Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 20 of 25
Found at i:3062006 original size:2 final size:2
Alignment explanation
Indices: 3061999--3062025 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3061989 GATTATAAAA
3061999 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
3062026 CCTTGGCAAC
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:3063589 original size:21 final size:22
Alignment explanation
Indices: 3063548--3063605 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
3063538 ATGATATAAA
* *
3063548 TATATTTA-ATTTTTTAAAAAT
1 TATATTTATATATTTAAAAAAT
3063569 TAT-TTTATATATTTAAAAAAT
1 TATATTTATATATTTAAAAAAT
*
3063590 TATATTTTTATATTTA
1 TATATTTATATATTTA
3063606 TATTTAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 17 0.53
22 11 0.34
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATATTTATATATTTAAAAAAT
Found at i:3063601 original size:22 final size:21
Alignment explanation
Indices: 3063563--3063605 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
3063553 TTAATTTTTT
3063563 AAAAATTATTTTATATATTTA
1 AAAAATTATTTTATATATTTA
*
3063584 AAAAATTATATTTTTATATTTA
1 AAAAATTAT-TTTATATATTTA
3063606 TATTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAAATTATTTTATATATTTA
Found at i:3064388 original size:2 final size:2
Alignment explanation
Indices: 3064381--3064418 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3064371 TGCAGTCTCT
3064381 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
3064419 AATTATGATT
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):
TA
Found at i:3064594 original size:2 final size:2
Alignment explanation
Indices: 3064587--3064613 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3064577 ATACTCTCAA
3064587 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
3064614 GAGAGAGAGA
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:3064618 original size:2 final size:2
Alignment explanation
Indices: 3064613--3064653 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3064603 ATATATATAT
3064613 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
3064654 AGATTTTGAA
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:3064893 original size:27 final size:28
Alignment explanation
Indices: 3064863--3064922 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
3064853 ATATATTCGA
*
3064863 TATAAATATATTT-AA-TTTTTTAAAATT
1 TATAAATAT-TTTAAATTTTTTTAAAAAT
*
3064890 TATATATATTTTAAAATTTTTTTAAAAAT
1 TATAAATATTTT-AAATTTTTTTAAAAAT
3064919 TATA
1 TATA
3064923 TTTTTATACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 3 0.11
27 8 0.29
28 2 0.07
29 15 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TATAAATATTTTAAATTTTTTTAAAAAT
Found at i:3068394 original size:20 final size:19
Alignment explanation
Indices: 3068344--3068421 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 19
3068334 GGTAAAAAGA
3068344 CATAATGTATCGATACATT
1 CATAATGTATCGATACATT
* *
3068363 GCAGAATATATCGATACATT
1 -CATAATGTATCGATACATT
*
3068383 CATACATGTATCGATATATT
1 CATA-ATGTATCGATACATT
* * *
3068403 GAAAAATGTATTGATACAT
1 -CATAATGTATCGATACAT
3068422 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 3 0.06
20 42 0.89
21 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:3068419 original size:40 final size:39
Alignment explanation
Indices: 3068344--3068421 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
3068334 GGTAAAAAGA
* *
3068344 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* * *
3068383 CATACATGTATCGATATATTGAAAAATGTATTGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
3068422 CTGGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:3069934 original size:20 final size:20
Alignment explanation
Indices: 3069909--3069949 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3069899 TAGTCATCGT
3069909 TGGTTACTTCACCCTTTGAG
1 TGGTTACTTCACCCTTTGAG
3069929 TGGTTACTTCACCCTTTGAG
1 TGGTTACTTCACCCTTTGAG
3069949 T
1 T
3069950 TTTGATTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (20 bp):
TGGTTACTTCACCCTTTGAG
Found at i:3070668 original size:16 final size:15
Alignment explanation
Indices: 3070646--3070687 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
3070636 ATAAATCTTA
3070646 AATTTTAATAATTGTT
1 AATTTTAATAATT-TT
*
3070662 TATTTTAA-AATTTT
1 AATTTTAATAATTTT
*
3070676 AATTTTATTAAT
1 AATTTTAATAAT
3070688 ATATTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 8 0.36
15 7 0.32
16 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
AATTTTAATAATTTT
Found at i:3071285 original size:29 final size:29
Alignment explanation
Indices: 3071222--3071286 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
3071212 TATTTTGTTA
*
3071222 TATCAAAAATTTCTTAACTTTTAATTTAG
1 TATCAAAAAATTCTTAACTTTTAATTTAG
*
3071251 -ACCAAACAAATTCTT-ACTTTTTAATTT-G
1 TATCAAA-AAATTCTTAAC-TTTTAATTTAG
3071279 TATCAAAA
1 TATCAAAA
3071287 TAAATTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (29 bp):
TATCAAAAAATTCTTAACTTTTAATTTAG
Found at i:3071394 original size:29 final size:28
Alignment explanation
Indices: 3071350--3071423 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 28
3071340 TTCATTTGAT
* * *
3071350 ATAAAAGATTTGTTTAGTTACAAT-CAA
1 ATAAAAGATTTATTTAGATACAATAAAA
3071377 ATGATAAAGATTTATTTAGATACAATAAAA
1 AT-A-AAAGATTTATTTAGATACAATAAAA
3071407 ATAAATAGATTTATTTA
1 ATAAA-AGATTTATTTA
3071424 AGAAAAGCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.05
28 3 0.08
29 31 0.77
30 4 0.10
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (28 bp):
ATAAAAGATTTATTTAGATACAATAAAA
Found at i:3072303 original size:16 final size:16
Alignment explanation
Indices: 3072284--3072316 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3072274 TATATTTATA
3072284 TAATA-AAATAAACTTT
1 TAATATAAATAAA-TTT
3072300 TAATATAAATAAATTT
1 TAATATAAATAAATTT
3072316 T
1 T
3072317 CTACTGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAAATAAATTT
Found at i:3074272 original size:20 final size:20
Alignment explanation
Indices: 3074210--3074286 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
3074200 TTTTACCCAG
* *
3074210 ATGTATCGATATATTTTTTA
1 ATGTATCGATATATTCTTCA
* * *
3074230 ATATATCGATATATGT-ATGA
1 ATGTATCGATATAT-TCTTCA
3074250 ATGTATCGATATATTCTTCA
1 ATGTATCGATATATTCTTCA
* *
3074270 ATGTACCGATAAATTCT
1 ATGTATCGATATATTCT
3074287 ATCTTTTTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (20 bp):
ATGTATCGATATATTCTTCA
Found at i:3074334 original size:20 final size:20
Alignment explanation
Indices: 3074309--3074346 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
3074299 AGATGTATCG
3074309 ATAATGTATCGATACATTGA
1 ATAATGTATCGATACATTGA
3074329 ATAATGTATCGATACATT
1 ATAATGTATCGATACATT
3074347 TAGTTAAAAT
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:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (20 bp):
ATAATGTATCGATACATTGA
Found at i:3084549 original size:24 final size:24
Alignment explanation
Indices: 3084516--3084594 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
3084506 ATTTGAATTG
* *
3084516 AATTATTATTTATATGATAAATA-A
1 AATTTTTATTTAAAT-ATAAATATA
* *
3084540 TATTTTTATTTAAATTTAAATATA
1 AATTTTTATTTAAATATAAATATA
* **
3084564 AATTTTTATTTAAAAATATTTAT-
1 AATTTTTATTTAAATATAAATATA
3084587 AATTTTTA
1 AATTTTTA
3084595 ATATTATTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 14 0.31
24 31 0.69
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (24 bp):
AATTTTTATTTAAATATAAATATA
Found at i:3084997 original size:19 final size:19
Alignment explanation
Indices: 3084977--3085025 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
3084967 GTTTTTAATA
3084977 AAAAT-TATATTATTAAAT
1 AAAATATATATTATTAAAT
* *
3084995 AAAATATATATTTTTAATT
1 AAAATATATATTATTAAAT
**
3085014 ATGATATATATT
1 AAAATATATATT
3085026 TAATAGATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
AAAATATATATTATTAAAT
Found at i:3088171 original size:34 final size:34
Alignment explanation
