Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 204 of 222
Found at i:64600630 original size:54 final size:55
Alignment explanation
Indices: 64600442--64600661 Score: 292
Period size: 54 Copynumber: 4.1 Consensus size: 55
64600432 CACGTGAGCC
* * *
64600442 AAGGCTCAACTCACTTCTCGCAATATAAGTTGATTTTTG-AAAACAGAATTTACAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTA-AA
*
64600497 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAATAG-----AAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAAAAACAGAAATTAAA
* *
64600550 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
*
64600604 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAA
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
64600659 AAG
1 AAG
64600662 TAGAAATTGA
Statistics
Matches: 149, Mismatches: 6, Indels: 20
0.85 0.03 0.11
Matches are distributed among these distances:
50 14 0.09
53 34 0.23
54 53 0.36
55 36 0.24
58 6 0.04
59 6 0.04
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (55 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAA
Found at i:64600641 original size:107 final size:107
Alignment explanation
Indices: 64600442--64600641 Score: 330
Period size: 107 Copynumber: 1.9 Consensus size: 107
64600432 CACGTGAGCC
* *
64600442 AAGGCTCAACTCACTTCTCGCAATATAAGTTGATTTTTGAAAACAGAATTTACAAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAACAGAAATTA-AAAAGGCTCAAC
64600507 TCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAATAGAAA
65 TCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAATAGAAA
* * *
64600550 AAGGCTCAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAAAATAGAAATT-AAAAGGCTCAAC
1 AAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTG-AAAACAGAAATTAAAAAGGCTCAAC
64600614 TCACCTCTCGCAATATGAGTTGATTTTT
65 TCACCTCTCGCAATATGAGTTGATTTTT
64600642 GAAAAACAGA
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
107 40 0.47
108 36 0.42
109 10 0.12
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (107 bp):
AAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTGAAAACAGAAATTAAAAAGGCTCAACT
CACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAATAGAAA
Found at i:64600659 original size:14 final size:14
Alignment explanation
Indices: 64600640--64600674 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
64600630 GAGTTGATTT
64600640 TTGAAAAACAGAAA
1 TTGAAAAACAGAAA
**
64600654 TTGAAAAGTAGAAA
1 TTGAAAAACAGAAA
64600668 TTGAAAA
1 TTGAAAA
64600675 TATCTCAGCG
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:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:64600823 original size:105 final size:105
Alignment explanation
Indices: 64600643--64600831 Score: 283
Period size: 105 Copynumber: 1.8 Consensus size: 105
64600633 TTGATTTTTG
** * * *
64600643 AAAAACAGAAATTGAAAAGTAGAAATTGAAAATATCTCAGCGTGCCCTGAGGCTCAACTCACCTC
1 AAAAACAGAAATTGAAAAACAGAAATTGAAAAGACCTCAGCGTGCCCTGAGACTCAACTCACCTC
64600708 TTGCAATATGAGTTGATTTTTTTTGAAACACAGAAATTAA
66 TTGCAATATGAGTTGATTTTTTTTGAAACACAGAAATTAA
* *
64600748 AAAAACA-AAATT-AAAAACAGAATTTGAAAAGACCTCAGCATGTGGCCTGAGACTCAACTCACC
1 AAAAACAGAAATTGAAAAACAGAAATTGAAAAGACCTCAGC--GTGCCCTGAGACTCAACTCACC
64600811 TCTTGCAATATGAGTTGATTT
64 TCTTGCAATATGAGTTGATTT
64600832 GAAAAGTAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
103 22 0.29
104 5 0.07
105 48 0.64
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.26
Consensus pattern (105 bp):
AAAAACAGAAATTGAAAAACAGAAATTGAAAAGACCTCAGCGTGCCCTGAGACTCAACTCACCTC
TTGCAATATGAGTTGATTTTTTTTGAAACACAGAAATTAA
Found at i:64600904 original size:85 final size:86
Alignment explanation
Indices: 64600760--64601006 Score: 306
Period size: 85 Copynumber: 2.8 Consensus size: 86
64600750 AAACAAAATT
* * *
64600760 AAAAACAGAATTTGAAAAGACCTCAGCATGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCA-GTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
64600825 TTGATTTGAAAAG-TAGAATT-A
65 TTGATTTGAAAAGATAG-ATTGA
* * * *
64600846 GTAAAGCAGAAATTGAAAATACCTCAGC-GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAA
1 -AAAAACAGAAATTGAAAATACCTCAGCAGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGA
64600909 GTTGATTTTTGAAAAGCATAGATTGA
64 GTTGA--TTTGAAAAG-ATAGATTGA
*
64600935 AAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAGCA-GTG-GCCTGAGGCTCAACTCACCTCTTGCAATATGA
64600999 GTTGATTT
64 GTTGATTT
64601007 TTGAAAAACA
Statistics
Matches: 138, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 32 0.23
88 30 0.22
89 4 0.03
90 33 0.24
92 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.26
Consensus pattern (86 bp):
AAAAACAGAAATTGAAAATACCTCAGCAGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAGT
TGATTTGAAAAGATAGATTGA
Found at i:64600994 original size:90 final size:89
Alignment explanation
Indices: 64600760--64601013 Score: 335
Period size: 90 Copynumber: 2.9 Consensus size: 89
64600750 AAACAAAATT
* * *
64600760 AAAAACAGAATTTGAAAAGACCTCAGCATGTGGCCTGAGACTCAACTCACCTCTTGCAATATGAG
1 AAAAACAGAAATTGAAAATACCTCAGCATGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
64600825 TTGA--TTTGAAAAGTAGAATTAG
66 TTGATTTTTGAAAAGTAGAATTAG
* * * *
64600847 TAAAGCAGAAATTGAAAATACCTCAGC--GT-GCCTTGAGGCTCAACTCACCTCTCGCAATATAA
1 AAAAACAGAAATTGAAAATACCTCAGCATGTGGCC-TGAGGCTCAACTCACCTCTTGCAATATGA
64600909 GTTGATTTTTGAAAAGCATAG-ATT-G
65 GTTGATTTTTGAAAAG--TAGAATTAG
*
64600934 AAAAAACATAAATTGAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTTGCAATATG
1 -AAAAACAGAAATTGAAAATACCTCAGCATGTG-GCCTGAGGCTCAACTCACCTCTTGCAATATG
64600998 AGTTGATTTTTGAAAA
64 AGTTGATTTTTGAAAA
64601014 ACAAAAATTA
Statistics
Matches: 145, Mismatches: 12, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
84 3 0.02
85 33 0.23
87 33 0.23
88 27 0.19
89 3 0.02
90 43 0.30
92 3 0.02
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (89 bp):
AAAAACAGAAATTGAAAATACCTCAGCATGTGGCCTGAGGCTCAACTCACCTCTTGCAATATGAG
TTGATTTTTGAAAAGTAGAATTAG
Found at i:64601476 original size:192 final size:192
Alignment explanation
Indices: 64601133--64601739 Score: 1165
Period size: 192 Copynumber: 3.2 Consensus size: 192
64601123 ATCTCCGTTC
64601133 TGAGGCTCAACTCA-TT-TCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
64601196 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
66 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
64601261 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCT
131 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCT
64601323 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
64601388 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
66 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
64601453 AACTCACTTCTCGCAATATGAGTTGA--TTTTT-AAAAA-TTAAAAATACCTCAACGTGTCT
131 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCT
64601511 TGAGGCT-AACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
64601575 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
66 CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
64601640 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCT
131 AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCT
64601702 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
64601740 CCTTGGAAAG
Statistics
Matches: 410, Mismatches: 0, Indels: 12
0.97 0.00 0.03
Matches are distributed among these distances:
187 148 0.36
188 29 0.07
189 10 0.02
190 24 0.06
191 31 0.08
192 168 0.41
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (192 bp):
TGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAAAGGCTTAACT
CACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGCCCCGAGGCTC
AACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTGTCT
Found at i:64601536 original size:65 final size:66
Alignment explanation
Indices: 64601378--64601739 Score: 275
Period size: 69 Copynumber: 5.5 Consensus size: 66
64601368 AAAAATTAAA
* * ** ** * ** *
64601378 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTT-TTA-A-AAATTAAAAATACCTCAACGTGT
**
64601443 CCCG
63 CTTG
64601447 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAATTAAAAATACCTCAACGTGTCTT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAATTAAAAATACCTCAACGTGTCTT
64601512 G
66 G
* * *
64601513 AGGCT-AACTCATTTCTCGCAATATGAGTTGATTTTGAAAAA-CAAAAAT---T-AA--------
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAATTAAAAATACCTCAACGTGTCTT
*
64601564 A
66 G
* * ** ** * ** *
64601565 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTT-TTA-A-AAATTAAAAATACCTCAACGTGT
**
64601630 CCCG
63 CTTG
64601634 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTTTAAAAAATTTAAAAATACCTCAACGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGA--TTTTT-AAAAA-TTAAAAATACCTCAACGTG
64601699 TCTTG
62 TCTTG
*
64601704 AGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
64601740 CCTTGGAAAG
Statistics
Matches: 233, Mismatches: 39, Indels: 43
0.74 0.12 0.14
Matches are distributed among these distances:
52 5 0.02
53 25 0.11
54 1 0.00
55 1 0.00
56 3 0.01
57 6 0.03
60 3 0.01
61 1 0.00
64 6 0.03
65 34 0.15
66 26 0.11
67 1 0.00
68 5 0.02
69 62 0.27
70 50 0.21
71 4 0.02
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (66 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAATTAAAAATACCTCAACGTGTCTT
G
Found at i:64601667 original size:122 final size:118
Alignment explanation
Indices: 64601447--64601669 Score: 293
Period size: 118 Copynumber: 1.9 Consensus size: 118
64601437 GCGTGCCCCG
* ** ** * * **
64601447 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAATTAAAAATACCTCAACGTGTCTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAAAAACTAAAAATACCTCAACGTGCCCC
*
64601512 GAGGCTAACTCATTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
66 GAGGCTAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
* **
64601565 AGGCTTAACTCACCTCTCGCAATATGAGTCAATTTAAAACATAAACTAAAAATACCTCGGCGTGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTCAATTT-AAA-A-AAACTAAAAATACCTCAACGTGC
64601630 CCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT
63 CCCGAGGCT-AACTCACTTCTCGCAATATGAGTTGATTTT
64601670 TTTAAAAAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
118 31 0.35
119 1 0.01
120 1 0.01
121 26 0.30
122 29 0.33
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (118 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTCAATTTAAAAAAACTAAAAATACCTCAACGTGCCCC
GAGGCTAACTCACTTCTCGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
