Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 6 of 167
Found at i:1661045 original size:24 final size:22
Alignment explanation
Indices: 1661018--1661068 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1661008 ATATATGCAC
*
1661018 ATATATATATTAAGATATATGG
1 ATATATATAATAAGATATATGG
*
1661040 ATATATATAATAAGATATATAG
1 ATATATATAATAAGATATATGG
1661062 ATATATA
1 ATATATA
1661069 ACTAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (22 bp):
ATATATATAATAAGATATATGG
Found at i:1661069 original size:20 final size:21
Alignment explanation
Indices: 1661020--1661078 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
1661010 ATATGCACAT
* *
1661020 ATATATATTAAGATATATGGAT
1 ATATATAATAAGATATAT-GAG
1661042 ATATATAATAAGATATAT-AG
1 ATATATAATAAGATATATGAG
1661062 ATATATAACTAA-ATATA
1 ATATATAA-TAAGATATA
1661079 ATATTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.41
21 3 0.09
22 17 0.50
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (21 bp):
ATATATAATAAGATATATGAG
Found at i:1670076 original size:34 final size:34
Alignment explanation
Indices: 1670030--1670096 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
1670020 GTGTGAGTGT
* **
1670030 GGGTGTTTATATATAGTTTATGTATATATAATGC
1 GGGTGTTCATATATAACTTATGTATATATAATGC
1670064 GGGTGTTCATATATAACTTATGTATATATAATG
1 GGGTGTTCATATATAACTTATGTATATATAATG
1670097 AGAGAGTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.45
Consensus pattern (34 bp):
GGGTGTTCATATATAACTTATGTATATATAATGC
Found at i:1691036 original size:22 final size:24
Alignment explanation
Indices: 1690991--1691037 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
1690981 AGACATAAAA
* *
1690991 ATTTTATGTTAAAATAGTTGTTAT
1 ATTTTATGTTAAAATAGCTATTAT
1691015 ATTTT-TGTT-AAATAGCTATTAT
1 ATTTTATGTTAAAATAGCTATTAT
1691037 A
1 A
1691038 CGCAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 4 0.19
24 5 0.24
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.53
Consensus pattern (24 bp):
ATTTTATGTTAAAATAGCTATTAT
Found at i:1691052 original size:25 final size:27
Alignment explanation
Indices: 1691023--1691075 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
1691013 ATATTTTTGT
1691023 TAAA-TAGCT-ATTATACGCAAATATA
1 TAAATTAGCTAATTATACGCAAATATA
** *
1691048 TAAATTATTTAATTATACGCATATATA
1 TAAATTAGCTAATTATACGCAAATATA
1691075 T
1 T
1691076 TATCATAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 3 0.13
27 16 0.70
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (27 bp):
TAAATTAGCTAATTATACGCAAATATA
Found at i:1715753 original size:42 final size:41
Alignment explanation
Indices: 1715701--1715780 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 41
1715691 CATTAAAGCT
* *
1715701 TGAACTTTTTTTTTGT-TTAAGTTAATCTCTAAACTTAAAAG
1 TGAACTTTTTTTTTGTCAT-AGTCAATCTCTAAACTTAAAAG
*
1715742 TGAACTTTTTTTTTTGTCATAGTCAATCTCTAAATTTAA
1 TGAAC-TTTTTTTTTGTCATAGTCAATCTCTAAACTTAA
1715781 CAATTATTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
41 5 0.15
42 28 0.82
43 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (41 bp):
TGAACTTTTTTTTTGTCATAGTCAATCTCTAAACTTAAAAG
Found at i:1722193 original size:28 final size:28
Alignment explanation
Indices: 1722153--1722209 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1722143 ATCTGGATTC
* *
1722153 TAAACCCTAGACCATAGACCTTAAACTT
1 TAAACCATAGACCATAGACCTCAAACTT
* *
1722181 TAAACCATCGACCTTAGACCTCAAACTT
1 TAAACCATAGACCATAGACCTCAAACTT
1722209 T
1 T
1722210 GGACCCCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.26
Consensus pattern (28 bp):
TAAACCATAGACCATAGACCTCAAACTT
Found at i:1722206 original size:21 final size:21
Alignment explanation
Indices: 1722163--1722206 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1722153 TAAACCCTAG
* *
1722163 ACCATAGACCTTAAACTTTAA
1 ACCATAGACCTTAAACCTCAA
* *
1722184 ACCATCGACCTTAGACCTCAA
1 ACCATAGACCTTAAACCTCAA
1722205 AC
1 AC
1722207 TTTGGACCCC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.32, G:0.07, T:0.23
Consensus pattern (21 bp):
ACCATAGACCTTAAACCTCAA
Found at i:1724653 original size:50 final size:49
Alignment explanation
Indices: 1724598--1724696 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 49
1724588 TGCTTGGAAC
* *
1724598 ACCTTCCGAGGTAAACTTTATTTTTGTATATCATTGATGTGTGTTGGCT
1 ACCTTCCAAGGTAAACTTTATTTTCGTATATCATTGATGTGTGTTGGCT
1724647 NACCTTCCAAGGTAAACTTTATTTTCGTATATCATTGATGTGTGTTGGCT
1 -ACCTTCCAAGGTAAACTTTATTTTCGTATATCATTGATGTGTGTTGGCT
1724697 TCTTTTTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.21, C:0.15, G:0.19, T:0.43
Consensus pattern (49 bp):
ACCTTCCAAGGTAAACTTTATTTTCGTATATCATTGATGTGTGTTGGCT
Found at i:1726896 original size:39 final size:39
Alignment explanation
Indices: 1726848--1726930 Score: 139
Period size: 39 Copynumber: 2.1 Consensus size: 39
1726838 ATCATGGCGG
* * *
1726848 TCGGTTTGGTGCGTACTGTTTCAGTACTAACATGGAACA
1 TCGGCTTGGTGCGCACTGTTTCAGTACTAAAATGGAACA
1726887 TCGGCTTGGTGCGCACTGTTTCAGTACTAAAATGGAACA
1 TCGGCTTGGTGCGCACTGTTTCAGTACTAAAATGGAACA
1726926 TCGGC
1 TCGGC
1726931 CGTTTTTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (39 bp):
TCGGCTTGGTGCGCACTGTTTCAGTACTAAAATGGAACA
Found at i:1732113 original size:2 final size:2
Alignment explanation
Indices: 1732106--1732142 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1732096 GATTGTTCAG
1732106 TA TA TA 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 TA TA TA T
1732143 GATGTGCCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1734030 original size:45 final size:45
Alignment explanation
Indices: 1733966--1734058 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
1733956 AATCCGAGAA
1733966 CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
1 CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
* *
1734011 CTGTGATTGCTTACAAGGTATGCCGTTCCTTTTAGAGAGTTAGCT
1 CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
1734056 CTG
1 CTG
1734059 GTTTATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (45 bp):
CTGTGATTGCTTACAAGGTATGCCATTCCTTTTACAGAGTTAGCT
Found at i:1738401 original size:3 final size:3
Alignment explanation
Indices: 1738380--1738527 Score: 260
Period size: 3 Copynumber: 48.7 Consensus size: 3
1738370 CGTCTGATAC
* *
1738380 TAT TAT TTT TAT TCCT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1738426 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1738474 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1738522 GTAT TA
1 -TAT TA
1738528 GTGTATACTT
Statistics
Matches: 139, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
3 134 0.96
4 5 0.04
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1738611 original size:41 final size:41
Alignment explanation
Indices: 1738558--1738639 Score: 98
Period size: 41 Copynumber: 2.0 Consensus size: 41
1738548 TATATATATG
* *
1738558 TAGTAATCTTTTATTACTTT-ATTTTTA-TATTATTATTATTA
1 TAGTAATCTTTTA-TA-TTTCAATATTATTATTATTATTATTA
1738599 TAGTAA-CTTTTTATATTTCAATATTATTATTATTATTATTA
1 TAGTAATC-TTTTATATTTCAATATTATTATTATTATTATTA
1738640 GTATATGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
39 3 0.08
40 8 0.22
41 25 0.69
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (41 bp):
TAGTAATCTTTTATATTTCAATATTATTATTATTATTATTA
Found at i:1738672 original size:21 final size:20
Alignment explanation
Indices: 1738626--1738694 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 20
1738616 TCAATATTAT
1738626 TATTATTATTAT-TA-GTATA
1 TATT-TTATTATATATGTATA
*
1738645 TGTTTTATTATATATGTATA
1 TATTTTATTATATATGTATA
1738665 TATCTTTAATATATATATACGTATA
1 TAT-TTT-AT-TATATAT--GTATA
1738690 TATTT
1 TATTT
1738695 ATGTAGTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
18 7 0.17
19 5 0.12
20 7 0.17
21 3 0.07
22 2 0.05
23 7 0.17
24 2 0.05
25 8 0.20
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.57
Consensus pattern (20 bp):
TATTTTATTATATATGTATA
Found at i:1738756 original size:11 final size:11
Alignment explanation
Indices: 1738740--1738808 Score: 52
Period size: 11 Copynumber: 6.0 Consensus size: 11
1738730 TTATTTCTAA
1738740 TATGTATATAT
1 TATGTATATAT
*
1738751 TATGTAAATATT
1 TATGTATATA-T
1738763 CTAATGT-TATAT
1 -T-ATGTATATAT
*
1738775 TATATATATAT
1 TATGTATATAT
*
1738786 T-TTTCATATTAT
1 TATGT-ATA-TAT
1738798 TATGTATATAT
1 TATGTATATAT
1738809 GTTTTTAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
10 5 0.11
11 22 0.48
12 9 0.20
13 6 0.13
14 4 0.09
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (11 bp):
TATGTATATAT
Found at i:1739070 original size:3 final size:3
Alignment explanation
Indices: 1739062--1739087 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1739052 TAATTTACTG
1739062 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
1739088 CACTATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1742611 original size:9 final size:9
Alignment explanation
Indices: 1742597--1742631 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1742587 ACTGCAGAAG
*
1742597 ACGAGGAGT
1 ACGAGGAAT
1742606 ACGAGGAAT
1 ACGAGGAAT
*
1742615 ATGAGGAAT
1 ACGAGGAAT
1742624 ACGAGGAA
1 ACGAGGAA
1742632 GAGGCTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.37, T:0.11
Consensus pattern (9 bp):
ACGAGGAAT
Found at i:1746836 original size:31 final size:31
Alignment explanation
Indices: 1746801--1746870 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
1746791 CTTAACAGCC
* *
