Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold148
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: 1464219
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 85296 characters in sequence are not A, C, G, or T
File 2 of 9
Found at i:173752 original size:21 final size:22
Alignment explanation
Indices: 173727--173769 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
173717 TGTAAAATTT
173727 TAAATCGATT-TAATATTTTTA
1 TAAATCGATTATAATATTTTTA
*
173748 TAAATTGATTGATAATATTTTT
1 TAAATCGATT-ATAATATTTTT
173770 TTAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
23 10 0.53
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.53
Consensus pattern (22 bp):
TAAATCGATTATAATATTTTTA
Found at i:174037 original size:23 final size:22
Alignment explanation
Indices: 174007--174051 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
173997 TTATTAAATT
*
174007 TTATTATTTAT-AAAATATATAA
1 TTATTATTT-TCAAAATACATAA
174029 TTATATATTTTCAAAATACATAA
1 TTAT-TATTTTCAAAATACATAA
174052 AAAATAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
TTATTATTTTCAAAATACATAA
Found at i:174150 original size:20 final size:21
Alignment explanation
Indices: 174105--174150 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
174095 TATAAATTAT
174105 TTTATATACTATTTATATGTTA
1 TTTA-ATACTATTTATATGTTA
174127 -TTAATACTATTTATAT-TTA
1 TTTAATACTATTTATATGTTA
174146 TTTAA
1 TTTAA
174151 ATTTAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.13
20 17 0.74
21 3 0.13
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTAATACTATTTATATGTTA
Found at i:180311 original size:28 final size:29
Alignment explanation
Indices: 180259--180314 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
180249 TAGATTGACT
180259 TATATTTTATATTTTTAAATTTTTTTAAA
1 TATATTTTATATTTTTAAATTTTTTTAAA
* *
180288 TATATTTTTTA-TTTTAACTTTTTTTAA
1 TATATTTTATATTTTTAAATTTTTTTAA
180315 TTTAATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (29 bp):
TATATTTTATATTTTTAAATTTTTTTAAA
Found at i:180954 original size:2 final size:2
Alignment explanation
Indices: 180947--180977 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
180937 CTGTTCGCAT
180947 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
180978 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:180982 original size:2 final size:2
Alignment explanation
Indices: 180977--181011 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
180967 ACACACACAC
180977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
181012 GTGTTCATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:182924 original size:39 final size:40
Alignment explanation
Indices: 182881--182968 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
182871 GGTCGACACT
* *
182881 GCCACCCAATTACATATTT-GATTCTCGTGAATTGGCATA
1 GCCACCCAACTACATATTTAAATTCTCGTGAATTGGCATA
* * *
182920 GCCACCCAACTGCATATTTAAATTTTCGTGGATTGGCATA
1 GCCACCCAACTACATATTTAAATTCTCGTGAATTGGCATA
182960 GCCACCCAA
1 GCCACCCAA
182969 ATACTAACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 17 0.40
40 26 0.60
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (40 bp):
GCCACCCAACTACATATTTAAATTCTCGTGAATTGGCATA
Found at i:192966 original size:21 final size:20
Alignment explanation
Indices: 192942--192980 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
192932 TATTTTTATT
192942 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TA-AAAATATA
192963 TAAATATTAATAAAAATA
1 TAAATATTAATAAAAATA
192981 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATATTAATAAAAATATA
Found at i:193059 original size:7 final size:7
Alignment explanation
Indices: 193037--193068 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
193027 AAGTTAGATC
193037 AAATTTA
1 AAATTTA
193044 AAA-TT-
1 AAATTTA
193049 AAATTTA
1 AAATTTA
193056 AAATTTA
1 AAATTTA
193063 AAATTT
1 AAATTT
193069 TTTCAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
5 3 0.13
6 4 0.17
7 16 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:195774 original size:20 final size:19
Alignment explanation
Indices: 195742--195781 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
195732 AATTACATAC
* *
195742 CTTTTTTTCTTTTATCTTA
1 CTTTTTTCCTTTTATATTA
195761 CTTTTTTCCTTTTTATATTA
1 CTTTTTTCC-TTTTATATTA
195781 C
1 C
195782 CATATATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTTTCCTTTTATATTA
Found at i:195937 original size:17 final size:19
Alignment explanation
Indices: 195915--195965 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 19
195905 ATATATCACG
195915 TTTTTTATTTTAATT-A-A
1 TTTTTTATTTTAATTGATA
* *
195932 TTTTTTATTATATTTGATA
1 TTTTTTATTTTAATTGATA
195951 TTTTATTATTTTAAT
1 TTTT-TTATTTTAAT
195966 ATTATTTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 13 0.48
18 1 0.04
19 5 0.19
20 8 0.30
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTTTTATTTTAATTGATA
Found at i:195968 original size:28 final size:28
Alignment explanation
Indices: 195920--195982 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 28
195910 TCACGTTTTT
*
195920 TATTTTAATTAATTTTTTATTATATT-TGA
1 TATTTT-ATTAATTTTATATTAT-TTATGA
195949 TATTTTATT-ATTTTAATATTATTTATGA
1 TATTTTATTAATTTT-ATATTATTTATGA
195977 -ATTTTA
1 TATTTTA
195983 AAAATTTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 13 0.42
28 12 0.39
29 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (28 bp):
TATTTTATTAATTTTATATTATTTATGA
Found at i:197709 original size:19 final size:18
Alignment explanation
Indices: 197676--197714 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
197666 TTTATTATTT
*
197676 TATTTTTATAAATTTTAA
1 TATTTTTATAAATTTAAA
*
197694 TATTTTTATTACATTTAAA
1 TATTTTTA-TAAATTTAAA
197713 TA
1 TA
197715 AATCTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTTTATAAATTTAAA
Found at i:197738 original size:29 final size:29
Alignment explanation
Indices: 197706--197810 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 29
197696 TTTTTATTAC
*
197706 ATTTAAATAAATCTTAATTTTTAATTTAT
1 ATTTAAATAAATCTTAACTTTTAATTTAT
* *
197735 ATTTAAATAAA-CTTTAACCTTTAAATTAT
1 ATTTAAATAAATC-TTAACTTTTAATTTAT
* *
197764 ATATAACA-AAATTCTCTAACTTTTAATTTAA
1 ATTTAA-ATAAA-TCT-TAACTTTTAATTTAT
* *
197795 ACTTAAATATATCTTA
1 ATTTAAATAAATCTTA
197811 TAACATAAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 1 0.02
29 34 0.57
30 6 0.10
31 19 0.32
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTAAATAAATCTTAACTTTTAATTTAT
Found at i:198169 original size:29 final size:28
Alignment explanation
Indices: 198102--198170 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
198092 ACTTTTTATT
198102 TAAAATA-AAAACTTAATTAGATATAAA
1 TAAAATATAAAACTTAATTAGATATAAA
* *
198129 TAAAATGATAAAGACTTATTTTGATAT-AA
1 TAAAAT-ATAAA-ACTTAATTAGATATAAA
198158 TAAAAATATAAAA
1 T-AAAATATAAAA
198171 TTTTTATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 6 0.17
28 2 0.06
29 11 0.31
30 17 0.47
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (28 bp):
TAAAATATAAAACTTAATTAGATATAAA
Found at i:198413 original size:37 final size:37
Alignment explanation
Indices: 198365--198438 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
198355 CACTTACAAT
*
198365 AATTATACTATAATTAATCAATCAACATTCAAAATTA
1 AATTACACTATAATTAATCAATCAACATTCAAAATTA
*
198402 AATTACACTATAATTAATCAATCAATATTCAAAATTA
1 AATTACACTATAATTAATCAATCAACATTCAAAATTA
198439 TGTAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (37 bp):
AATTACACTATAATTAATCAATCAACATTCAAAATTA
Found at i:199551 original size:21 final size:21
Alignment explanation
Indices: 199525--199566 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
199515 AAGCACTCGT
199525 TTTGGCTTTTTCTCTTTCTTA
1 TTTGGCTTTTTCTCTTTCTTA
