTGAAAA
3685071 GGAAGAGTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (28 bp):
ATCCTTGAAAAAGCTAAGGTTTTGCCTG
Found at i:3685104 original size:34 final size:34
Alignment explanation
Indices: 3685065--3685211 Score: 118
Period size: 34 Copynumber: 4.3 Consensus size: 34
3685055 GCCTGATTTT
* * *
3685065 TGAAAAGGAAGAGTGTGGGTTATGCCTGCTCATG
1 TGAAAAGGCAGTGTGTGGGTTATGCCTGATCATG
* * *
3685099 TGAAAAGGCAGTGTGTGGGTTGTGCTTGATCTTG
1 TGAAAAGGCAGTGTGTGGGTTATGCCTGATCATG
* * * *
3685133 TGAAAAAGCAGTGTGT-GGTTATGCTTGATCTTC
1 TGAAAAGGCAGTGTGTGGGTTATGCCTGATCATG
* * * * *
3685166 TCGAAAAGGTAATGTGTAAAGGTTATGCTTGATCCT-
1 T-GAAAAGGCAGTGTGT--GGGTTATGCCTGATCATG
3685202 TGAAAAGGCA
1 TGAAAAGGCA
3685212 ATTTTCATAA
Statistics
Matches: 95, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
33 16 0.17
34 55 0.58
35 8 0.08
36 1 0.01
37 15 0.16
ACGTcount: A:0.27, C:0.11, G:0.31, T:0.31
Consensus pattern (34 bp):
TGAAAAGGCAGTGTGTGGGTTATGCCTGATCATG
Found at i:3688135 original size:26 final size:26
Alignment explanation
Indices: 3688106--3688188 Score: 64
Period size: 26 Copynumber: 3.1 Consensus size: 26
3688096 ATCTTTTAAA
3688106 AATTGACTTCTTTTTTTCTCATAATC
1 AATTGACTTCTTTTTTTCTCATAATC
* * * *
3688132 AATT--TTTCACTGTTTATGTCTACTTAA-G
1 AATTGACTT--CT-TTT-TTTCT-CATAATC
3688160 AATTGACTTCTTTTTTTCTCATAATC
1 AATTGACTTCTTTTTTTCTCATAATC
3688186 AAT
1 AAT
3688189 CTCCAGAATT
Statistics
Matches: 41, Mismatches: 8, Indels: 16
0.63 0.12 0.25
Matches are distributed among these distances:
24 2 0.05
25 4 0.10
26 13 0.32
27 6 0.15
28 10 0.24
29 4 0.10
30 2 0.05
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.52
Consensus pattern (26 bp):
AATTGACTTCTTTTTTTCTCATAATC
Found at i:3688259 original size:14 final size:14
Alignment explanation
Indices: 3688237--3688270 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3688227 TTTTTCAATT
3688237 TAAACCTTAAACCC
1 TAAACCTTAAACCC
*
3688251 TAAATCTTAAACCC
1 TAAACCTTAAACCC
3688265 TAAACC
1 TAAACC
3688271 CTTTAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:3696295 original size:20 final size:20
Alignment explanation
Indices: 3696270--3696325 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
3696260 CCTAAAGAAT
*
3696270 ATCTATAGATAGATGAG-CAA
1 ATCTATACATAGATG-GCCAA
*
3696290 ATCTATCCATAGATGGCCAA
1 ATCTATACATAGATGGCCAA
3696310 ATCTAT-CTATAGATGG
1 ATCTATAC-ATAGATGG
3696326 AAACCATCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (20 bp):
ATCTATACATAGATGGCCAA
Found at i:3698012 original size:21 final size:21
Alignment explanation
Indices: 3697985--3698036 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
3697975 CTTTAAATCA
*
3697985 ATCAATAGATGTTCATCATCT
1 ATCAATAGATGTCCATCATCT
*
3698006 ATTAATAGATGTCCATCATCT
1 ATCAATAGATGTCCATCATCT
3698027 ATCAATAGAT
1 ATCAATAGAT
3698037 CAATTCAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
ATCAATAGATGTCCATCATCT
Found at i:3709518 original size:12 final size:12
Alignment explanation
Indices: 3709505--3709547 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
3709495 AAATGAATAT
3709505 ATACATATAT--
1 ATACATATATAC
*
3709515 ATATATATATAC
1 ATACATATATAC
*
3709527 ATACATACATAC
1 ATACATATATAC
3709539 ATACATATA
1 ATACATATA
3709548 GTGGATCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (12 bp):
ATACATATATAC
Found at i:3711404 original size:24 final size:27
Alignment explanation
Indices: 3711358--3711415 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 27
3711348 TGCAAAATAC
*
3711358 AAAACAATAATAATAATACAGAAAAAT-
1 AAAA-AATAATAATAATAAAGAAAAATG
3711385 AAAAAATAA-AA-AATAAAGAAAAATG
1 AAAAAATAATAATAATAAAGAAAAATG
3711410 AAAAAA
1 AAAAAA
3711416 GAGATAGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 12 0.41
25 8 0.28
26 5 0.17
27 4 0.14
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.14
Consensus pattern (27 bp):
AAAAAATAATAATAATAAAGAAAAATG
Found at i:3715681 original size:15 final size:18
Alignment explanation
Indices: 3715643--3715682 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 18
3715633 TATTTTTTTA
3715643 ATTTTAATAGTATTGAAT
1 ATTTTAATAGTATTGAAT
*
3715661 AATTTAA-A-TATT-AAT
1 ATTTTAATAGTATTGAAT
3715676 ATTTTAA
1 ATTTTAA
3715683 GTTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.45
16 4 0.20
17 1 0.05
18 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTTAATAGTATTGAAT
Found at i:3716958 original size:16 final size:15
Alignment explanation
Indices: 3716937--3716966 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
3716927 ATAAAGAAAA
3716937 GAAATAAAAATTAAAG
1 GAAAT-AAAATTAAAG
3716953 GAAATAAAATTAAA
1 GAAATAAAATTAAA
3716967 ATAAAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (15 bp):
GAAATAAAATTAAAG
Found at i:3740509 original size:20 final size:20
Alignment explanation
Indices: 3740480--3740517 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3740470 TCTTCACATA
3740480 TATGACGTGAGCTTAATTAT
1 TATGACGTGAGCTTAATTAT
*
3740500 TATGATGTGAGCTTAATT
1 TATGACGTGAGCTTAATT
3740518 CCTCCCCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (20 bp):
TATGACGTGAGCTTAATTAT
Found at i:3745066 original size:77 final size:77
Alignment explanation
Indices: 3744932--3745136 Score: 220
Period size: 77 Copynumber: 2.7 Consensus size: 77
3744922 AAACGATGAT
