Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold47
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: 2157611
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 149227 characters in sequence are not A, C, G, or T
File 3 of 15
Found at i:236245 original size:25 final size:25
Alignment explanation
Indices: 236212--236262 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
236202 ATCCCAACAC
* *
236212 ATATCTAAATATTTTTATTTAAATAT
1 ATATCTAAATACTTATA-TTAAATAT
236238 ATAT-TAAATACTTATATTAAATAT
1 ATATCTAAATACTTATATTAAATAT
236262 A
1 A
236263 AATAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
25 10 0.43
26 4 0.17
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
ATATCTAAATACTTATATTAAATAT
Found at i:236560 original size:27 final size:30
Alignment explanation
Indices: 236525--236605 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 30
236515 GTATTCACAT
236525 TATATTATTTTTTATTATAATTATATTTAA
1 TATATTATTTTTTATTATAATTATATTTAA
* * * *
236555 AATATTATATATTA--AT-ATAATATTTAA
1 TATATTATTTTTTATTATAATTATATTTAA
* *
236582 TATATTATATTTTATTTTAATTAT
1 TATATTATTTTTTATTATAATTAT
236606 TTTCTCATAT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
27 22 0.55
28 2 0.05
29 1 0.03
30 15 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TATATTATTTTTTATTATAATTATATTTAA
Found at i:236563 original size:14 final size:14
Alignment explanation
Indices: 236544--236593 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
236534 TTTTATTATA
236544 ATTATATTTAAAAT
1 ATTATATTTAAAAT
236558 ATTATATATT--AAT
1 ATTATAT-TTAAAAT
* *
236571 ATAATATTTAATAT
1 ATTATATTTAAAAT
236585 ATTATATTT
1 ATTATATTT
236594 TATTTTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 2 0.07
13 9 0.30
14 17 0.57
15 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTATATTTAAAAT
Found at i:238043 original size:2 final size:2
Alignment explanation
Indices: 238038--238072 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
238028 ATTAACCCTA
* *
238038 AT AT AT AT AG AT AC 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 A
238073 GAGAGAGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:240670 original size:2 final size:2
Alignment explanation
Indices: 240663--240732 Score: 97
Period size: 2 Copynumber: 35.5 Consensus size: 2
240653 AATAGGATTT
240663 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
* * **
240705 T- TA TC CA CC TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
240733 GAGAGTTCTT
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:241020 original size:2 final size:2
Alignment explanation
Indices: 241013--241041 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
241003 AGTAAATCAA
241013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
241042 CATGATCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:249677 original size:2 final size:2
Alignment explanation
Indices: 249672--249711 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
249662 ATAACATCAA
* * *
249672 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AG AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
249712 TGGAGGATGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:249908 original size:14 final size:14
Alignment explanation
Indices: 249884--249926 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 14
249874 GATCTTGAAC
249884 TAAAAAA-AATAAT
1 TAAAAAATAATAAT
249897 TAAAAAATAATATAAT
1 TAAAAAAT-A-ATAAT
*
249913 TAAAATATAATAAT
1 TAAAAAATAATAAT
249927 ATGACTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 7 0.27
14 5 0.19
15 2 0.08
16 12 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAAAATAATAAT
Found at i:249913 original size:16 final size:16
Alignment explanation
Indices: 249892--249924 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
249882 ACTAAAAAAA
249892 ATAATTAAAAAATAAT
1 ATAATTAAAAAATAAT
*
249908 ATAATTAAAATATAAT
1 ATAATTAAAAAATAAT
249924 A
1 A
249925 ATATGACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATTAAAAAATAAT
Found at i:250747 original size:21 final size:22
Alignment explanation
Indices: 250696--250747 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
250686 TACGATTTAA
* *
250696 ATTAGTTTAATCTAATATAAATT
1 ATTA-TTTAATCTAATAAAAAAT
250719 ATTATTTAAT-TAATAAAAAAAT
1 ATTATTTAATCTAAT-AAAAAAT
250741 ATT-TTTA
1 ATTATTTA
250748 TATAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 8 0.31
22 14 0.54
23 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTATTTAATCTAATAAAAAAT
Found at i:251313 original size:23 final size:22
Alignment explanation
Indices: 251280--251327 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
251270 TATGAATAAA
251280 TTAAAGCTTATTCAATAAATTAT
1 TTAAAGCTTATTCAA-AAATTAT
* * *
251303 TTAAAGTTTATTTAAAACTTAT
1 TTAAAGCTTATTCAAAAATTAT
251325 TTA
1 TTA
251328 TTGATCAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (22 bp):
TTAAAGCTTATTCAAAAATTAT
Found at i:251383 original size:43 final size:46
Alignment explanation
Indices: 251336--251423 Score: 130
Period size: 43 Copynumber: 2.0 Consensus size: 46
251326 TATTGATCAA
*
251336 TTATAATATAATTAATATTA-TTAT-TATTTA-TATTTTAT-TTTAT
1 TTATAATATAATTAATAATATTTATAT-TTTATTATTTTATATTTAT
251379 TTATAATATAATTAATAATATTTATATTTTATTATTTTATATTTA
1 TTATAATATAATTAATAATATTTATATTTTATTATTTTATATTTA
251424 AAATTAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
43 19 0.47
44 8 0.20
45 9 0.22
46 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (46 bp):
TTATAATATAATTAATAATATTTATATTTTATTATTTTATATTTAT
Found at i:251441 original size:40 final size:37
Alignment explanation
Indices: 251342--251433 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
251332 TCAATTATAA
* * * *
251342 TATAATTAATATTATTATTATTTATATTTTATTTTATT
1 TATAA-TAAAATTAATAATATTTATATTTTATTATATT
*
251380 TATAATATAATTAATAATATTTATATTTTATTAT-TT
1 TATAATAAAATTAATAATATTTATATTTTATTATATT
*
251416 TATATTTAAAATTAATAA
1 TATA-ATAAAATTAATAA
251434 ACATATTTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
36 6 0.13
37 35 0.76
38 5 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (37 bp):
TATAATAAAATTAATAATATTTATATTTTATTATATT
Found at i:253898 original size:32 final size:33
Alignment explanation
Indices: 253846--253925 Score: 99
Period size: 32 Copynumber: 2.4 Consensus size: 33
253836 AATAAATAAT
* * **
253846 TTAAAATATTATATATTTATATAAATTTTAGTATA
1 TTAATATATT-TAT-TTTATAAAAATTTTAAAATA
253881 TTAATA-ATTTATTTTATAAAAATTTTAAAATA
1 TTAATATATTTATTTTATAAAAATTTTAAAATA
253913 TTAATATATTTAT
1 TTAATATATTTAT
253926 ATCGTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
32 23 0.57
33 9 0.22
34 3 0.08
35 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (33 bp):
TTAATATATTTATTTTATAAAAATTTTAAAATA
Found at i:254623 original size:14 final size:14
Alignment explanation
Indices: 254604--254631 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
254594 ATATAATATT
254604 TTTATATTATATAA
1 TTTATATTATATAA
254618 TTTATATTATATAA
1 TTTATATTATATAA
254632 AAATATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATATTATATAA
Found at i:254952 original size:2 final size:2
Alignment explanation
Indices: 254945--254992 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
254935 TGAGAGCTTT
*
254945 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA -A TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
254984 TA T- TA TA TA
1 TA TA TA TA TA
254993 ATTTTTTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:255143 original size:27 final size:28
Alignment explanation
Indices: 255107--255195 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 28
255097 TTGGTTTTGA
255107 TTTTAAAATTAATAAT-ATTAATTAAAT
1 TTTTAAAATTAATAATAATTAATTAAAT
* * *
255134 TTTTAAAATTAATCGTATTGATTAAATAAAT
1 TTTTAAAATTAA---TAATAATTAATTAAAT
255165 ATTTTAAAATTAA-AATAATTAAATT-AAT
1 -TTTTAAAATTAATAATAATT-AATTAAAT
255193 TTT
1 TTT
255196 AAGTAGATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
27 15 0.29
28 8 0.16
29 3 0.06
30 3 0.06
31 10 0.20
32 12 0.24
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (28 bp):
TTTTAAAATTAATAATAATTAATTAAAT
Found at i:255545 original size:17 final size:17
Alignment explanation
Indices: 255509--255545 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
255499 CAAACTAATC
*
255509 AAATAAATTAATTTTTA
1 AAATAAATTAATTTTAA
*
255526 AAATCAATTAATTTTAA
1 AAATAAATTAATTTTAA
255543 AAA
1 AAA
255546 CTTAATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATAAATTAATTTTAA
Found at i:255976 original size:21 final size:22
Alignment explanation
Indices: 255934--255976 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
255924 AAGAAATTGA
* *
255934 TTAATATTAAAAAATTATATTT
1 TTAATATTAAAAAATAAAATTT
*
255956 TTAATATT-TAAAATAAAATTT
1 TTAATATTAAAAAATAAAATTT
255977 AAATAAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTAATATTAAAAAATAAAATTT
Found at i:256156 original size:11 final size:11
Alignment explanation
Indices: 256114--256156 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
256104 ATAAAAATAT
*
256114 TTTAAAATTAA
1 TTTAAAATAAA
*
256125 TTTATAATTAAA
1 TTTA-AAATAAA
*
256137 TTAAAAATAAA
1 TTTAAAATAAA
256148 TTTAAAATA
1 TTTAAAATA
256157 TTTAACATAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TTTAAAATAAA
Found at i:256271 original size:21 final size:22
Alignment explanation
Indices: 256245--256286 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
256235 TAAATTTTTA
256245 TTATTTTATAATTAA-AAATAT
1 TTATTTTATAATTAATAAATAT
*
256266 TTATTTTGTAATTAATAAATA
1 TTATTTTATAATTAATAAATA
256287 ATATATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTATTTTATAATTAATAAATAT
Found at i:256315 original size:27 final size:27
Alignment explanation
Indices: 256223--256315 Score: 75
Period size: 27 Copynumber: 3.4 Consensus size: 27
256213 TAAAAATAAT
* * *
256223 TTTAAAATTAAT-TAAATT-TTTATTAT
1 TTTAAAATTAATAT-ATTTATTTTTTAA
* * *
256249 TTTATAATTAAAAATATTTATTTTGTAA
1 TTTAAAATT-AATATATTTATTTTTTAA
*
256277 -TTAATAAATAATATATTTATTTTTTAA
1 TTTAA-AATTAATATATTTATTTTTTAA
256304 TTTAAAATTAAT
1 TTTAAAATTAAT
256316 TTAAAAAAGT
Statistics
Matches: 51, Mismatches: 11, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
26 8 0.16
27 30 0.59
28 13 0.25
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (27 bp):
TTTAAAATTAATATATTTATTTTTTAA
Found at i:256381 original size:20 final size:21
Alignment explanation
Indices: 256348--256391 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
256338 TAAAATTGGA
256348 TAAAATAAATAAATAT-TTTT
1 TAAAATAAATAAATATATTTT
256368 TAAATATAAA-AAATATATTTT
1 TAAA-ATAAATAAATATATTTT
256389 TAA
1 TAA
256392 TAAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAATAAATAAATATATTTT
Found at i:256395 original size:24 final size:24
Alignment explanation
Indices: 256347--256421 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 24
256337 TTAAAATTGG
*
256347 ATAAA-ATAAATAA-ATATTTTT-
1 ATAAATATAAAAAATATATTTTTA
256368 -TAAATATAAAAAATATATTTTTA
1 ATAAATATAAAAAATATATTTTTA
* * *
256391 ATAAAAATTAAAAAATAAATTATTA
1 ATAAATA-TAAAAAATATATTTTTA
*
256416 AAAAAT
1 ATAAAT
256422 TGGGAGGGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.09
21 7 0.16
22 8 0.19
24 5 0.12