199546 TTTGGCTTTTTCTCTTTCTTA
1 TTTGGCTTTTTCTCTTTCTTA
199567 GATTGATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.19, G:0.10, T:0.67
Consensus pattern (21 bp):
TTTGGCTTTTTCTCTTTCTTA
Found at i:202253 original size:2 final size:2
Alignment explanation
Indices: 202248--202280 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
202238 AAGAAAAGAA
202248 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 A
202281 AAATGATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:203461 original size:18 final size:17
Alignment explanation
Indices: 203438--203481 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
203428 AAGTATCTTC
*
203438 ATAAAATATTTTAAATA
1 ATAAAATATTTAAAATA
*
203455 TATAAAAAATTTAAAATA
1 -ATAAAATATTTAAAATA
*
203473 ATTAAATAT
1 ATAAAATAT
203482 ATTCATATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAATATTTAAAATA
Found at i:203769 original size:18 final size:18
Alignment explanation
Indices: 203748--203802 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
203738 TAATAATTTA
203748 TATTATTTTAATTTAAAT
1 TATTATTTTAATTTAAAT
* * *
203766 TATTATTTAAATAATAAAA
1 TATTATTTTAAT-TTAAAT
*
203785 TATTATTTTTATTTAAAT
1 TATTATTTTAATTTAAAT
203803 ATAATTATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATTTTAATTTAAAT
Found at i:203779 original size:36 final size:36
Alignment explanation
Indices: 203721--203815 Score: 111
Period size: 37 Copynumber: 2.6 Consensus size: 36
203711 TATTAAATCA
* **
203721 AATTTAAATATAAATTTTAATAAT-TTATATTATTTT
1 AATTTAAATAT-AATTTAAATAATAAAATATTATTTT
*
203757 AATTTAAATTATTATTTAAATAATAAAATATTATTTT
1 AATTTAAA-TATAATTTAAATAATAAAATATTATTTT
*
203794 TATTTAAATATAATTATAAATA
1 AATTTAAATATAATT-TAAATA
203816 TAATATAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
36 24 0.48
37 26 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
AATTTAAATATAATTTAAATAATAAAATATTATTTT
Found at i:203788 original size:19 final size:18
Alignment explanation
Indices: 203747--203792 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
203737 TTAATAATTT
* *
203747 ATATTATTTTAATTTAAA
1 ATATTATTTAAATATAAA
*
203765 TTATTATTTAAATAATAAA
1 ATATTATTTAAAT-ATAAA
203784 ATATTATTT
1 ATATTATTT
203793 TTATTTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTATTTAAATATAAA
Found at i:206182 original size:21 final size:20
Alignment explanation
Indices: 206158--206196 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
206148 TATTTTTATT
206158 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TA-AAAATATA
206179 TAAATATTAATAAAAATA
1 TAAATATTAATAAAAATA
206197 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATATTAATAAAAATATA
Found at i:206270 original size:12 final size:13
Alignment explanation
Indices: 206253--206283 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
206243 AAGTTAGATC
206253 AAATTTAAAA-TT
1 AAATTTAAAATTT
206265 AAATTTAAAATTT
1 AAATTTAAAATTT
206278 AAATTT
1 AAATTT
206284 TTTTCAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAATTTAAAATTT
Found at i:208966 original size:18 final size:18
Alignment explanation
Indices: 208939--208974 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
208929 TTACATACCT
* *
208939 TTTTTTCTTTTATCTTAC
1 TTTTTCCTTTTATATTAC
208957 TTTTTCCTTTTATATTAC
1 TTTTTCCTTTTATATTAC
208975 CATATATGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTTCCTTTTATATTAC
Found at i:209151 original size:22 final size:20
Alignment explanation
Indices: 209105--209154 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
209095 ATATATTACA
209105 TTTT-TTATTTTGATTAATT
1 TTTTATTATTTTGATTAATT
209124 TTTTATTATATTTGATT-A-T
1 TTTTATTAT-TTTGATTAATT
*
209143 GTTTATTATTTT
1 TTTTATTATTTT
209155 AATATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 13 0.46
20 5 0.18
21 7 0.25
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (20 bp):
TTTTATTATTTTGATTAATT
Found at i:210889 original size:19 final size:18
Alignment explanation
Indices: 210856--210894 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
210846 TTTATTATTT
*
210856 TATTTTTATAAATTTGAA
1 TATTTTTATAAATTTAAA
*
210874 TATTTTTATTACATTTAAA
1 TATTTTTA-TAAATTTAAA
210893 TA
1 TA
210895 AATCTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTTTATAAATTTAAA
Found at i:210944 original size:29 final size:28
Alignment explanation
Indices: 210881--210990 Score: 71
Period size: 29 Copynumber: 3.8 Consensus size: 28
210871 GAATATTTTT
* * *
210881 ATTACATTTAAATAAATCTTAATTTTTA
1 ATTATATTTAAATAAATCTTAACTTTAA
210909 ATGTATATTTAAATAAA-CTTTAACCTTTAA
1 AT-TATATTTAAATAAATC-TTAA-CTTTAA
*
210939 ATTATATATAACA-AAATTCTCTAACTTTTAA
1 ATTATATTTAA-ATAAA-TCT-TAAC-TTTAA
* * * *
210970 TTTAAACTTAAATATATCTTA
1 ATTATATTTAAATAAATCTTA
210991 TAACATAAAC
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
28 3 0.05
29 30 0.47
30 13 0.20
31 18 0.28
ACGTcount: A:0.44, C:0.10, G:0.01, T:0.45
Consensus pattern (28 bp):
ATTATATTTAAATAAATCTTAACTTTAA
Found at i:211348 original size:29 final size:28
Alignment explanation
Indices: 211281--211349 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
211271 ACTTTTTATT
211281 TAAAATA-AAAACTTAATTAGATATAAA
1 TAAAATATAAAACTTAATTAGATATAAA
* *
211308 TAAAATGATAAAGACTTATTTTGATAT-AA
1 TAAAAT-ATAAA-ACTTAATTAGATATAAA
211337 TAAAAATATAAAA
1 T-AAAATATAAAA
211350 TTTTTATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 6 0.17
28 2 0.06
29 11 0.31
30 17 0.47
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (28 bp):
TAAAATATAAAACTTAATTAGATATAAA
Found at i:211592 original size:37 final size:37
Alignment explanation
Indices: 211544--211617 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
211534 CACTTACAAT
*
211544 AATTATACTATAATTAATCAATCAACATTCAAAATTA
1 AATTACACTATAATTAATCAATCAACATTCAAAATTA
*
211581 AATTACACTATAATTAATCAATCAATATTCAAAATTA
1 AATTACACTATAATTAATCAATCAACATTCAAAATTA
211618 TGTAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (37 bp):
AATTACACTATAATTAATCAATCAACATTCAAAATTA
Found at i:212730 original size:21 final size:21
Alignment explanation
Indices: 212704--212745 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
212694 AAGCACTCGT
212704 TTTGGCTTTTTCTCTTTCTTA
1 TTTGGCTTTTTCTCTTTCTTA
212725 TTTGGCTTTTTCTCTTTCTTA
1 TTTGGCTTTTTCTCTTTCTTA
212746 GATTGATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.19, G:0.10, T:0.67
Consensus pattern (21 bp):
TTTGGCTTTTTCTCTTTCTTA
Found at i:215430 original size:2 final size:2
Alignment explanation
Indices: 215425--215461 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
215415 AAGAAAAGAA
215425 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 A
215462 AAATGATAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:216952 original size:18 final size:18
Alignment explanation
Indices: 216931--216985 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
216921 TAATAATTTA
216931 TATTATTTTAATTTAAAT
1 TATTATTTTAATTTAAAT
* * *
216949 TATTATTTAAATAATAAAA
1 TATTATTTTAAT-TTAAAT
*
216968 TATTATTTTTATTTAAAT
1 TATTATTTTAATTTAAAT
216986 ATAATTATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTATTTTAATTTAAAT
Found at i:216962 original size:36 final size:36
Alignment explanation
Indices: 216904--216998 Score: 111
Period size: 37 Copynumber: 2.6 Consensus size: 36
216894 TATTAAATCA
* **
216904 AATTTAAATATAAATTTTAATAAT-TTATATTATTTT
1 AATTTAAATAT-AATTTAAATAATAAAATATTATTTT
*
216940 AATTTAAATTATTATTTAAATAATAAAATATTATTTT
1 AATTTAAA-TATAATTTAAATAATAAAATATTATTTT
*
216977 TATTTAAATATAATTATAAATA
1 AATTTAAATATAATT-TAAATA
216999 TAATATAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
36 24 0.48
37 26 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (36 bp):