1746801 TAGTGACTTGAATAAAAAATTTCAAATAGTT
1 TAGTGACTTAAATAAAAAATTTCAAATAATT
* * *
1746832 TAGTGACTTAAATGAAAACTTTTAAATAATT
1 TAGTGACTTAAATAAAAAATTTCAAATAATT
1746863 TAGTGACT
1 TAGTGACT
1746871 ATTTTGTAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (31 bp):
TAGTGACTTAAATAAAAAATTTCAAATAATT
Found at i:1747703 original size:32 final size:30
Alignment explanation
Indices: 1747661--1747722 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1747651 AAAGATTGAT
* *
1747661 TAATAACCAAATTTAACTGAATAAAAAAAGAA
1 TAATAACCAAA-TTAAC-CAAAAAAAAAAGAA
*
1747693 TAATACCCAAATTAACCAAAAAAAAAAGAA
1 TAATAACCAAATTAACCAAAAAAAAAAGAA
1747723 GAAAATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 12 0.44
31 5 0.19
32 10 0.37
ACGTcount: A:0.65, C:0.13, G:0.05, T:0.18
Consensus pattern (30 bp):
TAATAACCAAATTAACCAAAAAAAAAAGAA
Found at i:1762732 original size:18 final size:16
Alignment explanation
Indices: 1762711--1762750 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 16
1762701 AAATATAACG
1762711 ATATATAAAAATAATACT
1 ATATATAAAAA-AATA-T
1762729 ATATAT-AAAAAATAT
1 ATATATAAAAAAATAT
1762744 ATATATA
1 ATATATA
1762751 CCCATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 4 0.19
17 4 0.19
18 6 0.29
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATATAAAAAAATAT
Found at i:1762779 original size:22 final size:23
Alignment explanation
Indices: 1762724--1762793 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
1762714 TATAAAAATA
*
1762724 ATACTATATATAAAAAATATATAT
1 ATACTA-ATATAATAAATATATAT
**
1762748 ATACCCATATAATAAA-ATATAT
1 ATACTAATATAATAAATATATAT
* *
1762770 GTACTAATATTAAT-AATAAATAT
1 ATACTAATA-TAATAAATATATAT
1762793 A
1 A
1762794 ATAGGGATAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
22 14 0.39
23 18 0.50
24 4 0.11
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (23 bp):
ATACTAATATAATAAATATATAT
Found at i:1762793 original size:43 final size:41
Alignment explanation
Indices: 1762694--1762794 Score: 105
Period size: 43 Copynumber: 2.4 Consensus size: 41
1762684 ATAGTAGGTA
*
1762694 TAATAATAAATATAACGATATATAAAAATAATACTATATAT
1 TAATAATAAATATAACCATATATAAAAATAATACTATATAT
* * * *
1762735 AAAAAATATATATATACCCATATAATAAAATATATGTACTA-ATAT
1 TAATAATA-A-ATATAACCATAT-ATAAAA-ATA-ATACTATATAT
1762780 TAATAATAAATATAA
1 TAATAATAAATATAA
1762795 TAGGGATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
41 6 0.13
42 1 0.02
43 15 0.32
44 7 0.15
45 13 0.28
46 5 0.11
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (41 bp):
TAATAATAAATATAACCATATATAAAAATAATACTATATAT
Found at i:1762863 original size:27 final size:28
Alignment explanation
Indices: 1762817--1762873 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 28
1762807 AGATATAATA
* *
1762817 ATATATACATAATATGGTATT-AAAAAT
1 ATATATACATAACATAGTATTCAAAAAT
* *
1762844 ATATATACGTAACATAGTATTCAAGAAT
1 ATATATACATAACATAGTATTCAAAAAT
1762872 AT
1 AT
1762874 GTACATGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (28 bp):
ATATATACATAACATAGTATTCAAAAAT
Found at i:1762953 original size:9 final size:10
Alignment explanation
Indices: 1762940--1762973 Score: 54
Period size: 9 Copynumber: 3.6 Consensus size: 10
1762930 AACATTAAAA
1762940 ATATATATA-
1 ATATATATAC
1762949 ATATATATAC
1 ATATATATAC
1762959 A-ATATATAC
1 ATATATATAC
1762968 ATATAT
1 ATATAT
1762974 TTAGAAATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATATAC
Found at i:1763068 original size:21 final size:23
Alignment explanation
Indices: 1763019--1763071 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
1763009 CATACGCTAC
1763019 ATAATTAATCTTAATAAAACTAAA
1 ATAATTAATCTTAAT-AAACTAAA
1763043 ATAATTAATCTTAAT-AA-TAAA
1 ATAATTAATCTTAATAAACTAAA
*
1763064 GTAATTAA
1 ATAATTAA
1763072 AAAGGATCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 11 0.39
22 2 0.07
24 15 0.54
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAATTAATCTTAATAAACTAAA
Found at i:1764129 original size:29 final size:27
Alignment explanation
Indices: 1764095--1764155 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 27
1764085 AAAATGGGGT
1764095 TTGGGCTTCTGTTGGGTTAATTTTGAGTG
1 TTGGGCTTC--TTGGGTTAATTTTGAGTG
1764124 TTGGG---CTTGGGTTAATTTTGAGTG
1 TTGGGCTTCTTGGGTTAATTTTGAGTG
*
1764148 TTGAGCTT
1 TTGGGCTT
1764156 GAGTAGGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
24 22 0.79
26 1 0.04
29 5 0.18
ACGTcount: A:0.11, C:0.07, G:0.34, T:0.48
Consensus pattern (27 bp):
TTGGGCTTCTTGGGTTAATTTTGAGTG
Found at i:1764133 original size:24 final size:24
Alignment explanation
Indices: 1764106--1764156 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1764096 TGGGCTTCTG
*
1764106 TTGGGTTAATTTTGAGTGTTGGGC
1 TTGGGTTAATTTTGAGTGTTGAGC
1764130 TTGGGTTAATTTTGAGTGTTGAGC
1 TTGGGTTAATTTTGAGTGTTGAGC
1764154 TTG
1 TTG
1764157 AGTAGGTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.14, C:0.04, G:0.35, T:0.47
Consensus pattern (24 bp):
TTGGGTTAATTTTGAGTGTTGAGC
Found at i:1766021 original size:17 final size:17
Alignment explanation
Indices: 1765979--1766022 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1765969 TGCTTTTTTC
1765979 TAAAATAAATGCAAAAAA
1 TAAAA-AAATGCAAAAAA
** *
1765997 CGAGAAAATGCAAAAAA
1 TAAAAAAATGCAAAAAA
1766014 TAAAAAAAT
1 TAAAAAAAT
1766023 AGTAAAAAAA
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
17 18 0.90
18 2 0.10
ACGTcount: A:0.70, C:0.07, G:0.09, T:0.14
Consensus pattern (17 bp):
TAAAAAAATGCAAAAAA
Found at i:1769853 original size:21 final size:23
Alignment explanation
Indices: 1769828--1769871 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1769818 AATTTAAAAA
1769828 TACTTT-T-AAAATAATATTTAT
1 TACTTTGTAAAAATAATATTTAT
1769849 TACTTTGTAAAAATAATATTTAT
1 TACTTTGTAAAAATAATATTTAT
1769872 AACTCCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (23 bp):
TACTTTGTAAAAATAATATTTAT
Found at i:1769884 original size:23 final size:23
Alignment explanation
Indices: 1769835--1769885 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1769825 AAATACTTTT
* ***
1769835 AAAATAATATTTATTACTTTGTA
1 AAAATAATATTTATAACTCCATA
*
1769858 AAAATAATATTTATAACTCCATC
1 AAAATAATATTTATAACTCCATA
1769881 AAAAT
1 AAAAT
1769886 CTTAATAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (23 bp):
AAAATAATATTTATAACTCCATA
Found at i:1773568 original size:15 final size:15
Alignment explanation
Indices: 1773534--1773588 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
1773524 ATATGTTCTG
* *
1773534 ATTGAAATGGTAAA-
1 ATTGAGATGTTAAAC
1773548 ATTGAGATGTTAAAC
1 ATTGAGATGTTAAAC
1773563 ATTGAGATGTTAAAC
1 ATTGAGATGTTAAAC
*
1773578 ATTGTGATGTT
1 ATTGAGATGTT
1773589 TTAGCTTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
14 12 0.32
15 25 0.68
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (15 bp):
ATTGAGATGTTAAAC
Found at i:1774377 original size:232 final size:229
Alignment explanation
Indices: 1773700--1774379 Score: 803
Period size: 232 Copynumber: 2.9 Consensus size: 229
1773690 GAATAAATTG
* * *
1773700 GAATGTATTCTTATTTATTAATAGGTTTTGGGTTCACGTGACTTGCAGTGGCAAACGCTTGTCAA
1 GAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTGTCAA
* * * *
1773765 AAAGTATTTATAATTAATCAGATAGGCGGTTTTGCG-TTATTGTTAAGG-ATTTTAGGTTTTTAT
66 AAAGTATTTGTAATTAATCA-ATAGGCGATTTTG-GTTTATTATT-AGGAATTTTAGATTTTTAT
* * *
1773828 TGGATAATGGGAAGTTTTAAATTTCAAGATTTGTTTGAAATATTTAATAATGTGATTTACAATAA
128 TGGATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAAT-TGATTTATAATAA
* * *
1773893 TGAGG-TTATTTTTTTCATTTGGTAATAGGTCTTTTATTG
192 TGAGGTTTA-TTTTTT-ATTTGTTAATAGGTCTTTTACTA
* * * * *
1773932 GAATGTTTTCTTATTTATTGATAGGTTTTCAGTTCACATGACTCACGGTGGCAAACGCTTGTCAA
1 GAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTGTCAA
* * * * * *
1773997 AAAGTATTTGTAACTAATTCAATATGC-AGTTTCGGTTTATTATTAGGAATCTTCGATTTTAATT
66 AAAGTATTTGTAATTAA-TCAATAGGCGA-TTTTGGTTTATTATTAGGAATTTTAGATTTTTATT
* * *
1774061 GGATAATGGGAAGTTTCAAATTTCAAGATTTGTTCAAAATATTTAATAATTTGATTTTTAATATT
129 GGATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAA-TTGATTTATAATAAT
* * ** *
1774126 GAGGTTCAGTTTTTATTTGTTAATATTTTTTTTCACTA
193 GAGGTTTATTTTTTATTTGTTAATAGGTCTTTT-ACTA
* *** * **
1774164 GAATGTATTCTTATTTATTAATAGGTTTTTGGTTCACATGACTCGCAACAGTAAATACTTGTCAA
1 GAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTGTCAA
*
1774229 AAAGTATTTGTAATTAATCATATAGGCGATTTTGGTTTATTATTAGGAATTTTATGTTTTTTATT
66 AAAGTATTTGTAATTAATCA-ATAGGCGATTTTGGTTTATTATTAGGAATTTTA-GATTTTTATT
* * * * *
1774294 AGATAATAGAAAGTTTCGAATATCAAGATTTGTTTAAAATATTTAATAACTTGATTTATAATAAT
129 GGATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAA-TTGATTTATAATAAT
1774359 G-GGTTTATTTTTTATTTGTTA
193 GAGGTTTATTTTTTATTTGTTA
1774380 CTTTGGTATT
Statistics
Matches: 376, Mismatches: 62, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
231 22 0.06
232 282 0.75
233 72 0.19
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (229 bp):
GAATGTATTCTTATTTATTAATAGGTTTTCGGTTCACATGACTCGCAGTGGCAAACGCTTGTCAA
AAAGTATTTGTAATTAATCAATAGGCGATTTTGGTTTATTATTAGGAATTTTAGATTTTTATTGG
ATAATGGGAAGTTTCAAATTTCAAGATTTGTTTAAAATATTTAATAATTGATTTATAATAATGAG
GTTTATTTTTTATTTGTTAATAGGTCTTTTACTA
Found at i:1775891 original size:76 final size:77
Alignment explanation
Indices: 1775783--1775928 Score: 206
Period size: 78 Copynumber: 1.9 Consensus size: 77
1775773 ATAAGGGCAC
* *
1775783 TATAATAAGTTTAAATAAGAGATGAAATTATGCTAAA-TCAAA-AAAAAAATTAAATCTCAAATT