25 19 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAAATATAAAAAATATATTTTTA
Found at i:256422 original size:23 final size:25
Alignment explanation
Indices: 256369--256420 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
256359 AATATTTTTT
* *
256369 AAATATAAAAAATATATTTTTAATAA
1 AAAT-TAAAAAATAAATTATTAATAA
256395 AAATTAAAAAATAAATTATTAA-AA
1 AAATTAAAAAATAAATTATTAATAA
256419 AA
1 AA
256421 TTGGGAGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 16 0.67
26 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATTAAAAAATAAATTATTAATAA
Found at i:257749 original size:32 final size:31
Alignment explanation
Indices: 257701--257763 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
257691 TTAAAATATT
* *
257701 ATTTATTTATATAATTTTTAATATATTAATA
1 ATTTATTTATAAAATTTTTAAGATATTAATA
*
257732 ATTTATTTTATAAAATTTTTTAGATATTAATA
1 ATTTA-TTTATAAAATTTTTAAGATATTAATA
257764 TAATTATATC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 5 0.18
32 23 0.82
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (31 bp):
ATTTATTTATAAAATTTTTAAGATATTAATA
Found at i:257788 original size:27 final size:27
Alignment explanation
Indices: 257758--257820 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
257748 TTTTTAGATA
*
257758 TTAATATAATTATATCTTATTTAT-TTT
1 TTAATAT-ATTATATCTTAATTATATTT
* *
257785 TTAATGTATTATATTTTAATTATATTT
1 TTAATATATTATATCTTAATTATATTT
*
257812 TTAAAATAT
1 TTAATATAT
257821 GTACATGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 14 0.47
27 16 0.53
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
TTAATATATTATATCTTAATTATATTT
Found at i:258375 original size:24 final size:26
Alignment explanation
Indices: 258321--258373 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
258311 AAACTTAATT
*
258321 TATTTTTTTAATTATATACTATATAA
1 TATTTTTATAATTATATACTATATAA
* *
258347 TATTTTTATATTTATATATTATATAA
1 TATTTTTATAATTATATACTATATAA
258373 T
1 T
258374 TTATATTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTTTTATAATTATATACTATATAA
Found at i:258835 original size:2 final size:2
Alignment explanation
Indices: 258828--258889 Score: 87
Period size: 2 Copynumber: 33.0 Consensus size: 2
258818 TGAGAGCTTT
258828 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
*
258870 T- TA -A TA -A TT TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
258890 ATTTTTTTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
1 4 0.07
2 50 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:259065 original size:27 final size:27
Alignment explanation
Indices: 259008--259065 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
258998 TTTGATTTTA
*
259008 AAATTTTTAAAATTAATAATATTAATT
1 AAATTTTTAAAATTAATAATATTAATC
** *
259035 AAATTTTTAAAATTAATCGTATTGATC
1 AAATTTTTAAAATTAATAATATTAATC
259062 AAAT
1 AAAT
259066 AAATATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (27 bp):
AAATTTTTAAAATTAATAATATTAATC
Found at i:259186 original size:7 final size:7
Alignment explanation
Indices: 259176--259231 Score: 51
Period size: 7 Copynumber: 7.9 Consensus size: 7
259166 ATAAAAAATA
259176 ATTATAT
1 ATTATAT
259183 ATTATAT
1 ATTATAT
*
259190 GTTATAT
1 ATTATAT
*
259197 AATAT-T
1 ATTATAT
*
259203 AATTACAT
1 -ATTATAT
*
259211 ATGATAT
1 ATTATAT
259218 ATTATTAT
1 ATTA-TAT
259226 ATTATA
1 ATTATA
259232 AAATTTTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
6 1 0.03
7 29 0.76
8 8 0.21
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (7 bp):
ATTATAT
Found at i:259205 original size:28 final size:26
Alignment explanation
Indices: 259174--259229 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
259164 TCATAAAAAA
* * *
259174 TAATTATATATTATATGTTATATAATAT
1 TAATTACATATGATATATTAT-T-ATAT
259202 TAATTACATATGATATATTATTATAT
1 TAATTACATATGATATATTATTATAT
259228 TA
1 TA
259230 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.24
27 1 0.04
28 18 0.72
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (26 bp):
TAATTACATATGATATATTATTATAT
Found at i:259408 original size:61 final size:61
Alignment explanation
Indices: 259332--259447 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
259322 TTGAAAATCT
* * * *
259332 ACAATCGACTGAACTAATCGAACAAATCGATTTTTAATATTAATTAATTTCAAAACCATCG
1 ACAATCGACTGAACTAATCAAACAAATCAATTTTTAAAATCAATTAATTTCAAAACCATCG
* *
259393 ACAATCGA-TCGAACTAATCAAATAAATCAATTTTTAAAATCAATTAATTTTAAAA
1 ACAATCGACT-GAACTAATCAAACAAATCAATTTTTAAAATCAATTAATTTCAAAA
259448 ACTTAATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 1 0.02
61 47 0.98
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.32
Consensus pattern (61 bp):
ACAATCGACTGAACTAATCAAACAAATCAATTTTTAAAATCAATTAATTTCAAAACCATCG
Found at i:259746 original size:21 final size:19
Alignment explanation
Indices: 259722--259764 Score: 68
Period size: 21 Copynumber: 2.2 Consensus size: 19
259712 AAACTTATCT
259722 TTAATTTTATTATTATATATA
1 TTAATTTTA-TATTA-ATATA
259743 TTAATTTTATATTAATATA
1 TTAATTTTATATTAATATA
259762 TTA
1 TTA
259765 TCTTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 8 0.36
20 5 0.23
21 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATTTTATATTAATATA
Found at i:260043 original size:20 final size:22
Alignment explanation
Indices: 260001--260044 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
259991 TCACTAAATT
*
260001 TTTAAATAATAATAATTAATTAA
1 TTTAAATAAAAATAATT-ATTAA
260024 TTTAAATAAAAAT-ATT-TTAA
1 TTTAAATAAAAATAATTATTAA
260044 T
1 T
260045 AAATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTAAATAAAAATAATTATTAA
Found at i:260092 original size:11 final size:11
Alignment explanation
Indices: 260030--260100 Score: 54
Period size: 11 Copynumber: 6.3 Consensus size: 11
260020 TTAATTTAAA
*
260030 TAAAAATATTT
1 TAAAAATAATT
260041 TAATAAATATATTT
1 TAA-AAATA-A-TT
**
260055 TAAAGTTAATT
1 TAAAAATAATT
* * *
260066 TATAATTAAAT
1 TAAAAATAATT
260077 TAAAAATAATT
1 TAAAAATAATT
260088 TAAAAAT-ATT
1 TAAAAATAATT
260098 TAA
1 TAA
260101 CATAAAATAT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
10 6 0.12
11 28 0.58
12 6 0.12
13 3 0.06
14 5 0.10
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (11 bp):
TAAAAATAATT
Found at i:260115 original size:14 final size:14
Alignment explanation
Indices: 260090--260118 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
260080 AAATAATTTA
260090 AAAATATTTAACAT
1 AAAATATTTAACAT
260104 AAAATATTTAACAT
1 AAAATATTTAACAT
260118 A
1 A
260119 CCTTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATATTTAACAT
Found at i:260378 original size:27 final size:26
Alignment explanation
Indices: 260335--260402 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
260325 GAGTAAATAC
*
260335 ATATTTTT--TAAATATTAAAAAAAGT
1 ATATTTTTAATAAAAATTAAAAAAA-T
260360 ATATTTTTAATAAAAATTAAAAAAAT
1 ATATTTTTAATAAAAATTAAAAAAAT
* *
260386 AAATTATTAA-AAAAATT
1 ATATTTTTAATAAAAATT
260403 GGGAGGGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 15 0.39
26 9 0.24
27 14 0.37
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (26 bp):
ATATTTTTAATAAAAATTAAAAAAAT
Found at i:260388 original size:15 final size:16
Alignment explanation
Indices: 260368--260401 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
260358 GTATATTTTT
260368 AATAAA-AATTAAAAA
1 AATAAATAATTAAAAA
*
260383 AATAAATTATTAAAAA
1 AATAAATAATTAAAAA
260399 AAT
1 AAT
260402 TGGGAGGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAATAATTAAAAA
Found at i:264028 original size:17 final size:16
Alignment explanation
Indices: 264006--264039 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
263996 TAGCGAGTAT
264006 AAAATTTAAATTAAAAA
1 AAAATTTAAA-TAAAAA
*
264023 AAAATTTATATAAAAA
1 AAAATTTAAATAAAAA
264039 A
1 A
264040 GTATATTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTTAAATAAAAA
Found at i:265013 original size:2 final size:2
Alignment explanation
Indices: 265006--265047 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
264996 TGTCAGTTGA
265006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
265048 GAGGAACTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:265262 original size:18 final size:19
Alignment explanation
Indices: 265239--265289 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
265229 CACATTCATG
265239 TCATATTAATATTATTTT-
1 TCATATTAATATTATTTTA
*
265257 TCATATTATTATT-TTTTA
1 TCATATTAATATTATTTTA
* *
265275 TCATGTTCATATTAT
1 TCATATTAATATTAT
265290 ATCTAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 22 0.81
19 1 0.04
ACGTcount: A:0.29, C:0.08, G:0.02, T:0.61
Consensus pattern (19 bp):
TCATATTAATATTATTTTA
Found at i:266166 original size:2 final size:2
Alignment explanation
Indices: 266159--266191 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
266149 CTATACATAC
266159 AT 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 AT A
266192 AATCTGTTCA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:267367 original size:18 final size:18
Alignment explanation
Indices: 267344--267380 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
267334 AAGCATAAAT
267344 TTTTATTATTCTTTTATA
1 TTTTATTATTCTTTTATA
*
267362 TTTTATTATTTTTTTATA
1 TTTTATTATTCTTTTATA
267380 T
1 T
267381 GGATAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTATTCTTTTATA
Found at i:267458 original size:21 final size:19
Alignment explanation
Indices: 267416--267458 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
267406 TCTAAATGGA
*
267416 TTTAATTTTTTATTATTCT
1 TTTAATTTTTTATTATTAT
*
267435 TTTACATTTTATTATTTTTAT
1 TTTA-ATTTT-TTATTATTAT
267456 TTT
1 TTT
267459 TTTATATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 5 0.25
21 11 0.55
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTAATTTTTTATTATTAT
Found at i:267872 original size:96 final size:98
Alignment explanation
Indices: 267698--267898 Score: 237
Period size: 96 Copynumber: 2.1 Consensus size: 98
267688 CATATCATAA
* * * * *
267698 TTATATTAAATATATTATCAACTACAATAAAATTGAAATAATGAGAAAATTCAAACACTAATCCT
1 TTAT-TTAAATATAATATCAACTACAATAAAATCGAAACAATAAGAAAATTCAAACACTAATCAT
*
267763 TTTAATTTACATCACAATATTATTTTG-CCTGGAC
65 TTCAATTTACATCACAATATTATTTTGCCCT-GAC
* * * *
267797 TTATTTAAA-ATAATATCAACTACATTAAAATCGAAACAATAAG-AGATTCAAATACTAGTCATT
1 TTATTTAAATATAATATCAACTACAATAAAATCGAAACAATAAGAAAATTCAAACACTAATCATT
* ** *
267860 TCAATTTGCATCACCCTTTTATTTTGCCCTGAC
66 TCAATTTACATCACAATATTATTTTGCCCTGAC
267893 TTATTT
1 TTATTT
267899 TCCAATTTCA
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
96 46 0.53
97 32 0.37
98 5 0.06
99 4 0.05
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.37
Consensus pattern (98 bp):
TTATTTAAATATAATATCAACTACAATAAAATCGAAACAATAAGAAAATTCAAACACTAATCATT
TCAATTTACATCACAATATTATTTTGCCCTGAC
Found at i:269253 original size:24 final size:24
Alignment explanation
Indices: 269226--269286 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
269216 TTGGTTTATA
269226 TAATTATTTTTAAAATTTAAAATT
1 TAATTATTTTTAAAATTTAAAATT
** ** *
269250 TAATTAAATTTATTATTTAAATTT
1 TAATTATTTTTAAAATTTAAAATT
*
269274 TAA-TATTTATAAA
1 TAATTATTTTTAAA
269287 TAAATTTTTT
Statistics
Matches: 27, Mismatches: 10, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TAATTATTTTTAAAATTTAAAATT
Found at i:273576 original size:14 final size:14
Alignment explanation