AATTTAAATATAATTTAAATAATAAAATATTATTTT
Found at i:216971 original size:19 final size:18
Alignment explanation
Indices: 216930--216975 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
216920 TTAATAATTT
* *
216930 ATATTATTTTAATTTAAA
1 ATATTATTTAAATATAAA
*
216948 TTATTATTTAAATAATAAA
1 ATATTATTTAAAT-ATAAA
216967 ATATTATTT
1 ATATTATTT
216976 TTATTTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTATTTAAATATAAA
Found at i:219371 original size:21 final size:20
Alignment explanation
Indices: 219347--219385 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
219337 TATTTTTATT
219347 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TA-AAAATATA
219368 TAAATATTAATAAAAATA
1 TAAATATTAATAAAAATA
219386 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATATTAATAAAAATATA
Found at i:219464 original size:7 final size:7
Alignment explanation
Indices: 219442--219473 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
219432 AAGTTAGATC
219442 AAATTTA
1 AAATTTA
219449 AAA-TT-
1 AAATTTA
219454 AAATTTA
1 AAATTTA
219461 AAATTTA
1 AAATTTA
219468 AAATTT
1 AAATTT
219474 TTTCAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
5 3 0.13
6 4 0.17
7 16 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:222349 original size:20 final size:20
Alignment explanation
Indices: 222307--222357 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
222297 ATATATTACA
*
222307 TTTT-TTATTTTGATTAATT
1 TTTTATTATTTTGATTAATG
222326 TTTTATTATATTTGATT-ATG
1 TTTTATTAT-TTTGATTAATG
222346 TTTTATTATTTT
1 TTTTATTATTTT
222358 AATATTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 7 0.24
20 15 0.52
21 7 0.24
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.73
Consensus pattern (20 bp):
TTTTATTATTTTGATTAATG
Found at i:224101 original size:19 final size:18
Alignment explanation
Indices: 224068--224106 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
224058 TTTATTATTT
*
224068 TATTTTTATAAATTTTAA
1 TATTTTTATAAATTTAAA
*
224086 TATTTTTATTACATTTAAA
1 TATTTTTA-TAAATTTAAA
224105 TA
1 TA
224107 AATCTTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTTTATAAATTTAAA
Found at i:224130 original size:29 final size:29
Alignment explanation
Indices: 224098--224202 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 29
224088 TTTTTATTAC
*
224098 ATTTAAATAAATCTTAATTTTTAATTTAT
1 ATTTAAATAAATCTTAACTTTTAATTTAT
* *
224127 ATTTAAATAAA-CTTTAACCTTTAAATTAT
1 ATTTAAATAAATC-TTAACTTTTAATTTAT
* *
224156 ATATAACA-AAATTCTCTAACTTTTAATTTAA
1 ATTTAA-ATAAA-TCT-TAACTTTTAATTTAT
* *
224187 ACTTAAATATATCTTA
1 ATTTAAATAAATCTTA
224203 TAACATAAAC
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 1 0.02
29 34 0.57
30 6 0.10
31 19 0.32
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTAAATAAATCTTAACTTTTAATTTAT
Found at i:224561 original size:29 final size:28
Alignment explanation
Indices: 224494--224562 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
224484 ACTTTTTATT
224494 TAAAATA-AAAACTTAATTAGATATAAA
1 TAAAATATAAAACTTAATTAGATATAAA
* *
224521 TAAAATGATAAAGACTTATTTTGATAT-AA
1 TAAAAT-ATAAA-ACTTAATTAGATATAAA
224550 TAAAAATATAAAA
1 T-AAAATATAAAA
224563 TTTTTATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 6 0.17
28 2 0.06
29 11 0.31
30 17 0.47
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (28 bp):
TAAAATATAAAACTTAATTAGATATAAA
Found at i:224805 original size:37 final size:37
Alignment explanation
Indices: 224757--224830 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
224747 CACTTACAAT
*
224757 AATTATACTATAATTAATCAATCAACATTCAAAATTA
1 AATTACACTATAATTAATCAATCAACATTCAAAATTA
*
224794 AATTACACTATAATTAATCAATCAATATTCAAAATTA
1 AATTACACTATAATTAATCAATCAACATTCAAAATTA
224831 TGTAAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (37 bp):
AATTACACTATAATTAATCAATCAACATTCAAAATTA
Found at i:225942 original size:21 final size:21
Alignment explanation
Indices: 225916--225957 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
225906 AAGCACTCGT
225916 TTTGGCTTTTTCTCTTTCTTA
1 TTTGGCTTTTTCTCTTTCTTA
225937 TTTGGCTTTTTCTCTTTCTTA
1 TTTGGCTTTTTCTCTTTCTTA
225958 GATTGATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.19, G:0.10, T:0.67
Consensus pattern (21 bp):
TTTGGCTTTTTCTCTTTCTTA
Found at i:227044 original size:2 final size:2
Alignment explanation
Indices: 227037--227067 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
227027 AATAAGGAAA
227037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
227068 CACAAGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:228646 original size:2 final size:2
Alignment explanation
Indices: 228641--228671 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
228631 AAGAAAAGAA
228641 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 A
228672 AAATGATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:233729 original size:50 final size:49
Alignment explanation
Indices: 233650--233758 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 49
233640 CAGATATCTA
233650 AATTAATATTTAATAATTAAAAATATTTTTATTTAA-ATTTAATTATAAAT
1 AATTAATA-TTAATAATTAAAAATATTTTTATTTAATA-TTAATTATAAAT
**
233700 ATATTAATATTAAT-A-TAAAAATAATTTTTTATTTTTTATTAATTATAAAT
1 A-ATTAATATTAATAATTAAAAAT-A-TTTTTATTTAATATTAATTATAAAT
*
233750 AATAAATAT
1 AATTAATAT
233759 AGATAATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
48 7 0.13
49 9 0.17
50 28 0.54
51 8 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (49 bp):
AATTAATATTAATAATTAAAAATATTTTTATTTAATATTAATTATAAAT
Found at i:233768 original size:141 final size:142
Alignment explanation
Indices: 233509--233782 Score: 462
Period size: 141 Copynumber: 1.9 Consensus size: 142
233499 TTCGATTGAG
233509 TTAATATCTAAAAAATAAAAATATTTTTATTTAAATTTAATTATAAAATATATATTAATATTAAT
1 TTAATATCTAAAAAATAAAAATATTTTTATTTAAATTTAATTAT-AAATATATATTAATATTAAT
* *
233574 ATAAAAATAATTTTTTATTTTTATTAATTATAAACAGTAAATATAGATAATATAAATGAATCAAA
65 ATAAAAATAATTTTTTATTTTTATTAATTATAAACAATAAATATAGATAATATAAACGAATCAAA
233639 TCAGATATCTAAA
130 TCAGATATCTAAA
* * *
233652 TTAATATTTAATAATTAAAAATATTTTTATTTAAATTTAATTAT-AA-ATATATTAATATTAATA
1 TTAATATCTAAAAAATAAAAATATTTTTATTTAAATTTAATTATAAATATATATTAATATTAATA
*
233715 TAAAAATAATTTTTTATTTTTTATTAATTATAAATAATAAATATAGATAATATAAACGAATCAAA
66 TAAAAATAATTTTTTA-TTTTTATTAATTATAAACAATAAATATAGATAATATAAACGAATCAAA
233780 TCA
130 TCA
233783 AATCGAATTC
Statistics
Matches: 124, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
140 33 0.27
141 50 0.40
143 41 0.33
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (142 bp):
TTAATATCTAAAAAATAAAAATATTTTTATTTAAATTTAATTATAAATATATATTAATATTAATA
TAAAAATAATTTTTTATTTTTATTAATTATAAACAATAAATATAGATAATATAAACGAATCAAAT
CAGATATCTAAA
Found at i:234450 original size:27 final size:28
Alignment explanation
Indices: 234380--234450 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 28
234370 AATATTGTTA
*
234380 TTTTAATATATATTT-AATAATTAAAATT
1 TTTTAA-ATTTATTTAAATAATTAAAATT
* * *
234408 TTTTATATTGA-ATAAATAATT-AAATT
1 TTTTAAATTTATTTAAATAATTAAAATT
234434 TTTTAAATTTATTTAAA
1 TTTTAAATTTATTTAAA
234451 ATTTGATATG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
26 15 0.44
27 14 0.41
28 5 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (28 bp):
TTTTAAATTTATTTAAATAATTAAAATT
Found at i:243264 original size:8 final size:8
Alignment explanation
Indices: 243251--243280 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
243241 ATAAAATAAT
243251 TATTTTAA
1 TATTTTAA
*
243259 TATTTTGA
1 TATTTTAA
243267 TATTTTAA
1 TATTTTAA
243275 TATTTT
1 TATTTT
243281 TGAATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (8 bp):
TATTTTAA
Found at i:243529 original size:17 final size:17
