Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 17 of 19
Found at i:3559378 original size:18 final size:18
Alignment explanation
Indices: 3559334--3559372 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
3559324 ATTTAAAAAG
*
3559334 AAAATATGTTTTATTATTA
1 AAAATAT-TTTTATAATTA
3559353 AAAATATTTTTATAATTA
1 AAAATATTTTTATAATTA
3559371 AA
1 AA
3559373 TTTATTGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
AAAATATTTTTATAATTA
Found at i:3559385 original size:30 final size:32
Alignment explanation
Indices: 3559343--3559405 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 32
3559333 GAAAATATGT
3559343 TTTATTATTAAAAATA-TTTTTA-TAATTAAA
1 TTTATTATTAAAAATATTTTTTATTAATTAAA
*
3559373 TTTATTGA-TAAAATTATTTTTTATTAATTAAA
1 TTTATT-ATTAAAAATATTTTTTATTAATTAAA
3559405 T
1 T
3559406 AATAATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 13 0.45
31 7 0.24
32 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
TTTATTATTAAAAATATTTTTTATTAATTAAA
Found at i:3559610 original size:21 final size:21
Alignment explanation
Indices: 3559568--3559618 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
3559558 CGTTATATAA
* *
3559568 TAAAAATATTAATATTTATTT
1 TAAAAATAATAATATTAATTT
3559589 TAAAAA-AATAATATTAATTT
1 TAAAAATAATAATATTAATTT
* *
3559609 TTAAATTAAT
1 TAAAAATAAT
3559619 CAAACTTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAAATAATAATATTAATTT
Found at i:3560631 original size:17 final size:19
Alignment explanation
Indices: 3560581--3560631 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 19
3560571 CATTATCATA
3560581 AAAATAA-ATA-TAATATT
1 AAAATAATATATTAATATT
3560598 AAAATAATATTATTAATA-T
1 AAAATAATA-TATTAATATT
3560617 -AAATAATATATTAAT
1 AAAATAATATATTAAT
3560632 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
17 14 0.45
18 9 0.29
19 3 0.10
20 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAATATATTAATATT
Found at i:3563142 original size:19 final size:19
Alignment explanation
Indices: 3563118--3563158 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3563108 TAAGAATAAA
*
3563118 TTTTTTT-CTTTTTTTTCCT
1 TTTTTTTAC-TTTGTTTCCT
3563137 TTTTTTTACTTTGTTTCCT
1 TTTTTTTACTTTGTTTCCT
3563156 TTT
1 TTT
3563159 ATTAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTTTACTTTGTTTCCT
Found at i:3563985 original size:190 final size:194
Alignment explanation
Indices: 3563684--3564036 Score: 450
Period size: 190 Copynumber: 1.8 Consensus size: 194
3563674 ATTTTTTCTA
* * * *
3563684 CTTAAGAAATTAATTTTAATGACTTCATTAGTCTCAAAATAAAAAAAATTTATTATTTCATCCGG
1 CTTAAGAAACTAATTTTAATGACTTAATTAGTCTC-AAATAAAAAAAATCTATTACTTCATCCGG
* * * * *
3563749 AAAGGACTTATGCATTTAAGCTCTTCCTTAAATTACGTAGTATTTGAATATCTAAATAATTTC-T
65 AAAGGACTTACGCATTTAAACTCTTCCTTAAATTACATAATATTTGAATATCTAAATAATATCTT
* *
3563813 AAAAAAGAATATCATATTTTAAAAATAAATTTTCTTTGTTTTCTTTTATTTTTTTCGTTCTTTTC
130 AAAAAAGAATATCACATATTAAAAATAAATTTTCTTTGTTTTCTTTTATTTTTTTCGTTCTTTTC
* **
3563878 CTTAAGAAACTAATTTTAATGACTTAATTAG-CTC-AA-AACAAAAATCTATTACTTCA-CTTGA
1 CTTAAGAAACTAATTTTAATGACTTAATTAGTCTCAAATAAAAAAAATCTATTACTTCATCCGGA
*
3563939 TAA-GACATTACGCATTTAAACT-TTCTCTTAAATTATATAATATTTGAATATCTAAATAATATC
66 -AAGGAC-TTACGCATTTAAACTCTTC-CTTAAATTACATAATATTTGAATATCTAAATAATATC
* * * *
3564002 TTAAGAAATAATGTCACATATTAAAAATAATTTTT
128 TTAAAAAAGAATATCACATATTAAAAATAAATTTT
3564037 TTTCATTATT
Statistics
Matches: 136, Mismatches: 19, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
189 9 0.07
190 65 0.48
191 30 0.22
193 3 0.02
194 29 0.21
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.42
Consensus pattern (194 bp):
CTTAAGAAACTAATTTTAATGACTTAATTAGTCTCAAATAAAAAAAATCTATTACTTCATCCGGA
AAGGACTTACGCATTTAAACTCTTCCTTAAATTACATAATATTTGAATATCTAAATAATATCTTA
AAAAAGAATATCACATATTAAAAATAAATTTTCTTTGTTTTCTTTTATTTTTTTCGTTCTTTTC
Found at i:3565253 original size:12 final size:11
Alignment explanation
Indices: 3565217--3565253 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3565207 ACATTTGTAC
3565217 AAAA-AAAAA-
1 AAAAGAAAAAG
3565226 AAAAGAAAAAG
1 AAAAGAAAAAG
3565237 AAAAGAAAGAAG
1 AAAAGAAA-AAG
3565249 AAAAG
1 AAAAG
3565254 GTCTACACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 4 0.16
10 5 0.20
11 8 0.32
12 8 0.32
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:3571056 original size:17 final size:17
Alignment explanation
Indices: 3571012--3571070 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
3571002 TTTAATAGGT
3571012 TAATA-ATTTATATTATA
1 TAATATATTT-TATTATA
*
3571029 TAATATTTTTTATTATA
1 TAATATATTTTATTATA
**
3571046 TTTTATATTTTATT-T-
1 TAATATATTTTATTATA
3571061 TAAT-TATTTT
1 TAATATATTTT
3571071 TTTTGTGTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 6 0.17
15 2 0.06
16 1 0.03
17 23 0.66
18 3 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TAATATATTTTATTATA
Found at i:3574015 original size:99 final size:99
Alignment explanation
Indices: 3573844--3574125 Score: 483
Period size: 99 Copynumber: 2.8 Consensus size: 99
3573834 GAGAAAGGCT
* *
3573844 GGCCGGCCAAAGGGTTCAAAGAATAAGCAGAAAAGGCTTAGTGATGAAAAACTTGGACCGTCAAG
1 GGCCGGCCAAAGGGTTCAAAGAATAAGCAGAAAAGGCCTAGTGATGAAAAACTTGGACTGTCAAG
* * *
3573909 TGAACAGCAGACCTTGCCAAAGAAAGTTGGCCGC
66 TGAACAGCAGACCTTGCAAAAAAAAGCTGGCCGC
*
3573943 GGCCGGCCAAAGGGTTCCAAGAATAAGCAGAAAAGGCCTAGTGATGAAAAACTTGGACTGTCAAG
1 GGCCGGCCAAAGGGTTCAAAGAATAAGCAGAAAAGGCCTAGTGATGAAAAACTTGGACTGTCAAG
*
3574008 TGAACAGCAGACCTCGCAAAAAAAAGCTGGCCGC
66 TGAACAGCAGACCTTGCAAAAAAAAGCTGGCCGC
* *
3574042 GGCCGGCCAAAGGGTTCAAAGAATAAGCAGAAAAGGCCCAGTAATGAAAAACTTGGACTGTCAAG
1 GGCCGGCCAAAGGGTTCAAAGAATAAGCAGAAAAGGCCTAGTGATGAAAAACTTGGACTGTCAAG
3574107 TGAACAGCAGACCTTGCAA
66 TGAACAGCAGACCTTGCAA
3574126 TCAAAGGATA
Statistics
Matches: 172, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 172 1.00
ACGTcount: A:0.38, C:0.21, G:0.27, T:0.14
Consensus pattern (99 bp):
GGCCGGCCAAAGGGTTCAAAGAATAAGCAGAAAAGGCCTAGTGATGAAAAACTTGGACTGTCAAG
TGAACAGCAGACCTTGCAAAAAAAAGCTGGCCGC
Found at i:3590040 original size:28 final size:26
Alignment explanation
Indices: 3589993--3590072 Score: 70
Period size: 28 Copynumber: 2.9 Consensus size: 26
3589983 TTGATTTTTT
* *
3589993 TTATAATCGGGAGGTACTCCAACCCCG
1 TTATTATCGGG-GATACTCCAACCCCG
* *
3590020 TTATGTCATCGGGGATACTCCAATCTCG
1 TTAT-T-ATCGGGGATACTCCAACCCCG
*
3590048 TTATTTTCGAGGGGATACTCCAACC
1 TTATTATC--GGGGATACTCCAACC
3590073 TCGATTTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
26 2 0.05
27 5 0.12
28 30 0.70
29 6 0.14
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (26 bp):
TTATTATCGGGGATACTCCAACCCCG
Found at i:3590129 original size:51 final size:51
Alignment explanation
Indices: 3590058--3590174 Score: 159
Period size: 51 Copynumber: 2.3 Consensus size: 51
3590048 TTATTTTCGA
*
3590058 GGGGATACTCCAACCTCGATTTTA-TTTCTAAAATACCAAATTTTC-ATAATC
1 GGGGATACTCCAACCTCGATTTTATTTTC-AAAACACC-AATTTTCTATAATC
*
3590109 GGGGATACTTCAA-CTCCGATTTTATTTTCAAAACACCAATTTTCTATAATC
1 GGGGATACTCCAACCT-CGATTTTATTTTCAAAACACCAATTTTCTATAATC
*
3590160 AGGGATACTCCAACC
1 GGGGATACTCCAACC
3590175 CTGTTATTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
50 9 0.16
51 44 0.76
52 5 0.09
ACGTcount: A:0.32, C:0.23, G:0.11, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGATTTTATTTTCAAAACACCAATTTTCTATAATC
Found at i:3590272 original size:131 final size:130
Alignment explanation
Indices: 3590031--3590272 Score: 303
Period size: 131 Copynumber: 1.9 Consensus size: 130
