Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, whole genome shotgun sequence
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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 111 of 133
Found at i:21587001 original size:123 final size:122
Alignment explanation
Indices: 21586783--21587028 Score: 411
Period size: 123 Copynumber: 2.0 Consensus size: 122
21586773 CTAAACCCCG
* *
21586783 TTTCCATGTATTTGATCCAGTTTGAGGTTCTTTACACCTTGGCTTTTAGAATGATTCACCCATAG
1 TTTCCATGCACTTGATCCAGTTTGAGGTTCTTTACACCTTGGCTTTTAGAATGATTCACCCATAG
* *
21586848 ATCATCTGAGCTTTAGAACCCACTGTCTCCAATTCACTGGTACAGGTCATGTGCTAT
66 ATCATCTGAGCTTTAAAACCCACTGTCTCCAACTCACTGGTACAGGTCATGTGCTAT
* * *
21586905 TTTCCATGCACTTGATCCAGTTTGAGGTTGTTTTACACCTTGGCTTTTATAATGATTCACCCATT
1 TTTCCATGCACTTGATCCAGTTTGAGGTT-CTTTACACCTTGGCTTTTAGAATGATTCACCCATA
*
21586970 GATCATCTGAGCTTTAAAACCCACTGTCTCCAACTCACTGGTACATGTCATGTGCTAT
65 GATCATCTGAGCTTTAAAACCCACTGTCTCCAACTCACTGGTACAGGTCATGTGCTAT
21587028 T
1 T
21587029 GCTCTTAACC
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
122 27 0.23
123 88 0.77
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (122 bp):
TTTCCATGCACTTGATCCAGTTTGAGGTTCTTTACACCTTGGCTTTTAGAATGATTCACCCATAG
ATCATCTGAGCTTTAAAACCCACTGTCTCCAACTCACTGGTACAGGTCATGTGCTAT
Found at i:21590777 original size:27 final size:27
Alignment explanation
Indices: 21590730--21590789 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
21590720 AAAATTAATA
21590730 ATAATT-AATATTATTTATTTAAAA-T
1 ATAATTAAATATTATTTATTTAAAATT
21590755 ATGAATTAAATATTTATTT-TTTAAAATT
1 AT-AATTAAATA-TTATTTATTTAAAATT
21590783 ATAATTA
1 ATAATTA
21590790 TTTTATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
25 2 0.06
26 4 0.13
27 16 0.52
28 9 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
ATAATTAAATATTATTTATTTAAAATT
Found at i:21591265 original size:20 final size:17
Alignment explanation
Indices: 21591226--21591265 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
21591216 TTAAATCAAA
*
21591226 AATAGTAAAATCACTTT
1 AATAATAAAATCACTTT
21591243 AATAATAAAATCA-TCTT
1 AATAATAAAATCACT-TT
21591260 AATAAT
1 AATAAT
21591266 TACATTACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.05
17 20 0.95
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.35
Consensus pattern (17 bp):
AATAATAAAATCACTTT
Found at i:21592717 original size:16 final size:15
Alignment explanation
Indices: 21592696--21592725 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21592686 AGAGTGACTT
21592696 AAAATAAATAATAATA
1 AAAATAAAT-ATAATA
21592712 AAAATAAATATAAT
1 AAAATAAATATAAT
21592726 TAATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAATATAATA
Found at i:21593147 original size:23 final size:23
Alignment explanation
Indices: 21593112--21593156 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
21593102 TCATCAAATC
21593112 AAATTATCATTTTTATTTATTTA
1 AAATTATCATTTTTATTTATTTA
*
21593135 AAATTATTC-TTTTTTTTTATTT
1 AAATTA-TCATTTTTATTTATTT
21593157 TGTTAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
AAATTATCATTTTTATTTATTTA
Found at i:21603991 original size:23 final size:23
Alignment explanation
Indices: 21603964--21604041 Score: 69
Period size: 22 Copynumber: 3.6 Consensus size: 23
21603954 TTTTTATATT
21603964 ATATAATATTATTTAAAAATTAA
1 ATATAATATTATTTAAAAATTAA
*
21603987 ATAT-ATTTTATTTCAAAAA-TAA
1 ATATAATATTATTT-AAAAATTAA
* *
21604009 AT-TAATTATAATTT-AAAATCAA
1 ATATAA-TATTATTTAAAAATTAA
21604031 ATA-AA-ATTATT
1 ATATAATATTATT
21604042 CATGATAATA
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
20 5 0.11
21 5 0.11
22 20 0.44
23 15 0.33
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATAATATTATTTAAAAATTAA
Found at i:21605165 original size:16 final size:15
Alignment explanation
Indices: 21605144--21605173 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21605134 AGAGTGACTT
21605144 AAAATAAATAATAATA
1 AAAATAAAT-ATAATA
21605160 AAAATAAATATAAT
1 AAAATAAATATAAT
21605174 TAATTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATAAATATAATA
Found at i:21605193 original size:33 final size:33
Alignment explanation
Indices: 21605161--21605223 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 33
21605151 ATAATAATAA
* *
21605161 AAAT-AAATATAATTAATTTA-ATTTTTTAAAT
1 AAATCAAATATAATAAATTAACATTTTTTAAAT
*
21605192 AATTCAAATATAATAAATTAACATTTTTTAAA
1 AAATCAAATATAATAAATTAACATTTTTTAAA
21605224 AGACAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 3 0.11
32 14 0.52
33 10 0.37
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (33 bp):
AAATCAAATATAATAAATTAACATTTTTTAAAT
Found at i:21605600 original size:22 final size:23
Alignment explanation
Indices: 21605560--21605603 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
21605550 TCATCAAATC
21605560 AAATTATCATTTTTATTTATTTA
1 AAATTATCATTTTTATTTATTTA
21605583 AAATTATTC-TTTTT-TTTATTT
1 AAATTA-TCATTTTTATTTATTT
21605604 TGTTAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 11 0.55
24 2 0.10
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (23 bp):
AAATTATCATTTTTATTTATTTA
Found at i:21613171 original size:14 final size:15
Alignment explanation
Indices: 21613148--21613185 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
21613138 ATTTTGAGTT
*
21613148 AAATTTAAATTTAA-
1 AAATTAAAATTTAAC
21613162 AAATTAAAATTTAATC
1 AAATTAAAATTTAA-C
21613178 AAATTAAA
1 AAATTAAA
21613186 GTCGAGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.62
16 8 0.38
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTAAAATTTAAC
Found at i:21614864 original size:2 final size:2
Alignment explanation
Indices: 21614857--21614883 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21614847 TTTTTGTTTT
21614857 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 T
21614884 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:21615710 original size:11 final size:11
Alignment explanation
Indices: 21615694--21615721 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
21615684 TTTTATCAGT
21615694 AAATGCATTAG
1 AAATGCATTAG
21615705 AAATGCATTAG
1 AAATGCATTAG
21615716 AAATGC
1 AAATGC
21615722 TGATTACTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (11 bp):
AAATGCATTAG
Found at i:21624758 original size:30 final size:30
Alignment explanation
Indices: 21624723--21624786 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
21624713 AAATGTGCTG
*
21624723 TTTATTGATTATTTTCTTTTGAATGATCAA
1 TTTATTGATTATTTTCTTTTAAATGATCAA
21624753 TTTATTGATTATTTTCTTTTAAATGATCAA
1 TTTATTGATTATTTTCTTTTAAATGATCAA
21624783 TTTA
1 TTTA
21624787 CCGTCTTCAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.28, C:0.06, G:0.08, T:0.58
Consensus pattern (30 bp):
TTTATTGATTATTTTCTTTTAAATGATCAA
Found at i:21634139 original size:18 final size:17
Alignment explanation
Indices: 21634110--21634149 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
21634100 TCAAATACAA
21634110 ATATATTATTTATCTAT
1 ATATATTATTTATCTAT
*
21634127 ATATATCTATTTATCTGT
1 ATATAT-TATTTATCTAT
21634145 ATATA
1 ATATA
21634150 AAAATATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (17 bp):
ATATATTATTTATCTAT
Found at i:21634413 original size:17 final size:17
Alignment explanation
Indices: 21634393--21634427 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
21634383 AATTTAAACG
*
21634393 AATTTTTTTTATTATTA
1 AATTTTTTTTATAATTA
21634410 AATTTTTTTTATAATTA
1 AATTTTTTTTATAATTA
21634427 A
1 A
21634428 GCTGCAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AATTTTTTTTATAATTA
Found at i:21636266 original size:50 final size:50
Alignment explanation
Indices: 21636204--21636301 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
21636194 TGCTAATTTA
* * *
21636204 ATATTGTAAGCTTACATTTTGTTTCAAATTACCATTTTGATGTTGTTAGC
1 ATATTGTAAGCTTAAATTTTATTTCAAATTACCATTATGATGTTGTTAGC
*
21636254 ATATTG-ATAGCTTAAATTTTATTTCAAATTATCATTATGATGTTGTTA
1 ATATTGTA-AGCTTAAATTTTATTTCAAATTACCATTATGATGTTGTTA
21636302 ACAGTTAGGG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 1 0.02
50 42 0.98
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (50 bp):
ATATTGTAAGCTTAAATTTTATTTCAAATTACCATTATGATGTTGTTAGC
Found at i:21636911 original size:21 final size:20
Alignment explanation
Indices: 21636885--21636962 Score: 84
Period size: 21 Copynumber: 3.8 Consensus size: 20
21636875 AATCATAGAT
* *
21636885 GTAGCTATTGATCCCCTTCTA
1 GTAGCTCTTGAT-CCTTTCTA
*
21636906 GTAGCTCTCGATCCTTTCTTA
1 GTAGCTCTTGATCCTTTC-TA
*
21636927 GTAACTCTTGATCCTTTACTA
1 GTAGCTCTTGATCCTTT-CTA
*
21636948 GTAGCTTTTGATCCT
1 GTAGCTCTTGATCCT
21636963 CTACCAGTAG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 5 0.10
21 42 0.88
22 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.42
Consensus pattern (20 bp):
GTAGCTCTTGATCCTTTCTA
Found at i:21641971 original size:11 final size:11
Alignment explanation
Indices: 21641955--21641992 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
21641945 TTATTAAAAC
21641955 TTAATAGTAAA
1 TTAATAGTAAA
* *
21641966 TTAATAATAAC
1 TTAATAGTAAA
21641977 TTAATAGTAAA
1 TTAATAGTAAA
21641988 TTAAT
1 TTAAT
21641993 GATAATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (11 bp):
TTAATAGTAAA
Found at i:21641980 original size:22 final size:22
Alignment explanation
Indices: 21641930--21642004 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
21641920 TGCAACCAGT
* *
21641930 ATAACATAATAGT-AATTATTA
1 ATAACTTAATAGTAAATTAATA
21641951 A-AACTTAATAGTAAATTAATA
1 ATAACTTAATAGTAAATTAATA
*
21641972 ATAACTTAATAGTAAATTAATG
1 ATAACTTAATAGTAAATTAATA
*
21641994 ATAATTTAATA
1 ATAACTTAATA
21642005 ATTAATAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
20 10 0.21
21 9 0.19
22 29 0.60
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.37
Consensus pattern (22 bp):
ATAACTTAATAGTAAATTAATA
Found at i:21642014 original size:25 final size:25
Alignment explanation
Indices: 21641986--21642047 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
21641976 CTTAATAGTA
*
21641986 AATTAATGATAATTTAAT-AATTAAT
1 AATTAAT-ATAATTTAATAAATCAAT
**
21642011 AATTAATAATTTTTTAATAAATCAAT
1 AATTAAT-ATAATTTAATAAATCAAT
21642037 AA-TAATATAAT
1 AATTAATATAAT
21642048 AAATGTATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
24 3 0.10
25 19 0.63
26 8 0.27
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
AATTAATATAATTTAATAAATCAAT
Found at i:21642017 original size:11 final size:10
Alignment explanation
