Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 9 of 195
Found at i:1760745 original size:39 final size:38
Alignment explanation
Indices: 1760691--1760935 Score: 233
Period size: 39 Copynumber: 6.3 Consensus size: 38
1760681 TCAGATCTTT
* *
1760691 AATTTAAAGTTTGTTGCTTATGATTAAATGAGCTTTTG
1 AATTTAAAGTTTGTTGCCTCTGATTAAATGAGCTTTTG
* * * *
1760729 AAATTTAAAGTTTGTTGTCTTTGGTTAAATGAGCTTGTG
1 -AATTTAAAGTTTGTTGCCTCTGATTAAATGAGCTTTTG
* * * * *
1760768 AATTTAAAGTTTTTTACCTCTGATGAGA-GAAGCCTTTTA
1 AATTTAAAGTTTGTTGCCTCTGATTAAATG-AG-CTTTTG
* * *
1760807 ACATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTG
1 A-ATTTAAAGTTTGTTGCCTCTGATTAAATGAGCTTTTG
* * * *
1760846 GATTTAAAGTTTGTTGCCTCTGATGAGAGGAGCCTTTTG
1 AATTTAAAGTTTGTTGCCTCTGATTAAATGAG-CTTTTG
* *
1760885 AATTTAAAGTTTGTTACCTCTG-GTAAGATGAGCTTTTTG
1 AATTTAAAGTTTGTTGCCTCTGATTAA-ATGAGC-TTTTG
1760924 AATTTAAAGTTT
1 AATTTAAAGTTT
1760936 TATAGCCTCT
Statistics
Matches: 167, Mismatches: 32, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
37 1 0.01
38 52 0.31
39 90 0.54
40 23 0.14
41 1 0.01
ACGTcount: A:0.27, C:0.09, G:0.21, T:0.44
Consensus pattern (38 bp):
AATTTAAAGTTTGTTGCCTCTGATTAAATGAGCTTTTG
Found at i:1760819 original size:78 final size:77
Alignment explanation
Indices: 1760723--1760945 Score: 295
Period size: 78 Copynumber: 2.8 Consensus size: 77
1760713 ATTAAATGAG
* *
1760723 CTTTTGAAATTTAAAGTTTGTTGTCTTTGGTTAAATGAGCTTGTGAATTTAAAGTTTTTTACCTC
1 CTTTT-AAATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCTTTTGAATTTAAAGTTTTTTACCTC
1760788 TGATGAGAGAAGC
65 TGATGAGAGAAGC
* * * *
1760801 CTTTTAACATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGGATTTAAAGTTTGTTGCCTC
1 CTTTTAA-ATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCTTTTGAATTTAAAGTTTTTTACCTC
*
1760866 TGATGAGAGGAGC
65 TGATGAGAGAAGC
* * * *
1760879 CTTTTGAATTTAAAGTTTGTTACCTCTGG-TAAGATGAGCTTTTTGAATTTAAAGTTTTATAGCC
1 CTTTTAAATTTAAAGTTTGTTGCCTTTGGTTAA-ATGAGC-TTTTGAATTTAAAGTTTTTTA-CC
1760943 TCT
63 TCT
1760946 ATTTAGATGA
Statistics
Matches: 126, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
76 3 0.02
77 27 0.21
78 91 0.72
79 5 0.04
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (77 bp):
CTTTTAAATTTAAAGTTTGTTGCCTTTGGTTAAATGAGCTTTTGAATTTAAAGTTTTTTACCTCT
GATGAGAGAAGC
Found at i:1760902 original size:117 final size:117
Alignment explanation
Indices: 1760692--1760906 Score: 299
Period size: 117 Copynumber: 1.8 Consensus size: 117
1760682 CAGATCTTTA
* * * * *
1760692 ATTTAAAGTTTGTTGCTTATGATTAAATGAGCTTTTGAAATTTAAAGTTTGTTGTCTTTGGTTAA
1 ATTTAAAGTTTGTTGCTTATGATTAAAGGAGCTTTTGAAATTTAAAGTTTGTTGCCTCTGATGAA
* *
1760757 ATGAGCTTGTGAATTTAAAGTTTTTTACCTCTGATGAGAGAAGCCTTTTAAC
66 AGGAGCTTGTGAATTTAAAGTTTGTTACCTCTGATGAGAGAAGCCTTTTAAC
* *
1760809 ATTTAAAGTTTGTTGCCTT-TGGTTAAAGGAGCTTTTG-GATTTAAAGTTTGTTGCCTCTGATGA
1 ATTTAAAGTTTGTTG-CTTATGATTAAAGGAGCTTTTGAAATTTAAAGTTTGTTGCCTCTGATGA
* *
1760872 GAGGAGCCTTTTGAATTTAAAGTTTGTTACCTCTG
65 AAGGAG-CTTGTGAATTTAAAGTTTGTTACCTCTG
1760907 GTAAGATGAG
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
116 25 0.29
117 57 0.67
118 3 0.04
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.44
Consensus pattern (117 bp):
ATTTAAAGTTTGTTGCTTATGATTAAAGGAGCTTTTGAAATTTAAAGTTTGTTGCCTCTGATGAA
AGGAGCTTGTGAATTTAAAGTTTGTTACCTCTGATGAGAGAAGCCTTTTAAC
Found at i:1761120 original size:3 final size:3
Alignment explanation
Indices: 1761112--1761158 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
1761102 TTTTATTCTT
* *
1761112 TTA TTA TTA TTA TTA -TA TAA TT- TTGT TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
1761156 TTA
1 TTA
1761159 ATCTTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
2 4 0.11
3 32 0.84
4 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1761565 original size:12 final size:11
Alignment explanation
Indices: 1761536--1761563 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1761526 AATTTTTTAG
1761536 AATTTTGAAAA
1 AATTTTGAAAA
1761547 AATTTTGAAAA
1 AATTTTGAAAA
1761558 AATTTT
1 AATTTT
1761564 TGGGTCACCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (11 bp):
AATTTTGAAAA
Found at i:1763723 original size:29 final size:28
Alignment explanation
Indices: 1763671--1763749 Score: 70
Period size: 29 Copynumber: 2.7 Consensus size: 28
1763661 ATTTTTTTTC
* * * *
1763671 TTTATT-TATTGAGATAAATTTTTACAT
1 TTTATTATATTTAAATAAATCTTTAAAT
1763698 ATTTATTATATTTAAATAAATCTTTAAAT
1 -TTTATTATATTTAAATAAATCTTTAAAT
1763727 TTTAATTTTTATATTTAAATAAA
1 TTT-A---TTATATTTAAATAAA
1763750 CGTTAATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
28 9 0.21
29 18 0.43
32 15 0.36
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (28 bp):
TTTATTATATTTAAATAAATCTTTAAAT
Found at i:1763825 original size:30 final size:29
Alignment explanation
Indices: 1763769--1763834 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
1763759 AAATCAATTT
1763769 TTTATTTGAATACAAATAAAAAATAAAAAA
1 TTTATTTGAATACAAATAAAAAAT-AAAAA
* * ** *
1763799 TTTATTTGAATATAATTAAAGCATAAAAG
1 TTTATTTGAATACAAATAAAAAATAAAAA
1763828 TTTATTT
1 TTTATTT
1763835 AAAAAATGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (29 bp):
TTTATTTGAATACAAATAAAAAATAAAAA
Found at i:1774084 original size:18 final size:18
Alignment explanation
Indices: 1774051--1774085 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1774041 TGAACCACTT
*
1774051 CCATTCCCTTGGTTCTTC
1 CCATTCCCCTGGTTCTTC
*
1774069 CCATTCCCCTGTTTCTT
1 CCATTCCCCTGGTTCTT
1774086 TGTGAGGGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.40, G:0.09, T:0.46
Consensus pattern (18 bp):
CCATTCCCCTGGTTCTTC
Found at i:1776018 original size:46 final size:45
Alignment explanation
Indices: 1775937--1776032 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 45
1775927 ATAATTAATA
* * ** *
1775937 ATATTTGTTATTTAACACAATATTAAATATTTTTTCTTGTACAAT
1 ATATGTGTTATTTAACACAATATTAAACAAATTTTCTTATACAAT
1775982 ACTATGTGTTATTTAACACAATATTAAACAAATTTTCTTATAC-AT
1 A-TATGTGTTATTTAACACAATATTAAACAAATTTTCTTATACAAT
1776027 ATATGT
1 ATATGT
1776033 AAATTTACAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
44 5 0.11
45 4 0.09
46 36 0.80
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (45 bp):
ATATGTGTTATTTAACACAATATTAAACAAATTTTCTTATACAAT
Found at i:1780600 original size:30 final size:30
Alignment explanation
Indices: 1780566--1780623 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1780556 AATCACTAAA
* *
1780566 TTTTAATTTATATTTAAATAAACTTTTATC
1 TTTTAATTAATATATAAATAAACTTTTATC
*
1780596 TTTTAATTAATATATAAATAAATTTTTA
1 TTTTAATTAATATATAAATAAACTTTTA
1780624 ATATAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTTAATTAATATATAAATAAACTTTTATC
Found at i:1788424 original size:21 final size:20
Alignment explanation
Indices: 1788398--1788437 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1788388 TTTTATTTAA
1788398 AATTATCAAAATATTAATATT
1 AATTATCAAAATA-TAATATT
*
1788419 AATTATTAAAATATAATAT
1 AATTATCAAAATATAATAT
1788438 GTTATCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTATCAAAATATAATATT
Found at i:1794868 original size:17 final size:17
Alignment explanation
Indices: 1794848--1794880 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1794838 AGATCAATAT
1794848 AATATTTAAAATTTAAA
1 AATATTTAAAATTTAAA
*
1794865 AATATTTAATATTTAA
1 AATATTTAAAATTTAA
1794881 TTTATTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATATTTAAAATTTAAA
Found at i:1807537 original size:12 final size:12
Alignment explanation
Indices: 1807522--1807546 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1807512 AATTAAAATT
1807522 TGAATTCATTTA
1 TGAATTCATTTA
1807534 TGAATTCATTTA
1 TGAATTCATTTA
1807546 T
1 T
1807547 TAGGTCATTG
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TGAATTCATTTA
Found at i:1807811 original size:15 final size:16
Alignment explanation
Indices: 1807783--1807815 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
1807773 CTAGTATATT
1807783 TTAACAATAAAAAAAA
1 TTAACAATAAAAAAAA
1807799 TTAACAA-AAAAAAAA
1 TTAACAATAAAAAAAA
1807814 TT
1 TT
1807816 GTAGTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (16 bp):
TTAACAATAAAAAAAA
Found at i:1807954 original size:23 final size:23
Alignment explanation
Indices: 1807902--1807969 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
1807892 TATGTTATAA
* *
1807902 ATATAAAATATAAAAATAA-TATT
1 ATATAAAATTTAATAATAATTA-T
*
1807925 ATTTAAAATTTAATAATAATTAT
1 ATATAAAATTTAATAATAATTAT
1807948 ATAT-AAATTTAATAA-AATTAT
