Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold144
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: 3311329
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
File 13 of 21
Found at i:1834832 original size:21 final size:19
Alignment explanation
Indices: 1834799--1834841 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
1834789 TTAAAAAAAC
1834799 TTTTTTCAATCAAAG-CTTT
1 TTTTTTCAATC-AAGTCTTT
1834818 TTTTTTCTAACTCAAGTCTTT
1 TTTTTTC-AA-TCAAGTCTTT
1834839 TTT
1 TTT
1834842 AACAGTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTTTTCAATCAAGTCTTT
Found at i:1838233 original size:25 final size:23
Alignment explanation
Indices: 1838205--1838271 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 23
1838195 ATATTTTTAA
1838205 TATTTATACTATGATATTATATATT
1 TATTT-TACTATGATA-TATATATT
*
1838230 TATTTTTCGTATG--ATATATATT
1 TATTTTAC-TATGATATATATATT
*
1838252 TATTTTTA-TATGATAAATAT
1 TA-TTTTACTATGATATATAT
1838272 TATAAAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
21 4 0.11
22 10 0.29
23 10 0.29
24 2 0.06
25 9 0.26
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (23 bp):
TATTTTACTATGATATATATATT
Found at i:1838263 original size:21 final size:22
Alignment explanation
Indices: 1838222--1838272 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
1838212 ACTATGATAT
*
1838222 TATATATTTATTTTTCGTATGA
1 TATATATTTATTTTTCATATGA
1838244 TATATATTTATTTTT-ATATGA
1 TATATATTTATTTTTCATATGA
*
1838265 TAAATATT
1 TATATATT
1838273 ATAAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (22 bp):
TATATATTTATTTTTCATATGA
Found at i:1838984 original size:29 final size:29
Alignment explanation
Indices: 1838936--1838999 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 29
1838926 CATATCATAT
*
1838936 TTATTTTTTTATTATATTGTG-T-TTTAA
1 TTATTTTTTTATTATATTGTGCTGTATAA
1838963 TTATTTTTTCATATTGAT-TTGTGCTGTATAA
1 TTATTTTTT--TATT-ATATTGTGCTGTATAA
1838994 TTATTT
1 TTATTT
1839000 GATATTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 9 0.29
29 9 0.29
30 3 0.10
31 10 0.32
ACGTcount: A:0.22, C:0.03, G:0.09, T:0.66
Consensus pattern (29 bp):
TTATTTTTTTATTATATTGTGCTGTATAA
Found at i:1845010 original size:20 final size:19
Alignment explanation
Indices: 1844987--1845032 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1844977 TATAATTAAA
1844987 TTTAAATAAAAATATATTAT
1 TTTAAATAAAAA-ATATTAT
* *
1845007 TTTAATTAAAAAATTTTAT
1 TTTAAATAAAAAATATTAT
*
1845026 TTCAAAT
1 TTTAAAT
1845033 TAAATTAACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAAATAAAAAATATTAT
Found at i:1849830 original size:23 final size:24
Alignment explanation
Indices: 1849804--1849856 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 24
1849794 AAATAAAAAA
1849804 TTAAAAATGTTATAAT-TTA-ATTT
1 TTAAAAAT-TTATAATATTATATTT
*
1849827 TT--AAATTTATTATATTATATTT
1 TTAAAAATTTATAATATTATATTT
1849849 TTAAAAAT
1 TTAAAAAT
1849857 AAATTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 6 0.24
21 7 0.28
22 6 0.24
23 2 0.08
24 4 0.16
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TTAAAAATTTATAATATTATATTT
Found at i:1855249 original size:2 final size:2
Alignment explanation
Indices: 1855242--1855276 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1855232 CCTGTACTTA
1855242 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1855277 ACACACATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1859518 original size:9 final size:9
Alignment explanation
Indices: 1859499--1859528 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1859489 AAACTCTATA
1859499 TAAAA-AAT
1 TAAAATAAT
1859507 TAAAATAAT
1 TAAAATAAT
1859516 TAAAATAAT
1 TAAAATAAT
1859525 TAAA
1 TAAA
1859529 CTAAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.24
9 16 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
TAAAATAAT
Found at i:1861477 original size:16 final size:18
Alignment explanation
Indices: 1861442--1861480 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1861432 TTTTAACAGA
1861442 ATAATTGAAATAATATAT
1 ATAATTGAAATAATATAT
1861460 ATAATTGAAATAATATAT
1 ATAATTGAAATAATATAT
1861478 ATA
1 ATA
1861481 TATATATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
ATAATTGAAATAATATAT
Found at i:1864534 original size:2 final size:2
Alignment explanation
Indices: 1864527--1864556 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1864517 ATTCTATCGA
1864527 AT 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 AT
1864557 CATGCTCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1867092 original size:20 final size:19
Alignment explanation
Indices: 1867067--1867115 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
1867057 TCATATTATA
*
1867067 ATTTTAT-TTAATATATAAT
1 ATTTTATATAAATAT-TAAT
1867086 ATATTTATATAAATATTAAT
1 AT-TTTATATAAATATTAAT
1867106 ATTTTA-ATAA
1 ATTTTATATAA
1867116 TTCTTTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 4 0.15
19 6 0.22
20 11 0.41
21 6 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTATATAAATATTAAT
Found at i:1867705 original size:19 final size:19
Alignment explanation
Indices: 1867662--1867705 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1867652 TAAATGTGAT
1867662 AATTTATATATTTATATTA
1 AATTTATATATTTATATTA
**
1867681 TTTTTATATA-TTATAATTA
1 AATTTATATATTTAT-ATTA
1867700 AATTTA
1 AATTTA
1867706 AAATATTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTATATATTTATATTA
Found at i:1867780 original size:17 final size:17
Alignment explanation
Indices: 1867734--1867780 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
1867724 TAAATTTTAA
*
1867734 TAAATTTATAATTTATGT
1 TAAA-TTATATTTTATGT
*
1867752 TATATTATATTTTATGTT
1 TAAATTATATTTTATG-T
1867770 TAAATTA-ATTT
1 TAAATTATATTT
1867781 ATTCTTACCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (17 bp):
TAAATTATATTTTATGT
Found at i:1868029 original size:19 final size:20
Alignment explanation
Indices: 1867992--1868029 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1867982 ATTATATTTT
*
1867992 TATATTTTAATATAATATAA
1 TATATTTTAAAATAATATAA
*
1868012 TATA-TTTAAAATATTATA
1 TATATTTTAAAATAATATA
1868030 TTTATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TATATTTTAAAATAATATAA
Found at i:1868081 original size:18 final size:17
Alignment explanation
Indices: 1867968--1868077 Score: 61
Period size: 18 Copynumber: 6.4 Consensus size: 17
1867958 AAAATTTATG
*
1867968 ATTTTTATATTTATATTAT
1 ATTTTTATA-TTATA-TAA
*
1867987 ATTTTTATATTTTAATATA
1 ATTTTTATATTAT-ATA-A
**
1868006 ATATAATATATT-TA-AA
1 AT-TTTTATATTATATAA
*
1868022 A-TATTATATTTATATAA
1 ATTTTTATA-TTATATAA
*
1868039 A-TTTTA-A-TATATCA
1 ATTTTTATATTATATAA
1868053 ATTATTTATATTATATAA
1 ATT-TTTATATTATATAA
1868071 ATTTTTA
1 ATTTTTA
1868078 ATATATTTAT
Statistics
Matches: 73, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
14 13 0.18
15 3 0.04
16 9 0.12
17 13 0.18
18 15 0.21
19 13 0.18
20 7 0.10
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTTATATTATATAA
Found at i:1868097 original size:32 final size:32
Alignment explanation
Indices: 1868009--1868098 Score: 103
Period size: 33 Copynumber: 2.8 Consensus size: 32
1867999 TAATATAATA
*
1868009 TAATATATTTAAAATATTATATTTATATAAATTT
1 TAATATATTT-ATATATTATA-TTATATAAATTT
**
1868043 TAATATATCAAT-TATTTATATTATATAAATTTT
1 TAATATATTTATATA-TTATATTATATAAA-TTT
1868076 TAATATATTTATATATT-TATTAT
1 TAATATATTTATATATTATATTAT
1868099 GTATCATCTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
32 17 0.35
33 21 0.44
34 10 0.21
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (32 bp):
TAATATATTTATATATTATATTATATAAATTT
Found at i:1871585 original size:1 final size:1
Alignment explanation
Indices: 1871579--1871604 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
1871569 AACACAATGC
1871579 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
1871605 TTCTCTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1874482 original size:2 final size:2
Alignment explanation
Indices: 1874477--1874505 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1874467 TTTTTTACCC
1874477 AT 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 AT A
1874506 GTAAAAGTGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1874913 original size:17 final size:15
Alignment explanation
Indices: 1874868--1874922 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
1874858 AATTATGCCT
*
1874868 TTTATAATTAATCAA
1 TTTATAATTAATTAA
*
1874883 TTTTTAA-TACATTATTA
1 TTTATAATTA-ATTA--A
1874900 TTTATAATTAATTAA
1 TTTATAATTAATTAA
1874915 TTT-TAATT
1 TTTATAATT
1874923 GGTGAATAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
14 7 0.21
15 13 0.39
17 11 0.33
18 2 0.06
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTATAATTAATTAA
Found at i:1876799 original size:14 final size:15
Alignment explanation
Indices: 1876765--1876801 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1876755 CATATCTCAA
1876765 AAAATTCTTTAATATT
1 AAAATT-TTTAATATT
1876781 AAAATTTTTAATA-T
1 AAAATTTTTAATATT
1876795 AAAATTT
1 AAAATTT
1876802 AAGCTATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 7 0.33
16 6 0.29
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
AAAATTTTTAATATT
Found at i:1877685 original size:2 final size:2
Alignment explanation
Indices: 1877680--1877714 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1877670 TCTTTCTTTA
1877680 AT AT AT AT 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 AT AT AT AT A
1877715 AACATATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1883488 original size:32 final size:32
Alignment explanation
Indices: 1883452--1883520 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
1883442 ATGTAAAATA
1883452 TTATAAATTTATATAATATTT-ATAAATATTTT
1 TTATAAATTTATAT-ATATTTCATAAATATTTT
** * **
1883484 TTATATTTTTATATTTATTTCATATTTATTTT
1 TTATAAATTTATATATATTTCATAAATATTTT
1883516 TTATA
1 TTATA
1883521 TTTTATTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 5 0.16
32 26 0.84
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (32 bp):
TTATAAATTTATATATATTTCATAAATATTTT
Found at i:1883489 original size:19 final size:20
Alignment explanation
Indices: 1883452--1883512 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 20
1883442 ATGTAAAATA
* *
1883452 TTATAA-ATTTATATAATAT
1 TTATAATATTTATTTCATAT
1883471 TTATAAATATTT-TTT-ATAT
1 TTAT-AATATTTATTTCATAT
*
1883490 TT-TTATATTTATTTCATAT
1 TTATAATATTTATTTCATAT
1883509 TTAT
1 TTAT
1883513 TTTTTATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 6 0.17
18 4 0.11
19 16 0.46
20 5 0.14
21 4 0.11
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATAATATTTATTTCATAT
Found at i:1883521 original size:24 final size:23
Alignment explanation
Indices: 1883483--1883564 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 23
1883473 ATAAATATTT
1883483 TTTATATTTTTATATTTATTTCATA
1 TTTAT-TTTTTATATTTATTT-ATA
1883508 TTTATTTTTTATATTTTATTT-TAA
1 TTTATTTTTTATA-TTTATTTAT-A
* * *
1883532 TTAATTTTTAATATTGTGTTTATA
1 TTTATTTTTTATATT-TATTTATA
1883556 -TTATTTTTT
1 TTTATTTTTT
1883565 GTATATTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
23 10 0.21
24 25 0.52
25 13 0.27
ACGTcount: A:0.26, C:0.01, G:0.02, T:0.71
Consensus pattern (23 bp):
TTTATTTTTTATATTTATTTATA
Found at i:1885320 original size:21 final size:22
Alignment explanation
Indices: 1885285--1885325 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1885275 ATTCGTATCA