* *** * * * *
3744932 GTTTAACACTTTTAGTTTTTAAAAA-AGTGCATCGTTATTTAAGTGTAAATAATTGATGGAATAT
1 GTTTAACACTTTTAGGTCCAAAAAAGAGTGCCTTGTTATTTAGGTGTAAATAAATGATGGAATAT
*
3744996 TAAC-ATGA-AGTC
66 T-ACTATGATA-AC
*
3745008 GTTTAACACTTTTAGGTCCAAAAAACTA-TGCCTTGTTATTTAGGTGTAAATAAATGATGGAATA
1 GTTTAACACTTTTAGGTCCAAAAAA-GAGTGCCTTGTTATTTAGGTGTAAATAAATGATGGAATA
3745072 TTACTATGATAAC
65 TTACTATGATAAC
* * * * *
3745085 GTTTCACCCTTTTAGGTCCAAAAAAGAGTGCTTTGTTTTTTAGATGTAAATA
1 GTTTAACACTTTTAGGTCCAAAAAAGAGTGCCTTGTTATTTAGGTGTAAATA
3745137 GGATATGGAT
Statistics
Matches: 109, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
76 24 0.22
77 83 0.76
78 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (77 bp):
GTTTAACACTTTTAGGTCCAAAAAAGAGTGCCTTGTTATTTAGGTGTAAATAAATGATGGAATAT
TACTATGATAAC
Found at i:3747272 original size:73 final size:73
Alignment explanation
Indices: 3747186--3747347 Score: 184
Period size: 73 Copynumber: 2.2 Consensus size: 73
3747176 AGAGACATTA
* * * * **
3747186 TTAGTCGACTAAGAGCTTACTG-CTAGAAACTGGGTTCA-AAGACAGAAATGACTTAATCGACCA
1 TTAGTCAACTAAGAGCTCACTGTC-AGAAACTGGGATCAGAAGACAAAAACAACTTAATCGACCA
*
3747249 ACAAGGATTG
65 ACAAGCA-TG
* ** *
3747259 TTAGTCAATTAAGAGCTCACTGTCAGAAGTTGGGATCAGAAGACAAAAACAACTTAATCGACTAA
1 TTAGTCAACTAAGAGCTCACTGTCAGAAACTGGGATCAGAAGACAAAAACAACTTAATCGACCAA
*
3747324 GAAGCATG
66 CAAGCATG
3747332 TTAGTCAACTAAGAGC
1 TTAGTCAACTAAGAGC
3747348 ATTCTGTTTG
Statistics
Matches: 74, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
73 47 0.64
74 27 0.36
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (73 bp):
TTAGTCAACTAAGAGCTCACTGTCAGAAACTGGGATCAGAAGACAAAAACAACTTAATCGACCAA
CAAGCATG
Found at i:3757254 original size:8 final size:7
Alignment explanation
Indices: 3757226--3757251 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3757216 TCAATAATCT
3757226 AAAAATA
1 AAAAATA
3757233 AAAAATA
1 AAAAATA
3757240 AAAAATA
1 AAAAATA
3757247 AAAAA
1 AAAAA
3757252 ATACATCTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:3758507 original size:19 final size:21
Alignment explanation
Indices: 3758469--3758507 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3758459 ATGATCAACA
3758469 AAAAGTCACAAAATGCTCATC
1 AAAAGTCACAAAATGCTCATC
3758490 AAAA-TCACAAAA-GCTCAT
1 AAAAGTCACAAAATGCTCAT
3758508 TAGACTACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.51, C:0.23, G:0.08, T:0.18
Consensus pattern (21 bp):
AAAAGTCACAAAATGCTCATC
Found at i:3759240 original size:16 final size:15
Alignment explanation
Indices: 3759221--3759250 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3759211 TAGAAAATTT
3759221 AACACAAATAAAAAAA
1 AACACAAA-AAAAAAA
3759237 AACACAAAAAAAAA
1 AACACAAAAAAAAA
3759251 TCTAAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.83, C:0.13, G:0.00, T:0.03
Consensus pattern (15 bp):
AACACAAAAAAAAAA
Found at i:3761227 original size:183 final size:181
Alignment explanation
Indices: 3760812--3761264 Score: 536
Period size: 183 Copynumber: 2.5 Consensus size: 181
3760802 TTTGATCTAC
* * *
3760812 AAATTATGAAATGAAAATATGAAATATGAAGTAACAAAAAGGAAAGTAAAATCATTA-CT--TTC
1 AAATTATGAAATGAAAATATGAAATATGAAGTAATAAAAAGGAAAGCAAAGTCATTACCTACTTC
** * * * * *
3760874 CCTTTGTAATTTTTTTTTTAATTTACCTTGAGGTATTGCTTGGGCTTGAAATTCTCGCTTGGCAT
66 TTTTTGTAA-TTTTTTTTTAATTTACCTTGAGGTACTGCTTGAGCTTGAAATCCTCACTTGGCAA
* * * * ** * *
3760939 CATCTACTACTTACTCATTTCTCATTTCTTGAACTAGAATTCTTGATCTACA
130 CATCCACTACTTACTCATTTCTCATCTCTTGAACCAAAATTCCAGATATAAA
3760991 AAATTATGAAATGAAAATATGAAATATGAAGTAATAAAAAGGAAAGCAAAGTCATTACCTACTTG
1 AAATTATGAAATGAAAATATGAAATATGAAGTAATAAAAAGGAAAGCAAAGTCATTACCTACTT-
* * *
3761056 CTTTTTGCAATTTTCTTTTAATTTACCTTGAGGTACTGCTTGAGCTTGAAATCCTTACTTGGCAA
65 CTTTTTGTAATTTTTTTTTAATTTACCTTGAGGTACTGCTTGAGCTTGAAATCCTCACTTGGCAA
* * * * * * *
3761121 CATCCCCTATTTGCTCATTTGTTA-CTCTTGAGCCAAAATTTCCAGCTATAAA
130 CATCCACTACTTACTCATTTCTCATCTCTTGAACCAAAA-TTCCAGATATAAA
* * * *
3761173 AACATTATGAAATGAAAATATAAAATATAAAGTAATAAAAAGGAAAACAAAGTCATTACCCACTT
1 AA-ATTATGAAATGAAAATATGAAATATGAAGTAATAAAAAGGAAAGCAAAGTCATTACCTACTT
*
3761238 ACTTTCTGTAATTTTTTTTTAATTTAC
65 -CTTTTTGTAATTTTTTTTTAATTTAC
3761265 TTGGAGACAG
Statistics
Matches: 232, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
179 54 0.23
180 2 0.01
181 10 0.04
182 78 0.34
183 88 0.38
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (181 bp):
AAATTATGAAATGAAAATATGAAATATGAAGTAATAAAAAGGAAAGCAAAGTCATTACCTACTTC
TTTTTGTAATTTTTTTTTAATTTACCTTGAGGTACTGCTTGAGCTTGAAATCCTCACTTGGCAAC
ATCCACTACTTACTCATTTCTCATCTCTTGAACCAAAATTCCAGATATAAA
Found at i:3761645 original size:20 final size:19
Alignment explanation
Indices: 3761615--3761656 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
3761605 TGTTAACATA
3761615 TATAATTTTTATAAATATT
1 TATAATTTTTATAAATATT
*
3761634 TATAACTTTTTATTAATATT
1 TATAA-TTTTTATAAATATT
3761654 TAT
1 TAT
3761657 TTGTACTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TATAATTTTTATAAATATT
Found at i:3767884 original size:3 final size:3
Alignment explanation
Indices: 3767878--3767909 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3767868 AATAATAACA
3767878 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
3767910 ATTTAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:3768934 original size:2 final size:2
