Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 5 of 349
Found at i:1542700 original size:12 final size:12
Alignment explanation
Indices: 1542680--1542726 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
1542670 GATTTAATAT
*
1542680 ATGTATATGTAC
1 ATGTATATGTAA
*
1542692 ATGTCTATGTAA
1 ATGTATATGTAA
1542704 ATGTATAAATGTAA
1 ATGTAT--ATGTAA
1542718 ATGTATATG
1 ATGTATATG
1542727 AATCTTACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 18 0.60
14 12 0.40
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (12 bp):
ATGTATATGTAA
Found at i:1542717 original size:14 final size:14
Alignment explanation
Indices: 1542698--1542724 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1542688 GTACATGTCT
1542698 ATGTAAATGTATAA
1 ATGTAAATGTATAA
1542712 ATGTAAATGTATA
1 ATGTAAATGTATA
1542725 TGAATCTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (14 bp):
ATGTAAATGTATAA
Found at i:1548725 original size:17 final size:17
Alignment explanation
Indices: 1548686--1548729 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1548676 GGGTAGCAAA
*
1548686 AGCAAAGGCAGCAGTAGC
1 AGCAAA-GCAGCAGCAGC
*
1548704 -CCAAAGCAGCAGCAGC
1 AGCAAAGCAGCAGCAGC
1548720 AGCAAAGCAG
1 AGCAAAGCAG
1548730 GTAAGGGGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.41, C:0.27, G:0.30, T:0.02
Consensus pattern (17 bp):
AGCAAAGCAGCAGCAGC
Found at i:1549249 original size:12 final size:13
Alignment explanation
Indices: 1549222--1549254 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1549212 AGAATAAATA
*
1549222 AATAATTTACTAT
1 AATAAATTACTAT
1549235 AATAAATTA-TAT
1 AATAAATTACTAT
1549247 AATAAATT
1 AATAAATT
1549255 CTCGAAATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
AATAAATTACTAT
Found at i:1553269 original size:20 final size:21
Alignment explanation
Indices: 1553246--1553284 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1553236 TTAAATATAA
1553246 AAAAATTT-AAAATAATATTG
1 AAAAATTTCAAAATAATATTG
* *
1553266 AAAACTTTCAAATTAATAT
1 AAAAATTTCAAAATAATAT
1553285 ATAATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (21 bp):
AAAAATTTCAAAATAATATTG
Found at i:1555419 original size:58 final size:58
Alignment explanation
Indices: 1555329--1555446 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
1555319 CAGTCAAAGA
1555329 CAGTTTTGGTGTTGGTCTCATGCAAAGACCTTACACAAAAACTTCATCAAATCCCTCC
1 CAGTTTTGGTGTTGGTCTCATGCAAAGACCTTACACAAAAACTTCATCAAATCCCTCC
1555387 CAGTTTTGGTGTTGGTCTCATGCAAAGACCTTACACAAAAACTTCATCAAATCCCTCC
1 CAGTTTTGGTGTTGGTCTCATGCAAAGACCTTACACAAAAACTTCATCAAATCCCTCC
1555445 CA
1 CA
1555447 TTCCATTGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (58 bp):
CAGTTTTGGTGTTGGTCTCATGCAAAGACCTTACACAAAAACTTCATCAAATCCCTCC
Found at i:1555590 original size:19 final size:19
Alignment explanation
Indices: 1555566--1555607 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
1555556 AGGAGATTGT
* *
1555566 TATTTTGCTATTTTTTTAC
1 TATTTTACTATTATTTTAC
1555585 TATTTTACTATTATTTTAC
1 TATTTTACTATTATTTTAC
1555604 TATT
1 TATT
1555608 GTTATTATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.21, C:0.10, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTACTATTATTTTAC
Found at i:1555621 original size:19 final size:19
Alignment explanation
Indices: 1555566--1555621 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
1555556 AGGAGATTGT
* **
1555566 TATTTTGCTATTTTTTTAC
1 TATTTTACTATTAGTTTAC
*
1555585 TATTTTACTATTATTTTAC
1 TATTTTACTATTAGTTTAC
*
1555604 TATTGTTATTATT-GTTTA
1 TATT-TTACTATTAGTTTA
1555622 AATATTCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 25 0.78
20 7 0.22
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.66
Consensus pattern (19 bp):
TATTTTACTATTAGTTTAC
Found at i:1558878 original size:70 final size:70
Alignment explanation
Indices: 1558760--1558930 Score: 195
Period size: 70 Copynumber: 2.5 Consensus size: 70
1558750 CTGGTCTTAG
* * *** * *
1558760 CTTTAAATTTAGTCGAAA-CTTAATATAATTATTGGATATCGAAGAATTTCA-AACTAATATAT-
1 CTTTAAATTTAGTCAAAACCCTAATATAATTATCAAATATCAAAAAATTTCAGAA-TAATATATA
*
1558822 AGCTCAA
65 ACCT-AA
* *
1558829 CTTTAAATTTAGTCAAAACCCTAATATGATTATCAAATATTAAAAAATTTCAGAATAATATATAA
1 CTTTAAATTTAGTCAAAACCCTAATATAATTATCAAATATCAAAAAATTTCAGAATAATATATAA
*
1558894 CCTGA
66 CCTAA
*
1558899 TTTTAAATTTAGTCAAAACCCTAATATAATTA
1 CTTTAAATTTAGTCAAAACCCTAATATAATTA
1558931 CTAAATAGAC
Statistics
Matches: 86, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
69 17 0.20
70 64 0.74
71 5 0.06
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.36
Consensus pattern (70 bp):
CTTTAAATTTAGTCAAAACCCTAATATAATTATCAAATATCAAAAAATTTCAGAATAATATATAA
CCTAA
Found at i:1564863 original size:14 final size:14
Alignment explanation
Indices: 1564844--1564910 Score: 64
Period size: 14 Copynumber: 4.7 Consensus size: 14
1564834 GTTTGCAGGT
*
1564844 AAAATGTTTTCCGG
1 AAAATGATTTCCGG
*
1564858 AAAATGATTTCTGG
1 AAAATGATTTCCGG
* * *
1564872 AAAATAATTTCTTGA
1 AAAATGATTTC-CGG
1564887 AAAATGATTTCTC-G
1 AAAATGATTTC-CGG
1564901 AAAATGATTT
1 AAAATGATTT
1564911 ACTTTTCTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
14 32 0.71
15 13 0.29
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (14 bp):
AAAATGATTTCCGG
Found at i:1564896 original size:15 final size:14
Alignment explanation
Indices: 1564857--1564910 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
1564847 ATGTTTTCCG
*
1564857 GAAAATGATTTCTG
1 GAAAATGATTTCTT
*
1564871 GAAAATAATTTCTT
1 GAAAATGATTTCTT
*
1564885 GAAAAATGATTTCTC
1 G-AAAATGATTTCTT
1564900 GAAAATGATTT
1 GAAAATGATTT
1564911 ACTTTTCTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 23 0.66
15 12 0.34
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (14 bp):
GAAAATGATTTCTT
Found at i:1578737 original size:16 final size:17
Alignment explanation
Indices: 1578712--1578745 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1578702 TTCAAAACTA
1578712 TACATAAACTTT-ATTT
1 TACATAAACTTTAATTT
*
1578728 TACATTAACTTTAATTT
1 TACATAAACTTTAATTT
1578745 T
1 T
1578746 TTTTCTCTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (17 bp):
TACATAAACTTTAATTT
Found at i:1581832 original size:32 final size:32
Alignment explanation
Indices: 1581794--1581859 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1581784 TTACTCACTC
1581794 TATTTTATATTGATTAGATTGTAATTGTAATT
1 TATTTTATATTGATTAGATTGTAATTGTAATT
*
1581826 TATTTTATATTGATTTGATTGTAATTGTAATT
1 TATTTTATATTGATTAGATTGTAATTGTAATT
1581858 TA
1 TA
1581860 GAGAATTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (32 bp):
TATTTTATATTGATTAGATTGTAATTGTAATT
Found at i:1583907 original size:9 final size:10
Alignment explanation
Indices: 1583885--1583921 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1583875 AATGACTCCT
*
1583885 AAAATTTTTG
1 AAAATTTTTA
1583895 AAAATTTTTA
1 AAAATTTTTA
1583905 AAAA-TTTTA
1 AAAATTTTTA
1583914 AAAATTTT
1 AAAATTTT
1583922 CATTATACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:1589324 original size:21 final size:20
Alignment explanation
Indices: 1589298--1589337 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1589288 CCACAACCTA
1589298 ATATTAATTTCTATATTTTTT
1 ATATTAATTT-TATATTTTTT
* *
1589319 ATATTACTTTTTTATTTTT
1 ATATTAATTTTATATTTTT
1589338 ATTATAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
ATATTAATTTTATATTTTTT
Found at i:1589880 original size:13 final size:13
Alignment explanation
Indices: 1589859--1589896 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1589849 TCTAAAAGCA
* *
1589859 TTTATATAATATT
1 TTTAAATAATAAT
1589872 TTTAAATAATAAT
1 TTTAAATAATAAT
1589885 TTT-AATAATAAT
1 TTTAAATAATAAT
1589897 ATTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTAAATAATAAT
Found at i:1595569 original size:31 final size:31
Alignment explanation
Indices: 1595534--1595601 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
1595524 TAAAAGCTAG
1595534 TGACTT-AATTGAAAACGTTT-GAATAATTCAA
1 TGACTTGAATT-AAAAC-TTTCGAATAATTCAA
* *
1595565 TGACTTGAATTAAAACTTTCGAATAATTTAG
1 TGACTTGAATTAAAACTTTCGAATAATTCAA
1595596 TGACTT
1 TGACTT
1595602 TTTGGTAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 3 0.09
31 26 0.79
32 4 0.12
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (31 bp):
TGACTTGAATTAAAACTTTCGAATAATTCAA
Found at i:1609644 original size:18 final size:18
Alignment explanation
Indices: 1609613--1609661 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1609603 AAATTTAAGT
* * *
1609613 AAATATATTAAGATCAAA
1 AAATAAATTTAGATAAAA
1609631 AAATAAATTTAGATAAAA
1 AAATAAATTTAGATAAAA
*
1609649 AAAGAAA-TTAGAT
1 AAATAAATTTAGAT
1609662 TTATTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (18 bp):
AAATAAATTTAGATAAAA
Found at i:1610199 original size:19 final size:20
Alignment explanation
Indices: 1610157--1610211 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
1610147 CAAAAATTAT
*
1610157 AAAATAATTTTCACAAATTTC
1 AAAATAATTTTTA-AAATTTC
1610178 AAAATAATTTTTAAAA-TTC
1 AAAATAATTTTTAAAATTTC
*
1610197 AAAAT-ATTTATAAAA
1 AAAATAATTTTTAAAA
1610212 ATCCTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 9 0.28
19 8 0.25
20 3 0.09
21 12 0.38
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATTTTTAAAATTTC
Found at i:1610212 original size:19 final size:19
Alignment explanation
Indices: 1610157--1610213 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1610147 CAAAAATTAT
*
1610157 AAAATAATTTTCACAAATTTC
1 AAAATAATTTT-A-AAAATTC
*
1610178 AAAATAATTTTTAAAATTC
1 AAAATAATTTTAAAAATTC
1610197 AAAAT-ATTTATAAAAAT
1 AAAATAATTT-TAAAAAT
1610214 CCTAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 4 0.12
19 17 0.53
21 11 0.34