Indices: 273531--273576 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
273521 ATTTTTTTAA
*
273531 TTTTTAAATTATAT
1 TTTTTAAAATATAT
*
273545 TTTTTAAAAAATAT
1 TTTTTAAAATATAT
273559 TTTTTAAAATAT-T
1 TTTTTAAAATATAT
273572 TTTTT
1 TTTTT
273577 CGAATTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 6 0.21
14 23 0.79
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTAAAATATAT
Found at i:273728 original size:22 final size:22
Alignment explanation
Indices: 273703--273793 Score: 67
Period size: 22 Copynumber: 4.0 Consensus size: 22
273693 TATTAATTAT
273703 TAAATTTTAATAAAATAAAAAA
1 TAAATTTTAATAAAATAAAAAA
* *
273725 TAAAATTTAATTAAATTTTAAAAAA
1 TAAATTTTAA-TAAA--ATAAAAAA
* * * *
273750 T-TATATTAAAAAAATTAAAATAT
1 TAAATTTTAATAAAA-TAAAA-AA
*
273773 TAATTTTTAATAAAATAAAAA
1 TAAATTTTAATAAAATAAAAA
273794 TTTTAAAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
22 15 0.29
23 14 0.27
24 14 0.27
25 8 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATTTTAATAAAATAAAAAA
Found at i:274152 original size:22 final size:25
Alignment explanation
Indices: 274125--274184 Score: 81
Period size: 23 Copynumber: 2.5 Consensus size: 25
274115 ATAAGTAGTT
274125 TAAATTTATTTTATTT-TAAAA-TA
1 TAAATTTATTTTATTTGTAAAAGTA
*
274148 T-AATTTATTTTTATTTGTAAAAGTT
1 TAAATTTA-TTTTATTTGTAAAAGTA
274173 TAAATTTATTTT
1 TAAATTTATTTT
274185 TTATTTAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 6 0.19
23 9 0.28
24 5 0.16
25 6 0.19
26 6 0.19
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (25 bp):
TAAATTTATTTTATTTGTAAAAGTA
Found at i:274178 original size:26 final size:24
Alignment explanation
Indices: 274092--274190 Score: 96
Period size: 24 Copynumber: 4.0 Consensus size: 24
274082 GATATGATTA
*
274092 TAAAAGTTTAATTTAATTTTT-TTA
1 TAAAAGTTTAATTT-ATTTTTATTT
*
274116 TAAGTAGTTTAAATTTA-TTTTATTT
1 TAA-AAGTTT-AATTTATTTTTATTT
*
274141 TAAAA-TATAATTTATTTTTATTT
1 TAAAAGTTTAATTTATTTTTATTT
274164 GTAAAAGTTTAAATTTATTTTTTATTT
1 -TAAAAGTTT-AATTTA-TTTTTATTT
274191 AATTATGCGA
Statistics
Matches: 62, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
22 6 0.10
23 10 0.16
24 13 0.21
25 13 0.21
26 11 0.18
27 9 0.15
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (24 bp):
TAAAAGTTTAATTTATTTTTATTT
Found at i:274342 original size:74 final size:73
Alignment explanation
Indices: 274138--274360 Score: 224
Period size: 74 Copynumber: 3.1 Consensus size: 73
274128 ATTTATTTTA
* * *
274138 TTTTAAAATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTT-ATTTAA-T-TATGCG
1 TTTTAAAATATAATTTATTTTTATTTATAAAAATTTAAATTTATTTTTTAATTTAATTATATACG
274200 ATTTAAAT
66 ATTTAAAT
* * * * * * * *
274208 TTTTAAAATATAATTTATTTTAATTTATAAAAAATTAAATATAATTTTTAGGTATGATTATATAT
1 TTTTAAAATATAATTTATTTTTATTTATAAAAATTTAAATTTATTTTTTA-ATTTAATTATATAC
*
274273 G-TTTATAT
65 GATTTAAAT
* * *
274281 TTTT-TATTATGAAATTTATTTTTATTTACAAAAATTTAATATTTATTTTTTAATTTAATTATAT
1 TTTTAAAATAT--AATTTATTTTTATTTATAAAAATTTAA-ATTTATTTTTTAATTTAATTATAT
*
274345 A-AATTTAAAT
63 ACGATTTAAAT
274355 TTTTAA
1 TTTTAA
274361 GTGCTGTGAT
Statistics
Matches: 119, Mismatches: 25, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
70 43 0.36
72 7 0.06
73 11 0.09
74 48 0.40
75 10 0.08
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (73 bp):
TTTTAAAATATAATTTATTTTTATTTATAAAAATTTAAATTTATTTTTTAATTTAATTATATACG
ATTTAAAT
Found at i:274674 original size:19 final size:19
Alignment explanation
Indices: 274631--274673 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
274621 ATAAAATATT
274631 ATTTTTTGATATTATTTAA
1 ATTTTTTGATATTATTTAA
*
274650 AATTTTTGATATTA-TT-A
1 ATTTTTTGATATTATTTAA
274667 ATTTTTT
1 ATTTTTT
274674 TATAGTATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (19 bp):
ATTTTTTGATATTATTTAA
Found at i:274912 original size:156 final size:156
Alignment explanation
Indices: 274568--274943 Score: 466
Period size: 156 Copynumber: 2.5 Consensus size: 156
274558 ATTGATCTAG
*
274568 AAAAATAAAAAGATTTAGTTTAATATAGTTTTAGATTATACTTTTTAATTAATAT-AAA-A--TA
1 AAAAATAAAAAGATTTAGTTTAATATAGTTTTAGATTATATTTTTTAATTAATATAAAATATTTA
* * ** * *
274629 -TT--ATTTTTTGATATTATTTAAAATTTTTGATATTATTAATTTTTTTATAGTATGCTTTTTTA
66 TTTAGATTTTTTGATATTATTTAAAATTTATAATATTATTAATTTTTTTATAACATACTTGTTTA
* * *
274691 TTATGTTAAAATATATTTAAGACATC
131 ATATATCAAAATATATTTAAGACATC
** *
274717 AAAAATAAAAAGGCTTAATTTAATATAGTTTT-GATTATATTTTTTAATTAATATAAAATATTTA
1 AAAAATAAAAAGATTTAGTTTAATATAGTTTTAGATTATATTTTTTAATTAATATAAAATATTTA
* *
274781 TTTAGATACTTTTTGATGTTATTTAAGATTTATAATATTATTAA-TTTTTTATAACATACTTGTT
66 TTTAGAT--TTTTTGATATTATTTAAAATTTATAATATTATTAATTTTTTTATAACATACTTGTT
* *
274845 TAATATATCAAAATATATTTAAGATATT
129 TAATATATCAAAATATATTTAAGACATC
* * * * *
274873 AAAAGTAAAAA-ATTTAGTTTAATATAATTTTAAATTATATTTTTTAATTAATATAAAATGTTTG
1 AAAAATAAAAAGATTTAGTTTAATATAGTTTTAGATTATATTTTTTAATTAATATAAAATATTTA
274937 TTTAGAT
66 TTTAGAT
274944 GTGAGATTTA
Statistics
Matches: 192, Mismatches: 25, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
148 21 0.11
149 32 0.17
150 1 0.01
152 2 0.01
153 2 0.01
155 18 0.09
156 85 0.44
157 31 0.16
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (156 bp):
AAAAATAAAAAGATTTAGTTTAATATAGTTTTAGATTATATTTTTTAATTAATATAAAATATTTA
TTTAGATTTTTTGATATTATTTAAAATTTATAATATTATTAATTTTTTTATAACATACTTGTTTA
ATATATCAAAATATATTTAAGACATC
Found at i:275643 original size:2 final size:2
Alignment explanation
Indices: 275636--275673 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
275626 TATATGCATA
275636 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
275674 GCATGCAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:279162 original size:19 final size:19
Alignment explanation
Indices: 279134--279170 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
279124 TATCCAAATT
279134 AATCAAAATATTTAAACAA
1 AATCAAAATATTTAAACAA
* *
279153 AATCAGAATATTTCAACA
1 AATCAAAATATTTAAACA
279171 TGTACTATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.27
Consensus pattern (19 bp):
AATCAAAATATTTAAACAA
Found at i:279354 original size:2 final size:2
Alignment explanation
Indices: 279343--279374 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
279333 AACTATACAA
279343 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
279375 AACTCAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:280500 original size:13 final size:13
Alignment explanation
Indices: 280464--280502 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
280454 TAAAAATATA
280464 TTAAATTTTAAAAT
1 TTAAATTTT-AAAT
*
280478 TTAAAATTTAAAT
1 TTAAATTTTAAAT
*
280491 TTAGATTTTAAA
1 TTAAATTTTAAA
280503 AATCTGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (13 bp):
TTAAATTTTAAAT
Found at i:285895 original size:32 final size:32
Alignment explanation
Indices: 285830--286070 Score: 118
Period size: 34 Copynumber: 7.4 Consensus size: 32
285820 TCTATGACAC
* * *
285830 CCTTTTAAGTCCACAACTCTGTGGCACCTTTT
1 CCTTTTAAGCCCATAACACTGTGGCACCTTTT
*
285862 TCTTTTCAAAGCCCATAACACT-TGGCACCTTTT
1 CCTTTT--AAGCCCATAACACTGTGGCACCTTTT
* *
285895 CCTTTTAAGTCCATAACTCTGTGGCA-C---T
1 CCTTTTAAGCCCATAACACTGTGGCACCTTTT
* *
285923 -CTTTTAAGTCCATAAC-TTCGTGGCACCTTTTT
1 CCTTTTAAGCCCATAACACT-GTGGCACC-TTTT
* * * * **
285955 CTTTTTAAAGCCTACAACTCTGTGATACTCTTTTT
1 CCTTTT-AAGCCCATAACACTGTGGCAC-C-TTTT
* * * *
285990 CCTTTTAAGTCCACAACTCTGTGACACCCTTTT
1 CCTTTTAAGCCCATAACACTGTGGCA-CCTTTT
* * * * *
286023 CCCTTTTAAGTCCAGAGCTCCGTGGCACCTTTTT
1 -CCTTTTAAGCCCATAACACTGTGGCACC-TTTT
*
286057 CATTTTAAAGCCCA
1 CCTTTT-AAGCCCA
286071 CAACTCCGTA
Statistics
Matches: 167, Mismatches: 25, Indels: 32
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.01
27 22 0.13
28 2 0.01
31 13 0.08
32 11 0.07
33 31 0.19
34 74 0.44
35 13 0.08
ACGTcount: A:0.21, C:0.29, G:0.12, T:0.38
Consensus pattern (32 bp):
CCTTTTAAGCCCATAACACTGTGGCACCTTTT
Found at i:285954 original size:27 final size:27
Alignment explanation
Indices: 285896--285953 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
285886 GCACCTTTTC
285896 CTTTTAAGTCCATAACTCTGTGGCACT
1 CTTTTAAGTCCATAACTCTGTGGCACT
285923 CTTTTAAGTCCATAACT-TCGTGGCAC-
1 CTTTTAAGTCCATAACTCT-GTGGCACT
285949 CTTTT
1 CTTTT
285954 TCTTTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.40
Consensus pattern (27 bp):
CTTTTAAGTCCATAACTCTGTGGCACT
Found at i:286023 original size:68 final size:67
Alignment explanation
Indices: 285923--287027 Score: 486
Period size: 68 Copynumber: 16.8 Consensus size: 67
285913 CTGTGGCACT
* * * **
285923 CTTTTAAGTCCATAACT-TCGTGGCACCTTTTTCTTTTTAAAG-CCTACAACTCTGTGATACTCT
1 CTTTTAAGTCCACAACTCT-GTGACACCTTTTTCTTTTT-AAGTCC-ACAACTCCGTGGCACTCT
285986 TTTTC
63 TTTTC
* * * *
285991 CTTTTAAGTCCACAACTCTGTGACACCCTTTTCCCTTTTAAGTCCAGAGCTCCGTGGCAC-CTTT
1 CTTTTAAGTCCACAACTCTGTGACA-CCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACTCTTT
286055 TTC
65 TTC
* * * *
286058 ATTTTAAAGCCCACAACTCCGTAGGAC-CCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCACT-
1 CTTTT-AAGTCCACAACTCTGT--GACACCTTTTT-CTTTTTAAGTCCACAACTCCGTGGCACTC
286121 TTTTTC
62 TTTTTC
* * *
286127 CTTTTCAAATCCCACAACTCCATG-GCACACTTTTTTCTTTTTAAGTCCACAACTCCGTGGTA-T
1 CTTTT-AAGT-CCACAACT-C-TGTG-ACACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACT
286190 CCTTTTTC
61 -CTTTTTC
** * * * * * *
286198 CTTTTAAGTTTATAGCTCCGT-AGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTT
1 CTTTTAAGTCCACAACTCTGTGA-CACCTTTTTCTTTT-TAAGTCCACAACTCCGTGGCACTCTT
286262 TTTC
64 TTTC
* * * * * *
286266 TTTTTAAGTCCACAACTCTGTGACGCCTTTTTCTTTTCAAAG-CTCACAACTCTGTGACGC-CTT
1 CTTTTAAGTCCACAACTCTGTGACACCTTTTTCTTTT-TAAGTC-CACAACTCCGTGGCACTCTT
286329 TTT-
64 TTTC
* * * * *
286332 CTTTTCGAAGCCCACAACTCTGTGGCACCTTTTTTTTCTTTTAAGTCCACAACTCCATGACAC-C
1 CTTTT--AAGTCCACAACTCTGTGACACC-TTTTTCT-TTTTAAGTCCACAACTCCGTGGCACTC
286396 TTTTT-
62 TTTTTC
* * * * *
286401 CTTTTCAAAG-CTCAGAACTCCGTGACACC--TTTC----AAAGCCCACAACTCTGTGGC-CTC-
1 CTTTT--AAGTC-CACAACTCTGTGACACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACTCT
286457 ---T-
63 TTTTC
* * * * * * *
286458 -TTTAAATTTC-CAACTCTGTGGCACTTTTTTCTTTTCAAAGCCCACAACTCCGTGGCAC-C--T
1 CTTTTAAGTCCACAACTCTGTGACACCTTTTTCTTTT-TAAGTCCACAACTCCGTGGCACTCTTT
286518 TT-
65 TTC
* * * * * *
286520 C---AAAGCCCACAACACCGTGACACCCTTTTTCCTTTTAAGTCCACAACTTCGTGGCAC-CTTT
1 CTTTTAAGTCCACAACTCTGTGACA-CCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACTCTTT
286581 TTC
65 TTC
** * *
286584 CTTTTAAG-CTCACAACTCCATGGCACC-----C-TTTTAAGTTCACAACTCCGTGGCA-TCTTT
1 CTTTTAAGTC-CACAACTCTGTGACACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACTCTTT
286641 TTC
65 TTC
** * * * * * *
286644 TCTTCAAAGCCCACAACT-TCGTGGCACC-TTTTCTTTTCAAAGCCCATAACTCCGTGGCAC-AT
1 -CTTTTAAGTCCACAACTCT-GTGACACCTTTTTCTTTT-TAAGTCCACAACTCCGTGGCACTCT
286706 TTTT-
63 TTTTC
* * * * * * **
286710 CTTTTCAAAGCCCACAACTCTGTGGCATCTTTTTCTTTTCAAAG-CCTACAACTCTGTGGTACAA
1 CTTTT--AAGTCCACAACTCTGTGACACCTTTTTCTTTT-TAAGTCC-ACAACTCCGTGGCACTC
286774 TTTTTC
62 TTTTTC
* ** * ** * *
286780 CTTTTAAGTCCACAACTTTGTGGTACCTTTTTCTTTTCAAAACCCACAACTCTGTGGTA-TCATT
1 CTTTTAAGTCCACAACTCTGTGACACCTTTTTCTTTT-TAAGTCCACAACTCCGTGGCACTC-TT
286844 TTTC
64 TTTC
* * * * *
286848 ATTTTAAGTCCACAATTCCGTGGCACC-----C-TTTTAAGTCTACAACTCCGTGGCATCCTTTT
