Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3
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: 6198200
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 200361 characters in sequence are not A, C, G, or T
File 18 of 32
Found at i:2775943 original size:15 final size:16
Alignment explanation
Indices: 2775913--2775947 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
2775903 AAGTGGTGTT
2775913 AAAGAAGAAGAAGAAG
1 AAAGAAGAAGAAGAAG
*
2775929 AAAGAATAA-AAGAAG
1 AAAGAAGAAGAAGAAG
2775944 AAAG
1 AAAG
2775948 CATTGGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (16 bp):
AAAGAAGAAGAAGAAG
Found at i:2777116 original size:3 final size:3
Alignment explanation
Indices: 2777110--2777162 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
2777100 GCGGAAAAAA
* *
2777110 AAT AAT AAAG AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2777156 AAT AAT A
1 AAT AAT A
2777163 GTAGGGCTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 43 0.96
4 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2781359 original size:26 final size:26
Alignment explanation
Indices: 2781333--2781385 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
2781323 ATATTTTTAT
*
2781333 ATTAATATTTATATATTTTATTATATA
1 ATTAA-ATTTACATATTTTATTATATA
2781360 ATTAAATTTACATATTTTATTA-ATA
1 ATTAAATTTACATATTTTATTATATA
2781385 A
1 A
2781386 AACAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.16
26 16 0.64
27 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
ATTAAATTTACATATTTTATTATATA
Found at i:2781890 original size:16 final size:17
Alignment explanation
Indices: 2781871--2781937 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
2781861 ATATGATAAC
2781871 TATATTTA-AAATATTT
1 TATATTTACAAATATTT
* *
2781887 TATATTTATAAAAATTT
1 TATATTTACAAATATTT
* * *
2781904 TA-A-ATATAAATAATT
1 TATATTTACAAATATTT
2781919 TATATTATACAAA-ATTT
1 TATATT-TACAAATATTT
2781936 TA
1 TA
2781938 AATATTTATA
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
15 11 0.28
16 10 0.25
17 14 0.35
18 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (17 bp):
TATATTTACAAATATTT
Found at i:2781913 original size:15 final size:15
Alignment explanation
Indices: 2781893--2781942 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
2781883 ATTTTATATT
2781893 TATAAAAATTTTAAA
1 TATAAAAATTTTAAA
*
2781908 TATAAATAA-TTTATAT
1 TATAAA-AATTTTA-AA
2781924 TATACAAAATTTTAAA
1 TATA-AAAATTTTAAA
2781940 TAT
1 TAT
2781943 TTATATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
15 10 0.34
16 13 0.45
17 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAAAAATTTTAAA
Found at i:2781915 original size:32 final size:32
Alignment explanation
Indices: 2781879--2781960 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 32
2781869 ACTATATTTA
*
2781879 AAATATTTTATATTTATA-AAAATTTTAAATAT
1 AAATAATTTATA-TTATACAAAATTTTAAATAT
2781911 AAATAATTTATATTATACAAAATTTTAAATAT
1 AAATAATTTATATTATACAAAATTTTAAATAT
** *
2781943 TTATATATTTTTATTATA
1 AAATA-ATTTATATTATA
2781961 TTTGTATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
31 5 0.11
32 28 0.64
33 11 0.25
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
AAATAATTTATATTATACAAAATTTTAAATAT
Found at i:2782451 original size:18 final size:18
Alignment explanation
Indices: 2782428--2782465 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2782418 TTAATTTTTT
2782428 AATAATAATAATA-AGAAC
1 AATAATAAT-ATACAGAAC
*
2782446 AATAATAGTATACAGAAC
1 AATAATAATATACAGAAC
2782464 AA
1 AA
2782466 AAAGCTAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.21
Consensus pattern (18 bp):
AATAATAATATACAGAAC
Found at i:2786984 original size:19 final size:19
Alignment explanation
Indices: 2786960--2787002 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2786950 TTTGTCAAAT
2786960 TTTTTAAATAAATTT-TATA
1 TTTTT-AATAAATTTATATA
* *
2786979 TTTTTATTATATTTATATA
1 TTTTTAATAAATTTATATA
2786998 TTTTT
1 TTTTT
2787003 TATTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTAATAAATTTATATA
Found at i:2787017 original size:20 final size:19
Alignment explanation
Indices: 2786971--2787016 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
2786961 TTTTAAATAA
2786971 ATTT-TATATTTTTATTAT
1 ATTTATATATTTTTATTAT
2786989 ATTTATATATTTTTTATT-T
1 ATTTATATA-TTTTTATTAT
2787008 -TTTATATAT
1 ATTTATATAT
2787017 AAAAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 1 0.04
18 12 0.46
19 5 0.19
20 8 0.31
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTATATATTTTTATTAT
Found at i:2794742 original size:11 final size:11
Alignment explanation
Indices: 2794726--2794750 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2794716 CAACTACTCA
2794726 TATATATTTTT
1 TATATATTTTT
2794737 TATATATTTTT
1 TATATATTTTT
2794748 TAT
1 TAT
2794751 TCACGTAATA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATATATTTTT
Found at i:2800721 original size:1 final size:1
Alignment explanation
Indices: 2800715--2800740 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2800705 ATGTCACCAA
2800715 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
2800741 AAAAAATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2806731 original size:2 final size:2
Alignment explanation
Indices: 2806718--2806763 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2806708 AATCTAACTT
* *
2806718 TC TC TG TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2806760 TC TC
1 TC TC
2806764 GATCGATTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.46, G:0.02, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2816307 original size:4 final size:4
Alignment explanation
Indices: 2816298--2816322 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2816288 GAAAAAATAT
2816298 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
2816323 AAAATTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:2820153 original size:20 final size:21
Alignment explanation
Indices: 2820114--2820153 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2820104 TTAAAAAAGA
*
2820114 AAATCAAATATCAATAAAATC
1 AAATCAAATATAAATAAAATC
*
2820135 AAATC-AATATAAATTAAAT
1 AAATCAAATATAAATAAAAT
2820154 TCCAAATTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCAAATATAAATAAAATC
Found at i:2820806 original size:22 final size:23
Alignment explanation
Indices: 2820776--2820821 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
2820766 AGTTAATTAA
* *
2820776 ATATTAATTTAATTAAA-AATAT
1 ATATAAATTAAATTAAATAATAT
2820798 ATATAAATTAAATTAAATAATAT
1 ATATAAATTAAATTAAATAATAT
2820821 A
1 A
2820822 ATGAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATATAAATTAAATTAAATAATAT
Found at i:2820831 original size:21 final size:21
Alignment explanation
Indices: 2820786--2820833 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 21
2820776 ATATTAATTT
2820786 AATTAAAAATATATATAAATTA
1 AATTAAAAATATATATAAA-TA
2820808 AATTAAATAATATA-ATGAAA-A
1 AATTAAA-AATATATAT-AAATA
2820829 AATTA
1 AATTA
2820834 TATGCACGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.25
22 9 0.38
23 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AATTAAAAATATATATAAATA
Found at i:2821172 original size:13 final size:14
Alignment explanation
Indices: 2821119--2821194 Score: 54
Period size: 13 Copynumber: 5.6 Consensus size: 14
2821109 TAATATATTT
*
2821119 TTTA-ATATTTACA
1 TTTATATATTTATA
2821132 -TTATA-ATATTATA
1 TTTATATAT-TTATA
* *
2821145 TTTGTATGATATATA
