Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr10
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: 21822658
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 1067834 characters in sequence are not A, C, G, or T
File 6 of 59
Found at i:1839288 original size:43 final size:43
Alignment explanation
Indices: 1839227--1839324 Score: 142
Period size: 43 Copynumber: 2.3 Consensus size: 43
1839217 TATATCAACT
* *
1839227 AGTCACACAATACTTAAAAACTAGTCACGTAATGTCCAAAGTC
1 AGTCACACAATACCTAAAAACTAGTCACGTAATATCCAAAGTC
* * *
1839270 AGTCACATAATGCCTAAAAACTAGTCACGTAATATCTAAAGTC
1 AGTCACACAATACCTAAAAACTAGTCACGTAATATCCAAAGTC
*
1839313 AGTCACGCAATA
1 AGTCACACAATA
1839325 TCCAAAGTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.23
Consensus pattern (43 bp):
AGTCACACAATACCTAAAAACTAGTCACGTAATATCCAAAGTC
Found at i:1839296 original size:22 final size:22
Alignment explanation
Indices: 1839200--1839302 Score: 77
Period size: 22 Copynumber: 4.7 Consensus size: 22
1839190 AATATATATC
* *
1839200 AACTAGTCACACAATG-CTATATC
1 AACTAGTCACATAATGCCTA-A-A
* * *
1839223 AACTAGTCACACAATACTTAAA
1 AACTAGTCACATAATGCCTAAA
*
1839245 AACTAGTCACGTAATGTCC-AAA
1 AACTAGTCACATAATG-CCTAAA
**
1839267 GTC-AGTCACATAATGCCTAAA
1 AACTAGTCACATAATGCCTAAA
*
1839288 AACTAGTCACGTAAT
1 AACTAGTCACATAAT
1839303 ATCTAAAGTC
Statistics
Matches: 63, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
20 2 0.03
21 15 0.24
22 27 0.43
23 17 0.27
24 2 0.03
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.24
Consensus pattern (22 bp):
AACTAGTCACATAATGCCTAAA
Found at i:1839308 original size:22 final size:22
Alignment explanation
Indices: 1839223--1839326 Score: 70
Period size: 22 Copynumber: 4.8 Consensus size: 22
1839213 ATGCTATATC
**
1839223 AACTAGTCACACAATA-CTTAAA
1 AACTAGTCACGTAATATC-TAAA
* *
1839245 AACTAGTCACGTAATGTCCAAA
1 AACTAGTCACGTAATATCTAAA
** * **
1839267 GTC-AGTCACATAATGCCTAAA
1 AACTAGTCACGTAATATCTAAA
1839288 AACTAGTCACGTAATATCTAAA
1 AACTAGTCACGTAATATCTAAA
** *
1839310 GTC-AGTCACGCAATATC
1 AACTAGTCACGTAATATC
1839327 CAAAGTCAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
21 29 0.46
22 33 0.52
23 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.24
Consensus pattern (22 bp):
AACTAGTCACGTAATATCTAAA
Found at i:1858325 original size:21 final size:20
Alignment explanation
Indices: 1858288--1858326 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1858278 GTTAAGATTG
1858288 ATTTTTTAAATAATTTTAGA
1 ATTTTTTAAATAATTTTAGA
* *
1858308 ATTTATTTATATATTTTTA
1 ATTT-TTTAAATAATTTTA
1858327 TATGGATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTTTTAAATAATTTTAGA
Found at i:1859079 original size:2 final size:2
Alignment explanation
Indices: 1859072--1859143 Score: 99
Period size: 2 Copynumber: 35.0 Consensus size: 2
1859062 TGCAAGTTGG
* * *
1859072 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AGG NT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T A-T AT AT AT AT
1859116 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1859144 GGGGGAAACC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 61 0.95
3 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1867855 original size:82 final size:84
Alignment explanation
Indices: 1867714--1867876 Score: 224
Period size: 82 Copynumber: 2.0 Consensus size: 84
1867704 GATACTTTAC
* * ** * *
1867714 TTCCTGGTGAGAGTATATGTTATAGATTCTTTGTTATTTTTGGCTGCTATATTTTAACTTAAATT
1 TTCCTGGTAAGAGTATATGTAATAGATTCTTTAATATTTTTGGCTACTATATTTCAACTTAAATT
1867779 CTTTTGTCATAATTTATGA
66 CTTTTGTCATAATTTATGA
*
1867798 TTCCTGGTAAGAGTAT-T-TAATGGATTCTTTAATATTTCTT-GCTACTATATTTCAACTTAAAT
1 TTCCTGGTAAGAGTATATGTAATAGATTCTTTAATATTT-TTGGCTACTATATTTCAACTTAAAT
*
1867860 TCTTTTGTTATAATTTA
65 TCTTTTGTCATAATTTA
1867877 CGTGCCTTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
82 52 0.74
83 3 0.04
84 15 0.21
ACGTcount: A:0.26, C:0.10, G:0.13, T:0.51
Consensus pattern (84 bp):
TTCCTGGTAAGAGTATATGTAATAGATTCTTTAATATTTTTGGCTACTATATTTCAACTTAAATT
CTTTTGTCATAATTTATGA
Found at i:1889313 original size:2 final size:2
Alignment explanation
Indices: 1889306--1889369 Score: 80
Period size: 2 Copynumber: 33.0 Consensus size: 2
1889296 TTTAATTCCC
* *
1889306 CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT NT -T AC- CT C- CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT CT CT
1889346 CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT
1889370 TTGCACCCGA
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
1 3 0.05
2 53 0.95
ACGTcount: A:0.02, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1891322 original size:25 final size:25
Alignment explanation
Indices: 1891265--1891327 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 25
1891255 ACACTAAAGA
1891265 GAGAAATCAACTTAATAGTAAGTAT
1 GAGAAATCAACTTAATAGTAAGTAT
*
1891290 GAG----GAACTTAATAGTAAGTAT
1 GAGAAATCAACTTAATAGTAAGTAT
1891311 GAGAAATCAACTTAATA
1 GAGAAATCAACTTAATA
1891328 CAAATATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
21 20 0.62
25 12 0.38
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (25 bp):
GAGAAATCAACTTAATAGTAAGTAT
Found at i:1899409 original size:70 final size:70
Alignment explanation
Indices: 1899296--1899429 Score: 250
Period size: 70 Copynumber: 1.9 Consensus size: 70
1899286 GGTAGTATAT
1899296 CAAGTTTCATCAAAAATAACAACTGTTGTTCATTCCAAATGTTTAGTTAAGTGGTTGTAGTTTGA
1 CAAGTTTCATCAAAAATAACAACTGTTGTTCATTCCAAATGTTTAGTTAAGTGGTTGTAGTTTGA
1899361 ACTAC
66 ACTAC
**
1899366 CAAGTTTCATTGAAAATAACAACTGTTGTTCATTCCAAATGTTTAGTTAAGTGGTTGTAGTTTG
1 CAAGTTTCATCAAAAATAACAACTGTTGTTCATTCCAAATGTTTAGTTAAGTGGTTGTAGTTTG
1899430 GTTAACTCTG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (70 bp):
CAAGTTTCATCAAAAATAACAACTGTTGTTCATTCCAAATGTTTAGTTAAGTGGTTGTAGTTTGA
ACTAC
Found at i:1907677 original size:33 final size:33
Alignment explanation
Indices: 1907639--1907715 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 33
1907629 TTTGTAATGT
1907639 TATAAT-TAA-AATAAAAAATATTAAAATAAAACA
1 TATAATATAAGAAT-AAAAA-ATTAAAATAAAACA
* *
1907672 TATAATATAAGAATTATAAATTAAAAT-AAA-A
1 TATAATATAAGAATAAAAAATTAAAATAAAACA
*
1907703 TAAAATATAAGAA
1 TATAATATAAGAA
1907716 ATTAAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
31 13 0.33
32 3 0.08
33 14 0.36
34 6 0.15
35 3 0.08
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (33 bp):
TATAATATAAGAATAAAAAATTAAAATAAAACA
Found at i:1907681 original size:14 final size:15
Alignment explanation
Indices: 1907643--1907674 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1907633 TAATGTTATA
1907643 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
1907658 ATTAAAATAAAACAT
1 ATTAAAATAAAAAAT
1907673 AT
1 AT
1907675 AATATAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:1907713 original size:31 final size:33
Alignment explanation
Indices: 1907658--1907724 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 33
1907648 AATAAAAAAT
*
1907658 ATTAAAATAAAACATATAATATAAG-AATTATAA
1 ATTAAAATAAAACATAAAATATAAGAAATTA-AA
1907691 ATTAAAAT-AAA-ATAAAATATAAGAAATTAAA
1 ATTAAAATAAAACATAAAATATAAGAAATTAAA
1907722 ATT
1 ATT
1907725 TATATAATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 16 0.50
32 8 0.25
33 8 0.25
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (33 bp):
ATTAAAATAAAACATAAAATATAAGAAATTAAA
Found at i:1907802 original size:34 final size:32
Alignment explanation
Indices: 1907749--1907835 Score: 93
Period size: 34 Copynumber: 2.6 Consensus size: 32
1907739 AAATGAAATT
*
1907749 AAAATAAAATATATAATATAAAAAATTATATTAA
1 AAAATAAAATA-A-AATATAAAAAATTATAATAA
* **
1907783 AGAAATGAAAATAAAATATATAAGGTTATAATAA
1 A-AAAT-AAAATAAAATATAAAAAATTATAATAA
1907817 AAAATAAAAATAAAATATA
1 AAAAT-AAAATAAAATATA
1907836 TTTAAGAGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 17 0.37
34 18 0.39
35 5 0.11
36 6 0.13
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (32 bp):
AAAATAAAATAAAATATAAAAAATTATAATAA
Found at i:1909892 original size:2 final size:2
Alignment explanation
Indices: 1909850--1909884 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1909840 GCAGTCACAA
*
1909850 AT AT AT AT AT AT AT AG AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1909885 TTTATATACG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1910981 original size:1 final size:1
Alignment explanation
Indices: 1910975--1911026 Score: 86
Period size: 1 Copynumber: 52.0 Consensus size: 1
1910965 NNNNNNNNNN