1 CTTTTAAGTCCACAACTCTGTGACACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCA--C----
286907 TCTTTTTTC
60 TC-TTTTTC
* ** * *
286916 CTCTTAAGTCCACAACTCCATGTCACC-----C-TTTTAAGTCCACAACTCTGTGGCAC-CTTTT
1 CTTTTAAGTCCACAACTCTGTGACACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACTCTTTT
286974 T-
66 TC
* * *
286975 CTTTTCAAAGCCCACAACTCCGTGGCACCTTATTT-TTTTTAAGTCCACAACTC
1 CTTTT--AAGTCCACAACTCTGTGACACCTT-TTTCTTTTTAAGTCCACAACTC
287028 TGTGACACAT
Statistics
Matches: 818, Mismatches: 134, Indels: 171
0.73 0.12 0.15
Matches are distributed among these distances:
53 11 0.01
54 3 0.00
55 4 0.00
56 3 0.00
57 1 0.00
59 4 0.00
60 59 0.07
61 103 0.13
62 15 0.02
63 4 0.00
64 1 0.00
65 4 0.00
66 15 0.02
67 106 0.13
68 299 0.37
69 118 0.14
70 49 0.06
71 18 0.02
72 1 0.00
ACGTcount: A:0.21, C:0.30, G:0.11, T:0.37
Consensus pattern (67 bp):
CTTTTAAGTCCACAACTCTGTGACACCTTTTTCTTTTTAAGTCCACAACTCCGTGGCACTCTTTT
TC
Found at i:286330 original size:102 final size:101
Alignment explanation
Indices: 285936--287079 Score: 574
Period size: 102 Copynumber: 11.6 Consensus size: 101
285926 TTAAGTCCAT
* *
285936 AACTTCGTGGCAC-CTTTTTCTTTTTAAAG-CCTACAACTCTGTGATACTCTTTTTCCTTTTAAG
1 AACTCCGTGGCACTCTTTTTCTTTTT-AAGTCC-ACAACTCTGTGACAC-CTTTTTCCTTTTAAG
* * * *
285999 -TCCACAACTCTGTGACACCCTTTTCCCTTTT--AAGTCCAG
63 CT-CACAACTCCGTGACA-CCTTTT-TCTTTTCAAAGCCCAC
* * * *
286038 AGCTCCGTGGCAC-CTTTTTCATTTTAAAGCCCACAACTCCGTAGGAC-CCTTTTTCCCTTTTAA
1 AACTCCGTGGCACTCTTTTTC-TTTTTAAGTCCACAACTCTGT--GACACCTTTTT-CCTTTTAA
* * *
286101 G-TCCACAACTCCGTGGCACTTTTTTCCTTTTCAAATCCCAC
62 GCT-CACAACTCCGTGACACCTTTTT-CTTTTCAAAGCCCAC
* * * ** *
286142 AACTCCATGGCACACTTTTTTCTTTTTAAGTCCACAACTCCGTGGTATCCTTTTTCCTTTTAAGT
1 AACTCCGTGGCACTC-TTTTTCTTTTTAAGTCCACAACTCTGTGACA-CCTTTTTCCTTTTAAGC
* * *
286207 TTATAGCTCCGT-AGCACCTTTTTCTTTTCAAAGCCCAC
64 TCACAACTCCGTGA-CACCTTTTTCTTTTCAAAGCCCAC
* *
286245 AACTCCGTGGCACTTTTTTTCTTTTTAAGTCCACAACTCTGTGACGCCTTTTT-CTTTTCAAAGC
1 AACTCCGTGGCACTCTTTTTCTTTTTAAGTCCACAACTCTGTGACACCTTTTTCCTTTT--AAGC
* * *
286309 TCACAACTCTGTGACGCCTTTTTCTTTTCGAAGCCCAC
64 TCACAACTCCGTGACACCTTTTTCTTTTCAAAGCCCAC
* * **
286347 AACTCTGTGGCAC-CTTTTTTTTCTTTTAAGTCCACAACTCCATGACACCTTTTT-CTTTTCAAA
1 AACTCCGTGGCACTC-TTTTTCT-TTTTAAGTCCACAACTCTGTGACACCTTTTTCCTTTT--AA
*
286410 GCTCAGAACTCCGTGACA-C-----C-TTTCAAAGCCCAC
62 GCTCACAACTCCGTGACACCTTTTTCTTTTCAAAGCCCAC
* * * * * *
286443 AACTCTGTGG--C-C----TCTTTTAAATTTC-CAACTCTGTGGCA-CTTTTTTCTTTTCAAAGC
1 AACTCCGTGGCACTCTTTTTCTTTTTAAGTCCACAACTCTGTGACACCTTTTTCCTTTT--AAGC
* *
286499 CCACAACTCCGTGGCA-C-----C-TTTCAAAGCCCAC
64 TCACAACTCCGTGACACCTTTTTCTTTTCAAAGCCCAC
* * * * *
286530 AACACCGTGACACCCTTTTTCCTTTTAAGTCCACAACT-TCGTGGCACCTTTTTCCTTTTAAGCT
1 AACTCCGTGGCACTCTTTTTCTTTTTAAGTCCACAACTCT-GTGACACCTTTTTCCTTTTAAGCT
* * **
286594 CACAACTCCATGGCACC-----CTTTT--AAGTTCAC
65 CACAACTCCGTGACACCTTTTTCTTTTCAAAGCCCAC
** * *
286624 AACTCCGTGGCA-TCTTTTTCTCTTCAAAGCCCACAACT-TCGTGGCACC-TTTT-CTTTTCAAA
1 AACTCCGTGGCACTCTTTTTCT-TTTTAAGTCCACAACTCT-GTGACACCTTTTTCCTTTT--AA
* * * *
286685 GCCCATAACTCCGTGGCACATTTTTCTTTTCAAAGCCCAC
62 GCTCACAACTCCGTGACACCTTTTTCTTTTCAAAGCCCAC
* * *
286725 AACTCTGTGGCA-TCTTTTTCTTTTCAAAG-CCTACAACTCTGTGGTACA-ATTTTTCCTTTTAA
1 AACTCCGTGGCACTCTTTTTCTTTT-TAAGTCC-ACAACTCTGT-G-ACACCTTTTTCCTTTTAA
** ** *
286787 G-TCCACAACTTTGTGGTACCTTTTTCTTTTCAAAACCCAC
62 GCT-CACAACTCCGTGACACCTTTTTCTTTTCAAAGCCCAC
* * * * * *
286827 AACTCTGTGGTA-TCATTTTTCATTTTAAGTCCACAATTCCGTGGCA-C-----CCTTTTAAG-T
1 AACTCCGTGGCACTC-TTTTTCTTTTTAAGTCCACAACTCTGTGACACCTTTTTCCTTTTAAGCT
* * *
286884 CTACAACTCCGTGGCATCCTTTTTCTTTTTTCCTCTTAAGTCCAC
65 C-ACAACTCCGTGACA-CCTTTTTC---TTT--TC-AAAGCCCAC
* * *
286929 AACTCCATGTCAC-C-----C-TTTTAAGTCCACAACTCTGTGGCACCTTTTT-CTTTTCAAAGC
1 AACTCCGTGGCACTCTTTTTCTTTTTAAGTCCACAACTCTGTGACACCTTTTTCCTTTT--AAGC
* * * *
286986 CCACAACTCCGTGGCACCTTATTT-TTTT-TAAGTCCAC
64 TCACAACTCCGTGACACCTT-TTTCTTTTCAAAGCCCAC
* * * * * * * *
287023 AACTCTGTGACAC-ATTTTTCTTTTCAAAGCCCATAACTCCGTGGCACCATTTTTCCT
1 AACTCCGTGGCACTCTTTTTCTTTT-TAAGTCCACAACTCTGTGACACC-TTTTTCCT
287080 CCAAAAGTCC
Statistics
Matches: 840, Mismatches: 122, Indels: 159
0.75 0.11 0.14
Matches are distributed among these distances:
86 6 0.01
87 56 0.07
88 7 0.01
89 3 0.00
90 1 0.00
92 5 0.01
93 11 0.01
94 107 0.13
95 56 0.07
96 47 0.06
97 1 0.00
98 3 0.00
99 9 0.01
100 19 0.02
101 71 0.08
102 225 0.27
103 131 0.16
104 48 0.06
105 28 0.03
106 6 0.01
ACGTcount: A:0.21, C:0.30, G:0.11, T:0.37
Consensus pattern (101 bp):
AACTCCGTGGCACTCTTTTTCTTTTTAAGTCCACAACTCTGTGACACCTTTTTCCTTTTAAGCTC
ACAACTCCGTGACACCTTTTTCTTTTCAAAGCCCAC
Found at i:286331 original size:275 final size:263
Alignment explanation
Indices: 285829--286801 Score: 741
Period size: 275 Copynumber: 3.7 Consensus size: 263
285819 CTCTATGACA
* * *
285829 CCCTTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTTTCAAAGCCCATAACACTTGGCACCTTT
1 CCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACACATGGCACCTTT
* * * *
285894 TCCTTTTAAGTCCATAACTCTGTGGCACTCTTTTAAGTCCATAACTTCGTGGCACCTTTTTCTTT
66 TCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTAAGTCCATAACTCCGTAGCACCTTTTTCTTT
* * * *
285959 TTAAAGCCTACAACTCTGTGATACTCTTTTTCCTTTTAAGTCCACAACTCTGTGACACCCTTTTC
131 TCAAAGCCCACAACTCCGTGACACTCTTTTTCCTTTTAAGTCCACAACTCTGTGACACCCTTTTC
*
286024 CCTTTTAAGTCCAGAGCTCCGTGGCACCTTTTTCATTTT-AAAGCCCACAACTCCGTAGG-ACCC
196 CCTTTTAAGTCCAGAGCTCCGTGACACCTTTTTC-TTTTCAAAGCCCACAACTCCGT-GGCACCC
286087 TTTTT
259 TTTTT
* * *
286092 CCCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCCTTTTCAAATCCCACAACTCCATGGCACAC
1 CCCTTTTAAGTCCACAACTCCGTGGCACCTTTTT-CTTTTCAAAGCCCACAAC-ACATGGCAC-C
* * ** *
286157 TTTTTTCTTTTTAAGTCCACAACTCCGTGGTATCCTTTTTCCTTTTAAGTTTATAGCTCCGTAGC
63 --TTTTCCTTTTAAGTCCACAACTCCGTGGCA--C----T-CTTTTAAGTCCATAACTCCGTAGC
* * *
286222 ACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTTCTTTTTAAGTCCACAACTCTGT
119 ACCTTTTTCTTTTCAAAGCCCACAACTCCGTGACACTCTTTTTCCTTTTAAGTCCACAACTCTGT
* * * * *
286287 GAC-GCCTTTT-TCTTTTCAAAGCTCACA-A-CTCTGTGACGCCTTTTTCTTTTCGAAGCCCACA
184 GACACCCTTTTCCCTTTT--AAG-TC-CAGAGCTCCGTGACACCTTTTTCTTTTCAAAGCCCACA
* *
286348 ACTCTGTGGCACCTTTTTT
245 ACTCCGTGGCACCCTTTTT
** * * * * * * *
286367 TTCTTTTAAGTCCACAACTCCATGACACCTTTTTCTTTTCAAAGCTCAGAACTCCGTGACACC-T
1 CCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAAC-ACATGGCACCTT
* * * * * * *
286431 TT-C---AAAGCCCACAACTCTGTGGC-CTCTTTTAAATTTCC--AACTCTGTGGCACTTTTTTC
65 TTCCTTTTAAGTCCACAACTCCGTGGCACTCTTTT-AA-GTCCATAACTCCGTAGCACCTTTTTC
* * * * *
286489 TTTTCAAAGCCCACAACTCCGTGGCAC-C--TTT-C---AAAGCCCACAACACCGTGACACCCTT
128 TTTTCAAAGCCCACAACTCCGTGACACTCTTTTTCCTTTTAAGTCCACAACTCTGTGACACCCTT
* * * * * * *
286547 TTTCCTTTTAAGTCCACAACTTCGTGGCACCTTTTTCCTTTT--AAGCTCACAACTCCATGGCA-
193 TTCCCTTTTAAGTCCAGAGCTCCGTGACACCTTTTT-CTTTTCAAAGCCCACAACTCCGTGGCAC
286609 -------
257 CCTTTTT
* * * * *
286609 CCCTTTTAAGTTCACAACTCCGTGGCATCTTTTTCTCTTCAAAGCCCACAACTTCGTGGCACCTT
1 CCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAAC-ACATGGCACCTT
* * * * * * *
286674 TT-CTTTTCAAAGCCCATAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAACTCTGTGGCAT
65 TTCCTTTT--AAGTCCACAACTCCGTGGCAC-----TCTTTT--AAGTCCATAACTCCGTAGCAC
* * ** ** *
286738 CTTTTTCTTTTCAAAGCCTACAACTCTGTGGTACAATTTTTCCTTTTAAGTCCACAACTTTGTG
121 CTTTTTCTTTTCAAAGCCCACAACTCCGTGACACTCTTTTTCCTTTTAAGTCCACAACTCTGTG
286802 GTACCTTTTT
Statistics
Matches: 569, Mismatches: 94, Indels: 94
0.75 0.12 0.12
Matches are distributed among these distances:
242 52 0.09
243 4 0.01
248 17 0.03
249 3 0.01
250 20 0.04
251 32 0.06
252 11 0.02
253 5 0.01
254 8 0.01
255 6 0.01
256 42 0.07
258 48 0.08
259 6 0.01
260 2 0.00
263 46 0.08
264 16 0.03
265 7 0.01
266 17 0.03
268 26 0.05
270 4 0.01
273 6 0.01
274 36 0.06
275 150 0.26
276 3 0.01
277 2 0.00
ACGTcount: A:0.21, C:0.30, G:0.12, T:0.37
Consensus pattern (263 bp):
CCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACACATGGCACCTTT
TCCTTTTAAGTCCACAACTCCGTGGCACTCTTTTAAGTCCATAACTCCGTAGCACCTTTTTCTTT
TCAAAGCCCACAACTCCGTGACACTCTTTTTCCTTTTAAGTCCACAACTCTGTGACACCCTTTTC
CCTTTTAAGTCCAGAGCTCCGTGACACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCCTT
TTT
Found at i:286420 original size:34 final size:34
Alignment explanation
Indices: 285936--287077 Score: 364
Period size: 34 Copynumber: 34.6 Consensus size: 34
285926 TTAAGTCCAT
* * *
285936 AACTTCGTGGCACCTTTTTCTTTTTAAAGC-CTAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTC-AC
* *
285970 AACTCTGTGATACTCTTTTTCCTTTT--AAG-TCCAC
1 AACTCCGTGACAC-CTTTTT-CTTTTCAAAGCT-CAC
* *
286004 AACTCTGTGACACCCTTTTCCCTTTT--AAG-TC-C
1 AACTCCGTGACA-CCTTTT-TCTTTTCAAAGCTCAC
* *
286036 AGAGCTCCGTGGCACCTTTTTCATTTT-AAAGCCCAC
1 A-A-CTCCGTGACACCTTTTTC-TTTTCAAAGCTCAC
286072 AACTCCGTAGGAC-CCTTTTTCCCTTTT--AAG-TCCAC
1 AACTCCGT--GACACCTTTTT--CTTTTCAAAGCT-CAC
* * * *
286107 AACTCCGTGGCACTTTTTTCCTTTTCAAATCCCAC
1 AACTCCGTGACACCTTTTT-CTTTTCAAAGCTCAC
* * *
286142 AACTCCATGGCACACTTTTTTCTTTT-TAAG-TCCAC
1 AACTCCGT-G-ACACCTTTTTCTTTTCAAAGCT-CAC
** * * *
286177 AACTCCGTGGTATCCTTTTTCCTTTT--AAGTTTAT
1 AACTCCGTGACA-CCTTTTT-CTTTTCAAAGCTCAC
* *
286211 AGCTCCGT-AGCACCTTTTTCTTTTCAAAGCCCAC
1 AACTCCGTGA-CACCTTTTTCTTTTCAAAGCTCAC
* * *
286245 AACTCCGTGGCACTTTTTTTCTTTT-TAAG-TCCAC
1 AACTCCGTGACAC-CTTTTTCTTTTCAAAGCT-CAC
* *
286279 AACTCTGTGACGCCTTTTTCTTTTCAAAGCTCAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
* * * *
286313 AACTCTGTGACGCCTTTTTCTTTTCGAAGCCCAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
* * * **
286347 AACTCTGTGGCACCTTTTTTTTCTTTTAAG-TCCAC
1 AACTCCGTGACACCTTTTTCTT-TTCAAAGCT-CAC
* *
286382 AACTCCATGACACCTTTTTCTTTTCAAAGCTCAG
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
*
286416 AACTCCGTGACA-C-----C-TTTCAAAGCCCAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
* * **
286443 AACTCTGTG--GCC----TCTTTT-AAATTTC-C
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
* * * *
286469 AACTCTGTGGCACTTTTTTCTTTTCAAAGCCCAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
* *
286503 AACTCCGTGGCA-C-----C-TTTCAAAGCCCAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
*
286530 AACACCGTGACACCCTTTTTCCTTTT--AAG-TCCAC
1 AACTCCGTGACA-CCTTTTT-CTTTTCAAAGCT-CAC
* *
286564 AACTTCGTGGCACCTTTTTCCTTTT--AAGCTCAC
1 AACTCCGTGACACCTTTTT-CTTTTCAAAGCTCAC
* * *
286597 AACTCCATGGCACC-----CTTTT--AAGTTCAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
* * * *
286624 AACTCCGTGGCATCTTTTTCTCTTCAAAGCCCAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
* * * *
286658 AACTTCGTGGCACC-TTTTCTTTTCAAAGCCCAT
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
* * *
286691 AACTCCGTGGCACATTTTTCTTTTCAAAGCCCAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
* * *
286725 AACTCTGTGGCATCTTTTTCTTTTCAAAGC-CTAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTC-AC
* *
286759 AACTCTGTGGTACA-ATTTTTCCTTTT--AAG-TCCAC
1 AACTCCGT-G-ACACCTTTTT-CTTTTCAAAGCT-CAC
** ** * *
286793 AACTTTGTGGTACCTTTTTCTTTTCAAAACCCAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
* ** *
286827 AACTCTGTGGTATCATTTTTCATTTT--AAG-TCCAC
1 AACTCCGTGACA-CCTTTTTC-TTTTCAAAGCT-CAC
* *
286861 AATTCCGTGGCACC-----CTTTT--AAG-TCTAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTC-AC