Found at i:64613577 original size:18 final size:17
Alignment explanation
Indices: 64613505--64613666 Score: 150
Period size: 17 Copynumber: 9.4 Consensus size: 17
64613495 ACGATATTTT
64613505 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
**
64613523 TTTTCAAAACACCG-AAA
1 TTTTTGAAACA-CGAAAA
* **
64613540 -TTTTGAAAACAAGAGGA
1 TTTTTG-AAACACGAAAA
*
64613557 TTTTTGAAATACGAAAA
1 TTTTTGAAACACGAAAA
*
64613574 ATTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
*
64613592 TTTTTGAAACACGGAAA
1 TTTTTGAAACACGAAAA
64613609 TTTTTGAAA-ACGAAAA
1 TTTTTGAAACACGAAAA
*
64613625 TTTTTGAAACACAAAAA
1 TTTTTGAAACACGAAAA
*
64613642 TTTTTAGAAGACACTAAAA
1 TTTTT-GAA-ACACGAAAA
*
64613661 ATTTTG
1 TTTTTG
64613667 GAAAATGGAT
Statistics
Matches: 117, Mismatches: 19, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
16 19 0.16
17 56 0.48
18 30 0.26
19 12 0.10
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:64613583 original size:35 final size:33
Alignment explanation
Indices: 64613537--64613645 Score: 123
Period size: 35 Copynumber: 3.2 Consensus size: 33
64613527 CAAAACACCG
*
64613537 AAATTTTGAAAACAAGAGGATTTTTGAAATACGAA
1 AAATTTTGAAAACAAGA--ATTTTTGAAACACGAA
* *
64613572 AAATTTTGAAAACACGAAAATTTTTGAAACACGGA
1 AAATTTTGAAAACA--AGAATTTTTGAAACACGAA
*
64613607 AATTTTTGAAAACGAA-AATTTTTGAAACAC-AA
1 AAATTTTGAAAAC-AAGAATTTTTGAAACACGAA
64613639 AAATTTT
1 AAATTTT
64613646 TAGAAGACAC
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
32 7 0.11
33 14 0.22
34 1 0.02
35 40 0.62
36 1 0.02
37 2 0.03
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (33 bp):
AAATTTTGAAAACAAGAATTTTTGAAACACGAA
Found at i:64613881 original size:20 final size:19
Alignment explanation
Indices: 64613843--64613889 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
64613833 AATATATTTT
64613843 TTTTTGAAACACGAGAAAAA
1 TTTTTGAAACACG-GAAAAA
*
64613863 TTTTTGAAGGCAC-GAAAAA
1 TTTTTGAA-ACACGGAAAAA
64613882 -TTTTGAAA
1 TTTTTGAAA
64613890 AATAGAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 8 0.33
21 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (19 bp):
TTTTTGAAACACGGAAAAA
Found at i:64621376 original size:132 final size:132
Alignment explanation
Indices: 64621027--64621361 Score: 465
Period size: 132 Copynumber: 2.5 Consensus size: 132
64621017 GAATAAACCA
* * * * * * * **
64621027 TTGAAAATAGCAGATCCTGTCTCCCCAAGCAGTGGCGGAGCAGATCAAAGACGGCAAATCTTATC
1 TTGAAGATTGCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATC
* * * *
64621092 TTCTCAAGATAGTGGAGAAGTAGATTTAAGTCATTAATCCTATCTCCCTGAGCAGCAGTGGAGTA
66 TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAATCCTATCTCCCTGAGCAACAGTGGAGTA
64621157 GG
131 GG
* *
64621159 TTGAAGATTGCAGAT-TCTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTAT
1 TTGAAGATTGCAGATCT-TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTAT
* * **
64621223 CTTCCCAAGATAGTGGAGAAGCAGATTTAGGCCATTAGTCCTATCTCTTTGAGCAACAGTGGAGT
65 CTTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAATCCTATCTCCCTGAGCAACAGTGGAGT
64621288 AGG
130 AGG
* *
64621291 TTGAAGATTGCAGATCTTGTCTCCCTAAGCAATAGTGGAGTAGATCGAAGACGGTGAATCTTATC
1 TTGAAGATTGCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATC
64621356 TTCCCA
66 TTCCCA
64621362 TCGTAGTGGG
Statistics
Matches: 178, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
132 177 0.99
133 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.27
Consensus pattern (132 bp):
TTGAAGATTGCAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCTTATC
TTCCCAAGATAGTGGAGAAGCAGATTTAAGCCATTAATCCTATCTCCCTGAGCAACAGTGGAGTA
GG
Found at i:64622139 original size:10 final size:9
Alignment explanation
Indices: 64622112--64622153 Score: 54
Period size: 8 Copynumber: 4.9 Consensus size: 9
64622102 ATTTTTCCAG
64622112 CTTA-TTTA
1 CTTATTTTA
64622120 CTTA-TTTA
1 CTTATTTTA
64622128 CTTATTTTTA
1 CTTA-TTTTA
64622138 CTTATTTTA
1 CTTATTTTA
64622147 -TTATTTT
1 CTTATTTT
64622154 TTATTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 19 0.59
9 5 0.16
10 8 0.25
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (9 bp):
CTTATTTTA
Found at i:64622139 original size:18 final size:18
Alignment explanation
Indices: 64622116--64622154 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
64622106 TTCCAGCTTA
64622116 TTTACTTA-TTTACTTATT
1 TTTACTTATTTTA-TTATT
64622134 TTTACTTATTTTATTATT
1 TTTACTTATTTTATTATT
64622152 TTT
1 TTT
64622155 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTACTTATTTTATTATT
Found at i:64622150 original size:26 final size:25
Alignment explanation
Indices: 64622112--64622161 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
64622102 ATTTTTCCAG
64622112 CTTATTTACTTATTTACTTATTTTTA
1 CTTATTTACTTATTT-CTTATTTTTA
*
64622138 CTTATTTTA-TTATTTTTTATTTTT
1 CTTA-TTTACTTATTTCTTATTTTT
64622162 TTAAAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 10 0.45
27 4 0.18
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (25 bp):
CTTATTTACTTATTTCTTATTTTTA
Found at i:64628906 original size:40 final size:42
Alignment explanation
Indices: 64628808--64628907 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 42
64628798 ATTGATCTCG
* *
64628808 GTTTCGCACACTTAGTGC-CAGTCATTTAACATCATTATTTA
1 GTTTCGCACACTTAGTGCTCAGTCATTCAACATCATCATTTA
*
64628849 GTTTCGCACACTTAGTGCTC-GAT-ATTCAACCTCATCATTTA
1 GTTTCGCACACTTAGTGCTCAG-TCATTCAACATCATCATTTA
64628890 G-TTCGCACACTTAGTGCT
1 GTTTCGCACACTTAGTGCT
64628908 AATCAGATAG
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
40 17 0.31
41 35 0.65
42 2 0.04
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (42 bp):
GTTTCGCACACTTAGTGCTCAGTCATTCAACATCATCATTTA
Found at i:64630234 original size:51 final size:51
Alignment explanation
Indices: 64630174--64630305 Score: 176
Period size: 51 Copynumber: 2.6 Consensus size: 51
64630164 TGATAGGTCG
* *
64630174 CATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGT-TTCGATCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAAT-GATCA
* * * * * *
64630225 CGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATGGTAATGGTCA
1 CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATGATCA
64630276 CATGTGTAGTACTATGTGCAGGCTACTATG
1 CATGTGTAGTACTATGTGCAGGCTACTATG
64630306 TGAACCGAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
51 69 0.99
52 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.33
Consensus pattern (51 bp):
CATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTAATGATCA
Found at i:64630307 original size:26 final size:26
Alignment explanation
Indices: 64630227--64630307 Score: 64
Period size: 26 Copynumber: 3.2 Consensus size: 26
64630217 TTCGATCACG
64630227 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * *
64630253 CGTGTA-T-CGGATG-GTAATGG-TCAC-A
1 TGTGTAGTAC-TATGTG-CA-GGCT-ACTA
64630278 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
64630304 TGTG
1 TGTG
64630308 AACCGAACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 18
0.62 0.09 0.28
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:64630365 original size:45 final size:45
Alignment explanation
Indices: 64630309--64630401 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
64630299 TACTATGTGA
* * *
64630309 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTACGTGCTGAATCC
*
64630354 ACCGGACATCATTGATTAATAAGGTGGTTGCTACGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTACGTGCTGAATCC
64630399 ACC
1 ACC
64630402 TAGTATCTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTACGTGCTGAATCC
Found at i:64630709 original size:26 final size:26
Alignment explanation
Indices: 64630673--64630725 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
64630663 ATTGAAGCTG
64630673 AATGAGTCTATTTTCACATAAAAGAA
1 AATGAGTCTATTTTCACATAAAAGAA
64630699 AATGAGTCTATTTTCACATAAAAGAA
1 AATGAGTCTATTTTCACATAAAAGAA
64630725 A
1 A
64630726 CAGAGCAAGC
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:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (26 bp):
AATGAGTCTATTTTCACATAAAAGAA
Found at i:64631982 original size:21 final size:20
Alignment explanation
Indices: 64631933--64631989 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
64631923 ATTAAATGGA
64631933 AATTGCAAATGATATTATTTG
1 AATTG-AAATGATATTATTTG
64631954 AATT-AAATGA-ATTATTGTGG
1 AATTGAAATGATATTATT-T-G
*
64631974 TATTGAAATGTATATT
1 AATTGAAATG-ATATT
64631990 GGATTGAGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 6 0.20
19 7 0.23
20 4 0.13
21 9 0.30
22 1 0.03
23 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.16, T:0.44
Consensus pattern (20 bp):
AATTGAAATGATATTATTTG
Found at i:64634055 original size:13 final size:13
Alignment explanation
Indices: 64634037--64634062 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64634027 CGTATATTAG
64634037 AAGGATTATATAA
1 AAGGATTATATAA
64634050 AAGGATTATATAA
1 AAGGATTATATAA
64634063 GTAATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (13 bp):
AAGGATTATATAA
Found at i:64634572 original size:31 final size:30
Alignment explanation
Indices: 64634521--64634580 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
64634511 CCACGTATGA
* *
64634521 ATATGAAATATATATTATATATTCCTAAAT
1 ATATGAAAGATATATAATATATTCCTAAAT
64634551 ATATGAAAAGATATATAATATATTCCTAAA
1 ATATG-AAAGATATATAATATATTCCTAAA
64634581 AGATATACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (30 bp):
ATATGAAAGATATATAATATATTCCTAAAT
Found at i:64635012 original size:59 final size:59
Alignment explanation
Indices: 64634937--64635061 Score: 169
Period size: 59 Copynumber: 2.1 Consensus size: 59
64634927 CCCATCCTAA
* * * * *
64634937 ATTGCATTCCTAACAAAGTGACAATCCACTTCAATTGCAATATGCAAGGCAAATTAACT
1 ATTGCATCCCAAACAAAGTGACAATACACTTCAATTGCAACATGCAACGCAAATTAACT
* * * *
64634996 ATTGCATCCCAAACAAAGTGACAATACACTTTAATTGCAACATGCAACGTAGATTGACT
1 ATTGCATCCCAAACAAAGTGACAATACACTTCAATTGCAACATGCAACGCAAATTAACT
64635055 ATTGCAT
1 ATTGCAT
64635062 ATTTAAATAT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (59 bp):
ATTGCATCCCAAACAAAGTGACAATACACTTCAATTGCAACATGCAACGCAAATTAACT
Found at i:64638210 original size:27 final size:27
Alignment explanation
Indices: 64638168--64638219 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
64638158 AAATGTGAAA
*
64638168 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
64638195 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
