Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 5 of 344
Found at i:1742702 original size:30 final size:31
Alignment explanation
Indices: 1742663--1742726 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
1742653 TGTTAACAAT
* * **
1742663 AAAACTTAAATTTTTAAATTTAAAAA-ATAA
1 AAAAATTAAATTCTTAAAAATAAAAATATAA
1742693 AAAAATTAAATTCTTAAAAATAAAAATATAA
1 AAAAATTAAATTCTTAAAAATAAAAATATAA
1742724 AAA
1 AAA
1742727 CAAAAATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (31 bp):
AAAAATTAAATTCTTAAAAATAAAAATATAA
Found at i:1756439 original size:25 final size:25
Alignment explanation
Indices: 1756405--1756456 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1756395 NNNNNNNNTC
1756405 ACTTGAAAGATTTAAAGAAATAATT
1 ACTTGAAAGATTTAAAGAAATAATT
1756430 ACTTGAAAGATTTAAAGAAATAATT
1 ACTTGAAAGATTTAAAGAAATAATT
1756455 AC
1 AC
1756457 ACAGTGGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.31
Consensus pattern (25 bp):
ACTTGAAAGATTTAAAGAAATAATT
Found at i:1765816 original size:29 final size:29
Alignment explanation
Indices: 1765784--1765846 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1765774 TGTTAACAAT
* *
1765784 AAAACTTAAATTTTTAAATTTAAAAA-ATA
1 AAAACTTAAATTCTTAAA-ATAAAAATATA
*
1765813 AAAAATTAAATTCTTAAAATAAAAATATA
1 AAAACTTAAATTCTTAAAATAAAAATATA
1765842 AAAAC
1 AAAAC
1765847 AAAAATGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (29 bp):
AAAACTTAAATTCTTAAAATAAAAATATA
Found at i:1765821 original size:21 final size:21
Alignment explanation
Indices: 1765797--1765837 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1765787 ACTTAAATTT
1765797 TTAAATT-TAAAAAATAAAAAA
1 TTAAATTCT-AAAAATAAAAAA
*
1765818 TTAAATTCTTAAAATAAAAA
1 TTAAATTCTAAAAATAAAAA
1765838 TATAAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
TTAAATTCTAAAAATAAAAAA
Found at i:1772566 original size:15 final size:15
Alignment explanation
Indices: 1772546--1772577 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1772536 TTAAACGAAA
1772546 ATTTTAATAGTAATG
1 ATTTTAATAGTAATG
1772561 ATTTTAATAGTAATG
1 ATTTTAATAGTAATG
1772576 AT
1 AT
1772578 GGGTTTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (15 bp):
ATTTTAATAGTAATG
Found at i:1778450 original size:40 final size:39
Alignment explanation
Indices: 1778369--1778457 Score: 99
Period size: 40 Copynumber: 2.3 Consensus size: 39
1778359 GCCAATACAT
* * **
1778369 TTGGTTCGTTGGACAACTTCATAGCATTACAGCCATTCA
1 TTGGTTCATTGGACAACTTCATAGCATAACAGCCAGCCA
*
1778408 TTGGTTCCATTGGACAACTTCCATCGCATAACAG-CAGCCA
1 TTGGTT-CATTGGACAACTT-CATAGCATAACAGCCAGCCA
*
1778448 TTGCTTCATT
1 TTGGTTCATT
1778458 TGTTTCAGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
39 10 0.24
40 21 0.50
41 11 0.26
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (39 bp):
TTGGTTCATTGGACAACTTCATAGCATAACAGCCAGCCA
Found at i:1781334 original size:39 final size:39
Alignment explanation
Indices: 1781281--1781359 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1781271 CAAGATGAAG
1781281 TTTTTAAGTTCAAAAACAAGACCTTAAAGTTCCATATCT
1 TTTTTAAGTTCAAAAACAAGACCTTAAAGTTCCATATCT
1781320 TTTTTAAGTTCAAAAACAAGACCTTAAAGTTCCATATCT
1 TTTTTAAGTTCAAAAACAAGACCTTAAAGTTCCATATCT
1781359 T
1 T
1781360 ATAAAATTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.37
Consensus pattern (39 bp):
TTTTTAAGTTCAAAAACAAGACCTTAAAGTTCCATATCT
Found at i:1786800 original size:64 final size:64
Alignment explanation
Indices: 1786726--1786854 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
1786716 GAAATCTCAT
1786726 GTTATTTAAATATAAGAAAGGCTTGACATCTATTTTGATAAGATTAATAAAAGAAGTTTCACGC
1 GTTATTTAAATATAAGAAAGGCTTGACATCTATTTTGATAAGATTAATAAAAGAAGTTTCACGC
1786790 GTTATTTAAATATAAGAAAGGCTTGACATCTATTTTGATAAGATTAATAAAAGAAGTTTCACGC
1 GTTATTTAAATATAAGAAAGGCTTGACATCTATTTTGATAAGATTAATAAAAGAAGTTTCACGC
1786854 G
1 G
1786855 ATAAACATGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (64 bp):
GTTATTTAAATATAAGAAAGGCTTGACATCTATTTTGATAAGATTAATAAAAGAAGTTTCACGC
Found at i:1788127 original size:19 final size:19
Alignment explanation
Indices: 1788103--1788144 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1788093 AATTATATTT
1788103 TAATTTTTAAAAATGATAA
1 TAATTTTTAAAAATGATAA
1788122 TAATTTTTAAAAATGATAA
1 TAATTTTTAAAAATGATAA
1788141 -AATT
1 TAATT
1788145 ATGATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
TAATTTTTAAAAATGATAA
Found at i:1795093 original size:30 final size:28
Alignment explanation
Indices: 1795057--1795127 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 28
1795047 ATAACTGAAG
*
1795057 CTAAATTTTAAAAATTGAAAAG-TAAAAGAA
1 CTAAATTTTAAAAA-TG-AAAGCAAAAAG-A
*
1795087 CTAAATTCTTGAAAATGAAAGCAAAAAGA
1 CTAAATT-TTAAAAATGAAAGCAAAAAGA
1795116 CTAAATTTTAAA
1 CTAAATTTTAAA
1795128 TTCTCAAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 4 0.11
29 12 0.33
30 14 0.39
31 6 0.17
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.27
Consensus pattern (28 bp):
CTAAATTTTAAAAATGAAAGCAAAAAGA
Found at i:1795254 original size:33 final size:32
Alignment explanation
Indices: 1795158--1795280 Score: 147
Period size: 32 Copynumber: 3.7 Consensus size: 32
1795148 CTATATAAAA
* *
1795158 AATAGATTGATACCCTGTGCATTGGGATATAT
1 AATAGTTTGATACCCTGTGCATTTGGATATAT
1795190 AATAGTTTGATACCCTGTGCATTTGGATATAT
1 AATAGTTTGATACCCTGTGCATTTGGATATAT
* *
1795222 AATGGTTTGATACCTTGTGCAATTTGGTTATATTAT
1 AATAGTTTGATACCCTGTGC-ATTTGG--ATA-TAT
*
1795258 AAAGTAGTTCGATACCCTGTGCA
1 -AA-TAGTTTGATACCCTGTGCA
1795281 CTGCATAGAA
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
32 48 0.62
33 6 0.08
35 3 0.04
36 3 0.04
37 3 0.04
38 15 0.19
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.38
Consensus pattern (32 bp):
AATAGTTTGATACCCTGTGCATTTGGATATAT
Found at i:1802540 original size:24 final size:22
Alignment explanation
Indices: 1802512--1802557 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1802502 AGATTATTTC
*
1802512 ATTTTAAACCTTTACATATTTTAT
1 ATTTTAAA-CTTTA-ATATATTAT
1802536 ATTTTAAACTTTAATATATTAT
1 ATTTTAAACTTTAATATATTAT
1802558 GCAGCTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 5 0.24
24 8 0.38
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTTAAACTTTAATATATTAT
Found at i:1804310 original size:23 final size:23
Alignment explanation
Indices: 1804276--1804322 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1804266 TATATCGAAA
1804276 AGTTTATAAGCATTTAAGACAAT
1 AGTTTATAAGCATTTAAGACAAT
*
1804299 AGTTTATTAGCATTTAAGACAAT
1 AGTTTATAAGCATTTAAGACAAT
1804322 A
1 A
1804323 ATAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (23 bp):
AGTTTATAAGCATTTAAGACAAT
Found at i:1804386 original size:38 final size:38
Alignment explanation
Indices: 1804333--1804411 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
1804323 ATAAATGAAT
*
1804333 AGTTGAAGAATGACCAAAACATGCCTAACGTCATGATG
1 AGTTGAAGAAGGACCAAAACATGCCTAACGTCATGATG
*
1804371 AGTTGAAGAAGGACCAAAACATGCCTAACGTCATGGTG
1 AGTTGAAGAAGGACCAAAACATGCCTAACGTCATGATG
1804409 AGT
1 AGT
1804412 AGGTAGGGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (38 bp):
AGTTGAAGAAGGACCAAAACATGCCTAACGTCATGATG
Found at i:1812040 original size:30 final size:30
Alignment explanation
Indices: 1812006--1812067 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1811996 CGAGCAGTAT
1812006 GTGCCAATTTTCACCTCTAATATCTACCGA
1 GTGCCAATTTTCACCTCTAATATCTACCGA
1812036 GTGCCAATTTTCACCTCTAATATCTACCGA
1 GTGCCAATTTTCACCTCTAATATCTACCGA
1812066 GT
1 GT
1812068 CGTCAGCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (30 bp):
GTGCCAATTTTCACCTCTAATATCTACCGA
Found at i:1824697 original size:30 final size:31
Alignment explanation
Indices: 1824663--1824733 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
1824653 AAAACTTAGC
1824663 AGCTCAGTGACTTAAACAAAAACTTTT-AAT
1 AGCTCAGTGACTTAAACAAAAACTTTTGAAT