* *
286888 AACTCCGTGGCATCCTTTTTCTTTTTTCCTCTTAAG-TCCAC
1 AACTCCGTGACA-CCTTTTTC---TTT--TC-AAAGCT-CAC
* *
286929 AACTCCATGTCACC-----CTTTT--AAG-TCCAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCT-CAC
* * *
286956 AACTCTGTGGCACCTTTTTCTTTTCAAAGCCCAC
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
* *
286990 AACTCCGTGGCACCTTATTT-TTTT-TAAG-TCCAC
1 AACTCCGTGACACCTT-TTTCTTTTCAAAGCT-CAC
* * * *
287023 AACTCTGTGACACATTTTTCTTTTCAAAGCCCAT
1 AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
*
287057 AACTCCGTGGCACCATTTTTC
1 AACTCCGTGACACC-TTTTTC
287078 CTCCAAAAGT
Statistics
Matches: 864, Mismatches: 133, Indels: 221
0.71 0.11 0.18
Matches are distributed among these distances:
26 12 0.01
27 111 0.13
28 9 0.01
29 1 0.00
30 1 0.00
32 35 0.04
33 135 0.16
34 370 0.43
35 124 0.14
36 36 0.04
37 10 0.01
38 1 0.00
40 2 0.00
41 16 0.02
42 1 0.00
ACGTcount: A:0.21, C:0.30, G:0.11, T:0.37
Consensus pattern (34 bp):
AACTCCGTGACACCTTTTTCTTTTCAAAGCTCAC
Found at i:286446 original size:27 final size:27
Alignment explanation
Indices: 286403--286543 Score: 97
Period size: 27 Copynumber: 5.0 Consensus size: 27
286393 ACCTTTTTCT
* * *
286403 TTTCAAAGCTCAGAACTCCGTGACACC
1 TTTCAAAGCCCACAACTCCGTGGCACC
*
286430 TTTCAAAGCCCACAACTCTGTGGC-CTC
1 TTTCAAAGCCCACAACTCCGTGGCAC-C
* *** *
286457 TTTTAAATTTC-CAACTCTGTGGCACTTTTTTC
1 TTTCAAAGCCCACAACTCCGTGGCAC------C
286489 TTTTCAAAGCCCACAACTCCGTGGCACC
1 -TTTCAAAGCCCACAACTCCGTGGCACC
* *
286517 TTTCAAAGCCCACAACACCGTGACACC
1 TTTCAAAGCCCACAACTCCGTGGCACC
286544 CTTTTTCCTT
Statistics
Matches: 90, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
26 13 0.14
27 54 0.60
28 1 0.01
32 2 0.02
33 7 0.08
34 13 0.14
ACGTcount: A:0.26, C:0.34, G:0.13, T:0.28
Consensus pattern (27 bp):
TTTCAAAGCCCACAACTCCGTGGCACC
Found at i:286642 original size:27 final size:27
Alignment explanation
Indices: 286583--286635 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
286573 GCACCTTTTT
286583 CCTTTTAAGCTCACAACTCCATGGCAC
1 CCTTTTAAGCTCACAACTCCATGGCAC
* *
286610 CCTTTTAAGTTCACAACTCCGTGGCA
1 CCTTTTAAGCTCACAACTCCATGGCA
286636 TCTTTTTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.34, G:0.13, T:0.28
Consensus pattern (27 bp):
CCTTTTAAGCTCACAACTCCATGGCAC
Found at i:286658 original size:94 final size:95
Alignment explanation
Indices: 286475--286796 Score: 291
Period size: 94 Copynumber: 3.3 Consensus size: 95
286465 TTCCAACTCT
* * *
286475 GTGGCA-CTTTTTTCTTTTCAAAGCCCACAACTCCGTGGCA-CCTTTCAAAGCCCACAACACCGT
1 GTGGCACCTTTTTCCTTTT-AAAGCCCACAACTCCGTGGCACCCTTT-TAAGCCCACAACTCCGT
* * ** *
286538 GACACCCTTTTTC-CTTTTAAGTCCACAACTTC
64 GGCA-TCTTTTTCTCTTCAAAGCCCACAACTTC
* * **
286570 GTGGCACCTTTTTCCTTTT-AAGCTCACAACTCCATGGCACCCTTTTAAGTTCACAACTCCGTGG
1 GTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGG
286634 CATCTTTTTCTCTTCAAAGCCCACAACTTC
66 CATCTTTTTCTCTTCAAAGCCCACAACTTC
* *
286664 GTGGCACC-TTTT-CTTTTCAAAGCCCATAACTCCGTGGCACATTTTTCTTTTCAAAGCCCACAA
1 GTGGCACCTTTTTCCTTTT-AAAGCCCACAACTCCGTGGCAC-----CCTTTT--AAGCCCACAA
* * *
286727 CTCTGTGGCATCTTTTTCTTTTCAAAGCCTACAAC-TC
58 CTCCGTGGCATCTTTTTCTCTTCAAAGCCCACAACTTC
* * *
286764 TGTGGTACAATTTTTCCTTTT-AAGTCCACAACT
1 -GTGGCAC-CTTTTTCCTTTTAAAGCCCACAACT
286797 TTGTGGTACC
Statistics
Matches: 186, Mismatches: 25, Indels: 25
0.79 0.11 0.11
Matches are distributed among these distances:
92 5 0.03
93 11 0.06
94 76 0.41
95 11 0.06
96 11 0.06
99 5 0.03
100 2 0.01
101 46 0.25
102 10 0.05
103 4 0.02
104 5 0.03
ACGTcount: A:0.22, C:0.31, G:0.12, T:0.34
Consensus pattern (95 bp):
GTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGG
CATCTTTTTCTCTTCAAAGCCCACAACTTC
Found at i:286889 original size:27 final size:27
Alignment explanation
Indices: 286849--286906 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
286839 TCATTTTTCA
*
286849 TTTTAAGTCCACAATTCCGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
286876 TTTTAAGTCTACAACTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
286903 TTTT
1 TTTT
286907 TCTTTTTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:286969 original size:27 final size:27
Alignment explanation
Indices: 286919--286974 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
286909 TTTTTTCCTC
*
286919 TTAAGTCCACAACTCCATGTCACCCTT
1 TTAAGTCCACAACTCCATGGCACCCTT
** *
286946 TTAAGTCCACAACTCTGTGGCACCTTT
1 TTAAGTCCACAACTCCATGGCACCCTT
286973 TT
1 TT
286975 CTTTTCAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (27 bp):
TTAAGTCCACAACTCCATGGCACCCTT
Found at i:287128 original size:27 final size:26
Alignment explanation
Indices: 287084--287136 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
287074 TTTCCTCCAA
*
287084 AAGTCCATAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTT
* *
287111 AAGTCCACAATTCTGTGGCACCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTT
287137 CTTTCTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (26 bp):
AAGTCCACAACTCCGTGGCACCTTTT
Found at i:287186 original size:32 final size:32
Alignment explanation
Indices: 287150--287276 Score: 136
Period size: 32 Copynumber: 4.0 Consensus size: 32
287140 TCTAAAATTC
* *
287150 ACACAAGTCGGTGGCAACCTTTTCTAAAGCCT
1 ACACAAGTCGATGGCAACCTCTTCTAAAGCCT
*
287182 ACACAAGTCGATGGCAACC-CTTCTAAAGCCC
1 ACACAAGTCGATGGCAACCTCTTCTAAAGCCT
** *
287213 ACGTAAGTCGATGGCAACCCTCTT-AAAAGCCT
1 ACACAAGTCGATGGCAA-CCTCTTCTAAAGCCT
* *
287245 ACACAAGTCGGTGGC-ATCTCTTTCT-AAGCCT
1 ACACAAGTCGATGGCAACCTC-TTCTAAAGCCT
287276 A
1 A
287277 ATGTCATTGG
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
30 3 0.04
31 35 0.44
32 38 0.48
33 3 0.04
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (32 bp):
ACACAAGTCGATGGCAACCTCTTCTAAAGCCT
Found at i:287401 original size:52 final size:52
Alignment explanation
Indices: 287328--287749 Score: 219
Period size: 52 Copynumber: 7.9 Consensus size: 52
287318 CATATCTTTC
* * * *
287328 TAAGTCAAATAGT-GCTGGCCTTGAATTAGCACATTGGCACATTTTTC-TTTT
1 TAAGTCAAATA-TCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCATCTT
* * * *
287379 ATAAGTCTAATATCGCTAGCCTTGAATCAACATATTGGCACCTTTGTCATCTT
1 -TAAGTCAAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCATCTT
* * * *
287432 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTC-TTTATCA-CTCC
1 TAAGTCAAATATCGCTGGCCTTGAATCAGCATATTGGC-ACATTTGTCATCT-T
* * ** * * * * *
287484 TAAGCCCAATATCATTGACCTTGAATTAGCATATTGACACCTTTTTCATTCTT
1 TAAGTCAAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCA-TCTT
* * * * * * * * *
287537 CTCAATTTTATGTCCAATGTTGCTAGCCTTGAATTAGCACATTGGCACCTTTTTC-TTTCT
1 -T--A----A-GTCAAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCATCT-T
* * * * ** * * *
287597 TAAGTCCAATATTGCTAGCCTTGAATCAGTATATTAACGCCTTTCTCATCTT
1 TAAGTCAAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCATCTT
* * * * *
287649 TGAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATC-TTTATCATCTT
1 TAAGTCAAATATCGCTGGCCTTGAATCAGCATATTGGCA-CATTTGTCATCTT
* * * *
287701 TGAA-TCTAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCAT
1 T-AAGTCAAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCAT
287750 TCTTCTCATC
Statistics
Matches: 293, Mismatches: 57, Indels: 40
0.75 0.15 0.10
Matches are distributed among these distances:
51 5 0.02
52 234 0.80
53 9 0.03
54 3 0.01
56 1 0.00
57 1 0.00
59 3 0.01
60 2 0.01
61 35 0.12
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.37
Consensus pattern (52 bp):
TAAGTCAAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTGTCATCTT
Found at i:287468 original size:104 final size:102
Alignment explanation
Indices: 287328--287749 Score: 337
Period size: 104 Copynumber: 4.0 Consensus size: 102
287318 CATATCTTTC
* * * *
287328 TAAGTCAAATAGT-GCTGGCCTTGAATTAGCACATTGGCACATTTTTCTTTTATAAGTCTAATAT
1 TAAGTCCAATA-TCGCTGGCCTTGAATCAGCACATTGGCAC-TTTATCTTTT-TAAGTCCAATAT
* *
287392 CGCTAGCCTTGAATCAACATATTGGCACCTTTGTCATCTT
63 CGCTAGCCTTGAATCAACATATTGACACCTTTATCATCTT
* * * ** *
287432 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTATCACTCCTAAGCCCAATATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC-ACTTTATC-TTTTTAAGTCCAATATC
* * * * *
287497 -ATTGACCTTGAATTAGCATATTGACACCTTTTTCATTCTT
64 GCTAG-CCTTGAATCAACATATTGACACCTTTATCA-TCTT
* * * * *
287537 CTCAATTTTATGTCCAATGTTGCTAGCCTTGAATTAGCACATTGGCACCTTTTTCTTTCTTAAGT
1 -T--A----A-GTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTATCTTT-TTAAGT
* ** * * *
287602 CCAATATTGCTAGCCTTGAATCAGTATATTAACGCCTTTCTCATCTT
56 CCAATATCGCTAGCCTTGAATCAACATATTGACACCTTTATCATCTT
* * * *
287649 TGAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTATCATCTTTGAA-TCTAATAT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CTTTATC-T-TTTTAAGTCCAATAT
* *
287713 CGCTGGCCTTGAATCAACATATTGGCACCTTTATCAT
63 CGCTAGCCTTGAATCAACATATTGACACCTTTATCAT
287750 TCTTCTCATC
Statistics
Matches: 249, Mismatches: 51, Indels: 36
0.74 0.15 0.11
Matches are distributed among these distances:
103 3 0.01
104 150 0.60
105 11 0.04
106 3 0.01
108 1 0.00
111 1 0.00
112 6 0.02
113 72 0.29
114 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.37
Consensus pattern (102 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACTTTATCTTTTTAAGTCCAATATCGC
TAGCCTTGAATCAACATATTGACACCTTTATCATCTT
Found at i:287725 original size:217 final size:217
Alignment explanation
Indices: 287340--287757 Score: 572
Period size: 217 Copynumber: 1.9 Consensus size: 217
287330 AGTCAAATAG
* *
287340 TGCTGGCCTTGAATTAGCACATTGGCACATTTTTCTTTTATAAGTCTAATATCGCTAGCCTTGAA
1 TGCTAGCCTTGAATTAGCACATTGGCACATTTTTCTTTTATAAGTCCAATATCGCTAGCCTTGAA
** * *
287405 TCAACATATTGGCACCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC
66 TCAACATATTAACACCTTTCTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC
* * * * *
287470 GTCTTTATCACTCCTAAGCCCAATATCATTGACCTTGAATTAGCATATTGACACCTTTTTCATTC
131 ATCTTTATCACTCCTAAGCCCAATATCACTGACCTTGAATCAACATATTGACACCTTTATCATTC
287535 TTCTCAATTTTATGTCCAATGT
196 TTCTCAATTTTATGTCCAATGT
* *
287557 TGCTAGCCTTGAATTAGCACATTGGCACCTTTTTCTTTCT-TAAGTCCAATATTGCTAGCCTTGA
1 TGCTAGCCTTGAATTAGCACATTGGCACATTTTTCTTT-TATAAGTCCAATATCGCTAGCCTTGA
** * * *
287621 ATCAGTATATTAACGCCTTTCTCATCTTTGAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG
65 ATCAACATATTAACACCTTTCTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGG
* * * * * *
287686 CATCTTTATCA-TCTTTGAA-TCTAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCA
130 CATCTTTATCACTC-CT-AAGCCCAATATCACTGACCTTGAATCAACATATTGACACCTTTATCA
287749 TTCTTCTCA
193 TTCTTCTCA
287758 TCTTTAAGCC
Statistics
Matches: 174, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
216 2 0.01
217 169 0.97
218 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (217 bp):
TGCTAGCCTTGAATTAGCACATTGGCACATTTTTCTTTTATAAGTCCAATATCGCTAGCCTTGAA
TCAACATATTAACACCTTTCTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC
ATCTTTATCACTCCTAAGCCCAATATCACTGACCTTGAATCAACATATTGACACCTTTATCATTC
TTCTCAATTTTATGTCCAATGT
Found at i:287791 original size:61 final size:61
Alignment explanation
Indices: 287708--287824 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
287698 CTTTGAATCT
* *
287708 AATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCATTCTTCTCATCTTTAAGCCC
1 AATATCGCTGGCCGTGAATCAACATATTGGCACCTCTATCATTCTTCTCATCTTTAAGCCC
* ** * *
287769 AATATTGCTGGCCGTGTCTCAACATATTGGCACCTCTGTCATTTTTCTCATCTTTA
1 AATATCGCTGGCCGTGAATCAACATATTGGCACCTCTATCATTCTTCTCATCTTTA
287825 TCATCTTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.38
Consensus pattern (61 bp):
AATATCGCTGGCCGTGAATCAACATATTGGCACCTCTATCATTCTTCTCATCTTTAAGCCC
Found at i:287800 original size:217 final size:217
Alignment explanation
Indices: 287357--287803 Score: 533
Period size: 217 Copynumber: 2.1 Consensus size: 217
287347 CTTGAATTAG
* * **
287357 CACATTGGCACATTTTTCTTTTATAAGTCTAATATCGCTAGCCTTGAATCAACATATTGGCACCT
1 CACATTGGCACCTTTTTCTTTTATAAGTCCAATATCGCTAGCCTTGAATCAACATATTAACACCT
* * *
287422 TTGTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTATCACTCCTAA
66 TTCTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTTATCACTCCTAA
* * * * * *
287487 GCCCAATATCATTGACCTTGAATTAGCATATTGACACCTTTTTCATTCTTCTCAATTTTATGTCC
131 GCCCAATATCACTGACCTTGAATCAACATATTGACACCTTTATCATTCTTCTCAATTTTAAGCCC
* * * *
287552 AATGTTGCTAGCCTTGAATTAG
196 AATATTGCTAGCCGTGAATCAA
* ** *
287574 CACATTGGCACCTTTTTCTTTCT-TAAGTCCAATATTGCTAGCCTTGAATCAGTATATTAACGCC
1 CACATTGGCACCTTTTTCTTT-TATAAGTCCAATATCGCTAGCCTTGAATCAACATATTAACACC
* * *
287638 TTTCTCATCTTTGAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTATCA-TCTTT
65 TTTCTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTTATCACTC-CT
* * * * *
287702 GAA-TCTAATATCGCTGGCCTTGAATCAACATATTGGCACCTTTATCATTCTTCTC-ATCTTTAA
129 -AAGCCCAATATCACTGACCTTGAATCAACATATTGACACCTTTATCATTCTTCTCAAT-TTTAA
* **
287765 GCCCAATATTGCTGGCCGTGTCTCAA
192 GCCCAATATTGCTAGCCGTGAATCAA
*
287791 CATATTGGCACCT
1 CACATTGGCACCT
287804 CTGTCATTTT
Statistics
Matches: 193, Mismatches: 33, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
216 4 0.02
217 186 0.96
218 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (217 bp):
CACATTGGCACCTTTTTCTTTTATAAGTCCAATATCGCTAGCCTTGAATCAACATATTAACACCT
TTCTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCATCTTTATCACTCCTAA
GCCCAATATCACTGACCTTGAATCAACATATTGACACCTTTATCATTCTTCTCAATTTTAAGCCC
AATATTGCTAGCCGTGAATCAA
Found at i:291192 original size:13 final size:13
Alignment explanation
Indices: 291174--291198 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291164 ATTCGCATTC
291174 ATATTTTCAAAAT
1 ATATTTTCAAAAT
291187 ATATTTTCAAAA
1 ATATTTTCAAAA
291199 ATTTTGAAGG
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATTTTCAAAAT
Found at i:296574 original size:79 final size:79
Alignment explanation
Indices: 296304--296849 Score: 542
Period size: 79 Copynumber: 7.0 Consensus size: 79
296294 TTTTCTGATG
* * * * * * * *
296304 AGAAATTTAATATTTTGGAGATAATAGCGGGGTTGGAGTATCCCTTTGAAAATAATGGGGTTGAA
1 AGAAA-TTAATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCTTCGAAAATAACGGGGTTGGA
* * *
296369 GTATCTCCGGTTGTGA
65 GTATCCCCGATTAT-A
** * * * * *
296385 A-AAATCGATGA--TTAGGAAATAAAATCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTAG
1 AGAAATTAAT-ATTTTA-GAAATAAAATCGGGGTTAGAGTATCCCTTCGAAAATAACGGGGTTGG
*
296447 AGTATCTCCG-----A
64 AGTATCCCCGATTATA
* * *
296458 A-AAATTAATATTTTAGAAATAAGATCGGGGTTAGAGTATCCGTTCGGAAATAACGGGGTTGGAG
1 AGAAATTAATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCTTCGAAAATAACGGGGTTGGAG
296522 TATCCCCGATTATA
66 TATCCCCGATTATA
* * * * *
296536 AGAAATTAATATTTTAGAAAGAAAA-CTGGGGTTTGAGTATTCCTTTGAAAATAACGGGGTTAGA
1 AGAAATTAATATTTTAGAAATAAAATC-GGGGTTAGAGTATCCCTTCGAAAATAACGGGGTTGGA
*
296600 GTATCCCCGATTGTGA
65 GTATCCCCGATTAT-A
** * * * *
296616 AG-AATCGATGA-TTTAGAAATAAAATCAGGATTGGAGTATCCTTTCGAAAATAACGGGGTTGGA
1 AGAAATTAAT-ATTTTAGAAATAAAATCGGGGTTAGAGTATCCCTTCGAAAATAACGGGGTTGGA
*
296679 GTATCCCCGATTATG
65 GTATCCCCGATTATA
* * * * *
296694 AGAAATTAATATTTTGGAAATAAGATCGGGGCTAGAGTATCCCCTCGGAAATAACGGGGTTGGAG
1 AGAAATTAATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCTTCGAAAATAACGGGGTTGGAG
296759 TATCCCCGATTATA
66 TATCCCCGATTATA
* *
296773 AGAAATTAATATTTTAGAAATAAAACCGGGGTTTGAGTATCCCCTT-GAAAATAACGGGGTTGGA
1 AGAAATTAATATTTTAGAAATAAAATCGGGGTTAGAGTAT-CCCTTCGAAAATAACGGGGTTGGA
*
296837 GTATCTCCGATTA
65 GTATCCCCGATTA
296850 AGAAAAATTG
Statistics
Matches: 385, Mismatches: 63, Indels: 36
0.80 0.13 0.07
Matches are distributed among these distances:
72 1 0.00
73 58 0.15
74 3 0.01
78 8 0.02
79 301 0.78
80 13 0.03
81 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (79 bp):
AGAAATTAATATTTTAGAAATAAAATCGGGGTTAGAGTATCCCTTCGAAAATAACGGGGTTGGAG
TATCCCCGATTATA
Found at i:296781 original size:237 final size:230
Alignment explanation
Indices: 296304--296857 Score: 768
Period size: 237 Copynumber: 2.4 Consensus size: 230
296294 TTTTCTGATG
* * * * * * *
296304 AGAAATTTAATATTTTGGAGATAATAGCGGGGTTGGAGTATCCCTTTGAAAATAATGGGGTTGAA
1 AGAAA-TTAATATTTTAGAAAGAAAACCGGGGTTTGAGTATCCCTTTGAAAATAACGGGGTTG-A
* * *
296369 GTATCTCCGGTTGTGAAAAATCGATGATTAGGAAATAAAATCGGGATTGGAGTATCCCCTCGGAA
64 GTATCTCCGATTGTGAAAAATCGATGATTAGGAAATAAAATCAGGATTGGAGTATCCCCTCGAAA
* *
296434 ATAACGGGGTTAGAGTATCTCCGAAAAATTAATATTTTAGAAATAAGATCGGGGTTAGAGTATCC
129 ATAACGGGGTTAGAGTATCCCCGAAAAATTAATATTTTAGAAATAAGATCGGGGCTAGAGTATCC
**
296499 GTTCGGAAATAACGGGGTTGGAGTATCCCCGATTATA
194 CCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATA
* *
296536 AGAAATTAATATTTTAGAAAGAAAACTGGGGTTTGAGTATTCCTTTGAAAATAACGGGGTTAGAG
1 AGAAATTAATATTTTAGAAAGAAAACCGGGGTTTGAGTATCCCTTTGAAAATAACGGGGTT-GAG
* * **
296601 TATCCCCGATTGTGAAGAATCGATGATTTA-GAAATAAAATCAGGATTGGAGTATCCTTTCGAAA
65 TATCTCCGATTGTGAAAAATCGATGA-TTAGGAAATAAAATCAGGATTGGAGTATCCCCTCGAAA
* *
296665 ATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTGGAAATAAGATCGGGGCTAGA
129 ATAACGGGGTTAGAGTATCCCCG---A--A-AAATTAATATTTTAGAAATAAGATCGGGGCTAGA
296730 GTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATA
188 GTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATA
* *
296773 AGAAATTAATATTTTAGAAATAAAACCGGGGTTTGAGTATCCCCTTGAAAATAACGGGGTTGGAG
1 AGAAATTAATATTTTAGAAAGAAAACCGGGGTTTGAGTATCCCTTTGAAAATAACGGGGTT-GAG
**
296838 TATCTCCGATTAAGAAAAAT
65 TATCTCCGATTGTGAAAAAT
296858 TGAGGAACTT
Statistics
Matches: 283, Mismatches: 31, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
231 123 0.43
232 9 0.03
234 1 0.00
236 1 0.00
237 149 0.53
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (230 bp):
AGAAATTAATATTTTAGAAAGAAAACCGGGGTTTGAGTATCCCTTTGAAAATAACGGGGTTGAGT
ATCTCCGATTGTGAAAAATCGATGATTAGGAAATAAAATCAGGATTGGAGTATCCCCTCGAAAAT
AACGGGGTTAGAGTATCCCCGAAAAATTAATATTTTAGAAATAAGATCGGGGCTAGAGTATCCCC
TCGGAAATAACGGGGTTGGAGTATCCCCGATTATA
Found at i:299234 original size:34 final size:33
Alignment explanation
Indices: 299191--299255 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
299181 AACTTCCTAG
*
299191 ATGTATCGATACAAAGAATAGATGTATCGATATA
1 ATGTATCGATACAAAGAA-AAATGTATCGATATA
*
299225 ATGTATCGATACACAGAAAAATGTATCGATA
1 ATGTATCGATACAAAGAAAAATGTATCGATA
299256 CATTTCCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 12 0.41
34 17 0.59
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATATA
Found at i:300213 original size:61 final size:60
Alignment explanation
Indices: 300105--300880 Score: 842
Period size: 61 Copynumber: 13.2 Consensus size: 60
300095 ATAAAGTGCA
** * ** *
300105 TCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCATGGGGGCTTTGAAACGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAA-GGAAAGGCG
* * * * **
300166 TCCTACTTTTTGGGGACTAGAAGGTGCCACCAACTCATGTGGGCTTTGAAATGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAA-GGAAAGGCG
* *
300227 TCCTGCTTTTTGGGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGGAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAGGCG
* *
300288 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAGAGAGAAA-GCA
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-GAAAGGCG
* ** *
300349 TCCTGCT-TCTTGAGGACAGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAGGCG
1 TCCTGCTCT-TTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
*
300409 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGGAAATGCG
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAGGAAAGGCG
* * * *
300470 TCCTGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGTGTGGGCTTT-ACAGAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGA-A-AGGAAAGGCG
* ** * *
300531 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAA------TGGGCTTTGAAAGGAGAGGCA
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
* * *
300585 TCCTGCTCTTTGAGGGCTGGAATGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA-GCA
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-GAAAGGCG
* **
300646 TCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTT-----GAAAGGCG
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
* *
300701 TCCTACTCTTTGAGGACTGGGAA-GTGCCACCAACTTATGTGGGCTTT---A--AAAGGCG
1 TCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
* * *
300756 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTT-----GAAAGGCA
1 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
300811 TCCTGCTCTTTGAGGACTGGGAA-GTGCCACCAACTTGTGTGGGCTTT---A--AAAGGCG
1 TCCTGCTCTTTGAGGACT-GGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
300866 TCCTGCTCTTTGAGG
1 TCCTGCTCTTTGAGG
300881 GCTAAAAAGT
Statistics
Matches: 632, Mismatches: 59, Indels: 54
0.85 0.08 0.07
Matches are distributed among these distances:
54 43 0.07
55 163 0.26
56 8 0.01
59 4 0.01
60 59 0.09
61 345 0.55
62 10 0.02
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (60 bp):
TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAGGCG
Found at i:300473 original size:182 final size:180
Alignment explanation
Indices: 300102--300857 Score: 903
Period size: 182 Copynumber: 4.3 Consensus size: 180
300092 AAAATAAAGT
** ** * * *
300102 GCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCATGGGGGCTTTGAAACG-GAAAGGCG
1 GCATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAGA-GAGAAA-GCA
* * ** * *
300166 TCCTACTTTTTGGGGACTA-GAAGGTGCCACCAACTCATGTGGGCTTTGAAATGGAAAGGCGTCC
64 TCCTACTCTTTGAGGAC-AGGAAAATGCCACCAACTTATGTGGGCTTTGAAA-GGAGAGGCGTCC
* *
300230 TGCTTTTTGGGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGGAAA
127 TGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGGAAA
* *
300284 GGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAGAGAGAAAGCA
1 -GCATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTG-AGAGAGAAAGCA
* *
300349 TCCTGCT-TCTTGAGGACAGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGAGAGGCGTCCT
64 TCCTACTCT-TTGAGGACAGGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGAGAGGCGTCCT
300413 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGGAAA
128 GCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGGAAA
* * * * *
300466 TGCGTCCTGCTCTTTGAGGACTGGAAGGTGCCACTAACTTGTGTGGGCTTTACAGAGAAAAAGCA
1 -GCATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT-GAGAGAGAAAGCA
* * * *
300531 TCCTGCTCTTTGAGGACTGAAAAATGCCACC-A---A--TGGGCTTTGAAAGGAGAGGCATCCTG
64 TCCTACTCTTTGAGGACAGGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGAGAGGCGTCCTG
* *
300590 CTCTTTGAGGGCTGGAATGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA
129 CTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAG-GAAA
* * *