64638220 GGTTCATTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.25, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:64638336 original size:103 final size:103
Alignment explanation
Indices: 64638091--64638356 Score: 401
Period size: 103 Copynumber: 2.6 Consensus size: 103
64638081 TTGTATATAA
** *
64638091 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
64638155 TTGAAATGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAA-GTGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
* **
64638195 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACTGTATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
*
64638260 TGAAA-TGAAAAGGGGGTTGCTATGTGCTGATTCCCTCG
66 TGAAAGTGAAAA-GGGGTTGCTATGTGCTGATTCCCCCG
* * *
64638298 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTAGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
64638357 ATAACGGTTA
Statistics
Matches: 147, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
102 6 0.04
103 78 0.53
104 62 0.42
105 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAAGTGAAAAGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:64645980 original size:208 final size:208
Alignment explanation
Indices: 64645727--64646161 Score: 537
Period size: 208 Copynumber: 2.1 Consensus size: 208
64645717 AAATTGTTGT
* * * *
64645727 GTTTTGTGAGTTTTTAGTAATGTAAAAATTTTTTAAAAATAATTTTATAGTTATTTTGTTAATAG
1 GTTTTGTGATTTTTTAGTAATGT--AAATTTTTAAAAAATAATTTTATAGTTATTTTGTCAATAA
* * *
64645792 TTTATGATTATG-T-TATAAATTGTTAGTG-T-TTT-GTGTTTTGTTATTTTTTAGTAACGT-AA
64 TTTATGATTAGGTTATATAAATTCTTAGTGTTATTTAGTGTTTTGTGATTTTTTAGTAACGTAAA
* * *
64645851 TTTCTTTTAAAATAAATGTTATAGTTATTTATTTTGTTAGTAATTTATGGGATTAGG-T-TATAA
129 TTTCTTTTAAAA-AAATATT-TA--TAGTTATTTGGTTAGTAATTTAT--GATTAGGTTATATAA
*
64645914 ATTGTTAGTATTTAGTTTAGG
188 ATGGTTAGTATTTAGTTTAGG
*
64645935 GTTTTGTGATTTTTTAGTAATGT-AATTTTTAAAAAAAAATAATTTTATAGTTATTTTGTCAGTA
1 GTTTTGTGATTTTTTAGTAATGTAAATTTTT---AAAAAATAATTTTATAGTTATTTTGTCAATA
*
64645999 ATTTATGATTAGGTTATATAAATTCTTAGTGTTTAGTTTAGTGTTTTGTGATTTTTTAGTAATGT
63 ATTTATGATTAGGTTATATAAATTCTTAGTG-TTA-TTTAGTGTTTTGTGATTTTTTAGTAACGT
*
64646064 AAATTTTTTTTAAAAAAATATTTATAGTTATTTGGTTAGTAATTTATGATTAGGTTATATAAATG
126 AAATTTCTTTTAAAAAAATATTTATAGTTATTTGGTTAGTAATTTATGATTAGGTTATATAAATG
* * *
64646129 GTTAGTGTTTGGTTTAGT
191 GTTAGTATTTAGTTTAGG
64646147 GTTTTGTGATTTTTT
1 GTTTTGTGATTTTTT
64646162 TTAAATTTAA
Statistics
Matches: 197, Mismatches: 17, Indels: 22
0.83 0.07 0.09
Matches are distributed among these distances:
205 7 0.04
208 61 0.31
209 1 0.01
210 21 0.11
211 1 0.01
212 59 0.30
214 5 0.03
215 29 0.15
216 13 0.07
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (208 bp):
GTTTTGTGATTTTTTAGTAATGTAAATTTTTAAAAAATAATTTTATAGTTATTTTGTCAATAATT
TATGATTAGGTTATATAAATTCTTAGTGTTATTTAGTGTTTTGTGATTTTTTAGTAACGTAAATT
TCTTTTAAAAAAATATTTATAGTTATTTGGTTAGTAATTTATGATTAGGTTATATAAATGGTTAG
TATTTAGTTTAGG
Found at i:64646003 original size:106 final size:107
Alignment explanation
Indices: 64645725--64646161 Score: 517
Period size: 106 Copynumber: 4.2 Consensus size: 107
64645715 ATAAATTGTT
* * *
64645725 GTGTTTTGTGAGTTTTTAGTAATGTAAAAATTTTTT-AAAAATA-ATTTTATAGTTATTTTGTTA
1 GTGTTTTGTGATTTTTTAGTAATGT-AAATTTTTTTAAAAAAAATATTTTATAGTTATTTTGTTA
* * *
64645788 ATAGTTTATGATTATG-T-TATAAATTGTTAGTG--T--TTT-
65 GTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTA
* * * * * *
64645824 GTGTTTTGTTATTTTTTAGTAACGT-AATTTCTTTTAAAATAAATGTTATAGTTATTTATTTTGT
1 GTGTTTTGTGATTTTTTAGTAATGTAAATTT-TTTTAAAAAAAATATTTTA--TAGTTATTTTGT
*
64645888 TAGTAATTTATGGGATTAGG-T-TATAAATTGTTAGTATTTAGTTTA
63 TAGTAATTTAT--GATTAGGTTATATAAATTGTTAGTGTTTAGTTTA
* * *
64645933 GGGTTTTGTGATTTTTTAGTAATGT-AA-TTTTTAAAAAAAAATAATTTTATAGTTATTTTGTCA
1 GTGTTTTGTGATTTTTTAGTAATGTAAATTTTTTTAAAAAAAAT-ATTTTATAGTTATTTTGTTA
*
64645996 GTAATTTATGATTAGGTTATATAAATTCTTAGTGTTTAGTTTA
65 GTAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTA
* *
64646039 GTGTTTTGTGATTTTTTAGTAATGTAAATTTTTTTTAAAAAAATA-TTTATAGTTATTTGGTTAG
1 GTGTTTTGTGATTTTTTAGTAATGTAAATTTTTTTAAAAAAAATATTTTATAGTTATTTTGTTAG
* *
64646103 TAATTTATGATTAGGTTATATAAATGGTTAGTGTTTGGTTTA
66 TAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTA
64646145 GTGTTTTGTGATTTTTT
1 GTGTTTTGTGATTTTTT
64646162 TTAAATTTAA
Statistics
Matches: 289, Mismatches: 32, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
97 4 0.01
98 4 0.01
99 27 0.09
100 4 0.01
102 20 0.07
104 28 0.10
105 1 0.00
106 141 0.49
107 14 0.05
108 22 0.08
109 24 0.08
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (107 bp):
GTGTTTTGTGATTTTTTAGTAATGTAAATTTTTTTAAAAAAAATATTTTATAGTTATTTTGTTAG
TAATTTATGATTAGGTTATATAAATTGTTAGTGTTTAGTTTA
Found at i:64647296 original size:50 final size:50
Alignment explanation
Indices: 64647238--64647339 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
64647228 TGTAGTAGAC
*
64647238 ATAGGCGAATGCCTCAAATTGTTGCAGTCGTGGACACTTTACCGAATGCT
1 ATAGGCGAATGCCTCAAATTGTTGCAGTCATGGACACTTTACCGAATGCT
*
64647288 ATAGGCGAATGCCTCATATTGTTGCAGTCATGGACACTTTACCGAATGCT
1 ATAGGCGAATGCCTCAAATTGTTGCAGTCATGGACACTTTACCGAATGCT
64647338 AT
1 AT
64647340 TCTTGGCATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (50 bp):
ATAGGCGAATGCCTCAAATTGTTGCAGTCATGGACACTTTACCGAATGCT
Found at i:64648281 original size:33 final size:33
Alignment explanation
Indices: 64648212--64648287 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
64648202 TACCACTTCA
* ** *
64648212 GTACTCCAGTCATCTCGGTTCGTATCCACTACC
1 GTACTCCACTCATCTCGGCCCGTATCCACCACC
* **
64648245 GTACTCCACTCCTCTCGGCCCGTATCCACCGTC
1 GTACTCCACTCATCTCGGCCCGTATCCACCACC
64648278 GTACTCCACT
1 GTACTCCACT
64648288 ACTTCCGGCT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.16, C:0.42, G:0.14, T:0.28
Consensus pattern (33 bp):
GTACTCCACTCATCTCGGCCCGTATCCACCACC
Found at i:64648580 original size:75 final size:72
Alignment explanation
Indices: 64648451--64648640 Score: 226
Period size: 75 Copynumber: 2.6 Consensus size: 72
64648441 TCAAACCATC
* *
64648451 AATTTTAAGGG-TTTTTGTAATTTAAATA-AA-TTTATATTTATGTAATGAATTTTTTGCCATTT
1 AATTTTATGGGTTTTTTGTAATTTAAATATAACTTTGTA-TTATGTAATGAATTTTTTGCCATTT
*
64648513 TAGTTATT
65 AAGTTATT
*
64648521 AATTTTA-GGGTTTTTTTGTAATTTAAATAGTCAACTTTGTACTTATGTAATGACTTTTTTGCCA
1 AATTTTATGGG-TTTTTTGTAATTTAAATA-T-AACTTTGTA-TTATGTAATGAATTTTTTGCCA
64648585 TTTAAGTTATT
62 TTTAAGTTATT
* **
64648596 AATTTTATGGGTCTTTTACAATTTAAATAATAAACTTTGTATTAT
1 AATTTTATGGGTTTTTTGTAATTTAAAT-AT-AACTTTGTATTAT
64648641 TTATGTAAAA
Statistics
Matches: 104, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
69 3 0.03
70 7 0.07
71 17 0.16
74 6 0.06
75 67 0.64
76 4 0.04
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.52
Consensus pattern (72 bp):
AATTTTATGGGTTTTTTGTAATTTAAATATAACTTTGTATTATGTAATGAATTTTTTGCCATTTA
AGTTATT
Found at i:64651623 original size:19 final size:19
Alignment explanation
Indices: 64651569--64651623 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
64651559 ATTCAGAAGC
* *
64651569 TAACAAAATTAGTAAC--C
1 TAACAAAATTACTAACAAA
* **
64651586 TAACAAAATAACTTTCAAA
1 TAACAAAATTACTAACAAA
64651605 TAACAAAATTACTAACAAA
1 TAACAAAATTACTAACAAA
64651624 ACTCTTCATT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 12 0.43
19 16 0.57
ACGTcount: A:0.58, C:0.16, G:0.02, T:0.24
Consensus pattern (19 bp):
TAACAAAATTACTAACAAA
Found at i:64655026 original size:106 final size:106
Alignment explanation
Indices: 64654839--64655048 Score: 298
Period size: 106 Copynumber: 2.0 Consensus size: 106
64654829 AAAATGAGTA
* *
64654839 TTCTTATTTTTAGGGATTCGAGATATCGTGCCCTAACTTACACGGCATAATTCTCTTCTTGATTA
1 TTCTTATTTTTAGGGATTCGAGACATCGTGCCCTAACTTACACGGCATAATTCTCTTCTCGATTA
*
64654904 ACTCGAAATACGAAGACATTCTTCATAAAATTTGATTTAGT
66 ACTCGAAATACAAAGACATTCTTCATAAAATTTGATTTAGT
* * * * *
64654945 TTCTTATTTTTGGGGATTCGAGACATCGTGTCCTAACTTATGA-GGCATGATTTTCTT-TCCGAT
1 TTCTTATTTTTAGGGATTCGAGACATCGTGCCCTAACTTA-CACGGCATAATTCTCTTCT-CGAT
* *
64655008 TGACTCGAAATACAAAGACATTTTTCATAAAATTTGATTTA
64 TAACTCGAAATACAAAGACATTCTTCATAAAATTTGATTTA
64655049 ATTAACGATA
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
105 1 0.01
106 90 0.98
107 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.40
Consensus pattern (106 bp):
TTCTTATTTTTAGGGATTCGAGACATCGTGCCCTAACTTACACGGCATAATTCTCTTCTCGATTA
ACTCGAAATACAAAGACATTCTTCATAAAATTTGATTTAGT
Found at i:64657130 original size:8 final size:8
Alignment explanation
Indices: 64657095--64657122 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
64657085 TATTAATTAG
64657095 ATTTTATT
1 ATTTTATT
64657103 ATTTTATT
1 ATTTTATT
64657111 ATTTTATT
1 ATTTTATT
64657119 ATTT
1 ATTT
64657123 ATTTATTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTATT
Found at i:64658939 original size:30 final size:31
Alignment explanation
Indices: 64658899--64658958 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
64658889 ATGGATATTG
*
64658899 AGTCAAATATG-GCACTCAACCTTTAAAAAAA
1 AGTCAAATATGACCAC-CAACCTTTAAAAAAA
64658930 AGTC-AATATGACCACCAACCTTTAAAAAA
1 AGTCAAATATGACCACCAACCTTTAAAAAA
64658959 TAATTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.48, C:0.22, G:0.08, T:0.22
Consensus pattern (31 bp):
AGTCAAATATGACCACCAACCTTTAAAAAAA
Found at i:64659076 original size:10 final size:9
Alignment explanation
Indices: 64659057--64659105 Score: 50
Period size: 10 Copynumber: 5.4 Consensus size: 9
64659047 TTCATAATGA
64659057 TTTTTGAAT
1 TTTTTGAAT
64659066 TTTTATGAAT
1 TTTT-TGAAT
64659076 TTTTAT-ATAT
1 TTTT-TGA-AT
64659086 TTTTTGAA-
1 TTTTTGAAT
64659094 -TTTTGAAT
1 TTTTTGAAT
64659102 TTTT
1 TTTT
64659106 AGTTATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
7 7 0.20
9 10 0.29
10 18 0.51
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.67
Consensus pattern (9 bp):
TTTTTGAAT
Found at i:64659079 original size:18 final size:18
Alignment explanation
Indices: 64659056--64659124 Score: 63
Period size: 18 Copynumber: 3.8 Consensus size: 18
64659046 CTTCATAATG
64659056 ATTTTTGAATTTTTATGA
1 ATTTTTGAATTTTTATGA
*
64659074 ATTTTT-ATATATTTTTTGA
1 ATTTTTGA-AT-TTTTATGA
*
64659093 A-TTTTGAATTTTTA-GTT
1 ATTTTTGAATTTTTATG-A
*
64659110 ATTTTAGAATTTTTA
1 ATTTTTGAATTTTTA
64659125 AATTATTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
16 1 0.02
17 6 0.14
18 26 0.62
19 9 0.21
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.64
Consensus pattern (18 bp):
ATTTTTGAATTTTTATGA