Alignment explanation
Indices: 243499--243531 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
243489 TAATTTTAAT
243499 ATATATAAATAATATAA
1 ATATATAAATAATATAA
243516 ATATGATAAA-AATATA
1 ATAT-ATAAATAATATA
243532 TTTATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
ATATATAAATAATATAA
Found at i:243530 original size:30 final size:29
Alignment explanation
Indices: 243465--243532 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
243455 TTAACATCTT
* *
243465 AAAATATATATAACAATTTAAATATAATT
1 AAAATATATATAACAATATAAATATAATA
** * *
243494 TTAATATATATAAATAATATAAATATGATA
1 AAAATATATAT-AACAATATAAATATAATA
243524 AAAATATAT
1 AAAATATAT
243533 TTATTATTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (29 bp):
AAAATATATATAACAATATAAATATAATA
Found at i:244251 original size:14 final size:14
Alignment explanation
Indices: 244208--244254 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
244198 ACAAATTATT
244208 ATATAATTAATAAAA
1 ATATAATT-ATAAAA
* **
244223 ATAT-TTTATTTAA
1 ATATAATTATAAAA
244236 ATATAATTATAAAA
1 ATATAATTATAAAA
244250 ATATA
1 ATATA
244255 TAAATTATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
13 8 0.32
14 13 0.52
15 4 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATAATTATAAAA
Found at i:244273 original size:14 final size:15
Alignment explanation
Indices: 244249--244277 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
244239 TAATTATAAA
244249 AATATATAAATTATT
1 AATATATAAATTATT
244264 AATATA-AAATTATT
1 AATATATAAATTATT
244278 GTTTTAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATATAAATTATT
Found at i:244884 original size:6 final size:6
Alignment explanation
Indices: 244873--244903 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
244863 ATTAAGTTAT
244873 AAATAA AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA A
244904 TTTTATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:245356 original size:22 final size:22
Alignment explanation
Indices: 245266--245356 Score: 57
Period size: 25 Copynumber: 4.1 Consensus size: 22
245256 TTTATTTTAT
245266 TATT-TTTTATATTATT-AA-AA
1 TATTATTTT-TATTATTAAATAA
* * *
245286 TGTTATTTTTA-TA-TGAATATT
1 TATTATTTTTATTATTAAATA-A
*
245307 TATATATTTTTATAATTAAATAAAAA
1 TAT-TATTTTTATTATTAAAT---AA
245333 TATTATTTTTATTATTAAATAA
1 TATTATTTTTATTATTAAATAA
245355 TA
1 TA
245357 ATTTAAACTG
Statistics
Matches: 54, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
18 1 0.02
19 4 0.07
20 6 0.11
21 6 0.11
22 12 0.22
23 1 0.02
24 4 0.07
25 16 0.30
26 3 0.06
27 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
TATTATTTTTATTATTAAATAA
Found at i:246250 original size:12 final size:12
Alignment explanation
Indices: 246207--246252 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
246197 ATTTTTATCT
246207 AAATTTAAA-TA
1 AAATTTAAATTA
*
246218 AAATTTAATTTCA
1 AAATTTAAATT-A
246231 AAATTTAAATTA
1 AAATTTAAATTA
*
246243 ATATTTAAAT
1 AAATTTAAAT
246253 ATTAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
11 8 0.27
12 11 0.37
13 11 0.37
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
AAATTTAAATTA
Found at i:247845 original size:13 final size:13
Alignment explanation
Indices: 247827--247852 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
247817 CAAGTTTTTG
247827 TGTATCGATACAT
1 TGTATCGATACAT
247840 TGTATCGATACAT
1 TGTATCGATACAT
247853 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:247877 original size:19 final size:18
Alignment explanation
Indices: 247807--247877 Score: 53
Period size: 19 Copynumber: 4.0 Consensus size: 18
247797 TACAAGCCAA
*
247807 TGTATCGATACAAGTTTTTG
1 TGTATCGATACAA--TTTGG
247827 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
247840 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
247859 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
247878 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:250218 original size:21 final size:21
Alignment explanation
Indices: 250194--250240 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
250184 TTTGATGCTG
250194 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
250214 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
250235 ATTTTG
1 ATTTTG
250241 TAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:250383 original size:13 final size:13
Alignment explanation
Indices: 250361--250399 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
250351 ATAATCACCC
*
250361 TGTATTGATACAA
1 TGTATCGATACAA
250374 TGTATCGATACAA
1 TGTATCGATACAA
250387 TGTATCGATACAA
1 TGTATCGATACAA
250400 AGAAAAATGT
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:0.38, C:0.13, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:252492 original size:15 final size:15
Alignment explanation
Indices: 252472--252501 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
252462 GTTCATCAAT
252472 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
252487 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
252502 CCCAATTTGA
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:0.20, G:0.17, T:0.50
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:256595 original size:13 final size:13
Alignment explanation
Indices: 256577--256601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
256567 CAAGTTTTTG
256577 TGTATCGATACAA
1 TGTATCGATACAA
256590 TGTATCGATACA
1 TGTATCGATACA
256602 TACTTGGTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:256617 original size:32 final size:32
Alignment explanation
Indices: 256554--256621 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 32
256544 CGTTACAAGC
* *
256554 CAATGTATCGATACAAGTTTTTGTGTATCGATA
1 CAATGTATCGATACAAG-CTTGGTGTATCGATA
256587 CAATGTATCGATACATA-CTTGGTGTATCGATA
1 CAATGTATCGATACA-AGCTTGGTGTATCGATA
256619 CAA
1 CAA
256622 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 16 0.50
33 15 0.47
34 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACAAGCTTGGTGTATCGATA
Found at i:256627 original size:19 final size:18
Alignment explanation
Indices: 256557--256627 Score: 53
Period size: 19 Copynumber: 4.0 Consensus size: 18
256547 TACAAGCCAA
*
256557 TGTATCGATACAAGTTTTTG
1 TGTATCGATACAA--TTTGG
256577 TGTATCGATACAA-----
1 TGTATCGATACAATTTGG
*
256590 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
256609 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
256628 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 12 0.28
14 1 0.02
18 1 0.02
19 16 0.37
20 13 0.30
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:257489 original size:18 final size:18
Alignment explanation
Indices: 257466--257533 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 18
257456 TTATTCAAAA
257466 AAATTCATTCATCTAAAT
1 AAATTCATTCATCTAAAT
*
257484 --A--CATTCATTTAAAT
1 AAATTCATTCATCTAAAT
* *
257498 AAATTCATTCACCCAAAT
1 AAATTCATTCATCTAAAT
* *
257516 ATATTTATTCATCTAAAT
1 AAATTCATTCATCTAAAT
257534 GTATCTTTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
14 12 0.32
16 2 0.05
18 24 0.63
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTCATTCATCTAAAT
Found at i:257962 original size:13 final size:15
Alignment explanation
Indices: 257944--257975 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
257934 GATAGATTGG
257944 TTTACTT-TATAT-A
1 TTTACTTGTATATGA
257957 TTTACTTGTATATGA
1 TTTACTTGTATATGA
257972 TTTA
1 TTTA
257976 AAGTTAACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.59
Consensus pattern (15 bp):
TTTACTTGTATATGA
Found at i:259509 original size:22 final size:22
Alignment explanation
Indices: 259445--259512 Score: 93
Period size: 22 Copynumber: 3.1 Consensus size: 22
259435 TAAAAACATT
* *
259445 ATCATTGATATTC-TAGCTTTGC