3590021 TATGTCATCG
* * * * *
3590031 GGGATACTCCAATCTCGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATTTCTAAAATACCA
1 GGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCTCAATTTTACTTCCAAAACACCA
* * *
3590096 AATTTTCATAATCGGGGATACTTCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCA
66 AATTTTCATAATCGGGGATACTCCAACTCCGATTTTATCTCCAAAACACCAATTTTCTATAATCA
*
3590161 GGGATACTCCAACC-CTGTTATTTTTCGAGGGGATACTCTAATCC-CAATTTTACTTCCAAAACA
1 GGGATACTCCAACCTC-GTTA-TTTTCGAGGGGATACTCCAA-CCTCAATTTTACTTCCAAAACA
* * *
3590224 CCGATTTTTCATAATCGGGGATACTCCAGC-CTCG-TTGTTATCTCCAAAA
63 CCAAATTTTCATAATCGGGGATACTCCAACTC-CGATT-TTATCTCCAAAA
3590273 TATTAGATTT
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
129 1 0.01
130 20 0.21
131 72 0.76
132 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (130 bp):
GGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAACCTCAATTTTACTTCCAAAACACCA
AATTTTCATAATCGGGGATACTCCAACTCCGATTTTATCTCCAAAACACCAATTTTCTATAATCA
Found at i:3592406 original size:4 final size:4
Alignment explanation
Indices: 3592399--3592495 Score: 86
Period size: 4 Copynumber: 24.2 Consensus size: 4
3592389 GTAAGTACTT
* * * * * *
3592399 TATA TATA TATA TATA TGTA TATA TATA TATG TATG TATG TATG TATG
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * *
3592447 TATG TATG TATG TATG TGTA TATT TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
3592495 T
1 T
3592496 TCTCCTACTT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 85 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (4 bp):
TATA
Found at i:3594072 original size:2 final size:2
Alignment explanation
Indices: 3594065--3594093 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3594055 GTTTATAGTT
3594065 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3594094 GAATATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3595019 original size:25 final size:22
Alignment explanation
Indices: 3594972--3595032 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
3594962 ACTAATATTT
3594972 ATAATAATATTTTATATATTAA
1 ATAATAATATTTTATATATTAA
*
3594994 ATAATTAATTATTTTAATGTATTAA
1 ATAA-TAA-TATTTT-ATATATTAA
*
3595019 A-AATAATAATTTAT
1 ATAATAATATTTTAT
3595033 CTGGTATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.06
22 9 0.26
23 6 0.18
24 8 0.24
25 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATAATAATATTTTATATATTAA
Found at i:3595030 original size:23 final size:24
Alignment explanation
Indices: 3594972--3595030 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
3594962 ACTAATATTT
3594972 ATAATAAT-ATTTT-ATATATTAA
1 ATAATAATAATTTTAATATATTAA
* *
3594994 ATAATTAATTATTTTAATGTATTAA
1 ATAA-TAATAATTTTAATATATTAA
3595019 A-AATAATAATTT
1 ATAATAATAATTT
3595031 ATCTGGTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 4 0.12
23 12 0.38
24 7 0.22
25 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
ATAATAATAATTTTAATATATTAA
Found at i:3598348 original size:2 final size:2
Alignment explanation
Indices: 3598341--3598392 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3598331 TACATTGCTC
3598341 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3598383 CT CT CT CT CT
1 CT CT CT CT CT
3598393 TTTAACTTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3601175 original size:12 final size:12
Alignment explanation
Indices: 3601161--3601192 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
3601151 AGAGCGAGCG
3601161 AGAGACAGAG--
1 AGAGACAGAGAC
3601171 AGAGACAGAGAC
1 AGAGACAGAGAC
3601183 AGAGACAGAG
1 AGAGACAGAG
3601193 GGAGGGAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
12 10 0.50
ACGTcount: A:0.50, C:0.12, G:0.38, T:0.00
Consensus pattern (12 bp):
AGAGACAGAGAC
Found at i:3601180 original size:6 final size:6
Alignment explanation
Indices: 3601161--3601192 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
3601151 AGAGCGAGCG
3601161 AGAGAC AGAG-- AGAGAC AGAGAC AGAGAC AGAG
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAG
3601193 GGAGGGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.17
6 20 0.83
ACGTcount: A:0.50, C:0.12, G:0.38, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:3601785 original size:14 final size:14
Alignment explanation
Indices: 3601752--3601785 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3601742 AGTATTTGAT
*
3601752 TAAATTTAATTATA
1 TAAATTTAATTAAA
*
3601766 TTAATTTAATTAAA
1 TAAATTTAATTAAA
3601780 TAAATT
1 TAAATT
3601786 ATTAAAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAAATTTAATTAAA
Found at i:3601911 original size:21 final size:21
Alignment explanation
Indices: 3601842--3601913 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
3601832 TTTATATTTT
3601842 TTAAAATTTATTATTTAAAAA
1 TTAAAATTTATTATTTAAAAA
* * **
3601863 TTATAA-TAATTATTTATGATATTT
1 TTAAAATTTATTATTTA--A-A-AA
3601887 TTAAAATTTATTATTTAAAAA
1 TTAAAATTTATTATTTAAAAA
3601908 TTAAAA
1 TTAAAA
3601914 AACTTACTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
20 9 0.24
21 11 0.29
22 2 0.05
23 2 0.05
24 5 0.13
25 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (21 bp):
TTAAAATTTATTATTTAAAAA
Found at i:3602357 original size:12 final size:12
Alignment explanation
Indices: 3602325--3602368 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
3602315 AAATTCAATA
*
3602325 AAAATAATATATT
1 AAAATAA-AAATT
3602338 AAATATAAAAATT
1 AAA-ATAAAAATT
3602351 AAAATAAAAATT
1 AAAATAAAAATT
3602363 ACAAAT
1 A-AAAT
3602369 TTTTTAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 10 0.36
13 14 0.50
14 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATAAAAATT
Found at i:3604035 original size:23 final size:23
Alignment explanation
Indices: 3604009--3604158 Score: 90
Period size: 23 Copynumber: 6.0 Consensus size: 23
3603999 AATTCATATA
3604009 TTTATATTATATTAATATAATTT
1 TTTATATTATATTAATATAATTT
3604032 TTTATA-TATTATTAATTATAAAATTAT
1 TTTATATTA-TATTAA-TAT--AATT-T
* * *
3604059 TATATATTTTTATATATTAATAATTT
1 TTTATA-TTATAT-TAAT-ATAATTT
* *
3604085 AGATTATATAGATATTAATAT-ATTT
1 --TTTATAT-TATATTAATATAATTT
*
3604110 ATTTATATTATATTTAA-ATTATTT
1 -TTTATATTATA-TTAATATAATTT
*
3604134 TTTATATTATATTATATTTAATTT
1 TTTATATTATATTA-ATATAATTT
3604158 T
1 T
3604159 ATTTACATAA
Statistics
Matches: 98, Mismatches: 13, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
22 5 0.05
23 29 0.30
24 23 0.23
25 4 0.04
26 7 0.07
27 14 0.14
28 11 0.11
29 5 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (23 bp):
TTTATATTATATTAATATAATTT
Found at i:3604196 original size:10 final size:10
Alignment explanation
Indices: 3604165--3604198 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3604155 TTTTATTTAC
3604165 ATAAATTAAA
1 ATAAATTAAA
* *
3604175 ACAAATAAAA
1 ATAAATTAAA
3604185 ATAAATTAAA
1 ATAAATTAAA
3604195 ATAA
1 ATAA
3604199 TTCACGTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (10 bp):
ATAAATTAAA
Found at i:3605962 original size:17 final size:17
Alignment explanation
Indices: 3605940--3605974 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3605930 TTTGGGTACA
*
3605940 TGCAGTATAGAAGAAAT
1 TGCAGTATACAAGAAAT
3605957 TGCAGTATACAAGAAAT
1 TGCAGTATACAAGAAAT
3605974 T
1 T
3605975 TCTCGACAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.26
Consensus pattern (17 bp):
TGCAGTATACAAGAAAT
Found at i:3606261 original size:21 final size:22
Alignment explanation
Indices: 3606228--3606277 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3606218 AGGGAACCTT