Indices: 3088101--3088318 Score: 278
Period size: 34 Copynumber: 6.5 Consensus size: 34
3088091 GTCACAGTGG
* * *
3088101 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * **
3088134 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGTC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
3088168 ATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
3088201 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
3088235 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
3088269 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3088303 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
3088319 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
33 40 0.25
34 120 0.75
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:3088284 original size:68 final size:67
Alignment explanation
Indices: 3088101--3088320 Score: 305
Period size: 67 Copynumber: 3.3 Consensus size: 67
3088091 GTCACAGTGG
* * * * *
3088101 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
*
3088166 TC
66 CC
* ** * *
3088168 ATTGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
3088233 CC
66 CC
* * *
3088235 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
3088300 GCC
65 GCC
3088303 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
3088321 GTTTTTACCA
Statistics
Matches: 133, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
67 73 0.55
68 60 0.45
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:3091473 original size:18 final size:18
Alignment explanation
Indices: 3091433--3091473 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
3091423 ATTAAACACG
3091433 AAAA-AAATAATATATAT
1 AAAATAAATAATATATAT
3091450 ACAAATAAATGAATATAT-T
1 A-AAATAAAT-AATATATAT
3091469 AAAAT
1 AAAAT
3091474 TTATATAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.05
18 7 0.33
19 6 0.29
20 7 0.33
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAATAAATAATATATAT
Found at i:3092372 original size:2 final size:2
Alignment explanation
Indices: 3092365--3092405 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
3092355 TCATATTTGC
* * *
3092365 AT AT AT AT GT AT GT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3092406 CACACTTTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3095992 original size:20 final size:21
Alignment explanation
Indices: 3095964--3096003 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3095954 GTATATGTAA
3095964 TAAATATATAATTA-ATTATAT
1 TAAATATAT-ATTAGATTATAT
3095985 TAAA-ATATATTAGATTATA
1 TAAATATATATTAGATTATA
3096004 ATTATTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TAAATATATATTAGATTATAT
Found at i:3097725 original size:31 final size:31
Alignment explanation
Indices: 3097647--3097740 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 31
3097637 GTAAAACTTA
* *
3097647 AAAAATATATATTAAAAAATTATTAATATTTT
1 AAAAAT-TAAATTAAAAAATTATCAATATTTT
* *
3097679 AAAACTT-AATAAAAAAATTATCAA-ATTATT
1 AAAAATTAAATTAAAAAATTATCAATATT-TT
3097709 AAAAATTAAATT-AAAAA-TAT--ATATTTT
1 AAAAATTAAATTAAAAAATTATCAATATTTT
3097736 AAAAA
1 AAAAA
3097741 ATATATTATA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
27 8 0.15
28 3 0.06
29 6 0.11
30 27 0.51
31 4 0.08
32 5 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (31 bp):
AAAAATTAAATTAAAAAATTATCAATATTTT
Found at i:3097747 original size:14 final size:15
Alignment explanation
Indices: 3097719--3097747 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3097709 AAAAATTAAA
3097719 TTAAAAATATATATT
1 TTAAAAATATATATT
3097734 TTAAAAA-ATATATT
1 TTAAAAATATATATT
3097748 ATAAGTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAAAATATATATT
Found at i:3097999 original size:20 final size:20
Alignment explanation
Indices: 3097953--3098021 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
3097943 TCATACCCTG
* *
3097953 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
** *
3097973 AAATATCGATACATGTATGA
1 ATGTATCGATACATGTATCA
* *
3097993 ATGTATCGATATAT-TCTACA
1 ATGTATCGATACATGTAT-CA
3098013 ATGTATCGA
1 ATGTATCGA
3098022 GATATTATGT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 2 0.05
20 36 0.95
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:3098970 original size:24 final size:24
Alignment explanation
Indices: 3098938--3098994 Score: 100
Period size: 22 Copynumber: 2.5 Consensus size: 24
3098928 AGCCTTTGAC
3098938 CATGCATTTTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
3098962 CATGCA--TTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
3098984 CATGCATTTTT
1 CATGCATTTTT
3098995 AACATGTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 22 0.71
24 9 0.29
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.63
Consensus pattern (24 bp):
CATGCATTTTTTTTTATTATGTTT
Found at i:3099001 original size:20 final size:21
Alignment explanation
Indices: 3098947--3099001 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
3098937 CCATGCATTT
**
3098947 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
3098968 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
3098990 -TTTTTAACATGT
1 TTTTTTAACATGT
3099002 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:3105165 original size:35 final size:32
Alignment explanation
Indices: 3105088--3105165 Score: 77
Period size: 34 Copynumber: 2.3 Consensus size: 32
3105078 CCTTTAAATG
3105088 ACAAAAAAAAGTCAAAAGCAAAAGCACAAAGAA-A
1 ACAAAAAAAAGTCAAAAGCAAAAG-A-AAA-AAGA
* *
3105122 AGAAAAAAAAGTGCAAAAGCAAAATAAAAAAGGA
1 ACAAAAAAAAGT-CAAAAGCAAAAGAAAAAA-GA
*
3105156 ACAACAAAAA
1 ACAAAAAAAA
3105166 TAAAAAACGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
32 2 0.05
33 3 0.08
34 21 0.57
35 11 0.30
ACGTcount: A:0.72, C:0.12, G:0.13, T:0.04
Consensus pattern (32 bp):
ACAAAAAAAAGTCAAAAGCAAAAGAAAAAAGA
Found at i:3105713 original size:198 final size:197
Alignment explanation
Indices: 3105331--3105728 Score: 778
Period size: 198 Copynumber: 2.0 Consensus size: 197
3105321 TGTCATGTGA
3105331 ACTGATGAACCTGTTTTTTAAGGAAATGTTCTTTTTAGCAAAAAACTTGGTGAGACACAAGCTTT
1 ACTGATGAACCTGTTTTTTAAGGAAATGTTCTTTTTAGCAAAAAACTTGGTGAGACACAAGCTTT
3105396 GAAACTCACCCAATCCTACAAAAAAAAATAAAAAACCTTTTTCACCCTAAAGCTAGTCAAAAACC
66 GAAACTCACCCAATCCTACAAAAAAAAATAAAAAACCTTTTTCACCCTAAAGCTAGTCAAAAACC
3105461 TCTTAAACACCTAAACAAGGGGCAACTCAAAACAACTTGGAAAAATCTTAAGGGTCTTCAAAGGT
131 TCTTAAACACCTAAACAAGGGGCAACTCAAAACAACTTGGAAAAATCTTAAGGGTCTTCAAAGGT
3105526 CG
196 CG
*
3105528 ACTGATGAACCTGTTTTTTAGGGAAATGTTCTTTTTAGCAAAAAACTTGGTGAGACACAAGCTTT
1 ACTGATGAACCTGTTTTTTAAGGAAATGTTCTTTTTAGCAAAAAACTTGGTGAGACACAAGCTTT
3105593 GAAACTCACCCAATCCTACAAAAAAAAATAAAAAAACCTTTTTCACCCTAAAGCTAGTCAAAAAC
66 GAAACTCACCCAATCCTACAAAAAAAAAT-AAAAAACCTTTTTCACCCTAAAGCTAGTCAAAAAC
3105658 CTCTTAAACACCTAAACAAGGGGCAACTCAAAACAACTTGGAAAAATCTTAAGGGTCTTCAAAGG
130 CTCTTAAACACCTAAACAAGGGGCAACTCAAAACAACTTGGAAAAATCTTAAGGGTCTTCAAAGG
3105723 TCG
195 TCG
3105726 ACT
1 ACT
3105729 CATCCCAATC
Statistics
Matches: 199, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
197 93 0.47
198 106 0.53
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (197 bp):
ACTGATGAACCTGTTTTTTAAGGAAATGTTCTTTTTAGCAAAAAACTTGGTGAGACACAAGCTTT
GAAACTCACCCAATCCTACAAAAAAAAATAAAAAACCTTTTTCACCCTAAAGCTAGTCAAAAACC
TCTTAAACACCTAAACAAGGGGCAACTCAAAACAACTTGGAAAAATCTTAAGGGTCTTCAAAGGT
CG
Found at i:3106757 original size:27 final size:27
Alignment explanation
Indices: 3106680--3107389 Score: 1134
Period size: 27 Copynumber: 26.0 Consensus size: 27
3106670 TGGCATTTCT
*
3106680 TTTTGAAGTCCACAACTCCGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
3106708 TTTTAAAGTCCACAACTCTGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* *
3106736 TTTTAAATCCACAACTCCGTGGCACTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
3106763 TTTTAAAGTCCACAACTCCGAGGCACTC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
3106791 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
3106819 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