Alignment explanation
Indices: 3768927--3768965 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3768917 GTTGATAGTA
3768927 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3768966 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3768970 original size:2 final size:2
Alignment explanation
Indices: 3768965--3768997 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3768955 ATATATATAT
3768965 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3768998 ATAGTTGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3771551 original size:15 final size:15
Alignment explanation
Indices: 3771531--3771599 Score: 111
Period size: 15 Copynumber: 4.6 Consensus size: 15
3771521 ATTACAATGC
* *
3771531 AATGTGATTACAGGT
1 AATGTGATTGCAAGT
3771546 AATGTGATTGCAAGT
1 AATGTGATTGCAAGT
3771561 AATGTGATTGCAAGT
1 AATGTGATTGCAAGT
*
3771576 AATGTGATTGCAAGC
1 AATGTGATTGCAAGT
3771591 AATGTGATT
1 AATGTGATT
3771600 ACAGGTAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:3771565 original size:30 final size:30
Alignment explanation
Indices: 3771529--3771607 Score: 131
Period size: 30 Copynumber: 2.6 Consensus size: 30
3771519 ACATTACAAT
3771529 GCAATGTGATTACAGGTAATGTGATTGCAA
1 GCAATGTGATTACAGGTAATGTGATTGCAA
* * *
3771559 GTAATGTGATTGCAAGTAATGTGATTGCAA
1 GCAATGTGATTACAGGTAATGTGATTGCAA
3771589 GCAATGTGATTACAGGTAA
1 GCAATGTGATTACAGGTAA
3771608 AATAACATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (30 bp):
GCAATGTGATTACAGGTAATGTGATTGCAA
Found at i:3771858 original size:23 final size:22
Alignment explanation
Indices: 3771840--3771979 Score: 69
Period size: 21 Copynumber: 6.3 Consensus size: 22
3771830 TATTTATTAG
3771840 TATAATAT-TTTATATTTTATT
1 TATAATATATTTATATTTTATT
*
3771861 TTTAATATATTTATATTTT-TGT
1 TATAATATATTTATATTTTAT-T
*
3771883 TATTAAT-T-TTTATATAATATCATT
1 TA-TAATATATTTATAT--T-TTATT
* * *
3771907 TCTTAAATATATTTATAATAT-TT
1 T-AT-AATATATTTATATTTTATT
* * *
3771930 TATATTTTATTTTTA-TTTATTAT
1 TATAATATATTTATATTTTA-T-T
3771953 TATAATAT-TTTATATTTTATT
1 TATAATATATTTATATTTTATT
*
3771974 TTTAAT
1 TATAAT
3771980 NNNNNNNNNN
Statistics
Matches: 88, Mismatches: 16, Indels: 30
0.66 0.12 0.22
Matches are distributed among these distances:
20 2 0.02
21 30 0.34
22 21 0.24
23 19 0.22
24 4 0.05
25 5 0.06
26 1 0.01
27 6 0.07
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (22 bp):
TATAATATATTTATATTTTATT
Found at i:3771946 original size:27 final size:27
Alignment explanation
Indices: 3771827--3771979 Score: 81
Period size: 27 Copynumber: 5.7 Consensus size: 27
3771817 CATATATTTT
*
3771827 TTTTATTTATTA-GTATAATATTTTATA
1 TTTTATTT-TTATTTATAATATTTTATA
* * *
3771854 TTTTATTTTTAATATATTTATATTTT-TG
1 TTTTATTTTT-ATTTA-TAATATTTTATA
*
3771882 TTATTAATTTTTA--TATAATA--TCAT-
1 TT-TT-ATTTTTATTTATAATATTTTATA
** *
3771906 TTCTTAAATATATTTATAATATTTTATA
1 TT-TTATTTTTATTTATAATATTTTATA
*
3771934 TTTTATTTTTATTTAT--TATTATAATA
1 TTTTATTTTTATTTATAATATT-TTATA
*
3771960 TTTTATATTTTATTTTTAAT
1 TTTTAT-TTTTATTTATAAT
3771980 NNNNNNNNNN
Statistics
Matches: 96, Mismatches: 15, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
23 4 0.04
24 5 0.05
25 12 0.12
26 16 0.17
27 34 0.35
28 7 0.07
29 12 0.12
30 6 0.06
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (27 bp):
TTTTATTTTTATTTATAATATTTTATA
Found at i:3771958 original size:58 final size:55
Alignment explanation
Indices: 3771740--3771960 Score: 209
Period size: 58 Copynumber: 3.9 Consensus size: 55
3771730 CTAATTATTA
**
3771740 AAATATAAGTTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTT
1 AAATATATTTTTAATAT-TTTATA-TTTTT-TT-TT-ATTTTTATATAATATCATTTCTT
** *
3771800 AAATATATTTTTAATATCATATA-TTTTTTTTATTTATTAGTATAATAT--TTT-AT
1 AAATATATTTTTAATATTTTATATTTTTTTTTATTT-TTA-TATAATATCATTTCTT
* *
3771853 -ATTTTATTTTTAATATATTTATATTTTTGTTATTAATTTTTATATAATATCATTTCTT
1 AAATATATTTTTAATAT-TTTATATTTTT-TT-TT-ATTTTTATATAATATCATTTCTT
*
3771911 AAATATATTTATAATATTTTATATTTTATTTTTATTTATTATTATAATAT
1 AAATATATTTTTAATATTTTATATTTT-TTTTTATTT-TTA-TATAATAT
3771961 TTTATATTTT
Statistics
Matches: 134, Mismatches: 13, Indels: 30
0.76 0.07 0.17
Matches are distributed among these distances:
52 14 0.10
53 5 0.04
54 11 0.08
55 15 0.11
56 19 0.14
57 16 0.12
58 21 0.16
59 18 0.13
60 15 0.11
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (55 bp):
AAATATATTTTTAATATTTTATATTTTTTTTTATTTTTATATAATATCATTTCTT
Found at i:3774027 original size:18 final size:18
Alignment explanation
Indices: 3773984--3774031 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
3773974 CTAGTAGCTT
*
3773984 ACAAATTAAAAATGACAC
1 ACAAATGAAAAATGACAC
*
3774002 ACAAATGAAAAATGACTC
1 ACAAATGAAAAATGACAC
**
3774020 ACCCATGAAAAA
1 ACAAATGAAAAA
3774032 AGAAACCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.58, C:0.19, G:0.08, T:0.15
Consensus pattern (18 bp):
ACAAATGAAAAATGACAC
Found at i:3780189 original size:21 final size:21
Alignment explanation
Indices: 3780164--3780212 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
3780154 TCAATGCAGT
* *
3780164 TAATACTTTTATTTATAAATTA
1 TAATAATTTTATTAAT-AATTA
3780186 -AATAAATTTTATTAATAATTA
1 TAAT-AATTTTATTAATAATTA
3780207 TAATAA
1 TAATAA
3780213 AAAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATAATTTTATTAATAATTA
Found at i:3780195 original size:22 final size:22
