Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 325 of 335
Found at i:95394459 original size:3 final size:3
Alignment explanation
Indices: 95394453--95394501 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
95394443 CTGCTGCTGG
95394453 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
95394501 T
1 T
95394502 CTGTTAAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:95394687 original size:30 final size:30
Alignment explanation
Indices: 95394618--95394690 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
95394608 GGAAACTGTT
*
95394618 AGTTAGTGACTGTTTTGTCACTTTTTTATA
1 AGTTAGTGACTGCTTTGTCACTTTTTTATA
*
95394648 ACGTTAGTGACTGCTTTGTTA-TTTTTTGA-A
1 A-GTTAGTGACTGCTTTGTCACTTTTTT-ATA
95394678 AGTTAAGTGACTG
1 AGTT-AGTGACTG
95394691 AAATGAAACC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 3 0.08
30 17 0.45
31 18 0.47
ACGTcount: A:0.22, C:0.10, G:0.21, T:0.48
Consensus pattern (30 bp):
AGTTAGTGACTGCTTTGTCACTTTTTTATA
Found at i:95395412 original size:3 final size:3
Alignment explanation
Indices: 95395404--95395446 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
95395394 ACTTTCCACC
95395404 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
95395447 AAAAGGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:95398149 original size:13 final size:14
Alignment explanation
Indices: 95398123--95398151 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
95398113 AATTATTGAA
95398123 TTACTAATTTAACC
1 TTACTAATTTAACC
95398137 TTACTAA-TTAACC
1 TTACTAATTTAACC
95398150 TT
1 TT
95398152 TAAATCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (14 bp):
TTACTAATTTAACC
Found at i:95407464 original size:24 final size:24
Alignment explanation
Indices: 95407436--95407490 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
95407426 AAGTCTAATT
*
95407436 CTAATCAATATG-AAATATATTATG
1 CTAAT-AATATGCAAATATATTATA
95407460 CTAATAA-ATGCTAAATATATTATA
1 CTAATAATATGC-AAATATATTATA
95407484 CTAATAA
1 CTAATAA
95407491 ATATTACATC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 3 0.11
23 2 0.07
24 23 0.82
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.36
Consensus pattern (24 bp):
CTAATAATATGCAAATATATTATA
Found at i:95412593 original size:3 final size:3
Alignment explanation
Indices: 95412585--95412629 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
95412575 CCCCGACCTG
95412585 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
95412630 AAACGGTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:95412914 original size:14 final size:13
Alignment explanation
Indices: 95412880--95412918 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
95412870 TAAAACTAGG
* *
95412880 AAATTCTATATAA
1 AAATTCTAAAAAA
95412893 AAATTCTAAAAAA
1 AAATTCTAAAAAA
95412906 AAATCTCTAAAAA
1 AAAT-TCTAAAAA
95412919 TGTTATTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 15 0.65
14 8 0.35
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATTCTAAAAAA
Found at i:95415924 original size:14 final size:14
Alignment explanation
Indices: 95415901--95415930 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
95415891 TTGAAATTAT
95415901 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
95415915 GTTGATTTGGATTG
1 GTTGAATTGGATTG
95415929 GT
1 GT
95415931 CTCGATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:95420899 original size:13 final size:13
Alignment explanation
Indices: 95420842--95420900 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
95420832 AATTTTATGT
*
95420842 ATATATAAAATAA
1 ATATTTAAAATAA
* *
95420855 ATAATTAAAATAT
1 ATATTTAAAATAA
*
95420868 ATATGTTGAAATAAA
1 ATAT-TTAAAAT-AA
*
95420883 ATATTTTAAATAA
1 ATATTTAAAATAA
95420896 ATATT
1 ATATT
95420901 ACAATTATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 20 0.54
14 12 0.32
15 5 0.14
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:95420925 original size:15 final size:16
Alignment explanation
Indices: 95420905--95420935 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
95420895 AATATTACAA
95420905 TTATTAA-AAATAATT
1 TTATTAATAAATAATT
95420920 TTATTAATAAATAATT
1 TTATTAATAAATAATT
95420936 AAAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATTAATAAATAATT
Found at i:95420931 original size:34 final size:33
Alignment explanation
Indices: 95420880--95420950 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 33
95420870 ATGTTGAAAT
*
95420880 AAAATATTTTAAATAAAT-ATTACAATTAT-TA
1 AAAATATTTTAAATAAATAATTAAAATTATATA
*
95420911 AAAATAATTTTATTAATAAATAATTAAAATTTTATA
1 AAAAT-ATTTTA--AATAAATAATTAAAATTATATA
95420947 AAAA
1 AAAA
95420951 ATCATAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 5 0.15
32 6 0.18
34 7 0.21
35 9 0.27
36 6 0.18
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
AAAATATTTTAAATAAATAATTAAAATTATATA
Found at i:95421319 original size:28 final size:29
Alignment explanation
Indices: 95421287--95421347 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
95421277 AATTTACAAG
95421287 AATTGAATC-AAATAAAAATT-ATGTATAA
1 AATTGAA-CAAAATAAAAATTCATGTATAA
* * *
95421315 AATTGCACAAAATCAAAATTCATGTATAG
1 AATTGAACAAAATAAAAATTCATGTATAA
95421344 AATT
1 AATT
95421348 ACACATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.04
28 16 0.57
29 11 0.39
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (29 bp):
AATTGAACAAAATAAAAATTCATGTATAA
Found at i:95421342 original size:29 final size:28
Alignment explanation
Indices: 95421296--95421352 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
95421286 GAATTGAATC
*
95421296 AAATAAAAATTATGTATAAAATTGCACA
1 AAATAAAAATTATGTATAAAATTACACA
* *
95421324 AAATCAAAATTCATGTATAGAATTACACA
1 AAATAAAAATT-ATGTATAAAATTACACA
95421353 TTAAATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.54, C:0.11, G:0.07, T:0.28
Consensus pattern (28 bp):
AAATAAAAATTATGTATAAAATTACACA
Found at i:95422956 original size:39 final size:40
Alignment explanation
Indices: 95422883--95422963 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
95422873 ATAACTTTTA
**
95422883 TTTTATTGTTAATTTTTTTTACTATTTTATAGGTATTTGC
1 TTTTATTGTTAATTTTTGCTACTATTTTATAGGTATTTGC
95422923 TTTTATTGTTAA-TTTTGCTACTATTTTATAGGTATTTGC
1 TTTTATTGTTAATTTTTGCTACTATTTTATAGGTATTTGC
95422962 TT
1 TT
95422964 GCTAAGTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 27 0.69
40 12 0.31
ACGTcount: A:0.20, C:0.06, G:0.11, T:0.63
Consensus pattern (40 bp):
TTTTATTGTTAATTTTTGCTACTATTTTATAGGTATTTGC
Found at i:95423784 original size:27 final size:27
Alignment explanation
Indices: 95423754--95423807 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
95423744 ACGAGTAAAA
95423754 TATTCAAACTCAACTATGTTATTATCG
1 TATTCAAACTCAACTATGTTATTATCG
95423781 TATTCAAACTCAACTATGTTATTATCG
1 TATTCAAACTCAACTATGTTATTATCG
95423808 AATAGAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (27 bp):
TATTCAAACTCAACTATGTTATTATCG
Found at i:95427141 original size:17 final size:17
Alignment explanation
Indices: 95427119--95427152 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
95427109 GGGCTGAGAA
95427119 TCCTAAGAGAAAACATC
1 TCCTAAGAGAAAACATC
95427136 TCCTAAGAGAAAACATC
1 TCCTAAGAGAAAACATC
95427153 AGTACTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (17 bp):
TCCTAAGAGAAAACATC
Found at i:95427934 original size:14 final size:14
Alignment explanation
Indices: 95427915--95427943 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
95427905 GTAATGGGAT
95427915 TATTTCTTGACTGA