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAATTTTAAAAATTC
Found at i:1619687 original size:20 final size:20
Alignment explanation
Indices: 1619662--1619705 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1619652 AAAATTATTT
*
1619662 AATAAAATAATAATTTTATA
1 AATAAAATAATAATCTTATA
1619682 AATAAAATAATAATCTTATA
1 AATAAAATAATAATCTTATA
1619702 AATA
1 AATA
1619706 TAACAGTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAAAATAATAATCTTATA
Found at i:1620901 original size:20 final size:19
Alignment explanation
Indices: 1620872--1620910 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1620862 AAATTACAGG
*
1620872 AAAATGAAAGTAAAAAGAA
1 AAAATGAAAGCAAAAAGAA
1620891 AAAATTGAAAGCAAAAAGAA
1 AAAA-TGAAAGCAAAAAGAA
1620911 TTAAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAATGAAAGCAAAAAGAA
Found at i:1622300 original size:13 final size:12
Alignment explanation
Indices: 1622267--1622300 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
1622257 TTTTAATCAA
1622267 TTTTTTTTGTTT
1 TTTTTTTTGTTT
1622279 TTTGTTTTTGTTT
1 TTT-TTTTTGTTT
1622292 TTTTCTTTT
1 TTTT-TTTT
1622301 AATTATTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:1622357 original size:39 final size:38
Alignment explanation
Indices: 1622229--1622357 Score: 127
Period size: 39 Copynumber: 3.3 Consensus size: 38
1622219 TTTGTTTTCC
*
1622229 TTTTTTTTTTTAATTATCTGTGTTTCCATTTTAATCAAT
1 TTTTTTTTTTTAATTATTTGTGTTTCCATTTTAATC-AT
* * * * *
1622268 TTTTTTTGTTTT-TTGTTTTTGTTTTTTTC-TTTTAATTAT
1 TTTTTTT-TTTTAAT-TATTTG-TGTTTCCATTTTAATCAT
*
1622307 TTTCCTTTTTTTAATTATTTGTGTTTCCATTTTAATCAT
1 TTT-TTTTTTTTAATTATTTGTGTTTCCATTTTAATCAT
1622346 TTTTTTGTTTTT
1 TTTTTT-TTTTT
1622358 TTTTCTTTTA
Statistics
Matches: 70, Mismatches: 13, Indels: 14
0.72 0.13 0.14
Matches are distributed among these distances:
38 7 0.10
39 39 0.56
40 19 0.27
41 5 0.07
ACGTcount: A:0.14, C:0.08, G:0.06, T:0.72
Consensus pattern (38 bp):
TTTTTTTTTTTAATTATTTGTGTTTCCATTTTAATCAT
Found at i:1622407 original size:48 final size:47
Alignment explanation
Indices: 1622315--1622407 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 47
1622305 ATTTTCCTTT
* **
1622315 TTTTAATTATTTGTGTTTCCATTTTAATCATTTTTTTGTTTTTTTTTC
1 TTTTAATTATTTGTGTTTCCATTTTAACCACCTTTTTG-TTTTTTTTC
*
1622363 TTTTAATTATTTTTGTTTCCATTTTGAACCAACCTTTTTGTTTTT
1 TTTTAATTATTTGTGTTTCCATTTT-AACC-ACCTTTTTGTTTTT
1622408 ATGCTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
48 24 0.62
49 8 0.21
50 7 0.18
ACGTcount: A:0.16, C:0.11, G:0.06, T:0.67
Consensus pattern (47 bp):
TTTTAATTATTTGTGTTTCCATTTTAACCACCTTTTTGTTTTTTTTC
Found at i:1624005 original size:65 final size:65
Alignment explanation
Indices: 1623880--1623999 Score: 151
Period size: 65 Copynumber: 1.9 Consensus size: 65
1623870 AAAAATACGC
* **
1623880 AAGTACTTAATTGGGACAAGAAAAAAAAGAGCTCAAGTATCAAATTAAATATTAAAACTAAACTT
1 AAGTACTTAATTGGGACAAGAAAAAAAAGAGCTCAAGTATCAAATTAAAAAAAAAAACTAAACTT
1623945 AAGTACTTAATTGCGG-CAA-AAAAAAAA-A-CTCAAGTATC-AATTAGAAAAACAAAAA
1 AAGTACTTAATTG-GGACAAGAAAAAAAAGAGCTCAAGTATCAAATTA-AAAAA-AAAAA
1624000 TACTAATTTG
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
61 5 0.10
62 13 0.27
63 5 0.10
64 8 0.16
65 16 0.33
66 2 0.04
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (65 bp):
AAGTACTTAATTGGGACAAGAAAAAAAAGAGCTCAAGTATCAAATTAAAAAAAAAAACTAAACTT
Found at i:1626239 original size:3 final size:3
Alignment explanation
Indices: 1626231--1626256 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1626221 TCGTTTTTGA
1626231 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
1626257 TCAGGCTAAT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1641990 original size:31 final size:31
Alignment explanation
Indices: 1641922--1641983 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
1641912 ATGGTCATTG
1641922 AACTATTCGAA-AGTTTTCATTTAAGTCACTA
1 AACTATTC-AAGAGTTTTCATTTAAGTCACTA
1641953 AACTATTCAAGAGTTTTCATTTAAGTCACTA
1 AACTATTCAAGAGTTTTCATTTAAGTCACTA
1641984 GGCTATTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (31 bp):
AACTATTCAAGAGTTTTCATTTAAGTCACTA
Found at i:1642747 original size:32 final size:32
Alignment explanation
Indices: 1642709--1642773 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
1642699 GAGAACAACT
1642709 ATCAAGTTCAAGAATTAAAACCCGAATGTGAA
1 ATCAAGTTCAAGAATTAAAACCCGAATGTGAA
1642741 ATCAAGTTCAAGAATTAAAACCCGAATGTGAA
1 ATCAAGTTCAAGAATTAAAACCCGAATGTGAA
1642773 A
1 A
1642774 ATAATTATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (32 bp):
ATCAAGTTCAAGAATTAAAACCCGAATGTGAA
Found at i:1645295 original size:12 final size:12
Alignment explanation
Indices: 1645278--1645319 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
1645268 ATTACGACGA
1645278 AAACTTTCATTG
1 AAACTTTCATTG
1645290 AAAC-TT-ATTTG
1 AAACTTTCA-TTG
1645301 AAAACTTTCATTG
1 -AAACTTTCATTG
1645314 AAACTT
1 AAACTT
1645320 ATTTGTGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 1 0.04
11 5 0.19
12 14 0.54
13 5 0.19
14 1 0.04
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (12 bp):
AAACTTTCATTG
Found at i:1645303 original size:24 final size:24
Alignment explanation
Indices: 1645276--1645324 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1645266 TAATTACGAC
1645276 GAAAACTTTCATTGAAACTTATTT
1 GAAAACTTTCATTGAAACTTATTT
1645300 GAAAACTTTCATTGAAACTTATTT
1 GAAAACTTTCATTGAAACTTATTT
1645324 G
1 G
1645325 TGACTATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (24 bp):
GAAAACTTTCATTGAAACTTATTT
Found at i:1645316 original size:13 final size:13
Alignment explanation
Indices: 1645276--1645316 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
1645266 TAATTACGAC
1645276 GAAAACTTTCATT
1 GAAAACTTTCATT
1645289 G-AAAC-TT-ATTT
1 GAAAACTTTCA-TT
1645300 GAAAACTTTCATT
1 GAAAACTTTCATT
1645313 GAAA
1 GAAA
1645317 CTTATTTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 1 0.04
11 5 0.21
12 8 0.33
13 9 0.38
14 1 0.04
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (13 bp):
GAAAACTTTCATT
Found at i:1646026 original size:23 final size:23
Alignment explanation
Indices: 1645996--1646043 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1645986 CAATTGGGAC
* *
1645996 AAAAAAATTCAAGTATCAAATTG
1 AAAAAAATTCAAGTACCAAAGTG
*
1646019 AAAAAAATTCAGGTACCAAAGTG
1 AAAAAAATTCAAGTACCAAAGTG
1646042 AA
1 AA
1646044 TATTGAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.21
Consensus pattern (23 bp):
AAAAAAATTCAAGTACCAAAGTG
Found at i:1652515 original size:16 final size:15
Alignment explanation
Indices: 1652493--1652535 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1652483 ACGATGCTTT
**
1652493 AAAAAATATTTTTAA
1 AAAAAATAAATTTAA
1652508 ATAAAAATAAATTTAA
1 A-AAAAATAAATTTAA
1652524 AAAAAATTAAAT
1 AAAAAA-TAAAT
1652536 ATGGACGAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 18 0.75
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAAAATAAATTTAA
Found at i:1666918 original size:79 final size:79
Alignment explanation
Indices: 1666549--1667073 Score: 454
Period size: 79 Copynumber: 6.6 Consensus size: 79
1666539 AACATCGTTG
* * * * * * *
1666549 GTTTTTCCTCTTGAAAATTCTCAGAAAATATTCACAGATTCACTCAAAGGAAATATAG-AAATAG
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATT-ACTC-AAGGAAATACAGCAAA-AG
*
1666613 CAAAAGGGTATCAGAATT
63 CAAAAGGGCATCA-AATT
* *
1666631 GGTTTCCCTTCATGCAAATTCCAAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAGAA-C
1 GTTTTCCC-TCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAA-AAGC
*
1666695 AAAAAGGGCA-CAAACTA
64 -AAAAGGGCATCAAA-TT
* * * * *
1666712 GTTTTCCCTCAGGCGAATTCCCATAAAATTTTCACAAATTACTCAAGCAAATACAGCAAGAGCAA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAAAGCAA
*
1666777 AAGGGAATCAACATT
66 AAGGGCATCAA-ATT
** * ** *
1666792 GTTTTCCCTCATGCAAATTCCCAGAAAAAATTCACAGAGAACT-AAGGAAATACATCAAAAGCAA
1 GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAAAGCAA
*
1666856 AAGGACATCAAATT
66 AAGGGCATCAAATT
** * *
1666870 -TGGTCTCCTCTTGCAAATTCCCAGAAAATTTTCACAAATTACTGAAGGAAATACAGCAAAAGCA
1 GTTTTC-CCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAAAGCA
* *
1666934 AAAGGGTATCGAATT
65 AAAGGGCATCAAATT
* * * * * * *
1666949 GATTTCTCC-CATTCAAATT-CCAGAAAAAATTTCACAAATTATTCAAGCAAATACAACAAGAGC
1 GTTTTC-CCTCATGCAAATTCCCAG-AAAATTTTCACAAATTACTCAAGGAAATACAGCAAAAGC
* * ***
1667012 AAAAGGGTACCTAACCA
64 AAAAGGGCATC-AAATT
* * *
1667029 GTGTTCCCTCAAT-CAAATTCCCAGAAAAAATTTCACATATTACTC
1 GTTTTCCCTC-ATGCAAATTCCCAG-AAAATTTTCACAAATTACTC
1667074 CAGAAAAACT
Statistics
Matches: 362, Mismatches: 65, Indels: 33
0.79 0.14 0.07
Matches are distributed among these distances:
77 3 0.01
78 38 0.10
79 120 0.33
80 105 0.29
81 48 0.13
82 21 0.06
83 27 0.07
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (79 bp):
GTTTTCCCTCATGCAAATTCCCAGAAAATTTTCACAAATTACTCAAGGAAATACAGCAAAAGCAA
AAGGGCATCAAATT
Found at i:1671804 original size:75 final size:75
Alignment explanation
Indices: 1671677--1671829 Score: 261
Period size: 75 Copynumber: 2.0 Consensus size: 75
1671667 CTTCGTTCTC
* *
1671677 CAAAGGATTGTCCTAATATAACATAGCCAGCGACAAAAAGAATCAAATTACAGCATTTAAACTTC
1 CAAAGGATTGTCCTAATATAACATAGCCAGCAACAAAAAGAATCAAACTACAGCATTTAAACTTC
1671742 AATAATACAG
66 AATAATACAG
* *
1671752 CAAAGGATTGTCCTGATATAACATAGCCAGCAACAAAAAGAATCAGACTACAGCATTTAAACTTC
1 CAAAGGATTGTCCTAATATAACATAGCCAGCAACAAAAAGAATCAAACTACAGCATTTAAACTTC
*
1671817 AATAGTACAG
66 AATAATACAG
1671827 CAA
1 CAA
1671830 CATGAGGCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.22
Consensus pattern (75 bp):
CAAAGGATTGTCCTAATATAACATAGCCAGCAACAAAAAGAATCAAACTACAGCATTTAAACTTC
AATAATACAG
Found at i:1675185 original size:150 final size:146
Alignment explanation