* *
1910975 GGGGGGGGGGGGGGGGGGGGGGGAGGGGCGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1911027 AGGGATTGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.02, C:0.02, G:0.96, T:0.00
Consensus pattern (1 bp):
G
Found at i:1911017 original size:29 final size:29
Alignment explanation
Indices: 1910975--1911030 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
1910965 NNNNNNNNNN
1910975 GGGGGGGGGGGGGGGGGGGGGGGAGGGGC
1 GGGGGGGGGGGGGGGGGGGGGGGAGGGGC
1911004 GGGGGGGGGGGGGGGGGGGGGGGAGGG
1 GGGGGGGGGGGGGGGGGGGGGGGAGGG
1911031 ATTGATCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.04, C:0.02, G:0.95, T:0.00
Consensus pattern (29 bp):
GGGGGGGGGGGGGGGGGGGGGGGAGGGGC
Found at i:1916091 original size:21 final size:21
Alignment explanation
Indices: 1916065--1916106 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
1916055 CGGTTTTAAA
1916065 ATTTTTTATTTAATAAATATAT
1 ATTTTTTATTTAA-AAATATAT
1916087 ATTTTTTATTTAAAAATATA
1 ATTTTTTATTTAAAAATATA
1916107 AGTTTGTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTTATTTAAAAATATAT
Found at i:1921194 original size:30 final size:29
Alignment explanation
Indices: 1921122--1921194 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
1921112 TTTAATAAAA
1921122 AAATAAATTTTTAT-TTTTTATTAAATTT
1 AAATAAATTTTTATATTTTTATTAAATTT
* * * *
1921150 AATTGAGA-TATTATATTTTTATTTGAATTT
1 AAAT-AAATTTTTATATTTTTA-TTAAATTT
1921180 AAATAAATTTTTATA
1 AAATAAATTTTTATA
1921195 ATTAATAGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
28 8 0.24
29 10 0.29
30 16 0.47
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (29 bp):
AAATAAATTTTTATATTTTTATTAAATTT
Found at i:1928839 original size:2 final size:2
Alignment explanation
Indices: 1928806--1928831 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1928796 GCAATTTCTG
1928806 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1928832 TTTATATAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1929198 original size:2 final size:2
Alignment explanation
Indices: 1929191--1929217 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1929181 CAATTTTCAA
1929191 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
1929218 ACAGAACAAA
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:1929244 original size:2 final size:2
Alignment explanation
Indices: 1929237--1929263 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1929227 AACATGNCTA
1929237 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
1929264 ACAGACAAAA
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:1940703 original size:15 final size:15
Alignment explanation
Indices: 1940683--1940713 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1940673 TTCATGTATG
*
1940683 ATTAATGATTAATTA
1 ATTAATCATTAATTA
1940698 ATTAATCATTAATTA
1 ATTAATCATTAATTA
1940713 A
1 A
1940714 AATATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (15 bp):
ATTAATCATTAATTA
Found at i:1942618 original size:20 final size:21
Alignment explanation
Indices: 1942590--1942628 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1942580 ACTTTTTTTA
*
1942590 TTTTTTTAAAAAAT-TACCCC
1 TTTTCTTAAAAAATCTACCCC
*
1942610 TTTTCTTAAGAAATCTACC
1 TTTTCTTAAAAAATCTACC
1942629 AATAGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.44
Consensus pattern (21 bp):
TTTTCTTAAAAAATCTACCCC
Found at i:1959674 original size:3 final size:3
Alignment explanation
Indices: 1959659--1959688 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1959649 GTAGAATCCA
*
1959659 TAT TAT TAG TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1959689 CAAATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1964485 original size:14 final size:13
Alignment explanation
Indices: 1964425--1964493 Score: 57
Period size: 14 Copynumber: 4.9 Consensus size: 13
1964415 ATCGGATAAA
*
1964425 ATTTTATATATCAT
1 ATTTTATAT-TTAT
*
1964439 ATTTAACTATTTAT
1 ATTTTA-TATTTAT
*
1964453 ATTTTATACATTAT
1 ATTTTATA-TTTAT
1964467 AATTTTATATTTAGT
1 -ATTTTATATTTA-T
*
1964482 ATTTTAAATTTA
1 ATTTTATATTTA
1964494 AATATAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 2 0.04
14 31 0.69
15 12 0.27
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (13 bp):
ATTTTATATTTAT
Found at i:1965169 original size:12 final size:13
Alignment explanation
Indices: 1965147--1965176 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1965137 TCACAAGTTG
1965147 AAAAGCCAAAACC
1 AAAAGCCAAAACC
1965160 AAAA-CCAAAACC
1 AAAAGCCAAAACC
1965172 AAAAG
1 AAAAG
1965177 AAGTTGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.27, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAGCCAAAACC
Found at i:1966590 original size:196 final size:196
Alignment explanation
Indices: 1966243--1966635 Score: 693
Period size: 196 Copynumber: 2.0 Consensus size: 196
1966233 TAATTTTTTT
* * *
1966243 AAAAGAAAAATTGTGAAGAGAAATGAACAAGGCTCTTATGGTGTAATGAATAGATGGTCATGTTA
1 AAAAGAAAAATTCTGAAGAGAAATGAACAAGCCTCTTATGGTGTAATGAATAGATGGGCATGTTA
1966308 GTAAGTAAGCAGGCCATGAGGTGGGAGTTTGTTTGTGTGCATCAAAGTAAAGCTCAGTAGATGAG
66 GTAAGTAAGCAGGCCATGAGGTGGGAGTTTGTTTGTGTGCATCAAAGTAAAGCTCAGTAGATGAG
1966373 GCTGCAATCTGCATCTCATCTTAAAATGAGCATTAACAAACAAAAAAAAAAAAAACAAAG-AAAT
131 GCTGCAATCTGCATCTCATCTTAAAATGAGCATTAAC-AACAAAAAAAAAAAAAACAAAGAAAAT
1966437 TC
195 TC
1966439 ANAAAG-AAAATTCTGAAGAGAAATGAACAAGCCTCTTA-GGTTGTAATGAATAGATGGGCATGT
1 A-AAAGAAAAATTCTGAAGAGAAATGAACAAGCCTCTTATGG-TGTAATGAATAGATGGGCATGT
* *
1966502 TAGTATGTAAGCAGGTCATGAGGTGGGAGTTTGTTTGTGTGCATCAAAGTAAAGCTCAGTAGATG
64 TAGTAAGTAAGCAGGCCATGAGGTGGGAGTTTGTTTGTGTGCATCAAAGTAAAGCTCAGTAGATG
1966567 AGGCTGCAATCTGCATCTCATCTTAAAATGAGCATTAACAACAAAAAAAAAAAAAACAAAGAAAA
129 AGGCTGCAATCTGCATCTCATCTTAAAATGAGCATTAACAACAAAAAAAAAAAAAACAAAGAAAA
1966632 TTC
194 TTC
1966635 A
1 A
1966636 GTAAAAAAAT
Statistics
Matches: 189, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
195 24 0.13
196 161 0.85
197 4 0.02
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.24
Consensus pattern (196 bp):
AAAAGAAAAATTCTGAAGAGAAATGAACAAGCCTCTTATGGTGTAATGAATAGATGGGCATGTTA
GTAAGTAAGCAGGCCATGAGGTGGGAGTTTGTTTGTGTGCATCAAAGTAAAGCTCAGTAGATGAG
GCTGCAATCTGCATCTCATCTTAAAATGAGCATTAACAACAAAAAAAAAAAAAACAAAGAAAATT
C
Found at i:1975261 original size:25 final size:24
Alignment explanation
Indices: 1975233--1975299 Score: 125
Period size: 24 Copynumber: 2.8 Consensus size: 24
1975223 AAATTTAATA
1975233 TTTATTATTTTAATAAATAAATTTT
1 TTTATTATTTTAATAAAT-AATTTT
1975258 TTTATTATTTTAATAAATAATTTT
1 TTTATTATTTTAATAAATAATTTT
1975282 TTTATTATTTTAATAAAT
1 TTTATTATTTTAATAAAT
1975300 TGAAGAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 24 0.57
25 18 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTATTATTTTAATAAATAATTTT
Found at i:1976660 original size:18 final size:18
Alignment explanation
Indices: 1976621--1976657 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1976611 ATTAAGTAAA
1976621 TTAAAAAGTTAAAAAAAT
1 TTAAAAAGTTAAAAAAAT
*
1976639 TTAAAAAG-TAAAATAAT
1 TTAAAAAGTTAAAAAAAT
1976656 TT
1 TT
1976658 TAATTAAGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
TTAAAAAGTTAAAAAAAT
Found at i:1985633 original size:16 final size:17
Alignment explanation
Indices: 1985606--1985638 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1985596 TTAATTGTGA
*
1985606 TTTTTAACAATTTTCTT
1 TTTTTAACAATTATCTT
1985623 TTTTTAA-AATTATCTT
1 TTTTTAACAATTATCTT
1985639 GGCAATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTAACAATTATCTT
Found at i:1989749 original size:2 final size:2
Alignment explanation
Indices: 1989742--1989769 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1989732 TAGTTATAGA
1989742 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1989770 GGAGGGGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1998442 original size:28 final size:28
Alignment explanation
Indices: 1998410--1998473 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
1998400 AAACTTTTTA
1998410 AATAAATATTTATTCTTTTAATGAGTTC
1 AATAAATATTTATTCTTTTAATGAGTTC
1998438 AATAAAGT-TTTATTCTTTTAATGAGTTC
1 AATAAA-TATTTATTCTTTTAATGAGTTC
1998466 AATAAATA
1 AATAAATA
1998474 AATTTTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 1 0.03
28 32 0.94
29 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (28 bp):
AATAAATATTTATTCTTTTAATGAGTTC
Found at i:1998481 original size:32 final size:30
Alignment explanation
Indices: 1998408--1998482 Score: 100
Period size: 28 Copynumber: 2.5 Consensus size: 30