Indices: 21641936--21642013 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 10
21641926 CAGTATAACA
*
21641936 TAATAGTAAT
1 TAATAATAAT
*
21641946 TATTAA-AACT
1 TAATAATAA-T
*
21641956 TAATAGTAAAT
1 TAATAAT-AAT
21641967 TAATAATAACT
1 TAATAATAA-T
*
21641978 TAATAGTAAAT
1 TAATAAT-AAT
*
21641989 TAATGATAAT
1 TAATAATAAT
21641999 T--TAATAAT
1 TAATAATAAT
21642007 TAATAAT
1 TAATAAT
21642014 TAATAATTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
8 7 0.13
9 2 0.04
10 19 0.37
11 20 0.38
12 4 0.08
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (10 bp):
TAATAATAAT
Found at i:21642019 original size:22 final size:22
Alignment explanation
Indices: 21641955--21642049 Score: 84
Period size: 22 Copynumber: 4.3 Consensus size: 22
21641945 TTATTAAAAC
* * *
21641955 TTAATAGTAAATTAATAATAAC
1 TTAATAATAAATCAATAATAAT
* * *
21641977 TTAATAGTAAATTAATGATAAT
1 TTAATAATAAATCAATAATAAT
*
21641999 TTAATAATTAAT-AATTAATAAT
1 TTAATAATAAATCAA-TAATAAT
**
21642021 TTTTTAATAAATCAATAATAAT
1 TTAATAATAAATCAATAATAAT
*
21642043 ATAATAA
1 TTAATAA
21642050 ATGTATAACA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
21 2 0.03
22 56 0.93
23 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (22 bp):
TTAATAATAAATCAATAATAAT
Found at i:21642171 original size:22 final size:22
Alignment explanation
Indices: 21642143--21642214 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
21642133 CAAAAAAAAG
* *
21642143 TGATAACTTAGTTATTAATTAT
1 TGATAACTTAGTAATAAATTAT
*
21642165 TGATAACTTAGTAATAAATTAA
1 TGATAACTTAGTAATAAATTAT
*
21642187 T-ACTAACTTAATAATAAATTAT
1 TGA-TAACTTAGTAATAAATTAT
*
21642209 TAATAA
1 TGATAA
21642215 TATATTAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
21 1 0.02
22 41 0.95
23 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (22 bp):
TGATAACTTAGTAATAAATTAT
Found at i:21642197 original size:11 final size:11
Alignment explanation
Indices: 21642167--21642214 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
21642157 TTAATTATTG
*
21642167 ATAACTTAGTA
1 ATAACTTAATA
*
21642178 ATAAATTAATA
1 ATAACTTAATA
*
21642189 CTAACTTAATA
1 ATAACTTAATA
* *
21642200 ATAAATTATTA
1 ATAACTTAATA
21642211 ATAA
1 ATAA
21642215 TATATTAGTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (11 bp):
ATAACTTAATA
Found at i:21642289 original size:22 final size:22
Alignment explanation
Indices: 21642263--21642323 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
21642253 TCATAGTAGC
*
21642263 AAATC-ATAAATAACTTATTAGT
1 AAATCAAT-AATAACTTAATAGT
*
21642285 AAATCAATAATAATTTAATAGT
1 AAATCAATAATAACTTAATAGT
*
21642307 AAAT-AATTGATAACTTA
1 AAATCAA-TAATAACTTA
21642324 GTAATTAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (22 bp):
AAATCAATAATAACTTAATAGT
Found at i:21642488 original size:96 final size:96
Alignment explanation
Indices: 21642384--21642566 Score: 312
Period size: 96 Copynumber: 1.9 Consensus size: 96
21642374 ATCATTGACG
* * *
21642384 ATTTAATAATTAATTAGTAATAACTTAATAGTAAATCATACATAATTTAATATAATCAGTAATAA
1 ATTTAATAATTAATCAGTAATAACTTAATAATAAATCATACATAATTTAATATAACCAGTAATAA
*
21642449 TTTGATAATGAATTATATATAAGCATTGATA
66 TTTGATAATGAATCATATATAAGCATTGATA
* *
21642480 ATTTAATAATTAATCAGTAATAACTTAATAATAAATCATGCATAATTTAATATAACCAGTGATAA
1 ATTTAATAATTAATCAGTAATAACTTAATAATAAATCATACATAATTTAATATAACCAGTAATAA
21642545 TTTGATAATGAATCATATATAA
66 TTTGATAATGAATCATATATAA
21642567 TTTAGCAATT
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (96 bp):
ATTTAATAATTAATCAGTAATAACTTAATAATAAATCATACATAATTTAATATAACCAGTAATAA
TTTGATAATGAATCATATATAAGCATTGATA
Found at i:21642524 original size:22 final size:22
Alignment explanation
Indices: 21642477--21642570 Score: 79
Period size: 22 Copynumber: 4.4 Consensus size: 22
21642467 ATAAGCATTG
*
21642477 ATAATTTAATAATTAATCAGTA
1 ATAATTTAATAATAAATCAGTA
* *
21642499 ATAACTTAATAATAAATCA-TGC
1 ATAATTTAATAATAAATCAGT-A
* *
21642521 ATAATTTAAT-AT-AACCAGTG
1 ATAATTTAATAATAAATCAGTA
* *
21642541 ATAATTTGATAATGAATCA-TA
1 ATAATTTAATAATAAATCAGTA
21642562 TATAATTTA
1 -ATAATTTA
21642571 GCAATTAATG
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
20 13 0.23
21 7 0.12
22 37 0.65
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.38
Consensus pattern (22 bp):
ATAATTTAATAATAAATCAGTA
Found at i:21642560 original size:42 final size:44
Alignment explanation
Indices: 21642477--21642570 Score: 111
Period size: 42 Copynumber: 2.2 Consensus size: 44
21642467 ATAAGCATTG
* *
21642477 ATAATTTAATAATTAATCAGTAATAACTTAATAATAAATCATGC
1 ATAATTTAATAATTAACCAGTAATAACTTAATAATAAATCATAC
* * * * *
21642521 ATAATTTAAT-A-TAACCAGTGATAATTTGATAATGAATCATAT
1 ATAATTTAATAATTAACCAGTAATAACTTAATAATAAATCATAC
21642563 ATAATTTA
1 ATAATTTA
21642571 GCAATTAATG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 32 0.74
43 1 0.02
44 10 0.23
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.38
Consensus pattern (44 bp):
ATAATTTAATAATTAACCAGTAATAACTTAATAATAAATCATAC
Found at i:21642565 original size:32 final size:32
Alignment explanation
Indices: 21642433--21642566 Score: 80
Period size: 32 Copynumber: 4.2 Consensus size: 32
21642423 ACATAATTTA
* *
21642433 ATATAATCAGTAATAATTTGATAATGAATTAT
1 ATATAACCAGTAATAATTTGATAATGAATCAT
* * * * *
21642465 ATATAAGCATTGATAATTTAATAATTAATCAGT
1 ATATAACCAGTAATAATTTGATAATGAATCA-T
* * * *
21642498 A-ATAACTTAATAATAAATCATGCATAAT---TTA-
1 ATATAAC-CAGTAAT-AAT-TTG-ATAATGAATCAT
*
21642529 ATATAACCAGTGATAATTTGATAATGAATCAT
1 ATATAACCAGTAATAATTTGATAATGAATCAT
21642561 ATATAA
1 ATATAA
21642567 TTTAGCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 20
0.66 0.16 0.18
Matches are distributed among these distances:
28 5 0.07
29 2 0.03
30 3 0.04
31 7 0.09
32 40 0.54
33 8 0.11
34 3 0.04
35 1 0.01
36 5 0.07
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (32 bp):
ATATAACCAGTAATAATTTGATAATGAATCAT
Found at i:21642635 original size:8 final size:8
Alignment explanation
Indices: 21642622--21642679 Score: 52
Period size: 8 Copynumber: 7.8 Consensus size: 8
21642612 TAGTAAATCA
21642622 ATAATAAT
1 ATAATAAT
21642630 ATAATAAT
1 ATAATAAT
21642638 A-AAT-AT
1 ATAATAAT
*
21642644 ATAAAAAT
1 ATAATAAT
*
21642652 ATAATAGT
1 ATAATAAT
21642660 A-AATAAT
1 ATAATAAT
*
21642667 -TGATAAT
1 ATAATAAT
*
21642674 TTAATA
1 ATAATA
21642680 GTAAGTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
6 3 0.08
7 15 0.38
8 22 0.55
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (8 bp):
ATAATAAT
Found at i:21642640 original size:22 final size:21
Alignment explanation
Indices: 21642589--21642769 Score: 102
Period size: 22 Copynumber: 8.4 Consensus size: 21
21642579 TGATAATTTT
** * *
21642589 ATAGTAAATAACCACAATTTA
1 ATAGTAAATAATAATAATATA
21642610 AGTAGTAAATCAATAATAATATA
1 A-TAGTAAAT-AATAATAATATA
* *
21642633 ATAATAAATATATAAAAATATA
1 ATAGTAAATA-ATAATAATATA
* *
21642655 ATAGTAAATAATTGATAATTTA
1 ATAGTAAATAA-TAATAATATA
* *
21642677 ATAGTAAGT--TTATAAGT-TA
1 ATAGTAAATAATAATAA-TATA
*
21642696 ATAGTAAATCACTAATAACTAATA
1 ATAGTAAAT-AATAATAA-T-ATA
* *
21642720 ATA--AAATACTAATAATGTA
1 ATAGTAAATAATAATAATATA
* * *
21642739 ATTGTAAATCAATAATAATTTG
1 ATAGTAAAT-AATAATAATATA
21642761 ATAGTAAAT
1 ATAGTAAAT
21642770 TAGTTTATCA
Statistics
Matches: 126, Mismatches: 21, Indels: 25
0.73 0.12 0.15
Matches are distributed among these distances:
19 19 0.15
20 2 0.02
21 15 0.12
22 76 0.60
23 9 0.07
24 5 0.04
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (21 bp):
ATAGTAAATAATAATAATATA
Found at i:21642765 original size:84 final size:86
Alignment explanation
Indices: 21642607--21642767 Score: 213
Period size: 84 Copynumber: 1.9 Consensus size: 86
21642597 TAACCACAAT
*
21642607 TTAAGTAGTAAATCAATAATAATATAATAATAAATATATAAAAATATAATAGTAAATAATTGATA
1 TTAAGTAGTAAATCAATAATAATATAATAATAAATATATAAAAATATAATAGTAAATAATTAATA
21642672 ATTTAATAGTAAGTTTATAAG
66 ATTTAATAGTAAGTTTATAAG
* * * * *
21642693 TTAA-TAGTAAATCACTAATAA-CTAATAATAAA-ATACTAATAATGTAATTGTAAATCAA-TAA
1 TTAAGTAGTAAATCAATAATAATATAATAATAAATATA-TAAAAATATAATAGTAAAT-AATTAA
*
21642754 TAATTTGATAGTAA
64 TAATTTAATAGTAA
21642768 ATTAGTTTAT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
83 3 0.05
84 41 0.62
85 18 0.27
86 4 0.06
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.35
Consensus pattern (86 bp):
TTAAGTAGTAAATCAATAATAATATAATAATAAATATATAAAAATATAATAGTAAATAATTAATA
ATTTAATAGTAAGTTTATAAG
Found at i:21642907 original size:11 final size:11
Alignment explanation
Indices: 21642893--21642989 Score: 70
Period size: 11 Copynumber: 8.8 Consensus size: 11
21642883 AAATTATTTT
*
21642893 ATAATTTAATG
1 ATAAATTAATG
*
21642904 ATAAA-TAATTC
1 ATAAATTAA-TG
*
21642915 ATAACTTAATG
1 ATAAATTAATG
*
21642926 ATAAATTAATC
1 ATAAATTAATG
*
21642937 ATAAATTAATA
1 ATAAATTAATG
***
21642948 ATAAATCGTTG
1 ATAAATTAATG
* *
21642959 CTAACTTAATG
1 ATAAATTAATG
*
21642970 ATAAATCAATG
1 ATAAATTAATG
*
21642981 ATAATTTAA
1 ATAAATTAA
21642990 GTGTTAATCA
Statistics
Matches: 63, Mismatches: 21, Indels: 4
0.72 0.24 0.05
Matches are distributed among these distances:
10 3 0.05
11 57 0.90
12 3 0.05
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.37
Consensus pattern (11 bp):
ATAAATTAATG
Found at i:21642946 original size:44 final size:44
Alignment explanation
Indices: 21642893--21642989 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
21642883 AAATTATTTT
* *
21642893 ATAATTTAATGATAAATAATT-CATAACTTAATGATAAATTAATC
1 ATAATTTAATAATAAATAATTGC-TAACTTAATGATAAATCAATC
* ** *
21642937 ATAAATTAATAATAAATCGTTGCTAACTTAATGATAAATCAATG
1 ATAATTTAATAATAAATAATTGCTAACTTAATGATAAATCAATC
21642981 ATAATTTAA
1 ATAATTTAA
21642990 GTGTTAATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 44 0.98
45 1 0.02
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.37
Consensus pattern (44 bp):
ATAATTTAATAATAAATAATTGCTAACTTAATGATAAATCAATC
Found at i:21642989 original size:22 final size:22
Alignment explanation
Indices: 21642849--21643009 Score: 94
Period size: 22 Copynumber: 7.3 Consensus size: 22
21642839 TAAATCATCA
* **
21642849 ATAATTTAGTGATAAAT-AAAA
1 ATAATTTAATGATAAATCAATG
* * * * *
21642870 ATAATTTAATAAAAAATTATTTT
1 ATAATTTAATGATAAATCA-ATG
*
21642893 ATAATTTAATGATAAAT-AATTC
1 ATAATTTAATGATAAATCAA-TG
* * *
21642915 ATAACTTAATGATAAATTAATC
1 ATAATTTAATGATAAATCAATG
* * **
21642937 ATAAATTAATAATAAATCGTTG
1 ATAATTTAATGATAAATCAATG
* *
21642959 CTAACTTAATGATAAATCAATG
1 ATAATTTAATGATAAATCAATG
* *
21642981 ATAATTTAAGTG-TTAATCATTG