1885285 TGTTTATATTATTTTTATATTG
1 TGTTTATATTATTTTTATATTG
*
1885307 TGTTT-TATTTTTTTTATAT
1 TGTTTATATTATTTTTATAT
1885326 ATATGTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (22 bp):
TGTTTATATTATTTTTATATTG
Found at i:1886157 original size:15 final size:15
Alignment explanation
Indices: 1886126--1886176 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
1886116 TTTAAATAAT
*
1886126 TTTTATTAATTATAA
1 TTTTATTAATTAAAA
1886141 TTTT-TTAATTAAAAA
1 TTTTATTAATT-AAAA
*
1886156 TTTTATAAATATTAAAA
1 TTTTAT-TA-ATTAAAA
1886173 TTTT
1 TTTT
1886177 CAGCGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 6 0.20
15 11 0.37
16 1 0.03
17 9 0.30
18 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTATTAATTAAAA
Found at i:1886897 original size:16 final size:18
Alignment explanation
Indices: 1886873--1886905 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1886863 TATTAGGGTT
1886873 ATTTATTTAAT-TTTAAA
1 ATTTATTTAATATTTAAA
1886890 ATTT-TTTAATATTTAA
1 ATTTATTTAATATTTAA
1886906 GAGAAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTATTTAATATTTAAA
Found at i:1887013 original size:23 final size:25
Alignment explanation
Indices: 1886987--1887040 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
1886977 TAGCTCGTTC
1886987 AATTTTATAATTATATA-A-TATAT
1 AATTTTATAATTATATACATTATAT
* *
1887010 AATTTTATATTTTTATACATTATAT
1 AATTTTATAATTATATACATTATAT
1887035 AATTTT
1 AATTTT
1887041 TACATATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 15 0.56
24 1 0.04
25 11 0.41
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
AATTTTATAATTATATACATTATAT
Found at i:1887021 original size:7 final size:8
Alignment explanation
Indices: 1886987--1887040 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
1886977 TAGCTCGTTC
1886987 AATTTTAT
1 AATTTTAT
*
1886995 AATTATAT
1 AATTTTAT
*
1887003 AA-TATAT
1 AATTTTAT
1887010 AATTTTAT
1 AATTTTAT
*
1887018 ATTTTTAT
1 AATTTTAT
*
1887026 ACATTATAT
1 A-ATTTTAT
1887035 AATTTT
1 AATTTT
1887041 TACATATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
7 7 0.18
8 25 0.66
9 6 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
AATTTTAT
Found at i:1887048 original size:15 final size:17
Alignment explanation
Indices: 1886987--1887045 Score: 63
Period size: 15 Copynumber: 3.7 Consensus size: 17
1886977 TAGCTCGTTC
1886987 AATTTTATA-ATTATAT
1 AATTTTATACATTATAT
* *
1887003 AA-TATATA-ATTTTAT
1 AATTTTATACATTATAT
*
1887018 ATTTTTATACATTATAT
1 AATTTTATACATTATAT
1887035 AATTTT-TACAT
1 AATTTTATACAT
1887046 ATAAAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 12 0.34
16 12 0.34
17 11 0.31
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTTATACATTATAT
Found at i:1887149 original size:23 final size:23
Alignment explanation
Indices: 1887106--1887149 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1887096 TTATATTTTA
*
1887106 AAATTTAATAAAAATATTAAAGT
1 AAATTTAATAAAAATAATAAAGT
*
1887129 AAATTTTA-AAAAATAAATAAA
1 AAATTTAATAAAAAT-AATAAA
1887150 AACTAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (23 bp):
AAATTTAATAAAAATAATAAAGT
Found at i:1890489 original size:8 final size:8
Alignment explanation
Indices: 1890449--1890597 Score: 69
Period size: 8 Copynumber: 18.8 Consensus size: 8
1890439 ATTTAATATG
1890449 AATAATAA
1 AATAATAA
*
1890457 AAAAATAA
1 AATAATAA
1890465 AA-AATAA
1 AATAATAA
*
1890472 AA-AA-AT
1 AATAATAA
1890478 AATAATAA
1 AATAATAA
*
1890486 AATAGTAA
1 AATAATAA
* *
1890494 TAATTGATTA
1 -AA-TAATAA
* *
1890504 ATTAATTA
1 AATAATAA
* *
1890512 ATTAATTA
1 AATAATAA
*
1890520 ATTAA-AA
1 AATAATAA
* *
1890527 AACAAAAA
1 AATAATAA
1890535 AATAATAA
1 AATAATAA
1890543 AATAAATAA
1 AAT-AATAA
1890552 AA-AAT-A
1 AATAATAA
*
1890558 AATAATTA
1 AATAATAA
1890566 AATAA-AA
1 AATAATAA
1890573 ATATACATAA
1 A-ATA-ATAA
*
1890583 AATAAAAA
1 AATAATAA
1890591 CAATAAT
1 -AATAAT
1890598 TAATTAATTT
Statistics
Matches: 112, Mismatches: 17, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
6 6 0.05
7 23 0.21
8 58 0.52
9 19 0.17
10 6 0.05
ACGTcount: A:0.70, C:0.02, G:0.01, T:0.26
Consensus pattern (8 bp):
AATAATAA
Found at i:1890494 original size:11 final size:11
Alignment explanation
Indices: 1890449--1890589 Score: 53
Period size: 11 Copynumber: 12.9 Consensus size: 11
1890439 ATTTAATATG
1890449 AATAAT-AAA-
1 AATAATAAAAT
1890458 AA-AATAAAA-
1 AATAATAAAAT
*
1890467 AATAAAAAAAT
1 AATAATAAAAT
1890478 AATAATAAAAT
1 AATAATAAAAT
* *
1890489 AGTAAT-AATT
1 AATAATAAAAT
* * *
1890499 GATTAATTAATT
1 -AATAATAAAAT
* *
1890511 AATTAATTAATT
1 AA-TAATAAAAT
* * *
1890523 AAAAAACAAAAA
1 -AATAATAAAAT
1890535 AATAATAAAAT
1 AATAATAAAAT
1890546 AAATAA-AAAAT
1 -AATAATAAAAT
*
1890557 AAATAATTAAAT
1 -AATAATAAAAT
* *
1890569 AAAAATATACAT
1 AATAATA-AAAT
1890581 AA-AATAAAA
1 AATAATAAAA
1890590 ACAATAATTA
Statistics
Matches: 103, Mismatches: 19, Indels: 19
0.73 0.13 0.13
Matches are distributed among these distances:
8 3 0.03
9 7 0.07
10 11 0.11
11 49 0.48
12 31 0.30
13 2 0.02
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:1890509 original size:4 final size:4
Alignment explanation
Indices: 1890494--1890524 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1890484 AAAATAGTAA
*
1890494 TAAT TGAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAA
1890525 AAAACAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:1890548 original size:23 final size:22
Alignment explanation
Indices: 1890522--1890573 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
1890512 ATTAATTAAT
1890522 TAAAAAACAAAAAAATAATAAAA
1 TAAAAAA-AAAAAAATAATAAAA
* *
1890545 TAAATAAAAAATAAATAATTAAA
1 TAAA-AAAAAAAAAATAATAAAA
1890568 TAAAAA
1 TAAAAA
1890574 TATACATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.08
23 21 0.81
24 3 0.12
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (22 bp):
TAAAAAAAAAAAAATAATAAAA
Found at i:1890870 original size:15 final size:14
Alignment explanation
Indices: 1890850--1890886 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
1890840 ACATTTCGTG
1890850 CATTGCATTGCATTT
1 CATTGCATTGC-TTT
1890865 CATTGCATTGCTTT
1 CATTGCATTGCTTT
1890879 CA-TGCATT
1 CATTGCATT
1890887 AATGCTGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 6 0.27
14 5 0.23
15 11 0.50
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.46
Consensus pattern (14 bp):
CATTGCATTGCTTT
Found at i:1890929 original size:33 final size:33
Alignment explanation
Indices: 1890891--1890976 Score: 154
Period size: 33 Copynumber: 2.6 Consensus size: 33
1890881 TGCATTAATG
1890891 CTGCTGCAAACGGTAGCAATCAACAACATTAAA
1 CTGCTGCAAACGGTAGCAATCAACAACATTAAA
* *
1890924 CTGCTGCAAATGGTAGCAATCAACAACATTAAG
1 CTGCTGCAAACGGTAGCAATCAACAACATTAAA
1890957 CTGCTGCAAACGGTAGCAAT
1 CTGCTGCAAACGGTAGCAAT
1890977 GAAGAAAGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (33 bp):
CTGCTGCAAACGGTAGCAATCAACAACATTAAA
Found at i:1891826 original size:22 final size:23
Alignment explanation
Indices: 1891749--1891832 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
1891739 AAGAAATGGC
* * *
1891749 AGCAAA-ACTAGCAAAAATAGCA
1 AGCAAACACCAGCAAAAACAGTA
* *
1891771 AGCAAATACCAACAAAAACAGTA
1 AGCAAACACCAGCAAAAACAGTA
*
1891794 AGCAAATACCAGCAAAAACAAG-A
1 AGCAAACACCAGCAAAAAC-AGTA
1891817 AG-AAACACCAGCAAAA
1 AGCAAACACCAGCAAAA
1891833 TAGCAATCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
22 19 0.35
23 33 0.61
24 2 0.04
ACGTcount: A:0.61, C:0.21, G:0.12, T:0.06
Consensus pattern (23 bp):
AGCAAACACCAGCAAAAACAGTA
Found at i:1893128 original size:184 final size:184
Alignment explanation
Indices: 1892737--1893177 Score: 532
Period size: 184 Copynumber: 2.4 Consensus size: 184
1892727 TTTTTATGCC
* * * * *
1892737 CACTTGAGTCATGTTTTAATATTCTTATGGTTTTCTGTAGGGGTATGAAAAATTTTAAAACTTTT
1 CACTCGAGTCATATTTTCATATTCCTATGGTTTTCCGTAGGGGTATGAAAAATTTTAAAACTTTT
* * **** *
1892802 CGTATCTCTTGGTTTTCTGTCGGGTACGAAATGTAATTATCGAAACTAATTTTAAAATTTAGAAA
66 CGTATCTCCTGGTTTTCCGTCAAACACGAAACGTAATTATCGAAACTAATTTTAAAATTTAGAAA
* * *
1892867 AAAATTTCAGTTTCCCTATATTAATTTTTTTAAAAAAATGTGCGATCGTTTATT
131 AAAAATTCAGTTTCCCTAAATTAATTTTTTTAAAAAAATGTGCGATCATTTATT
* * *
1892921 TACTTGAGTCATATTTTCATATTCCTATGGGTTTTCCGTAGGGGTATGAAAATTTTTAAAA-TCT
1 CACTCGAGTCATATTTTCATATTCCTAT-GGTTTTCCGTAGGGGTATGAAAAATTTTAAAACT-T
* *
1892985 TTCGTATTTCCTGGTTTTCCGTCAAACACGAAACGTAATTATCGAAACT-ATTTTTAAATTTAGA
64 TTCGTATCTCCTGGTTTTCCGTCAAACACGAAACGTAATTATCGAAACTAATTTTAAAATTTAGA
* * *
1893049 AAAAAAATT-AGTTTCCTTAAATTAATTTTTTCTAAAAAAATGTGTGATCATTTGTT
129 AAAAAAATTCAGTTTCCCTAAATTAATTTTTT-TAAAAAAATGTGCGATCATTTATT
* * * * * *
1893105 CACTCGGGTCATATTTTCATATTCTTGTAGGTGTT-CGTAGGAGTAT-AAAAGATTTCGAAAACT
1 CACTCGAGTCATATTTTCATATTCCTAT-GGTTTTCCGTAGGGGTATGAAAA-ATTT-TAAAACT
1893168 TTTCGTATCT
63 TTTCGTATCT
1893178 TTTCGGGTTT
Statistics
Matches: 219, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
182 4 0.02
183 33 0.15
184 109 0.50
185 73 0.33
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (184 bp):
CACTCGAGTCATATTTTCATATTCCTATGGTTTTCCGTAGGGGTATGAAAAATTTTAAAACTTTT
CGTATCTCCTGGTTTTCCGTCAAACACGAAACGTAATTATCGAAACTAATTTTAAAATTTAGAAA
AAAAATTCAGTTTCCCTAAATTAATTTTTTTAAAAAAATGTGCGATCATTTATT
Found at i:1897107 original size:61 final size:61
Alignment explanation
Indices: 1897012--1897129 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 61
1897002 TGTTACTTTC
* * * *
1897012 ATCCAATTGTCATCACTTTTCTTTGACATCACATTATTTTCATCTTAGCACTTATTTAGAT
1 ATCCAATCGTCATAACTTTTCTTTGACATCACATTAATTTCATCTTAGCACTCATTTAGAT
1897073 ATCCAATCGTCATAACTTTTCTTTGACATCACATTAATTTCATCTTAGCACTCATTT
1 ATCCAATCGTCATAACTTTTCTTTGACATCACATTAATTTCATCTTAGCACTCATTT
1897130 GTATAGATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.27, C:0.23, G:0.06, T:0.44
Consensus pattern (61 bp):
ATCCAATCGTCATAACTTTTCTTTGACATCACATTAATTTCATCTTAGCACTCATTTAGAT
Found at i:1900455 original size:20 final size:20
Alignment explanation
Indices: 1900430--1900504 Score: 89
Period size: 20 Copynumber: 3.7 Consensus size: 20
1900420 ACATAAGTTT
*
1900430 TGTATCCATACATGATTCAA
1 TGTATCGATACATGATTCAA
* *
1900450 TGTATCGATACATTA-CCTATA
1 TGTATCGATACATGATTC-A-A
*
1900471 TGTATCGATACATTATTCAA
1 TGTATCGATACATGATTCAA
1900491 TGTATCGATACATG
1 TGTATCGATACATG
1900505 CAGGCAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
19 1 0.02
20 28 0.60
21 17 0.36
22 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.37
Consensus pattern (20 bp):
TGTATCGATACATGATTCAA
Found at i:1915603 original size:15 final size:15
Alignment explanation
Indices: 1915583--1915612 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1915573 CTAATTTGCC
1915583 ATTGTCAACAAAATT
1 ATTGTCAACAAAATT
*
1915598 ATTGTCAAGAAAATT
1 ATTGTCAACAAAATT
1915613 TTGCTAACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (15 bp):
ATTGTCAACAAAATT
Found at i:1915729 original size:32 final size:32
Alignment explanation
Indices: 1915684--1915866 Score: 212
Period size: 32 Copynumber: 5.8 Consensus size: 32
1915674 ATCCCTTCTC
*
1915684 AAAA-CCCACACAAGTCGGTGGCAACCTTTTT
1 AAAAGCCCACACAAGTTGGTGGCAACCTTTTT
* * *
1915715 AAAAGCCCACACAAGTTAGTGGTAACCCTTTCT
1 AAAAGCCCACACAAGTTGGTGGCAA-CCTTTTT
* *
1915748 -AAAGCCCACACAAGTTAGTGGTAACCTTCTTT
1 AAAAGCCCACACAAGTTGGTGGCAACCTT-TTT
*
1915780 -AAAGCCCACAAAAGTTGGTGGCAACCTTCTTT
1 AAAAGCCCACACAAGTTGGTGGCAACCTT-TTT
* * * *