* *
3606228 AAAAAAAAGTAAAAGGGAAAGG
1 AAAAAATAGTAAAAGGAAAAGG
*
3606250 AAAAAATA-TAAAATGAAAAGG
1 AAAAAATAGTAAAAGGAAAAGG
*
3606271 TAAAAAT
1 AAAAAAT
3606278 GAACAGCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (22 bp):
AAAAAATAGTAAAAGGAAAAGG
Found at i:3609484 original size:2 final size:2
Alignment explanation
Indices: 3609477--3609520 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3609467 CTTCGCTATC
3609477 AT AT AT AT 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 AT AT AT AT
3609519 AT
1 AT
3609521 TCAAAGGAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3610628 original size:28 final size:28
Alignment explanation
Indices: 3610580--3610650 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 28
3610570 TAATACTTAA
* **
3610580 ATAATATTA-AAAT-ATTAAAATTTATTT
1 ATAATATTATATATAATT-AAATTTAAAT
3610607 ATATATATT-TATATAATTAAATTTAAAT
1 ATA-ATATTATATATAATTAAATTTAAAT
3610635 ATAATATTATATATAA
1 ATAATATTATATATAA
3610651 AAAAATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 8 0.22
28 26 0.70
29 3 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
ATAATATTATATATAATTAAATTTAAAT
Found at i:3611166 original size:14 final size:14
Alignment explanation
Indices: 3611147--3611173 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3611137 TTAATAAATT
3611147 TTAATATTTATATC
1 TTAATATTTATATC
3611161 TTAATATTTATAT
1 TTAATATTTATAT
3611174 TTTTTTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAATATTTATATC
Found at i:3611367 original size:33 final size:33
Alignment explanation
Indices: 3611305--3611368 Score: 78
Period size: 33 Copynumber: 1.9 Consensus size: 33
3611295 TTTTAAATAA
**
3611305 TTAAAAAATAAAAATAAATAATTTTTAAAATTT
1 TTAAAAAATAAAAATAAATAATTAATAAAATTT
3611338 TTAAAAAATAAAAATCTAAA-AA-TAATAAAAT
1 TTAAAAAATAAAAA--TAAATAATTAATAAAAT
3611369 AAAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 21 0.78
34 2 0.07
35 4 0.15
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (33 bp):
TTAAAAAATAAAAATAAATAATTAATAAAATTT
Found at i:3612421 original size:17 final size:20
Alignment explanation
Indices: 3612377--3612423 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3612367 ATTTACTATA
3612377 TATTTAATATTAAAATTATT
1 TATTTAATATTAAAATTATT
*
3612397 TATTTAATATT-TAATT-TT
1 TATTTAATATTAAAATTATT
3612415 T-TTTAATAT
1 TATTTAATAT
3612424 AACCTTCTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 8 0.31
18 3 0.12
19 4 0.15
20 11 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTAATATTAAAATTATT
Found at i:3612734 original size:22 final size:22
Alignment explanation
Indices: 3612693--3612749 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
3612683 TGTATATTAT
*
3612693 TTTTATCATAGTTAAATTCATA-G
1 TTTTAT-ATACTTAAATTCA-AGG
*
3612716 TTTTATATACTTGAATTCAAGG
1 TTTTATATACTTAAATTCAAGG
3612738 TTTTATATACTT
1 TTTTATATACTT
3612750 TATAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 1 0.03
22 24 0.77
23 6 0.19
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTTATATACTTAAATTCAAGG
Found at i:3613376 original size:21 final size:20
Alignment explanation
Indices: 3613343--3613383 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3613333 AATAATTAAT
3613343 ATTAAATTCTTAATACTATA
1 ATTAAATTCTTAATACTATA
* *
3613363 ATTATATTCTTTAATATTATA
1 ATTAAATTC-TTAATACTATA
3613384 TTTTATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTAAATTCTTAATACTATA
Found at i:3613550 original size:21 final size:23
Alignment explanation
Indices: 3613512--3613556 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
3613502 TGACATTATT
3613512 ATTTATTTATATTATTAAAATTA
1 ATTTATTTATATTATTAAAATTA
* *
3613535 ATTT-TTT-TATTGTTAAATTTA
1 ATTTATTTATATTATTAAAATTA
3613556 A
1 A
3613557 AAGTTATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 3 0.15
23 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTATTTATATTATTAAAATTA
Found at i:3614046 original size:20 final size:20
Alignment explanation
Indices: 3614008--3614046 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3613998 AATTTTATTT
*
3614008 TATTATAATTATATTTAAAA
1 TATTATAATTATATATAAAA
3614028 TATTATATATT-TATATAAA
1 TATTATA-ATTATATATAAA
3614047 TTTTAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATTATATATAAAA
Found at i:3614095 original size:22 final size:21
Alignment explanation
Indices: 3614046--3614092 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3614036 ATTTATATAA
*
3614046 ATTTTA-ATAAATTAATAATTT
1 ATTTTATATAAATT-TTAATTT
*
3614067 ATATTATATAAATTTTAATTT
1 ATTTTATATAAATTTTAATTT
3614088 ATTTT
1 ATTTT
3614093 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTATATAAATTTTAATTT
Found at i:3615344 original size:14 final size:14
Alignment explanation
Indices: 3615325--3615352 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3615315 TTAATGTTAA
3615325 TATATACATATATT
1 TATATACATATATT
3615339 TATATACATATATT
1 TATATACATATATT
3615353 GTTTTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATACATATATT
Found at i:3624458 original size:2 final size:2
Alignment explanation
Indices: 3624453--3624499 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
3624443 AGAAACGGTA
* *
3624453 AG AG AG AG AC AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3624495 A- AG AG
1 AG AG AG
3624500 GGGGGGGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.53, C:0.02, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3624937 original size:24 final size:23
Alignment explanation
Indices: 3624883--3624952 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
3624873 ATTAAATTTT
3624883 AATAAAATAATTATT--TTATAAAA
1 AATAAAATAA-TATTAATT-TAAAA
3624906 AATAAAAATAATATTAATTTAATAA
1 AAT-AAAATAATATTAATTTAA-AA
* *
3624931 AATAAAATATTATAAATTTAAA
1 AATAAAATAATATTAATTTAAA
3624953 TTTTTTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
23 8 0.20
24 26 0.63
25 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
AATAAAATAATATTAATTTAAAA
Found at i:3626000 original size:2 final size:2
Alignment explanation
Indices: 3625993--3626026 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3625983 ACGCTTTTGC
3625993 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
3626027 GAGAAACCAT
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:3627583 original size:76 final size:76
Alignment explanation
Indices: 3627453--3627607 Score: 267
Period size: 76 Copynumber: 2.0 Consensus size: 76
3627443 TTTTACATGA
* *
3627453 TGGCAATTGTAAAAGAAGCTATAAATGTTAAGGGTGGTTAAAAAAGGGGATTTAAAGGATAAAGG
1 TGGCAATTGTAAAAGAAGATATAAATGTTAAGGGTGGTTAAAAAAGGGGATTTAAAAGATAAAGG
3627518 TTGTTTATTGT
66 TTGTTTATTGT
*
3627529 TGGCAATTGTAAAAGAAGATATAAATGTTACGGGTGGTTAAAAAAAGGGG-TTTAAAAGATAAAG
1 TGGCAATTGTAAAAGAAGATATAAATGTTAAGGGTGGTT-AAAAAAGGGGATTTAAAAGATAAAG
3627593 GTTGTTTATTGT
65 GTTGTTTATTGT
3627605 TGG
1 TGG
3627608 GTTCTTTAGG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
76 65 0.87
77 10 0.13
ACGTcount: A:0.38, C:0.03, G:0.28, T:0.32
Consensus pattern (76 bp):
TGGCAATTGTAAAAGAAGATATAAATGTTAAGGGTGGTTAAAAAAGGGGATTTAAAAGATAAAGG
TTGTTTATTGT
Found at i:3633722 original size:25 final size:24
Alignment explanation
Indices: 3633656--3633722 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 24
3633646 AAAATATATA
* *
3633656 ATTTAATTTAATTTATTATTTATTT
1 ATTTAATTTAA-ATATAATTTATTT
* * *
3633681 ATTTAATTAAAAAATAATTTTTTT
1 ATTTAATTTAAATATAATTTATTT
3633705 ATTTAAATTTAAATATAA