1 TATTTCTTGACTGA
95427929 TATTTCTTGACTGA
1 TATTTCTTGACTGA
95427943 T
1 T
95427944 GTTTTGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.52
Consensus pattern (14 bp):
TATTTCTTGACTGA
Found at i:95429697 original size:13 final size:13
Alignment explanation
Indices: 95429681--95429710 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
95429671 AAATTTAACT
*
95429681 AATAAATAAATAA
1 AATAAATAAAAAA
95429694 AATAAATAAAAAA
1 AATAAATAAAAAA
95429707 AATA
1 AATA
95429711 TAAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AATAAATAAAAAA
Found at i:95434734 original size:41 final size:42
Alignment explanation
Indices: 95434673--95434769 Score: 110
Period size: 45 Copynumber: 2.3 Consensus size: 42
95434663 AAGTACCACA
*
95434673 TTTAAAA-AATAAATTAG-TTTTA-ATTAAAGTTTTATTCATT
1 TTTAAAATAA-AAATTAGTTTTTATATTAAAGTTTCATTCATT
*
95434713 TTTAAAACTAAAAATTAGTTTTTTATTATTAAAGTTTCATTTATT
1 TTTAAAA-TAAAAATTAG-TTTTTA-TATTAAAGTTTCATTCATT
*
95434758 TTTACAATAAAA
1 TTTAAAATAAAA
95434770 TTGACATGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
40 7 0.15
41 7 0.15
42 2 0.04
43 5 0.10
44 5 0.10
45 22 0.46
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (42 bp):
TTTAAAATAAAAATTAGTTTTTATATTAAAGTTTCATTCATT
Found at i:95436518 original size:19 final size:20
Alignment explanation
Indices: 95436496--95436543 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
95436486 ATTAAGCCCA
95436496 AAAAAAAAAC-CTAA-CCCC
1 AAAAAAAAACACTAACCCCC
*
95436514 TAAAAAAAACACTAACCCCC
1 AAAAAAAAACACTAACCCCC
95436534 AAATAAAAAA
1 AAA-AAAAAA
95436544 ACCAAGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.36
19 4 0.16
20 6 0.24
21 6 0.24
ACGTcount: A:0.65, C:0.27, G:0.00, T:0.08
Consensus pattern (20 bp):
AAAAAAAAACACTAACCCCC
Found at i:95436518 original size:20 final size:20
Alignment explanation
Indices: 95436492--95436546 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
95436482 GCCCATTAAG
95436492 CCCAAAAAAAAAACCTAACC
1 CCCAAAAAAAAAACCTAACC
* *
95436512 CCTAAAAAAAACA-CTAACC
1 CCCAAAAAAAAAACCTAACC
95436531 CCCAAATAAAAAAACC
1 CCCAAA-AAAAAAACC
95436547 AAGAAACCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 11 0.38
20 17 0.59
21 1 0.03
ACGTcount: A:0.60, C:0.33, G:0.00, T:0.07
Consensus pattern (20 bp):
CCCAAAAAAAAAACCTAACC
Found at i:95437798 original size:25 final size:24
Alignment explanation
Indices: 95437770--95437838 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 24
95437760 ATTATCATGA
*
95437770 TTATTATATATTAGTGTATATTTTT
1 TTATTATATATTA-TGTATATGTTT
95437795 TTATTATATATATATGTATATGTTT
1 TTATTATATAT-TATGTATATGTTT
*
95437820 TTAATATAT-TTATGTATAT
1 TTATTATATATTATGTATAT
95437839 ACTTATGTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.22
24 1 0.02
25 29 0.71
26 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (24 bp):
TTATTATATATTATGTATATGTTT
Found at i:95437839 original size:25 final size:24
Alignment explanation
Indices: 95437774--95437839 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 24
95437764 TCATGATTAT
95437774 TATATATTAGTGTATAT-TTTTTTATTA
1 TATAT-TTA-TGTATATATTTTTTA--A
* *
95437801 TATATATATGTATAT-GTTTTTAA
1 TATATTTATGTATATATTTTTTAA
95437824 TATATTTATGTATATA
1 TATATTTATGTATATA
95437840 CTTATGTAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 15 0.43
25 13 0.37
26 2 0.06
27 5 0.14
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (24 bp):
TATATTTATGTATATATTTTTTAA
Found at i:95437951 original size:24 final size:25
Alignment explanation
Indices: 95437922--95437977 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
95437912 TATGTATATC
*
95437922 TATATAT-TTTTCGTATATAGTATG-
1 TATATATGTTTTC-AATATAGTATGT
*
95437946 TATATATGTTTTCAATATTGTATGT
1 TATATATGTTTTCAATATAGTATGT
95437971 TATATAT
1 TATATAT
95437978 ATTATTGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (25 bp):
TATATATGTTTTCAATATAGTATGT
Found at i:95438058 original size:19 final size:19
Alignment explanation
Indices: 95438034--95438070 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
95438024 CTATTTTATA
*
95438034 TATATTTCTAATATCATTG
1 TATATTTCTAACATCATTG
95438053 TATATTTCTAACATCATT
1 TATATTTCTAACATCATT
95438071 ACTATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATTTCTAACATCATTG
Found at i:95438155 original size:9 final size:9
Alignment explanation
Indices: 95438138--95438172 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
95438128 ATCATTTCTA
95438138 ATATATATT
1 ATATATATT
*
95438147 ATATGTATT
1 ATATATATT
*
95438156 TTATATATT
1 ATATATATT
95438165 ATATATAT
1 ATATATAT
95438173 ATTTTAATGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (9 bp):
ATATATATT
Found at i:95438332 original size:21 final size:21
Alignment explanation
Indices: 95438308--95438347 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
95438298 ATTTTGTACG
*
95438308 TATCATTATTATATCTATTTT
1 TATCACTATTATATCTATTTT
* *
95438329 TATCCCTATTATATTTATT
1 TATCACTATTATATCTATT
95438348 GTTAATACTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (21 bp):
TATCACTATTATATCTATTTT
Found at i:95438469 original size:37 final size:35
Alignment explanation
Indices: 95438404--95438473 Score: 81
Period size: 37 Copynumber: 1.9 Consensus size: 35
95438394 TTATATATAG
95438404 TATTATTTTCATACATTATCATATTTATTATTATACC
1 TATTATTTTCATA-ATTATCATATTTATT-TTATACC
95438441 TATTATTTTCACT-ATTATCACT-TATTATTTTAT
1 TATTATTTTCA-TAATTATCA-TAT-TTATTTTAT
95438474 TTTAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
36 12 0.40
37 17 0.57
38 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (35 bp):
TATTATTTTCATAATTATCATATTTATTTTATACC
Found at i:95440770 original size:35 final size:35
Alignment explanation
Indices: 95440726--95440892 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
95440716 TCCTCATTGA
** *
95440726 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
95440761 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
95440801 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
95440836 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
95440871 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
95440893 CTTTGCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:95440809 original size:75 final size:73
Alignment explanation
Indices: 95440721--95440892 Score: 226
Period size: 75 Copynumber: 2.4 Consensus size: 73
95440711 GGTTTTCCTC
** * * **
95440721 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
95440785 TCAGTATGG
65 TCAGTATGG
*
95440794 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
95440859 CTCAGTATGG
64 CTCAGTATGG
95440869 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
95440893 CTTTGCCATG
Statistics
Matches: 89, Mismatches: 7, Indels: 9
0.85 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 58 0.65
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:95445267 original size:35 final size:35
Alignment explanation
Indices: 95445201--95445276 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
95445191 AATAAAATTT
*
95445201 AAATATTTTTAAATTATATTCATAATAAAAT-ATCA
1 AAATATTTTCAAATTATATTCATAATAAAATAAT-A
* *
95445236 AAATATTTTACAAATTATATTTA-AATCAAATAATA
1 AAATATTTT-CAAATTATATTCATAATAAAATAATA
95445271 AAATAT
1 AAATAT
95445277 AAATTAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 23 0.64
36 13 0.36
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (35 bp):
AAATATTTTCAAATTATATTCATAATAAAATAATA