* ** *
1824693 AGCTCAATGACTTAAATGAAAATTTTTGAAT
1 AGCTCAGTGACTTAAACAAAAACTTTTGAAT
*
1824724 AGTTCAGTGA
1 AGCTCAGTGA
1824734 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 23 0.68
31 11 0.32
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (31 bp):
AGCTCAGTGACTTAAACAAAAACTTTTGAAT
Found at i:1827627 original size:48 final size:48
Alignment explanation
Indices: 1827509--1827629 Score: 199
Period size: 48 Copynumber: 2.5 Consensus size: 48
1827499 AGCCGTAACA
* *
1827509 GCTGAACCCATAAAGCAGGAGGTTACTAATACTCCATCAGTCTCGAAG
1 GCTGAATCCATAAAGCAGGATGTTACTAATACTCCATCAGTCTCGAAG
*
1827557 GCTGAATTCATAAAGCAGGATGTTACTAATACTCCATCAGTCTCGAAG
1 GCTGAATCCATAAAGCAGGATGTTACTAATACTCCATCAGTCTCGAAG
1827605 GCTGAATCCATAAAGC-GAGATGTTA
1 GCTGAATCCATAAAGCAG-GATGTTA
1827630 ATACTACTGC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 1 0.01
48 67 0.99
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (48 bp):
GCTGAATCCATAAAGCAGGATGTTACTAATACTCCATCAGTCTCGAAG
Found at i:1837115 original size:16 final size:17
Alignment explanation
Indices: 1837094--1837134 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1837084 AAGATAAATT
1837094 TTTTAAATTT-AACTC-A
1 TTTTAAATTTGAA-TCAA
1837110 TTTTAAATTTGAATCAA
1 TTTTAAATTTGAATCAA
1837127 TTTTAAAT
1 TTTTAAAT
1837135 ATCATTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTTAAATTTGAATCAA
Found at i:1837440 original size:13 final size:13
Alignment explanation
Indices: 1837422--1837476 Score: 85
Period size: 13 Copynumber: 4.2 Consensus size: 13
1837412 TTAGTTTGGC
1837422 AGTGCTTTTGAAA
1 AGTGCTTTTGAAA
1837435 AGTGCTTTTGAAA
1 AGTGCTTTTGAAA
1837448 AGTGC-TTTGAAAA
1 AGTGCTTTTG-AAA
*
1837461 ATTGCTTTTGAAA
1 AGTGCTTTTGAAA
1837474 AGT
1 AGT
1837477 TTAGTTTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
12 4 0.11
13 30 0.79
14 4 0.11
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (13 bp):
AGTGCTTTTGAAA
Found at i:1849686 original size:16 final size:16
Alignment explanation
Indices: 1849667--1849701 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1849657 GTTTCATGTT
* *
1849667 TTTCTAGTTTAGATTA
1 TTTCGAGTTTAAATTA
1849683 TTTCGAGTTTAAATTA
1 TTTCGAGTTTAAATTA
1849699 TTT
1 TTT
1849702 TAAATTCAAA
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:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTCGAGTTTAAATTA
Found at i:1853472 original size:7 final size:7
Alignment explanation
Indices: 1853460--1853487 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1853450 GAATAGGGCA
1853460 GCAACAG
1 GCAACAG
1853467 GCAACAG
1 GCAACAG
1853474 GCAACAG
1 GCAACAG
1853481 GCAACAG
1 GCAACAG
1853488 AATCAGACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.29, T:0.00
Consensus pattern (7 bp):
GCAACAG
Found at i:1857638 original size:16 final size:16
Alignment explanation
Indices: 1857619--1857651 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1857609 AATAATTAGT
1857619 AATATAAAACAGTAGG
1 AATATAAAACAGTAGG
1857635 AATATAAAACAGTAGG
1 AATATAAAACAGTAGG
1857651 A
1 A
1857652 TCGAATCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (16 bp):
AATATAAAACAGTAGG
Found at i:1858222 original size:13 final size:13
Alignment explanation
Indices: 1858204--1858245 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
1858194 AAATTTTTTT
1858204 TAAATATTATCAC
1 TAAATATTATCAC
1858217 TAAATA--ATC-C
1 TAAATATTATCAC
1858227 TAAATATTATCAC
1 TAAATATTATCAC
1858240 TAAATA
1 TAAATA
1858246 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 3 0.12
13 13 0.50
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAATATTATCAC
Found at i:1858232 original size:23 final size:23
Alignment explanation
Indices: 1858204--1858247 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1858194 AAATTTTTTT
1858204 TAAATATTATCACTAAATAATCC
1 TAAATATTATCACTAAATAATCC
1858227 TAAATATTATCACTAAATAAT
1 TAAATATTATCACTAAATAAT
1858248 TTAAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAATATTATCACTAAATAATCC
Found at i:1860773 original size:16 final size:16
Alignment explanation
Indices: 1860752--1860784 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1860742 TAATATCAAC
1860752 TCAATTTTAGAGATTT
1 TCAATTTTAGAGATTT
1860768 TCAATTTTAGAGATTT
1 TCAATTTTAGAGATTT
1860784 T
1 T
1860785 AAGTATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (16 bp):
TCAATTTTAGAGATTT
Found at i:1866372 original size:31 final size:31
Alignment explanation
Indices: 1866337--1866397 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
1866327 TAAAATAGTC
*
1866337 ATTGAATTATTT-AAAAGTTTCCATTTAAGTT
1 ATTGAAATATTTGAAAA-TTTCCATTTAAGTT
**
1866368 ATTGAAATATTTGAAAATTTTTATTTAAGT
1 ATTGAAATATTTGAAAATTTCCATTTAAGT
1866398 CACTAGGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (31 bp):
ATTGAAATATTTGAAAATTTCCATTTAAGTT
Found at i:1871016 original size:31 final size:31
Alignment explanation
Indices: 1870981--1871045 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1870971 TTAACAATCT
1870981 AATGACTTAAATAAAAAGTTTT-GAATAGTTC
1 AATGACTTAAATAAAAA-TTTTCGAATAGTTC
* *
1871012 AATGACTTGAATGAAAATTTTCGAATAGTTC
1 AATGACTTAAATAAAAATTTTCGAATAGTTC
1871043 AAT
1 AAT
1871046 TATTATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (31 bp):
AATGACTTAAATAAAAATTTTCGAATAGTTC
Found at i:1872105 original size:15 final size:15
Alignment explanation
Indices: 1872087--1872137 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
1872077 TTTAAGGAAA
1872087 AAAATAAATATTTTG
1 AAAATAAATATTTTG
* * **
1872102 AAAATAGATGTTTCA
1 AAAATAAATATTTTG
*
1872117 AAAATGAATATTTTG
1 AAAATAAATATTTTG
1872132 AAAATA
1 AAAATA
1872138 GATGTTTCAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (15 bp):
AAAATAAATATTTTG
Found at i:1872120 original size:30 final size:30
Alignment explanation
Indices: 1872086--1872152 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
1872076 TTTTAAGGAA
1872086 AAAAATAAATATTTTGAAAATAGATGTTTC
1 AAAAATAAATATTTTGAAAATAGATGTTTC
*
1872116 AAAAATGAATATTTTGAAAATAGATGTTTC
1 AAAAATAAATATTTTGAAAATAGATGTTTC
1872146 AAAAATA
1 AAAAATA
1872153 TTAATTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.34
Consensus pattern (30 bp):
AAAAATAAATATTTTGAAAATAGATGTTTC
Found at i:1872150 original size:15 final size:15
Alignment explanation
Indices: 1872102--1872152 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
1872092 AAATATTTTG
1872102 AAAATAGATGTTTCA
1 AAAATAGATGTTTCA
* **
1872117 AAAAT-GAATATTTTG
1 AAAATAG-ATGTTTCA
1872132 AAAATAGATGTTTCA
1 AAAATAGATGTTTCA
1872147 AAAATA
1 AAAATA
1872153 TTAATTTTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33
Consensus pattern (15 bp):
AAAATAGATGTTTCA
Found at i:1876886 original size:19 final size:20
Alignment explanation
Indices: 1876854--1876891 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1876844 AATATTTTAA
*
1876854 TTTAAATATATAAATTATAT
1 TTTAAATATATAAAATATAT
1876874 TTTAAATAT-TAAAATATA
1 TTTAAATATATAAAATATA
1876892 ACTGTTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATATATAAAATATAT
Found at i:1876907 original size:22 final size:21
Alignment explanation
Indices: 1876877--1876933 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
1876867 ATTATATTTT
1876877 AAATATTAAAATATAACTGTTAC
1 AAAT-TTAAAATATAA-TGTTAC
*
1876900 AAATTTAAATATATAATGTTAT
1 AAATTTAAA-ATATAATGTTAC
*
1876922 ATATTTAAAATA
1 AAATTTAAAATA
1876934 AATCTTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (21 bp):
AAATTTAAAATATAATGTTAC
Found at i:1881194 original size:21 final size:22
Alignment explanation
Indices: 1881154--1881200 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
1881144 CTCTGCTCAA
*
1881154 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
*
1881175 ACTCCACCTGCTGTGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