1 ATAATTTAA-TGATAAATCAATG
21643003 ATAATTT
1 ATAATTT
21643010 TTTTTTATAT
Statistics
Matches: 109, Mismatches: 26, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
21 14 0.13
22 76 0.70
23 19 0.17
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (22 bp):
ATAATTTAATGATAAATCAATG
Found at i:21643306 original size:22 final size:22
Alignment explanation
Indices: 21643281--21643783 Score: 125
Period size: 22 Copynumber: 22.9 Consensus size: 22
21643271 AAAACAAGTG
* *
21643281 ATAATTTAATAATTAATTATTA
1 ATAATTTAATAATAAATTAATA
* *
21643303 ATAACTTAATAATAAATCAATA
1 ATAATTTAATAATAAATTAATA
* *
21643325 ATAATTTAGTAGTAAATTAAT-
1 ATAATTTAATAATAAATTAATA
* * *
21643346 ATAATTTAACAGTAAATCAAT-
1 ATAATTTAATAATAAATTAATA
* * *
21643367 TTGAATTTAATAGT-AATTAATTG
1 AT-AATTTAATAATAAATTAA-TA
* *
21643390 ATAAACTTT-ATAGTAAA-TCATAA
1 AT-AA-TTTAATAATAAATTAAT-A
** * *
21643413 ATAGCTTAATAATAAATCAATG
1 ATAATTTAATAATAAATTAATA
* * *
21643435 ATAATTTAATAATTAATCATTA
1 ATAATTTAATAATAAATTAATA
* *
21643457 AAAACTTAA-AAGTAAATTAAT-
1 ATAATTTAATAA-TAAATTAATA
* * * *
21643478 ATAACTTAGGAATAGTAAATTATTG
1 ATAA-TT--TAATAATAAATTAATA
* * * * * *
21643503 ATAACTTAATAGTTAATCAGTG
1 ATAATTTAATAATAAATTAATA
* * * *
21643525 ATAACTTAATAATTAA-TCATGG
1 ATAATTTAATAATAAATTAAT-A
* *
21643547 ATAATTTAAT-ATAAATTAGTG
1 ATAATTTAATAATAAATTAATA
* * *
21643568 ATAACTTGATAATAAA-TCATA
1 ATAATTTAATAATAAATTAATA
* ** *
21643589 GTTAATTTAATAATAAATTTGTG
1 -ATAATTTAATAATAAATTAATA
* *
21643612 ATAATTTTATAGTAAA-TAATAA
1 ATAATTTAATAATAAATTAAT-A
* * * **
21643634 AAAACTAAATGGTAAA-TACATA
1 ATAATTTAATAATAAATTA-ATA
** * * *
21643656 ATAACAT-ATATTAAATCATTA
1 ATAATTTAATAATAAATTAATA
* *
21643677 ATAATTT-ATATATAAATTATTG
1 ATAATTTAATA-ATAAATTAATA
* * *
21643699 ATAACTTGATAATAAATTACTA
1 ATAATTTAATAATAAATTAATA
* * * *
21643721 ATAACTTAATTACAAATTAGTA
1 ATAATTTAATAATAAATTAATA
* ** *
21643743 CTAATTTAATTCTAAATCAATA
1 ATAATTTAATAATAAATTAATA
* *
21643765 ATAATTTTATAGTAAATTA
1 ATAATTTAATAATAAATTA
21643784 GTTAATCATT
Statistics
Matches: 353, Mismatches: 104, Indels: 48
0.70 0.21 0.10
Matches are distributed among these distances:
21 65 0.18
22 246 0.70
23 21 0.06
24 16 0.05
25 5 0.01
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (22 bp):
ATAATTTAATAATAAATTAATA
Found at i:21643331 original size:44 final size:44
Alignment explanation
Indices: 21643281--21643783 Score: 217
Period size: 44 Copynumber: 11.4 Consensus size: 44
21643271 AAAACAAGTG
* *
21643281 ATAATTTAATAATTAATTATTAATAACTTAATAATAAATCAATA
1 ATAATTTAATAATAAATTATTGATAACTTAATAATAAATCAATA
* * * * * *
21643325 ATAATTTAGTAGTAAATTAAT-ATAATTTAACAGTAAATCAAT-
1 ATAATTTAATAATAAATTATTGATAACTTAATAATAAATCAATA
* * * *
21643367 TTGAATTTAATAGT-AATTAATTGATAAACTTTATAGTAAATC-ATAA
1 AT-AATTTAATAATAAATT-ATTGAT-AACTTAATAATAAATCAAT-A
** * * * * *
21643413 ATAGCTTAATAATAAATCAATGATAATTTAATAATTAATCATTA
1 ATAATTTAATAATAAATTATTGATAACTTAATAATAAATCAATA
* * * * * * *
21643457 AAAACTTAA-AAGTAAATTAAT-ATAACTTAGGAATAGTAAATTATTG
1 ATAATTTAATAA-TAAATTATTGATAACTT---AATAATAAATCAATA
* * * * * * *
21643503 ATAACTTAATAGTTAATCAGTGATAACTTAATAATTAATC-ATGG
1 ATAATTTAATAATAAATTATTGATAACTTAATAATAAATCAAT-A
* *
21643547 ATAATTTAAT-ATAAATTAGTGATAACTTGATAATAAATC-ATA
1 ATAATTTAATAATAAATTATTGATAACTTAATAATAAATCAATA
* * * *
21643589 GTTAATTTAATAATAAATT-TGTGATAATTTTATAGTAAAT-AATAA
1 -ATAATTTAATAATAAATTAT-TGATAACTTAATAATAAATCAAT-A
* * * ** * * * * *
21643634 AAAACTAAATGGTAAA-TACATAATAACAT-ATATTAAATCATTA
1 ATAATTTAATAATAAATTA-TTGATAACTTAATAATAAATCAATA
* * *
21643677 ATAATTT-ATATATAAATTATTGATAACTTGATAATAAATTACTA
1 ATAATTTAATA-ATAAATTATTGATAACTTAATAATAAATCAATA
* * * * * **
21643721 ATAACTTAATTACAAATTAGT-ACTAATTTAATTCTAAATCAATA
1 ATAATTTAATAATAAATTATTGA-TAACTTAATAATAAATCAATA
* *
21643765 ATAATTTTATAGTAAATTA
1 ATAATTTAATAATAAATTA
21643784 GTTAATCATT
Statistics
Matches: 340, Mismatches: 91, Indels: 56
0.70 0.19 0.11
Matches are distributed among these distances:
42 7 0.02
43 100 0.29
44 166 0.49
45 30 0.09
46 29 0.09
47 8 0.02
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (44 bp):
ATAATTTAATAATAAATTATTGATAACTTAATAATAAATCAATA
Found at i:21643572 original size:90 final size:90
Alignment explanation
Indices: 21643399--21643606 Score: 217
Period size: 90 Copynumber: 2.3 Consensus size: 90
21643389 GATAAACTTT
* * *
21643399 ATAGTAAATCATAAATAGCTTAATAATAAATCAATGATAATTTAATAATTAATCATTAAAAACTT
1 ATAGTAAATCATAAATAACTTAATAATAAATCAATGATAACTTAATAATTAATCATGAAAAACTT
21643464 AAAAGTAAATTAATATAACTTAGGA
66 AAAAGTAAATTAATATAACTTAGGA
* ** * * * * * *
21643489 ATAGTAAATTATTGATAACTTAATAGTTAATCAGTGATAACTTAATAATTAATCATGGATAATTT
1 ATAGTAAATCATAAATAACTTAATAATAAATCAATGATAACTTAATAATTAATCATGAAAAACTT
* *
21643554 AATA-TAAATTAGTGATAACTT--G-
66 AAAAGTAAATTAAT-ATAACTTAGGA
* ** *
21643576 ATAATAAATCATAGTTAATTTAATAATAAAT
1 ATAGTAAATCATAAATAACTTAATAATAAAT
21643607 TTGTGATAAT
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
87 24 0.25
88 1 0.01
89 8 0.08
90 63 0.66
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.37
Consensus pattern (90 bp):
ATAGTAAATCATAAATAACTTAATAATAAATCAATGATAACTTAATAATTAATCATGAAAAACTT
AAAAGTAAATTAATATAACTTAGGA
Found at i:21643586 original size:65 final size:65
Alignment explanation
Indices: 21643488--21643730 Score: 190
Period size: 65 Copynumber: 3.7 Consensus size: 65
21643478 ATAACTTAGG
* * *
21643488 AATAGTAAATTATTGATAACTTAATAGTTAATCAGTGATAACTTAATAATTAATCATGGATAATT
1 AATAGTAAATTATTGATAACTTAATAATAAATCA-TAATAACTTAATAATTAATCATGGATAATT
21643553 T
65 T
* * * * * *
21643554 AATA-TAAATTAGTGATAACTTGATAATAAATCATAGTTAATTTAATAATAAAT-TTGTGATAAT
1 AATAGTAAATTATTGATAACTTAATAATAAATCATA-ATAACTTAATAATTAATCATG-GATAAT
21643617 TT
64 TT
* * ** * * ** * **
21643619 TATAGTAAATAATAAAAAACTAAATGGTAAATACATAATAACAT-AT-ATTAAATCATTAATAAT
1 AATAGTAAATTATTGATAACTTAATAATAAAT-CATAATAACTTAATAATT-AATCATGGATAAT
21643682 TT
64 TT
* *
21643684 ATATA-TAAATTATTGATAACTTGATAATAAATTACTAATAACTTAAT
1 A-ATAGTAAATTATTGATAACTTAATAATAAATCA-TAATAACTTAAT
21643731 TACAAATTAG
Statistics
Matches: 131, Mismatches: 37, Indels: 18
0.70 0.20 0.10
Matches are distributed among these distances:
64 6 0.05
65 89 0.68
66 32 0.24
67 4 0.03
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (65 bp):
AATAGTAAATTATTGATAACTTAATAATAAATCATAATAACTTAATAATTAATCATGGATAATTT
Found at i:21643791 original size:30 final size:30
Alignment explanation
Indices: 21643757--21643813 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
21643747 TTTAATTCTA
*
21643757 AATCAATAATAATTTTATAGTAAATTAGTT
1 AATCAATAATAACTTTATAGTAAATTAGTT
* *
21643787 AATCATTAATAACTTTGTAGTAAATTA
1 AATCAATAATAACTTTATAGTAAATTA
21643814 TCGATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (30 bp):
AATCAATAATAACTTTATAGTAAATTAGTT
Found at i:21644240 original size:20 final size:23
Alignment explanation
Indices: 21644190--21644250 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
21644180 CACAAATTTA
* *
21644190 ATCAATAATTATA-AAAAAATAT
1 ATCAAAAATTACACAAAAAATAT
*
21644212 ATCACAAATTAC-CAAAAAAT-T
1 ATCAAAAATTACACAAAAAATAT
21644233 A-CAAAAATTACACAAAAA
1 ATCAAAAATTACACAAAAA
21644251 TGTTATCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 9 0.27
21 8 0.24
22 16 0.48
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.23
Consensus pattern (23 bp):
ATCAAAAATTACACAAAAAATAT
Found at i:21644302 original size:21 final size:20
Alignment explanation
Indices: 21644278--21644360 Score: 87
Period size: 21 Copynumber: 4.0 Consensus size: 20
21644268 CAAATATTGT
*
21644278 CAAAATTATATCAAAGATCAC
1 CAAAATTATATCAAAG-TTAC
21644299 CAAAATTATATCATAAGTTAC
1 CAAAATTATATCA-AAGTTAC
*
21644320 C-AAATGAATATCAAATGTTAC
1 CAAAAT-TATATCAAA-GTTAC
*
21644341 CAAAATTTTATCAAAAGTTA
1 CAAAATTATATC-AAAGTTA
21644361 TTGAAATCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
20 6 0.11
21 37 0.70
22 10 0.19
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.30
Consensus pattern (20 bp):
CAAAATTATATCAAAGTTAC
Found at i:21653095 original size:24 final size:26
Alignment explanation
Indices: 21653068--21653146 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 26
21653058 ATTATATTAA
*
21653068 TAAAATTATTT-ATA-TTTAATTTTT
1 TAAAATTATTTAATATTTTAATATTT
21653092 TAAAA--ATTTAATATTTTAATATTT
1 TAAAATTATTTAATATTTTAATATTT
*
21653116 TAATAATTATGTCAATA--TTAATATTT
1 TAA-AATTAT-TTAATATTTTAATATTT
*
21653142 GAAAA
1 TAAAA
21653147 AGAATAAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
22 4 0.09
23 3 0.07
24 17 0.37
25 4 0.09
26 11 0.24
27 2 0.04
28 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (26 bp):
TAAAATTATTTAATATTTTAATATTT
Found at i:21653109 original size:8 final size:8
Alignment explanation
Indices: 21653082--21653120 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
21653072 ATTATTTATA
*
21653082 TTTAATTT
1 TTTAATAT
* *
21653090 TTTAAAAA
1 TTTAATAT
21653098 TTTAATAT
1 TTTAATAT
21653106 TTTAATAT
1 TTTAATAT
21653114 TTTAATA
1 TTTAATA
21653121 ATTATGTCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TTTAATAT
Found at i:21657241 original size:2 final size:2
Alignment explanation
Indices: 21657236--21657262 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21657226 TTCGATAATT
21657236 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
21657263 TGGTATGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21666428 original size:21 final size:20
Alignment explanation
Indices: 21666404--21666451 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
21666394 TCTACAAAAT
21666404 TAAATATATTTTTTATTACAA
1 TAAATATATTTTTT-TTACAA
*
21666425 TAAAT-T-TTTTTTTTATAA
1 TAAATATATTTTTTTTACAA
*
21666443 TACATATAT
1 TAAATATAT
21666452 ACAATTCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 9 0.39
19 7 0.30
20 2 0.09
21 5 0.22
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAATATATTTTTTTTACAA
Found at i:21666744 original size:20 final size:20
Alignment explanation
Indices: 21666719--21666757 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21666709 CTAATTGATT
* *
21666719 AGATTTTTTTTTTTTTTTAC
1 AGATTTATTCTTTTTTTTAC
21666739 AGATTTATTCTTTTTTTTA
1 AGATTTATTCTTTTTTTTA
21666758 TTTGTTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.72
Consensus pattern (20 bp):
AGATTTATTCTTTTTTTTAC
Found at i:21671587 original size:5 final size:5
Alignment explanation
Indices: 21671577--21671611 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
