Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 159 of 210
Found at i:48117854 original size:29 final size:29
Alignment explanation
Indices: 48117821--48117876 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
48117811 AAAATATTAG
48117821 TTAACCTAA-ATTAACCTAATGGAATTTAA
1 TTAACCTAAGA-TAACCTAATGGAATTTAA
*
48117850 TTAACCTAAGATATCCTAATGGAATTT
1 TTAACCTAAGATAACCTAATGGAATTT
48117877 CCTATTCCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (29 bp):
TTAACCTAAGATAACCTAATGGAATTTAA
Found at i:48117925 original size:19 final size:19
Alignment explanation
Indices: 48117901--48117937 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
48117891 CGGCCTATGA
48117901 TCAATTAAATCCCTAATTG
1 TCAATTAAATCCCTAATTG
* *
48117920 TCAATTAAGTCGCTAATT
1 TCAATTAAATCCCTAATT
48117938 ACCCTCAACT
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:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (19 bp):
TCAATTAAATCCCTAATTG
Found at i:48125390 original size:13 final size:15
Alignment explanation
Indices: 48125362--48125394 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
48125352 GTTCAAGTCA
48125362 TTTTATGTTATTTTG
1 TTTTATGTTATTTTG
48125377 TTTTAT-TT-TTTTG
1 TTTTATGTTATTTTG
48125390 TTTTA
1 TTTTA
48125395 GTATATTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 2 0.11
15 6 0.33
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (15 bp):
TTTTATGTTATTTTG
Found at i:48128135 original size:30 final size:30
Alignment explanation
Indices: 48128099--48128158 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
48128089 GAGTTTAATG
48128099 TTTAGTTAGGGTATTTTTACTTATTTTTAT
1 TTTAGTTAGGGTATTTTTACTTATTTTTAT
48128129 TTTAGTTAGGGTATTTTTACTTATTTTTAT
1 TTTAGTTAGGGTATTTTTACTTATTTTTAT
48128159 AGTGGTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.03, G:0.13, T:0.63
Consensus pattern (30 bp):
TTTAGTTAGGGTATTTTTACTTATTTTTAT
Found at i:48135400 original size:9 final size:10
Alignment explanation
Indices: 48135381--48135417 Score: 53
Period size: 9 Copynumber: 4.0 Consensus size: 10
48135371 TGAGTTTTCG
48135381 AATTCGAATA
1 AATTCGAATA
48135391 AATT-GAAT-
1 AATTCGAATA
48135399 AATTCGAAT-
1 AATTCGAATA
48135408 AATTCGAATA
1 AATTCGAATA
48135418 TCAAACTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 4 0.16
9 17 0.68
10 4 0.16
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (10 bp):
AATTCGAATA
Found at i:48143017 original size:19 final size:19
Alignment explanation
Indices: 48142993--48143030 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
48142983 CTTTGGTGTC
48142993 TCGTGCAACATTATACATA
1 TCGTGCAACATTATACATA
*
48143012 TCGTGCAATATTATACATA
1 TCGTGCAACATTATACATA
48143031 CTTGTGGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
TCGTGCAACATTATACATA
Found at i:48144329 original size:6 final size:6
Alignment explanation
Indices: 48144318--48144342 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48144308 ATTTATGGCT
48144318 GGCAGG GGCAGG GGCAGG GGCAGG G
1 GGCAGG GGCAGG GGCAGG GGCAGG G
48144343 TCTTTAGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.68, T:0.00
Consensus pattern (6 bp):
GGCAGG
Found at i:48145047 original size:32 final size:32
Alignment explanation
Indices: 48145006--48145071 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
48144996 ACTTCAATAT
*
48145006 TAGATCAAATAGTGACAAGTATATTTCTTAAC
1 TAGATCAAATAGTAACAAGTATATTTCTTAAC
48145038 TAGATCAAATAGTAACAAGTATATTTCTTAAC
1 TAGATCAAATAGTAACAAGTATATTTCTTAAC
48145070 TA
1 TA
