Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr1
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: 35726063
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1821929 characters in sequence are not A, C, G, or T
File 6 of 109
Found at i:1880676 original size:40 final size:39
Alignment explanation
Indices: 1880613--1880742 Score: 147
Period size: 37 Copynumber: 3.3 Consensus size: 39
1880603 TTTGGCATCT
*
1880613 AGTGTCTCATCGGATAATTCGAAGTAATAAATTGACACCC
1 AGTGTCTCATCGGATAATCCGAAGT-ATAAATTGACACCC
* * *
1880653 AGTGTCTCATCGGCTAAACCGAAG--TAAATTGGCACCC
1 AGTGTCTCATCGGATAATCCGAAGTATAAATTGACACCC
* * * *
1880690 AGCGCCTCATCGAATTAATCTGAAGTAGTAAATTGACACCC
1 AGTGTCTCATCGGA-TAATCCGAAGTA-TAAATTGACACCC
1880731 AGTGTCTCATCG
1 AGTGTCTCATCG
1880743 ACTCGAAGTC
Statistics
Matches: 73, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
37 22 0.30
38 8 0.11
40 21 0.29
41 22 0.30
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (39 bp):
AGTGTCTCATCGGATAATCCGAAGTATAAATTGACACCC
Found at i:1881708 original size:35 final size:36
Alignment explanation
Indices: 1881662--1881752 Score: 98
Period size: 35 Copynumber: 2.6 Consensus size: 36
1881652 TTTATCATTA
* *
1881662 TAATATAATAATATATATACT-TA-ACTTTTAAGTTT
1 TAATATTATAATATATATACTATATA-TTTTAACTTT
* *
1881697 TAATATTATAATGT-TATAATATATATTTTAACTTT
1 TAATATTATAATATATATACTATATATTTTAACTTT
*
1881732 AAATATTTATAATATATATAC
1 TAATA-TTATAATATATATAC
1881753 ACTTATGCTC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
34 5 0.11
35 27 0.60
36 9 0.20
37 4 0.09
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (36 bp):
TAATATTATAATATATATACTATATATTTTAACTTT
Found at i:1886442 original size:18 final size:17
Alignment explanation
Indices: 1886419--1886454 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
1886409 GGTTAATATG
1886419 TAATTTGGTACTTGAATT
1 TAATTTGGTACTT-AATT
1886437 TAATTTGGTACTTAATT
1 TAATTTGGTACTTAATT
1886454 T
1 T
1886455 TTTAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.53
Consensus pattern (17 bp):
TAATTTGGTACTTAATT
Found at i:1887629 original size:2 final size:2
Alignment explanation
Indices: 1887622--1887647 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1887612 TAAAAATAAA
1887622 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
1887648 CACATGTCAT
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:1889994 original size:22 final size:22
Alignment explanation
Indices: 1889969--1890016 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 22
1889959 ACCTTGATTT
*
1889969 TATTAATTTTTTAAATATAAAA
1 TATTAATATTTTAAATATAAAA
* *
1889991 TATT--TATTTTATATATAAAT
1 TATTAATATTTTAAATATAAAA
1890011 TATTAA
1 TATTAA
1890017 AAAATAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
20 17 0.81
22 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTAATATTTTAAATATAAAA
Found at i:1890006 original size:20 final size:20
Alignment explanation
Indices: 1889977--1890014 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1889967 TTTATTAATT
1889977 TTTTAAATATAAAATATTTA
1 TTTTAAATATAAAATATTTA
* *
1889997 TTTTATATATAAATTATT
1 TTTTAAATATAAAATATT
1890015 AAAAAATAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAAATATAAAATATTTA
Found at i:1895270 original size:29 final size:30
Alignment explanation
Indices: 1895220--1895292 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 30
1895210 AACTATACAT
*
1895220 GAACTATGATTTAATGTGCAATTGTATATATA
1 GAACTTTGATTT--TGTGCAATTGTATATATA
*
1895252 -AACTTTGATTTTGTGCAATTTTATATATA
1 GAACTTTGATTTTGTGCAATTGTATATATA
*
1895281 GAATTTTGATTT
1 GAACTTTGATTT
1895293 GATCTAATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 17 0.46
30 10 0.27
31 10 0.27
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (30 bp):
GAACTTTGATTTTGTGCAATTGTATATATA
Found at i:1895507 original size:29 final size:31
Alignment explanation
Indices: 1895422--1895541 Score: 99
Period size: 31 Copynumber: 3.9 Consensus size: 31
1895412 AATATGTATG
1895422 ATTAA-ATCAAAATTAAAGTTTAAAT-TATATA
1 ATTAACATC-AAATTAAAGTTT-AATGTATATA
* * * *
1895453 TTTGA-ATCACAATTAGAGTTTCATGTATATA
1 ATTAACATCA-AATTAAAGTTTAATGTATATA
1895484 ATT-ACATCAAATTAAAGTTT-ATGTATATA
1 ATTAACATCAAATTAAAGTTTAATGTATATA
* * *
1895513 ATTACACATTAAATCAAAATTT-ATGTATA
1 ATTA-ACATCAAATTAAAGTTTAATGTATA
1895542 ATTTTGAGAT
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
29 12 0.16
30 14 0.19
31 49 0.65
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (31 bp):
ATTAACATCAAATTAAAGTTTAATGTATATA
Found at i:1896482 original size:11 final size:11
Alignment explanation
Indices: 1896468--1896518 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1896458 ACGTTTTAGA
*
1896468 ATTTTTTATAT
1 ATTTTTTAAAT
1896479 ATTTTTTAAAT
1 ATTTTTTAAAT
1896490 ATAATTTTTGAAAT
1 AT--TTTTT-AAAT
*
1896504 -TTTTATAAAT
1 ATTTTTTAAAT
1896514 ATTTT
1 ATTTT
1896519 GAGTTGTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
10 4 0.12
11 20 0.59
13 6 0.18
14 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
ATTTTTTAAAT
Found at i:1896520 original size:20 final size:20
Alignment explanation
Indices: 1896481--1896566 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
1896471 TTTTATATAT
*
1896481 TTTTTAAATATAATTTTTGAAA
1 TTTTTAAA-ATTA-TTTTGAAA
*
1896503 TTTTTATAAA-TATTTTG-AG
1 TTTTTA-AAATTATTTTGAAA
* * * *
1896522 TTGTAAAAATTATCTTGAAT
1 TTTTTAAAATTATTTTGAAA
1896542 TTTTTAAAATTATTTTGAAA
1 TTTTTAAAATTATTTTGAAA
1896562 TTTTT
1 TTTTT
1896567 GTTAAGAGAG
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
18 3 0.06
19 11 0.22
20 27 0.53
21 1 0.02
22 7 0.14
23 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.07, T:0.56
Consensus pattern (20 bp):
TTTTTAAAATTATTTTGAAA
Found at i:1899171 original size:16 final size:15
Alignment explanation
Indices: 1899150--1899187 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
1899140 TTAGTCACTT
1899150 AAAATTTATAAAATTA
1 AAAATTTATAAAA-TA
*
1899166 AAAATTTATATAATA
1 AAAATTTATAAAATA
1899181 AAAATTT
1 AAAATTT
1899188 TCTATTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATTTATAAAATA
Found at i:1903409 original size:27 final size:27
Alignment explanation
Indices: 1903356--1903411 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
1903346 TATGTTGTTG
*
1903356 ATGATGAAGATGAGGAGGAAGAAGAAA
1 ATGATGAAGATGAGGAAGAAGAAGAAA
** * *
1903383 ATGATGAAGATTTGGAAGAGGAGGAAA
1 ATGATGAAGATGAGGAAGAAGAAGAAA
1903410 AT
1 AT
1903412 CGTAACCGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (27 bp):
ATGATGAAGATGAGGAAGAAGAAGAAA
Found at i:1913711 original size:2 final size:2
Alignment explanation
Indices: 1913704--1913748 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1913694 GATAACTACT
1913704 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC T-
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1913744 TC TC T
1 TC TC T
1913749 TTTTAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1925532 original size:69 final size:69
Alignment explanation
Indices: 1925368--1925544 Score: 239
Period size: 69 Copynumber: 2.6 Consensus size: 69
1925358 TTAGATTTTC
* * * *
1925368 AAGGGCAGATATATTTCCATAGAATTGATTAGAAGAGAGGTCTAAAGATTCAAGCAATGTTAAGC
1 AAGGGCAGATATATTTCCAGAGAACTGATTAGTAGAGAGGTCCAAAGATTCAAGCAATGTTAAGC
*
1925433 TCTT
66 TCTG
* * *
1925437 AAGTGCAGATATATATCCAGAGAACTGATTAGTAGAGAGGTCCAAAGATTCAAGCAATTTTAAGC
1 AAGGGCAGATATATTTCCAGAGAACTGATTAGTAGAGAGGTCCAAAGATTCAAGCAATGTTAAGC
1925502 TCTG
66 TCTG
* * *
1925506 AAGGGCAGATATATTTTCGGAAAACTGATT-GTAAGAGAG
1 AAGGGCAGATATATTTCCAGAGAACTGATTAGT-AGAGAG
1925545 AGATAACATT
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
68 2 0.02
69 92 0.98
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (69 bp):
AAGGGCAGATATATTTCCAGAGAACTGATTAGTAGAGAGGTCCAAAGATTCAAGCAATGTTAAGC
TCTG
Found at i:1931028 original size:33 final size:33
Alignment explanation
Indices: 1930986--1931053 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
1930976 GATATATTTC
1930986 CAGAGAATTGATTAGAAGAGAGGCCCAAAGATT
1 CAGAGAATTGATTAGAAGAGAGGCCCAAAGATT
1931019 CAGAGAATTGATTAGAAGAGAGGCCCAAAGATT
1 CAGAGAATTGATTAGAAGAGAGGCCCAAAGATT
1931052 CA
1 CA
1931054 AGCAATGTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.13, G:0.26, T:0.18
Consensus pattern (33 bp):
CAGAGAATTGATTAGAAGAGAGGCCCAAAGATT
Found at i:1931138 original size:69 final size:69
Alignment explanation
Indices: 1931027--1931316 Score: 454
Period size: 69 Copynumber: 4.2 Consensus size: 69
1931017 TTCAGAGAAT
* *
1931027 TGATTAGAAGAGAGGCCCAAAGATTCAAGCAATGTTAGGCTCTGAAGGGCAGATATATTTCCAAA
1 TGATTAGAAGAGAGGTCCAAAGATTCAAGCAATGTTAGGCTCTGAAGGGCAGATATATTTCCAGA
1931092 AAAC
66 AAAC
* *
1931096 TGATTAGAAGAGAGGTCCAAAGATGCAAGCAATGTTAGGCTCTGAATGGCAGATATATTTCCAGA
1 TGATTAGAAGAGAGGTCCAAAGATTCAAGCAATGTTAGGCTCTGAAGGGCAGATATATTTCCAGA
*
1931161 GAAC
66 AAAC
1931165 TGATTAGAAGAGAGGTCCAAAGATTCAAGCAATGTTAGGCTCTGAAGGGCAGATATATTTCCAGA
1 TGATTAGAAGAGAGGTCCAAAGATTCAAGCAATGTTAGGCTCTGAAGGGCAGATATATTTCCAGA
*
1931230 TAAC
66 AAAC
* * * ** * *
1931234 TGATTAGAAGAGAGGTTCAAAGATTCAAGCAATTTTAGGCTCTTAAGGATAGATATATTTTCGGA
1 TGATTAGAAGAGAGGTCCAAAGATTCAAGCAATGTTAGGCTCTGAAGGGCAGATATATTTCCAGA
1931299 AAAC
66 AAAC
*
1931303 TGATTGGAAGAGAG
1 TGATTAGAAGAGAG
1931317 AGATAACATT
Statistics
Matches: 204, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 204 1.00
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (69 bp):
TGATTAGAAGAGAGGTCCAAAGATTCAAGCAATGTTAGGCTCTGAAGGGCAGATATATTTCCAGA
AAAC
Found at i:1940908 original size:27 final size:26
Alignment explanation
Indices: 1940877--1940933 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1940867 TTACCATTAT
1940877 TTAAAAGATTATAA-TTGAAAAAAATGA
1 TTAAAAGA-TA-AATTTGAAAAAAATGA
* *
1940904 TTAAAATATAAATTTGAAAAAAATTA
1 TTAAAAGATAAATTTGAAAAAAATGA
1940930 TTAA
1 TTAA
1940934 TCCCCTTGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 18 0.67
27 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (26 bp):
TTAAAAGATAAATTTGAAAAAAATGA
Found at i:1941204 original size:29 final size:29