Found at i:95445819 original size:25 final size:25
Alignment explanation
Indices: 95445785--95445835 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
95445775 TTTTGAATAG
* * *
95445785 AAAACGTGCTATTAGAAGTAGACTA
1 AAAACATGCTATCAGAAGCAGACTA
95445810 AAAACATGCTATCAGAAGCAGACTA
1 AAAACATGCTATCAGAAGCAGACTA
95445835 A
1 A
95445836 TCAAATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.18, T:0.20
Consensus pattern (25 bp):
AAAACATGCTATCAGAAGCAGACTA
Found at i:95452419 original size:39 final size:39
Alignment explanation
Indices: 95452365--95452444 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
95452355 GTAGTTATAC
*
95452365 ATGCAAATGTTGGATCAATCCAGCAGTCAACATAGACTA
1 ATGCAAATATTGGATCAATCCAGCAGTCAACATAGACTA
95452404 ATGCAAATATTGGATCAATCCAGCAGTCAACATAGACTA
1 ATGCAAATATTGGATCAATCCAGCAGTCAACATAGACTA
95452443 AT
1 AT
95452445 ACCCTCACTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (39 bp):
ATGCAAATATTGGATCAATCCAGCAGTCAACATAGACTA
Found at i:95457223 original size:18 final size:18
Alignment explanation
Indices: 95457202--95457266 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
95457192 CCGGCTCCTC
*
95457202 CACCAAACCCACCACCGG
1 CACCAAACCCACCACCAG
* *
95457220 CACC-AGCTCCACCACCAC
1 CACCAAAC-CCACCACCAG
* *
95457238 CAACGAACCCACCACCAG
1 CACCAAACCCACCACCAG
*
95457256 CTCCAAACCCA
1 CACCAAACCCA
95457267 AATCCAGCAC
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
17 2 0.06
18 32 0.89
19 2 0.06
ACGTcount: A:0.34, C:0.55, G:0.08, T:0.03
Consensus pattern (18 bp):
CACCAAACCCACCACCAG
Found at i:95457229 original size:30 final size:30
Alignment explanation
Indices: 95457177--95457236 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
95457167 GAAACCTCCT
* * * *
95457177 AACCCACCACCTCCGCCGGCTCCTCCACCA
1 AACCCACCACCGCCACCAGCTCCACCACCA
*
95457207 AACCCACCACCGGCACCAGCTCCACCACCA
1 AACCCACCACCGCCACCAGCTCCACCACCA
95457237 CCAACGAACC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.58, G:0.10, T:0.07
Consensus pattern (30 bp):
AACCCACCACCGCCACCAGCTCCACCACCA
Found at i:95460149 original size:16 final size:15
Alignment explanation
Indices: 95460125--95460154 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
95460115 TTAACATATA
95460125 AAAATTATATAAAAG
1 AAAATTATATAAAAG
95460140 AAAATATATATAAAA
1 AAAAT-TATATAAAA
95460155 ATTAGTTTAT
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:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AAAATTATATAAAAG
Found at i:95461049 original size:21 final size:20
Alignment explanation
Indices: 95461025--95461076 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 20
95461015 TTTCCTTTGC
*
95461025 TTTTTAAAAATATTTTTTTTAT
1 TTTTTAAAAATA--ATTTTTAT
95461047 TTTTT-AAAATAATTTTTAT
1 TTTTTAAAAATAATTTTTAT
95461066 TTTTTAAAAAT
1 TTTTTAAAAAT
95461077 TGAAAAACAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 12 0.43
20 5 0.18
21 6 0.21
22 5 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTTAAAAATAATTTTTAT
Found at i:95461285 original size:16 final size:17
Alignment explanation
Indices: 95461260--95461295 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
95461250 ATAAAAAAAC
95461260 TTTTATTATTTTTTAAT
1 TTTTATTATTTTTTAAT
*
95461277 TTTTA-TATTTTTTTAT
1 TTTTATTATTTTTTAAT
95461293 TTT
1 TTT
95461296 CTAACAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTATTATTTTTTAAT
Found at i:95472483 original size:16 final size:15
Alignment explanation
Indices: 95472443--95472489 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
95472433 TAATAATCAT
95472443 TTAATTTTA-AATAA
1 TTAATTTTATAATAA
95472457 TTACATTTTATAATAA
1 TTA-ATTTTATAATAA
* *
95472473 CTTAATATTATTATAA
1 -TTAATTTTATAATAA
95472489 T
1 T
95472490 AAAATGACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 3 0.11
15 7 0.25
16 15 0.54
17 3 0.11
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAATTTTATAATAA
Found at i:95474417 original size:14 final size:16
Alignment explanation
Indices: 95474381--95474418 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
95474371 AATTGATAAA
95474381 TATT-TTTTTAATATC
1 TATTATTTTTAATATC
95474396 TATTATTTTTAATAT-
1 TATTATTTTTAATATC
95474411 T-TTATTTT
1 TATTATTTT
95474419 ACACCTACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 10 0.45
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTTTTAATATC
Found at i:95485849 original size:48 final size:48
Alignment explanation
Indices: 95485778--95485875 Score: 169
Period size: 48 Copynumber: 2.0 Consensus size: 48
95485768 AATGTTGAAG
*
95485778 ACATCATCTTTCTGTACCGGTACAATTCTGTTGCATTTATATCACGTT
1 ACATCATCTTTCTGTACCGGTACAATTCCGTTGCATTTATATCACGTT
* *
95485826 ACATCATCTTTCTGTATCGGTACAGTTCCGTTGCATTTATATCACGTT
1 ACATCATCTTTCTGTACCGGTACAATTCCGTTGCATTTATATCACGTT
95485874 AC
1 AC
95485876 CGGAATCACA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (48 bp):
ACATCATCTTTCTGTACCGGTACAATTCCGTTGCATTTATATCACGTT
Found at i:95492375 original size:2 final size:2
Alignment explanation
Indices: 95492368--95492404 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
95492358 AAATTATAAT
*
95492368 TA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
95492405 TTTTATGGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:95492380 original size:10 final size:10
Alignment explanation
Indices: 95492362--95492410 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
95492352 GCAAATAAAT
*
95492362 TATAATTATA
1 TATATTTATA
95492372 TATATTTATA
1 TATATTTATA
*
95492382 TATATATATA
1 TATATTTATA
*
95492392 TATATATATA
1 TATATTTATA
*
95492402 TATTTTTAT
1 TATATTTAT
95492411 GGTATCTCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TATATTTATA
Found at i:95494095 original size:64 final size:62
Alignment explanation
Indices: 95493989--95494109 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 62
95493979 AGGTTTGATG
* *
95493989 GGTGAGAAGTGAAATGAATGGTTGTGTTTTAATAGAAGGTTTCAAGGGTGAGAGATTTCTTA
1 GGTGAGAACTGAAATGAATGGTTGTGTTTTAATAGAAGGTTTCAAGGGTGACAGATTTCTTA
* * *
95494051 GGTGAGGACTGAAATGAATGATTTTGTGCTTTT-ATAGAAGGTTTCATGGGTGACAGATT
1 GGTGAGAACTGAAATGAATG--GTTGTG-TTTTAATAGAAGGTTTCAAGGGTGACAGATT
95494110 ACTTTTTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 18 0.35
64 29 0.57
65 4 0.08
ACGTcount: A:0.29, C:0.05, G:0.31, T:0.35
Consensus pattern (62 bp):
GGTGAGAACTGAAATGAATGGTTGTGTTTTAATAGAAGGTTTCAAGGGTGACAGATTTCTTA
Found at i:95498574 original size:2 final size:2
Alignment explanation
Indices: 95498569--95498599 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
95498559 AATAAATACA
95498569 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
95498600 GGTGAAAAAC
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:95506697 original size:136 final size:137
Alignment explanation
Indices: 95506453--95506738 Score: 504
Period size: 136 Copynumber: 2.1 Consensus size: 137
95506443 CATTGGGCCT
** *
95506453 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
95506518 AGCCCCTTATTCAGATAACAGTATGACCCATAGGCCCATTTCAAAATACAT-GCAACATCAAT-A
66 AGCCCCTTATTCAGATAACAGTATGACCCATAGGCCCATTTCAAAATACATAG-AACATCAATAA
95506581 ACATATGC
130 ACATATGC
95506589 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
* *
95506654 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATAGAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGACCCATAGGCCCATTTCAAAATACATAGAACATCAATAAA
95506719 CATATGC
131 CATATGC
95506726 AAGCCCATTTGGG
1 AAGCCCATTTGGG
95506739 GAGACTACTC
Statistics