Indices: 1675002--1675750 Score: 582
Period size: 150 Copynumber: 5.0 Consensus size: 146
1674992 GTTTTGAGTG
* * * * * *
1675002 AATTTGAGATAGGAAGTAACAAAAAACGAGGCAATTAGACTGAAAGGTATCGAAATAAAATTGAA
1 AATTCGAGATATGAAGTTA-AAAAAACAAGGCAATTAGACT-AAAGGTATTGAAATAAATTTGAA
* * *
1675067 AAAAAAACACAAAAAACCAGAGTCAAGAACACCACGAAAGATCAAATGCTCAAGCGAATAACCAA
64 AAAAAAA-A-AAAAAACCAGAGCCAAGAACACCACGAAAGATCAAATGCTCAAACGAACAACCAA
*
1675132 TAAATCGGA-GATTTTCAGCAA
127 TAAA-C-AATGATTTTCAGCAA
* * *
1675153 AATTAGAGATATGAAGTTAAAAAAACAAGGCAAATAGAGTAAAGGGTATTGAAATAAATTTGAAA
1 AATTCGAGATATGAAGTTAAAAAAACAAGGCAATTAGACTAAA-GGTATTGAAATAAATTTGAAA
** *
1675218 AAAAAAAAACCTAACTCAGAGCCAAGAACACCATGAAAGATCAAATGCTCAAACGAACAACCAAT
65 AAAAAAAAA-AAAAC-CAGAGCCAAGAACACCACGAAAGATCAAATGCTCAAACGAACAACCAAT
1675283 ATAACAATGATTTTCAGCAA
128 A-AACAATGATTTTCAGCAA
* * * *
1675303 AA-TCGAGCTAGGAAGTTTAAAAAAAAAAAAAAACCAAGGCACTTAGACTAAAGAGTATTGAGAT
1 AATTCGAGATATGAAG-TT--------AAAAAAA-CAAGGCAATTAGACTAAAG-GTATTGAAAT
* *
1675367 AAATTTGAAAAGAAAAAAAAACACCTAACCCAGAGCCAAAAACACCATGAAAGATCAAATGCTCA
55 AAATTTGAAAA-AAAAAAAAA-A---AA-CCAGAGCCAAGAACACCACGAAAGATCAAATGCTCA
* * *
1675432 AGCGAATAACCAATAAAACAATGATTTTCAGCGA
114 AACGAACAACCAAT-AAACAATGATTTTCAGCAA
*** * *
1675466 AA-TCGA-ACTAT-AA---AAAAAAAGGGGGCAATTAGAGTAAAGGGTATTGGAATAAATTTG--
1 AATTCGAGA-TATGAAGTTAAAAAAACAAGGCAATTAGACTAAA-GGTATTGAAATAAATTTGAA
* * ** * *
1675523 ----AAAAAAAAACCCAGAGCCAAGAATC-TCACCCAAGCTCGAATGCTCAAACGAACAACCAAT
64 AAAAAAAAAAAAAACCAGAGCCAAGAA-CACCACGAAAGATCAAATGCTCAAACGAACAACCAAT
1675583 AAAGCAATGATTTTCAGC-A
128 AAA-CAATGATTTTCAGCAA
* * * * *
1675602 AATTCGAGCTATGAAGTTAAAAAAACAAGGCAATTATACTAAAGAGAATTGAAATAAAATCG-AA
1 AATTCGAGATATGAAGTTAAAAAAACAAGGCAATTAGACTAAAG-GTATTGAAATAAATTTGAAA
* * ** * * * * *
1675666 AAAACACACTAACCCAAAGCCAAGAATC-TCACCAAAGCTCAAATGCTCAAACGAACAACCAA-A
65 AAAAAAAAAAAAACCAGAGCCAAGAA-CACCACGAAAGATCAAATGCTCAAACGAACAACCAATA
1675729 AACAAAAATGATTTTCAGCAA
129 AAC---AATGATTTTCAGCAA
1675750 A
1 A
1675751 TTCTAGCTGG
Statistics
Matches: 491, Mismatches: 64, Indels: 89
0.76 0.10 0.14
Matches are distributed among these distances:
136 6 0.01
137 60 0.12
138 4 0.01
140 1 0.00
141 34 0.07
142 7 0.01
144 1 0.00
145 3 0.01
146 52 0.11
147 13 0.03
148 4 0.01
149 46 0.09
150 114 0.23
151 18 0.04
158 8 0.02
159 35 0.07
160 8 0.02
162 2 0.00
163 73 0.15
164 2 0.00
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (146 bp):
AATTCGAGATATGAAGTTAAAAAAACAAGGCAATTAGACTAAAGGTATTGAAATAAATTTGAAAA
AAAAAAAAAAAACCAGAGCCAAGAACACCACGAAAGATCAAATGCTCAAACGAACAACCAATAAA
CAATGATTTTCAGCAA
Found at i:1675593 original size:300 final size:307
Alignment explanation
Indices: 1675064--1675626 Score: 736
Period size: 300 Copynumber: 1.8 Consensus size: 307
1675054 AAATAAAATT
* *
1675064 GAAAAAAAAACACAAAAAACCAGAGTCAAGAACACCACGAAAGATCAAATGCTCAAGCGAATAAC
1 GAAAAAAAAACACAAAAAACCAGAGCCAAAAACACCACGAAAGATCAAATGCTCAAGCGAATAAC
* *
1675129 CAATAAATCGGAGATTTTCAGCAAAATTAGAGATATGAAGTTAAAAAAACAAGGCAAATAGAGTA
66 CAATAAAACGAAGATTTTCAGCAAAATTAGAGATATGAA--TAAAAAAACAAGGCAAATAGAGTA
**
1675194 AAGGGTATTGAAATAAATTTGAAAAAAAAAAAACCTAACTCAGAGCCAAGAACACCATGAAAGAT
129 AAGGGTATTGAAATAAATTTG--AAAAAAAAAACC--ACTCAGAGCCAAGAACACCACCAAAGAT
1675259 CAAATGCTCAAACGAACAACCAATATAACAATGATTTTCAGCAAAATCGAGCTAGGAAGTTTAAA
190 CAAATGCTCAAACGAACAACCAATATAACAATGATTTTCAGCAAAATCGAGCTAGGAAG-TTAAA
1675324 AAAAAAAAAAAACCAAGGCACTTAGACTAAAGAGTATTGAGATAAATTTGAAAA
254 AAAAAAAAAAAACCAAGGCACTTAGACTAAAGAGTATTGAGATAAATTTGAAAA
** * *
1675378 GAAAAAAAAACAC-CTAACCCAGAGCCAAAAACACCATGAAAGATCAAATGCTCAAGCGAATAAC
1 GAAAAAAAAACACAAAAAACCAGAGCCAAAAACACCACGAAAGATCAAATGCTCAAGCGAATAAC
* * *** *
1675442 CAATAAAAC-AATGATTTTCAGCGAAA-TCGA-ACTAT-AA-AAAAAAAGGGGGCAATTAGAGTA
66 CAATAAAACGAA-GATTTTCAGCAAAATTAGAGA-TATGAATAAAAAAACAAGGCAAATAGAGTA
* * * * *
1675502 AAGGGTATTGGAATAAATTTG-AAAAAAAAA-C-C-CAGAGCCAAGAATC-TCACCCAAGCTCGA
129 AAGGGTATTGAAATAAATTTGAAAAAAAAAACCACTCAGAGCCAAGAA-CACCACCAAAGATCAA
* *
1675562 ATGCTCAAACGAACAACCAATA-AAGCAATGATTTTCAGCAAATTCGAGCTATGAAGTTAAAAAA
193 ATGCTCAAACGAACAACCAATATAA-CAATGATTTTCAGCAAAATCGAGCTAGGAAGTTAAAAAA
1675626 A
257 A
1675627 CAAGGCAATT
Statistics
Matches: 222, Mismatches: 23, Indels: 23
0.83 0.09 0.09
Matches are distributed among these distances:
299 11 0.05
300 71 0.32
301 2 0.01
304 1 0.00
305 9 0.04
308 39 0.18
311 3 0.01
312 7 0.03
313 66 0.30
314 13 0.06
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.17
Consensus pattern (307 bp):
GAAAAAAAAACACAAAAAACCAGAGCCAAAAACACCACGAAAGATCAAATGCTCAAGCGAATAAC
CAATAAAACGAAGATTTTCAGCAAAATTAGAGATATGAATAAAAAAACAAGGCAAATAGAGTAAA
GGGTATTGAAATAAATTTGAAAAAAAAAACCACTCAGAGCCAAGAACACCACCAAAGATCAAATG
CTCAAACGAACAACCAATATAACAATGATTTTCAGCAAAATCGAGCTAGGAAGTTAAAAAAAAAA
AAAAACCAAGGCACTTAGACTAAAGAGTATTGAGATAAATTTGAAAA
Found at i:1675668 original size:137 final size:137
Alignment explanation
Indices: 1675416--1675758 Score: 364
Period size: 146 Copynumber: 2.4 Consensus size: 137
1675406 AAACACCATG
* * * *
1675416 AAAGATCAAATGCTCAAGCGAATAACCAATAAAACAATGATTTTCAGCGAAA-TCGAACTATAAA
1 AAAGCTCAAATGCTCAAACGAACAACCAATAAAACAATGATTTTCAGC-AAATTCGAGCTATAAA
*** * * * * * * * * * *
1675480 AAAAAAGGGGGCAATTAGAGTAAAGGGTATTGGAATAAATTTGAAAAAAAAACCCAGAGCCAAGA
65 AAAAAACAAGGCAATTAGACTAAAGAGAATTGAAATAAAATCGAACACACAACCCAAAGCCAAGA
1675545 ATCTCACC
130 ATCTCACC
* * *
1675553 CAAGCTCGAATGCTCAAACGAACAACCAATAAAGCAATGATTTTCAGCAAATTCGAGCTATGAAG
1 AAAGCTCAAATGCTCAAACGAACAACCAATAAAACAATGATTTTCAGCAAATTCGAGCTAT-AA-
*
1675618 TTAAAAAAACAAGGCAATTATACTAAAGAGAATTGAAATAAAATCGAAAAAACACACTAACCCAA
64 --AAAAAAACAAGGCAATTAGACTAAAGAGAATTGAAATAAAATCG----AACACAC-AACCCAA
1675683 AGCCAAGAATCTCACC
122 AGCCAAGAATCTCACC
* * *
1675699 AAAGCTCAAATGCTCAAACGAACAACCAAAAACAAAAATGATTTTCAGCAAATTCTAGCT
1 AAAGCTCAAATGCTCAAACGAACAACCAATAA-AACAATGATTTTCAGCAAATTCGAGCT
1675759 GGGAATTGAA
Statistics
Matches: 168, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
136 3 0.02
137 50 0.30
138 2 0.01
141 34 0.20
145 4 0.02
146 51 0.30
147 24 0.14
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.18
Consensus pattern (137 bp):
AAAGCTCAAATGCTCAAACGAACAACCAATAAAACAATGATTTTCAGCAAATTCGAGCTATAAAA
AAAAACAAGGCAATTAGACTAAAGAGAATTGAAATAAAATCGAACACACAACCCAAAGCCAAGAA
TCTCACC
Found at i:1675711 original size:146 final size:142
Alignment explanation
Indices: 1675382--1675758 Score: 410
Period size: 137 Copynumber: 2.7 Consensus size: 142
1675372 TGAAAAGAAA
* * ** * * *
1675382 AAAAAACAC-CTAACCCAGAGCCAA-AAACACCATGAAAGATCAAATGCTCAAGCGAATAACCAA
1 AAAAAACACACTAACCCAGAGCCAAGAATC-TCACCAAAGCTCAAATGCTCAAACGAACAACCAA
* *** * * *
1675445 TAAAACAATGATTTTCAGCGAAA-TCGAACTATAAAAAAAAAGGGGGCAATTAGAGTAAAGGGTA
65 TAAAACAATGATTTTCAGC-AAATTCGAGCTATAAAAAAAAACAAGGCAATTAGACTAAAGAGAA
* * *
1675509 TTGGAATAAATTTG
129 TTGAAATAAAATCG
* *
1675523 -AAAAA-A-A--AACCCAGAGCCAAGAATCTCACCCAAGCTCGAATGCTCAAACGAACAACCAAT
1 AAAAAACACACTAACCCAGAGCCAAGAATCTCACCAAAGCTCAAATGCTCAAACGAACAACCAAT
* *
1675583 AAAGCAATGATTTTCAGCAAATTCGAGCTATGAAGTTAAAAAAACAAGGCAATTATACTAAAGAG
66 AAAACAATGATTTTCAGCAAATTCGAGCTAT-AA---AAAAAAACAAGGCAATTAGACTAAAGAG
1675648 AATTGAAATAAAATCG
127 AATTGAAATAAAATCG
* *
1675664 AAAAAACACACTAACCCAAAGCCAAGAATCTCACCAAAGCTCAAATGCTCAAACGAACAACCAAA
1 AAAAAACACACTAACCCAGAGCCAAGAATCTCACCAAAGCTCAAATGCTCAAACGAACAACCAAT
* *
1675729 AACAAAAATGATTTTCAGCAAATTCTAGCT
66 AA-AACAATGATTTTCAGCAAATTCGAGCT
1675759 GGGAATTGAA
Statistics
Matches: 195, Mismatches: 28, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
136 3 0.02
137 65 0.33
138 5 0.03
139 1 0.01
140 5 0.03
141 34 0.17
142 5 0.03
143 1 0.01
144 1 0.01
146 51 0.26
147 24 0.12
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (142 bp):
AAAAAACACACTAACCCAGAGCCAAGAATCTCACCAAAGCTCAAATGCTCAAACGAACAACCAAT
AAAACAATGATTTTCAGCAAATTCGAGCTATAAAAAAAAACAAGGCAATTAGACTAAAGAGAATT
GAAATAAAATCG
Found at i:1676674 original size:30 final size:30
Alignment explanation
Indices: 1676637--1676708 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
1676627 TGATACGTTG
*
1676637 AACTTTGATTTGGTGT-AATTATACACATGA
1 AACTTTGATTTGGT-TCAAATATACACATGA
* * *
1676667 AATTTTGATTGTGGTTCAAATGTATACATGA
1 AACTTTGATT-TGGTTCAAATATACACATGA
1676698 AACTTTGATTT
1 AACTTTGATTT
1676709 TGATTCAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (30 bp):
AACTTTGATTTGGTTCAAATATACACATGA
Found at i:1676698 original size:31 final size:31
Alignment explanation
Indices: 1676661--1676723 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1676651 GTAATTATAC
* *
1676661 ACATGAAATTTTGATTGTGGTTCAAATGTAT
1 ACATGAAACTTTGATTGTGATTCAAATGTAT
* *
1676692 ACATGAAACTTTGATTTTGATTCAATTGTAT
1 ACATGAAACTTTGATTGTGATTCAAATGTAT
1676723 A
1 A
1676724 TATTTAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (31 bp):
ACATGAAACTTTGATTGTGATTCAAATGTAT
Found at i:1680436 original size:37 final size:39
Alignment explanation
Indices: 1680384--1680472 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 39
1680374 ATTTAACCTG
* * *
1680384 ATTTACTATTTTAAAAAATAATTTTATATATAAT-TAAA-T
1 ATTTA-TATATTAAAAAATAAATATAT-TATAATGTAAATT
*
1680423 ATTTA-ATATTAAAAATTAAATATATTATAATGTAAATT
1 ATTTATATATTAAAAAATAAATATATTATAATGTAAATT
1680461 ATTTATATATTA
1 ATTTATATATTA
1680473 GGATTTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
36 6 0.14
37 20 0.47
38 6 0.14
39 11 0.26
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (39 bp):
ATTTATATATTAAAAAATAAATATATTATAATGTAAATT
Found at i:1682839 original size:60 final size:60
Alignment explanation
Indices: 1682764--1682888 Score: 198
Period size: 60 Copynumber: 2.1 Consensus size: 60
1682754 TGAATAGTTA
*