1 TATAATAAGTTTAAATAAGAGATGAAACTATGCCAAATTCAAATAAAAAAATTAAATCTCAAATT
1775846 TGAACTTGAAAA
66 TGAACTTGAAAA
* * * * *
1775858 TATAATAAGTTTAGATAAAGAGATGAAACTATGCCAAATTGAAATAAAAGAATTTACTCTCAAAT
1 TATAATAAGTTTAAAT-AAGAGATGAAACTATGCCAAATTCAAATAAAAAAATTAAATCTCAAAT
1775923 TTGAAC
65 TTGAAC
1775929 ATAAGTTGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
75 15 0.25
76 19 0.31
77 4 0.07
78 23 0.38
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.29
Consensus pattern (77 bp):
TATAATAAGTTTAAATAAGAGATGAAACTATGCCAAATTCAAATAAAAAAATTAAATCTCAAATT
TGAACTTGAAAA
Found at i:1777591 original size:30 final size:31
Alignment explanation
Indices: 1777551--1777609 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
1777541 CTTGTTAGGA
*
1777551 GTAACTGTCTTACAGTTAGT-TGGTTAGCTTT
1 GTAACTGTCTT-CAGTTAATATGGTTAGCTTT
*
1777582 GTAAC-GTCTTTAGTTAATATGGTTAGCT
1 GTAACTGTCTTCAGTTAATATGGTTAGCT
1777610 GTTAGCTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 14 0.56
31 5 0.20
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (31 bp):
GTAACTGTCTTCAGTTAATATGGTTAGCTTT
Found at i:1782124 original size:30 final size:31
Alignment explanation
Indices: 1782084--1782142 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
1782074 CATGTTAGGA
*
1782084 GTAACTGTCTTACAGTTAGT-TGGTTAGCTTT
1 GTAACTGTCTT-CAGTTAATATGGTTAGCTTT
*
1782115 GTAAC-GTCTTTAGTTAATATGGTTAGCT
1 GTAACTGTCTTCAGTTAATATGGTTAGCT
1782143 GTTAGCTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.24
30 14 0.56
31 5 0.20
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.44
Consensus pattern (31 bp):
GTAACTGTCTTCAGTTAATATGGTTAGCTTT
Found at i:1799919 original size:69 final size:69
Alignment explanation
Indices: 1799808--1799943 Score: 254
Period size: 69 Copynumber: 2.0 Consensus size: 69
1799798 GTATTCCTCA
1799808 AATTTCCATAATCCCTTGGATTGTAGGATTTTTTCTATAATTATGCAGATTTTCTTTTACTCTGT
1 AATTTCCATAATCCCTTGGATTGTAGGATTTTTTCTATAATTATGCAGATTTTCTTTTACTCTGT
1799873 TTCC
66 TTCC
**
1799877 AATTTCCATAATCCCTTGGATTGTAGGATTTTTTCTATAATTATGGGGATTTTCTTTTACTCTGT
1 AATTTCCATAATCCCTTGGATTGTAGGATTTTTTCTATAATTATGCAGATTTTCTTTTACTCTGT
1799942 TT
66 TT
1799944 ACTTACATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.50
Consensus pattern (69 bp):
AATTTCCATAATCCCTTGGATTGTAGGATTTTTTCTATAATTATGCAGATTTTCTTTTACTCTGT
TTCC
Found at i:1801151 original size:109 final size:112
Alignment explanation
Indices: 1800931--1801152 Score: 324
Period size: 109 Copynumber: 2.0 Consensus size: 112
1800921 TGAATTTAGC
* * * *
1800931 CCTCATGTATCCCCTTTCAGTCAATTTAGGTATTATAGTATTATTATTCTTTTTTGAGCTAAATT
1 CCTCATGTATACACTTTCAATCAATTTAGCTATTATAGTA-TATTATTCTTTTTTGAGCTAAATT
* * * *
1800996 TGACTGATTAACCTTTCAAAAAGTGTCCAATTGCTTTTCTTTAATGGA
65 TGACTGATTAACCTTTCAAAAAATATCAAATTACTTTTCTTTAATGGA
*
1801044 CCTCATGTATACACTTTCAATCAATTTAGCTATTATAG-A-ATTATTCTTTTTTGAGTTAAATTT
1 CCTCATGTATACACTTTCAATCAATTTAGCTATTATAGTATATTATTCTTTTTTGAGCTAAATTT
*
1801107 GACT-ATTAACCTTTCAAAAAATATCAAATTATTTTTCTTTAATGGA
66 GACTGATTAACCTTTCAAAAAATATCAAATTACTTTTCTTTAATGGA
1801153 AATACTAACT
Statistics
Matches: 99, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
109 37 0.37
110 27 0.27
112 1 0.01
113 34 0.34
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (112 bp):
CCTCATGTATACACTTTCAATCAATTTAGCTATTATAGTATATTATTCTTTTTTGAGCTAAATTT
GACTGATTAACCTTTCAAAAAATATCAAATTACTTTTCTTTAATGGA
Found at i:1805512 original size:22 final size:22
Alignment explanation
Indices: 1805487--1805532 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1805477 GATATTTGTG
* * *
1805487 TTTGCAAACTACTCAAATTTAA
1 TTTGAAAAATACTCAAATTCAA
*
1805509 TTTGAAAAATATTCAAATTCAA
1 TTTGAAAAATACTCAAATTCAA
1805531 TT
1 TT
1805533 CCGTAATATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (22 bp):
TTTGAAAAATACTCAAATTCAA
Found at i:1806748 original size:33 final size:33
Alignment explanation
Indices: 1806706--1806772 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1806696 CAGATATTGC
1806706 AGTGAAAAATAAAAGCCGTAGGAGTTAAAGTAT
1 AGTGAAAAATAAAAGCCGTAGGAGTTAAAGTAT
1806739 AGTGAAAAATAAAAGCCGTAGGAGTTAAAGTAT
1 AGTGAAAAATAAAAGCCGTAGGAGTTAAAGTAT
1806772 A
1 A
1806773 CTTACTTCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.49, C:0.06, G:0.24, T:0.21
Consensus pattern (33 bp):
AGTGAAAAATAAAAGCCGTAGGAGTTAAAGTAT
Found at i:1810663 original size:14 final size:15
Alignment explanation
Indices: 1810644--1810676 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1810634 AGTTTCAAAT
1810644 TTATGGATGAAGC-A
1 TTATGGATGAAGCAA
1810658 TTATGGATGAAGCAA
1 TTATGGATGAAGCAA
1810673 TTAT
1 TTAT
1810677 CAAAGGATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (15 bp):
TTATGGATGAAGCAA
Found at i:1812000 original size:45 final size:45
Alignment explanation
Indices: 1811914--1812002 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
1811904 ACCCGATCGA
* *
1811914 GGTTTCATTCCATGATCAATGATCAATCCATCATTGTGGGGGGGG
1 GGTTTCATTCCATGATCAATGATCAATCCATCATGGGGGGGGGGG
1811959 GGTTTCATTCCATGATCAAATGATCAATCCATCA-GGGGGGGGGG
1 GGTTTCATTCCATGATC-AATGATCAATCCATCATGGGGGGGGGG
1812003 AAGCCTCCAC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 25 0.61
46 16 0.39
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (45 bp):
GGTTTCATTCCATGATCAATGATCAATCCATCATGGGGGGGGGGG
Found at i:1812001 original size:46 final size:45
Alignment explanation
Indices: 1811914--1812002 Score: 142
Period size: 46 Copynumber: 2.0 Consensus size: 45
1811904 ACCCGATCGA
** *
1811914 GGTTTCATTCCATGATCAATGATCAATCCATCATTGTGGGGGGGG
1 GGTTTCATTCCATGATCAATGATCAATCCATCAGGGGGGGGGGGG
1811959 GGTTTCATTCCATGATCAAATGATCAATCCATCAGGGGGGGGGG
1 GGTTTCATTCCATGATC-AATGATCAATCCATCAGGGGGGGGGG
1812003 AAGCCTCCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 17 0.43
46 23 0.57
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (45 bp):
GGTTTCATTCCATGATCAATGATCAATCCATCAGGGGGGGGGGGG
Found at i:1815104 original size:20 final size:20
Alignment explanation
Indices: 1815079--1815122 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
1815069 ACTACTACAT
1815079 GATTAATTAATTATTCATTA
1 GATTAATTAATTATTCATTA
1815099 GATTAATTAATTATTCATTA
1 GATTAATTAATTATTCATTA
1815119 GATT
1 GATT
1815123 TTCTACTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.50
Consensus pattern (20 bp):
GATTAATTAATTATTCATTA
Found at i:1819289 original size:46 final size:46
Alignment explanation
Indices: 1819222--1819396 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
1819212 TGTAACCCGC
1819222 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
* *
1819268 CCATAAGTGAACTCTGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * ** *
1819318 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
1819361 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
1819397 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 62 0.58
47 25 0.23
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:1819342 original size:93 final size:93
Alignment explanation
Indices: 1819230--1819400 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
1819220 GCCCATAAGT
** * *
1819230 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCTGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1819295 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
1819323 GAACTCGGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
1819388 CGAGTTCGGATGC
66 CGAGCTCGGATGC
1819401 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:1823027 original size:15 final size:17
Alignment explanation
Indices: 1822997--1823029 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1822987 TAAAAAATTT
1822997 AAAATTATTCAAAAATA
1 AAAATTATTCAAAAATA
1823014 AAAATTA-T-AAAAATA
1 AAAATTATTCAAAAATA
1823029 A
1 A
1823030 TTAAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATTATTCAAAAATA
Found at i:1827493 original size:45 final size:44
Alignment explanation
Indices: 1827441--1827642 Score: 268
Period size: 45 Copynumber: 4.6 Consensus size: 44
1827431 CGGGCTTCGG
*
1827441 GCCTAGCAGGCTATGATGCCGGTGAAATACTATTCGGGCCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATA-TATTCGGGCCTTTGA
* *
1827486 GCCTAGCAGGCTATGATGCCGGTGAGATATCATTCGGGCCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATAT-ATTCGGGCCTTTGA
*
1827531 GCCTAGCAGGCTATAATGCCGGTGAGATACTATTCGGG-CTTTCGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATA-TATTCGGGCCTTT-GA
* *
1827576 GCCTAGCAGGTTATAATGCCGGTGAAATGATA-TCGGGCC-TCGA
1 GCCTAGCAGGCTATAATGCCGGTGAAAT-ATATTCGGGCCTTTGA
*
1827619 GCCTAGCAGGCGA-AATGCCGGTGA
1 GCCTAGCAGGCTATAATGCCGGTGA
1827643 TTAGAGAAAA
Statistics
Matches: 145, Mismatches: 7, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
42 11 0.08
43 13 0.09
44 11 0.08
45 108 0.74
46 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.24
Consensus pattern (44 bp):
GCCTAGCAGGCTATAATGCCGGTGAAATATATTCGGGCCTTTGA
Found at i:1827595 original size:90 final size:88
Alignment explanation
Indices: 1827422--1827642 Score: 295
Period size: 90 Copynumber: 2.5 Consensus size: 88
1827412 TGTTTATCAA
* * * *
1827422 AAATGATATCGGGCTTCGGGCCTAGCAGGCTATGATGCCGGTGAAATACTATTCGGGCCTTTGAG
1 AAATCATATCGGGCCTCGAGCCTAGCAGGCTATAATGCCGGTGAAATACTATTCGGGCCTTTGAG
*
1827487 CCTAGCAGGCTATGATGCCGGTG
66 CCTAGCAGGCTATAATGCCGGTG
* *
1827510 AGATATCAT-TCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATACTATTCGGG-CTTT