Matches: 143, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
136 120 0.84
137 23 0.16
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAAAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGACCCATAGGCCCATTTCAAAATACATAGAACATCAATAAA
CATATGC
Found at i:95508556 original size:26 final size:26
Alignment explanation
Indices: 95508520--95508654 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
95508510 CATGAAATTC
95508520 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
95508546 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
95508572 TTATCATGGAACATTTA-CTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
95508597 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
95508623 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
95508649 TTATCA
1 TTATCA
95508655 ATTTGTATCA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 23 0.23
26 79 0.77
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:95508606 original size:51 final size:52
Alignment explanation
Indices: 95508520--95508654 Score: 245
Period size: 51 Copynumber: 2.6 Consensus size: 52
95508510 CATGAAATTC
* *
95508520 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
95508572 TTATCATGGAACATTTA-CTAACCTATTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
95508623 TTATCATGGAACATTTACCTAACCTATTATCA
1 TTATCATGGAACATTTACCTAACCTATTATCA
95508655 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
51 50 0.62
52 30 0.38
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.33
Consensus pattern (52 bp):
TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
Found at i:95513548 original size:12 final size:12
Alignment explanation
Indices: 95513531--95513585 Score: 110
Period size: 12 Copynumber: 4.6 Consensus size: 12
95513521 AGTACTACCT
95513531 CGGCCTCGACCA
1 CGGCCTCGACCA
95513543 CGGCCTCGACCA
1 CGGCCTCGACCA
95513555 CGGCCTCGACCA
1 CGGCCTCGACCA
95513567 CGGCCTCGACCA
1 CGGCCTCGACCA
95513579 CGGCCTC
1 CGGCCTC
95513586 TTCCCCGAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.15, C:0.51, G:0.25, T:0.09
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:95515013 original size:135 final size:137
Alignment explanation
Indices: 95514770--95515054 Score: 529
Period size: 135 Copynumber: 2.1 Consensus size: 137
95514760 CATTGGGCCT
**
95514770 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
95514835 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
95514899 CATATGC
131 CATATGC
95514906 AAGCCCATTTGGGTAACAGTGGTACTGGGCCA-AGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
95514970 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
95515035 CATATGC
131 CATATGC
95515042 AAGCCCATTTGGG
1 AAGCCCATTTGGG
95515055 GAGACTACTC
Statistics
Matches: 145, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
135 93 0.64
136 52 0.36
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAA
CATATGC
Found at i:95516874 original size:26 final size:26
Alignment explanation
Indices: 95516838--95516972 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
95516828 CATGAAATTC
95516838 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
95516864 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
95516890 TTATCATGGAACATTTA-CTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
95516915 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
95516941 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
95516967 TTATCA
1 TTATCA
95516973 ATTTGTATCA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 23 0.23
26 79 0.77
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:95516924 original size:51 final size:52
Alignment explanation
Indices: 95516838--95516972 Score: 245
Period size: 51 Copynumber: 2.6 Consensus size: 52
95516828 CATGAAATTC
* *
95516838 TTATCATGAAACATTTACCTAACCCATTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
95516890 TTATCATGGAACATTTA-CTAACCTATTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
95516941 TTATCATGGAACATTTACCTAACCTATTATCA
1 TTATCATGGAACATTTACCTAACCTATTATCA
95516973 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
51 50 0.62
52 30 0.38
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.33
Consensus pattern (52 bp):
TTATCATGGAACATTTACCTAACCTATTATCATGAAACATTTACCTAACCCA
Found at i:95517901 original size:13 final size:14
Alignment explanation
Indices: 95517880--95517923 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
95517870 TAGGACCTTC
*
95517880 TAGATTTTA-GATT
1 TAGAATTTATGATT
*
95517893 TAGAATTTATGGTT
1 TAGAATTTATGATT
*
95517907 TAGAATTTATGGTT
1 TAGAATTTATGATT
95517921 TAG
1 TAG
95517924 GGTTATGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 8 0.29
14 20 0.71
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (14 bp):
TAGAATTTATGATT
Found at i:95517908 original size:14 final size:14
Alignment explanation
Indices: 95517891--95517923 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
95517881 AGATTTTAGA
95517891 TTTAGAATTTATGG
1 TTTAGAATTTATGG
95517905 TTTAGAATTTATGG
1 TTTAGAATTTATGG
95517919 TTTAG
1 TTTAG
95517924 GGTTATGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (14 bp):
TTTAGAATTTATGG
Found at i:95518718 original size:5 final size:5
Alignment explanation
Indices: 95518708--95518733 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
95518698 ACTTTTATTA
95518708 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
95518734 TTTGGATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:95519565 original size:20 final size:18
Alignment explanation
Indices: 95519540--95519577 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
95519530 TTATCATTAT
95519540 ACATATTATTTATTACAATA
1 ACATATT-TTTATT-CAATA
95519560 ACATATTTTTATTCAATA
1 ACATATTTTTATTCAATA
95519578 TTTTTTGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (18 bp):
ACATATTTTTATTCAATA
Found at i:95520223 original size:17 final size:17
Alignment explanation
Indices: 95520203--95520250 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
95520193 AAACCCTAAA
95520203 ATTTAAAATTTTATATT
1 ATTTAAAATTTTATATT
*
95520220 ATTTTTAAA-TTTATATT
1 A-TTTAAAATTTTATATT
95520237 ATTAATAAAATTTT
1 ATT--TAAAATTTT
95520251 TAATTAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.08
17 10 0.40
18 10 0.40
19 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAAAATTTTATATT
Found at i:95521172 original size:22 final size:20
Alignment explanation
Indices: 95521147--95521187 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
95521137 TTTATTTAAG
95521147 AAATAATTAAATTAAAAAATTA
1 AAATAATTAAA--AAAAAATTA
*
95521169 AAATATTTAAAAAAAAATT
1 AAATAATTAAAAAAAAATT
95521188 TATTTAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATTAAAAAAAAATTA
Found at i:95521191 original size:16 final size:16
Alignment explanation
Indices: 95521130--95521195 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
95521120 TCTATAAATG
*
95521130 AAAAATATTTATTTAA
1 AAAAAAATTTATTTAA
* * * *
95521146 GAAATAATTAAATTAA
1 AAAAAAATTTATTTAA
*
95521162 AAAATTAAA-ATATTTAA
1 AAAA--AAATTTATTTAA
95521179 AAAAAAATTTATTTAA
1 AAAAAAATTTATTTAA
95521195 A
1 A
95521196 GACATTGAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
15 3 0.08
16 22 0.61
17 9 0.25
18 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AAAAAAATTTATTTAA
Found at i:95522310 original size:20 final size:20
Alignment explanation
Indices: 95522282--95522325 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