1 ATTT-AATTTAAATATAA
3633723 AATATATAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 13 0.38
25 21 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTAATTTAAATATAATTTATTT
Found at i:3634996 original size:25 final size:23
Alignment explanation
Indices: 3634934--3635014 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 23
3634924 TATTTTATTT
*
3634934 AATAAATAAAT-AAA-TAATA-A
1 AATATATAAATAAAATTAATATA
* * *
3634954 AATAAATACAATACAATTTAATTTA
1 AATATATA-AATA-AAATTAATATA
*
3634979 ATATATTTAAATAAAATTAATATA
1 A-ATATATAAATAAAATTAATATA
3635003 AATATATAAATA
1 AATATATAAATA
3635015 TTTAATATAT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
20 8 0.17
21 3 0.06
23 12 0.25
24 14 0.29
25 6 0.12
26 5 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
AATATATAAATAAAATTAATATA
Found at i:3635037 original size:22 final size:21
Alignment explanation
Indices: 3634974--3635041 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 21
3634964 ATACAATTTA
** *
3634974 ATTTAATATATTTAAATAAA-
1 ATTTAATATAAATATATAAAT
3634994 A-TTAATATAAATATATAAAT
1 ATTTAATATAAATATATAAAT
* **
3635014 ATTTAATATATATTATATTTAT
1 ATTTAATATA-AATATATAAAT
3635036 ATTTAA
1 ATTTAA
3635042 AATTTTAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 15 0.38
20 2 0.05
21 8 0.21
22 14 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTAATATAAATATATAAAT
Found at i:3636532 original size:5 final size:5
Alignment explanation
Indices: 3636522--3636554 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
3636512 TAATCAGCAG
3636522 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAA
3636555 TATTAGCAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:3637958 original size:13 final size:13
Alignment explanation
Indices: 3637940--3637973 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
3637930 AAATGTATTA
3637940 TATATTAATTAAT
1 TATATTAATTAAT
3637953 TATATTAATTAAT
1 TATATTAATTAAT
*
3637966 TAAATTAA
1 TATATTAA
3637974 ATTTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATTAATTAAT
Found at i:3638774 original size:23 final size:22
Alignment explanation
Indices: 3638729--3638774 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
3638719 TACGATTTTA
*
3638729 AATAAATTTATGATAATTTAAT
1 AATAAATTTATGATAATTAAAT
3638751 AATAAATTTAATG-TCAATTAAAT
1 AATAAATTT-ATGAT-AATTAAAT
3638774 A
1 A
3638775 TATTATTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (22 bp):
AATAAATTTATGATAATTAAAT
Found at i:3639119 original size:21 final size:23
Alignment explanation
Indices: 3639095--3639142 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
3639085 CATTATAAAA
3639095 ATAAAAAACTTAA-TTAAAT-TT
1 ATAAAAAACTTAATTTAAATATT
* *
3639116 ATAAATAATTTAATTTAAATATT
1 ATAAAAAACTTAATTTAAATATT
3639139 ATAA
1 ATAA
3639143 TACTCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 6 0.26
23 6 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATAAAAAACTTAATTTAAATATT
Found at i:3639630 original size:31 final size:31
Alignment explanation
Indices: 3639594--3639668 Score: 84
Period size: 30 Copynumber: 2.4 Consensus size: 31
3639584 TTAATATTTA
*
3639594 AAAATTATTTAATATATAA-TTGTATT-TACAT
1 AAAATT-TTTAATATATAACTTG-ATTCTAAAT
*
3639625 AAAATTTTAAAT-TATAACTTGATTCTAAAT
1 AAAATTTTTAATATATAACTTGATTCTAAAT
3639655 AAATATTTTTAATA
1 AAA-ATTTTTAATA
3639669 AAAATAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 8 0.22
30 15 0.41
31 14 0.38
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (31 bp):
AAAATTTTTAATATATAACTTGATTCTAAAT
Found at i:3639689 original size:19 final size:18
Alignment explanation
Indices: 3639651--3639735 Score: 66
Period size: 19 Copynumber: 4.4 Consensus size: 18
3639641 ACTTGATTCT
3639651 AAATAAATATTT-TTAATAA
1 AAATAAATATTTATT--TAA
3639670 AAATAAATATTTCATTT-A
1 AAATAAATATTT-ATTTAA
*
3639688 AAATAAAATATTATAAATTAA
1 AAAT-AAATATT-T-ATTTAA
*
3639709 AAATTAAAAATTTATTTAA
1 AAA-TAAATATTTATTTAA
*
3639728 ATATAAAT
1 AAATAAAT
3639736 TAAAATATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
18 9 0.17
19 27 0.50
20 5 0.09
21 12 0.22
22 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATAAATATTTATTTAA
Found at i:3639718 original size:23 final size:22
Alignment explanation
Indices: 3639692--3639740 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
3639682 CATTTAAAAT
3639692 AAAATATTA-TAAATTAAAAATTA
1 AAAAT-TTATTAAA-TAAAAATTA
*
3639715 AAAATTTATTTAAATATAAATTA
1 AAAATTTA-TTAAATAAAAATTA
3639738 AAA
1 AAA
3639741 TATAAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.13
23 16 0.70
24 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAATTTATTAAATAAAAATTA
Found at i:3640025 original size:25 final size:25
Alignment explanation
Indices: 3639979--3640027 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
3639969 TATAATATAA
* * * *
3639979 ATAAATTTAAAATTTTTTAAATTTG
1 ATAAATTAAAAATATATAAAATTTG
3640004 ATAAATTAAAAATATATAAAATTT
1 ATAAATTAAAAATATATAAAATTT
3640028 AATTATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (25 bp):
ATAAATTAAAAATATATAAAATTTG
Found at i:3647029 original size:2 final size:2
Alignment explanation
Indices: 3647022--3647046 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3647012 GCTTTCCTTT
3647022 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
3647047 TTTTCAACTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3647362 original size:24 final size:23
Alignment explanation
Indices: 3647334--3647389 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
3647324 TCTCCTCCTC
*
3647334 CAATTCCTCATCGGTTTCTCGTTT
1 CAATTCCTCATC-ATTTCTCGTTT
* * *
3647358 CAATTTCTCTTCATTTCTCTTTT
1 CAATTCCTCATCATTTCTCGTTT
*
3647381 CGATTCCTC
1 CAATTCCTC
3647390 TGTTTCCTGA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.12, C:0.30, G:0.07, T:0.50
Consensus pattern (23 bp):
CAATTCCTCATCATTTCTCGTTT
Found at i:3650666 original size:28 final size:28
Alignment explanation
Indices: 3650626--3650713 Score: 167
Period size: 28 Copynumber: 3.1 Consensus size: 28
3650616 CTATTTTCTG
3650626 AATACCACTAATGATACCATTGCAATTT
1 AATACCACTAATGATACCATTGCAATTT
3650654 AATACCACTAATGATACCATTGCAATTT
1 AATACCACTAATGATACCATTGCAATTT
*
3650682 AATGCCACTAATGATACCATTGCAATTT
1 AATACCACTAATGATACCATTGCAATTT
3650710 AATA
1 AATA
3650714 GTCTATGATT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (28 bp):
AATACCACTAATGATACCATTGCAATTT
Found at i:3651395 original size:2 final size:2
Alignment explanation
Indices: 3651388--3651425 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3651378 TCTTAAATTC
*
3651388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3651426 GTATGTTATA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3654487 original size:25 final size:25
Alignment explanation
Indices: 3654455--3654509 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
3654445 CCTCCGAAAT
3654455 AATG-TCATTTTCATAGATATGTCA
1 AATGCTCATTTTCATAGATATGTCA
3654479 AATGCTCATTTTCATAGATATGTCA
1 AATGCTCATTTTCATAGATATGTCA
3654504 AATGCT
1 AATGCT
3654510 GCAGAATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.40
Consensus pattern (25 bp):
AATGCTCATTTTCATAGATATGTCA
Found at i:3658139 original size:22 final size:22
Alignment explanation
Indices: 3658100--3658141 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3658090 ATTGAATTAA
*
3658100 TTAAATTTTAGTTGTTTATATT
1 TTAAATTTTAATTGTTTATATT
3658122 TTAAATTTTAAATT-TTTATA
1 TTAAATTTT-AATTGTTTATA