Alignment explanation
Indices: 3780170--3780213 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3780160 CAGTTAATAC
*
3780170 TTTTATTTATAAATTA-AATAAA
1 TTTTATTAAT-AATTATAATAAA
3780192 TTTTATTAATAATTATAATAAA
1 TTTTATTAATAATTATAATAAA
3780214 AAATATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTATTAATAATTATAATAAA
Found at i:3781554 original size:29 final size:29
Alignment explanation
Indices: 3781492--3781554 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
3781482 CTATGTTGGA
* *
3781492 AAAAAATATTGTTGCTACACGTCATGTTG
1 AAAAAATATTATTGCTACACGTCATATTG
* * * *
3781521 CAAAAATATTATTGGTACACGTTATATTT
1 AAAAAATATTATTGCTACACGTCATATTG
3781550 AAAAA
1 AAAAA
3781555 TTTTTTTTAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (29 bp):
AAAAAATATTATTGCTACACGTCATATTG
Found at i:3783531 original size:19 final size:20
Alignment explanation
Indices: 3783506--3783545 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3783496 GAGAGAGAAA
* *
3783506 AAAAAATGTATTTTTATTTT
1 AAAAATTGTATATTTATTTT
*
3783526 AAAAATTTTATATTTATTTT
1 AAAAATTGTATATTTATTTT
3783546 TAAGGTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
AAAAATTGTATATTTATTTT
Found at i:3800803 original size:2 final size:2
Alignment explanation
Indices: 3800796--3800820 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3800786 NNNNNNNNNN
3800796 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3800821 GCACACATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3801534 original size:21 final size:22
Alignment explanation
Indices: 3801509--3801552 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
3801499 AAGTGATTAA
3801509 TTTAAGTTATTTTA-ATTAAAT
1 TTTAAGTTATTTTATATTAAAT
*
3801530 TTTAAGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATATTAAAT
3801552 T
1 T
3801553 ACTTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATATTAAAT
Found at i:3807748 original size:78 final size:78
Alignment explanation
Indices: 3807591--3807741 Score: 180
Period size: 78 Copynumber: 1.9 Consensus size: 78
3807581 CCATCAGAAC
* * * * * * *
3807591 AACCAATGGCTACTTAGACTGAAGATTGCTTTGGATACTGGAGAGACACCAACAAAATGAATTCA
1 AACCAATGGATACTTAGACTGAAGATTACTTTGAACACTGAAAAGACACCAACAAAATGAACTCA
3807656 ATTGCCAACGTTT
66 ATTGCCAACGTTT
* * * *
3807669 AACCAATGGATACTTAGATTGAAG-TCTACTTTGAACACTGAAAAGACACCTA-TAAATGCACTC
1 AACCAATGGATACTTAGACTGAAGAT-TACTTTGAACACTGAAAAGACACCAACAAAATGAACTC
3807732 AATTGCCAAC
65 AATTGCCAAC
3807742 ATTTTAAGCC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
77 19 0.31
78 42 0.69
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (78 bp):
AACCAATGGATACTTAGACTGAAGATTACTTTGAACACTGAAAAGACACCAACAAAATGAACTCA
ATTGCCAACGTTT
Found at i:3809035 original size:2 final size:2
Alignment explanation
Indices: 3809028--3809053 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3809018 TAATTTTCTT
3809028 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
3809054 CCTCCCTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3813973 original size:22 final size:22
Alignment explanation
Indices: 3813945--3813986 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3813935 AAATCCACAG
*
3813945 AGATTGAAATCAGGAAATACAC
1 AGATTGAAATCAAGAAATACAC
3813967 AGATTGAAATCAAGAAATAC
1 AGATTGAAATCAAGAAATAC
3813987 TATATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.19
Consensus pattern (22 bp):
AGATTGAAATCAAGAAATACAC
Found at i:3820976 original size:153 final size:151
Alignment explanation
Indices: 3820699--3821002 Score: 563
Period size: 153 Copynumber: 2.0 Consensus size: 151
3820689 GGTTTAGTAA
3820699 TTTTACATTTCTTTGCTGAGAAAACTTAAAATATTATTATCACATTCCTGTATGGGCATAGGTAT
1 TTTTACATTTCTTTGCTGAGAAAACTTAAAATATTATTATCACATTCCTGTATGGGCATAGGTAT
*
3820764 AATCAGATTCTTCAAGGTGACTTAATAAAGCTCAAAAATGGAGAATGAAATAGTGCAGGATATGG
66 AATCAGATTCTTCAAGGTGACGTAATAAAGCTCAAAAATGGAGAATGAAATAGTGCAGGATAT-G
*
3820829 GGATACTACATCTAATGTTGTT
130 GAATACTACATCTAATGTTGTT
3820851 TTTTACATTTCTTTGCTGAGAAAACTTAAAATATTTATTATCACATTCCTGTATGGGCATAGGTA
1 TTTTACATTTCTTTGCTGAGAAAACTTAAAATA-TTATTATCACATTCCTGTATGGGCATAGGTA
3820916 TAATCAGATTCTTCAAGGTGACGTAATAAAGCTCAAAAATGGAGAATGAAATAGTGCAGGATATG
65 TAATCAGATTCTTCAAGGTGACGTAATAAAGCTCAAAAATGGAGAATGAAATAGTGCAGGATATG
*
3820981 GAATACTACATCTAATTTTGTT
130 GAATACTACATCTAATGTTGTT
3821003 ACCCCTTTCA
Statistics
Matches: 148, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
152 54 0.36
153 94 0.64
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (151 bp):
TTTTACATTTCTTTGCTGAGAAAACTTAAAATATTATTATCACATTCCTGTATGGGCATAGGTAT
AATCAGATTCTTCAAGGTGACGTAATAAAGCTCAAAAATGGAGAATGAAATAGTGCAGGATATGG
AATACTACATCTAATGTTGTT
Found at i:3836393 original size:19 final size:19
Alignment explanation
Indices: 3836369--3836405 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3836359 AAACATCTCT
* *
3836369 AAAATAGAAAAGAATAAAG
1 AAAATAAAAAAAAATAAAG
3836388 AAAATAAAAAAAAATAAA
1 AAAATAAAAAAAAATAAA
3836406 ATCCCTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (19 bp):
AAAATAAAAAAAAATAAAG
Found at i:3838247 original size:25 final size:25
Alignment explanation
Indices: 3838219--3838266 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
3838209 TGATGATTCT
*
3838219 TAATCCCTACAATTATGGTAATTTC
1 TAATCCCAACAATTATGGTAATTTC