95522272 AAATTTATTA
95522282 AAAACTAAAGA-ATATATAAT
1 AAAACTAAA-ATATATATAAT
* *
95522302 AAAATTAAAATATTTATAAT
1 AAAACTAAAATATATATAAT
95522322 AAAA
1 AAAA
95522326 AACTCAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAACTAAAATATATATAAT
Found at i:95523267 original size:17 final size:16
Alignment explanation
Indices: 95523225--95523267 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
95523215 TAAAAATTAT
* *
95523225 AATTAAATTAATATAA
1 AATTAAATAAATAAAA
95523241 AATATAAATAAATAAAA
1 AAT-TAAATAAATAAAA
95523258 AATTAGAATA
1 AATTA-AATA
95523268 TAATTTGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (16 bp):
AATTAAATAAATAAAA
Found at i:95524042 original size:12 final size:12
Alignment explanation
Indices: 95524027--95524055 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
95524017 ACGAAGACTT
95524027 CGAGGAAGAAGA
1 CGAGGAAGAAGA
95524039 CGAGGAAGAAGA
1 CGAGGAAGAAGA
95524051 -GAGGA
1 CGAGGA
95524056 GGAGAGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.48, C:0.07, G:0.45, T:0.00
Consensus pattern (12 bp):
CGAGGAAGAAGA
Found at i:95524238 original size:15 final size:15
Alignment explanation
Indices: 95524208--95524252 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
95524198 GGAGGAAGTG
* *
95524208 GAGGAGGAAGAAGAA
1 GAGGAAGAAGAGGAA
* *
95524223 GATGAAGATGAGGAA
1 GAGGAAGAAGAGGAA
95524238 GAGGAAGAAGAGGAA
1 GAGGAAGAAGAGGAA
95524253 AGTGAGAGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.44, T:0.04
Consensus pattern (15 bp):
GAGGAAGAAGAGGAA
Found at i:95524258 original size:24 final size:23
Alignment explanation
Indices: 95524199--95524268 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 23
95524189 AACGGCGAAG
*
95524199 GAGGAAGTGGAGGAGGAAGAAGAA
1 GAGGAAGT-GAGGAAGAAGAAGAA
* *
95524223 GATGAAGATGAGGAAGAGGAAGAA
1 GAGGAAG-TGAGGAAGAAGAAGAA
95524247 GAGGAAAGTGAGAGAAGGAAGA
1 GAGG-AAGTGAG-GAA-GAAGA
95524269 GAAAGATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
24 26 0.70
25 7 0.19
26 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.46, T:0.06
Consensus pattern (23 bp):
GAGGAAGTGAGGAAGAAGAAGAA
Found at i:95525573 original size:18 final size:18
Alignment explanation
Indices: 95525550--95525595 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
95525540 TTTATGTAGC
95525550 TGAAGTTCTCTTCTTAGT
1 TGAAGTTCTCTTCTTAGT
95525568 TGAAGTTCTCTTCTTAGT
1 TGAAGTTCTCTTCTTAGT
95525586 TGAAGTTCTC
1 TGAAGTTCTC
95525596 CTAATTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.48
Consensus pattern (18 bp):
TGAAGTTCTCTTCTTAGT
Found at i:95531672 original size:14 final size:14
Alignment explanation
Indices: 95531653--95531686 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
95531643 AATAGTAGAC
95531653 ATCGAAATTCATAA
1 ATCGAAATTCATAA
95531667 ATCG-AATTCATAA
1 ATCGAAATTCATAA
95531680 ATCGAAA
1 ATCGAAA
95531687 GATAATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.50, C:0.15, G:0.09, T:0.26
Consensus pattern (14 bp):
ATCGAAATTCATAA
Found at i:95532707 original size:38 final size:38
Alignment explanation
Indices: 95532663--95532741 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
95532653 TATATTGAAA
*
95532663 ATAAGGTTAAATTTTGCTATTAGTCACAGTATATATAT
1 ATAAGGTTAAATTTTACTATTAGTCACAGTATATATAT
95532701 ATAAGGTTAAATTTTACTATTAGTCACAGTATATATAT
1 ATAAGGTTAAATTTTACTATTAGTCACAGTATATATAT
95532739 ATA
1 ATA
95532742 TATATATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (38 bp):
ATAAGGTTAAATTTTACTATTAGTCACAGTATATATAT
Found at i:95532737 original size:2 final size:2
Alignment explanation
Indices: 95532730--95532755 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
95532720 TTAGTCACAG
95532730 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
95532756 AAAGGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:95532775 original size:54 final size:54
Alignment explanation
Indices: 95532692--95532799 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
95532682 TTAGTCACAG
*
95532692 TATATATATATAAGGTTAAATTTTACTATTAGTCACAGTATATATATATATATA
1 TATATATATAAAAGGTTAAATTTTACTATTAGTCACAGTATATATATATATATA
*
95532746 TATATATATAAAAGGTTAAATTTTGCTATTAGTCACAGTATATATATATATATA
1 TATATATATAAAAGGTTAAATTTTACTATTAGTCACAGTATATATATATATATA
95532800 AAACTTTAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.44
Consensus pattern (54 bp):
TATATATATAAAAGGTTAAATTTTACTATTAGTCACAGTATATATATATATATA
Found at i:95534858 original size:12 final size:12
Alignment explanation
Indices: 95534841--95534866 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
95534831 AAATAATCAG
95534841 ATAGCCACATGT
1 ATAGCCACATGT
95534853 ATAGCCACATGT
1 ATAGCCACATGT
95534865 AT
1 AT
95534867 CTTATGCTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (12 bp):
ATAGCCACATGT
Found at i:95540134 original size:19 final size:19
Alignment explanation
Indices: 95540110--95540158 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
95540100 TCACTATTAA
95540110 TCGTTTTTATTATATCTGC
1 TCGTTTTTATTATATCTGC
95540129 TCGTTTTTATTATATCTGC
1 TCGTTTTTATTATATCTGC
*
95540148 TCTTTTTTATT
1 TCGTTTTTATT
95540159 TAATGTGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.14, C:0.14, G:0.08, T:0.63
Consensus pattern (19 bp):
TCGTTTTTATTATATCTGC
Found at i:95547581 original size:18 final size:18
Alignment explanation
Indices: 95547560--95547596 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
95547550 GTCTATTTGG
* *
95547560 TTTAAAGTAAATAAATTA
1 TTTAAAATAAAAAAATTA
95547578 TTTAAAATAAAAAAATTA
1 TTTAAAATAAAAAAATTA
95547596 T
1 T
95547597 AAAAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (18 bp):
TTTAAAATAAAAAAATTA
Found at i:95550905 original size:31 final size:31
Alignment explanation
Indices: 95550870--95550931 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
95550860 AGAACACATA
95550870 AATTCTTTAGATAAAACAATACTAAATACAC
1 AATTCTTTAGATAAAACAATACTAAATACAC
95550901 AATTCTTTAGATAAAACAATACTAAATACAC
1 AATTCTTTAGATAAAACAATACTAAATACAC
95550932 GATAGTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.29
Consensus pattern (31 bp):
AATTCTTTAGATAAAACAATACTAAATACAC
Found at i:95554113 original size:24 final size:24
Alignment explanation
Indices: 95554081--95554141 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
95554071 ACAGACCGAT
* *
95554081 TACAAATACAGATGCA-ATTACATA
1 TACATATACAGATGCAGA-TACAGA
* *
95554105 TACATATACAGATGTAGATACAGG
1 TACATATACAGATGCAGATACAGA
95554129 TACATATACAGAT
1 TACATATACAGAT
95554142 CCTACCCCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 31 0.97
25 1 0.03
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (24 bp):
TACATATACAGATGCAGATACAGA
Found at i:95556758 original size:30 final size:30
Alignment explanation
Indices: 95556722--95556790 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
95556712 GCCCAGAATA
** *
95556722 CCACACGTTCGTATGGTCTACCCGTGTGAC
1 CCACACGCCCGTATGGTCCACCCGTGTGAC
* *
95556752 CCACACGCCCGTGTGGTCCACTCGTGTGAC
1 CCACACGCCCGTATGGTCCACCCGTGTGAC
*
95556782 CCATACGCC
1 CCACACGCC
95556791 TGTGTGGCCT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.16, C:0.39, G:0.23, T:0.22
Consensus pattern (30 bp):
CCACACGCCCGTATGGTCCACCCGTGTGAC
Found at i:95556796 original size:30 final size:30
Alignment explanation
Indices: 95556735--95556797 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
95556725 CACGTTCGTA
*
95556735 TGGTCTACCCGTGTGACCCACACGCCCGTG
1 TGGTCCACCCGTGTGACCCACACGCCCGTG