1998398 CAAAACTTTT
*
1998408 TAAATAAATATTTATTCTTTTAATGAGTTC
1 TAAATAAATTTTTATTCTTTTAATGAGTTC
*
1998438 --AATAAAGTTTTATTCTTTTAATGAGTTC
1 TAAATAAATTTTTATTCTTTTAATGAGTTC
1998466 AATAAATAAATTTTTAT
1 --TAAATAAATTTTTAT
1998483 AACTAACTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 26 0.68
32 12 0.32
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (30 bp):
TAAATAAATTTTTATTCTTTTAATGAGTTC
Found at i:2002076 original size:16 final size:17
Alignment explanation
Indices: 2002055--2002087 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2002045 TTATACTTTC
2002055 AAATAAAAAG-TAACAA
1 AAATAAAAAGTTAACAA
*
2002071 AAATAACAAGTTAACAA
1 AAATAAAAAGTTAACAA
2002088 CCAAACATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.70, C:0.09, G:0.06, T:0.15
Consensus pattern (17 bp):
AAATAAAAAGTTAACAA
Found at i:2015398 original size:6 final size:6
Alignment explanation
Indices: 2015387--2015435 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
2015377 CTTCCTCTCC
* * *
2015387 CTTTCT CTTTCT CTTCCTT CCTTTCC CTTTCC CTTTCT CTTTCT CTTTC
1 CTTTCT CTTTCT CTTTC-T -CTTTCT CTTTCT CTTTCT CTTTCT CTTTC
2015436 CCTCTTTTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
6 32 0.86
7 1 0.03
8 4 0.11
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (6 bp):
CTTTCT
Found at i:2015420 original size:32 final size:33
Alignment explanation
Indices: 2015383--2015554 Score: 107
Period size: 33 Copynumber: 4.9 Consensus size: 33
2015373 TCGACTTCCT
* *
2015383 CTCCCTTTCTCTTTCTC-TTCCTTCCTTTCCCT
1 CTCCCTTTCTCTTTCTCTTTCCCTCCTTTCCCG
* *
2015415 TTCCCTTTCTCTTTCTCTTTCCCTCTTTTCCCG
1 CTCCCTTTCTCTTTCTCTTTCCCTCCTTTCCCG
* ** *
2015448 CTCCCTTTCCCGCTCTCTTTCACGCTCTCTCTTCTCTCT
1 CTCCCTTTCTCTTTCTCTTTC-C-CTC-CT-TTC-C-CG
* * *
2015487 ATCCCTCTCTCTTTC-CTTCTCCCTCGCTCTTTCC-
1 CTCCCTTTCTCTTTCTCTT-TCCCTC-CT-TTCCCG
*
2015521 CTCTCTTTCTCTTTCTCTCGTTCCCTCTCTTTCC
1 CTCCCTTTCTCTTTCTCT--TTCCCTC-CTTTCC
2015555 TCTCTCTCCC
Statistics
Matches: 107, Mismatches: 22, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
32 16 0.15
33 29 0.27
34 13 0.12
35 9 0.08
36 10 0.09
37 12 0.11
38 5 0.05
39 13 0.12
ACGTcount: A:0.01, C:0.47, G:0.03, T:0.49
Consensus pattern (33 bp):
CTCCCTTTCTCTTTCTCTTTCCCTCCTTTCCCG
Found at i:2015442 original size:26 final size:26
Alignment explanation
Indices: 2015377--2015427 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
2015367 TTTCCCTCGA
* *
2015377 CTTCCTCTCCCTTTCTCTTTCTCTTC
1 CTTCCTTTCCCTTTCCCTTTCTCTTC
2015403 CTTCCTTTCCCTTTCCCTTTCTCTT
1 CTTCCTTTCCCTTTCCCTTTCTCTT
2015428 TCTCTTTCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (26 bp):
CTTCCTTTCCCTTTCCCTTTCTCTTC
Found at i:2015475 original size:12 final size:12
Alignment explanation
Indices: 2015428--2015477 Score: 61
Period size: 12 Copynumber: 4.4 Consensus size: 12
2015418 CCTTTCTCTT
2015428 TCTCTTT-CC-C
1 TCTCTTTCCCGC
2015438 TCT-TTTCCCGC
1 TCTCTTTCCCGC
*
2015449 TCCCTTTCCCGC
1 TCTCTTTCCCGC
*
2015461 TCTCTTTCACGC
1 TCTCTTTCCCGC
2015473 TCTCT
1 TCTCT
2015478 CTTCTCTCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 3 0.09
10 5 0.15
11 3 0.09
12 23 0.68
ACGTcount: A:0.02, C:0.48, G:0.06, T:0.44
Consensus pattern (12 bp):
TCTCTTTCCCGC
Found at i:2015477 original size:2 final size:2
Alignment explanation
Indices: 2015472--2015572 Score: 50
Period size: 2 Copynumber: 52.5 Consensus size: 2
2015462 CTCTTTCACG
* * * *
2015472 CT CT CT CT -T CT CT CT AT CC CT CT CT CT TT C- CT -T CT CC CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * * * * *
2015511 CG CT CT TT CC CT CT CT TT CT CT TT CT CT CGT -T CC CT CT CT TT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT
*
2015553 C- CT CT CT CT CC CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C
2015573 GATGCTTTTC
Statistics
Matches: 69, Mismatches: 24, Indels: 12
0.66 0.23 0.11
Matches are distributed among these distances:
1 5 0.07
2 63 0.91
3 1 0.01
ACGTcount: A:0.01, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2015486 original size:21 final size:19
Alignment explanation
Indices: 2015472--2015571 Score: 68
Period size: 18 Copynumber: 5.4 Consensus size: 19
2015462 CTCTTTCACG
2015472 CTCTCTCTTCTCTCTATCC
1 CTCTCTCTTCTCTCTATCC
*
2015491 CTCTCTCTT-TC-CTTCTCC
1 CTCTCTCTTCTCTC-TATCC
* * * *
2015509 CTCGCTCTT-TCCCTCTCT
1 CTCTCTCTTCTCTCTATCC
*
2015527 TTCTCT-TTCTCTCGT-TCC
1 CTCTCTCTTCTCTC-TATCC
*
2015545 CTCTCT-TTCCTCTCTCTCC
1 CTCTCTCTT-CTCTCTATCC
2015564 CTCTCTCT
1 CTCTCTCT
2015572 CGATGCTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
17 3 0.05
18 37 0.56
19 25 0.38
20 1 0.02
ACGTcount: A:0.01, C:0.48, G:0.02, T:0.49
Consensus pattern (19 bp):
CTCTCTCTTCTCTCTATCC
Found at i:2015530 original size:24 final size:24
Alignment explanation
Indices: 2015503--2015553 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
2015493 CTCTCTTTCC
*
2015503 TTCTCCCTCGCTCTTTCCCTCTCT
1 TTCTCCCTCGCTCGTTCCCTCTCT
** *
2015527 TTCTCTTTCTCTCGTTCCCTCTCT
1 TTCTCCCTCGCTCGTTCCCTCTCT
2015551 TTC
1 TTC
2015554 CTCTCTCTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.00, C:0.45, G:0.04, T:0.51
Consensus pattern (24 bp):
TTCTCCCTCGCTCGTTCCCTCTCT
Found at i:2017181 original size:26 final size:26
Alignment explanation
Indices: 2017146--2017199 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
2017136 TCCTCTAAGC
2017146 TTTATCATCTAAAAATCAATAAGCTT
1 TTTATCATCTAAAAATCAATAAGCTT
* * *
2017172 TTTATGATCTAGAAGTCAATAAGCTT
1 TTTATCATCTAAAAATCAATAAGCTT
2017198 TT
1 TT
2017200 ATTCCTCAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (26 bp):
TTTATCATCTAAAAATCAATAAGCTT
Found at i:2020220 original size:3 final size:3
Alignment explanation
Indices: 2020212--2020252 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2020202 AATATAAGTG
2020212 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2020253 AATGCGAAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2040341 original size:2 final size:2
Alignment explanation
Indices: 2040334--2040361 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2040324 GTTCCTTCCA
2040334 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2040362 CCTCCCGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2042405 original size:2 final size:2
Alignment explanation
Indices: 2042394--2042447 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
2042384 TTAAAAATTT
2042394 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2042435 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
2042448 TAAAAAGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2050549 original size:27 final size:27
Alignment explanation
Indices: 2050499--2050554 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
2050489 TTTCCCATAT
2050499 ATACTTACCATATATTCATTATTCAAGGG
1 ATACTTACCATATATTCA-TATTC-AGGG
2050528 ATACTTACCATATAATT-A-ATTCAGGG
1 ATACTTACCATAT-ATTCATATTCAGGG
2050554 A
1 A
2050555 ATAACCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 5 0.19
27 4 0.15
29 14 0.54
30 3 0.12
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (27 bp):
ATACTTACCATATATTCATATTCAGGG
Found at i:2054298 original size:2 final size:2
Alignment explanation
Indices: 2054291--2054320 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2054281 ATTTACCATC
*
2054291 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2054321 ACTATTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2059127 original size:3 final size:3
Alignment explanation
Indices: 2059119--2059147 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2059109 TCTATTCTTT
2059119 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2059148 TTAGGACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2059707 original size:41 final size:40
Alignment explanation
Indices: 2059645--2059722 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 40
2059635 TCTTAATTTT
*
2059645 ATAATTTTGGTGATTCGTTTTACTTTTACCTTCTTCATCTC
1 ATAATTTTGGCGATTCGTTTTACTTTTACC-TCTTCATCTC
* *
2059686 ATAATTTTGGCGATTCTTTTTATTTTTACCTCTTCAT
1 ATAATTTTGGCGATTCGTTTTACTTTTACCTCTTCAT
2059723 TTCTTACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 7 0.21
41 27 0.79
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.55
Consensus pattern (40 bp):
ATAATTTTGGCGATTCGTTTTACTTTTACCTCTTCATCTC
Found at i:2061246 original size:63 final size:63
Alignment explanation
Indices: 2061083--2061275 Score: 183
Period size: 63 Copynumber: 3.1 Consensus size: 63