Found at i:64659123 original size:26 final size:26
Alignment explanation
Indices: 64659056--64659136 Score: 78
Period size: 26 Copynumber: 3.0 Consensus size: 26
64659046 CTTCATAATG
64659056 ATTTTTGAATTTTTATGAATTTTTA-TAT
1 ATTTTTGAA-TTTT-TGAATTTTTAGT-T
64659084 ATTTTTTGAA-TTTTGAATTTTTAGTT
1 A-TTTTTGAATTTTTGAATTTTTAGTT
* *
64659110 ATTTTAGAATTTTTAAATTATTT-GTT
1 ATTTTTGAATTTTTGAATT-TTTAGTT
64659136 A
1 A
64659137 ATGTGGCATA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
25 7 0.15
26 24 0.51
27 7 0.15
28 1 0.02
29 8 0.17
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (26 bp):
ATTTTTGAATTTTTGAATTTTTAGTT
Found at i:64661995 original size:11 final size:11
Alignment explanation
Indices: 64661979--64662086 Score: 54
Period size: 11 Copynumber: 10.5 Consensus size: 11
64661969 AATTAATCAT
64661979 ATTAATATTAA
1 ATTAATATTAA
64661990 ATTAATA--AA
1 ATTAATATTAA
* *
64661999 A-TATTATCTAG
1 ATTAATAT-TAA
*
64662010 ATAAATATTAA
1 ATTAATATTAA
*
64662021 ATTAA-ATTTA
1 ATTAATATTAA
* * *
64662031 A-T-ATCTCAC
1 ATTAATATTAA
64662040 ATTAATATTAA
1 ATTAATATTAA
64662051 ATTAATA--AA
1 ATTAATATTAA
*
64662060 A-TACTATCTAA
1 ATTAATAT-TAA
*
64662071 ATAAATATTAA
1 ATTAATATTAA
64662082 ATTAA
1 ATTAA
64662087 ATTTAATATC
Statistics
Matches: 68, Mismatches: 18, Indels: 22
0.63 0.17 0.20
Matches are distributed among these distances:
8 9 0.13
9 9 0.13
10 6 0.09
11 36 0.53
12 8 0.12
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.40
Consensus pattern (11 bp):
ATTAATATTAA
Found at i:64662003 original size:16 final size:15
Alignment explanation
Indices: 64661982--64662086 Score: 51
Period size: 15 Copynumber: 6.9 Consensus size: 15
64661972 TAATCATATT
64661982 AATATTAAATTAATAA
1 AATATTAAATTAAT-A
64661998 AATATT--ATCTAGATA
1 AATATTAAAT-TA-ATA
64662013 AATATTAAA-T--TA
1 AATATTAAATTAATA
*
64662025 AAT-TTAATATCTCACATT
1 AATATTAA-AT-T-A-ATA
64662043 AATATTAAATTAATAA
1 AATATTAAATTAAT-A
* ** *
64662059 AATACTATCTAAATA
1 AATATTAAATTAATA
64662074 AATATTAAATTAA
1 AATATTAAATTAA
64662087 ATTTAATATC
Statistics
Matches: 66, Mismatches: 10, Indels: 27
0.64 0.10 0.26
Matches are distributed among these distances:
11 4 0.06
12 6 0.09
14 3 0.05
15 22 0.33
16 19 0.29
17 2 0.03
18 6 0.09
19 4 0.06
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (15 bp):
AATATTAAATTAATA
Found at i:64662020 original size:31 final size:31
Alignment explanation
Indices: 64661982--64662086 Score: 124
Period size: 31 Copynumber: 3.4 Consensus size: 31
64661972 TAATCATATT
* *
64661982 AATATTAAATTAATAAAATATTATCTAGATA
1 AATATTAAATTAATAAAATAATATCTAAATA
** * *
64662013 AATATTAAATT-A-AATTTAATATCTCACATT
1 AATATTAAATTAATAAAATAATATCT-AAATA
*
64662043 AATATTAAATTAATAAAATACTATCTAAATA
1 AATATTAAATTAATAAAATAATATCTAAATA
64662074 AATATTAAATTAA
1 AATATTAAATTAA
64662087 ATTTAATATC
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
29 9 0.15
30 15 0.25
31 28 0.46
32 9 0.15
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (31 bp):
AATATTAAATTAATAAAATAATATCTAAATA
Found at i:64662075 original size:61 final size:61
Alignment explanation
Indices: 64661979--64662108 Score: 224
Period size: 61 Copynumber: 2.1 Consensus size: 61
64661969 AATTAATCAT
* *
64661979 ATTAATATTAAATTAATAAAATATTATCTAGATAAATATTAAATTAAATTTAATATCTCAC
1 ATTAATATTAAATTAATAAAATACTATCTAAATAAATATTAAATTAAATTTAATATCTCAC
*
64662040 ATTAATATTAAATTAATAAAATACTATCTAAATAAATATTAAATTAAATTTAATATCTCAT
1 ATTAATATTAAATTAATAAAATACTATCTAAATAAATATTAAATTAAATTTAATATCTCAC
*
64662101 TTTAATAT
1 ATTAATAT
64662109 ATAGATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (61 bp):
ATTAATATTAAATTAATAAAATACTATCTAAATAAATATTAAATTAAATTTAATATCTCAC
Found at i:64663521 original size:12 final size:12
Alignment explanation
Indices: 64663506--64663535 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
64663496 AATGATTAAA
64663506 TAAATTAAAAAT
1 TAAATTAAAAAT
*
64663518 TAAATTAGAAAT
1 TAAATTAAAAAT
64663530 TAAATT
1 TAAATT
64663536 CGGATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (12 bp):
TAAATTAAAAAT
Found at i:64664667 original size:136 final size:136
Alignment explanation
Indices: 64664423--64664693 Score: 524
Period size: 136 Copynumber: 2.0 Consensus size: 136
64664413 TTCTATTTTT
*
64664423 GGCTTTTACAAAGTCAAAAGAATATGATAAGTCCTTAACTTTTTCCACATTTTTTATTCGACCTC
1 GGCTTTTACAAAGTCAAAAGAATATGATAAGTCCTTAACTTTTTCCACATTTTTTATTCAACCTC
64664488 ATTTCATTGATTGTGTTTCAATTTGGTCATTTCCTGGTCGTTTTTTACTCTTAGCGTCCCAATTG
66 ATTTCATTGATTGTGTTTCAATTTGGTCATTTCCTGGTCGTTTTTTACTCTTAGCGTCCCAATTG
64664553 CATCCA
131 CATCCA
*
64664559 GGCTTTTACAAAGTCAGAAGAATATGATAAGTCCTTAACTTTTTCCACATTTTTTATTCAACCTC
1 GGCTTTTACAAAGTCAAAAGAATATGATAAGTCCTTAACTTTTTCCACATTTTTTATTCAACCTC
64664624 ATTTCATTGATTGTGTTTCAATTTGGTCATTTCCTGGTCGTTTTTTACTCTTAGCGTCCCAATTG
66 ATTTCATTGATTGTGTTTCAATTTGGTCATTTCCTGGTCGTTTTTTACTCTTAGCGTCCCAATTG
64664689 CATCC
131 CATCC
64664694 CTGATAAGAT
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 133 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (136 bp):
GGCTTTTACAAAGTCAAAAGAATATGATAAGTCCTTAACTTTTTCCACATTTTTTATTCAACCTC
ATTTCATTGATTGTGTTTCAATTTGGTCATTTCCTGGTCGTTTTTTACTCTTAGCGTCCCAATTG
CATCCA
Found at i:64665905 original size:25 final size:25
Alignment explanation
Indices: 64665877--64665930 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
64665867 GAATATTTTG
* * *
64665877 TAAAGATTTTGTGGTGAACTCTCTA
1 TAAAGACTTTATGGCGAACTCTCTA
* *
64665902 TAAAGCCTTTATGGCGAACTCTCTG
1 TAAAGACTTTATGGCGAACTCTCTA
64665927 TAAA
1 TAAA
64665931 ACATTCTTGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (25 bp):
TAAAGACTTTATGGCGAACTCTCTA
Found at i:64670116 original size:3 final size:3
Alignment explanation
Indices: 64670108--64670144 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
64670098 TTTCGTGTCT
64670108 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
64670145 GTCATTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:64673803 original size:5 final size:5
Alignment explanation
Indices: 64673795--64673829 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
64673785 ATCACATTTC
**
64673795 CCCTG CCCTG AACTG CCCTG CCCTG CCCTG CCCTG
1 CCCTG CCCTG CCCTG CCCTG CCCTG CCCTG CCCTG
64673830 GTATCTTAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.06, C:0.54, G:0.20, T:0.20
Consensus pattern (5 bp):
CCCTG
Found at i:64679948 original size:16 final size:16
Alignment explanation
Indices: 64679927--64679961 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
64679917 TTGTGTTTTG
*
64679927 TTTTGACTGCATGACA
1 TTTTGACTACATGACA
*
64679943 TTTTGACTACATGGCA
1 TTTTGACTACATGACA
64679959 TTT
1 TTT
64679962 CATTATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (16 bp):
TTTTGACTACATGACA
Found at i:64682607 original size:12 final size:13
Alignment explanation
Indices: 64682578--64682609 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
64682568 ATTCAATCCA
64682578 AAAAAATAAGAAC
1 AAAAAATAAGAAC
64682591 AAAAAATAAGAAC
1 AAAAAATAAGAAC
64682604 AAAAAA
1 AAAAAA
64682610 CAAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.06, T:0.06
Consensus pattern (13 bp):
AAAAAATAAGAAC
Found at i:64685172 original size:252 final size:252
Alignment explanation
Indices: 64684727--64685222 Score: 796
Period size: 252 Copynumber: 2.0 Consensus size: 252
64684717 TACTTCTCTG
* * *
64684727 GCGGTGTAGGGGACCAGATTAAAGCTACGACGACGAATCTCGTTTCCCCGACATTACAGTTAAAT
1 GCGGTGTAGGGGACCAGATTAAAGCCACAACGACGAATCTCGTTTCCCCAACATTACAGTTAAAT
* * *
64684792 AGATTGAAGCCACAACGGCAAATCTTACTTCTCCGGCATTGCAACGGAGCAGATTGAAGCCACGA
66 AGATTAAAGCCACAACGACAAATCTTACTTCCCCGGCATTGCAACGGAGCAGATTGAAGCCACGA
* * *
64684857 CGGTGAATCTTATCTTCCTCGCATTAAGACTTGGATTAGCTAAAGTGGAGCGGATTAAGGCTGTG
131 CGGTGAATCTTATCTCCCTCGCATTAAGACTTAGATTAGCTAAAGTGGAGCGGATTAAGGCTGTA
* *
64684922 GGCAGCAAATCCTATCTCTTTGGCATTACAGTGGAATGGATTGAAGCCATGATGATA
196 GACAGCAAATCCTATCTCTTTGGCATTACAGTGGAATAGATTGAAGCCATGATGATA
* *
64684979 GCGGTGTAGGGGACCAGATTGAAGCCACAAC-AGCGAATCTCGTTTCCCCAACATTTCAGTTAAA
1 GCGGTGTAGGGGACCAGATTAAAGCCACAACGA-CGAATCTCGTTTCCCCAACATTACAGTTAAA
* * *
64685043 TAGATTAAAGCCACAACGACGAATCTTACTTCCCCGGCGTTGCAGCGGAGCAGATTGAAGCCACG
65 TAGATTAAAGCCACAACGACAAATCTTACTTCCCCGGCATTGCAACGGAGCAGATTGAAGCCACG
* * *
64685108 ATGGTGAATCTTATCTCCCTGGCGTTAAGACTTAGATTAGCTAAAGTGGAGCGGATTAAGGCTGT
130 ACGGTGAATCTTATCTCCCTCGCATTAAGACTTAGATTAGCTAAAGTGGAGCGGATTAAGGCTGT
*
64685173 AGACAGCGAATCCTATCTCTTTGGCATTACAGTGGAATAGATTGAAGCCA
195 AGACAGCAAATCCTATCTCTTTGGCATTACAGTGGAATAGATTGAAGCCA
64685223 AAACGTCAAA
Statistics
Matches: 223, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
251 1 0.00
252 222 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.25
Consensus pattern (252 bp):
GCGGTGTAGGGGACCAGATTAAAGCCACAACGACGAATCTCGTTTCCCCAACATTACAGTTAAAT
AGATTAAAGCCACAACGACAAATCTTACTTCCCCGGCATTGCAACGGAGCAGATTGAAGCCACGA
CGGTGAATCTTATCTCCCTCGCATTAAGACTTAGATTAGCTAAAGTGGAGCGGATTAAGGCTGTA
GACAGCAAATCCTATCTCTTTGGCATTACAGTGGAATAGATTGAAGCCATGATGATA
Found at i:64685283 original size:50 final size:50
Alignment explanation
Indices: 64685202--64685693 Score: 365
Period size: 50 Copynumber: 9.8 Consensus size: 50
64685192 TTTGGCATTA
* * * * *
64685202 CAGTGGAATAGATTGAAGCCAAAACGTCAAATCTTACTTCCCTAGCAGTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTG
* * * * * * * *
64685252 TAGTGGAACAGATTGAAGCTACGACGGCAAATCTTATTTCCCCGACATTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTG
* ** * ** *
64685302 CAATTAAATAGATTGAAGCCACAACGATGAATCTTACTTCCCTGGCGGTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTG
* * * * * ** * * *
64685352 TAGTGGAATAGATTGAAGCTACGACGGTGAATCTTGTTTCCCCGACATTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTG
* * ** * *
64685402 TAATTAAATAGATTGAAGCCACAACGGCGAATCTTACTTCACTGGC-GATG
1 CAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAG-TG
** * ** * * *
64685452 CAGTGGAACAGATTGAAGTTACAACGGTGAATCTTGTTTCCTTGACATTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTG
* ** * * * *
64685502 CAATTAAAAAGATTGAAGCCACAATGGTGAATCTTACTTCCCTGGCGGTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTG
** * * * * *
64685552 CAGTGGAACAGATTGAAGGTACAACGACGAATCTTACTTCCCCGACATTA
1 CAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTG
* ** * * *
64685602 CAATTAAAAAGATTGAAGCCACAATGGCAAATCTTACTTCCCTGGCAGTG
1 CAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTG
* * *
64685652 CAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGCTTCCC
1 CAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCC
64685694 CGACATTACA
Statistics
Matches: 326, Mismatches: 114, Indels: 4
0.73 0.26 0.01
Matches are distributed among these distances:
50 326 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (50 bp):
CAGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCAGTG
Found at i:64685385 original size:100 final size:100
Alignment explanation
Indices: 64685208--64685719 Score: 657
Period size: 100 Copynumber: 5.1 Consensus size: 100
64685198 ATTACAGTGG
* * * * *
64685208 AATAGATTGAAGCCAAAAC-GTCAAATCTTACTTCCCTAGCAGTGTAGTGGAACAGATTGAAGCT
1 AATAGATTGAAGCCACAACGGT-GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCT
* * *
64685272 ACGACGGCAAATCTTATTTCCCCGACATTGCAATTA
65 ACAACGGCGAATCTTGTTTCCCCGACATTGCAATTA
* * *
64685308 AATAGATTGAAGCCACAACGATGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTA
1 AATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTA
* * *
64685373 CGACGGTGAATCTTGTTTCCCCGACATTGTAATTA
66 CAACGGCGAATCTTGTTTCCCCGACATTGCAATTA
* * * *
64685408 AATAGATTGAAGCCACAACGGCGAATCTTACTTCACTGGCGATGCAGTGGAACAGATTGAAGTTA
1 AATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTA
* **
64685473 CAACGGTGAATCTTGTTTCCTTGACATTGCAATTA
66 CAACGGCGAATCTTGTTTCCCCGACATTGCAATTA
* * *
64685508 AAAAGATTGAAGCCACAATGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGGTA
1 AATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTA
* ** *
64685573 CAACGACGAATCTTACTTCCCCGACATTACAATTA
66 CAACGGCGAATCTTGTTTCCCCGACATTGCAATTA
* * ** *
64685608 AAAAGATTGAAGCCACAATGGCAAATCTTACTTCCCTGGCAGTGCAGTGGAACAGATTGAAGCTA
1 AATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTA
* * * *
64685673 CAACAGCGAATCTTGCTTCCCCGACATTACAGTTA
66 CAACGGCGAATCTTGTTTCCCCGACATTGCAATTA
* *
64685708 ATTAGACTGAAG
1 AATAGATTGAAG
64685720 ATAGCGAATC
Statistics
Matches: 366, Mismatches: 45, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
100 365 1.00
101 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (100 bp):
AATAGATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTA
CAACGGCGAATCTTGTTTCCCCGACATTGCAATTA
Found at i:64685877 original size:44 final size:44
Alignment explanation
Indices: 64685829--64685924 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 44
64685819 GTATTATCCT
* * * *
64685829 CCTGAAGTGGCA-TGGGGCAGACTGAAGATAGCGAGTCTTATCTC
1 CCTGAAGTGACAGTGGAGCAGACTGAAGATA-CGAATCCTATCTC
* * * *
64685873 CCTGAAGTTATAGTGGAGCAGACTGAAGCTACTAATCCTATCTC
1 CCTGAAGTGACAGTGGAGCAGACTGAAGATACGAATCCTATCTC
64685917 CCTGAAGT
1 CCTGAAGT
64685925 TGCAATAGAG
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 27 0.63
45 16 0.37
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (44 bp):
CCTGAAGTGACAGTGGAGCAGACTGAAGATACGAATCCTATCTC
Found at i:64686154 original size:88 final size:88
Alignment explanation
Indices: 64686005--64686204 Score: 228
Period size: 88 Copynumber: 2.3 Consensus size: 88
64685995 ATATCAAACA
* * * * * *
64686005 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTAGAAGATACAAGTCTTATCTCCCTGAAGTTGCAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGCTAAAACATACAAGTCTCATCCCCCTGAAGTTGCAGC
*
64686070 GGAGCAGG-TAGAAGATACAAGTC
66 AGAG-AGGATAGAAGATACAAGTC
*
64686093 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAACCAT-CAA-TCTCGTCCCCCTGAAGTTGCA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAG-CTAAAA-CATACAAGTCTCATCCCCCTGAAGTTGCA
* * *
64686156 GCAGAGTGGATTGAAGCTACAAGTC
64 GCAGAGAGGATAGAAGATACAAGTC
* *
64686181 GTATCTCTCTGAAG-TGCAGTGGAG
1 TTATCTCCCTGAAGTTGCAGTGGAG
64686205 TAGATCGAAG
Statistics
Matches: 96, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
87 12 0.12
88 75 0.78
89 7 0.07
90 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (88 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGCTAAAACATACAAGTCTCATCCCCCTGAAGTTGCAGC
AGAGAGGATAGAAGATACAAGTC
Found at i:64686156 original size:44 final size:44
Alignment explanation
Indices: 64686005--64686120 Score: 232
Period size: 44 Copynumber: 2.6 Consensus size: 44
64685995 ATATCAAACA
64686005 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTAGAAGATACAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTAGAAGATACAAGTC
64686049 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTAGAAGATACAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGGTAGAAGATACAAGTC
64686093 TTATCTCCCTGAAGTTGCAGTGGAGCAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAG
64686121 ACTAAAACCA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (44 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGGTAGAAGATACAAGTC
Found at i:64687451 original size:3 final size:3
Alignment explanation
Indices: 64687436--64687528 Score: 57
Period size: 3 Copynumber: 31.3 Consensus size: 3
64687426 AGGTTTTTTT
* * * *
64687436 TTA TT- TTA ATA TTA TTA ATA TTG TTA -TA TTGCA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT--A TTA TTA TTA TTA
* * * * * *
64687481 -TA TTT TTA TTA TTA TTA CTA TTA TTA ATA TAA TAA TAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
64687528 T
1 T
64687529 AACCATGTAT
Statistics
Matches: 69, Mismatches: 16, Indels: 10
0.73 0.17 0.11
Matches are distributed among these distances:
2 6 0.09
3 61 0.88
5 2 0.03
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:64693257 original size:21 final size:21
Alignment explanation
Indices: 64693231--64693271 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
64693221 ATCTGCTCAA
* *
64693231 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
64693252 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
64693272 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:64712238 original size:18 final size:17
Alignment explanation
Indices: 64712210--64712244 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
64712200 ATTATTAAGA
*
64712210 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
64712227 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
64712245 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:64712493 original size:45 final size:44
Alignment explanation
Indices: 64712404--64712498 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
64712394 TTACACCTCT
*
64712404 ATTACATTCAACCAAACACAGGATTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
*** *
64712448 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACACAGGA-TTACTATTACACCTCTATTCC
64712493 ATTACA
1 ATTACA
64712499 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 20 0.44
45 25 0.56
ACGTcount: A:0.34, C:0.27, G:0.06, T:0.33
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAGGATTACTATTACACCTCTATTCC
Found at i:64712526 original size:16 final size:16
Alignment explanation
Indices: 64712479--64712528 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
64712469 GATTTGCTAT
* *
64712479 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
64712495 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
64712511 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
64712527 TA
1 TA
64712529 TAGCGAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.34, C:0.36, G:0.00, T:0.30
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:64720121 original size:21 final size:22
Alignment explanation
Indices: 64720087--64720131 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
64720077 AGTTCATCGT
* *
64720087 TTTAGGAATCTTATTTTTTTTA
1 TTTAGCAATCTTATCTTTTTTA
64720109 TTTAGCAA-CTTATCTTTTTTA
1 TTTAGCAATCTTATCTTTTTTA
64720130 TT
1 TT
64720132 AATTTAGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.22, C:0.09, G:0.07, T:0.62
Consensus pattern (22 bp):
TTTAGCAATCTTATCTTTTTTA
Found at i:64722639 original size:60 final size:60
Alignment explanation
Indices: 64722540--64722658 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
64722530 TTATTTTTTA
* *
64722540 TAATTATTTTAAAATTAATTTGTTAGTAATTTAATATTATGTTATAAACTGTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTATGTTATAAACTGTTGTGTTTG
* * *
64722600 TAATTATTTTAAAATTATTTTATTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTATGTTATAAACTGTTGTGTTT
64722659 AGTTTAGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 54 1.00
ACGTcount: A:0.33, C:0.01, G:0.12, T:0.55
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAAGATTATGTTATAAACTGTTGTGTTTG
Found at i:64724432 original size:15 final size:14
Alignment explanation
Indices: 64724409--64724463 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
64724399 TTTGAATTTT
*
64724409 TTTTTATTTTAAAA
1 TTTTAATTTTAAAA
*
64724423 TTTTTAATTTTTAAA
1 -TTTTAATTTTAAAA
*
64724438 TTTCAATTTTTAAAA
1 TTTTAA-TTTTAAAA
64724453 -TTTAATTTTAA
1 TTTTAATTTTAA
64724464 TTATTAGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
13 6 0.18
14 9 0.26
15 19 0.56
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAATTTTAAAA
Found at i:64724456 original size:21 final size:20
Alignment explanation
Indices: 64724421--64724465 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
64724411 TTTATTTTAA
**
64724421 AATTTTTAATTTTTAAATTTC
1 AATTTTTAAAATTT-AATTTC
*
64724442 AATTTTTAAAATTTAATTTT
1 AATTTTTAAAATTTAATTTC
64724462 AATT
1 AATT
64724466 ATTAGTATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTTTTAAAATTTAATTTC
Found at i:64724459 original size:14 final size:14
Alignment explanation
Indices: 64724415--64724461 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
64724405 TTTTTTTTTA
64724415 TTTTAAAATTTTTAAT
1 TTTTAAAA--TTTAAT
64724431 TTTT-AAATTTCAAT
1 TTTTAAAATTT-AAT
64724445 TTTTAAAATTTAAT
1 TTTTAAAATTTAAT
64724459 TTT
1 TTT
64724462 AATTATTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.10
14 13 0.45
15 9 0.31
16 4 0.14
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTAAAATTTAAT
Found at i:64729786 original size:15 final size:15
Alignment explanation
Indices: 64729768--64729811 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
64729758 TCGTCCACCT
*
64729768 CCTCCTCCGCCTCCG
1 CCTCCTCCACCTCCG
*
64729783 CCTCCCCCACCTCCG
1 CCTCCTCCACCTCCG
*
64729798 CCCCCTCCACCTCC
1 CCTCCTCCACCTCC
64729812 TCCGGCACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.05, C:0.73, G:0.07, T:0.16
Consensus pattern (15 bp):
CCTCCTCCACCTCCG
Found at i:64736572 original size:21 final size:24
Alignment explanation
