Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold43
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: 2559314
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13088 characters in sequence are not A, C, G, or T
File 18 of 19
Found at i:2178676 original size:18 final size:19
Alignment explanation
Indices: 2178655--2178692 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2178645 AAATTGAGTT
*
2178655 ATTTATTTAA-ATTTTAAA
1 ATTTATCTAATATTTTAAA
2178673 ATTTATCTAATATTTTAAA
1 ATTTATCTAATATTTTAAA
2178692 A
1 A
2178693 AATTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTATCTAATATTTTAAA
Found at i:2181256 original size:24 final size:25
Alignment explanation
Indices: 2181194--2181256 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
2181184 ATATGACACG
*
2181194 AATTAAATAATTAAAATAAAATATA
1 AATTAAATTATTAAAATAAAATATA
* **
2181219 AATTTATATT-TTAAAAT-TTATATA
1 AA-TTAAATTATTAAAATAAAATATA
2181243 AATTAAATTATTAA
1 AATTAAATTATTAA
2181257 TGTATGTGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 6 0.19
24 11 0.35
25 9 0.29
26 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATTAAATTATTAAAATAAAATATA
Found at i:2182429 original size:2 final size:2
Alignment explanation
Indices: 2182422--2182459 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2182412 TTATTTTGGG
2182422 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
2182460 CTGTTGTAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2186968 original size:23 final size:21
Alignment explanation
Indices: 2186923--2186969 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
2186913 AGGTTTTGTT
*
2186923 TTATAAAAATAATTAATTTAA
1 TTATAAAAATAATTAATTAAA
*
2186944 TTATATAAATAAATTAAATTAAA
1 TTATAAAAAT-AATT-AATTAAA
2186967 TTA
1 TTA
2186970 AATTTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 4 0.18
23 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTATAAAAATAATTAATTAAA
Found at i:2188163 original size:21 final size:22
Alignment explanation
Indices: 2188139--2188179 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2188129 TTTATTTTAT
2188139 TATT-TTTTTAAAAAATTAATA
1 TATTATTTTTAAAAAATTAATA
* *
2188160 TATTATTTTTATAAATTTAA
1 TATTATTTTTAAAAAATTAA
2188180 GAAAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTATTTTTAAAAAATTAATA
Found at i:2188290 original size:20 final size:18
Alignment explanation
Indices: 2188265--2188304 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
2188255 AAAATTATCA
*
2188265 ATTATTTTATTTAATATAAT
1 ATTATTTT-TATAA-ATAAT
2188285 ATTATTTTTATAAATAAT
1 ATTATTTTTATAAATAAT
2188303 AT
1 AT
2188305 ATTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 4 0.21
20 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATTTTTATAAATAAT
Found at i:2188317 original size:24 final size:23
Alignment explanation
Indices: 2188276--2188323 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
2188266 TTATTTTATT
* *
2188276 TAATATAATATTATTTTTATAAA
1 TAATATAATATTAATTTTAAAAA
*
2188299 TAATATATTAATTAATTTTAAAAA
1 TAATATAAT-ATTAATTTTAAAAA
2188323 T
1 T
2188324 TCTTAAGTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TAATATAATATTAATTTTAAAAA
Found at i:2188522 original size:25 final size:24
Alignment explanation
Indices: 2188491--2188569 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 24
2188481 TCGACATTAA
2188491 ATTTTATAATTTGTATATTTATATT
1 ATTTTATAATTT-TATATTTATATT
*
2188516 ATTTTATATATTTTATTATATAATAATT
1 ATTTTATA-ATTTTA-TAT-TTAT-ATT
*
2188544 ATATTTAAAATATTTTATATTTATAT
1 AT-TTT-ATA-ATTTTATATTTATAT
2188570 AAAATTAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
25 10 0.22
26 7 0.16
27 5 0.11
28 8 0.18
29 6 0.13
30 9 0.20
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (24 bp):
ATTTTATAATTTTATATTTATATT
Found at i:2188532 original size:17 final size:18
Alignment explanation
Indices: 2188491--2188534 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
2188481 TCGACATTAA
*
2188491 ATTTTATAATTTGTATAT
1 ATTTTATTATTTGTATAT
*
2188509 -TTATATTATTT-TATAT
1 ATTTTATTATTTGTATAT
2188525 ATTTTATTAT
1 ATTTTATTAT
2188535 ATAATAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
ATTTTATTATTTGTATAT
Found at i:2188609 original size:58 final size:58
Alignment explanation
Indices: 2188532--2188674 Score: 163
Period size: 58 Copynumber: 2.5 Consensus size: 58
2188522 TATATTTTAT
*
2188532 TATATAATAATTATA-TTTAAAATATTTTATATTTATA-TAAAATTAAATATATTAATAAT-A
1 TATATTAT-ATTATATTTTAAAATATTTTATATTTATATTAAAA-T-AATA-A-TAATAATAA
* *
2188592 TATATTATA-TA-ATTTTAAAATATTTTTTATTTATATTATAATAATAATAATAATAA
1 TATATTATATTATATTTTAAAATATTTTATATTTATATTAAAATAATAATAATAATAA
*
2188648 TATTTTATATTATATTTT-AAATATTTT
1 TATATTATATTATATTTTAAAATATTTT
2188675 TTTATGTTAG
Statistics
Matches: 74, Mismatches: 4, Indels: 13
0.81 0.04 0.14
Matches are distributed among these distances:
55 7 0.09
56 10 0.14
57 16 0.22
58 29 0.39
59 5 0.07
60 7 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (58 bp):
TATATTATATTATATTTTAAAATATTTTATATTTATATTAAAATAATAATAATAATAA
Found at i:2189873 original size:8 final size:8
Alignment explanation
Indices: 2189843--2189901 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
2189833 TTAATGTGAT
2189843 TATATTTA
1 TATATTTA
2189851 -ATATTTA
1 TATATTTA
* *
2189858 AATTTTTA
1 TATATTTA
2189866 TATATTTA
1 TATATTTA
* *
2189874 AAAATTATA
1 TATATT-TA
2189883 TATAATTT-
1 TAT-ATTTA
2189891 TATATTTA
1 TATATTTA
2189899 TAT
1 TAT
2189902 TTAAAAACAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
7 11 0.28
8 22 0.55
9 4 0.10
10 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TATATTTA
Found at i:2190629 original size:3 final size:3
Alignment explanation
Indices: 2190621--2190657 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2190611 AATAACGCCA
2190621 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
2190658 GCTGCTGCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:2190662 original size:3 final size:3
Alignment explanation
Indices: 2190656--2190680 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2190646 TCTTCTTCTT
2190656 CTG CTG CTG CTG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG C
2190681 AAGAAACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.32, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:2190966 original size:3 final size:3
Alignment explanation
Indices: 2190954--2190985 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2190944 GTTTGCTCGC
2190954 TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2190986 AGAATTTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:2195406 original size:2 final size:2
Alignment explanation
Indices: 2195399--2195434 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2195389 AATCAAAATG
2195399 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
2195435 TGGAGTTTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2199030 original size:3 final size:3
Alignment explanation
Indices: 2199022--2199087 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
2199012 AAATATTTAC
* * * * * * *
2199022 TAT TAT TAT TTT TAT TAT TAC TAC TAC TAC TAC TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2199070 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