1 TTTATAT-ATTTATA
2821160 TTTAT-TATTTATA
1 TTTATATATTTATA
*
2821173 -TGATATATTTATTA
1 TTTATATATTTA-TA
2821187 TTTATATA
1 TTTATATA
2821195 ATATATATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
12 8 0.17
13 17 0.35
14 7 0.15
15 14 0.29
16 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (14 bp):
TTTATATATTTATA
Found at i:2821174 original size:22 final size:22
Alignment explanation
Indices: 2821149--2821202 Score: 85
Period size: 20 Copynumber: 2.5 Consensus size: 22
2821139 ATTATATTTG
2821149 TATGATATATATTTATTATTTA
1 TATGATATATATTTATTATTTA
2821171 TATG--ATATATTTATTATTTA
1 TATGATATATATTTATTATTTA
*
2821191 TATAATATATAT
1 TATGATATATAT
2821203 AAATACAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 19 0.66
22 10 0.34
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
TATGATATATATTTATTATTTA
Found at i:2821316 original size:33 final size:34
Alignment explanation
Indices: 2821279--2821342 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
2821269 AAATCAAAGA
*
2821279 TAAGTTTATTTTTTAAAATTGAT-TTTTTTTGTT
1 TAAGTTTATTTTTTAAAATTAATATTTTTTTGTT
*
2821312 TAAGTTTATTTTTTAAACTTAATATTTTTTT
1 TAAGTTTATTTTTTAAAATTAATATTTTTTT
2821343 AAAAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.27, C:0.02, G:0.06, T:0.66
Consensus pattern (34 bp):
TAAGTTTATTTTTTAAAATTAATATTTTTTTGTT
Found at i:2822080 original size:16 final size:16
Alignment explanation
Indices: 2822061--2822118 Score: 80
Period size: 16 Copynumber: 3.6 Consensus size: 16
2822051 TTTAGGTCAT
*
2822061 TTTTTATTTTAAGTTA
1 TTTTAATTTTAAGTTA
*
2822077 TTTTAATTTTAAATTA
1 TTTTAATTTTAAGTTA
* *
2822093 TTTTAAATTCAAGTTA
1 TTTTAATTTTAAGTTA
2822109 TTTTAATTTT
1 TTTTAATTTT
2822119 TGATCGTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (16 bp):
TTTTAATTTTAAGTTA
Found at i:2822269 original size:24 final size:23
Alignment explanation
Indices: 2822225--2822269 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
2822215 AAATATTTTA
*
2822225 ATTTAGATCATTTTAGATTAATT
1 ATTTAGATCATTTAAGATTAATT
* *
2822248 ATTTAGGTCAATTTAAGTTTAA
1 ATTTAGATC-ATTTAAGATTAA
2822270 ATCGTTGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (23 bp):
ATTTAGATCATTTAAGATTAATT
Found at i:2822409 original size:6 final size:5
Alignment explanation
Indices: 2822380--2822422 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
2822370 TTAACTTTTT
2822380 AATTA AATTA AATTA AATTAA AATATA AA-TA AATT- AATTA AAT
1 AATTA AATTA AATTA AATT-A AAT-TA AATTA AATTA AATTA AAT
2822423 CTTTTAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
4 8 0.24
5 18 0.53
6 7 0.21
7 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATTA
Found at i:2825101 original size:17 final size:17
Alignment explanation
Indices: 2825079--2825163 Score: 70
Period size: 16 Copynumber: 5.0 Consensus size: 17
2825069 CGATAAAAAT
2825079 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
2825096 ATTTTA-ATGTA-ATAA
1 ATTTTATATTTATATAA
*
2825111 TAATTTATA-TTATATAA
1 -ATTTTATATTTATATAA
*
2825128 ATTTTAAATATTTATAT-T
1 ATTTT--ATATTTATATAA
*
2825146 ATTTTTTATATTATATAA
1 ATTTTATAT-TTATATAA
2825164 TATATTAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 15
0.71 0.09 0.20
Matches are distributed among these distances:
15 4 0.08
16 18 0.34
17 17 0.32
18 8 0.15
19 6 0.11
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:2825832 original size:25 final size:24
Alignment explanation
Indices: 2825804--2825850 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2825794 ATATTAATTT
**
2825804 TATTATTTGTATAATATAAAATACA
1 TATTATTTAAATAA-ATAAAATACA
*
2825829 TATTTTTTAAATAAATAAAATA
1 TATTATTTAAATAAATAAAATA
2825851 ATAAATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
TATTATTTAAATAAATAAAATACA
Found at i:2833627 original size:16 final size:16
Alignment explanation
Indices: 2833606--2833636 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2833596 TTTGATCAAA
*
2833606 TAATTAATTTAAATTG
1 TAATTAACTTAAATTG
2833622 TAATTAACTTAAATT
1 TAATTAACTTAAATT
2833637 TTAAATATTA
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:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (16 bp):
TAATTAACTTAAATTG
Found at i:2833636 original size:22 final size:21
Alignment explanation
Indices: 2833607--2833662 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
2833597 TTGATCAAAT
2833607 AATT-AATTTAAAT-TGTAATTA
1 AATTAAATTTAAATAT-TAA-TA
*
2833628 ACTTAAATTTTAAATATTAATA
1 AATTAAA-TTTAAATATTAATA
2833650 AATTAAATTTAAA
1 AATTAAATTTAAA
2833663 ATAATTCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 9 0.30
22 10 0.33
23 10 0.33
24 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTAAATTTAAATATTAATA
Found at i:2833639 original size:23 final size:22
Alignment explanation
Indices: 2833613--2833665 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2833603 AAATAATTAA
*
2833613 TTTAAAT-TGTAATTAACTTAAAT
1 TTTAAATAT-TAA-TAAATTAAAT
2833636 TTTAAATATTAATAAATTAAAT
1 TTTAAATATTAATAAATTAAAT
*
2833658 TTAAAATA
1 TTTAAATA
2833666 ATTCAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 16 0.59
23 10 0.37
24 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
TTTAAATATTAATAAATTAAAT
Found at i:2833664 original size:22 final size:22
Alignment explanation
Indices: 2833630--2833682 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2833620 TGTAATTAAC
*
2833630 TTAAATTTTAAAT-ATTAATAAA
1 TTAAATTTAAAATAATTAA-AAA
* *
2833652 TTAAATTTAAAATAATTCAAAT
1 TTAAATTTAAAATAATTAAAAA
2833674 TTAAATTTA
1 TTAAATTTA
2833683 CTCAACTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TTAAATTTAAAATAATTAAAAA
Found at i:2833679 original size:15 final size:15
Alignment explanation
Indices: 2833637--2833678 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
2833627 AACTTAAATT
*
2833637 TTAAATATTAATA-AA
1 TTAAAT-TTAAAATAA
2833652 TTAAATTTAAAATAA
1 TTAAATTTAAAATAA
2833667 TTCAAATTTAAA
1 TT-AAATTTAAA
2833679 TTTACTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 10 0.42
16 9 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAATTTAAAATAA
Found at i:2838934 original size:17 final size:17
Alignment explanation
Indices: 2838894--2838945 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
2838884 AATTTTTTTG
*
2838894 ATAAAAATATTAATTTAA
1 ATAAAAATAAT-ATTTAA
2838912 AT-AAAATAATATTTAA
1 ATAAAAATAATATTTAA
* *
2838928 TTAAAAAT-ATATTAAA
1 ATAAAAATAATATTTAA
2838944 AT
1 AT
2838946 TTAATTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 15 0.52
17 12 0.41
18 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAAAATAATATTTAA
Found at i:2838947 original size:22 final size:20
Alignment explanation
Indices: 2838922--2838969 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
2838912 ATAAAATAAT
2838922 ATTTAATTAAAAATATATTAAA
1 ATTTAATTAAAAAT-T-TTAAA
*
2838944 ATTTAATTTAAAATTTTAAA
1 ATTTAATTAAAAATTTTAAA
*
2838964 ACTTAA
1 ATTTAA
2838970 ATTCAATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 1 0.04
22 13 0.54
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAATTAAAAATTTTAAA
Found at i:2839074 original size:26 final size:26
Alignment explanation
Indices: 2839045--2839095 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
2839035 TATTATGTAA
2839045 ATATTAAAAAATATATTAAAATATTT
1 ATATTAAAAAATATATTAAAATATTT
** * *
2839071 ATATTTTAAAATTTATTAAATTATT
1 ATATTAAAAAATATATTAAAATATT
2839096 AAAAATTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATTAAAAAATATATTAAAATATTT
Found at i:2840021 original size:21 final size:22
Alignment explanation
Indices: 2839986--2840036 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
2839976 GTGTTTGAAT
*
2839986 ATTTAAAAAATTATTTTTAAAA
1 ATTTTAAAAATTATTTTTAAAA
*
2840008 ATTTTAAAAA-TATTTTTGAAA
1 ATTTTAAAAATTATTTTTAAAA
2840029 ATTTTAAA
1 ATTTTAAA
2840037 CTTTTTAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
ATTTTAAAAATTATTTTTAAAA
Found at i:2845223 original size:2 final size:2
Alignment explanation
Indices: 2845216--2845246 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2845206 AAGACTGAGC
*
2845216 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2845247 AATTTTGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2848841 original size:2 final size:2
Alignment explanation
Indices: 2848836--2848870 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2848826 TCTCTCTCTC
2848836 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2848871 TTCTGCATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2850608 original size:2 final size:2
Alignment explanation
Indices: 2850601--2850650 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
2850591 GCTGCACTCA
* *
2850601 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T- TT TC TC TC AC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
2850642 TC TT TC TC T
1 TC TC TC TC T
2850651 GATATGATCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:2851167 original size:16 final size:15
Alignment explanation
Indices: 2851139--2851169 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2851129 ATTGTAATTT
2851139 TTTAAAAAATATATA
1 TTTAAAAAATATATA
2851154 TTTAAAATAATATATA
1 TTTAAAA-AATATATA
2851170 ATTAGATGTT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTTAAAAAATATATA
Found at i:2855645 original size:19 final size:18
Alignment explanation
Indices: 2855621--2855656 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2855611 CATTAAAAAA
2855621 TAATTTAAATATAATATAT
1 TAATTTAAATA-AATATAT
*
2855640 TAATTTATATAAATATA
1 TAATTTAAATAAATATA
2855657 AAATATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTTAAATAAATATAT
Found at i:2856249 original size:2 final size:2
Alignment explanation
Indices: 2856242--2856271 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2856232 GAAAACACCT
2856242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2856272 CATACAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2856471 original size:10 final size:9
Alignment explanation
Indices: 2856456--2856516 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 9
2856446 ATAGACAGAG
2856456 ATTTATTTGT
1 ATTTATTT-T
2856466 ATTTA-TTT
1 ATTTATTTT
2856474 ATTTATTTT
1 ATTTATTTT
2856483 AAAATTTATTTGT
1 ---ATTTATTT-T
2856496 ATTTATTTTAT
1 ATTTA-TTT-T
2856507 ATTTATTTT
1 ATTTATTTT
2856516 A
1 A
2856517 ATATTTAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
8 6 0.14
9 7 0.16
10 13 0.30
11 9 0.20
12 8 0.18
13 1 0.02
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (9 bp):
ATTTATTTT
Found at i:2856492 original size:30 final size:32
Alignment explanation
Indices: 2856456--2856523 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 32
2856446 ATAGACAGAG
2856456 ATTTATTTGTATTTA-TT-TATTTATTTTAAA
1 ATTTATTTGTATTTATTTATATTTATTTTAAA
*
2856486 ATTTATTTGTATTTATTTTATATTTATTTTAAT
1 ATTTATTTGTATTTA-TTTATATTTATTTTAAA
2856519 ATTTA
1 ATTTA
2856524 AATTATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 15 0.44
32 2 0.06
33 17 0.50
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (32 bp):
ATTTATTTGTATTTATTTATATTTATTTTAAA
Found at i:2856498 original size:22 final size:20
Alignment explanation
Indices: 2856466--2856533 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
2856456 ATTTATTTGT
2856466 ATTTA-TTTATTTATTTTAAA
1 ATTTATTTTATTTATTTT-AA
*
2856486 ATTTATTTGTATTTATTTTAT
1 ATTTATTT-TATTTATTTTAA
*
2856507 ATTTATTTTA-ATA-TTTAA
1 ATTTATTTTATTTATTTTAA
2856525 ATTATATTT
1 ATT-TATTT
2856534 AAATTTAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
18 7 0.17
19 7 0.17
20 7 0.17
21 11 0.26
22 10 0.24
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (20 bp):
ATTTATTTTATTTATTTTAA
Found at i:2856511 original size:11 final size:11
Alignment explanation
Indices: 2856473--2856534 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
2856463 TGTATTTATT
2856473 TATTTATTTTAA
1 TATTTATTTT-A
* *
2856485 AATTTA-TTTG
1 TATTTATTTTA
2856495 TATTTATTTTA
1 TATTTATTTTA
2856506 TATTTATTTTAA
1 TATTTATTTT-A
**
2856518 TATTTAAATTA
1 TATTTATTTTA
2856529 TATTTA
1 TATTTA
2856535 AATTTAGTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
10 5 0.12
11 23 0.55
12 14 0.33
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTATTTTA
Found at i:2859304 original size:6 final size:6
Alignment explanation
Indices: 2859293--2859324 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2859283 CACCGATGCT
2859293 TCACCA TCACCA TCACCA TCACCA TCACCA TC
1 TCACCA TCACCA TCACCA TCACCA TCACCA TC
2859325 GCAGTCTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (6 bp):
TCACCA
Found at i:2862553 original size:2 final size:2
Alignment explanation
Indices: 2862536--2862572 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2862526 TAGAAAAGTC
*
2862536 AT AT GT AT AT -T 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
2862573 TGTTCCTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2866867 original size:11 final size:11
Alignment explanation
Indices: 2866851--2866947 Score: 66
Period size: 10 Copynumber: 9.3 Consensus size: 11
2866841 TTAATTTATG
2866851 TATTTATATTA
1 TATTTATATTA
2866862 TATTTAT-TTA
1 TATTTATATTA
2866872 T-TTTATATTA
1 TATTTATATTA
*
2866882 T-TATA-ATTA
1 TATTTATATTA
* *
2866891 TATTTAAAATA
1 TATTTATATTA
2866902 T-TTTATATT-
1 TATTTATATTA
*
2866911 TATTT-TAATTT
1 TATTTAT-ATTA
*
2866922 TA-ATATATTAA
1 TATTTATATT-A
2866933 TAATTTATATTA
1 T-ATTTATATTA
2866945 TAT
1 TAT
2866948 AAAATTTAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 20
0.71 0.08 0.21
Matches are distributed among these distances:
9 12 0.18
10 30 0.44
11 17 0.25
12 3 0.04
13 6 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTATATTA
Found at i:2866868 original size:6 final size:6
Alignment explanation
Indices: 2866851--2866997 Score: 54
Period size: 5 Copynumber: 26.5 Consensus size: 6
2866841 TTAATTTATG
*
2866851 TATTTA TA-TTA TA-TT- TATTTA T-TTTA TATTATTA TAATTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TA-T-TTA TATTTA TATTTA
** * *
2866897 -AAATA T-TTTA TATTTA T-TTTA -ATTT- TA-ATA TATTAA TAATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA T-ATTTA
* * ** * *
2866940 TA-TTA TA-TAA AATTTA -AAATA TTTTTA TATTTA TA-TCA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
*
2866984 T-TTTA TTTTTA TAT
1 TATTTA TATTTA TAT
2866998 CATAATATAT
Statistics
Matches: 103, Mismatches: 22, Indels: 32
0.66 0.14 0.20
Matches are distributed among these distances:
4 3 0.03
5 50 0.49
6 39 0.38
7 6 0.06
8 5 0.05
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (6 bp):
TATTTA
Found at i:2866871 original size:15 final size:15
Alignment explanation
Indices: 2866851--2866915 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
2866841 TTAATTTATG
2866851 TATTTATATTATATT
1 TATTTATATTATATT
*
2866866 TATTTATTTTATA-T
1 TATTTATATTATATT
2866880 TA-TTATAATTATATT
1 TATTTAT-ATTATATT