* * *
3838244 TAATTCCAATAATTATGTTAATT
1 TAATCCCAACAATTATGGTAATT
3838267 AATAAAAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (25 bp):
TAATCCCAACAATTATGGTAATTTC
Found at i:3842449 original size:2 final size:2
Alignment explanation
Indices: 3842442--3842485 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3842432 TAACAGCAGC
*
3842442 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3842484 AT
1 AT
3842486 GTCCATGTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3850070 original size:2 final size:2
Alignment explanation
Indices: 3850063--3850092 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3850053 GTTGGATCTA
3850063 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
3850093 CATCCTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:3852166 original size:28 final size:28
Alignment explanation
Indices: 3852112--3852166 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
3852102 AGCTTTGATC
* * *
3852112 TTGGTGTGTAATATTTACTGTTGAAGTT
1 TTGGTGTGTAATATTTACAGCTAAAGTT
3852140 TTGGTGTGTAATATCTTA-AGCTAAAGT
1 TTGGTGTGTAATAT-TTACAGCTAAAGT
3852167 GGGTAATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.25, C:0.05, G:0.24, T:0.45
Consensus pattern (28 bp):
TTGGTGTGTAATATTTACAGCTAAAGTT
Found at i:3862269 original size:75 final size:74
Alignment explanation
Indices: 3862138--3862345 Score: 266
Period size: 75 Copynumber: 2.9 Consensus size: 74
3862128 CTATGACGTA
* * * * * * *
3862138 ACACATTATGTACAAAAACATGTTACACGTCATGATTAGGTTGTTACATGTTATGTTGAAAAAAA
1 ACACGTTATGGACAAAAATATGTTACATG-CATGATTAAGTTGTTACACGTCATGTTGAAAAAAA
3862203 TACTGTTGTT
65 TACTGTTGTT
*
3862213 ACACGTTATGGACAAAAATATGTTACATGCCATGGTTAAGTTGTTACACGTCATGTTGAAAAAAA
1 ACACGTTATGGACAAAAATATGTTACATG-CATGATTAAGTTGTTACACGTCATGTTGAAAAAAA
3862278 TACTGTTGTT
65 TACTGTTGTT
* *
3862288 AAACGTCATGGACAAAAATATGTT--AT--A--ATTAAGTTGTTACACGTCATGTTGAAAAAAA
1 ACACGTTATGGACAAAAATATGTTACATGCATGATTAAGTTGTTACACGTCATGTTGAAAAAAA
3862346 ATATATTTTT
Statistics
Matches: 121, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
68 30 0.25
70 1 0.01
73 2 0.02
75 88 0.73
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (74 bp):
ACACGTTATGGACAAAAATATGTTACATGCATGATTAAGTTGTTACACGTCATGTTGAAAAAAAT
ACTGTTGTT
Found at i:3864135 original size:5 final size:5
Alignment explanation
Indices: 3864121--3864149 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3864111 GAAATAAAAA
3864121 TAAA- TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
3864150 AAAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TAAAT
Found at i:3864143 original size:15 final size:14
Alignment explanation
Indices: 3864118--3864152 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
3864108 TTGGAAATAA
3864118 AAATAAA-TAAATT
1 AAATAAATTAAATT
3864131 AAATTAAATTAAATT
1 AAA-TAAATTAAATT
3864146 AAATAAA
1 AAATAAA
3864153 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 8 0.40
15 9 0.45
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATAAATTAAATT
Found at i:3864158 original size:15 final size:15
Alignment explanation
Indices: 3864122--3864158 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3864112 AAATAAAAAT
*
3864122 AAATAAATTAAATTA
1 AAATAAATTAAATAA
*
3864137 AATTAAATTAAATAA
1 AAATAAATTAAATAA
3864152 AAATAAA
1 AAATAAA
3864159 AAAAGAGTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAAATTAAATAA
Found at i:3876687 original size:20 final size:20
Alignment explanation
Indices: 3876662--3876699 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3876652 AATACCCAGT
3876662 AATGTATCGATACATTTAGG
1 AATGTATCGATACATTTAGG
*
3876682 AATGTATTGATACATTTA
1 AATGTATCGATACATTTA
3876700 CATGGGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTTAGG
Found at i:3882062 original size:30 final size:30
Alignment explanation
Indices: 3881985--3882063 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
3881975 AGTATTACAA
* * *
3881985 TTATACTTTCTTGAAAAAGTAGTGTAAAGG
1 TTATACCTCCTTGAAAAGGTAGTGTAAAGG
3882015 TTATACCTCCTTGAAAAGGTAGTGCT-AAGG
1 TTATACCTCCTTGAAAAGGTAGTG-TAAAGG
*
3882045 TTATATCTCCGTT-AAAAGG
1 TTATACCTCC-TTGAAAAGG
3882064 GTAGAGAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 40 0.93
31 3 0.07
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (30 bp):
TTATACCTCCTTGAAAAGGTAGTGTAAAGG
Found at i:3882177 original size:39 final size:39
Alignment explanation
Indices: 3882077--3882201 Score: 144
Period size: 39 Copynumber: 3.2 Consensus size: 39
3882067 GAGAGATTAG
* * * *
3882077 ACTTGACCCTAAAAAGGTTGTGACTTGTCTAAAGGTTAT
1 ACTTGATCTTAAAAAGGTAGTGACTTGTATAAAGGTTAT
* *
3882116 ACTGGATCTTAAAAAGGCAGTGACTTGTATAAAGGTTAT
1 ACTTGATCTTAAAAAGGTAGTGACTTGTATAAAGGTTAT
* * *
3882155 ACTTGATCTTAAAAAAGTAGTGATTTGTGTAGAA-GTTAT
1 ACTTGATCTTAAAAAGGTAGTGACTTGTATA-AAGGTTAT
*
3882194 GCTTGATC
1 ACTTGATC
3882202 CTTGAAAGGC
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 71 0.97
40 2 0.03
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (39 bp):
ACTTGATCTTAAAAAGGTAGTGACTTGTATAAAGGTTAT
Found at i:3884463 original size:20 final size:20
Alignment explanation
Indices: 3884438--3884498 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
3884428 GCCTAGCAAG
3884438 ACAACCCCAACCTAGCCCAA
1 ACAACCCCAACCTAGCCCAA
3884458 ACAACCCCAACCTAGCCCAA