** * * *
3106846 TTCAAATTCCACAACTCTGTGGCACTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3106873 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
3106901 TTTTAAGTCCACAACTCTGTGGCA-CC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3106927 TTTCAAAGTCCACAACTCCGTGGCACCC
1 TTT-TAAGTCCACAACTCCGTGGCACCC
3106955 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3106982 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
*
3107010 TTTTAAGTCCACAACTCCGTGGCATCTC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
3107038 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3107065 TTTTAAGTCCACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
3107092 TTTTAAGTCCACAACTCCGTAGCACCT
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3107119 TTTTAAGTCCACAACTCCGTGGCACTC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3107146 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3107173 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3107200 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3107227 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3107254 TTTTAAGTCCACAACTCCGTGGCATCCC
1 TTTTAAGTCCACAACTCCGTGGCA-CCC
* *
3107282 TTTTAAGACCACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3107309 TTTTAAGTCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3107336 TTTTAAGTCCACAACTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
*
3107363 TTTTAAATCCACAACTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
3107390 ATTTCAAAGC
Statistics
Matches: 635, Mismatches: 41, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
26 5 0.01
27 442 0.70
28 188 0.30
ACGTcount: A:0.24, C:0.35, G:0.14, T:0.27
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:3107431 original size:32 final size:32
Alignment explanation
Indices: 3107372--3108248 Score: 1487
Period size: 32 Copynumber: 27.6 Consensus size: 32
3107362 CTTTTAAATC
* * *
3107372 CACAACTCCGTGGC-ACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
* *
3107403 CACAAGTCGGTGGCAACCAATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
3107435 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3107467 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
3107499 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3107531 CACAAGTCGGTGGC-A---ATT-CAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
* *
3107558 TACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3107590 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3107622 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3107654 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3107686 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3107718 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3107750 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
3107782 CACAAGTCGGTGGCAGCCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
3107814 CACAAGTCGGTGGCAGCCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
3107846 CACAAGTCGGTGGTAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3107878 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3107910 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3107942 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
3107974 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
3108006 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
3108038 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
*
3108070 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
* *
3108102 CACAAGTCGGTGGCAACCCATTTCAAAACCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
3108134 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
* *
3108166 CACAAGTCGGTGGCAACTCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
**
3108198 CACAAGTCGGTGGCAACCCATTTAAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
** *
3108230 TGCAAGTCAGTGGCAACCC
1 CACAAGTCGGTGGCAACCC
3108249 TTTTCAAATC
Statistics
Matches: 816, Mismatches: 24, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
27 22 0.03
28 4 0.00
31 16 0.02
32 774 0.95
ACGTcount: A:0.31, C:0.35, G:0.19, T:0.14
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
Found at i:3108830 original size:20 final size:20
Alignment explanation
Indices: 3108784--3108834 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
3108774 TCATACCCTG
* *
3108784 ATATATCGATACATTTTTCA
1 ATATATCGATACATGTATCA
*
3108804 ATATATCGATACATGTATGA
1 ATATATCGATACATGTATCA
*
3108824 ATGTATCGATA
1 ATATATCGATA
3108835 TATTCTACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (20 bp):
ATATATCGATACATGTATCA
Found at i:3109801 original size:24 final size:24
Alignment explanation
Indices: 3109769--3109825 Score: 100
Period size: 22 Copynumber: 2.5 Consensus size: 24
3109759 AGCCTTTGAC
3109769 CATGCATTTTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
3109793 CATGCA--TTTTTTTATTATGTTT
1 CATGCATTTTTTTTTATTATGTTT
3109815 CATGCATTTTT
1 CATGCATTTTT
3109826 AACATGTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 22 0.71
24 9 0.29
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.63
Consensus pattern (24 bp):
CATGCATTTTTTTTTATTATGTTT
Found at i:3109832 original size:20 final size:21
Alignment explanation
Indices: 3109778--3109832 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
3109768 CCATGCATTT
**
3109778 TTTTTTATTATGTTTCATGCA
1 TTTTTTAACATGTTTCATGCA
**
3109799 TTTTTTTATTATGTTTCATGCA
1 -TTTTTTAACATGTTTCATGCA
3109821 -TTTTTAACATGT
1 TTTTTTAACATGT
3109833 CCAGCATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 10 0.32
22 21 0.68
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (21 bp):
TTTTTTAACATGTTTCATGCA
Found at i:3112589 original size:16 final size:16
Alignment explanation
Indices: 3112570--3112609 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3112560 TTAAAGAGTT
3112570 AAAAATTTAAAGTTAA
1 AAAAATTTAAAGTTAA
*
3112586 AAAAATTTAAATTTAA
1 AAAAATTTAAAGTTAA
*
3112602 AAATATTT
1 AAAAATTT
3112610 GAAATTGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAAATTTAAAGTTAA
Found at i:3113275 original size:8 final size:8
Alignment explanation
Indices: 3113264--3113288 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3113254 TGATTAAAAA
3113264 ATTAAATT
1 ATTAAATT
3113272 ATTAAATT
1 ATTAAATT
3113280 ATTAAATT
1 ATTAAATT
3113288 A
1 A
3113289 AACAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTAAATT
Found at i:3114098 original size:19 final size:19
Alignment explanation
Indices: 3114074--3114110 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3114064 AAATTTACTT
*
3114074 TATTTTTTAAATTCAAATC
1 TATTTTTGAAATTCAAATC
3114093 TATTTTTGAAATTCAAAT
1 TATTTTTGAAATTCAAAT
3114111 TTCGACCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.51
Consensus pattern (19 bp):
TATTTTTGAAATTCAAATC
Found at i:3114621 original size:27 final size:27
Alignment explanation
Indices: 3114591--3114646 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
3114581 TAATACTCAA
3114591 TATATAAATAAAATTA-TTATATAATTT
1 TATATAAATAAAATTACTTAT-TAATTT
** *
3114618 TATATTTATATAATTACTTATTAATTT
1 TATATAAATAAAATTACTTATTAATTT
3114645 TA
1 TA
3114647 AAAATTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
TATATAAATAAAATTACTTATTAATTT
Found at i:3114891 original size:64 final size:66
Alignment explanation
Indices: 3114821--3114947 Score: 152
Period size: 64 Copynumber: 2.0 Consensus size: 66
3114811 AGCCCTTGAC
* *
3114821 TAAAAT-AATCTAAATAAAAAATAGTTCTAATCTAAAAGAAAATTAAATCC-AAAAT-ACTTAAA
1 TAAAATAAATCTAAATAAAAAATACTT-AAATCTAAAAGAAAATTAAATCCAAAAATAACTTAAA
3114883 TT
65 TT
* ** * * *
3114885 TAAAATAAATTTAAATCCAAAATACTTAAATTTAAAATAAATTTAAATCCAAAAATAACTTAA
1 TAAAATAAATCTAAATAAAAAATACTTAAATCTAAAAGAAAATTAAATCCAAAAATAACTTAA
3114948 TCTGAACTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
64 25 0.48
65 21 0.40
66 6 0.12
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (66 bp):