Alignment explanation
Indices: 1941163--1941225 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
1941153 TAAATTTTGT
* *
1941163 TTAAAATTTATTAAATAACAATTAATTAA
1 TTAAAACTGATTAAATAACAATTAATTAA
** *
1941192 TTAAAACTGATTAAATATTAATTAATTAT
1 TTAAAACTGATTAAATAACAATTAATTAA
1941221 TTAAA
1 TTAAA
1941226 CTCTTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (29 bp):
TTAAAACTGATTAAATAACAATTAATTAA
Found at i:1941496 original size:21 final size:20
Alignment explanation
Indices: 1941463--1941509 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1941453 AAATTAAATA
*
1941463 ATAAAAAACTTAATTTAATT
1 ATAAAAAAATTAATTTAATT
1941483 ATAAAAAATATTAATATT-A-T
1 ATAAAAAA-ATTAAT-TTAATT
1941503 ATAAAAA
1 ATAAAAA
1941510 TAATATGTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 16 0.67
21 6 0.25
22 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAAAAAATTAATTTAATT
Found at i:1946054 original size:69 final size:69
Alignment explanation
Indices: 1945974--1946288 Score: 468
Period size: 69 Copynumber: 4.6 Consensus size: 69
1945964 TTAGACTTTC
* * *
1945974 AAGGGCAGATATATTTCCAGAGAACTGATTTGAAGAGAGGTCCAATGATTCAAGCAATGTTAGGC
1 AAGGGCAGATATATTTCCAGAGAACTGATTAGAAGAGAGGTCCAAAGATGCAAGCAATGTTAGGC
1946039 TCTG
66 TCTG
* *
1946043 AAGGGTAGATATATTTCCAGAAAACTGATTAGAAGAGAGGTCCAAAGATGCAAGCAATGTTAGGC
1 AAGGGCAGATATATTTCCAGAGAACTGATTAGAAGAGAGGTCCAAAGATGCAAGCAATGTTAGGC
1946108 TCTG
66 TCTG
* * *
1946112 AATGGCAGATATATTTCCAGAGAACTGATTACAAGAGAGGTCCAAAGATGCAAGCAATGTTAGAC
1 AAGGGCAGATATATTTCCAGAGAACTGATTAGAAGAGAGGTCCAAAGATGCAAGCAATGTTAGGC
* *
1946177 TTTC
66 TCTG
* *
1946181 AAGGGCAGATATATTTCCAGAGAACTGATTAGAAGAGAGGTCCAAAGATTCAAGCAATTTTAGGC
1 AAGGGCAGATATATTTCCAGAGAACTGATTAGAAGAGAGGTCCAAAGATGCAAGCAATGTTAGGC
*
1946246 TCTT
66 TCTG
** * * *
1946250 AAGGATAGATATATTTCCGGAAAACTGATTGGAAGAGAG
1 AAGGGCAGATATATTTCCAGAGAACTGATTAGAAGAGAG
1946289 TGATAACATT
Statistics
Matches: 222, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 222 1.00
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.25
Consensus pattern (69 bp):
AAGGGCAGATATATTTCCAGAGAACTGATTAGAAGAGAGGTCCAAAGATGCAAGCAATGTTAGGC
TCTG
Found at i:1947046 original size:2 final size:2
Alignment explanation
Indices: 1947000--1947028 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1946990 GCAGCACATT
1947000 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1947029 TAAATCTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1956874 original size:3 final size:3
Alignment explanation
Indices: 1956866--1956910 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
1956856 ATTAATCTTG
1956866 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1956911 CTCATTTATA
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:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1963190 original size:44 final size:42
Alignment explanation
Indices: 1963088--1963237 Score: 144
Period size: 44 Copynumber: 3.5 Consensus size: 42
1963078 TGTTTGTGGT
* *
1963088 CTTAGTCTGCTCCACTGTAA-CTTCAGGGAGATAAGA--CTAG
1 CTTAATCTGCTCCACTGTAATC-TCAGGGAGATAAGACTCTGG
* *
1963128 ATGTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGG
1 CT-TAATCTGCTCCACTGTAATCTCAGGGAGATAAGA-CTCTGG
* * *
1963172 CTTCAATCTGCTCCACTGTAACCTCAAGGAGATAAGACTGGTGG
1 CTT-AATCTGCTCCACTGTAATCTCAGGGAGATAAGACT-CTGG
* *
1963216 CCTAAATCTGCTCCACTTTAAT
1 -CTTAATCTGCTCCACTGTAAT
1963238 GGATTTTCAA
Statistics
Matches: 90, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
40 1 0.01
41 30 0.33
42 1 0.01
43 3 0.03
44 53 0.59
45 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (42 bp):
CTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGACTCTGG
Found at i:1963534 original size:3 final size:3
Alignment explanation
Indices: 1963526--1963580 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
1963516 ATTAATCTTG
1963526 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1963574 TAT TAT T
1 TAT TAT T
1963581 TACTCATTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1968355 original size:6 final size:6
Alignment explanation
Indices: 1968346--1968385 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
1968336 TTCAAAAAAA
1968346 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
1968386 AGAAGAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:1968412 original size:12 final size:12
Alignment explanation
Indices: 1968346--1968419 Score: 64
Period size: 12 Copynumber: 6.3 Consensus size: 12
1968336 TTCAAAAAAA
*
1968346 AAAATCAAAATC
1 AAAATAAAAATC
*
1968358 AAAATCAAAATC
1 AAAATAAAAATC
*
1968370 AAAATCAAAATC
1 AAAATAAAAATC
*
1968382 AAAA-AGAAGA--
1 AAAATA-AAAATC
*
1968392 AAAAGAAAAATC
1 AAAATAAAAATC
*
1968404 AAAATAAAAATG
1 AAAATAAAAATC
1968416 AAAA
1 AAAA
1968420 GAGAGAAGGA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
10 7 0.13
11 1 0.02
12 45 0.85
ACGTcount: A:0.73, C:0.09, G:0.05, T:0.12
Consensus pattern (12 bp):
AAAATAAAAATC
Found at i:1968419 original size:18 final size:18
Alignment explanation
Indices: 1968346--1968419 Score: 71
Period size: 18 Copynumber: 4.2 Consensus size: 18
1968336 TTCAAAAAAA
*
1968346 AAAATCAAAATCAAAATC
1 AAAATCAAAATAAAAATC
*
1968364 AAAATCAAAATCAAAATC
1 AAAATCAAAATAAAAATC
* * **
1968382 AAAA--AGAAGAAAAAGA
1 AAAATCAAAATAAAAATC
*
1968398 AAAATCAAAATAAAAATG
1 AAAATCAAAATAAAAATC
1968416 AAAA
1 AAAA
1968420 GAGAGAAGGA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
16 11 0.24
18 34 0.76
ACGTcount: A:0.73, C:0.09, G:0.05, T:0.12
Consensus pattern (18 bp):
AAAATCAAAATAAAAATC
Found at i:1970730 original size:12 final size:11
Alignment explanation
Indices: 1970715--1970771 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 11
1970705 TCAAAAAAAA
1970715 AAAATCAAAATC
1 AAAAT-AAAATC
*
1970727 AAAATCAAAAGC
1 AAAAT-AAAATC
* *
1970739 AGAAAAAAAATAA
1 A-AAATAAAAT-C
1970752 AAAATAAAATC
1 AAAATAAAATC
1970763 AAAATAAAA
1 AAAATAAAA
1970772 GAAAAAAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
11 9 0.24
12 24 0.65
13 4 0.11
ACGTcount: A:0.75, C:0.09, G:0.04, T:0.12
Consensus pattern (11 bp):
AAAATAAAATC
Found at i:1970761 original size:42 final size:42
Alignment explanation
Indices: 1970708--1970790 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1970698 ATCCAATTCA
** *
1970708 AAAAAAAAAAATCAAAATCAAAA-TCAAAAGCAGAAAAAAAAT
1 AAAAAAAAAAATCAAAAT-AAAAGAAAAAAGAAGAAAAAAAAT
*
1970750 AAAAAATAAAATCAAAATAAAAGAAAAAAGAAGAAAAAAAA
1 AAAAAAAAAAATCAAAATAAAAGAAAAAAGAAGAAAAAAAA
1970791 GATGTTAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 4 0.11
42 32 0.89
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.08
Consensus pattern (42 bp):
AAAAAAAAAAATCAAAATAAAAGAAAAAAGAAGAAAAAAAAT
Found at i:1970778 original size:30 final size:30
Alignment explanation
Indices: 1970709--1970766 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1970699 TCCAATTCAA
*
1970709 AAAAAAAAAATCAAAATCAAAATCAAAAGC
1 AAAAAAAAAATAAAAATCAAAATCAAAAGC
*
1970739 AGAAAAAAAATAAAAAAT-AAAATCAAAA
1 AAAAAAAAAAT-AAAAATCAAAATCAAAA
1970767 TAAAAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.78, C:0.09, G:0.03, T:0.10
Consensus pattern (30 bp):
AAAAAAAAAATAAAAATCAAAATCAAAAGC
Found at i:1971674 original size:14 final size:15
Alignment explanation
Indices: 1971650--1971678 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1971640 TTTAAGTCGA
1971650 AAAAGATGAAAAATG
1 AAAAGATGAAAAATG
1971665 AAAA-ATGAAAAATG
1 AAAAGATGAAAAATG
1971679 GAGAGGCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (15 bp):
AAAAGATGAAAAATG
Found at i:1973067 original size:44 final size:43
Alignment explanation
Indices: 1972970--1974122 Score: 299
Period size: 44 Copynumber: 26.7 Consensus size: 43
1972960 AAGTAGTAGA
* * * * * *
1972970 TCTTATTTCTCTGAAGTTGCAGTAGAGTAGAT-CGT-ATCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGCAGG
*
1973011 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGTAAGCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAGTAAGCAGG
* * * * **
1973055 TCTTATCCCCCTGAAGTTACAGTGGGGCAGATCGAAG-ATGGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-G-AGTA-AGCAGG
* * *
1973100 TCTTATATCCCTGAGGTTGCAGTGGAGCAGAT-AG-AAGCAGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGCAG---G
* * * * * * *
1973144 TCCTATCTCCCTGAAGTTACAGAGGAGCGGATTAAAGT-AGTAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-GAGTAAGCAGG
* * * * *
1973188 TCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT-CGT-ATCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGCAGG
* * *
1973229 TCTTATCTCCCTGAAGTTGTAGCGGAGTAGACTGAGTAAGCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAGTAAGCAGG
* * * * **
1973273 TCTTATCCCCCTGAAGTTGCAATGGGGCAGATCGAAG-ATGGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-G-AGTA-AGCAGG
* * **
1973318 TCTTATCTCCCTGAGGTTGCAGTGGAGTAGAT-AG-AAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAG-C-A-GG
* * * * * * * *
1973362 TCCTATCTCCCTAAAGTTACAGAGGAGCGGATTAAAGTAA-TAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-GAGTAAGCAGG
* * * * *
1973406 TCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT-CGT-ATCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGCAGG
* * * * *
1973447 TCTTATCTCCCTGAAGTTGCAGCGGATCAGACTTAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAGTAAGCAGG
* * * * * **
1973491 TCTCATCCCCCTGAAGTTACAGTGGGGCAGATCGAAG-ATGACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-G-AGTAAG-CAGG
* * * * **
1973536 TCTTATCTCCTTGAGGTTGCAATGGAGCAAAT-AG-AAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAG-C-A-GG
* * * * * * *
1973580 TCCTATCTCCCTGAAGTTACAGAGGAGCGGATTAAAGT-AGTAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-GAGTAAGCAGG
* ** * * **
1973624 TCTTACCTCTTTGAAGTTGCAGTAGAGCAGACGA--AAGCTACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGC-A-GG
* * * * * * *
1973667 TCCTATCTCCCTGAAGTTACAGTGGAGCGGACTAAAATCA-CAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-GAGTAAGCAGG
* * ** * * **
1973711 TCTTATCTCTCTGAAGTTGTAGTATAGCAGAT-CGCATCCA-G