48145072 AAATGACATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.42, C:0.12, G:0.11, T:0.35
Consensus pattern (32 bp):
TAGATCAAATAGTAACAAGTATATTTCTTAAC
Found at i:48147986 original size:18 final size:18
Alignment explanation
Indices: 48147965--48148004 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
48147955 TAATAAATTT
*
48147965 TATTTTAATTT-TTAAAAA
1 TATTTAAATTTATT-AAAA
48147983 TATTTAAATTTATTAAAA
1 TATTTAAATTTATTAAAA
48148001 TATT
1 TATT
48148005 AATATAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTAAATTTATTAAAA
Found at i:48151782 original size:21 final size:21
Alignment explanation
Indices: 48151743--48151783 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48151733 CATGTCAAAA
48151743 TATTATTGTCATATATTATGC
1 TATTATTGTCATATATTATGC
*
48151764 TATTGATTGTCA-ATGTTATG
1 TATT-ATTGTCATATATTATG
48151784 TTAACGTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (21 bp):
TATTATTGTCATATATTATGC
Found at i:48152247 original size:38 final size:36
Alignment explanation
Indices: 48152168--48152280 Score: 163
Period size: 38 Copynumber: 3.1 Consensus size: 36
48152158 AGCTTCAGCC
* * *
48152168 GATTTGCTCCCTTGTTTCTTTTCTTTTCTTTTCTGCC
1 GATTTGCTCCC-AGTTTATTTTCTTTTCTTTTCTGCA
*
48152205 GATTTGCTCCCAGTTTATTTTCTTTTTTTTTTTCTGCA
1 GATTTGCTCCCAGTTTATTTTC--TTTTCTTTTCTGCA
48152243 GATTTGCTCCCAGTTTATTTTCTTTTCTTTTCTGCA
1 GATTTGCTCCCAGTTTATTTTCTTTTCTTTTCTGCA
48152279 GA
1 GA
48152281 ATAATTCTGG
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
36 24 0.35
37 11 0.16
38 34 0.49
ACGTcount: A:0.09, C:0.22, G:0.12, T:0.58
Consensus pattern (36 bp):
GATTTGCTCCCAGTTTATTTTCTTTTCTTTTCTGCA
Found at i:48154221 original size:28 final size:27
Alignment explanation
Indices: 48154190--48154277 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 27
48154180 ATTTATTAGT
48154190 TATAATTATTTTAAATTTTATTAAATCA
1 TATAATTATTTTAAATTTTATTAAAT-A
* * *
48154218 TAT-ATT-TTAATTAAAATATATTTAATA
1 TATAATTATT--TTAAATTTTATTAAATA
*
48154245 T-TAATTATTTCAAATTTTATTAAATTA
1 TATAATTATTTTAAATTTTATTAAA-TA
48154272 TATAAT
1 TATAAT
48154278 ATAGTATCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
26 14 0.30
27 11 0.23
28 22 0.47
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (27 bp):
TATAATTATTTTAAATTTTATTAAATA
Found at i:48154364 original size:14 final size:15
Alignment explanation
Indices: 48154343--48154391 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
48154333 AATTTTATTA
48154343 AATT-ATATAT-TTT
1 AATTAATATATGTTT
48154356 AATTAATATATGTTT
1 AATTAATATATGTTT
*
48154371 AA-TAATAATTATGTTA
1 AATTAAT-A-TATGTTT
48154387 AATTA
1 AATTA
48154392 TCTTTTATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.13
14 10 0.33
15 6 0.20
16 8 0.27
17 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
AATTAATATATGTTT
Found at i:48154401 original size:120 final size:121
Alignment explanation
Indices: 48154277--48154510 Score: 418
Period size: 120 Copynumber: 1.9 Consensus size: 121
48154267 AATTATATAA
48154277 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATCAAGAATTTTATT
1 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATCAAGAATTTTATT
*
48154342 AAATTATATATTTTAATTA-ATATATGTTTAATAATAATTATG-TTAAATTATCTTT
66 AAATTATATATTTTAATTATA-ATATATTTAATAATAATTATGTTTAAATTATCTTT
*
48154397 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATT
1 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATCAAGAATTTTATT
*
48154462 AAATTATATATTTTAATTATAATATATTTAATAATTATTATGTTTAAAT
66 AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