1 A-A-ATCATATCGGGCC-TCGAGCCTAGCAGGCTATAATGCCGGTGAAATACTATTCGGGCCTTT
*
1827573 CGAGCCTAGCAGGTTATAATGCCGGTG
63 -GAGCCTAGCAGGCTATAATGCCGGTG
* *
1827600 AAATGATATCGGGCCTCGAGCCTAGCAGGCGA-AATGCCGGTGA
1 AAATCATATCGGGCCTCGAGCCTAGCAGGCTATAATGCCGGTGA
1827643 TTAGAGAAAA
Statistics
Matches: 117, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
87 11 0.09
88 20 0.17
89 19 0.16
90 67 0.57
ACGTcount: A:0.23, C:0.22, G:0.31, T:0.24
Consensus pattern (88 bp):
AAATCATATCGGGCCTCGAGCCTAGCAGGCTATAATGCCGGTGAAATACTATTCGGGCCTTTGAG
CCTAGCAGGCTATAATGCCGGTG
Found at i:1828412 original size:30 final size:30
Alignment explanation
Indices: 1828345--1828405 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
1828335 TGTGAAAAGA
1828345 AAAGTTTTAAATTGATTGAAATTTTTCGGC
1 AAAGTTTTAAATTGATTGAAATTTTTCGGC
*
1828375 AAAGTTTTAAATTGATTGAAATTTTTTGGC
1 AAAGTTTTAAATTGATTGAAATTTTTCGGC
1828405 A
1 A
1828406 CGGTTTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.44
Consensus pattern (30 bp):
AAAGTTTTAAATTGATTGAAATTTTTCGGC
Found at i:1830769 original size:14 final size:14
Alignment explanation
Indices: 1830750--1830777 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1830740 CCTCACAATA
1830750 ATGTTATCTCTAGG
1 ATGTTATCTCTAGG
1830764 ATGTTATCTCTAGG
1 ATGTTATCTCTAGG
1830778 GAGAGAATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (14 bp):
ATGTTATCTCTAGG
Found at i:1838670 original size:21 final size:19
Alignment explanation
Indices: 1838641--1838679 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1838631 TTTCTTCTAA
1838641 TAATATTATTGAAAAGTAAC
1 TAATATTATT-AAAAGTAAC
*
1838661 TAATCATTATTTAAAGTAA
1 TAAT-ATTATTAAAAGTAA
1838680 ACTGACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (19 bp):
TAATATTATTAAAAGTAAC
Found at i:1838953 original size:13 final size:12
Alignment explanation
Indices: 1838933--1838962 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
1838923 TTTTTAATTT
1838933 AAATTTTAAAAA
1 AAATTTTAAAAA
1838945 AAATATTTAAAAA
1 AAAT-TTTAAAAA
1838958 AAATT
1 AAATT
1838963 GGTGATCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATTTTAAAAA
Found at i:1843622 original size:96 final size:96
Alignment explanation
Indices: 1843461--1843791 Score: 644
Period size: 96 Copynumber: 3.4 Consensus size: 96
1843451 CACTTTGTTA
*
1843461 TTATAGTGGAATTTATTATTGCCTCTACTTGTAGATGTAGGTTTTAAGTTCGTTGAATCATGTGT
1 TTAT-GTGAAATTTATTATTGCCTCTACTTGTAGATGTAGGTTTTAAGTTCGTTGAATCATGTGT
1843526 TTCCTATTATTTATGGTCATATTTCCTTTTAT
65 TTCCTATTATTTATGGTCATATTTCCTTTTAT
1843558 TTATGTGAAATTTATTATTGCCTCTACTTGTAGATGTAGGTTTTAAGTTCGTTGAATCATGTGTT
1 TTATGTGAAATTTATTATTGCCTCTACTTGTAGATGTAGGTTTTAAGTTCGTTGAATCATGTGTT
1843623 TCCTATTATTTATGGTCATATTTCCTTTTAT
66 TCCTATTATTTATGGTCATATTTCCTTTTAT
1843654 TTATGTGAAATTTATTATTGCCTCTACTTGTAGATGTAGGTTTTAAGTTCGTTGAATCATGTGTT
1 TTATGTGAAATTTATTATTGCCTCTACTTGTAGATGTAGGTTTTAAGTTCGTTGAATCATGTGTT
1843719 TCCTATTATTTATGGTCATATTTCCTTTTAT
66 TCCTATTATTTATGGTCATATTTCCTTTTAT
1843750 TTATGTGAAATTTATTATTGCCTCTACTTGTAGATGTAGGTT
1 TTATGTGAAATTTATTATTGCCTCTACTTGTAGATGTAGGTT
1843792 ACTTGCATGA
Statistics
Matches: 233, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
96 229 0.98
97 4 0.02
ACGTcount: A:0.22, C:0.11, G:0.16, T:0.50
Consensus pattern (96 bp):
TTATGTGAAATTTATTATTGCCTCTACTTGTAGATGTAGGTTTTAAGTTCGTTGAATCATGTGTT
TCCTATTATTTATGGTCATATTTCCTTTTAT
Found at i:1846300 original size:16 final size:16
Alignment explanation
Indices: 1846281--1846326 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
1846271 ACTTGTTCCA
1846281 AACATGAGTTGTTTTG
1 AACATGAGTTGTTTTG
*
1846297 AACAT-AGTTGTTTTT
1 AACATGAGTTGTTTTG
*
1846312 AACAAGAGTTGTTTT
1 AACATGAGTTGTTTT
1846327 ATGGTGATGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.46
Consensus pattern (16 bp):
AACATGAGTTGTTTTG
Found at i:1846327 original size:15 final size:15
Alignment explanation
Indices: 1846281--1846327 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1846271 ACTTGTTCCA
*
1846281 AACATGAGTTGTTTT
1 AACAAGAGTTGTTTT
*
1846296 GAAC-ATAGTTGTTTTT
1 -AACAAGAGTTG-TTTT
1846312 AACAAGAGTTGTTTT
1 AACAAGAGTTGTTTT
1846327 A
1 A
1846328 TGGTGATGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (15 bp):
AACAAGAGTTGTTTT
Found at i:1854221 original size:19 final size:17
Alignment explanation
Indices: 1854199--1854246 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
1854189 AAAAACAACC
1854199 TTGTAATAAATAATTTATT
1 TTGTAATAAATAA--TATT
1854218 TTGTATATAAAATAATATT
1 TTGTA-AT-AAATAATATT
1854237 TT-TAATAAAT
1 TTGTAATAAAT
1854247 TTTAATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.15
17 2 0.07
18 2 0.07
19 11 0.41
20 2 0.07
21 6 0.22
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTGTAATAAATAATATT
Found at i:1871282 original size:31 final size:30
Alignment explanation
Indices: 1871247--1871307 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
1871237 GAAACAGAAT
*
1871247 GAAAGCAAACGAAAC-AGAGAAGAACAGGGGA
1 GAAAG-AAACGAAACAAGA-AAGAAAAGGGGA
* *
1871278 GAAAGAAAGGAAAGAAGAAAGAAAAGGGGA
1 GAAAGAAACGAAACAAGAAAGAAAAGGGGA
1871308 AATAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.59, C:0.07, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAACGAAACAAGAAAGAAAAGGGGA
Found at i:1871868 original size:39 final size:39
Alignment explanation
Indices: 1871761--1871895 Score: 123
Period size: 39 Copynumber: 3.4 Consensus size: 39
1871751 GACCTCGAGT
* * *
1871761 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGCTAG-TC
** ** *
1871802 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
*
1871840 CGATGAGACACTGGGTGTCAACTATTACTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTATTACTTCG-GCTAGTC
*
1871879 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
1871896 CCATATTGGT
Statistics
Matches: 76, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
38 19 0.25
39 36 0.47
40 4 0.05
41 15 0.20
42 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGCTAGTC
Found at i:1873505 original size:131 final size:129
Alignment explanation
Indices: 1873271--1873600 Score: 477
Period size: 131 Copynumber: 2.6 Consensus size: 129
1873261 CTATTCATTC
*
1873271 AAAAATTCTTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCAGGGAATCGTGCCCTA-TCGT
1 AAAAATTC-TTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTACT-GT
* **
1873335 GCTGGGTTGCAATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTGGAATTTCACTCATGTCT
64 GCTGGGTTGCAATTTCCCGTTTGCTCAAAATAATCGAATATTCCTTTAAAATTTCACTCATGT-T
1873400 TT
128 TT
* *
1873402 AAAAATTCTTCAAAACGAAGGAAATGTTTGGTGTTTGGCAATTCGGGGAATCGTGCCCTACTGTG
1 AAAAATTCTT-AAAACGAAGGAAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTACTGTG
1873467 CTGGGTTGCAATTTCCCGTTTGCTCAAAATAATCGAATATTCCTTTAAAATTTCACTCATGTTTT
65 CTGGGTTGCAATTTCCCGTTTGCTCAAAATAATCGAATATTCCTTTAAAATTTCACTCATGTTTT
** * * * * **
1873532 CTAAATTC-TAAAAC-AAAGCAATGTTCAATGTTTGGAAATTCGGGGAATCGTGCCCTACCATGC
1 AAAAATTCTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTACTGTGC
1873595 TGGGTT
66 TGGGTT
1873601 TCGATTTTTT
Statistics
Matches: 181, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
127 47 0.26
128 5 0.03
129 1 0.01
130 11 0.06
131 116 0.64
132 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (129 bp):
AAAAATTCTTAAAACGAAGGAAATGTTCGATGTTTGGCAATTCGGGGAATCGTGCCCTACTGTGC
TGGGTTGCAATTTCCCGTTTGCTCAAAATAATCGAATATTCCTTTAAAATTTCACTCATGTTTT
Found at i:1888425 original size:24 final size:24
Alignment explanation
Indices: 1888401--1888449 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1888391 TTGGAAGGTT
1888401 TTTA-CTCTGCT-GTTTTGGCACG
1 TTTATCTCTGCTAGTTTTGGCACG
* *
1888423 TTTATGTCTGCTATTTTTGGCACG
1 TTTATCTCTGCTAGTTTTGGCACG
1888447 TTT
1 TTT
1888450 CTTAGGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 6 0.26
24 13 0.57
ACGTcount: A:0.10, C:0.18, G:0.20, T:0.51
Consensus pattern (24 bp):
TTTATCTCTGCTAGTTTTGGCACG
Found at i:1908701 original size:22 final size:23
Alignment explanation
Indices: 1908673--1908716 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1908663 CAAAAAGTTA
1908673 AAAAGTTATCATTGAA-TTATTC
1 AAAAGTTATCATTGAAGTTATTC
* *
1908695 AAAAGTTTTCATTTAAGTTATT
1 AAAAGTTATCATTGAAGTTATT
1908717 TTGGTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (23 bp):
AAAAGTTATCATTGAAGTTATTC
Found at i:1909958 original size:15 final size:15
Alignment explanation
Indices: 1909911--1909958 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1909901 CTAAAATGGT
*
1909911 AATTTTAAAATTTAA
1 AATTTTAAATTTTAA
**
1909926 TTTTTTATAATTTATAA
1 AATTTTA-AATTT-TAA
1909943 AATTTTAAATTTTAA
1 AATTTTAAATTTTAA
1909958 A
1 A
1909959 TTAATAATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 9 0.35
16 9 0.35
17 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATTTTAAATTTTAA
Found at i:1912729 original size:30 final size:30
Alignment explanation
Indices: 1912695--1912756 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1912685 CATTAATTAA
1912695 TTGTTCTGATAAAATCGATATATTGAAAAT
1 TTGTTCTGATAAAATCGATATATTGAAAAT
1912725 TTGTTCTGATAAAATCGATATATTGAAAAT
1 TTGTTCTGATAAAATCGATATATTGAAAAT
1912755 TT
1 TT
1912757 TTTTGGTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (30 bp):
TTGTTCTGATAAAATCGATATATTGAAAAT
Found at i:1916503 original size:14 final size:14
Alignment explanation