1915812 AAAA-CCCACATAAGTCGGTGGCAACCCTTTC
1 AAAAGCCCACACAAGTTGGTGGCAACCTTTTT
1915843 AAAAGCCCACACAAGTTGGTGGCA
1 AAAAGCCCACACAAGTTGGTGGCA
1915867 TTTCTTTCTA
Statistics
Matches: 133, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
31 14 0.11
32 110 0.83
33 9 0.07
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (32 bp):
AAAAGCCCACACAAGTTGGTGGCAACCTTTTT
Found at i:1915852 original size:96 final size:96
Alignment explanation
Indices: 1915688--1915864 Score: 266
Period size: 96 Copynumber: 1.8 Consensus size: 96
1915678 CTTCTCAAAA
* * * *
1915688 CCCACACAAGTCGGTGGCAACCTTTTTAAAAGCCCACACAAGTTAGTGGTAACCCTTTCTAAAGC
1 CCCACAAAAGTCGGTGGCAACCTTTTTAAAAGCCCACACAAGTCAGTGGCAACCCTTTCAAAAGC
1915753 CCACACAAGTTAGTGGTAACCTTCTTTAAAG
66 CCACACAAGTTAGTGGTAACCTTCTTTAAAG
* * *
1915784 CCCACAAAAGTTGGTGGCAACCTTCTTTAAAA-CCCACATAAGTCGGTGGCAACCCTTTCAAAAG
1 CCCACAAAAGTCGGTGGCAACCTT-TTTAAAAGCCCACACAAGTCAGTGGCAACCCTTTCAAAAG
*
1915848 CCCACACAAGTTGGTGG
65 CCCACACAAGTTAGTGG
1915865 CATTTCTTTC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
96 65 0.90
97 7 0.10
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (96 bp):
CCCACAAAAGTCGGTGGCAACCTTTTTAAAAGCCCACACAAGTCAGTGGCAACCCTTTCAAAAGC
CCACACAAGTTAGTGGTAACCTTCTTTAAAG
Found at i:1915936 original size:43 final size:43
Alignment explanation
Indices: 1915870--1915961 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
1915860 GGTGGCATTT
* *
1915870 CTTTCTAAGCCTAATGTCACTGGCCTTGAATCAACACATTGGCA
1 CTTT-TAAGCCTAATATCACTGGCCTTGAATCAACACATTGGAA
* * *
1915914 CTTTTAAGTCTAATATCGCTGGCCTTGAATCAACATATTGGAA
1 CTTTTAAGCCTAATATCACTGGCCTTGAATCAACACATTGGAA
1915957 CTTTT
1 CTTTT
1915962 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 39 0.91
44 4 0.09
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (43 bp):
CTTTTAAGCCTAATATCACTGGCCTTGAATCAACACATTGGAA
Found at i:1915994 original size:52 final size:49
Alignment explanation
Indices: 1915916--1916154 Score: 228
Period size: 49 Copynumber: 4.8 Consensus size: 49
1915906 CATTGGCACT
*
1915916 TTTAAGTCTAATATCGCTGGCCTTGAATCAACATATTGGAACTTTTTCCATC
1 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGAAC--TTT-CATC
* * *
1915968 TTTAAGTCTAATATCGCTGACCTTGAATCAGCACATT-AACACCTTTGCCATC
1 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGA-A-CTTT--CATC
* * * * * *
1916020 TTTAAATCTAATGTCGCTGGCCTTGAATCGGTATATTGGCACTTTCATT
1 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGAACTTTCATC
* * * **
1916069 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCATCATC
1 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGAACTTTCATC
** ** *
1916118 TTTAAGTCCGATATCATTGGCCTTGAATCAACATATT
1 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATT
1916155 AGCATTTTTA
Statistics
Matches: 158, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
49 77 0.49
51 8 0.05
52 72 0.46
53 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (49 bp):
TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGAACTTTCATC
Found at i:1916087 original size:49 final size:50
Alignment explanation
Indices: 1915916--1916315 Score: 234
Period size: 52 Copynumber: 7.8 Consensus size: 50
1915906 CATTGGCACT
* * * *
1915916 TTTAAGTCTAATATCGCTGGCCTTGAATCAACATATTGGAACTTTTTCCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC--TTTACATC
* * * ** *
1915968 TTTAAGTCTAATATCGCTGACCTTGAATCAGCACATTAACACCTTTGCCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTT-ACATC
* * * * * *
1916020 TTTAAATCTAATGTCGCTGGCCTTGAATCGGTATATTGGCACTTT-CATT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTACATC
* **
1916069 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCAT-CATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTACATC
* ** * * *
1916118 TTTAAGTCCGATATCATTGGCCTTGAATCAACATATTAGCATTTTTAACAT-
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTTT-ACATC
* * * * * *
1916169 TCCTAAGCCCAATGTCACTGGCCTTGAATCAGTACATTGGCATTCTTCT-CATC
1 T-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA--CTT-TACATC
* * * * * * * * * ** *
1916222 TTCAAGTCTAATGTCACTAG-CTGTGAATTAGCACATTGACATTTTTTGTATT
1 TTTAAGTCCAATATCGCTGGCCT-TGAATCAGCATATTGGCA--CTTTACATC
* * *
1916274 TTTAAGCCCAATATCGCTGGCCTTAAATCAACATATTGGCAC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1916316 ATTTCTCATC
Statistics
Matches: 272, Mismatches: 64, Indels: 26
0.75 0.18 0.07
Matches are distributed among these distances:
49 80 0.29
50 1 0.00
51 11 0.04
52 172 0.63
53 7 0.03
54 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.36
Consensus pattern (50 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTTTACATC
Found at i:1917150 original size:20 final size:20
Alignment explanation
Indices: 1917124--1917194 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1917114 ACCTAGATGC
*
1917124 ATCGATACATGATTCAATGT
1 ATCGATACATTATTCAATGT
* *
1917144 GTCGATACATTA-CCTAGATGT
1 ATCGATACATTATTC-A-ATGT
*
1917165 ATCGATACATTATTTAATGT
1 ATCGATACATTATTCAATGT
1917185 ATCGATACAT
1 ATCGATACAT
1917195 ACAGACAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 25 0.60
21 16 0.38
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (20 bp):
ATCGATACATTATTCAATGT
Found at i:1917169 original size:41 final size:41
Alignment explanation
Indices: 1917112--1917194 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
1917102 CATCTGGTAT
*
1917112 TTACCTAGATGCATCGATACATGATTCAATGTGTCGATACA
1 TTACCTAGATGCATCGATACATGATTCAATGTATCGATACA
* * *
1917153 TTACCTAGATGTATCGATACATTATTTAATGTATCGATACA
1 TTACCTAGATGCATCGATACATGATTCAATGTATCGATACA
1917194 T
1 T
1917195 ACAGACAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (41 bp):
TTACCTAGATGCATCGATACATGATTCAATGTATCGATACA
Found at i:1920612 original size:44 final size:44
Alignment explanation
Indices: 1920564--1920754 Score: 181
Period size: 44 Copynumber: 4.3 Consensus size: 44
1920554 CATACGATTG
1920564 CCACCCTAGTCAAATTTTTCTCATTTTGATTTGACGTATGGTTA
1 CCACCCTAGTCAAATTTTTCTCATTTTGATTTGACGTATGGTTA
* * * **
1920608 CCACCTTAATCAGATTCTTT-TCATTTCAATTTGACGTATGGTTA
1 CCACCCTAGTCAAATT-TTTCTCATTTTGATTTGACGTATGGTTA
*** * *
1920652 CCACCCTAGTCAAA-TCCACATCTTTTCTG-TCTGACGTATGGTTA
1 CCACCCTAGTCAAATTTTTC-TCATTT-TGATTTGACGTATGGTTA
* * * * * *
1920696 ACACCCTAGTTAGATTTTTCTTATTCTGATTTGATGTATGGTTA
1 CCACCCTAGTCAAATTTTTCTCATTTTGATTTGACGTATGGTTA
*
1920740 CCACCCTGGTCAAAT
1 CCACCCTAGTCAAAT
1920755 CTCTTTCTTT
Statistics
Matches: 111, Mismatches: 30, Indels: 12
0.73 0.20 0.08
Matches are distributed among these distances:
43 3 0.03
44 103 0.93
45 5 0.05
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.40
Consensus pattern (44 bp):
CCACCCTAGTCAAATTTTTCTCATTTTGATTTGACGTATGGTTA
Found at i:1920711 original size:88 final size:88
Alignment explanation
Indices: 1920595--1920755 Score: 218
Period size: 88 Copynumber: 1.8 Consensus size: 88
1920585 CATTTTGATT
* *
1920595 TGACGTATGGTTACCACCTTAATCAGATTCTTTTCAT-TTC-AATTTGACGTATGGTTACCACCC
1 TGACGTATGGTTAACACCCTAATCAGA-T-TTTTCATATTCTAATTTGACGTATGGTTACCACCC
1920658 TAGTCAAATCCACATCTTTTCTGTC
64 TAGTCAAATCCACATCTTTTCTGTC
* * * * * *
1920683 TGACGTATGGTTAACACCCTAGTTAGATTTTTCTTATTCTGATTTGATGTATGGTTACCACCCTG
1 TGACGTATGGTTAACACCCTAATCAGATTTTTCATATTCTAATTTGACGTATGGTTACCACCCTA
1920748 GTCAAATC
66 GTCAAATC
1920756 TCTTTCTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
86 6 0.10
87 4 0.06
88 53 0.84
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (88 bp):
TGACGTATGGTTAACACCCTAATCAGATTTTTCATATTCTAATTTGACGTATGGTTACCACCCTA
GTCAAATCCACATCTTTTCTGTC
Found at i:1920975 original size:42 final size:42
Alignment explanation
Indices: 1920927--1921607 Score: 340
Period size: 42 Copynumber: 16.2 Consensus size: 42
1920917 TTGACTGTTG
* *
1920927 GCTTTGAACTTGGAGACTTTTTTACCCTCAGTCTGCCTGTCA
1 GCTTTGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCA
* * ** * ** * *
1920969 ACTTTGACCCTGGAGACTGCCTCACTTTAAGTCTGCTTGTCA
1 GCTTTGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCA
* * *
1921011 GCTTTGACCTTAGAGACTTTCTTA-CCTACAGTCTGTCTGTCG
1 GCTTTGACCTTGGAGACTTTCTTACCCT-CAGTCTGCCTGTCA
** * * *
1921053 GCTTTGACCTTGGAGACTGCCTCA-CCTCAAGTCTGCCTATCG
1 GCTTTGACCTTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCA
* * * *
1921095 GCTTTGACCCTAGAGACTTTCTTA-CTTACAGTCTGCCTAT-A
1 GCTTTGACCTTGGAGACTTTCTTACCCT-CAGTCTGCCTGTCA
* * * *
1921136 GGCTTTGACC-TGAGAGA-TTGCCT-CACCTCAAGTATACCTGTCA
1 -GCTTTGACCTTG-GAGACTTTCTTAC-CCTC-AGTCTGCCTGTCA
* *
1921179 GCTTTGACTTTGGAGACTTTGTTACCCTCAGTCTGCCTGTC-
1 GCTTTGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCA
* ** * * * *
1921220 GACTTTGACCTTGGAAACTGCCTCA-CCTTATGTTTGCTTGTCA
1 G-CTTTGACCTTGGAGACTTTCTTACCCTCA-GTCTGCCTGTCA
* * * * * *
1921263 ACTTTGACTTTGGAGACTTTTTTACCCTTAGTCTACCTGTCG
1 GCTTTGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCA
* * * * *
1921305 GTTTTAACCCTGAAGA-TTGCTTTA-CCTCAAGTCTGCCTGTCA
1 GCTTTGACCTTGGAGACTTTC-TTACCCTC-AGTCTGCCTGTCA
** * * **
1921347 GCTTTGACCTTAAAGACTTTCTTA-CCT-ATGGTCTGCTTATTG
1 GCTTTGACCTTGGAGACTTTCTTACCCTCA--GTCTGCCTGTCA
* * * * *
1921389 GCTTTGACCCTCGAGA-TTGCCTTA-CCTCAAGTTTGCCTGTCG
1 GCTTTGACCTTGGAGACTT-TCTTACCCTC-AGTCTGCCTGTCA
* * * *
1921431 GTTTTGACCCTAGAGACTTTCTTACCCTCAGTCTACCTGTC-
1 GCTTTGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCA
* * ** * * * *
1921472 GACTTTGACCCTAGAGACTACCTCA-CCTCAAGTTTGCCTATCG
1 G-CTTTGACCTTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCA
* * *
1921515 GCTTTGACTTTGGAGACTTTCTTA-CCTACAGTTTGCTTGTCA
1 GCTTTGACCTTGGAGACTTTCTTACCCT-CAGTCTGCCTGTCA
* * * * *
1921557 -ATGTTGACCTTGGAGAC-TGCCTAACCTCAAGTTTGCCTGTCA
1 GCT-TTGACCTTGGAGACTTTCTTACCCTC-AGTCTGCCTGTCA
1921599 GCTTTGACC
1 GCTTTGACC
1921608 CTAAAGACTG
Statistics
Matches: 481, Mismatches: 124, Indels: 68
0.71 0.18 0.10
Matches are distributed among these distances:
40 1 0.00
41 31 0.06
42 419 0.87
43 28 0.06
44 2 0.00
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (42 bp):
GCTTTGACCTTGGAGACTTTCTTACCCTCAGTCTGCCTGTCA
Found at i:1921068 original size:84 final size:84
Alignment explanation
Indices: 1920910--1921616 Score: 654
Period size: 84 Copynumber: 8.4 Consensus size: 84
1920900 TTTTAACTTT
* ** * * * *
1920910 CTCAAGTTTGACTGTTGGCTTTGAACTTGGAGACTTTTTTACCCTCAGTCTGCCTGTCAACTTTG
1 CTCAAGTTTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCCTCAGTCTGCCTGTCGACTTTG
1920975 ACCCTGGAGACTGCCTCAC
66 ACCCTGGAGACTGCCTCAC
* * * * * *
1920994 TTTAAGTCTGCTTGTCAGCTTTGACCTTAGAGACTTTCTTA-CCTACAGTCTGTCTGTCGGCTTT
1 CTCAAGTTTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCCT-CAGTCTGCCTGTCGACTTT
*
1921058 GACCTTGGAGACTGCCTCAC
65 GACCCTGGAGACTGCCTCAC
* * * * * * * *
1921078 CTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTCTTA-CTTACAGTCTGCCTATAGGCTTT
1 CTCAAGTTTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCCT-CAGTCTGCCTGTCGACTTT
*
1921142 GA-CCTGAGAGATTGCCTCAC
65 GACCCTG-GAGACTGCCTCAC
* * * * *
1921162 CTCAAGTATACCTGTCAGCTTTGACTTTGGAGACTTTGTTACCCTCAGTCTGCCTGTCGACTTTG
1 CTCAAGTTTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCCTCAGTCTGCCTGTCGACTTTG
* *
1921227 ACCTTGGAAACTGCCTCAC
66 ACCCTGGAGACTGCCTCAC
* * * * * * * * * ** *
1921246 CTTATGTTTGCTTGTCAACTTTGACTTTGGAGACTTTTTTACCCTTAGTCTACCTGTCGGTTTTA
1 CTCAAGTTTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCCTCAGTCTGCCTGTCGACTTTG
* * * *
1921311 ACCCTGAAGATTGCTTTAC
66 ACCCTGGAGACTGCCTCAC
* * * * * *