1 ATATAAAATTTAATAATAATTAT
1807969 A
1 A
1807970 AATATATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.17
22 11 0.28
23 20 0.50
24 2 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAAAATTTAATAATAATTAT
Found at i:1807966 original size:21 final size:21
Alignment explanation
Indices: 1807916--1807978 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1807906 AAAATATAAA
* *
1807916 AATAATATTATTTA-AAATTT
1 AATAAAATTATATATAAATTT
1807936 AATAATAATTATATATAAATTT
1 AATAA-AATTATATATAAATTT
* *
1807958 AATAAAATTATAAATATATTT
1 AATAAAATTATATATAAATTT
1807979 TATATTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 5 0.14
21 21 0.57
22 11 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATAAAATTATATATAAATTT
Found at i:1808040 original size:18 final size:18
Alignment explanation
Indices: 1807994--1808046 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1807984 TTTTATATCG
*
1807994 ATATAAATTATAACATATA
1 ATATAAA-TATAAAATATA
* **
1808013 ATTTTTATATAAAATATA
1 ATATAAATATAAAATATA
1808031 ATATAAATATATAAAT
1 ATATAAATATA-AAAT
1808047 TTTAATATTT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAAATATAAAATATA
Found at i:1816930 original size:6 final size:6
Alignment explanation
Indices: 1816919--1816948 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1816909 TTCATTTAAA
1816919 AAATAT AAATAT AAATAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT
1816949 TTTATTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATAT
Found at i:1821631 original size:17 final size:17
Alignment explanation
Indices: 1821609--1821642 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1821599 TTTTTAAGGT
1821609 ATCCTAAATATGTGTGC
1 ATCCTAAATATGTGTGC
1821626 ATCCTAAATATGTGTGC
1 ATCCTAAATATGTGTGC
1821643 TTTGTCTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (17 bp):
ATCCTAAATATGTGTGC
Found at i:1830114 original size:10 final size:10
Alignment explanation
Indices: 1830085--1830127 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
1830075 TTGCATAATA
*
1830085 TATATATATA
1 TATATATATG
1830095 TATATATATG
1 TATATATATG
*
1830105 TATATGTATG
1 TATATATATG
* *
1830115 TATGTATGTG
1 TATATATATG
1830125 TAT
1 TAT
1830128 GCCATCCTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (10 bp):
TATATATATG
Found at i:1833011 original size:6 final size:6
Alignment explanation
Indices: 1833000--1833030 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1832990 GTTGGTTCAT
*
1833000 CAGAGC CAGAGC CAGAGC CAGAGC CAAAGC C
1 CAGAGC CAGAGC CAGAGC CAGAGC CAGAGC C
1833031 TGAGTTCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.35, C:0.35, G:0.29, T:0.00
Consensus pattern (6 bp):
CAGAGC
Found at i:1834530 original size:101 final size:99
Alignment explanation
Indices: 1834392--1834683 Score: 361
Period size: 101 Copynumber: 2.9 Consensus size: 99
1834382 TTATAATAAA
* * **
1834392 CATAAATATGTATATTAACAAATATAAAAAACAACAAATTAATTCAATAATCTATAATAGAACAC
1 CATAAATATGTATATTAA-AAATACAATAAATGACAAATTAATTCAATAA-CTATAATAGAACAC
* * *
1834457 GTATAAGTCAATAAACTTGTTCCAACTTACAGTATT
64 GTATAAATTAATAAACTTGTTACAACTTACAGTATT
* * * *
1834493 TATAAATATGTATATTGAAAAATACAATAAATGACAAATTAATTCAATAACATATAATGGACCGC
1 CATAAATATGTATATT-AAAAATACAATAAATGACAAATTAATTCAATAAC-TATAATAGAACAC
* * *
1834558 GTATAAATTAATAAATTTGTTACAATTTATAGTATT
64 GTATAAATTAATAAACTTGTTACAACTTACAGTATT
* *
1834594 CATAAATATGTATATTCAAAAATACAATAAATGACAAAGTAATTCAATAA-TATAATAAAACACG
1 CATAAATATGTATATT-AAAAATACAATAAATGACAAATTAATTCAATAACTATAATAGAACACG
* * *
1834658 TGTAAATTGATAAACTTGTTATAACT
65 TATAAATTAATAAACTTGTTACAACT
1834684 CATAACAAAT
Statistics
Matches: 163, Mismatches: 26, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
99 31 0.19
100 1 0.01
101 129 0.79
102 2 0.01
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.33
Consensus pattern (99 bp):
CATAAATATGTATATTAAAAATACAATAAATGACAAATTAATTCAATAACTATAATAGAACACGT
ATAAATTAATAAACTTGTTACAACTTACAGTATT
Found at i:1851291 original size:42 final size:44
Alignment explanation
Indices: 1851209--1851296 Score: 153
Period size: 42 Copynumber: 2.0 Consensus size: 44
1851199 ACATGAACAT
1851209 AAAACCTTAATCAGAACTTAAAGAAGATTCTATACATAATAAACC
1 AAAACCTTAATCAGAACTT-AAGAAGATTCTATACATAATAAACC
1851254 AAAACCTTAATCAGAACTT-A-AAGATTCTATACATAATAAACC
1 AAAACCTTAATCAGAACTTAAGAAGATTCTATACATAATAAACC
1851296 A
1 A
1851297 TGACAGAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
42 23 0.53
43 1 0.02
45 19 0.44
ACGTcount: A:0.51, C:0.18, G:0.06, T:0.25
Consensus pattern (44 bp):
AAAACCTTAATCAGAACTTAAGAAGATTCTATACATAATAAACC
Found at i:1852841 original size:14 final size:13
Alignment explanation
Indices: 1852823--1852847 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1852813 CGAAATGTTT
1852823 TTTTTTTCTTTTG
1 TTTTTTTCTTTTG
1852836 TTTTTTTCTTTT
1 TTTTTTTCTTTT
1852848 TCTTTTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (13 bp):
TTTTTTTCTTTTG
Found at i:1852847 original size:19 final size:18
Alignment explanation
Indices: 1852820--1852861 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
1852810 AAGCGAAATG
*
1852820 TTTTTTTTTTCTTTTGTT
1 TTTTTTTTTTCTTTTCTT
1852838 TTTTTCTTTTTCTTTTCTT
1 TTTTT-TTTTTCTTTTCTT
1852857 TTTTT
1 TTTTT
1852862 GTCTGATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (18 bp):
TTTTTTTTTTCTTTTCTT
Found at i:1852853 original size:13 final size:12
Alignment explanation
Indices: 1852820--1852861 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
1852810 AAGCGAAATG
1852820 TTTTTTTTTTCT
1 TTTTTTTTTTCT
1852832 TTTGTTTTTTTC-
1 TTT-TTTTTTTCT
*
1852844 TTTTTCTTTTCT
1 TTTTTTTTTTCT
1852856 TTTTTT
1 TTTTTT
1852862 GTCTGATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 7 0.27
12 11 0.42
13 8 0.31
ACGTcount: A:0.00, C:0.10, G:0.02, T:0.88
Consensus pattern (12 bp):
TTTTTTTTTTCT
Found at i:1856760 original size:2 final size:2
Alignment explanation
Indices: 1856753--1856782 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1856743 ATAATAATTG
1856753 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
1856783 GGAATGATGG
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:1858266 original size:22 final size:23
Alignment explanation
Indices: 1858214--1858267 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 23
1858204 AAAAAACATA
*
1858214 ATATAAAATATAAAATTTATACTT
1 ATATAAAATAT-AAATTTATAATT
*
1858238 AT-T-AAATAT-CATTTATAATT
1 ATATAAAATATAAATTTATAATT
1858258 ATATAAAATA
1 ATATAAAATA
1858268 ATTAAGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 11 0.42
21 1 0.04
22 11 0.42
23 1 0.04
24 2 0.08
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATAAAATATAAATTTATAATT
Found at i:1874387 original size:20 final size:20
Alignment explanation
Indices: 1874362--1874399 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1874352 TAATACCAAT
* *
1874362 TATTTTTATTAATTTTGACC
1 TATTTTGATGAATTTTGACC
1874382 TATTTTGATGAATTTTGA
1 TATTTTGATGAATTTTGA
1874400 TAGAATAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.05, G:0.11, T:0.58
Consensus pattern (20 bp):
TATTTTGATGAATTTTGACC
Found at i:1874475 original size:19 final size:20
Alignment explanation
Indices: 1874437--1874476 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1874427 AAATGTGAAA
*
1874437 TATATTTTGTAATTTTTAACT
1 TATATTTTGT-ATATTTAACT
1874458 TATATTTTGT-TATTTAACT
1 TATATTTTGTATATTTAACT
1874477 ATTTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
21 10 0.56
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (20 bp):
TATATTTTGTATATTTAACT
Found at i:1874556 original size:11 final size:12
Alignment explanation
Indices: 1874542--1874572 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1874532 TTTCTTTATT
1874542 TTTATTTTA-AC
1 TTTATTTTATAC
1874553 TTTATTTTATAC
1 TTTATTTTATAC
1874565 TTTATTTT
1 TTTATTTT
1874573 TTAAAACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.47
12 10 0.53
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTATTTTATAC
Found at i:1877535 original size:22 final size:22
Alignment explanation
Indices: 1877509--1877553 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1877499 TATGAAAGAG
*
1877509 CTCAAATGGTTTTGTAAAACCC
1 CTCAAATGGTTTTGCAAAACCC
1877531 CTCAAATGGTTTTGCAAAACCC
1 CTCAAATGGTTTTGCAAAACCC
1877553 C
1 C
1877554 AACTTTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (22 bp):
CTCAAATGGTTTTGCAAAACCC
Found at i:1883355 original size:22 final size:22
Alignment explanation