48154511 ATGATTAAAT
Statistics
Matches: 109, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
120 102 0.94
121 7 0.06
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (121 bp):
TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATCAAGAATTTTATT
AAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATTATCTTT
Found at i:48154735 original size:45 final size:46
Alignment explanation
Indices: 48154630--48154742 Score: 136
Period size: 45 Copynumber: 2.6 Consensus size: 46
48154620 AGTTTTTTCC
48154630 ATTATGCTATTACACCTCTATT-C----CATTCAACCAAACACAAG
1 ATTATGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAG
* *
48154671 ATTAT--TATTACGCCTCTATTCCATTACATTCAACCAAACA-ATTG
1 ATTATGCTATTACACCTCTATTCCATTACATTCAACCAAACACA-AG
48154715 ATT-TGCTATTACACCTCTATTCCATTAC
1 ATTATGCTATTACACCTCTATTCCATTAC
48154743 GCTTCTATTC
Statistics
Matches: 61, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
39 14 0.23
40 1 0.02
41 5 0.08
43 2 0.03
44 18 0.30
45 21 0.34
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (46 bp):
ATTATGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAG
Found at i:48154749 original size:16 final size:16
Alignment explanation
Indices: 48154722--48154770 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
48154712 TTGATTTGCT
*
48154722 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
*
48154738 ATTACGCTTCTATTCC
1 ATTACGCCTCTATTCC
*
48154754 ATTACGCCTCTAATCC
1 ATTACGCCTCTATTCC
48154770 A
1 A
48154771 ATACAGCGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.24, C:0.35, G:0.04, T:0.37
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:48156299 original size:27 final size:27
Alignment explanation
Indices: 48156269--48156335 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
48156259 CCTATCAGGT
48156269 AGGCGCCAATGAAGGTGCCTCACAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
*
48156296 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCACAGAG
48156323 AGGCGCCAATGAA
1 AGGCGCCAATGAA
48156336 TATTGTAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.31, C:0.24, G:0.33, T:0.12
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCACAGAG
Found at i:48156434 original size:21 final size:21
Alignment explanation
Indices: 48156405--48156448 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
48156395 TGGATTAGTA
*
48156405 TTTTGTATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
48156426 TTTTATATGAATATTGTAATT
1 TTTTATATGAATATTGTAATT
48156447 TT
1 TT
48156449 GTGTTTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
TTTTATATGAATATTGTAATT
Found at i:48156581 original size:16 final size:16
Alignment explanation
Indices: 48156538--48156581 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
48156528 AAAATCAAAT
* *
48156538 AAAATTTAATTATATA
1 AAAATTAAATTATACA
* *
48156554 AAAGTTACATTATACA
1 AAAATTAAATTATACA
48156570 AAAATTAAATTA
1 AAAATTAAATTA
48156582 GTTAACAACA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (16 bp):
AAAATTAAATTATACA
Found at i:48156657 original size:38 final size:38
Alignment explanation
Indices: 48156614--48156695 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
48156604 AAAAAGTCAG
48156614 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
48156652 TTATAATTAAACTTTTAATAAGATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
48156690 TTATAA
1 TTATAA
48156696 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:48156821 original size:60 final size:60
Alignment explanation