1 ACAACCCCAACCTAGCCCAA
* * *
3884478 ACAAGCCTAACCTAGCTCAA
1 ACAACCCCAACCTAGCCCAA
3884498 A
1 A
3884499 TGAGCCTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.41, C:0.44, G:0.07, T:0.08
Consensus pattern (20 bp):
ACAACCCCAACCTAGCCCAA
Found at i:3884504 original size:20 final size:20
Alignment explanation
Indices: 3884446--3884554 Score: 121
Period size: 20 Copynumber: 5.5 Consensus size: 20
3884436 AGACAACCCC
* * *
3884446 AACCTAGCCCAAACAACCCC
1 AACCTAGCTCAAACAAGCCT
*
3884466 AACCTAGCCCAAACAAGCCT
1 AACCTAGCTCAAACAAGCCT
**
3884486 AACCTAGCTCAAATGAGCCT
1 AACCTAGCTCAAACAAGCCT
*
3884506 AACCTATGC-CAAACAAGCTT
1 AACCTA-GCTCAAACAAGCCT
* *
3884526 AACCTAACTCAGACAAGCCT
1 AACCTAGCTCAAACAAGCCT
3884546 AACCTAGCT
1 AACCTAGCT
3884555 TAGATCAGCC
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
19 1 0.01
20 72 0.96
21 2 0.03
ACGTcount: A:0.39, C:0.37, G:0.10, T:0.15
Consensus pattern (20 bp):
AACCTAGCTCAAACAAGCCT
Found at i:3887230 original size:234 final size:234
Alignment explanation
Indices: 3886797--3887250 Score: 642
Period size: 234 Copynumber: 1.9 Consensus size: 234
3886787 CCAAAAGTAT
*
3886797 AACTCAGAAACTTGGTGACCAAGAAAAGGCATGGCACAACTAGACAAAAGTGGAGCAACTAAATT
1 AACTCAGAAACTTAGTGACCAAGAAAAGGCATGGCACAACTAGACAAAAGTGGAGCAACTAAATT
* * * * * * * * * * *
3886862 CAAGCTTGAATTCAAATTTTATAGCTAGTCTATAGTGAATAATCGAGACCTTGAGGAAAAAGAAT
66 CAAGCTTGAATTCAAATTTTAGAGCAAGTCCACAATAAAGAACCAAGACCTTAAGGAAAAAAAAT
* * * * *
3886927 CGATTCTCTAAGATTGCAAAGGTGTCACCTTTATGCCTAGTTGTAGAAGAACCAACACCTTATAA
131 CAATTCTCCAAGATTGCAAAAGTGTCACCTTTATGCCCAGTTGTAGAAGAACCAACACCTTAAAA
3886992 TAAAAGAA-TCGATTCTTCAAAGATAGAAGTTAGTTTTTG
196 TAAAAGAACT-GATTCTTCAAAGATAGAAGTTAGTTTTTG
* ** * * *
3887031 AACTTAGAAACTTAGTGACCAAG-AAAGGCATGGCACAGTTGGACAAAAGTGGAGCGATTAAATT
1 AACTCAGAAACTTAGTGACCAAGAAAAGGCATGGCACAACTAGACAAAAGTGGAGCAACTAAATT
3887095 CAAGCTTGAATTCAAATTTTAGAGCAAGTCCACAATAAAGAACCAAGACCTTAAGGTAAAAAAAA
66 CAAGCTTGAATTCAAATTTTAGAGCAAGTCCACAATAAAGAACCAAGACCTTAAGG-AAAAAAAA
* * *
3887160 TCAATTCTCCAATATTGTAAAAGTGTCACCTTTATGCCCAGTTGTAGAAGAATCAACACCTTAAA
130 TCAATTCTCCAAGATTGCAAAAGTGTCACCTTTATGCCCAGTTGTAGAAGAACCAACACCTTAAA
3887225 ATAAAAGAACTGATTCTTCAAAGATA
195 ATAAAAGAACTGATTCTTCAAAGATA
3887251 AAAAGCTACA
Statistics
Matches: 192, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
233 82 0.43
234 109 0.57
235 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (234 bp):
AACTCAGAAACTTAGTGACCAAGAAAAGGCATGGCACAACTAGACAAAAGTGGAGCAACTAAATT
CAAGCTTGAATTCAAATTTTAGAGCAAGTCCACAATAAAGAACCAAGACCTTAAGGAAAAAAAAT
CAATTCTCCAAGATTGCAAAAGTGTCACCTTTATGCCCAGTTGTAGAAGAACCAACACCTTAAAA
TAAAAGAACTGATTCTTCAAAGATAGAAGTTAGTTTTTG
Found at i:3896237 original size:3 final size:3
Alignment explanation
Indices: 3896229--3896253 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3896219 TTGAGGAAAG
3896229 GGT GGT GGT GGT GGT GGT GGT GGT G
1 GGT GGT GGT GGT GGT GGT GGT GGT G
3896254 TAATTGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:3899957 original size:2 final size:2
Alignment explanation
Indices: 3899950--3899979 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3899940 ATCACCTCCA
3899950 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3899980 TAAACTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3904403 original size:27 final size:27
Alignment explanation
Indices: 3904373--3904452 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
3904363 CGAGCTACTA
*
3904373 ATGAATACATTTAACTACCAGAAGTGG
1 ATGAATACATTTAACTACCAAAAGTGG
*
3904400 ATGAATACATTT-AGTCACCAAAAGTGG
1 ATGAATACATTTAACT-ACCAAAAGTGG
* *
3904427 ATGAATACTTTTAACTACCAACAGTG
1 ATGAATACATTTAACTACCAAAAGTG
3904453 AATAAATAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 42 0.91
28 2 0.04
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (27 bp):
ATGAATACATTTAACTACCAAAAGTGG
Found at i:3908724 original size:60 final size:60
Alignment explanation
Indices: 3908643--3908758 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
3908633 GTAGCAGCCA
* * *
3908643 ATGAATTTCAAGCATTGCGTGTATCATC-TTAGGAATTATAGGAATGGTGTGTAACATCTT
1 ATGAATTTCAAGCATTGCGTGTAACAACATT-GGAATTATAGGAATGGCGTGTAACATCTT
* *
3908703 ATGAATTTTAAGCA-TGACGTGTAACAACATTGGAATTTTAGGAATGGCGTGTAACA
1 ATGAATTTCAAGCATTG-CGTGTAACAACATTGGAATTATAGGAATGGCGTGTAACA
3908759 ATTTATTCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 2 0.04
60 45 0.92
61 2 0.04
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.34
Consensus pattern (60 bp):
ATGAATTTCAAGCATTGCGTGTAACAACATTGGAATTATAGGAATGGCGTGTAACATCTT
Found at i:3908725 original size:30 final size:29
Alignment explanation
Indices: 3908643--3908728 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 29
3908633 GTAGCAGCCA
* *
3908643 ATGAATTTCAAGCATTGCGTGTATCATCTT
1 ATGAATTTTAAGCA-TGCGTGTAACATCTT
* * * * *
3908673 AGGAATTATAGGAATGGTGTGTAACATCTT
1 ATGAATTTTAAGCAT-GCGTGTAACATCTT
3908703 ATGAATTTTAAGCATGACGTGTAACA
1 ATGAATTTTAAGCATG-CGTGTAACA
3908729 ACATTGGAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
29 2 0.05
30 40 0.95
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (29 bp):
ATGAATTTTAAGCATGCGTGTAACATCTT
Found at i:3916393 original size:26 final size:24
Alignment explanation
Indices: 3916364--3916417 Score: 72