1881197 ACTC
1 ACTC
1881201 ACTCCTTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.23
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:1885363 original size:8 final size:8
Alignment explanation
Indices: 1885350--1885375 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1885340 TCCACTTCCG
1885350 TCACCTCT
1 TCACCTCT
1885358 TCACCTCT
1 TCACCTCT
1885366 TCACCTCT
1 TCACCTCT
1885374 TC
1 TC
1885376 TTTTCAAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.50, G:0.00, T:0.38
Consensus pattern (8 bp):
TCACCTCT
Found at i:1886011 original size:29 final size:30
Alignment explanation
Indices: 1885979--1886041 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 30
1885969 TTAAGTTTTG
** *
1885979 AATTTGATTATTATTCTCAC-TTGGGTCTA
1 AATTTGACAATTATTCTCACATTGGGTATA
1886008 AA-TTGACAATTATTCTCACATTGGGTATA
1 AATTTGACAATTATTCTCACATTGGGTATA
1886037 AATTT
1 AATTT
1886042 TTTGGTCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 15 0.52
29 12 0.41
30 2 0.07
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (30 bp):
AATTTGACAATTATTCTCACATTGGGTATA
Found at i:1889912 original size:50 final size:50
Alignment explanation
Indices: 1889844--1889945 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
1889834 TACAGAAAGA
1889844 TAATCAATGGAGGGAAATTAAAGACACTGAGAAACAAACCTGTTACAGGG
1 TAATCAATGGAGGGAAATTAAAGACACTGAGAAACAAACCTGTTACAGGG
1889894 TAATCAATGGAGGGAAATTAAAGACACTGAGAAACAAACCTGTTACAGGG
1 TAATCAATGGAGGGAAATTAAAGACACTGAGAAACAAACCTGTTACAGGG
1889944 TA
1 TA
1889946 GAAGCTGATC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.19
Consensus pattern (50 bp):
TAATCAATGGAGGGAAATTAAAGACACTGAGAAACAAACCTGTTACAGGG
Found at i:1891271 original size:51 final size:51
Alignment explanation
Indices: 1891211--1891312 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
1891201 CCCTATATGC
1891211 ATGGGATAGAAATCAACTAAAGGATATGTGGCAGAAATGGAAAATAAGATT
1 ATGGGATAGAAATCAACTAAAGGATATGTGGCAGAAATGGAAAATAAGATT
1891262 ATGGGATAGAAATCAACTAAAGGATATGTGGCAGAAATGGAAAATAAGATT
1 ATGGGATAGAAATCAACTAAAGGATATGTGGCAGAAATGGAAAATAAGATT
1891313 TTGGTACTCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (51 bp):
ATGGGATAGAAATCAACTAAAGGATATGTGGCAGAAATGGAAAATAAGATT
Found at i:1891297 original size:25 final size:25
Alignment explanation
Indices: 1891218--1891299 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
1891208 TGCATGGGAT
1891218 AGAAATCAACTAAAGGATATGTGGC
1 AGAAATCAACTAAAGGATATGTGGC
* * *
1891243 AGAAATGGAA--AATAAGATTATG-GGAT
1 AGAAAT-CAACTAA-AGGA-TATGTGG-C
1891269 AGAAATCAACTAAAGGATATGTGGC
1 AGAAATCAACTAAAGGATATGTGGC
1891294 AGAAAT
1 AGAAAT
1891300 GGAAAATAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
24 2 0.05
25 23 0.52
26 17 0.39
27 2 0.05
ACGTcount: A:0.48, C:0.07, G:0.24, T:0.21
Consensus pattern (25 bp):
AGAAATCAACTAAAGGATATGTGGC
Found at i:1895748 original size:25 final size:26
Alignment explanation
Indices: 1895713--1895762 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
1895703 GCGTTTTCAT
* *
1895713 TATTTTTATATTCAAAACA-ATTTTC
1 TATTTTCATATACAAAACATATTTTC
1895738 TATTTTCATATACAAAACATATTTT
1 TATTTTCATATACAAAACATATTTT
1895763 TTCAATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (26 bp):
TATTTTCATATACAAAACATATTTTC
Found at i:1895903 original size:13 final size:13
Alignment explanation
Indices: 1895885--1895909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1895875 TTTTAAAAGT
1895885 ATTTTCTATTTTA
1 ATTTTCTATTTTA
1895898 ATTTTCTATTTT
1 ATTTTCTATTTT
1895910 TTAAAATTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTCTATTTTA
Found at i:1904437 original size:16 final size:16
Alignment explanation
Indices: 1904416--1904449 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1904406 CTCTCAAATT
*
1904416 TTTAATTATTTTTTAA
1 TTTAATTATTGTTTAA
1904432 TTTAATTATTGTTTAA
1 TTTAATTATTGTTTAA
1904448 TT
1 TT
1904450 GATTCATCAT
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:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTAATTATTGTTTAA
Found at i:1904781 original size:16 final size:16
Alignment explanation
Indices: 1904760--1904790 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1904750 TTCGAGTCAT
1904760 TTTTGAATTTAAGTTG
1 TTTTGAATTTAAGTTG
1904776 TTTTGAATTTAAGTT
1 TTTTGAATTTAAGTT
1904791 TGAAGGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (16 bp):
TTTTGAATTTAAGTTG
Found at i:1911138 original size:20 final size:20
Alignment explanation
Indices: 1911113--1911184 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
1911103 TTGTATGATA
1911113 AATTTTATAATTTTTTTACG
1 AATTTTATAATTTTTTTACG
*
1911133 AATTTTAT-ATTTCTTTAC-
1 AATTTTATAATTTTTTTACG
* *
1911151 -ATTTTTTAATTTTCTTACG
1 AATTTTATAATTTTTTTACG
* *
1911170 ACTTTATAAAATTTT
1 AATTT-TATAATTTT
1911185 ATAAATTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
17 6 0.15
18 8 0.20
19 9 0.22
20 11 0.27
21 7 0.17
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (20 bp):
AATTTTATAATTTTTTTACG
Found at i:1911149 original size:19 final size:20
Alignment explanation
Indices: 1911113--1911162 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1911103 TTGTATGATA
*
1911113 AATTTTATAATTTTTTTACG
1 AATTTTATAATTTCTTTACG
1911133 AATTTTAT-ATTTCTTTAC-
1 AATTTTATAATTTCTTTACG
*
1911151 -ATTTTTTAATTT
1 AATTTTATAATTT
1911163 TCTTACGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.22
18 4 0.15
19 9 0.33
20 8 0.30
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (20 bp):
AATTTTATAATTTCTTTACG
Found at i:1911194 original size:37 final size:36
Alignment explanation
Indices: 1911110--1911194 Score: 82
Period size: 37 Copynumber: 2.3 Consensus size: 36
1911100 TTTTTGTATG
* *
1911110 ATAAATTTTATAATTTTTTTACGAATTTTATATTTCT
1 ATAAATTTT-TAATTTTCTTACGAATTTTAAATTTCT
* * *
1911147 TTACATTTTTTAATTTTCTTACGACTTTATAAAATTT-T
1 ATA-AATTTTTAATTTTCTTACGAATTT-T-AAATTTCT
1911185 ATAAATTTTT
1 ATAAATTTTT
1911195 CTATATTTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
37 24 0.63
38 9 0.24
39 5 0.13
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (36 bp):
ATAAATTTTTAATTTTCTTACGAATTTTAAATTTCT
Found at i:1911233 original size:18 final size:17
Alignment explanation
Indices: 1911212--1911330 Score: 71
Period size: 19 Copynumber: 6.6 Consensus size: 17
1911202 TTCTATATAC
*
1911212 TATAATTTTTATGGTTTT
1 TATAATTTTTAT-ATTTT
** *
1911230 TATAAAAATTTACAATTTTT
1 TAT-AATTTTTA-TATTT-T
1911250 TATATATTTTTTATGATTTT
1 TATA-AT-TTTTAT-ATTTT
1911270 TATAA-TTTTA-ATTTT
1 TATAATTTTTATATTTT
* *
1911285 TAAAATTTTTATAACTTT
1 TATAATTTTTAT-ATTTT
*
1911303 TATTAATTTTTATTTTTT
1 TA-TAATTTTTATATTTT
*
1911321 TATCATTTTT
1 TATAATTTTT
1911331 TACTACATGT
Statistics
Matches: 78, Mismatches: 13, Indels: 21
0.70 0.12 0.19
Matches are distributed among these distances:
15 9 0.12
16 5 0.06
17 12 0.15
18 14 0.18
19 20 0.26
20 10 0.13
21 8 0.10
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (17 bp):
TATAATTTTTATATTTT
Found at i:1911269 original size:9 final size:8
Alignment explanation
Indices: 1911247--1911330 Score: 53
Period size: 9 Copynumber: 9.6 Consensus size: 8
1911237 ATTTACAATT
1911247 TTTTATATA
1 TTTT-TATA
1911256 TTTTTTATGA
1 -TTTTTAT-A
1911266 TTTTTATA
1 TTTTTATA
*
1911274 ATTTTA-A
1 TTTTTATA
*
1911281 TTTTTAAAA
1 TTTTT-ATA
1911290 TTTTTATAA
1 TTTTTAT-A
*
1911299 CTTTTATTAA
1 TTTTTA-T-A
*
1911309 TTTTTATT
1 TTTTTATA
1911317 TTTTTATCA
1 TTTTTAT-A
1911326 TTTTT
1 TTTTT
1911331 TACTACATGT
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
7 5 0.08
8 15 0.25
9 28 0.46
10 13 0.21
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.69
Consensus pattern (8 bp):
TTTTTATA
Found at i:1915911 original size:26 final size:26
Alignment explanation
Indices: 1915881--1915933 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1915871 TACATCAATT