* * *
95556765 TGGTCCACTCGTGTGACCCATACGCCTGTG
1 TGGTCCACCCGTGTGACCCACACGCCCGTG
95556795 TGG
1 TGG
95556798 CCTACACGGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.13, C:0.35, G:0.29, T:0.24
Consensus pattern (30 bp):
TGGTCCACCCGTGTGACCCACACGCCCGTG
Found at i:95560514 original size:13 final size:13
Alignment explanation
Indices: 95560496--95560521 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
95560486 CAATAATTTA
95560496 AAATTTAAAAAAT
1 AAATTTAAAAAAT
95560509 AAATTTAAAAAAT
1 AAATTTAAAAAAT
95560522 TAATACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTTAAAAAAT
Found at i:95560853 original size:30 final size:30
Alignment explanation
Indices: 95560819--95560878 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
95560809 AGACAGTGAG
95560819 AGCCTTATATAATTGACCTCAGCTTTCCTC
1 AGCCTTATATAATTGACCTCAGCTTTCCTC
*
95560849 AGCCTTGTATAATTGACCTCAGCTTTCCTC
1 AGCCTTATATAATTGACCTCAGCTTTCCTC
95560879 TTCTTCAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.37
Consensus pattern (30 bp):
AGCCTTATATAATTGACCTCAGCTTTCCTC
Found at i:95568231 original size:44 final size:45
Alignment explanation
Indices: 95568136--95568269 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
95568126 ACAGGACAGT
* *
95568136 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
95568182 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
95568226 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
95568270 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.49
45 1 0.01
46 37 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:95573612 original size:14 final size:15
Alignment explanation
Indices: 95573585--95573622 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
95573575 CAATTTTTTG
95573585 TATTTTATAAATATA
1 TATTTTATAAATATA
*
95573600 TATTTTA-AAATATT
1 TATTTTATAAATATA
95573614 TAATTTTAT
1 T-ATTTTAT
95573623 TCATTAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTTTATAAATATA
Found at i:95581778 original size:3 final size:3
Alignment explanation
Indices: 95581772--95581801 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
95581762 TAATAAAGTA
95581772 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
95581802 TTGCTTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:95582927 original size:7 final size:7
Alignment explanation
Indices: 95582915--95582946 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
95582905 ACTTTAATTC
95582915 TTTCCCT
1 TTTCCCT
95582922 TTTCCCT
1 TTTCCCT
95582929 TTTCCCT
1 TTTCCCT
*
95582936 TTTCCAT
1 TTTCCCT
95582943 TTTC
1 TTTC
95582947 AAGGCAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTCCCT
Found at i:95583563 original size:3 final size:3
Alignment explanation
Indices: 95583557--95583594 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
95583547 AATAAATCAT
95583557 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
95583595 TTGTTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:95583700 original size:22 final size:22
Alignment explanation
Indices: 95583657--95583701 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
95583647 TGTAATAAGA
***
95583657 TTTTAATTTAACATGCTTAATT
1 TTTTAATTTAACATGAACAATT
*
95583679 TTTTAATTTAACTTGAACAATT
1 TTTTAATTTAACATGAACAATT
95583701 T
1 T
95583702 CACTCGATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTTAATTTAACATGAACAATT
Found at i:95589542 original size:26 final size:27
Alignment explanation
Indices: 95589494--95589545 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
95589484 TTCTATTTTT
* * *
95589494 CTATTTCACTTTTTTGTTTTTTCTTTC
1 CTATTTCAATTTTATGTTCTTTCTTTC
95589521 CTATTTCAATTTTAT-TTCTTTCTTT
1 CTATTTCAATTTTATGTTCTTTCTTT
95589546 TCTTCCTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.12, C:0.17, G:0.02, T:0.69
Consensus pattern (27 bp):
CTATTTCAATTTTATGTTCTTTCTTTC
Found at i:95589547 original size:27 final size:28
Alignment explanation
Indices: 95589489--95589547 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
95589479 TCTCCTTCTA
* * * *
95589489 TTTTTCTATTTCACTTTTTTGTTTTTTC
1 TTTTCCTATTTCAATTTTATGTTCTTTC
95589517 -TTTCCTATTTCAATTTTAT-TTCTTTC
1 TTTTCCTATTTCAATTTTATGTTCTTTC
95589543 TTTTC
1 TTTTC
95589548 TTCCTATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 6 0.23
27 20 0.77
ACGTcount: A:0.10, C:0.17, G:0.02, T:0.71
Consensus pattern (28 bp):
TTTTCCTATTTCAATTTTATGTTCTTTC
Found at i:95590100 original size:21 final size:21
Alignment explanation
Indices: 95590074--95590116 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
95590064 AATGATACTA
95590074 AGATGAATTTGCTAATTTGAG
1 AGATGAATTTGCTAATTTGAG
95590095 AGATGAATTTGCTAATTTGAG
1 AGATGAATTTGCTAATTTGAG
95590116 A
1 A
95590117 AGAGGGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (21 bp):
AGATGAATTTGCTAATTTGAG
Found at i:95592730 original size:30 final size:28
Alignment explanation
Indices: 95592690--95592746 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
95592680 AAATTTTTAA
95592690 TAAATAAAAAATTTATAAAT-TTATAAATAT
1 TAAATAAAAAA--TATAAATATT-TAAATAT
*
95592720 TAAATTAAAAATATAAATATTTAAATA
1 TAAATAAAAAATATAAATATTTAAATA
95592747 AATTTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 13 0.52
29 2 0.08
30 10 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAATAAAAAATATAAATATTTAAATAT
Found at i:95597928 original size:15 final size:16
Alignment explanation
Indices: 95597901--95597931 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
95597891 CGACACAAAA
95597901 AAAAAATTAATTTTTT
1 AAAAAATTAATTTTTT
95597917 AAAAAATT-ATTTTTT
1 AAAAAATTAATTTTTT
95597932 CTGATGGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AAAAAATTAATTTTTT
Found at i:95599221 original size:18 final size:19
Alignment explanation
Indices: 95599187--95599222 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
95599177 ACAAAATAAT
*
95599187 TCAAAATAATTTTTAAAAA
1 TCAAAATAATTTATAAAAA
95599206 TCAAAAT-ATTTATAAAA
1 TCAAAATAATTTATAAAA
95599223 TTTTCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (19 bp):
TCAAAATAATTTATAAAAA
Found at i:95599231 original size:20 final size:20
Alignment explanation
Indices: 95599206--95599276 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 20
95599196 TTTTTAAAAA
95599206 TCAAAATATTTATAAAATTT
1 TCAAAATATTTATAAAATTT
*
95599226 TC-AAA-ATTTAT--ACTTT
1 TCAAAATATTTATAAAATTT
*
95599242 T-TAAATA-TTATAAAATTT
1 TCAAAATATTTATAAAATTT
* * *
95599260 TTAAAAAAATTATAAAA
1 TCAAAATATTTATAAAA
95599277 AAATAAAGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
16 12 0.29
17 1 0.02
18 11 0.27
19 7 0.17
20 10 0.24
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
TCAAAATATTTATAAAATTT
Found at i:95599262 original size:18 final size:18
Alignment explanation
Indices: 95599209--95599264 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
95599199 TTAAAAATCA
*
95599209 AAATATTTATAAAATTTTC
1 AAATA-TTATAAAATTTTT
* *
95599228 AAA-ATT-TATACTTTTT
1 AAATATTATAAAATTTTT
95599244 AAATATTATAAAATTTTT
1 AAATATTATAAAATTTTT
95599262 AAA
1 AAA
95599265 AAAATTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
16 10 0.33
17 5 0.17
18 12 0.40
19 3 0.10
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (18 bp):
AAATATTATAAAATTTTT
Found at i:95600230 original size:35 final size:34
Alignment explanation
Indices: 95600181--95600273 Score: 114
Period size: 35 Copynumber: 2.7 Consensus size: 34
95600171 CGTAACTCGC
*