Period size: 26 Copynumber: 2.2 Consensus size: 24
3916354 CTAAGAAGAA
*
3916364 AAGAGAAAGGAGAGGAGAAGGAAGGC
1 AAGAGAAAGGAGAGGA-AA-GAAAGC
*
3916390 AAGAGAAAGTAGAGGAAAGAAAGC
1 AAGAGAAAGGAGAGGAAAGAAAGC
3916414 AAGA
1 AAGA
3916418 AAGAGAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 9 0.35
25 2 0.08
26 15 0.58
ACGTcount: A:0.56, C:0.04, G:0.39, T:0.02
Consensus pattern (24 bp):
AAGAGAAAGGAGAGGAAAGAAAGC
Found at i:3924728 original size:18 final size:18
Alignment explanation
Indices: 3924678--3924733 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
3924668 ACATATGAGT
*
3924678 AAATAAAATAGAAATGAA
1 AAATAAAATAAAAATGAA
3924696 AAA-AAAAGTAAAAAT-AA
1 AAATAAAA-TAAAAATGAA
*
3924713 AAATAATAATATAAATTGAA
1 AAATAA-AATA-AAAATGAA
3924733 A
1 A
3924734 GAAAAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 9 0.29
18 13 0.42
19 6 0.19
20 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (18 bp):
AAATAAAATAAAAATGAA
Found at i:3926247 original size:21 final size:22
Alignment explanation
Indices: 3926218--3926261 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3926208 AAGTGATTAA
3926218 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
3926239 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
3926261 T
1 T
3926262 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:3926955 original size:12 final size:12
Alignment explanation
Indices: 3926909--3926954 Score: 76
Period size: 12 Copynumber: 3.8 Consensus size: 12
3926899 AGAGATTTTT
3926909 GAGGCAGCAAGA
1 GAGGCAGCAAGA
3926921 GAGGCAGCAAGA
1 GAGGCAGCAAGA
3926933 GAGGCAGCAA-A
1 GAGGCAGCAAGA
3926944 GGAGGCAGCAA
1 -GAGGCAGCAA
3926955 AAACTATTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 1 0.03
12 32 0.97
ACGTcount: A:0.41, C:0.17, G:0.41, T:0.00
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:3932841 original size:12 final size:12
Alignment explanation
Indices: 3932826--3932873 Score: 80
Period size: 12 Copynumber: 4.0 Consensus size: 12
3932816 AGAGATTTTT
3932826 GAGGCAGCAAGA
1 GAGGCAGCAAGA
3932838 GAGGCAGCAAGA
1 GAGGCAGCAAGA
3932850 GAGGCAGCAA-A
1 GAGGCAGCAAGA
3932861 GGAGGCAGCAAGA
1 -GAGGCAGCAAGA
3932874 AACTATTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 1 0.03
12 32 0.94
13 1 0.03
ACGTcount: A:0.42, C:0.17, G:0.42, T:0.00
Consensus pattern (12 bp):
GAGGCAGCAAGA
Found at i:3934799 original size:31 final size:30
Alignment explanation
Indices: 3934736--3934799 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
3934726 TTTATACATA
* *
3934736 GCATGTAACAACATTTAACTTGCTAGACATG
1 GCATGTAACAACA-TTAAATTGCTAGAAATG
3934767 GCATGTAACAACA-TAAATTGCCTAGTAAATG
1 GCATGTAACAACATTAAATTG-CTAG-AAATG
3934798 GC
1 GC
3934800 GTCTAGCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 6 0.21
30 4 0.14
31 19 0.66
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (30 bp):
GCATGTAACAACATTAAATTGCTAGAAATG
Found at i:3941344 original size:2 final size:2
Alignment explanation
Indices: 3941313--3941358 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
3941303 GCAGTTTTGA
* * *
3941313 AT AT -T AT A- AT AT AA AT AT AT AC AT AC AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3941353 AT AT AT
1 AT AT AT
3941359 CAAATATTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3953075 original size:6 final size:6
Alignment explanation
Indices: 3953064--3953089 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3953054 CTCCTAGATT
3953064 CCCCAG CCCCAG CCCCAG CCCCAG CC
1 CCCCAG CCCCAG CCCCAG CCCCAG CC
3953090 GGGAACAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.69, G:0.15, T:0.00
Consensus pattern (6 bp):
CCCCAG
Found at i:3961449 original size:142 final size:142
Alignment explanation
Indices: 3961212--3961490 Score: 481
Period size: 142 Copynumber: 2.0 Consensus size: 142
3961202 CCTTTGGTAC
* * * *
3961212 TGAAATGACAAAATTGAATGACCTAAATGTGTTTTAAAATTTAGTCAAAGTGGTTTTGAGCTTGA
1 TGAAATGACAAAATTGAATAACCTAAATATGTTTTAAAATTAAGTCAAAGTGGTTTTGAACTTGA
3961277 AGAACAATTCTCAAAGAAGTTTAAAGTTAATTGTACAAAGAAAAATCTTTTAAACTCTTAAAATC
66 AGAACAATTCTCAAAGAAGTTTAAAGTTAATTGTACAAAGAAAAATCTTTTAAACTCTTAAAATC
3961342 TCAAGTTGTTTT
131 TCAAGTTGTTTT
*
3961354 TGAAATGACAAAATTGAATAACCTAAATATGTTTTGAAATTAAGTCAAAGT-GTTTGTGAACTTG
1 TGAAATGACAAAATTGAATAACCTAAATATGTTTTAAAATTAAGTCAAAGTGGTTT-TGAACTTG
3961418 AAGAACAATTCTCAAAGAAGTTTGAAA-TTAATTGTACAAAGAAAAATCTTTTAAACTCTTAAAA
65 AAGAACAATTCTCAAAGAAGTTT-AAAGTTAATTGTACAAAGAAAAATCTTTTAAACTCTTAAAA
3961482 TCTCAAGTT
129 TCTCAAGTT
3961491 CTAACATAAA
Statistics
Matches: 130, Mismatches: 5, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
141 4 0.03
142 123 0.95
143 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (142 bp):
TGAAATGACAAAATTGAATAACCTAAATATGTTTTAAAATTAAGTCAAAGTGGTTTTGAACTTGA
AGAACAATTCTCAAAGAAGTTTAAAGTTAATTGTACAAAGAAAAATCTTTTAAACTCTTAAAATC
TCAAGTTGTTTT
Found at i:3964336 original size:14 final size:16
Alignment explanation
Indices: 3964324--3964355 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3964314 TAATTTATTT
3964324 ATTTTTCTCTATTTTC
1 ATTTTTCTCTATTTTC
3964340 ATTTTTCT-T-TTTTC
1 ATTTTTCTCTATTTTC
3964354 AT
1 AT
3964356 CCTCTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 1 0.06
16 8 0.50
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTCTCTATTTTC
Found at i:3964644 original size:2 final size:2
Alignment explanation
Indices: 3964637--3964661 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3964627 TTTAGTTCAT
3964637 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3964662 GTATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3971392 original size:23 final size:24
Alignment explanation
Indices: 3971345--3971392 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3971335 TAAACCAATT
**
3971345 TTTATTAAAAGTGTAAGTATTAAA
1 TTTATTAAAAGTGTAAGTAAAAAA
*
3971369 TTTATTAAAATTG-AAGTAAAAAA
1 TTTATTAAAAGTGTAAGTAAAAAA
3971392 T
1 T
3971393 AAAATTAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (24 bp):
TTTATTAAAAGTGTAAGTAAAAAA
Found at i:3973686 original size:20 final size:20
Alignment explanation
Indices: 3973661--3973700 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3973651 CATTAATCCT
3973661 CAAATTTCTTTTTTAGTAGA
1 CAAATTTCTTTTTTAGTAGA
3973681 CAAATTTCTTTTTTAGTAGA
1 CAAATTTCTTTTTTAGTAGA
3973701 AATTAATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
CAAATTTCTTTTTTAGTAGA
Found at i:3975546 original size:31 final size:30
Alignment explanation
Indices: 3975511--3975569 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
3975501 ATACCTTTAG
*
3975511 AGAAAATGTAGATTAACA-ATTATACCTCCAT
1 AGAAAAGGTAG-TTAA-AGATTATACCTCCAT
*
3975542 AGAAAAGGTAGTTAAAGGTTATACCTCC
1 AGAAAAGGTAGTTAAAGATTATACCTCC
3975570 TAAAAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 1 0.04
30 14 0.56
31 10 0.40
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (30 bp):
AGAAAAGGTAGTTAAAGATTATACCTCCAT
Found at i:3985954 original size:35 final size:35
Alignment explanation
Indices: 3985882--3986013 Score: 106
Period size: 35 Copynumber: 3.6 Consensus size: 35
3985872 AAACATTACC
* * *
3985882 TTTTCAAGAA-GAGCAAGCATAACCTTTGCATTACCT
1 TTTTCAA-AAGGAGCAAGCATAACCTCTACACT-CCT
* *
3985918 TTTT-AAAAGGAGCAAGCATAACTTCTACGCTTCCTTT
1 TTTTCAAAAGGAGCAAGCATAACCTCTACAC-TCC--T
* *
3985955 CCTTTTCAATAGGAGCAAGCATAACCTCTACACTACT
1 --TTTTCAAAAGGAGCAAGCATAACCTCTACACTCCT
* *
3985992 TTTTCAAGAGGAGGAAGCATAA
1 TTTTCAAAAGGAGCAAGCATAA
3986014 TCTCATTACC
Statistics
Matches: 78, Mismatches: 11, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
34 2 0.03
35 40 0.51
36 5 0.06
37 2 0.03
39 6 0.08
40 23 0.29
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (35 bp):
TTTTCAAAAGGAGCAAGCATAACCTCTACACTCCT
Found at i:3986071 original size:30 final size:30
Alignment explanation
Indices: 3986030--3986087 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
3986020 TACCTTTTGC
3986030 TTGGAGGTATAA-TTAGTACTACCTTTTCTAG
1 TTGGAGGTATAACTT--TACTACCTTTTCTAG
3986061 TTGG-GGTATAACCTTTACTACCTTTTC
1 TTGGAGGTATAA-CTTTACTACCTTTTC
3986088 AAGGAGGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
30 19 0.76
31 4 0.16
32 2 0.08
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.43
Consensus pattern (30 bp):
TTGGAGGTATAACTTTACTACCTTTTCTAG
Found at i:3999202 original size:59 final size:59
Alignment explanation
Indices: 3999087--3999245 Score: 162
Period size: 59 Copynumber: 2.7 Consensus size: 59
3999077 CATGCAATAT
* * * * * *
3999087 ACATGTCTAGCACCAAACCTTGCCAGATAAGCAT--CAAGCATGTGTCTTACCAATTGC
1 ACATGTTTAGCACCAAGCCTTACTAGATAGGCATCACAAGCATATGTCTTACCAATTGC
* * * * *
3999144 ACATGTTTAGTACCGAGCTTTGCTAGATAGGCATCACAAGCATATGTCTTATTC-ATTGC
1 ACATGTTTAGCACCAAGCCTTACTAGATAGGCATCACAAGCATATGTCTTA-CCAATTGC
** *
3999203 ACATGTTTAGCATTAAGCCTTACTAGATAGGCATCAGAAGCAT
1 ACATGTTTAGCACCAAGCCTTACTAGATAGGCATCACAAGCAT
3999246 TGTGCTTCAT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
57 27 0.33
59 55 0.66
60 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (59 bp):
ACATGTTTAGCACCAAGCCTTACTAGATAGGCATCACAAGCATATGTCTTACCAATTGC
Found at i:4004601 original size:21 final size:21
Alignment explanation
Indices: 4004561--4004602 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4004551 AATAAATTAG
**
4004561 AACTCTAGGTTAACGGCTTAA
1 AACTCTAGGTTAACAACTTAA
4004582 AACTCTAGGTTAACAACTTAA
1 AACTCTAGGTTAACAACTTAA
4004603 GCCTATCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (21 bp):
AACTCTAGGTTAACAACTTAA
Found at i:4004859 original size:50 final size:50
Alignment explanation
Indices: 4004790--4004895 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
4004780 AGTTGTTTAA
*
4004790 ATTTTTGCACTAAGTGAAATGATTTGTCAATTCTCTATGGGAACAAATTT
1 ATTTTAGCACTAAGTGAAATGATTTGTCAATTCTCTATGGGAACAAATTT
4004840 ATTTTAGCACTAAGTGAAATGATTTGTCAATTCTCTATGGGAACAAATTT
1 ATTTTAGCACTAAGTGAAATGATTTGTCAATTCTCTATGGGAACAAATTT
4004890 ACTTTT
1 A-TTTT
4004896 CATTGTATTA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 50 0.93
51 4 0.07
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (50 bp):
ATTTTAGCACTAAGTGAAATGATTTGTCAATTCTCTATGGGAACAAATTT
Found at i:4010796 original size:31 final size:31
Alignment explanation
Indices: 4010758--4010821 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
4010748 GGATTATCTG
4010758 GTTCTACGCAAGGGATTTGTAGTAAAATGAA
1 GTTCTACGCAAGGGATTTGTAGTAAAATGAA
4010789 GTTCTACGCAAGGGATTTGTAGTAAAATGAA
1 GTTCTACGCAAGGGATTTGTAGTAAAATGAA
4010820 GT
1 GT
4010822 AAGTTCTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.27, T:0.30
Consensus pattern (31 bp):
GTTCTACGCAAGGGATTTGTAGTAAAATGAA
Done.