2061073 CCCAAACAAT
* ** * * * * *
2061083 TTTTCAATTTTTATAATTTATTTATATTTTTTAAAAATTTTATAATTTCGCCTCTCCAATAAT
1 TTTTAAATTTTTATAACATATTTTTATTTTTTAGAAATTTTATAATTTCACCTCTACAATAAA
* *** ** *
2061146 TTTTAAATTTTTATAACTTGCCTTTACATTTTAGAAATTTTATAATTTCACTTCTACAA-AAA
1 TTTTAAATTTTTATAACATATTTTTATTTTTTAGAAATTTTATAATTTCACCTCTACAATAAA
* * * *
2061208 TTTTAAATTTTTTCTAACATATTTTTATTTTTTTGAAATTTTATAATTTTATCC-CTACAATAAT
1 TTTTAAA-TTTTTATAACATATTTTTATTTTTTAGAAATTTTATAATTTCA-CCTCTACAATAAA
2061272 TTTT
1 TTTT
2061276 TGTTTAGTGA
Statistics
Matches: 103, Mismatches: 24, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
62 9 0.09
63 87 0.84
64 7 0.07
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (63 bp):
TTTTAAATTTTTATAACATATTTTTATTTTTTAGAAATTTTATAATTTCACCTCTACAATAAA
Found at i:2072393 original size:44 final size:44
Alignment explanation
Indices: 2072330--2072419 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
2072320 AGAAAGAATC
2072330 TTGGAACAGCAAACATCTTTCATCTTTATTGTTTTCTTATGTTA
1 TTGGAACAGCAAACATCTTTCATCTTTATTGTTTTCTTATGTTA
*
2072374 TTGGAACAGCAAATATCTTTCATCTTTATTGTTTTCTTATGTTA
1 TTGGAACAGCAAACATCTTTCATCTTTATTGTTTTCTTATGTTA
2072418 TT
1 TT
2072420 ATACAAGCAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.50
Consensus pattern (44 bp):
TTGGAACAGCAAACATCTTTCATCTTTATTGTTTTCTTATGTTA
Found at i:2088750 original size:11 final size:11
Alignment explanation
Indices: 2088736--2088765 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2088726 AAAACCACAG
2088736 AAAAACAAACC
1 AAAAACAAACC
2088747 AAAAACAAACC
1 AAAAACAAACC
*
2088758 AAGAACAA
1 AAAAACAA
2088766 CCCAGAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.73, C:0.23, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAACAAACC
Found at i:2103222 original size:19 final size:20
Alignment explanation
Indices: 2103189--2103227 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2103179 TGTACCAAAA
* *
2103189 ATAAGCATATCATCA-ACAT
1 ATAAGCAAATAATCACACAT
2103208 ATAAGCAAATAATCACACAT
1 ATAAGCAAATAATCACACAT
2103228 TCACTATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.21, G:0.05, T:0.23
Consensus pattern (20 bp):
ATAAGCAAATAATCACACAT
Found at i:2110919 original size:17 final size:17
Alignment explanation
Indices: 2110892--2110933 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2110882 AAATGTCTTT
*
2110892 TATACTTTAAAAATAT-
1 TATATTTTAAAAATATA
*
2110908 TATAATTTTAAATATATA
1 TAT-ATTTTAAAAATATA
2110926 TATATTTT
1 TATATTTT
2110934 CTTTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 3 0.14
17 16 0.73
18 3 0.14
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATTTTAAAAATATA
Found at i:2111369 original size:14 final size:15
Alignment explanation
Indices: 2111342--2111370 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2111332 AAGAAAAAGG
2111342 AAAAAAATAGAATTA
1 AAAAAAATAGAATTA
2111357 AAAAAAATA-AATTA
1 AAAAAAATAGAATTA
2111371 TTTGTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAAAAATAGAATTA
Found at i:2111474 original size:47 final size:45
Alignment explanation
Indices: 2111375--2111491 Score: 134
Period size: 47 Copynumber: 2.6 Consensus size: 45
2111365 AAATTATTTG
*
2111375 TAAATT-TTAAAATATTAAT-TTTTATATATAATTTTAATATTAT
1 TAAATTATTAAAATATTAATATTTTAAATATAATTTTAATATTAT
* *
2111418 TAAAATATTAAAATATTAATATTTTAAACTATTAATGTTTTAT-TTAT
1 TAAATTATTAAAATATTAATATTTTAAA-TA-TAAT-TTTAATATTAT
*
2111465 TAAATTATTAATATATTAA-ACTTTTAA
1 TAAATTATTAAAATATTAATA-TTTTAA
2111492 TGAGCATAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
43 5 0.08
44 13 0.21
45 6 0.10
46 3 0.05
47 31 0.49
48 5 0.08
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (45 bp):
TAAATTATTAAAATATTAATATTTTAAATATAATTTTAATATTAT
Found at i:2111483 original size:16 final size:15
Alignment explanation
Indices: 2111375--2111492 Score: 84
Period size: 16 Copynumber: 7.7 Consensus size: 15
2111365 AAATTATTTG
*
2111375 TAAATTTTAAAATAT
1 TAAATTTTAATATAT
*
2111390 T-AATTTTTATATA-
1 TAAATTTTAATATAT
2111403 T-AATTTTAATATTAT
1 TAAATTTTAATA-TAT
* *
2111418 TAAAATATTAAAATAT
1 T-AAATTTTAATATAT
2111434 TAATATTTTAA-ACTAT
1 TAA-ATTTTAATA-TAT
* *
2111450 T-AATGTTTTATTTAT
1 TAAAT-TTTAATATAT
2111465 TAAATTATTAATATAT
1 TAAATT-TTAATATAT
2111481 TAAACTTTTAAT
1 TAAA-TTTTAAT
2111493 GAGCATAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 21
0.73 0.09 0.19
Matches are distributed among these distances:
13 10 0.12
14 14 0.17
15 15 0.18
16 33 0.40
17 10 0.12
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.53
Consensus pattern (15 bp):
TAAATTTTAATATAT
Found at i:2111561 original size:19 final size:19
Alignment explanation
Indices: 2111532--2111601 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 19
2111522 TATTTTAATC
2111532 ATAATAATATTAAATTATAA
1 ATAA-AATATTAAATTATAA
2111552 ATAAAATATTATTAATTA-AA
1 ATAAAATATTA--AATTATAA
*
2111572 ATATTAATAATTAAATTAT-A
1 ATA-AAAT-ATTAAATTATAA
*
2111592 CTAAAATATT
1 ATAAAATATT
2111602 GATATTTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
18 3 0.07
19 10 0.24
20 17 0.40
21 8 0.19
22 4 0.10
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
ATAAAATATTAAATTATAA
Found at i:2111573 original size:15 final size:15
Alignment explanation
Indices: 2111548--2111651 Score: 65
Period size: 15 Copynumber: 7.1 Consensus size: 15
2111538 ATATTAAATT
*
2111548 ATAAATAAAATATTA
1 ATAATTAAAATATTA
*
2111563 TTAATTAAAATATTA
1 ATAATTAAAATATTA
2111578 ATAATT--AA-ATT-
1 ATAATTAAAATATTA
* *
2111589 AT-ACTAAAATATTG
1 ATAATTAAAATATTA
* *
2111603 ATATTTAAATTATTA
1 ATAATTAAAATATTA
* * *
2111618 ATTATTAATATTTTA
1 ATAATTAAAATATTA
2111633 ATTAATTATAAATTATTA
1 A-TAATTA-AAA-TATTA
2111651 A
1 A
2111652 CATTTAAAAA
Statistics
Matches: 65, Mismatches: 16, Indels: 13
0.69 0.17 0.14
Matches are distributed among these distances:
10 2 0.03
11 2 0.03
12 5 0.08
13 5 0.08
14 2 0.03
15 37 0.57
16 5 0.08
17 2 0.03
18 5 0.08
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (15 bp):
ATAATTAAAATATTA
Found at i:2111580 original size:40 final size:39
Alignment explanation
Indices: 2111536--2111634 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 39
2111526 TTAATCATAA
2111536 TAATATTAAATTATAAATAAAATATT-ATTAATTAAAATAT
1 TAATATTAAATTAT-AATAAAATATTGA-TAATTAAAATAT
* * *
2111576 TAATAATTAAATTATACTAAAATATTGATATTTAAATTAT
1 TAAT-ATTAAATTATAATAAAATATTGATAATTAAAATAT
*
2111616 TAATTATTAATATTTTAAT
1 TAA-TATTAA-ATTATAAT
2111635 TAATTATAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
40 32 0.64
41 18 0.36
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (39 bp):
TAATATTAAATTATAATAAAATATTGATAATTAAAATAT
Found at i:2111600 original size:25 final size:25
Alignment explanation
Indices: 2111568--2111615 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2111558 TATTATTAAT
2111568 TAAAATATTAATAATTAAATTATAC
1 TAAAATATTAATAATTAAATTATAC
* *
2111593 TAAAATATTGATATTTAAATTAT
1 TAAAATATTAATAATTAAATTAT
2111616 TAATTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TAAAATATTAATAATTAAATTATAC
Found at i:2123217 original size:2 final size:2
Alignment explanation
Indices: 2123210--2123270 Score: 72
Period size: 2 Copynumber: 31.5 Consensus size: 2
2123200 AAGTTCATTA
* * *
2123210 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AA AN GT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2123250 AT CT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
2123271 AAAGATTTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2123454 original size:9 final size:10
Alignment explanation
Indices: 2123436--2123464 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
2123426 TTGGAATCTC
2123436 AGAGAAAGAA
1 AGAGAAAGAA
2123446 AGA-AAAGAA
1 AGAGAAAGAA
2123455 AGAGAAAGAA
1 AGAGAAAGAA
2123465 GTAGAACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (10 bp):
AGAGAAAGAA
Found at i:2127506 original size:19 final size:18
Alignment explanation
Indices: 2127471--2127506 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2127461 TGTCCCCTTG
*
2127471 AGGATTTTTTTTTTTGTA
1 AGGATTTTTTTTATTGTA
2127489 AGGATTTTTCTTTATTGT
1 AGGATTTTT-TTTATTGT
2127507 TTTCCCCCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.64
Consensus pattern (18 bp):
AGGATTTTTTTTATTGTA
Found at i:2136128 original size:2 final size:2
Alignment explanation
Indices: 2136116--2136151 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2136106 TGGCAGAATA
*