2199088 AAGAGAAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:2199365 original size:2 final size:2
Alignment explanation
Indices: 2199358--2199395 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2199348 CCGCCATCAC
2199358 AG AG AG AG 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
2199396 TTTTCGTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2199698 original size:18 final size:18
Alignment explanation
Indices: 2199668--2199702 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2199658 ATTAATAATA
2199668 TATATGTTTATAAATTTT
1 TATATGTTTATAAATTTT
2199686 TATAT-TTTAATAAATTT
1 TATATGTTT-ATAAATTT
2199703 AATTAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
TATATGTTTATAAATTTT
Found at i:2200444 original size:2 final size:2
Alignment explanation
Indices: 2200437--2200463 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2200427 AGTGGTAAGT
2200437 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 T
2200464 GTAGGGAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2204968 original size:24 final size:23
Alignment explanation
Indices: 2204938--2204999 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 23
2204928 TTAAAAAATA
2204938 AAAATAAGAATAATATTA-TATATT
1 AAAATAA-AATAATA-TAGTATATT
*
2204962 AAAATAATATTAATATAGTATATT
1 AAAATAA-AATAATATAGTATATT
2204986 ATAAATAAAATAAT
1 A-AAATAAAATAAT
2205000 TATATAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 2 0.06
24 25 0.76
25 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (23 bp):
AAAATAAAATAATATAGTATATT
Found at i:2205009 original size:5 final size:5
Alignment explanation
Indices: 2204947--2205091 Score: 71
Period size: 5 Copynumber: 30.4 Consensus size: 5
2204937 AAAAATAAGA
* * * * *
2204947 ATAAT ATTAT AT-AT -TAAA ATAAT ATTAAT ATAGT ATATT ATAA- ATAAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT
* * *
2204995 ATAAT -T-AT ATAAT AT-AT A-ACT ATATT ATTAAATT ATAAT ATATT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-T-AA-T ATAAT ATAAT
* *
2205039 TTAAT AT-AT ATAAT AAAAT ATAAT ATAAT AT--T ATAAT ATGAAT -T-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AAT ATAAT
2205085 ATAAT AT
1 ATAAT AT
2205092 GATACGAAAT
Statistics
Matches: 107, Mismatches: 16, Indels: 34
0.68 0.10 0.22
Matches are distributed among these distances:
3 8 0.07
4 19 0.18
5 65 0.61
6 11 0.10
7 2 0.02
8 2 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (5 bp):
ATAAT
Found at i:2205010 original size:27 final size:26
Alignment explanation
Indices: 2204938--2205011 Score: 70
Period size: 27 Copynumber: 3.0 Consensus size: 26
2204928 TTAAAAAATA
2204938 AAAATAAGAATAA-TAT-T-ATATATT
1 AAAATAA-AATAATTATATAATATATT
*
2204962 AAAAT--AAT-ATTAATATAGTATATT
1 AAAATAAAATAATT-ATATAATATATT
2204986 ATAAATAAAATAATTATATAATATAT
1 A-AAATAAAATAATTATATAATATAT
2205012 AACTATATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
20 1 0.03
21 4 0.10
22 2 0.05
23 1 0.03
24 12 0.30
25 4 0.10
27 13 0.32
28 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (26 bp):
AAAATAAAATAATTATATAATATATT
Found at i:2205024 original size:38 final size:38
Alignment explanation
Indices: 2204965--2205048 Score: 88
Period size: 38 Copynumber: 2.3 Consensus size: 38
2204955 ATATATTAAA
2204965 ATAATAT-TAATATAGTATATTATAAATAAAATA-ATTAT
1 ATAATATATAATATAGTATATTA-AAATAAAATATATT-T
* *
2205003 ATAATATATAACTATA-T-TATTAAATTATAATATATTT
1 ATAATATATAA-TATAGTATATTAAAATAAAATATATTT
2205040 -TAATATATA
1 ATAATATATA
2205049 TAATAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
36 9 0.22
37 9 0.22
38 15 0.37
39 4 0.10
40 4 0.10
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (38 bp):
ATAATATATAATATAGTATATTAAAATAAAATATATTT
Found at i:2205089 original size:14 final size:13
Alignment explanation
Indices: 2205044--2205093 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 13
2205034 ATATTTTAAT
2205044 ATATATAATA--A
1 ATATATAATATGA
2205055 A-ATATAATAT-A
1 ATATATAATATGA
2205066 ATATTATAATATGA
1 ATA-TATAATATGA
2205080 ATTATATAATATGA
1 A-TATATAATATGA
2205094 TACGAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
10 8 0.24
11 3 0.09
12 1 0.03
13 8 0.24
14 12 0.35
15 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
ATATATAATATGA
Found at i:2206261 original size:16 final size:15
Alignment explanation
Indices: 2206213--2206264 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 15
2206203 TCTTTTTTAA
2206213 AAAATTATTAATATATT
1 AAAATTATTAA-ATA-T
*
2206230 AACATTTATATAAATAT
1 AA-AATTAT-TAAATAT
2206247 AAAATATATTAAATAT
1 AAAAT-TATTAAATAT
2206263 AA
1 AA
2206265 TTATAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 11 0.37
17 8 0.27
18 8 0.27
19 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATTATTAAATAT
Found at i:2208124 original size:2 final size:2
Alignment explanation
Indices: 2208117--2208148 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2208107 AACTTCAACC
2208117 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
2208149 CAATTTGGTC
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:2212626 original size:2 final size:2
Alignment explanation
Indices: 2212619--2212657 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2212609 CAGGTCTTTC
2212619 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2212658 ACTTCCCTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2218687 original size:160 final size:160
Alignment explanation
Indices: 2218423--2218744 Score: 644
Period size: 160 Copynumber: 2.0 Consensus size: 160
2218413 AAGTCGTATC
2218423 AGTCCTTTCTGCGCATATCAAAACAAAACAGGTGCCCATCCTAGAAAACAGTAAGGACGTCAAAG
1 AGTCCTTTCTGCGCATATCAAAACAAAACAGGTGCCCATCCTAGAAAACAGTAAGGACGTCAAAG
2218488 GAAGCACTGCATAACCATTGATTGCTAGCCACTTAATTAACTTATCGTACCAACGAAACATTTGG
66 GAAGCACTGCATAACCATTGATTGCTAGCCACTTAATTAACTTATCGTACCAACGAAACATTTGG
2218553 GCTTCACTTTTGCATAAAACAATTGAAAAA
131 GCTTCACTTTTGCATAAAACAATTGAAAAA
2218583 AGTCCTTTCTGCGCATATCAAAACAAAACAGGTGCCCATCCTAGAAAACAGTAAGGACGTCAAAG
1 AGTCCTTTCTGCGCATATCAAAACAAAACAGGTGCCCATCCTAGAAAACAGTAAGGACGTCAAAG
2218648 GAAGCACTGCATAACCATTGATTGCTAGCCACTTAATTAACTTATCGTACCAACGAAACATTTGG
66 GAAGCACTGCATAACCATTGATTGCTAGCCACTTAATTAACTTATCGTACCAACGAAACATTTGG
2218713 GCTTCACTTTTGCATAAAACAATTGAAAAA
131 GCTTCACTTTTGCATAAAACAATTGAAAAA
2218743 AG
1 AG
2218745 GCTTGACTTT
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (160 bp):
AGTCCTTTCTGCGCATATCAAAACAAAACAGGTGCCCATCCTAGAAAACAGTAAGGACGTCAAAG
GAAGCACTGCATAACCATTGATTGCTAGCCACTTAATTAACTTATCGTACCAACGAAACATTTGG
GCTTCACTTTTGCATAAAACAATTGAAAAA
Found at i:2221333 original size:21 final size:22
Alignment explanation
Indices: 2221298--2221340 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2221288 ATCTTTACCA
2221298 TAAGATAAAACTTTCTTTTTTT
1 TAAGATAAAACTTTCTTTTTTT
*
2221320 TAAG-TAAAATTTTCTTTTTTT
1 TAAGATAAAACTTTCTTTTTTT
2221341 ATAAAGGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (22 bp):
TAAGATAAAACTTTCTTTTTTT
Found at i:2221453 original size:3 final size:3
Alignment explanation
Indices: 2221445--2221482 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2221435 AAGGAATATA
2221445 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 AA