TAAAATAAATCTAAATAAAAAATACTTAAATCTAAAAGAAAATTAAATCCAAAAATAACTTAAAT
T
Found at i:3114899 original size:32 final size:32
Alignment explanation
Indices: 3114853--3114947 Score: 154
Period size: 32 Copynumber: 2.9 Consensus size: 32
3114843 AGTTCTAATC
* *
3114853 TAAAAGAAAATTAAATCCAAAATACTTAAATT
1 TAAAATAAATTTAAATCCAAAATACTTAAATT
3114885 TAAAATAAATTTAAATCCAAAATACTTAAATT
1 TAAAATAAATTTAAATCCAAAATACTTAAATT
3114917 TAAAATAAATTTAAATCCAAAAATAACTTAA
1 TAAAATAAATTTAAATCC-AAAAT-ACTTAA
3114948 TCTGAACTAC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 48 0.81
33 5 0.08
34 6 0.10
ACGTcount: A:0.59, C:0.09, G:0.01, T:0.31
Consensus pattern (32 bp):
TAAAATAAATTTAAATCCAAAATACTTAAATT
Found at i:3114947 original size:17 final size:16
Alignment explanation
Indices: 3114863--3114947 Score: 75
Period size: 17 Copynumber: 5.2 Consensus size: 16
3114853 TAAAAGAAAA
3114863 TTAAATCCAAAAT-AC
1 TTAAATCCAAAATAAC
** *
3114878 TTAAATTTAAAATAAAT
1 TTAAATCCAAAAT-AAC
3114895 TTAAATCCAAAAT-AC
1 TTAAATCCAAAATAAC
** *
3114910 TTAAATTTAAAATAAAT
1 TTAAATCCAAAAT-AAC
3114927 TTAAATCCAAAAATAAC
1 TTAAATCC-AAAATAAC
3114944 TTAA
1 TTAA
3114948 TCTGAACTAC
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
15 23 0.43
17 25 0.47
18 5 0.09
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (16 bp):
TTAAATCCAAAATAAC
Found at i:3115204 original size:21 final size:22
Alignment explanation
Indices: 3115187--3115232 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3115177 TTAATTCTTT
*
3115187 TAAATTT-TATAATGATTCTAA
1 TAAATTTATAGAATGATTCTAA
* *
3115208 TAAATTTATAGAATGAGTCAAA
1 TAAATTTATAGAATGATTCTAA
3115230 TAA
1 TAA
3115233 TTATTCTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (22 bp):
TAAATTTATAGAATGATTCTAA
Found at i:3118394 original size:37 final size:37
Alignment explanation
Indices: 3118344--3118414 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
3118334 CAAGTGTCGT
3118344 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAA
1 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAA
3118381 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGG
1 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGG
3118415 CAGACTTGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.28, C:0.06, G:0.39, T:0.27
Consensus pattern (37 bp):
ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAA
Found at i:3120461 original size:20 final size:19
Alignment explanation
Indices: 3120407--3120461 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
3120397 AAAACCCTTA
*
3120407 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
3120427 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
3120447 AATGTATCGATACAT
1 AAAGTATCGATACAT
3120462 GAAAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:3120558 original size:20 final size:20
Alignment explanation
Indices: 3120513--3120564 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
3120503 GTAGCCAAAC
* **
3120513 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
3120533 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
3120552 TTGTATCGATACA
1 TTGTATCGATACA
3120565 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:3120630 original size:20 final size:22
Alignment explanation
Indices: 3120599--3120642 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
3120589 CTATATTTTT
3120599 CAAATATGTATCGATACA-TCA
1 CAAATATGTATCGATACATTCA
3120620 CAAAT-TGTATCGATACATTCA
1 CAAATATGTATCGATACATTCA
3120641 CA
1 CA
3120643 CGGGAAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (22 bp):
CAAATATGTATCGATACATTCA
Found at i:3125760 original size:13 final size:13
Alignment explanation
Indices: 3125742--3125780 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3125732 ACATTTTTCT
3125742 TTGTATCGATACA
1 TTGTATCGATACA
3125755 TTGTATCGATACA
1 TTGTATCGATACA
*
3125768 CTGTATCGATACA
1 TTGTATCGATACA
3125781 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3128247 original size:20 final size:19
Alignment explanation
Indices: 3128193--3128247 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
3128183 AAAACCCTTA
*
3128193 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
3128213 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
3128233 AATGTATCGATACAT
1 AAAGTATCGATACAT
3128248 GAAAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:3128336 original size:13 final size:13
Alignment explanation
Indices: 3128318--3128343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3128308 TACACCAAGT
3128318 ATGTATCGATACA
1 ATGTATCGATACA
3128331 ATGTATCGATACA
1 ATGTATCGATACA
3128344 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3128341 original size:32 final size:33
Alignment explanation
Indices: 3128300--3128363 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
3128290 TAGCCAAACT
* **
3128300 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
3128332 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
3128364 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:3131480 original size:34 final size:34
Alignment explanation
Indices: 3131413--3131662 Score: 351
Period size: 34 Copynumber: 7.4 Consensus size: 34
3131403 TGGTTGATAA
* * *
3131413 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
3131446 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
3131480 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
3131513 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
3131547 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
3131581 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
3131615 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
3131649 TGTTGATTAAATGG
1 TGTTGATTAAATGG
3131663 TGGTTTTTAC
Statistics
Matches: 196, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
33 40 0.20
34 156 0.80
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:3132026 original size:19 final size:19
Alignment explanation
Indices: 3131970--3132032 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
3131960 TGGTTGTCGA
**
3131970 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
3131989 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
3132008 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
3132027 GTTACT
1 GGTACT
3132033 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:3136167 original size:34 final size:34
Alignment explanation
Indices: 3136098--3136349 Score: 355
Period size: 34 Copynumber: 7.5 Consensus size: 34
3136088 AAGTGGGAGA
* * *
3136098 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
3136131 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
3136165 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
3136198 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
3136232 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
3136266 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
3136300 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
3136334 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
3136350 TGGTTTTTAC
Statistics
Matches: 198, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
33 42 0.21
34 156 0.79
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:3136772 original size:17 final size:15
Alignment explanation
Indices: 3136750--3136783 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
3136740 TTGAATCATA
3136750 TAAATTTTTGTGTTTTT
1 TAAATTTTT-T-TTTTT
3136767 TAAATTTTTTTTTTT
1 TAAATTTTTTTTTTT
3136782 TA
1 TA
3136784 CATCTTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 1 0.06
17 9 0.53
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TAAATTTTTTTTTTT
Found at i:3140892 original size:37 final size:37
Alignment explanation
Indices: 3140837--3140949 Score: 208
Period size: 37 Copynumber: 3.1 Consensus size: 37
3140827 CAAGTGTCGT
*
3140837 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
1 ACATCAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