Indices: 64736548--64736590 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
64736538 AAATTTATTA
64736548 TTAA-GCTTT-ATT-TTAACAATT
1 TTAACGCTTTCATTCTTAACAATT
*
64736569 TTAACGTTTTCATTCTTAACAA
1 TTAACGCTTTCATTCTTAACAA
64736591 GCATTATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 3 0.17
24 7 0.39
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.49
Consensus pattern (24 bp):
TTAACGCTTTCATTCTTAACAATT
Found at i:64738947 original size:28 final size:27
Alignment explanation
Indices: 64738916--64738983 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
64738906 ATGTTTTTGA
** *
64738916 ATTTATTTTTTTAATAATTATAATTTAT
1 ATTTATTTTTAAAATAA-CATAATTTAT
*
64738944 ATTTATTTTTAAAATAACATTATTTAT
1 ATTTATTTTTAAAATAACATAATTTAT
64738971 ATTTATTTTTAAA
1 ATTTATTTTTAAA
64738984 TCCTTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.58
28 15 0.42
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (27 bp):
ATTTATTTTTAAAATAACATAATTTAT
Found at i:64740858 original size:49 final size:50
Alignment explanation
Indices: 64740765--64740866 Score: 179
Period size: 49 Copynumber: 2.1 Consensus size: 50
64740755 TAAAACAACC
*
64740765 ATAGTTATGGTAGTTGTGCTTCCCTCCCCTTCAATGTAATAATATATATA
1 ATAGTTATGGTAGTTGTGATTCCCTCCCCTTCAATGTAATAATATATATA
*
64740815 ATAGTTATGGTAGTTGTGATT-CCTCTCCTTCAATGTAATAATATATATA
1 ATAGTTATGGTAGTTGTGATTCCCTCCCCTTCAATGTAATAATATATATA
64740864 ATA
1 ATA
64740867 AAACCTAAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
49 30 0.60
50 20 0.40
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (50 bp):
ATAGTTATGGTAGTTGTGATTCCCTCCCCTTCAATGTAATAATATATATA
Found at i:64746601 original size:12 final size:12
Alignment explanation
Indices: 64746586--64746665 Score: 63
Period size: 12 Copynumber: 6.4 Consensus size: 12
64746576 TTCTTTCTCC
64746586 CTTTTTTTCTTT
1 CTTTTTTTCTTT
*
64746598 CTTTCTTTCTTT
1 CTTTTTTTCTTT
* *
64746610 C-TTTTCTGTTT
1 CTTTTTTTCTTT
* *
64746621 CATTTTTGCTTTGT
1 CTTTTTTTC-TT-T
*
64746635 CTCTTTTTCTATTT
1 CT-TTTTT-TCTTT
64746649 CTTTTTTTCTTT
1 CTTTTTTTCTTT
64746661 CTTTT
1 CTTTT
64746666 ATTTATTTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 10
0.71 0.15 0.14
Matches are distributed among these distances:
11 8 0.15
12 25 0.48
13 7 0.13
14 5 0.10
15 7 0.13
ACGTcount: A:0.03, C:0.19, G:0.04, T:0.75
Consensus pattern (12 bp):
CTTTTTTTCTTT
Found at i:64746680 original size:13 final size:13
Alignment explanation
Indices: 64746644--64746682 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
64746634 TCTCTTTTTC
64746644 TATTTCTTTT-TT
1 TATTTCTTTTATT
*
64746656 TCTTTCTTTTATT
1 TATTTCTTTTATT
*
64746669 TATTTATTTTATT
1 TATTTCTTTTATT
64746682 T
1 T
64746683 TAATATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (13 bp):
TATTTCTTTTATT
Found at i:64753257 original size:3 final size:3
Alignment explanation
Indices: 64753249--64753277 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
64753239 ACAGTCTAAC
64753249 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
64753278 TAATTTCCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:64765905 original size:19 final size:19
Alignment explanation
Indices: 64765865--64765905 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
64765855 TAAGATTGTC
*
64765865 AAAATATCTAAAAAAATTG
1 AAAATATCTAAAAAAATGG
64765884 AAAA-ATCTAAAAAATATGG
1 AAAATATCTAAAAAA-ATGG
64765903 AAA
1 AAA
64765906 GATTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.22
Consensus pattern (19 bp):
AAAATATCTAAAAAAATGG
Found at i:64766426 original size:33 final size:34
Alignment explanation
Indices: 64766362--64766426 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
64766352 TAATTTTTAT
*
64766362 TTTCTAAATTTTTTTGTTTTTTTAATAGAAAAAA
1 TTTCTAAATTTTTTTATTTTTTTAATAGAAAAAA
* *
64766396 TTTCTATATTTTTTTATTTTTTTCAT-GAAAA
1 TTTCTAAATTTTTTTATTTTTTTAATAGAAAA
64766427 TAGGATTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 5 0.18
34 23 0.82
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (34 bp):
TTTCTAAATTTTTTTATTTTTTTAATAGAAAAAA
Found at i:64767638 original size:23 final size:23
Alignment explanation
Indices: 64767605--64767677 Score: 103
Period size: 23 Copynumber: 3.1 Consensus size: 23
64767595 AGTTATACTA
*
64767605 TTGCATCGAAGTGTCACTTTCAT
1 TTGCATCGAAGTGCCACTTTCAT
*
64767628 TTGCA-CAGAAGTGCCACATTTCAA
1 TTGCATC-GAAGTGCCAC-TTTCAT
64767652 TTGCATCGAAGTGCCACTTTCAT
1 TTGCATCGAAGTGCCACTTTCAT
64767675 TTG
1 TTG
64767678 TGCGCATAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
22 1 0.02
23 22 0.50
24 20 0.45
25 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (23 bp):
TTGCATCGAAGTGCCACTTTCAT
Found at i:64767655 original size:24 final size:23
Alignment explanation
Indices: 64767604--64767673 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 23
64767594 CAGTTATACT
*
64767604 ATTGCATCGAAGTGTCACTTTCA
1 ATTGCATCGAAGTGCCACTTTCA
*
64767627 TTTGCA-CAGAAGTGCCACATTTCA
1 ATTGCATC-GAAGTGCCAC-TTTCA
64767651 ATTGCATCGAAGTGCCACTTTCA
1 ATTGCATCGAAGTGCCACTTTCA
64767674 TTTGTGCGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 1 0.02
23 19 0.46
24 20 0.49
25 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.31
Consensus pattern (23 bp):
ATTGCATCGAAGTGCCACTTTCA
Found at i:64768208 original size:28 final size:28
Alignment explanation
Indices: 64768176--64768232 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
64768166 TGTTGCTTTT
64768176 TCCACATTATGATGGTTACACTTTCTCC
1 TCCACATTATGATGGTTACACTTTCTCC
64768204 TCCACATTATGATGGTTACACTTTCTCC
1 TCCACATTATGATGGTTACACTTTCTCC
64768232 T
1 T
64768233 ATACAGTGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.28, G:0.11, T:0.40
Consensus pattern (28 bp):
TCCACATTATGATGGTTACACTTTCTCC
Found at i:64770509 original size:26 final size:25
Alignment explanation
Indices: 64770471--64770520 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
64770461 CCTAATTCCT
*
64770471 AAAAAACCTTAACCCTAACAAAATA
1 AAAAAACCCTAACCCTAACAAAATA
*
64770496 AAAAAAGCCCTAACCCTATCAAAAT
1 AAAAAA-CCCTAACCCTAACAAAAT
64770521 TTTTCTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.56, C:0.26, G:0.02, T:0.16
Consensus pattern (25 bp):
AAAAAACCCTAACCCTAACAAAATA
Found at i:64774540 original size:21 final size:20
Alignment explanation
Indices: 64774516--64774561 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
64774506 AATCTTAGGC
* *
64774516 TAAAAATTATTAGAAAATCTA
1 TAAAAATAATTAAAAAATC-A
64774537 TAAAAATAATTAAAAAATCA
1 TAAAAATAATTAAAAAATCA
64774557 TAAAA
1 TAAAA
64774562 TTTAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (20 bp):
TAAAAATAATTAAAAAATCA
Found at i:64785791 original size:20 final size:21
Alignment explanation
Indices: 64785755--64785793 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
64785745 AAAAGACGGT
64785755 CAAAATAGTTTCTTAAAGAGC
1 CAAAATAGTTTCTTAAAGAGC
64785776 CAAAA-AGTTTGC-TAAAGA
1 CAAAATAGTTT-CTTAAAGA
64785794 ATGAGAGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (21 bp):
CAAAATAGTTTCTTAAAGAGC
Found at i:64800308 original size:27 final size:27
Alignment explanation
Indices: 64800259--64800317 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
64800249 CCCGATATAT
*
64800259 GGCTC-TTCGTGAGCTTCTCGATTAAA
1 GGCTCTTTCATGAGCTTCTCGATTAAA
* * *
64800285 GGCTCTTTCATGATCTTCTTGATTAAT
1 GGCTCTTTCATGAGCTTCTCGATTAAA
64800312 GGCTCT
1 GGCTCT
64800318 CCAGAACTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (27 bp):
GGCTCTTTCATGAGCTTCTCGATTAAA
Found at i:64800420 original size:24 final size:24
Alignment explanation
Indices: 64800393--64800454 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
64800383 TGGCTCTTTG
*
64800393 GAGCTACCCGTTATTAGCTCGTAT
1 GAGCTTCCCGTTATTAGCTCGTAT
* * *
64800417 GAGCTTCCTGATTA-TGGCTCTTAT
1 GAGCTTCCCG-TTATTAGCTCGTAT
64800441 GAGCTTCCCGTTAT
1 GAGCTTCCCGTTAT
64800455 ACAGCCCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 3 0.10
24 25 0.81
25 3 0.10
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (24 bp):
GAGCTTCCCGTTATTAGCTCGTAT
Found at i:64800495 original size:25 final size:25
Alignment explanation
Indices: 64800415--64800511 Score: 106
Period size: 25 Copynumber: 3.9 Consensus size: 25
64800405 ATTAGCTCGT
* **
64800415 ATGAGCTTCCTGAT-TATGGCTCTT
1 ATGAGCTTCCTGTTATATGGCTCAC
* ** * *
64800439 ATGAGCTTCCCGTTATACAGCCCAG
1 ATGAGCTTCCTGTTATATGGCTCAC
*
64800464 ATAAGCTTCCTGTTATATGGCTCAC
1 ATGAGCTTCCTGTTATATGGCTCAC
64800489 ATGAGCTTCCTGTTATATGGCTC
1 ATGAGCTTCCTGTTATATGGCTC
64800512 GAGAGATGGC
Statistics
Matches: 58, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
24 12 0.21
25 46 0.79
ACGTcount: A:0.21, C:0.25, G:0.20, T:0.35
Consensus pattern (25 bp):
ATGAGCTTCCTGTTATATGGCTCAC
Found at i:64800522 original size:12 final size:12
Alignment explanation
Indices: 64800505--64800529 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
64800495 TTCCTGTTAT
64800505 ATGGCTCGAGAG
1 ATGGCTCGAGAG
64800517 ATGGCTCGAGAG
1 ATGGCTCGAGAG
64800529 A
1 A
64800530 GAGCATCCTG
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:0.28, C:0.16, G:0.40, T:0.16
Consensus pattern (12 bp):
ATGGCTCGAGAG
Found at i:64801743 original size:42 final size:42
Alignment explanation
Indices: 64801682--64801773 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
64801672 CCTAAATTGG
64801682 ACACGGCCGTAGACACGGGCGTGTCTCTTGGCCATGTGAGCC
1 ACACGGCCGTAGACACGGGCGTGTCTCTTGGCCATGTGAGCC
*
64801724 AGACGGCCGTAGACACGGGCGTGTCTCTTGGCCATGTGAGCC
1 ACACGGCCGTAGACACGGGCGTGTCTCTTGGCCATGTGAGCC
64801766 ACACGGCC
1 ACACGGCC
64801774 TGGCCATATG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.17, C:0.32, G:0.34, T:0.17
Consensus pattern (42 bp):
ACACGGCCGTAGACACGGGCGTGTCTCTTGGCCATGTGAGCC
Found at i:64806202 original size:29 final size:28
Alignment explanation
Indices: 64806134--64806203 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 28
64806124 AGGGGTCTGA
*
64806134 TGCCGCCTGACAACATTCCTCCAAATGG
1 TGCCGCCTGACAACATCCCTCCAAATGG
* * ** **
64806162 TGTCGCTTGACAATGTCCCTCCACCTGGG
1 TGCCGCCTGACAACATCCCTCCAAAT-GG
64806191 TGCCGCCTGACAA
1 TGCCGCCTGACAA
64806204 ATCTCTTCCA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
28 19 0.59
29 13 0.41
ACGTcount: A:0.20, C:0.36, G:0.21, T:0.23
Consensus pattern (28 bp):
TGCCGCCTGACAACATCCCTCCAAATGG
Found at i:64819158 original size:21 final size:21
Alignment explanation