Indices: 1916486--1916520 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1916476 TGTTGTCATT
1916486 TTATTATCATATTG
1 TTATTATCATATTG
**
1916500 TTATTATTTTATTG
1 TTATTATCATATTG
1916514 TTATTAT
1 TTATTAT
1916521 TTAGATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (14 bp):
TTATTATCATATTG
Found at i:1916521 original size:14 final size:14
Alignment explanation
Indices: 1916495--1916522 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1916485 TTTATTATCA
1916495 TATTGTTATTATTT
1 TATTGTTATTATTT
1916509 TATTGTTATTATTT
1 TATTGTTATTATTT
1916523 AGATATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (14 bp):
TATTGTTATTATTT
Found at i:1916588 original size:31 final size:31
Alignment explanation
Indices: 1916550--1916610 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1916540 TATTTTATTA
*
1916550 TTAATTTTGCTATTATTTTAAAAGTATTTGC
1 TTAATTTTGCTACTATTTTAAAAGTATTTGC
*
1916581 TTAATTTTGCTACTATTTTAGAAGTATTTG
1 TTAATTTTGCTACTATTTTAAAAGTATTTG
1916611 TTTATTAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.11, T:0.54
Consensus pattern (31 bp):
TTAATTTTGCTACTATTTTAAAAGTATTTGC
Found at i:1917135 original size:22 final size:19
Alignment explanation
Indices: 1917087--1917127 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1917077 TTCACCGCTA
1917087 CTATTTTTCAGAACAATTC
1 CTATTTTTCAGAACAATTC
1917106 CTATTTTTCAGAACAATTC
1 CTATTTTTCAGAACAATTC
1917125 CTA
1 CTA
1917128 ATATTTTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (19 bp):
CTATTTTTCAGAACAATTC
Found at i:1919021 original size:121 final size:121
Alignment explanation
Indices: 1918806--1919023 Score: 305
Period size: 121 Copynumber: 1.8 Consensus size: 121
1918796 CTCATGCATT
* * * * *
1918806 TGAAATTTCAAAAGGATATTTGGCTATCTGGTCAAACGGTAAGTCGAAACCTAGCACGATTGGGT
1 TGAAACTTCAAAAGGATATTTAGCTATCTGGTCAAACGGAAAATCGAAACCTAGCACGATTGGGC
* **
1918871 ACGATTTCTCGAATTTCTAAATGCAAAATATTGCCTCAAATTTAAGAAAACATGAA
66 ACGATTTCTCGAATTTCCAAACACAAAATATTGCCTCAAATTTAAGAAAACATGAA
* *
1918927 TGAAACTTCAAAAGGATATTTAGTTAT-TCGGTCAAACGGAAAATCGAAACTTAGCACG-TTAGG
1 TGAAACTTCAAAAGGATATTTAGCTATCT-GGTCAAACGGAAAATCGAAACCTAGCACGATT-GG
*
1918990 GCACGATTTCTCGAATTTCCAAACACGAAATATT
64 GCACGATTTCTCGAATTTCCAAACACAAAATATT
1919024 TTCTTATTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
120 3 0.04
121 81 0.96
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (121 bp):
TGAAACTTCAAAAGGATATTTAGCTATCTGGTCAAACGGAAAATCGAAACCTAGCACGATTGGGC
ACGATTTCTCGAATTTCCAAACACAAAATATTGCCTCAAATTTAAGAAAACATGAA
Found at i:1922118 original size:98 final size:98
Alignment explanation
Indices: 1921947--1922137 Score: 280
Period size: 98 Copynumber: 1.9 Consensus size: 98
1921937 GACCTGACAC
1921947 GATCTCCTCTACTGTAACCTTAAAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAATCTC
1 GATCTCCTCTACTGTAACCTTAAAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAATCTC
*
1922012 AGGCAGATAGGATTACTATCTTCAATCTAATGT
66 AGGCAGATAGGATTACTAGCTTCAATCTAATGT
* * * * *
1922045 GATCTGCTCTACTGTAA-CTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTGTAA-CT
1 GATCTCCTCTACTGTAACCTT-AAAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAATC-
1922108 TCAGAG-AGATAGGATTACTAGCTTCAATCT
64 TCAG-GCAGATAGGATTACTAGCTTCAATCT
1922138 GCTCCGCTGT
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
97 4 0.05
98 79 0.94
99 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (98 bp):
GATCTCCTCTACTGTAACCTTAAAGAGATAAGATCCTTTATTTTAATCCACTCCACTATAATCTC
AGGCAGATAGGATTACTAGCTTCAATCTAATGT
Found at i:1922194 original size:46 final size:45
Alignment explanation
Indices: 1922046--1922601 Score: 240
Period size: 46 Copynumber: 12.7 Consensus size: 45
1922036 ATCTAATGTG
* * **
1922046 ATCTGCTCTACTGTAA-CTTCAGAGAGATAAGATCTTTTATT-TT-A
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-TTGAATTCTTCA
* * * * *
1922090 ATCCGCTCCACTGTAA-CTTCAGAGAGATAGGA-TT-ACTAGCTTCA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTTGAAT-TCTTCA
* *
1922134 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTGAAATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTG-AATTCTTCA
* * * *
1922180 GTCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATCTTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTGAATTC-TTCA
* * ** * *
1922226 GTCTGCTCCACTGTGATCTCAGGGAGATAAGACCTG-A---TGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTGAATTCTTCA
* * *
1922267 ATCTACTCTACTGTAA-CTTCAGGGAGATAAGATCCTT-TATT-TT-A
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TTGAATTCTTCA
** * * *
1922311 ATCCACTCCGCTGTAA-CTTCAGGGAGATAGGA--T-AGTGTCTTCA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTTGAAT-TCTTCA
* * *
1922354 ATCTGCTCCGCTGTAATCTGAGGGAGATAAGATTTGAAATTCTTTA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTG-AATTCTTCA
* * * ** * * *
1922400 GTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTG----GTGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTGAATTCTTCA
* * * *
1922441 ATCTGCTCTACTGTAA-CTTCAGAGAGAT-A-A---G-ATCCTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATTTGAATTCTTCA
* * * * *
1922480 ATCCGCTCCACTGTAATCTTAGGGAGATAGGA-TTG-CTATATTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTGAAT-TCTTCA
* * **
1922524 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTG-AATTCTTCA
* * *
1922570 GTCTGTTCCACCGTAATCTCAGGG-GAATAAGA
1 ATCTGCTCCACTGTAATCTCAGGGAG-ATAAGA
1922602 CCTTTTATGA
Statistics
Matches: 394, Mismatches: 82, Indels: 70
0.72 0.15 0.13
Matches are distributed among these distances:
36 1 0.00
39 24 0.06
40 6 0.02
41 54 0.14
42 4 0.01
43 33 0.08
44 116 0.29
45 13 0.03
46 138 0.35
47 5 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (45 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTGAATTCTTCA
Found at i:1922412 original size:174 final size:170
Alignment explanation
Indices: 1922181--1922604 Score: 595
Period size: 174 Copynumber: 2.5 Consensus size: 170
1922171 AATTCTTCGG
* * *
1922181 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAA-TCTTTCGGTCTGCTCCACTGTGATCT
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTT-GGTCTGTTCCACTGTAATCT
*
1922245 CAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGGGAGATAAGATCCTTTATTTT
65 CAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCC-----TTT
* * *
1922310 AATCCACTCCGCTGTAA-CTTCAGGGAGATAGGATAG-TGTCTTCAA
125 AATCCACTCCACTGTAATCTT-AGGGAGATAGGATAGCTATATTCAA
* * *
1922355 TCTGCTCCGCTGTAATCTGAGGGAGATAAGATTTGAAATTCTTTAGTCTGTTCCACTGTAATCTC
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATCTC
* * * *
1922420 AGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCG
66 AGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCA
*
1922485 CTCCACTGTAATCTTAGGGAGATAGGATTGCTATATTCAA
131 CTCCACTGTAATCTTAGGGAGATAGGATAGCTATATTCAA
* *
1922525 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTTGGTCTGTTCCACCGTAATCTC
1 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATCTC
1922590 AGGG-GAATAAGACCT
66 AGGGAG-ATAAGACCT
1922605 TTTATGATGA
Statistics
Matches: 225, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
169 32 0.14
170 83 0.37
174 105 0.47
175 5 0.02
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (170 bp):
TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTGTAATCTC
AGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAATCCA
CTCCACTGTAATCTTAGGGAGATAGGATAGCTATATTCAA
Found at i:1922507 original size:39 final size:42
Alignment explanation
Indices: 1922050--1922558 Score: 169
Period size: 44 Copynumber: 11.7 Consensus size: 42
1922040 AATGTGATCT
* * * *
1922050 GCTCTACTGTAA-CTTCAGAGAGATAAGATCTTTTATTTTAATCC
1 GCTCCACTGTAATCTT-AGGGAGATAAGATC-TATA-TTCAATCC
* * *
1922094 GCTCCACTGTAA-CTTCAGAGAGATAGGAT-TACTAGCTTCAATCT
1 GCTCCACTGTAATCTT-AGGGAGATAAGATCTA-TA--TTCAATCC
* * * * *
1922138 GCTCCGCTGTAATCTCAGGGAGATAAGATTTGAAATTC-TTCGGTC
1 GCTCCACTGTAATCTTAGGGAGATAAGATCT-ATATTCAATC---C
* * ** *
1922183 TGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATCTTTCGGTCT
1 -GCTCCACTGTAATCTTAGGGAGATAAGATCT---AT-ATTCAATCC
* * * * * * *
1922230 GCTCCACTGTGATCTCAGGGAGATAAGACCT-GATGCGATCT
1 GCTCCACTGTAATCTTAGGGAGATAAGATCTATATTCAATCC
* * * *
1922271 ACTCTACTGTAA-CTTCAGGGAGATAAGATCCTTTATTTTAATCC
1 GCTCCACTGTAATCTT-AGGGAGATAAGAT-CTATA-TTCAATCC
* * * * * * *
1922315 ACTCCGCTGTAA-CTTCAGGGAGATAGGATAGTGTCTTCAATCT
1 GCTCCACTGTAATCTT-AGGGAGATAAGAT-CTATATTCAATCC
* * * * * *
1922358 GCTCCGCTGTAATCTGAGGGAGATAAGATTTGAAATTCTTTAGTCT
1 GCTCCACTGTAATCTTAGGGAGATAAGATCT-ATATTC---AATCC
* * * * ** * * *
1922404 GTTCCACTGTAATCTCAGGGAAATAAGACCT-GGTGCGATCT
1 GCTCCACTGTAATCTTAGGGAGATAAGATCTATATTCAATCC
* * *
1922445 GCTCTACTGTAA-CTTCAGAGAGATAAGATC-CT-TT-AATCC
1 GCTCCACTGTAATCTT-AGGGAGATAAGATCTATATTCAATCC
* *
1922484 GCTCCACTGTAATCTTAGGGAGATAGGATTGCTATATTCAATCT
1 GCTCCACTGTAATCTTAGGGAGATAAGA-T-CTATATTCAATCC
* *
1922528 GCTCCGCTGTAATCTCAGGGAGATAAGATCT
1 GCTCCACTGTAATCTTAGGGAGATAAGATCT
1922559 GCAATTCTTT
Statistics
Matches: 353, Mismatches: 82, Indels: 62
0.71 0.16 0.12
Matches are distributed among these distances:
39 24 0.07
40 9 0.03
41 52 0.15
42 9 0.03
43 41 0.12
44 120 0.34
45 4 0.01
46 88 0.25
48 1 0.00
49 3 0.01
50 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (42 bp):
GCTCCACTGTAATCTTAGGGAGATAAGATCTATATTCAATCC
Found at i:1926507 original size:39 final size:38
Alignment explanation
Indices: 1926464--1926543 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 38