1 ATCATT-AGATTCTTAGCTTTTC
259467 ATCATTAGATTCTTAGCTTTTC
1 ATCATTAGATTCTTAGCTTTTC
*
259489 ATCGTTAGATTCTTAGCTTTTC
1 ATCATTAGATTCTTAGCTTTTC
259511 AT
1 AT
259513 TAAAAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
21 5 0.12
22 37 0.88
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.49
Consensus pattern (22 bp):
ATCATTAGATTCTTAGCTTTTC
Found at i:260610 original size:31 final size:30
Alignment explanation
Indices: 260543--260602 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
260533 TAGAATTTTT
260543 AAAAAAATCAAACCAAAATCTTAAATTTAAA
1 AAAAAAATCAAACCAAAATC-TAAATTTAAA
* *
260574 AAAAAAATCAAATCAAAATC-AATTTTAAA
1 AAAAAAATCAAACCAAAATCTAAATTTAAA
260603 TTTAAAAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 8 0.30
31 19 0.70
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.23
Consensus pattern (30 bp):
AAAAAAATCAAACCAAAATCTAAATTTAAA
Found at i:260954 original size:13 final size:13
Alignment explanation
Indices: 260936--260960 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
260926 ATTTTGCTAA
260936 GTATCGATACATT
1 GTATCGATACATT
260949 GTATCGATACAT
1 GTATCGATACAT
260961 AGCATTGGCA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:261044 original size:14 final size:14
Alignment explanation
Indices: 261025--261054 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
261015 TCATGTATCG
261025 ATACATCACTGTTC
1 ATACATCACTGTTC
*
261039 ATACATCGCTGTTC
1 ATACATCACTGTTC
261053 AT
1 AT
261055 CACTGTACAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.37
Consensus pattern (14 bp):
ATACATCACTGTTC
Found at i:261046 original size:22 final size:21
Alignment explanation
Indices: 260988--261046 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
260978 AATCTCATTT
* *
260988 TCACTGTTCATAA-CTATTCA
1 TCACTGTTCATAATCGATACA
* *
261008 TAACTGTTCATGTATCGATACA
1 TCACTGTTCAT-AATCGATACA
261030 TCACTGTTCATACATCG
1 TCACTGTTCATA-ATCG
261047 CTGTTCATCA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 10 0.33
21 1 0.03
22 19 0.63
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (21 bp):
TCACTGTTCATAATCGATACA
Found at i:261139 original size:22 final size:22
Alignment explanation
Indices: 261111--261153 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
261101 ATTCATCACA
*
261111 GTATCGATACATTACTGTTCAT
1 GTATCGATACATCACTGTTCAT
261133 GTATCGATACATCACTGTTCA
1 GTATCGATACATCACTGTTCA
261154 CATTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (22 bp):
GTATCGATACATCACTGTTCAT
Found at i:261238 original size:20 final size:19
Alignment explanation
Indices: 261190--261228 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
261180 ATAATTTCAA
261190 ATGCATGTATCGATACATT
1 ATGCATGTATCGATACATT
*
261209 ATGAATTGTATCGATACATT
1 ATGCA-TGTATCGATACATT
261229 GGAGCATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
ATGCATGTATCGATACATT
Found at i:263354 original size:84 final size:84
Alignment explanation
Indices: 263181--263341 Score: 209
Period size: 84 Copynumber: 1.9 Consensus size: 84
263171 ACTCAAAGAA
* * * *
263181 GAAAATAAATCAATAAGTGTAGAGATTAATATTCTTAAAAAGAAATTAAGTGAATTAGAGAAGAA
1 GAAAATAAATCAATAAGTGTAGAAAATAATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
*
263246 TATGAAAGAGTTACAAAAT
66 TAAGAAAGAGTTACAAAAT
* * * *
263265 GAAAATAAATCAATGAGTTTAGAAAATAAT-TCTTTTAAAAAGAAAATAAATGAATTAGAGGAGA
1 GAAAATAAATCAATAAGTGTAGAAAATAATAT-TCTTAAAAAGAAAATAAATGAATTAGAGAAGA
263329 A-AAGAAATGAGTT
65 ATAAGAAA-GAGTT
263342 GCAAGTGGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
83 6 0.09
84 60 0.91
ACGTcount: A:0.54, C:0.03, G:0.17, T:0.26
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATAATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAA
TAAGAAAGAGTTACAAAAT
Found at i:264322 original size:25 final size:20
Alignment explanation
Indices: 264271--264312 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
264261 GTTTTTGTGC
264271 TTAATTGAATTTGTGTTCAA
1 TTAATTGAATTTGTGTTCAA
264291 TTAATTGAATTTGTGTTCAA
1 TTAATTGAATTTGTGTTCAA
264311 TT
1 TT
264313 CTTTGAATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (20 bp):
TTAATTGAATTTGTGTTCAA
Found at i:266475 original size:13 final size:13
Alignment explanation
Indices: 266457--266481 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
266447 ATTTTGCTAA
266457 GTATCGATACATT
1 GTATCGATACATT
266470 GTATCGATACAT
1 GTATCGATACAT
266482 AGCATTGGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:266645 original size:22 final size:22
Alignment explanation
Indices: 266617--266659 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
266607 ATTCATCACA
*
266617 GTATCGATACATTACTGTTCAT
1 GTATCGATACATCACTGTTCAT
266639 GTATCGATACATCACTGTTCA
1 GTATCGATACATCACTGTTCA
266660 CACTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (22 bp):
GTATCGATACATCACTGTTCAT
Found at i:266744 original size:20 final size:21
Alignment explanation
Indices: 266698--266744 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
266688 AATTTCAAAT
266698 GCATGTATCAATACATTATGA
1 GCATGTATCAATACATTATGA
266719 --ATTGTATCAATACATT-TGA
1 GCA-TGTATCAATACATTATGA
266738 GCATGTA
1 GCATGTA
266745 AGTGCTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 4 0.17
20 18 0.78
21 1 0.04
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (21 bp):
GCATGTATCAATACATTATGA
Found at i:272671 original size:3 final size:3
Alignment explanation
Indices: 272663--272709 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
272653 ACGATACTTG
272663 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
272710 ATTTAGTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:273101 original size:29 final size:31
Alignment explanation
Indices: 273075--273136 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
273065 CATAATCTAG
*
273075 AATTTAAAAA-AAATC-CAATCAAAATCTTA
1 AATTAAAAAATAAATCACAATCAAAATCTTA
*
273104 AATTAAAAAATAAATCAGAATC-AAAT-TTA
1 AATTAAAAAATAAATCACAATCAAAATCTTA
273133 AATT
1 AATT
273137 TAAGAATCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 16 0.55
30 9 0.31
31 4 0.14
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (31 bp):
AATTAAAAAATAAATCACAATCAAAATCTTA
Found at i:275019 original size:38 final size:38
Alignment explanation
Indices: 274968--275045 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
274958 ACATGAAGGA
*
274968 ACAAATCAAGTCAAGGAATCAAAGATAAGTATGGTTAC
1 ACAAATCAAGTCAAGGAATCAAAGATAAGTATGCTTAC
275006 ACAAATCAAGTCAAGGAATCAAAGATAAGTATGCTTAC
1 ACAAATCAAGTCAAGGAATCAAAGATAAGTATGCTTAC
275044 AC
1 AC
275046 TTGACTATGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (38 bp):
ACAAATCAAGTCAAGGAATCAAAGATAAGTATGCTTAC
Found at i:275035 original size:19 final size:19
Alignment explanation
Indices: 274975--275035 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
274965 GGAACAAATC
274975 AAGTCAAGGAATCAAAGAT
1 AAGTCAAGGAATCAAAGAT
* *
274994 AAGT-ATGG-TTACACAA-AT
1 AAGTCAAGGAAT-CA-AAGAT
275012 CAAGTCAAGGAATCAAAGAT
1 -AAGTCAAGGAATCAAAGAT
275032 AAGT
1 AAGT
275036 ATGCTTACAC
Statistics
Matches: 32, Mismatches: 4, Indels: 12
0.67 0.08 0.25
Matches are distributed among these distances:
17 1 0.03
18 7 0.22
19 16 0.50
20 7 0.22
21 1 0.03
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (19 bp):
AAGTCAAGGAATCAAAGAT
Found at i:278147 original size:10 final size:10
Alignment explanation
Indices: 278134--278160 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
278124 CCATAGTTAG
278134 ATTAGAAGCC
1 ATTAGAAGCC
278144 ATTAGAAGCC
1 ATTAGAAGCC
278154 ATTAGAA
1 ATTAGAA
278161 TACTTCTAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (10 bp):
ATTAGAAGCC
Found at i:279743 original size:48 final size:49