1682764 GGTGACCAAAAAAGAAATGTACTAATAGTTGAGTGACCATTTTGTAACTTTTCATAG-CTG
1 GGTGACCAAAAAAGAAATGTACTAATACTTGAGTGACCATTTTGTAACTTTTCATAGTC-G
* * *
1682824 GGTGACCAAAGAAGAAATTTACTAATACTTGAGTGACTATTTTGTAACTTTTCATAGTCG
1 GGTGACCAAAAAAGAAATGTACTAATACTTGAGTGACCATTTTGTAACTTTTCATAGTCG
1682884 GGTGA
1 GGTGA
1682889 AAAAATGAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 59 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.33
Consensus pattern (60 bp):
GGTGACCAAAAAAGAAATGTACTAATACTTGAGTGACCATTTTGTAACTTTTCATAGTCG
Found at i:1686496 original size:18 final size:18
Alignment explanation
Indices: 1686460--1686497 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1686450 AAAATATTTA
*
1686460 TTTTGATGTTTTTAGTAT
1 TTTTGATGTTTATAGTAT
1686478 TTTTGATGTATTATA-TAT
1 TTTTGATGT-TTATAGTAT
1686496 TT
1 TT
1686498 AAAAATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (18 bp):
TTTTGATGTTTATAGTAT
Found at i:1687498 original size:28 final size:29
Alignment explanation
Indices: 1687467--1687524 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
1687457 AAAGTGATTT
1687467 AAATG-AAATAATTA-GGGCTAAAATGATA
1 AAATGAAAAT-ATTAGGGGCTAAAATGATA
*
1687495 AAATGAAAATATTAGGGGCTAAAATTATA
1 AAATGAAAATATTAGGGGCTAAAATGATA
1687524 A
1 A
1687525 TTAAGCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.26
Consensus pattern (29 bp):
AAATGAAAATATTAGGGGCTAAAATGATA
Found at i:1694576 original size:31 final size:29
Alignment explanation
Indices: 1694520--1694578 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1694510 TATAAAATAA
** *
1694520 ATATAATTCATGCAAAAAAATTTAAAAAT
1 ATATAATTCATAAAAAAAAAATTAAAAAT
1694549 ATATAATTCATAAAAAAATAAGATTAAAAA
1 ATATAATTCATAAAAAAA-AA-ATTAAAAA
1694579 AATTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.64
30 2 0.08
31 7 0.28
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (29 bp):
ATATAATTCATAAAAAAAAAATTAAAAAT
Found at i:1696917 original size:237 final size:234
Alignment explanation
Indices: 1696491--1697081 Score: 767
Period size: 237 Copynumber: 2.5 Consensus size: 234
1696481 TTATCAAGAT
* * * * * *
1696491 ATTGAGACTACCCCTTCAAGATTTTGTTGTCCATAGATAACCATGTATTTAGCCTTTATTTATTC
1 ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTA-T-
* * * * *
1696556 CCCCCTATATAATAAAATTGGTCAAATTTCATTGAAAGTATCTCTATTATTTGTTTTTTCACAAA
64 -CCCCTA-ATAATAAAATCGGTCAAATTTCATAGAAAGTCTCTCTATTATTTTTTTTTTCAAAAA
* * * *
1696621 TTTAGCCTCTCTACTATAATTTAATAATTTCTTAGTTGATTGGAGGGTACCGAATCAAGTTACAG
127 TTTAACCTCTCTACTATAATTTAATAATTTCTTAGGTGAGTGGAGAGTACCGAATCAAGTTACAG
*
1696686 TTCAAGAGAGTGGGATTACATCAACAAAGTTTGAATAATGGTC
192 TTCAAGAGAGTGGGATTACATCAACAAAGTTTGAATAATGATC
*
1696729 ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAAACATGAATTTAGCCTTTATTTATCC
1 ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATCC
* *
1696794 CCATAAATAATAAAATCGGTCAAATTTCATAGAAACTCCCTCTATTATTTTTTTTTTCCAAAAAT
66 CC-T-AATAATAAAATCGGTCAAATTTCATAGAAAGTCTCTCTATTATTTTTTTTTT-CAAAAAT
* * * * *
1696859 TTAATCTCTCTATTATAATTTGATCATTTCTTGGGTGAGTGGAGAGTACCGAATCAAGTTACAGT
128 TTAACCTCTCTACTATAATTTAATAATTTCTTAGGTGAGTGGAGAGTACCGAATCAAGTTACAGT
* *
1696924 TCAAGAGAGTGGGATTATATCAACAAAGTTTGACTAATGATC
193 TCAAGAGAGTGGGATTACATCAACAAAGTTTGAATAATGATC
* * * * * *
1696966 ATTGAGAGTGTCCTTTTCAAGATTTTGCTGCCCAAATATAACCATGAATTTAGCCTTTATTTTTT
1 ATTGAGAATG-CCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATC
** *
1697031 CCC---T-ATAAAATCAATCAAATTTCATAGAAAGTCTCTTTATTATTTTTTTTT
65 CCCTAATAATAAAATCGGTCAAATTTCATAGAAAGTCTCTCTATTATTTTTTTTT
1697082 ACGGATTTAA
Statistics
Matches: 311, Mismatches: 38, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
232 42 0.14
233 1 0.00
235 4 0.01
236 46 0.15
237 112 0.36
238 106 0.34
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (234 bp):
ATTGAGAATGCCCTTTCAAGATTTTGTTGTCCAAATATAACCATGAATTTAGCCTTTATTTATCC
CCTAATAATAAAATCGGTCAAATTTCATAGAAAGTCTCTCTATTATTTTTTTTTTCAAAAATTTA
ACCTCTCTACTATAATTTAATAATTTCTTAGGTGAGTGGAGAGTACCGAATCAAGTTACAGTTCA
AGAGAGTGGGATTACATCAACAAAGTTTGAATAATGATC
Found at i:1705251 original size:29 final size:27
Alignment explanation
Indices: 1705219--1705289 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 27
1705209 TTGGAATTTT
1705219 AAATATAAAAAATAGGACTAAATTCCTGA
1 AAATATAAAAAATAGGACTAAATT-CT-A
1705248 AAATA-AAAGTAAAT-GGACTAAATTCTA
1 AAATATAAA--AAATAGGACTAAATTCTA
*
1705275 AATATATAAAGAATA
1 AA-ATATAAAAAATA
1705290 CATGGACTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
27 6 0.17
28 8 0.22
29 18 0.50
30 4 0.11
ACGTcount: A:0.58, C:0.07, G:0.10, T:0.25
Consensus pattern (27 bp):
AAATATAAAAAATAGGACTAAATTCTA
Found at i:1705613 original size:27 final size:25
Alignment explanation
Indices: 1705575--1705627 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
1705565 TGAATCTGAA
1705575 ATTTTAAATAAATTTACTATTTTTTTT
1 ATTTTAAATAAA-TTA-TATTTTTTTT
* *
1705602 ATTTTAATTAAATTATCTTTTTTTT
1 ATTTTAAATAAATTATATTTTTTTT
1705627 A
1 A
1705628 CCAAAACAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 11 0.46
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTTAAATAAATTATATTTTTTTT
Found at i:1708839 original size:21 final size:21
Alignment explanation
Indices: 1708798--1708840 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1708788 AAAACAATCG
*
1708798 TTGAATTTTGAAACGTTTTAA
1 TTGAATTTTGAAACGTATTAA
*
1708819 TTGAATTTTTTAAA-GTATTAA
1 TTGAA-TTTTGAAACGTATTAA
1708840 T
1 T
1708841 ATCGTCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (21 bp):
TTGAATTTTGAAACGTATTAA
Found at i:1709877 original size:20 final size:20
Alignment explanation
Indices: 1709852--1709892 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1709842 AAAATTATTC
1709852 TATTTAGTAACGGAATAAGT
1 TATTTAGTAACGGAATAAGT
1709872 TATTTAGTAACGGAATAAGT
1 TATTTAGTAACGGAATAAGT
1709892 T
1 T
1709893 TTAACGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.37
Consensus pattern (20 bp):
TATTTAGTAACGGAATAAGT
Found at i:1718199 original size:23 final size:24
Alignment explanation
Indices: 1718161--1718209 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1718151 TTTGAATCAG
1718161 TTTTCTTTAATGTTTAATAA-TTAT
1 TTTTCTTTAATGTTT-ATAATTTAT
*
1718185 TTTTCTTT-ATTTTTATAATTTAT
1 TTTTCTTTAATGTTTATAATTTAT
1718208 TT
1 TT
1718210 AATTAAATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 11 0.48
24 8 0.35
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTCTTTAATGTTTATAATTTAT
Found at i:1721788 original size:30 final size:28
Alignment explanation
Indices: 1721741--1721806 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 28
1721731 TTTGGGTCAG
*
1721741 GACTAAAATTTTAAAATTAAAAAGTACAAT
1 GACTAAAATTATAAAATTAAAAA-TAC-AT
*
1721771 GACTAAAATTGAT-AAATTTAAAATACAT
1 GACTAAAATT-ATAAAATTAAAAATACAT
1721799 GAACTAAA
1 G-ACTAAA
1721807 TCCACAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 3 0.09
29 9 0.28
30 19 0.59
31 1 0.03
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.29
Consensus pattern (28 bp):
GACTAAAATTATAAAATTAAAAATACAT
Found at i:1723468 original size:22 final size:24
Alignment explanation
Indices: 1723428--1723477 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
1723418 GTAATTTGAC
* **
1723428 AAAAAAAATATAAGTTTAAGGGTT
1 AAAAAAAATATAAGATTAAAAGTT
1723452 AAAAAAAAT-TAA-ATTAAAAGTT
1 AAAAAAAATATAAGATTAAAAGTT
1723474 AAAA
1 AAAA
1723478 TAATTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 11 0.48
23 3 0.13
24 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (24 bp):
AAAAAAAATATAAGATTAAAAGTT
Found at i:1724716 original size:13 final size:13
Alignment explanation
Indices: 1724694--1724724 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1724684 ACGATTTAAC
*
1724694 GATCAGTATGGTA
1 GATCAATATGGTA
1724707 GATCAATATGGTA
1 GATCAATATGGTA
1724720 GATCA
1 GATCA
1724725 GTACATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.29
Consensus pattern (13 bp):
GATCAATATGGTA
Found at i:1725442 original size:21 final size:19
Alignment explanation
Indices: 1725410--1725454 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
1725400 TTTCGGTTAT
*
1725410 CTTTTTTTAATTTTTAGTG
1 CTTTTTTGAATTTTTAGTG
1725429 ACTTTTTCTGAATTTTTAGTG
1 -CTTTTT-TGAATTTTTAGTG
1725450 CTTTT
1 CTTTT
1725455 AAGTGATAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.16, C:0.09, G:0.11, T:0.64
Consensus pattern (19 bp):
CTTTTTTGAATTTTTAGTG
Found at i:1727728 original size:30 final size:29
Alignment explanation
Indices: 1727659--1727728 Score: 68
Period size: 30 Copynumber: 2.3 Consensus size: 29
1727649 GGGTTTGCTT
* * *
1727659 AAAATTTTCAAAAATTTTAGAGACTTAATT
1 AAAATTTT-AAAAATTATAGAGACATAATG
* *
1727689 AGAATTTTTAAAAATTATAGAAGGCATAATG
1 A-AAATTTTAAAAATTATAG-AGACATAATG
1727720 AAAATTTTA
1 AAAATTTTA
1727729 GAATCACATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
30 18 0.56
31 14 0.44
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (29 bp):
AAAATTTTAAAAATTATAGAGACATAATG
Found at i:1730906 original size:60 final size:60
Alignment explanation
Indices: 1730753--1730911 Score: 171
Period size: 59 Copynumber: 2.7 Consensus size: 60
1730743 TTTGGCATTT
* * *
1730753 GAGTTTGGCTTTAATGTTCAATTTAGTACCTAAGTTTTTTGTGTCCTAATTTAATATCTA
1 GAGTTTGGATTTAATGTTCAATTTAGTACCTGAGTTTTTTGTGTCCTAATTTAATAACTA
* * * * **
1730813 -AGTTTGGTTTTAATGTTCAATTTTGTACTTGAGTTTTTCTTTGTCC-CGTTTAA-ACACTA
1 GAGTTTGGATTTAATGTTCAATTTAGTACCTGAGTTTTT-TGTGTCCTAATTTAATA-ACTA
* * *
1730872 GAGTTTGGATTCAATGTTTAGTTTAGTACCTGAGTTTTTT
1 GAGTTTGGATTTAATGTTCAATTTAGTACCTGAGTTTTTT
1730912 TGTATGTTTA
Statistics
Matches: 82, Mismatches: 14, Indels: 7
0.80 0.14 0.07
Matches are distributed among these distances:
58 1 0.01
59 43 0.52
60 38 0.46