Indices: 64819132--64819172 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
64819122 ATCTGCTCAA
*
64819132 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGTTGTGGAGTAC
64819153 ACTCCACCTGTTGTGGAGTA
1 ACTCCACCTGTTGTGGAGTA
64819173 TTGCTCGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGTTGTGGAGTAC
Found at i:64827068 original size:13 final size:13
Alignment explanation
Indices: 64827049--64827090 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
64827039 TTTTTAATCT
64827049 AATATATATTTTA
1 AATATATATTTTA
* *
64827062 TATATATATATTA
1 AATATATATTTTA
*
64827075 AATATATATTTAA
1 AATATATATTTTA
64827088 AAT
1 AAT
64827091 GGGTCGGGCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATATATATTTTA
Found at i:64827070 original size:15 final size:15
Alignment explanation
Indices: 64827050--64827083 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
64827040 TTTTAATCTA
**
64827050 ATATATATTTTATAT
1 ATATATATTAAATAT
64827065 ATATATATTAAATAT
1 ATATATATTAAATAT
64827080 ATAT
1 ATAT
64827084 TTAAAATGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATATTAAATAT
Found at i:64832649 original size:69 final size:67
Alignment explanation
Indices: 64832559--64832694 Score: 209
Period size: 69 Copynumber: 2.0 Consensus size: 67
64832549 TTTATATTTT
* *
64832559 AATTTTGTAATTTATTTTTTTCAAATTTCTTTTAGAAATTAAAATATTTAAATTTTAAGATTTTG
1 AATTTTGTAATTTATTATTTTCAAATTTCTTTTAGAAATTAAAATATTTAAAATTTAAGATTTTG
64832624 AA
66 AA
* * *
64832626 AATTTTGGATAATTTATTATTTTCAATTTTTTTTTGGAAATTAAAATATTTAAAATTTAAGATTT
1 AATTTT-G-TAATTTATTATTTTCAAATTTCTTTTAGAAATTAAAATATTTAAAATTTAAGATTT
64832691 TGAA
64 TGAA
64832695 TTAATCTAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 6 0.10
68 1 0.02
69 55 0.89
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (67 bp):
AATTTTGTAATTTATTATTTTCAAATTTCTTTTAGAAATTAAAATATTTAAAATTTAAGATTTTG
AA
Found at i:64835610 original size:35 final size:35
Alignment explanation
Indices: 64835558--64835754 Score: 166
Period size: 35 Copynumber: 5.6 Consensus size: 35
64835548 ACTCTCTATT
*
64835558 TTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGTTGGATTAGCTCTTATGAGCA
* *
64835593 TTAGTGTGTTTCAGTTGGATTAGCTCTTACGAGCA
1 TTGGTGTGTTTCAGTTGGATTAGCTCTTATGAGCA
* ** * *
64835628 TTGGTGTGTTTCGGAGGGATTAACTCTTACGAGCA
1 TTGGTGTGTTTCAGTTGGATTAGCTCTTATGAGCA
* * *
64835663 TTAAAGTGT-TTTGAAG--GGATTAGCTCTTATTAGCA
1 TT--GGTGTGTTT-CAGTTGGATTAGCTCTTATGAGCA
* * * * * *
64835698 TTGGTATGTTTCAGATGGATTGGCTTTTCTAAGCA
1 TTGGTGTGTTTCAGTTGGATTAGCTCTTATGAGCA
**
64835733 TCTGGTGTGTTTTGGTTGGATT
1 T-TGGTGTGTTTCAGTTGGATT
64835755 GTCGATGTAC
Statistics
Matches: 130, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
33 5 0.04
34 3 0.02
35 98 0.75
36 19 0.15
37 5 0.04
ACGTcount: A:0.19, C:0.11, G:0.28, T:0.42
Consensus pattern (35 bp):
TTGGTGTGTTTCAGTTGGATTAGCTCTTATGAGCA
Found at i:64835672 original size:70 final size:70
Alignment explanation
Indices: 64835558--64835718 Score: 193
Period size: 70 Copynumber: 2.3 Consensus size: 70
64835548 ACTCTCTATT
* * * *
64835558 TTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCATT--AGTGTGTTT-CAGTTGGATTAGCTCT
1 TTGGTGTGTTTCGGATGGATTAACTCTTACGAGCATTAAAGTGT-TTTGAAG--GGATTAGCTCT
64835620 TACGAGCA
63 TACGAGCA
* *
64835628 TTGGTGTGTTTCGGAGGGATTAACTCTTACGAGCATTAAAGTGTTTTGAAGGGATTAGCTCTTAT
1 TTGGTGTGTTTCGGATGGATTAACTCTTACGAGCATTAAAGTGTTTTGAAGGGATTAGCTCTTAC
*
64835693 TAGCA
66 GAGCA
* *
64835698 TTGGTATGTTTCAGATGGATT
1 TTGGTGTGTTTCGGATGGATT
64835719 GGCTTTTCTA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
70 68 0.87
71 3 0.04
72 7 0.09
ACGTcount: A:0.20, C:0.11, G:0.28, T:0.40
Consensus pattern (70 bp):
TTGGTGTGTTTCGGATGGATTAACTCTTACGAGCATTAAAGTGTTTTGAAGGGATTAGCTCTTAC
GAGCA
Found at i:64844044 original size:452 final size:452
Alignment explanation
Indices: 64843200--64844107 Score: 1816
Period size: 452 Copynumber: 2.0 Consensus size: 452
64843190 AAAAAGAGCG
64843200 TCGATTCTGATCCAATTTCTTTTTTAGAAAACTTTATTGATAAACAAAATTCTTTACATAAAATG
1 TCGATTCTGATCCAATTTCTTTTTTAGAAAACTTTATTGATAAACAAAATTCTTTACATAAAATG
64843265 AATTATAGATATGGCTTTGCCCTAATGCTCAGAGCTTTAACTTCTTTCAACAATGAAGCCAACTC
66 AATTATAGATATGGCTTTGCCCTAATGCTCAGAGCTTTAACTTCTTTCAACAATGAAGCCAACTC
64843330 CTGACCCCGATCCGATTCCAGCTCGTACTTTACACTTAAAACGTCAGTCTGAATCGCCATTGCTT
131 CTGACCCCGATCCGATTCCAGCTCGTACTTTACACTTAAAACGTCAGTCTGAATCGCCATTGCTT
64843395 GTAAATGATCAGCTACCTCCCGGATCTAAGCCACGGCCTTGCCCATAATGTAATCTCTGTTCTGA
196 GTAAATGATCAGCTACCTCCCGGATCTAAGCCACGGCCTTGCCCATAATGTAATCTCTGTTCTGA
64843460 ATTTGATTCTGAGAATGATAAAGTTGTTCCTTCCAATACTCTTCATTTCCTTCCAAGAATTCGAT
261 ATTTGATTCTGAGAATGATAAAGTTGTTCCTTCCAATACTCTTCATTTCCTTCCAAGAATTCGAT
64843525 CATTTGCCCACAGCTTTGTAATGTATTCTCCAGTTCCTCTATCCTCTTTTTCATTTCTTCAATCT
326 CATTTGCCCACAGCTTTGTAATGTATTCTCCAGTTCCTCTATCCTCTTTTTCATTTCTTCAATCT
64843590 TGCCCAGGCTTGCTTTTAATTCTATTACAGAATTACGGCCTCTATACCGAATGAGTGATCTC
391 TGCCCAGGCTTGCTTTTAATTCTATTACAGAATTACGGCCTCTATACCGAATGAGTGATCTC
64843652 TCGATTCTGATCCAATTTCTTTTTTAGAAAACTTTATTGATAAACAAAATTCTTTACATAAAATG
1 TCGATTCTGATCCAATTTCTTTTTTAGAAAACTTTATTGATAAACAAAATTCTTTACATAAAATG
64843717 AATTATAGATATGGCTTTGCCCTAATGCTCAGAGCTTTAACTTCTTTCAACAATGAAGCCAACTC
66 AATTATAGATATGGCTTTGCCCTAATGCTCAGAGCTTTAACTTCTTTCAACAATGAAGCCAACTC
64843782 CTGACCCCGATCCGATTCCAGCTCGTACTTTACACTTAAAACGTCAGTCTGAATCGCCATTGCTT
131 CTGACCCCGATCCGATTCCAGCTCGTACTTTACACTTAAAACGTCAGTCTGAATCGCCATTGCTT
64843847 GTAAATGATCAGCTACCTCCCGGATCTAAGCCACGGCCTTGCCCATAATGTAATCTCTGTTCTGA
196 GTAAATGATCAGCTACCTCCCGGATCTAAGCCACGGCCTTGCCCATAATGTAATCTCTGTTCTGA
64843912 ATTTGATTCTGAGAATGATAAAGTTGTTCCTTCCAATACTCTTCATTTCCTTCCAAGAATTCGAT
261 ATTTGATTCTGAGAATGATAAAGTTGTTCCTTCCAATACTCTTCATTTCCTTCCAAGAATTCGAT
64843977 CATTTGCCCACAGCTTTGTAATGTATTCTCCAGTTCCTCTATCCTCTTTTTCATTTCTTCAATCT
326 CATTTGCCCACAGCTTTGTAATGTATTCTCCAGTTCCTCTATCCTCTTTTTCATTTCTTCAATCT
64844042 TGCCCAGGCTTGCTTTTAATTCTATTACAGAATTACGGCCTCTATACCGAATGAGTGATCTC
391 TGCCCAGGCTTGCTTTTAATTCTATTACAGAATTACGGCCTCTATACCGAATGAGTGATCTC
64844104 TCGA
1 TCGA
64844108 GCTCCATTAT
Statistics
Matches: 456, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
452 456 1.00
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (452 bp):
TCGATTCTGATCCAATTTCTTTTTTAGAAAACTTTATTGATAAACAAAATTCTTTACATAAAATG
AATTATAGATATGGCTTTGCCCTAATGCTCAGAGCTTTAACTTCTTTCAACAATGAAGCCAACTC
CTGACCCCGATCCGATTCCAGCTCGTACTTTACACTTAAAACGTCAGTCTGAATCGCCATTGCTT
GTAAATGATCAGCTACCTCCCGGATCTAAGCCACGGCCTTGCCCATAATGTAATCTCTGTTCTGA
ATTTGATTCTGAGAATGATAAAGTTGTTCCTTCCAATACTCTTCATTTCCTTCCAAGAATTCGAT
CATTTGCCCACAGCTTTGTAATGTATTCTCCAGTTCCTCTATCCTCTTTTTCATTTCTTCAATCT
TGCCCAGGCTTGCTTTTAATTCTATTACAGAATTACGGCCTCTATACCGAATGAGTGATCTC
Found at i:64847143 original size:6 final size:7
Alignment explanation
Indices: 64847126--64847157 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
64847116 TCTATTTACA
64847126 GAAAAAT
1 GAAAAAT
64847133 GAAAAAT
1 GAAAAAT
64847140 -AAAAAT
1 GAAAAAT
64847146 G-AAAAT
1 GAAAAAT
64847152 GAAAAA
1 GAAAAA
64847158 ATCGCCCCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 12 0.52
7 11 0.48
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
GAAAAAT
Found at i:64847156 original size:13 final size:14
Alignment explanation
Indices: 64847126--64847157 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
64847116 TCTATTTACA
64847126 GAAAAATGAAAAAT
1 GAAAAATGAAAAAT
64847140 -AAAAATG-AAAAT
1 GAAAAATGAAAAAT
64847152 GAAAAA
1 GAAAAA
64847158 ATCGCCCCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (14 bp):
GAAAAATGAAAAAT
Found at i:64848959 original size:18 final size:19
Alignment explanation
Indices: 64848936--64848972 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
64848926 AAACATATCA
64848936 GATTAA-AACTATT-TAATT
1 GATTAATAA-TATTATAATT
64848954 GATTAATAATATTATAATT
1 GATTAATAATATTATAATT
64848973 TTAGCAACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (19 bp):
GATTAATAATATTATAATT
Found at i:64852678 original size:45 final size:45
Alignment explanation
Indices: 64852520--64852697 Score: 164
Period size: 45 Copynumber: 4.0 Consensus size: 45
64852510 CACACAATAC
* * * *
64852520 CACCCTTATAGTCAATAGTA-CTCGGTGAAATCAGCACATAGCAAC
1 CACCTTTATATTCATTAGTATC-CGGTGAAATCAGCACATAGCAAT
* * * *
64852565 CACTTTTATACTCAATAGTA-CCGGGTGAATTCAGCACATAGCAAT
1 CACCTTTATATTCATTAGTATCC-GGTGAAATCAGCACATAGCAAT
** * *
64852610 CA-CTTATATAACCATTGGCATCCGGTGAAATCAGCACATAGCAAT
1 CACCTT-TATATTCATTAGTATCCGGTGAAATCAGCACATAGCAAT
* * **
64852655 CACCTTTATTTTCATTAATATCCGGTGGGATCAGCACATAGCA
1 CACCTTTATATTCATTAGTATCCGGTGAAATCAGCACATAGCA
64852698 TCCACCTATA
Statistics
Matches: 109, Mismatches: 20, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
44 3 0.03
45 101 0.93
46 5 0.05
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (45 bp):
CACCTTTATATTCATTAGTATCCGGTGAAATCAGCACATAGCAAT
Found at i:64852708 original size:90 final size:90
Alignment explanation
Indices: 64852542--64852708 Score: 214
Period size: 90 Copynumber: 1.9 Consensus size: 90
64852532 CAATAGTACT
* *
64852542 CGGTGAAATCAGCACATAGCAACCACTTTTATACTCAATAGTACCGGGTGAATTCAGCACATAGC
1 CGGTGAAATCAGCACATAGCAACCACCTTTATACTCAATAATACCGGGTGAATTCAGCACATAGC
*
64852607 AATCACTTATATAACCATTGGCATC
66 AATCACCTATATAACCATTGGCATC
* ** * *
64852632 CGGTGAAATCAGCACATAGCAATCACCTTTATTTTCATTAATATCC-GGTGGGA-TCAGCACATA
1 CGGTGAAATCAGCACATAGCAACCACCTTTATACTCAATAATA-CCGGGT-GAATTCAGCACATA
64852695 GC-ATCCACCTATAT
64 GCAAT-CACCTATAT
64852709 TTCCAACGAT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
89 2 0.03
90 60 0.91
91 4 0.06
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.27
Consensus pattern (90 bp):
CGGTGAAATCAGCACATAGCAACCACCTTTATACTCAATAATACCGGGTGAATTCAGCACATAGC
AATCACCTATATAACCATTGGCATC
Found at i:64852721 original size:45 final size:45
Alignment explanation
Indices: 64852542--64852723 Score: 118
Period size: 45 Copynumber: 4.0 Consensus size: 45
64852532 CAATAGTACT
* * * * * *
64852542 CGGTGAAATCAGCACATAGCAACCACTTTTA-TACTCAATAGTA-C
1 CGGTGAAATCAGCACATAGCAATCACCTATATTTC-CAACAATATC
* * ** *****
64852586 CGGGTGAATTCAGCACATAGCAATCACTTATATAACCATTGGCATC
1 C-GGTGAAATCAGCACATAGCAATCACCTATATTTCCAACAATATC
* * **
64852632 CGGTGAAATCAGCACATAGCAATCACCTTTATTTTCATTAATATC
1 CGGTGAAATCAGCACATAGCAATCACCTATATTTCCAACAATATC
** *
64852677 CGGTGGGATCAGCACATAGC-ATCCACCTATATTTCCAACGATATC
1 CGGTGAAATCAGCACATAGCAAT-CACCTATATTTCCAACAATATC