1915881 AAAATTTAAATTTAAATCTAAAAATA
1 AAAATTTAAATTTAAATCTAAAAATA
*
1915907 AAAATTTAAGTTTAAATCTAAAAATA
1 AAAATTTAAATTTAAATCTAAAAATA
1915933 A
1 A
1915934 CGTCCATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (26 bp):
AAAATTTAAATTTAAATCTAAAAATA
Found at i:1922060 original size:21 final size:21
Alignment explanation
Indices: 1922034--1922074 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1922024 AGACGAGCAA
* *
1922034 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1922055 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1922075 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1929156 original size:23 final size:22
Alignment explanation
Indices: 1929104--1929156 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
1929094 TCCACGTCTT
*
1929104 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
1929126 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
1929149 TTTCTTTT
1 TTTCTTTT
1929157 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:1939603 original size:12 final size:13
Alignment explanation
Indices: 1939581--1939639 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
1939571 ATTGGGAAAC
1939581 AAAATTTAAATAT
1 AAAATTTAAATAT
1939594 AAAA-TTAAATAT
1 AAAATTTAAATAT
1939606 AAATATTTAAA-AT
1 AAA-ATTTAAATAT
* *
1939619 ATATATTTATATAT
1 A-AAATTTAAATAT
*
1939633 CAAATTT
1 AAAATTT
1939640 TATTTTTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 11 0.29
13 19 0.50
14 8 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAATTTAAATAT
Found at i:1939632 original size:27 final size:28
Alignment explanation
Indices: 1939580--1939641 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 28
1939570 AATTGGGAAA
1939580 CAAA-ATTT-AAATATAAAATTAAATAT
1 CAAATATTTAAAATATAAAATTAAATAT
* * *
1939606 -AAATATTTAAAATATATATTTATATAT
1 CAAATATTTAAAATATAAAATTAAATAT
1939633 CAAAT-TTTA
1 CAAATATTTA
1939642 TTTTTAATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 3 0.10
26 4 0.13
27 19 0.63
28 4 0.13
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (28 bp):
CAAATATTTAAAATATAAAATTAAATAT
Found at i:1940391 original size:10 final size:10
Alignment explanation
Indices: 1940376--1940409 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1940366 TGAATTTTTT
*
1940376 TCGAATCGAA
1 TCGAATCGAG
1940386 TCGAATCGAG
1 TCGAATCGAG
*
1940396 TCAAATCGAG
1 TCGAATCGAG
1940406 TCGA
1 TCGA
1940410 GTTAACGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (10 bp):
TCGAATCGAG
Found at i:1949146 original size:7 final size:6
Alignment explanation
Indices: 1949119--1949144 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1949109 TATTATCACC
1949119 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
1949145 ATCTTGTGCT
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):
AATAAA
Found at i:1958646 original size:15 final size:15
Alignment explanation
Indices: 1958626--1958663 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1958616 GTTTCGTTTG
1958626 TTTTTTATAT-TAATT
1 TTTTTTATATAT-ATT
*
1958641 TTTTTTACATATATT
1 TTTTTTATATATATT
1958656 TTTTTTAT
1 TTTTTTAT
1958664 CTGAATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTATATATATT
Found at i:1959176 original size:18 final size:18
Alignment explanation
Indices: 1959153--1959197 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1959143 TTTATTAATC
*
1959153 TTTTTTCGATTTTTTTTA
1 TTTTTTAGATTTTTTTTA
1959171 TTTTTTAGATTTTTTTTGA
1 TTTTTTAGATTTTTTTT-A
1959190 TATTTTTA
1 T-TTTTTA
1959198 TTTTGTGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 16 0.67
19 2 0.08
20 6 0.25
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.76
Consensus pattern (18 bp):
TTTTTTAGATTTTTTTTA
Found at i:1959195 original size:28 final size:29
Alignment explanation
Indices: 1959131--1959201 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 29
1959121 TTTATATTAT
1959131 TATTTATTTATGTTTATTAATCTTTTTTCGA
1 TATTT-TTTAT-TTTATTAATCTTTTTTCGA
* *
1959162 TTTTTTTTATTTT-TTAGAT-TTTTTTTGA
1 TATTTTTTATTTTATTA-ATCTTTTTTCGA
1959190 TA-TTTTTATTTT
1 TATTTTTTATTTT
1959202 GTGATGGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 10 0.28
28 12 0.33
29 5 0.14
30 5 0.14
31 4 0.11
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (29 bp):
TATTTTTTATTTTATTAATCTTTTTTCGA
Found at i:1961275 original size:23 final size:23
Alignment explanation
Indices: 1961239--1961282 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1961229 TTCAAATTTT
*
1961239 AAAAATTAAAAAATATAAAAAGA
1 AAAAATTAAAAAATAAAAAAAGA
**
1961262 AAAAATTACCAAATAAAAAAA
1 AAAAATTAAAAAATAAAAAAA
1961283 ATCCATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAAATTAAAAAATAAAAAAAGA
Found at i:1967288 original size:20 final size:20
Alignment explanation
Indices: 1967248--1967289 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1967238 CATCAATAAT
* *
1967248 AATAATAAGAATAATCGTAA
1 AATAATAAGAAAAATAGTAA
*
1967268 AATAATAAGAAAAATATTAA
1 AATAATAAGAAAAATAGTAA
1967288 AA
1 AA
1967290 AAAAACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (20 bp):
AATAATAAGAAAAATAGTAA
Found at i:1968831 original size:30 final size:29
Alignment explanation
Indices: 1968774--1968831 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
1968764 ATTTTGACCA
* * *
1968774 TTTTAAAATGATAAAATTTTAATTTAATT
1 TTTTAAAATGATAAAAATATAAATTAATT
*
1968803 TTTTAAAAATTATAAAAATATAAATTAAT
1 TTTT-AAAATGATAAAAATATAAATTAAT
1968832 ATAATGATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTTAAAATGATAAAAATATAAATTAATT
Found at i:1973164 original size:33 final size:33
Alignment explanation
Indices: 1973126--1973192 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1973116 TATTTATTAC
1973126 TGATACTTTAATAGCGATTTTCTAACTTGTCTT
1 TGATACTTTAATAGCGATTTTCTAACTTGTCTT
1973159 TGATACTTTAATAGCGATTTTCTAACTTGTCTT
1 TGATACTTTAATAGCGATTTTCTAACTTGTCTT
1973192 T
1 T
1973193 ACATATTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (33 bp):
TGATACTTTAATAGCGATTTTCTAACTTGTCTT
Found at i:1974608 original size:16 final size:15
Alignment explanation
Indices: 1974589--1974618 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1974579 TTCAACTAAT
1974589 TTTTGAGTTGGAATTA
1 TTTTGAGTT-GAATTA
1974605 TTTTGAGTTGAATT
1 TTTTGAGTTGAATT
1974619 TGGATTGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (15 bp):
TTTTGAGTTGAATTA
Found at i:1976802 original size:16 final size:16
Alignment explanation
Indices: 1976781--1976812 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1976771 TTTTAAGTGG
1976781 GATTATTTTAGATTCA
1 GATTATTTTAGATTCA
1976797 GATTATTTTAGATTCA
1 GATTATTTTAGATTCA
1976813 ATCAATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
GATTATTTTAGATTCA
Found at i:1983167 original size:23 final size:23
Alignment explanation
Indices: 1983109--1983170 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
1983099 CGAAATGTAA
*
1983109 TTATAATTTTTTTATTGATTAAT
1 TTATAATTTTATTATTGATTAAT
* * * *
1983132 ATGTAAGTGTATT-TTGTATTAAT
1 TTATAATTTTATTATTG-ATTAAT
1983155 TTATAATTTTATTATT
1 TTATAATTTTATTATT
1983171 TTTGAAAAGA
Statistics
Matches: 28, Mismatches: 9, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
22 3 0.11
23 23 0.82
24 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (23 bp):
TTATAATTTTATTATTGATTAAT
Found at i:1983372 original size:12 final size:12
Alignment explanation
Indices: 1983355--1983388 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1983345 CGACCCGCCC
1983355 ATATTAATTTTT
1 ATATTAATTTTT
*
1983367 ATATTATTTTTT
1 ATATTAATTTTT
*
1983379 ATATAAATTT
1 ATATTAATTT
1983389 AAAAAACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:1983633 original size:22 final size:22
Alignment explanation
Indices: 1983608--1983650 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1983598 TATCCAAACA