1926454 CTTCTTCCGT
1926464 TCTAGACTTCGCGATCATATCGTCAACATAGACTTCGGA
1 TCTAGACTTCGCGATCATATCGTCAACATAGACTTC-GA
*
1926503 TCTAGACTTTGCGATCATATCGTCAACATAGACTTCGA
1 TCTAGACTTCGCGATCATATCGTCAACATAGACTTCGA
1926541 TCT
1 TCT
1926544 CTTTGTGCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 5 0.12
39 35 0.88
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (38 bp):
TCTAGACTTCGCGATCATATCGTCAACATAGACTTCGA
Found at i:1934497 original size:70 final size:70
Alignment explanation
Indices: 1934384--1934523 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
1934374 TTTAGCCATC
1934384 TCGGATTTAAAAATGAGATCGCGACCAGTAAGTTTGGACGTGATTTTTTAATCCCGAGGCCATCT
1 TCGGATTTAAAAATGAGATCGCGACCAGTAAGTTTGGACGTGATTTTTTAATCCCGAGGCCATCT
1934449 AAAAT
66 AAAAT
*
1934454 TCGGATTTAAAAATGAGATCGCGACCAGTAAGTTTGGACGTGATTTTTTTATCCCGAGGCCATCT
1 TCGGATTTAAAAATGAGATCGCGACCAGTAAGTTTGGACGTGATTTTTTAATCCCGAGGCCATCT
1934519 AAAAT
66 AAAAT
1934524 CTGAGTTTAG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (70 bp):
TCGGATTTAAAAATGAGATCGCGACCAGTAAGTTTGGACGTGATTTTTTAATCCCGAGGCCATCT
AAAAT
Found at i:1936182 original size:18 final size:19
Alignment explanation
Indices: 1936159--1936194 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1936149 TCGAAAAAAA
1936159 AATAAACAA-AAAATAAAC
1 AATAAACAATAAAATAAAC
1936177 AATAAACAATAAAATAAA
1 AATAAACAATAAAATAAA
1936195 GAGTAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (19 bp):
AATAAACAATAAAATAAAC
Found at i:1938455 original size:21 final size:20
Alignment explanation
Indices: 1938431--1938473 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
1938421 CGATCTACAA
*
1938431 GGGAAAGGGAAAACAAATAG
1 GGGAAAGAGAAAACAAATAG
1938451 NGGGAAAGAGAAAACAAATAG
1 -GGGAAAGAGAAAACAAATAG
1938472 GG
1 GG
1938474 TAAGCATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.53, C:0.05, G:0.35, T:0.05
Consensus pattern (20 bp):
GGGAAAGAGAAAACAAATAG
Found at i:1941133 original size:23 final size:25
Alignment explanation
Indices: 1941101--1941146 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1941091 TCCATATTAA
1941101 TTCTAGA-TTTA-TTTTTAGTAAGT
1 TTCTAGATTTTATTTTTTAGTAAGT
*
1941124 TTCTATATTTTATTTTTTAGTAA
1 TTCTAGATTTTATTTTTTAGTAA
1941147 AATATAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 4 0.20
25 10 0.50
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.61
Consensus pattern (25 bp):
TTCTAGATTTTATTTTTTAGTAAGT
Found at i:1941306 original size:27 final size:27
Alignment explanation
Indices: 1941267--1941341 Score: 73
Period size: 27 Copynumber: 2.8 Consensus size: 27
1941257 ATATAAATAA
* *
1941267 AAAAATCTA-AAATTTTATAAATCTA-T
1 AAAAATCTATAAA-TTTATAAAACAACT
* * *
1941293 AAAAATGTATAAATATATAAAAGAACT
1 AAAAATCTATAAATTTATAAAACAACT
*
1941320 AAAAATTTATAAATTTATAAAA
1 AAAAATCTATAAATTTATAAAA
1941342 AAATATATAA
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
26 16 0.40
27 24 0.60
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (27 bp):
AAAAATCTATAAATTTATAAAACAACT
Found at i:1941342 original size:18 final size:18
Alignment explanation
Indices: 1941174--1941361 Score: 62
Period size: 16 Copynumber: 10.7 Consensus size: 18
1941164 GTTTTTATTT
1941174 TAAA-ATATAAAAATATA
1 TAAATATATAAAAATATA
*
1941191 TACA-AT-TAAAAATATA
1 TAAATATATAAAAATATA
* *
1941207 TAGAA-A-ACAAATAATATTT
1 TA-AATATATAAA-AATA-TA
*
1941226 TAAAAATATAAAAA-AT-
1 TAAATATATAAAAATATA
*
1941242 TACGAA-ATAT-AATATATA
1 TA--AATATATAAAAATATA
*
1941260 TAAATA-A-AAAAATCTA
1 TAAATATATAAAAATATA
* * *
1941276 -AAAT-TTTATAAATCTA
1 TAAATATATAAAAATATA
* * *
1941292 TAAAAATGTATAAATATA
1 TAAATATATAAAAATATA
* *
1941310 TAAA-AGAACTAAAAATTTA
1 TAAATA-TA-TAAAAATATA
*
1941329 TAAATTTATAAAAAAATATA
1 TAAA--TATATAAAAATATA
1941349 TAAATATATAAAA
1 TAAATATATAAAA
1941362 TAACTAAAAA
Statistics
Matches: 129, Mismatches: 21, Indels: 41
0.68 0.11 0.21
Matches are distributed among these distances:
15 4 0.03
16 34 0.26
17 22 0.17
18 33 0.26
19 18 0.14
20 16 0.12
21 1 0.01
22 1 0.01
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (18 bp):
TAAATATATAAAAATATA
Found at i:1941345 original size:20 final size:20
Alignment explanation
Indices: 1941320--1941361 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1941310 TAAAAGAACT
* *
1941320 AAAAATTTATAAATTTATAA
1 AAAAATATATAAATATATAA
1941340 AAAAATATATAAATATATAA
1 AAAAATATATAAATATATAA
1941360 AA
1 AA
1941362 TAACTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATATATAAATATATAA
Found at i:1941367 original size:47 final size:44
Alignment explanation
Indices: 1941255--1941371 Score: 148
Period size: 47 Copynumber: 2.6 Consensus size: 44
1941245 GAAATATAAT
* *
1941255 ATATATAAATA-A-AAAAATCTAAAATTTTATAAATCTATAAAA
1 ATATATAAATATATAAAAAACTAAAAATTTATAAATCTATAAAA
* *
1941297 ATGTATAAATATATAAAAGAACTAAAAATTTATAAATTTATAAAAAA
1 ATATATAAATATATAAAA-AACTAAAAATTTATAAATCTAT--AAAA
1941344 ATATATAAATATATAAAATAACTAAAAA
1 ATATATAAATATATAAAA-AACTAAAAA
1941372 ATACATCTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
42 10 0.16
43 1 0.02
44 4 0.06
45 19 0.30
47 30 0.47
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (44 bp):
ATATATAAATATATAAAAAACTAAAAATTTATAAATCTATAAAA
Found at i:1941718 original size:16 final size:16
Alignment explanation
Indices: 1941696--1941742 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
1941686 TGAAAAATAT
*
1941696 AAAAAATATAAATTTA
1 AAAAAATATAAAATTA
*
1941712 TAAAAATATATACAATTA
1 -AAAAA-ATATAAAATTA
1941730 AAAAAATATAAAA
1 AAAAAATATAAAA
1941743 AGGCCTGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.27
17 10 0.38
18 9 0.35
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAATATAAAATTA
Found at i:1941722 original size:18 final size:18
Alignment explanation
Indices: 1941693--1941739 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1941683 ATTTGAAAAA
1941693 TATAAAAA-ATATA-AATT
1 TATAAAAATATATACAA-T
1941710 TATAAAAATATATACAAT
1 TATAAAAATATATACAAT
*
1941728 TAAAAAAATATA
1 TATAAAAATATA
1941740 AAAAGGCCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 8 0.30
18 17 0.63
19 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TATAAAAATATATACAAT
Found at i:1950703 original size:9 final size:10
Alignment explanation
Indices: 1950689--1950773 Score: 79
Period size: 9 Copynumber: 8.7 Consensus size: 10
1950679 ACCAAAGGTT
1950689 TAAATAA-AA
1 TAAATAATAA
*
1950698 TAAATAAAAA
1 TAAATAATAA
**
1950708 TAAATAGGAA
1 TAAATAATAA
*
1950718 GAAATAATAA
1 TAAATAATAA
*
1950728 T-AATAATGA
1 TAAATAATAA
1950737 T-AATAATAA
1 TAAATAATAA
1950746 T-AATAATAA
1 TAAATAATAA
1950755 TAAACTCAATAA
1 TAAA-T-AATAA
1950767 TAAATAA
1 TAAATAA
1950774 AATGATAGGA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
9 32 0.50
10 21 0.33
11 2 0.03
12 9 0.14
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (10 bp):
TAAATAATAA
Found at i:1950769 original size:3 final size:3
Alignment explanation
Indices: 1950720--1950757 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1950710 AATAGGAAGA
*
1950720 AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1950758 ACTCAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1951975 original size:16 final size:19
Alignment explanation
Indices: 1951954--1951989 Score: 51
Period size: 16 Copynumber: 2.1 Consensus size: 19
1951944 AGTATAAATG
1951954 ATATAC-AA-AAC-AATAT
1 ATATACGAATAACTAATAT
1951970 ATATACGAATAACTAATAT
1 ATATACGAATAACTAATAT
1951989 A
1 A
1951990 CACAAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.35
17 2 0.12
18 3 0.18
19 6 0.35
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.28
Consensus pattern (19 bp):
ATATACGAATAACTAATAT
Found at i:1952118 original size:14 final size:14
Alignment explanation
Indices: 1952099--1952131 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1952089 AAAACAGAAT
1952099 GAAAATATACAA-AA
1 GAAAATA-ACAACAA
1952113 GAAAATAACAACAA
1 GAAAATAACAACAA
1952127 GAAAA
1 GAAAA
1952132 AAAAAAGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.73, C:0.09, G:0.09, T:0.09
Consensus pattern (14 bp):
GAAAATAACAACAA
Found at i:1952622 original size:24 final size:24
Alignment explanation
Indices: 1952590--1952635 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1952580 GGAGTGGTTT
* *
1952590 AGTGGGGTGATGGAGTTAGTGGCA
1 AGTGAGGTGACGGAGTTAGTGGCA
1952614 AGTGAGGTGACGGAGTTAGTGG
1 AGTGAGGTGACGGAGTTAGTGG
1952636 TCGGTTTAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.04, G:0.50, T:0.24
Consensus pattern (24 bp):
AGTGAGGTGACGGAGTTAGTGGCA
Found at i:1954610 original size:177 final size:176
Alignment explanation
Indices: 1954301--1954690 Score: 627
Period size: 177 Copynumber: 2.2 Consensus size: 176
1954291 GAGATACTTC
*
1954301 AGCTTTCTCTGGTCTTTCATTGTATGTTTCACCAACACGACATTCATGAGTTTCCACCGACTTAG
1 AGCTTTCTCTGG-CTTTCATTGTATGTTTCACCAACACGACATTCATAAGTTTCCACCGACTTAG
* *
1954366 TAGCATTTTCTTCTATCTCGGCATTAACATTGTCAAAATTGAATTCTTTAAGTGACCCAAGAGTG
65 TAGCATTTTCTTCTATCTCGCCATTAACATTGTCAAAATTGAATTCTTTAACTGACCCAAGAGTG
*
1954431 ATGGATCGGTTCTTATGGTTCTGTGGTTTGCCTTCCCCATCTGCTGG
130 ATGGATCGGTTCTTATGGTGCTGTGGTTTGCCTTCCCCATCTGCTGG
* * *
1954478 AGCTTGCTCTGGCCTTTCATTGTATGTTTCACCAACACGACCTTCATAAGTTTCCACTGACTTAG
1 AGCTTTCTCTGG-CTTTCATTGTATGTTTCACCAACACGACATTCATAAGTTTCCACCGACTTAG
* * * *
1954543 TAGCATTTTCTTCTATCTCTCCATTAATATTGTCGAAATTGAATTCTTTAACTGACCCGAGAGTG