1921330 CTCAAGTCTGCCTGTCAGCTTTGACCTTAAAGACTTTCTTA-CCT-ATGGTCTGCTTATTGGCTT
1 CTCAAGTTTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCCTCA--GTCTGCCTGTCGACTT
* * *
1921393 TGACCCTCGAGATTGCCTTAC
64 TGACCCTGGAGACTGCCTCAC
* * * *
1921414 CTCAAGTTTGCCTGTCGGTTTTGACCCTAGAGACTTTCTTACCCTCAGTCTACCTGTCGACTTTG
1 CTCAAGTTTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCCTCAGTCTGCCTGTCGACTTTG
* *
1921479 ACCCTAGAGACTACCTCAC
66 ACCCTGGAGACTGCCTCAC
* * * * * * *
1921498 CTCAAGTTTGCCTATCGGCTTTGACTTTGGAGACTTTCTTA-CCTACAGTTTGCTTGTC-AATGT
1 CTCAAGTTTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCCT-CAGTCTGCCTGTCGACT-T
* *
1921561 TGACCTTGGAGACTGCCTAAC
64 TGACCCTGGAGACTGCCTCAC
* *
1921582 CTCAAGTTTGCCTGTCAGCTTTGACCCTAAAGACT
1 CTCAAGTTTGCCTGTCAGCTTTGACCTTAGAGACT
1921617 GCTTGTTGGT
Statistics
Matches: 503, Mismatches: 110, Indels: 20
0.79 0.17 0.03
Matches are distributed among these distances:
82 1 0.00
83 14 0.03
84 479 0.95
85 8 0.02
86 1 0.00
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.36
Consensus pattern (84 bp):
CTCAAGTTTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCCTCAGTCTGCCTGTCGACTTTG
ACCCTGGAGACTGCCTCAC
Found at i:1921197 original size:168 final size:169
Alignment explanation
Indices: 1920910--1922194 Score: 815
Period size: 168 Copynumber: 7.8 Consensus size: 169
1920900 TTTTAACTTT
* ** * * * * * * **
1920910 CTCAAGTTTGACTGTTGGCTTTGAACTTGGAGACTTTTTTACCCTCAGTCTGCCTGTCAACTTTG
1 CTCAAGTTTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCTTCAGTCTACCTGTCGGCTTTG
* * *
1920975 ACCCTG-GAGACTGCCTCACTTTAAGTCTGCTTGTCAGCTTTGACCTTAGAGACTTTCTTACCTA
66 ACCCTGAGAGACTGCCTCACCTCAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCTA
*
1921039 CAGTCTG-TCTGTCGGCTTTGACCTTGGAGACTGCCTCAC
131 CAGTCTGCT-TGTCGACTTTGACCTTGGAGACTGCCTCAC
* * * * * *
1921078 CTCAAGTCTGCCTATCGGCTTTGACCCTAGAGACTTTCTTA-CTTACAGTCTGCCTATAGGCTTT
1 CTCAAGTTTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCTT-CAGTCTACCTGTCGGCTTT
* * * * * *
1921142 GA-CCTGAGAGATTGCCTCACCTCAAGTATACCTGTCAGCTTTGACTTTGGAGACTTTGTTACCC
65 GACCCTGAGAGACTGCCTCACCTCAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTA-CC
* *
1921206 T-CAGTCTGCCTGTCGACTTTGACCTTGGAAACTGCCTCAC
129 TACAGTCTGCTTGTCGACTTTGACCTTGGAGACTGCCTCAC
* * * * ** * * *
1921246 CTTATGTTTGCTTGTCAACTTTGACTTTGGAGACTTTTTTACCCTT-AGTCTACCTGTCGGTTTT
1 CTCAAGTTTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTA-CCTTCAGTCTACCTGTCGGCTTT
* * * * *
1921310 AACCCTGA-AGATTGCTTTACCTCAAGTCTGCCTGTCAGCTTTGACCTTAAAGACTTTCTTACCT
65 GACCCTGAGAGACTGCCTCACCTCAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCT
** * * * * * * *
1921374 ATGGTCTGCTTATTGGCTTTGACCCTCGAGATTGCCTTAC
130 ACAGTCTGCTTGTCGACTTTGACCTTGGAGACTGCCTCAC
* * * *
1921414 CTCAAGTTTGCCTGTCGGTTTTGACCCTAGAGACTTTCTTACCCTCAGTCTACCTGTCGACTTTG
1 CTCAAGTTTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCTTCAGTCTACCTGTCGGCTTTG
* * * * * *
1921479 ACCCT-AGAGACTACCTCACCTCAAGTTTGCCTATCGGCTTTGACTTTGGAGACTTTCTTACCTA
66 ACCCTGAGAGACTGCCTCACCTCAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCTA
* * *
1921543 CAGTTTGCTTGTC-AATGTTGACCTTGGAGACTGCCTAAC
131 CAGTCTGCTTGTCGACT-TTGACCTTGGAGACTGCCTCAC
* * *
1921582 CTCAAGTTTGCCTGTCAGCTTTGACCCTA-A-A------GA-C-T--G-CT---TGTTGGTTTTG
1 CTCAAGTTTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCTTCAGTCTACCTGTCGGCTTTG
* * ** * * * *
1921631 ACCCT-AGACTGCCTCACCTCAAGTC-TG-CT---TGTCAGCTTTGACCCTGGAGACTTTTTTAC
66 ACCCTGAGA--GACT-GCCTCACCTCAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTAC
** * * * *
1921690 CTTTAGTCTGCCTGTTGGCTTTGACCTTGGAGACTGCCTTAC
128 CTACAGTCTGCTTGTCGACTTTGACCTTGGAGACTGCCTCAC
* * * * * ** *
1921732 CTCAAGTCTGCCTGTC-GTCTTTGACCTTGGAGACTTTTTTACCCTT-ACTCTGTCTGTTGGCTT
1 CTCAAGTTTGCCTGTCAG-CTTTGACCCTAGAGACTTTCTTA-CCTTCAGTCTACCTGTCGGCTT
*
1921795 TGACCCT-AGAGACTGCCTCACCTCAAGTCTGCCTGTC-GACTTTGACCTTGGAGACTTTCTTAC
64 TGACCCTGAGAGACTGCCTCACCTCAAGTCTGCCTGTCAG-CTTTGACCTTAGAGACTTTCTTA-
* * * * * * **
1921858 CCT-TAGTCTACCTGTTAGA-TTT-AGCCCTAGAGACTATCTCAC
127 CCTACAGTCTGCTTG-TCGACTTTGA-CCTTGGAGACTGCCTCAC
* * * * * * * * *
1921900 ATCAAGTCTACCTGCCAGCTTTGACCTTGGAGACTTTCTTACCCTCAGT-TCGCCTATCGGCTTT
1 CTCAAGTTTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCTTCAGTCT-ACCTGTCGGCTTT
* * * * *
1921964 GA-CCTTAGAGACTGCCTCACCTTAAGTCTACCTGTC-GACTTTGACCCTGGAGACTTT-TTACC
65 GACCCTGAGAGACTGCCTCACCTCAAGTCTGCCTGTCAG-CTTTGACCTTAGAGACTTTCTTA-C
* * * * * * *
1922026 CT-TAGTGTGCCTATCGGCTTGGATCTTGGAGACTGCCTCAC
128 CTACAGTCTGCTTGTCGACTTTGACCTTGGAGACTGCCTCAC
* * * ** * * * * * * *
1922067 CTCAAATCTGCCTATTGGCTTTGACTCTGGAGACTTTTTTACCTTCAGTCTGCTTGTCGGTTTTA
1 CTCAAGTTTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCTTCAGTCTACCTGTCGGCTTTG
* *** * * * * **
1922132 ACCTTG-GAGACTTTTTTACCCTC-AGTTTGCCTGTCAACTTTGACCTTGGAGACTGCCTTACCT
66 ACCCTGAGAGACTGCCTCA-CCTCAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCT
1922195 CAAATCTGCT
Statistics
Matches: 874, Mismatches: 191, Indels: 105
0.75 0.16 0.09
Matches are distributed among these distances:
149 1 0.00
150 81 0.09
151 2 0.00
152 17 0.02
153 1 0.00
154 4 0.00
155 10 0.01
156 1 0.00
158 2 0.00
159 1 0.00
160 2 0.00
161 1 0.00
163 9 0.01
164 4 0.00
165 2 0.00
166 21 0.02
167 140 0.16
168 558 0.64
169 14 0.02
170 3 0.00
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.36
Consensus pattern (169 bp):
CTCAAGTTTGCCTGTCAGCTTTGACCCTAGAGACTTTCTTACCTTCAGTCTACCTGTCGGCTTTG
ACCCTGAGAGACTGCCTCACCTCAAGTCTGCCTGTCAGCTTTGACCTTAGAGACTTTCTTACCTA
CAGTCTGCTTGTCGACTTTGACCTTGGAGACTGCCTCAC
Found at i:1921699 original size:42 final size:42
Alignment explanation
Indices: 1921646--1922203 Score: 374
Period size: 42 Copynumber: 13.3 Consensus size: 42
1921636 AGACTGCCTC
* * * * *
1921646 ACCTCAAGTCTGCTTGTCAGCTTTGACCCTGGAGACTTTTTT
1 ACCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* * **
1921688 ACCTTTAGTCTGCCTGTTGGCTTTGACCTTGGAGACTGCCTT
1 ACCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* * *
1921730 ACCTCAAGTCTGCCTGTCGTCTTTGACCTTGGAGACTTTTTT
1 ACCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* * * * * ** *
1921772 ACCCTT-ACTCTGTCTGTTGGCTTTGACCCTAGAGACTGCCTC
1 A-CCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* *
1921814 ACCTCAAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCTT
1 ACCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* ** * * * * *
1921856 ACCCTT-AGTCTACCTGTTAGATTT-AGCCCTAGAGACTATCTC
1 A-CCTTAAGTCTGCCTGTCGGCTTTGA-CCTTGGAGACTTTCTT
* * * * *
1921898 ACATCAAGTCTACCTGCCAGCTTTGACCTTGGAGACTTTCTT
1 ACCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* * * * ** *
1921940 ACCCTCAGT-TCGCCTATCGGCTTTGACCTTAGAGACTGCCTC
1 ACCTTAAGTCT-GCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* * *
1921982 ACCTTAAGTCTACCTGTCGACTTTGACCCTGGAGACTTT-TT
1 ACCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* * * * ** *
1922023 ACCCTT-AGTGTGCCTATCGGCTTGGATCTTGGAGACTGCCTC
1 A-CCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* * * * *
1922065 ACCTCAAATCTGCCTATTGGCTTTGA-CTCTGGAGACTTTTTT
1 ACCTTAAGTCTGCCTGTCGGCTTTGACCT-TGGAGACTTTCTT
* * * * *
1922107 ACCTTCAGTCTGCTTGTCGGTTTTAACCTTGGAGACTTTTTT
1 ACCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* * * ** **
1922149 ACCCTCAGTTTGCCTGTCAACTTTGACCTTGGAGACTGCCTT
1 ACCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* *
1922191 ACCTCAAATCTGC
1 ACCTTAAGTCTGC
1922204 TTAGACCTGG
Statistics
Matches: 383, Mismatches: 120, Indels: 26
0.72 0.23 0.05
Matches are distributed among these distances:
41 38 0.10
42 335 0.87
43 10 0.03
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (42 bp):
ACCTTAAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
Found at i:1921763 original size:84 final size:84
Alignment explanation
Indices: 1921615--1922185 Score: 559
Period size: 84 Copynumber: 6.8 Consensus size: 84
1921605 ACCCTAAAGA
* * * * *
1921615 CTGCTTGTTGGTTTTGACCCT--AGACTGCCTCACCTCAAGTCTGCTTGTC-AGCTTTGACCCTG
1 CTGCCTGTTGGCTTTGACCTTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGA-CTTTGACCTTG
*
1921677 GAGACTTTTTTACCTTTAGT
65 GAGACTTTTTTACCCTTAGT
* * *
1921697 CTGCCTGTTGGCTTTGACCTTGGAGACTGCCTTACCTCAAGTCTGCCTGTCGTCTTTGACCTTGG
1 CTGCCTGTTGGCTTTGACCTTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGACTTTGACCTTGG
*
1921762 AGACTTTTTTACCCTTACT
66 AGACTTTTTTACCCTTAGT
* *
1921781 CTGTCTGTTGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGACTTTGACCTTGG
1 CTGCCTGTTGGCTTTGACCTTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGACTTTGACCTTGG
*
1921846 AGACTTTCTTACCCTTAGT
66 AGACTTTTTTACCCTTAGT
* * * * ** * * *
1921865 CTACCTGTTAGATTT-AGCCCTAGAGACTATCTCACATCAAGTCTACCTG-CCAGCTTTGACCTT
1 CTGCCTGTTGGCTTTGA-CCTTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGA-CTTTGACCTT
* *
1921928 GGAGACTTTCTTACCCTCAGT
64 GGAGACTTTTTTACCCTTAGT
* * * * *
1921949 -TCGCCTATCGGCTTTGACCTTAGAGACTGCCTCACCTTAAGTCTACCTGTCGACTTTGACCCTG
1 CT-GCCTGTTGGCTTTGACCTTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGACTTTGACCTTG
1922013 GAGAC-TTTTTACCCTTAGT
65 GAGACTTTTTTACCCTTAGT
* * * * * * * * * *
1922032 GTGCCTATCGGCTTGGATCTTGGAGACTGCCTCACCTCAAATCTGCCTATTGGCTTTGA-CTCTG
1 CTGCCTGTTGGCTTTGACCTTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGACTTTGACCT-TG
1922096 GAGACTTTTTTA-CCTTCAGT
65 GAGACTTTTTTACCCTT-AGT
* * * * * *** * * *
1922116 CTGCTTGTCGGTTTTAACCTTGGAGACTTTTTTACCCTC-AGTTTGCCTGTCAACTTTGACCTTG
1 CTGCCTGTTGGCTTTGACCTTAGAGACTGCCTCA-CCTCAAGTCTGCCTGTCGACTTTGACCTTG
1922180 GAGACT
65 GAGACT
1922186 GCCTTACCTC
Statistics
Matches: 408, Mismatches: 67, Indels: 26
0.81 0.13 0.05
Matches are distributed among these distances:
82 19 0.05
83 75 0.18
84 305 0.75
85 9 0.02
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (84 bp):
CTGCCTGTTGGCTTTGACCTTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGACTTTGACCTTGG
AGACTTTTTTACCCTTAGT
Found at i:1921766 original size:150 final size:151
Alignment explanation
Indices: 1921475--1921757 Score: 365
Period size: 150 Copynumber: 1.9 Consensus size: 151
1921465 ACCTGTCGAC
* * **
1921475 TTTGACCCTAGAGACTACCTCACCTCAAGTTTGCCTATCGGCTTTGACTTTGGAGACTTTCTTAC
1 TTTGACCCTA-AGACTACCTCACCTCAAGTCTGCCTATCAGCTTTGACCCTGGAGACTTTCTTAC
* * *
1921540 CTACAGTTTGCTTGTCAATGTTGACCTTGGAGACTGCCTAACCTCAAGTTTGCCTGTCAGCTTTG
65 CTACAGTCTGCCTGTCAATGTTGACCTTGGAGACTGCCTAACCTCAAGTCTGCCTGTCAGCTTTG
1921605 ACCCTAAAGACTGCTTGTTGGT
130 ACCCTAAAGACTGCTTGTTGGT
* * * *
1921627 TTTGACCCT-AGACTGCCTCACCTCAAGTCTGCTTGTCAGCTTTGACCCTGGAGACTTTTTTACC
1 TTTGACCCTAAGACTACCTCACCTCAAGTCTGCCTATCAGCTTTGACCCTGGAGACTTTCTTACC
** *** *
1921691 TTTAGTCTGCCTGTTGGCT-TTGACCTTGGAGACTGCCTTACCTCAAGTCTGCCTGTC-GTCTTT
66 TACAGTCTGCCTG-TCAATGTTGACCTTGGAGACTGCCTAACCTCAAGTCTGCCTGTCAG-CTTT
1921754 GACC
129 GACC
1921758 TTGGAGACTT
Statistics
Matches: 112, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
149 1 0.01
150 100 0.89
151 2 0.02
152 9 0.08
ACGTcount: A:0.17, C:0.28, G:0.20, T:0.35
Consensus pattern (151 bp):
TTTGACCCTAAGACTACCTCACCTCAAGTCTGCCTATCAGCTTTGACCCTGGAGACTTTCTTACC
TACAGTCTGCCTGTCAATGTTGACCTTGGAGACTGCCTAACCTCAAGTCTGCCTGTCAGCTTTGA
CCCTAAAGACTGCTTGTTGGT
Found at i:1921821 original size:234 final size:234
Alignment explanation
Indices: 1921379--1921841 Score: 549
Period size: 234 Copynumber: 2.0 Consensus size: 234