21671567 ATAATTTTAT
21671577 TAATA TAATA TAATA TAATA TAACTA TAAATA TAA
1 TAATA TAATA TAATA TAATA TAA-TA T-AATA TAA
21671612 ATACAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 20 0.71
6 6 0.21
7 2 0.07
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (5 bp):
TAATA
Found at i:21675106 original size:23 final size:23
Alignment explanation
Indices: 21675071--21675119 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
21675061 AGAATAAAAA
21675071 AAATATTATAGATATTAAATTTT
1 AAATATTATAGATATTAAATTTT
**
21675094 AAAT-TTATCAGATATTATCTTTT
1 AAATATTAT-AGATATTAAATTTT
21675117 AAA
1 AAA
21675120 AATAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (23 bp):
AAATATTATAGATATTAAATTTT
Found at i:21676791 original size:21 final size:19
Alignment explanation
Indices: 21676759--21676797 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
21676749 ATTTTTTAAT
*
21676759 AAATTTTTAAAATTAATTA
1 AAATTTTTAAAAATAATTA
21676778 AAATTTATTAAAAAATAATT
1 AAATTT-TT-AAAAATAATT
21676798 TTTGAGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTTTTAAAAATAATTA
Found at i:21679236 original size:159 final size:159
Alignment explanation
Indices: 21679010--21679323 Score: 522
Period size: 159 Copynumber: 2.0 Consensus size: 159
21679000 AGTAAAAATG
* *
21679010 GACACCAATCTAATTAAACTAACAAACTTGCATCAAACAAACCAATATATAATGAGGGAGAAGGC
1 GACACCAATCCAATTAAACTAACAAACTTGCATCAAACAAACCAATATACAATGAGGGAGAAGGC
* *
21679075 AACAAACATAAAAGAAAAA-GGAGCTTTGTTCATGAAAATGATAAGATCCATACAAAAAGACAAA
66 AACAAACATAAAA-AAAAAGGGAGCTTTGTTCATGAAAATGACAAGAACCATACAAAAAGACAAA
*
21679139 GAAGGCTACCTTTGCTCTTTCTTTTTTCTC
130 GAAAGCTACCTTTGCTCTTTCTTTTTTCTC
* * *
21679169 GACACCAATCCAATTAAACTAACAAACTTGCATCAAACAGACCAGTATACAGTGAGGGAGAAGGC
1 GACACCAATCCAATTAAACTAACAAACTTGCATCAAACAAACCAATATACAATGAGGGAGAAGGC
* *
21679234 AACAAACATAAAAAAAAAGGGAGCTTTGTTTATGGAAATGACAAGAACCATACAAAAAGACAAAG
66 AACAAACATAAAAAAAAAGGGAGCTTTGTTCATGAAAATGACAAGAACCATACAAAAAGACAAAG
21679299 AAAGCTACCTTTGCTCTTTCTTTTT
131 AAAGCTACCTTTGCTCTTTCTTTTT
21679324 CCTCCAAAGA
Statistics
Matches: 144, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
158 5 0.03
159 139 0.97
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (159 bp):
GACACCAATCCAATTAAACTAACAAACTTGCATCAAACAAACCAATATACAATGAGGGAGAAGGC
AACAAACATAAAAAAAAAGGGAGCTTTGTTCATGAAAATGACAAGAACCATACAAAAAGACAAAG
AAAGCTACCTTTGCTCTTTCTTTTTTCTC
Found at i:21680424 original size:145 final size:145
Alignment explanation
Indices: 21680032--21680493 Score: 417
Period size: 145 Copynumber: 3.2 Consensus size: 145
21680022 ATTTTAAATA
* * *
21680032 AGGGATATTTTCATAATTTCATA-TTTTTTGAGGTACTGTTATGATTTTAAATGTATCAAAAATC
1 AGGGATATTTTGATAATTTCATACTTTTTT-AGGTACTGTTATGATTTCAAATGCATCAAAAATC
* *
21680096 ATGAAATATTATGAAA-TAAAA-AT-----TTTCATGAAAATACGAGCTTGAGATGGCCAAATTA
65 ATGAAATATTATGAAATTAAAATATAAAAGTTTCATGAAAATACGAGCTTGAGAAGGTCAAATTA
** *
21680154 CCTAAATACCCTTGA-
130 CAAAAATACCCTTTAT
* * ** * *
21680169 AGGATAAGAGTATTTTGGTAATTTCACACTTTATTGGGGGTATTGTTATGATTTCAAATGCATAA
1 AGG----GA-TATTTTGATAATTTCATACTTT-TT-TAGGTACTGTTATGATTTCAAATGCATCA
* * * *
21680234 AAAATCATAAAATATTATGAAATTAAGATCTAAAAAGTTTTATGAAAATACGAGCTTGAGAAGGT
59 AAAATCATGAAATATTATGAAATTAAAATAT-AAAAGTTTCATGAAAATACGAGCTTGAGAAGGT
21680299 CAAATTACAAAAATA-CCTTTAT
123 CAAATTACAAAAATACCCTTTAT
* ** * * * *
21680321 AGGGATATTTTGATAATTTTATACTTTTTTAGGTACAATTGTGATTTCAAATGCACCAAAATTTA
1 AGGGATATTTTGATAATTTCATACTTTTTTAGGTACTGTTATGATTTCAAATGCATCAAAAATCA
*** ** * *
21680386 TGAAATATTATGAAATTAAAATATAAAGAGTTTCATGAAAATTTAAGCTAAAAAAGGTTAAATTA
66 TGAAATATTATGAAATTAAAATATAAA-AGTTTCATGAAAATACGAGCTTGAGAAGGTCAAATTA
*
21680451 CAAAAAAACCCTTT-T
130 CAAAAATACCCTTTAT
* **
21680466 AGGGGTATTTT-AGTAATTTTTTACTTTT
1 AGGGATATTTTGA-TAATTTCATACTTTT
21680494 CAGTGCAATA
Statistics
Matches: 260, Mismatches: 45, Indels: 32
0.77 0.13 0.09
Matches are distributed among these distances:
137 3 0.01
141 2 0.01
142 15 0.06
143 3 0.01
144 50 0.19
145 112 0.43
146 8 0.03
147 19 0.07
148 2 0.01
151 5 0.02
152 41 0.16
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (145 bp):
AGGGATATTTTGATAATTTCATACTTTTTTAGGTACTGTTATGATTTCAAATGCATCAAAAATCA
TGAAATATTATGAAATTAAAATATAAAAGTTTCATGAAAATACGAGCTTGAGAAGGTCAAATTAC
AAAAATACCCTTTAT
Found at i:21689326 original size:16 final size:17
Alignment explanation
Indices: 21689294--21689330 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
21689284 ATAAGATAAT
21689294 TTATTTATTTATCAAAA
1 TTATTTATTTATCAAAA
*
21689311 TTATTT-TTTTTCAAAA
1 TTATTTATTTATCAAAA
21689327 TTAT
1 TTAT
21689331 ATAATTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTTATTTATCAAAA
Found at i:21692989 original size:13 final size:12
Alignment explanation
Indices: 21692967--21693017 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
21692957 TAATAATTTA
*
21692967 AAATACAATATG
1 AAATATAATATG
*
21692979 ATAATATAATACG
1 A-AATATAATATG
21692992 -AATATAATATG
1 AAATATAATATG
*
21693003 AATATAAAATATG
1 AA-ATATAATATG
21693016 AA
1 AA
21693018 TGTGATACGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 10 0.31
12 2 0.06
13 20 0.62
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (12 bp):
AAATATAATATG
Found at i:21693018 original size:24 final size:24
Alignment explanation
Indices: 21692968--21693018 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
21692958 AATAATTTAA
*
21692968 AATACAATATGATAATATAATACG
1 AATACAATATGATAATAAAATACG
* *
21692992 AATATAATATGA-ATATAAAATATG
1 AATACAATATGATA-ATAAAATACG
21693016 AAT
1 AAT
21693019 GTGATACGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (24 bp):
AATACAATATGATAATAAAATACG
Found at i:21693590 original size:28 final size:29
Alignment explanation
Indices: 21693525--21693594 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
21693515 CATTTTTTAA
*
21693525 AAATAAAATTTTATATTTTTATTATATTT
1 AAATAAAATTTTATATTTTTATTATATCT
21693554 AAATAAAATTTTAT-TTTTTATTTATATCT
1 AAATAAAATTTTATATTTTTA-TTATATCT
* *
21693583 AGATAAATTTTT
1 AAATAAAATTTT
21693595 TAAATAAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 6 0.16
29 31 0.84
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (29 bp):
AAATAAAATTTTATATTTTTATTATATCT
Found at i:21693653 original size:30 final size:29
Alignment explanation
Indices: 21693618--21693745 Score: 107
Period size: 30 Copynumber: 4.3 Consensus size: 29
21693608 GGTTTATATA
*
21693618 AAAAATTTATTTGGATACAAATTAAAAATT
1 AAAAATTTATTTGAATA-AAATTAAAAATT
* * *
21693648 AAAAATTTATTT-AGGTGTAAATTAAAATTT
1 AAAAATTTATTTGA-AT-AAAATTAAAAATT
* *
21693678 AAGAATTTATTTGAATATAA-TAAAAATTT
1 AAAAATTTATTTGAATAAAATTAAAAA-TT
* *
21693707 ATAAATTTATTTAAATAAAATTATAAAATT
1 AAAAATTTATTTGAATAAAATTA-AAAATT
*
21693737 CAAATATTT
1 -AAAAATTT
21693746 TTATTATTTT
Statistics
Matches: 76, Mismatches: 15, Indels: 13
0.73 0.14 0.12
Matches are distributed among these distances:
28 5 0.07
29 20 0.26
30 40 0.53
31 11 0.14
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (29 bp):
AAAAATTTATTTGAATAAAATTAAAAATT
Found at i:21694052 original size:22 final size:22
Alignment explanation
Indices: 21694022--21694076 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
21694012 GAAAAATAAC
*
21694022 TTTTCTTT-CTCTCCTTTCTATT
1 TTTTTTTTCCTCTCCTTTC-ATT
*
21694044 TTTTTTTTCCTTTCCTTTCATT
1 TTTTTTTTCCTCTCCTTTCATT
*
21694066 TATTTTGTTCC
1 T-TTTTTTTCC
21694077 ATAGCTTAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.05, C:0.24, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTTTTCCTCTCCTTTCATT
Found at i:21694059 original size:23 final size:23
Alignment explanation
Indices: 21694033--21694076 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
21694023 TTTCTTTCTC
*
21694033 TCCTTTCTATTT-TTTTTTTCCTT
1 TCCTTTC-ATTTATTTTGTTCCTT
21694056 TCCTTTCATTTATTTTGTTCC
1 TCCTTTCATTTATTTTGTTCC
21694077 ATAGCTTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.07, C:0.23, G:0.02, T:0.68
Consensus pattern (23 bp):
TCCTTTCATTTATTTTGTTCCTT
Found at i:21696261 original size:13 final size:13
Alignment explanation
Indices: 21696240--21696273 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
21696230 GAAAGTAATC
21696240 ATATATAATAT-T
1 ATATATAATATAT
21696252 ATATTATAATATAT
1 ATA-TATAATATAT
21696266 ATATATAA
1 ATATATAA
21696274 CTTAATAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 13 0.65
14 4 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATAATATAT
Found at i:21702561 original size:16 final size:16
Alignment explanation
Indices: 21702540--21702570 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21702530 AAAAAAGAAG
21702540 AACAAAATGGAAAGGA
1 AACAAAATGGAAAGGA
*
21702556 AACAAACTGGAAAGG
1 AACAAAATGGAAAGG
21702571 GTTGGTGCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.10, G:0.26, T:0.06
Consensus pattern (16 bp):
AACAAAATGGAAAGGA
Found at i:21702654 original size:25 final size:25
Alignment explanation
Indices: 21702626--21702695 Score: 96
Period size: 20 Copynumber: 3.0 Consensus size: 25
21702616 TCCTGCCACT
*
21702626 ACCCCAGCAATCATACCACCCCCTC
1 ACCCCAGCGATCATACCACCCCCTC
21702651 ACCCCAGCGATCATACCA----CT-
1 ACCCCAGCGATCATACCACCCCCTC
21702671 ACCCCAGCGATCATACCACCCCCTC
1 ACCCCAGCGATCATACCACCCCCTC
21702696 TTCCAGTCCC
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
20 18 0.46
21 2 0.05
24 2 0.05
25 17 0.44
ACGTcount: A:0.27, C:0.53, G:0.07, T:0.13
Consensus pattern (25 bp):
ACCCCAGCGATCATACCACCCCCTC
Found at i:21703970 original size:28 final size:27
Alignment explanation
Indices: 21703911--21703972 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 27
21703901 TTTTTATAGA
* *
21703911 AAGCATAAGGCAAAACGACGTCGTTTT
1 AAGCATAAGCCAAAACGACGTCGTTTC
*
21703938 GAGCATAAGACCAAAACGACGTCGTTTC
1 AAGCATAAG-CCAAAACGACGTCGTTTC
21703966 AAGCATA
1 AAGCATA
21703973 GAGGATCTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (27 bp):
AAGCATAAGCCAAAACGACGTCGTTTC
Found at i:21704674 original size:48 final size:49
Alignment explanation
Indices: 21704629--21704764 Score: 145
Period size: 49 Copynumber: 2.8 Consensus size: 49
21704619 ATTCTTAATT
*
21704629 TTCAAAATCCT-AAATCCAAAACCC-C-TAAAAATCCAAAATCCCTTAAA
1 TTCAAAACCCTAAAATCCAAAACCCTCAT-AAAATCCAAAATCCCTTAAA
* **
21704676 TTCAAACCCCTAAAATCTGAAACCCTCATAAAATCCAAAATCCCTTAAA
1 TTCAAAACCCTAAAATCCAAAACCCTCATAAAATCCAAAATCCCTTAAA
* * ** *
21704725 -TCCAAACCTTTAAAATCTGAAACCCTCTTAAAATCCAAAA