2136116 TC TC CC TC TC TC TC TC TC TC T- TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2136152 TTAACTCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2136142 original size:13 final size:13
Alignment explanation
Indices: 2136124--2136149 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2136114 TATCTCCCTC
2136124 TCTCTCTCTCTCT
1 TCTCTCTCTCTCT
2136137 TCTCTCTCTCTCT
1 TCTCTCTCTCTCT
2136150 CTTTAACTCA
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:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (13 bp):
TCTCTCTCTCTCT
Found at i:2136142 original size:15 final size:15
Alignment explanation
Indices: 2136122--2136152 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2136112 AATATCTCCC
2136122 TCTCTCTCTCTCTCT
1 TCTCTCTCTCTCTCT
2136137 TCTCTCTCTCTCTCT
1 TCTCTCTCTCTCTCT
2136152 T
1 T
2136153 TAACTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTCTCTCTCTCTCT
Found at i:2138092 original size:82 final size:82
Alignment explanation
Indices: 2137988--2138148 Score: 214
Period size: 82 Copynumber: 2.0 Consensus size: 82
2137978 ACTCTGATAT
* * ** * * *
2137988 CACTTGTCACAAATTTATTTTTCGACCCAAAAGACATACTTATTAAGTGATCGAAGATCTTTGTT
1 CACTTGTCACAAACTCATTTTTCGACCCAAAAGACATACTTATTAAGTGATAAAAAATCCTTATT
2138053 TATAAACTTAAAACTTG
66 TATAAACTTAAAACTTG
* * * * *
2138070 CACTTGTCACAGACTCATTTTTCGATCTAAAAGATATACTTGTTAAGTGATAAAAAATCCTTATT
1 CACTTGTCACAAACTCATTTTTCGACCCAAAAGACATACTTATTAAGTGATAAAAAATCCTTATT
2138135 TATAAACTTAAAAC
66 TATAAACTTAAAAC
2138149 CCGCTTCATC
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (82 bp):
CACTTGTCACAAACTCATTTTTCGACCCAAAAGACATACTTATTAAGTGATAAAAAATCCTTATT
TATAAACTTAAAACTTG
Found at i:2141055 original size:12 final size:12
Alignment explanation
Indices: 2141038--2141074 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
2141028 CCAGGGTGCT
2141038 GGTGCTGACATG
1 GGTGCTGACATG
2141050 GGTGCTGACATG
1 GGTGCTGACATG
*
2141062 GGTGCTGGCATG
1 GGTGCTGACATG
2141074 G
1 G
2141075 ATGATGATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.14, C:0.16, G:0.46, T:0.24
Consensus pattern (12 bp):
GGTGCTGACATG
Found at i:2146073 original size:26 final size:24
Alignment explanation
Indices: 2146020--2146077 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 24
2146010 AACAAAATTT
*
2146020 TTAATTATTTTATTTATATTTAAA
1 TTAATTATTTAATTTATATTTAAA
*
2146044 --AATTATTTAATTTAGTTTTTTAAA
1 TTAATTATTTAATTTA--TATTTAAA
2146068 TTAATTATTT
1 TTAATTATTT
2146078 TTCGATTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 13 0.46
24 7 0.25
26 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTAATTATTTAATTTATATTTAAA
Found at i:2158873 original size:36 final size:37
Alignment explanation
Indices: 2158799--2158876 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
2158789 TTTTTTGAGA
2158799 TTTTTTTAAATATTTTAAATGAAATTTCTTTACTTTT
1 TTTTTTTAAATATTTTAAATGAAATTTCTTTACTTTT
2158836 TTTTTTTAAATATTTTAAATGAAATTTCTTTACTTTT
1 TTTTTTTAAATATTTTAAATGAAATTTCTTTACTTTT
2158873 TTTT
1 TTTT
2158877 ATGTTCATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (37 bp):
TTTTTTTAAATATTTTAAATGAAATTTCTTTACTTTT
Found at i:2158992 original size:47 final size:47
Alignment explanation
Indices: 2158941--2159079 Score: 235
Period size: 47 Copynumber: 3.0 Consensus size: 47
2158931 GTGAAATTTA
2158941 ATAATTGTCTCATATACAAATAAAAATTACTTATAATCAAATTTTTT
1 ATAATTGTCTCATATACAAATAAAAATTACTTATAATCAAATTTTTT
*
2158988 ATAATTGT-TGCGTATACAAATAAAAATTACTTATAATCAAATTTTTT
1 ATAATTGTCT-CATATACAAATAAAAATTACTTATAATCAAATTTTTT
* *
2159035 ATAATTGTCTCATATACAAATAAAAATTAATAATAATCAAATTTT
1 ATAATTGTCTCATATACAAATAAAAATTACTTATAATCAAATTTT
2159080 AAAAAATATA
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
46 1 0.01
47 84 0.98
48 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (47 bp):
ATAATTGTCTCATATACAAATAAAAATTACTTATAATCAAATTTTTT
Found at i:2160180 original size:79 final size:79
Alignment explanation
Indices: 2160079--2160231 Score: 247
Period size: 79 Copynumber: 1.9 Consensus size: 79
2160069 TAAAAATTAC
* *
2160079 TTATAAGTTTGTGAGGAAAAAAAACTAAAGAAATGATGAGGAAAA-AAGAATGAAAGTGGGAAAT
1 TTATAAGGTTGTGAGGAAAAAAAACTAAAGAAATGATGA-GAAAACAAGAATGAAAGAGGGAAAT
2160143 AAGAACATTATTTTG
65 AAGAACATTATTTTG
*
2160158 TTATAAGGTTGTGA-GAGAAAAAAATTAAAGAAATGATGAGAAAACAAGAATGAAAGAGGGAAAT
1 TTATAAGGTTGTGAGGA-AAAAAAACTAAAGAAATGATGAGAAAACAAGAATGAAAGAGGGAAAT
2160222 AAGAACATTA
65 AAGAACATTA
2160232 AAAAATATAA
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
78 7 0.10
79 62 0.90
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.22
Consensus pattern (79 bp):
TTATAAGGTTGTGAGGAAAAAAAACTAAAGAAATGATGAGAAAACAAGAATGAAAGAGGGAAATA
AGAACATTATTTTG
Found at i:2161610 original size:53 final size:55
Alignment explanation
Indices: 2161531--2161640 Score: 170
Period size: 54 Copynumber: 2.0 Consensus size: 55
2161521 TTTTACTGAA
* *
2161531 TTTTGTTTGCTTTTTTTTTATGCTCATTCTAAGATGAGA-TTTTATAATCAAATT
1 TTTTCTTTGCTTTTCTTTTATGCTCATTCTAAGATGAGATTTTTATAATCAAATT
* *
2161585 TTTTCTTTGC-TTTCTTTTATTCTCATTTTAAGATGAGATTTTTATAATCAAATT
1 TTTTCTTTGCTTTTCTTTTATGCTCATTCTAAGATGAGATTTTTATAATCAAATT
2161639 TT
1 TT
2161641 AAAAAATACA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
53 25 0.49
54 26 0.51
ACGTcount: A:0.24, C:0.10, G:0.09, T:0.57
Consensus pattern (55 bp):
TTTTCTTTGCTTTTCTTTTATGCTCATTCTAAGATGAGATTTTTATAATCAAATT
Found at i:2161877 original size:79 final size:80
Alignment explanation
Indices: 2161746--2161907 Score: 272
Period size: 79 Copynumber: 2.0 Consensus size: 80
2161736 CCTTTTCCCA
* * * *
2161746 CTTCACCTGCTTACATAGTAACATGAGCCTTTATTAATCACAACATAAGAGGC-TTGTTTAGTTC
1 CTTCACCTGCTAACATACTAACATGAGCATCTATTAATCACAACATAAGAGGCTTTGTTTAGTTC
2161810 TGTTCTTTGCATGTT
66 TGTTCTTTGCATGTT
2161825 CTTCACCTGCTAACATACTAACATGAGCATCTATTAATCACAACATAAGAGGCTTTTGTTTAGTT
1 CTTCACCTGCTAACATACTAACATGAGCATCTATTAATCACAACATAAGAGGC-TTTGTTTAGTT
2161890 CTGTTCTTTGCATGTT
65 CTGTTCTTTGCATGTT
2161906 CT
1 CT
2161908 AATGGCTGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
79 49 0.64
81 28 0.36
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (80 bp):
CTTCACCTGCTAACATACTAACATGAGCATCTATTAATCACAACATAAGAGGCTTTGTTTAGTTC
TGTTCTTTGCATGTT
Found at i:2169048 original size:26 final size:24
Alignment explanation
Indices: 2168994--2169058 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 24
2168984 ATAAGAACTT
*
2168994 ATTTGATCTAAAATTAAAATATAAAA
1 ATTTGAT-T-AAATTAAAAAATAAAA
*
2169020 ATTTGATTAAATGTAAAAAACTAATA
1 ATTTGATTAAAT-TAAAAAA-TAAAA
2169046 ATTT-ATTTAAATT
1 ATTTGA-TTAAATT
2169059 TTTATGAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 4 0.12
25 9 0.26
26 21 0.62
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (24 bp):
ATTTGATTAAATTAAAAAATAAAA
Found at i:2189945 original size:43 final size:43
Alignment explanation
Indices: 2189890--2189974 Score: 152
Period size: 43 Copynumber: 2.0 Consensus size: 43
2189880 TCCTGTTATA
2189890 AAGTTAGATTAATCCCACAAGACTTGAAGTAGAATAGATAAAG
1 AAGTTAGATTAATCCCACAAGACTTGAAGTAGAATAGATAAAG
* *
2189933 AAGTTAGATTAATCCCATAAGACTTGAAGTGGAATAGATAAA
1 AAGTTAGATTAATCCCACAAGACTTGAAGTAGAATAGATAAA
2189975 AGAAAAGAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.46, C:0.11, G:0.19, T:0.25
Consensus pattern (43 bp):
AAGTTAGATTAATCCCACAAGACTTGAAGTAGAATAGATAAAG
Found at i:2190435 original size:21 final size:21
Alignment explanation
Indices: 2190410--2190453 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2190400 AAAAAGGTTT
2190410 AAGTT-TAATTTTAAATTATAA
1 AAGTTGTAATTTTAAATT-TAA
*
2190431 AAGTTGTTATTTTAAATTTAA
1 AAGTTGTAATTTTAAATTTAA
2190452 AA
1 AA
2190454 ATTAATTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (21 bp):
AAGTTGTAATTTTAAATTTAA
Found at i:2194587 original size:77 final size:77
Alignment explanation
Indices: 2194458--2194608 Score: 205
Period size: 77 Copynumber: 2.0 Consensus size: 77
2194448 AATAGTTACC
** * ** * *
2194458 TTATAAAAAAACAACCATTCATTCTATAAGATATAACTTTTGAGTTATAATATGAAAAGATAACT
1 TTATAAAAAAACAACCACCCATTCTATAAGACATAACTTTTGAACTACAATATGAAAAAATAACT
2194523 TTTCATATCACG
66 TTTCATATCACG
* *
2194535 TTATAAAAAGACAACCACCCATTCTATAAGACAT-ACTTTTTGAACTACAATATTAAAAAATAAC
1 TTATAAAAAAACAACCACCCATTCTATAAGACATAAC-TTTTGAACTACAATATGAAAAAATAAC
2194599 TTTTCATATC
65 TTTTCATATC
2194609 CAAACTTTTG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
76 2 0.03
77 62 0.97
ACGTcount: A:0.44, C:0.16, G:0.06, T:0.34