3658142 ATTAAATAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
TTAAATTTTAATTGTTTATATT
Found at i:3658983 original size:12 final size:12
Alignment explanation
Indices: 3658961--3659010 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
3658951 CTAAACATAT
*
3658961 ATTTCATTATTA
1 ATTTTATTATTA
*
3658973 ATTTTAATATTA
1 ATTTTATTATTA
3658985 ATATTATATTATTA
1 AT-TT-TATTATTA
*
3658999 ATATTATTATTA
1 ATTTTATTATTA
3659011 TAATAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 20 0.62
13 3 0.09
14 9 0.28
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTTATTATTA
Found at i:3658985 original size:6 final size:6
Alignment explanation
Indices: 3658968--3659010 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
3658958 TATATTTCAT
* *
3658968 TATTAA TTTTAA TATTAA TATTATA TTATTAA TATTAT TATTA
1 TATTAA TATTAA TATTAA TATTA-A -TATTAA TATTAA TATTA
3659011 TAATAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
6 25 0.78
7 2 0.06
8 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (6 bp):
TATTAA
Found at i:3658999 original size:20 final size:19
Alignment explanation
Indices: 3658968--3659012 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
3658958 TATATTTCAT
3658968 TATTA-ATTTTAATATTAA
1 TATTATATTTTAATATTAA
*
3658986 TATTATATTATTAATATTAT
1 TATTATATT-TTAATATTAA
3659006 TATTATA
1 TATTATA
3659013 ATAATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 3 0.12
20 16 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTATATTTTAATATTAA
Found at i:3659017 original size:17 final size:17
Alignment explanation
Indices: 3658983--3659034 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
3658973 ATTTTAATAT
3658983 TAATATTA-TATTAT--
1 TAATATTATTATTATAA
3658997 TAATATTATTATTATAA
1 TAATATTATTATTATAA
*
3659014 TAATTATTTTTA-TATAA
1 TAA-TATTATTATTATAA
3659031 TAAT
1 TAAT
3659035 TATTTTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 8 0.24
15 6 0.18
16 1 0.03
17 11 0.33
18 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATATTATTATTATAA
Found at i:3659035 original size:17 final size:17
Alignment explanation
Indices: 3659009--3659042 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3658999 ATATTATTAT
3659009 TATAATAATTATTTTTA
1 TATAATAATTATTTTTA
3659026 TATAATAATTATTTTTA
1 TATAATAATTATTTTTA
3659043 ATTTCATCAA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATAATAATTATTTTTA
Found at i:3659645 original size:7 final size:8
Alignment explanation
Indices: 3659616--3659645 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
3659606 TTTATATAAT
3659616 TATTTTAA
1 TATTTTAA
3659624 TATTTTAA
1 TATTTTAA
3659632 TATTTTAA
1 TATTTTAA
3659640 -ATTTTA
1 TATTTTA
3659646 TAAATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATTTTAA
Found at i:3659652 original size:16 final size:16
Alignment explanation
Indices: 3659617--3659667 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
3659607 TTATATAATT
*
3659617 ATTTTAATATTTTAAT
1 ATTTTAATATTTTAAA
3659633 ATTTTAA-ATTTTATAA
1 ATTTTAATATTTTA-AA
**
3659649 ATTTTTTTATTTTTAAA
1 ATTTTAATA-TTTTAAA
3659666 AT
1 AT
3659668 ATAATTATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 13 0.45
17 5 0.17
18 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTAATATTTTAAA
Found at i:3666761 original size:29 final size:28
Alignment explanation
Indices: 3666708--3666774 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
3666698 TAAAAGCTTT
3666708 TTAAATATA-TTAAAATTTTAAATATAATA
1 TTAAATATATTTAAAATTTT-AATAT-ATA
* *
3666737 TTAATTATATTTAAATATTTT-ATATTTA
1 TTAAATATATTTAAA-ATTTTAATATATA
3666765 TTAAATATAT
1 TTAAATATAT
3666775 CATATTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 11 0.33
29 12 0.36
30 5 0.15
31 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TTAAATATATTTAAAATTTTAATATATA
Found at i:3666779 original size:18 final size:18
Alignment explanation
Indices: 3666747--3666781 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3666737 TTAATTATAT
* *
3666747 TTAAATATTTTATATTTA
1 TTAAATATATCATATTTA
3666765 TTAAATATATCATATTT
1 TTAAATATATCATATTT
3666782 TTTTTAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAAATATATCATATTTA
Found at i:3666793 original size:2 final size:2
Alignment explanation
Indices: 3666788--3666816 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3666778 ATTTTTTTTA
3666788 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
3666817 AAATTAAGAA
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:3667767 original size:20 final size:20
Alignment explanation
Indices: 3667713--3667768 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
3667703 TAAATGAGAT
*
3667713 AAAATATAAA-AAATA-ATA
1 AAAATTTAAATAAATATATA
** *
3667731 AAAATTTTTTATTAATATATA
1 AAAA-TTTAAATAAATATATA
3667752 AAAATTTAAATAAATAT
1 AAAATTTAAATAAATAT
3667769 GTTATATTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
18 4 0.14
19 3 0.11
20 14 0.50
21 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATTTAAATAAATATATA
Found at i:3668645 original size:36 final size:36
Alignment explanation
Indices: 3668603--3668673 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
3668593 TTCCATTCCA
*
3668603 AATCATTTTCAAAATATTATTAAAGTTTACTAAAAT
1 AATCATTTCCAAAATATTATTAAAGTTTACTAAAAT
*
3668639 AATCATTTCCAAAATATTATTAAAGTTTATTAAAA
1 AATCATTTCCAAAATATTATTAAAGTTTACTAAAA
3668674 AAATTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (36 bp):
AATCATTTCCAAAATATTATTAAAGTTTACTAAAAT
Found at i:3671283 original size:2 final size:2
Alignment explanation
Indices: 3671276--3671306 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3671266 TAAATAGTTT
3671276 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3671307 GCACACCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3671810 original size:14 final size:14
Alignment explanation
Indices: 3671791--3671821 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3671781 AATAATTTTG
3671791 AATATAATTAATAT
1 AATATAATTAATAT
*
3671805 AATATATTTAATAT
1 AATATAATTAATAT
3671819 AAT
1 AAT
3671822 TTTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATAATTAATAT
Found at i:3674425 original size:17 final size:16
Alignment explanation
Indices: 3674405--3674454 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
3674395 TAAATTTAAA
3674405 AAATAATTTTTAATATT
1 AAATAATTTTTAA-ATT
*
3674422 AAATAATAATTTAAATT
1 AAATAAT-TTTTAAATT
*
3674439 AAATTA-TTTTAAATT
1 AAATAATTTTTAAATT
3674454 A
1 A
3674455 CTTAAAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 9 0.31
17 15 0.52
18 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATAATTTTTAAATT
Found at i:3674451 original size:15 final size:16
Alignment explanation
Indices: 3674412--3674454 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
3674402 AAAAAATAAT
3674412 TTTTAATATTAAATAATA
1 TTTTAA-ATTAAAT-ATA
*
3674430 ATTTAAATTAAAT-TA
1 TTTTAAATTAAATATA
3674445 TTTTAAATTA
1 TTTTAAATTA
3674455 CTTAAAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 11 0.48
17 7 0.30
18 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTTAAATTAAATATA
Found at i:3676408 original size:14 final size:14
Alignment explanation
Indices: 3676391--3676423 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3676381 AAAATAATTT
3676391 TATATAACAATAAA
1 TATATAACAATAAA
3676405 TATAT-ACAATAAA
1 TATATAACAATAAA
*
3676418 AATATA
1 TATATA
3676424 TTTACAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (14 bp):
TATATAACAATAAA