Alignment explanation
Indices: 279657--279763 Score: 164
Period size: 48 Copynumber: 2.2 Consensus size: 49
279647 TTGTTCAAAA
* *
279657 TATCGATACATCTGGATTTTTCCAGAATGTATCGATACAATGTAACTTG
1 TATCGATACATCTGGAGTTTTCCAGAATGTATCAATACAATGTAACTTG
*
279706 TATCGATACATCTGG-GTTTTCCAG-ATCGTATCAATACAATGTAATTTG
1 TATCGATACATCTGGAGTTTTCCAGAAT-GTATCAATACAATGTAACTTG
279754 TATCGATACA
1 TATCGATACA
279764 ATATGTATCG
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
47 2 0.04
48 37 0.69
49 15 0.28
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (49 bp):
TATCGATACATCTGGAGTTTTCCAGAATGTATCAATACAATGTAACTTG
Found at i:279772 original size:15 final size:15
Alignment explanation
Indices: 279752--279781 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
279742 CAATGTAATT
279752 TGTATCGATACAATA
1 TGTATCGATACAATA
279767 TGTATCGATACAATA
1 TGTATCGATACAATA
279782 CTAATGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (15 bp):
TGTATCGATACAATA
Found at i:286110 original size:26 final size:26
Alignment explanation
Indices: 286079--286138 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
286069 TTGCATTTCA
*
286079 GCAGCTGTCGATTTCTTCTCTTCGTT
1 GCAGCTGTCGATTTCTTCTCTTCATT
*
286105 GTAGCTGTCGATTTCTTCTCTTCATT
1 GCAGCTGTCGATTTCTTCTCTTCATT
286131 GCAGCTGT
1 GCAGCTGT
286139 TTCGTTCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.45
Consensus pattern (26 bp):
GCAGCTGTCGATTTCTTCTCTTCATT
Found at i:286146 original size:26 final size:27
Alignment explanation
Indices: 286079--286166 Score: 71
Period size: 26 Copynumber: 3.4 Consensus size: 27
286069 TTGCATTTCA
*
286079 GCAGCTG--TCGATTTCTTCTCTTCGTT
1 GCAGCTGTTTCGA-TTCTTCTCTTCATT
*
286105 GTAGCTG--TCGATTTCTTCTCTTCATT
1 GCAGCTGTTTCGA-TTCTTCTCTTCATT
* *
286131 GCAGCTGTTTCG-TTCTTGT-TGCATT
1 GCAGCTGTTTCGATTCTTCTCTTCATT
*
286156 GCAGTTGTTTC
1 GCAGCTGTTTC
286167 AGCAGCTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
25 15 0.28
26 36 0.67
28 3 0.06
ACGTcount: A:0.09, C:0.23, G:0.20, T:0.48
Consensus pattern (27 bp):
GCAGCTGTTTCGATTCTTCTCTTCATT
Found at i:286233 original size:23 final size:23
Alignment explanation
Indices: 286163--286222 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
286153 ATTGCAGTTG
286163 TTTCAGCAGCTTAATTGCATCTA
1 TTTCAGCAGCTTAATTGCATCTA
286186 TTTCAGCAGCTTAATTGCATCTA
1 TTTCAGCAGCTTAATTGCATCTA
286209 TTTCAGCAGCTTAA
1 TTTCAGCAGCTTAA
286223 CTGTAGCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (23 bp):
TTTCAGCAGCTTAATTGCATCTA
Found at i:286480 original size:54 final size:54
Alignment explanation
Indices: 286390--286503 Score: 174
Period size: 54 Copynumber: 2.1 Consensus size: 54
286380 CATGCTACCA
* * *
286390 TTTCCTGTTTCTTCAGCCTCCATGTTCATACATGAAAGCATGCGTGAAATGCCG
1 TTTCTTGTTTCTTCAGCCTCCATGTTCATACATGAAAACATGCATGAAATGCCG
***
286444 TTTCTTGTTTCTTCAGCCTCCATGTTCATGTGTGAAAACATGCATGAAATGCCG
1 TTTCTTGTTTCTTCAGCCTCCATGTTCATACATGAAAACATGCATGAAATGCCG
286498 TTTCTT
1 TTTCTT
286504 TTCCTATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.38
Consensus pattern (54 bp):
TTTCTTGTTTCTTCAGCCTCCATGTTCATACATGAAAACATGCATGAAATGCCG
Found at i:287508 original size:27 final size:27
Alignment explanation
Indices: 287470--287525 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
287460 ATAAAAGAAA
287470 TCCACATCCACTAAACGAACTTTGCAT
1 TCCACATCCACTAAACGAACTTTGCAT
287497 TCCACATCCACTAAACGAACTTTGCAT
1 TCCACATCCACTAAACGAACTTTGCAT
287524 TC
1 TC
287526 ATGATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.34, G:0.07, T:0.27
Consensus pattern (27 bp):
TCCACATCCACTAAACGAACTTTGCAT
Found at i:287662 original size:7 final size:7
Alignment explanation
Indices: 287652--287789 Score: 68
Period size: 7 Copynumber: 18.6 Consensus size: 7
287642 TTTTATATAT
*
287652 AAAATTA
1 AAAATAA
287659 AAAATAAA
1 AAAAT-AA
287667 AAAATAA
1 AAAATAA
287674 AAAATTAATA
1 AAAA-T-A-A
287684 AAAATCAA
1 AAAAT-AA
*
287692 ATAATAA
1 AAAATAA
287699 AATAAT-A
1 AA-AATAA
* *
287706 ACAATGA
1 AAAATAA
*
287713 AAAAT-C
1 AAAATAA
287719 AAAATCCAA
1 AAAAT--AA
287728 AAAA-AA
1 AAAATAA
287734 AAACA-AA
1 AAA-ATAA
287741 AAAATAA
1 AAAATAA
287748 AAAATTAAA
1 AAAA-T-AA
287757 AAAATAA
1 AAAATAA
*
287764 TAAAATGA
1 -AAAATAA
* *
287772 TAAATCA
1 AAAATAA
287779 AAAATAA
1 AAAATAA
287786 AAAA
1 AAAA
287790 AAGAAATACA
Statistics
Matches: 104, Mismatches: 13, Indels: 28
0.72 0.09 0.19
Matches are distributed among these distances:
6 14 0.13
7 49 0.47
8 23 0.22
9 13 0.12
10 5 0.05
ACGTcount: A:0.76, C:0.05, G:0.01, T:0.17
Consensus pattern (7 bp):
AAAATAA
Found at i:287671 original size:8 final size:8
Alignment explanation
Indices: 287658--287790 Score: 69
Period size: 8 Copynumber: 16.6 Consensus size: 8
287648 ATATAAAATT
287658 AAAAATAA
1 AAAAATAA
287666 AAAAATAA
1 AAAAATAA
*
287674 AAAATTAA
1 AAAAATAA
*
287682 TAAAAATCA
1 -AAAAATAA
*
287691 AATAATAA
1 AAAAATAA
*
287699 AATAAT--
1 AAAAATAA
* *
287705 AACAAT-G
1 AAAAATAA
287712 AAAAATCAA
1 AAAAAT-AA
*
287721 AATCCAAAAAA
1 AA---AAATAA
*
287732 AAAAACAA
1 AAAAATAA
287740 AAAAATAA
1 AAAAATAA
*
287748 AAAATTAA
1 AAAAATAA
287756 AAAAATAA
1 AAAAATAA
* *
287764 TAAAAT-G
1 AAAAATAA
* *
287771 ATAAAT-C
1 AAAAATAA
287778 AAAAATAA
1 AAAAATAA
287786 AAAAA
1 AAAAA
287791 AGAAATACAT
Statistics
Matches: 97, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
6 5 0.05
7 14 0.14
8 63 0.65
9 8 0.08
11 4 0.04
12 3 0.03
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.17
Consensus pattern (8 bp):
AAAAATAA
Found at i:287702 original size:19 final size:17
Alignment explanation
Indices: 287653--287769 Score: 55
Period size: 17 Copynumber: 6.6 Consensus size: 17
287643 TTTATATATA
*
287653 AAATTAAAAATAAAAA-
1 AAATAAAAAATAAAAAC
*
287669 AATAAAAAATTAATAAAAATC
1 AA-ATAAAA--AATAAAAA-C
*
287690 AAATAATAAAATAATAAC
1 AAATAA-AAAATAAAAAC
* *
287708 -AATGAAAAATCAAAATCC
1 AAATAAAAAAT-AAAA-AC
*
287726 AAA-AAAAAA-AACAAAA
1 AAATAAAAAATAA-AAAC
*
287742 AAATAAAAAATTAAAA-
1 AAATAAAAAATAAAAAC
287758 AAATAATAAAAT
1 AAATAA-AAAAT
287770 GATAAATCAA
Statistics
Matches: 77, Mismatches: 11, Indels: 25
0.68 0.10 0.22
Matches are distributed among these distances:
16 18 0.23
17 27 0.35
18 8 0.10
19 17 0.22
20 3 0.04
21 4 0.05
ACGTcount: A:0.76, C:0.05, G:0.01, T:0.18
Consensus pattern (17 bp):
AAATAAAAAATAAAAAC
Found at i:288230 original size:41 final size:41
Alignment explanation
Indices: 288185--288317 Score: 151
Period size: 41 Copynumber: 3.3 Consensus size: 41
288175 ACACCGGCAG
* * **
288185 CAGCTTCCAGTAGCAGGAACATCAAAAACCAACACCAACAA
1 CAGCTTCCAGTAGCAAGAGCATCCGAAACCAACACCAACAA
* * * *
288226 CAGCTTCCAGT-CCATGAGCACCCGAAACCAACACCAACAG
1 CAGCTTCCAGTAGCAAGAGCATCCGAAACCAACACCAACAA
* * * *
288266 CAGCTTTCAGCAGCAAGAGCATCCGAAACCAATACCAGCAA
1 CAGCTTCCAGTAGCAAGAGCATCCGAAACCAACACCAACAA
288307 CAGCTTCCAGT
1 CAGCTTCCAGT
288318 CCACGAGCAC
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
40 31 0.42
41 43 0.58
ACGTcount: A:0.38, C:0.35, G:0.15, T:0.12
Consensus pattern (41 bp):
CAGCTTCCAGTAGCAAGAGCATCCGAAACCAACACCAACAA
Found at i:288261 original size:40 final size:40
Alignment explanation
Indices: 288210--288356 Score: 154
Period size: 40 Copynumber: 3.6 Consensus size: 40
288200 GGAACATCAA
*
288210 AAACCAACACCAACAACAGCTTCCAGTCCATGAGCACCCG
1 AAACCAACACCAACAACAGCTTCCAGTCCAAGAGCACCCG
* * *
288250 AAACCAACACCAACAGCAGCTTTCAG-CAGCAAGAGCATCCG
1 AAACCAACACCAACAACAGCTTCCAGTC--CAAGAGCACCCG
* * *
288291 AAACCAATACCAGCAACAGCTTCCAGTCCACGAGCACCC-
1 AAACCAACACCAACAACAGCTTCCAGTCCAAGAGCACCCG
** * *
288330 AGAACCAATGCCAGCAGCAGCTTCCAG
1 A-AACCAACACCAACAACAGCTTCCAG
288357 CAGTAGGAGC
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.02
40 56 0.62