Consensus pattern (77 bp):
TTATAAAAAAACAACCACCCATTCTATAAGACATAACTTTTGAACTACAATATGAAAAAATAACT
TTTCATATCACG
Found at i:2195480 original size:2 final size:2
Alignment explanation
Indices: 2195473--2195529 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
2195463 AATGTTATGA
* *
2195473 AT AT AT AT AT AT AT AT AT AT AT A- AT -T GT AT AA AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2195512 AT AT AT A- AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2195530 AGTATTACTA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
1 4 0.09
2 42 0.91
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2196458 original size:2 final size:2
Alignment explanation
Indices: 2196397--2196440 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2196387 TGTTAGTCCT
2196397 TA TA TA TA TA TA TA -A TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2196437 TA TA
1 TA TA
2196441 GATTAAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2199750 original size:21 final size:22
Alignment explanation
Indices: 2199721--2199764 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2199711 TCTTATGGTT
*
2199721 TTTGTTGTA-GGGTGTTGTTTC
1 TTTGCTGTATGGGTGTTGTTTC
2199742 TTTGCTGTATTGGGTGTTGTTTC
1 TTTGCTGTA-TGGGTGTTGTTTC
2199765 AGTTCTCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.05, C:0.07, G:0.32, T:0.57
Consensus pattern (22 bp):
TTTGCTGTATGGGTGTTGTTTC
Found at i:2200421 original size:14 final size:14
Alignment explanation
Indices: 2200402--2200435 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
2200392 ATTTTCTAGT
2200402 CAAATACTTTAATA
1 CAAATACTTTAATA
2200416 CAAATACTTTAATA
1 CAAATACTTTAATA
2200430 CAAATA
1 CAAATA
2200436 TCTAGTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (14 bp):
CAAATACTTTAATA
Found at i:2210114 original size:22 final size:22
Alignment explanation
Indices: 2210087--2210128 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
2210077 TAGATAAAAT
2210087 AAAATACCTCAAAAGCAATTGA
1 AAAATACCTCAAAAGCAATTGA
2210109 AAAATACCTCAAAAGCAATT
1 AAAATACCTCAAAAGCAATT
2210129 CAAGTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.19, G:0.07, T:0.19
Consensus pattern (22 bp):
AAAATACCTCAAAAGCAATTGA
Found at i:2212660 original size:1 final size:1
Alignment explanation
Indices: 2212654--2212678 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2212644 AATGATTTCT
2212654 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
2212679 GGTTTGGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2214757 original size:9 final size:9
Alignment explanation
Indices: 2214722--2214764 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
2214712 GTTCCTTTTA
2214722 TTACAATCT
1 TTACAATCT
*
2214731 TTACTAATCA
1 TTAC-AATCT
*
2214741 GT-CAATCT
1 TTACAATCT
2214749 TTACAATCT
1 TTACAATCT
2214758 TTACAAT
1 TTACAAT
2214765 AATTATGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 5 0.18
9 18 0.64
10 5 0.18
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (9 bp):
TTACAATCT
Found at i:2220692 original size:14 final size:15
Alignment explanation
Indices: 2220675--2220716 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2220665 ATAATATTAA
2220675 ATTA-TAAATAAAAT
1 ATTAGTAAATAAAAT
* *
2220689 ATTATTAATTAAAAT
1 ATTAGTAAATAAAAT
*
2220704 ATTAGTAATTAAA
1 ATTAGTAAATAAA
2220717 TTATATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTAGTAAATAAAAT
Found at i:2220694 original size:22 final size:20
Alignment explanation
Indices: 2220664--2220704 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
2220654 NNNNNNNNNN
2220664 AATAATATTAAATTATAAATAA
1 AATAATATT-AATTA-AAATAA
*
2220686 AATATTATTAATTAAAATA
1 AATAATATTAATTAAAATA
2220705 TTAGTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATAATATTAATTAAAATAA
Found at i:2220703 original size:15 final size:15
Alignment explanation
Indices: 2220683--2220725 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2220673 AAATTATAAA
2220683 TAAAATATTATTAAT
1 TAAAATATTATTAAT
*
2220698 TAAAATATTAGTAAT
1 TAAAATATTATTAAT
*
2220713 TAAATTA-TATTAA
1 TAAAATATTATTAA
2220726 AATATTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAAAATATTATTAAT
Found at i:2220729 original size:25 final size:25
Alignment explanation
Indices: 2220692--2220745 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
2220682 ATAAAATATT
2220692 ATTA-ATTAAAATA-TTAGTAATTAA
1 ATTATATTAAAATATTTA-TAATTAA
*
2220716 ATTATATTAAAATATTTATATTTAA
1 ATTATATTAAAATATTTATAATTAA
2220741 ATTAT
1 ATTAT
2220746 TAATATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.15
25 20 0.74
26 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
ATTATATTAAAATATTTATAATTAA
Found at i:2220746 original size:15 final size:15
Alignment explanation
Indices: 2220717--2220765 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2220707 AGTAATTAAA
*
2220717 TTATA-TTAAAATAT
1 TTATATTTAAATTAT
2220731 TTATATTTAAATTAT
1 TTATATTTAAATTAT
* * *
2220746 TAATATTTTAATTAA
1 TTATATTTAAATTAT
2220761 TTATA
1 TTATA
2220766 AATTATTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATATTTAAATTAT
Found at i:2220763 original size:16 final size:15
Alignment explanation
Indices: 2220722--2220779 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
2220712 TTAAATTATA
* *
2220722 TTAAAATATTTATAT
1 TTAAATTATTAATAT
2220737 TTAAATTATTAATAT
1 TTAAATTATTAATAT
*
2220752 TT---TAATTAAT-T
1 TTAAATTATTAATAT
*
2220763 ATAAATTATTAATAT
1 TTAAATTATTAATAT
2220778 TT
1 TT
2220780 TAAAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
11 2 0.06
12 7 0.21
14 7 0.21
15 17 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAAATTATTAATAT
Found at i:2231550 original size:24 final size:24
Alignment explanation
Indices: 2231523--2231571 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2231513 AATTTTATAA
*
2231523 AATAGATTAACAGTTATAAAATTC
1 AATACATTAACAGTTATAAAATTC
2231547 AATACATTAACAGTTATAAAATTC
1 AATACATTAACAGTTATAAAATTC
2231571 A
1 A
2231572 TTTTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (24 bp):
AATACATTAACAGTTATAAAATTC
Found at i:2233816 original size:28 final size:29
Alignment explanation
Indices: 2233768--2233833 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
2233758 ATGCATTTTG
**
2233768 GTAATTTTTCAATTT-TTGGGGCAAAAAT
1 GTAATTTTTCAATTTACGGGGGCAAAAAT
* * *
2233796 GTAATTTTTCACTTTACGGGGGTAAAAGT
1 GTAATTTTTCAATTTACGGGGGCAAAAAT
2233825 GTAATTTTT
1 GTAATTTTT
2233834 AAAAATTTGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.44
Consensus pattern (29 bp):
GTAATTTTTCAATTTACGGGGGCAAAAAT
Found at i:2243200 original size:71 final size:71
Alignment explanation
Indices: 2243133--2243300 Score: 327
Period size: 71 Copynumber: 2.4 Consensus size: 71
2243123 CATAGAAGTG
2243133 CCAATCAAATTCAACTCAGTATTCTTCATTCTTTTTTCCTCGCTTCCTTCTCTTCGTTGCTTCTA
1 CCAATCAAATTCAACTCAGTATTCTTCATTCTTTTTTCCTCGCTTCCTTCTCTTCGTTGCTTCTA
2243198 GAAATA
66 GAAATA
*
2243204 CCAATCAAATTCAACTCAGTATTCTCCATTCTTTTTTCCTCGCTTCCTTCTCTTCGTTGCTTCTA
1 CCAATCAAATTCAACTCAGTATTCTTCATTCTTTTTTCCTCGCTTCCTTCTCTTCGTTGCTTCTA
2243269 GAAATA
66 GAAATA
2243275 CCAATCAAATTCAACTCAGTATTCTT
1 CCAATCAAATTCAACTCAGTATTCTT
2243301 TTTCTTTAAA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 95 1.00
ACGTcount: A:0.23, C:0.29, G:0.07, T:0.42
Consensus pattern (71 bp):
CCAATCAAATTCAACTCAGTATTCTTCATTCTTTTTTCCTCGCTTCCTTCTCTTCGTTGCTTCTA
GAAATA
Found at i:2255152 original size:269 final size:269
Alignment explanation
Indices: 2254672--2255208 Score: 860
Period size: 269 Copynumber: 2.0 Consensus size: 269
2254662 TCTCTCTAGA
* * * * *
2254672 ATTTGCTTTTGATGAAGAACTTTGGCAAGGGGATGATGAAACAGAGCAACTACTTGAATAGCCAC
1 ATTTGCTTTTAACGAAGAACTTTGGCAAAGGGATGACGAAACAGAGCAACTACTTAAATAGCCAC
* * *
2254737 TATGTTCCTTGAGTTAATTTGCACTTGATCCTTTAGAGGAAGCAAGTTGTGTGGAAGTAACTTCT
66 TATGTTCCTTGAGTTAATTTGCACTTGATCCTTTAGAAGAAGCAAGTTGTATGGAAGAAACTTCT
* **
2254802 TCAAAACTTAGGGAAGAAGCATCATATAAAGGATTTTGGTTGAGGACTGGGAAAGTTTGCTAATA
131 TCAAAACTTAGGGAAGAAGCATCATATAAAGGATTTTGGTTGAAGACTAAGAAAGTTTGCTAATA
* *
2254867 CAATTTAGTTAGAGCTTATGTCTTTCTCCGAGTACCATATGGATGTGTTGGAACATCTGTGCTTA
196 CAATTTAGTAAGAGCTTATGTCTTTCTCCGAGTACCATATGGATATGTTGGAACATCTGTGCTTA
2254932 ATGATGAGG
261 ATGATGAGG
* * * *
2254941 ATTTGCTTTTAACGAAGAACTTTTGCAAAGGGATGACGAAATAGAGCTACTGCTTAAATAGCCA-
1 ATTTGCTTTTAACGAAGAACTTTGGCAAAGGGATGACGAAACAGAGCAACTACTTAAATAGCCAC
* *
2255005 TCATGTTCCTTGAGTTGATTTGCACTTGATCCTTTGGAAGAAGCAAGTTGTATGGAAGAAACTTC