2221483 ATTTAGAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2224103 original size:13 final size:13
Alignment explanation
Indices: 2224082--2224119 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
2224072 TATTTAACTA
2224082 TTATTTATATGTT
1 TTATTTATATGTT
* *
2224095 TTTTTTATAT-TA
1 TTATTTATATGTT
2224107 TTATTTATATGTT
1 TTATTTATATGTT
2224120 ATAATAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (13 bp):
TTATTTATATGTT
Found at i:2224249 original size:19 final size:19
Alignment explanation
Indices: 2224225--2224294 Score: 52
Period size: 19 Copynumber: 3.4 Consensus size: 19
2224215 ATATATAATT
2224225 AATTTATTATTTATTTTTA
1 AATTTATTATTTATTTTTA
*
2224244 AATTTAATT-TTTATATTTA
1 AATTT-ATTATTTATTTTTA
* *
2224263 TATAATATTCATATTATTTTTA
1 AAT-TTATT-AT-TTATTTTTA
2224285 TAATTATATT
1 -AATT-TATT
2224295 TAATATATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
19 19 0.50
20 4 0.11
21 1 0.03
22 8 0.21
23 6 0.16
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (19 bp):
AATTTATTATTTATTTTTA
Found at i:2224262 original size:6 final size:6
Alignment explanation
Indices: 2224213--2224375 Score: 61
Period size: 6 Copynumber: 26.8 Consensus size: 6
2224203 ATTTAATTAA
* * * * *
2224213 ATATAT ATAATT A-ATTT ATTATTT ATTTTT AAATTT AATTTTT ATATTT
1 ATATTT ATATTT ATATTT A-TATTT ATATTT ATATTT -ATATTT ATATTT
* * * *
2224262 ATA-TA ATATTC ATA-TT ATTTTT ATAATT ATATTT AATATATT ATA--T
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT -ATAT-TT ATATTT
** * **
2224308 ATAAAT ATATTA ATAATTT ATATTAT ATATTAT AATACAT ATATTT ATATATT
1 ATATTT ATATTT AT-ATTT ATATT-T ATATT-T -ATATTT ATATTT ATAT-TT
*
2224361 -T-TTT ATGTTT ATATT
1 ATATTT ATATTT ATATT
2224376 ATTTGTATGT
Statistics
Matches: 117, Mismatches: 25, Indels: 30
0.68 0.15 0.17
Matches are distributed among these distances:
4 6 0.05
5 13 0.11
6 61 0.52
7 32 0.27
8 5 0.04
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (6 bp):
ATATTT
Found at i:2224302 original size:26 final size:28
Alignment explanation
Indices: 2224250--2224305 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
2224240 TTTAAATTTA
* *
2224250 ATTTTTATATTTATATAATATTCATATT
1 ATTTTTATAATTATATAATAATCATATT
*
2224278 ATTTTTATAATTATAT-TTAAT-ATATT
1 ATTTTTATAATTATATAATAATCATATT
2224304 AT
1 AT
2224306 ATATAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.28
27 3 0.12
28 15 0.60
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
ATTTTTATAATTATATAATAATCATATT
Found at i:2224315 original size:22 final size:21
Alignment explanation
Indices: 2224301--2224361 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 21
2224291 TATTTAATAT
*
2224301 ATTATATATAAATATATTAATA
1 ATTATATATATATAT-TTAATA
2224323 ATT-TATATTATATATTATAATA
1 ATTATATA-TATATATT-TAATA
*
2224345 CA-TATATTTATATATTT
1 -ATTATATATATATATTT
2224362 TTTATGTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
21 6 0.18
22 23 0.70
23 4 0.12
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATATATATATATTTAATA
Found at i:2224826 original size:12 final size:12
Alignment explanation
Indices: 2224804--2224842 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2224794 ACACCTTCAA
2224804 ATTTAAAATATAT
1 ATTT-AAATATAT
2224817 ATTTAAATATAT
1 ATTTAAATATAT
* *
2224829 ATATATATATAT
1 ATTTAAATATAT
2224841 AT
1 AT
2224843 AATCAAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATTTAAATATAT
Found at i:2226298 original size:12 final size:12
Alignment explanation
Indices: 2226239--2226305 Score: 68
Period size: 12 Copynumber: 5.7 Consensus size: 12
2226229 ATAGACTTTT
*
2226239 TATAATATTAAA
1 TATAATATAAAA
*
2226251 TACT-ATATAATTA
1 TA-TAATATAA-AA
2226264 TATAATATAAAA
1 TATAATATAAAA
2226276 -ATAAT-TAAAA
1 TATAATATAAAA
*
2226286 TAAAATATAAAA
1 TATAATATAAAA
2226298 TATAATAT
1 TATAATAT
2226306 GATATAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
10 5 0.11
11 9 0.20
12 21 0.47
13 10 0.22
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (12 bp):
TATAATATAAAA
Found at i:2226299 original size:29 final size:28
Alignment explanation
Indices: 2226255--2226375 Score: 95
Period size: 29 Copynumber: 4.2 Consensus size: 28
2226245 ATTAAATACT
*
2226255 ATATAATTATATAATATAAAAATAATTAAA
1 ATATAA-TATAAAATATAAAAAT-ATTAAA
* * *
2226285 ATAAAATATAAAATATAATATGATATAAAA
1 ATATAATATAAAATATAA-A-AATATTAAA
* *
2226315 AT-TAATATAAATATTTTAAAATATTAAA
1 ATATAATATAAA-ATATAAAAATATTAAA
* *
2226343 AT-TTATATAAAATAT-AAAATATTTATA
1 ATATAATATAAAATATAAAAATA-TTAAA
2226370 ATATAA
1 ATATAA
2226376 CAAAATACTT
Statistics
Matches: 73, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
26 6 0.08
27 9 0.12
28 19 0.26
29 20 0.27
30 17 0.23
31 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (28 bp):
ATATAATATAAAATATAAAAATATTAAA
Found at i:2226355 original size:19 final size:20
Alignment explanation
Indices: 2226261--2226369 Score: 66
Period size: 20 Copynumber: 5.2 Consensus size: 20
2226251 TACTATATAA
*
2226261 TTATATAATATA-AAAATAAT
1 TTATATAAAATATAAAAT-AT
* *
2226281 TAAAATAAAATATAAAATAT
1 TTATATAAAATATAAAATAT
2226301 AATATGATATAAAAATTAATATAAATA-
1 --T-T-ATAT-AAAA-T-ATA-AAATAT
*
2226328 TT-T-TAAAATATTAAA-AT
1 TTATATAAAATATAAAATAT
2226345 TTATATAAAATATAAAATAT
1 TTATATAAAATATAAAATAT
2226365 TTATA
1 TTATA
2226370 ATATAACAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 26
0.68 0.07 0.25
Matches are distributed among these distances:
16 1 0.01
17 5 0.07
18 3 0.04
19 12 0.17
20 22 0.32
21 6 0.09
22 2 0.03
24 4 0.06
25 5 0.07
26 1 0.01
27 3 0.04
28 5 0.07
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.39
Consensus pattern (20 bp):
TTATATAAAATATAAAATAT
Found at i:2226369 original size:18 final size:18
Alignment explanation
Indices: 2226291--2226370 Score: 67
Period size: 18 Copynumber: 4.3 Consensus size: 18
2226281 TAAAATAAAA
* *
2226291 TATAAAATATAATATGATA
1 TATAAAATATAAAAT-ATT
2226310 TA-AAAATTAATATAAATATT
1 TATAAAA-T-ATA-AAATATT
2226330 T-TAAAATATTAAAAT-TT
1 TATAAAATA-TAAAATATT
2226347 ATATAAAATATAAAATATT
1 -TATAAAATATAAAATATT
2226366 TATAA
1 TATAA
2226371 TATAACAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
17 2 0.04
18 21 0.41
19 15 0.29
20 10 0.20
21 3 0.06
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (18 bp):
TATAAAATATAAAATATT
Found at i:2226856 original size:27 final size:29
Alignment explanation
Indices: 2226821--2226876 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
2226811 ATTTATTAAC
*
2226821 TTTTAAAAATATATATT-ATTTTATAATA
1 TTTTAAAAATATATATTAATTTTAAAATA
*
2226849 TTTT-AAAATTTATATTAATTTTAAAATA
1 TTTTAAAAATATATATTAATTTTAAAATA
2226877 AAATATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
TTTTAAAAATATATATTAATTTTAAAATA
Found at i:2226860 original size:17 final size:18
Alignment explanation
Indices: 2226840--2226875 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2226830 TATATATTAT
2226840 TTTATAAT-ATTTTAAAA
1 TTTATAATAATTTTAAAA
*
2226857 TTTATATTAATTTTAAAA
1 TTTATAATAATTTTAAAA
2226875 T
1 T
2226876 AAAATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATAATAATTTTAAAA
Found at i:2226875 original size:45 final size:47
Alignment explanation