41 32 0.35
42 1 0.01
ACGTcount: A:0.37, C:0.37, G:0.16, T:0.10
Consensus pattern (40 bp):
AAACCAACACCAACAACAGCTTCCAGTCCAAGAGCACCCG
Found at i:288309 original size:81 final size:81
Alignment explanation
Indices: 288174--288452 Score: 285
Period size: 81 Copynumber: 3.4 Consensus size: 81
288164 CAAAGAAAAA
* * * ** *
288174 AACACCGGCAGCAGCTTCCAGTAGCAGGAACATCAAAAACCAACACCAACAACAGCTTCCAGTCC
1 AACACCAGCAGCAGCTTCCAGCAGCAGGAGCATCCGAAACCAATACCAACAACAGCTTCCAGTCC
*
288239 ATGAGCACCCGAAACC
66 ACGAGCACCCGAAACC
* * * *
288255 AACACCAACAGCAGCTTTCAGCAGCAAGAGCATCCGAAACCAATACCAGCAACAGCTTCCAGTCC
1 AACACCAGCAGCAGCTTCCAGCAGCAGGAGCATCCGAAACCAATACCAACAACAGCTTCCAGTCC
288320 ACGAGCACCC-AGAACC
66 ACGAGCACCCGA-AACC
** * * * * *
288336 AATGCCAGCAGCAGCTTCCAGCAGTAGGAGCAT-CGAAA-AAACTAACACCGATAGCAGTTTCCA
1 AACACCAGCAGCAGCTTCCAGCAGCAGGAGCATCCGAAACCAA-TACCAAC-A-A-CAGCTTCCA
* *
288399 ATCCACGAGCACCTGAAACC
62 GTCCACGAGCACCCGAAACC
* * *
288419 AACACCAGCAGCAGCTTTCAACAGTAGGAGCATC
1 AACACCAGCAGCAGCTTCCAGCAGCAGGAGCATC
288453 AAAAAACTAA
Statistics
Matches: 164, Mismatches: 27, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
79 2 0.01
80 11 0.07
81 96 0.59
82 1 0.01
83 53 0.32
84 1 0.01
ACGTcount: A:0.37, C:0.34, G:0.18, T:0.12
Consensus pattern (81 bp):
AACACCAGCAGCAGCTTCCAGCAGCAGGAGCATCCGAAACCAATACCAACAACAGCTTCCAGTCC
ACGAGCACCCGAAACC
Found at i:288432 original size:40 final size:39
Alignment explanation
Indices: 288210--288562 Score: 146
Period size: 40 Copynumber: 8.7 Consensus size: 39
288200 GGAACATCAA
* * * *
288210 AAACCAACACCAACAACAGCTTCCAGTCCATGAGCACCCG
1 AAACCAACACCAGCAGCAGCTTCCAATCCACGAGCA-CCG
* * * *
288250 AAACCAACACCAACAGCAGCTTTCAGCA-GCAAGAGCATCCG
1 AAACCAACACCAGCAGCAGCTTCCA--ATCCACGAGCA-CCG
* * * *
288291 AAACCAATACCAGCAACAGCTTCCAGTCCACGAGCACCC
1 AAACCAACACCAGCAGCAGCTTCCAATCCACGAGCACCG
** * *
288330 AGAACCAATGCCAGCAGCAGCTTCCAGCAGT--AGGAGCATCG
1 A-AACCAACACCAGCAGCAGCTTCCA--A-TCCACGAGCACCG
* * *
288371 AAAAAACTAACACC-GATAGCAGTTTCCAATCCACGAGCACCTG
1 ---AAACCAACACCAG-CAGCAGCTTCCAATCCACGAGCACC-G
* * * **
288414 AAACCAACACCAGCAGCAGCTTTCAA-CAGTAGGAGCATCAAA
1 AAACCAACACCAGCAGCAGCTTCCAATC--CACGAGCA-C-CG
* * * **
288456 AAACTAACATC-GACAGCAGCTTCC-A-GCAGCAGAAGCATCTA
1 AAACCAACACCAG-CAGCAGCTTCCAATCCA-C-G-AGCA-CCG
* * * *
288497 AAACCAACACCAGCGGCAGCTTCTAGTCCACGAGCACCCA
1 AAACCAACACCAGCAGCAGCTTCCAATCCACGAGCA-CCG
288537 AAACCAACACCAGCAGCAGCTTCCAA
1 AAACCAACACCAGCAGCAGCTTCCAA
288563 CAGCAGGAGC
Statistics
Matches: 234, Mismatches: 53, Indels: 52
0.69 0.16 0.15
Matches are distributed among these distances:
39 5 0.02
40 102 0.44
41 69 0.29
42 36 0.15
43 21 0.09
44 1 0.00
ACGTcount: A:0.38, C:0.34, G:0.16, T:0.12
Consensus pattern (39 bp):
AAACCAACACCAGCAGCAGCTTCCAATCCACGAGCACCG
Found at i:288500 original size:123 final size:124
Alignment explanation
Indices: 288344--288638 Score: 369
Period size: 123 Copynumber: 2.4 Consensus size: 124
288334 CCAATGCCAG
* * * *
288344 CAGCAGCTTCCAGCAGTAGGAGCATCGAAAAAACTAACACC-GATAGCAGTTTCCAATCCACGAG
1 CAGCAGCTTCCAGCAGTAGGAGCATC--TAAAACCAACACCAG-CAGCAGCTTCCAATCCACGAG
** * * * * *
288408 CACCTGAAACCAACACCAGCAGCAGCTTTCAACAGTAGGAGCAT-CAAAAAACTAACATCGA
63 CACCCAAAACCAACACCAGCAGCAGCTTCCAACAGCAGGAGCATAAAAAAAACCAACACCGA
* * * * *
288469 CAGCAGCTTCCAGCAGCAGAAGCATCTAAAACCAACACCAGCGGCAGCTTCTAGTCCACGAGCAC
1 CAGCAGCTTCCAGCAGTAGGAGCATCTAAAACCAACACCAGCAGCAGCTTCCAATCCACGAGCAC
288534 CCAAAACCAACACCAGCAGCAGCTTCCAACAGCAGGAGCATAAAAAAAACCAACACCGA
66 CCAAAACCAACACCAGCAGCAGCTTCCAACAGCAGGAGCATAAAAAAAACCAACACCGA
* * * *
288593 CAGTAGATTCCAGCAGTAGGAGCATCTGAAACCAACACCATCAGCA
1 CAGCAGCTTCCAGCAGTAGGAGCATCTAAAACCAACACCAGCAGCA
288639 ATGTCCAATA
Statistics
Matches: 145, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
123 67 0.46
124 54 0.37
125 24 0.17
ACGTcount: A:0.39, C:0.31, G:0.18, T:0.12
Consensus pattern (124 bp):
CAGCAGCTTCCAGCAGTAGGAGCATCTAAAACCAACACCAGCAGCAGCTTCCAATCCACGAGCAC
CCAAAACCAACACCAGCAGCAGCTTCCAACAGCAGGAGCATAAAAAAAACCAACACCGA
Found at i:288501 original size:83 final size:83
Alignment explanation
Indices: 288174--288519 Score: 278
Period size: 81 Copynumber: 4.2 Consensus size: 83
288164 CAAAGAAAAA
* ** * * * * * *
288174 AACACCGGCAGCAGCTTCCAGTAGCAGGAACATC--AAAAACCAACACCAACAACAGCTTCCAGT
1 AACACCAGCAGCAGCTTCCAACAGTAGGAGCATCGAAAAAACTAACACCGACAGCAGCTTCCAAT
* **
288237 CCATGAGCACCCGAAACC
66 CCACGAGCACCTAAAACC
* * * * * * * *
288255 AACACCAACAGCAGCTTTCAGCAGCAAGAGCATCCG---AAACCAATACC-AGCAACAGCTTCCA
1 AACACCAGCAGCAGCTTCCAACAGTAGGAGCAT-CGAAAAAACTAACACCGA-CAGCAGCTTCCA
* * *
288316 GTCCACGAGCACCCAGAACC
64 ATCCACGAGCACCTAAAACC
** * * *
288336 AATGCCAGCAGCAGCTTCCAGCAGTAGGAGCATCGAAAAAACTAACACCGATAGCAGTTTCCAAT
1 AACACCAGCAGCAGCTTCCAACAGTAGGAGCATCGAAAAAACTAACACCGACAGCAGCTTCCAAT
*
288401 CCACGAGCACCTGAAACC
66 CCACGAGCACCTAAAACC
* *
288419 AACACCAGCAGCAGCTTTCAACAGTAGGAGCATC-AAAAAACTAACATCGACAGCAGCTTCC-A-
1 AACACCAGCAGCAGCTTCCAACAGTAGGAGCATCGAAAAAACTAACACCGACAGCAGCTTCCAAT
* *
288481 GCAGCAGAAGCATCTAAAACC
66 CCA-C-G-AGCACCTAAAACC
*
288502 AACACCAGCGGCAGCTTC
1 AACACCAGCAGCAGCTTC
288520 TAGTCCACGA
Statistics
Matches: 218, Mismatches: 37, Indels: 18
0.80 0.14 0.07
Matches are distributed among these distances:
80 5 0.02
81 95 0.44
82 26 0.12
83 91 0.42
84 1 0.00
ACGTcount: A:0.38, C:0.33, G:0.17, T:0.12
Consensus pattern (83 bp):
AACACCAGCAGCAGCTTCCAACAGTAGGAGCATCGAAAAAACTAACACCGACAGCAGCTTCCAAT
CCACGAGCACCTAAAACC
Found at i:288764 original size:71 final size:71
Alignment explanation
Indices: 288673--288838 Score: 199
Period size: 71 Copynumber: 2.3 Consensus size: 71
288663 CCACAACAAA
* * * * *
288673 TTCTAGCAGCTCCAGCAGCTTCCACAGTAGTCTTCAGTAGCTCCCACAG-TAGCCTCCAGCAGTT
1 TTCTAGCAGCTCCAGCAGCTTCCACAGTAGCCTCCAGCAGCTCCCA-AGACAGCCTCCAGCAGCT
288737 CAGCAAC
65 CAGCAAC
* * * * *
288744 TTTTAGCAGCTCCAGCAGCTTCCACGGTAGCCTCCAGCAGCTCCCATGACAGCCTCTAGTAGCTC
1 TTCTAGCAGCTCCAGCAGCTTCCACAGTAGCCTCCAGCAGCTCCCAAGACAGCCTCCAGCAGCTC
288809 AGCAAC
66 AGCAAC
* * *
288815 TTCCAGCAACTCCAACAGCTTCCA
1 TTCTAGCAGCTCCAGCAGCTTCCA
288839 TCGCAACCTC
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
70 1 0.01
71 79 0.99
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.22
Consensus pattern (71 bp):
TTCTAGCAGCTCCAGCAGCTTCCACAGTAGCCTCCAGCAGCTCCCAAGACAGCCTCCAGCAGCTC
AGCAAC
Found at i:288797 original size:22 final size:22
Alignment explanation
Indices: 288753--288808 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
288743 CTTTTAGCAG
* **
288753 CTCCAGCAGCTTCCACGGTAGC
1 CTCCAGCAGCTCCCACGACAGC
*
288775 CTCCAGCAGCTCCCATGACAGC
1 CTCCAGCAGCTCCCACGACAGC
* *
288797 CTCTAGTAGCTC
1 CTCCAGCAGCTC
288809 AGCAACTTCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.41, G:0.20, T:0.20
Consensus pattern (22 bp):
CTCCAGCAGCTCCCACGACAGC
Found at i:289228 original size:12 final size:12
Alignment explanation
Indices: 289211--289237 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
289201 TAAGTTTTTT
289211 AAAAAAAACAAA
1 AAAAAAAACAAA
289223 AAAAAAAACAAA
1 AAAAAAAACAAA
289235 AAA
1 AAA
289238 TGAAAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:300622 original size:13 final size:13
Alignment explanation
Indices: 300604--300630 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
300594 ATAAGCTGCT
300604 TTGTATCGATACA
1 TTGTATCGATACA
300617 TTGTATCGATACA
1 TTGTATCGATACA
300630 T
1 T
300631 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:300661 original size:21 final size:19
Alignment explanation
Indices: 300615--300671 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
300605 TGTATCGATA
*
300615 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGGT
300634 CATTGTATCGATACATGGT