Found at i:3677238 original size:33 final size:33
Alignment explanation
Indices: 3677157--3677239 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 33
3677147 TTGACTAATA
*
3677157 AAAATATAAATTATTAATTTTTAAAAAATATTCAT
1 AAAA-ATAAATT-TTAATTTATAAAAAATATTCAT
*
3677192 AAAAATAATATTTTAATTTATAAAAAA-ATTTACT
1 AAAAATAA-ATTTTAATTTATAAAAAATATTCA-T
*
3677226 GAAAATAAATTTTA
1 AAAAATAAATTTTA
3677240 CTTCAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
33 10 0.23
34 26 0.60
35 7 0.16
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (33 bp):
AAAAATAAATTTTAATTTATAAAAAATATTCAT
Found at i:3678347 original size:20 final size:20
Alignment explanation
Indices: 3678324--3678362 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3678314 AATATATTAC
* *
3678324 ATAAAAATTAAATTAAAATT
1 ATAAAAATAAAATAAAAATT
*
3678344 ATAATAATAAAATAAAAAT
1 ATAAAAATAAAATAAAAAT
3678363 AAAAGTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
ATAAAAATAAAATAAAAATT
Found at i:3684837 original size:38 final size:37
Alignment explanation
Indices: 3684782--3684863 Score: 146
Period size: 38 Copynumber: 2.2 Consensus size: 37
3684772 AACTATACTA
3684782 TCAATCAAAAAAAGAACTATATGTAATATTAAAATGCT
1 TCAAT-AAAAAAAGAACTATATGTAATATTAAAATGCT
3684820 TCAATAAAAAAATGAACTATATGTAATATTAAAATGCT
1 TCAATAAAAAAA-GAACTATATGTAATATTAAAATGCT
3684858 TCAATA
1 TCAATA
3684864 CAACAGATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
37 7 0.16
38 36 0.84
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.30
Consensus pattern (37 bp):
TCAATAAAAAAAGAACTATATGTAATATTAAAATGCT
Found at i:3684853 original size:22 final size:22
Alignment explanation
Indices: 3684790--3684855 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 22
3684780 TATCAATCAA
*
3684790 AAAAAGAACTATATGTAATATT
1 AAAATGAACTATATGTAATATT
*
3684812 AAAATG--CT-TCA-ATAA-A--
1 AAAATGAACTAT-ATGTAATATT
3684828 AAAATGAACTATATGTAATATT
1 AAAATGAACTATATGTAATATT
3684850 AAAATG
1 AAAATG
3684856 CTTCAATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 16
0.63 0.06 0.31
Matches are distributed among these distances:
16 6 0.18
18 4 0.12
19 8 0.24
20 4 0.12
22 11 0.33
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (22 bp):
AAAATGAACTATATGTAATATT
Found at i:3690926 original size:33 final size:33
Alignment explanation
Indices: 3690889--3690955 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
3690879 CAATGTTCTA
*
3690889 TGATTAGTCTGTTTGATACTCAATTCTTTGGTT
1 TGATTAGTCTGTTTGATACACAATTCTTTGGTT
*
3690922 TGATTAGTCTGTTTGATACACCATTCTTTGGTT
1 TGATTAGTCTGTTTGATACACAATTCTTTGGTT
3690955 T
1 T
3690956 TTCAGAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.51
Consensus pattern (33 bp):
TGATTAGTCTGTTTGATACACAATTCTTTGGTT
Found at i:3695942 original size:3 final size:3
Alignment explanation
Indices: 3695936--3695970 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3695926 AATAATAATA
3695936 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3695971 AATGTACAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3697004 original size:2 final size:2
Alignment explanation
Indices: 3696989--3697025 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
3696979 TACCTACAAT
* *
3696989 TA TA TA TG TG 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
3697026 TAAGCGAATT
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:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3703837 original size:2 final size:2
Alignment explanation
Indices: 3703825--3703858 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
3703815 AATCTAAATA
3703825 AT AT CAT 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 A
3703859 CCGAAATCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3704344 original size:2 final size:2
Alignment explanation
Indices: 3704337--3704362 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3704327 AGATCCATAG
3704337 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
3704363 ATGCAGCTAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:3705224 original size:18 final size:18
Alignment explanation
Indices: 3705203--3705255 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
3705193 ATATTTTCTA
3705203 ATTAATAAATTTTAATAT
1 ATTAATAAATTTTAATAT
3705221 ATTAAT-AA-TTT-ATAT
1 ATTAATAAATTTTAATAT
*
3705236 -TAAATAAATTTTAATAT
1 ATTAATAAATTTTAATAT
3705253 ATT
1 ATT
3705256 CATTCTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 6 0.21
17 6 0.21
18 7 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTAATAAATTTTAATAT
Found at i:3707424 original size:44 final size:46
Alignment explanation
Indices: 3707363--3707453 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 46
3707353 GTATTGTTAA
* * * *
3707363 ATTTATTATTAATTTTTATGTAAAT-TTTTTATTAATAAATTAAATT
1 ATTTATTATTAATTTTTAT-TAAATAATTTTAATAAAAAAATAAATT
3707409 ATTTA-TATTAA-TTTTATTAAATAATTTTAATAAAAAAATAAATT
1 ATTTATTATTAATTTTTATTAAATAATTTTAATAAAAAAATAAATT
3707453 A
1 A
3707454 AGTATACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 5 0.12
44 24 0.60
45 6 0.15
46 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (46 bp):
ATTTATTATTAATTTTTATTAAATAATTTTAATAAAAAAATAAATT
Found at i:3707427 original size:23 final size:23
Alignment explanation
Indices: 3707363--3707435 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
3707353 GTATTGTTAA
3707363 ATTTATTATTAATTTTTATGTAAATT
1 ATTTA-TATTAA-TTTTAT-TAAATT
**
3707389 -TTT-TATTAA-TAAATTAAATT
1 ATTTATATTAATTTTATTAAATT
*
3707409 ATTTATATTAATTTTATTAAATA
1 ATTTATATTAATTTTATTAAATT
3707432 ATTT
1 ATTT
3707436 TAATAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
20 6 0.15
21 6 0.15
22 6 0.15
23 18 0.46
25 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (23 bp):
ATTTATATTAATTTTATTAAATT
Found at i:3707586 original size:22 final size:23
Alignment explanation
Indices: 3707539--3707607 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 23
3707529 TGTTAATATT
* *
3707539 ATTTAATAAAATTAA-AGTAAATA
1 ATTTAAT-TAATTAATAATAAATA
3707562 ATTTAATTAATTAATAATAAA-A
1 ATTTAATTAATTAATAATAAATA
3707584 ATTTAA-TAATATAATTTAATAAAT
1 ATTTAATTAAT-TAA--TAATAAAT
3707608 TAAAAGTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
21 4 0.10
22 16 0.41
23 12 0.31
24 7 0.18
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (23 bp):
ATTTAATTAATTAATAATAAATA
Found at i:3707591 original size:14 final size:13
Alignment explanation
Indices: 3707572--3707605 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3707562 ATTTAATTAA
3707572 TTAATAATAAAAAT
1 TTAATAAT-AAAAT
*
3707586 TTAATAATATAAT
1 TTAATAATAAAAT
3707599 TTAATAA
1 TTAATAA
3707606 ATTAAAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAATAATAAAAT
Found at i:3707598 original size:35 final size:34
Alignment explanation
Indices: 3707542--3707610 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
3707532 TAATATTATT
*
3707542 TAATAAAATTAAAGTAAATAATTTAATTAATTAA
1 TAATAAAATTAAAGTAAATAATTTAATAAATTAA
*
3707576 TAATAAAAATTTAA-TAATATAATTTAATAAATTAA
1 TAAT-AAAATTAAAGTAA-ATAATTTAATAAATTAA
3707611 AAGTTTGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 7 0.23
35 24 0.77
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (34 bp):
TAATAAAATTAAAGTAAATAATTTAATAAATTAA
Found at i:3714631 original size:22 final size:22
Alignment explanation
Indices: 3714604--3714649 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3714594 GATATTCGTC
3714604 TGTTTGATAGATTAAATTTATA