Indices: 2226814--2226901 Score: 112
Period size: 45 Copynumber: 1.9 Consensus size: 47
2226804 TAATTTTATT
* *
2226814 TATTAACTTTTAAAAAT-ATATA-TTATTTTATAATATTTTAAAATTTA
1 TATTAACTTTTAAAAATAAAATATTTATTTT-T-ATATTATAAAATTTA
2226861 TATTAA-TTTT-AAAATAAAATATTTATTTTTATATTATAAAA
1 TATTAACTTTTAAAAATAAAATATTTATTTTTATATTATAAAA
2226902 ATATAAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
45 15 0.41
46 9 0.24
47 13 0.35
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (47 bp):
TATTAACTTTTAAAAATAAAATATTTATTTTTATATTATAAAATTTA
Found at i:2226888 original size:19 final size:18
Alignment explanation
Indices: 2226847--2226889 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2226837 TATTTTATAA
**
2226847 TATTTTAAAATTTATATT
1 TATTTTAAAATAAATATT
*
2226865 AATTTTAAAATAAAATATT
1 TATTTTAAAAT-AAATATT
2226884 TATTTT
1 TATTTT
2226890 TATATTATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTAAAATAAATATT
Found at i:2229193 original size:17 final size:17
Alignment explanation
Indices: 2229161--2229198 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2229151 TAAGTTTAAA
2229161 ATTTAAATTTTATTATC
1 ATTTAAATTTTATTATC
*
2229178 ATTTATAATTTT-TTATT
1 ATTTA-AATTTTATTATC
2229195 ATTT
1 ATTT
2229199 TTAAGCTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTAAATTTTATTATC
Found at i:2230367 original size:22 final size:23
Alignment explanation
Indices: 2230332--2230378 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2230322 TTTGTATCAC
*
2230332 TTTAATAATTTTATTTATAA-AT
1 TTTAATAATTTTATATATAAGAT
2230354 TTTAA-AATTATTATATATAAGAT
1 TTTAATAATT-TTATATATAAGAT
2230377 TT
1 TT
2230379 ATTTTTACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 4 0.18
22 14 0.64
23 4 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTAATAATTTTATATATAAGAT
Found at i:2231342 original size:16 final size:16
Alignment explanation
Indices: 2231321--2231365 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2231311 TTATATTAAA
2231321 AATATTTTATATTTTT
1 AATATTTTATATTTTT
*
2231337 ATTATTTTA-ATTTTTT
1 AATATTTTATA-TTTTT
*
2231353 AATAATTTATATT
1 AATATTTTATATT
2231366 ATGAAAGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
AATATTTTATATTTTT
Found at i:2231407 original size:14 final size:13
Alignment explanation
Indices: 2231381--2231426 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2231371 AGTTTTGAAA
2231381 TATATATTTATTAT
1 TATAT-TTTATTAT
2231395 TATATTTTAATTAT
1 TATATTTT-ATTAT
*
2231409 TTTA-TTTA-TAT
1 TATATTTTATTAT
2231420 TATATTT
1 TATATTT
2231427 GTGTAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 6 0.21
12 3 0.11
13 6 0.21
14 13 0.46
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATATTTTATTAT
Found at i:2240196 original size:21 final size:23
Alignment explanation
Indices: 2240138--2240197 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 23
2240128 AAAATAAATG
2240138 TCAAATATAAATAT-TTATTATA
1 TCAAATATAAATATATTATTATA
**
2240160 T-ATTTATAAATTTATATT-TTAT-
1 TCAAATATAAA--TATATTATTATA
2240182 TCAAATATAAATATAT
1 TCAAATATAAATATAT
2240198 ATAGTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 9
0.70 0.09 0.21
Matches are distributed among these distances:
21 12 0.40
22 2 0.07
23 14 0.47
24 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (23 bp):
TCAAATATAAATATATTATTATA
Found at i:2240388 original size:39 final size:39
Alignment explanation
Indices: 2240344--2240422 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
2240334 AAAGGAAGGA
2240344 AAAAGTAAATAATGTTAAAGAGTTAAAAAGGTCTTGTTT
1 AAAAGTAAATAATGTTAAAGAGTTAAAAAGGTCTTGTTT
*
2240383 AAAAGTAAATAATGTTAAAGAGTTAAAAAGGTTTTGTTT
1 AAAAGTAAATAATGTTAAAGAGTTAAAAAGGTCTTGTTT
2240422 A
1 A
2240423 TCTTTCTTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.47, C:0.01, G:0.18, T:0.34
Consensus pattern (39 bp):
AAAAGTAAATAATGTTAAAGAGTTAAAAAGGTCTTGTTT
Found at i:2242331 original size:17 final size:19
Alignment explanation
Indices: 2242309--2242345 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
2242299 AAAAATAATT
2242309 AAAAAAGA-TAT-AATATA
1 AAAAAAGATTATGAATATA
*
2242326 AAAAAATATTATGAATATA
1 AAAAAAGATTATGAATATA
2242345 A
1 A
2242346 TAAGTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 3 0.18
19 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAAAAGATTATGAATATA
Found at i:2252040 original size:2 final size:2
Alignment explanation
Indices: 2252033--2252061 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2252023 TCACACCCAC
2252033 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
2252062 CAGATTAATT
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:2255251 original size:12 final size:12
Alignment explanation
Indices: 2255244--2255309 Score: 52
Period size: 11 Copynumber: 5.7 Consensus size: 12
2255234 AAATTTGTTT
2255244 TATTATTTATTA
1 TATTATTTATTA
**
2255256 TATTA-TTAAAA
1 TATTATTTATTA
2255267 TATTATTT-TTA
1 TATTATTTATTA
2255278 TATTAATATT-TATA
1 TATT-AT-TTAT-TA
2255292 TATT-TTTATTA
1 TATTATTTATTA
2255303 -ATTATTT
1 TATTATTT
2255310 TAAATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
10 3 0.07
11 21 0.48
12 11 0.25
13 3 0.07
14 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TATTATTTATTA
Found at i:2255301 original size:6 final size:7
Alignment explanation
Indices: 2255242--2255309 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
2255232 AAAAATTTGT
2255242 TTTATTA
1 TTTATTA
2255249 TTTATTA
1 TTTATTA
2255256 TATTATTAA
1 T-TTATT-A
**
2255265 AATATTA
1 TTTATTA
2255272 TTT-TTA
1 TTTATTA
*
2255278 TATTAATA
1 T-TTATTA
2255286 TTTATATA
1 TTTAT-TA
2255294 TTT-TTA
1 TTTATTA
*
2255300 TTAATTA
1 TTTATTA
2255307 TTT
1 TTT
2255310 TAAATAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
6 8 0.17
7 21 0.45
8 17 0.36
9 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTATTA
Found at i:2256265 original size:20 final size:22
Alignment explanation
Indices: 2256240--2256280 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2256230 AATATAAATT
2256240 TATTTA-TTT-TTAAAATTTTA
1 TATTTACTTTATTAAAATTTTA
*
2256260 TATTTACTTTATTAATATTTT
1 TATTTACTTTATTAAAATTTT
2256281 CAAATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTTACTTTATTAAAATTTTA
Found at i:2257228 original size:20 final size:21
Alignment explanation
Indices: 2257198--2257245 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
2257188 CTTCTTCAGG
*
2257198 ATTTT-CTTTTCC-CTCCTTC
1 ATTTTCCTTTTCCTCTCCTCC
2257217 ATTTTCCTTTTCCTCTCCTCC
1 ATTTTCCTTTTCCTCTCCTCC
2257238 ATTTTCCT
1 ATTTTCCT
2257246 CTCAATAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 5 0.19
20 7 0.27
21 14 0.54
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTCCTTTTCCTCTCCTCC
Found at i:2257331 original size:2 final size:2
Alignment explanation
Indices: 2257324--2257352 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2257314 AATCGAAAGC
2257324 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
2257353 AGGGATTAAT
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:2258806 original size:75 final size:75
Alignment explanation
Indices: 2258735--2258873 Score: 165
Period size: 75 Copynumber: 1.9 Consensus size: 75
2258725 CTTGATCGTC
* * * * * *