** *
2866895 TAAAATATTTTATATT
1 T-ATTTATATTATATT
2866911 TATTT
1 TATTT
2866916 TAATTTTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
13 4 0.10
14 8 0.20
15 16 0.40
16 9 0.22
17 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTATATTATATT
Found at i:2866878 original size:20 final size:19
Alignment explanation
Indices: 2866840--2866882 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
2866830 AAGAAGTAAA
2866840 ATTA-ATTTATGTATTTAT
1 ATTATATTTATGTATTTAT
*
2866858 ATTATATTTATTTATTTTAT
1 ATTATATTTATGTA-TTTAT
2866878 ATTAT
1 ATTAT
2866883 TATAATTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.18
19 8 0.36
20 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
ATTATATTTATGTATTTAT
Found at i:2866926 original size:25 final size:26
Alignment explanation
Indices: 2866857--2866940 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 26
2866847 TATGTATTTA
2866857 TATTATATTTA-TTT-ATTTT-ATAT
1 TATTATATTTATTTTAATTTTAATAT
*
2866880 TATTATAATTATATTTAA----AATAT
1 TATTATATTTAT-TTTAATTTTAATAT
2866903 T-TTATATTTATTTTAATTTTAATA-
1 TATTATATTTATTTTAATTTTAATAT
2866927 TATTAATAATTTAT
1 TATT-AT-ATTTAT
2866941 ATTATATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
21 5 0.10
22 9 0.19
23 15 0.31
24 1 0.02
25 9 0.19
26 3 0.06
27 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TATTATATTTATTTTAATTTTAATAT
Found at i:2867007 original size:60 final size:59
Alignment explanation
Indices: 2866851--2867007 Score: 153
Period size: 60 Copynumber: 2.7 Consensus size: 59
2866841 TTAATTTATG
* * *
2866851 TATTTATATTATATTTA-TTTA-TTTTATATTATTATA-ATTATATTTAAAATATTTTA
1 TATTTATATTATATTTATTTTATTTTTATATTATAATATATAAAATTTAAAATATTTTA
* ** * * *
2866907 TATTTATTTTA-ATTT-TAATATATTAATAATTTATATTATATAAAATTTAAAATATTTTTA
1 TATTTATATTATATTTATTTTATTTTTAT-A-TTATAATATATAAAATTTAAAATA-TTTTA
* *
2866967 TATTTATATCATATTTATTTTATTTTTATATCATAATATAT
1 TATTTATATTATATTTATTTTATTTTTATATTATAATATAT
2867008 TTTGATTATT
Statistics
Matches: 76, Mismatches: 17, Indels: 12
0.72 0.16 0.11
Matches are distributed among these distances:
55 6 0.08
56 14 0.18
57 1 0.01
58 6 0.08
59 13 0.17
60 23 0.30
61 5 0.07
62 8 0.11
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (59 bp):
TATTTATATTATATTTATTTTATTTTTATATTATAATATATAAAATTTAAAATATTTTA
Found at i:2867008 original size:23 final size:23
Alignment explanation
Indices: 2866957--2867010 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
2866947 TAAAATTTAA
2866957 AATAT-TTTTATATTTATATCAT
1 AATATATTTTATATTTATATCAT
* *
2866979 -ATTTATTTTATTTTTATATCAT
1 AATATATTTTATATTTATATCAT
2867001 AATATATTTT
1 AATATATTTT
2867011 GATTATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.11
22 16 0.59
23 8 0.30
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (23 bp):
AATATATTTTATATTTATATCAT
Found at i:2877216 original size:27 final size:27
Alignment explanation
Indices: 2877176--2877227 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
2877166 AAAATAAAAT
2877176 AAAATAATAAAAAATAATAATTTTATA
1 AAAATAATAAAAAATAATAATTTTATA
*
2877203 AAAATAA-AATAAAATAATTATTTTA
1 AAAATAATAA-AAAATAATAATTTTA
2877228 AAATTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AAAATAATAAAAAATAATAATTTTATA
Found at i:2877218 original size:24 final size:25
Alignment explanation
Indices: 2877181--2877230 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
2877171 AAAATAAAAT
2877181 AATAAAAAATAATAATT-TTATAAA
1 AATAAAAAATAATAATTATTATAAA
*
2877205 AATAAAATAA-AATAATTATTTTAAA
1 AATAAAA-AATAATAATTATTATAAA
2877230 A
1 A
2877231 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
AATAAAAAATAATAATTATTATAAA
Found at i:2877252 original size:35 final size:36
Alignment explanation
Indices: 2877194--2877261 Score: 113
Period size: 34 Copynumber: 1.9 Consensus size: 36
2877184 AAAAAATAAT
2877194 AATTTTATAAAAATAAAATAAAAT-AATTATTTTAA
1 AATTTTATAAAAATAAAATAAAATAAATTATTTTAA
2877229 AATTTT-TAAAAATAAAATCAAAATAAATTATTT
1 AATTTTATAAAAATAAAAT-AAAATAAATTATTT
2877262 AATAAACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 12 0.39
35 11 0.35
36 8 0.26
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (36 bp):
AATTTTATAAAAATAAAATAAAATAAATTATTTTAA
Found at i:2877263 original size:35 final size:35
Alignment explanation
Indices: 2877161--2877261 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 35
2877151 AAATTTTTAC
* * ***
2877161 TTATTAAAATAAAATAAAATAATAAAAAATAATAATT
1 TTATAAAAATAAAATAAAATAAT-TATTTTAA-AATT
2877198 TTATAAAAATAAAATAAAATAATTATTTTAAAATT
1 TTATAAAAATAAAATAAAATAATTATTTTAAAATT
2877233 TT-TAAAAATAAAATCAAAATAAATTATTT
1 TTATAAAAATAAAAT-AAAAT-AATTATTT
2877262 AATAAACTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
34 12 0.21
35 11 0.19
36 12 0.21
37 22 0.39
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (35 bp):
TTATAAAAATAAAATAAAATAATTATTTTAAAATT
Found at i:2877315 original size:21 final size:22
Alignment explanation
Indices: 2877271--2877318 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 22
2877261 TAATAAACTT
2877271 TATATTTTACAAATTAAATAAA
1 TATATTTTACAAATTAAATAAA
*
2877293 TATATTATTAAAATAATTAAATAAA
1 TATATT-TT-ACA-AATTAAATAAA
2877318 T
1 T
2877319 TCATAATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 2 0.09
24 2 0.09
25 12 0.55
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TATATTTTACAAATTAAATAAA
Found at i:2887418 original size:23 final size:23
Alignment explanation
Indices: 2887388--2887434 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
2887378 TCCAACTAAA
2887388 AAAATGGCAGAATAACAATGTAG
1 AAAATGGCAGAATAACAATGTAG
*
2887411 AAAATGGCAGAATAATAATGTAG
1 AAAATGGCAGAATAACAATGTAG
2887434 A
1 A
2887435 TTAACGCAAT
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:0.53, C:0.06, G:0.21, T:0.19
Consensus pattern (23 bp):
AAAATGGCAGAATAACAATGTAG
Found at i:2893088 original size:41 final size:41
Alignment explanation
Indices: 2893032--2893115 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
2893022 ATTCAAAGAG
2893032 AAAAAAAAATTACGTGAAAGGATTTTTTTTAAAAATTATTA
1 AAAAAAAAATTACGTGAAAGGATTTTTTTTAAAAATTATTA
*
2893073 AAAAAAAAATTACGTGAAAGGATTTTTTTTTAAAATTATTA
1 AAAAAAAAATTACGTGAAAGGATTTTTTTTAAAAATTATTA
2893114 AA
1 AA
2893116 TCCCAAGCTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (41 bp):
AAAAAAAAATTACGTGAAAGGATTTTTTTTAAAAATTATTA
Found at i:2902563 original size:34 final size:34
Alignment explanation
Indices: 2902498--2902681 Score: 244
Period size: 34 Copynumber: 5.4 Consensus size: 34
2902488 TATGGCCTAC
* *
2902498 TTGTTGATTAAAT-GGTGATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * *
2902531 TTGTTGACTAAATGGGAAATTTGATAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
*
2902565 TTGTTGATTAAATGGGAGATTTAGTAGCTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * * *
2902599 TTATTGATTAAATGGGTGATTTGGTGGTTTACCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
* * *
2902633 TTGTTGACTAAATGGGAGATTTGGTAGGTTGCCA
1 TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
2902667 TTGTTGATTAAATGG
1 TTGTTGATTAAATGG
2902682 TGGTTTTTAC
Statistics
Matches: 129, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
33 12 0.09
34 117 0.91
ACGTcount: A:0.27, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TTGTTGATTAAATGGGAGATTTGGTAGCTTACCA
Found at i:2903044 original size:19 final size:19
Alignment explanation
Indices: 2902988--2903050 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2902978 TGGTTGTCGA