66 T-ATGTTCCTTGAGTTAATTTGCACTTGATCCTTTAGAAGAAGCAAGTTGTATGGAAGAAACTTC
* *
2255070 TTCAGAACTTAGGGAAGAAGCATCATATAAAGGATTTTGGTTGAAGACTAAGAAAGTTTGCTCAT
130 TTCAAAACTTAGGGAAGAAGCATCATATAAAGGATTTTGGTTGAAGACTAAGAAAGTTTGCTAAT
*
2255135 ACAATTTAGTAAGAGCTTCTGTCTTTCTCCGAGTACCATATGGATATGTTGGAACATCTGTGCTT
195 ACAATTTAGTAAGAGCTTATGTCTTTCTCCGAGTACCATATGGATATGTTGGAACATCTGTGCTT
2255200 AATGATGAG
260 AATGATGAG
2255209 ATTGGAAAAA
Statistics
Matches: 245, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
268 1 0.00
269 244 1.00
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (269 bp):
ATTTGCTTTTAACGAAGAACTTTGGCAAAGGGATGACGAAACAGAGCAACTACTTAAATAGCCAC
TATGTTCCTTGAGTTAATTTGCACTTGATCCTTTAGAAGAAGCAAGTTGTATGGAAGAAACTTCT
TCAAAACTTAGGGAAGAAGCATCATATAAAGGATTTTGGTTGAAGACTAAGAAAGTTTGCTAATA
CAATTTAGTAAGAGCTTATGTCTTTCTCCGAGTACCATATGGATATGTTGGAACATCTGTGCTTA
ATGATGAGG
Found at i:2255565 original size:52 final size:54
Alignment explanation
Indices: 2255509--2255643 Score: 170
Period size: 54 Copynumber: 2.5 Consensus size: 54
2255499 TCGGACTTTG
** * *
2255509 TCTTGATCACAAACT-TCACTT-A-ATCTTTGCTTCAA-AGGTCTTGATGACTTAA
1 TCTTGATCACAAACTAT-ACTTGATATCTTCCCTTCAAGA-GTCTTCACGACTTAA
*
2255561 TCTTGATCACAAACTATATTTGATATCTTCCCTTCAAGAGTCTTCACGACTTAA
1 TCTTGATCACAAACTATACTTGATATCTTCCCTTCAAGAGTCTTCACGACTTAA
*
2255615 TCTTGATCACGAACTATACTTGATATCTT
1 TCTTGATCACAAACTATACTTGATATCTT
2255644 GATCAGGAAC
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
52 18 0.25
53 2 0.03
54 51 0.71
55 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (54 bp):
TCTTGATCACAAACTATACTTGATATCTTCCCTTCAAGAGTCTTCACGACTTAA
Found at i:2255671 original size:23 final size:23
Alignment explanation
Indices: 2255641--2255725 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
2255631 TACTTGATAT
*
2255641 CTTGATCAGGAACTTCGTTGCCA
1 CTTGATCATGAACTTCGTTGCCA
* * *
2255664 CTTGATCACGAACTTCGTTGTCG
1 CTTGATCATGAACTTCGTTGCCA
* * ** *
2255687 GTTGATCATGTACTTCACTGCTA
1 CTTGATCATGAACTTCGTTGCCA
2255710 CTTGATCATGAACTTC
1 CTTGATCATGAACTTC
2255726 ACTTGATATC
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (23 bp):
CTTGATCATGAACTTCGTTGCCA
Found at i:2261036 original size:431 final size:432
Alignment explanation
Indices: 2260195--2261038 Score: 1633
Period size: 431 Copynumber: 2.0 Consensus size: 432
2260185 TTTTTCTTCT
2260195 AAAACACTTATATATATAATATTAATATAAATAATATAATTTTAAAACATTAAGTTTAAAAACAA
1 AAAACACTTATATATATAATATTAATATAAATAATATAATTTTAAAACATTAAGTTTAAAAACAA
2260260 ATAGGAATTAAAAAAATCCGAATAAAATTTTAAAAGAAAAATAAAGAATATCTGACGTGTCACCG
66 ATAGGAATTAAAAAAATCCGAATAAAATTTTAAAAGAAAAATAAAGAATATCTGACGTGTCACCG
2260325 CAAGGCAAATAAAAAAAGGAAAAAGAAATCCGACGTGGCGAAAATAGGATTCCAATCCATCGTCC
131 CAAGGCAAATAAAAAAAGGAAAAAGAAATCCGACGTGGCGAAAATAGGATTCCAATCCATCGTCC
2260390 TCGACTCCACTTTCTTCCCTCGCTTCCTTCTCTTCACTCTTTCTTGATCGACAGAAAAACCAATC
196 TCGACTCCACTTTCTTCCCTCGCTTCCTTCTCTTCACTCTTTCTTGATCGACAGAAAAACCAATC
2260455 AAATTCAGCTCATAAGTATTCTTTTTCTTTAGGTGTCCTTCTTCAATGGCTTCCTCCAAGCGACT
261 AAATTCAGCTCATAAGTATTCTTTTTCTTTAGGTGTCCTTCTTCAATGGCTTCCTCCAAGCGACT
2260520 CTCCTTCTCCAAAAGCAACTCCAAGGTTTCTATTTCTTGAAAGGCGTCGGTTTCGGTTTATTGAT
326 CTCCTTCTCCAAAAGCAACTCCAAGGTTTCTATTTCTTGAAAGGCGTCGGTTTCGGTTTATTGAT
2260585 CATTTCTTCTTCTTCTTCTTTTCTTCCTTAAGGTGTTACTTA
391 CATTTCTTCTTCTTCTTCTTTTCTTCCTTAAGGTGTTACTTA
2260627 NAAAACAACTTATATATATATATATT-ATAT-AATAAT-T-ATTTTAAAACATTAAGTTTAAAAA
1 -AAAAC-ACTTATATATATA-ATATTAATATAAATAATATAATTTTAAAACATTAAGTTTAAAAA
2260688 CAAATAGGAATTAAAAAAATCCGAATAAAATTTTAAAAGAAAAATAAAGAATATCTGACGTGTCA
63 CAAATAGGAATTAAAAAAATCCGAATAAAATTTTAAAAGAAAAATAAAGAATATCTGACGTGTCA
2260753 CCGCAAGGCAAATAAAAAAAGGAAAAAGAAATCCGACGTGGCGAAAATAGGATTCCAATCCATCG
128 CCGCAAGGCAAATAAAAAAAGGAAAAAGAAATCCGACGTGGCGAAAATAGGATTCCAATCCATCG
2260818 TCCTCGACTCCACTTTCTTCCCTCGCTTCCTTCTCTTCACTCTTTCTTGATCGACAGAAAAACCA
193 TCCTCGACTCCACTTTCTTCCCTCGCTTCCTTCTCTTCACTCTTTCTTGATCGACAGAAAAACCA
2260883 ATCAAATTCAGCTCATAAGTATTCTTTTTCTTTAGGTGTCCTTCTTCAATGGCTTCCTCCAAGCG
258 ATCAAATTCAGCTCATAAGTATTCTTTTTCTTTAGGTGTCCTTCTTCAATGGCTTCCTCCAAGCG
2260948 ACTCTCCTTCTCCAAAAGCAACTCCAAGGTTTCTATTTCTTGAAAGGCGTCGGTTTCGGTTTATT
323 ACTCTCCTTCTCCAAAAGCAACTCCAAGGTTTCTATTTCTTGAAAGGCGTCGGTTTCGGTTTATT
2261013 GATCATTTCTTCTTCTTCTTCTTTTC
388 GATCATTTCTTCTTCTTCTTCTTTTC
2261039 GAATTTTAAG
Statistics
Matches: 409, Mismatches: 0, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
431 375 0.92
432 1 0.00
433 11 0.03
434 17 0.04
435 5 0.01
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (432 bp):
AAAACACTTATATATATAATATTAATATAAATAATATAATTTTAAAACATTAAGTTTAAAAACAA
ATAGGAATTAAAAAAATCCGAATAAAATTTTAAAAGAAAAATAAAGAATATCTGACGTGTCACCG
CAAGGCAAATAAAAAAAGGAAAAAGAAATCCGACGTGGCGAAAATAGGATTCCAATCCATCGTCC
TCGACTCCACTTTCTTCCCTCGCTTCCTTCTCTTCACTCTTTCTTGATCGACAGAAAAACCAATC
AAATTCAGCTCATAAGTATTCTTTTTCTTTAGGTGTCCTTCTTCAATGGCTTCCTCCAAGCGACT
CTCCTTCTCCAAAAGCAACTCCAAGGTTTCTATTTCTTGAAAGGCGTCGGTTTCGGTTTATTGAT
CATTTCTTCTTCTTCTTCTTTTCTTCCTTAAGGTGTTACTTA
Found at i:2262504 original size:37 final size:37
Alignment explanation
Indices: 2262454--2262527 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2262444 ACTTAGGCCT
2262454 CAGGTGATAAGACTATATATGTTTACAATGAAGTGCA
1 CAGGTGATAAGACTATATATGTTTACAATGAAGTGCA
2262491 CAGGTGATAAGACTATATATGTTTACAATGAAGTGCA
1 CAGGTGATAAGACTATATATGTTTACAATGAAGTGCA
2262528 TTTTACTTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.30
Consensus pattern (37 bp):
CAGGTGATAAGACTATATATGTTTACAATGAAGTGCA
Found at i:2265867 original size:16 final size:14
Alignment explanation
Indices: 2265846--2265884 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 14
2265836 CACGACCAGG
2265846 TTTTTCTTTCTTTTCC
1 TTTTTCTTT-TTTT-C
2265862 TTTTTCTTTTTTTC
1 TTTTTCTTTTTTTC
2265876 TTTTT-TTTT
1 TTTTTCTTTT
2265885 GTCAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 4 0.17
16 9 0.39
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTCTTTTTTTC
Found at i:2270125 original size:2 final size:2
Alignment explanation
Indices: 2270118--2270144 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2270108 ATTAGAGTCG
2270118 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2270145 GTCAATTACT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2270872 original size:129 final size:129
Alignment explanation
Indices: 2270721--2270965 Score: 352
Period size: 130 Copynumber: 1.9 Consensus size: 129
2270711 ATTTTATTTA
2270721 TAATTTAAATGTTATTATGATTATTTATTTTTACAT-TATTTTA-TTTTAAACATTAATAATGTA
1 TAATTTAAATGTTATTATGATTATTTATTTTTA-ATCTATTTTATTTTTAAACATTAATAATGTA
*
2270784 TAATTTATTAAAAATATTAAAAAATGAT-AGTTTAAATATTAATATTTTATTTGTACTTTAATCA
65 TAATTTATTAAAAACATTAAAAAATGATCA-TTTAAATATTAATATTTTATTTGTACTTTAATCA
2270848 T
129 T
* * * *
2270849 TAATATTAAATGTTATTATGATTATTTATTTTTATTCTATTTTATTTTTTAATATTAATAATTTA
1 TAAT-TTAAATGTTATTATGATTATTTATTTTTAATCTATTTTATTTTTAAACATTAATAATGTA
* * * * *
2270914 TATTTTATTAATAACATTAATAATTTATCATTTAAATATTAATATTTTATTT
65 TAATTTATTAAAAACATTAAAAAATGATCATTTAAATATTAATATTTTATTT
2270966 ATAAATTAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
128 5 0.05
129 36 0.35
130 61 0.59
131 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (129 bp):
TAATTTAAATGTTATTATGATTATTTATTTTTAATCTATTTTATTTTTAAACATTAATAATGTAT
AATTTATTAAAAACATTAAAAAATGATCATTTAAATATTAATATTTTATTTGTACTTTAATCAT
Found at i:2270974 original size:26 final size:26
Alignment explanation
Indices: 2270936--2270988 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2270926 AACATTAATA
* *
2270936 ATTTATCATTTAAATATTAATATTTT
1 ATTTATAAATTAAATATTAATATTTT
* *
2270962 ATTTATAAATTAATTATTAATGTTTT
1 ATTTATAAATTAAATATTAATATTTT
2270988 A
1 A
2270989 AATATTAGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
ATTTATAAATTAAATATTAATATTTT
Found at i:2270989 original size:41 final size:41
Alignment explanation
Indices: 2270913--2271015 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
2270903 TTAATAATTT
* *
2270913 ATATTTTATTAATAACATTAATAATTTATCATTTAAATATTA
1 ATATTTTATTTATAA-ATTAATAATTAATCATTTAAATATTA
* **
2270955 ATATTTTATTTATAAATTAATTATTAATGTTTTAAATATTA
1 ATATTTTATTTATAAATTAATAATTAATCATTTAAATATTA
* *
2270996 GTATTTTATTTATAATTTAA
1 ATATTTTATTTATAAATTAA
2271016 ATTTGATTAT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 40 0.74
42 14 0.26
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (41 bp):
ATATTTTATTTATAAATTAATAATTAATCATTTAAATATTA