2258735 AATATTCATTCTGATCGTTAGATTTATGATT-ATCATTTAAA-TCTTGACTACCAAAAAGACAAA
1 AATATTCATTCTAACCATCAGACTTATG-TTCATCACTTAAATTCTT-ACTACCAAAAAGACAAA
2258798 ACTCTGATCATA
64 ACTCTGATCATA
* * *
2258810 AATATTTATTCTAACCATCAGACTTATGTTCATCACTTAAATTCTTATTACCAAAAAGATAAAA
1 AATATTCATTCTAACCATCAGACTTATGTTCATCACTTAAATTCTTACTACCAAAAAGACAAAA
2258874 TTCTAATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
74 2 0.04
75 47 0.89
76 4 0.08
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (75 bp):
AATATTCATTCTAACCATCAGACTTATGTTCATCACTTAAATTCTTACTACCAAAAAGACAAAAC
TCTGATCATA
Found at i:2260568 original size:2 final size:2
Alignment explanation
Indices: 2260561--2260587 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2260551 AGACAAAGCA
2260561 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
2260588 ATACTAAAAG
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:2261845 original size:19 final size:19
Alignment explanation
Indices: 2261821--2261888 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
2261811 CTTAGCATCT
2261821 TTTTTACTA-GTATATATAA
1 TTTTTA-TATGTATATATAA
* *
2261840 TTTTTATATTTATCTATAA
1 TTTTTATATGTATATATAA
2261859 TTTTT-TCAT-TATA-ATAA
1 TTTTTAT-ATGTATATATAA
2261876 TTTATTTATATGT
1 -TT-TTTATATGT
2261889 GGTCTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
17 4 0.10
18 8 0.20
19 26 0.65
20 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTTTATATGTATATATAA
Found at i:2261972 original size:25 final size:24
Alignment explanation
Indices: 2261914--2261972 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
2261904 ATTATTAAAA
* *
2261914 AAATATTTAATATTAATTATGTTT
1 AAATATATAATATTAATTATATTT
2261938 AAA-ATATAATATTTAAATT-TATTT
1 AAATATATAATA-TT-AATTATATTT
*
2261962 AAATATCTAAT
1 AAATATATAAT
2261973 TATCGTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 7 0.24
24 12 0.41
25 10 0.34
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
AAATATATAATATTAATTATATTT
Found at i:2267393 original size:20 final size:20
Alignment explanation
Indices: 2267347--2267406 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 20
2267337 AAATTATATT
*
2267347 AATATTTTAA-AATAAATAA
1 AATATTTAAATAATAAATAA
2267366 AATATTTAAATAATAATATAA
1 AATATTTAAATAATAA-ATAA
2267387 AAT-TTTAAAT-ATAAACTAA
1 AATATTTAAATAATAAA-TAA
2267406 A
1 A
2267407 TTTTGATGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 1 0.03
19 17 0.46
20 12 0.32
21 7 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AATATTTAAATAATAAATAA
Found at i:2275341 original size:23 final size:23
Alignment explanation
Indices: 2275314--2275358 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2275304 ATATTATTAC
* *
2275314 TTAAATATGATTGGTTGAAATTT
1 TTAAAAATGATTGCTTGAAATTT
*
2275337 TTAAAAATTATTGCTTGAAATT
1 TTAAAAATGATTGCTTGAAATT
2275359 GATGTTTAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (23 bp):
TTAAAAATGATTGCTTGAAATTT
Found at i:2279108 original size:15 final size:15
Alignment explanation
Indices: 2279088--2279117 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2279078 TTGGTGGAGG
*
2279088 TGGTGGGGATGGTGA
1 TGGTGGCGATGGTGA
2279103 TGGTGGCGATGGTGA
1 TGGTGGCGATGGTGA
2279118 GCTTTGGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.57, T:0.27
Consensus pattern (15 bp):
TGGTGGCGATGGTGA
Found at i:2280316 original size:16 final size:17
Alignment explanation
Indices: 2280295--2280327 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2280285 TATAACATGA
2280295 TATTT-AAAAAAATAAC
1 TATTTAAAAAAAATAAC
2280311 TATTTAAAAAAAATAAC
1 TATTTAAAAAAAATAAC
2280328 GAAGAGTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (17 bp):
TATTTAAAAAAAATAAC
Found at i:2280539 original size:3 final size:3
Alignment explanation
Indices: 2280531--2280555 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2280521 CTTGTTTTGC
2280531 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
2280556 CTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:2282750 original size:30 final size:30
Alignment explanation
Indices: 2282714--2282773 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
2282704 CAGAATAATA
2282714 TGCACCTTCAACCAAAAC-AAAGTCATCTTC
1 TGCACCTTCAA-CAAAACAAAAGTCATCTTC
* *
2282744 TGCACCTTCAACTAAGCAAAAGTCATCTTC
1 TGCACCTTCAACAAAACAAAAGTCATCTTC
2282774 CACAGTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.35, C:0.32, G:0.08, T:0.25
Consensus pattern (30 bp):
TGCACCTTCAACAAAACAAAAGTCATCTTC
Found at i:2282834 original size:54 final size:54
Alignment explanation
Indices: 2282752--2282860 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
2282742 TCTGCACCTT
* * *
2282752 CAACTAAGCAAAAGTCATCTTCCACAGTTTCCTGAATGGTATTCTCTAAATCTG
1 CAACTAAGCAAAAGTCATCCTCCACAGTTTCCTGAATGGTACTCTCGAAATCTG
2282806 CAACTAAGCAAAAGTCATCCTCCACAGTTTCCTGAATGGTACTCTCGAAATCTG
1 CAACTAAGCAAAAGTCATCCTCCACAGTTTCCTGAATGGTACTCTCGAAATCTG
2282860 C
1 C
2282861 CATGTCCTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.28
Consensus pattern (54 bp):
CAACTAAGCAAAAGTCATCCTCCACAGTTTCCTGAATGGTACTCTCGAAATCTG
Found at i:2290360 original size:9 final size:9
Alignment explanation
Indices: 2290346--2290379 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
2290336 AGACCACCTA
2290346 AAGGGATCG
1 AAGGGATCG
2290355 AAGGGATCG
1 AAGGGATCG
2290364 AAGGGATCG
1 AAGGGATCG
2290373 AAGGGAT
1 AAGGGAT
2290380 AGCATAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.35, C:0.09, G:0.44, T:0.12
Consensus pattern (9 bp):
AAGGGATCG
Found at i:2292052 original size:19 final size:20
Alignment explanation
Indices: 2292028--2292077 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2292018 TGAGCTATTG
2292028 ATGAATGAAG-GATTCAAAT
1 ATGAATGAAGAGATTCAAAT
2292047 ATGAAT-AGAGAGATTCAAAT
1 ATGAATGA-AGAGATTCAAAT
2292067 ATGAATAGAAG
1 ATGAAT-GAAG
2292078 CTTCTTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 8 0.30
20 15 0.56
21 2 0.07
22 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.22, T:0.24
Consensus pattern (20 bp):
ATGAATGAAGAGATTCAAAT
Found at i:2292063 original size:20 final size:20
Alignment explanation
Indices: 2292038--2292075 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2292028 ATGAATGAAG
2292038 GATTCAAATATGAATAGAGA
1 GATTCAAATATGAATAGAGA
2292058 GATTCAAATATGAATAGA
1 GATTCAAATATGAATAGA
2292076 AGCTTCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.26
Consensus pattern (20 bp):
GATTCAAATATGAATAGAGA
Found at i:2293882 original size:31 final size:28
Alignment explanation
Indices: 2293834--2293894 Score: 77
Period size: 31 Copynumber: 2.1 Consensus size: 28
2293824 ATCTAATTAT
* *
2293834 AAAATATATAAATATTAATTTAAATATA
1 AAAATATATAAATATTAAATTAAACATA
2293862 AAAATAATATAAATAAATTAAATTAAACATA
1 AAAAT-ATATAAAT--ATTAAATTAAACATA
2293893 AA
1 AA
2293895 TTTAAGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.18
29 8 0.29
31 15 0.54
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (28 bp):
AAAATATATAAATATTAAATTAAACATA
Found at i:2293904 original size:26 final size:26
Alignment explanation
Indices: 2293821--2293893 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
2293811 TTATTTTATT
*
2293821 TAAATCTAATTAT-AAAAT-ATATAAA
1 TAAAT-TAAATATAAAAATAATATAAA