Indices: 48156728--48156849 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 60
48156718 ATATTAATCT
* * * *
48156728 AAACACAACAACTTATAGCTTAATCCTAAATTACTAATAAATTAAATTT-T-AAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATT--ATTTATAAAATAATTAC
*
48156788 AAACACAAAAATTTATAACATAATCCTAAATTACTAACAAATTATTTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTATTTATAAAATAATTAC
48156848 AA
1 AA
48156850 TATTCATACA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 4 0.07
59 1 0.02
60 50 0.91
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCTAAATTACTAACAAATTATTTATAAAATAATTAC
Found at i:48156868 original size:21 final size:21
Alignment explanation
Indices: 48156837--48156976 Score: 113
Period size: 21 Copynumber: 6.2 Consensus size: 21
48156827 AATTATTTAT
48156837 AAAATAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATAC
48156859 AAAAAATTACAATATTACAATATATC
1 AAAAAATTACAATATT-C---ATA-C
*** *
48156885 CCGACATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
48156906 --AAAATTACAATATTACAATATTC
1 AAAAAATTACAATATT-C-ATA--C
*
48156929 ATACAAAATTACAATATTCATAT
1 A-A-AAAATTACAATATTCATAC
48156952 AAAAAATTACAATATTCATAC
1 AAAAAATTACAATATTCATAC
48156973 AAAA
1 AAAA
48156977 TACTAATTCA
Statistics
Matches: 97, Mismatches: 8, Indels: 27
0.73 0.06 0.20
Matches are distributed among these distances:
19 12 0.12
20 1 0.01
21 38 0.39
22 9 0.09
23 2 0.02
25 7 0.07
26 14 0.14
27 14 0.14
ACGTcount: A:0.54, C:0.15, G:0.01, T:0.31
Consensus pattern (21 bp):
AAAAAATTACAATATTCATAC
Found at i:48156877 original size:8 final size:8
Alignment explanation
Indices: 48156864--48156967 Score: 52
Period size: 8 Copynumber: 12.4 Consensus size: 8
48156854 CATACAAAAA
48156864 ATTACAAT
1 ATTACAAT
48156872 ATTACAAT
1 ATTACAAT
* * *
48156880 ATATCCCGAC
1 AT-T-ACAAT
48156890 ATTACAAT
1 ATTACAAT
*
48156898 ATTCATACAAA
1 A-T--TACAAT
48156909 ATTACAAT
1 ATTACAAT
48156917 ATTACAAT
1 ATTACAAT
*
48156925 ATTCATACAAA
1 A-T--TACAAT
48156936 ATTACAAT
1 ATTACAAT
48156944 ATT-C-AT
1 ATTACAAT
* *
48156950 A-TAAAAA
1 ATTACAAT
48156957 ATTACAAT
1 ATTACAAT
48156965 ATT
1 ATT
48156968 CATACAAAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 22
0.66 0.13 0.21
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 3 0.04
8 42 0.59
9 4 0.06
10 6 0.08
11 12 0.17
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.34
Consensus pattern (8 bp):
ATTACAAT
Found at i:48156914 original size:19 final size:19
Alignment explanation
Indices: 48156911--48157050 Score: 108
Period size: 19 Copynumber: 7.1 Consensus size: 19
48156901 CATACAAAAT
*
48156911 TACAATATTACAATATTCA
1 TACAAAATTACAATATTCA
48156930 TACAAAATTACAATATTCATA
1 TACAAAATTACAATATTC--A
*
48156951 TAAAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
*
48156970 TACAAAA-TACTA-ATTCAA
1 TACAAAATTACAATATTC-A
*
48156988 AACTATAAA-TACAAATTTAATT-A
1 TAC-A-AAATTAC-AA--T-ATTCA
* *
48157011 TAAAATAATTACAATATTAA
1 TACAA-AATTACAATATTCA
48157031 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
48157050 T
1 T
48157051 TGGCGCCTCT
Statistics
Matches: 98, Mismatches: 10, Indels: 26
0.73 0.07 0.19
Matches are distributed among these distances:
17 4 0.04
18 7 0.07
19 42 0.43
20 12 0.12
21 20 0.20
22 5 0.05
23 5 0.05
25 3 0.03
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (19 bp):
TACAAAATTACAATATTCA
Found at i:48156926 original size:27 final size:27
Alignment explanation
Indices: 48156890--48156967 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
48156880 ATATCCCGAC