3140874 ACATCAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
1 ACATCAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
*
3140911 ACATCAACTTGTAGAATGGGGTGGGATTGAGAGGTAG
1 ACATCAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
3140948 AC
1 AC
3140950 TTGGCTTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 74 1.00
ACGTcount: A:0.28, C:0.08, G:0.39, T:0.25
Consensus pattern (37 bp):
ACATCAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
Found at i:3142822 original size:30 final size:29
Alignment explanation
Indices: 3142777--3142836 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 29
3142767 ATATATATAT
3142777 TATATTTTTCATTACTT-CTAAATTTTAAA
1 TATATTTTTCATTACTTGC-AAATTTTAAA
*
3142806 TATATTTTTGCATTACTTGCAACTTTTAAA
1 TATATTTTT-CATTACTTGCAAATTTTAAA
3142836 T
1 T
3142837 GTTATTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 9 0.32
30 18 0.64
31 1 0.04
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (29 bp):
TATATTTTTCATTACTTGCAAATTTTAAA
Found at i:3144984 original size:19 final size:17
Alignment explanation
Indices: 3144950--3145017 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 17
3144940 AATTTAACAT
3144950 AAAAATAATAAATATTA
1 AAAAATAATAAATATTA
3144967 AAAAATAATACGAATATTA
1 AAAAATAATA--AATATTA
* *
3144986 TATAAATATATAAATATTTT
1 -AAAAATA-ATAAATA-TTA
*
3145006 AAAAATTATAAA
1 AAAAATAATAAA
3145018 ATATAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
17 10 0.24
18 5 0.12
19 16 0.38
20 8 0.19
21 3 0.07
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (17 bp):
AAAAATAATAAATATTA
Found at i:3145035 original size:16 final size:17
Alignment explanation
Indices: 3145012--3145057 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
3145002 TTTTAAAAAT
3145012 TATAAAATATAAATTT-
1 TATAAAATATAAATTTA
3145028 TA-ATAAATCA-AAATTTA
1 TATA-AAAT-ATAAATTTA
3145045 TATAAAATATAAA
1 TATAAAATATAAA
3145058 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
15 1 0.04
16 13 0.52
17 10 0.40
18 1 0.04
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
TATAAAATATAAATTTA
Found at i:3145104 original size:27 final size:28
Alignment explanation
Indices: 3145037--3145111 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 28
3145027 TTAATAAATC
*
3145037 AAAATTTATATAAAATATAAAAAATTTTA
1 AAAATTAATATAAAATA-AAAAAATTTTA
* * *
3145066 AACA-TAATTATAAGATAATAAAA-TTTA
1 AAAATTAA-TATAAAATAAAAAAATTTTA
3145093 AAAATTAATATAAAATAAA
1 AAAATTAATATAAAATAAA
3145112 TATATAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
27 16 0.43
28 10 0.27
29 11 0.30
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (28 bp):
AAAATTAATATAAAATAAAAAAATTTTA
Found at i:3156705 original size:23 final size:24
Alignment explanation
Indices: 3156660--3156709 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
3156650 TTATCATAAG
*
3156660 TTAATAATTAATATCTTATTAATT
1 TTAATAAATAATATCTTATTAATT
3156684 TTAATAAATATATAT-TTA-TAATT
1 TTAATAAATA-ATATCTTATTAATT
3156707 TTA
1 TTA
3156710 TATTATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 12 0.50
25 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAATAAATAATATCTTATTAATT
Found at i:3156724 original size:17 final size:17
Alignment explanation
Indices: 3156688--3156738 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 17
3156678 TTAATTTTAA
3156688 TAAATATATATTTATAATTT
1 TAAAT-TATATTT-T-ATTT
*
3156708 TATATTATATTTTATTT
1 TAAATTATATTTTATTT
3156725 TAAATTATATTTTA
1 TAAATTATATTTTA
3156739 ATTATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 17 0.59
18 1 0.03
19 7 0.24
20 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAAATTATATTTTATTT
Found at i:3156735 original size:22 final size:23
Alignment explanation
Indices: 3156698--3156770 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 23
3156688 TAAATATATA
3156698 TTTATAATTTTATATTATATTTTAT
1 TTTATAA--TTATATTATATTTTAT
* *
3156723 TTTA-AATTATATTTTA-ATTATT
1 TTTATAATTATATTATATTTTA-T
*
3156745 TTTATTATATATATATATATTTTAT
1 TTTATAAT-TATAT-TATATTTTAT
3156770 T
1 T
3156771 AGCATGTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
21 3 0.08
22 14 0.37
23 2 0.05
24 7 0.18
25 9 0.24
26 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTATAATTATATTATATTTTAT
Found at i:3157198 original size:20 final size:20
Alignment explanation
Indices: 3157175--3157232 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
3157165 TATAATTTTT
*
3157175 TTATTATA-ATTATATTTAAA
1 TTATTATATATT-TATATAAA
3157195 TTATTATATATTTATATAAA
1 TTATTATATATTTATATAAA
* *
3157215 TTTTTATTTATTTATATA
1 TTATTATATATTTATATA
3157233 TTTATATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 31 0.91
21 3 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTATATATTTATATAAA
Found at i:3157233 original size:44 final size:43
Alignment explanation
Indices: 3157159--3157244 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 43
3157149 AAGCAGATAG
3157159 TATTTATATAATTTTTTTATTATAATTATATTTAAATTATTATA
1 TATTTATATAATTTTTTTATTATAATTATATTTAAATT-TTATA
*
3157203 TATTTATATAAATTTTTATTTATT-T-A-TATATTTATATTTTAT
1 TATTTATAT-AA-TTTT-TTTATTATAATTATATTTAAATTTTAT
3157245 TTATATTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
43 4 0.11
44 20 0.53
45 3 0.08
46 5 0.13
47 6 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (43 bp):
TATTTATATAATTTTTTTATTATAATTATATTTAAATTTTATA
Found at i:3157254 original size:34 final size:33
Alignment explanation
Indices: 3157173--3157285 Score: 90
Period size: 34 Copynumber: 3.4 Consensus size: 33
3157163 TATATAATTT
* * *
3157173 TTTTA-TTATAATTATATTTAAATTA-TTATATA
1 TTTTATTTAT-ATTTTATTTTAATTATTTTTATA
* * *
3157205 -TTTATATAAATTTT-TATTTATTTATATATTTATA
1 TTTTATTTATATTTTAT-TTTAATTAT-T-TTTATA
3157239 TTTTATTTATATTTTATTTTAATTATTTTATATA
1 TTTTATTTATATTTTATTTTAATTATTTT-TATA
*
3157273 TTTTATTCATATT
1 TTTTATTTATATT
3157286 ATATAATTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 14
0.72 0.11 0.16
Matches are distributed among these distances:
30 1 0.02
31 14 0.22
32 2 0.03
33 3 0.05
34 22 0.35
35 20 0.32
36 1 0.02
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (33 bp):
TTTTATTTATATTTTATTTTAATTATTTTTATA
Found at i:3157955 original size:11 final size:11
Alignment explanation
Indices: 3157941--3157992 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
3157931 AATATTAATA
3157941 ATTTATATTAT
1 ATTTATATTAT
*
3157952 ATTTATTTTAT
1 ATTTATATTAT
* *
3157963 TTTTATGTTAT
1 ATTTATATTAT
3157974 A-TTATATT-T
1 ATTTATATTAT
3157983 -TTTATATTAT
1 ATTTATATTAT
3157993 TTAATTTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 8 0.24
10 7 0.21
11 19 0.56
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:3157963 original size:27 final size:28
Alignment explanation
Indices: 3157932--3158010 Score: 85
Period size: 27 Copynumber: 2.9 Consensus size: 28
3157922 ATATAATTAA
*
3157932 ATATTAATAATTTATATTATATTTATTT
1 ATATTATTAATTTATATTATATTTATTT
*
3157960 -TATT-TTTATGTTATATTATATTT-TTT
1 ATATTATTAAT-TTATATTATATTTATTT
*
3157986 ATATTATTTAATTT-TATCATATTTA
1 ATATTA-TTAATTTATATTATATTTA
3158011 AAATTACTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
26 6 0.14
27 30 0.71
28 2 0.05
29 4 0.10
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (28 bp):
ATATTATTAATTTATATTATATTTATTT
Found at i:3157967 original size:22 final size:22
Alignment explanation
Indices: 3157942--3158002 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 22
3157932 ATATTAATAA
3157942 TTTATATTATATTTATTTTATT
1 TTTATATTATATTTATTTTATT
* *
3157964 TTTATGTTATA-TTA-TAT-TT
1 TTTATATTATATTTATTTTATT
*
3157983 TTTATATTAT-TTAATTTTAT
1 TTTATATTATATTTATTTTAT
3158003 CATATTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
19 13 0.42
20 4 0.13
21 4 0.13
22 10 0.32
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTATATTATATTTATTTTATT
Found at i:3157999 original size:17 final size:17
Alignment explanation
Indices: 3157948--3158000 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