1921369 TACCTATGGT
* * * * *
1921379 CTGCTTATTGGCTTTGACCCTCGAGATTGCCTTACCTCAAGTTTGCCTGTCGGTTTTGACCCTAG
1 CTGCTTATTGGCTTTGACCCTC-AGACTGCCTCACCTCAAGTCTGCCTGTCAGCTTTGACCCTAG
*
1921444 AGACTTTCTTACCCTCAGTCTACCTGTCGACTTTGACCCTAGAGACTACCTCACCTCAAGTTTGC
65 AGACTTTCTTACCCTCAGTCTACCTGTCGACTTTGACCCTAGAGACTACCTCACCTCAAGTCTGC
* * * * *
1921509 CTATCGGCTTTGACTTTGGAGACTTTCTTACCTACAGTTTGCTTGTCAATGTTGACCTTGGAGAC
130 CTATCGGCTTTGACCTTGGAGACTTTCTTACCTACAGTCTGCTTGGC-ATGTTGACCCTAGAGAC
*
1921574 TGCCTAACCTCAAGTTTGCCTGTC-AGCTTTGACCCTAAAGA
194 TGCCTAACCTCAAGTCTGCCTGTCGA-CTTTGACCCTAAAGA
* * * *
1921615 CTGCTTGTTGGTTTTGACCCT-AGACTGCCTCACCTCAAGTCTGCTTGTCAGCTTTGACCCTGGA
1 CTGCTTATTGGCTTTGACCCTCAGACTGCCTCACCTCAAGTCTGCCTGTCAGCTTTGACCCTAGA
* * * * * * * * * *
1921679 GACTTTTTTACCTTTAGTCTGCCTGTTGGCTTTGACCTTGGAGACTGCCTTACCTCAAGTCTGCC
66 GACTTTCTTACCCTCAGTCTACCTGTCGACTTTGACCCTAGAGACTACCTCACCTCAAGTCTGCC
* * * *
1921744 TGTCGTCTTTGACCTTGGAGACTTTTTTACCCTTACTCTGTCTG-TTGGC-T-TTGACCCTAGAG
131 TATCGGCTTTGACCTTGGAGACTTTCTTA-CC-TA--CAGTCTGCTTGGCATGTTGACCCTAGAG
*
1921806 ACTGCCTCACCTCAAGTCTGCCTGTCGACTTTGACC
192 ACTGCCTAACCTCAAGTCTGCCTGTCGACTTTGACC
1921842 TTGGAGACTT
Statistics
Matches: 191, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
234 157 0.82
235 4 0.02
236 21 0.11
237 4 0.02
238 5 0.03
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (234 bp):
CTGCTTATTGGCTTTGACCCTCAGACTGCCTCACCTCAAGTCTGCCTGTCAGCTTTGACCCTAGA
GACTTTCTTACCCTCAGTCTACCTGTCGACTTTGACCCTAGAGACTACCTCACCTCAAGTCTGCC
TATCGGCTTTGACCTTGGAGACTTTCTTACCTACAGTCTGCTTGGCATGTTGACCCTAGAGACTG
CCTAACCTCAAGTCTGCCTGTCGACTTTGACCCTAAAGA
Found at i:1921866 original size:126 final size:126
Alignment explanation
Indices: 1921652--1922203 Score: 438
Period size: 126 Copynumber: 4.4 Consensus size: 126
1921642 CCTCACCTCA
* * *** * ** * *
1921652 AGTCTGCTTGTCAGCTTTGACCCTGGAGACTTTTTTACCTTTAGTCTGCCTGTTGGCTTTGACCT
1 AGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCT
* * *
1921717 TGGAGACTGCCTTACCTCAAGTCTGCCTGTCGTCTTTGACCTTGGAGACTTTTTTACCCTT
66 TGGAGACTGCCTTACCTTAAGTCTACCTGTCGTCTTTGACCCTGGAGACTTTTTTACCCTT
* * ** * * * *
1921778 ACTCTGTCTGTTGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGACTTTGACCT
1 AGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCT
** * * * * * * * *
1921843 TGGAGACTTTCTTACCCTT-AGTCTACCTGTTAG-ATTT-AGCCCTAGAGACTATCTCA-CATCA
66 TGGAGACTGCCTTA-CCTTAAGTCTACCTG-TCGTCTTTGA-CCCTGGAGACTTTTTTACCCT-T
* * ** *
1921904 AGTCTACCTGCCAGCTTTGACCTTGGAGACTTTCTTACCCTC-AGT-TCGCCTATCGGCTTTGAC
1 AGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCA-CCTCAAGTCT-GCCTATCGGCTTTGAC
* * *
1921967 CTTAGAGACTGCCTCACCTTAAGTCTACCTGTCGACTTTGACCCTGGAGAC-TTTTTACCCTT
64 CTTGGAGACTGCCTTACCTTAAGTCTACCTGTCGTCTTTGACCCTGGAGACTTTTTTACCCTT
* * * * * * *
1922029 AGTGTGCCTATCGGCTTGGATCTTGGAGACTGCCTCACCTCAAATCTGCCTATTGGCTTTGA-CT
1 AGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCT
*** * * * * * *
1922093 CTGGAGACTTTTTTACCTTCAGTCTGCTTGTCGGT-TTTAACCTTGGAGACTTTTTTACCCTC
66 -TGGAGACTGCCTTACCTTAAGTCTACCTGTC-GTCTTTGACCCTGGAGACTTTTTTACCCTT
* * * *
1922155 AGTTTGCCTGTCAACTTTGACCTTGGAGACTGCCTTACCTCAAATCTGC
1 AGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGC
1922204 TTAGACCTGG
Statistics
Matches: 328, Mismatches: 83, Indels: 30
0.74 0.19 0.07
Matches are distributed among these distances:
124 6 0.02
125 92 0.28
126 220 0.67
127 10 0.03
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (126 bp):
AGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCACCTCAAGTCTGCCTATCGGCTTTGACCT
TGGAGACTGCCTTACCTTAAGTCTACCTGTCGTCTTTGACCCTGGAGACTTTTTTACCCTT
Found at i:1921921 original size:318 final size:318
Alignment explanation
Indices: 1921328--1921925 Score: 763
Period size: 318 Copynumber: 1.9 Consensus size: 318
1921318 AGATTGCTTT
* * *
1921328 ACCTCAAGTCTGCCTGTCAGCTTTGACCTTAAAGACTTTCTTACCTATGGTCTGCTTATTGGCTT
1 ACCTCAAGTCTGCCTGTCAGCTTTGACCCTAAAGACTTTCTTACCTATAGTCTGCCTATTGGCTT
* *
1921393 TGACCCTCGAGATTGCCTTACCTCAAGTTTGCCTGTCGGTTTTGACCCTAGAGACTTTCTTACCC
66 TGACCCTCGAGACTGCCTTACCTCAAGTCTGCCTGTCGGTTTTGACCCTAGAGACTTTCTTACCC
* * *
1921458 TCAGTCTACCTGTCGACTTTGACCCTAGAGACTACCTCACCTCAAGTTTGCCTATCGGCTTTGAC
131 TCACTCTACCTGTCGACTTTGACCCTAGAGACTACCTCACCTCAAGTCTGCCTATCGACTTTGAC
* * * * * * * *
1921523 TTTGGAGACTTTCTTACCTACAGTTTGCTTGTCAATGTTGACCTTGGAGACTGCCTAACCTCAAG
196 CTTGGAGACTTTCTTACCTACAGTCTACCTGTCAATGTTGACCCTAGAGACTACCTAACATCAAG
* * *
1921588 TTTGCCTGTCAGCTTTGACCCTAAAGACTGCTTGTTGGTTTTGACCCTAGACTGCCTC
261 TCTACCTGCCAGCTTTGACCCTAAAGACTGCTTGTTGGTTTTGACCCTAGACTGCCTC
* ** * * *
1921646 ACCTCAAGTCTGCTTGTCAGCTTTGACCCTGGAGACTTTTTTACCTTTAGTCTGCCTGTTGGCTT
1 ACCTCAAGTCTGCCTGTCAGCTTTGACCCTAAAGACTTTCTTACCTATAGTCTGCCTATTGGCTT
* * * * *
1921711 TGACCTTGGAGACTGCCTTACCTCAAGTCTGCCTGTC-GTCTTTGACCTTGGAGACTTTTTTACC
66 TGACCCTCGAGACTGCCTTACCTCAAGTCTGCCTGTCGGT-TTTGACCCTAGAGACTTTCTTACC
* ** * * * *
1921775 CTTACTCTGTCTGTTGGCTTTGACCCTAGAGACTGCCTCACCTCAAGTCTGCCTGTCGACTTTGA
130 CTCACTCTACCTGTCGACTTTGACCCTAGAGACTACCTCACCTCAAGTCTGCCTATCGACTTTGA
* * * *
1921840 CCTTGGAGACTTTCTTACCCT-TAGTCTACCTGTTAGAT-TT-AGCCCTAGAGACTATCTCACAT
195 CCTTGGAGACTTTCTTA-CCTACAGTCTACCTGTCA-ATGTTGA-CCCTAGAGACTACCTAACAT
1921902 CAAGTCTACCTGCCAGCTTTGACC
257 CAAGTCTACCTGCCAGCTTTGACC
1921926 TTGGAGACTT
Statistics
Matches: 235, Mismatches: 41, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
317 3 0.01
318 227 0.97
319 5 0.02
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (318 bp):
ACCTCAAGTCTGCCTGTCAGCTTTGACCCTAAAGACTTTCTTACCTATAGTCTGCCTATTGGCTT
TGACCCTCGAGACTGCCTTACCTCAAGTCTGCCTGTCGGTTTTGACCCTAGAGACTTTCTTACCC
TCACTCTACCTGTCGACTTTGACCCTAGAGACTACCTCACCTCAAGTCTGCCTATCGACTTTGAC
CTTGGAGACTTTCTTACCTACAGTCTACCTGTCAATGTTGACCCTAGAGACTACCTAACATCAAG
TCTACCTGCCAGCTTTGACCCTAAAGACTGCTTGTTGGTTTTGACCCTAGACTGCCTC
Found at i:1922741 original size:10 final size:10
Alignment explanation
Indices: 1922726--1922766 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
1922716 CTTTAACATG
1922726 AATAATAAAA
1 AATAATAAAA
1922736 AATAATAAAA
1 AATAATAAAA
1922746 AATAA-AAATA
1 AATAATAAA-A
1922756 GAATAATAAAA
1 -AATAATAAAA
1922767 TAGTAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.11
10 16 0.57
11 6 0.21
12 3 0.11
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (10 bp):
AATAATAAAA
Found at i:1922821 original size:14 final size:14
Alignment explanation
Indices: 1922798--1922847 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
1922788 TTAATTAATT
1922798 AAAA-AAATAATAA
1 AAAATAAATAATAA
1922811 AAAATAAATAATTAA
1 AAAATAAATAA-TAA
*
1922826 ATAAATATAT-ATAA
1 A-AAATAAATAATAA
1922840 AATAATAA
1 AA-AATAA
1922848 CAATAATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
13 5 0.16
14 14 0.45
15 5 0.16
16 7 0.23
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATAAATAATAA
Found at i:1922822 original size:26 final size:27
Alignment explanation
Indices: 1922793--1922844 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
1922783 ATTAATTAAT
1922793 TAATTAAAAAAATA-ATAAAAAATAAA
1 TAATTAAAAAAATATATAAAAAATAAA
* *
1922819 TAATTAAATAAATATATATAAAATAA
1 TAATTAAAAAAATATATAAAAAATAA
1922845 TAACAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (27 bp):
TAATTAAAAAAATATATAAAAAATAAA
Found at i:1922854 original size:9 final size:8
Alignment explanation
Indices: 1922729--1922854 Score: 56
Period size: 8 Copynumber: 16.8 Consensus size: 8
1922719 TAACATGAAT
1922729 AATAA-AA
1 AATAATAA
1922736 AATAATAA
1 AATAATAA
1922744 AA-AAT-A
1 AATAATAA
*
1922750 AA-AATAG
1 AATAATAA
1922757 AATAATAA
1 AATAATAA
*
1922765 AATAGT--
1 AATAATAA
**
1922771 AATAATTG
1 AATAATAA
* *
1922779 ATTAATTA
1 AATAATAA
* *
1922787 ATTAATTA
1 AATAATAA
* *
1922795 ATTAAAAA
1 AATAATAA
1922803 AATAATAA
1 AATAATAA
1922811 AA-AAT-A
1 AATAATAA
*
1922817 AATAATTA
1 AATAATAA
1922825 AAT-A-AA
1 AATAATAA
*
1922831 TATATATAA
1 AATA-ATAA
1922840 AATAATAA
1 AATAATAA
1922848 CAATAAT
1 -AATAAT
1922855 TAATTATTTT
Statistics
Matches: 95, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
6 17 0.18
7 17 0.18
8 50 0.53
9 11 0.12
ACGTcount: A:0.67, C:0.01, G:0.02, T:0.29
Consensus pattern (8 bp):
AATAATAA
Found at i:1923105 original size:15 final size:14
Alignment explanation
Indices: 1923085--1923121 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
1923075 ACATTTCGTG
1923085 CATTGCATTGCATTT
1 CATTGCATTGC-TTT
1923100 CATTGCATTGCTTT
1 CATTGCATTGCTTT
1923114 CA-TGCATT
1 CATTGCATT
1923122 AAAGCTGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 6 0.27
14 5 0.23
15 11 0.50
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.46
Consensus pattern (14 bp):
CATTGCATTGCTTT
Found at i:1923309 original size:31 final size:31
Alignment explanation
Indices: 1923261--1923337 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
1923251 AAGTAATGAA
* *
1923261 GCTAC-ATCAAAACAATAAGAAG-AATCTGAT
1 GCTACAATGAAAATAATAAGAAGAAATC-GAT
*
1923291 GCTGCAATGAAAATAATAAGAAGAAATCGAT
1 GCTACAATGAAAATAATAAGAAGAAATCGAT
*
1923322 GCTACAATGAAGATAA
1 GCTACAATGAAAATAA
1923338 AAAACGGATA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 4 0.10
31 32 0.80
32 4 0.10
ACGTcount: A:0.51, C:0.13, G:0.17, T:0.19
Consensus pattern (31 bp):
GCTACAATGAAAATAATAAGAAGAAATCGAT
Found at i:1924017 original size:23 final size:23
Alignment explanation
Indices: 1923933--1924017 Score: 66
Period size: 23 Copynumber: 3.7 Consensus size: 23
1923923 AAGCAACAGT
* *
1923933 AGCAAA-ACCAGCAAAAATAGCA
1 AGCAAACACTAGCAAAAACAGCA
* * **
1923955 AGCAAATACCAAAAAAAACAGCA
1 AGCAAACACTAGCAAAAACAGCA
* * *
1923978 AGCAAATACTTGGAAAAACAAG-A
1 AGCAAACACTAGCAAAAAC-AGCA
1924001 AGCAAACACTAGCAAAA
1 AGCAAACACTAGCAAAA
1924018 TAGCAATCAA
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
22 6 0.12
23 43 0.84
24 2 0.04
ACGTcount: A:0.60, C:0.20, G:0.13, T:0.07
Consensus pattern (23 bp):
AGCAAACACTAGCAAAAACAGCA
Found at i:1929912 original size:23 final size:23
Alignment explanation
Indices: 1929869--1929912 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1929859 TTTATTTTAG
* *
1929869 ATTTTTAAAATTTTATCTTTTTC
1 ATTTTTAAAATTTAATATTTTTC
1929892 ATTTTTAATAA-TTAATATTTT
1 ATTTTTAA-AATTTAATATTTT
1929913 GGATAATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 16 0.89
24 2 0.11
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTTTAAAATTTAATATTTTTC
Found at i:1932761 original size:40 final size:40
Alignment explanation
Indices: 1932708--1932799 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
1932698 CCATTCGTTA
* *
1932708 ACTTATAGGTTTTGTCCCAGTTAACCTTACTTATTCATTG
1 ACTTATAGATTTTGTCCCAGTTAACCTTACCTATTCATTG
* ** * * **
1932748 ACTTGTAGATTTTGTCTTAGTTAACTTTTCCTATTTGTTG
1 ACTTATAGATTTTGTCCCAGTTAACCTTACCTATTCATTG
1932788 ACTTATAGATTT
1 ACTTATAGATTT
1932800 ATCTTGGTCA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.22, C:0.15, G:0.13, T:0.50
Consensus pattern (40 bp):
ACTTATAGATTTTGTCCCAGTTAACCTTACCTATTCATTG
Found at i:1932818 original size:40 final size:39
Alignment explanation
Indices: 1932745--1932839 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
1932735 TACTTATTCA
* * * *
1932745 TTGACTTGTAGATTTTGTCTTAGTTAACTTTTCCTATTTG
1 TTGACTTATAGATTTTATCTTAGTCAACTTTTCC-ATTAG
*
1932785 TTGACTTATAGA-TTTATCTTGGTCAACTCTTTCCATTAG
1 TTGACTTATAGATTTTATCTTAGTCAACT-TTTCCATTAG
* *
1932824 TTGACTTGTAGGTTTT