64852722 CG
1 CG
64852724 ATCCATTCCA
Statistics
Matches: 111, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
44 3 0.03
45 104 0.94
46 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (45 bp):
CGGTGAAATCAGCACATAGCAATCACCTATATTTCCAACAATATC
Found at i:64853195 original size:50 final size:49
Alignment explanation
Indices: 64853133--64853268 Score: 184
Period size: 50 Copynumber: 2.7 Consensus size: 49
64853123 TCACATATCG
* *
64853133 GTGCCGATGCCATGTCCCAGACATGGCCTTACACTG-ACTCTCCTCTGTCC
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGCACT-T-CTCGGTCC
* *
64853183 GTGCCGATGCCATGTCCTAGACATGGTCTTACACTAGCACTTCTCGGTCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACT-GCACTTCTCGGTCC
* *
64853233 GCGCCAATGCCATGTCCCAGACATGGTCTTACACTG
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTG
64853269 GCACACTCGC
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
49 1 0.01
50 71 0.92
51 2 0.03
52 3 0.04
ACGTcount: A:0.18, C:0.34, G:0.21, T:0.26
Consensus pattern (49 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTGCACTTCTCGGTCC
Found at i:64857931 original size:27 final size:26
Alignment explanation
Indices: 64857840--64857933 Score: 64
Period size: 27 Copynumber: 3.3 Consensus size: 26
64857830 TGTATCATTA
*
64857840 TATTAAATTATTTAAATATTATTTATTATT
1 TATTAAA-T-TTTAAATA--ATTTATTAAT
*
64857870 ATATTTGAAATTTTAAAATATTTTATGT-AT
1 -TA-TT-AAATTTT-AAATAATTTAT-TAAT
*
64857900 CATTAAATTTATAAATAATTTATTAAT
1 TATTAAATTT-TAAATAATTTATTAAT
64857927 TATTAAA
1 TATTAAA
64857934 ATGTATTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
26 1 0.02
27 24 0.46
28 3 0.06
29 1 0.02
30 6 0.12
31 6 0.12
32 8 0.15
33 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (26 bp):
TATTAAATTTTAAATAATTTATTAAT
Found at i:64866588 original size:6 final size:6
Alignment explanation
Indices: 64866579--64866606 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
64866569 TATATTTATA
64866579 GGATAG GGATAG GGATAG GGATAG GGAT
1 GGATAG GGATAG GGATAG GGATAG GGAT
64866607 CAAAAAGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.50, T:0.18
Consensus pattern (6 bp):
GGATAG
Found at i:64866886 original size:11 final size:11
Alignment explanation
Indices: 64866870--64866895 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
64866860 AGTCCAAACC
64866870 ACCTGTTTTCT
1 ACCTGTTTTCT
64866881 ACCTGTTTTCT
1 ACCTGTTTTCT
64866892 ACCT
1 ACCT
64866896 ACTGAGTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.12, C:0.31, G:0.08, T:0.50
Consensus pattern (11 bp):
ACCTGTTTTCT
Found at i:64869481 original size:16 final size:16
Alignment explanation
Indices: 64869456--64869487 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
64869446 GATTTGGGAG
*
64869456 ATTTTCTTTTTATTTT
1 ATTTTATTTTTATTTT
64869472 ATTTTATTTTTATTTT
1 ATTTTATTTTTATTTT
64869488 TTTCTGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (16 bp):
ATTTTATTTTTATTTT
Found at i:64875414 original size:23 final size:24
Alignment explanation
Indices: 64875366--64875429 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
64875356 TAAGGCTATA
*
64875366 AAAATATTAAAAAACTTAGAAATT
1 AAAATATTAAAAAATTTAGAAATT
*
64875390 AAAATA-TAGAAAAATTTA-AATTT
1 AAAATATTA-AAAAATTTAGAAATT
64875413 AAACATATTAAAAAATT
1 AAA-ATATTAAAAAATT
64875430 AAAGAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 9 0.26
24 24 0.69
25 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (24 bp):
AAAATATTAAAAAATTTAGAAATT
Found at i:64880700 original size:18 final size:19
Alignment explanation
Indices: 64880679--64880720 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
64880669 ACTCTTTTAT
64880679 TTTTATTAT-TTT-ATCGTG
1 TTTT-TTATGTTTAATCGTG
*
64880697 TTTTTTATGTTTAATCTTG
1 TTTTTTATGTTTAATCGTG
64880716 TTTTT
1 TTTTT
64880721 ATCTTGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 7 0.33
19 10 0.48
ACGTcount: A:0.14, C:0.05, G:0.10, T:0.71
Consensus pattern (19 bp):
TTTTTTATGTTTAATCGTG
Found at i:64889219 original size:6 final size:7
Alignment explanation
Indices: 64889179--64889217 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
64889169 AAATATATAT
64889179 ATTTTT-
1 ATTTTTA
64889185 ATTTTTA
1 ATTTTTA
*
64889192 TTTTTTA
1 ATTTTTA
64889199 ATTTTTA
1 ATTTTTA
64889206 ATTTTTA
1 ATTTTTA
64889213 ATTTT
1 ATTTT
64889218 AAAATACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
ATTTTTA
Found at i:64889250 original size:20 final size:23
Alignment explanation
Indices: 64889225--64889275 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 23
64889215 TTTAAAATAC
64889225 TTTTAAAAT-ATTTTTT-AT-TT
1 TTTTAAAATAATTTTTTAATGTT
64889245 TTTT-AAATAATTTTTTAATGTT
1 TTTTAAAATAATTTTTTAATGTT
64889267 TATTTAAAA
1 T-TTTAAAA
64889276 AATGGGCCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.15
20 11 0.42
21 2 0.08
22 3 0.12
23 3 0.12
24 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTAAAATAATTTTTTAATGTT
Found at i:64894054 original size:14 final size:14
Alignment explanation
Indices: 64894009--64894054 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
64893999 TTTAACCTAA
64894009 AAAAATATTTA-T-
1 AAAAATATTTATTC
64894021 AAAAATGATTCTAGTTC
1 AAAAAT-ATT-TA-TTC
64894038 AAAAATATTTATTC
1 AAAAATATTTATTC
64894052 AAA
1 AAA
64894055 TATCTGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 6 0.21
13 3 0.10
14 8 0.28
15 2 0.07
16 4 0.14
17 6 0.21
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (14 bp):
AAAAATATTTATTC
Found at i:64895534 original size:23 final size:23
Alignment explanation
Indices: 64895482--64895529 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
64895472 GGGGACGGTT
*
64895482 TTATTTATTTAATATTAATATAA
1 TTATTTACTTAATATTAATATAA
*
64895505 TTTTTTACTTAAT-TT--TATAA
1 TTATTTACTTAATATTAATATAA
64895525 TTATT
1 TTATT
64895530 ATTTATAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTTACTTAATATTAATATAA
Found at i:64909866 original size:9 final size:9
Alignment explanation
Indices: 64909848--64909878 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
64909838 TTTAGTTAAA
64909848 AATTAACCG
1 AATTAACCG
*
64909857 AATTACCCG
1 AATTAACCG
64909866 AATTAACCG
1 AATTAACCG
64909875 AATT
1 AATT
64909879 GAATCACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:64910203 original size:18 final size:18
Alignment explanation
Indices: 64910180--64910223 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
64910170 AATATTTATG
*
64910180 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGATA
64910198 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
*
64910216 CTTGGGTT
1 ATTGGGTT
64910224 TGGATTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.11, C:0.02, G:0.45, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:64911202 original size:7 final size:7
Alignment explanation
Indices: 64911190--64911214 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
64911180 AGGAAAAAAA
64911190 AATAAAC
1 AATAAAC
64911197 AATAAAC
1 AATAAAC
64911204 AATAAAC
1 AATAAAC
64911211 AATA
1 AATA
64911215 CAATTGACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (7 bp):
AATAAAC
Found at i:64913540 original size:26 final size:26
Alignment explanation
Indices: 64913507--64913569 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
64913497 TTTACTTGAG
64913507 TAAAATTTTGACAATTTTACCCTCT-A
1 TAAAATTTTGACAATTTTACCC-CTAA
**
64913533 TAAAATTTTGATGATTTTACCCCTAA
1 TAAAATTTTGACAATTTTACCCCTAA
64913559 TAAAATTTTGA
1 TAAAATTTTGA
64913570 GAAATTCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
25 2 0.06
26 32 0.94
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (26 bp):
TAAAATTTTGACAATTTTACCCCTAA
Found at i:64925674 original size:18 final size:18
Alignment explanation
Indices: 64925646--64925680 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
64925636 AATCGTTTCG
64925646 TACCATATTTGTATACATA
1 TACCATATTTGTA-ACATA
64925665 TACC-TATTTGTAACAT
1 TACCATATTTGTAACAT
64925681 GTACTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (18 bp):
TACCATATTTGTAACATA
Found at i:64927092 original size:89 final size:89
Alignment explanation
Indices: 64926941--64927111 Score: 324
Period size: 89 Copynumber: 1.9 Consensus size: 89
64926931 TAAAACAGTT
*
64926941 TTACAAATTAGTACATGGGCTAGCTAAATCAAACTCCCATTACCTCAAAAACATAAAAATTACAA
1 TTACAAATTAGTACACGGGCTAGCTAAATCAAACTCCCATTACCTCAAAAACATAAAAATTACAA
64927006 GAAAAAGACTAGGTGAGTCGAATA
66 GAAAAAGACTAGGTGAGTCGAATA
*
64927030 TTACAACTTAGTACACGGGCTAGCTAAATCAAACTCCCATTACCTCAAAAACATAAAAATTACAA
1 TTACAAATTAGTACACGGGCTAGCTAAATCAAACTCCCATTACCTCAAAAACATAAAAATTACAA
64927095 GAAAAAGACTAGGTGAG
66 GAAAAAGACTAGGTGAG
64927112 CCTAATATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (89 bp):
TTACAAATTAGTACACGGGCTAGCTAAATCAAACTCCCATTACCTCAAAAACATAAAAATTACAA
GAAAAAGACTAGGTGAGTCGAATA
Found at i:64932748 original size:15 final size:14
Alignment explanation
Indices: 64932718--64932745 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
64932708 ATTACGTCAT
64932718 TTCTATTTTTTAAA
1 TTCTATTTTTTAAA
64932732 TTCTATTTTTTAAA
1 TTCTATTTTTTAAA
64932746 ATTTAGGGAA
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:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (14 bp):
TTCTATTTTTTAAA
Found at i:64935581 original size:19 final size:20
Alignment explanation
Indices: 64935557--64935603 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
64935547 TTATATTTTG
64935557 TATATATAATGT-ACG-AATA
1 TATATATAATGTGA-GTAATA
*
64935576 TATATAT-GTGTGAGTAATA
1 TATATATAATGTGAGTAATA
64935595 TATATATAA
1 TATATATAA
64935604 ATTCTTGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.45, C:0.02, G:0.13, T:0.40
Consensus pattern (20 bp):
TATATATAATGTGAGTAATA
Found at i:64936425 original size:41 final size:41
Alignment explanation
Indices: 64936380--64936501 Score: 219
Period size: 41 Copynumber: 3.0 Consensus size: 41
64936370 AGGCTTAGCA
64936380 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAG
64936421 CCTAGCAGGCTAAGTGCCGGT-AATCTGAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGAA-CTGAATCAGGTTATAAG
*
64936462 CCTAGCAGGCTAAGTGTCGGTGAACTGAATCAGGTTATAA
1 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
64936502 ATGAAACACC
Statistics
Matches: 78, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
40 2 0.03
41 74 0.95
42 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAG
Done.