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (60 bp):
GAGTTTGGATTTAATGTTCAATTTAGTACCTGAGTTTTTTGTGTCCTAATTTAATAACTA
Found at i:1738277 original size:6 final size:7
Alignment explanation
Indices: 1738256--1738280 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1738246 AATAAAAAAT
1738256 AATTAAA
1 AATTAAA
1738263 AATTAAA
1 AATTAAA
1738270 AATTAAA
1 AATTAAA
1738277 AATT
1 AATT
1738281 TTAATATTTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:1739036 original size:62 final size:61
Alignment explanation
Indices: 1738914--1739037 Score: 144
Period size: 61 Copynumber: 2.0 Consensus size: 61
1738904 TAAATTGATA
* * *
1738914 AAAAATAAATAATGTAATCATATTTTAATATAATTATTATTTAATATAATTTAATAAAAAT
1 AAAAATAAATAATGTAATAATATTTTAATATAAATATTATTTAATATAAATTAATAAAAAT
* * * *
1738975 AAAAATATATAATTTAATAATGTTTTTAATATAAATATT-TTT-ATATTAAATTATATTAAAAT
1 AAAAATAAATAATGTAATAAT-ATTTTAATATAAATATTATTTAATA-TAAATTA-ATAAAAAT
1739037 A
1 A
1739038 TTTTTTAGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
60 3 0.06
61 27 0.51
62 23 0.43
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (61 bp):
AAAAATAAATAATGTAATAATATTTTAATATAAATATTATTTAATATAAATTAATAAAAAT
Found at i:1739038 original size:32 final size:31
Alignment explanation
Indices: 1739009--1739070 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
1738999 TTTAATATAA
*
1739009 ATATT-TTTATATTAAATTATATTAAAATAT
1 ATATTATTTATATTAAATTATAGTAAAATAT
* *
1739039 TTTTTAGTTTATATTAAATTATAGTAAAATAT
1 ATATTA-TTTATATTAAATTATAGTAAAATAT
1739071 TTAAAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 3 0.11
32 24 0.89
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (31 bp):
ATATTATTTATATTAAATTATAGTAAAATAT
Found at i:1742275 original size:8 final size:9
Alignment explanation
Indices: 1742252--1742278 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1742242 TTTGGCTACC
1742252 TATTTTTAA
1 TATTTTTAA
1742261 TATTTTTAA
1 TATTTTTAA
1742270 TATTTTTAA
1 TATTTTTAA
1742279 AGTCAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATTTTTAA
Found at i:1744686 original size:20 final size:20
Alignment explanation
Indices: 1744662--1744708 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1744652 ATTTAATTTA
*
1744662 ATTGCATTGTGTG-TTGTTT
1 ATTGCATTGGGTGTTTGTTT
1744681 ACTTGC-TTGGGTGTTTGTTT
1 A-TTGCATTGGGTGTTTGTTT
1744701 -TTGCATTG
1 ATTGCATTG
1744709 CGTATGAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 10 0.42
ACGTcount: A:0.09, C:0.09, G:0.28, T:0.55
Consensus pattern (20 bp):
ATTGCATTGGGTGTTTGTTT
Found at i:1747483 original size:30 final size:30
Alignment explanation
Indices: 1747413--1747487 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
1747403 CGAAGCCTTT
*
1747413 TAAAATTTTTTAAAATTTTAATTATCTCCC
1 TAAAAATTTTTAAAATTTTAATTATCTCCC
* *
1747443 TTAAAGTTTTTAAAAGTTTTAATTATAC-CCC
1 TAAAAATTTTTAAAA-TTTTAATTAT-CTCCC
1747474 -AAAAATTTTTAAAA
1 TAAAAATTTTTAAAA
1747488 AATTTGATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
30 25 0.64
31 13 0.33
32 1 0.03
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.45
Consensus pattern (30 bp):
TAAAAATTTTTAAAATTTTAATTATCTCCC
Found at i:1752125 original size:23 final size:23
Alignment explanation
Indices: 1752082--1752139 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
1752072 ATTATTAAAT
*
1752082 TTATTATATTATATAATCTAATA
1 TTATTATATTATATAATCTAACA
1752105 TTATTAGTA-TATATACA-CTAACA
1 TTATTA-TATTATATA-ATCTAACA
*
1752128 TATATTAAATTA
1 T-TATTATATTA
1752140 ACAAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (23 bp):
TTATTATATTATATAATCTAACA
Found at i:1753280 original size:59 final size:58
Alignment explanation
Indices: 1753110--1753282 Score: 166
Period size: 60 Copynumber: 2.9 Consensus size: 58
1753100 CACACACAAA
* * ** *
1753110 AAAAAAAAGCTTATGTACTAAATTGAACATTGAAGTCAAATTTAGGTACTTGATTGAGAT
1 AAAAAAAA-CTTATGTACCAAATTGAACATTGAAGTCAAATTAAGG-ACTAAATTGAGAC
* * * * * * *
1753170 AAAGAAAAAGTCATGTACCAAAGTAAACATTGAAGCCAAACTTAAGTACTAAATTGTGAC
1 AAA-AAAAACTTATGTACCAAATTGAACATTGAAGTCAAA-TTAAGGACTAAATTGAGAC
* * *
1753230 AAAAAAAACTTAAGTACCAAATTGAATATTAAAGTCAAATTCAAGGACTAAAT
1 AAAAAAAACTTATGTACCAAATTGAACATTGAAGTCAAATT-AAGGACTAAAT
1753283 AATATATTAA
Statistics
Matches: 89, Mismatches: 21, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
58 2 0.02
59 38 0.43
60 40 0.45
61 9 0.10
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.26
Consensus pattern (58 bp):
AAAAAAAACTTATGTACCAAATTGAACATTGAAGTCAAATTAAGGACTAAATTGAGAC
Found at i:1754192 original size:15 final size:17
Alignment explanation
Indices: 1754171--1754211 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
1754161 TAACCCTTTA
1754171 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
1754187 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
1754203 AAAATTATA
1 AAAATTATA
1754212 TTTTTTACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:1765519 original size:21 final size:22
Alignment explanation
Indices: 1765493--1765556 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 22
1765483 GAAAGCTTTG
1765493 TTTTTAATGGTTTGGTCTTAAT
1 TTTTTAATGGTTTGGTCTTAAT
***
1765515 TTTTAGTAAAAAATTTGGTCTTAA-
1 TTTT--T-AATGGTTTGGTCTTAAT
1765539 TTTTTAATGGTTTGGTCT
1 TTTTTAATGGTTTGGTCT
1765557 CCAATATTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
21 10 0.30
22 5 0.15
24 5 0.15
25 13 0.39
ACGTcount: A:0.23, C:0.05, G:0.17, T:0.55
Consensus pattern (22 bp):
TTTTTAATGGTTTGGTCTTAAT
Found at i:1766659 original size:2 final size:2
Alignment explanation
Indices: 1766652--1766678 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1766642 GAAGGTATTA
1766652 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1766679 AGCGTGCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1767610 original size:20 final size:18
Alignment explanation
Indices: 1767570--1767614 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
1767560 TAAAAAAGTA
1767570 TAAAAAATTATTAAATAT
1 TAAAAAATTATTAAATAT
* *
1767588 TAAAATAATATATTTAATTT
1 TAAAA-AAT-TATTAAATAT
1767608 TAAAAAA
1 TAAAAAA
1767615 AATAATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 5 0.22
20 13 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAAAATTATTAAATAT
Found at i:1774894 original size:16 final size:15
Alignment explanation
Indices: 1774873--1774920 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
1774863 GATGGGAATA
1774873 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
1774889 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
1774904 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
1774920 A
1 A
1774921 ATATTAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:1774903 original size:8 final size:8
Alignment explanation
Indices: 1774869--1774920 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
1774859 CAATGATGGG
*
1774869 AATAATAA
1 AATATTAA
1774877 AATATATAA
1 AATAT-TAA
1774886 AATA-TAA
1 AATATTAA
1774893 AATATTAA
1 AATATTAA
*
1774901 AATATCAA
1 AATATTAA
*
1774909 AATATTAG
1 AATATTAA
1774917 AATA
1 AATA
1774921 ATATTAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:1774920 original size:24 final size:24
Alignment explanation
Indices: 1774868--1774923 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1774858 ACAATGATGG
*
1774868 GAATAATAAAATATATAAAATATA
1 GAATAATAAAATATACAAAATATA
* *
1774892 AAATATTAAAATAT-CAAAATATTA
1 GAATAATAAAATATACAAAATA-TA
1774916 GAATAATA
1 GAATAATA
1774924 TTAATTAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (24 bp):
GAATAATAAAATATACAAAATATA
Found at i:1775083 original size:23 final size:22
Alignment explanation
Indices: 1775032--1775085 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
1775022 ATACTACATC
1775032 AATATGTACATAT-ATA--AAA
1 AATATGTACATATAATATTAAA
**
1775051 AATAAATACATGATAATATTAAA
1 AATATGTACAT-ATAATATTAAA
1775074 AATATGTACATA
1 AATATGTACATA
1775086 ATATAGTGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 9 0.33
20 2 0.07
21 3 0.11
22 1 0.04
23 12 0.44
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
AATATGTACATATAATATTAAA
Found at i:1775132 original size:22 final size:24
Alignment explanation
Indices: 1775048--1775133 Score: 81
Period size: 25 Copynumber: 3.7 Consensus size: 24
1775038 TACATATATA
* *
1775048 AAAAATAAATACATGATAATA--TT
1 AAAAATATATACATAAT-ATAGGTT
*
1775071 AAAAATATGTACATAATATAGTGTT
1 AAAAATATATACATAATATAG-GTT
*
1775096 AAAAATACATACATAATATA-GTT
1 AAAAATATATACATAATATAGGTT
*
1775119 -AAGATATATACATAA
1 AAAAATATATACATAA
1775134 GATAACATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
22 16 0.30
23 17 0.32
25 20 0.38
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (24 bp):
AAAAATATATACATAATATAGGTT
Found at i:1775209 original size:47 final size:45
Alignment explanation
Indices: 1775158--1775288 Score: 117
Period size: 47 Copynumber: 2.9 Consensus size: 45
1775148 AAAAAAATCT
1775158 ATATATATAAATAATATAATATTAAAGATATATAAAAATAGTATAAA
1 ATATATATAAATAATATAATATTAAAGATATATAAAAATA-T-TAAA
** * *
1775205 ATATATATACGTAATATAAAATTTAAA-ATATACCT-AATATATTAAA
1 ATATATATAAATAATATAATA-TTAAAGATATA--TAAAAATATTAAA
* * * *
1775251 AGA-ATATATATAATATAATATT-AAGAAATATAATAATA
1 ATATATATAAATAATATAATATTAAAGATATATAAAAATA
1775289 ACAAAAAAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
42 1 0.01
43 6 0.09
44 6 0.09
45 14 0.21
46 6 0.09
47 24 0.35
48 10 0.15
49 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (45 bp):
ATATATATAAATAATATAATATTAAAGATATATAAAAATATTAAA
Found at i:1775213 original size:11 final size:11
Alignment explanation
Indices: 1775158--1775213 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
1775148 AAAAAAATCT