1 TTCAAAACC-CTAAAATCCAAAACCCTCATAAAATCCAAAA
21704765 CCCCCCAAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
47 9 0.12
48 17 0.22
49 50 0.65
50 1 0.01
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.23
Consensus pattern (49 bp):
TTCAAAACCCTAAAATCCAAAACCCTCATAAAATCCAAAATCCCTTAAA
Found at i:21704692 original size:31 final size:31
Alignment explanation
Indices: 21704631--21704690 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
21704621 TCTTAATTTT
21704631 CAAAATCCTAAATCCAAAACCCCTAAAAATC
1 CAAAATCCTAAATCCAAAACCCCTAAAAATC
*
21704662 CAAAATCCCTTAAATTC-AAACCCCTAAAA
1 CAAAAT-CC-TAAATCCAAAACCCCTAAAA
21704691 TCTGAAACCC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 6 0.23
32 14 0.54
33 6 0.23
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (31 bp):
CAAAATCCTAAATCCAAAACCCCTAAAAATC
Found at i:21704698 original size:16 final size:16
Alignment explanation
Indices: 21704640--21704768 Score: 73
Period size: 18 Copynumber: 7.9 Consensus size: 16
21704630 TCAAAATCCT
*
21704640 AAATCCAAAACCCCTAA
1 AAATCTAAAACCCCT-A
* * *
21704657 AAATCCAAAATCCCTT
1 AAATCTAAAACCCCTA
*
21704673 AAAT-TCAAACCCCTA
1 AAATCTAAAACCCCTA
*
21704688 AAATCTGAAACCCTCATA
1 AAATCTAAAACCC-C-TA
* * *
21704706 AAATCCAAAATCCCTT
1 AAATCTAAAACCCCTA
* **
21704722 AAATC-CAAACCTTTA
1 AAATCTAAAACCCCTA
*
21704737 AAATCTGAAACCCTCTTA
1 AAATCTAAAACCC-C-TA
*
21704755 AAATCCAAAACCCC
1 AAATCTAAAACCCC
21704769 CCAAATCCAA
Statistics
Matches: 85, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
15 21 0.25
16 22 0.26
17 17 0.20
18 25 0.29
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.21
Consensus pattern (16 bp):
AAATCTAAAACCCCTA
Found at i:21704720 original size:49 final size:49
Alignment explanation
Indices: 21704656--21704779 Score: 185
Period size: 49 Copynumber: 2.5 Consensus size: 49
21704646 AAAACCCCTA
*
21704656 AAAATCCAAAATCCCTTAAATTCAAACCCCTAAAATCTGAAACCCTCAT
1 AAAATCCAAAATCCCTTAAATCCAAACCCCTAAAATCTGAAACCCTCAT
** *
21704705 AAAATCCAAAATCCCTTAAATCCAAACCTTTAAAATCTGAAACCCTCTT
1 AAAATCCAAAATCCCTTAAATCCAAACCCCTAAAATCTGAAACCCTCAT
* **
21704754 AAAATCCAAAACCCCCCAAATCCAAA
1 AAAATCCAAAATCCCTTAAATCCAAA
21704780 ATCCCAAACC
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 68 1.00
ACGTcount: A:0.46, C:0.31, G:0.02, T:0.21
Consensus pattern (49 bp):
AAAATCCAAAATCCCTTAAATCCAAACCCCTAAAATCTGAAACCCTCAT
Found at i:21704748 original size:65 final size:66
Alignment explanation
Indices: 21704640--21704784 Score: 147
Period size: 65 Copynumber: 2.2 Consensus size: 66
21704630 TCAAAATCCT
* **
21704640 AAATCCAAAACCCCTAAAAATCCAAAATCCCTTAAATTCAAACCC-C-TAAAATCTGAAACCCTC
1 AAATCCAAAATCCCTAAAAATCCAAAATCCCTTAAATTCAAACCCTCTTAAAATCCAAAACCC-C
*
21704703 ATA
65 -CA
* * *
21704706 AAATCCAAAATCCCT-TAAATCC-AAA-CCTTTAAAATCTGAAACCCTCTTAAAATCCAAAACCC
1 AAATCCAAAATCCCTAAAAATCCAAAATCCCTT-AAAT-TCAAACCCTCTTAAAATCCAAAACCC
*
21704768 CCC
64 CCA
21704771 AAATCCAAAATCCC
1 AAATCCAAAATCCC
21704785 AAACCTTTAA
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
63 4 0.06
64 7 0.10
65 27 0.40
66 16 0.24
67 13 0.19
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.20
Consensus pattern (66 bp):
AAATCCAAAATCCCTAAAAATCCAAAATCCCTTAAATTCAAACCCTCTTAAAATCCAAAACCCCC
A
Found at i:21708453 original size:19 final size:20
Alignment explanation
Indices: 21708413--21708453 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
21708403 TTTGAACTTT
*
21708413 TAATTTTAATGATTAAACAA
1 TAATTTTAATGATTAAAAAA
*
21708433 TAATTTTAATTA-TAAAAAA
1 TAATTTTAATGATTAAAAAA
21708452 TA
1 TA
21708454 TAATCTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
TAATTTTAATGATTAAAAAA
Found at i:21730266 original size:17 final size:17
Alignment explanation
Indices: 21730244--21730276 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21730234 TAGTAAATCA
21730244 TACATCA-AGCACTTGAC
1 TACATCACAGC-CTTGAC
21730261 TACATCACAGCCTTGA
1 TACATCACAGCCTTGA
21730277 TATGGATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.24
Consensus pattern (17 bp):
TACATCACAGCCTTGAC
Found at i:21734657 original size:36 final size:36
Alignment explanation
Indices: 21734609--21734679 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
21734599 CCTACCAAAC
*
21734609 TTTCAATATTAAAATTCCTGTCCCAATAGAAGAAAA
1 TTTCAATATTAAAATGCCTGTCCCAATAGAAGAAAA
*
21734645 TTTCAATGTTAAAATGCCTGTCCCAATAGAAGAAA
1 TTTCAATATTAAAATGCCTGTCCCAATAGAAGAAA
21734680 TTTATCATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (36 bp):
TTTCAATATTAAAATGCCTGTCCCAATAGAAGAAAA
Found at i:21737497 original size:20 final size:20
Alignment explanation
Indices: 21737460--21737499 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
21737450 ATAAACAAAT
*
21737460 CTCTTGGATAAGATAGTTGA
1 CTCTTGGATAAGACAGTTGA
*
21737480 CTCTTGGATAAGGCAGTTGA
1 CTCTTGGATAAGACAGTTGA
21737500 GAATAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (20 bp):
CTCTTGGATAAGACAGTTGA
Found at i:21738144 original size:29 final size:29
Alignment explanation
Indices: 21738063--21738140 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
21738053 AAATAGGCAT
*
21738063 CAAATTCTAAGAATTTTTAAATTTGAGAT
1 CAAATTCTAAGAATTTTTAAATTTGAGAC
* ** *
21738092 TAAATTCTAAGAATCATTAAATTTGGGAC
1 CAAATTCTAAGAATTTTTAAATTTGAGAC
21738121 CAAATTCTAAG-ATTTTTAAA
1 CAAATTCTAAGAATTTTTAAA
21738141 ATTTATTAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
28 7 0.17
29 34 0.83
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.38
Consensus pattern (29 bp):
CAAATTCTAAGAATTTTTAAATTTGAGAC
Found at i:21739728 original size:15 final size:16
Alignment explanation
Indices: 21739698--21739731 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
21739688 TCCTCTTAAA
*
21739698 ATTATAATTATTTTAT
1 ATTATAAATATTTTAT
21739714 ATTATAAAT-TTTTAT
1 ATTATAAATATTTTAT
21739729 ATT
1 ATT
21739732 TTTAGACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATAAATATTTTAT
Found at i:21741967 original size:52 final size:52
Alignment explanation
Indices: 21741879--21742035 Score: 163
Period size: 52 Copynumber: 3.0 Consensus size: 52
21741869 TAGACAAAAA
* * * *
21741879 GACTTGCAAAAAAAGAATTCTAAGAA-AAAGATGATTCTTAATAGGTAAGTTT
1 GACTTACAAGAAAAGAATTTTAAGAAGAAAGA-GATTCTTAATAGGCAAGTTT
* * *
21741931 GACTTACAAGAAAAGAATTTTAAAAAGAAAGGGATTCTTAATAGGCAAATTT
1 GACTTACAAGAAAAGAATTTTAAGAAGAAAGAGATTCTTAATAGGCAAGTTT
* * * * * * * *
21741983 AATTTACAGGAGAATAATTTTAAGAGGAAAGAGATTTTTAATGGGCAAGTTT
1 GACTTACAAGAAAAGAATTTTAAGAAGAAAGAGATTCTTAATAGGCAAGTTT
21742035 G
1 G
21742036 TATGGTTATA
Statistics
Matches: 85, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
52 81 0.95
53 4 0.05
ACGTcount: A:0.45, C:0.06, G:0.20, T:0.29
Consensus pattern (52 bp):
GACTTACAAGAAAAGAATTTTAAGAAGAAAGAGATTCTTAATAGGCAAGTTT
Found at i:21742200 original size:37 final size:37
Alignment explanation
Indices: 21742151--21742225 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
21742141 CGTCTTATGG
21742151 GTGTGTATGTTTATTTGTGAGTGGACTATAGGAGATT
1 GTGTGTATGTTTATTTGTGAGTGGACTATAGGAGATT
21742188 GTGTGTATGTTTATTTGTGAGTGGACTATAGGAGATT
1 GTGTGTATGTTTATTTGTGAGTGGACTATAGGAGATT
21742225 G
1 G
21742226 AGAGGTTCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.21, C:0.03, G:0.33, T:0.43
Consensus pattern (37 bp):
GTGTGTATGTTTATTTGTGAGTGGACTATAGGAGATT
Found at i:21743869 original size:15 final size:16
Alignment explanation
Indices: 21743837--21743870 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21743827 AATATAGAGG
**
21743837 AAAAATAAATTTGAAA
1 AAAAATAAAACTGAAA
21743853 AAAAATAAAACTGAAA
1 AAAAATAAAACTGAAA
21743869 AA
1 AA
21743871 TTAAAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAAATAAAACTGAAA
Found at i:21745390 original size:18 final size:18
Alignment explanation
Indices: 21745367--21745404 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
21745357 AAACGATATG
*
21745367 ATTCATCTGCCGTAAGAA
1 ATTCATCTGCCATAAGAA
*
21745385 ATTCATCTTCCATAAGAA
1 ATTCATCTGCCATAAGAA
21745403 AT
1 AT
21745405 AAAATCAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (18 bp):
ATTCATCTGCCATAAGAA
Found at i:21746660 original size:34 final size:35
Alignment explanation
Indices: 21746621--21746689 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
21746611 TTTTTTATTT
*
21746621 TAATTTT-T-TTATACTTTTTTTAAACCAAAGTTTA
1 TAATTTTATATTATA-TTTTTTCAAACCAAAGTTTA
*
21746655 TAATTTTATATTTTATTTTTTCAAACCAAAGTTTA
1 TAATTTTATATTATATTTTTTCAAACCAAAGTTTA
21746690 CAAGTATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 7 0.23
35 20 0.65
36 4 0.13
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (35 bp):
TAATTTTATATTATATTTTTTCAAACCAAAGTTTA
Found at i:21746710 original size:36 final size:34
Alignment explanation
Indices: 21746635--21746714 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 34
21746625 TTTTTTATAC
*
21746635 TTTTTTT-AAACCAAAGTTTATAATTTTATATTT
1 TTTTTTTCAAACCAAAGTTTACAATTTTATATTT
*
21746668 TATTTTTTCAAACCAAAGTTTACAAGTATTTCA-GTTT
1 T-TTTTTTCAAACCAAAGTTTACAA-T-TTT-ATATTT
21746705 TTTTTTTCAA
1 TTTTTTTCAA
21746715 GAAAACAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
33 1 0.03
34 6 0.15
35 15 0.38
36 10 0.25
37 7 0.17
38 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.05, T:0.54
Consensus pattern (34 bp):
TTTTTTTCAAACCAAAGTTTACAATTTTATATTT
Found at i:21751694 original size:48 final size:49
Alignment explanation
Indices: 21751526--21752089 Score: 452
Period size: 45 Copynumber: 11.8 Consensus size: 49
21751516 TTTAAAATTT
* * * *
21751526 AAAAAACTCATTTAATCAGAGGC-TCAACAACTTAAAAAATTC--C-TG
1 AAAAAACTCCTCTAAGCAGAGGCTTCAACAACTTTAAAAATTCATCTTG
** * * * *
21751571 AAAATGCTCATATCAGGAGAGGC-TCAACAACTTTAAAAA-T--TCTT-
1 AAAAAACTCCTCTAAGCAGAGGCTTCAACAACTTTAAAAATTCATCTTG
21751615 AAAAATACTCCTCTCAA-CAGAGGC-TCAACAACTTTAAAAATTCATCTTG
1 AAAAA-ACTCCTCT-AAGCAGAGGCTTCAACAACTTTAAAAATTCATCTTG
*
21751664 AAAAAACTCCTCTAAGCAGAGACTTC-ACAACTTTAAAAATT--T-TTG
1 AAAAAACTCCTCTAAGCAGAGGCTTCAACAACTTTAAAAATTCATCTTG
** * *
21751709 AAAATGCTCCTCTTAA-TATAGGCTT-AACAACTTT-AAAATATCATCTTG
1 AAAAAACTCCTC-TAAGCAGAGGCTTCAACAACTTTAAAAAT-TCATCTTG
* *
21751757 AGAAAAAGCTCATCTAAGCAGAGGCTT-AACGACTTTAAAAATCTCATCTTG
1 A-AAAAA-CTCCTCTAAGCAGAGGCTTCAACAACTTTAAAAAT-TCATCTTG
* * * *
21751808 AAAAAGCTCATCTAAGCAGAGGC-TCCACAACTTTAAAAATTCATATTG
1 AAAAAACTCCTCTAAGCAGAGGCTTCAACAACTTTAAAAATTCATCTTG
** ** * * *
21751856 AAAAGGCTTATCTAAGCAAAGGC-TCCATAACTTTAAAAA-T--TCTTG