1 TTGACTTATAGATTTT
1932840 GTCCTGATTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
39 27 0.59
40 19 0.41
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.52
Consensus pattern (39 bp):
TTGACTTATAGATTTTATCTTAGTCAACTTTTCCATTAG
Found at i:1932840 original size:79 final size:78
Alignment explanation
Indices: 1932745--1932916 Score: 186
Period size: 79 Copynumber: 2.2 Consensus size: 78
1932735 TACTTATTCA
* * ** * * * **
1932745 TTGACTTGTAGATTTTGT-CTTAGTTAACTTTTCCTATTTGTTGACTTATAGATTT-ATCTTGGT
1 TTGACTTGTAGGTTTTGTCCTGA-TTAACTCATCCTATATGTTGACGTATAGATTTCATCCTCAT
*
1932808 CAACTCTTTCCATT
65 CAACTCTTCCCATT
* *
1932822 AGTTGACTTGTAGGTTTTGTCCTGATTAACTCATCCTATATGTTGACGTGTAGGTTTCATCCTCA
1 --TTGACTTGTAGGTTTTGTCCTGATTAACTCATCCTATATGTTGACGTATAGATTTCATCCTCA
1932887 TCAACTCTTCCCATT
64 TCAACTCTTCCCATT
*
1932902 TTGACTTGTAAGTTT
1 TTGACTTGTAGGTTT
1932917 CATCTCGGTT
Statistics
Matches: 78, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
78 14 0.18
79 43 0.55
80 21 0.27
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.47
Consensus pattern (78 bp):
TTGACTTGTAGGTTTTGTCCTGATTAACTCATCCTATATGTTGACGTATAGATTTCATCCTCATC
AACTCTTCCCATT
Found at i:1932853 original size:40 final size:40
Alignment explanation
Indices: 1932770--1932916 Score: 108
Period size: 40 Copynumber: 3.8 Consensus size: 40
1932760 TGTCTTAGTT
* * * * *
1932770 AACT-TTTCCTATTTGTTGACTTATA-GATTTATCTTGGTC
1 AACTCTTTCC-ATTAGTTGACTTGTAGGTTTTATCCTGATC
* *
1932809 AACTCTTTCCATTAGTTGACTTGTAGGTTTTGTCCTGATT
1 AACTCTTTCCATTAGTTGACTTGTAGGTTTTATCCTGATC
* * * *
1932849 AACTC-ATCC-TATATGTTGACGTGTAGGTTTCATCCTCATC
1 AACTCTTTCCAT-TA-GTTGACTTGTAGGTTTTATCCTGATC
* *
1932889 AACTCTTCCCATT--TTGACTTGTAAGTTT
1 AACTCTTTCCATTAGTTGACTTGTAGGTTT
1932917 CATCTCGGTT
Statistics
Matches: 85, Mismatches: 17, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
38 14 0.16
39 22 0.26
40 45 0.53
41 3 0.04
42 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (40 bp):
AACTCTTTCCATTAGTTGACTTGTAGGTTTTATCCTGATC
Found at i:1932917 original size:38 final size:39
Alignment explanation
Indices: 1932807--1932920 Score: 122
Period size: 40 Copynumber: 2.9 Consensus size: 39
1932797 TTTATCTTGG
* ** *
1932807 TCAACTCTTTCCATTAGTTGACTTGTAGGTTTTGTCCTGA
1 TCAACTCTTCCCATT-GTTGACTTGTAGGTTTCATCCTCA
* * * *
1932847 TTAACTCATCCTATATGTTGACGTGTAGGTTTCATCCTCA
1 TCAACTCTTCCCAT-TGTTGACTTGTAGGTTTCATCCTCA
*
1932887 TCAACTCTTCCCATT-TTGACTTGTAAGTTTCATC
1 TCAACTCTTCCCATTGTTGACTTGTAGGTTTCATC
1932921 TCGGTTAACC
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
38 17 0.28
39 1 0.02
40 41 0.68
41 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.14, T:0.43
Consensus pattern (39 bp):
TCAACTCTTCCCATTGTTGACTTGTAGGTTTCATCCTCA
Found at i:1933222 original size:65 final size:63
Alignment explanation
Indices: 1933132--1933313 Score: 181
Period size: 64 Copynumber: 2.8 Consensus size: 63
1933122 AGACATAAGA
* ** * *
1933132 TTACATCCTAGTCATCTTCATTTGACTAGATCAGTTTTATG-CTAGTAAACTCTTTTAAACCTAG
1 TTACATCCTGGTCATCTTCGCTTGACTAGATCA-TTTT-TGCCTAGTAAAC-CCTCTAAACCTAG
1933196 G
63 G
* * *
1933197 TTACATTCTGGTCATCCTT-GCTTGACT-GAATCATTTTTGCTCTAGTCAACCCTCTAGACCTAG
1 TTACATCCTGGTCAT-CTTCGCTTGACTAG-ATCATTTTTGC-CTAGTAAACCCTCTAAACCTAG
1933260 G
63 G
* * *
1933261 TTACATCCTGGTCATCTTCGCTTGACTATATCAATTTTGCCCTAGTCAACCCT
1 TTACATCCTGGTCATCTTCGCTTGACTAGATCATTTTTG-CCTAGTAAACCCT
1933314 TTATATTGGT
Statistics
Matches: 99, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
63 5 0.05
64 59 0.60
65 32 0.32
66 3 0.03
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.38
Consensus pattern (63 bp):
TTACATCCTGGTCATCTTCGCTTGACTAGATCATTTTTGCCTAGTAAACCCTCTAAACCTAGG
Found at i:1933272 original size:64 final size:64
Alignment explanation
Indices: 1933021--1933313 Score: 196
Period size: 66 Copynumber: 4.5 Consensus size: 64
1933011 TTCTTATTCA
* * ** * ** * *
1933021 TTGACTATATCAGTTTTGCCCTAATCAACTATTTTAGACCTATGACTACATTCTGGTCA-CTTTT
1 TTGACTATATCAATTTTGCCCTAGTCAAC-CCTCTAGACCTA-GGTTACATCCTGGTCATC-TTC
*
1933085 GT
63 GC
* * * * * * * * * *
1933087 TTGATTGTATCAGTTTTGCACTCGTCAACCCTTTTAGACATAAGATTACATCCTAGTCATCTTCA
1 TTGACTATATCAATTTTGCCCTAGTCAACCC-TCTAGACCT-AGGTTACATCCTGGTCATCTTCG
*
1933152 T
64 C
* * *** * * * * *
1933153 TTGACTAGATCAGTTTTATGCTAGTAAACTCTTTTAAACCTAGGTTACATTCTGGTCATCCTT-G
1 TTGACTATATCAATTTTGCCCTAGTCAAC-CCTCTAGACCTAGGTTACATCCTGGTCAT-CTTCG
1933217 C
64 C
* *
1933218 TTGACTGA-ATCATTTTTGCTCTAGTCAACCCTCTAGACCTAGGTTACATCCTGGTCATCTTCGC
1 TTGACT-ATATCAATTTTGCCCTAGTCAACCCTCTAGACCTAGGTTACATCCTGGTCATCTTCGC
1933282 TTGACTATATCAATTTTGCCCTAGTCAACCCT
1 TTGACTATATCAATTTTGCCCTAGTCAACCCT
1933314 TTATATTGGT
Statistics
Matches: 179, Mismatches: 40, Indels: 18
0.76 0.17 0.08
Matches are distributed among these distances:
63 4 0.02
64 55 0.31
65 37 0.21
66 80 0.45
67 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (64 bp):
TTGACTATATCAATTTTGCCCTAGTCAACCCTCTAGACCTAGGTTACATCCTGGTCATCTTCGC
Found at i:1933564 original size:130 final size:128
Alignment explanation
Indices: 1933336--1933569 Score: 292
Period size: 129 Copynumber: 1.8 Consensus size: 128
1933326 TGCCCTAGTT
* * * ** *
1933336 AACCTTTTAGAACTAAGTTATATCTTAGTCATTTTTGCTTGACTGTATTAGTTTTGCTTTGGTAA
1 AACCCTTTAGAACTAAGTTACATCTTAGTCATTTTTGCTAGACTGTATTAGTTTTGCCCTGATAA
* **
1933401 ACCATTTTGACCTAGGTTACATCCTGGTCATCTTTGCTTAATTTTATCTATTTCTCCATGATC
66 ACCATTTTGACCAAGGTTACATCCTAATCATCTTTGCTTAATTTTATCTATTTCTCCATGATC
* *
1933464 AACCCTTTAG-ACGTAAGTTACATCTTGGTCATCTTTTGCTAGATTGTATT-GATTTTGCCCTGA
1 AACCCTTTAGAAC-TAAGTTACATCTTAGTCAT-TTTTGCTAGACTGTATTAG-TTTTGCCCTGA
* * *
1933527 TTAACCCTTTTAGAGCAAGGTTACATCCTAATCATCTTTGCTT
63 TAAACCATTTT-GACCAAGGTTACATCCTAATCATCTTTGCTT
1933570 GACTACATTG
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
127 2 0.02
128 27 0.31
129 32 0.36
130 27 0.31
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (128 bp):
AACCCTTTAGAACTAAGTTACATCTTAGTCATTTTTGCTAGACTGTATTAGTTTTGCCCTGATAA
ACCATTTTGACCAAGGTTACATCCTAATCATCTTTGCTTAATTTTATCTATTTCTCCATGATC
Found at i:1933619 original size:64 final size:64
Alignment explanation
Indices: 1933544--1933665 Score: 190
Period size: 64 Copynumber: 1.9 Consensus size: 64
1933534 TTTTAGAGCA
* *
1933544 AGGTTACATCCTAATCATCTTTGCTTGACTACATTGGTTTTGCTTTAGTTAACATTTTAAACCT
1 AGGTTACATCCTAATCATCTTTGCTTGACTACATTGGTTTTGCCTTAGTCAACATTTTAAACCT
* ** *
1933608 AGGTTACATCCTAATCATTTTTGCTTGACTTTATTGGTTTTGCCTTAGTCAACCTTTT
1 AGGTTACATCCTAATCATCTTTGCTTGACTACATTGGTTTTGCCTTAGTCAACATTTT
1933666 TAGACCTAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (64 bp):
AGGTTACATCCTAATCATCTTTGCTTGACTACATTGGTTTTGCCTTAGTCAACATTTTAAACCT
Found at i:1936494 original size:10 final size:10
Alignment explanation
Indices: 1936479--1936503 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1936469 AAATCATTTG
1936479 TTTAGAATAT
1 TTTAGAATAT
1936489 TTTAGAATAT
1 TTTAGAATAT
1936499 TTTAG
1 TTTAG
1936504 TATTCCAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (10 bp):
TTTAGAATAT
Found at i:1937599 original size:145 final size:148
Alignment explanation
Indices: 1937399--1937669 Score: 352
Period size: 145 Copynumber: 1.9 Consensus size: 148
1937389 TGTCACCAGC
*
1937399 TCACTTTTATGCCAAAAGTGTGCATTTAGGATAGGTTTACCCTTGTACTTATCATTTTTGTG-TC
1 TCACTTTTATGCCAAAAGTGTGCATTTAGGATAGGTTCACCCTTGTACTTATCATTTTTGTGTTC
* * * * * *
1937463 TTTTAGGGTTGTTGAGATA-TTTAATGTCGAAAGTATACCT-AAAGGTA-TTTAAATAATTTCAT
66 -TTTAAGGTTATTAAGATACTTTAACGCCGAAAGTATACCTCAAAGGCATTTTAAATAATTTCAT
1937525 TAAAACCGAGTCTTAAGTG
130 TAAAACCGAGTCTTAAGTG
* * * * * * *
1937544 TCACTTTTATGCTACAGGTGTGCATTTAGGATATGTTCATCTTTTTACTTATCATTTTTGTGTTC
1 TCACTTTTATGCCAAAAGTGTGCATTTAGGATAGGTTCACCCTTGTACTTATCATTTTTGTGTTC
* * *
1937609 TTTAAGGTTATTAAGATACTTTCACGCCGAAAGTATAGCTCAAAGGCATTTTAGATAATTT
66 TTTAAGGTTATTAAGATACTTTAACGCCGAAAGTATACCTCAAAGGCATTTTAAATAATTT
1937670 TTCTAGAATT
Statistics
Matches: 105, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
145 69 0.66
146 19 0.18
147 6 0.06
148 11 0.10
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (148 bp):
TCACTTTTATGCCAAAAGTGTGCATTTAGGATAGGTTCACCCTTGTACTTATCATTTTTGTGTTC
TTTAAGGTTATTAAGATACTTTAACGCCGAAAGTATACCTCAAAGGCATTTTAAATAATTTCATT
AAAACCGAGTCTTAAGTG
Found at i:1938060 original size:38 final size:37
Alignment explanation
Indices: 1938006--1938083 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 37
1937996 GTTTCTCTAA
*
1938006 TTTTTTGGTGGAGGAACAAAAGAGGATGATAAAAAACT
1 TTTTTTAGTGGAGGAACAAAAGAGGATGATAAAAAA-T
*
1938044 TTTTTTAGTGGGGGAACAAAAGAGGATGATAAAAAAT
1 TTTTTTAGTGGAGGAACAAAAGAGGATGATAAAAAAT
1938081 TTT
1 TTT
1938084 CGTATTTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 4 0.11
38 34 0.89
ACGTcount: A:0.41, C:0.04, G:0.26, T:0.29
Consensus pattern (37 bp):
TTTTTTAGTGGAGGAACAAAAGAGGATGATAAAAAAT
Found at i:1938319 original size:13 final size:13
Alignment explanation
Indices: 1938301--1938326 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1938291 AACTCTCGAA
1938301 CCCTTTATATGAT
1 CCCTTTATATGAT
1938314 CCCTTTATATGAT
1 CCCTTTATATGAT
1938327 TATGTTATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
CCCTTTATATGAT
Found at i:1939518 original size:34 final size:34
Alignment explanation
Indices: 1939475--1939547 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
1939465 GAGATAGAAT
*
1939475 TTATCATAATCTCTAAAAACAATCAAAATAAAAC
1 TTATCATAATCTCTAAAAACAATCAAAATAAAAA
* * * * *
1939509 TTATCATAATTTCTAAGAATAGTCAAGATAAAAA
1 TTATCATAATCTCTAAAAACAATCAAAATAAAAA
1939543 TTATC
1 TTATC
1939548 CAAATCCTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.32
Consensus pattern (34 bp):
TTATCATAATCTCTAAAAACAATCAAAATAAAAA
Found at i:1939649 original size:18 final size:18
Alignment explanation
Indices: 1939623--1939661 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1939613 TATCATTATC
*
1939623 ATATTCATATCAAAATTT
1 ATATCCATATCAAAATTT
1939641 ATATCCATATCAAAATTT
1 ATATCCATATCAAAATTT
1939659 ATA
1 ATA
1939662 AAATATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATCCATATCAAAATTT
Found at i:1941789 original size:30 final size:33
Alignment explanation
Indices: 1941728--1941786 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
1941718 CAAATAATTT
1941728 ATATATTATTATTAATAATAATATATTAAATAC
1 ATATATTATTATTAATAATAATATATTAAATAC
1941761 ATATATTATT-TT-ATAATAA-AT-TTAAA
1 ATATATTATTATTAATAATAATATATTAAA
1941787 ATATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 5 0.19
30 2 0.08
31 7 0.27
32 2 0.08
33 10 0.38
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (33 bp):
ATATATTATTATTAATAATAATATATTAAATAC
Found at i:1943352 original size:22 final size:23
Alignment explanation
Indices: 1943307--1943352 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
1943297 AGAAATAAGT
1943307 TTAAATATTTTTCAAGTAATAAA
1 TTAAATATTTTTCAAGTAATAAA
1943330 TTAAATATTTTTCAAGTAA-AAA
1 TTAAATATTTTTCAAGTAATAAA
1943352 T
1 T
1943353 AATTTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAAATATTTTTCAAGTAATAAA
Found at i:1950994 original size:40 final size:39
Alignment explanation
Indices: 1950934--1951029 Score: 131
Period size: 40 Copynumber: 2.4 Consensus size: 39
1950924 TTTTACCCAG
* *
1950934 ATGTATTGATACATTTTTCAATATATCGATACATGTATGA-
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TAT-AT
* *
1950974 ATGTATCGATACATTCTTCAATGTATCGATACATTCTAT