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGCAGG
* * **
1973752 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACGA--AAGCTATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGC-A-GG
* * * * * * *
1973795 TCCTATCTCCCTAAAGTTGCAGTGGAGCATATTA-AAATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAA--GCAGG
* * * * * * **
1973839 TCTTATCTCTCTGAAGTTGTAATAGAGCAGAT-CGCATCCA-G
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGCAGG
* * * * * *
1973880 TCTTATCTCCCTAAAGTTGCAGTGGAGCGGATTA-AAATCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAA--GCAGG
* * * * * **
1973924 TCTTATCTCTCTGAAGTTGCAGTAGAGCAAAT-CGCATCCA-G
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGCAGG
* * * **
1973965 TTTTATCTCCCTGAAGTTGTAGTGGAGCAGACGA--AAGCTACAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGC-A-GG
* * * * * * *
1974008 TCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTA-AAACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAA--GCAGG
* * * * * * **
1974052 TCTTATCTCTCTTACGTTGCAGTAGAGCAGAT-CGT-ATCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGCAGG
*
1974093 CCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1974123 GTTGAAAATA
Statistics
Matches: 805, Mismatches: 239, Indels: 136
0.68 0.20 0.12
Matches are distributed among these distances:
40 5 0.01
41 203 0.25
42 23 0.03
43 96 0.12
44 358 0.44
45 102 0.13
46 3 0.00
47 13 0.02
48 2 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGTAAGCAGG
Found at i:1973301 original size:218 final size:218
Alignment explanation
Indices: 1972915--1974119 Score: 1298
Period size: 218 Copynumber: 5.6 Consensus size: 218
1972905 ACAGATCGGT
* * *
1972915 GAAGCCGATAATCCTATCTTCCTGAAATTACAGAGGAGCGGATTAAAGTAGTAGATCTTATTTCT
1 GAAGCCGATAATCCTATCTCCCTGAAGTTACAGAGGAGCGGATTAAAGTAGTAGATCTTATCTCT
*
1972980 CTGAAGTTGCAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGCAGACTG
66 CTGAAGTTGCAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGACTG
*
1973045 AGTAAGCAGGTCTTATCCCCCTGAAGTTACAGTGGGGCAGATCGAAGATGGCAAATCTTATATCC
131 AGTAAGCAGGTCTTATCCCCCTGAAGTTACAGTGGGGCAGATCGAAGATGGCAAATCTTATCTCC
1973110 CTGAGGTTGCAGTGGAGCAGATA
196 CTGAGGTTGCAGTGGAGCAGATA
*
1973133 GAAGCAGATAATCCTATCTCCCTGAAGTTACAGAGGAGCGGATTAAAGTAGTAGATCTTATCTCT
1 GAAGCCGATAATCCTATCTCCCTGAAGTTACAGAGGAGCGGATTAAAGTAGTAGATCTTATCTCT
*
1973198 CTGAAGTTGCAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAAGTTGTAGCGGAGTAGACTG
66 CTGAAGTTGCAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGACTG
* *
1973263 AGTAAGCAGGTCTTATCCCCCTGAAGTTGCAATGGGGCAGATCGAAGATGGCAAATCTTATCTCC
131 AGTAAGCAGGTCTTATCCCCCTGAAGTTACAGTGGGGCAGATCGAAGATGGCAAATCTTATCTCC
*
1973328 CTGAGGTTGCAGTGGAGTAGATA
196 CTGAGGTTGCAGTGGAGCAGATA
* *
1973351 GAAGCCGATAATCCTATCTCCCTAAAGTTACAGAGGAGCGGATTAAAGTAATAGATCTTATCTCT
1 GAAGCCGATAATCCTATCTCCCTGAAGTTACAGAGGAGCGGATTAAAGTAGTAGATCTTATCTCT
1973416 CTGAAGTTGCAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAAGTTGCAGCGGA-TCAGACT
66 CTGAAGTTGCAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGT-AGACT
* * * * *
1973480 TAGAAAGCAAGTCTCATCCCCCTGAAGTTACAGTGGGGCAGATCGAAGATGACAAATCTTATCTC
130 GAGTAAGCAGGTCTTATCCCCCTGAAGTTACAGTGGGGCAGATCGAAGATGGCAAATCTTATCTC
* * *
1973545 CTTGAGGTTGCAATGGAGCAAATA
195 CCTGAGGTTGCAGTGGAGCAGATA
*
1973569 GAAGCCGATAATCCTATCTCCCTGAAGTTACAGAGGAGCGGATTAAAGTAGTAGATCTTACCTCT
1 GAAGCCGATAATCCTATCTCCCTGAAGTTACAGAGGAGCGGATTAAAGTAGTAGATCTTATCTCT
* * * * * * * **
1973634 TTGAAGTTGCAGTAGAGCAGA-CGAAAGCTACA-ATCCTATCTCCCTGAAGTTACAGTGGAGCGG
66 CTGAAGTTGCAGTAGAGTAGATCG-TA--T-CAGGTCTTATCTCCCTGAAGTTGCAGCGGAGTAG
* * * * * * ** *** * * *
1973697 ACTAAAATCA-CAGATCTTATCTCTCTGAAGTTGTAGTATAGCAGATCG--CAT--CCAGTCTTA
127 ACT-GAGTAAGCAGGTCTTATCCCCCTGAAGTTACAGTGGGGCAGATCGAAGATGGCAAATCTTA
* * *
1973757 TCTCCCTGAAGTTACAGTGGAGCAGA-C
191 TCTCCCTGAGGTTGCAGTGGAGCAGATA
* * * * ** * *
1973784 GAAAG-CTATAATCCTATCTCCCTAAAGTTGCAGTGGAGCATATTAAAATCA-CAGATCTTATCT
1 G-AAGCCGATAATCCTATCTCCCTGAAGTTACAGAGGAGCGGATTAAAGT-AGTAGATCTTATCT
* * * * * * **
1973847 CTCTGAAGTTGTAATAGAGCAGATCGCATCCA-GTCTTATCTCCCTAAAGTTGCAGTGGAGCGGA
64 CTCTGAAGTTGCAGTAGAGTAGATCGTAT-CAGGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGA
* * * * * * * * * * * * * * *
1973911 TTAAAATCA-CAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAAATCG--CAT--CCAGTTTTAT
128 CT-GAGTAAGCAGGTCTTATCCCCCTGAAGTTACAGTGGGGCAGATCGAAGATGGCAAATCTTAT
* * *
1973971 CTCCCTGAAGTTGTAGTGGAGCAGA-C
192 CTCCCTGAGGTTGCAGTGGAGCAGATA
* * * * * ** *
1973997 GAAAG-CTACAATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCA-CAGATCTTATCT
1 G-AAGCCGATAATCCTATCTCCCTGAAGTTACAGAGGAGCGGATT-AAAGTAGTAGATCTTATCT
* * * *** *
1974060 CTCTTACGTTGCAGTAGAGCAGATCGTATCAAACCTTATCTCCCTGAAGTTGCAGTGGAG
64 CTCTGAAGTTGCAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAG
1974120 CAGGTTGAAA
Statistics
Matches: 877, Mismatches: 98, Indels: 29
0.87 0.10 0.03
Matches are distributed among these distances:
212 2 0.00
213 213 0.24
214 3 0.00
215 69 0.08
216 34 0.04
217 3 0.00
218 493 0.56
220 56 0.06
221 4 0.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (218 bp):
GAAGCCGATAATCCTATCTCCCTGAAGTTACAGAGGAGCGGATTAAAGTAGTAGATCTTATCTCT
CTGAAGTTGCAGTAGAGTAGATCGTATCAGGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGACTG
AGTAAGCAGGTCTTATCCCCCTGAAGTTACAGTGGGGCAGATCGAAGATGGCAAATCTTATCTCC
CTGAGGTTGCAGTGGAGCAGATA
Found at i:1973681 original size:87 final size:85
Alignment explanation
Indices: 1973578--1974120 Score: 282
Period size: 85 Copynumber: 6.4 Consensus size: 85
1973568 AGAAGCCGAT
* * * * *
1973578 AATCCTATCTCCCTGAAGTTACAGAGGAGCGGATTAAAGT-AGTAGATCTTACCTCTTTGAAGTT
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGACTAAAATCA-CAGATCTTACCTCTCTGAAGTT
1973642 GCAGTAGAGCAGA-CGAAAGCTAC
65 GCAGTAGAGCAGATCG-AA--TAC
*
1973665 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGACTAAAATCACAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGACTAAAATCACAGATCTTACCTCTCTGAAGTTG
* * * *
1973730 TAGTATAGCAGATCGCATCC
66 CAGTAGAGCAGATCGAATAC
* * * * * * * * * *
1973750 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGAC-GAAAGCTATA-ATCCTATCTCCCTAAAGTT
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGACTAAAATC-ACAGATCTTACCTCTCTGAAGTT
* * **
1973813 GCAGTGGAGCATATTAAAATCAC
65 GCAGTAGAGCAGA-TCGAAT-AC
* * ** * * * *** * * *
1973836 AGATCTTATCTCTCTGAAGTTGTAATAGAGCAGA-TCGCATC-CAG-TCTTATCTCCCTAAAGTT
1 A-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGACTAAAATCACAGATCTTACCTCTCTGAAGTT
* * **
1973898 GCAGTGGAGCGGATTAAAATCAC
65 GCAGTAGAGCAGA-TCGAAT-AC
* * * * * * *** * * *
1973921 AGATCTTATCTCTCTGAAGTTGCAGTAGAGC-AAATCGCATC-CAG-TTTTATCTCCCTGAAGTT
1 A-ATCCTATCTCCCTGAAGTTACAGTGGAGCGGACTAAAATCACAGATCTTACCTCTCTGAAGTT
* *
1973983 GTAGTGGAGCAGA-CGAAAGCTAC
65 GCAGTAGAGCAGATCG-AA--TAC
* * * * * * *
1974006 AATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTTACGTTG
1 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGACTAAAATCACAGATCTTACCTCTCTGAAGTTG
*
1974071 CAGTAGAGCAGATCGTAT-C
66 CAGTAGAGCAGATCGAATAC
* *
1974090 AAACCTTATCTCCCTGAAGTTGCAGTGGAGC
1 AATCC-TATCTCCCTGAAGTTACAGTGGAGC
1974121 AGGTTGAAAA
Statistics
Matches: 370, Mismatches: 69, Indels: 36
0.78 0.15 0.08
Matches are distributed among these distances:
84 62 0.17
85 175 0.47
86 6 0.02
87 122 0.33
88 5 0.01
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (85 bp):
AATCCTATCTCCCTGAAGTTACAGTGGAGCGGACTAAAATCACAGATCTTACCTCTCTGAAGTTG
CAGTAGAGCAGATCGAATAC
Found at i:1973790 original size:128 final size:128
Alignment explanation
Indices: 1973635--1973907 Score: 447
Period size: 128 Copynumber: 2.1 Consensus size: 128
1973625 CTTACCTCTT
* * *
1973635 TGAAGTTGCAGTAGAGCAGACGAAAGCTACAATCCTATCTCCCTGAAGTTACAGTGGAGCGGACT
1 TGAAGTTGCAGTGGAGCAGACGAAAGCTACAATCCTATCTCCCTAAAGTTACAGTGGAGCAGACT
* *
1973700 AAAATCACAGATCTTATCTCTCTGAAGTTGTAGTATAGCAGATCGCATCCAGTCTTATCTCCC
66 AAAATCACAGATCTTATCTCTCTGAAGTTGTAATAGAGCAGATCGCATCCAGTCTTATCTCCC
* * * * *
1973763 TGAAGTTACAGTGGAGCAGACGAAAGCTATAATCCTATCTCCCTAAAGTTGCAGTGGAGCATATT
1 TGAAGTTGCAGTGGAGCAGACGAAAGCTACAATCCTATCTCCCTAAAGTTACAGTGGAGCAGACT
1973828 AAAATCACAGATCTTATCTCTCTGAAGTTGTAATAGAGCAGATCGCATCCAGTCTTATCTCCC
66 AAAATCACAGATCTTATCTCTCTGAAGTTGTAATAGAGCAGATCGCATCCAGTCTTATCTCCC
*
1973891 TAAAGTTGCAGTGGAGC
1 TGAAGTTGCAGTGGAGC
1973908 GGATTAAAAT
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
128 133 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (128 bp):
TGAAGTTGCAGTGGAGCAGACGAAAGCTACAATCCTATCTCCCTAAAGTTACAGTGGAGCAGACT
AAAATCACAGATCTTATCTCTCTGAAGTTGTAATAGAGCAGATCGCATCCAGTCTTATCTCCC
Found at i:1973906 original size:85 final size:85
Alignment explanation
Indices: 1973798--1973995 Score: 324
Period size: 85 Copynumber: 2.3 Consensus size: 85
1973788 GCTATAATCC
* *
1973798 TATCTCCCTAAAGTTGCAGTGGAGCATATTAAAATCACAGATCTTATCTCTCTGAAGTTGTAATA
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAATA
*
1973863 GAGCAGATCGCATCCAGTCT
66 GAGCAAATCGCATCCAGTCT
* *
1973883 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGTA
1 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAATA
*
1973948 GAGCAAATCGCATCCAGTTT
66 GAGCAAATCGCATCCAGTCT
* *
1973968 TATCTCCCTGAAGTTGTAGTGGAGCAGA
1 TATCTCCCTAAAGTTGCAGTGGAGCAGA
1973996 CGAAAGCTAC
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 104 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (85 bp):
TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAATA
GAGCAAATCGCATCCAGTCT
Found at i:1974015 original size:128 final size:128
Alignment explanation
Indices: 1973883--1974122 Score: 390
Period size: 128 Copynumber: 1.9 Consensus size: 128
1973873 CATCCAGTCT
*
1973883 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGTA
1 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
* *** *
1973948 GAGCAAATCGCATCCAGTTTTATCTCCCTGAAGTTGTAGTGGAGCAGACGAAAGCTACAATCC
66 GAGCAAATCGCATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGCTACAATCC
* *
1974011 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTTACGTTGCAGTA
1 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
* *
1974076 GAGCAGATCGTATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAG
66 GAGCAAATCGCATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAG
1974123 GTTGAAAATA
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
128 102 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.28
Consensus pattern (128 bp):
TATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
GAGCAAATCGCATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGCTACAATCC
Found at i:1974135 original size:128 final size:129
Alignment explanation
Indices: 1973878--1974146 Score: 380
Period size: 128 Copynumber: 2.1 Consensus size: 129
1973868 GATCGCATCC
* *
1973878 AGTCTTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTG
1 AGTCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* *** * *
1973943 CAGTAGAGCAAATCGCATCCAGTTTTATCTCCCTGAAGTTGTAGTGGAGCAGACGAAAGCTACA
66 CAGTAGAGCAAATCGCATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGATACA
* *
1974007 A-TCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTTACGTTG
1 AGTCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
* * **
1974071 CAGTAGAGCAGATCGTATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAA-ATACA
66 CAGTAGAGCAAATCGCATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCA-GACGAAAGATACA
*
1974135 AGTCTTATCTCC
1 AGTCCTATCTCC
1974147 TTGACGTTGT
Statistics
Matches: 123, Mismatches: 15, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
128 108 0.88
129 15 0.12
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (129 bp):
AGTCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTG
CAGTAGAGCAAATCGCATCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACGAAAGATACA
Found at i:1974881 original size:11 final size:10
Alignment explanation
Indices: 1974858--1974890 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1974848 GTTTTGAATC
1974858 TTTTTCA-TT
1 TTTTTCATTT
1974867 TTTTTCTATTT
1 TTTTTC-ATTT
1974878 TTTTTCATTT
1 TTTTTCATTT
1974888 TTT
1 TTT
1974891 CTTTTACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 8 0.36
11 8 0.36
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:1978447 original size:25 final size:25
Alignment explanation
Indices: 1978410--1978462 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1978400 TAAAATCTAT
* * *
1978410 TTAAAATTTATTACATATCAATTAA
1 TTAAAAATGATTAAATATCAATTAA
* *
1978435 TTAAAAATGATTAAATATTAATTTA
1 TTAAAAATGATTAAATATCAATTAA
1978460 TTA
1 TTA
1978463 GAATCGGTGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (25 bp):
TTAAAAATGATTAAATATCAATTAA
Found at i:1982858 original size:16 final size:16
Alignment explanation
Indices: 1982834--1982864 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1982824 CATAAATATT
*
1982834 TTTTTAAAATATATAC
1 TTTTAAAAATATATAC
1982850 TTTTAAAAATATATA
1 TTTTAAAAATATATA
1982865 TGTAAAATTT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTAAAAATATATAC
Found at i:1990390 original size:15 final size:15
Alignment explanation
Indices: 1990349--1990390 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1990339 AATCTAATAG
1990349 TAATTATTATT-AAT
1 TAATTATTATTAAAT
1990363 TAATTAGTT-TTAAAT
1 TAATTA-TTATTAAAT
*
1990378 TAATTTTTATTAA
1 TAATTATTATTAA
1990391 GATGACAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TAATTATTATTAAAT
Found at i:1990967 original size:20 final size:20
Alignment explanation
Indices: 1990942--1990983 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1990932 AATCATTTTA
*
1990942 AATTTG-AATAAAAAATTCAT
1 AATTTGTAA-AAAAAAATCAT
1990962 AATTTGTAAAAAAAAATCAT
1 AATTTGTAAAAAAAAATCAT
1990982 AA
1 AA
1990984 AAGCTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (20 bp):
AATTTGTAAAAAAAAATCAT
Found at i:1994983 original size:16 final size:16
Alignment explanation
Indices: 1994962--1995004 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
1994952 TATTATTATT
1994962 ATTTAT-TTAAATTGTA
1 ATTTATATT-AATTGTA
1994978 ATTTATATTAATTGTA
1 ATTTATATTAATTGTA
*
1994994 TTATTATATTA
1 AT-TTATATTA
1995005 TGGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (16 bp):
ATTTATATTAATTGTA
Found at i:1995000 original size:17 final size:17
Alignment explanation
Indices: 1994958--1995004 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1994948 TAATTATTAT
1994958 TATTATT-TATTTAAATTG
1 TATTATTATA-TT-AATTG
*
1994976 TAAT-TTATATTAATTG
1 TATTATTATATTAATTG
1994992 TATTATTATATTA
1 TATTATTATATTA
1995005 TGGAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 8 0.32
17 12 0.48
18 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
TATTATTATATTAATTG
Found at i:1996150 original size:39 final size:40
Alignment explanation
Indices: 1996107--1996184 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
1996097 GGAATGCTGG
*
1996107 ATATTGTTTTG-ATTACTG-AGTGAATTGTGAAAATACTGA
1 ATATTGTTATGTA-TACTGCAGTGAATTGTGAAAATACTGA
* * *
1996146 ATATTGTTATGTATATTGCATTGAATTGTGAAATTACTG
1 ATATTGTTATGTATACTGCAGTGAATTGTGAAAATACTG
1996185 GAGTAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 14 0.42
40 19 0.58
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (40 bp):
ATATTGTTATGTATACTGCAGTGAATTGTGAAAATACTGA
Found at i:2003337 original size:21 final size:21
Alignment explanation
Indices: 2003291--2003337 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
2003281 AAAATAATAT
* * *
2003291 AACACAATAAAATTTTATACA
1 AACATAATAAAATATTATAAA
2003312 AACATAATAAAA-ATTATAAA
1 AACATAATAAAATATTATAAA
2003332 ATACAT
1 A-ACAT
2003338 TATTAATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.28
Consensus pattern (21 bp):
AACATAATAAAATATTATAAA
Found at i:2003836 original size:35 final size:35
Alignment explanation
Indices: 2003794--2003864 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
2003784 ACGGTAAATC
2003794 AAAGTATAGCTTTAGCCAAAAAATGTAATGAGTAA
1 AAAGTATAGCTTTAGCCAAAAAATGTAATGAGTAA
2003829 AAAGTATAGCTTTAGCCAAAAAATGTAATGAGTAA
1 AAAGTATAGCTTTAGCCAAAAAATGTAATGAGTAA
2003864 A
1 A
2003865 CTACACTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.25
Consensus pattern (35 bp):
AAAGTATAGCTTTAGCCAAAAAATGTAATGAGTAA
Found at i:2012030 original size:12 final size:12
Alignment explanation
Indices: 2012013--2012068 Score: 51
Period size: 12 Copynumber: 4.5 Consensus size: 12
2012003 TGTTCATTCA
2012013 TTCATCAAGTTT
1 TTCATCAAGTTT
2012025 TTCATCAAGTGTTTT
1 TTCATCAA--G-TTT
**
2012040 TTCATCAAGTCA
1 TTCATCAAGTTT
*
2012052 TTAATCAAG-TT
1 TTCATCAAGTTT
2012063 TTCATC
1 TTCATC
2012069 TGTGGAATAC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
11 5 0.14
12 17 0.49
13 1 0.03
14 1 0.03
15 11 0.31
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.46
Consensus pattern (12 bp):
TTCATCAAGTTT
Found at i:2017206 original size:6 final size:6
Alignment explanation
Indices: 2017174--2017216 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
2017164 AAAAATAAAC
* *
2017174 ATTTTA ATTTTA ATTTTT ATTTATTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT A-TT-TTT ATTTTT ATTTTT ATTTT
2017217 GCAGGGAGAC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
6 26 0.76
7 4 0.12
8 4 0.12
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (6 bp):
ATTTTT
Found at i:2017990 original size:3 final size:3
Alignment explanation
Indices: 2017984--2018008 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2017974 ACAAAAAAAT
2017984 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2018009 AAATAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2031098 original size:28 final size:28
Alignment explanation
Indices: 2031042--2031105 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
2031032 TTTTTTTGGT
* **
2031042 ATATTTTGGTAAATAAAAAAAAATTATA
1 ATATTTTGATAAATAAAAAAAAAGGATA
2031070 ATATTTTGATAAATAAAAAAAAAGGATA
1 ATATTTTGATAAATAAAAAAAAAGGATA
*
2031098 ACATTTTG
1 ATATTTTG
2031106 GTTATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (28 bp):
ATATTTTGATAAATAAAAAAAAAGGATA
Found at i:2032517 original size:22 final size:22
Alignment explanation
Indices: 2032489--2032532 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2032479 AACTTTAAAC
2032489 AGAAATTACAAAGAAACCAAGG
1 AGAAATTACAAAGAAACCAAGG
*
2032511 AGAAATTACAAAGAAACTAAGG
1 AGAAATTACAAAGAAACCAAGG
2032533 CTAGTTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.59, C:0.11, G:0.18, T:0.11
Consensus pattern (22 bp):
AGAAATTACAAAGAAACCAAGG
Found at i:2032677 original size:22 final size:22
Alignment explanation
Indices: 2032649--2032691 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2032639 TACTAACTTT
2032649 AAAGAGAAATTACAAAGAAACC
1 AAAGAGAAATTACAAAGAAACC
2032671 AAAGAGAAATTACAAAGAAAC
1 AAAGAGAAATTACAAAGAAAC
2032692 TAAGGCTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.65, C:0.12, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAGAGAAATTACAAAGAAACC
Found at i:2032701 original size:164 final size:169
Alignment explanation
Indices: 2032430--2032844 Score: 687
Period size: 164 Copynumber: 2.4 Consensus size: 169
2032420 GTTTAGCTTT
* * *
2032430 GTTTTATACAAGTTATTAGATCAAATGTAAATCAACAACTAATCCTACTAACTTTAAACAGAAAT
1 GTTTTATACAAGTCATTACATCAAATGTAAATCAACAACTAATCCTACTAACTTTAAAGAGAAAT
*
2032495 TACAAAGAAACCAAGGAGAAATTACAAAGAAACTAAGGCTAGTTACATAGAAAAAAACTGAACAA
66 TACAAAGAAACCAAAGAGAAATTACAAAGAAACTAAGGCTAGTTACATAGAAAAAAACTGAACAA
2032560 CTAACCCTACCAACTTTG-A-A-G-AT-GTTTTATACAA
131 CTAACCCTACCAACTTTGAAGATGTATAGTTTTATACAA
2032594 GTTTTATACAAGTCATTACATCAAATGTAAATCAACAACTAATCCTACTAACTTTAAAGAGAAAT
1 GTTTTATACAAGTCATTACATCAAATGTAAATCAACAACTAATCCTACTAACTTTAAAGAGAAAT
2032659 TACAAAGAAACCAAAGAGAAATTACAAAGAAACTAAGGCTAGTTACATAGAAAAAAACTGAACAA
66 TACAAAGAAACCAAAGAGAAATTACAAAGAAACTAAGGCTAGTTACATAGAAAAAAACTGAACAA
2032724 CTAACCCTACCAACTTTGAAGATGTTTTATACAAGTTTTATACAA
131 CTAACCCTACCAACTTTGAAGATG---TAT---AGTTTTATACAA
* *
2032769 GTTTTATACAAGTCATTACATCAAATGTAAATCAACAACTAATCCTACTAACTTTGAAGACAAAT
1 GTTTTATACAAGTCATTACATCAAATGTAAATCAACAACTAATCCTACTAACTTTAAAGAGAAAT