300643 GCATCCTGCTCTTTGAGGATTGGAAAATGCCACCAACTTGTGTGGGCTTTGA-A-AG---GCGTC
1 GCATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAGAGAGAAAGCATC
* * *
300703 CTACTCTTTGAGGACTGGGAAGTGCCACCAACTTATGTGGGCTTT--AA--A-AGGCGTCCTGCT
66 CTACTCTTTGAGGACAGGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGAGAGGCGTCCTGCT
* *
300763 CTTTGAGGACTGAAAGGTGCCACCAACTCGTGTGGGCTTTG-AAA-G---
131 CTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGGAAA
*
300808 GCATCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTT
1 GCATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTT
300858 AAAAGGCGTC
Statistics
Matches: 512, Mismatches: 48, Indels: 44
0.85 0.08 0.07
Matches are distributed among these distances:
165 47 0.09
168 1 0.00
170 32 0.06
171 49 0.10
172 1 0.00
173 1 0.00
174 4 0.01
175 1 0.00
176 124 0.24
177 4 0.01
181 1 0.00
182 152 0.30
183 89 0.17
184 6 0.01
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (180 bp):
GCATCCTGCTCTTTGAGGACTGGAAAGTGCCACCAACTTGTGTGGGCTTTGAGAGAGAAAGCATC
CTACTCTTTGAGGACAGGAAAATGCCACCAACTTATGTGGGCTTTGAAAGGAGAGGCGTCCTGCT
CTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGGAAA
Found at i:301874 original size:9 final size:8
Alignment explanation
Indices: 301862--301924 Score: 60
Period size: 8 Copynumber: 8.0 Consensus size: 8
301852 TTTTTCTCTT
301862 TTTTCTTTG
1 TTTT-TTTG
*
301871 TTTTGTT-
1 TTTTTTTG
301878 TTTTTTTG
1 TTTTTTTG
301886 TTTTTTT-
1 TTTTTTTG
301893 TTGTTTTT-
1 TT-TTTTTG
*
301901 TTGTTTTG
1 TTTTTTTG
*
301909 TTTTTTGG
1 TTTTTTTG
301917 TTTTTTTG
1 TTTTTTTG
301925 AAAAAGAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
7 12 0.27
8 29 0.64
9 4 0.09
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (8 bp):
TTTTTTTG
Found at i:301875 original size:5 final size:5
Alignment explanation
Indices: 301867--301912 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
301857 CTCTTTTTTC
* *
301867 TTTGT TTTGT TTTTT TTTGT TTTTT TTTG- TTT-T TTTGT TTTGT TTT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTT
301913 TTGGTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
4 6 0.17
5 29 0.83
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (5 bp):
TTTGT
Found at i:301879 original size:15 final size:15
Alignment explanation
Indices: 301861--301907 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
301851 TTTTTTCTCT
301861 TTTTTCTTTGTTTTG
1 TTTTTCTTTGTTTTG
*
301876 TTTTTTTTTGTTTT-
1 TTTTTCTTTGTTTTG
*
301890 TTTTTGTTT-TTTTG
1 TTTTTCTTTGTTTTG
301904 TTTT
1 TTTT
301908 GTTTTTTGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 4 0.14
14 12 0.41
15 13 0.45
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (15 bp):
TTTTTCTTTGTTTTG
Found at i:301879 original size:25 final size:25
Alignment explanation
Indices: 301850--301913 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
301840 TCTTCTTCTT
*
301850 TTTTTTTCTCTTTTTTCTTTGTTTTG
1 TTTTTTTCT-GTTTTTCTTTGTTTTG
* *
301876 TTTTTTTTTGTTTTTTTTTGTTTT-
1 TTTTTTTCTGTTTTTCTTTGTTTTG
*
301900 TTTGTTT-TGTTTTT
1 TTTTTTTCTGTTTTT
301914 TGGTTTTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 7 0.21
24 6 0.18
25 13 0.38
26 8 0.24
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (25 bp):
TTTTTTTCTGTTTTTCTTTGTTTTG
Found at i:301880 original size:28 final size:28
Alignment explanation
Indices: 301848--301913 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
301838 ATTCTTCTTC
301848 TTTTTTTTTCTCTTTTTTCT-TTGTTTTG
1 TTTTTTTTTCT-TTTTTTCTGTTGTTTTG
* * *
301876 TTTTTTTTTGTTTTTTTTTGTTTTTTTG
1 TTTTTTTTTCTTTTTTTCTGTTGTTTTG
301904 TTTTGTTTTT
1 TTTT-TTTTT
301914 TGGTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 7 0.21
28 21 0.64
29 5 0.15
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (28 bp):
TTTTTTTTTCTTTTTTTCTGTTGTTTTG
Found at i:301883 original size:20 final size:18
Alignment explanation
Indices: 301848--301924 Score: 73
Period size: 19 Copynumber: 4.0 Consensus size: 18
301838 ATTCTTCTTC
* *
301848 TTTTTTTTTCTCTTTTTTC
1 TTTTTTTTT-TTTTTTTTG
*
301867 TTTGTTTTGTTTTTTTTTG
1 TTT-TTTTTTTTTTTTTTG
*
301886 TTTTTTTTTGTTTTTTTG
1 TTTTTTTTTTTTTTTTTG
301904 TTTTGTTTTTTGGTTTTTTTG
1 TTTT-TTTTTT--TTTTTTTG
301925 AAAAAGAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
18 17 0.35
19 18 0.38
20 5 0.10
21 8 0.17
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTTTTTTTTTG
Found at i:301919 original size:13 final size:13
Alignment explanation
Indices: 301891--301920 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
301881 TTTTGTTTTT
*
301891 TTTTGTTTTTTTG
1 TTTTGTTTTTTGG
301904 TTTTGTTTTTTGG
1 TTTTGTTTTTTGG
301917 TTTT
1 TTTT
301921 TTTGAAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (13 bp):
TTTTGTTTTTTGG
Found at i:301923 original size:1 final size:1
Alignment explanation
Indices: 301848--301914 Score: 53
Period size: 1 Copynumber: 67.0 Consensus size: 1
301838 ATTCTTCTTC
* * * * * * * * *
301848 TTTTTTTTTCTCTTTTTTCTTTGTTTTGTTTTTTTTTGTTTTTTTTTGTTTTTTTGTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
301913 TT
1 TT
301915 GGTTTTTTTG
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.04, G:0.09, T:0.87
Consensus pattern (1 bp):
T
Found at i:314302 original size:79 final size:78
Alignment explanation
Indices: 314195--314765 Score: 650
Period size: 79 Copynumber: 7.2 Consensus size: 78
314185 GAGATAATAG
* * * * **
314195 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGA
1 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAAT-A
314260 -TTAGGAAATAAAAT
65 TTTA-GAAATAAAAT
* *
314274 CGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATAT
1 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATA-
*
314339 TTTAGAAATAAGAT
65 TTTAGAAATAAAAT
* * * *
314353 CGGGGTTAGAGTATTCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTAT-AAGAAATTAATA
1 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAA-AAATTAATA
*
314417 TTTTATAAATAAAAT
65 -TTTAGAAATAAAAT
* * * * **
314432 CAGGG-TTAGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAATCGATG
1 C-GGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAAT-
314496 ATTTAGAAATAAAAT
64 ATTTAGAAATAAAAT
* *
314511 CGGGATTGGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTATGAGAAATTAATAT
1 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATA-
* *
314576 TTTGGAAATAAGAT
65 TTTAGAAATAAAAT
* * * *
314590 CGGGGTTAGAGTATCCCCTCAAAAACAACGGGGTTGGAGTATCCCCGATTAT-AAGAAATTAATA
1 CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAA-AAATTAATA
*
314654 TTTTAGAAATAAAAC
65 -TTTAGAAATAAAAT
* * * * ** *
314669 CGAGG-TTGGAGTATCCCTTTGAAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTG
1 CG-GGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATA
*
314733 TTTCGAAAATAAAAT
65 TTTAG-AAATAAAAT
314748 C-GGAGTTGGAGTATCCCC
1 CGGGA-TTGGAGTATCCCC
314766 GATTGTGAAA
Statistics
Matches: 423, Mismatches: 55, Indels: 28
0.84 0.11 0.06
Matches are distributed among these distances:
77 2 0.00
78 11 0.03
79 398 0.94
80 12 0.03
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.27
Consensus pattern (78 bp):
CGGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATAT
TTAGAAATAAAAT
Found at i:314589 original size:237 final size:235
Alignment explanation
Indices: 314168--314765 Score: 914
Period size: 237 Copynumber: 2.5 Consensus size: 235
314158 TTTCCCGATG
* * * *
314168 AGAAATTTAATATTTTGGAGATAATAGCGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGA
1 AGAAA-TTAATATTTTAGAAATAA-AACAGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGA
* *
314233 GTATCCCCGGTTGTGAAAAATCGATGA-TTAGGAAATAAAATCGGGATTGGAGTATCCCCTCGGA
64 GTATCCCCGATTGTG-AAAATCGATGATTTA-GAAATAAAATCGGGATTGGAGTATCCCCTCGAA
314297 AATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAGATCGGGGTTAG
127 AATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAGATCGGGGTTAG
* ** *
314362 AGTATTCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATA
192 AGTATCCCCTCAAAAACAACGGGGTTGGAGTATCCCCGATTATA
* *
314406 AGAAATTAATATTTTATAAATAAAATCAGGGTTAGAGTATCCCCTTGAAAATAACGGGGTTGGAG
1 AGAAATTAATATTTTAGAAATAAAA-CAGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAG
314471 TATCCCCGATTGTGAAGAATCGATGATTTAGAAATAAAATCGGGATTGGAGTATCCCCTCGAAAA
65 TATCCCCGATTGTGAA-AATCGATGATTTAGAAATAAAATCGGGATTGGAGTATCCCCTCGAAAA
* *
314536 TAATGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTGGAAATAAGATCGGGGTTAGAG
129 TAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAGATCGGGGTTAGAG
314601 TATCCCCTCAAAAACAACGGGGTTGGAGTATCCCCGATTATA
194 TATCCCCTCAAAAACAACGGGGTTGGAGTATCCCCGATTATA
* *
314643 AGAAATTAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCTTTGAAAATAACGGGGTTGGAG
1 AGAAATTAATATTTTAGAAATAAAACAG-GGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAG
* * *
314708 TATCCCCGATTGTGGAAAATTGGTG-TTTCGAAAATAAAATC-GGAGTTGGAGTATCCCC
65 TATCCCCGATTGT-GAAAATCGATGATTTAG-AAATAAAATCGGGA-TTGGAGTATCCCC
314766 GATTGTGAAA
Statistics
Matches: 332, Mismatches: 21, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
236 12 0.04
237 309 0.93
238 11 0.03
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.28
Consensus pattern (235 bp):
AGAAATTAATATTTTAGAAATAAAACAGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGT
ATCCCCGATTGTGAAAATCGATGATTTAGAAATAAAATCGGGATTGGAGTATCCCCTCGAAAATA
ACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTTAGAAATAAGATCGGGGTTAGAGTA
TCCCCTCAAAAACAACGGGGTTGGAGTATCCCCGATTATA
Found at i:317154 original size:13 final size:13
Alignment explanation
Indices: 317136--317161 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
317126 CAAAGAATAG
317136 ATGTATCGATACA
1 ATGTATCGATACA
317149 ATGTATCGATACA
1 ATGTATCGATACA
317162 CAGAAAAATA
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:317158 original size:34 final size:33
Alignment explanation
Indices: 317115--317181 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 33
317105 AACTTCCTAG
* *
317115 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAA-AAATATATCGATACA
*
317149 ATGTATCGATACACAGAAAAATATATCGATACA
1 ATGTATCGATACAAAGAAAAATATATCGATACA
317182 TTTCCTTGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 13 0.43
34 17 0.57
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.25
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATATATCGATACA
Found at i:317237 original size:19 final size:20
Alignment explanation
Indices: 317213--317266 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
317203 AGCGATACAT
*
317213 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTGAA
**
317232 TGTATCGATACATTTACTGAA
1 TGTATCGATACA-AAACTGAA
317253 TGTATCGATACAAA
1 TGTATCGATACAAA
317267 TTATTGGAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACAAAACTGAA
Found at i:317345 original size:21 final size:21
Alignment explanation
Indices: 317321--317398 Score: 147
Period size: 21 Copynumber: 3.7 Consensus size: 21
317311 ACATTTGTAG
317321 AATGTATCGATACATTCCACA
1 AATGTATCGATACATTCCACA
*
317342 AATGTATCGATATATTCCACA
1 AATGTATCGATACATTCCACA
317363 AATGTATCGATACATTCCACA
1 AATGTATCGATACATTCCACA
317384 AATGTATCGATACAT
1 AATGTATCGATACAT
317399 CTGGATAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (21 bp):
AATGTATCGATACATTCCACA
Found at i:318784 original size:34 final size:33