1 TGTTTGATAGATTAAATTTATA
3714626 TGTTTGATAGATTAAATTTATA
1 TGTTTGATAGATTAAATTTATA
3714648 TG
1 TG
3714650 AATCGAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (22 bp):
TGTTTGATAGATTAAATTTATA
Found at i:3714786 original size:14 final size:14
Alignment explanation
Indices: 3714739--3714786 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
3714729 TTCAAATTTA
3714739 ATTATAAAAAT-AT
1 ATTATAAAAATAAT
* *
3714752 ATATATAAAACTATT
1 AT-TATAAAAATAAT
*
3714767 AATATAAAAATAAT
1 ATTATAAAAATAAT
3714781 ATTATA
1 ATTATA
3714787 TATATATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
13 2 0.07
14 23 0.85
15 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTATAAAAATAAT
Found at i:3716329 original size:14 final size:14
Alignment explanation
Indices: 3716289--3716342 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
3716279 CATTTTTTTT
*
3716289 ATAAAGTTTAATTAA
1 ATAAA-TTTATTTAA
* *
3716304 ATAAAATAATTTAA
1 ATAAATTTATTTAA
3716318 ATAAATTTATTT-A
1 ATAAATTTATTTAA
*
3716331 ATCAATTTATTT
1 ATAAATTTATTT
3716343 CTTTTATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 12 0.36
14 16 0.48
15 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (14 bp):
ATAAATTTATTTAA
Found at i:3725119 original size:30 final size:30
Alignment explanation
Indices: 3725085--3725148 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
3725075 ACTGATAATA
3725085 ATTATATTT-TAGAATAAGTAT-AAATTTATC
1 ATTATATTTATAGAATAA-T-TCAAATTTATC
* *
3725115 ATTATATTTATGGGATAATTCAAATTTATC
1 ATTATATTTATAGAATAATTCAAATTTATC
3725145 ATTA
1 ATTA
3725149 ATTATGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 23 0.77
31 6 0.20
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.47
Consensus pattern (30 bp):
ATTATATTTATAGAATAATTCAAATTTATC
Found at i:3727073 original size:42 final size:39
Alignment explanation
Indices: 3726979--3727134 Score: 109
Period size: 40 Copynumber: 4.0 Consensus size: 39
3726969 CGTAAATTTA
3726979 AATATAA-TATAA-T-TAAAAAA-AT-TAAAATTTAATAT
1 AATATAATTATAAGTATAAAAAATATATAAAATTT-ATAT
* *
3727014 AAT-TATTTTTTAA--ATAAATAAATATAT-AAATTTATAT
1 AATATA-ATTATAAGTATAAA-AAATATATAAAATTTATAT
*
3727051 AATATATATTATTAAAGTATAAAAAATTATATAAAATATTTTA-
1 AATATA-ATTA-T-AAGTATAAAAAA-TATATAAAAT-TTATAT
*
3727094 AATATAATTATAATTATATAAAAATATATGAAAA-TTATAT
1 AATATAATTATAAGTATA-AAAAATATAT-AAAATTTATAT
3727134 A
1 A
3727135 GACACAAAAA
Statistics
Matches: 97, Mismatches: 7, Indels: 29
0.73 0.05 0.22
Matches are distributed among these distances:
34 2 0.02
35 3 0.03
36 8 0.08
37 10 0.10
38 13 0.13
39 6 0.06
40 14 0.14
41 13 0.13
42 14 0.14
43 10 0.10
44 4 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (39 bp):
AATATAATTATAAGTATAAAAAATATATAAAATTTATAT
Found at i:3727090 original size:30 final size:28
Alignment explanation
Indices: 3727032--3727116 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 28
3727022 TTTAAATAAA
* *
3727032 TAAATATATAAATTTATATAATATATATTAT
1 TAAATATAAAAAATTATATAA-A-ATATT-T
3727063 TAAAGTATAAAAAATTATATAAAATATTT
1 TAAA-TATAAAAAATTATATAAAATATTT
*
3727092 TAAATATAATTATAATTATATAAAA
1 TAAATATAA--AAAATTATATAAAA
3727117 ATATATGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 5 0.10
29 5 0.10
30 18 0.38
31 5 0.10
32 15 0.31
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (28 bp):
TAAATATAAAAAATTATATAAAATATTT
Found at i:3727132 original size:11 final size:10
Alignment explanation
Indices: 3727036--3727134 Score: 58
Period size: 10 Copynumber: 9.6 Consensus size: 10
3727026 AATAAATAAA
*
3727036 TATATAAATT
1 TATATAAAAT
*
3727046 TATATAATAT
1 TATATAAAAT
* *
3727056 ATATTATTAAAG
1 -TA-TATAAAAT
*
3727068 TATAAAAAAT
1 TATATAAAAT
3727078 TATATAAAA-
1 TATATAAAAT
* *
3727087 TATTTTAAA-
1 TATATAAAAT
*
3727096 TATAATTATAAT
1 TAT-A-TAAAAT
*
3727108 TATATAAAAA
1 TATATAAAAT
3727118 TATATGAAAAT
1 TATAT-AAAAT
3727129 TATATA
1 TATATA
3727135 GACACAAAAA
Statistics
Matches: 66, Mismatches: 17, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
9 10 0.15
10 31 0.47
11 17 0.26
12 8 0.12
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (10 bp):
TATATAAAAT
Found at i:3728410 original size:150 final size:150
Alignment explanation
Indices: 3728133--3728433 Score: 498
Period size: 150 Copynumber: 2.0 Consensus size: 150
3728123 ATTGAGCCTA
* *
3728133 TATGAATTACTGGAGTTTATTGCGTATTATTTGATTCAACGATCATTAAGAATTATTTAGTGGGA
1 TATGAATTACTGGAGTTAATTGCGTATTATTTGATCCAACGATCATTAAGAATTATTTAGTGGGA
* * *
3728198 TGACTAATTATAATATATTTATATATTTCAATATCGAAGTTAAAACAGTTTGTTAAT-TTTTAAT
66 TGAATAATTATAATATATTTATATATTTCAATATCGAAGTTAAAACAGTTTGTTAATGTTTAAAA
3728262 TTTTTATAATGTTTCTGATTT
131 TTTTTATAATGTTT-TGATTT
* *
3728283 TATGAATTACTGGAGTTAATTGTGTATTATTTGATCCAACGATCATTAAGAATTGTTTAGTGGGA
1 TATGAATTACTGGAGTTAATTGCGTATTATTTGATCCAACGATCATTAAGAATTATTTAGTGGGA
*
3728348 TGAATAATTATAATATATTTATATATTTCAATTTCGAAGTTAAAAACAGTTTGTTAA-GTTTAAA
66 TGAATAATTATAATATATTTATATATTTCAATATCGAAGTT-AAAACAGTTTGTTAATGTTTAAA
3728412 ATTTTTATAATGTTTTGATTT
130 ATTTTTATAATGTTTTGATTT
3728433 T
1 T
3728434 GGTATGTAGC
Statistics
Matches: 141, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
150 107 0.76
151 34 0.24
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.47
Consensus pattern (150 bp):
TATGAATTACTGGAGTTAATTGCGTATTATTTGATCCAACGATCATTAAGAATTATTTAGTGGGA
TGAATAATTATAATATATTTATATATTTCAATATCGAAGTTAAAACAGTTTGTTAATGTTTAAAA
TTTTTATAATGTTTTGATTT
Found at i:3730949 original size:2 final size:2
Alignment explanation
Indices: 3730942--3730971 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3730932 CTTTGTTTAT
3730942 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
3730972 AATAGTCATG
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:3732469 original size:146 final size:144
Alignment explanation
Indices: 3732192--3732479 Score: 378
Period size: 146 Copynumber: 2.0 Consensus size: 144
3732182 CATGCACGTA
* * * * * *
3732192 TTGTTTTTGAGGAACTTCTAAGAATAAAAGAACTAGTTATTCGGGACTTCTGAACTTGTGAAAAG
1 TTGTTTTTGAGCAACGTCGAAGAATAAAAGAACTAATTATTCAGGACTTCTAAACTTGTGAAAAG
* * *
3732257 GAAAGAAAAATAGAAGGGACAAAACCAACTCACACGAGCTTGCTGATTTGACAATGTGTTCCAAT
66 GAAAAAAAAATAGAAGGGACAAAACCAACTCACACGAGCTTGCTGATTTGACAAGGGGTTCCAAT
3732322 AAGATTAAGTTGTT
131 AAGATTAAGTTGTT
* * * * * *
3732336 TTGTTTTTGAGCAACGTCGAAGAATAAATGTACTAATTATTTAGGACTTTTAAATTTGTGAAATG
1 TTGTTTTTGAGCAACGTCGAAGAATAAAAGAACTAATTATTCAGGACTTCTAAACTTGTGAAAAG
* * * *
3732401 GAAGAAAAAAAATAGAGGGGACAAAACCAGCTCATACGAGCTTGCTGATTTGACAAGGGGTTCGA
66 G-A-AAAAAAAATAGAAGGGACAAAACCAACTCACACGAGCTTGCTGATTTGACAAGGGGTTCCA
*
3732466 ATAAGATTAGGTTG
129 ATAAGATTAAGTTG
3732480 GTTGGTCTTT
Statistics
Matches: 122, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
144 54 0.44
145 1 0.01
146 67 0.55
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (144 bp):
TTGTTTTTGAGCAACGTCGAAGAATAAAAGAACTAATTATTCAGGACTTCTAAACTTGTGAAAAG
GAAAAAAAAATAGAAGGGACAAAACCAACTCACACGAGCTTGCTGATTTGACAAGGGGTTCCAAT
AAGATTAAGTTGTT
Found at i:3734860 original size:18 final size:19
Alignment explanation
Indices: 3734828--3734865 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3734818 ATAATGTCTA
*
3734828 AAATATTAAATATTTATAT
1 AAATATTAAAAATTTATAT
3734847 AAAT-TTAAAAATTTATAT
1 AAATATTAAAAATTTATAT
3734865 A
1 A
3734866 TATAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATATTAAAAATTTATAT
Found at i:3734870 original size:22 final size:23
Alignment explanation