Indices: 1883316--1883359 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1883306 TACCTTCCCC
*
1883316 TCCCTTCTCTCTCTTTTTCTCT
1 TCCCTTCTCTCTCCTTTTCTCT
1883338 TCCCATTCTCT-TCCTTTTCTCT
1 TCCC-TTCTCTCTCCTTTTCTCT
1883360 CCTCCTCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.57
Consensus pattern (22 bp):
TCCCTTCTCTCTCCTTTTCTCT
Found at i:1887058 original size:3 final size:3
Alignment explanation
Indices: 1887050--1887094 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1887040 AAGCGACAAC
1887050 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1887095 TTGTTTATTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1887532 original size:2 final size:2
Alignment explanation
Indices: 1887525--1887552 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1887515 ATTCACATAC
1887525 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
1887553 CATTCGAAAA
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):
AT
Found at i:1888917 original size:12 final size:12
Alignment explanation
Indices: 1888900--1888924 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1888890 CACCAATGTT
1888900 AGATTACCATCC
1 AGATTACCATCC
1888912 AGATTACCATCC
1 AGATTACCATCC
1888924 A
1 A
1888925 CATTGCCAAG
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:0.36, C:0.32, G:0.08, T:0.24
Consensus pattern (12 bp):
AGATTACCATCC
Found at i:1893845 original size:46 final size:47
Alignment explanation
Indices: 1893774--1893864 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 47
1893764 AAAAATGCAA
* *
1893774 CACATATCACAATTATCTACAATCTTTCTGCAAATACTTAATTCAAG
1 CACATAACACAATAATCTACAATCTTTCTGCAAATACTTAATTCAAG
* *
1893821 CACATAACA-AATAATCTCCAATCTTTCTGCAAGTACTTAATTCA
1 CACATAACACAATAATCTACAATCTTTCTGCAAATACTTAATTCA
1893865 TAAACAGTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
46 32 0.80
47 8 0.20
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.33
Consensus pattern (47 bp):
CACATAACACAATAATCTACAATCTTTCTGCAAATACTTAATTCAAG
Found at i:1894125 original size:16 final size:16
Alignment explanation
Indices: 1894104--1894135 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1894094 TAGAAGATAG
1894104 AACTAGAATGATTCAA
1 AACTAGAATGATTCAA
1894120 AACTAGAATGATTCAA
1 AACTAGAATGATTCAA
1894136 TTGCAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (16 bp):
AACTAGAATGATTCAA
Found at i:1900712 original size:32 final size:32
Alignment explanation
Indices: 1900676--1900742 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
1900666 TATAATATAT
* *
1900676 AATTTTGATATAAAATATAATATAAATACATA
1 AATTTTAATATAAAATATAATAAAAATACATA
*** *
1900708 AATTTTAATATTTTATATGATAAAAATACATA
1 AATTTTAATATAAAATATAATAAAAATACATA
1900740 AAT
1 AAT
1900743 CATCTTTAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (32 bp):
AATTTTAATATAAAATATAATAAAAATACATA
Found at i:1902755 original size:13 final size:12
Alignment explanation
Indices: 1902731--1902765 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1902721 ATATTTTTTA
1902731 TTAATATAAATT
1 TTAATATAAATT
1902743 TTAATATATAATT
1 TTAATATA-AATT
*
1902756 TTTATATAAA
1 TTAATATAAA
1902766 ATATGATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TTAATATAAATT
Found at i:1902787 original size:31 final size:32
Alignment explanation
Indices: 1902745--1902820 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
1902735 TATAAATTTT
*
1902745 AATATATAATTTTT-ATATAAAATATGATATA
1 AATATAAAATTTTTAATATAAAATATGATATA
***
1902776 AATATAAAATTTTTTAATATTTTATATGATATA
1 AATATAAAA-TTTTTAATATAAAATATGATATA
1902809 AATATATAAATT
1 AATATA-AAATT
1902821 ATCATATCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 8 0.21
32 5 0.13
33 22 0.58
34 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
AATATAAAATTTTTAATATAAAATATGATATA
Found at i:1903293 original size:29 final size:29
Alignment explanation
Indices: 1903256--1903319 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
1903246 TATAATAAAA
*
1903256 TATTTAATGTGATATTTATA-TATAAAATT
1 TATTTAATGTGATATTTAAATTAT-AAATT
*
1903285 TTTTTAATGTGATATTTAAATTATAAATT
1 TATTTAATGTGATATTTAAATTATAAATT
1903314 TATTTA
1 TATTTA
1903320 TTAATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (29 bp):
TATTTAATGTGATATTTAAATTATAAATT
Found at i:1906844 original size:2 final size:2
Alignment explanation
Indices: 1906837--1906882 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
1906827 GGGAACACCA
* *
1906837 AT AT AT AT AT CT AT AC 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 AT AT AT AT AT AT
1906879 -T AT A
1 AT AT A
1906883 ATGAAACAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1908230 original size:16 final size:15
Alignment explanation
Indices: 1908209--1908238 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1908199 GTATACGATA
1908209 ATATAATAAAAATATG
1 ATATAA-AAAAATATG
1908225 ATATAAAAAAATAT
1 ATATAAAAAAATAT
1908239 AAAAATAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (15 bp):
ATATAAAAAAATATG
Found at i:1914874 original size:3 final size:3
Alignment explanation
Indices: 1914866--1914898 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1914856 TTTCACAGGT
1914866 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1914899 AGTTGTGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1916235 original size:22 final size:25
Alignment explanation
Indices: 1916177--1916235 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 25
1916167 AATTTAAAAT
*
1916177 TATAATATAATAATTTTTATATTATA
1 TATATTATAA-AATTTTTATATTATA
1916203 TATATT-T-AAATTTTTAT-TTAT-
1 TATATTATAAAATTTTTATATTATA
1916224 T-TATTATAAAAT
1 TATATTATAAAAT
1916236 AAATACGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
20 4 0.13
21 2 0.07
22 8 0.27
23 9 0.30
24 1 0.03
25 1 0.03
26 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATATTATAAAATTTTTATATTATA
Found at i:1916378 original size:22 final size:22
Alignment explanation
Indices: 1916350--1916407 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
1916340 TTCGTAAGTT
1916350 ATTCGAATTTGATTTGAATAAA
1 ATTCGAATTTGATTTGAATAAA
1916372 ATTCGAATTTGATTTGAATAAA
1 ATTCGAATTTGATTTGAATAAA
1916394 ATTCGAATTTGATT
1 ATTCGAATTTGATT
1916408 CGATTATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (22 bp):
ATTCGAATTTGATTTGAATAAA
Found at i:1916408 original size:11 final size:11
Alignment explanation
Indices: 1916350--1916410 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
1916340 TTCGTAAGTT
1916350 ATTCGAATTTG
1 ATTCGAATTTG
* ***
1916361 ATTTGAATAAA
1 ATTCGAATTTG
1916372 ATTCGAATTTG
1 ATTCGAATTTG
* ***
1916383 ATTTGAATAAA
1 ATTCGAATTTG
1916394 ATTCGAATTTG
1 ATTCGAATTTG
1916405 ATTCGA
1 ATTCGA
1916411 TTATTATCGA
Statistics
Matches: 34, Mismatches: 16, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.41
Consensus pattern (11 bp):
ATTCGAATTTG
Found at i:1921988 original size:10 final size:10
Alignment explanation
Indices: 1921973--1921998 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1921963 TTATTATATG
1921973 CTCTCTGTCT
1 CTCTCTGTCT
1921983 CTCTCTGTCT
1 CTCTCTGTCT
1921993 CTCTCT
1 CTCTCT
1921999 CTCACACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (10 bp):
CTCTCTGTCT
Found at i:1925668 original size:16 final size:16
Alignment explanation
Indices: 1925644--1925677 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1925634 TACCTCTCAG
1925644 CACAAGACAAGTATAT
1 CACAAGACAAGTATAT
*
1925660 CACAGGACAAGTATAT
1 CACAAGACAAGTATAT
1925676 CA
1 CA
1925678 TTCCACCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.18
Consensus pattern (16 bp):
CACAAGACAAGTATAT
Found at i:1928970 original size:5 final size:5
Alignment explanation
Indices: 1928960--1928999 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
1928950 TTCTTTGGTG
* *
1928960 TTTTC TTTTC TTTTC -TTTC TTTTC TTTTC TATTC GTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
1929000 CTGCTTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 4 0.13
5 26 0.87
ACGTcount: A:0.03, C:0.20, G:0.03, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:1928980 original size:14 final size:14
Alignment explanation
Indices: 1928961--1928999 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
1928951 TCTTTGGTGT
1928961 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
1928975 TTTCTTTTCTTTTC
1 TTTCTTTTCTTTTC
*
1928989 TATTCGTTTCT
1 T-TTCTTTTCT
1929000 CTGCTTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 15 0.65
15 8 0.35