1 AAAAAACTCCTCTAAGCAGAGGCTTCAACAACTTTAAAAATTCATCTTG
**
21751901 AAAATGCTCCTCTCAA-CAGAGGC-TCAACAACTTT-AAAATTCTTATCTTG
1 AAAAAACTCCTCT-AAGCAGAGGCTTCAACAACTTTAAAAATTC--ATCTTG
* *
21751950 GAAAAACTCCTCTAAGTAGAGG-TTCAACAACTTT-AAAATATCATCTTGAG
1 AAAAAACTCCTCTAAGCAGAGGCTTCAACAACTTTAAAAAT-TCATCTT--G
* *
21752000 AAAAAAGCTCCTCTAAGTAGAGG-TTCAACAATTTTAAAAATCTCATCTTG
1 AAAAAA-CTCCTCTAAGCAGAGGCTTCAACAACTTTAAAAAT-TCATCTTG
* *
21752050 AAAAAGCTCCTATAAGCAGAGGC-TCAACAACTTTAAAAAT
1 AAAAAACTCCTCTAAGCAGAGGCTTCAACAACTTTAAAAAT
21752090 CTATCTTTTC
Statistics
Matches: 432, Mismatches: 52, Indels: 66
0.79 0.09 0.12
Matches are distributed among these distances:
44 15 0.03
45 118 0.27
46 8 0.02
47 4 0.01
48 87 0.20
49 109 0.25
50 38 0.09
51 41 0.09
52 12 0.03
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.28
Consensus pattern (49 bp):
AAAAAACTCCTCTAAGCAGAGGCTTCAACAACTTTAAAAATTCATCTTG
Found at i:21752091 original size:49 final size:48
Alignment explanation
Indices: 21751542--21752089 Score: 508
Period size: 49 Copynumber: 11.5 Consensus size: 48
21751532 CTCATTTAAT
* * * * *
21751542 CAGAGGCTCAACAACTTAAAAAATTC--C-TGAAAATGCTCATATCAG
1 CAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCCTCTAAG
* *
21751587 GAGAGGCTCAACAACTTTAAAAA-T--TCTT-AAAAATACTCCTCTCAA-
1 CAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAA-GCTCCTCT-AAG
*
21751632 CAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAACTCCTCTAAG
1 CAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCCTCTAAG
* *
21751680 CAGAGACTTC-ACAACTTTAAAAATT--T-TTGAAAATGCTCCTCTTAA-
1 CAGAGGC-TCAACAACTTTAAAAATTCATCTTGAAAAAGCTCCTC-TAAG
* * * *
21751725 TATAGGCTTAACAACTTT-AAAATATCATCTTGAGAAAAAGCTCATCTAAG
1 CAGAGGCTCAACAACTTTAAAAAT-TCATCTT--GAAAAAGCTCCTCTAAG
* * *
21751775 CAGAGGCTTAACGACTTTAAAAATCTCATCTTGAAAAAGCTCATCTAAG
1 CAGAGGCTCAACAACTTTAAAAAT-TCATCTTGAAAAAGCTCCTCTAAG
* * * **
21751824 CAGAGGCTCCACAACTTTAAAAATTCATATTGAAAAGGCTTATCTAAG
1 CAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCCTCTAAG
* * * *
21751872 CAAAGGCTCCATAACTTTAAAAA-T--TCTTGAAAATGCTCCTCTCAA-
1 CAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCCTCT-AAG
21751917 CAGAGGCTCAACAACTTT-AAAATTCTTATCTTGGAAAAA-CTCCTCTAAG
1 CAGAGGCTCAACAACTTTAAAAATTC--ATCTT-GAAAAAGCTCCTCTAAG
* *
21751966 TAGAGGTTCAACAACTTT-AAAATATCATCTTGAGAAAAAAGCTCCTCTAAG
1 CAGAGGCTCAACAACTTTAAAAAT-TCATCTT--G-AAAAAGCTCCTCTAAG
* * * *
21752017 TAGAGGTTCAACAATTTTAAAAATCTCATCTTGAAAAAGCTCCTATAAG
1 CAGAGGCTCAACAACTTTAAAAAT-TCATCTTGAAAAAGCTCCTCTAAG
21752066 CAGAGGCTCAACAACTTTAAAAAT
1 CAGAGGCTCAACAACTTTAAAAAT
21752090 CTATCTTTTC
Statistics
Matches: 424, Mismatches: 46, Indels: 62
0.80 0.09 0.12
Matches are distributed among these distances:
44 16 0.04
45 105 0.25
46 8 0.02
47 4 0.01
48 84 0.20
49 117 0.28
50 39 0.09
51 39 0.09
52 12 0.03
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (48 bp):
CAGAGGCTCAACAACTTTAAAAATTCATCTTGAAAAAGCTCCTCTAAG
Found at i:21756261 original size:32 final size:32
Alignment explanation
Indices: 21756166--21756262 Score: 82
Period size: 32 Copynumber: 3.2 Consensus size: 32
21756156 ATTCTTTGAA
*
21756166 AACTTTGATTTTCAAGGAAAATTGATACTTTC
1 AACTTTGATTTTCAAAGAAAATTGATACTTTC
* * * *
21756198 AACTTT--TCTCCAAA-AATATT--T--TTTGGA
1 AACTTTGATTTTCAAAGAAAATTGATACTTT--C
21756225 AACTTTGATTTTCAAAGAAAATTGATACTTTC
1 AACTTTGATTTTCAAAGAAAATTGATACTTTC
21756257 AACTTT
1 AACTTT
21756263 TCCTTAAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 18
0.64 0.12 0.24
Matches are distributed among these distances:
25 3 0.06
27 7 0.15
29 11 0.23
30 10 0.21
32 13 0.28
34 3 0.06
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (32 bp):
AACTTTGATTTTCAAAGAAAATTGATACTTTC
Found at i:21756264 original size:59 final size:59
Alignment explanation
Indices: 21755765--21756264 Score: 579
Period size: 59 Copynumber: 8.4 Consensus size: 59
21755755 TTGTGCAGAA
* * *
21755765 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTCCTTT-GAAACTTT-AATTTCGAGG
1 AAAATTGATACTTTCAACTTTTCTCCAAAAATATT-TTTTGGAAACTTTGATTTTCAAGG
** * * *
21755823 AAAATTGATACTTTCAACTTTTC-CTCAAAAATTGATTTTTTTTTTAAA-TTT-AATTTCGAGA
1 AAAATTGATACTTTCAACTTTTCTC-CAAAAA-T-A--TTTTTTGGAAACTTTGATTTTCAAGG
* * * * * *
21755884 AAAATTGATACTTTCAACTTTTTTTCAAAAACTTTTTTTTTTGAAAATTT-ATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCTCCAAAAA--TATTTTTTGGAAACTTTGATTTTCAAGG
* *
21755944 AAAATTGATACTTTCAACTTTTTTCCCAAAAATATTTTTTTTGGAAACTTTGATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCT-CCAAAAATA--TTTTTTGGAAACTTTGATTTTCAAGG
21756006 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGGAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGGAAACTTTGATTTTCAAGG
* * * * *
21756065 AAAATTGATATTTTCAACTTTTC-CTCAAAAACCT-TTTTTTTGAAA-TTTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCTC-CAAAAA--TATTTTTTGGAAACTTTGATTTTCAAGG
* *
21756124 AAAATTGATACTTTCAACTTTT-TCCCAAAAATATTCTTTGAAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCT-CCAAAAATATTTTTTGGAAACTTTGATTTTCAAGG
*
21756183 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGGAAACTTTGATTTTCAAAG
1 AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGGAAACTTTGATTTTCAAGG
21756242 AAAATTGATACTTTCAACTTTTC
1 AAAATTGATACTTTCAACTTTTC
21756265 CTTAAAAACC
Statistics
Matches: 389, Mismatches: 32, Indels: 41
0.84 0.07 0.09
Matches are distributed among these distances:
57 2 0.01
58 38 0.10
59 191 0.49
60 46 0.12
61 72 0.19
62 40 0.10
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTGGAAACTTTGATTTTCAAGG
Found at i:21756381 original size:17 final size:17
Alignment explanation
Indices: 21756322--21756393 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
21756312 TAAATAAAAT
21756322 AATAAAAC-AAAATAAA
1 AATAAAACAAAAATAAA
* * *
21756338 AGTGAAAATAAATAAAAAA
1 AAT-AAAACAAA-AATAAA
21756357 AGAGTAAAACAAAAATAAA
1 A-A-TAAAACAAAAATAAA
* *
21756376 AATAAAATAAAGATAAA
1 AATAAAACAAAAATAAA
21756393 A
1 A
21756394 GAATATTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
16 2 0.05
17 18 0.42
18 3 0.07
19 12 0.28
20 7 0.16
21 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (17 bp):
AATAAAACAAAAATAAA
Found at i:21756391 original size:11 final size:11
Alignment explanation
Indices: 21756330--21756393 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 11
21756320 ATAATAAAAC
*
21756330 AAAATAAAAGTG
1 AAAATAAAA-TA
21756342 AAAAT-AAATA
1 AAAATAAAATA
*
21756352 AAAA-AAGAGTA
1 AAAATAA-AATA
21756363 AAACA-AAAATA
1 AAA-ATAAAATA
21756374 AAAATAAAATA
1 AAAATAAAATA
*
21756385 AAGATAAAA
1 AAAATAAAA
21756394 GAATATTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 7 0.16
11 29 0.66
12 8 0.18
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.14
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:21757283 original size:8 final size:9
Alignment explanation
Indices: 21757265--21757315 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
21757255 TCAACCAGAT
21757265 AAATAAAAA
1 AAATAAAAA
21757274 AAATAAAAAA
1 AAAT-AAAAA
**
21757284 AAATAAATC
1 AAATAAAAA
21757293 AAATAAAAA
1 AAATAAAAA
*
21757302 TAAATCAAAA
1 -AAATAAAAA
21757312 AAAT
1 AAAT
21757316 TAACAGATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 18 0.51
10 17 0.49
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (9 bp):
AAATAAAAA
Found at i:21757289 original size:19 final size:19
Alignment explanation
Indices: 21757265--21757315 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
21757255 TCAACCAGAT
21757265 AAATAAAAAAAATAAAAAA
1 AAATAAAAAAAATAAAAAA
** *
21757284 AAATAAATCAAATAAAAAT
1 AAATAAAAAAAATAAAAAA
*
21757303 AAATCAAAAAAAT
1 AAATAAAAAAAAT
21757316 TAACAGATAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (19 bp):
AAATAAAAAAAATAAAAAA
Found at i:21757302 original size:15 final size:15
Alignment explanation
Indices: 21757265--21757314 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
21757255 TCAACCAGAT
21757265 AAATAAAAA-AAAT-
1 AAATAAAAATAAATC
*
21757278 AAAAAAAAATAAATC
1 AAATAAAAATAAATC
21757293 AAATAAAAATAAATC
1 AAATAAAAATAAATC
21757308 AAA-AAAA
1 AAATAAAA
21757315 TTAACAGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
13 8 0.24
14 8 0.24
15 17 0.52
ACGTcount: A:0.82, C:0.04, G:0.00, T:0.14
Consensus pattern (15 bp):
AAATAAAAATAAATC
Found at i:21757326 original size:21 final size:21
Alignment explanation
Indices: 21757301--21757364 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
21757291 TCAAATAAAA
21757301 ATAAATCAAAAAAATTAACAG
1 ATAAATCAAAAAAATTAACAG
*
21757322 ATAAATTAAAATTAAA-TAACAG
1 ATAAATCAAAA--AAATTAACAG
* *
21757344 AT-AATACATAAATATTAACAG
1 ATAAAT-CAAAAAAATTAACAG
21757365 GAAAAAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 2 0.06
21 19 0.54
22 11 0.31
23 3 0.09
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (21 bp):
ATAAATCAAAAAAATTAACAG
Found at i:21757332 original size:32 final size:28
Alignment explanation
Indices: 21757260--21757340 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 28
21757250 AATTTTCAAC
21757260 CAGATAAATAAAAA-AAATAAAAAAAAA
1 CAGATAAATAAAAATAAATAAAAAAAAA
* *
21757287 TAAATCAAATAAAAATAAATCAAAAAAATTAA
1 CAGAT-AAATAAAAATAAAT-AAAAAAA--AA
*
21757319 CAGATAAATTAAAATTAAATAA
1 CAGATAAA-TAAAAATAAATAA
21757341 CAGATAATAC
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
27 3 0.07
28 9 0.21
29 4 0.09
30 7 0.16
31 5 0.12
32 15 0.35
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (28 bp):
CAGATAAATAAAAATAAATAAAAAAAAA
Found at i:21764927 original size:2 final size:2
Alignment explanation
Indices: 21764920--21764950 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21764910 TAGCCTTATT
21764920 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 T
21764951 TAAACTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21767373 original size:2 final size:2
Alignment explanation
Indices: 21767366--21767396 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
21767356 TATTGTCCTA
21767366 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 A
21767397 CCCACAAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21767769 original size:2 final size:2
Alignment explanation
Indices: 21767738--21767801 Score: 91
Period size: 2 Copynumber: 33.5 Consensus size: 2
21767728 GATTTTTATG
21767738 TA TA T- TA TA -A TA TA -A TA TGA TA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