48156890 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
48156917 ATTACAATATTCATACAAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
48156944 ATT-C-ATA-T-A-A-AAAATTACAAT
1 ATTACAATATTCATACAAAATTACAAT
48156965 ATT
1 ATT
48156968 CATACAAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
21 14 0.27
22 1 0.02
23 1 0.02
24 1 0.02
25 3 0.06
26 1 0.02
27 30 0.59
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.35
Consensus pattern (27 bp):
ATTACAATATTCATACAAAATTACAAT
Found at i:48156971 original size:67 final size:63
Alignment explanation
Indices: 48156911--48157049 Score: 157
Period size: 61 Copynumber: 2.3 Consensus size: 63
48156901 CATACAAAAT
* * * *
48156911 TACAATATTACAATATTC-ATAC-AAAATTAC-AATATTCA-TATAAAA-AATTACAATATTCA
1 TACAAAATTACAATATTCAAAACTAAAAATACAAAT-TTAATTATAAAATAATTACAATATTCA
* * *
48156970 TACAAAA-TACTA-ATTCAAAACTATAAATACAAATTTAATTATAAAATAATTACAATATTAA
1 TACAAAATTACAATATTCAAAACTAAAAATACAAATTTAATTATAAAATAATTACAATATTCA
48157031 TACAAAATTACAATATTCA
1 TACAAAATTACAATATTCA
48157050 TTGGCGCCTC
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
57 4 0.06
58 7 0.11
59 15 0.23
60 10 0.15
61 20 0.31
62 4 0.06
63 5 0.08
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (63 bp):
TACAAAATTACAATATTCAAAACTAAAAATACAAATTTAATTATAAAATAATTACAATATTCA
Found at i:48157084 original size:27 final size:27
Alignment explanation
Indices: 48157046--48157112 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
48157036 AATTACAATA
48157046 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
*
48157073 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
48157100 TTCATTGGCGCCT
1 TTCATTGGCGCCT
48157113 ACCTGATAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:48158997 original size:28 final size:28
Alignment explanation
Indices: 48158966--48159024 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
48158956 ATAATTCTAG
* * * *
48158966 AAAGTACATATATATATATATATATTAT
1 AAAGAACATATAAACATATATAGATTAT
**
48158994 AAAGAATGTATAAACATATATAGATTAT
1 AAAGAACATATAAACATATATAGATTAT
48159022 AAA
1 AAA
48159025 ATATGAAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.54, C:0.03, G:0.07, T:0.36
Consensus pattern (28 bp):
AAAGAACATATAAACATATATAGATTAT
Found at i:48159325 original size:10 final size:10
Alignment explanation
Indices: 48159310--48159335 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
48159300 AAATACAATA
48159310 ATAATACTAT
1 ATAATACTAT
48159320 ATAATACTAT
1 ATAATACTAT
48159330 ATAATA
1 ATAATA
48159336 TCATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATACTAT
Found at i:48159444 original size:13 final size:13
Alignment explanation
Indices: 48159428--48159457 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
48159418 AATTTAAAAT
48159428 AAAACAGAATTTG
1 AAAACAGAATTTG
*
48159441 AAAACTGAATTTG
1 AAAACAGAATTTG
48159454 AAAA
1 AAAA
48159458 TAAAATAAAA
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:0.57, C:0.07, G:0.13, T:0.23
Consensus pattern (13 bp):
AAAACAGAATTTG
Found at i:48162034 original size:11 final size:11
Alignment explanation
Indices: 48162018--48162042 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
48162008 AATAATTAAT
48162018 ATTATGTGTTA
1 ATTATGTGTTA
48162029 ATTATGTGTTA
1 ATTATGTGTTA
48162040 ATT
1 ATT
48162043 TCAAGACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (11 bp):
ATTATGTGTTA
Found at i:48163137 original size:2 final size:2
Alignment explanation
Indices: 48163132--48163163 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