Found at i:2271150 original size:158 final size:158
Alignment explanation
Indices: 2270849--2271191 Score: 478
Period size: 158 Copynumber: 2.2 Consensus size: 158
2270839 CTTTAATCAT
* *
2270849 TAATATTAAATGTTATTATGATTATTTATTTTTATTCTATTTTATTTTTTAATATTAATAATTTA
1 TAAT-TTAAATGTTATTATGATTATTTATTCTTATTCTATTTTATTTTTAAATATTAATAATTTA
* * * *
2270914 TATTTTATTAATAACATTAATAATTTATCATTTAAATATTAATATTTTATTTATAAATTAATTAT
65 TATTTTATTAATAACATTAATAATTGATCATTTAAACATTAATATTTTATTTATAAATTAATCAC
* * * *
2270979 TAATGTTTTAAATATTAGTATTTTATTTA
130 TAATATTTAAAATACTACTATTTTATTTA
2271008 TAATTTAAAT-TTGATTATGATTATTTATTCTTATT-TAATTTTATCTTTTAAATATTAATAATT
1 TAATTTAAATGTT-ATTATGATTATTTATTCTTATTCT-ATTTTAT-TTTTAAATATTAATAATT
* * * * *
2271071 TATATTTT-TTTA-AATATTAATAATTGATCATTTAAGCATTAATGTTTTATTTATAATTTAATC
63 TATATTTTATTAATAACATTAATAATTGATCATTTAAACATTAATATTTTATTTATAAATTAATC
2271134 ACTAATATTATAAAATACTACTATTTTATTTA
128 ACTAATATT-TAAAATACTACTATTTTATTTA
2271166 TAATTTAAATGTTATTATGATTATTT
1 TAATTTAAATGTTATTATGATTATTT
2271192 TTTATTTTAT
Statistics
Matches: 164, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
157 54 0.33
158 79 0.48
159 31 0.19
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (158 bp):
TAATTTAAATGTTATTATGATTATTTATTCTTATTCTATTTTATTTTTAAATATTAATAATTTAT
ATTTTATTAATAACATTAATAATTGATCATTTAAACATTAATATTTTATTTATAAATTAATCACT
AATATTTAAAATACTACTATTTTATTTA
Found at i:2271325 original size:16 final size:16
Alignment explanation
Indices: 2271304--2271334 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2271294 TATTTTTTAT
*
2271304 TTATAATTTAAATATA
1 TTATAATTAAAATATA
2271320 TTATAATTAAAATAT
1 TTATAATTAAAATAT
2271335 GAAAATATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATAATTAAAATATA
Found at i:2297280 original size:22 final size:22
Alignment explanation
Indices: 2297253--2297298 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2297243 TGATTAAGAA
*
2297253 GAAAAAGCAACACAAGAAATAAG
1 GAAAAGGCAACACAA-AAATAAG
* *
2297276 GAAAAGGGAGCACAAAAATAAG
1 GAAAAGGCAACACAAAAATAAG
2297298 G
1 G
2297299 TTTACATCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.61, C:0.11, G:0.24, T:0.04
Consensus pattern (22 bp):
GAAAAGGCAACACAAAAATAAG
Found at i:2307039 original size:28 final size:30
Alignment explanation
Indices: 2307008--2307072 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
2306998 TATTTAAAAA
2307008 ATTTTAAATAAATTA-TTATTTT-TATTAT
1 ATTTTAAATAAATTATTTATTTTATATTAT
** *
2307036 ATTTT--ATTTATTATTTATTTTATATTTT
1 ATTTTAAATAAATTATTTATTTTATATTAT
2307064 ATTTTAAAT
1 ATTTTAAAT
2307073 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 6 0.20
27 7 0.23
28 15 0.50
30 2 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (30 bp):
ATTTTAAATAAATTATTTATTTTATATTAT
Found at i:2307044 original size:16 final size:15
Alignment explanation
Indices: 2307023--2307067 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 15
2307013 AAATAAATTA
2307023 TTATTTTTATTATATT
1 TTATTTTTATT-TATT
2307039 TTATTTATTATTTATT
1 TTATTT-TTATTTATT
2307055 TTATATTTTATTT
1 TTAT-TTTTATTT
2307068 TAAATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTTATTTATT
Found at i:2307046 original size:23 final size:23
Alignment explanation
Indices: 2307020--2307067 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
2307010 TTTAAATAAA
2307020 TTATTATTT-TTATTATATTTTAT
1 TTATTATTTATT-TTATATTTTAT
2307043 TTATTATTTATTTTATATTTTAT
1 TTATTATTTATTTTATATTTTAT
2307066 TT
1 TT
2307068 TAAATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (23 bp):
TTATTATTTATTTTATATTTTAT
Found at i:2307050 original size:12 final size:12
Alignment explanation
Indices: 2307020--2307067 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
2307010 TTTAAATAAA
2307020 TTATTATTTT-T
1 TTATTATTTTAT
2307031 ATTA-TATTTTAT
1 -TTATTATTTTAT
2307043 TTATTA-TTTAT
1 TTATTATTTTAT
2307054 TT-TATATTTTAT
1 TTAT-TATTTTAT
2307066 TT
1 TT
2307068 TAAATTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 1 0.03
11 18 0.56
12 13 0.41
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTATTATTTTAT
Found at i:2307068 original size:12 final size:12
Alignment explanation
Indices: 2307032--2307074 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
2307022 ATTATTTTTA
2307032 TTATATTTTA-T
1 TTATATTTTATT
2307043 TTAT-TATTTATT
1 TTATAT-TTTATT
2307055 TTATATTTTATT
1 TTATATTTTATT
*
2307067 TTAAATTT
1 TTATATTT
2307075 AAAAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 1 0.04
11 8 0.29
12 18 0.64
13 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTATATTTTATT
Found at i:2307074 original size:23 final size:23
Alignment explanation
Indices: 2307032--2307075 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2307022 ATTATTTTTA
*
2307032 TTATATTTTATTTATTATTTATT
1 TTATATTTTATTTATAATTTATT
2307055 TTATATTTTATTT-TAAATTTA
1 TTATATTTTATTTAT-AATTTA
2307076 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATATTTTATTTATAATTTATT
Found at i:2307222 original size:28 final size:26
Alignment explanation
Indices: 2307167--2307245 Score: 113
Period size: 26 Copynumber: 3.0 Consensus size: 26
2307157 ATAATAGATA
*
2307167 ATGACATCACATACCGATATAGTATC
1 ATGACGTCACATACCGATATAGTATC
2307193 ATGACGTCACATACCGAGATATAGTATC
1 ATGACGTCACATACC--GATATAGTATC
* *
2307221 ATGACGCCACATATCGATATAGTAT
1 ATGACGTCACATACCGATATAGTAT
2307246 GATAACATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
26 24 0.50
28 24 0.50
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (26 bp):
ATGACGTCACATACCGATATAGTATC
Found at i:2313523 original size:2 final size:2
Alignment explanation
Indices: 2313518--2313577 Score: 63
Period size: 2 Copynumber: 31.0 Consensus size: 2
2313508 GGGGAGGAGG
* * *
2313518 GA GA GA GA GA GA GA GA GA GA GA GA -A CA -A NGG GA GG GA G- GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -GA GA GA GA GA GA
2313558 GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA
2313578 AACACAAAGT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.47, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2313560 original size:38 final size:36
Alignment explanation
Indices: 2313509--2313581 Score: 112
Period size: 38 Copynumber: 2.0 Consensus size: 36
2313499 AGGGGGGGGG
2313509 GGGAGGAGGGAGAGAGAGAGAGAGAGAGAGAGAACAA
1 GGGAGGAGGGAGAGAGAGAGAGAGAGAGAGA-AACAA
2313546 NGGGAGG-GAGGAGAGAGAGAGAGAGAGAGAGAAACA
1 -GGGAGGAG-GGAGAGAGAGAGAGAGAGAGAGAAACA
2313582 CAAAGTAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
37 5 0.15
38 29 0.85
ACGTcount: A:0.45, C:0.03, G:0.51, T:0.00
Consensus pattern (36 bp):
GGGAGGAGGGAGAGAGAGAGAGAGAGAGAGAAACAA
Found at i:2328878 original size:15 final size:14
Alignment explanation
Indices: 2328830--2328879 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
2328820 AGCAACGTTT
*
2328830 GGAAGAAAGAAAGA
1 GGAAAAAAGAAAGA
*
2328844 GAGAAAAATGAAAGA
1 G-GAAAAAAGAAAGA
2328859 -G-AAAAAGAGAAGA
1 GGAAAAAAGA-AAGA
2328872 GGAAAAAA
1 GGAAAAAA
2328880 AATTTCTGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
12 6 0.21
13 5 0.17
14 2 0.07
15 16 0.55
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (14 bp):
GGAAAAAAGAAAGA
Found at i:2328981 original size:30 final size:31
Alignment explanation
Indices: 2328915--2328981 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
2328905 AAAAGACCAC
2328915 AAAGCCCTCGACAGAATAAAAAACTACCAAA
1 AAAGCCCTCGACAGAATAAAAAACTACCAAA
*
2328946 GAAGCCCTCGACAGAATAAAAAACTA-CAAA
1 AAAGCCCTCGACAGAATAAAAAACTACCAAA
2328976 AAAGCC
1 AAAGCC
2328982 TTTCAAATCC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 9 0.26
31 25 0.74
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (31 bp):
AAAGCCCTCGACAGAATAAAAAACTACCAAA
Found at i:2330559 original size:74 final size:74
Alignment explanation
Indices: 2330438--2330589 Score: 286
Period size: 74 Copynumber: 2.1 Consensus size: 74
2330428 AATACAAAAA
*
2330438 AACAACATGAACTTGAAAACGAAATCAAAATAACAATATCTTTAATCACTCTTGTTTGTTTCTAC
1 AACAACATGAACTTAAAAACGAAATCAAAATAACAATATCTTTAATCACTCTTGTTTGTTTCTAC
2330503 TATCTTTTG
66 TATCTTTTG
*
2330512 AACAACATGAACTTAAAAACGAAATCAGAATAACAATATCTTTAATCACTCTTGTTTGTTTCTAC
1 AACAACATGAACTTAAAAACGAAATCAAAATAACAATATCTTTAATCACTCTTGTTTGTTTCTAC
2330577 TATCTTTTG
66 TATCTTTTG
2330586 AACA
1 AACA
2330590 GTTAATACAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.36
Consensus pattern (74 bp):
AACAACATGAACTTAAAAACGAAATCAAAATAACAATATCTTTAATCACTCTTGTTTGTTTCTAC
TATCTTTTG
Done.