2032834 TACAAAGAAAC
66 TACAAAGAAAC
2032845 TAAGGCTAGT
Statistics
Matches: 234, Mismatches: 6, Indels: 11
0.93 0.02 0.04
Matches are distributed among these distances:
164 144 0.62
165 1 0.00
166 1 0.00
167 1 0.00
171 2 0.01
175 85 0.36
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (169 bp):
GTTTTATACAAGTCATTACATCAAATGTAAATCAACAACTAATCCTACTAACTTTAAAGAGAAAT
TACAAAGAAACCAAAGAGAAATTACAAAGAAACTAAGGCTAGTTACATAGAAAAAAACTGAACAA
CTAACCCTACCAACTTTGAAGATGTATAGTTTTATACAA
Found at i:2032763 original size:11 final size:11
Alignment explanation
Indices: 2032747--2032781 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
2032737 CTTTGAAGAT
2032747 GTTTTATACAA
1 GTTTTATACAA
2032758 GTTTTATACAA
1 GTTTTATACAA
2032769 GTTTTATACAA
1 GTTTTATACAA
2032780 GT
1 GT
2032782 CATTACATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (11 bp):
GTTTTATACAA
Found at i:2038671 original size:27 final size:27
Alignment explanation
Indices: 2038639--2038693 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
2038629 ATGTTGGAAA
2038639 TGAAACTCTCAATAGCCATCCAAATAT
1 TGAAACTCTCAATAGCCATCCAAATAT
*
2038666 TGAAACTGTCAATAGCCATCCAAATAT
1 TGAAACTCTCAATAGCCATCCAAATAT
2038693 T
1 T
2038694 CAAAAGCTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (27 bp):
TGAAACTCTCAATAGCCATCCAAATAT
Found at i:2045583 original size:19 final size:19
Alignment explanation
Indices: 2045543--2045585 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2045533 ACTACAAAAT
* *
2045543 AATTCAAAATATTTTTTAA
1 AATTCAAAATATATTATAA
2045562 AATTCAAAATA-ATTATACA
1 AATTCAAAATATATTATA-A
2045581 AATTC
1 AATTC
2045586 CTAATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTCAAAATATATTATAA
Found at i:2045613 original size:21 final size:21
Alignment explanation
Indices: 2045588--2045650 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
2045578 ACAAATTCCT
2045588 AATTTTATATATTTTTTAAAA
1 AATTTTATATATTTTTTAAAA
* * *
2045609 AATTTTA-AAAATTTATAAATA
1 AATTTTATATATTTTTTAAA-A
*
2045630 AATTTTAT-TTTTTTTCTAAAA
1 AATTTTATATATTTTT-TAAAA
2045651 TAATAATTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
20 9 0.28
21 19 0.59
22 4 0.12
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTTTATATATTTTTTAAAA
Found at i:2048328 original size:20 final size:20
Alignment explanation
Indices: 2048303--2048347 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
2048293 GAACCAGACT
*
2048303 GAACCGGGCGGTCGGACCGG
1 GAACCGGGCGGTCGGACCAG
2048323 GAACCGGGCGGTCGGACCAG
1 GAACCGGGCGGTCGGACCAG
2048343 GAACC
1 GAACC
2048348 AGCCAGGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.31, G:0.44, T:0.04
Consensus pattern (20 bp):
GAACCGGGCGGTCGGACCAG
Found at i:2050892 original size:16 final size:16
Alignment explanation
Indices: 2050871--2050912 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2050861 AAAATTTATA
*
2050871 TTTTCTATCTTTCCAT
1 TTTTCTATCTTTCCAC
2050887 TTTTCTA-CTTTTCCAC
1 TTTTCTATC-TTTCCAC
*
2050903 ATTTCTATCT
1 TTTTCTATCT
2050913 ACTCTACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.14, C:0.26, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTCTATCTTTCCAC
Found at i:2059280 original size:15 final size:16
Alignment explanation
Indices: 2059254--2059283 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2059244 ATTTAAATTT
2059254 TTTTATAATTAATAAA
1 TTTTATAATTAATAAA
2059270 TTTTA-AATTAATAA
1 TTTTATAATTAATAA
2059284 TGATAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTATAATTAATAAA
Found at i:2061147 original size:81 final size:82
Alignment explanation
Indices: 2061043--2061205 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 82
2061033 CAATCAAGCA
2061043 AGTAGATCGATTTTGATATCTTCAATTTCAATCAATTTATTTTAAATAATATTTATATATATATA
1 AGTAGATCGATTTTGATATCTTCAATTTCAATCAATTTATTTTAAATAATATTTATATATATATA
2061108 TATATATTAGGATTTTT
66 TATATATTAGGATTTTT
2061125 AGTAGATCGA-TTTGATATCTTCAATTTCAATCAATTTATTTTAAATAATATTTATATATATATA
1 AGTAGATCGATTTTGATATCTTCAATTTCAATCAATTTATTTTAAATAATATTTATATATATATA
2061189 TATATATTAGGATTTTT
66 TATATATTAGGATTTTT
2061206 CCCAATTCGG
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 71 0.88
82 10 0.12
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (82 bp):
AGTAGATCGATTTTGATATCTTCAATTTCAATCAATTTATTTTAAATAATATTTATATATATATA
TATATATTAGGATTTTT
Found at i:2061325 original size:31 final size:31
Alignment explanation
Indices: 2061290--2061355 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
2061280 CAACATAGTT
*
2061290 ATTGAATTATTCGAATTTTTTTATTTAAGTC
1 ATTGAATTATTCGAAATTTTTTATTTAAGTC
*
2061321 ATTGAATTATTTGAAATTTTTTATTTAAGTC
1 ATTGAATTATTCGAAATTTTTTATTTAAGTC
2061352 ATTG
1 ATTG
2061356 GACTGTTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.55
Consensus pattern (31 bp):
ATTGAATTATTCGAAATTTTTTATTTAAGTC
Found at i:2065301 original size:1 final size:1
Alignment explanation
Indices: 2065297--2065324 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2065287 TCCTCCTCCA
2065297 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
2065325 AAATAGTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2068965 original size:21 final size:21
Alignment explanation
Indices: 2068915--2068966 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
2068905 AGGAGGCTTC
* *
2068915 AAAGAAGGAAGAATAGACGTG
1 AAAGAAGGGAGAAGAGACGTG
2068936 AAAGAAGGGAGAAGAGACGTG
1 AAAGAAGGGAGAAGAGACGTG
*
2068957 AACGAAGGGA
1 AAAGAAGGGA
2068967 CATAATTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.38, T:0.06
Consensus pattern (21 bp):
AAAGAAGGGAGAAGAGACGTG
Found at i:2070250 original size:21 final size:22
Alignment explanation
Indices: 2070221--2070263 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2070211 TCTTAGCAAC
2070221 TAAATAACTCAAT-TTTTTTTTA
1 TAAATAACTC-ATGTTTTTTTTA
2070243 TAAA-AACTCATGTTTTTTTTA
1 TAAATAACTCATGTTTTTTTTA
2070264 AGAAAAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 2 0.10
21 14 0.70
22 4 0.20
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
TAAATAACTCATGTTTTTTTTA
Found at i:2072734 original size:24 final size:24
Alignment explanation
Indices: 2072703--2072751 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2072693 ACTCCACTAA
2072703 TCTCTTTTTAGGAATACAATAATC
1 TCTCTTTTTAGGAATACAATAATC
2072727 TCTCTTTTTAGGAATACAATAATC
1 TCTCTTTTTAGGAATACAATAATC
2072751 T
1 T
2072752 TCAGGATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (24 bp):
TCTCTTTTTAGGAATACAATAATC
Found at i:2077503 original size:15 final size:15
Alignment explanation
Indices: 2077483--2077513 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2077473 ACAACAACAT
2077483 AACTCTTGAACTTTC
1 AACTCTTGAACTTTC
*
2077498 AACTCTTGACCTTTC
1 AACTCTTGAACTTTC
2077513 A
1 A
2077514 CTTACATAAC
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:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTCTTGAACTTTC
Found at i:2078821 original size:11 final size:12
Alignment explanation
Indices: 2078798--2078826 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
2078788 TATAAAATTT
2078798 AAAAATCATTAA
1 AAAAATCATTAA
2078810 AAAAATCA-TAA
1 AAAAATCATTAA
2078821 AAAAAT
1 AAAAAT
2078827 TTTATAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAATCATTAA
Found at i:2085289 original size:24 final size:24
Alignment explanation
Indices: 2085252--2085324 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
2085242 GGTAAGACAT
2085252 TTTCCACAGCTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
* *
2085276 TTTCCACTGTTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
*
2085300 TTTCCACAGCTCCTCTATTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
2085324 T
1 T
2085325 ATCGATTGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.12, C:0.47, G:0.04, T:0.37
Consensus pattern (24 bp):
TTTCCACAGCTCCTCTCTTCACCC
Found at i:2097233 original size:29 final size:30
Alignment explanation
Indices: 2097169--2097234 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
2097159 ATAAATCTCA
* * *
2097169 AATT-TATACATGAATTTTGATTTAATGTGC
1 AATTGTATACATGAACTTTAATTT-AGGTGC
2097199 AATTGTATACATGAACTTTAATTT-GGTGC
1 AATTGTATACATGAACTTTAATTTAGGTGC
2097228 AATTGTA
1 AATTGTA
2097235 CACGTGAAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 11 0.34
30 4 0.12
31 17 0.53
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (30 bp):
AATTGTATACATGAACTTTAATTTAGGTGC
Found at i:2097242 original size:29 final size:30
Alignment explanation
Indices: 2097195--2097251 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
2097185 TTGATTTAAT
* *
2097195 GTGCAATTGTATACATG-AACTTTAATTTG
1 GTGCAATTGTACACATGAAACTCTAATTTG
*
2097224 GTGCAATTGTACACGTGAAACTCTAATT
1 GTGCAATTGTACACATGAAACTCTAATT
2097252 GTTGTTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (30 bp):
GTGCAATTGTACACATGAAACTCTAATTTG
Found at i:2097473 original size:29 final size:30
Alignment explanation
Indices: 2097441--2097504 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
2097431 AAATTTTATT
*
2097441 TATAAAATTGCACA-AAATCAAAGTTCATG
1 TATAAAATTGCACATAAACCAAAGTTCATG
* *
2097470 TATACAATTGCACATTAAACCATAGTTCATG
1 TATAAAATTGCACA-TAAACCAAAGTTCATG
2097501 TATA
1 TATA
2097505 GTTTTGAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 13 0.43
31 17 0.57
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (30 bp):
TATAAAATTGCACATAAACCAAAGTTCATG
Found at i:2098385 original size:13 final size:13
Alignment explanation
Indices: 2098367--2098391 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2098357 ATTTACAAGA
2098367 TTACATAATCAAT
1 TTACATAATCAAT
2098380 TTACATAATCAA
1 TTACATAATCAA
2098392 ATCAAATCTA
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:2104634 original size:26 final size:26
Alignment explanation
Indices: 2104605--2104725 Score: 91
Period size: 26 Copynumber: 4.4 Consensus size: 26
2104595 GTAAATGTCG
2104605 AATTTTTTAAACATTTAATATATTAA
1 AATTTTTTAAACATTTAATATATTAA
* * * *
2104631 AATTTTTTAAATCAGTAAATACTAATAT
1 AATTTTTTAAA-CATTTAATA-TATTAA
* ** **
2104659 AATTGTAATTAATTATTTCAAGTA-ATGTCG