48163122 AAAAAATCTA
48163132 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
48163164 TCAAACACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:48166364 original size:42 final size:42
Alignment explanation
Indices: 48166317--48166398 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
48166307 ACAACGCTCC
48166317 CGGATGAACATTTCCCTAATTTCAAAGTAA-AATTCTAAAGCA
1 CGGATGAACATTTCCCTAATTTC-AAGTAACAATTCTAAAGCA
* *
48166359 CGGATGAACATTTCTCTAATTTCAAGTAACAATTTTAAAG
1 CGGATGAACATTTCCCTAATTTCAAGTAACAATTCTAAAG
48166399 AATCCTAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 6 0.16
42 31 0.84
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (42 bp):
CGGATGAACATTTCCCTAATTTCAAGTAACAATTCTAAAGCA
Found at i:48167874 original size:12 final size:12
Alignment explanation
Indices: 48167857--48167882 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48167847 ATACATTTAA
48167857 AAACATTAAAAC
1 AAACATTAAAAC
48167869 AAACATTAAAAC
1 AAACATTAAAAC
48167881 AA
1 AA
48167883 TAAACAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (12 bp):
AAACATTAAAAC
Found at i:48168129 original size:33 final size:33
Alignment explanation
Indices: 48168086--48168150 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
48168076 AACAATAATA
* **
48168086 AAACACCACAAAAAGTAGCA-TCAAAACAACACC
1 AAACAACACAAAAAACAGCACT-AAAACAACACC
48168119 AAACAACACAAAAAACAGCACTAAAACAACAC
1 AAACAACACAAAAAACAGCACTAAAACAACAC
48168151 AAAAAATAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.62, C:0.29, G:0.05, T:0.05
Consensus pattern (33 bp):
AAACAACACAAAAAACAGCACTAAAACAACACC
Found at i:48168144 original size:12 final size:12
Alignment explanation
Indices: 48168119--48168156 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
48168109 AAACAACACC
48168119 AAACAACACAAA
1 AAACAACACAAA
* *
48168131 AAACAGCAC-TA
1 AAACAACACAAA
48168142 AAACAACACAAA
1 AAACAACACAAA
48168154 AAA
1 AAA
48168157 TAGCACCACC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.71, C:0.24, G:0.03, T:0.03
Consensus pattern (12 bp):
AAACAACACAAA
Found at i:48168149 original size:23 final size:24
Alignment explanation
Indices: 48168118--48168181 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
48168108 AAAACAACAC
*
48168118 CAAACAACACAAAAAACAGCACTA
1 CAAACAACACAAAAAACAGCACCA
*
48168142 -AAACAACACAAAAAATAGCACCA
1 CAAACAACACAAAAAACAGCACCA
* *
48168165 CCAACAACACCAAAAAC
1 CAAACAACACAAAAAAC
48168182 TTGCAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 21 0.62
24 13 0.38
ACGTcount: A:0.62, C:0.31, G:0.03, T:0.03
Consensus pattern (24 bp):
CAAACAACACAAAAAACAGCACCA
Found at i:48169123 original size:30 final size:31
Alignment explanation
Indices: 48169077--48169139 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 31
48169067 GGGGATGGGA
*
48169077 TGGGAGGGGAGAAAAAGTTATGGGGGGAAAG
1 TGGGAGGGGAGAAAAAGTTATGGGAGGAAAG
* *
48169108 TGGGA-GGGAGTAAAAGTTTTGGGAGGAAAG
1 TGGGAGGGGAGAAAAAGTTATGGGAGGAAAG
48169138 TG
1 TG
48169140 AAAAGTTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.33, C:0.00, G:0.49, T:0.17
Consensus pattern (31 bp):
TGGGAGGGGAGAAAAAGTTATGGGAGGAAAG
Found at i:48174291 original size:50 final size:50
Alignment explanation
Indices: 48174226--48174750 Score: 383
Period size: 50 Copynumber: 10.5 Consensus size: 50
48174216 TTAAAAGTAG
* * * *
48174226 GATTCGCCATTGTGGCTTCAATCTTTTTAACTGCAATGTCGGGGAAGCAA
1 GATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAA
* * *
48174276 GATTCGCTGTGGTGGCTTTAATATTTTTAACTGCAATGCCAGGGAAGCAA