65 TAGCATTTTCTTCTATCTCGCCATTAACATTGTCAAAATTGAATTCTTTAACTGACCCAAGAGTG
*
1954608 ATGGATCGGTTCTTATGGTGCTGTGGTTTGCCTTCCCTATCTGCTGG
130 ATGGATCGGTTCTTATGGTGCTGTGGTTTGCCTTCCCCATCTGCTGG
* *
1954655 AGCTTTCTCTGGTTTTCCGTTGTATGTTTCACCAAC
1 AGCTTTCTCTGGCTTT-CATTGTATGTTTCACCAAC
1954691 TCTACATACA
Statistics
Matches: 196, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
176 3 0.02
177 193 0.98
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (176 bp):
AGCTTTCTCTGGCTTTCATTGTATGTTTCACCAACACGACATTCATAAGTTTCCACCGACTTAGT
AGCATTTTCTTCTATCTCGCCATTAACATTGTCAAAATTGAATTCTTTAACTGACCCAAGAGTGA
TGGATCGGTTCTTATGGTGCTGTGGTTTGCCTTCCCCATCTGCTGG
Found at i:1954720 original size:177 final size:175
Alignment explanation
Indices: 1954301--1954740 Score: 612
Period size: 177 Copynumber: 2.5 Consensus size: 175
1954291 GAGATACTTC
* *
1954301 AGCTTTCTCTGGTCTTTCATTGTATGTTTCACCAACACGACATTCATGAGTTTCCACCGACTTAG
1 AGCTTTCTCTGGT-TTTCATTGTATGTTTCACCAACACGACATTCA-GAATTTCCAACGACTTAG
** *
1954366 TAGCATTTTCTTCTATCTCGGCATTAACATTGTCAAAATTGAATTCTTTAAGTGACCCAAGAGTG
64 TAGCATTTTCTTCTATCTCTCCATTAACATTGTCAAAATTGAATTCTTTAACTGACCCAAGAGTG
*
1954431 ATGGATCGGTTCTTATGGTTCTGTGGTTTGCCTTCCCCATCTGCTGG
129 ATGGATCGGTTCTTATGGTGCTGTGGTTTGCCTTCCCCATCTGCTGG
* * * *
1954478 AGCTTGCTCTGGCCTTTCATTGTATGTTTCACCAACACGACCTTCATAAGTTTCC-ACTGACTTA
1 AGCTTTCTCTGG-TTTTCATTGTATGTTTCACCAACACGACATTCAGAA-TTTCCAAC-GACTTA
* * *
1954542 GTAGCATTTTCTTCTATCTCTCCATTAATATTGTCGAAATTGAATTCTTTAACTGACCCGAGAGT
63 GTAGCATTTTCTTCTATCTCTCCATTAACATTGTCAAAATTGAATTCTTTAACTGACCCAAGAGT
*
1954607 GATGGATCGGTTCTTATGGTGCTGTGGTTTGCCTTCCCTATCTGCTGG
128 GATGGATCGGTTCTTATGGTGCTGTGGTTTGCCTTCCCCATCTGCTGG
* * * * *
1954655 AGCTTTCTCTGGTTTTCCGTTGTATGTTTCACCAACTCTACATACAGAATTATCCAACAACTTAG
1 AGCTTTCTCTGGTTTT-CATTGTATGTTTCACCAACACGACATTCAGAATT-TCCAACGACTTAG
* * *
1954720 TGGCGTTTTCTTCTCTCTCTC
64 TAGCATTTTCTTCTATCTCTC
1954741 TTGCTGCTTC
Statistics
Matches: 231, Mismatches: 26, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
176 7 0.03
177 222 0.96
178 2 0.01
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (175 bp):
AGCTTTCTCTGGTTTTCATTGTATGTTTCACCAACACGACATTCAGAATTTCCAACGACTTAGTA
GCATTTTCTTCTATCTCTCCATTAACATTGTCAAAATTGAATTCTTTAACTGACCCAAGAGTGAT
GGATCGGTTCTTATGGTGCTGTGGTTTGCCTTCCCCATCTGCTGG
Found at i:1957205 original size:20 final size:22
Alignment explanation
Indices: 1957163--1957206 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1957153 GAGAAAAAAT
* *
1957163 AAAAAATTATATAATTTTTTTA
1 AAAAAATTATATAATATTCTTA
1957185 AAAAAATTAT-TAA-ATTCTTA
1 AAAAAATTATATAATATTCTTA
1957205 AA
1 AA
1957207 TCAAAAATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 3 0.15
22 10 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAAATTATATAATATTCTTA
Found at i:1986943 original size:105 final size:106
Alignment explanation
Indices: 1986800--1987026 Score: 402
Period size: 105 Copynumber: 2.1 Consensus size: 106
1986790 AAAGTTTTAT
*
1986800 TTTTATTTATTTATTTATTTATTTTACTTAGTTTAAATTTTTATATTCAGTCCAAGAGTCCCAAA
1 TTTT-TTT-TTTAGTTATTTATTTTACTTAGTTTAAATTTTTATATTCAGTCCAAGAGTCCCAAA
* *
1986865 TAAAATACCCTTGGCCGAATTTCCATATTAAAATAATTAGGAG
64 TAAAAGACCATTGGCCGAATTTCCATATTAAAATAATTAGGAG
1986908 -TTTTTTTTTAGTTATTTATTTTACTTAGTTTAAATTTTTATATTCAGTCCAAGAGTCCCAAATA
1 TTTTTTTTTTAGTTATTTATTTTACTTAGTTTAAATTTTTATATTCAGTCCAAGAGTCCCAAATA
1986972 AAAGACCATTGGCCGAATTTCCATATTAAAATAATTAGGAG
66 AAAGACCATTGGCCGAATTTCCATATTAAAATAATTAGGAG
1987013 TTTTTTTTTTAGTT
1 TTTTTTTTTTAGTT
1987027 TTAGTTTTAG
Statistics
Matches: 115, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
105 96 0.83
106 16 0.14
107 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (106 bp):
TTTTTTTTTTAGTTATTTATTTTACTTAGTTTAAATTTTTATATTCAGTCCAAGAGTCCCAAATA
AAAGACCATTGGCCGAATTTCCATATTAAAATAATTAGGAG
Found at i:1995302 original size:24 final size:25
Alignment explanation
Indices: 1995256--1995307 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
1995246 AAGTATTCAC
1995256 TTTAATTGATTAATATTTTAATA-A
1 TTTAATTGATTAATATTTTAATATA
*
1995280 TTTAATT-ATTAATTTTTTAAATATA
1 TTTAATTGATTAATATTTT-AATATA
1995305 TTT
1 TTT
1995308 TTAGTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 10 0.40
24 11 0.44
25 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTAATTGATTAATATTTTAATATA
Found at i:1995592 original size:19 final size:19
Alignment explanation
Indices: 1995565--1995601 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1995555 GACGTCACCT
*
1995565 TATTTAAAAGTTTAAATAA
1 TATTGAAAAGTTTAAATAA
1995584 TATTGAAAAGTTTAAATA
1 TATTGAAAAGTTTAAATA
1995602 TATACAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (19 bp):
TATTGAAAAGTTTAAATAA
Found at i:1999869 original size:8 final size:9
Alignment explanation
Indices: 1999840--1999873 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1999830 ATTCCCTGTG
*
1999840 AAAATTTAA
1 AAAAATTAA
1999849 AAAGAATTAA
1 AAA-AATTAA
1999859 AAAAATTAA
1 AAAAATTAA
1999868 AAAAAT
1 AAAAAT
1999874 AACGTGATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (9 bp):
AAAAATTAA
Found at i:2001243 original size:66 final size:68
Alignment explanation
Indices: 2001173--2001298 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 68
2001163 CAATTTTGTC
* * *
2001173 TTTTTTAGTCACCAAAATGGAAACATCC-AATATCCAAGATAGTTGGGTGA-CAAAAAAAAGTTT
1 TTTTTTAGTCACCAAAATGGAAACATCCAAAAATCCAAAATAGTTAGGTGATCAAAAAAAAGTTT
2001236 GCT
66 GCT
* * * *
2001239 TTTTTTGGTCTCCAGAATGGAGACATCCAAAAATCCAAAATAGTTAGGTGATCAAAAAAA
1 TTTTTTAGTCACCAAAATGGAAACATCCAAAAATCCAAAATAGTTAGGTGATCAAAAAAA
2001299 GATAAAATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 24 0.47
67 19 0.37
68 8 0.16
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (68 bp):
TTTTTTAGTCACCAAAATGGAAACATCCAAAAATCCAAAATAGTTAGGTGATCAAAAAAAAGTTT
GCT
Found at i:2003997 original size:26 final size:26
Alignment explanation
Indices: 2003961--2004013 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
2003951 GGAGAGGAGA
2003961 TTATGACATTTAAGATAGTTGAAGGC
1 TTATGACATTTAAGATAGTTGAAGGC
2003987 TTATGACATTTAAGATAGTTGAAGGC
1 TTATGACATTTAAGATAGTTGAAGGC
2004013 T
1 T
2004014 GGGAAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.08, G:0.23, T:0.36
Consensus pattern (26 bp):
TTATGACATTTAAGATAGTTGAAGGC
Found at i:2004195 original size:15 final size:15
Alignment explanation
Indices: 2004175--2004206 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2004165 GGAGCCTGCT
2004175 CTAATATTCCTTTTG
1 CTAATATTCCTTTTG
2004190 CTAATATTCCTTTTG
1 CTAATATTCCTTTTG
2004205 CT
1 CT
2004207 GAAGTTGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.06, T:0.53
Consensus pattern (15 bp):
CTAATATTCCTTTTG
Found at i:2006559 original size:27 final size:28
Alignment explanation
Indices: 2006529--2006625 Score: 88
Period size: 28 Copynumber: 3.2 Consensus size: 28
2006519 CTTTTTTTAA
2006529 TTTTAAAATTAGAACTAAATTGATAAAT
1 TTTTAAAATTAGAACTAAATTGATAAAT
* *
2006557 TTTATAAATATTGAGGGA-TAAATTTATTTAAAT
1 TTT-TAAA-ATT-A-GAACTAAATTGA--TAAAT
* *
2006590 TTTTAGAATTAGAACTAAAATGATAAAT
1 TTTTAAAATTAGAACTAAATTGATAAAT
2006618 TTTGTAAA
1 TTT-TAAA
2006626 TATTGAGGGC
Statistics
Matches: 54, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
28 11 0.20
29 9 0.17
30 10 0.19
31 11 0.20
32 5 0.09
33 8 0.15
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.41
Consensus pattern (28 bp):
TTTTAAAATTAGAACTAAATTGATAAAT
Found at i:2006675 original size:61 final size:61
Alignment explanation
Indices: 2006529--2006707 Score: 191
Period size: 61 Copynumber: 2.9 Consensus size: 61
2006519 CTTTTTTTAA
* * * *
2006529 TTTTAAAATTAGAACTAAATTGATAAATTTTATAAATATTGAGGGATAAATTTATTTAAAT
1 TTTTAGAATTAGAACTAAATTGATAAATTTTGTAAATATTGAGGGATAAATTTGTTGAAAT
* *
2006590 TTTTAGAATTAGAACTAAAATGATAAATTTTGTAAATATTGAGGGCTAAATTTGTTG-AAT
1 TTTTAGAATTAGAACTAAATTGATAAATTTTGTAAATATTGAGGGATAAATTTGTTGAAAT
* * * ** * * *
2006650 ATTTTAGATTTAAGATC-GAATTGATAAAACTTGTAAACATTGAAAGGTTAAATTTGTT
1 -TTTTAGAATT-AGAACTAAATTGATAAATTTTGTAAATATTG-AGGGATAAATTTGTT
2006708 ATTAGGCTAA
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
60 3 0.03
61 80 0.80
62 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.14, T:0.41
Consensus pattern (61 bp):
TTTTAGAATTAGAACTAAATTGATAAATTTTGTAAATATTGAGGGATAAATTTGTTGAAAT
Found at i:2016600 original size:79 final size:79
Alignment explanation
Indices: 2016469--2016625 Score: 224
Period size: 79 Copynumber: 2.0 Consensus size: 79
2016459 AAGATGATGG
* * *
2016469 TTCACAGTACCCCTGGCTCAACCAGTAAGCTAGGTCAAACCAGAGATCAACCACCCAATGATCCG
1 TTCACAGTACCCCTGGCTCAACCAGTAAGCTAGGACAAACAAGAGATCAACCACCCAAAGATCCG
2016534 GACCCGAAGTAGCA
66 GACCCGAAGTAGCA
* * * * * * *
2016548 TTCACAGTATCCCTGGTTCACCCAGTAAGTTAGGACGAACAAGAGATGAACCACGCAAAGATCCG
1 TTCACAGTACCCCTGGCTCAACCAGTAAGCTAGGACAAACAAGAGATCAACCACCCAAAGATCCG
2016613 GACCCGAAGTAGC
66 GACCCGAAGTAGC
2016626 CAAACCAGCT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.16
Consensus pattern (79 bp):
TTCACAGTACCCCTGGCTCAACCAGTAAGCTAGGACAAACAAGAGATCAACCACCCAAAGATCCG
GACCCGAAGTAGCA
Found at i:2022634 original size:17 final size:18
Alignment explanation
Indices: 2022601--2022635 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2022591 TAAAAAATGA
2022601 TTAGGTCTAATTATGATT
1 TTAGGTCTAATTATGATT
*
2022619 TTAGTTCTAA-TATGATT
1 TTAGGTCTAATTATGATT
2022636 AAATTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (18 bp):