21767777 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 T
21767802 TAGATGTTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
1 4 0.07
2 51 0.89
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:21768140 original size:2 final size:2
Alignment explanation
Indices: 21768130--21768173 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
21768120 TATATTTTTA
*
21768130 AT AT GAT AT AT AA 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 AT AT AT AT AT AT
21768173 A
1 A
21768174 AGATTAGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:21768157 original size:375 final size:378
Alignment explanation
Indices: 21767750--21768439 Score: 1074
Period size: 375 Copynumber: 1.8 Consensus size: 378
21767740 TATTATAATA
*
21767750 TAATATGATATAATATATATATATATATATATATATATATATATATAT-ATATTAGAT-G-T-T-
1 TAATATGATATAATATATATATATATATATATATATATATATATATATAAGATTAGATAGATGTA
* *
21767810 TACCATGCAATCAACCCTTGATCTA-AGGATTACAAGTTAGTTCCAACCGTGTTTCATGTGAGTA
66 TACCATGCAATC-ACCCCT--TC-AGAGGATTACAAGTTAGCTCCAACCGTGTTTCATGTGAGTA
* * *
21767874 AAGTTAACGGTGACTTGATTTAAATAAGATAAAGCACATAATGGATAAAAGATTTGGATAAATTT
127 AAGTTAACGGTGACTTGATTTAAATAAGACAAAGCACATAATGGATAAAAGATTGGGATAAACTT
* * *
21767939 AATTTATACAATTTTGAAACATTGAATCATTGATTGGATTGTAATTTGAAACATTGAAAATTTGA
192 AATCTAT--AATTTTGAAACATTGAATAATTGATTGGATTGTAATTTGAAACATTGAAAAATTGA
* *
21768004 TTAGATAAAATTATTTGGTAAATAATTTAAATTTAATAATTATTTATTGGATCTTATATGTCAAA
255 TTAGATAAAATTATTTGATAAATAACTTAAATTTAATAATTATTTATTGGATCTTATATGTCAAA
21768069 AATTTAGATTCCTATATATGTATTCAAATGACATACTTTATCAGATATTCATATATTTT
320 AATTTAGATTCCTATATATGTATTCAAATGACATACTTTATCAGATATTCATATATTTT
21768128 TAATATGATAT-ATA-A-ATATATATATATATATATATATATATATATAAGATTAGATAGATGTA
1 TAATATGATATAATATATATATATATATATATATATATATATATATATAAGATTAGATAGATGTA
* *
21768190 TGCCATGTAATCACCCCTTCAGAGGATTACAAGTTAGCTCCAACCGTGTTTCATGTGAGTAAAGT
66 TACCATGCAATCACCCCTTCAGAGGATTACAAGTTAGCTCCAACCGTGTTTCATGTGAGTAAAGT
* * * *
21768255 TAACGGTGGCTTTATTTAAATAAGGCAAAGCACATAATGGATAAAAGATTGGGATAAACTTACTC
131 TAACGGTGACTTGATTTAAATAAGACAAAGCACATAATGGATAAAAGATTGGGATAAACTTAATC
*
21768320 TATGATTTTGAAACATTGAATAATTGATTGGATTGTAATTTGAAACATTGAAAAATTGATTAGAT
196 TATAATTTTGAAACATTGAATAATTGATTGGATTGTAATTTGAAACATTGAAAAATTGATTAGAT
** *
21768385 AGGATTATTTGATAAATAACTTAAATTTAATAATTATTTATTGGGTCTTATATGT
261 AAAATTATTTGATAAATAACTTAAATTTAATAATTATTTATTGGATCTTATATGT
21768440 AGGGATGGCA
Statistics
Matches: 285, Mismatches: 21, Indels: 15
0.89 0.07 0.05
Matches are distributed among these distances:
375 139 0.49
376 10 0.04
377 108 0.38
378 12 0.04
379 6 0.02
380 10 0.04
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (378 bp):
TAATATGATATAATATATATATATATATATATATATATATATATATATAAGATTAGATAGATGTA
TACCATGCAATCACCCCTTCAGAGGATTACAAGTTAGCTCCAACCGTGTTTCATGTGAGTAAAGT
TAACGGTGACTTGATTTAAATAAGACAAAGCACATAATGGATAAAAGATTGGGATAAACTTAATC
TATAATTTTGAAACATTGAATAATTGATTGGATTGTAATTTGAAACATTGAAAAATTGATTAGAT
AAAATTATTTGATAAATAACTTAAATTTAATAATTATTTATTGGATCTTATATGTCAAAAATTTA
GATTCCTATATATGTATTCAAATGACATACTTTATCAGATATTCATATATTTT
Found at i:21768225 original size:377 final size:375
Alignment explanation
Indices: 21767750--21768439 Score: 1075
Period size: 377 Copynumber: 1.8 Consensus size: 375
21767740 TATTATAATA
* *
21767750 TAATATGATATAATATATATATATATATATATATATATATATATATATATATTAGATGTTTACCA
1 TAATATGATATAATAAATATATATATATATATATATATATATATATATAGATTAGATGTTTACCA
* *
21767815 TGCAATCAACCCTTGATCTAAGGATTACAAGTTAGTTCCAACCGTGTTTCATGTGAGTAAAGTTA
66 TGCAATCAACCCCT-ATCTAAGGATTACAAGTTAGCTCCAACCGTGTTTCATGTGAGTAAAGTTA
* * * *
21767880 ACGGTGACTTGATTTAAATAAGATAAAGCACATAATGGATAAAAGATTTGGATAAATTTAATTTA
130 ACGGTGACTTGATTTAAATAAGACAAAGCACATAATGGATAAAAGATTGGGATAAACTTAATCTA
* *
21767945 TACAATTTTGAAACATTGAATCATTGATTGGATTGTAATTTGAAACATTGAAAATTTGATTAGAT
195 T--AATTTTGAAACATTGAATAATTGATTGGATTGTAATTTGAAACATTGAAAAATTGATTAGAT
* *
21768010 AAAATTATTTGGTAAATAATTTAAATTTAATAATTATTTATTGGATCTTATATGTCAAAAATTTA
258 AAAATTATTTGATAAATAACTTAAATTTAATAATTATTTATTGGATCTTATATGTCAAAAATTTA
21768075 GATTCCTATATATGTATTCAAATGACATACTTTATCAGATATTCATATATTTT
323 GATTCCTATATATGTATTCAAATGACATACTTTATCAGATATTCATATATTTT
21768128 TAATATGATAT-ATAAATATATATATATATATATATATATATATATA-AGATTAGATAGATGTAT
1 TAATATGATATAATAAATATATATATATATATATATATATATATATATAGATTAGAT-G-T-T-T
* *
21768191 GCCATGTAATC-ACCCCT-TC-AGAGGATTACAAGTTAGCTCCAACCGTGTTTCATGTGAGTAAA
62 ACCATGCAATCAACCCCTATCTA-AGGATTACAAGTTAGCTCCAACCGTGTTTCATGTGAGTAAA
* * * *
21768253 GTTAACGGTGGCTTTATTTAAATAAGGCAAAGCACATAATGGATAAAAGATTGGGATAAACTTAC
126 GTTAACGGTGACTTGATTTAAATAAGACAAAGCACATAATGGATAAAAGATTGGGATAAACTTAA
*
21768318 TCTATGATTTTGAAACATTGAATAATTGATTGGATTGTAATTTGAAACATTGAAAAATTGATTAG
191 TCTATAATTTTGAAACATTGAATAATTGATTGGATTGTAATTTGAAACATTGAAAAATTGATTAG
** *
21768383 ATAGGATTATTTGATAAATAACTTAAATTTAATAATTATTTATTGGGTCTTATATGT
256 ATAAAATTATTTGATAAATAACTTAAATTTAATAATTATTTATTGGATCTTATATGT
21768440 AGGGATGGCA
Statistics
Matches: 285, Mismatches: 22, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
375 109 0.38
376 9 0.03
377 139 0.49
378 12 0.04
379 6 0.02
380 10 0.04
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (375 bp):
TAATATGATATAATAAATATATATATATATATATATATATATATATATAGATTAGATGTTTACCA
TGCAATCAACCCCTATCTAAGGATTACAAGTTAGCTCCAACCGTGTTTCATGTGAGTAAAGTTAA
CGGTGACTTGATTTAAATAAGACAAAGCACATAATGGATAAAAGATTGGGATAAACTTAATCTAT
AATTTTGAAACATTGAATAATTGATTGGATTGTAATTTGAAACATTGAAAAATTGATTAGATAAA
ATTATTTGATAAATAACTTAAATTTAATAATTATTTATTGGATCTTATATGTCAAAAATTTAGAT
TCCTATATATGTATTCAAATGACATACTTTATCAGATATTCATATATTTT
Found at i:21768633 original size:20 final size:21
Alignment explanation
Indices: 21768597--21768648 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
21768587 CTCAAAATTA
21768597 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
21768619 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
21768640 AT-AAATATT
1 ATAAAATATT
21768649 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:21768639 original size:21 final size:22
Alignment explanation
Indices: 21768597--21768648 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
21768587 CTCAAAATTA
21768597 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
21768619 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
21768640 AT-AAATATT
1 ATAAAATATT
21768649 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:21768656 original size:30 final size:30
Alignment explanation
Indices: 21768621--21768681 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
21768611 TTTAAAATAT
* * * *
21768621 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATAATTA
*
21768651 AAAATATCATTATATAAATATATATAATTA
1 AAAATATCATTATATAAATATAAATAATTA
21768681 A
1 A
21768682 TTAATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATAATTA
Found at i:21769146 original size:4 final size:4
Alignment explanation
Indices: 21769139--21769188 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
21769129 ACGCACACAC
* * * * *
21769139 ATAT ATAT ATAT ATAT ATAT GTAT GTAT GTAT GTAT GTAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
21769187 AT
1 AT
21769189 GTATGTATGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:21769182 original size:30 final size:30
Alignment explanation
Indices: 21769146--21769203 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
21769136 CACATATATA
21769146 TATATATATATATGTATGTATGTATGTATG
1 TATATATATATATGTATGTATGTATGTATG
21769176 TATATATATATATGTATGTATGTATGTA
1 TATATATATATATGTATGTATGTATGTA
21769204 AAAATAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (30 bp):
TATATATATATATGTATGTATGTATGTATG
Found at i:21769189 original size:26 final size:26
Alignment explanation
Indices: 21769150--21769203 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
21769140 TATATATATA
*
21769150 TATATATATGTATGTATGTATGTATG
1 TATATATATATATGTATGTATGTATG
21769176 TATATATATATATGTATGTATGTATG
1 TATATATATATATGTATGTATGTATG
21769202 TA
1 TA
21769204 AAAATAAGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (26 bp):
TATATATATATATGTATGTATGTATG
Found at i:21769193 original size:4 final size:4
Alignment explanation
Indices: 21769156--21769203 Score: 64
Period size: 4 Copynumber: 12.5 Consensus size: 4
21769146 TATATATATA
* *
21769156 TATG TATG TATG TATG TATG TA-- TATA TATA TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
21769202 TA
1 TA
21769204 AAAATAAGAG
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 2 0.05
4 39 0.95
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:21771645 original size:17 final size:18
Alignment explanation
Indices: 21771623--21771656 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21771613 TTGATATCAT
21771623 ATAATTATAAC-CATAAA
1 ATAATTATAACTCATAAA
*
21771640 ATAATTTTAACTCATAA
1 ATAATTATAACTCATAA
21771657 TATTAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAATTATAACTCATAAA
Found at i:21774342 original size:21 final size:24
Alignment explanation
Indices: 21774318--21774366 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
21774308 TTTTACATTG
21774318 AAATTTTA-TAGTT-T-TTATATA
1 AAATTTTATTAGTTATATTATATA
21774339 AAA-TTTATTAGTTATATTATATA
1 AAATTTTATTAGTTATATTATATA
*
21774362 TAATT
1 AAATT
21774367 AAGTTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 8 0.35
22 1 0.04
23 9 0.39
24 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
AAATTTTATTAGTTATATTATATA
Found at i:21774366 original size:23 final size:21
Alignment explanation
Indices: 21774332--21774387 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
21774322 TTTATAGTTT
*
21774332 TTATATAAAATTTATTAGTTATA
1 TTATATATAATTTA--AGTTATA
*
21774355 TTATATATAA-TTAAGTTTTA
1 TTATATATAATTTAAGTTATA
21774375 TATATATATAATT
1 T-TATATATAATT
21774388 GTATATCCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 7 0.24
21 9 0.31
22 4 0.14
23 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TTATATATAATTTAAGTTATA
Found at i:21775768 original size:10 final size:10
Alignment explanation
Indices: 21775755--21775788 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
21775745 TGAAATATTT
21775755 TAAAATTAAA
1 TAAAATTAAA
*
21775765 TAAAATCAAA
1 TAAAATTAAA
*
21775775 TAAAATTAAT
1 TAAAATTAAA
21775785 TAAA
1 TAAA
21775789 TGCAAGACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAAATTAAA
Found at i:21775928 original size:376 final size:376
Alignment explanation
Indices: 21774801--21776276 Score: 2097