Alignment explanation
Indices: 318741--318810 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
318731 CCGTTACAAG
*
318741 CAATGTATCGATACAATT-TCATCATGTATCGAAA
1 CAATGTATCGATAC-ATTATC-CCATGTATCGAAA
*
318775 CAATGTATCGATACATTATCCCATGTATCGATA
1 CAATGTATCGATACATTATCCCATGTATCGAAA
318808 CAA
1 CAA
318811 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 17 0.52
34 16 0.48
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (33 bp):
CAATGTATCGATACATTATCCCATGTATCGAAA
Found at i:318883 original size:19 final size:20
Alignment explanation
Indices: 318840--318893 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
318830 TGCCAATCTT
**
318840 ATGTATCGATACAATTGTCC
1 ATGTATCGATACAATTGAAC
318860 ATGTATCGATACAATT-AAC
1 ATGTATCGATACAATTGAAC
318879 ATGTATCGATACAAT
1 ATGTATCGATACAAT
318894 GTATCGATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACAATTGAAC
Found at i:318897 original size:13 final size:13
Alignment explanation
Indices: 318879--318905 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
318869 TACAATTAAC
318879 ATGTATCGATACA
1 ATGTATCGATACA
318892 ATGTATCGATACA
1 ATGTATCGATACA
318905 A
1 A
318906 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:320350 original size:51 final size:51
Alignment explanation
Indices: 320223--320358 Score: 148
Period size: 51 Copynumber: 2.6 Consensus size: 51
320213 AAATTGGTAT
* *** *
320223 TTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATTAAAGGAAAATTGGTG
1 TTTTGGAAATAAAATCGG-GTTGGAGTATCCCCGATTAAAGAAAAATCAATA
* * *
320275 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCGATT-ATGAAAAATCAATA
1 TTTTGGAAATAAAATC-GGGTTGGAGTATCCCCGATTAAAGAAAAATCAATA
* *
320326 TTTTGGAAATAAAGTCGGGATTGGAGTAGCCCC
1 TTTTGGAAATAAAATCGGG-TTGGAGTATCCCC
320359 TCAGAAATAA
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
50 3 0.04
51 33 0.47
52 32 0.46
53 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (51 bp):
TTTTGGAAATAAAATCGGGTTGGAGTATCCCCGATTAAAGAAAAATCAATA
Found at i:320377 original size:28 final size:27
Alignment explanation
Indices: 320341--320407 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
320331 GAAATAAAGT
*
320341 CGGGATTGGAGTAGCCCCTCA-GAAATAA
1 CGGGGTTGGAGTAGCCCC-CATG-AATAA
* * *
320369 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTAGCCCCCATGAATAA
320396 CGGGGTTGGAGT
1 CGGGGTTGGAGT
320408 GTCCCCGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 17 0.50
28 17 0.50
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (27 bp):
CGGGGTTGGAGTAGCCCCCATGAATAA
Found at i:320503 original size:51 final size:53
Alignment explanation
Indices: 320400--320522 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 53
320390 GATTAACGGG
* * * *
320400 GTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTG-TTTTTGAAAATAAAATCGGA
320454 GTTGGAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAAAATAAAATCGGA
*
320505 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
320523 GTGGAGAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 35 0.56
52 2 0.03
53 8 0.13
54 18 0.29
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAAAATAAAATCGGA
Found at i:322894 original size:13 final size:13
Alignment explanation
Indices: 322876--322901 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
322866 ACAAAGATCC
322876 ATGTATCGATACA
1 ATGTATCGATACA
322889 ATGTATCGATACA
1 ATGTATCGATACA
322902 CAGAAAAATG
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:322897 original size:33 final size:33
Alignment explanation
Indices: 322855--322921 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
322845 AAAATTTCCA
***
322855 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
322888 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
322921 A
1 A
322922 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:323038 original size:21 final size:20
Alignment explanation
Indices: 323012--323090 Score: 95
Period size: 21 Copynumber: 3.8 Consensus size: 20
323002 GTTGGGACCC
323012 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTA-AA
* *
323033 TGTATCGATACATTCCGCAAA
1 TGTATCGATACATT-TGTAAA
**
323054 TGTATCGATACATTCTACAAA
1 TGTATCGATACATT-TGTAAA
323075 TGTATCGATACATTTG
1 TGTATCGATACATTTG
323091 GATAATTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 1 0.02
21 49 0.94
22 2 0.04
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATTTGTAAA
Found at i:323894 original size:20 final size:20
Alignment explanation
Indices: 323871--323917 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 20
323861 TTTAATTGTG
*
323871 TTTAATTATACTGCTAGATT
1 TTTAACTATACTGCTAGATT
323891 TTTACAAACTATACTGCTAGATT
1 TTT---AACTATACTGCTAGATT
323914 TTTA
1 TTTA
323918 CACATAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
20 4 0.17
23 19 0.83
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.47
Consensus pattern (20 bp):
TTTAACTATACTGCTAGATT
Found at i:324768 original size:21 final size:21
Alignment explanation
Indices: 324736--324778 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
324726 TGTATCATAC
324736 ATAATATAAATTACATAATAT
1 ATAATATAAATTACATAATAT
* *
324757 ATAA-ATACAATTATATAGTAT
1 ATAATATA-AATTACATAATAT
324778 A
1 A
324779 CTTGTCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAATATAAATTACATAATAT
Found at i:330222 original size:23 final size:23
Alignment explanation
Indices: 330187--330239 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
330177 AACGAAGCAT
* *
330187 TTTTAAT-TTTATA-TTATTAATA
1 TTTTAATATATATACTT-TTAAAA
330209 TTTTAATATATATACTTTTAAAA
1 TTTTAATATATATACTTTTAAAA
*
330232 TTATAATA
1 TTTTAATA
330240 AATAAGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 7 0.27
23 17 0.65
24 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTAATATATATACTTTTAAAA
Found at i:330253 original size:20 final size:21
Alignment explanation
Indices: 330228--330271 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
330218 ATATACTTTT
330228 AAAATTA-TAATAA-ATAAGAA
1 AAAATTATTAATAATATAA-AA
330248 AAAATTATTAATAATATAAAA
1 AAAATTATTAATAATATAAAA
330269 AAA
1 AAA
330272 TTTAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 11 0.50
22 4 0.18
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
AAAATTATTAATAATATAAAA
Found at i:332228 original size:20 final size:19
Alignment explanation
Indices: 332200--332248 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
332190 CAAATTTTAT
*
332200 ATAAATATAATATCTAAAAA
1 ATAAATATAA-AACTAAAAA
*
332220 ATAATTATAAAACTAAAAA
1 ATAAATATAAAACTAAAAA
332239 ATAAATATAA
1 ATAAATATAA
332249 CACGAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
ATAAATATAAAACTAAAAA
Found at i:334176 original size:19 final size:19
Alignment explanation
Indices: 334147--334184 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
334137 GCCATATTAC
334147 TAAAAAAACT-ATTTTTTA
1 TAAAAAAACTAATTTTTTA
334165 TAAAAAATACTAATTTTTTA
1 TAAAAAA-ACTAATTTTTTA
334185 ATTTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAAAAACTAATTTTTTA
Found at i:337888 original size:2 final size:2
Alignment explanation
Indices: 337883--337910 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
337873 GAATCATGTA
337883 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
337911 TTACAATTTA
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:338463 original size:2 final size:2
Alignment explanation
Indices: 338458--338509 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
338448 ATATATGTGC
*
338458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
338500 AT AT AT AT AT
1 AT AT AT AT AT
338510 GCACCCACCT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:338759 original size:24 final size:24
Alignment explanation
Indices: 338713--338762 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
338703 ATTTATTAAA
*
338713 ATAATAAAAATAAAATTAAATATG
1 ATAATAAAAATAAAATAAAATATG
*
338737 ATAA-AAAAATATAATAAAGATATG
1 ATAATAAAAATAAAATAAA-ATATG
338761 AT
1 AT
338763 TGTGTTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (24 bp):
ATAATAAAAATAAAATAAAATATG
Found at i:338872 original size:14 final size:15
Alignment explanation
Indices: 338849--338877 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
338839 TTTAATAAGT
338849 TTTTTAAAATTTAAA
1 TTTTTAAAATTTAAA
338864 TTTTT-AAATTTAAA
1 TTTTTAAAATTTAAA
338878 AATAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTTAAAATTTAAA
Found at i:342293 original size:81 final size:81
Alignment explanation
Indices: 342071--342293 Score: 245
Period size: 78 Copynumber: 2.8 Consensus size: 81
342061 TTGGGTTAAA
* * * *
342071 CTGTGGTATCATAGATTTATGCTATGGTGTTGATCTAAGTTGACTTGTACGAATTGCATTTGTAA
1 CTGTGGTATCATAAAGTTATGTTATGGTGTTGATCTAAGTTGACTTGTATGAATTGCATTTGTAA
* *
342136 TCTACTTGGGGTGAAG
66 TCTACTTGAGCTGAAG
* * * * * *
342152 CTGTGCTATC-T-TAGGT-TGTTATGGTGTTGATCTAAGTTTACTTGAATGAATTGCACTTGTAA
1 CTGTGGTATCATAAAGTTATGTTATGGTGTTGATCTAAGTTGACTTGTATGAATTGCATTTGTAA
* * *
342214 TCTAGTTGAGCTTATG
66 TCTACTTGAGCTGAAG
** * * *
342230 CTGTGGTATCATAAAGTTATGTTATGGTGTCAATGTTAGTTGACTTGTATGAATTGCTTTTGTA
1 CTGTGGTATCATAAAGTTATGTTATGGTGTTGATCTAAGTTGACTTGTATGAATTGCATTTGTA
342294 TTTAGAGTTT
Statistics
Matches: 114, Mismatches: 25, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
78 61 0.54
79 3 0.03
80 4 0.04
81 46 0.40
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.43
Consensus pattern (81 bp):
CTGTGGTATCATAAAGTTATGTTATGGTGTTGATCTAAGTTGACTTGTATGAATTGCATTTGTAA
TCTACTTGAGCTGAAG
Found at i:345767 original size:22 final size:21
Alignment explanation
Indices: 345739--345789 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
345729 ATTTAATTCT
345739 AATAATTTTTAAAAAATTTAAA
1 AATAATTTTTAAAAAA-TTAAA
*
345761 AATAATTTTTTAAAAATTAAA
1 AATAATTTTTAAAAAATTAAA
*
345782 AATTATTT
1 AATAATTT
345790 ATATTTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 12 0.44
22 15 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAATTTTTAAAAAATTAAA
Found at i:345775 original size:21 final size:22
Alignment explanation
Indices: 345739--345789 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
345729 ATTTAATTCT
*
345739 AATAATTTTTAAAAAATTTAAA
1 AATAATTTTTAAAAAAATTAAA
*
345761 AATAATTTTT-TAAAAATTAAA
1 AATAATTTTTAAAAAAATTAAA
*
345782 AATTATTT
1 AATAATTT
345790 ATATTTTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTTAAAAAAATTAAA
Found at i:346516 original size:22 final size:23
Alignment explanation
Indices: 346491--346548 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
346481 TAATAATAAG
346491 TTAATAATTAATGTATAAA-A-TA
1 TTAATAATTAATGT-TAAATATTA
* *
346513 TTAAAAATAAATGTTAAATATTA
1 TTAATAATTAATGTTAAATATTA
346536 TTAAATAATTAAT
1 TT-AATAATTAAT
346549 AATATTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.14
22 13 0.45
23 4 0.14
24 8 0.28
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (23 bp):
TTAATAATTAATGTTAAATATTA
Found at i:346806 original size:2 final size:2
Alignment explanation
Indices: 346762--346798 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
346752 TTTAATAAAG
346762 AT AT AT 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 AT AT AT A
346799 GCTATATAGA
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.