**
2902988 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
2903007 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
2903026 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
2903045 GTTACT
1 GGTACT
2903051 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:2907180 original size:34 final size:34
Alignment explanation
Indices: 2907114--2907298 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
2907104 AAGTGGGAGA
* *
2907114 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
2907147 ATTGTTGACTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2907181 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
2907215 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
2907249 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
2907283 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2907299 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:2910920 original size:50 final size:50
Alignment explanation
Indices: 2910856--2911014 Score: 264
Period size: 50 Copynumber: 3.2 Consensus size: 50
2910846 TATACTTAGA
*
2910856 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
2910906 GTCAACAATAATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
2910956 GTCAACAATTACGACCACCTCTCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
2911006 GTCAACAAT
1 GTCAACAAT
2911015 GGCAACAACT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 102 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:2915770 original size:4 final size:4
Alignment explanation
Indices: 2915761--2915791 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2915751 CCGGTCAGTG
*
2915761 ATGA ATGA ATGA ATGA ATGA ATGA ATCA ATG
1 ATGA ATGA ATGA ATGA ATGA ATGA ATGA ATG
2915792 TTTTCTCAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.03, G:0.23, T:0.26
Consensus pattern (4 bp):
ATGA
Found at i:2916129 original size:2 final size:2
Alignment explanation
Indices: 2916122--2916159 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2916112 CTGACAATTT
*
2916122 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2916160 AGAACATTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2916344 original size:3 final size:3
Alignment explanation
Indices: 2916336--2916380 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
2916326 GTTTGCTTCT
2916336 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT
2916381 TGAAAATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2917255 original size:12 final size:11
Alignment explanation
Indices: 2917219--2917268 Score: 50
Period size: 10 Copynumber: 4.5 Consensus size: 11
2917209 AATATTAATA
2917219 TAAAT-TTTTT
1 TAAATATTTTT
2917229 TAAA-ATTTTT
1 TAAATATTTTT
*
2917239 AAAATTATTTTT
1 TAAA-TATTTTT
2917251 TAAATAATTATTT
1 TAAAT-ATT-TTT
2917264 TAAAT
1 TAAAT
2917269 CTAAATAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 12 0.36
11 1 0.03
12 12 0.36
13 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
TAAATATTTTT
Found at i:2917265 original size:13 final size:12
Alignment explanation
Indices: 2917221--2917268 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
2917211 TATTAATATA
*
2917221 AATTTTTTTAA-
1 AATTTTTTAAAT
*
2917232 AATTTTTAAAAT
1 AATTTTTTAAAT
*
2917244 TATTTTTTAAAT
1 AATTTTTTAAAT
2917256 AATTATTTTAAAT
1 AATT-TTTTAAAT
2917269 CTAAATAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 9 0.30
12 13 0.43
13 8 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
AATTTTTTAAAT
Found at i:2917990 original size:2 final size:2
Alignment explanation
Indices: 2917944--2917975 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2917934 GTTTGACGTG
2917944 AT 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
2917976 TTAATGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2918922 original size:28 final size:28
Alignment explanation
Indices: 2918858--2918922 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
2918848 ATTAACGTAG
* *
2918858 AATTAATTA-ATTTTGTATATTTTTATT
1 AATTAATTATATTTTGTATATTTTAATA
**
2918885 AATTTTTTATATTATTG-ATATTTTAATA
1 AATTAATTATATT-TTGTATATTTTAATA
2918913 AATTAATTAT
1 AATTAATTAT
2918923 TAAATTTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 7 0.23
28 20 0.67
29 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (28 bp):
AATTAATTATATTTTGTATATTTTAATA
Found at i:2919118 original size:30 final size:30
Alignment explanation
Indices: 2919077--2919140 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 30
2919067 ATTTAAATGT
2919077 AATATACATAATT-TATATAAATAAAATATAA
1 AATATACATAATTATAT-TAAATAAAA-ATAA
2919108 AATATA-ATAATTATATTAAATAAAAATAA
1 AATATACATAATTATATTAAATAAAAATAA
2919137 AATA
1 AATA
2919141 ATTTTACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 8 0.25
30 15 0.47
31 9 0.28
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (30 bp):
AATATACATAATTATATTAAATAAAAATAA
Found at i:2919134 original size:31 final size:31
Alignment explanation
Indices: 2919077--2919140 Score: 98
Period size: 29 Copynumber: 2.1 Consensus size: 31
2919067 ATTTAAATGT
2919077 AATATACATAATTTATATAAATAAAATATAA
1 AATATACATAATTTATATAAATAAAATATAA
2919108 AATATA-ATAA-TTATATTAAATAAAA-ATAA
1 AATATACATAATTTATA-TAAATAAAATATAA
2919137 AATA
1 AATA
2919141 ATTTTACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 13 0.41
30 13 0.41
31 6 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (31 bp):
AATATACATAATTTATATAAATAAAATATAA
Found at i:2919548 original size:18 final size:21
Alignment explanation
Indices: 2919518--2919564 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
2919508 AAAATAAATA
*
2919518 TAATAATTAATTAT-ATATATTT
1 TAATAATTAA-TATGATAT-TAT
2919540 TAATAATTAATATGATATTAT
1 TAATAATTAATATGATATTAT
2919561 TAAT
1 TAAT
2919565 TATTCATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATAATTAATATGATATTAT
Found at i:2919565 original size:18 final size:18
Alignment explanation
Indices: 2919523--2919567 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2919513 AAATATAATA
*
2919523 ATTAATTATATATATTTT
1 ATTAATTATATATATATT
*
2919541 AATAATTA-ATATGATATT
1 ATTAATTATATAT-ATATT
2919559 ATTAATTAT
1 ATTAATTAT
2919568 TCATGTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTAATTATATATATATT
Found at i:2920042 original size:39 final size:41
Alignment explanation
Indices: 2919991--2920080 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 41
2919981 TTAATTTTTT
*
2919991 TTAATATA-TATACATTTAT-CTTTTAATAATT-AATCAAA
1 TTAATATATTATACATTTATACTTTTAATAATTGAATAAAA
* * *
2920029 TTAATATATTATACATTTATATTTTTAATTATTGATTAAAA
1 TTAATATATTATACATTTATACTTTTAATAATTGAATAAAA
*
2920070 TTAACATATTA
1 TTAATATATTA
2920081 ATTTTTTTAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
38 8 0.18
39 11 0.25
40 10 0.23
41 15 0.34
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (41 bp):
TTAATATATTATACATTTATACTTTTAATAATTGAATAAAA
Found at i:2923570 original size:2 final size:2
Alignment explanation
Indices: 2923563--2923594 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2923553 CAGCTTCAGC
2923563 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2923595 ATACACACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2924695 original size:2 final size:2
Alignment explanation
Indices: 2924688--2924717 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2924678 ATCGCATGAC