1 ATGTATCGATACATTCTTCAATATATCGATACATTATAT
1951013 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
1951030 ATCTTTTTAC
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.02
39 19 0.37
40 31 0.61
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATAT
Found at i:1951018 original size:19 final size:20
Alignment explanation
Indices: 1950934--1951031 Score: 105
Period size: 20 Copynumber: 5.0 Consensus size: 20
1950924 TTTTACCCAG
* *
1950934 ATGTATTGATACATT-TTTCA
1 ATGTATCGATACATTCTAT-A
* *
1950954 ATATATCGATACA-TGTATGA
1 ATGTATCGATACATTCTAT-A
1950974 ATGTATCGATACATTCT-TCA
1 ATGTATCGATACATTCTAT-A
1950994 ATGTATCGATACATTCTAT-
1 ATGTATCGATACATTCTATA
1951013 ATGTATCGATACATTCTAT
1 ATGTATCGATACATTCTAT
1951032 CTTTTTACCT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
19 20 0.29
20 45 0.66
21 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTCTATA
Found at i:1953393 original size:97 final size:96
Alignment explanation
Indices: 1953223--1953559 Score: 568
Period size: 97 Copynumber: 3.5 Consensus size: 96
1953213 AAAATTTTAT
* * * *
1953223 TCAT-GGGGATACTCTAACCCCATTCCTCCGAGGGGATACTCCAACCCTGCTTTTAAACTTTTCA
1 TCATCGGGGACACTCCAACCCCATTCCTCCGA-GGGATACTCCAACCCCGCTTTTAAACTTGTCA
1953287 AGATTCAAATCTTATTCTCGCTTAAATTGTCA
65 AGATTCAAATCTTATTCTCGCTTAAATTGTCA
*
1953319 TTATCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACTTGTCA
1 TCATCGGGGACACTCCAACCCCATTCCTCCGA-GGGATACTCCAACCCCGCTTTTAAACTTGTCA
*
1953384 AGATCCAAATCTTATTCTCGCTTAAATTGTCA
65 AGATTCAAATCTTATTCTCGCTTAAATTGTCA
*
1953416 TCATCGGGGACACTCCAACCCCATTCCTCCGAGGGATACTCCAACCTCGCTTTTAAACTTGTCAA
1 TCATCGGGGACACTCCAACCCCATTCCTCCGAGGGATACTCCAACCCCGCTTTTAAACTTGTCAA
*
1953481 GATTCAAATCTTATTCTCACTTAAATTGTCA
66 GATTCAAATCTTATTCTCGCTTAAATTGTCA
*
1953512 TCATCGGGGATACTCCAACCCCATTCCTCCGAGGGATACTCCAACCCC
1 TCATCGGGGACACTCCAACCCCATTCCTCCGAGGGATACTCCAACCCC
1953560 ATTTTTTTTT
Statistics
Matches: 228, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
96 110 0.48
97 118 0.52
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (96 bp):
TCATCGGGGACACTCCAACCCCATTCCTCCGAGGGATACTCCAACCCCGCTTTTAAACTTGTCAA
GATTCAAATCTTATTCTCGCTTAAATTGTCA
Found at i:1955454 original size:19 final size:19
Alignment explanation
Indices: 1955415--1955456 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1955405 GAGGAAGGAC
*
1955415 CATTTTTTTTATTGATGTT
1 CATTTTTTTTATTGATATT
* *
1955434 CATTTTTTTTCTTGCTATT
1 CATTTTTTTTATTGATATT
1955453 CATT
1 CATT
1955457 CTCATTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.12, G:0.07, T:0.67
Consensus pattern (19 bp):
CATTTTTTTTATTGATATT
Found at i:1965133 original size:5 final size:5
Alignment explanation
Indices: 1965123--1965175 Score: 83
Period size: 5 Copynumber: 11.0 Consensus size: 5
1965113 TTTACACCTA
*
1965123 AAAAC AAAAC AAAAC -AAAC AAAAC AAAAC AAAAC AAAAA AAAAC AAAA-
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
1965171 AAAAC
1 AAAAC
1965176 CAAGAAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
4 8 0.18
5 36 0.82
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:1965147 original size:19 final size:20
Alignment explanation
Indices: 1965122--1965175 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
1965112 CTTTACACCT
1965122 AAAAACAAAACAAAAC-AAA
1 AAAAACAAAACAAAACAAAA
*
1965141 CAAAACAAAACAAAACAAAA
1 AAAAACAAAACAAAACAAAA
1965161 AAAAACAAAA-AAAAC
1 AAAAACAAAACAAAAC
1965176 CAAGAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 20 0.62
20 12 0.38
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAACAAAACAAAACAAAA
Found at i:1965183 original size:10 final size:10
Alignment explanation
Indices: 1965122--1965184 Score: 74
Period size: 10 Copynumber: 6.4 Consensus size: 10
1965112 CTTTACACCT
1965122 AAAAACAAAA
1 AAAAACAAAA
*
1965132 CAAAAC-AAA
1 AAAAACAAAA
*
1965141 CAAAACAAAA
1 AAAAACAAAA
*
1965151 CAAAACAAAA
1 AAAAACAAAA
1965161 AAAAACAAAA
1 AAAAACAAAA
* *
1965171 AAAACCAAGA
1 AAAAACAAAA
1965181 AAAA
1 AAAA
1965185 TAGGAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
9 9 0.19
10 39 0.81
ACGTcount: A:0.83, C:0.16, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAACAAAA
Found at i:1965183 original size:19 final size:19
Alignment explanation
Indices: 1965122--1965184 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
1965112 CTTTACACCT
1965122 AAAAACAAAACAAAA-CAA
1 AAAAACAAAACAAAACCAA
*
1965140 ACAAAACAAAACAAAACAAAA
1 A-AAAACAAAACAAAAC-CAA
1965161 AAAAACAAAA-AAAACCAA
1 AAAAACAAAACAAAACCAA
1965179 GAAAAA
1 -AAAAA
1965185 TAGGAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 3 0.08
19 24 0.62
20 9 0.23
21 3 0.08
ACGTcount: A:0.83, C:0.16, G:0.02, T:0.00
Consensus pattern (19 bp):
AAAAACAAAACAAAACCAA
Found at i:1966491 original size:28 final size:28
Alignment explanation
Indices: 1966419--1966951 Score: 661
Period size: 28 Copynumber: 18.5 Consensus size: 28
1966409 CGTTCATCTC
* *
1966419 TTCAAAGCCCACAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
1966448 TTCAAAGCCCATAAGTCAGTGACACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
1966476 TTTAAAGCCCACAAGTTAGTGGTACTCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
1966505 TTCAAAGCCCATAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
1966534 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1966562 TTCAAAGCCCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
1966591 TTCAAAGCCCACAAGTTAGTGGCATCAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1966619 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
1966647 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1966675 TTCAAAGCCCACGTAAGTTAGTGGCACCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCT
* *
1966705 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
1966733 TTCAAAGCTCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
1966761 TTCAAAGCCCACGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
* **
1966791 TTCAAAGCCCACGCAAGTGAGTGGCACTATT
1 TTCAAAGCCCA--CAAGTCAGTGGCAC-CCT
1966822 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
1966850 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
1966878 TTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
1966907 TTCAAAGCCCACACGAGTCGGTGGTAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGG-CAC-CCT
1966939 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1966952 TGAGTTAATG
Statistics
Matches: 449, Mismatches: 44, Indels: 19
0.88 0.09 0.04
Matches are distributed among these distances:
28 218 0.49
29 123 0.27
30 70 0.16
31 19 0.04
32 19 0.04
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:1966510 original size:57 final size:57
Alignment explanation
Indices: 1966419--1966951 Score: 664
Period size: 57 Copynumber: 9.2 Consensus size: 57
1966409 CGTTCATCTC
* * * *
1966419 TTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCATAAGTCAGTGACACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * * *
1966476 TTTAAAGCCCACAAGTTAGTGGTACTCCTTTCAAAGCCCATAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
1966534 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCATAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * * *
1966591 TTCAAAGCCCACAAGTTAGTGGCA-TCATTTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
*
1966647 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACGTAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCAC--AAGTCAGTGGCACCCT
* *
1966705 TTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCTCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* **
1966761 TTCAAAGCCCACGCAAGTCAGTGGCAC-CCTTTCAAAGCCCACGCAAGTGAGTGGCACTATT
1 TTCAAAGCCCA--CAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCAC-CCT
1966822 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * *
1966878 TTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCCCACACGAGTCGGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA--AGTCAGTGG-CAC-CCT
1966939 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1966952 TGAGTTAATG
Statistics
Matches: 422, Mismatches: 37, Indels: 30
0.86 0.08 0.06
Matches are distributed among these distances:
56 90 0.21
57 153 0.36
58 101 0.24
59 36 0.09
60 15 0.04
61 27 0.06
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:1966569 original size:86 final size:84
Alignment explanation
Indices: 1966419--1966951 Score: 670
Period size: 86 Copynumber: 6.2 Consensus size: 84
1966409 CGTTCATCTC
* * * * * *
1966419 TTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCATAAGTCAGTGACACCCTTTTAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGC
* *
1966484 CCACAAGTTAGTGGTACTCCT
65 CCACAAGTCAGTGGCAC-CCT
* * * *
1966505 TTCAAAGCCCATAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGC
* *
1966570 CCATAAGTCAGTGGCACTCTT
65 CCACAAGTCAGTGGCAC-CCT
* * * *
1966591 TTCAAAGCCCACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCC
1966656 CACAAGTCAGTGGCACCCT
66 CACAAGTCAGTGGCACCCT
* *
1966675 TTCAAAGCCCACGTAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAG
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAG
*
1966740 CTCACAAGTCAGTGGCACCCT
64 CCCACAAGTCAGTGGCACCCT
* **
1966761 TTCAAAGCCCACGCAAGTCAGTGGCACCCTTTCAAAGCCCACGCAAGTGAGTGGCACTATTTTCA
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTTAGTGGCAC-CCTTTCA
1966826 AAGCCCACAAGTCAGTGGCACCCT
61 AAGCCCACAAGTCAGTGGCACCCT
*
1966850 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGC
* * *
1966915 CCACACGAGTCGGTGGTAACTCTT
65 CCACA--AGTCAGTGG-CAC-CCT
1966939 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1966952 TGAGTTAATG
Statistics
Matches: 405, Mismatches: 31, Indels: 19
0.89 0.07 0.04
Matches are distributed among these distances:
84 14 0.03
85 81 0.20
86 205 0.51
87 36 0.09
88 15 0.04
89 54 0.13
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (84 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCC
CACAAGTCAGTGGCACCCT
Found at i:1967565 original size:20 final size:20
Alignment explanation
Indices: 1967533--1967607 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
1967523 TTTTACCCAG
*
1967533 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1967553 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1967573 ATGTATCGATACATTGTTCA
1 ATGTATCGATACATTTTTCA
1967593 ATGTATCGATACATT
1 ATGTATCGATACATT
1967608 CTGTCTTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1969959 original size:97 final size:97
Alignment explanation
Indices: 1969802--1970147 Score: 566
Period size: 97 Copynumber: 3.6 Consensus size: 97
1969792 AAAATTTTAT
* * *
1969802 TCATCGGGGATACTCTAACCCCATTCCTCCGAGGGGATACTCCAACCTCGCTTTTAAACTTGTCA
1 TCATCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACTTGTCA
* *
1969867 AGATTCAAATCTTATTATCACTTAAATTGTCA
66 AGATTCAAATCTTATTCTCGCTTAAATTGTCA
* * *
1969899 TCATCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGATATTAAACTTGTTA
1 TCATCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACTTGTCA
*
1969964 AGATCCAAATCTTATTCTCGCTTAAATTGTCA
66 AGATTCAAATCTTATTCTCGCTTAAATTGTCA
* *
1969996 TCATCGGGGACACTCCAACCCCATTCCTCCGAGAGGATACTCCAAGCCCGCTTTTAAACTTGTCA
1 TCATCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACTTGTCA
*
1970061 AGATTCAAATCTTATTCTTGCTTAAATTGTCA
66 AGATTCAAATCTTATTCTCGCTTAAATTGTCA
* *
1970093 TCATCGGGGACACTCCAACCCCATTCCTCCGAAGGGATACTCCAACCCCGTTTTT