1983608 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
** *
1983630 ATAACAGTAAAATGGTAGCAA
1 ATAACAACAAAATAGTAGCAA
1983651 AATAGTGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.16
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:1985279 original size:20 final size:20
Alignment explanation
Indices: 1985254--1985293 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1985244 CGTAAAATGA
*
1985254 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
1985274 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
1985294 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:1985283 original size:34 final size:35
Alignment explanation
Indices: 1985239--1985305 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
1985229 CAGTAAAATA
*
1985239 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
1985273 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
1985306 CTAGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:1994566 original size:24 final size:24
Alignment explanation
Indices: 1994538--1994583 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1994528 AACGTGTATG
* *
1994538 ATTGAAATAAAATTAAAGTTTCGT
1 ATTGAAACAAAATTAAAATTTCGT
*
1994562 ATTGAAACACAATTAAAATTTC
1 ATTGAAACAAAATTAAAATTTC
1994584 ATGTACATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.35
Consensus pattern (24 bp):
ATTGAAACAAAATTAAAATTTCGT
Found at i:1997893 original size:26 final size:26
Alignment explanation
Indices: 1997864--1997914 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1997854 AAAGATAAAA
*
1997864 ATTTTATTTT-TTTAATCTTAAATTTC
1 ATTTT-TTTTGTTTAATCTCAAATTTC
*
1997890 ATTTTTTTTGTTTTATCTCAAATTT
1 ATTTTTTTTGTTTAATCTCAAATTT
1997915 TTTTAATCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.24, C:0.08, G:0.02, T:0.67
Consensus pattern (26 bp):
ATTTTTTTTGTTTAATCTCAAATTTC
Found at i:2001277 original size:14 final size:14
Alignment explanation
Indices: 2001255--2001285 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
2001245 TTTAGTCCTT
*
2001255 TTAAGTTTTTAAAA
1 TTAAATTTTTAAAA
2001269 TTAAATTTTTAAAA
1 TTAAATTTTTAAAA
2001283 TTA
1 TTA
2001286 TATGTTAGTT
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:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
TTAAATTTTTAAAA
Found at i:2006027 original size:21 final size:20
Alignment explanation
Indices: 2005989--2006030 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2005979 TTAATAGTTC
*
2005989 AAAAAATAAATTGTTAATAT
1 AAAAAATAAATTATTAATAT
*
2006009 AAAAAATATATTATATAATAT
1 AAAAAATAAATTAT-TAATAT
2006030 A
1 A
2006031 TATTATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAAATAAATTATTAATAT
Found at i:2006883 original size:16 final size:16
Alignment explanation
Indices: 2006858--2006893 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2006848 GGAGGTACAA
*
2006858 ATTT-AAGTTCCGATC
1 ATTTCAAGTTCAGATC
2006873 ATTTCAAGTTCAGATC
1 ATTTCAAGTTCAGATC
2006889 ATTTC
1 ATTTC
2006894 TGGTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (16 bp):
ATTTCAAGTTCAGATC
Found at i:2015802 original size:18 final size:18
Alignment explanation
Indices: 2015779--2015820 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2015769 CATTAATACA
*
2015779 AGAACCTGAAACAGAACC
1 AGAACCGGAAACAGAACC
* *
2015797 AGAACCGGAAGCCGAACC
1 AGAACCGGAAACAGAACC
2015815 AGAACC
1 AGAACC
2015821 AGAGCATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.31, G:0.21, T:0.02
Consensus pattern (18 bp):
AGAACCGGAAACAGAACC
Found at i:2015917 original size:3 final size:3
Alignment explanation
Indices: 2015909--2015953 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2015899 GTCACCCTTT
2015909 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
2015954 AAATCACTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:2020094 original size:132 final size:132
Alignment explanation
Indices: 2019861--2020109 Score: 331
Period size: 132 Copynumber: 1.9 Consensus size: 132
2019851 TAAAGGAATC
*
2019861 TTCGATCATTTTGGACAAACAGGAAATCGCAACCCAGCACGATAAGGCACGATTCCCCAAATTGC
1 TTCGATCATTTTGGACAAACAGGAAATCGCAACCCAACACGATAAGGCACGATTCCCCAAATTGC
* * * *
2019926 CAAACATCGAATATTACCTTCGTTTTGAAGAGTTTTTAGAAAACATGAATGAAGTTCCAAAGGGA
66 CAAACATCGAACATCACATTCGTTTTAAAGAGTTTTTAGAAAACATGAATGAAGTTCCAAAGGGA
2019991 CA
131 CA
* * * * * * *
2019993 TTCGATTATTTT-GAGCAAAC-GAGAAATTGCAACCCAACACGTTAGGGCACGATTTCGCGAATT
1 TTCGATCATTTTGGA-CAAACAG-GAAATCGCAACCCAACACGATAAGGCACGATTCCCCAAATT
* *
2020056 GCCAAATATCGAACATCACATTCGTTTTAAAGGATTTTTTAGAAAACATGAATG
64 GCCAAACATCGAACATCACATTCGTTTTAAA-GAGTTTTTAGAAAACATGAATG
2020110 GTTATAAAAC
Statistics
Matches: 100, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
131 3 0.03
132 76 0.76
133 21 0.21
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.27
Consensus pattern (132 bp):
TTCGATCATTTTGGACAAACAGGAAATCGCAACCCAACACGATAAGGCACGATTCCCCAAATTGC
CAAACATCGAACATCACATTCGTTTTAAAGAGTTTTTAGAAAACATGAATGAAGTTCCAAAGGGA
CA
Found at i:2032829 original size:33 final size:33
Alignment explanation
Indices: 2032758--2032822 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
2032748 ATAAAAACAC
* * *
2032758 CATTTCAAAATTTTTATATTAAAAGTTAGATTA
1 CATTTTAAAATTCTTATATTAAAAGTTAAATTA
*
2032791 CATTTTAAAATTCTTGTATTAAAAGTTAAATT
1 CATTTTAAAATTCTTATATTAAAAGTTAAATT
2032823 GTATTTTCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (33 bp):
CATTTTAAAATTCTTATATTAAAAGTTAAATTA
Found at i:2038925 original size:26 final size:27
Alignment explanation
Indices: 2038877--2038928 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
2038867 TCATATAAAT
*
2038877 AAAATAAATTATTATTTTAATATATTA
1 AAAATAAATTATTAGTTTAATATATTA
* *
2038904 AAAATAAATTCTT-GTTTCATATATT
1 AAAATAAATTATTAGTTTAATATATT
2038929 TACGGTGGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (27 bp):
AAAATAAATTATTAGTTTAATATATTA
Found at i:2039099 original size:15 final size:15
Alignment explanation
Indices: 2039047--2039102 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 15
2039037 AAATATTTTA
* *
2039047 ACATATAATTTATAC
1 ACATATAAATTATAT
*
2039062 ACATACAAA-TATAT
1 ACATATAAATTATAT
2039076 -C-T-T-AATTATAT
1 ACATATAAATTATAT
2039087 ACATATAAATTATAT
1 ACATATAAATTATAT
2039102 A
1 A
2039103 TGAATATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
10 2 0.06
11 5 0.16
12 2 0.06
13 2 0.06
14 5 0.16
15 16 0.50
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (15 bp):
ACATATAAATTATAT
Found at i:2040706 original size:25 final size:26
Alignment explanation
Indices: 2040665--2040714 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
2040655 GATTTTCTTT
2040665 TTTTTTTTAAATTAATACTACTAATTA
1 TTTTTTTTAAA-TAATACTACTAATTA
*
2040692 TTTTTTTTAAA-AATATTACTAAT
1 TTTTTTTTAAATAATACTACTAAT
2040715 AAAAAAGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.50
27 11 0.50
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTTTTTAAATAATACTACTAATTA
Found at i:2042275 original size:25 final size:25
Alignment explanation
Indices: 2042241--2042300 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
2042231 AAATTCAACT
2042241 TCAACTATTAAAATCGTTGAAATTC
1 TCAACTATTAAAATCGTTGAAATTC
2042266 TCAACTATTAAAATCGTTGAAATTC
1 TCAACTATTAAAATCGTTGAAATTC
2042291 TC--CTATTAAA
1 TCAACTATTAAA
2042301 TCCATTGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
23 8 0.23
25 27 0.77
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.37
Consensus pattern (25 bp):
TCAACTATTAAAATCGTTGAAATTC
Found at i:2050472 original size:184 final size:185
Alignment explanation
Indices: 2050201--2050547 Score: 468
Period size: 184 Copynumber: 1.9 Consensus size: 185
2050191 AATATCACAT
* * * *
2050201 GAGCCAACCTATATTATGTAACTAGTTCAAATGGCAAACCCTTTGCGGGGTTCGAACTTTGGATC