95600181 AACCCCAAACTCTTAAACCTTAAACCTGAACAATA
1 AACCCCAAA-TCTTAAACCTTAAACCTAAACAATA
* * *
95600216 AACTCCAAATTCTTAAACCTTAAACCTAAACATTG
1 AACCCCAAA-TCTTAAACCTTAAACCTAAACAATA
* *
95600251 AACCCCAAATCCTAAACATTAAA
1 AACCCCAAATCTTAAACCTTAAA
95600274 TCCAAAATCC
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
34 12 0.24
35 38 0.76
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23
Consensus pattern (34 bp):
AACCCCAAATCTTAAACCTTAAACCTAAACAATA
Found at i:95600281 original size:21 final size:21
Alignment explanation
Indices: 95600240--95600283 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
95600230 AAACCTTAAA
* *
95600240 CCTAAACATTGAACCCCAAAT
1 CCTAAACATTAAACCCAAAAT
*
95600261 CCTAAACATTAAATCCAAAAT
1 CCTAAACATTAAACCCAAAAT
95600282 CC
1 CC
95600284 CGAATCTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.32, G:0.02, T:0.20
Consensus pattern (21 bp):
CCTAAACATTAAACCCAAAAT
Found at i:95600492 original size:17 final size:18
Alignment explanation
Indices: 95600470--95600503 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
95600460 TTGTTTCTAA
95600470 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
95600487 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
95600504 AAGTTAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:95602315 original size:9 final size:9
Alignment explanation
Indices: 95602301--95602333 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
95602291 GTTGAATTTT
95602301 ATAATTTAA
1 ATAATTTAA
*
95602310 ATAATTCAA
1 ATAATTTAA
95602319 ATAATTTAA
1 ATAATTTAA
95602328 ATAATT
1 ATAATT
95602334 GATTGGTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (9 bp):
ATAATTTAA
Found at i:95609758 original size:8 final size:8
Alignment explanation
Indices: 95609745--95609778 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
95609735 ACAATTAATT
95609745 AATTTAAA
1 AATTTAAA
*
95609753 ATTTTAAA
1 AATTTAAA
95609761 AATTTAAA
1 AATTTAAA
*
95609769 AATTCAAA
1 AATTTAAA
95609777 AA
1 AA
95609779 AATATAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (8 bp):
AATTTAAA
Found at i:95611285 original size:14 final size:14
Alignment explanation
Indices: 95611251--95611298 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
95611241 AAATTTTTAA
*
95611251 TAAATAAAAAATAT
1 TAAATTAAAAATAT
*
95611265 ATAAAATTATAAATAT
1 -T-AAATTAAAAATAT
95611281 TAAATTAAAAATA-
1 TAAATTAAAAATAT
95611294 TAAAT
1 TAAAT
95611299 ATTTAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 5 0.17
14 11 0.38
15 2 0.07
16 11 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATTAAAAATAT
Found at i:95611295 original size:20 final size:21
Alignment explanation
Indices: 95611266--95611307 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
95611256 AAAAAATATA
*
95611266 TAAAATTATAAATA-TTAAAT
1 TAAAAATATAAATATTTAAAT
95611286 TAAAAATATAAATATTTAAAT
1 TAAAAATATAAATATTTAAAT
95611307 T
1 T
95611308 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAAATATAAATATTTAAAT
Found at i:95615940 original size:18 final size:20
Alignment explanation
Indices: 95615905--95615943 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
95615895 AAACCCTGAA
95615905 TTTTCTCTTTTCTTCTTTCT
1 TTTTCTCTTTTCTTCTTTCT
95615925 TTTTCTC-TTT-TTCTTTCT
1 TTTTCTCTTTTCTTCTTTCT
95615943 T
1 T
95615944 CCTTCCCCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 3 0.16
20 7 0.37
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCTCTTTTCTTCTTTCT
Found at i:95616222 original size:21 final size:22
Alignment explanation
Indices: 95616169--95616225 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
95616159 CAATTTAAAT
*
95616169 AATAATAACAATAACAATAATA
1 AATAATAATAATAACAATAATA
* *
95616191 ATTAA-ATATAA-AACTATAATA
1 AATAATA-ATAATAACAATAATA
95616212 AATAATAATAATAA
1 AATAATAATAATAA
95616226 TTTAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 18 0.64
22 10 0.36
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAATAATAATAACAATAATA
Found at i:95616463 original size:14 final size:14
Alignment explanation
Indices: 95616444--95616473 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
95616434 GATTAACTTC
*
95616444 ATAAATATTTTTTA
1 ATAAATATTTTCTA
95616458 ATAAATATTTTCTA
1 ATAAATATTTTCTA
95616472 AT
1 AT
95616474 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:95619359 original size:46 final size:46
Alignment explanation
Indices: 95619231--95619361 Score: 165
Period size: 46 Copynumber: 2.8 Consensus size: 46
95619221 TTTGACATGA
* * * * * *
95619231 TGCCATAGTGTCTTTCAACTACGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCACGC
* *
95619277 TGCCATGGTATCTTTCAACCGTGGTCTTATTCATTTCATGTCACGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGC
*
95619323 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
95619362 ATCAGAGAGC
Statistics
Matches: 73, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
45 4 0.05
46 69 0.95
ACGTcount: A:0.19, C:0.25, G:0.15, T:0.40
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCACGC
Found at i:95627515 original size:17 final size:15
Alignment explanation
Indices: 95627483--95627534 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
95627473 ATTACATTTA
95627483 TAATATAAAAAAAAT
1 TAATATAAAAAAAAT
95627498 TAATATAAAATTAAAAT
1 TAATATAAAA--AAAAT
* * *
95627515 TAAAATTAAAAATAT
1 TAATATAAAAAAAAT
95627530 TAATA
1 TAATA
95627535 AAACTTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 18 0.58
17 13 0.42
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATATAAAAAAAAT
Found at i:95627518 original size:12 final size:11
Alignment explanation
Indices: 95627488--95627525 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
95627478 ATTTATAATA
95627488 TAAAA-AAAAT
1 TAAAATAAAAT
*
95627498 TAATATAAAAT
1 TAAAATAAAAT
95627509 TAAAATTAAAAT
1 TAAAA-TAAAAT
95627521 TAAAA
1 TAAAA
95627526 ATATTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 4 0.17
11 9 0.38
12 11 0.46
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAATAAAAT
Found at i:95627534 original size:6 final size:6
Alignment explanation
Indices: 95627493--95627525 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
95627483 TAATATAAAA
*
95627493 AAAATT AATA-T AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
95627526 ATATTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:95632313 original size:23 final size:23
Alignment explanation
Indices: 95632283--95632330 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
95632273 GACAGGTACA
95632283 AAAAAACCATTTCAAACATTTCT
1 AAAAAACCATTTCAAACATTTCT
95632306 AAAAAACCATTTCAAACATTTCT
1 AAAAAACCATTTCAAACATTTCT
95632329 AA
1 AA
95632331 CTTTCCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAAACCATTTCAAACATTTCT
Found at i:95633132 original size:2 final size:2
Alignment explanation
Indices: 95633127--95633164 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
95633117 TATATGCGTG
95633127 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
95633165 TAGTGAATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:95635742 original size:21 final size:21
Alignment explanation
Indices: 95635718--95635758 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
95635708 CGTTGATCAC
95635718 CTTGCTCTTG-TGTTGTCACTA
1 CTTGCTC-TGATGTTGTCACTA
*
95635739 CTTGTTCTGATGTTGTCACT
1 CTTGCTCTGATGTTGTCACT
95635759 GATCGGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.10, C:0.22, G:0.20, T:0.49
Consensus pattern (21 bp):