Indices: 3734842--3734889 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
3734832 ATTAAATATT
3734842 TATATAAATTTAA-AAATTTATA
1 TATATAAATTTAATAAATTTATA
*
3734864 TATATAAATTTAATATATTTATA
1 TATATAAATTTAATAAATTTATA
3734887 TAT
1 TAT
3734890 TCATATTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATAAATTTAATAAATTTATA
Found at i:3735046 original size:15 final size:16
Alignment explanation
Indices: 3735016--3735049 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3735006 CCATTAAGCT
*
3735016 ATTTTTTTTATATTGC
1 ATTTTTGTTATATTGC
3735032 ATTTTTGTTAT-TTGC
1 ATTTTTGTTATATTGC
3735047 ATT
1 ATT
3735050 CTTTACTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.68
Consensus pattern (16 bp):
ATTTTTGTTATATTGC
Found at i:3735586 original size:2 final size:2
Alignment explanation
Indices: 3735581--3735614 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3735571 TTTTTGAATT
3735581 TA 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 TA
3735615 AATTTATTTT
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):
TA
Found at i:3742617 original size:2 final size:2
Alignment explanation
Indices: 3742610--3742638 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3742600 TTCTGGTTGG
3742610 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3742639 ATTATTATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3744321 original size:17 final size:18
Alignment explanation
Indices: 3744296--3744329 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3744286 TTAAAATTTG
*
3744296 TATATAATTTTT-ATTAT
1 TATAAAATTTTTGATTAT
3744313 TATAAAATTTTTGATTA
1 TATAAAATTTTTGATTA
3744330 AATTTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TATAAAATTTTTGATTAT
Found at i:3746669 original size:28 final size:28
Alignment explanation
Indices: 3746601--3746669 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
3746591 TTAAAAGTAT
*
3746601 AATAAAAATATATAATTTAAAAAATTTA
1 AATAAAAATATATTATTTAAAAAATTTA
**
3746629 AAT--ATTTGATATTATTATAAAAAA-TTA
1 AATAAAAAT-ATATTATT-TAAAAAATTTA
3746656 AATAAAAATATATT
1 AATAAAAATATATT
3746670 TAAAATAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
26 2 0.06
27 13 0.41
28 15 0.47
29 2 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (28 bp):
AATAAAAATATATTATTTAAAAAATTTA
Found at i:3746684 original size:16 final size:18
Alignment explanation
Indices: 3746654--3746693 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
3746644 TATAAAAAAT
3746654 TAAATAAAAATATATTTA
1 TAAATAAAAATATATTTA
*
3746672 -AAATAATAA-ATATTTA
1 TAAATAAAAATATATTTA
3746688 TAAATA
1 TAAATA
3746694 TTTAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAATAAAAATATATTTA
Found at i:3746747 original size:17 final size:17
Alignment explanation
Indices: 3746694--3746751 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
3746684 TTTATAAATA
3746694 TTTAAATAATCAAAT-TAT
1 TTTAAATAAT-AAATAT-T
** *
3746712 TTTATCTAAAAAATAATT
1 TTTAAATAATAAAT-ATT
3746730 TTTAAATAATAAATATT
1 TTTAAATAATAAATATT
3746747 TTTAA
1 TTTAA
3746752 TTTTTATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 12 0.38
18 19 0.59
19 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAATAATAAATATT
Found at i:3746798 original size:33 final size:34
Alignment explanation
Indices: 3746743--3746808 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 34
3746733 AAATAATAAA
** *
3746743 TATTTTTAATTTTTATTTTTAAATTATAATTTAT
1 TATTTTTAATTTCAATTATTAAATTATAATTTAT
3746777 TATTTTT-ATTTCAATTATTAAATTATAATTTA
1 TATTTTTAATTTCAATTATTAAATTATAATTTA
3746809 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (34 bp):
TATTTTTAATTTCAATTATTAAATTATAATTTAT
Found at i:3747992 original size:2 final size:2
Alignment explanation
Indices: 3747987--3748019 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3747977 CATAAATTGT
3747987 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3748020 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3749532 original size:2 final size:2
Alignment explanation
Indices: 3749525--3749567 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3749515 AAGATTTTAT
3749525 TA TA TA TA TA 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 TA TA TA TA TA
3749567 T
1 T
3749568 GGTAACTCTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3752170 original size:2 final size:2
Alignment explanation
Indices: 3752127--3752153 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3752117 ATTATTAAAC
3752127 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
3752154 CACGTGACTA
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:3753300 original size:2 final size:2
Alignment explanation
Indices: 3753295--3753332 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3753285 GGAAAAAAGG
3753295 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3753333 ACCAACATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3753955 original size:16 final size:17
Alignment explanation
Indices: 3753926--3753957 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3753916 TAAACATAAT
3753926 ATAAATTATTAAATATA
1 ATAAATTATTAAATATA
3753943 ATAAATT-TTAAATAT
1 ATAAATTATTAAATAT
3753958 TTGATATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAATTATTAAATATA
Found at i:3769402 original size:19 final size:20
Alignment explanation
Indices: 3769375--3769412 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
3769365 ATTTTATATG
3769375 AAAACAAAAATATTATATAC
1 AAAACAAAAATATTATATAC
* *
3769395 AAAA-AAAATTATTTTATA
1 AAAACAAAAATATTATATA
3769413 TATTGTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAACAAAAATATTATATAC
Found at i:3770456 original size:26 final size:27
Alignment explanation
Indices: 3770427--3770485 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 27
3770417 TAAAATTTAA
3770427 TTTAATTATTAATAAA-TAT-ATACTTT
1 TTTAATTATTAATAAATTATGATA-TTT
*
3770453 TTT-ATTATTTATAAATTATGATATTT
1 TTTAATTATTAATAAATTATGATATTT
3770479 TTGTAAT
1 TT-TAAT
3770486 ATATGTCCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
25 11 0.39
26 11 0.39
27 4 0.14
28 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (27 bp):
TTTAATTATTAATAAATTATGATATTT
Found at i:3772630 original size:2 final size:2
Alignment explanation
Indices: 3772623--3772661 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
3772613 ATATTATCAA
* * *
3772623 AT AT AT AT TT AT TT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3772662 ACAAGCTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3773894 original size:16 final size:17
Alignment explanation
Indices: 3773869--3773910 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
3773859 TTTTTAAAAA
3773869 ATAATA-TTTAATAATTT
1 ATAATATTTTAAT-ATTT
3773886 -TAA-ATTTTAATATTT
1 ATAATATTTTAATATTT
3773901 ATAATATTTT
1 ATAATATTTT
3773911 TTATTATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.23
16 12 0.55
17 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATAATATTTTAATATTT
Found at i:3773905 original size:9 final size:8
Alignment explanation
Indices: 3773870--3773910 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 8
3773860 TTTTAAAAAA
3773870 TAATA-TT
1 TAATATTT
3773877 TAATAATTT
1 TAAT-ATTT
3773886 TAA-ATTT
1 TAATATTT
3773893 TAATATTT
1 TAATATTT
3773901 ATAATATTT
1 -TAATATTT
3773910 T
1 T
3773911 TTATTATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 11 0.37
8 6 0.20
9 13 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TAATATTT
Done.