1 AATT-T-TTTAAACATTT-AA-TATAT-TAA
2104689 AATTTTTTAAACATTTAATATATTAA
1 AATTTTTTAAACATTTAATATATTAA
2104715 AATTTTTTAAA
1 AATTTTTTAAA
2104726 TCAGTAAATA
Statistics
Matches: 70, Mismatches: 17, Indels: 16
0.68 0.17 0.16
Matches are distributed among these distances:
26 25 0.36
27 11 0.16
28 16 0.23
29 5 0.07
30 11 0.16
31 2 0.03
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (26 bp):
AATTTTTTAAACATTTAATATATTAA
Found at i:2104702 original size:84 final size:85
Alignment explanation
Indices: 2104584--2104757 Score: 341
Period size: 84 Copynumber: 2.1 Consensus size: 85
2104574 AATAAATTCG
2104584 AATTATTTCAAGTAAATGTCGAATTTTTTAAACATTTAATATATTAAAATTTTTTAAATCAGTAA
1 AATTATTTCAAGTAAATGTCGAATTTTTTAAACATTTAATATATTAAAATTTTTTAAATCAGTAA
2104649 ATACTAATATAATTGTAATT
66 ATACTAATATAATTGTAATT
2104669 AATTATTTCAAGT-AATGTCGAATTTTTTAAACATTTAATATATTAAAATTTTTTAAATCAGTAA
1 AATTATTTCAAGTAAATGTCGAATTTTTTAAACATTTAATATATTAAAATTTTTTAAATCAGTAA
2104733 ATACTAATATAATTGTAATT
66 ATACTAATATAATTGTAATT
2104753 AATTA
1 AATTA
2104758 ATTATTTCTT
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 76 0.85
85 13 0.15
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (85 bp):
AATTATTTCAAGTAAATGTCGAATTTTTTAAACATTTAATATATTAAAATTTTTTAAATCAGTAA
ATACTAATATAATTGTAATT
Found at i:2107178 original size:20 final size:20
Alignment explanation
Indices: 2107153--2107192 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2107143 TCTTTCAATT
* *
2107153 TTAAAATGAAATTTTTAAAA
1 TTAAAAAGAAATATTTAAAA
*
2107173 TTAAAAAGATATATTTAAAA
1 TTAAAAAGAAATATTTAAAA
2107193 GATCATGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
TTAAAAAGAAATATTTAAAA
Found at i:2116331 original size:10 final size:10
Alignment explanation
Indices: 2116316--2116345 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
2116306 TAAAAGACCC
2116316 AAAATAAAAA
1 AAAATAAAAA
2116326 AAAATAAAAA
1 AAAATAAAAA
2116336 AAAAGTAAAA
1 AAAA-TAAAA
2116346 GCAAATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAATAAAAA
Found at i:2120274 original size:19 final size:17
Alignment explanation
Indices: 2120235--2120274 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 17
2120225 AAAATCTAAA
2120235 ATGAAAATTTTAAAAAG
1 ATGAAAATTTTAAAAAG
*
2120252 ATGAATATTGTTAAAATAG
1 ATGAAAATT-TTAAAA-AG
2120271 ATGA
1 ATGA
2120275 TGTAAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 6 0.30
19 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (17 bp):
ATGAAAATTTTAAAAAG
Found at i:2121294 original size:252 final size:244
Alignment explanation
Indices: 2120951--2121454 Score: 635
Period size: 252 Copynumber: 2.0 Consensus size: 244
2120941 AAAAAAAGAG
** *
2120951 AAAAACATAATTAAAGAAGGAAAAAAAGGAAGTAATAAAATGAAAATGAAAAATCTTACTTAAAC
1 AAAAACATAATTAAAG-AGGAAAAAAAACAAGTAATAAAATGAAAAAGAAAAATCTTACTTAAAC
* *
2121016 TCGAATATATCTCTGCCATGTTTTCTTAGCAACCAAACAGAATATAAACCTTAAACAAATGCATT
65 TCGAATATATCTCTGCCATATTTTCTTAGCAACCAAACAGAAGATAAACCTTAAACAAAT--A--
* * * *
2121081 TGATAGCTTCCAAGCATAAAT-TGCT-GAATATCAAGCTAAGTACTAAATTACTGAAGTAACTCA
126 T-AT---TT--AAACA-AAATCTGCTAG-ATATCAAGCTAAGTACTAAACTACTCAAGTAACTAA
* *
2121144 TATTTTAGGGGA-AAAA-TAATTCAGCAATTAGATTTCAAAATCAAAGAAATCTATCAAACA
183 CATTTTAGGGGACAAAAGTAATTCAGCAATTAGATTACAAAATCAAAGAAATCTATCAAACA
*
2121204 CAAAAACATAATTAAAG-GGAAAAAAAACAAGTAATAAATTGAAAAAGAAAAATCTTA-TATAAA
1 -AAAAACATAATTAAAGAGGAAAAAAAACAAGTAATAAAATGAAAAAGAAAAATCTTACT-TAAA
* * * *
2121267 CTCGGATATATGT-TAGCCATATTTTCTTAGCAACCAAACAGACGATAAACCTTAACCAAATATA
64 CTCGAATATATCTCT-GCCATATTTTCTTAGCAACCAAACAGAAGATAAACCTTAAACAAATATA
* * *
2121331 TTTAAACAAAATCTGGTAGTTCTCAAGCTAAGTACTAAACTACTCAAGTAACTAACATTTTAGGG
128 TTTAAACAAAATCTGCTAGATATCAAGCTAAGTACTAAACTACTCAAGTAACTAACATTTTAGGG
2121396 GACAAAAGTTAATTCAGCAATTAGATTACAAAATCAAAGAAATCTATCAAACA
193 GACAAAAG-TAATTCAGCAATTAGATTACAAAATCAAAGAAATCTATCAAACA
2121449 AAAAAC
1 AAAAAC
2121455 CAAGACGTAA
Statistics
Matches: 224, Mismatches: 19, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
241 4 0.02
242 49 0.22
243 5 0.02
244 8 0.04
245 43 0.19
247 2 0.01
248 1 0.00
250 1 0.00
251 2 0.01
252 93 0.42
254 16 0.07
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (244 bp):
AAAAACATAATTAAAGAGGAAAAAAAACAAGTAATAAAATGAAAAAGAAAAATCTTACTTAAACT
CGAATATATCTCTGCCATATTTTCTTAGCAACCAAACAGAAGATAAACCTTAAACAAATATATTT
AAACAAAATCTGCTAGATATCAAGCTAAGTACTAAACTACTCAAGTAACTAACATTTTAGGGGAC
AAAAGTAATTCAGCAATTAGATTACAAAATCAAAGAAATCTATCAAACA
Found at i:2128497 original size:19 final size:19
Alignment explanation
Indices: 2128466--2128511 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2128456 GGCCTGATTA
*
2128466 AAAAATT-ATTAAAATTTC
1 AAAAATTAATAAAAATTTC
2128484 AAAAATATAATAAAAATTTC
1 AAAAAT-TAATAAAAATTTC
2128504 AATAAATT
1 AA-AAATT
2128512 TTGGTTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 1 0.04
20 13 0.54
21 4 0.17
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTAATAAAAATTTC
Found at i:2130209 original size:13 final size:13
Alignment explanation
Indices: 2130191--2130223 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2130181 CTCCCTAACA
2130191 GCGGTCCTACGTG
1 GCGGTCCTACGTG
2130204 GCGGTCCTACGTG
1 GCGGTCCTACGTG
*
2130217 GCAGTCC
1 GCGGTCC
2130224 AAATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.33, G:0.36, T:0.21
Consensus pattern (13 bp):
GCGGTCCTACGTG
Found at i:2133432 original size:18 final size:17
Alignment explanation
Indices: 2133411--2133447 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
2133401 ATATTTTTAT
*
2133411 AAATTTATTTTTAAATAA
1 AAATTTAATTTTAAA-AA
2133429 AAATTTAATTTTAAAAA
1 AAATTTAATTTTAAAAA
2133446 AA
1 AA
2133448 TTAAATATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTAATTTTAAAAA
Found at i:2135325 original size:9 final size:9
Alignment explanation
Indices: 2135311--2135341 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2135301 GTTAAACGAA
2135311 TCGAGTTAT
1 TCGAGTTAT
*
2135320 TCGAGTTAA
1 TCGAGTTAT
2135329 TCGAGTTAT
1 TCGAGTTAT
2135338 TCGA
1 TCGA
2135342 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:2135411 original size:9 final size:9
Alignment explanation
Indices: 2135394--2135430 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2135384 TCAGTTTTCG
2135394 AATTCGAAT
1 AATTCGAAT
*
2135403 AACTCGAAT
1 AATTCGAAT
2135412 AATTCGAAT
1 AATTCGAAT
2135421 AATTCGAAT
1 AATTCGAAT
2135430 A
1 A
2135431 TCAAATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:2136267 original size:5 final size:5
Alignment explanation
Indices: 2136257--2136287 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
2136247 CTCGAAAATT
2136257 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
2136288 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:2139501 original size:34 final size:34
Alignment explanation
Indices: 2139456--2139520 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2139446 ACTGTATACG
* *
2139456 TGAACAGTACCGTCA-ACATGAATAGTATCGTGCA
1 TGAACAATACCGT-ATACATAAATAGTATCGTGCA
*
2139490 TGAACAATACCGTATACTTAAATAGTATCGT
1 TGAACAATACCGTATACATAAATAGTATCGT
2139521 AAACGGCCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 1 0.04
34 26 0.96
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (34 bp):
TGAACAATACCGTATACATAAATAGTATCGTGCA
Found at i:2161318 original size:31 final size:32
Alignment explanation
Indices: 2161269--2161339 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
2161259 CGCGTGAACA
* * * *
2161269 ATAGTAAAAGGATCAAAGTGAGAA-TTTCATT
1 ATAGTACAAGGATAAAAGTGAAAACTTTCACT
*
2161300 ATAGTACAAGGGTAAAAGTGAAAACTTTCACT
1 ATAGTACAAGGATAAAAGTGAAAACTTTCACT
2161332 ATAGTACA
1 ATAGTACA
2161340 TATCAAAGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (32 bp):
ATAGTACAAGGATAAAAGTGAAAACTTTCACT
Found at i:2161350 original size:30 final size:28
Alignment explanation
Indices: 2161280--2161364 Score: 75
Period size: 32 Copynumber: 2.9 Consensus size: 28
2161270 TAGTAAAAGG
* *
2161280 ATCAAAGTGAGAATTTCATTATAGTACA
1 ATCAAAGTGAAAATTTCACTATAGTACA
*
2161308 AGGGTAAAAGTGAAAACTTTCACTATAGTACA
1 A---TCAAAGTGAAAA-TTTCACTATAGTACA
*
2161340 TATCAAAGTG-AAA-TTCACTACAGTA
1 -ATCAAAGTGAAAATTTCACTATAGTA
2161365 TAAGGGCCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
27 11 0.23
28 1 0.02
29 3 0.06
30 7 0.15
31 10 0.21
32 14 0.30
33 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (28 bp):
ATCAAAGTGAAAATTTCACTATAGTACA
Found at i:2163967 original size:3 final size:3
Alignment explanation
Indices: 2163959--2163994 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
2163949 ATATAGGGTG
2163959 ATA ATA ATA ATA ATA ATA ATA ATA ATA GATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
2163995 GATTGAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2168140 original size:70 final size:70
Alignment explanation
Indices: 2168046--2168187 Score: 275
Period size: 70 Copynumber: 2.0 Consensus size: 70
2168036 CCCTGTCAAT
*
2168046 TTCGAAAGTGAGCAATTAAGGATAATTAATCACGGCATTAACGTCATCAGTCAATTGTACATAAT
1 TTCGAAAGTGAGCAATTAAGGATAATTAATCACGGCATTAACGTCATCAATCAATTGTACATAAT
2168111 TTTGA
66 TTTGA
2168116 TTCGAAAGTGAGCAATTAAGGATAATTAATCACGGCATTAACGTCATCAATCAATTGTACATAAT
1 TTCGAAAGTGAGCAATTAAGGATAATTAATCACGGCATTAACGTCATCAATCAATTGTACATAAT
2168181 TTTGA
66 TTTGA
2168186 TT
1 TT
2168188 GATATAACAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (70 bp):
TTCGAAAGTGAGCAATTAAGGATAATTAATCACGGCATTAACGTCATCAATCAATTGTACATAAT
TTTGA
Found at i:2171457 original size:114 final size:115
Alignment explanation
Indices: 2171318--2171524 Score: 407
Period size: 114 Copynumber: 1.8 Consensus size: 115
2171308 TATTTTAGAG
2171318 GTATTTGCTTGCAAAGTTACACCTATCTTAGTGTTGTTTAAATATAAATAATTTTTTAAATTTAT
1 GTATTTGCTTGCAAAGTTACACCTATCTTAGTGTTGTTTAAATATAAATAATTTTTTAAATTTAT
2171383 TTTCGAAGCATTTATTTTAATGTTTTTAGTGTATTTTATATATTATATTT
66 TTTCGAAGCATTTATTTTAATGTTTTTAGTGTATTTTATATATTATATTT
2171433 GTATTTGCTT-CAAAGTTACACCTATCTTAGTGTTGTTTAAATATAAATAATTTTTTAAATTTAT
1 GTATTTGCTTGCAAAGTTACACCTATCTTAGTGTTGTTTAAATATAAATAATTTTTTAAATTTAT