1 TCATCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTT
1970148 TTTTCAATCA
Statistics
Matches: 229, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 229 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (97 bp):
TCATCGGGGACACTCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACTTGTCA
AGATTCAAATCTTATTCTCGCTTAAATTGTCA
Found at i:1977335 original size:21 final size:21
Alignment explanation
Indices: 1977302--1977341 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1977292 TTTGTTATAT
*
1977302 ATTTTATTTTTATTTTTAATA
1 ATTTTATTTTTATATTTAATA
1977323 ATTTT-TTTATTATATTTAA
1 ATTTTATTT-TTATATTTAA
1977342 GAGATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTTATTTTTATATTTAATA
Found at i:1978172 original size:16 final size:16
Alignment explanation
Indices: 1978153--1978188 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1978143 CCGAAACTTA
*
1978153 AAATAATCCGAACTCG
1 AAATAATCCAAACTCG
*
1978169 AAATAATTCAAACTCG
1 AAATAATCCAAACTCG
1978185 AAAT
1 AAAT
1978189 GACTCGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.22
Consensus pattern (16 bp):
AAATAATCCAAACTCG
Found at i:1979787 original size:32 final size:32
Alignment explanation
Indices: 1979729--1979803 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
1979719 TTTTAAAGAC
1979729 TATTAAATTTTAAGAGTAAATATATTTAATATT
1 TATTAAATTTT-AGAGTAAATATATTTAATATT
* *
1979762 TATTAAATTTGT-GAGTAATTTTATTTAATATT
1 TATTAAATTT-TAGAGTAAATATATTTAATATT
* *
1979794 CATCAAATTT
1 TATTAAATTT
1979804 ATAAATAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 26 0.70
33 10 0.27
34 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.51
Consensus pattern (32 bp):
TATTAAATTTTAGAGTAAATATATTTAATATT
Found at i:1979813 original size:32 final size:32
Alignment explanation
Indices: 1979751--1979813 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
1979741 AGAGTAAATA
* * * * *
1979751 TATTTAATATTTATTAAATTTGTGAGTAATTT
1 TATTTAATATTCATCAAATTTATAAATAATTT
1979783 TATTTAATATTCATCAAATTTATAAATAATT
1 TATTTAATATTCATCAAATTTATAAATAATT
1979814 ATCATTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (32 bp):
TATTTAATATTCATCAAATTTATAAATAATTT
Found at i:1980605 original size:2 final size:2
Alignment explanation
Indices: 1980598--1980639 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1980588 ACATATTTCT
*
1980598 TA TA TA TA TA TA TA TA TA TA TA TA TA TG 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
1980640 AAAGAAAACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1990483 original size:45 final size:45
Alignment explanation
Indices: 1990434--1990524 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
1990424 TACTAAGGTT
1990434 TAATTGTATTCTGGTCATTATTGATAGGAATACTAAATATGCGCA
1 TAATTGTATTCTGGTCATTATTGATAGGAATACTAAATATGCGCA
*
1990479 TAATTGTATTTTGGTCATTATTGATAGGAATACTAAATATGCGCA
1 TAATTGTATTCTGGTCATTATTGATAGGAATACTAAATATGCGCA
1990524 T
1 T
1990525 TTCATGGCTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.40
Consensus pattern (45 bp):
TAATTGTATTCTGGTCATTATTGATAGGAATACTAAATATGCGCA
Found at i:1996152 original size:41 final size:40
Alignment explanation
Indices: 1996077--1996163 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 40
1996067 ATAATATTAA
*
1996077 AAATTAAAAAATATTTTTATATAAATATTTATAA-TTAAATTT
1 AAATAAAAAAATATTTTTATATAAATA--TATAATTTAAA-TT
*
1996119 AAATAAAAATAATTTTTATTATATAAATA-ATAATTTAAATT
1 AAATAAAAA-AATATTT-TTATATAAATATATAATTTAAATT
1996160 AAAT
1 AAAT
1996164 CTTTCTAAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
41 10 0.25
42 13 0.32
43 6 0.15
44 11 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (40 bp):
AAATAAAAAAATATTTTTATATAAATATATAATTTAAATT
Found at i:1996771 original size:2 final size:2
Alignment explanation
Indices: 1996764--1996802 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1996754 ATGCATAACC
1996764 TA TA TA TA TA 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 TA TA TA TA TA T
1996803 GTAGAAAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1996887 original size:80 final size:80
Alignment explanation
Indices: 1996778--1996935 Score: 298
Period size: 80 Copynumber: 2.0 Consensus size: 80
1996768 TATATATATA
* *
1996778 TATATATATATATATATATATATATGTAGAAAGATAATCTTAACGTGTAAAATCAGAAGGTAAAA
1 TATACATATATATATATATATATATGTAGAAAGATAATCTCAACGTGTAAAATCAGAAGGTAAAA
1996843 GATATTTGCTTCACC
66 GATATTTGCTTCACC
1996858 TATACATATATATATATATATATATGTAGAAAGATAATCTCAACGTGTAAAATCAGAAGGTAAAA
1 TATACATATATATATATATATATATGTAGAAAGATAATCTCAACGTGTAAAATCAGAAGGTAAAA
1996923 GATATTTGCTTCA
66 GATATTTGCTTCA
1996936 ACTTCCAGAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 76 1.00
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (80 bp):
TATACATATATATATATATATATATGTAGAAAGATAATCTCAACGTGTAAAATCAGAAGGTAAAA
GATATTTGCTTCACC
Found at i:1999885 original size:38 final size:38
Alignment explanation
Indices: 1999843--1999916 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
1999833 ATTTGAGTAT
* *
1999843 TCTCCCAACAAGGTTTTCAGAGTAATAGCAATGATTAC
1 TCTCCCAACAAGGTTTTCAAAGTAACAGCAATGATTAC
1999881 TCTCCCAACAAGGTTTTCAAAGTAACAGCAATGATT
1 TCTCCCAACAAGGTTTTCAAAGTAACAGCAATGATT
1999917 TCCTGGACCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (38 bp):
TCTCCCAACAAGGTTTTCAAAGTAACAGCAATGATTAC
Found at i:2004820 original size:15 final size:15
Alignment explanation
Indices: 2004800--2004829 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2004790 ATCCACATTT
*
2004800 CTTCTCTCATCTTTC
1 CTTCTCCCATCTTTC
2004815 CTTCTCCCATCTTTC
1 CTTCTCCCATCTTTC
2004830 TTTGTCCTCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.43, G:0.00, T:0.50
Consensus pattern (15 bp):
CTTCTCCCATCTTTC
Found at i:2012428 original size:15 final size:15
Alignment explanation
Indices: 2012408--2012440 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2012398 AGTGTCCTTA
2012408 TTCCTTCTCTCATCT
1 TTCCTTCTCTCATCT
2012423 TTCCTTCTCTCATCT
1 TTCCTTCTCTCATCT
2012438 TTC
1 TTC
2012441 TTTTCCCTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCCTTCTCTCATCT
Found at i:2015555 original size:21 final size:22
Alignment explanation
Indices: 2015511--2015558 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2015501 TTATATAAAT
* *
2015511 ATAATATAAAATTAATTAATAA
1 ATAATATAAAATAAAGTAATAA
*
2015533 ATAATATAATATAAAGT-ATAA
1 ATAATATAAAATAAAGTAATAA
2015554 ATAAT
1 ATAAT
2015559 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
ATAATATAAAATAAAGTAATAA
Found at i:2016468 original size:16 final size:16
Alignment explanation
Indices: 2016447--2016504 Score: 59
Period size: 15 Copynumber: 3.8 Consensus size: 16
2016437 ATCAAATTTA
2016447 TATAAATATAAAATAT
1 TATAAATATAAAATAT
*
2016463 TATAAATAT-AATTAT
1 TATAAATATAAAATAT
* *
2016478 AATATA-ATAAAATA-
1 TATAAATATAAAATAT
2016492 TATATAATATAAA
1 TATA-AATATAAA
2016505 TACATATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 5 0.15
15 14 0.42
16 14 0.42
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TATAAATATAAAATAT
Found at i:2016478 original size:22 final size:21
Alignment explanation
Indices: 2016446--2016493 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2016436 TATCAAATTT
*
2016446 ATATAAATATAAAATATTATAA
1 ATATAAATATAAAATAATA-AA
* *
2016468 ATATAATTATAATATAATAAA
1 ATATAAATATAAAATAATAAA
2016489 ATATA
1 ATATA
2016494 TATAATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAAATATAAAATAATAAA
Found at i:2016488 original size:30 final size:28
Alignment explanation
Indices: 2016447--2016503 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
2016437 ATCAAATTTA
2016447 TATAAATATAAAATAT-TATAAATATAAT
1 TATAAATATAAAATATATAT-AATATAAT
2016475 TATAATATAATAAAATATATATAATATAA
1 TATAA-AT-ATAAAATATATATAATATAA
2016504 ATACATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 5 0.19
29 2 0.08
30 16 0.62
31 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
TATAAATATAAAATATATATAATATAAT
Found at i:2016506 original size:25 final size:26
Alignment explanation
Indices: 2016446--2016512 Score: 57
Period size: 25 Copynumber: 2.6 Consensus size: 26
2016436 TATCAAATTT
* *
2016446 ATATAAATATAAAATATTATAAATATA
1 ATATAAATAT-ATATAATATAAATATA
* *
2016473 AT-TATAATATA-ATAAAATATATATA
1 ATATA-AATATATATAATATAAATATA
*
2016498 ATATAAATACATATA
1 ATATAAATATATATA
2016513 TTATCAGATC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
25 18 0.55
26 8 0.24
27 7 0.21
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATAAATATATATAATATAAATATA
Found at i:2016511 original size:19 final size:19
Alignment explanation
Indices: 2016448--2016513 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 19
2016438 TCAAATTTAT
*
2016448 ATAAATATA-A-AATAT-T
1 ATAAATATATATAATATAA
2016464 ATAAATATAATTATAATAT-A
1 ATAAATAT-A-TATAATATAA
2016484 ATAAAATATATATAATATAA
1 AT-AAATATATATAATATAA
*
2016504 ATACATATAT
1 ATAAATATAT
2016514 TATCAGATCT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
16 8 0.19
17 1 0.02
19 16 0.38
20 11 0.26
21 6 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAATATATATAATATAA
Found at i:2016751 original size:19 final size:19
Alignment explanation
Indices: 2016727--2016777 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 19
2016717 TTATATAAAA
*
2016727 TAAATATAATATAAATTAT
1 TAAATATAATATAAAATAT
2016746 TAAATAT-AT-TAAAATAT
1 TAAATATAATATAAAATAT
2016763 TAAATATAAATATAA
1 TAAATAT-AATATAA
2016778 CACTTATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 14 0.50
18 2 0.07
19 9 0.32
20 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAAATATAATATAAAATAT
Found at i:2016763 original size:17 final size:18
Alignment explanation
Indices: 2016727--2016840 Score: 68
Period size: 20 Copynumber: 6.1 Consensus size: 18
2016717 TTATATAAAA
*
2016727 TAAATATAATATAAATTAT
1 TAAATAT-ATATAAAATAT
2016746 TAAATATAT-TAAAATAT
1 TAAATATATATAAAATAT
* * *
2016763 TAAATATAAATATAACACT
1 TAAATATATATAAAATA-T
* * *
2016782 TATATTAAATATATAATAT
1 TA-AATATATATAAAATAT
* *
2016801 TAATTATATTTAAATATAT
1 TAAATATATATAAA-ATAT
* *
2016820 TATATTATATCATAATATAT
1 TA-AATATAT-ATAAAATAT
2016840 T
1 T
2016841 TATTTTTATT
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
17 15 0.20
18 16 0.21
19 19 0.25
20 23 0.30
21 3 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATATATATAAAATAT
Found at i:2016825 original size:24 final size:23
Alignment explanation
Indices: 2016751--2016826 Score: 84
Period size: 24 Copynumber: 3.3 Consensus size: 23
2016741 ATTATTAAAT
*
2016751 ATATTAA-AATATTAAATATA-A
1 ATATTAATTATATTAAATATATA
*
2016772 ATATAACACTTATATTAAATATATA
1 ATATTA-A-TTATATTAAATATATA
*
2016797 ATATTAATTATATTTAAATATATT
1 ATATTAATTATA-TTAAATATATA
2016821 ATATTA
1 ATATTA
2016827 TATCATAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 5 0.11
22 1 0.02
23 5 0.11
24 29 0.63
25 6 0.13
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
ATATTAATTATATTAAATATATA
Found at i:2017260 original size:15 final size:14
Alignment explanation
Indices: 2017226--2017264 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
2017216 ATGAATAAAG
2017226 TAATTA-ATTATTT
1 TAATTATATTATTT
2017239 TAATTATATTATTTT
1 TAATTATATTA-TTT
*
2017254 TATTTATATTA
1 TAATTATATTA
2017265 ATAATAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.26
14 4 0.17
15 13 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TAATTATATTATTT
Done.