1 GAGCCAACCTACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGGTTCGAACTTTGGATC
* * * *
2050266 ATTCTTATCAAACATTAGGACAAGTTTATAC-T-TAACTACCATTGAAGTTGCA-AAACATCATT
66 ATTCTTATCAAACATAAGGACAAGCTTATACATCTAACAACCATTGAA-AT-CAGAAACATCATT
**
2050328 CACAGTGACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCAC
129 CACAGCAACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCAC
* *
2050385 GAGCCAACCTACATTACGTAGCTAGTGCAAAAGGCGAACCCTTTG-GGGGATTCGAACTTTGGAT
1 GAGCCAACCTACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGG-TTCGAACTTTGGAT
* ** *
2050449 CGTTCTTATCAAATGTAAGGACAAGCTTATACATCTAACAATCATTGAAATCATGAAACATCATT
65 CATTCTTATCAAACATAAGGACAAGCTTATACATCTAACAACCATTGAAATCA-GAAACATCATT
* *
2050514 CACAGCAACATCAAGAATTGTTGGAATACTAATA
129 CACAGCAACATCAAGAATTGTCGAAATACTAATA
2050548 GACACTGTAC
Statistics
Matches: 140, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
183 4 0.03
184 82 0.59
185 2 0.01
186 52 0.37
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (185 bp):
GAGCCAACCTACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGGTTCGAACTTTGGATC
ATTCTTATCAAACATAAGGACAAGCTTATACATCTAACAACCATTGAAATCAGAAACATCATTCA
CAGCAACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCAC
Found at i:2053651 original size:16 final size:16
Alignment explanation
Indices: 2053630--2053661 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2053620 TTAAAAAAGA
2053630 TATTTTAACATTTAGC
1 TATTTTAACATTTAGC
2053646 TATTTTAACATTTAGC
1 TATTTTAACATTTAGC
2053662 CCTTGAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
TATTTTAACATTTAGC
Found at i:2056207 original size:54 final size:51
Alignment explanation
Indices: 2056100--2056223 Score: 133
Period size: 54 Copynumber: 2.4 Consensus size: 51
2056090 CCCTTCTCAT
* *
2056100 AATTTGATTTACAGTAATGCTGTCAGAAGCAGAGGTTGATTTCATTCTAGA
1 AATTTGATTTCCAGTAATGCTGACAGAAGCAGAGGTTGATTTCATTCTAGA
* * *
2056151 AATTTGATTTCCAGTAATGGTGCCACTAGAAGCAGAGTTTGATTCTC-TTCTGGA
1 AATTTGATTTCCAGTAATGCTG--AC-AGAAGCAGAGGTTGATT-TCATTCTAGA
* * *
2056205 AATTCGGTTTCCAGCAATG
1 AATTTGATTTCCAGTAATG
2056224 ATCCTCTCAG
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
51 20 0.33
53 1 0.02
54 38 0.62
55 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (51 bp):
AATTTGATTTCCAGTAATGCTGACAGAAGCAGAGGTTGATTTCATTCTAGA
Found at i:2056304 original size:54 final size:55
Alignment explanation
Indices: 2056246--2056425 Score: 142
Period size: 54 Copynumber: 3.3 Consensus size: 55
2056236 GTTATGGTTG
* *
2056246 ATTCCTTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGA-TTGGACATTA
1 ATTCCCTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGAGTTGGACGTTA
* ** ** * * * *
2056300 ATTCCGC-TCTAGGAAG-TTGATCCCCAGTAACAAGCC-CA-CCGGAAGTGGGA-GTTG
1 ATTCC-CTTCTA-GAAGTTTGGTTTCCAGTAATGA-CCTTATCAGG-AGTTGGACGTTA
*
2056354 ATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTT-GACGTTA
1 ATTCCCTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGAGTTGGACGTTA
2056408 ATTCCGC-TCTAGGAAGTT
1 ATTCC-CTTCTA-GAAGTT
2056426 GATCGCCAGT
Statistics
Matches: 93, Mismatches: 21, Indels: 23
0.68 0.15 0.17
Matches are distributed among these distances:
53 12 0.13
54 61 0.66
55 20 0.22
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.32
Consensus pattern (55 bp):
ATTCCCTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGAGTTGGACGTTA
Found at i:2056435 original size:108 final size:108
Alignment explanation
Indices: 2056242--2056475 Score: 389
Period size: 108 Copynumber: 2.2 Consensus size: 108
2056232 AGGGGTTATG
* *
2056242 GTTGATTCCTTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGACATTAATTCCGC
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGATTGGACATTAATTCCGC
*
2056307 TCTAGGAAGTTGATCCCCAGTAACAAGCCCACCGGAAGTGGGA
66 TCTAGGAAGTTGATCCCCAGTAACAAGCCCACCAGAAGTGGGA
*
2056350 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTT-GACGTTAATTCCG
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGA-TTGGACATTAATTCCG
* **
2056414 CTCTAGGAAGTTGATCGCCAGTAATGAGCCCACCAGAAGTGGGA
65 CTCTAGGAAGTTGATCCCCAGTAACAAGCCCACCAGAAGTGGGA
2056458 GTTGATTCCCTTCTAGAA
1 GTTGATTCCCTTCTAGAA
2056476 ATCTGAATTC
Statistics
Matches: 118, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
108 116 0.98
109 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (108 bp):
GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGATTGGACATTAATTCCGC
TCTAGGAAGTTGATCCCCAGTAACAAGCCCACCAGAAGTGGGA
Found at i:2056473 original size:54 final size:54
Alignment explanation
Indices: 2056307--2056473 Score: 153
Period size: 54 Copynumber: 3.1 Consensus size: 54
2056297 TTAATTCCGC
** *
2056307 TCTAGGAAGTTGATCCCCAGTAACAAGCCCACCGGAAGTGGGAGTTGATTCCCT
1 TCTAGGAAGTTGATCCCCAGTAATGAGCCCACCAGAAGTGGGAGTTGATTCCCT
* ** * * * * * *
2056361 TCTA-GAAGTTTGGTTTCCAATAATGA-CCTTATCAGGAGT-TGACGTTAATTCCGC-
1 TCTAGGAAG-TTGATCCCCAGTAATGAGCC-CACCAGAAGTGGGA-GTTGATTCC-CT
*
2056415 TCTAGGAAGTTGATCGCCAGTAATGAGCCCACCAGAAGTGGGAGTTGATTCCCT
1 TCTAGGAAGTTGATCCCCAGTAATGAGCCCACCAGAAGTGGGAGTTGATTCCCT
2056469 TCTAG
1 TCTAG
2056474 AAATCTGAAT
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
53 9 0.11
54 66 0.79
55 9 0.11
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (54 bp):
TCTAGGAAGTTGATCCCCAGTAATGAGCCCACCAGAAGTGGGAGTTGATTCCCT
Found at i:2064048 original size:22 final size:21
Alignment explanation
Indices: 2064008--2064049 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2063998 ATATAAGTAG
**
2064008 AAAAAATATAAAAGTAATTTA
1 AAAAAATATAAAAAAAATTTA
2064029 AAAAAATTATAAAAAAAATTT
1 AAAAAA-TATAAAAAAAATTT
2064050 CATAATGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAAATATAAAAAAAATTTA
Found at i:2066865 original size:18 final size:18
Alignment explanation
Indices: 2066816--2066865 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
2066806 GATCTCGACC
2066816 AAATTAATTCGATTAACT
1 AAATTAATTCGATTAACT
*
2066834 AAATTCGATT-GATTAACT
1 AAATT-AATTCGATTAACT
*
2066852 GAATTAATTCGATT
1 AAATTAATTCGATT
2066866 TTACCTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (18 bp):
AAATTAATTCGATTAACT
Found at i:2072365 original size:11 final size:11
Alignment explanation
Indices: 2072349--2072384 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2072339 GGGGAACCAT
2072349 AAAAAAAAAAC
1 AAAAAAAAAAC
2072360 AAAAAAAAAAC
1 AAAAAAAAAAC
*
2072371 AAAGAAAGAAAC
1 AAA-AAAAAAAC
2072383 AA
1 AA
2072385 TCACTAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.86, C:0.08, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:2072898 original size:10 final size:10
Alignment explanation
Indices: 2072883--2072907 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2072873 CCCCCCCCCC
2072883 AAAAAAAAGA
1 AAAAAAAAGA
2072893 AAAAAAAAGA
1 AAAAAAAAGA
2072903 AAAAA
1 AAAAA
2072908 GAAGTGATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:2080825 original size:13 final size:13
Alignment explanation
Indices: 2080807--2080832 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2080797 TTTGACCTCG
2080807 ATTTGATTGGTTA
1 ATTTGATTGGTTA
2080820 ATTTGATTGGTTA
1 ATTTGATTGGTTA
2080833 TCGATTTTTG
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:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
ATTTGATTGGTTA
Found at i:2081774 original size:46 final size:46
Alignment explanation
Indices: 2081712--2081892 Score: 229
Period size: 46 Copynumber: 3.9 Consensus size: 46
2081702 TTTGACATGA
* * * * * *
2081712 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCACGT
* ***
2081758 TACCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
* *
2081804 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
*
2081850 TGTCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
2081893 GAGAGCACAC
Statistics
Matches: 119, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 4 0.03