3157938 ATAATTTATA
*
3157948 TTATATTTATTTTA-TTT
1 TTATA-TTATTTAATTTT
*
3157965 TTATGTTATATTATATTTT
1 TTATATTAT-TTA-ATTTT
3157984 TTATATTATTTAATTTT
1 TTATATTATTTAATTTT
3158001 ATCATATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 4 0.13
17 11 0.37
18 4 0.13
19 11 0.37
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (17 bp):
TTATATTATTTAATTTT
Found at i:3158309 original size:19 final size:19
Alignment explanation
Indices: 3158287--3158323 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3158277 TAAAAAATTA
3158287 TTTTTAT-ATTAATATTTAT
1 TTTTTATAATTAA-ATTTAT
3158306 TTTTTATAATTAAATTTA
1 TTTTTATAATTAAATTTA
3158324 AATAAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATAATTAAATTTAT
Found at i:3158924 original size:29 final size:28
Alignment explanation
Indices: 3158892--3158961 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
3158882 AAATTAAATT
3158892 TATTTAAATTATTATTTAATAAATAAAAA
1 TATTTAAATTATTATTTAAT-AATAAAAA
** *
3158921 TATTTTTATT-TAAATTTAATAATAAAAA
1 TATTTAAATTAT-TATTTAATAATAAAAA
*
3158949 TATATAAA-TATTA
1 TATTTAAATTATTA
3158962 ATATAAATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
27 2 0.06
28 15 0.47
29 15 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TATTTAAATTATTATTTAATAATAAAAA
Found at i:3158962 original size:29 final size:29
Alignment explanation
Indices: 3158905--3158962 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
3158895 TTAAATTATT
* **
3158905 ATTTAATAAATAAAAATATTTTTATTTAA
1 ATTTAATAAATAAAAATATATAAATTTAA
3158934 ATTTAAT-AATAAAAATATATAAATATTAA
1 ATTTAATAAATAAAAATATATAAAT-TTAA
3158963 TATAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTTAATAAATAAAAATATATAAATTTAA
Found at i:3168869 original size:37 final size:36
Alignment explanation
Indices: 3168819--3168968 Score: 183
Period size: 37 Copynumber: 4.1 Consensus size: 36
3168809 CAAGTGTCGT
3168819 ACATTAACTTGTGGAATGGGGTAGGATTGAGAGGTAG
1 ACATTAACTTGTGGAATGGGGT-GGATTGAGAGGTAG
* *
3168856 ACATTACCTTGTGGAATGGGGTGAGATTGAGATGTAG
1 ACATTAACTTGTGGAATGGGGTG-GATTGAGAGGTAG
* * *
3168893 TCATTACCTTGTGGAATGGGGTGGGATTGAGAGGTAA
1 ACATTAACTTGTGGAATGGGGT-GGATTGAGAGGTAG
* * * *
3168930 ACATCAACTTGTGGAATAGGGTGGAATTAAAAGGTAG
1 ACATTAACTTGTGGAATGGGGTGG-ATTGAGAGGTAG
3168967 AC
1 AC
3168969 TTGGCTTTTT
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
36 3 0.03
37 94 0.96
38 1 0.01
ACGTcount: A:0.30, C:0.08, G:0.35, T:0.27
Consensus pattern (36 bp):
ACATTAACTTGTGGAATGGGGTGGATTGAGAGGTAG
Found at i:3172217 original size:31 final size:31
Alignment explanation
Indices: 3172181--3172239 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
3172171 GTTTTGGTGG
3172181 GTATTGTTAATACATATTTTGGCATTTTTAT
1 GTATTGTTAATACATATTTTGGCATTTTTAT
3172212 GTATTGTTAATACATATTTTGGCATTTT
1 GTATTGTTAATACATATTTTGGCATTTT
3172240 CCTTTTCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.07, G:0.14, T:0.54
Consensus pattern (31 bp):
GTATTGTTAATACATATTTTGGCATTTTTAT
Found at i:3175796 original size:16 final size:17
Alignment explanation
Indices: 3175769--3175809 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
3175759 TGCTAACAAA
*
3175769 TTATATTATTTAAA-AT
1 TTATATTTTTTAAATAT
*
3175785 TTTTATTTTTTAAATAT
1 TTATATTTTTTAAATAT
3175802 TTATATTT
1 TTATATTT
3175810 AATATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATATTTTTTAAATAT
Found at i:3176587 original size:2 final size:2
Alignment explanation
Indices: 3176582--3176629 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
3176572 ATATATATGT
* * *
3176582 AG AG AG AG AG AG AG AG AT AG AG AG AG CG AG AG AG AG AG GG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3176624 AG AG AG
1 AG AG AG
3176630 GAGTATTGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.50, T:0.02
Consensus pattern (2 bp):
AG
Found at i:3177368 original size:2 final size:2
Alignment explanation
Indices: 3177361--3177404 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3177351 AACATGTAAT
3177361 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
3177403 TA
1 TA
3177405 AACTAGATTT
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):
TA
Found at i:3179119 original size:55 final size:54
Alignment explanation
Indices: 3179052--3179169 Score: 150
Period size: 55 Copynumber: 2.1 Consensus size: 54
3179042 AATCAAGATC
* * * *
3179052 AATTTAAATTTAATT-TAAATTATT-ATTTCAATAATAATATTTTTATTTTTATTTA
1 AATTTAAATTTAATTAT-AATTATTAATAT-AAAAATAAT-TTTTTAATATTATTTA
3179107 AATTTAAATTTAATTATAATTATTAATATAAAAATAATTTTTTAATATTATTTA
1 AATTTAAATTTAATTATAATTATTAATATAAAAATAATTTTTTAATATTATTTA
3179161 AATATTAAA
1 AAT-TTAAA
3179170 ATAAATTTCG
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
54 17 0.30
55 35 0.62
56 4 0.07
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (54 bp):
AATTTAAATTTAATTATAATTATTAATATAAAAATAATTTTTTAATATTATTTA
Found at i:3179821 original size:25 final size:25
Alignment explanation
Indices: 3179809--3179859 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
3179799 ATTTTTAAAT
3179809 TTTTTTATCAATTTAATATTTAATA
1 TTTTTTATCAATTTAATATTTAATA
*
3179834 TTTTTTATCAA-AT-ATA-TTAATA
1 TTTTTTATCAATTTAATATTTAATA
3179856 TTTT
1 TTTT
3179860 AAATTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 10 0.40
23 3 0.12
24 1 0.04
25 11 0.44
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTTTTATCAATTTAATATTTAATA
Found at i:3180084 original size:13 final size:13
Alignment explanation
Indices: 3180066--3180091 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3180056 TTATATTTTA
3180066 CTAAAAAATTAAT
1 CTAAAAAATTAAT
3180079 CTAAAAAATTAAT
1 CTAAAAAATTAAT
3180092 ATCCTTAACA
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:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
CTAAAAAATTAAT
Found at i:3180145 original size:21 final size:21
Alignment explanation
Indices: 3180103--3180160 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
3180093 TCCTTAACAA
*
3180103 AAATAAAAATTT--AAATAAT
1 AAATAAATATTTAAAAATAAT
* * * *
3180122 AAATTAATTTTTTAAAATATT
1 AAATAAATATTTAAAAATAAT
3180143 AAATAAATATTTAAAAAT
1 AAATAAATATTTAAAAAT
3180161 TTACACAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
19 9 0.30
21 21 0.70
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATAAATATTTAAAAATAAT
Found at i:3180155 original size:20 final size:20
Alignment explanation
Indices: 3180103--3180158 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3180093 TCCTTAACAA
*
3180103 AAATAAAAATTT-AAATAAT
1 AAATAAATATTTAAAATAAT
* * *
3180122 AAATTAATTTTTTAAAATATT
1 AAA-TAAATATTTAAAATAAT
3180143 AAATAAATATTTAAAA
1 AAATAAATATTTAAAA
3180159 ATTTACACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.10
20 17 0.59
21 9 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATAAATATTTAAAATAAT
Found at i:3181794 original size:2 final size:2
Alignment explanation
Indices: 3181787--3181861 Score: 114
Period size: 2 Copynumber: 37.5 Consensus size: 2
3181777 ATTGCTGCTG
* *
3181787 TA TA TA TA TA TA TA TA TA TA TG TA TG 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
* *
3181829 TG TA TA TA TA TA TA TG 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 T
3181862 TGTAATTTGT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3182603 original size:17 final size:18
Alignment explanation
Indices: 3182570--3182608 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
3182560 TTTTTTGAGC
3182570 TTTTTTATTTTTAAATT-
1 TTTTTTATTTTTAAATTA
3182587 TTTTTTAATTTTT-AATTA
1 TTTTTT-ATTTTTAAATTA
3182605 TTTT
1 TTTT
3182609 ATATCCGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTTTATTTTTAAATTA
Found at i:3183785 original size:13 final size:13
Alignment explanation
Indices: 3183764--3183804 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
3183754 ATTTAAATTT
*
3183764 ATATAAAATATAA
1 ATATTAAATATAA
3183777 ATATTAAATATAA
1 ATATTAAATATAA
**
3183790 ATATTTTATATAA
1 ATATTAAATATAA