1775158 ATATATATAAATA
1 ATATATAT-AA-A
*
1775171 ATATAATATTAA
1 ATAT-ATATAAA
*
1775183 AGATATATAAA
1 ATATATATAAA
1775194 A-ATAGTATAAA
1 ATATA-TATAAA
1775205 ATATATATA
1 ATATATATA
1775214 CGTAATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 3 0.08
11 18 0.49
12 7 0.19
13 5 0.14
14 4 0.11
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (11 bp):
ATATATATAAA
Found at i:1775806 original size:30 final size:30
Alignment explanation
Indices: 1775770--1775884 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
1775760 TAGGTACAAG
*
1775770 TGGTGGTGGAGAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1775800 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
* *
1775830 TGGTGGTGGAAAAAGAGTGGCTAGTGGAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
1775860 TGGTGGTGGAAAAGGTGTGGCTAGT
1 TGGTGGTGGAAAAGGTGTGGCTAGT
1775885 TGAGAAAAGT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.21, C:0.03, G:0.50, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAAAAGGTGTGGCTAGTGGAGT
Found at i:1776757 original size:77 final size:77
Alignment explanation
Indices: 1776582--1776832 Score: 366
Period size: 77 Copynumber: 3.3 Consensus size: 77
1776572 ATGTGAACCC
* * * *
1776582 AAGGCTCAACTCACATCTCGCAATATGAGTTGA--TTTTTGAAAAACAGAAATTTAAAAATACCT
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAA-TTGAAAATAGCT
** *
1776645 CAG--CGTGTCCT
65 CAGCACGTGAGCA
*
1776656 GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATAGCTC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATAGCTC
1776721 AGCACGTGAGCA
66 AGCACGTGAGCA
* *
1776733 AAGGCTCAACTCACCTCTCACAATATGAGTTGATTCTTTTGAAAAGCAGAAATTGAAAATAGCTC
1 AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATAGCTC
1776798 AGCACGTGAGCA
66 AGCACGTGAGCA
*
1776810 AAGGCTCAACTCACTTCTCGCAA
1 AAGGCTCAACTCACCTCTCGCAA
1776833 AAGTAGATTT
Statistics
Matches: 160, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
74 31 0.19
75 13 0.08
76 16 0.10
77 100 0.62
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (77 bp):
AAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAGCAGAAATTGAAAATAGCTC
AGCACGTGAGCA
Found at i:1776923 original size:14 final size:14
Alignment explanation
Indices: 1776904--1776954 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1776894 GAGTTGATTT
*
1776904 TTGAAAAATATAAA
1 TTGAAAAATAGAAA
1776918 TTGAAAAAAATAGAAA
1 TTG--AAAAATAGAAA
**
1776934 TTGAAAAGCAGAAA
1 TTGAAAAATAGAAA
1776948 TT-AAAAA
1 TTGAAAAA
1776955 GACCTCAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 14 0.45
16 13 0.42
ACGTcount: A:0.65, C:0.02, G:0.12, T:0.22
Consensus pattern (14 bp):
TTGAAAAATAGAAA
Found at i:1776928 original size:16 final size:16
Alignment explanation
Indices: 1776907--1776940 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1776897 TTGATTTTTG
*
1776907 AAAAATATAAATTGAA
1 AAAAATAGAAATTGAA
1776923 AAAAATAGAAATTGAA
1 AAAAATAGAAATTGAA
1776939 AA
1 AA
1776941 GCAGAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
AAAAATAGAAATTGAA
Found at i:1777093 original size:75 final size:75
Alignment explanation
Indices: 1776934--1777175 Score: 317
Period size: 76 Copynumber: 3.2 Consensus size: 75
1776924 AAAATAGAAA
* * ** *
1776934 TTGAAAAGCAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTAAAAATACCTCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATAT
*
1776999 GAGTT-A-ATTT
64 GAGTTGATTTTT
* * * *
1777009 TTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTTTCGCAATATGA
1 TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
1777074 GTTGATTTTT
66 GTTGATTTTT
*
1777084 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAA-TTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
1777149 AGTTGATTTTT
65 AGTTGATTTTT
* **
1777160 TTTACGAACAGAAATT
1 TTGAAAAACAGAAATT
1777176 GAAGAACAGA
Statistics
Matches: 146, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
73 34 0.23
74 1 0.01
75 43 0.29
76 68 0.47
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.29
Consensus pattern (75 bp):
TTGAAAAACAGAAATTAAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTT
Found at i:1777184 original size:14 final size:14
Alignment explanation
Indices: 1777165--1777192 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1777155 TTTTTTTTAC
1777165 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1777179 GAACAGAAATTGAA
1 GAACAGAAATTGAA
1777193 AAGACCTCAG
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:0.57, C:0.07, G:0.21, T:0.14
Consensus pattern (14 bp):
GAACAGAAATTGAA
Found at i:1777238 original size:91 final size:88
Alignment explanation
Indices: 1777084--1777268 Score: 248
Period size: 89 Copynumber: 2.1 Consensus size: 88
1777074 GTTGATTTTT
* *
1777084 TTGAAAAACAGAAATTTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
* * *
1777149 AGTTGATTTTTTTTACGAACAGAAA
66 AGTT-A-ATTTTTGACAAACAGAAA
* *
1777174 TTGAAGAACAGAAA-TTGAAAAGACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAAT
1 TTGAAAAACAGAAATTTAAAAAGACCTCAGC--GTG-GCCTGAGGCTCAACTCACCTCTCGCAAT
1777237 ATGAGTTAATTTTTGACAAACAGAAA
63 ATGAGTTAATTTTTGACAAACAGAAA
1777263 TTGAAA
1 TTGAAA
1777269 TTACCTCAGC
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
89 34 0.40
90 14 0.17
91 34 0.40
92 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.26
Consensus pattern (88 bp):
TTGAAAAACAGAAATTTAAAAAGACCTCAGCGTGGCCTGAGGCTCAACTCACCTCTCGCAATATG
AGTTAATTTTTGACAAACAGAAA
Found at i:1777307 original size:73 final size:74
Alignment explanation
Indices: 1777174--1777342 Score: 232
Period size: 73 Copynumber: 2.3 Consensus size: 74
1777164 CGAACAGAAA
* *
1777174 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATAT
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCA-GTGACCCGAGGCTCAACTCACCTCTCGCAATAT
1777239 GAGTTAATTT
65 GAGTTAATTT
* ** * *
1777249 TTGACAAACAGAAATTGAAATTACCTCAGC-GTGTCCCGAGGCTCAACTCACCTTTCGCAATATG
1 TTGAAAAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
*
1777313 AGTTGATTT
66 AGTTAATTT
* *
1777322 TTGAAAAATATAAATTGAAAA
1 TTGAAAAACAGAAATTGAAAA
1777343 AACAGAAATT
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
73 56 0.68
75 26 0.32
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAAAGACCTCAGCAGTGACCCGAGGCTCAACTCACCTCTCGCAATATG
AGTTAATTT
Found at i:1777341 original size:14 final size:14
Alignment explanation
Indices: 1777322--1777371 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
1777312 GAGTTGATTT
* *
1777322 TTGAAAAATATAAA
1 TTGAAAAACAGAAA
1777336 TTGAAAAAACAGAAA
1 TTG-AAAAACAGAAA
*
1777351 TTGAAAAGCAGAAA
1 TTGAAAAACAGAAA
1777365 TT-AAAAA
1 TTGAAAAA
1777372 AGACCTCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.20
Consensus pattern (14 bp):
TTGAAAAACAGAAA
Found at i:1777373 original size:15 final size:15
Alignment explanation
Indices: 1777333--1777373 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1777323 TGAAAAATAT
1777333 AAATTGAAAAAA-CAG
1 AAATT-AAAAAAGCAG
*
1777348 AAATT-GAAAAGCAG
1 AAATTAAAAAAGCAG
1777362 AAATTAAAAAAG
1 AAATTAAAAAAG
1777374 ACCTCAGCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.18
14 8 0.36
15 10 0.45
ACGTcount: A:0.66, C:0.05, G:0.15, T:0.15
Consensus pattern (15 bp):
AAATTAAAAAAGCAG
Found at i:1777493 original size:78 final size:75
Alignment explanation
Indices: 1777351--1777522 Score: 218
Period size: 78 Copynumber: 2.2 Consensus size: 75
1777341 AAAACAGAAA
* * * *
1777351 TTGAAAAGCAGAAATTAAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCTTACAATA
1 TTGAAAA-CAGAAATTGAAAAAGACCTCAGCATGTAAGCCAAGACTCAACTCACCTCTCACAATA
1777416 TGAGTTGATTTTT
65 TGAGTTGA--TTT
* * * *
1777429 TTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAGGCTCAACTCACCTCTCGCAATA
1 TTGA-AAACAGAAATTGAAAAAGACCTCAGCATGTAAGCCAAGACTCAACTCACCTCTCACAATA
1777494 TGAGTTGATTT
65 TGAGTTGATTT
*
1777505 TTGAAAAACATAAATTGA
1 TTG-AAAACAGAAATTGA
1777523 GCAGAAATTG
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
76 18 0.22
77 1 0.01
78 61 0.73
79 3 0.04
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (75 bp):
TTGAAAACAGAAATTGAAAAAGACCTCAGCATGTAAGCCAAGACTCAACTCACCTCTCACAATAT
GAGTTGATTT
Found at i:1777521 original size:183 final size:177
Alignment explanation
Indices: 1777166--1777522 Score: 554
Period size: 183 Copynumber: 2.0 Consensus size: 177
1777156 TTTTTTTACG
* *
1777166 AACAGAAATTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCT
1 AACAGAAATTGAAGAACAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCT
* * *
1777231 CGCAATATGAGTTAATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAAC
66 CACAATATGAGTTAATTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCCAAGGCTCAAC
* *
1777296 TCACCTTTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAA
131 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAAAA
1777343 AACAGAAATTGAA-AAGCAGAAATTAAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCT
1 AACAGAAATTGAAGAA-CAGAAATT-AAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCT
* * *
1777407 CTTACAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATACCTCAGCGTGTAAGCCAAG
64 CTCACAATATGAGTT-A-ATTTTTGACAAACAGAAATTG-AAAATACCTCAGCGTGT--CCCAAG
1777472 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGA
124 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGA
1777523 GCAGAAATTG
Statistics
Matches: 163, Mismatches: 10, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
176 2 0.01
177 21 0.13
178 50 0.31
179 1 0.01
180 20 0.12
181 16 0.10
183 53 0.33
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (177 bp):
AACAGAAATTGAAGAACAGAAATTAAAAAGACCTCAGCATGTGAGCCGAGACTCAACTCACCTCT
CACAATATGAGTTAATTTTTGACAAACAGAAATTGAAAATACCTCAGCGTGTCCCAAGGCTCAAC
TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACATAAATTGAAAA
Found at i:1777522 original size:345 final size:337
Alignment explanation
Indices: 1777044--1777661 Score: 825
Period size: 345 Copynumber: 1.8 Consensus size: 337
1777034 TCAGCGTGTC
* * *
1777044 CCGAGGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTTAAAAATAC
1 CCGAGACTCAACTCACCTTTCACAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATAC
* * **
1777109 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTACGAACAGAAA
66 CTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGAAAAACAGAAA
*
1777174 TTGAAGAACAGAAATTGAAAAGACCTCAGCATGTGAG-C-CGAGGCTCAACTCACCTCTCGCAAT
130 TTG-AG--CAGAAATTGAAAAGACCTCA--ACG-G-GTCTCGAGGCTCAACTCACCTCTCGCAAT
* * *
1777237 ATGAGTT-AATTTTTGACAAACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACC
188 ATGAGTTGAATTTTTG---AACAGAAATTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACC
* *
1777301 TTTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGCAGAAAT
250 TCTCACAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGCAGAAAT
1777366 TAAAAAAGACCTCAGCATGTGAG
315 TAAAAAAGACCTCAGCATGTGAG
*
1777389 CCGAGACTCAACTCACCTCTT-ACAATATGAGTTGATTTTTTTGACAAACAGAAATTGAAAAATA
1 CCGAGACTCAACTCACCT-TTCACAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATA
*
1777453 CCTCAGCGTGTAAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAT
65 CCTCAGCGTGT---CCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAG
* * *
1777516 AAATTGAGCAGAAATTGAAAATACCTCAACGGGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
127 AAATTGAGCAGAAATTGAAAAGACCTCAACGGGTCTCGAGGCTCAACTCACCTCTCGCAATATGA
* ** * * ** *
1777581 GTTGATTTTTTGATGATAAATTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCTCTCACA
192 GTTGAATTTTTGAACAGAAATTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTCACA
1777646 ATATGAGTTGATTTTT
257 ATATGAGTTGATTTTT
1777662 TTGAATTAAA
Statistics
Matches: 240, Mismatches: 26, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
338 58 0.24
339 2 0.01
340 32 0.13
341 7 0.03
342 19 0.08
344 2 0.01
345 84 0.35
346 2 0.01
347 32 0.13
348 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (337 bp):
CCGAGACTCAACTCACCTTTCACAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAAATAC
CTCAGCGTGTCCTAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAACAGAAAT
TGAGCAGAAATTGAAAAGACCTCAACGGGTCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
AATTTTTGAACAGAAATTGAAAATACCTCAACGTGACCCGAGGCTCAACTCACCTCTCACAATAT
GAGTTGATTTTTGAAAAATATAAATTGAAAAAACAGAAATTGAAAAGCAGAAATTAAAAAAGACC
TCAGCATGTGAG
Found at i:1777648 original size:71 final size:71
Alignment explanation
Indices: 1777527--1777662 Score: 236
Period size: 71 Copynumber: 1.9 Consensus size: 71
1777517 AATTGAGCAG
* *
1777527 AAATTGAAAATACCTCAACGGGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGGGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTT
1777592 GATGAT
66 GATGAT
* *
1777598 AAATTGAAAATACCTCAATGTGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGGGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTT
1777663 TGAATTAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (71 bp):
AAATTGAAAATACCTCAACGGGACTTGAGGTTCAACTCACCTCTCACAATATGAGTTGATTTTTT
GATGAT
Found at i:1777919 original size:77 final size:74
Alignment explanation
Indices: 1777821--1778153 Score: 391
Period size: 74 Copynumber: 4.4 Consensus size: 74
1777811 TGGCCCGAGA
* * * *
1777821 CTCAACTCACCTCTCGCAATATGAGTTCATTCTTTTAAAAAGCAAAAATTGAAAATACCTCGGCA
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAA-CAGAAATTGAAAATACCTCAGC-
* * *
1777886 TGTGGCCCGATG
64 -GTGTCCTGAGG
* * *
1777898 CTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTGAAAATACCTCAA
1 CTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTTTAAAAACAGAAATTGAAAATACCTCAG
*
1777963 CGTGTCTTGAGG
63 CGTGTCCTGAGG
** * * * * *
1777975 CTCAACTCATTTCTCGTAATATAAGTTGA--ATTTTGAAAACAGAAATTGAAATTACCTCAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGAAATTGAAAATACCTCAGCGT
1778038 GTCCTGAGG
66 GTCCTGAGG
** * *
1778047 CTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTAACAACAGAAATTGAAATTACCTCAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGAAATTGAAAATACCTCAGCGT
1778112 GTCCTGAGG
66 GTCCTGAGG
*
1778121 CTCAACTCACCTCTAGCAATATGAGTTGATTTT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTT
1778154 GAAAAACAAA
Statistics
Matches: 225, Mismatches: 26, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
72 66 0.29
74 70 0.31
77 60 0.27
79 19 0.08
80 10 0.04
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (74 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTAAAAACAGAAATTGAAAATACCTCAGCGT
GTCCTGAGG
Found at i:1778032 original size:72 final size:72
Alignment explanation
Indices: 1777933--1778167 Score: 337
Period size: 72 Copynumber: 3.2 Consensus size: 72
1777923 TTGATTTTTT
* * * * *
1777933 TTTTGAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGTAATATA
1 TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATG
1777998 AGTTGAA
66 AGTTGAA
1778005 TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATG
1 TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATG
*
1778070 AGTTGATT
66 AGTTGA-A
* ** *
1778078 TTTTTAACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATAT
1 TTTTGAA-AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATAT
1778143 GAGTTG-A
65 GAGTTGAA
*
1778150 TTTTGAAAAACAAAAATT
1 TTTTG-AAAACAGAAATT
1778168 AAAAGGCTTA
Statistics
Matches: 147, Mismatches: 13, Indels: 6
0.89 0.08 0.04
Matches are distributed among these distances:
72 79 0.54
73 8 0.05
74 60 0.41
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (72 bp):
TTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATG
AGTTGAA
Found at i:1778114 original size:146 final size:147
Alignment explanation
Indices: 1777821--1778167 Score: 403
Period size: 146 Copynumber: 2.3 Consensus size: 147
1777811 TGGCCCGAGA
* * * * * *
1777821 CTCAACTCACCTCTCGCAATATGAGTTCATTCTTTTAAAAAGCAAAAATTGAAAATACCTCGGCA
1 CTCAACTCACCTCTAGCAATATAAGTTGA-T-TTTGAAAAA-CAAAAATTGAAATTACCTCAGC-
* * *
1777886 TGTGGCCCGATGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTTGAAAACAGAAATTG
62 -GTGTCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGA--TTTTTTTTGAAAACAGAAATTG
*
1777951 AAAATACCTCAACGTGTCTTGAGG
124 AAAATACCTCAACGTGTCCTGAGG
** * * *
1777975 CTCAACTCATTTCTCGTAATATAAGTTGAATTTTG-AAAACAGAAATTGAAATTACCTCAGCGTG
1 CTCAACTCACCTCTAGCAATATAAGTTG-ATTTTGAAAAACAAAAATTGAAATTACCTCAGCGTG
** * *
1778039 TCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTTTTTT-AACAACAGAAATTGAAATT
65 TCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTGAA-AACAGAAATTGAAAAT
*
1778102 ACCTCAGCGTGTCCTGAGG
129 ACCTCAACGTGTCCTGAGG
*
1778121 CTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATT
1 CTCAACTCACCTCTAGCAATATAAGTTGATTTTGAAAAACAAAAATT
1778168 AAAAGGCTTA
Statistics
Matches: 166, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
145 8 0.05
146 73 0.44
149 34 0.20
151 19 0.11
152 4 0.02
153 3 0.02
154 24 0.14
155 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (147 bp):
CTCAACTCACCTCTAGCAATATAAGTTGATTTTGAAAAACAAAAATTGAAATTACCTCAGCGTGT
CCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTGAAAACAGAAATTGAAAATAC
CTCAACGTGTCCTGAGG
Found at i:1778318 original size:70 final size:70
Alignment explanation
Indices: 1778171--1778345 Score: 203
Period size: 70 Copynumber: 2.5 Consensus size: 70
1778161 AAAAATTAAA
* * * * * **
1778171 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
1778235 CCCCG
66 CCCCG
*
1778240 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTGAAAA-AAAAATTAAAAATACCTCAACGT
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTT-AAAACAAAAACTAAAAATACCTCAACGT
* **
1778304 GTCTTG
65 GCCCCG
*
1778310 AGGCTCAACTGA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
1778346 CCTTGGAAAG
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
69 27 0.30
70 60 0.66
71 4 0.04
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACAAAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:1789611 original size:29 final size:30
Alignment explanation
Indices: 1789557--1789632 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
1789547 CCTTATACTA
* * *
1789557 TTAATAATATAGGGAGTAAATCGATCCA-T
1 TTAATAATAGAGGGATTAAATCGATCAAGT
* *
1789586 TTAATAATAGAGGGATTAATTTGATCAAGT
1 TTAATAATAGAGGGATTAAATCGATCAAGT
*
1789616 TCTTATAATAGAGGGAT
1 T-TAATAATAGAGGGAT
1789633 CTCACTTGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 23 0.59
30 2 0.05
31 14 0.36
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (30 bp):
TTAATAATAGAGGGATTAAATCGATCAAGT
Found at i:1790762 original size:32 final size:30
Alignment explanation
Indices: 1790713--1790852 Score: 92
Period size: 32 Copynumber: 4.6 Consensus size: 30
1790703 ACCCCCAAAA
*
1790713 AAGTTTA-AGTACTAAATTAAGAAAAAAGTGTC
1 AAGTTTAGA-TACCAAATT-AGAAAAAA-TGTC
*
1790745 AAGTTTAGATACCAAATTAGGAAAAAAAAGGTC
1 AAGTTTAGATACCAAATTA-G--AAAAAATGTC
* ** * *
1790778 AAGTTTGGGCA-CTAATTAGACCAAAAAAG--
1 AAGTTTAGATACCAAATTAGA--AAAAATGTC
1790807 -AGTTTAGATACCAAATTAGAAAAAATGTC
1 AAGTTTAGATACCAAATTAGAAAAAATGTC
* *
1790836 AAATTTAAATACCAAAT
1 AAGTTTAGATACCAAAT
1790853 ATTATATTAA
Statistics
Matches: 84, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
27 6 0.07
28 7 0.08
29 9 0.11
30 14 0.17
31 8 0.10
32 22 0.26
33 12 0.14
34 6 0.07
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (30 bp):
AAGTTTAGATACCAAATTAGAAAAAATGTC
Found at i:1794330 original size:29 final size:29
Alignment explanation