46 115 0.97
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCACGT
Found at i:2086979 original size:62 final size:62
Alignment explanation
Indices: 2086903--2087029 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
2086893 TTAAATTAAT
2086903 ATTTAAGAAGGATTTGATGAATATGGTGTTGAATTATGAATTCCTTTTTTATCTGAAAAATA
1 ATTTAAGAAGGATTTGATGAATATGGTGTTGAATTATGAATTCCTTTTTTATCTGAAAAATA
2086965 ATTTAAGAAGGATTTGATGAATATGGTGTTGAATTATGAATTCCTTTTTTATCTGAAAAATA
1 ATTTAAGAAGGATTTGATGAATATGGTGTTGAATTATGAATTCCTTTTTTATCTGAAAAATA
2087027 ATT
1 ATT
2087030 CAACCAGCTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (62 bp):
ATTTAAGAAGGATTTGATGAATATGGTGTTGAATTATGAATTCCTTTTTTATCTGAAAAATA
Found at i:2090969 original size:28 final size:28
Alignment explanation
Indices: 2090938--2090997 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
2090928 TAAAATATGA
*
2090938 TTATTCAGTAT-TAAATTAAATTTT-ATTT
1 TTATTCAATATAT-AATT-AATTTTAATTT
*
2090966 TTATTTAATATATAATTAATTTTAATTT
1 TTATTCAATATATAATTAATTTTAATTT
2090994 TTAT
1 TTAT
2090998 AATAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 6 0.21
28 21 0.75
29 1 0.04
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
TTATTCAATATATAATTAATTTTAATTT
Found at i:2091008 original size:28 final size:28
Alignment explanation
Indices: 2090951--2091039 Score: 76
Period size: 28 Copynumber: 3.1 Consensus size: 28
2090941 TTCAGTATTA
* *
2090951 AATTAAATTTT-ATTTTTAT-TTAATATAT
1 AATT-AATTTTAATTTTTATAATAA-AAAT
2090979 AATTAATTTTAATTTTTATAATAAAAAT
1 AATTAATTTTAATTTTTATAATAAAAAT
* **
2091007 AAATAA-TTTATATTTAAAGTAATAAAAAT
1 AATTAATTTTA-ATTTTTA-TAATAAAAAT
2091036 AATT
1 AATT
2091040 TAAATATTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 10 0.20
28 25 0.49
29 16 0.31
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
AATTAATTTTAATTTTTATAATAAAAAT
Found at i:2092513 original size:16 final size:19
Alignment explanation
Indices: 2092487--2092524 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
2092477 TCAATTTAGC
2092487 TAAATTAATTTT-TCAA-T
1 TAAATTAATTTTCTCAACT
2092504 TAAA-TAATTTTCTCAACT
1 TAAATTAATTTTCTCAACT
2092522 TAA
1 TAA
2092525 TTCTAATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATTAATTTTCTCAACT
Found at i:2094733 original size:17 final size:17
Alignment explanation
Indices: 2094707--2094748 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
2094697 ATAACACTAT
*
2094707 AATG-TAAATATTTTAA
1 AATGTTAAATATTTAAA
2094723 AATGTTAAATATTTAAA
1 AATGTTAAATATTTAAA
2094740 AATGTTAAA
1 AATGTTAAA
2094749 GATGTATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
AATGTTAAATATTTAAA
Found at i:2099657 original size:29 final size:29
Alignment explanation
Indices: 2099622--2099680 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
2099612 ACGTAAGATT
2099622 AATGAACAAATTAATCTTTCTATTAAAAA
1 AATGAACAAATTAATCTTTCTATTAAAAA
2099651 AATGAACAAATTAATCTTTCTATTAAAAA
1 AATGAACAAATTAATCTTTCTATTAAAAA
2099680 A
1 A
2099681 TTCATCCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (29 bp):
AATGAACAAATTAATCTTTCTATTAAAAA
Found at i:2099766 original size:28 final size:29
Alignment explanation
Indices: 2099734--2099790 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
2099724 TGCCTAAACA
*
2099734 AAAATGGATGAAATTTTTAATA-AATAAT
1 AAAATGCATGAAATTTTTAATAGAATAAT
2099762 AAAATGCATGAAATTTTTAATAGAATAAT
1 AAAATGCATGAAATTTTTAATAGAATAAT
2099791 TAATTTCCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 21 0.78
29 6 0.22
ACGTcount: A:0.53, C:0.02, G:0.11, T:0.35
Consensus pattern (29 bp):
AAAATGCATGAAATTTTTAATAGAATAAT
Found at i:2105097 original size:31 final size:32
Alignment explanation
Indices: 2105062--2105128 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
2105052 AAATCAATTT
2105062 AAAAGTTG-GAACTTTTTGTAGAATTAACCAA
1 AAAAGTTGAGAACTTTTTGTAGAATTAACCAA
* *
2105093 AAAAGTTGAGAACTTTTTGTGGAATTAACCCA
1 AAAAGTTGAGAACTTTTTGTAGAATTAACCAA
2105125 AAAA
1 AAAA
2105129 TAACATTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 8 0.24
32 25 0.76
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.30
Consensus pattern (32 bp):
AAAAGTTGAGAACTTTTTGTAGAATTAACCAA
Found at i:2117393 original size:23 final size:23
Alignment explanation
Indices: 2117366--2117411 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2117356 TTTTTAAAAG
2117366 AAATGACCAATTTACTTTTTGAT
1 AAATGACCAATTTACTTTTTGAT
* *
2117389 AAATGATCAATTTGCTTTTTGAT
1 AAATGACCAATTTACTTTTTGAT
2117412 CTAACGTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (23 bp):
AAATGACCAATTTACTTTTTGAT
Found at i:2122441 original size:25 final size:25
Alignment explanation
Indices: 2122413--2122461 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
2122403 GCCCAAACCT
2122413 GTGTAGATTTTTGATGAGGAAATCG
1 GTGTAGATTTTTGATGAGGAAATCG
*
2122438 GTGTAGATTTTTTATGAGGAAATC
1 GTGTAGATTTTTGATGAGGAAATC
2122462 CAAAAGTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.39
Consensus pattern (25 bp):
GTGTAGATTTTTGATGAGGAAATCG
Found at i:2122878 original size:4 final size:4
Alignment explanation
Indices: 2122871--2122967 Score: 140
Period size: 4 Copynumber: 24.2 Consensus size: 4
2122861 TGCATGTGTG
* * *
2122871 TGTA TGTA TGAA TGCA TGCA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
2122919 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTG TGTG TGTG TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
2122967 T
1 T
2122968 CTGTACTATA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 88 1.00
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:2124736 original size:199 final size:196
Alignment explanation
Indices: 2124357--2124926 Score: 759
Period size: 196 Copynumber: 2.9 Consensus size: 196
2124347 AGGCAAAATC
* * *
2124357 TATGTTGTTCGGACTCTTCATTTTTCTTGAAGCACCAGTGTTTGACAGATGGATATTACATGGAA
1 TATGTTGCTCAGACTCTTCATTTTTCTTGAAGCACCAGTGTTTGACACATGGATATTACATGGAA
* * *
2124422 AACCTTTGAAAAATGAAAAATCTAACGATACTCGTGTCAAATGCACACCCGTATTTGACACTCAC
66 AACCTTTG-AAAA-G-----TCTAACGATACTCGTGTTAAATACATACCCGTATTTGACACTCAC
* * * *
2124487 ACCCGAGTCCGAATAACATAGGGCAAAATTCACTATGTCAACTAACAATTGAGAGCTAGGGATCA
124 ACCAGAGTCCGAATAACATAGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAGCGATCA
2124552 CAAAATGA
189 CAAAATGA
**
2124560 TAGGTTGTTGCTCAGACTCTTCATTTTTCTTGAAGCACTC-GTGTCGGACACATGGATATTACAT
1 TA---TGTTGCTCAGACTCTTCATTTTTCTTGAAGCAC-CAGTGTTTGACACATGGATATTACAT
* * * * *
2124624 AGAAAACCTTTGAAAAGTCTAACAATACTC-TCATTAAATACATACCCATATTTGACACTTACAC
62 GGAAAACCTTTGAAAAGTCTAACGATACTCGT-GTTAAATACATACCCGTATTTGACACTCACAC
* *
2124688 CAGAGTCCGAATAACATAGGGCAAAATTAACTATGTCAACTGACAATTGACAGCAAGCGATCACA
126 CAGAGTCCGAATAACATAGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAGCGATCACA
* *
2124753 CAATGC
191 AAATGA
* * *
2124759 TATGTTGCTCAGGCTCTTCATTTTTCTTGAAGCACCAGTGTTTGACATATGTATATTACATGGAA
1 TATGTTGCTCAGACTCTTCATTTTTCTTGAAGCACCAGTGTTTGACACATGGATATTACATGGAA
* *
2124824 AACCTTTGAAAAGTCAAACGATACTCGTGTTAAATACATACCGGTATTTGACACTCACACCCA-A
66 AACCTTTGAAAAGTCTAACGATACTCGTGTTAAATACATACCCGTATTTGACACTCACA-CCAGA
*
2124888 GTCCGAGTAACATAGGGCAAAATTCACTATGTCAACTAA
130 GTCCGAATAACATAGGGCAAAATTCACTATGTCAACTAA
2124927 TAAATCAAGG
Statistics
Matches: 323, Mismatches: 36, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
195 1 0.00
196 143 0.44
197 4 0.01
198 1 0.00
199 103 0.32
203 2 0.01
204 1 0.00
205 4 0.01
206 63 0.20
207 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (196 bp):
TATGTTGCTCAGACTCTTCATTTTTCTTGAAGCACCAGTGTTTGACACATGGATATTACATGGAA
AACCTTTGAAAAGTCTAACGATACTCGTGTTAAATACATACCCGTATTTGACACTCACACCAGAG
TCCGAATAACATAGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAGCGATCACAAAATG
A
Found at i:2132572 original size:18 final size:18
Alignment explanation