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTCTTTTCTTTTC
Found at i:1929177 original size:3 final size:3
Alignment explanation
Indices: 1929169--1929193 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1929159 AATTATGGAT
1929169 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1929194 AGTGTTCAAG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1930783 original size:22 final size:23
Alignment explanation
Indices: 1930758--1930812 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
1930748 AATTTTATTT
*
1930758 AAATATATTAAAAA-TTAAATTA
1 AAATATAATAAAAATTTAAATTA
*
1930780 AAATATAATAAAAATTTAAATTT
1 AAATATAATAAAAATTTAAATTA
1930803 AAATACTAAT
1 AAATA-TAAT
1930813 TAACTGAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 13 0.45
23 12 0.41
24 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATATAATAAAAATTTAAATTA
Found at i:1931085 original size:27 final size:26
Alignment explanation
Indices: 1931032--1931089 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
1931022 TTATTTTATC
*
1931032 AAAAT-AATTTTTTATTTAAAATAAT
1 AAAATAAATTTTTAATTTAAAATAAT
* *
1931057 AAAATAAATTTGTTAATTTAATATGAT
1 AAAATAAATTT-TTAATTTAAAATAAT
1931084 AAAATA
1 AAAATA
1931090 TTATTTGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 5 0.18
26 5 0.18
27 18 0.64
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
AAAATAAATTTTTAATTTAAAATAAT
Found at i:1931384 original size:24 final size:23
Alignment explanation
Indices: 1931357--1931410 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
1931347 TTATTATAAA
* *
1931357 AATAAAAAAGATTTTATATTTGTT
1 AATAAAAAAGATTTTACA-TTATT
* *
1931381 AATATATAAATATTTTACATTATT
1 AATA-AAAAAGATTTTACATTATT
1931405 AATAAA
1 AATAAA
1931411 TCATTCAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 1 0.04
24 12 0.50
25 11 0.46
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
AATAAAAAAGATTTTACATTATT
Found at i:1940736 original size:24 final size:24
Alignment explanation
Indices: 1940662--1940736 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
1940652 TAAAAACCAA
*
1940662 CAAAAATAGAAAAACCCAGATGAT
1 CAAAAATAGAAAAACCCAAATGAT
** ** *
1940686 CAAAGAA-A-AAAAA-TGACAACCAA
1 CAAA-AATAGAAAAACCCA-AATGAT
1940709 CAAAAATAGAAAAACCCAAATGAT
1 CAAAAATAGAAAAACCCAAATGAT
1940733 CAAA
1 CAAA
1940737 GAAAAAAAAT
Statistics
Matches: 35, Mismatches: 11, Indels: 10
0.62 0.20 0.18
Matches are distributed among these distances:
22 3 0.09
23 12 0.34
24 17 0.49
25 3 0.09
ACGTcount: A:0.64, C:0.17, G:0.09, T:0.09
Consensus pattern (24 bp):
CAAAAATAGAAAAACCCAAATGAT
Found at i:1940747 original size:47 final size:47
Alignment explanation
Indices: 1940656--1940751 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
1940646 AAAGCTTAAA
*
1940656 AACCAACAAAAATAGAAAAACCCAGATGATCAAAGAAAAAAAATGAC
1 AACCAACAAAAATAGAAAAACCCAAATGATCAAAGAAAAAAAATGAC
1940703 AACCAACAAAAATAGAAAAACCCAAATGATCAAAGAAAAAAAATGAC
1 AACCAACAAAAATAGAAAAACCCAAATGATCAAAGAAAAAAAATGAC
1940750 AA
1 AA
1940752 TCTGGGTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.66, C:0.17, G:0.09, T:0.08
Consensus pattern (47 bp):
AACCAACAAAAATAGAAAAACCCAAATGATCAAAGAAAAAAAATGAC
Found at i:1942541 original size:23 final size:24
Alignment explanation
Indices: 1942515--1942561 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1942505 TAAAAAATAA
1942515 AAATATAAAATTTTAT-TTTTATT
1 AAATATAAAATTTTATATTTTATT
* *
1942538 AAATATATAATTTTTTATTTTATT
1 AAATATAAAATTTTATATTTTATT
1942562 TTAAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
AAATATAAAATTTTATATTTTATT
Found at i:1944912 original size:24 final size:24
Alignment explanation
Indices: 1944867--1944913 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1944857 TTTTATAAAA
* **
1944867 TTTTAAATTATATTATTTTATTAT
1 TTTTAAATTATATAATCATATTAT
*
1944891 TTTTATATTATATAATCATATTA
1 TTTTAAATTATATAATCATATTA
1944914 ATCATGTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
TTTTAAATTATATAATCATATTAT
Found at i:1945996 original size:22 final size:21
Alignment explanation
Indices: 1945971--1946030 Score: 75
Period size: 22 Copynumber: 2.8 Consensus size: 21
1945961 AATTTTACTT
1945971 ATAAATAATATTATATTAATAA
1 ATAAATAATATTA-ATTAATAA
* *
1945993 ATAAATAATGTTAATTCATAA
1 ATAAATAATATTAATTAATAA
*
1946014 ATAATATATTATTAATT
1 ATAA-ATAATATTAATT
1946031 GTCGTAACGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.33
22 22 0.67
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATAAATAATATTAATTAATAA
Found at i:1946672 original size:156 final size:156
Alignment explanation
Indices: 1946327--1946765 Score: 785
Period size: 156 Copynumber: 2.8 Consensus size: 156
1946317 GTTAGTTGTT
1946327 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
*
1946392 AGTATGCAAG-AAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGA-TATTTAAAG-AAAAT
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
1946454 CAAGATCAACCAATTAATTAATTATC
131 CAAGATCAACCAATTAATTAATTATC
* * *
1946480 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAACTTGAGAAAATTTCCTCACCTCAGG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
1946545 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
1946610 CAAGATCAACCAATTAATTAATTATC
131 CAAGATCAACCAATTAATTAATTATC
*
1946636 GGAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
* *
1946701 AGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAA
66 AGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAA
1946766 AGAAAAAAAA
Statistics
Matches: 272, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
153 72 0.26
154 38 0.14
155 8 0.03
156 113 0.42
157 41 0.15
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (156 bp):
GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
CAAGATCAACCAATTAATTAATTATC
Found at i:1946813 original size:16 final size:15
Alignment explanation
Indices: 1946794--1946823 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1946784 AAAATCAAAG
1946794 TCAAATAAAAAAAAAT
1 TCAAA-AAAAAAAAAT
1946810 TCAAAAAAAAAAAA
1 TCAAAAAAAAAAAA
1946824 AAAAACTTGG
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:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (15 bp):
TCAAAAAAAAAAAAT
Found at i:1946824 original size:16 final size:16
Alignment explanation
Indices: 1946794--1946824 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1946784 AAAATCAAAG
*
1946794 TCAAATAAAAAAAAAT
1 TCAAAAAAAAAAAAAT
1946810 TCAAAAAAAAAAAAA
1 TCAAAAAAAAAAAAA
1946825 AAAACTTGGA
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:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (16 bp):
TCAAAAAAAAAAAAAT
Found at i:1946853 original size:15 final size:15
Alignment explanation
Indices: 1946829--1946869 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1946819 AAAAAAAAAA
1946829 CTTGGAGCGGCTCGG
1 CTTGGAGCGGCTCGG
*
1946844 CTTGGTGCGGCTCGG
1 CTTGGAGCGGCTCGG
*
1946859 CTCGGAG-GGCT
1 CTTGGAGCGGCT
1946870 GAAACGCGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.05, C:0.27, G:0.46, T:0.22
Consensus pattern (15 bp):
CTTGGAGCGGCTCGG
Found at i:1947111 original size:19 final size:19
Alignment explanation
Indices: 1947082--1947126 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1947072 GAACGCCGGT
*
1947082 GCCGGATTCTGGAAATTTC
1 GCCGGAATCTGGAAATTTC
* *
1947101 GTCGGAATCTGGGAATTTC
1 GCCGGAATCTGGAAATTTC
1947120 GCCGGAA
1 GCCGGAA
1947127 GTTGGCCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (19 bp):
GCCGGAATCTGGAAATTTC
Found at i:1948033 original size:6 final size:6
Alignment explanation
Indices: 1948022--1948062 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
1948012 TCAACTCAAC
*
1948022 ATTTTT ATTTTT GA-TTTT -TTTTT ATTTTT GTTTTT ATTTTT
1 ATTTTT ATTTTT -ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1948063 TTGATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 4 0.13
6 25 0.83
7 1 0.03
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:1948040 original size:1 final size:1
Alignment explanation
Indices: 1948036--1948130 Score: 73
Period size: 1 Copynumber: 95.0 Consensus size: 1
1948026 TTATTTTTGA
* * * ** ** ** * *
1948036 TTTTTTTTTATTTTTGTTTTTATTTTTTTGATTTTTTTGATTTTTTTGATTTTTTTGTTTTTGTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
1948101 TTTTTGTTTTTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1948131 GGCCGAAGCT
Statistics
Matches: 71, Mismatches: 23, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.86
Consensus pattern (1 bp):