2171497 TTTCGAAGCATTTATTTTAATGTTTTTA
66 TTTCGAAGCATTTATTTTAATGTTTTTA
2171525 AATGTTTTTA
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
114 82 0.89
115 10 0.11
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (115 bp):
GTATTTGCTTGCAAAGTTACACCTATCTTAGTGTTGTTTAAATATAAATAATTTTTTAAATTTAT
TTTCGAAGCATTTATTTTAATGTTTTTAGTGTATTTTATATATTATATTT
Found at i:2177304 original size:21 final size:22
Alignment explanation
Indices: 2177259--2177305 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
2177249 AAAAGAAGAT
*
2177259 AAATAAAAAAAATAAATTAATA
1 AAATAAAAAAAATAAATTAAAA
* *
2177281 AAATTAAATAAAT-AATTAAAA
1 AAATAAAAAAAATAAATTAAAA
2177302 AAAT
1 AAAT
2177306 CACTCCCCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATAAAAAAAATAAATTAAAA
Found at i:2190217 original size:28 final size:28
Alignment explanation
Indices: 2190185--2190259 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
2190175 TAAATTATTT
*
2190185 TTAAATTGAATATTGAAATATTGAAATA
1 TTAAATTGAATATTGAAAAATTGAAATA
** *
2190213 TTAAATTGGAA-ATAAAAAAATTGAAGTA
1 TTAAATT-GAATATTGAAAAATTGAAATA
*
2190241 TCAAATTGAATATTGAAAA
1 TTAAATTGAATATTGAAAA
2190260 CTAAATGATA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.08
28 32 0.84
29 3 0.08
ACGTcount: A:0.53, C:0.01, G:0.12, T:0.33
Consensus pattern (28 bp):
TTAAATTGAATATTGAAAAATTGAAATA
Found at i:2198096 original size:195 final size:196
Alignment explanation
Indices: 2197845--2198221 Score: 528
Period size: 195 Copynumber: 1.9 Consensus size: 196
2197835 TTGGGAAAAA
* * **
2197845 AAAACAATGTAATTAATTGCTTAATTTTCCTGCAGTTTCTTTTCTCAGTAACCAAACACAAATTG
1 AAAACAATGTAATTAATTGATTAATTTTCCTGCAGTTCCTTTTCTCAGTAACCAAACACAAAAAG
* *
2197910 AATCAAACAAATCTAAG-AACAAGAAA-CCATCCTTTCCA-CACCAATTACTAG-AAAACCAAAT
66 AATCAAACAAATCTAAGAAACAA-AAAGCCATCCTTACCACCA-CAATAACTAGCAAAACCAAAT
2197971 TATGCATTTAACACTTCATTATCCAACCAAAAATTGGAACTTTCAAAATATAAAGTCATAAATCA
129 TATGCATTTAACACTTCATTATCCAACCAAAAATTGGAACTTTCAAAATATAAAGTCATAAATCA
2198036 GTT
194 GTT
* *
2198039 AAAACTAATGTAATTAATTGATTAATTTTCCTGGAGTTCCTTTTCTCAGTGACCAAACACAAAAA
1 AAAAC-AATGTAATTAATTGATTAATTTTCCTGCAGTTCCTTTTCTCAGTAACCAAACACAAAAA
* * * *
2198104 GAATCTAACAAATTTGAGAAACAAAAAGCCATTCTTACCACCACAATAACTAGCAAAACCAAATT
65 GAATCAAACAAATCTAAGAAACAAAAAGCCATCCTTACCACCACAATAACTAGCAAAACCAAATT
* ** * * **
2198169 CTGCATTTAGTATTTCATTATCCAACGAAAAATTTTAACTTTCAAAATATAAA
130 ATGCATTTAACACTTCATTATCCAACCAAAAATTGGAACTTTCAAAATATAAA
2198222 ACAAATAAAA
Statistics
Matches: 159, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
194 5 0.03
195 71 0.45
196 24 0.15
197 59 0.37
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.30
Consensus pattern (196 bp):
AAAACAATGTAATTAATTGATTAATTTTCCTGCAGTTCCTTTTCTCAGTAACCAAACACAAAAAG
AATCAAACAAATCTAAGAAACAAAAAGCCATCCTTACCACCACAATAACTAGCAAAACCAAATTA
TGCATTTAACACTTCATTATCCAACCAAAAATTGGAACTTTCAAAATATAAAGTCATAAATCAGT
T
Found at i:2202603 original size:6 final size:6
Alignment explanation
Indices: 2202592--2202616 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2202582 GAATCTCACG
2202592 TTTATT TTTATT TTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT T
2202617 GGAAATACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTATT
Found at i:2202609 original size:85 final size:85
Alignment explanation
Indices: 2202512--2202669 Score: 230
Period size: 85 Copynumber: 1.9 Consensus size: 85
2202502 ACATTTTCAC
* *
2202512 TTTTATTATTATTATTT-TCTT-GAAATAATGTGTTTGGTTGCCGAGAAACTGAAGTGAACAGTT
1 TTTTATTATTATT-TTTAT-TTGGAAATAATGTGTTTGGTTGCAGAGAAACTGAAGTAAACAGTT
2202575 TAAAAGAGAATCTCACGTTTAT
64 TAAAAGAGAATCTCACGTTTAT
* * * *
2202597 TTTTATTTTTATTTTTATTTGGAAATACTGTGTTTGGTTGCATAGAAACTGAAGTAAATAGTTTA
1 TTTTATTATTATTTTTATTTGGAAATAATGTGTTTGGTTGCAGAGAAACTGAAGTAAACAGTTTA
2202662 AAAGAGAA
66 AAAGAGAA
2202670 AATGAATACT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
84 5 0.08
85 60 0.92
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (85 bp):
TTTTATTATTATTTTTATTTGGAAATAATGTGTTTGGTTGCAGAGAAACTGAAGTAAACAGTTTA
AAAGAGAATCTCACGTTTAT
Found at i:2213886 original size:54 final size:56
Alignment explanation
Indices: 2213791--2214005 Score: 179
Period size: 57 Copynumber: 3.8 Consensus size: 56
2213781 ATCTTGGGCA
* * * * * *
2213791 AAAAAAAAGTTCAAGCCCCATTGTGGGAAGTATTGCCAAGTTCAGG-GC-CTTGAAT
1 AAAAAAAAGTTCAGGCCCCAATGTGAGAA-AATTGCTAAGTTCAGGACCACTTGAAT
* * *
2213846 AAAAAAAAGTTCAGGCCCCACTGTGAGAAAATTGCTAAGTTTAGGACCTAACTTGGAT
1 AAAAAAAAGTTCAGGCCCCAATGTGAGAAAATTGCTAAGTTCAGGACC--ACTTGAAT
* * * * * *
2213904 GAAACAAA-TTCAGGCCCCAATATGAGAAAATTGCTAAGTTTAGGACCTAACTTGGAC
1 AAAAAAAAGTTCAGGCCCCAATGTGAGAAAATTGCTAAGTTCAGGACC--ACTTGAAT
* *
2213961 GAAAAAAA-TTCAGGCCCCAATGT-AGGAAAAGTTGCCAAGTTCAGG
1 AAAAAAAAGTTCAGGCCCCAATGTGA-GAAAA-TTGCTAAGTTCAGG
2214006 CCCTAAAAAG
Statistics
Matches: 137, Mismatches: 17, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
54 13 0.09
55 27 0.20
56 1 0.01
57 72 0.53
58 24 0.18
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (56 bp):
AAAAAAAAGTTCAGGCCCCAATGTGAGAAAATTGCTAAGTTCAGGACCACTTGAAT
Found at i:2213921 original size:57 final size:57
Alignment explanation
Indices: 2213847--2214011 Score: 233
Period size: 57 Copynumber: 2.9 Consensus size: 57
2213837 GCCTTGAATA
* *
2213847 AAAAAAAGTTCAGGCCCCACTGTGAGAAAATTGCTAAGTTTAGGACCTAACTTGGATG
1 AAAAAAA-TTCAGGCCCCAATGTGAGAAAATTGCTAAGTTTAGGACCTAACTTGGACG
* *
2213905 AAACAAATTCAGGCCCCAATATGAGAAAATTGCTAAGTTTAGGACCTAACTTGGACG
1 AAAAAAATTCAGGCCCCAATGTGAGAAAATTGCTAAGTTTAGGACCTAACTTGGACG
* * *
2213962 AAAAAAATTCAGGCCCCAATGT-AGGAAAAGTTGCCAAGTTCAGGCCCTAA
1 AAAAAAATTCAGGCCCCAATGTGA-GAAAA-TTGCTAAGTTTAGGACCTAA
2214012 AAAGTAATTT
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
56 1 0.01
57 72 0.75
58 23 0.24
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (57 bp):
AAAAAAATTCAGGCCCCAATGTGAGAAAATTGCTAAGTTTAGGACCTAACTTGGACG
Found at i:2214643 original size:18 final size:18
Alignment explanation
Indices: 2214620--2214656 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2214610 TTTTTCACTC
2214620 TATATGCTAATGCATAGG
1 TATATGCTAATGCATAGG
2214638 TATATGCTAATGCATAGG
1 TATATGCTAATGCATAGG
2214656 T
1 T
2214657 GAACTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.35
Consensus pattern (18 bp):
TATATGCTAATGCATAGG
Found at i:2218981 original size:2 final size:2
Alignment explanation
Indices: 2218976--2219001 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2218966 AAAATCTTCA
2218976 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
2219002 TTGCTTCCTT
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:2223528 original size:19 final size:20
Alignment explanation
Indices: 2223495--2223533 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
2223485 TCTTCTTCTT
*
2223495 TTTTTTAAAATAA-TTATAA
1 TTTTTTAAAACAATTTATAA
*
2223514 TTTTTTAGAACAATTTATAA
1 TTTTTTAAAACAATTTATAA
2223534 AATTTTGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (20 bp):
TTTTTTAAAACAATTTATAA
Found at i:2223565 original size:20 final size:20
Alignment explanation
Indices: 2223528--2223588 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
2223518 TTAGAACAAT
**
2223528 TTATAAA-ATTTTGGAATTC
1 TTATAAATATTTTAAAATTC
2223547 TTATAAATATTTTAAAATT-
1 TTATAAATATTTTAAAATTC
*
2223566 TTGA-AAATTATTTTAAATTTC
1 TT-ATAAA-TATTTTAAAATTC
2223587 TT
1 TT
2223589 TTTGTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
19 12 0.34
20 21 0.60
21 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.52
Consensus pattern (20 bp):
TTATAAATATTTTAAAATTC
Found at i:2223582 original size:29 final size:29
Alignment explanation
Indices: 2223526--2223583 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2223516 TTTTAGAACA
* *
2223526 ATTTATAAAATTTTGGAATTCTTATAAAT
1 ATTTATAAAATTTTGAAATTATTATAAAT
*
2223555 ATTT-TAAAATTTTGAAAATTATTTTAAAT
1 ATTTATAAAATTTTG-AAATTATTATAAAT
2223584 TTCTTTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (29 bp):
ATTTATAAAATTTTGAAATTATTATAAAT
Found at i:2227673 original size:14 final size:14
Alignment explanation
Indices: 2227654--2227680 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2227644 CTAAATAACT
2227654 ATTAAATTAAATTA
1 ATTAAATTAAATTA
2227668 ATTAAATTAAATT
1 ATTAAATTAAATT
2227681 CCAAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAAATTAAATTA
Found at i:2229172 original size:31 final size:31
Alignment explanation
Indices: 2229126--2229184 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2229116 CACAAATTTG
*
2229126 TTAATTTTGGTCCCTAAATTTGTTAATTTTCT
1 TTAATTTTAGTCCCTAAATTT-TTAATTTTCT
2229158 TTAA-TTTAGTCCCTAAATTTTTAATTT
1 TTAATTTTAGTCCCTAAATTTTTAATTT
2229185 AGTCCTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 7 0.27
31 15 0.58
32 4 0.15
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.56
Consensus pattern (31 bp):
TTAATTTTAGTCCCTAAATTTTTAATTTTCT
Found at i:2229182 original size:20 final size:20
Alignment explanation
Indices: 2229157--2229195 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2229147 GTTAATTTTC
2229157 TTTAATTTAGTCCCTAAATT
1 TTTAATTTAGTCCCTAAATT
*
2229177 TTTAATTTAGTCCTTAAAT
1 TTTAATTTAGTCCCTAAAT
2229196 CTTGGATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (20 bp):
TTTAATTTAGTCCCTAAATT
Found at i:2229321 original size:22 final size:22
Alignment explanation
Indices: 2229277--2229322 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2229267 AAACATATAA
* * *
2229277 TTTTATATTTTGTTTTCTATTT
1 TTTTATATTTTATATACTATTT
2229299 TTTTATATTTTATATACT-TTT
1 TTTTATATTTTATATACTATTT
2229320 TTT
1 TTT
2229323 AAAGAAATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTTATATTTTATATACTATTT
Found at i:2229636 original size:17 final size:17
Alignment explanation
Indices: 2229614--2229666 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
2229604 TATTATATCA
2229614 ATATAATATAAAATATT
1 ATATAATATAAAATATT
* *
2229631 ATATAATATGAATATGAAT
1 ATATAATAT-AAAAT-ATT
*
2229650 ATATAATACAAAATATT
1 ATATAATATAAAATATT
2229667 TCTCTACCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 11 0.38