2924688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2924718 CACACACAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2925453 original size:2 final size:2
Alignment explanation
Indices: 2925446--2925486 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2925436 CTCATCTCCA
*
2925446 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2925487 GGGAAAAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2925848 original size:32 final size:28
Alignment explanation
Indices: 2925783--2925869 Score: 86
Period size: 32 Copynumber: 3.0 Consensus size: 28
2925773 ATTGTATCTG
* **
2925783 AAATA-TTATATATTTATATAAATAATA
1 AAATATTTATTTATTTATATAAATTTTA
*
2925810 ATATATTAATAATTTATTTTATATAAATTTTA
1 AAATATT--T-ATTTA-TTTATATAAATTTTA
*
2925842 AAATATTTATTTATTTATATTAATTTTA
1 AAATATTTATTTATTTATATAAATTTTA
2925870 TTTTTTTACA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
27 4 0.08
28 15 0.31
29 5 0.10
30 2 0.04
31 4 0.08
32 19 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
AAATATTTATTTATTTATATAAATTTTA
Found at i:2925861 original size:14 final size:15
Alignment explanation
Indices: 2925811--2925893 Score: 55
Period size: 14 Copynumber: 5.5 Consensus size: 15
2925801 TAAATAATAA
2925811 TATATTAATAATTTATTT
1 TATATTAAT--TTTA-TT
* *
2925829 TATATAAATTTTA-A
1 TATATTAATTTTATT
* *
2925843 AATATTTA-TTTATT
1 TATATTAATTTTATT
2925857 TATATTAATTTTATT
1 TATATTAATTTTATT
* *
2925872 T-TTTTACATTATATT
1 TATATTA-ATTTTATT
2925887 TATATTA
1 TATATTA
2925894 TATAAATATA
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
13 4 0.08
14 15 0.30
15 15 0.30
16 8 0.16
18 8 0.16
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATTAATTTTATT
Found at i:2925871 original size:19 final size:20
Alignment explanation
Indices: 2925847--2925892 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
2925837 TTTTAAAATA
*
2925847 TTTATTTATTTATATTA-AT
1 TTTATTTATTTACATTATAT
*
2925866 TTTATTTTTTTACATTATAT
1 TTTATTTATTTACATTATAT
2925886 TTATATT
1 TT-TATT
2925893 ATATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 15 0.65
20 4 0.17
21 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATTTATTTACATTATAT
Found at i:2930480 original size:3 final size:3
Alignment explanation
Indices: 2930472--2930503 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2930462 ATCAAAGCCT
2930472 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2930504 CAACAACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2931241 original size:24 final size:23
Alignment explanation
Indices: 2931210--2931255 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2931200 TATATTAATT
*
2931210 TAAATTT-AATTTATTTTAAAATA
1 TAAATTTAAATTT-TATTAAAATA
2931233 TAAATTTTAAATTTTATTAAAAT
1 TAAA-TTTAAATTTTATTAAAAT
2931256 TTATTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 11 0.55
25 5 0.25
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAAATTTAAATTTTATTAAAATA
Found at i:2931530 original size:72 final size:72
Alignment explanation
Indices: 2931426--2931652 Score: 233
Period size: 72 Copynumber: 3.2 Consensus size: 72
2931416 TGATTTTTTT
* * * *
2931426 AAATATTGAAAA-GAGCCACATTTTTTTATCCAAATCTATTACTCAAACTTTAAATTTTTATG-T
1 AAATATT-AAAACGAACCACAATTTTTTATCCAAATCTATTACTCAAACCTTAAATTTTTATGCA
*
2931489 AATCTGTTA
65 AACCT-TTA
* * *
2931498 AAATATTAAAACGAACCACAATCTTTTGTCCAAATCTATTATTCAAACCTTAAATTTTTATGCAA
1 AAATATTAAAACGAACCACAATTTTTTATCCAAATCTATTACTCAAACCTTAAATTTTTATGCAA
*
2931563 ACCTTTT
66 ACCTTTA
* * * ** **** *
2931570 AAATATTAAAACGAACTACACTTTTTTATCCAAATCCATTTTTCGTGTCTTAAATTTTTATACAA
1 AAATATTAAAACGAACCACAATTTTTTATCCAAATCTATTACTCAAACCTTAAATTTTTATGCAA
* *
2931635 ACCCTTC
66 ACCTTTA
2931642 AAATATTAAAA
1 AAATATTAAAA
2931653 AAACCTACAA
Statistics
Matches: 131, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
71 4 0.03
72 123 0.94
73 4 0.03
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (72 bp):
AAATATTAAAACGAACCACAATTTTTTATCCAAATCTATTACTCAAACCTTAAATTTTTATGCAA
ACCTTTA
Found at i:2936854 original size:11 final size:11
Alignment explanation
Indices: 2936840--2936911 Score: 55
Period size: 11 Copynumber: 6.8 Consensus size: 11
2936830 AAATAATTAA
2936840 AATATATTATT
1 AATATATTATT
*
2936851 AATATAATATT
1 AATATATTATT
2936862 AATATA-TA--
1 AATATATTATT
* *
2936870 AATATTTTA-A
1 AATATATTATT
*
2936880 AATTTAATT-TT
1 AATAT-ATTATT
2936891 ATATATATTATT
1 A-ATATATTATT
2936903 AATATATTA
1 AATATATTA
2936912 AATTTTATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
8 5 0.10
9 2 0.04
10 6 0.12
11 30 0.61
12 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
AATATATTATT
Found at i:2936871 original size:41 final size:41
Alignment explanation
Indices: 2936826--2936909 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 41
2936816 TATCAATAAG
2936826 ATAAAAATAATTAAAATAT-ATTATTA-ATATAATATTAATAT
1 ATAAAAAT-ATTAAAATATAATT-TTATATATAATATTAATAT
* * * *
2936867 ATAAATATTTTAAAATTTAATTTTATATATATTATTAATAT
1 ATAAAAATATTAAAATATAATTTTATATATAATATTAATAT
2936908 AT
1 AT
2936910 TAAATTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 11 0.30
41 26 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (41 bp):
ATAAAAATATTAAAATATAATTTTATATATAATATTAATAT
Found at i:2936933 original size:27 final size:27
Alignment explanation
Indices: 2936880--2936971 Score: 91
Period size: 27 Copynumber: 3.3 Consensus size: 27
2936870 AATATTTTAA
* *
2936880 AATTT-AATTTTATATATAT-TATTAAT
1 AATTTAAATTTTATATAAATATA-AAAT
2936906 -ATATTAAATTTTATATAAATATAAAAT
1 AAT-TTAAATTTTATATAAATATAAAAT
*
2936933 AATTTAAATATTATTATAATATAATAAAAT
1 AATTTAAATTTTA-TATAA-AT-ATAAAAT
2936963 AATTTAAAT
1 AATTTAAAT
2936972 ATAACAACTC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 25 0.45
28 9 0.16
29 2 0.04
30 16 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTTAAATTTTATATAAATATAAAAT
Found at i:2936960 original size:30 final size:27
Alignment explanation
Indices: 2936909--2936973 Score: 94
Period size: 30 Copynumber: 2.3 Consensus size: 27
2936899 TATTAATATA
*
2936909 TTAAATTTTATATAAATATAAAATAAT
1 TTAAATATTATATAAATATAAAATAAT
2936936 TTAAATATTATTATAATATAATAAAATAAT
1 TTAAATATTA-TATAA-AT-ATAAAATAAT
2936966 TTAAATAT
1 TTAAATAT
2936974 AACAACTCTC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 9 0.26
28 5 0.15
29 2 0.06
30 18 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TTAAATATTATATAAATATAAAATAAT
Found at i:2937568 original size:2 final size:2
Alignment explanation
Indices: 2937563--2937589 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2937553 ACACACACAC
2937563 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
2937590 ATTAAAGATT
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:2937682 original size:39 final size:34
Alignment explanation
Indices: 2937602--2937690 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 34
2937592 TAAAGATTTT
*
2937602 AAATT-TTTTTAATTTTAAAAAATAATTATTTAA
1 AAATTATTTTTAATTTTAAAAAATAATTATTAAA
2937635 AAATTATTTTTAATTTTAAAAAATAACTAATCAATTAAA
1 AAATTATTTTTAATTTTAAAAAATAA-T--T--ATTAAA
*
2937674 AAATTATTTTTTATTTT
1 AAATTATTTTTAATTTT
2937691 TTATTTATTA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
33 5 0.10
34 20 0.42
35 1 0.02
37 1 0.02
39 21 0.44
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (34 bp):
AAATTATTTTTAATTTTAAAAAATAATTATTAAA
Found at i:2938274 original size:17 final size:17
Alignment explanation
Indices: 2938236--2938278 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2938226 GTAAAATTAA