TTAGGTCTAATTATGATT
Found at i:2023468 original size:14 final size:14
Alignment explanation
Indices: 2023449--2023492 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
2023439 AACACTCGAC
2023449 GATTGGTTATAGAT
1 GATTGGTTATAGAT
2023463 GATTGGTTAT--A-
1 GATTGGTTATAGAT
2023474 GA-TGGTTATAGAT
1 GATTGGTTATAGAT
2023487 GATTGG
1 GATTGG
2023493 GAGATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 7 0.27
11 2 0.08
12 2 0.08
13 2 0.08
14 13 0.50
ACGTcount: A:0.27, C:0.00, G:0.32, T:0.41
Consensus pattern (14 bp):
GATTGGTTATAGAT
Found at i:2032667 original size:31 final size:31
Alignment explanation
Indices: 2032632--2032693 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2032622 AATGACTTAA
*
2032632 TAAATAAAAACTTCTCAATAGTTTAGTGACT
1 TAAATAAAAACTTCTCAATACTTTAGTGACT
* * *
2032663 TAAATGAAAACTTTTGAATACTTTAGTGACT
1 TAAATAAAAACTTCTCAATACTTTAGTGACT
2032694 ATTTTGTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (31 bp):
TAAATAAAAACTTCTCAATACTTTAGTGACT
Found at i:2034557 original size:49 final size:49
Alignment explanation
Indices: 2034482--2034579 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 49
2034472 CATGCAAACT
*
2034482 TATTAACTGATAATTAATGCGTACAATGGAGTG-TGTTGCTGTAAATTAG
1 TATTAACTGATAATTAATGCGCACAATGGAGTGCT-TTGCTGTAAATTAG
*
2034531 TATTAACTGCTAATTAATGCGCACAATGGAGTGCTTTGCTGTAAATTAG
1 TATTAACTGATAATTAATGCGCACAATGGAGTGCTTTGCTGTAAATTAG
2034580 AAGCCTAGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
49 45 0.98
50 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (49 bp):
TATTAACTGATAATTAATGCGCACAATGGAGTGCTTTGCTGTAAATTAG
Found at i:2044179 original size:32 final size:32
Alignment explanation
Indices: 2044143--2044210 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
2044133 AGTTTGGACC
2044143 TAACACGAAACATATTTAAAACATGTGAATCA
1 TAACACGAAACATATTTAAAACATGTGAATCA
2044175 TAACACGAAACATATTTAAAACATGTGAATCA
1 TAACACGAAACATATTTAAAACATGTGAATCA
2044207 -AACA
1 TAACA
2044211 ATAAGCAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.24
Consensus pattern (32 bp):
TAACACGAAACATATTTAAAACATGTGAATCA
Found at i:2044346 original size:30 final size:30
Alignment explanation
Indices: 2044303--2044378 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 30
2044293 TACTATTTAA
* *
2044303 AAAGTATATTTTTAT-AATTTTTAAAGGA-T
1 AAAGTAAAATTTTATCAA-TTTTAAAGGACT
*
2044332 TAAGTCAAAATTTTATCAATTTTAAAGGACT
1 AAAGT-AAAATTTTATCAATTTTAAAGGACT
*
2044363 AAAGTATAATTTTATC
1 AAAGTAAAATTTTATC
2044379 TTTACTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 4 0.10
30 28 0.72
31 7 0.18
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.43
Consensus pattern (30 bp):
AAAGTAAAATTTTATCAATTTTAAAGGACT
Found at i:2045192 original size:5 final size:5
Alignment explanation
Indices: 2045182--2045216 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
2045172 TTACGTGATA
2045182 AAAAT AAAAT AAAAT AAAAT AAAAT --AAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
2045217 TAATTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.11
5 25 0.89
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:2045202 original size:15 final size:13
Alignment explanation
Indices: 2045182--2045216 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 13
2045172 TTACGTGATA
2045182 AAAATAAAATAAAAT
1 AAAATAAAAT--AAT
2045197 AAAATAAAATAAT
1 AAAATAAAATAAT
2045210 AAAATAA
1 AAAATAA
2045217 TAATTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.50
15 10 0.50
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:2045220 original size:11 final size:11
Alignment explanation
Indices: 2045179--2045220 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
2045169 TAATTACGTG
*
2045179 ATAAAAATAAA
1 ATAATAATAAA
2045190 ATAA-AATAAA
1 ATAATAATAAA
2045200 ATAAAATAATAAA
1 AT--AATAATAAA
2045213 ATAATAAT
1 ATAATAAT
2045221 TTTATAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.29
11 10 0.36
12 2 0.07
13 8 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
ATAATAATAAA
Found at i:2046796 original size:31 final size:30
Alignment explanation
Indices: 2046725--2046798 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 30
2046715 TCAACCGGCT
* *
2046725 AATAGCTTAGTGACTTAAATGATAAGTTTC
1 AATAGTTTAGTGACTTAAATGAAAAGTTTC
* * *
2046755 ACATAATTTAGTGACTTAAATGAAAATTTTTG
1 A-ATAGTTTAGTGACTTAAATGAAAA-GTTTC
2046787 AATAGTTTAGTG
1 AATAGTTTAGTG
2046799 GCTATTTTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 1 0.03
31 31 0.86
32 4 0.11
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (30 bp):
AATAGTTTAGTGACTTAAATGAAAAGTTTC
Found at i:2054284 original size:85 final size:85
Alignment explanation
Indices: 2054184--2054354 Score: 288
Period size: 85 Copynumber: 2.0 Consensus size: 85
2054174 CTATTAGATA
** *
2054184 TATGATGAAATTTTTTTATGTTAAGCTTATACCTATGTTATCTAAGTTTCGTATAGAAGCTTTAT
1 TATGATGAAATTTTTTTATGTTAAGCTTATACCTATGCCATCTAAGTTTCATATAGAAGCTTTAT
2054249 CCTTTACCCCAAACAAATCT
66 CCTTTACCCCAAACAAATCT
* *
2054269 TATGATGAAATTTTTTTATGTTCAGCTTGTACCTATGCCATCTAAGTTTCATATAGAAGCTTTAT
1 TATGATGAAATTTTTTTATGTTAAGCTTATACCTATGCCATCTAAGTTTCATATAGAAGCTTTAT
*
2054334 CCTTTACCCCGAACAAATCT
66 CCTTTACCCCAAACAAATCT
2054354 T
1 T
2054355 GTCATAAGAA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 80 1.00
ACGTcount: A:0.29, C:0.18, G:0.11, T:0.42
Consensus pattern (85 bp):
TATGATGAAATTTTTTTATGTTAAGCTTATACCTATGCCATCTAAGTTTCATATAGAAGCTTTAT
CCTTTACCCCAAACAAATCT
Found at i:2062395 original size:24 final size:23
Alignment explanation
Indices: 2062361--2062408 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
2062351 AAATGTGTTT
2062361 TTTTCTTTTAATCTAAGTGAAAATA
1 TTTTCTTTTAATCTAA-T-AAAATA
*
2062386 TTTT-TTTTAATTTAATAAAATA
1 TTTTCTTTTAATCTAATAAAATA
2062408 T
1 T
2062409 CATGTCAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
23 1 0.05
24 10 0.45
25 4 0.18
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
TTTTCTTTTAATCTAATAAAATA
Found at i:2072118 original size:109 final size:109
Alignment explanation
Indices: 2071928--2072251 Score: 623
Period size: 109 Copynumber: 3.0 Consensus size: 109
2071918 AAAGGATCGG
* *
2071928 TGGCGACTCC-CTATTTATTTCAAAATCAAATGTCAAATTTCAAACTTTTTTCCATAAATCGCCA
1 TGGCGACTCCACTATTTATTTCAAAATCAAACGTCAAATTTCAAACTTTTTTCCATAAATCACCA
2071992 CAATTAGCGACCAAGCTACGCTAAAATTTTTACGTCGCTACAGC
66 CAATTAGCGACCAAGCTACGCTAAAATTTTTACGTCGCTACAGC
2072036 TGGCGACTCCACTATTTATTTCAAAATCAAACGTCAAATTTCAAACTTTTTTCCATAAATCACCA
1 TGGCGACTCCACTATTTATTTCAAAATCAAACGTCAAATTTCAAACTTTTTTCCATAAATCACCA
2072101 CAATTAGCGACCAAGCTACGCTAAAATTTTTACGTCGCTACAGC
66 CAATTAGCGACCAAGCTACGCTAAAATTTTTACGTCGCTACAGC
2072145 TGGCGACTCCACTATTTATTTCAAAATCAAACGTCAAATTTCAAACTTTTTTCCATAAATCACCA
1 TGGCGACTCCACTATTTATTTCAAAATCAAACGTCAAATTTCAAACTTTTTTCCATAAATCACCA
2072210 CAATTAGCGACCAAGCTACGCTAAAATTTTTACGTCGCTACA
66 CAATTAGCGACCAAGCTACGCTAAAATTTTTACGTCGCTACA
2072252 CAAACAATCC
Statistics
Matches: 213, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
108 10 0.05
109 203 0.95
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (109 bp):
TGGCGACTCCACTATTTATTTCAAAATCAAACGTCAAATTTCAAACTTTTTTCCATAAATCACCA
CAATTAGCGACCAAGCTACGCTAAAATTTTTACGTCGCTACAGC
Found at i:2073238 original size:22 final size:22
Alignment explanation
Indices: 2073213--2073256 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2073203 TCCGCCAAAG
*
2073213 TTAAATAAGTGTGGTGAAGCCA
1 TTAAATAAGTGTGGTCAAGCCA
2073235 TTAAATAAGTGTGGTCAAGCCA
1 TTAAATAAGTGTGGTCAAGCCA
2073257 CCAGAATTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (22 bp):
TTAAATAAGTGTGGTCAAGCCA
Found at i:2073782 original size:5 final size:5
Alignment explanation
Indices: 2073772--2073803 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
2073762 CAAATTCGCA
2073772 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA
2073804 TCACAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2078487 original size:16 final size:16
Alignment explanation
Indices: 2078446--2078505 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
2078436 AGATTAGGTA
2078446 GCAT-CATACATACAT
1 GCATACATACATACAT
* * *
2078461 GCTTACGTACATGCAT
1 GCATACATACATACAT
* *
2078477 ACATACATACATGCAT
1 GCATACATACATACAT
*
2078493 GCATATATACATA
1 GCATACATACATA
2078506 TATATATGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
15 3 0.09
16 32 0.91
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.28
Consensus pattern (16 bp):
GCATACATACATACAT
Found at i:2078497 original size:12 final size:12
Alignment explanation
Indices: 2078450--2078484 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2078440 TAGGTAGCAT
2078450 CATACATACATG
1 CATACATACATG
* *
2078462 CTTACGTACATG
1 CATACATACATG
2078474 CATACATACAT
1 CATACATACAT
2078485 ACATGCATGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.29
Consensus pattern (12 bp):
CATACATACATG
Found at i:2082153 original size:19 final size:17
Alignment explanation
Indices: 2082121--2082165 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
2082111 ATAAATATTT
2082121 TTAAAATAAAATAATAA
1 TTAAAATAAAATAATAA
2082138 TTAATAATAAATATAATAA
1 TTAA-AATAAA-ATAATAA
*
2082157 TTTAAATAA
1 TTAAAATAA
2082166 GTTTTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 4 0.16
18 11 0.44
19 10 0.40
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAATAAAATAATAA
Done.