1 CATTGTATCGATACATGGT
300653 CAAATTGTATCGATACATG
1 C--ATTGTATCGATACATG
300672 AAACTGGCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
19 19 0.54
21 16 0.46
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Consensus pattern (19 bp):
CATTGTATCGATACATGGT
Found at i:300737 original size:13 final size:13
Alignment explanation
Indices: 300716--300746 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
300706 CGATACATGG
*
300716 TACAATGTATCGA
1 TACATTGTATCGA
300729 TACATTGTATCGA
1 TACATTGTATCGA
300742 TACAT
1 TACAT
300747 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:300745 original size:33 final size:32
Alignment explanation
Indices: 300703--300766 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 32
300693 TCACTATTTA
300703 TATCGATACATG-GTACAATGTATCGATACATTG
1 TATCGATACATGAG-A-AATGTATCGATACATTG
300736 TATCGATACATGAAGAAATGTATCGATACAT
1 TATCGATACATG-AGAAATGTATCGATACAT
300767 AGCATGTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (32 bp):
TATCGATACATGAGAAATGTATCGATACATTG
Found at i:303401 original size:20 final size:19
Alignment explanation
Indices: 303376--303445 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
303366 ACCCTAAAAA
303376 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
303396 GTATCGATACAGATTGCAT
1 GTATCGATACACATTAAAT
*
303415 AGTATCGATACACA-CAATAT
1 -GTATCGATACACATTAA-AT
303435 GTATCGATACA
1 GTATCGATACA
303446 GGACATTGGC
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
19 15 0.37
20 26 0.63
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:303494 original size:53 final size:53
Alignment explanation
Indices: 303418--303551 Score: 241
Period size: 53 Copynumber: 2.5 Consensus size: 53
303408 ATTGCATAGT
*
303418 ATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCTAAATTTGC
1 ATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTGC
* *
303471 ATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTTGT
1 ATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTGC
303524 ATCGATACACACAATATGTATCGATACA
1 ATCGATACACACAATATGTATCGATACA
303552 TTGGCAGTAG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 78 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (53 bp):
ATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTTGC
Found at i:303700 original size:13 final size:13
Alignment explanation
Indices: 303682--303720 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
303672 TCACTATTCA
303682 TGTATCGATACAT
1 TGTATCGATACAT
* *
303695 TGTATCGATATAG
1 TGTATCGATACAT
303708 TGTATCGATACAT
1 TGTATCGATACAT
303721 CATAAACAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:304253 original size:34 final size:35
Alignment explanation
Indices: 304190--304256 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
304180 CTAAGTGATT
304190 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
304226 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
304257 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:308359 original size:13 final size:13
Alignment explanation
Indices: 308341--308369 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
308331 ACAACATTCC
308341 TTGTATCGATACA
1 TTGTATCGATACA
308354 TTGTATCGATACA
1 TTGTATCGATACA
308367 TTG
1 TTG
308370 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:310285 original size:36 final size:34
Alignment explanation
Indices: 310208--310312 Score: 183
Period size: 34 Copynumber: 3.0 Consensus size: 34
310198 AAAAAGGGGG
310208 AGAAGATAATCGTTTAAGGGGGAGAATTTTTTTT
1 AGAAGATAATCGTTTAAGGGGGAGAATTTTTTTT
310242 AGAAGATAATCGTTTAAGGGGGAGAATTTTTTTT
1 AGAAGATAATCGTTTAAGGGGGAGAATTTTTTTT
*
310276 AGAGGAGATAATCGTTTAAGGGGGAGAATATTTTTT
1 AGA--AGATAATCGTTTAAGGGGGAGAATTTTTTTT
310312 A
1 A
310313 AGGGGAGAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
34 37 0.54
36 31 0.46
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (34 bp):
AGAAGATAATCGTTTAAGGGGGAGAATTTTTTTT
Found at i:310312 original size:19 final size:18
Alignment explanation
Indices: 310254--310321 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
310244 AAGATAATCG
310254 TTTAAGGGGGAGAAT-TTT
1 TTTAA-GGGGAGAATATTT
* * **
310272 TTTTAGAGGAG-ATAATCG
1 TTTAAGGGGAGAAT-ATTT
310290 TTTAAGGGGGAGAATATTT
1 TTTAA-GGGGAGAATATTT
310309 TTTAAGGGGAGAA
1 TTTAAGGGGAGAA
310322 AAACGACAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
16 2 0.05
17 5 0.13
18 17 0.45
19 12 0.32
20 2 0.05
ACGTcount: A:0.32, C:0.01, G:0.32, T:0.34
Consensus pattern (18 bp):
TTTAAGGGGAGAATATTT
Found at i:310882 original size:13 final size:13
Alignment explanation
Indices: 310864--310907 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 13
310854 ACATGCTGCT
310864 TTGTATCGATACA
1 TTGTATCGATACA
310877 TTGTATCGATATGTTCA
1 TTGTATCGATA----CA
310894 TTGTATCGATACA
1 TTGTATCGATACA
310907 T
1 T
310908 GGTCAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
13 14 0.52
17 13 0.48
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:310995 original size:13 final size:13
Alignment explanation
Indices: 310974--311037 Score: 68
Period size: 13 Copynumber: 5.4 Consensus size: 13
310964 CGATACATGG
*
310974 TACAATGTATCGA
1 TACATTGTATCGA
310987 TACATTGTATCGA
1 TACATTGTATCGA
*
311000 TACA-TG-A-AGA
1 TACATTGTATCGA
311010 -A-A-TGTATCGA
1 TACATTGTATCGA
311020 TACATTGTATCGA
1 TACATTGTATCGA
311033 TACAT
1 TACAT
311038 GAAGAAATGT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
8 3 0.07
9 2 0.05
10 4 0.09
11 2 0.05
12 3 0.07
13 29 0.67
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:311000 original size:33 final size:32
Alignment explanation
Indices: 310958--311057 Score: 157
Period size: 33 Copynumber: 3.0 Consensus size: 32
310948 CTATCACTAT
310958 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
310991 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
311024 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
311057 T
1 T
311058 AGCATGTAAC
Statistics
Matches: 65, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
33 63 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:311017 original size:20 final size:20
Alignment explanation
Indices: 310992--311057 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
310982 ATCGATACAT
310992 TGTATCGATACATGAAGAAA
1 TGTATCGATACATGAAGAAA
311012 TGTATCGATACAT-------
1 TGTATCGATACATGAAGAAA
311025 TGTATCGATACATGAAGAAA
1 TGTATCGATACATGAAGAAA
311045 TGTATCGATACAT
1 TGTATCGATACAT
311058 AGCATGTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 13 0.33
20 26 0.67
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGAAGAAA
Found at i:314811 original size:13 final size:13
Alignment explanation
Indices: 314793--314817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
314783 ACACAAAGTA
314793 TGTATCGATACAT
1 TGTATCGATACAT
314806 TGTATCGATACA
1 TGTATCGATACA
314818 CCATAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:314814 original size:32 final size:33
Alignment explanation
Indices: 314773--314840 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
314763 GTAGCCAAAC
*
314773 TTGTATCGATACA-CA-AAGTATGTATCGATACA
1 TTGTATCGATACACCATAA-AATGTATCGATACA
314805 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
314838 TTG
1 TTG
314841 GCTTGTAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:315327 original size:34 final size:35
Alignment explanation
Indices: 315264--315330 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
315254 CTAAGTGATT
315264 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
315300 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
315331 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Done.