Period size: 375 Copynumber: 3.9 Consensus size: 376
21774791 TATTTTACAA
* * *
21774801 TTAAGAGTTGAATATTATAATTGGAAAAAAAAAAACACAAAATTATCCTATACTGATAACAATTA
1 TTAAGAGTTGAATATTATAATTGAAAAAAAAAAAACACAAAATTATCCTATAATGATGACAATTA
* *
21774866 AAGTTTTATTACCTTTAATATTAATTTAATTGAGAGTGATTTAAGGTAAATAATAATAGAAAATA
66 AAGTTTTATTACCTTTAATATGAATTTAATTGAGAGTGATTTAAAGTAAATAATAATAGAAAATA
*
21774931 AATGTAATTAATTTAATTTTTTAAAAATAATTCAAATATAAACAATACATTGAAATTATTTTAAA
131 AATGTAATTAATTTAATTTTTTAAAAATAATTCAAATATAATCAATACATTGAAA-TATTTTAAA
* * * * * * *
21774996 ATTTAAATAAAATCAAATAAAATTAATTAAATGCAAGACACATTTTGATTATTTAAGATAGACTA
195 ATTTAAATAAAATCAAATAAAATTAATTAAATGCAAGACACATGTCGATTGTTTAAAATTGTCCA
* * * ** *
21775061 CATGTTAAAATAATAGACCATCCATCTTAGAATTTTTTT-TTTTTTTTTGCAAAAAGTTTTGGCT
260 CATGTCAAAATAATAGACCATCCACCTT-GGATTTTTTTCTTTTTTACT--AAAAA-TTTTGACT
* * ** * *
21775125 TTTATACATTTATATAAGATATAAGATTGGAAAGTAGTTTTTTTCTTTTACATAAATGCAAT
321 TTTATATATTTATATAAGATATAAAATT-GAAA--AGTGATTTT-TTTTAC--ACATGTAAT
* * * * *
21775187 TTAAAAGTTGAATATTATAATTG-AAAAAAGAGAATACAAAATTATCCTATAATGATGGCAATTA
1 TTAAGAGTTGAATATTATAATTGAAAAAAAAAAAACACAAAATTATCCTATAATGATGACAATTA
* * * * *
21775251 AAGTTTTATTTATTACATTTAATATGAATTTAATTGAGAGTGATATAATGTTAATAGTAATAGAA
66 AAG---T-TTTATTACCTTTAATATGAATTTAATTGAGAGTGATTTAAAGTAAATAATAATAGAA
* *
21775316 AATAAATGTAATTAATTTAATTTTTT-TAAATAATTCAAATATAATCAATGCATTGAAATATTTT
127 AATAAATGTAATTAATTTAATTTTTTAAAAATAATTCAAATATAATCAATACATTGAAATATTTT
** * **
21775380 AAAATTTAAATAAAATCAAATAAAATTAATTAAAT-CAAGGTACATGTCGATTGTTTAAGATCAT
192 AAAATTTAAATAAAATCAAATAAAATTAATTAAATGCAAGACACATGTCGATTGTTTAAAATTGT
* *
21775444 CTATATGTCAAAATAATAGACCATCCACCTTGGA-TTTTTTCATTTTTTACTAAAAATTTTGACT
257 CCACATGTCAAAATAATAGACCATCCACCTTGGATTTTTTTC-TTTTTTACTAAAAATTTTGACT
21775508 TTTATATATTTATATAAGATATAAAATTGAAAAGTGATTTTTTTTACACATGTAAT
321 TTTATATATTTATATAAGATATAAAATTGAAAAGTGATTTTTTTTACACATGTAAT
* *
21775564 TTAAGAGTTGAATATTATAATTGAAAAAAAAAAGAACACAAAATTATCTTATAATGATGGCAATT
1 TTAAGAGTTGAATATTATAATTGAAAAAAAAAA-AACACAAAATTATCCTATAATGATGACAATT
* * *
21775629 AAAGTTTTATTATCTTTAATATAAATTTAATTGAGAGTGATTTAAAATAAATAATAATAGAAAAT
65 AAAGTTTTATTACCTTTAATATGAATTTAATTGAGAGTGATTTAAAGTAAATAATAATAGAAAAT
* **
21775694 AAAAGTAATTAATTTAATTTTTTTTAAATAATTCAAATATAATCAATACATTGAAATATTTTAAA
130 AAATGTAATTAATTTAATTTTTTAAAAATAATTCAAATATAATCAATACATTGAAATATTTTAAA
* *
21775759 A-TTAAATAAAATCAAATAAAATTAATTAAATGCAAGACATATGTTGATTGTTTAAAATTGTCCA
195 ATTTAAATAAAATCAAATAAAATTAATTAAATGCAAGACACATGTCGATTGTTTAAAATTGTCCA
*
21775823 CATGTCAAAATAATAAACCATCCACCTTGGATTTTTTTTCTTTTTTACTAAAAATTTTGACTTTT
260 CATGTCAAAATAATAGACCATCCACCTTGGA-TTTTTTTCTTTTTTACTAAAAATTTTGACTTTT
21775888 ATATATTTATATAAGATATAAAATTGAAAAGTGATTTTTTTTACACATGTAAT
324 ATATATTTATATAAGATATAAAATTGAAAAGTGATTTTTTTTACACATGTAAT
* *
21775941 TTAAGAGTTGAATATTATAATT-AAAAAAAGAAAACACAAAATTATCTTATAATGATGACAATTA
1 TTAAGAGTTGAATATTATAATTGAAAAAAAAAAAACACAAAATTATCCTATAATGATGACAATTA
*
21776005 AAGTTTTATTACCTTTAATATGAATTTAATTGAGAGTGATTTAAAGTAAATAATAATAAAAAATA
66 AAGTTTTATTACCTTTAATATGAATTTAATTGAGAGTGATTTAAAGTAAATAATAATAGAAAATA
* *
21776070 AACGTAATTAATTTAATTTTTTAAAAATAATTCAAATATAATCAATACATTCAAATATTTTAAAA
131 AATGTAATTAATTTAATTTTTTAAAAATAATTCAAATATAATCAATACATTGAAATATTTTAAAA
* *
21776135 TTTAAATAAAATCAAATAAAATTAATTAAATGCAAGACATATGTCAATTGTTTAAAATTGTCCAC
196 TTTAAATAAAATCAAATAAAATTAATTAAATGCAAGACACATGTCGATTGTTTAAAATTGTCCAC
* ** * * *
21776200 ATGTCAAAATAATAGATCATCCAACC-AAGATTTTTTCCTTTTTT-GTCAAAAACTTTGACTTTT
261 ATGTCAAAATAATAGACCATCC-ACCTTGGATTTTTTTCTTTTTTACT-AAAAATTTTGACTTTT
21776263 ATATATTTATATAA
324 ATATATTTATATAA
21776277 ATGTAATTTA
Statistics
Matches: 994, Mismatches: 81, Indels: 41
0.89 0.07 0.04
Matches are distributed among these distances:
374 1 0.00
375 299 0.30
376 188 0.19
377 132 0.13
378 14 0.01
379 39 0.04
380 7 0.01
382 4 0.00
383 33 0.03
384 11 0.01
385 40 0.04
386 78 0.08
387 41 0.04
388 30 0.03
389 77 0.08
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (376 bp):
TTAAGAGTTGAATATTATAATTGAAAAAAAAAAAACACAAAATTATCCTATAATGATGACAATTA
AAGTTTTATTACCTTTAATATGAATTTAATTGAGAGTGATTTAAAGTAAATAATAATAGAAAATA
AATGTAATTAATTTAATTTTTTAAAAATAATTCAAATATAATCAATACATTGAAATATTTTAAAA
TTTAAATAAAATCAAATAAAATTAATTAAATGCAAGACACATGTCGATTGTTTAAAATTGTCCAC
ATGTCAAAATAATAGACCATCCACCTTGGATTTTTTTCTTTTTTACTAAAAATTTTGACTTTTAT
ATATTTATATAAGATATAAAATTGAAAAGTGATTTTTTTTACACATGTAAT
Found at i:21780367 original size:3 final size:3
Alignment explanation
Indices: 21780359--21780404 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
21780349 CACTCATGGT
21780359 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
21780405 AAGTAACAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21782007 original size:21 final size:22
Alignment explanation
Indices: 21781982--21782029 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
21781972 ATCATAGTAA
21781982 CTTTC-ACCAGTAATCTCATCT
1 CTTTCGACCAGTAATCTCATCT
*
21782003 CTTTCGGGCCAGTAATCTCATCT
1 CTTTC-GACCAGTAATCTCATCT
21782026 CTTT
1 CTTT
21782030 TGGGCAGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.21
23 19 0.79
ACGTcount: A:0.19, C:0.31, G:0.10, T:0.40
Consensus pattern (22 bp):
CTTTCGACCAGTAATCTCATCT
Found at i:21782015 original size:23 final size:23
Alignment explanation
Indices: 21781988--21782034 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
21781978 GTAACTTTCA
21781988 CCAGTAATCTCATCTCTTTCGGG
1 CCAGTAATCTCATCTCTTTCGGG
*
21782011 CCAGTAATCTCATCTCTTTTGGG
1 CCAGTAATCTCATCTCTTTCGGG
21782034 C
1 C
21782035 AGAAGCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (23 bp):
CCAGTAATCTCATCTCTTTCGGG
Found at i:21784695 original size:38 final size:37
Alignment explanation
Indices: 21784617--21784698 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 37
21784607 AATACTTGTT
* * *
21784617 ATAAAAAATATTAAAATATTTTAATTTTTATTTAAGA
1 ATAAAAAATATTAAAATATTATAAATTTTATATAAGA
21784654 ATAAAAAATATATAAAATAATTAATAAATTTTA-ATAA-A
1 ATAAAAAATAT-TAAAAT-ATT-ATAAATTTTATATAAGA
21784692 ATAAAAA
1 ATAAAAA
21784699 TACATGAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
37 11 0.28
38 14 0.36
39 6 0.15
40 8 0.21
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (37 bp):
ATAAAAAATATTAAAATATTATAAATTTTATATAAGA
Found at i:21788788 original size:13 final size:14
Alignment explanation
Indices: 21788770--21788798 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
21788760 ACTCTTTTTT
21788770 TTATATTTTAA-AA
1 TTATATTTTAATAA
21788783 TTATATTTTAATAA
1 TTATATTTTAATAA
21788797 TT
1 TT
21788799 TTTTTTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATATTTTAATAA
Found at i:21794716 original size:11 final size:11
Alignment explanation
Indices: 21794700--21794724 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21794690 TTAATGTAAA
21794700 TTTTTTTTTCT
1 TTTTTTTTTCT
21794711 TTTTTTTTTCT
1 TTTTTTTTTCT
21794722 TTT
1 TTT
21794725 CTGGGCATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:21805028 original size:21 final size:20
Alignment explanation
Indices: 21804988--21805029 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
21804978 TATTTTATTT
*
21804988 TTTATTATTTTTGTTCTATG
1 TTTATTATTTTTGTTATATG
21805008 TTTATTTATTTTT-TTAATATG
1 TTTA-TTATTTTTGTT-ATATG
21805029 T
1 T
21805030 CAAGTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.71
Consensus pattern (20 bp):
TTTATTATTTTTGTTATATG
Found at i:21808582 original size:133 final size:136
Alignment explanation
Indices: 21808416--21808672 Score: 405
Period size: 133 Copynumber: 1.9 Consensus size: 136
21808406 CTAAAATTAA
* **
21808416 TGAAGAATTACATACAAAAACTATAAATGTAATTAATAATTAATGAAAAATACTCATAAAATCGT
1 TGAAGAATTACATACAAAAACTATAAATGTAATTAATAATTAATGAAAAAAACTCATAAAATAAT
*
21808481 TTTAAATAATGT-AAGAAAATTAG-CTTTT-TTATTAAATCATTTCCATAATTGACTAATTGAGA
66 TTTAAATAAT-TAAAGAAAATTAGTCTTTTATTATTAAATCATATCCATAATTGACTAATTGAGA
21808543 ATAAGGT
130 ATAAGGT
* *
21808550 TGAAGAATTGCATA-AAAAACTATAAATGTAATTAATAATTATTGAAAAAAACTCATAAAATAAT
1 TGAAGAATTACATACAAAAACTATAAATGTAATTAATAATTAATGAAAAAAACTCATAAAATAAT
* *
21808614 TTTAAATAATTAAAGAAAATTAGTGTTTTATTGTTAAATCATATCCATAATTGACTAAT
66 TTTAAATAATTAAAGAAAATTAGTCTTTTATTATTAAATCATATCCATAATTGACTAAT
21808673 GCCCCATTTG
Statistics
Matches: 112, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
132 1 0.01
133 67 0.60
134 17 0.15
135 27 0.24
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.35
Consensus pattern (136 bp):
TGAAGAATTACATACAAAAACTATAAATGTAATTAATAATTAATGAAAAAAACTCATAAAATAAT
TTTAAATAATTAAAGAAAATTAGTCTTTTATTATTAAATCATATCCATAATTGACTAATTGAGAA
TAAGGT
Found at i:21808973 original size:15 final size:15
Alignment explanation
Indices: 21808955--21808983 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21808945 TTTGTTATTT
21808955 TATATAAAAATAATA
1 TATATAAAAATAATA
21808970 TATATAAAAATAAT
1 TATATAAAAATAAT
21808984 TTTTAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TATATAAAAATAATA
Found at i:21809037 original size:53 final size:52
Alignment explanation
Indices: 21808978--21809104 Score: 145
Period size: 50 Copynumber: 2.4 Consensus size: 52
21808968 TATATATAAA
*
21808978 AATAATTTTTAAATATTTAATAAT-AAAATATTA-TTCTATATAAAAATAATTTT
1 AATAATTTTTAAA-ATTTAATAATAAAAATATTACTT-GATAT-AAAATAATTTT
* *
21809031 AGTAATTTTT--AATTTATTAATAAAAATATTACTTGATATAAAATAATTTT
1 AATAATTTTTAAAATTTAATAATAAAAATATTACTTGATATAAAATAATTTT
* *
21809081 AATAAATTTTAATAATTTATTAAT
1 AATAATTTTTAA-AATTTAATAAT
21809105 TTCACAAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
50 28 0.44
51 14 0.22
52 2 0.03
53 20 0.31
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (52 bp):
AATAATTTTTAAAATTTAATAATAAAAATATTACTTGATATAAAATAATTTT
Found at i:21809269 original size:63 final size:62
Alignment explanation
Indices: 21809195--21809316 Score: 181
Period size: 63 Copynumber: 2.0 Consensus size: 62
21809185 TATTATTATT
21809195 TTTATATTTAAATATATATTTCATCATTAACTTTAATATCATTACTATAATAATCAATCTACC
1 TTTATATTTAAATATATATTTCATCATTAACTTTAATATCATTACTAT-ATAATCAATCTACC
* * * * **
21809258 TTTATATTTAAATATATATTTTATTATTAATTTTAATTTTGTTACTATATAATCAATCT
1 TTTATATTTAAATATATATTTCATCATTAACTTTAATATCATTACTATATAATCAATCT
21809317 TATAATTATA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
62 11 0.21
63 42 0.79
ACGTcount: A:0.38, C:0.10, G:0.01, T:0.52
Consensus pattern (62 bp):
TTTATATTTAAATATATATTTCATCATTAACTTTAATATCATTACTATATAATCAATCTACC
Done.