3183803 AT
1 AT
3183805 TAAAAAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
ATATTAAATATAA
Found at i:3186006 original size:17 final size:18
Alignment explanation
Indices: 3185984--3186023 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
3185974 TTCTTCGCTC
*
3185984 ATATGTATAAA-AAATAT
1 ATATGTACAAATAAATAT
3186001 ATATGTACAAATAAATAT
1 ATATGTACAAATAAATAT
*
3186019 TTATG
1 ATATG
3186024 GATGCTAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (18 bp):
ATATGTACAAATAAATAT
Found at i:3188668 original size:2 final size:2
Alignment explanation
Indices: 3188663--3188717 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
3188653 TATGAACATA
* * * *
3188663 AT AT AT AT AT AT AT AT GT GT AT AT AT AT AT AT GT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3188705 AT AT AT AT GT AT A
1 AT AT AT AT AT AT A
3188718 CACAAACACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3188687 original size:16 final size:16
Alignment explanation
Indices: 3188666--3188717 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
3188656 GAACATAATA
3188666 TATATATATATATGTG
1 TATATATATATATGTG
*
3188682 TATATATATATATGTA
1 TATATATATATATGTG
* *
3188698 TATATTTATATATATG
1 TATATATATATATGTG
3188714 TATA
1 TATA
3188718 CACAAACACT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (16 bp):
TATATATATATATGTG
Found at i:3188687 original size:18 final size:18
Alignment explanation
Indices: 3188663--3188717 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
3188653 TATGAACATA
3188663 ATATATATATATATATG-
1 ATATATATATATATATGT
*
3188680 -TGTATATATATATATGT
1 ATATATATATATATATGT
*
3188697 ATATATTTATATATATGT
1 ATATATATATATATATGT
3188715 ATA
1 ATA
3188718 CACAAACACT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 15 0.45
18 18 0.55
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
ATATATATATATATATGT
Found at i:3189599 original size:6 final size:6
Alignment explanation
Indices: 3189588--3189612 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3189578 TATCATATTA
3189588 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
3189613 CATATCGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:3190673 original size:2 final size:2
Alignment explanation
Indices: 3190666--3190704 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3190656 ACCGGCCATG
3190666 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 T
3190705 GTGAATTAAG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3192614 original size:10 final size:9
Alignment explanation
Indices: 3192596--3192633 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
3192586 AAAATTCTTT
3192596 TATTATATA
1 TATTATATA
3192605 TA-TATATA
1 TATTATATA
3192613 TATTTATATA
1 TA-TTATATA
3192623 TACTTATATA
1 TA-TTATATA
3192633 T
1 T
3192634 TAAATGTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 8 0.31
9 2 0.08
10 16 0.62
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (9 bp):
TATTATATA
Found at i:3193226 original size:41 final size:41
Alignment explanation
Indices: 3193175--3193261 Score: 97
Period size: 41 Copynumber: 2.1 Consensus size: 41
3193165 TTTTATTTTT
*
3193175 AAATATAATTATGAAAA-AAACATCTAAACATAAAAAAATTAA
1 AAATATAATTA--AAAACAAACAACTAAACATAAAAAAATTAA
* * *
3193217 AAAT-TAATTAAAAATCAAATAAGTAAATATAAAAAAATTAA
1 AAATATAATTAAAAA-CAAACAACTAAACATAAAAAAATTAA
3193258 AAAT
1 AAAT
3193262 CTTATCTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
39 4 0.10
41 31 0.79
42 4 0.10
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (41 bp):
AAATATAATTAAAAACAAACAACTAAACATAAAAAAATTAA
Found at i:3193713 original size:16 final size:17
Alignment explanation
Indices: 3193693--3193726 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3193683 ATTTTTTATC
3193693 ATTTTT-ATT-CAAAAA
1 ATTTTTAATTACAAAAA
3193708 ATTTTTAATTACAAAAA
1 ATTTTTAATTACAAAAA
3193725 AT
1 AT
3193727 AAGAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 3 0.18
17 8 0.47
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTTTAATTACAAAAA
Found at i:3193902 original size:23 final size:24
Alignment explanation
Indices: 3193857--3193907 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
3193847 AACTTTGAAA
* *
3193857 TAAATTTATTAAAATATTTTTATT
1 TAAATTAATTAAAATATTATTATT
*
3193881 TAAATTAATT-AATTATTATTATT
1 TAAATTAATTAAAATATTATTATT
3193904 TAAA
1 TAAA
3193908 AATTTAGTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TAAATTAATTAAAATATTATTATT
Found at i:3193969 original size:9 final size:9
Alignment explanation
Indices: 3193935--3193961 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3193925 ATTGGTTAAA
3193935 GAAAAAAAT
1 GAAAAAAAT
3193944 GAAAAAAAT
1 GAAAAAAAT
3193953 GAAAAAAAT
1 GAAAAAAAT
3193962 AATAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:3195278 original size:20 final size:20
Alignment explanation
Indices: 3195226--3195279 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 20
3195216 AAAGTTTTTT
* *
3195226 TATATTTAA-ATATTAAATA
1 TATATTTAATTTAATAAATA
3195245 TA-A-TTAATAATTAATAAATA
1 TATATTTAAT--TTAATAAATA
3195265 TATATTTAATTTAAT
1 TATATTTAATTTAAT
3195280 TATATAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
17 4 0.14
18 1 0.04
19 2 0.07
20 15 0.54
21 1 0.04
22 5 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TATATTTAATTTAATAAATA
Found at i:3195285 original size:39 final size:38
Alignment explanation
Indices: 3195226--3195302 Score: 88
Period size: 39 Copynumber: 2.0 Consensus size: 38
3195216 AAAGTTTTTT
3195226 TATATTTAAATATTAAATAT-AATTAATAATTAATAAATA
1 TATATTTAAATATTAAATATAAATTAA-AATTAA-AAATA
3195265 TATATTT-AAT-TTAATTATATAAAATTAAAATTAAAAAT
1 TATATTTAAATATTAA--ATAT-AAATTAAAATTAAAAAT
3195303 TTTGAAGCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
37 4 0.12
38 3 0.09
39 15 0.44
40 6 0.18
41 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (38 bp):
TATATTTAAATATTAAATATAAATTAAAATTAAAAATA
Found at i:3195470 original size:5 final size:5
Alignment explanation
Indices: 3195455--3195500 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
3195445 AAATAAATTA
* *
3195455 TTAATT TTAAT TTAA- TTAAT TTAA- TCAAT TTAAT TTAAT ATAAT TT
1 TTAA-T TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TT
3195501 TTAATCATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
4 7 0.21
5 23 0.68
6 4 0.12
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (5 bp):
TTAAT
Found at i:3195473 original size:9 final size:9
Alignment explanation
Indices: 3195461--3195499 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
3195451 ATTATTAATT
3195461 TTAATTTAA
1 TTAATTTAA
3195470 TTAATTTAA
1 TTAATTTAA
*
3195479 TCAATTTAA
1 TTAATTTAA
*
3195488 TTTAATATAA
1 -TTAATTTAA
3195498 TT
1 TT
3195500 TTTAATCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (9 bp):
TTAATTTAA
Found at i:3195876 original size:23 final size:25
Alignment explanation
Indices: 3195823--3195879 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
3195813 GTTTATTGTG
**
3195823 ATTATAAATATAATATAGTATTATA
1 ATTATAAATATAATATAAAATTATA
3195848 A-T-TAAATATAATA-AAAATTA-A
1 ATTATAAATATAATATAAAATTATA
3195869 ATTATAAATAT
1 ATTATAAATAT
3195880 TATGATAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 2 0.07
22 6 0.21
23 18 0.64
24 1 0.04
25 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (25 bp):
ATTATAAATATAATATAAAATTATA
Found at i:3196926 original size:2 final size:2
Alignment explanation
Indices: 3196919--3196952 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3196909 CCTTCGAATC
3196919 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
3196953 TTCCAATTTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3197486 original size:27 final size:28
Alignment explanation
Indices: 3197440--3197492 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
3197430 TTTTGCTTAA
*
3197440 TTTAAAAAAATTATCTCATTATTTTACT
1 TTTAAAAAAACTATCTCATTATTTTACT
* *
3197468 TTTAAAATAACTATC-CATTTTTTTA