2293846 TATTAATTTAAATATAAAAATAATATAAA
1 TA--AA-TTAAATATAAAAATAATATAAA
*
2293875 TAAATTAAAT-TAAACATAA
1 TAAATTAAATATAAAAATAA
2293894 ATTTAAGTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
25 10 0.24
26 6 0.15
27 10 0.24
28 6 0.15
29 9 0.22
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (26 bp):
TAAATTAAATATAAAAATAATATAAA
Found at i:2295066 original size:26 final size:27
Alignment explanation
Indices: 2295016--2295111 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 27
2295006 TTGTTGATAT
*
2295016 AATTATTAATTTTAATTTAAATTAAAA
1 AATTATTAAATTTAATTTAAATTAAAA
2295043 AATTATTAAATTT-ATTTAAATTAAAA
1 AATTATTAAATTTAATTTAAATTAAAA
*
2295069 TTTAATCTAATTTAATTTAATTATAAA-T-AAA
1 ---AAT-T-ATTAAATTTAATT-TAAATTAAAA
*
2295100 AATTAATAAATT
1 AATTATTAAATT
2295112 ATATATATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 15
0.75 0.05 0.19
Matches are distributed among these distances:
26 19 0.33
27 13 0.22
28 3 0.05
29 3 0.05
30 1 0.02
31 11 0.19
32 4 0.07
33 4 0.07
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
AATTATTAAATTTAATTTAAATTAAAA
Found at i:2295893 original size:26 final size:27
Alignment explanation
Indices: 2295854--2295936 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 27
2295844 ATATTATGAT
*
2295854 TATATT-TATGATTTAATATTTTTTTAA
1 TATATTATAT-ATTTAATATTATTTTAA
**
2295881 -ATATTATATATTTATATAAAATTTTAA
1 TATATTATATATTTA-ATATTATTTTAA
2295908 TATATTATATATTT-ATATTAAATTTTAA
1 TATATTATATATTTAATATT--ATTTTAA
2295936 T
1 T
2295937 TTTTTTATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
26 13 0.28
27 12 0.26
28 21 0.46
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (27 bp):
TATATTATATATTTAATATTATTTTAA
Found at i:2295949 original size:28 final size:28
Alignment explanation
Indices: 2295875--2295936 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
2295865 TTTAATATTT
2295875 TTTTAA-ATATTATATATTTATATAAAA
1 TTTTAATATATTATATATTTATATAAAA
*
2295902 TTTTAATATATTATATATTTATATTAAA
1 TTTTAATATATTATATATTTATATAAAA
2295930 TTTTAAT
1 TTTTAAT
2295937 TTTTTTATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 6 0.18
28 27 0.82
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTAATATATTATATATTTATATAAAA
Found at i:2297279 original size:16 final size:14
Alignment explanation
Indices: 2297250--2297283 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
2297240 CGACTGACCT
2297250 TTTTATTTTCTTTC
1 TTTTATTTTCTTTC
2297264 TTTTATTTTATCTTTC
1 TTTTA-TTT-TCTTTC
2297280 TTTT
1 TTTT
2297284 GATTAAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 3 0.17
16 10 0.56
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTTTCTTTC
Found at i:2307409 original size:2 final size:2
Alignment explanation
Indices: 2307402--2307426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2307392 TCAGCCAAAG
2307402 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
2307427 CTGCTCTTAA
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2308458 original size:19 final size:18
Alignment explanation
Indices: 2308331--2308466 Score: 64
Period size: 17 Copynumber: 8.1 Consensus size: 18
2308321 TTAAAGCATA
2308331 TTTAATTATT-TA-TATAT
1 TTTAATT-TTATATTATAT
*
2308348 TTTTATTTTA-ATTATAT
1 TTTAATTTTATATTATAT
* *
2308365 TTAAATTTATATATAAATAT
1 TTTAATTT-TATAT-TATAT
* *
2308385 TTAAATATTA-A-TA-A-
1 TTTAATTTTATATTATAT
*
2308399 TTT-ATTTTATA-TAAAT
1 TTTAATTTTATATTATAT
*
2308415 TTTAA---TATCTT-TAT
1 TTTAATTTTATATTATAT
* *
2308429 ATTAATTTTATTTTATAT
1 TTTAATTTTATATTATAT
2308447 TTTAATTTTTATATTATAT
1 TTTAA-TTTTATATTATAT
2308466 T
1 T
2308467 AATAAAATGT
Statistics
Matches: 90, Mismatches: 14, Indels: 28
0.68 0.11 0.21
Matches are distributed among these distances:
13 5 0.06
14 14 0.16
15 3 0.03
16 7 0.08
17 23 0.26
18 10 0.11
19 17 0.19
20 11 0.12
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATTTTATATTATAT
Found at i:2309201 original size:2 final size:2
Alignment explanation
Indices: 2309196--2309221 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2309186 TCTCTCTCTC
2309196 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
2309222 AAATATTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2316731 original size:2 final size:2
Alignment explanation
Indices: 2316724--2316755 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2316714 CCTAACGGAA
2316724 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
2316756 TTAAATAAAT
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:2318871 original size:13 final size:13
Alignment explanation
Indices: 2318853--2318878 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2318843 TAATTAACTA
2318853 GAACTTTCAAAAT
1 GAACTTTCAAAAT
2318866 GAACTTTCAAAAT
1 GAACTTTCAAAAT
2318879 CGAGAGATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
GAACTTTCAAAAT
Found at i:2319022 original size:9 final size:10
Alignment explanation
Indices: 2319002--2319030 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
2318992 GTCCCACATT
2319002 AAAT-AAGAA
1 AAATCAAGAA
2319011 AAATCAAGAA
1 AAATCAAGAA
2319021 AAATCAAGAA
1 AAATCAAGAA
2319031 TAAGAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.10
Consensus pattern (10 bp):
AAATCAAGAA
Found at i:2325537 original size:34 final size:36
Alignment explanation
Indices: 2325463--2325537 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
2325453 TATATTTACA
*
2325463 ATTATCAAATTAACTTTTCTGGTTATTGTAGTCTAT
1 ATTATCAAATTAACTTTTCTGGTTATTGCAGTCTAT
*
2325499 ATTATCAAATTAACTTTTCTGGTT-TT-CATTCTAT
1 ATTATCAAATTAACTTTTCTGGTTATTGCAGTCTAT
2325533 ATTAT
1 ATTAT
2325538 GTGAAGCAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 11 0.30
35 2 0.05
36 24 0.65
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (36 bp):
ATTATCAAATTAACTTTTCTGGTTATTGCAGTCTAT
Found at i:2330565 original size:11 final size:11
Alignment explanation
Indices: 2330530--2330574 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
2330520 TTATCAATTC
*
2330530 AAATAAAA-AC
1 AAATAAAATAA
2330540 AAATAAAAT--
1 AAATAAAATAA
*
2330549 AAATAAACTAA
1 AAATAAAATAA
2330560 AAATAAAATAA
1 AAATAAAATAA
2330571 AAAT
1 AAAT
2330575 TACTGATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 8 0.27
10 8 0.27
11 14 0.47
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:2332228 original size:24 final size:26
Alignment explanation
Indices: 2332196--2332259 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
2332186 TTTTTTTCAC
* *
2332196 TCTTTTTTTTTCAATTTT-CTTTTTT
1 TCTTATTTTTTCAATTTTAATTTTTT
*
2332221 T-TTATTTTTTTAATTTTAATTTTTT
1 TCTTATTTTTTCAATTTTAATTTTTT
*
2332246 TCTTTTTTTTTCAA
1 TCTTATTTTTTCAA
2332260 AGCAAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 14 0.44
25 8 0.25
26 10 0.31
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (26 bp):
TCTTATTTTTTCAATTTTAATTTTTT
Found at i:2333286 original size:41 final size:41
Alignment explanation
Indices: 2333241--2333355 Score: 178
Period size: 41 Copynumber: 2.8 Consensus size: 41
2333231 CTCTTTTTTT
*
2333241 TTTGATAAGGCATTGGCACGTTAATAAAATAGAAGCTCTCG
1 TTTGATAAGGCATTGGCACGTTAATAAAATAGAAACTCTCG
* *
2333282 TTTGATAAGGC-GTGAGCACGTTAATAAAACAGAAACTCTCG
1 TTTGATAAGGCATTG-GCACGTTAATAAAATAGAAACTCTCG
*