18 8 0.28
19 10 0.34
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (17 bp):
ATATAATATAAAATATT
Found at i:2238945 original size:6 final size:6
Alignment explanation
Indices: 2238934--2238959 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2238924 CAAGAATATT
2238934 ACTTGC ACTTGC ACTTGC ACTTGC AC
1 ACTTGC ACTTGC ACTTGC ACTTGC AC
2238960 ATACTACTGA
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:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (6 bp):
ACTTGC
Found at i:2249962 original size:21 final size:21
Alignment explanation
Indices: 2249936--2249984 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2249926 TATTTAATTT
*
2249936 TATATA-ATATAATTTAAAAAA
1 TATATACATA-AAATTAAAAAA
2249957 TATATACATAAAATT-AAAAA
1 TATATACATAAAATTAAAAAA
2249977 TAT-TACAT
1 TATATACAT
2249985 TACATCAGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 5 0.19
20 8 0.31
21 10 0.38
22 3 0.12
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (21 bp):
TATATACATAAAATTAAAAAA
Found at i:2249976 original size:22 final size:21
Alignment explanation
Indices: 2249936--2249976 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2249926 TATTTAATTT
* *
2249936 TATATAATATAATTTAAAAAA
1 TATATAATAAAATTAAAAAAA
2249957 TATATACATAAAATTAAAAA
1 TATATA-ATAAAATTAAAAA
2249977 TATTACATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TATATAATAAAATTAAAAAAA
Found at i:2250466 original size:16 final size:17
Alignment explanation
Indices: 2250445--2250476 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2250435 TCTTTCACTT
2250445 TATTTATTT-ATCCATA
1 TATTTATTTAATCCATA
2250461 TATTTATTTAATCCAT
1 TATTTATTTAATCCAT
2250477 CCCCCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.31, C:0.12, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTTATTTAATCCATA
Found at i:2251428 original size:241 final size:242
Alignment explanation
Indices: 2250869--2251588 Score: 1033
Period size: 242 Copynumber: 3.0 Consensus size: 242
2250859 GGTCACTTGA
* *
2250869 GATTTTCTCTGATTTTTCTTATCTCTTGTTTGTTTTCTCGGAATTTCTGCATTTCCTCGTCTGGG
1 GATTTTCTCTGATTTTTCTTATCTCTTGTTTGTTTCCTCGGAATTTCTGCATTTTCTCGT-TGGG
* * * * * * *
2250934 TCATCTCCAATTTTTGATTGCTTTTATGTTTTGTTTTTCGTT--CATAATGAGTTCT-CTTCTAC
65 TCATCTCCAATATTTGATAGATTTTATGTTTTTTTTTTCATTGGC-T-AT-A-TTCTGCTCCT-T
** * * *
2250996 TCCTTTGTTTTGTTT-AATCATTAATTTCGATATGTTGTTTAAGATGATTG-ATTTTCTAATTAA
125 TGGTTTGTTTTTTTTAAATCATTAATTTGGATATGTTGTTTAAGATTATTGAATTTTCTAATTAA
* * *
2251059 ATTGGCTACACTGCATTTGATAATTCACTCTGATTTACTTGTTTATTATTACT
190 ATTGGCTACACTGCATTTGATAATTTACTCTGATTTATTTGTTTATGATTACT
* *
2251112 GATTTTCTCTGTTTTTTCTTATCTCTTGTTTGTTTCCTTGGAATTTCTGCATTTTCTCGTTGGGT
1 GATTTTCTCTGATTTTTCTTATCTCTTGTTTGTTTCCTCGGAATTTCTGCATTTTCTCGTTGGGT
2251177 CATCTCCAATATTTGATAGATTTTATGTTTTTTTTTTCATTGGCTATATTCTGCTCCTTTGGTTT
66 CATCTCCAATATTTGATAGATTTTATGTTTTTTTTTTCATTGGCTATATTCTGCTCCTTTGGTTT
* * *
2251242 TTTTTTTTTAAATCATTAATTTGGACATGTTGTTTAAGATTACTGAATTTTCTAATTAAATTGGC
131 GTTTTTTTTAAATCATTAATTTGGATATGTTGTTTAAGATTATTGAATTTTCTAATTAAATTGGC
*
2251307 TACATTGCATTTGATAATTTACTCTGATTTATTTGTTTATGATTACT
196 TACACTGCATTTGATAATTTACTCTGATTTATTTGTTTATGATTACT
2251354 GATTTTCTCTG-TTTTTCTTATCTCTTGTTTGTTTCCTCGGAATTTCTGCATTTTCTCGTTGGGT
1 GATTTTCTCTGATTTTTCTTATCTCTTGTTTGTTTCCTCGGAATTTCTGCATTTTCTCGTTGGGT
* *
2251418 CATCTCCAATATTTGATATATTTTA--ATTTTTTTTTCATTGGCTATATTCTGCTCCTTTGGTTT
66 CATCTCCAATATTTGATAGATTTTATGTTTTTTTTTTCATTGGCTATATTCTGCTCCTTTGGTTT
*
2251481 GTTTTTTTTAAATCATTAATTTGGATATGTTGTTTTAAGATTATTGAATTTTCTAATTAAATTAG
131 GTTTTTTTTAAATCATTAATTTGGATATGTTG-TTTAAGATTATTGAATTTTCTAATTAAATTGG
* ** * **
2251546 CTATACTGTGTTTGATAATTTGCTCTGATTTATAAGTTTATGA
195 CTACACTGCATTTGATAATTTACTCTGATTTATTTGTTTATGA
2251589 ATGTATTGCT
Statistics
Matches: 434, Mismatches: 37, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
239 67 0.15
240 81 0.19
241 112 0.26
242 116 0.27
243 57 0.13
244 1 0.00
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.54
Consensus pattern (242 bp):
GATTTTCTCTGATTTTTCTTATCTCTTGTTTGTTTCCTCGGAATTTCTGCATTTTCTCGTTGGGT
CATCTCCAATATTTGATAGATTTTATGTTTTTTTTTTCATTGGCTATATTCTGCTCCTTTGGTTT
GTTTTTTTTAAATCATTAATTTGGATATGTTGTTTAAGATTATTGAATTTTCTAATTAAATTGGC
TACACTGCATTTGATAATTTACTCTGATTTATTTGTTTATGATTACT
Found at i:2255210 original size:3 final size:3
Alignment explanation
Indices: 2255202--2255238 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2255192 CTTCCTTTAA
2255202 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2255239 AAGAATTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2257664 original size:104 final size:104
Alignment explanation
Indices: 2257305--2257998 Score: 521
Period size: 104 Copynumber: 6.6 Consensus size: 104
2257295 GTAGTATCTA
* * *
2257305 TATAGTAGTTGATGATTTCATTTGAACTATAGTTTGATTCGTAAAAGCTGAA-CAATGTATACAC
1 TATAGTAGTTGATGATTTCATTTGAACTATAGTTTGATTCGTAAAACCTGAATC-ATGGATACAT
* **
2257369 GAATTATTAAATTTTGGCATTCCGAAATTCATAGTATTGG
65 GAATTAGTAAATTTTGGCATTTAGAAATTCATAGTATTGG
* **
2257409 TATAGTAGTTGATGATTTCATTTGAACTATAGTTTGGTTCGTAAAACCTCG-ATCATGGATATTT
1 TATAGTAGTTGATGATTTCATTTGAACTATAGTTTGATTCGTAAAACCT-GAATCATGGATA-CA
* * * ** * *
2257473 TG-CTTGGTAACTTTTCCTCCTATTAAGGCAAACTACA-A-TATTGG
64 TGAATTAGTAAATTTT--GGC-ATTTA-G-AAA-TTCATAGTATTGG
* * ** * * *
2257517 TTTAGTAGTAGATGATTTGGTTTCAACTGTAGTTTGATTCGTAAAACCTGAATCATGGATACACG
1 TATAGTAGTTGATGATTTCATTTGAACTATAGTTTGATTCGTAAAACCTGAATCATGGATACATG
* *
2257582 AATCATTAAATTTTGGCATGTT-GAAATTCATAGTATTGG
66 AATTAGTAAATTTTGGCAT-TTAGAAATTCATAGTATTGG
* * * * ** *
2257621 TATAGTAGTTGATGATTTCATTTGAACTATATTTTGGTACGTAAAACCTCAATCATGGATATTTT
1 TATAGTAGTTGATGATTTCATTTGAACTATAGTTTGATTCGTAAAACCTGAATCATGGATACATG
** ** * * * * *
2257686 TCTCGGTAACTATTCCT-CCTATTACACAAATT-ACAGTATTGG
66 AATTAGTAA--ATT-TTGGC-ATT-TAGAAATTCATAGTATTGG
* * ** *
2257728 TTTAGTAGTTGGTGATTTGGTTTGAACTGTAGTTTGATTCGTAAAACCTGAATCATGGATACATG
1 TATAGTAGTTGATGATTTCATTTGAACTATAGTTTGATTCGTAAAACCTGAATCATGGATACATG
* * * *
2257793 AATTACTAAATTTTGGCATTTCGAAATTTATAGCATTGG
66 AATTAGTAAATTTTGGCATTTAGAAATTCATAGTATTGG
* * **
2257832 TATAGTAGTTGATGATTTCATTTGAACTATAGTTTGGTTCGTAAAACCTGAATCATGGTTATTTT
1 TATAGTAGTTGATGATTTCATTTGAACTATAGTTTGATTCGTAAAACCTGAATCATGGATA-CAT
* * * ** * * * *
2257897 G-CTTGGTAACTTTTCTCCTATTAACTCAAATT-ACAGTATAGG
65 GAATTAGTAAATTTT-GGC-ATTTA--GAAATTCATAGTATTGG
* * *
2257939 TATAGTAGTTGATGATTTCGTTT--ACTTATAGTTTGGTTCATAAAACCTGAATCATGGATA
1 TATAGTAGTTGATGATTTCATTTGAAC-TATAGTTTGATTCGTAAAACCTGAATCATGGATA
2257999 GTTACTCAGT
Statistics
Matches: 457, Mismatches: 105, Indels: 54
0.74 0.17 0.09
Matches are distributed among these distances:
102 3 0.01
103 9 0.02
104 201 0.44
105 14 0.03
106 43 0.09
107 103 0.23
108 77 0.17
109 4 0.01
110 3 0.01
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (104 bp):
TATAGTAGTTGATGATTTCATTTGAACTATAGTTTGATTCGTAAAACCTGAATCATGGATACATG
AATTAGTAAATTTTGGCATTTAGAAATTCATAGTATTGG
Found at i:2257840 original size:211 final size:210
Alignment explanation
Indices: 2257307--2257998 Score: 998
Period size: 211 Copynumber: 3.3 Consensus size: 210
2257297 AGTATCTATA
* * *
2257307 TAGTAGTTGATGATTTCATTTGAACTATAGTTTGATTCGTAAAAGCTGAA-CAATGTATACACGA
1 TAGTAGTTGATGATTTCGTTTGAACTATAGTTTGATTCGTAAAACCTGAATC-ATGGATACACGA
*
2257371 ATTATTAAATTTTGGCATTCCGAAATTCATAGTATTGGTATAGTAGTTGATGATTTCATTTGAAC
65 ATTATTAAATTTTGGCATTTCGAAATTCATAGTATTGGTATAGTAGTTGATGATTTCATTTGAAC
*
2257436 TATAGTTTGGTTCGTAAAACCTCGATCATGGATATTTTGCTTGGTAACTTTTCCTCCTATTA-AG
130 TATAGTTTGGTTCGTAAAACCTCAATCATGGATATTTTGCTTGGTAAC-TTTCCTCCTATTACA-
* *
2257500 GCAAACTACAATATTGGTT
193 -CAAATTACAGTATTGGTT
* * * *
2257519 TAGTAGTAGATGATTTGGTTTCAACTGTAGTTTGATTCGTAAAACCTGAATCATGGATACACGAA
1 TAGTAGTTGATGATTTCGTTTGAACTATAGTTTGATTCGTAAAACCTGAATCATGGATACACGAA
*
2257584 TCATTAAATTTTGGCATGTT-GAAATTCATAGTATTGGTATAGTAGTTGATGATTTCATTTGAAC
66 TTATTAAATTTTGGCAT-TTCGAAATTCATAGTATTGGTATAGTAGTTGATGATTTCATTTGAAC
* * * *
2257648 TATATTTTGGTACGTAAAACCTCAATCATGGATATTTTTCTCGGTAACTATTCCTCCTATTACAC
130 TATAGTTTGGTTCGTAAAACCTCAATCATGGATATTTTGCTTGGTAACT-TTCCTCCTATTACAC
2257713 AAATTACAGTATTGGTT
194 AAATTACAGTATTGGTT
* * * *
2257730 TAGTAGTTGGTGATTTGGTTTGAACTGTAGTTTGATTCGTAAAACCTGAATCATGGATACATGAA
1 TAGTAGTTGATGATTTCGTTTGAACTATAGTTTGATTCGTAAAACCTGAATCATGGATACACGAA
* * *
2257795 TTACTAAATTTTGGCATTTCGAAATTTATAGCATTGGTATAGTAGTTGATGATTTCATTTGAACT
66 TTATTAAATTTTGGCATTTCGAAATTCATAGTATTGGTATAGTAGTTGATGATTTCATTTGAACT
* * * *
2257860 ATAGTTTGGTTCGTAAAACCTGAATCATGGTTATTTTGCTTGGTAACTTTTCTCCTATTAACTCA
131 ATAGTTTGGTTCGTAAAACCTCAATCATGGATATTTTGCTTGGTAACTTTCCTCCTATT-ACACA
* *
2257925 AATTACAGTATAGGTA
195 AATTACAGTATTGGTT
* *
2257941 TAGTAGTTGATGATTTCGTTT--ACTTATAGTTTGGTTCATAAAACCTGAATCATGGATA
1 TAGTAGTTGATGATTTCGTTTGAAC-TATAGTTTGATTCGTAAAACCTGAATCATGGATA
2257999 GTTACTCAGT
Statistics
Matches: 434, Mismatches: 39, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
209 2 0.00
210 43 0.10
211 215 0.50
212 171 0.39
213 3 0.01
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (210 bp):
TAGTAGTTGATGATTTCGTTTGAACTATAGTTTGATTCGTAAAACCTGAATCATGGATACACGAA
TTATTAAATTTTGGCATTTCGAAATTCATAGTATTGGTATAGTAGTTGATGATTTCATTTGAACT
ATAGTTTGGTTCGTAAAACCTCAATCATGGATATTTTGCTTGGTAACTTTCCTCCTATTACACAA
ATTACAGTATTGGTT
Found at i:2262539 original size:8 final size:7
Alignment explanation
Indices: 2262497--2262537 Score: 73
Period size: 7 Copynumber: 5.7 Consensus size: 7
2262487 TTCTGAACCC
2262497 AAAAATA
1 AAAAATA
2262504 AAAAATA
1 AAAAATA
2262511 AAAAATA
1 AAAAATA
2262518 AAAAATAA
1 AAAAAT-A
2262526 AAAAATA
1 AAAAATA
2262533 AAAAA
1 AAAAA
2262538 ATGTTTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:2264069 original size:2 final size:2
Alignment explanation
Indices: 2264064--2264103 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2264054 GTATTGTGTG
*
2264064 TA TA TA TA TA TA TA TA TG 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
2264104 ACTCGAGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Done.