T
Found at i:1948055 original size:23 final size:23
Alignment explanation
Indices: 1948023--1948125 Score: 101
Period size: 23 Copynumber: 4.5 Consensus size: 23
1948013 CAACTCAACA
*
1948023 TTTTTATTTTTGATTTTTTT-TT
1 TTTTTGTTTTTGATTTTTTTGTT
1948045 ATTTTTGTTTTT-ATTTTTTTGATT
1 -TTTTTGTTTTTGATTTTTTTG-TT
1948069 TTTTTGATTTTTTTGATTTTTTTGTT
1 TTTTTG---TTTTTGATTTTTTTGTT
1948095 TTTGTT-TTTTTG--TTTTTT-TT
1 TTT-TTGTTTTTGATTTTTTTGTT
1948115 TTTTTGTTTTT
1 TTTTTGTTTTT
1948126 TTTTTGGCCG
Statistics
Matches: 71, Mismatches: 1, Indels: 19
0.78 0.01 0.21
Matches are distributed among these distances:
19 2 0.03
20 10 0.14
21 6 0.08
22 8 0.11
23 22 0.31
24 2 0.03
26 10 0.14
27 11 0.15
ACGTcount: A:0.07, C:0.00, G:0.09, T:0.84
Consensus pattern (23 bp):
TTTTTGTTTTTGATTTTTTTGTT
Found at i:1948074 original size:40 final size:38
Alignment explanation
Indices: 1948029--1948131 Score: 134
Period size: 40 Copynumber: 2.6 Consensus size: 38
1948019 AACATTTTTA
1948029 TTTTTGATTTTTTTTTATTTTTGTTTTTATTTTTTTGATT
1 TTTTTGATTTTTTTTT-TTTTTGTTTTTATTTTTTTG-TT
*
1948069 TTTTTGATTTTTTTGATTTTTTTGTTTTTGTTTTTTTGTT
1 TTTTTGATTTTTTT--TTTTTTTGTTTTTATTTTTTTGTT
**
1948109 TTTTTTTTTTTGTTTTTTTTTTG
1 TTTTTGATTTT-TTTTTTTTTTG
1948132 GCCGAAGCTC
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
39 8 0.14
40 25 0.44
41 22 0.39
42 2 0.04
ACGTcount: A:0.06, C:0.00, G:0.10, T:0.84
Consensus pattern (38 bp):
TTTTTGATTTTTTTTTTTTTTGTTTTTATTTTTTTGTT
Found at i:1948128 original size:14 final size:14
Alignment explanation
Indices: 1948023--1948130 Score: 110
Period size: 14 Copynumber: 7.6 Consensus size: 14
1948013 CAACTCAACA
*
1948023 TTTTTATTTTTGATTT
1 TTTTTTTTTTTG--TT
1948039 TTTTTTATTTTTGTT
1 TTTTTT-TTTTTGTT
* *
1948054 TTTATTTTTTTGAT
1 TTTTTTTTTTTGTT
**
1948068 TTTTTTGATTT-TT
1 TTTTTTTTTTTGTT
**
1948081 TTGATTTTTTTGTT
1 TTTTTTTTTTTGTT
*
1948095 TTTGTTTTTTTGTT
1 TTTTTTTTTTTGTT
1948109 TTTTTTTTTTTGTT
1 TTTTTTTTTTTGTT
1948123 TTTTTTTT
1 TTTTTTTT
1948131 GGCCGAAGCT
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
13 8 0.11
14 50 0.66
15 7 0.09
16 5 0.07
17 6 0.08
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTTTGTT
Found at i:1948129 original size:47 final size:49
Alignment explanation
Indices: 1948024--1948129 Score: 130
Period size: 47 Copynumber: 2.2 Consensus size: 49
1948014 AACTCAACAT
1948024 TTTTATTTTTGATTTTTTTTTATTTTTGTTTTTATTTTTTTGATTTTTTTG
1 TTTT-TTTTTGA-TTTTTTTTATTTTTGTTTTTATTTTTTTGATTTTTTTG
* * *
1948075 -ATTTTTTTGA-TTTTTTTGTTTTTGTTTTT-TTGTTTTT-TTTTTTTTG
1 TTTTTTTTTGATTTTTTTTATTTTTGTTTTTATT-TTTTTGATTTTTTTG
1948121 TTTTTTTTT
1 TTTTTTTTT
1948130 TGGCCGAAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
46 10 0.20
47 30 0.61
49 7 0.14
50 2 0.04
ACGTcount: A:0.07, C:0.00, G:0.08, T:0.85
Consensus pattern (49 bp):
TTTTTTTTTGATTTTTTTTATTTTTGTTTTTATTTTTTTGATTTTTTTG
Found at i:1948216 original size:40 final size:40
Alignment explanation
Indices: 1948138--1948831 Score: 848
Period size: 40 Copynumber: 17.0 Consensus size: 40
1948128 TTTGGCCGAA
* *
1948138 GCTCCTCTAAACAGAGACTCAAC-GACTTTTGAAAGTAAATT
1 GCTCCTCTAAACAGAG--GCAACGGACTTTGGAAAGTAAATT
1948179 GCTCCTCTAAACAGAGGCAACGGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGGACTTTGGAAAGTAAATT
* *
1948219 GCTCCTCTCAACAGAGGCACCAC-GACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCA--ACGGACTTTGG-AAAGTAAATT
* *
1948261 GCTCCTCTCAACAGAGGCACCAC-GACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGGACTTTGGAAAGTAAATT
*
1948302 GCTCCTCTAAACAGAGGCACCAC-GACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCA--ACGGACTTTGG-AAAGTAAATT
* *
1948344 GCTCCTCTCAACAGAGGCACCAC-GACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGGACTTTGGAAAGTAAATT
* *
1948385 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGGACTTTGGAAAGTAAATT
*
1948425 GCTCCTCTAAACAGAAGCACCAC-GACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGGACTTTGGAAAGTAAATT
*
1948466 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGGACTTTGGAAAGTAAATT
* *
1948506 GCTCCTCTCAACAGAGGCACCAC-GACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCA--ACGGACTTTGG-AAAGTAAATT
*
1948548 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGGACTTTGGAAAGTAAATT
* *
1948588 GCTCCTCTCAACAGAGGCACCAC-GACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCA--ACGGACTTTGG-AAAGTAAATT
*
1948630 GCTCCTCTAAACAGAGGCAACGAAC-TTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGGACTTTGG-AAAGTAAATT
* *
1948670 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGGACTTTGGAAAGTAAATT
* * * *
1948710 GCTCCTCTAAATAGAGGCAACGAACTTTGAAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAACGGACTTTG--GAAAGTAAATT
* *
1948752 GCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAACGG-ACTTTGGAAAGTAAATT
* *
1948793 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCAACGGACTTTGGAAAGTAAAT
1948832 ACTCCTAGAC
Statistics
Matches: 594, Mismatches: 38, Indels: 43
0.88 0.06 0.06
Matches are distributed among these distances:
39 8 0.01
40 228 0.38
41 182 0.31
42 170 0.29
43 6 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (40 bp):
GCTCCTCTAAACAGAGGCAACGGACTTTGGAAAGTAAATT
Found at i:1948278 original size:82 final size:81
Alignment explanation
Indices: 1948138--1948831 Score: 980
Period size: 82 Copynumber: 8.5 Consensus size: 81
1948128 TTTGGCCGAA
* *
1948138 GCTCCTCTAAACAGAGACTCAACG-ACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCA-AC
1 GCTCCTCTAAACAGAG--GCAACGAACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACAC
*
1948200 GGACTTTGGAAAGTAAATT
64 -GACTTTGAAAAGTAAATT
* * *
1948219 GCTCCTCTCAACAGAGGCACCACG-ACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCA--ACGAACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CA
1948283 CGACTTTGAAAAGTAAATT
63 CGACTTTGAAAAGTAAATT
* *
1948302 GCTCCTCTAAACAGAGGCACCACG-ACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCA
1 GCTCCTCTAAACAGAGGCA--ACGAACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CA
1948366 CGACTTTGAAAAGTAAATT
63 CGACTTTGAAAAGTAAATT
*
1948385 GCTCCTCTAAACAGAGGCAACGAACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAAGCACCACG
1 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CACG
*
1948449 ACTTTGGAAAGTAAATT
65 ACTTTGAAAAGTAAATT
*
1948466 GCTCCTCTAAACAGAGGCAACGAACTTTGG-AAAGTAAATTGCTCCTCTCAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CACG
*
1948530 ACTTTGGAAAAATAAATT
65 ACTTT-GAAAAGTAAATT
*
1948548 GCTCCTCTAAACAGAGGCAACGAACTTTGG-AAAGTAAATTGCTCCTCTCAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-CACG
*
1948612 ACTTTGGAAAAATAAATT
65 ACTTT-GAAAAGTAAATT
1948630 GCTCCTCTAAACAGAGGCAACGAAC-TTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCA-ACGA
1 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACACG-
1948693 ACTTTGAAAAGTAAATT
65 ACTTTGAAAAGTAAATT
* * *
1948710 GCTCCTCTAAATAGAGGCAACGAACTTTGAAAAAAATAAATTGCTCCTCTAAACAGAGGCA-ACG
1 GCTCCTCTAAACAGAGGCAACGAACTTTG-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACAC-
*
1948774 GAACTTTGAAAAATAAATT
64 G-ACTTTGAAAAGTAAATT
1948793 GCTCCTCTAAACAGAGGCAACGAACTTT-GAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAAT
1948832 ACTCCTAGAC
Statistics
Matches: 576, Mismatches: 24, Indels: 26
0.92 0.04 0.04
Matches are distributed among these distances:
79 2 0.00
80 38 0.07
81 162 0.28
82 209 0.36
83 163 0.28
84 2 0.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (81 bp):
GCTCCTCTAAACAGAGGCAACGAACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACACGA
CTTTGAAAAGTAAATT
Found at i:1948418 original size:123 final size:120
Alignment explanation
Indices: 1948138--1948831 Score: 979
Period size: 123 Copynumber: 5.7 Consensus size: 120
1948128 TTTGGCCGAA
* *
1948138 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1 GCTCCTCTAAACAGAG--GCAACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
1948202 ACTTTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
63 ACTTTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAATAAATT
*
1948261 GCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
* *
1948326 -ACTTTGGAAAAATAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGAAAAGTAAATT
62 AACTTTGG-AAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAATT
*
1948385 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAAGCACCACG-
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGA
* * *
1948449 ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTTGGAAAGTAAATT
63 ACTTTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACG-ACTTTGAAAAATAAATT
* *
1948506 GCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGA
1 GCTCCTCTAAACAGAGGCA--ACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
1948571 ACTTTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGGAAAAATAAATT
63 ACTTTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTT-GAAAAATAAATT
*
1948630 GCTCCTCTAAACAGAGGCAACGAACTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAAC
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAAC
* * *
1948695 TTTGAAAAGTAAATTGCTCCTCTAAATAGAGGCA--ACGAACTTTGAAAAAAATAAATT
65 TTTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACG-ACTTTG--AAAAATAAATT
*
1948752 GCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGAA
1 GCTCCTCTAAACAGAGGCAAC-G-ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
*
1948817 CTTTGAAAAGTAAAT
64 CTTTGGAAAGTAAAT
1948832 ACTCCTAGAC
Statistics
Matches: 528, Mismatches: 23, Indels: 40
0.89 0.04 0.07
Matches are distributed among these distances:
120 7 0.01
121 44 0.08
122 176 0.33
123 193 0.37
124 67 0.13
125 41 0.08
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (120 bp):
GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACT
TTGGAAAGTAAATTGCTCCTCTCAACAGAGGCACCACGACTTTGAAAAATAAATT
Found at i:1950031 original size:8 final size:8
Alignment explanation
Indices: 1950018--1950048 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1950008 TTCGGATCTC
1950018 TTTTTTCA
1 TTTTTTCA
1950026 TTTTTTCA
1 TTTTTTCA
*
1950034 TTTTCTCA
1 TTTTTTCA
1950042 TTTTTTC
1 TTTTTTC
1950049 TTCTTTCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1953981 original size:156 final size:156
Alignment explanation
Indices: 1953715--1954312 Score: 1115
Period size: 156 Copynumber: 3.8 Consensus size: 156
1953705 GTTAGTTGTT
1953715 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
*
1953780 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTATTTAAAGAAAAAT
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
1953845 CAAGATCAACCAATTAATTAATTATC
131 CAAGATCAACCAATTAATTAATTATC
* * *
1953871 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAACTTGAGAAAATTTCCTCACCTCAGG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
1953936 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
1954001 CAAGATCAACCAATTAATTAATTATC
131 CAAGATCAACCAATTAATTAATTATC
1954027 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
*
1954092 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTATTTAAAGAAAAAT
66 AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
1954157 CAAGATCAACCAATTAATTAATTATC
131 CAAGATCAACCAATTAATTAATTATC
*
1954183 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGG
1 GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
* *
1954248 AGTATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAA
66 AGTATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAA
1954313 AGAAAAAAAA
Statistics
Matches: 429, Mismatches: 12, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
156 389 0.91
157 40 0.09
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (156 bp):
GAAAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAG
AGTATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAT
CAAGATCAACCAATTAATTAATTATC
Found at i:1954366 original size:14 final size:13
Alignment explanation
Indices: 1954347--1954382 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1954337 AAAGTCAAAT
*
1954347 AAAAAAAAATTCA
1 AAAAAAAAAATCA
1954360 AAAAAAAAAATCA
1 AAAAAAAAAATCA
1954373 AAAAAAAAAA
1 AAAAAAAAAA
1954383 AAAAAACCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.86, C:0.06, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAAAAAAAATCA
Found at i:1954665 original size:18 final size:20
Alignment explanation
Indices: 1954642--1954686 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
1954632 GAACGCCGGT
*
1954642 GCCGGATTCT-GGAATT-TC
1 GCCGGAATCTGGGAATTGTC
1954660 GCCGGAATCTGGGAATTGTC
1 GCCGGAATCTGGGAATTGTC
1954680 GCCGGAA
1 GCCGGAA
1954687 GTTGGCCGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.38
19 6 0.25
20 9 0.38
ACGTcount: A:0.20, C:0.22, G:0.33, T:0.24
Consensus pattern (20 bp):
GCCGGAATCTGGGAATTGTC
Found at i:1954789 original size:30 final size:31
Alignment explanation
Indices: 1954749--1954817 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1954739 AAACTGGGTC
*
1954749 TGTCGCCGG-AACTTC-AAAGTTCGCCGGAAT
1 TGTCGCCGGAAAATTCAAAAG-TCGCCGGAAT
*
1954779 TGTCGTCGGAAAATTCAAAAGTCGCCGGAAT
1 TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
*
1954810 TTTCGCCG
1 TGTCGCCG
1954818 AAATCTGGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 8 0.24
31 21 0.64
32 4 0.12
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (31 bp):
TGTCGCCGGAAAATTCAAAAGTCGCCGGAAT
Found at i:1955397 original size:3 final size:3
Alignment explanation
Indices: 1955389--1955415 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1955379 AAAGATATAC
1955389 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1955416 GAATACATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1956254 original size:25 final size:25
Alignment explanation
Indices: 1956199--1956255 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
1956189 TATAATTATA
**
1956199 AAAAATTATTTATTATATTTAAATT
1 AAAAATTATTTAACATATTTAAATT
**
1956224 TGAAATTATTTGAACATATTTAAA-T
1 AAAAATTATTT-AACATATTTAAATT
1956249 AAAAATT
1 AAAAATT
1956256 TAAAATAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
AAAAATTATTTAACATATTTAAATT
Found at i:1958251 original size:31 final size:29
Alignment explanation
Indices: 1958211--1958272 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 29
1958201 CATTTTATTA
* *
1958211 ATGATATCATCTT-ATTTATTTTATTAATAAT
1 ATGACATCAT-TTAATTT-TTTTAAT-ATAAT
1958242 ATGACATCATTTAATTTTTTTAATATAAT
1 ATGACATCATTTAATTTTTTTAATATAAT
1958271 AT
1 AT
1958273 AAAATTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 7 0.25
30 8 0.29
31 13 0.46
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.53
Consensus pattern (29 bp):
ATGACATCATTTAATTTTTTTAATATAAT
Found at i:1958253 original size:26 final size:26
Alignment explanation
Indices: 1958202--1958266 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
1958192 AAATTTACCC
*
1958202 ATTTTATTAATGATATCATCTTATTT-
1 ATTTTATTAATAATATCATC-TATTTA
1958228 ATTTTATTAATAATATGACATC-ATTTA
1 ATTTTATTAATAATAT--CATCTATTTA
*
1958255 ATTTTTTTAATA
1 ATTTTATTAATA
1958267 TAATATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 19 0.56
27 11 0.32
28 4 0.12
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (26 bp):
ATTTTATTAATAATATCATCTATTTA
Found at i:1959312 original size:21 final size:21
Alignment explanation
Indices: 1959277--1959338 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
1959267 ATAATTTTTT
*
1959277 TTATGAATTTTTTTAATTATAA
1 TTAT-AATATTTTTAATTATAA
*
1959299 TTATAATATTTTTAACTATAA
1 TTATAATATTTTTAATTATAA
1959320 TTATAATAATTTTT-ATTAT
1 TTATAAT-ATTTTTAATTAT
1959339 TTTTTTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 26 0.72
22 10 0.28
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATAATATTTTTAATTATAA
Found at i:1963135 original size:22 final size:22
Alignment explanation
Indices: 1963107--1963150 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1963097 ATCAAAACCT
1963107 TGTTTGGAATTTTGAGCCAGTA
1 TGTTTGGAATTTTGAGCCAGTA
1963129 TGTTTGGAATTTTGAGCCAGTA
1 TGTTTGGAATTTTGAGCCAGTA
1963151 CTAACTCATC
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:0.23, C:0.09, G:0.27, T:0.41
Consensus pattern (22 bp):
TGTTTGGAATTTTGAGCCAGTA
Found at i:1971138 original size:22 final size:23
Alignment explanation
Indices: 1971103--1971145 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1971093 ATATTATAAA
1971103 TTTTTAAAATTTGAATCAATTAT
1 TTTTTAAAATTTGAATCAATTAT
* *
1971126 TTTTTTAAA-TTGATTCAATT
1 TTTTTAAAATTTGAATCAATT
1971146 CAAATTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (23 bp):
TTTTTAAAATTTGAATCAATTAT
Found at i:1972530 original size:20 final size:20
Alignment explanation
Indices: 1972476--1972531 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1972466 ATATTCAACT
1972476 TAAAATCAATTAACAATAAATA
1 TAAAATC-ATTAA-AATAAATA
1972498 -AAAAT-ATTCAAAATAAATA
1 TAAAATCATT-AAAATAAATA
*
1972517 TAAAATCACTAAAAT
1 TAAAATCATTAAAAT
1972532 TTTAAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 11 0.37