CTTGCTCTGATGTTGTCACTA
Found at i:95637739 original size:2 final size:2
Alignment explanation
Indices: 95637732--95637758 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
95637722 ACATTAAAAT
95637732 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
95637759 CACAACTATT
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:95640698 original size:16 final size:16
Alignment explanation
Indices: 95640677--95640707 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
95640667 GCTCATGCAG
*
95640677 ATTCATGCACGTAAGA
1 ATTCATGCACATAAGA
95640693 ATTCATGCACATAAG
1 ATTCATGCACATAAG
95640708 TTGTCCAGGT
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:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (16 bp):
ATTCATGCACATAAGA
Found at i:95645255 original size:16 final size:16
Alignment explanation
Indices: 95645234--95645264 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
95645224 GCTCATGCAG
*
95645234 ATTCATGCACGTAAGA
1 ATTCATGCACATAAGA
95645250 ATTCATGCACATAAG
1 ATTCATGCACATAAG
95645265 TTGTCCGGGT
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:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (16 bp):
ATTCATGCACATAAGA
Found at i:95647654 original size:2 final size:2
Alignment explanation
Indices: 95647647--95647673 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
95647637 GGCTAACAGG
95647647 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
95647674 AATGTAACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:95649616 original size:80 final size:80
Alignment explanation
Indices: 95649532--95649680 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
95649522 TATGGTAACC
* * * *
95649532 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
95649596 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
95649612 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
95649677 CCGG
66 CCGG
95649681 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:95649622 original size:40 final size:38
Alignment explanation
Indices: 95649573--95649680 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
95649563 ATCACGATTT
*
95649573 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
95649613 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
95649653 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
95649681 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:95657733 original size:80 final size:80
Alignment explanation
Indices: 95657649--95657797 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
95657639 TATGGTAACC
* * * *
95657649 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
95657713 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
95657729 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
95657794 CCGG
66 CCGG
95657798 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:95657739 original size:40 final size:38
Alignment explanation
Indices: 95657690--95657797 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
95657680 ATCACGATTT
*
95657690 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
95657730 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
95657770 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
95657798 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:95661753 original size:18 final size:18
Alignment explanation
Indices: 95661728--95661816 Score: 124
Period size: 18 Copynumber: 4.9 Consensus size: 18
95661718 ACCGTTTACA
*
95661728 GTACTATTCACGTATATG
1 GTACTATTCACGTATACG
*
95661746 GCACTATTCACGTATACG
1 GTACTATTCACGTATACG
*
95661764 GTACTATTCATGTATACG
1 GTACTATTCACGTATACG
*
95661782 ATACTATTCACGTATACG
1 GTACTATTCACGTATACG
* *
95661800 ATACTGTTCACGTATAC
1 GTACTATTCACGTATAC
95661817 CGTAGTTGGG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (18 bp):
GTACTATTCACGTATACG
Found at i:95668024 original size:98 final size:98
Alignment explanation
Indices: 95667855--95668049 Score: 320
Period size: 98 Copynumber: 2.0 Consensus size: 98
95667845 GCCATTGTGC
* * * * *
95667855 ACGGTGGCTGGCGACGGTCGCCAGGGCCAATCAGTGGCGGAGACTGGCTGGAGCCTTCGCCGGAG
1 ACGGTGGCCGACGACGGTCGCCACGGCCAATCAGTGGCAGAGACTGGCCGGAGCCTTCGCCGGAG
95667920 CACGCACCTGCAGAGAGAAAACAAAAGAACAAA
66 CACGCACCTGCAGAGAGAAAACAAAAGAACAAA
95667953 ACGGTGGCCGACGACGGTCGCCGACGG-CAATCAGTGGCAGAGACTGGCCGGAGCCTTCGCCGGA
1 ACGGTGGCCGACGACGGTCGCC-ACGGCCAATCAGTGGCAGAGACTGGCCGGAGCCTTCGCCGGA
*
95668017 GCACGCACCTGCAGAGAGAAAACAGAAGAACAA
65 GCACGCACCTGCAGAGAGAAAACAAAAGAACAA
95668050 TTTTTTTTTT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 87 0.97
99 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.34, T:0.09
Consensus pattern (98 bp):
ACGGTGGCCGACGACGGTCGCCACGGCCAATCAGTGGCAGAGACTGGCCGGAGCCTTCGCCGGAG
CACGCACCTGCAGAGAGAAAACAAAAGAACAAA
Found at i:95668522 original size:3 final size:3
Alignment explanation
Indices: 95668506--95669250 Score: 232
Period size: 3 Copynumber: 250.7 Consensus size: 3
95668496 TATTATCCAA
* *
95668506 ATT ATT GTT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * ** *
95668554 ATT ATT ATT ATT ATT ATT ACC ATT A-T ATTT GTT GCT ATT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT
* * * *
95668599 ATT ATT ATT TTT ATT ACTT CCATT ATT ATC ATT A-C ATT TTT CATGT
1 ATT ATT ATT ATT ATT A-TT --ATT ATT ATT ATT ATT ATT ATT -AT-T
* * * * *
95668645 CTT ATT CCTT TTCT ATT ATT ATTT ATT A-T ATT GTAT ATT ATT ATT A-G
1 ATT ATT -ATT AT-T ATT ATT A-TT ATT ATT ATT AT-T ATT ATT ATT ATT
* * * * * * *
95668692 ATT ATC A-T GTT ATT ATT -TCT -TT CTCT TTT ATT GTG A-T CTT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT ATT ATT ATT
** ** * * * *
95668735 ATT ATT ACC GCT ATT ACT ATT TTT ATT TTT ATT -TT TTT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* ** * * * * * * **
95668781 -TT ACT ACC AGT GTC GTT ATT -GT ACT ATT ATT ATT ACC ATT -TT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
95668825 A-T ATT -TCT CATT -TT -TT ACT A-C ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT AT-T -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
95668867 ATT ATT ATT ATT ATT ATT ATT ATT TTT ACT ATCT AAT A-T ATT ACT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
* * * *
95668912 A-T ACCTT ATT ATT ATT ATT ATT ACT ATT -GT ATT AGT ACT ATT ATT
1 ATT A--TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
95668957 ATT A-C ATT -TT CTT -TT -TT ATT ACT ATT ACT A-T ATT ACTT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT
* * * * * *
95668997 ATCT -TT ATT -TCCT ATT ATT GTT ATC ATT ATT ATT AAT ACT AAT ATA
1 AT-T ATT ATT AT--T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
95669043 AAT ATT CTT ATT ATT ACTT -TT ATT ATT ATC ATT AGT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
95669088 -TGT ACT ACT ATT ATT ATT ACT ATC ATT -TAT ATT -TC ATT ATT ATT
1 AT-T ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
* * * *
95669132 ATT AGT GTT ACT ATT -TCT ATT ATT GTT -TT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
95669176 ATT ATT ATT ATT ATT ATTT ATTT GTT ATT ATG GTT GTT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
*
95669223 ATT ACCTC ATT ATTT ATT ATT -TT ATT AT
1 ATT A--TT ATT A-TT ATT ATT ATT ATT AT
95669251 CGTCTATTAG
Statistics
Matches: 548, Mismatches: 132, Indels: 124
0.68 0.16 0.15
Matches are distributed among these distances:
2 55 0.10
3 447 0.82
4 36 0.07
5 9 0.02
6 1 0.00
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Done.