Indices: 2132549--2132598 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2132539 CGGCTGCAGT
*
2132549 GGCGGCTGAGGTGGCGGA
1 GGCGGCTGAGGCGGCGGA
* *
2132567 GGCGGCGGAGGCGGCGGT
1 GGCGGCTGAGGCGGCGGA
2132585 GGCCGGACTGAGGC
1 GG-CGG-CTGAGGC
2132599 AACTCGGTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 17 0.65
19 3 0.12
20 6 0.23
ACGTcount: A:0.10, C:0.22, G:0.60, T:0.08
Consensus pattern (18 bp):
GGCGGCTGAGGCGGCGGA
Found at i:2132573 original size:9 final size:9
Alignment explanation
Indices: 2132549--2132583 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2132539 CGGCTGCAGT
*
2132549 GGCGGCTGA
1 GGCGGCGGA
*
2132558 GGTGGCGGA
1 GGCGGCGGA
2132567 GGCGGCGGA
1 GGCGGCGGA
2132576 GGCGGCGG
1 GGCGGCGG
2132584 TGGCCGGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.09, C:0.20, G:0.66, T:0.06
Consensus pattern (9 bp):
GGCGGCGGA
Found at i:2135232 original size:13 final size:13
Alignment explanation
Indices: 2135214--2135279 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
2135204 AGTCTTGAAC
2135214 TTTAAACTTAAAT
1 TTTAAACTTAAAT
2135227 TTTAAACTT-AA-
1 TTTAAACTTAAAT
*
2135238 ---AATCTTAAAT
1 TTTAAACTTAAAT
*
2135248 TTTAAACTCAAAT
1 TTTAAACTTAAAT
* *
2135261 TCTAACCTTAAAT
1 TTTAAACTTAAAT
*
2135274 ATTAAA
1 TTTAAA
2135280 TTTGGAAGTT
Statistics
Matches: 39, Mismatches: 9, Indels: 10
0.67 0.16 0.17
Matches are distributed among these distances:
8 5 0.13
9 2 0.05
12 2 0.05
13 30 0.77
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTAAACTTAAAT
Found at i:2135253 original size:34 final size:33
Alignment explanation
Indices: 2135214--2135282 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 33
2135204 AGTCTTGAAC
* * *
2135214 TTTAAACTTAAATTTTAAACTTAAAATCTTAAAT
1 TTTAAACTCAAATTCTAAACTT-AAATATTAAAT
*
2135248 TTTAAACTCAAATTCTAACCTTAAATATTAAAT
1 TTTAAACTCAAATTCTAAACTTAAATATTAAAT
2135281 TT
1 TT
2135283 GGAAGTTAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 12 0.39
34 19 0.61
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (33 bp):
TTTAAACTCAAATTCTAAACTTAAATATTAAAT
Found at i:2139689 original size:16 final size:17
Alignment explanation
Indices: 2139668--2139701 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2139658 ATTGTTTTGA
*
2139668 ATTTTTGA-GTATTTTT
1 ATTTTTGATATATTTTT
2139684 ATTTTTGATATATTTTT
1 ATTTTTGATATATTTTT
2139701 A
1 A
2139702 ATTAAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (17 bp):
ATTTTTGATATATTTTT
Found at i:2141211 original size:24 final size:24
Alignment explanation
Indices: 2141184--2141231 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2141174 ACCGTCACTG
*
2141184 TCAGCATCACCATTACCATCACCA
1 TCAGCATCACAATTACCATCACCA
**
2141208 TCAGCATCACAATTGTCATCACCA
1 TCAGCATCACAATTACCATCACCA
2141232 CTATCAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.38, G:0.06, T:0.23
Consensus pattern (24 bp):
TCAGCATCACAATTACCATCACCA
Found at i:2141263 original size:57 final size:57
Alignment explanation
Indices: 2141193--2141375 Score: 255
Period size: 57 Copynumber: 3.3 Consensus size: 57
2141183 GTCAGCATCA
* * *
2141193 CCATTACCATCACCATCAGCATCACAATTGTCATCACCACTATCAACATCGCTATTG
1 CCATCACCGTCACCATCAGCATCACAATTGTCATCACCACTATCAACATCACTATTG
*
2141250 CCATCACCGTCACCATCAGCATCACAATTGTCATCACCACTATCAACATCCCTATTG
1 CCATCACCGTCACCATCAGCATCACAATTGTCATCACCACTATCAACATCACTATTG
* * * * * *
2141307 CCATCACCGTCACCTTCAGCATCACCATTGCCATCACC-C--TCAGCGTCACAATTG
1 CCATCACCGTCACCATCAGCATCACAATTGTCATCACCACTATCAACATCACTATTG
2141361 CCATCACCGTCACCA
1 CCATCACCGTCACCA
2141376 CTATCAGAAA
Statistics
Matches: 115, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
54 25 0.22
56 1 0.01
57 89 0.77
ACGTcount: A:0.28, C:0.40, G:0.08, T:0.23
Consensus pattern (57 bp):
CCATCACCGTCACCATCAGCATCACAATTGTCATCACCACTATCAACATCACTATTG
Found at i:2141343 original size:24 final size:24
Alignment explanation
Indices: 2141316--2141368 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2141306 GCCATCACCG
* *
2141316 TCACCTTCAGCATCACCATTGCCA
1 TCACCCTCAGCATCACAATTGCCA
*
2141340 TCACCCTCAGCGTCACAATTGCCA
1 TCACCCTCAGCATCACAATTGCCA
2141364 TCACC
1 TCACC
2141369 GTCACCACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.43, G:0.09, T:0.23
Consensus pattern (24 bp):
TCACCCTCAGCATCACAATTGCCA
Found at i:2145267 original size:48 final size:48
Alignment explanation
Indices: 2145195--2145293 Score: 180
Period size: 48 Copynumber: 2.1 Consensus size: 48
2145185 CGCTTCACTC
2145195 AAGAGATCTCGTCAAATGTCTGCCTCATCAAGACTCATTGCCTTATCA
1 AAGAGATCTCGTCAAATGTCTGCCTCATCAAGACTCATTGCCTTATCA
* *
2145243 AAGAGATCTCGTCAAATGTTTGCCTCATCAAGGCTCATTGCCTTATCA
1 AAGAGATCTCGTCAAATGTCTGCCTCATCAAGACTCATTGCCTTATCA
2145291 AAG
1 AAG
2145294 GCAAAGGCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (48 bp):
AAGAGATCTCGTCAAATGTCTGCCTCATCAAGACTCATTGCCTTATCA
Found at i:2145900 original size:21 final size:20
Alignment explanation
Indices: 2145868--2145906 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2145858 ATTTGTCCTT
2145868 AAAAAATTATTAAAAATTTC
1 AAAAAATTATTAAAAATTTC
*
2145888 AAAAAGTTCATTAAAAATT
1 AAAAAATT-ATTAAAAATT
2145907 ATATTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAAATTATTAAAAATTTC
Found at i:2149170 original size:31 final size:31
Alignment explanation
Indices: 2149088--2149173 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
2149078 TGGTGTCTAA
*
2149088 TATTTACAAAAGTGCTCAAATGAGGTAAAATC
1 TATTT-CAAAAGTGCTCAAATAAGGTAAAATC
*
2149120 T-TTTCGAAAA-TACTCAAATAAGTGCT-AAA-C
1 TATTTC-AAAAGTGCTCAAATAAG-G-TAAAATC
2149150 TATTTCAAAAGTGCTCAAATAAGG
1 TATTTCAAAAGTGCTCAAATAAGG
2149174 ACTTCTCAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
30 18 0.39
31 26 0.57
32 2 0.04
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (31 bp):
TATTTCAAAAGTGCTCAAATAAGGTAAAATC
Found at i:2152236 original size:13 final size:13
Alignment explanation
Indices: 2152205--2152239 Score: 56
Period size: 11 Copynumber: 2.8 Consensus size: 13
2152195 GTGTCGTATA
2152205 AATTTATACTTAT
1 AATTTATACTTAT
2152218 --TTTATACTTAT
1 AATTTATACTTAT
2152229 AATTTATACTT
1 AATTTATACTT
2152240 GCCTTTGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 11 0.55
13 9 0.45
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTTATACTTAT
Found at i:2152393 original size:4 final size:4
Alignment explanation
Indices: 2152378--2152416 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
2152368 TCTACTAAAT
*
2152378 TTAA TCTAA TTAA TTAA TTAA TTAA TTTA -TAA TTAA TTA
1 TTAA T-TAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
2152417 TGATGATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 2 0.06
4 25 0.81
5 4 0.13
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (4 bp):
TTAA
Found at i:2156021 original size:61 final size:60
Alignment explanation
Indices: 2155922--2156046 Score: 187
Period size: 61 Copynumber: 2.1 Consensus size: 60
2155912 TACATAGAGT
* *
2155922 TGAACATAGTAAAATAAGAAATTAAAATATTTCATTGAAATTGTTCATTTGGAAATTTCC
1 TGAACATAGTAAAATAAGAAATTAAAAGATTTCATTGAAATTGTTCATTTAGAAATTTCC
* * **
2155982 TGAATCATAGTAAAATAAGAAATTGAAAGATTTCGTTGAAATTGTTTGTTTAGAAATTTCC
1 TGAA-CATAGTAAAATAAGAAATTAAAAGATTTCATTGAAATTGTTCATTTAGAAATTTCC
2156043 TGAA
1 TGAA
2156047 AAGCTAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 4 0.07
61 54 0.93
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (60 bp):
TGAACATAGTAAAATAAGAAATTAAAAGATTTCATTGAAATTGTTCATTTAGAAATTTCC
Found at i:2162594 original size:7 final size:7
Alignment explanation
Indices: 2162582--2162610 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2162572 ATAATGATTG
2162582 ATTTATA
1 ATTTATA
2162589 ATTTATA
1 ATTTATA
2162596 ATTTATA
1 ATTTATA
2162603 ATTTATA
1 ATTTATA
2162610 A
1 A
2162611 ATAATAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTTATA
Done.