20 12 0.40
21 7 0.23
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (20 bp):
TAAAATCATTAAAATAAATA
Found at i:1973585 original size:10 final size:10
Alignment explanation
Indices: 1973562--1973602 Score: 50
Period size: 9 Copynumber: 4.2 Consensus size: 10
1973552 TGGGATTCGA
1973562 TTTTAAGTATT
1 TTTTAA-TATT
*
1973573 TTTTAATAAT
1 TTTTAATATT
1973583 TTTTAA-ATT
1 TTTTAATATT
1973592 TTTTAA-ATT
1 TTTTAATATT
1973601 TT
1 TT
1973603 GCCCTCTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 13 0.46
10 9 0.32
11 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTAATATT
Found at i:1974837 original size:12 final size:12
Alignment explanation
Indices: 1974822--1974856 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1974812 ATATAAGTTC
* *
1974822 ATATATATATAT
1 ATATATTTATAA
1974834 ATATATTTATAA
1 ATATATTTATAA
1974846 ATATATTTATA
1 ATATATTTATA
1974857 CTAAACTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATATTTATAA
Found at i:1975609 original size:6 final size:6
Alignment explanation
Indices: 1975594--1975663 Score: 54
Period size: 6 Copynumber: 11.8 Consensus size: 6
1975584 TTAAATATCC
* * * **
1975594 ATAAAA ATAAAT ATAAAA ATAAAT TTAAAAT ATTCAT -TAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT AT-AAAT ATAAAT ATAAAT ATAAAT
* *
1975642 ATAGAT ATGAAT AT-AAT ATAAA
1 ATAAAT ATAAAT ATAAAT ATAAA
1975664 GATTTAAAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
5 8 0.16
6 36 0.73
7 5 0.10
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:1976378 original size:13 final size:13
Alignment explanation
Indices: 1976362--1976386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1976352 TTTAATTAAT
1976362 AAATTTATATATA
1 AAATTTATATATA
1976375 AAATTTATATAT
1 AAATTTATATAT
1976387 TAATAATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATTTATATATA
Found at i:1976396 original size:26 final size:26
Alignment explanation
Indices: 1976271--1976413 Score: 88
Period size: 30 Copynumber: 5.0 Consensus size: 26
1976261 TGTAATATTT
*
1976271 TATTAATAAATAAATATAAAATTTTA
1 TATTAATAAATATATATAAAATTTTA
* * * * *
1976297 AATAAATACATATAAATTAAAATTTTT
1 TATTAATAAATATATA-TAAAATTTTA
** *
1976324 TATTAATAAAATATTATTATCTAATTTATT
1 TATTAAT-AAATA-TA-TATAAAATTT-TA
1976354 TAATTAATAAATTTATATATAAAATTTATA
1 T-ATTAATAAA--TATATATAAAATTT-TA
*
1976384 TATTAATAATATATCAAATATAAATTTTA
1 TATTAATAA-ATAT-ATATA-AAATTTTA
1976413 T
1 T
1976414 TGAGTTGTTT
Statistics
Matches: 90, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
26 11 0.12
27 14 0.16
28 7 0.08
29 23 0.26
30 25 0.28
31 8 0.09
32 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
TATTAATAAATATATATAAAATTTTA
Found at i:1991003 original size:17 final size:17
Alignment explanation
Indices: 1990965--1991016 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
1990955 CCAAATCACA
1990965 AGTGATGAGATCACCAAT
1 AGTGATGAGATCACC-AT
1990983 AGTGATGAGATCACCAT
1 AGTGATGAGATCACCAT
* *
1991000 AGTGATTAGATTACCAT
1 AGTGATGAGATCACCAT
1991017 GGTAGTCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 17 0.53
18 15 0.47
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (17 bp):
AGTGATGAGATCACCAT
Found at i:1995546 original size:2 final size:2
Alignment explanation
Indices: 1995539--1995569 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1995529 GCCTAACCAA
1995539 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 A
1995570 AATTATCCCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1997650 original size:16 final size:16
Alignment explanation
Indices: 1997629--1997661 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1997619 AAAAGATCAA
*
1997629 AGTATCATCGTCCATT
1 AGTATCATCATCCATT
1997645 AGTATCATCATCCATT
1 AGTATCATCATCCATT
1997661 A
1 A
1997662 TGAATAATGA
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:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (16 bp):
AGTATCATCATCCATT
Found at i:2000175 original size:127 final size:127
Alignment explanation
Indices: 1999949--2000193 Score: 427
Period size: 127 Copynumber: 1.9 Consensus size: 127
1999939 GCATAACAAA
* *
1999949 GCATTACCATAATCATCGTAATTATAGCAAAATTCAAATTGCTATAAATGATCTTATTCCGTATA
1 GCATTACCATAATCATCGTAATGATAGCAAAATTCAAATTGCTATAAATGATCTTATTCCATATA
* *
2000014 GATCTTCTAAGCAACTATTTATTAAAAGCATGCTCAAAGATCAAATCAAACTCCTTAACGAG
66 AATCTTCTAAGCAACTATTTATTAAAAGCATGCTCAAAGAACAAATCAAACTCCTTAACGAG
* * *
2000076 GCATTACCATAATCTTCGTAATGATAGTAAAATTCAAATTGCTATAATTGATCTTATTCCATATA
1 GCATTACCATAATCATCGTAATGATAGCAAAATTCAAATTGCTATAAATGATCTTATTCCATATA
2000141 AATCTTCTAAGCAACTATTTATTAAAAGCATGCTCAAAGAACAAATCAAACTC
66 AATCTTCTAAGCAACTATTTATTAAAAGCATGCTCAAAGAACAAATCAAACTC
2000194 TTTTGGCAGA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 111 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.32
Consensus pattern (127 bp):
GCATTACCATAATCATCGTAATGATAGCAAAATTCAAATTGCTATAAATGATCTTATTCCATATA
AATCTTCTAAGCAACTATTTATTAAAAGCATGCTCAAAGAACAAATCAAACTCCTTAACGAG
Found at i:2006398 original size:25 final size:25
Alignment explanation
Indices: 2006322--2006400 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 25
2006312 TAAAGAAGTT
* *
2006322 ATAATTAAATATATATTTATATAAAA
1 ATAATTAAATAAATA-TAATATAAAA
*
2006348 ATTATTAAATTAAAT-TAA-ATTAAAAA
1 ATAATTAAA-TAAATATAATA-T-AAAA
*
2006374 ATAATTAAACAAATATAATATAAAA
1 ATAATTAAATAAATATAATATAAAA
2006399 AT
1 AT
2006401 TAAATCAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
24 1 0.02
25 13 0.30
26 24 0.56
27 5 0.12
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATTAAATAAATATAATATAAAA
Found at i:2006423 original size:22 final size:22
Alignment explanation
Indices: 2006376--2006431 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
2006366 ATTAAAAAAT
*
2006376 AATTAAACAAATATAATATAAA
1 AATTAAACAAATATAATACAAA
* *
2006398 AATTAAATCAAAT-TCATACAAG
1 AATTAAA-CAAATATAATACAAA
*
2006420 AATTAAAAAAAT
1 AATTAAACAAAT
2006432 CTTATGATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 4 0.14
22 20 0.69
23 5 0.17
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.27
Consensus pattern (22 bp):
AATTAAACAAATATAATACAAA
Found at i:2006694 original size:18 final size:18
Alignment explanation
Indices: 2006672--2006714 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
2006662 TTATATAATC
*
2006672 ATATATTTTTATTAACTTTT
1 ATATATTTTTA--ATCTTTT
*
2006692 ATATATTTTTAATTTTTT
1 ATATATTTTTAATCTTTT
2006710 ATATA
1 ATATA
2006715 ATAAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
ATATATTTTTAATCTTTT
Found at i:2007519 original size:19 final size:20
Alignment explanation
Indices: 2007478--2007519 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
2007468 TATTTTATTC
* *
2007478 ATTAAAATAATAAAAATAT-
1 ATTAAAATAATAAAATTTTA
2007497 ATTAAAAT-ATAAAATTTTA
1 ATTAAAATAATAAAATTTTA
2007516 ATTA
1 ATTA
2007520 CACTCATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATTAAAATAATAAAATTTTA
Found at i:2009305 original size:9 final size:9
Alignment explanation
Indices: 2009291--2009316 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2009281 GTCTACCACC
2009291 ACCAGAACG
1 ACCAGAACG
2009300 ACCAGAACG
1 ACCAGAACG
2009309 ACCAGAAC
1 ACCAGAAC
2009317 TACCTTGCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.35, G:0.19, T:0.00
Consensus pattern (9 bp):
ACCAGAACG
Found at i:2017936 original size:12 final size:11
Alignment explanation
Indices: 2017919--2017957 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2017909 CACATAATTT
2017919 AAAATTTTAATA
1 AAAATTTT-ATA
2017931 AAAATTTTATA
1 AAAATTTTATA
* *
2017942 TAAATTTGATA
1 AAAATTTTATA
2017953 AAAAT
1 AAAAT
2017958 AAAATATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
AAAATTTTATA
Found at i:2032135 original size:17 final size:17
Alignment explanation
Indices: 2032115--2032166 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
2032105 ATTAGTTTAC
2032115 TTAATAAATAAATATAT
1 TTAATAAATAAATATAT
* *
2032132 TTAATAATTTAATTATAT
1 TTAATAA-ATAAATATAT
2032150 TTATTATAAAATAAATA
1 TTA--AT-AAATAAATA
2032167 AAATATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 7 0.26
18 11 0.41
20 7 0.26
21 2 0.07
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAATAAATAAATATAT
Found at i:2032356 original size:19 final size:19
Alignment explanation
Indices: 2032308--2032357 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
2032298 GTAGTAATCG
* *
2032308 TTATTTTATAT-AAATTAA
1 TTATTTTAAATCAAATAAA