1 TTTAAAAAAACTATCTCATTATTTTA
3197493 AAAAAATACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (28 bp):
TTTAAAAAAACTATCTCATTATTTTACT
Found at i:3197498 original size:24 final size:23
Alignment explanation
Indices: 3197471--3197519 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3197461 TTTTACTTTT
*
3197471 AAAATAACTATCCATTTTTTTAAA
1 AAAATAACTAT-AATTTTTTTAAA
*
3197495 AAAATACCTATAATTTTTTTAAA
1 AAAATAACTATAATTTTTTTAAA
3197518 AA
1 AA
3197520 TATTTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (23 bp):
AAAATAACTATAATTTTTTTAAA
Found at i:3200431 original size:4 final size:4
Alignment explanation
Indices: 3200422--3200448 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3200412 TCTCCCAAAG
3200422 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
3200449 TTTGCTAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3200711 original size:2 final size:2
Alignment explanation
Indices: 3200704--3200731 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3200694 AATATTTGAA
3200704 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
3200732 TTCTTTTATA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3201768 original size:5 final size:5
Alignment explanation
Indices: 3201746--3201780 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
3201736 TGACATACCC
3201746 AAAAT GAAAAT GAAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT -AAAAT -AAAAT AAAAT AAAAT AAAAT AAA
3201781 TAGCTTTCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:3202446 original size:22 final size:21
Alignment explanation
Indices: 3202421--3202463 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
3202411 AGTTTTTACT
*
3202421 CAAATTTTTTTATTTATAAATA
1 CAAATTTTTTT-TTAATAAATA
3202443 CAAATTTTTTTTTAATAAATA
1 CAAATTTTTTTTTAATAAATA
3202464 TCTTTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
CAAATTTTTTTTTAATAAATA
Found at i:3202452 original size:21 final size:22
Alignment explanation
Indices: 3202421--3202463 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3202411 AGTTTTTACT
3202421 CAAATTTTTTTATTT-ATAAATA
1 CAAATTTTTTT-TTTAATAAATA
3202443 CAAA-TTTTTTTTTAATAAATA
1 CAAATTTTTTTTTTAATAAATA
3202464 TCTTTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 13 0.65
22 4 0.20
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
CAAATTTTTTTTTTAATAAATA
Found at i:3204755 original size:13 final size:13
Alignment explanation
Indices: 3204737--3204763 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3204727 TAAGGATCAA
3204737 GTTTTAAGATTTT
1 GTTTTAAGATTTT
3204750 GTTTTAAGATTTT
1 GTTTTAAGATTTT
3204763 G
1 G
3204764 GCATATAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (13 bp):
GTTTTAAGATTTT
Found at i:3209007 original size:14 final size:14
Alignment explanation
Indices: 3208988--3209015 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3208978 GGTTTATTAT
3208988 TGCAGTCTGATCGG
1 TGCAGTCTGATCGG
3209002 TGCAGTCTGATCGG
1 TGCAGTCTGATCGG
3209016 CATCATTAGA
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:0.14, C:0.21, G:0.36, T:0.29
Consensus pattern (14 bp):
TGCAGTCTGATCGG
Found at i:3210334 original size:35 final size:37
Alignment explanation
Indices: 3210226--3210336 Score: 172
Period size: 37 Copynumber: 3.1 Consensus size: 37
3210216 CAAGTGTCGT
*
3210226 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGCTAG
1 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
*
3210263 ACATTACCTTGTGGAATGGGGTGGGATTGAGAGGTAG
1 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
* *
3210300 ACATCAACTTGTGGAAT-GGG-GGGATTGAGTGGTAG
1 ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
3210335 AC
1 AC
3210337 TTGGCTTTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
35 16 0.23
36 3 0.04
37 50 0.72
ACGTcount: A:0.26, C:0.09, G:0.39, T:0.26
Consensus pattern (37 bp):
ACATTAACTTGTGGAATGGGGTGGGATTGAGAGGTAG
Found at i:3212031 original size:37 final size:36
Alignment explanation
Indices: 3211958--3212033 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 36
3211948 TTTAAAATTT
*
3211958 TTTATAAATAAAATATCATAATATAATTTATATAAA
1 TTTATAAATAAAATATCATAATATAAATTATATAAA
3211994 TTTATATAATAATAATA-CATCAAATATAAATT-T-TAAA
1 TTTATA-AATAA-AATATCAT--AATATAAATTATATAAA
3212031 TTT
1 TTT
3212034 TACATATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
36 6 0.17
37 15 0.43
38 5 0.14
39 9 0.26
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (36 bp):
TTTATAAATAAAATATCATAATATAAATTATATAAA
Found at i:3212337 original size:17 final size:17
Alignment explanation
Indices: 3212317--3212351 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3212307 ATTATTAAAA
3212317 TAATATAATA-TTTATTT
1 TAAT-TAATACTTTATTT
3212334 TAATTAATACTTTATTT
1 TAATTAATACTTTATTT
3212351 T
1 T
3212352 TTAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TAATTAATACTTTATTT
Found at i:3214321 original size:17 final size:17
Alignment explanation
Indices: 3214299--3214365 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 17
3214289 ACTTAACATC
3214299 AAAATAATAAATATTAA
1 AAAATAATAAATATTAA
3214316 AAAATAATACGAATA-TAA
1 AAAATAATA--AATATTAA
*
3214334 TATAAATATATAAATATTTTA
1 -A-AAATA-ATAAATA-TTAA
*
3214355 AAAATTATAAA
1 AAAATAATAAA
3214366 ATATAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
17 9 0.22
18 8 0.20
19 13 0.32
20 6 0.15
21 5 0.12
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (17 bp):
AAAATAATAAATATTAA
Found at i:3214369 original size:38 final size:37
Alignment explanation
Indices: 3214300--3214371 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
3214290 CTTAACATCA
*
3214300 AAATAATAAATATTAAAAAATAATACGAATATAATAT
1 AAATAATAAATATTAAAAAATAATACAAATATAATAT
* *
3214337 AAATATATAAATATTTTAAAAATTATA-AAATATAA
1 AAATA-ATAAATA-TTAAAAAATAATACAAATATAA
3214372 ATTTTAACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 5 0.17
38 14 0.47
39 11 0.37
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (37 bp):
AAATAATAAATATTAAAAAATAATACAAATATAATAT
Found at i:3214406 original size:49 final size:48
Alignment explanation
Indices: 3214330--3214455 Score: 121
Period size: 49 Copynumber: 2.6 Consensus size: 48
3214320 TAATACGAAT
* * * * * *
3214330 ATAATATAAATATATAAATATTTTAAAAATTATAAAATATAAATTTTAAC
1 ATAATA-AAATTTATAAATAATATAAAAAATATAAAACAT-AATTATAAC
* *
3214380 AT-ATCAAAATTTATATAA-AATATAAAAAATCTTAAACATAATTATAAC
1 ATAAT-AAAATTTATA-AATAATATAAAAAATATAAAACATAATTATAAC
3214428 ATAATAAAATTTATAAATTAATATAAAA
1 ATAATAAAATTTATAAA-TAATATAAAA
3214456 TAAATATATA
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
47 2 0.03
48 20 0.32
49 36 0.57
50 5 0.08
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (48 bp):
ATAATAAAATTTATAAATAATATAAAAAATATAAAACATAATTATAAC
Found at i:3226036 original size:12 final size:12
Alignment explanation
Indices: 3226007--3226087 Score: 51
Period size: 12 Copynumber: 6.6 Consensus size: 12
3225997 TTTTAATAAA
3226007 TATATATTTATAAT
1 TATAT-TTTAT-AT
* *
3226021 TTTATATTATAT
1 TATATTTTATAT
* * *
3226033 TTTATTTAAAAT
1 TATATTTTATAT
3226045 TATATTTTA-AT
1 TATATTTTATAT
3226056 TAT-TTTTATCAT
1 TATATTTTAT-AT
3226068 ATATATTTTAT-T
1 -TATATTTTATAT
3226080 ATATATTT
1 -TATATTT
3226088 AAAATTATGT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
10 5 0.09
11 5 0.09
12 29 0.52
13 7 0.12
14 10 0.18
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (12 bp):
TATATTTTATAT
Found at i:3226510 original size:20 final size:19
Alignment explanation
Indices: 3226499--3226559 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 19
3226489 ATTATAATTA
3226499 TATTTAAATTATTATATATT
1 TATTTAAATTATT-TATATT
*
3226519 TATATAAA-T-TTT-TATT
1 TATTTAAATTATTTATATT
*
3226535 TATTTATA-TATTTATATT
1 TATTTAAATTATTTATATT
3226553 ATATTTA
1 -TATTTA
3226560 TATTTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
16 11 0.31
17 4 0.11
18 6 0.17
19 7 0.20
20 7 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTAAATTATTTATATT
Done.