2333323 TTTGATAAGGCATGGGCACGTTAATAAAATAGA
1 TTTGATAAGGCATTGGCACGTTAATAAAATAGA
2333356 GTTTCTATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.03
41 63 0.95
42 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.27
Consensus pattern (41 bp):
TTTGATAAGGCATTGGCACGTTAATAAAATAGAAACTCTCG
Found at i:2341123 original size:22 final size:22
Alignment explanation
Indices: 2341079--2341123 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2341069 ATAGTAATCA
* *
2341079 ATTTAATTTTTATCAATTTTAT
1 ATTTAATTTTTATCAAATATAT
2341101 ATTTAATTTATTAT-AAATATAT
1 ATTTAATTT-TTATCAAATATAT
2341123 A
1 A
2341124 AATTTATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTAATTTTTATCAAATATAT
Found at i:2343886 original size:17 final size:17
Alignment explanation
Indices: 2343857--2343899 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
2343847 TAAATTTTAT
2343857 TTTATTATTTTTATA-TA
1 TTTATT-TTTTTATATTA
2343874 TATTATTTTTTTATATTA
1 T-TTATTTTTTTATATTA
2343892 TTTATTTT
1 TTTATTTT
2343900 GAGTTTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTTTTTATATTA
Found at i:2343890 original size:13 final size:13
Alignment explanation
Indices: 2343850--2343899 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 13
2343840 TCAGAATTAA
2343850 ATTTTATTT-TATT
1 ATTTT-TTTATATT
2343863 ATTTTTATATATATT
1 ATTTTT-T-TATATT
2343878 ATTTTTTTATATT
1 ATTTTTTTATATT
2343891 ATTTATTTT
1 ATTT-TTTT
2343900 GAGTTTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
12 1 0.03
13 16 0.48
14 6 0.18
15 10 0.30
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
ATTTTTTTATATT
Found at i:2344146 original size:31 final size:31
Alignment explanation
Indices: 2344111--2344178 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
2344101 CTAATTATCT
* *
2344111 ATTAA-TATAATAATTAATATTATTATATTGC
1 ATTAATTATAATAA-CAATATTATAATATTGC
*
2344142 ATTAATTATTATAACAATATTATAATATT--
1 ATTAATTATAATAACAATATTATAATATTGC
2344171 ATTAATTA
1 ATTAATTA
2344179 ATTTTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.24
31 18 0.55
32 7 0.21
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTAATTATAATAACAATATTATAATATTGC
Found at i:2344573 original size:26 final size:26
Alignment explanation
Indices: 2344544--2344603 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
2344534 TAATTAATTA
* * *
2344544 ATATTTTAATTATATTTTTA-ATTTTT
1 ATATATTAATAAT-TTTTTATATATTT
2344570 ATATATTAATAATTTTTTATATATTT
1 ATATATTAATAATTTTTTATATATTT
2344596 ATA-ATTAA
1 ATATATTAA
2344604 AAAATTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 11 0.37
26 19 0.63
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
ATATATTAATAATTTTTTATATATTT
Found at i:2344586 original size:18 final size:18
Alignment explanation
Indices: 2344565--2344601 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
2344555 ATATTTTTAA
2344565 TTTTTATATATTAATAAT
1 TTTTTATATATTAATAAT
*
2344583 TTTTTATATATTTATAAT
1 TTTTTATATATTAATAAT
2344601 T
1 T
2344602 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTATATATTAATAAT
Found at i:2345324 original size:19 final size:19
Alignment explanation
Indices: 2345297--2345358 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
2345287 TTTAAATAAA
*
2345297 AATTATAATTATTATTTAT
1 AATTTTAATTATTATTTAT
*
2345316 AATTTTAATT-TTAATTTTT
1 AATTTTAATTATT-ATTTAT
* *
2345335 AATATTTATTATATTAATTAT
1 AAT-TTTAAT-TATTATTTAT
2345356 AAT
1 AAT
2345359 ATTATTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 2 0.06
19 17 0.50
20 5 0.15
21 8 0.24
22 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTAATTATTATTTAT
Found at i:2346674 original size:4 final size:4
Alignment explanation
Indices: 2346667--2346697 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2346657 TTCATAGGCT
2346667 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2346698 TGCTTTGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2346813 original size:4 final size:4
Alignment explanation
Indices: 2346804--2346828 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2346794 CCTTTGCTTC
2346804 CCCT CCCT CCCT CCCT CCCT CCCT C
1 CCCT CCCT CCCT CCCT CCCT CCCT C
2346829 ACCACATCTT
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:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (4 bp):
CCCT
Found at i:2347053 original size:22 final size:22
Alignment explanation
Indices: 2347008--2347076 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
2346998 AAAAATTTAA
* *
2347008 TTTAATTAATTAATA-TTATCAT
1 TTTAAATAA-TAATATTTATAAT
2347030 TTTAAA-AATAATATTTATTAAT
1 TTTAAATAATAATATTTA-TAAT
**
2347052 TTTAAATTTTAATATTTATAAT
1 TTTAAATAATAATATTTATAAT
2347074 TTT
1 TTT
2347077 TTTAAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 5 0.12
21 5 0.12
22 21 0.52
23 9 0.22
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTAAATAATAATATTTATAAT
Found at i:2347077 original size:23 final size:24
Alignment explanation
Indices: 2347038--2347086 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
2347028 ATTTTAAAAA
2347038 TAATATTTATTAA-TTTTAAATTT
1 TAATATTTATTAATTTTTAAATTT
2347061 TAATATTTA-TAATTTTTTTAAATTT
1 TAATATTTATTAA--TTTTTAAATTT
2347086 T
1 T
2347087 TTAAATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 3 0.13
23 9 0.39
25 11 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TAATATTTATTAATTTTTAAATTT
Found at i:2347225 original size:2 final size:2
Alignment explanation
Indices: 2347218--2347265 Score: 78
Period size: 2 Copynumber: 23.5 Consensus size: 2
2347208 TGTTTTTGCC
*
2347218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TCA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
2347261 TA TA T
1 TA TA T
2347266 TTTGTCAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2350168 original size:2 final size:2
Alignment explanation
Indices: 2350156--2350208 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
2350146 TTCTTTTGCT
*
2350156 TA TA AA 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
* *
2350198 TG TA CA TA TA T
1 TA TA TA TA TA T
2350209 TTTCATGCTG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2361586 original size:8 final size:8
Alignment explanation
Indices: 2361573--2361604 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
2361563 ATTAACTATT
2361573 TTAAAAAA
1 TTAAAAAA
2361581 TTAAAAAAA
1 TT-AAAAAA
2361590 TTAAAAAA
1 TTAAAAAA
2361598 TTAAAAA
1 TTAAAAA
2361605 TTAGTCAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
TTAAAAAA
Found at i:2361587 original size:9 final size:9
Alignment explanation
Indices: 2361575--2361604 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2361565 TAACTATTTT
2361575 AAAAAATTA
1 AAAAAATTA
2361584 AAAAAATT-
1 AAAAAATTA
2361592 AAAAAATTA
1 AAAAAATTA
2361601 AAAA
1 AAAA
2361605 TTAGTCAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAAATTA
Found at i:2362396 original size:6 final size:7
Alignment explanation
Indices: 2362376--2362405 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2362366 ACAACTAACT
2362376 AATAAAA
1 AATAAAA
2362383 AATAAAA
1 AATAAAA
2362390 AATAAAAA
1 AAT-AAAA
2362398 AATAAAA
1 AATAAAA
2362405 A
1 A
2362406 CAAAGTCCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AATAAAA