Indices: 1794278--1794336 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1794268 TTTGACTATA
* *
1794278 TAAAAAAAATTTAGGGTCGGAAATTTAAT
1 TAAAAAAAATTTAGGGTCGAAAATATAAT
*
1794307 TAAAAAAATTTTAGAGGTC-AAAATATAAT
1 TAAAAAAAATTTAG-GGTCGAAAATATAAT
1794336 T
1 T
1794337 TATCTTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (29 bp):
TAAAAAAAATTTAGGGTCGAAAATATAAT
Found at i:1796023 original size:14 final size:14
Alignment explanation
Indices: 1796004--1796034 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1795994 TCTTTATTTG
1796004 TTTTTTATCTCTTT
1 TTTTTTATCTCTTT
*
1796018 TTTTTTTTCTCTTT
1 TTTTTTATCTCTTT
1796032 TTT
1 TTT
1796035 GTAATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTATCTCTTT
Found at i:1799575 original size:4 final size:4
Alignment explanation
Indices: 1799566--1799608 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
1799556 TTATATATGT
1799566 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1799609 TATATATATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1802540 original size:3 final size:3
Alignment explanation
Indices: 1802526--1802563 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1802516 ACCACACAAT
*
1802526 TGA TGT TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1802564 GTAGCAGCAG
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:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (3 bp):
TGA
Found at i:1816021 original size:16 final size:17
Alignment explanation
Indices: 1816000--1816037 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1815990 CTAGCTTGAA
*
1816000 TTTTAA-ATTTTTTATT
1 TTTTAATATTTTTAATT
1816016 TTTTAATATTTTTAATT
1 TTTTAATATTTTTAATT
1816033 TTTTA
1 TTTTA
1816038 GATACATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTAATATTTTTAATT
Found at i:1816027 original size:9 final size:8
Alignment explanation
Indices: 1816000--1816037 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1815990 CTAGCTTGAA
*
1816000 TTTTAAAT
1 TTTTTAAT
1816008 TTTTT-AT
1 TTTTTAAT
1816015 TTTTTAAT
1 TTTTTAAT
1816023 ATTTTTAAT
1 -TTTTTAAT
1816032 TTTTTA
1 TTTTTA
1816038 GATACATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
7 7 0.26
8 12 0.44
9 8 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTAAT
Found at i:1816502 original size:31 final size:31
Alignment explanation
Indices: 1816455--1816515 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1816445 AGAGAATGCC
*
1816455 CAAAATATAAACGATCTAAAACGTGAGTGAA
1 CAAAATAGAAACGATCTAAAACGTGAGTGAA
* *
1816486 CAAAATAGAAATGATCTAAAACGTTAGTGA
1 CAAAATAGAAACGATCTAAAACGTGAGTGA
1816516 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.21
Consensus pattern (31 bp):
CAAAATAGAAACGATCTAAAACGTGAGTGAA
Found at i:1816675 original size:8 final size:8
Alignment explanation
Indices: 1816662--1816690 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1816652 CTGAATCTTA
1816662 TTTTTTCT
1 TTTTTTCT
1816670 TTTTTTCT
1 TTTTTTCT
1816678 TTTTTTCT
1 TTTTTTCT
1816686 TTTTT
1 TTTTT
1816691 GTGATGGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1817985 original size:17 final size:18
Alignment explanation
Indices: 1817958--1817991 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1817948 ATTTTTCATG
1817958 TCAACAAAAATTTTAAAT
1 TCAACAAAAATTTTAAAT
1817976 TCAA-AAAAATTTTAAA
1 TCAACAAAAATTTTAAA
1817992 AGTTCACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (18 bp):
TCAACAAAAATTTTAAAT
Found at i:1821240 original size:10 final size:11
Alignment explanation
Indices: 1821218--1821251 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1821208 TCTATTTCTG
1821218 TTTTATATTTA
1 TTTTATATTTA
1821229 TTTTAT-TTTA
1 TTTTATATTTA
*
1821239 TTTTATAATTA
1 TTTTATATTTA
1821250 TT
1 TT
1821252 CTGACATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTATATTTA
Found at i:1822088 original size:25 final size:25
Alignment explanation
Indices: 1822031--1822091 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
1822021 ATGAAGAGGA
*
1822031 TTAATTTTTTTTAATATTTTTAATT
1 TTAATATTTTTTAATATTTTTAATT
* *
1822056 ATAA-ATTTTTTAAT-TATTTTACTT
1 TTAATATTTTTTAATAT-TTTTAATT
1822080 TTAATATTTTTT
1 TTAATATTTTTT
1822092 TTAAACATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 19 0.63
25 10 0.33
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TTAATATTTTTTAATATTTTTAATT
Found at i:1822760 original size:6 final size:6
Alignment explanation
Indices: 1822749--1822774 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1822739 AAATGACCTA
1822749 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
1822775 TAAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:1823030 original size:23 final size:23
Alignment explanation
Indices: 1822984--1823031 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1822974 TTTTTTTTTT
*
1822984 ATTTTATTAAATAAATTATTAAA
1 ATTTTATTAAATAAATTATAAAA
*
1823007 ATTTTATTAAAATATATTA-AAAA
1 ATTTTATT-AAATAAATTATAAAA
1823030 AT
1 AT
1823032 AAAAAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
ATTTTATTAAATAAATTATAAAA
Found at i:1824750 original size:21 final size:22
Alignment explanation
Indices: 1824697--1824743 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1824687 TCGAGTTTAA
1824697 GCTCAAGCTTGTCAATATTTGG
1 GCTCAAGCTTGTCAATATTTGG
1824719 GCTCAAGCTTGTCAATATTTGG
1 GCTCAAGCTTGTCAATATTTGG
1824741 GCT
1 GCT
1824744 TAGCTTGGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (22 bp):
GCTCAAGCTTGTCAATATTTGG
Found at i:1824846 original size:81 final size:81
Alignment explanation
Indices: 1824711--1824872 Score: 315
Period size: 81 Copynumber: 2.0 Consensus size: 81
1824701 AAGCTTGTCA
*
1824711 ATATTTGGGCTCAAGCTTGTCAATATTTGGGCTTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
1 ATATTTGGGCTCAAGCTTGTCAATATTTGGGCCTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
1824776 AAATGGGTTACAAACT
66 AAATGGGTTACAAACT
1824792 ATATTTGGGCTCAAGCTTGTCAATATTTGGGCCTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
1 ATATTTGGGCTCAAGCTTGTCAATATTTGGGCCTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
1824857 AAATGGGTTACAAACT
66 AAATGGGTTACAAACT
1824873 CAAGGTTTAA
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (81 bp):
ATATTTGGGCTCAAGCTTGTCAATATTTGGGCCTAGCTTGGCTCAATTACACCCTTAAGAAGGAG
AAATGGGTTACAAACT
Found at i:1832558 original size:37 final size:37
Alignment explanation
Indices: 1832508--1832583 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
1832498 TTTCTTTTAG
* *
1832508 CTATATTAGTTTCAATTAGAAATTATCTATAGCTGCT
1 CTATATTAGTTTCAACTAGAAATTATATATAGCTGCT
1832545 CTATATTAGTTTCAACTAGAAATTATATATAGCTGCT
1 CTATATTAGTTTCAACTAGAAATTATATATAGCTGCT
1832582 CT
1 CT
1832584 TAATACAGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (37 bp):
CTATATTAGTTTCAACTAGAAATTATATATAGCTGCT
Found at i:1840487 original size:18 final size:18
Alignment explanation
Indices: 1840453--1840487 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1840443 GGCACAGTTT
*
1840453 AAAATGAAAATTTTAAAG
1 AAAATGAAAATTGTAAAG
*
1840471 AAAATGAATATTGTAAA
1 AAAATGAAAATTGTAAA
1840488 AATCACGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
AAAATGAAAATTGTAAAG
Found at i:1841738 original size:20 final size:20
Alignment explanation
Indices: 1841699--1841737 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1841689 TTCAAATTTT
1841699 TTAATAAATTTATATATATA
1 TTAATAAATTTATATATATA
1841719 TTAAT-AATTTATAT-TATA
1 TTAATAAATTTATATATATA
1841737 T
1 T
1841738 AAAATTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATAAATTTATATATATA
Found at i:1854972 original size:29 final size:29
Alignment explanation
Indices: 1854905--1854983 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 29
1854895 AATTGAATCA
1854905 AAATCAAAGTTTCATGTATATATATAAACC
1 AAATCAAA-TTTCATGTATATATATAAACC
* **
1854935 ACAATTCAAATTTCATGTGTATA-ATTGTACC
1 A-AA-TCAAATTTCATGTATATATA-TAAACC
*
1854966 AAATCAAAATTCATGTAT
1 AAATCAAATTTCATGTAT
1854984 CAAATTATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
29 13 0.32
30 4 0.10
31 19 0.46
32 5 0.12
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (29 bp):
AAATCAAATTTCATGTATATATATAAACC
Found at i:1855177 original size:56 final size:56
Alignment explanation
Indices: 1855081--1855195 Score: 176
Period size: 56 Copynumber: 2.1 Consensus size: 56
1855071 CTATGCATTG
*
1855081 TAATTTTTAAGGTTTTAGTTAAATAATTATTGATGCGTAAATTTATAAATTAACAC
1 TAATTTTTAAGGTTTTAGTTAAATAATTATCGATGCGTAAATTTATAAATTAACAC
* * * * *
1855137 TAATTTTTAGGGTTTTAGTTTAATGATTATCGATGTGTAAATTTATACATTAACAC
1 TAATTTTTAAGGTTTTAGTTAAATAATTATCGATGCGTAAATTTATAAATTAACAC
1855193 TAA
1 TAA
1855196 ATTACATGTG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (56 bp):
TAATTTTTAAGGTTTTAGTTAAATAATTATCGATGCGTAAATTTATAAATTAACAC
Found at i:1858339 original size:22 final size:24
Alignment explanation
Indices: 1858313--1858374 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 24
1858303 GAAATTAAAT
1858313 TATATATTTTTATAATAGTAA-AA
1 TATATATTTTTATAATAGTAATAA
* * **
1858336 -ATATAATTTTATTATTTTAATAA
1 TATATATTTTTATAATAGTAATAA
*
1858359 TTTATATTTTTATAAT
1 TATATATTTTTATAAT
1858375 TTTTAAAGGA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 16 0.53
23 2 0.07
24 12 0.40
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TATATATTTTTATAATAGTAATAA
Found at i:1858368 original size:15 final size:16
Alignment explanation
Indices: 1858338--1858376 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1858328 TAGTAAAAAT
1858338 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
1858355 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
1858370 ATAATTT
1 ATAATTT
1858377 TTAAAGGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Done.