*
2032326 TGATATTT-AATCAAATAAA
1 TTAT-TTTAAATCAAATAAA
2032345 TTATTTTAAATCA
1 TTATTTTAAATCA
2032358 TAAGTGATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 8 0.32
19 17 0.68
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (19 bp):
TTATTTTAAATCAAATAAA
Found at i:2036080 original size:15 final size:15
Alignment explanation
Indices: 2036062--2036154 Score: 79
Period size: 15 Copynumber: 6.4 Consensus size: 15
2036052 ATTGATAAAT
2036062 AATATTATATTAATA
1 AATATTATATTAATA
*
2036077 AATAATATATTAATA
1 AATATTATATTAATA
*
2036092 AA-ATTATTATAAATA
1 AATATTA-TATTAATA
*
2036107 AATATTATACTAAT-
1 AATATTATATTAATA
* *
2036121 -ATGTTAATGTTAATA
1 AATATT-ATATTAATA
*
2036136 AATAATAT-TTAA-A
1 AATATTATATTAATA
2036149 AATATT
1 AATATT
2036155 TTAATTATTA
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
13 10 0.16
14 13 0.21
15 32 0.52
16 7 0.11
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (15 bp):
AATATTATATTAATA
Found at i:2036084 original size:18 final size:18
Alignment explanation
Indices: 2036026--2036110 Score: 78
Period size: 18 Copynumber: 5.2 Consensus size: 18
2036016 TTTGTTAAGT
*
2036026 ATAATTTTA-ATT-ATAA
1 ATAATATTATATTAATAA
* *
2036042 ATAATACTATATTGATAA
1 ATAATATTATATTAATAA
2036060 ATAATATTATATTAATAA
1 ATAATATTATATTAATAA
2036078 AT-A-A-TATATTAATAA
1 ATAATATTATATTAATAA
*
2036093 A-ATTATTATA--AATAA
1 ATAATATTATATTAATAA
2036108 ATA
1 ATA
2036111 TTATACTAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
15 18 0.31
16 10 0.17
17 8 0.14
18 22 0.38
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (18 bp):
ATAATATTATATTAATAA
Found at i:2036091 original size:29 final size:31
Alignment explanation
Indices: 2036026--2036176 Score: 114
Period size: 32 Copynumber: 4.9 Consensus size: 31
2036016 TTTGTTAAGT
* * * *
2036026 ATAATTTTAATTATAAAT-AATACTATATTG
1 ATAATATTAATTATTAATAAATAATATATTA
* *
2036056 ATAAATAATATTATATTAATAAATAATATATTA
1 AT-AATATTAAT-TATTAATAAATAATATATTA
* * * *
2036089 ATAAAATT-ATTATAAATAAATATTATACTA
1 ATAATATTAATTATTAATAAATAATATATTA
* *
2036119 AT-ATGTTAA-TGTTAATAAATAATAT-TTA
1 ATAATATTAATTATTAATAAATAATATATTA
*
2036147 AAAATATTTTAATTATTAATAAATAATATA
1 ATAATA--TTAATTATTAATAAATAATATA
2036177 AAGAATAATA
Statistics
Matches: 91, Mismatches: 21, Indels: 15
0.72 0.17 0.12
Matches are distributed among these distances:
28 3 0.03
29 18 0.20
30 22 0.24
31 11 0.12
32 25 0.27
33 12 0.13
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (31 bp):
ATAATATTAATTATTAATAAATAATATATTA
Found at i:2036100 original size:32 final size:33
Alignment explanation
Indices: 2036044--2036176 Score: 115
Period size: 32 Copynumber: 4.3 Consensus size: 33
2036034 AATTATAAAT
* * *
2036044 AATACTATATTGATAAATAATATTATATTAATA
1 AATAATATATTAATAAATATTATTATATTAATA
2036077 AATAATATATTAATAAA-ATTATTATA--AATA
1 AATAATATATTAATAAATATTATTATATTAATA
* * * *
2036107 AATATTATACTAAT--ATGTTA--ATGTTAATA
1 AATAATATATTAATAAATATTATTATATTAATA
2036136 AATAATAT-TTAA-AAATATT-TTAATTATTAATA
1 AATAATATATTAATAAATATTATT-A-TATTAATA
2036168 AATAATATA
1 AATAATATA
2036177 AAGAATAATA
Statistics
Matches: 79, Mismatches: 11, Indels: 20
0.72 0.10 0.18
Matches are distributed among these distances:
27 2 0.03
28 4 0.05
29 18 0.23
30 16 0.20
31 1 0.01
32 23 0.29
33 15 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (33 bp):
AATAATATATTAATAAATATTATTATATTAATA
Found at i:2036109 original size:30 final size:31
Alignment explanation
Indices: 2036035--2036121 Score: 97
Period size: 30 Copynumber: 2.8 Consensus size: 31
2036025 TATAATTTTA
* *
2036035 ATTATAAAT-AATACTATATTGATAAATAAT
1 ATTATAAATAAATAATATATTAATAAATAAT
*
2036065 ATTATATTAATAAATAATATATTAATAAA-ATT
1 ATTATA--AATAAATAATATATTAATAAATAAT
* *
2036097 ATTATAAATAAATATTATACTAATA
1 ATTATAAATAAATAATATATTAATA
2036122 TGTTAATGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
30 23 0.47
32 11 0.22
33 15 0.31
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (31 bp):
ATTATAAATAAATAATATATTAATAAATAAT
Found at i:2036296 original size:17 final size:17
Alignment explanation
Indices: 2036245--2036300 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
2036235 AATATTATGA
*
2036245 TTAA-AATATAATTATTT
1 TTAATAATAT-ATAATTT
*
2036262 TTGAATATTA-ATAA-TT
1 TT-AATAATATATAATTT
2036278 TTAATAATATATAATTT
1 TTAATAATATATAATTT
2036295 TTAATA
1 TTAATA
2036301 TTTTAATAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 6 0.19
16 8 0.25
17 13 0.41
18 2 0.06
19 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
TTAATAATATATAATTT
Found at i:2036322 original size:26 final size:26
Alignment explanation
Indices: 2036269--2036322 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
2036259 TTTTTGAATA
*
2036269 TTAATAATTTTAATAATATATAATTT
1 TTAATAATTTTAATAATATATAAGTT
*
2036295 TTAAT-ATTTTAATAAGTATATTAGTT
1 TTAATAATTTTAATAA-TATATAAGTT
2036321 TT
1 TT
2036323 TTTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
TTAATAATTTTAATAATATATAAGTT
Found at i:2044702 original size:29 final size:29
Alignment explanation
Indices: 2044670--2044725 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2044660 GGCAATTGGA
* *
2044670 AATTTGTATAATTGCTATGATCAATTAGT
1 AATTTGTAAAATTGATATGATCAATTAGT
* *
2044699 AATTTGTAAAATTTATATTATCAATTA
1 AATTTGTAAAATTGATATGATCAATTA
2044726 AGAAAGGAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.46
Consensus pattern (29 bp):
AATTTGTAAAATTGATATGATCAATTAGT
Found at i:2048769 original size:11 final size:12
Alignment explanation
Indices: 2048744--2048768 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2048734 ATACCCTCAG
2048744 TTCCTTTTTTTT
1 TTCCTTTTTTTT
2048756 TTCCTTTTTTTT
1 TTCCTTTTTTTT
2048768 T
1 T
2048769 CTTTCAGATA
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTCCTTTTTTTT
Found at i:2059208 original size:7 final size:7
Alignment explanation
Indices: 2059193--2059232 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
2059183 TTTAAAAACA
*
2059193 AAATTAT
1 AAATAAT
2059200 AAATAAT
1 AAATAAT
2059207 AAATAAT
1 AAATAAT
2059214 AAATAAT
1 AAATAAT
2059221 ATAATAA-
1 A-AATAAT
2059228 AAATA
1 AAATA
2059233 TTAATAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
6 4 0.13
7 22 0.71
8 5 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAATAAT
Found at i:2059336 original size:12 final size:12
Alignment explanation
Indices: 2059319--2059344 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2059309 TTCACACTTC
2059319 AAAATTTTTTTA
1 AAAATTTTTTTA
2059331 AAAATTTTTTTA
1 AAAATTTTTTTA
2059343 AA
1 AA
2059345 TGAAATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AAAATTTTTTTA
Found at i:2059468 original size:42 final size:41
Alignment explanation
Indices: 2059448--2059531 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 41
2059438 TTGAAAATTT
**
2059448 ATTTTCAAAAAGTTTTAAAATTTAAAAAATTATAAAAAATA
1 ATTTTCAAAAAACTTTAAAATTTAAAAAATTATAAAAAATA
*
2059489 ATTTTTAAAAAACTTTAAAATTTTAAAAAATTATAAAATAATA
1 ATTTTCAAAAAACTTTAAAA-TTTAAAAAATTATAAAA-AATA
2059532 GTTAAACAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 17 0.45
42 17 0.45
43 4 0.11
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.38
Consensus pattern (41 bp):
ATTTTCAAAAAACTTTAAAATTTAAAAAATTATAAAAAATA
Found at i:2059527 original size:18 final size:18
Alignment explanation
Indices: 2059491--2059527 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2059481 AAAAAATAAT
2059491 TTTTAAAAAACTTTAAAA
1 TTTTAAAAAACTTTAAAA
2059509 TTTTAAAAAA-TTATAAAA
1 TTTTAAAAAACTT-TAAAA
2059527 T
1 T
2059528 AATAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TTTTAAAAAACTTTAAAA
Found at i:2071677 original size:2 final size:2
Alignment explanation
Indices: 2071670--2071707 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2071660 TTGATTCCCT
*
2071670 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2071708 AAGCTTAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:2081747 original size:30 final size:29
Alignment explanation
Indices: 2081680--2081748 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
2081670 TAATCGATAT
*
2081680 TATATAAAATATATTTAATTTAATTTAAAA
1 TATATAAAATATATTT-ATTTAATATAAAA
2081710 T-TAATAAAATATTATTT-TTTAATATAAATA
1 TAT-ATAAAATA-TATTTATTTAATATAAA-A
2081740 TATATAAAA
1 TATATAAAA
2081749 AAAATAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
29 11 0.32
30 17 0.50
31 6 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TATATAAAATATATTTATTTAATATAAAA
Done.