Found at i:2362728 original size:2 final size:2
Alignment explanation
Indices: 2362723--2362765 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2362713 TGTGTGTGTG
2362723 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
2362765 T
1 T
2362766 TTTGGGACTT
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:2365236 original size:14 final size:15
Alignment explanation
Indices: 2365217--2365246 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2365207 AGCTGGAGGA
2365217 AAAAAGAAAA-AAAG
1 AAAAAGAAAAGAAAG
2365231 AAAAAGAAAAGAAAG
1 AAAAAGAAAAGAAAG
2365246 A
1 A
2365247 GAAATACACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAGAAAG
Found at i:2375473 original size:2 final size:2
Alignment explanation
Indices: 2375466--2375506 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2375456 TCAAGCCAAA
2375466 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2375507 CGAAGGACCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2376070 original size:2 final size:2
Alignment explanation
Indices: 2376063--2376104 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2376053 GCCACTACAA
2376063 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
2376105 TCTGCTTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2376279 original size:24 final size:24
Alignment explanation
Indices: 2376219--2376290 Score: 63
Period size: 24 Copynumber: 2.8 Consensus size: 24
2376209 TTAAATTCAA
2376219 ATTTTATAAAACTTAAATTAAATTTG
1 ATTTT-TAAAA-TTAAATTAAATTTG
** * * *
2376245 ATAATTCAAATTCAATTAAATTTT
1 ATTTTTAAAATTAAATTAAATTTG
2376269 ATTTTTAAAATTTAAACTTAAA
1 ATTTTTAAAA-TTAAA-TTAAA
2376291 ACTCATTTCA
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
24 19 0.54
25 8 0.23
26 8 0.23
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (24 bp):
ATTTTTAAAATTAAATTAAATTTG
Found at i:2376767 original size:13 final size:13
Alignment explanation
Indices: 2376749--2376773 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2376739 ATTACAGAAA
2376749 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
2376762 AAAAAAAAAAAA
1 AAAAAAAAAAAA
2376774 ACTTAATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:2376767 original size:14 final size:14
Alignment explanation
Indices: 2376748--2376775 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2376738 CATTACAGAA
2376748 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
2376762 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
2376776 TTAATTAACA
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:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:2385854 original size:58 final size:57
Alignment explanation
Indices: 2385760--2385873 Score: 183
Period size: 58 Copynumber: 2.0 Consensus size: 57
2385750 AATAACATAG
* * *
2385760 ATAAAGAAATAAACTCAAGGTCTAACATAGATATGCAGCGGAAATATTATTTATGAA
1 ATAAAGAAATAAACTCAAGGTCTAACATAGAGATGCAGCAGAAACATTATTTATGAA
*
2385817 ATAAAGAAATAAAACTTAAGGTCTAACATAGAGATGCAGCAGAAACATTATTTATGA
1 ATAAAGAAAT-AAACTCAAGGTCTAACATAGAGATGCAGCAGAAACATTATTTATGA
2385874 TGAGGTCTGC
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 10 0.19
58 42 0.81
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (57 bp):
ATAAAGAAATAAACTCAAGGTCTAACATAGAGATGCAGCAGAAACATTATTTATGAA
Found at i:2387102 original size:16 final size:17
Alignment explanation
Indices: 2387075--2387107 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2387065 AATCCAACGC
2387075 CAAAAAACAAAAAAGAA
1 CAAAAAACAAAAAAGAA
*
2387092 CAAAAAA-AAAATAGAA
1 CAAAAAACAAAAAAGAA
2387108 GATCAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.82, C:0.09, G:0.06, T:0.03
Consensus pattern (17 bp):
CAAAAAACAAAAAAGAA
Found at i:2387671 original size:22 final size:22
Alignment explanation
Indices: 2387646--2387694 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2387636 AATTTATTTT
*
2387646 TATTTACAATTTAATTAT-AAAA
1 TATTT-CAATATAATTATAAAAA
*
2387668 TATTTTAATATAATTATAAAAA
1 TATTTCAATATAATTATAAAAA
2387690 TATTT
1 TATTT
2387695 TTTTAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTTCAATATAATTATAAAAA
Found at i:2398379 original size:2 final size:2
Alignment explanation
Indices: 2398372--2398412 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2398362 TTTGTACTTT
2398372 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2398413 CAAGTTCTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2398694 original size:20 final size:22
Alignment explanation
Indices: 2398642--2398696 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 22
2398632 ATTTTTATTT
2398642 AATTTTAATTATAAAAATATATA
1 AATTTTAA-TATAAAAATATATA
*
2398665 AATATTAATATAAAAATA-AT-
1 AATTTTAATATAAAAATATATA
*
2398685 TATTTTAATATA
1 AATTTTAATATA
2398697 TATAAATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.34
21 2 0.07
22 10 0.34
23 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTTTAATATAAAAATATATA
Found at i:2398697 original size:22 final size:24
Alignment explanation
Indices: 2398642--2398712 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 24
2398632 ATTTTTATTT
2398642 AATTTTAAT-TATAAAAATATATA
1 AATTTTAATATATAAAAATATATA
*
2398665 AATATT-A-ATATAAAAATA-AT-
1 AATTTTAATATATAAAAATATATA
* * *
2398685 TATTTTAATATATATAAATA-GTA
1 AATTTTAATATATAAAAATATATA
2398708 AATTT
1 AATTT
2398713 GGATAACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
20 4 0.11
21 3 0.08
22 22 0.58
23 9 0.24
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (24 bp):
AATTTTAATATATAAAAATATATA
Found at i:2402648 original size:23 final size:23
Alignment explanation
Indices: 2402618--2402664 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2402608 ACAGAGCTTG
2402618 GCCTGATATGCTATGTCATAAGT
1 GCCTGATATGCTATGTCATAAGT
2402641 GCCTGATATGCTATGTCATAAGT
1 GCCTGATATGCTATGTCATAAGT
2402664 G
1 G
2402665 GCTGTGTGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (23 bp):
GCCTGATATGCTATGTCATAAGT
Found at i:2407326 original size:40 final size:40
Alignment explanation
Indices: 2407261--2407345 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
2407251 TCTGAAAACA
*
2407261 TTAAAGAGACAAACTTGCAGTTAGCAAGAGAATTAAT-AG
1 TTAAAGAGACAAACTTGCAGTTAGCAAGAGAATCAATCAG
*
2407300 TTAAAGAGACCTAACTTGCA-TGTAGCAAGAGAATCAATCAG
1 TTAAAGAGA-CAAACTTGCAGT-TAGCAAGAGAATCAATCAG
2407341 TTAAA
1 TTAAA
2407346 CTTGAAACAG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
39 10 0.24
40 24 0.59
41 7 0.17
ACGTcount: A:0.45, C:0.13, G:0.19, T:0.24
Consensus pattern (40 bp):
TTAAAGAGACAAACTTGCAGTTAGCAAGAGAATCAATCAG
Found at i:2423174 original size:2 final size:2
Alignment explanation
Indices: 2423167--2423194 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2423157 GAGGGAAGGA
2423167 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
2423195 GGGTGGGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2443366 original size:1 final size:1
Alignment explanation
Indices: 2443360--2443399 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
2443350 AACAAGTTTC
* * *
2443360 TTTTTTTCTTTTTTCTTTTTTTTTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2443400 GGGTTTCTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.05, G:0.03, T:0.93
Consensus pattern (1 bp):
T
Done.