* *
2938236 ATAAATTTTATATGTTT
1 ATAATTTTTATATGTAT
2938253 ATAATTTTTATATG-AT
1 ATAATTTTTATATGTAT
2938269 ATTAATTTTT
1 A-TAATTTTT
2938279 TGTAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
ATAATTTTTATATGTAT
Found at i:2938375 original size:28 final size:28
Alignment explanation
Indices: 2938338--2938399 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
2938328 ACGTTAGTAT
** *
2938338 AAAAT-TAATATGTTAAATGTATATTAA
1 AAAATATAATATGTTAAATCAATATAAA
* *
2938365 AAAATATAATATTTTCAATCAATATAAA
1 AAAATATAATATGTTAAATCAATATAAA
2938393 AAAATAT
1 AAAATAT
2938400 TAAATTAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 5 0.17
28 24 0.83
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (28 bp):
AAAATATAATATGTTAAATCAATATAAA
Found at i:2938795 original size:33 final size:34
Alignment explanation
Indices: 2938749--2938818 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
2938739 ATTTTATATT
* *
2938749 TATAAATTTTAATATATTAATAAT-TTAT-TTTTA
1 TATAAATTCTAATAT-GTAATAATATTATATTTTA
2938782 TATAAATTCTAATATGTAATAATATTATATTTTA
1 TATAAATTCTAATATGTAATAATATTATATTTTA
2938816 TAT
1 TAT
2938819 TATTGTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 7 0.21
33 18 0.55
34 8 0.24
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (34 bp):
TATAAATTCTAATATGTAATAATATTATATTTTA
Found at i:2956290 original size:22 final size:22
Alignment explanation
Indices: 2956265--2956309 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
2956255 ATTTCGATAT
2956265 TTTATATCAT-TTATAAGTTTAA
1 TTTATATCATATTA-AAGTTTAA
*
2956287 TTTATATTATATTAAAGTTTAA
1 TTTATATCATATTAAAGTTTAA
2956309 T
1 T
2956310 ATATTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TTTATATCATATTAAAGTTTAA
Found at i:2959866 original size:161 final size:161
Alignment explanation
Indices: 2959683--2960002 Score: 631
Period size: 161 Copynumber: 2.0 Consensus size: 161
2959673 CATCAGCCAT
*
2959683 TGAAAAGTGTGATGAAAGATAGTGCAAAACAAGCTAAGTCTTCAATTTGATCATATTCTATCTGA
1 TGAAAAGTGTGATGAAAGATAGTACAAAACAAGCTAAGTCTTCAATTTGATCATATTCTATCTGA
2959748 TCCTAGCCCATATTTGAATATGTGAATTAAAAGTTTCAAAGCTAATTGGTACAGCAGAACTATAA
66 TCCTAGCCCATATTTGAATATGTGAATTAAAAGTTTCAAAGCTAATTGGTACAGCAGAACTATAA
2959813 TCTTTCTTAAACAAGAAACAAAATAATCCAC
131 TCTTTCTTAAACAAGAAACAAAATAATCCAC
2959844 TGAAAAGTGTGATGAAAGATAGTACAAAACAAGCTAAGTCTTCAATTTGATCATATTCTATCTGA
1 TGAAAAGTGTGATGAAAGATAGTACAAAACAAGCTAAGTCTTCAATTTGATCATATTCTATCTGA
2959909 TCCTAGCCCATATTTGAATATGTGAATTAAAAGTTTCAAAGCTAATTGGTACAGCAGAACTATAA
66 TCCTAGCCCATATTTGAATATGTGAATTAAAAGTTTCAAAGCTAATTGGTACAGCAGAACTATAA
2959974 TCTTTCTTAAACAAGAAACAAAATAATCC
131 TCTTTCTTAAACAAGAAACAAAATAATCC
2960003 TGCCCTTTCT
Statistics
Matches: 158, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 158 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (161 bp):
TGAAAAGTGTGATGAAAGATAGTACAAAACAAGCTAAGTCTTCAATTTGATCATATTCTATCTGA
TCCTAGCCCATATTTGAATATGTGAATTAAAAGTTTCAAAGCTAATTGGTACAGCAGAACTATAA
TCTTTCTTAAACAAGAAACAAAATAATCCAC
Found at i:2961616 original size:28 final size:27
Alignment explanation
Indices: 2961567--2961624 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
2961557 TTTAATTATT
2961567 AAATATATAAAAAATAATATTTTAATTG
1 AAATATATAAAAAATAATA-TTTAATTG
*
2961595 AAATA-ATAAAAACATCAA-ATTTATTTG
1 AAATATATAAAAA-AT-AATATTTAATTG
2961622 AAA
1 AAA
2961625 CTTAACGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 17 0.63
28 8 0.30
29 2 0.07
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (27 bp):
AAATATATAAAAAATAATATTTAATTG
Found at i:2969571 original size:27 final size:27
Alignment explanation
Indices: 2969508--2969597 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 27
2969498 TCAAAATATG
* *
2969508 TTTATTTTCATATA-TATATATATTTATA
1 TTTATATTCATATATTA-ATA-AATTATA
*
2969536 TTAATTATTCATATATTAATAAATTATA
1 TTTA-TATTCATATATTAATAAATTATA
* * *
2969564 TTTATATTTA-ATATTTATTATATTATA
1 TTTATATTCATATA-TTAATAAATTATA
2969591 -TTATATT
1 TTTATATT
2969598 TTTATATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
26 10 0.19
27 16 0.31
28 12 0.23
29 12 0.23
30 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTATATTCATATATTAATAAATTATA
Found at i:2969602 original size:8 final size:8
Alignment explanation
Indices: 2969564--2969615 Score: 61
Period size: 8 Copynumber: 6.2 Consensus size: 8
2969554 ATAAATTATA
2969564 TTTATA-T
1 TTTATATT
*
2969571 TTAATATT
1 TTTATATT
2969579 TATTATATT
1 T-TTATATT
2969588 ATATTATATT
1 -T-TTATATT
2969598 TTTATATT
1 TTTATATT
2969606 TTTATATT
1 TTTATATT
2969614 TT
1 TT
2969616 ACGTGTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
7 5 0.12
8 19 0.47
9 7 0.17
10 9 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
TTTATATT
Found at i:2969602 original size:34 final size:33
Alignment explanation
Indices: 2969514--2969606 Score: 90
Period size: 34 Copynumber: 2.8 Consensus size: 33
2969504 TATGTTTATT
2969514 TTCATATA-TATA-TATA-TTTATA-TTAATTA
1 TTCATATATTATATTATATTTTATATTTAATTA
2969543 TTCATATATTAATAAATTATA-TTTATATTTAA-TA
1 TTCATATATT-AT--ATTATATTTTATATTTAATTA
*
2969577 TTTATTATATTATATTATATTTTTATATTT
1 TTCA-TATATTATATTATA-TTTTATATTT
2969607 TTATATTTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
29 8 0.15
30 1 0.02
31 2 0.04
32 6 0.11
33 1 0.02
34 26 0.48
35 10 0.19
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (33 bp):
TTCATATATTATATTATATTTTATATTTAATTA
Found at i:2969615 original size:7 final size:7
Alignment explanation
Indices: 2969559--2969616 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
2969549 TATTAATAAA
2969559 TTATA-T
1 TTATATT
2969565 TTATATT
1 TTATATT
*
2969572 TAATA-T
1 TTATATT
*
2969578 TTATTATA
1 TTA-TATT
2969586 TTATATT
1 TTATATT
*
2969593 ATAT-TT
1 TTATATT
2969599 TTATATTT
1 TTATA-TT
2969607 TTATATT
1 TTATATT
2969614 TTA
1 TTA
2969617 CGTGTAATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
6 13 0.32
7 18 0.44
8 10 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATATT
Found at i:2970644 original size:17 final size:17
Alignment explanation
Indices: 2970622--2970679 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
2970612 ATACATATAA
2970622 ATAATATTAAAATTTAT
1 ATAATATTAAAATTTAT
2970639 ATAATA-T-AAA-TTAT
1 ATAATATTAAAATTTAT
2970653 -TAATATATCAAAATTTAT
1 ATAATAT-T-AAAATTTAT
2970671 ATAAATATT
1 AT-AATATT
2970680 TAATAATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 5 0.15
14 4 0.12
15 4 0.12
16 1 0.03
17 9 0.26
18 4 0.12
19 2 0.06
20 5 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATAATATTAAAATTTAT
Found at i:2970678 original size:18 final size:17
Alignment explanation
Indices: 2970624--2970678 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
2970614 ACATATAAAT
2970624 AATATTAAAATTTATAT-
1 AATA-TAAAATTTATATA
2970641 AATAT-AAA-TTAT-TA
1 AATATAAAATTTATATA
2970655 ATATATCAAAATTTATATA
1 A-ATAT-AAAATTTATATA
2970674 AATAT
1 AATAT
2970679 TTAATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 1 0.03
14 5 0.16
15 7 0.22
16 1 0.03
17 7 0.22
18 8 0.25
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATAAAATTTATATA
Found at i:2970915 original size:14 final size:14
Alignment explanation
Indices: 2970896--2970937 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
2970886 ATGTTATTAT
2970896 TTTTTTATAATTTA
1 TTTTTTATAATTTA
*
2970910 TTTTTTAAAATTTA
1 TTTTTTATAATTTA
*
2970924 ATTTTTATTAATTT
1 TTTTTTA-TAATTT
2970938 CATATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTTATAATTTA
Found at i:2971131 original size:17 final size:17
Alignment explanation
Indices: 2971111--2971161 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
2971101 TAAAACTTGA
2971111 TATTTTTTAATTAAATT
1 TATTTTTTAATTAAATT
*
2971128 TATTTTTTTACTTAAATT
1 TA-TTTTTTAATTAAATT
* *
2971146 AATTTTTTATTTAAAT
1 TATTTTTTAATTAAAT
2971162 CTTTTCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTTTAATTAAATT
Found at i:2971136 original size:18 final size:18
Alignment explanation
Indices: 2971113--2971153 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2971103 AAACTTGATA
*
2971113 TTTTTTAATTAAATTTAT
1 TTTTTTAATTAAATTAAT
*
2971131 TTTTTTACTTAAATTAAT
1 TTTTTTAATTAAATTAAT
2971149 TTTTT
1 TTTTT
2971154 ATTTAAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTTAATTAAATTAAT
Found at i:2979333 original size:6 final size:5
Alignment explanation
Indices: 2979288--2979317 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
2979278 GTTAAGAGGG
2979288 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
2979318 ACATGAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:2980080 original size:22 final size:20
Alignment explanation
Indices: 2980042--2980084 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
2980032 TATATGTTAA
*
2980042 ATAATTATATTAAAATTTAT
1 ATAAATATATTAAAATTTAT
2980062 ATAAATATATATAATAATTTAT
1 ATAAATATAT-TAA-AATTTAT
2980084 A
1 A
2980085 AATTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAAATATATTAAAATTTAT
Found at i:2980095 original size:24 final size:25
Alignment explanation
Indices: 2980065--2980117 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
2980055 AATTTATATA
*
2980065 AATATATATAATAATTTATAAATT-TT
1 AATATA-AT-ATAATATATAAATTATT
2980091 AATATAATATAATATATAAATTATT
1 AATATAATATAATATATAAATTATT
2980116 AA
1 AA
2980118 ATTTAATCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 13 0.52
25 6 0.24
26 6 0.24
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
AATATAATATAATATATAAATTATT
Found at i:2980106 original size:32 final size:32
Alignment explanation
Indices: 2980041--2980121 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 32
2980031 ATATATGTTA
*
2980041 AATAATTATATTAAAATTTATATAAATATATAT
1 AATAATT-TATTAAATTTTATATAAATATATAT
2980074 AATAATTTA-TAAATTTTA-ATATAATATA-AT
1 AATAATTTATTAAATTTTATATA-AATATATAT
*
2980104 ATATAAATTATTAAATTT
1 A-ATAATTTATTAAATTT
2980122 AATCTGAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
30 6 0.14
31 21 0.49
32 9 0.21
33 7 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
AATAATTTATTAAATTTTATATAAATATATAT
Found at i:2981480 original size:2 final size:2
Alignment explanation
Indices: 2981473--2981506 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2981463 GATATGTGAA
2981473 AT AT 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
2981507 CTACAAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2984374 original size:51 final size:52
Alignment explanation
Indices: 2984278--2984380 Score: 172
Period size: 51 Copynumber: 2.0 Consensus size: 52
2984268 CACTGACTGC
* **
2984278 TATATATATATATTCTCAAAACCTCTTTATAAACTATCTGGTAGATA-TATA
1 TATATATATATATTCTCAAAACCTCTTTACAAACTATCTAATAGATAGTATA
2984329 TATATATATATATTCTCAAAACCTCTTTACAAACTATCTAATAGATAGTATA
1 TATATATATATATTCTCAAAACCTCTTTACAAACTATCTAATAGATAGTATA
2984381 GTACAATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 44 0.92
52 4 0.08
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.40
Consensus pattern (52 bp):
TATATATATATATTCTCAAAACCTCTTTACAAACTATCTAATAGATAGTATA
Found at i:2985660 original size:27 final size:27
Alignment explanation
Indices: 2985595--2985657 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
2985585 AAAATTTATG
* *
2985595 TATTTATGAT-ATGTTTATAATATTTT
1 TATTTATAATAATGTTTAAAATATTTT
2985621 TATGTTATAATAATGTTTAAAATATTTT
1 TAT-TTATAATAATGTTTAAAATATTTT
2985649 ATATTTATA
1 -TATTTATA
2985658 TAAATGATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 3 0.09
27 6 0.19
28 20 0.62
29 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (27 bp):
TATTTATAATAATGTTTAAAATATTTT
Found at i:2985975 original size:2 final size:2
Alignment explanation
Indices: 2985963--2986012 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
2985953 CCTCTACATC
* *
2985963 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2986005 GT AT AT AT
1 AT AT AT AT
2986013 TAATTATTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2986215 original size:35 final size:35
Alignment explanation
Indices: 2986169--2986306 Score: 240
Period size: 35 Copynumber: 3.9 Consensus size: 35
2986159 TCTCAAGTTC
*
2986169 GGCTTAGATGTGGCCCGCACCAGCTGAACTACCTA
1 GGCTTAGATGTGGCCCGCACCAGCTGAACCACCTA
2986204 GGCTTAGATGTGGCCCGCACCAGCTGAACCACCTA
1 GGCTTAGATGTGGCCCGCACCAGCTGAACCACCTA
* * *
2986239 GGCTTAGATGTGGACCGCACCAGCTGAACCAACTC
1 GGCTTAGATGTGGCCCGCACCAGCTGAACCACCTA
2986274 GGCTTAGATGTGGCCCGCACCAGCTGAACCACC
1 GGCTTAGATGTGGCCCGCACCAGCTGAACCACC
2986307 CAATTTATTA
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 97 1.00
ACGTcount: A:0.23, C:0.33, G:0.26, T:0.17
Consensus pattern (35 bp):
GGCTTAGATGTGGCCCGCACCAGCTGAACCACCTA
Found at i:2987098 original size:3 final size:3
Alignment explanation
Indices: 2987090--2987133 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2987080 ATATATTTAA
2987090 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2987134 CATAATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2988491 original size:2 final size:2
Alignment explanation
Indices: 2988484--2988508 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2988474 TCTATCTATC
2988484 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
2988509 TATTGTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2989904 original size:2 final size:2
Alignment explanation
Indices: 2989897--2989925 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2989887 CAATATGTTG
2989897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2989926 AATAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2997484 original size:18 final size:19
Alignment explanation
Indices: 2997470--2997514 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
2997460 TACAATTCTT
2997470 TTTA-TATTT-TTAATTTA
1 TTTATTATTTATTAATTTA
2997487 TTTATTATTTATTAA--TA
1 TTTATTATTTATTAATTTA
*
2997504 TTTATTTTTTA
1 TTTATTATTTA
2997515 AAAATTCACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 16 0.64
18 5 0.20
19 4 0.16
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTATTATTTATTAATTTA
Found at i:2998961 original size:25 final size:23
Alignment explanation
Indices: 2998915--2998962 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
2998905 TACTGCTATC
*
2998915 TTTTATTGGCTAGATGTATAGAA
1 TTTTATTGGCTAAATGTATAGAA
*
2998938 TTTTATATGGCTGAAATGTGTAGAA
1 TTTTAT-TGGCT-AAATGTATAGAA
2998963 ATTAACCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.29
24 5 0.24
25 10 0.48
ACGTcount: A:0.31, C:0.04, G:0.23, T:0.42
Consensus pattern (23 bp):
TTTTATTGGCTAAATGTATAGAA
Found at i:3007568 original size:6 final size:6
Alignment explanation
Indices: 3007559--3007598 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
3007549 ATAAAAAATA
* *
3007559 TTATAT TTATAT TAATAT TATATTT TTATAT TTATAT TTA
1 TTATAT TTATAT TTATAT T-TATAT TTATAT TTATAT TTA
3007599 AATAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (6 bp):
TTATAT
Done.