1 GATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAA
* ** * * * *
48174326 GATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTAAGAAAGTAA
1 GATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGCC-AGGGAAGCAA
* * * *
48174377 GATTCGTCGTTGTGACTTTAATCCTTTTAACTGCAATGCCAGGAAAGCAA
1 GATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAA
* * ** ** * * *
48174427 GATTCACCGTTGTGGCTTTAATCTATTCCACTGC-ACCCCTGGGAGGTAA
1 GATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAA
* * * * *
48174476 GATTCGCTGATGTAGCTTTAATCTTTTTAACTGTAATGTC-GTGGAAGCAA
1 GATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGCCAG-GGAAGCAA
* ** * * * *
48174526 GATTCGCCGTTGTGGCTTTAATCTGTTCCACTGCACTGCCTGAGAGAGTAA
1 GATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGCCAGGGA-AGCAA
* * * * * **
48174577 GATTTGTCGTTGTGACTTTAATCCTTTTAACTACAATG-TTGGGAAAGCAA
1 GATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGCCAGGG-AAGCAA
* * * * ** * * * *
48174627 GATTCACCATTGTGGCTTTAATCTGTTCT-ATTGCACCGTCTGGGAGGTAA
1 GATTCGCCGTTGTGGCTTTAATCT-TTTTAACTGCAATGCCAGGGAAGCAA
* * * * * * * * *
48174677 AATTTGCGGCTGTAGCTCTAATCTTTTTAACCGCAATGTCAGGGAGGCAA
1 GATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAA
*
48174727 GATTCACCGTTGTGGCTTTAATCT
1 GATTCGCCGTTGTGGCTTTAATCT
48174751 GTTCCACTGC
Statistics
Matches: 355, Mismatches: 111, Indels: 18
0.73 0.23 0.04
Matches are distributed among these distances:
49 39 0.11
50 234 0.66
51 82 0.23
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (50 bp):
GATTCGCCGTTGTGGCTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAA
Found at i:48174413 original size:101 final size:100
Alignment explanation
Indices: 48174274--48174782 Score: 537
Period size: 101 Copynumber: 5.1 Consensus size: 100
48174264 TCGGGGAAGC
* * * *
48174274 AAGATTCGCTGTGGTGGCTTTAATATTTTTAACTGCAATGCCAGGGAAGCAAGATTCGCCGTTGT
1 AAGATTCGCTGTTGTGACTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAAGATTCACCGTTGT
*
48174339 GGCTTTAATCTGTTCCACTGCACTGCCTAAGAAAGT
66 GGCTTTAATCTGTTCCACTGCACCGCCT-AGAAAGT
* *
48174375 AAGATTCG-TCGTTGTGACTTTAATCCTTTTAACTGCAATGCCAGGAAAGCAAGATTCACCGTTG
1 AAGATTCGCT-GTTGTGACTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAAGATTCACCGTTG
* * * *
48174439 TGGCTTTAATCTATTCCACTGCACC-CCTGGGAGGT
65 TGGCTTTAATCTGTTCCACTGCACCGCCTAGAAAGT
* * * *
48174474 AAGATTCGCTGATGT-AGCTTTAATCTTTTTAACTGTAATGTC-GTGGAAGCAAGATTCGCCGTT
1 AAGATTCGCTGTTGTGA-CTTTAATCTTTTTAACTGCAATGCCAG-GGAAGCAAGATTCACCGTT
* *
48174537 GTGGCTTTAATCTGTTCCACTGCACTGCCTGAGAGAGT
64 GTGGCTTTAATCTGTTCCACTGCACCGCCT-AGAAAGT
* * * ** *
48174575 AAGATTTG-TCGTTGTGACTTTAATCCTTTTAACTACAATG-TTGGGAAAGCAAGATTCACCATT
1 AAGATTCGCT-GTTGTGACTTTAATCTTTTTAACTGCAATGCCAGGG-AAGCAAGATTCACCGTT
* * * * * *
48174638 GTGGCTTTAATCTGTTCTATTGCACCGTCTGGGAGGT
64 GTGGCTTTAATCTGTTCCACTGCACCGCCTAGAAAGT
* * * * * * * *
48174675 AAAATTTGCGGCTGT-AGCTCTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTG
1 AAGATTCGCTGTTGTGA-CTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAAGATTCACCGTTG
* * *
48174739 TGGCTTTAATCTGTTCCACTGCACCGCCTGGGAGGT
65 TGGCTTTAATCTGTTCCACTGCACCGCCTAGAAAGT
48174775 AAGATTCG
1 AAGATTCG
48174783 TAATCTTCAA
Statistics
Matches: 340, Mismatches: 55, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
98 2 0.01
99 80 0.24
100 99 0.29
101 158 0.46
102 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (100 bp):
AAGATTCGCTGTTGTGACTTTAATCTTTTTAACTGCAATGCCAGGGAAGCAAGATTCACCGTTGT
GGCTTTAATCTGTTCCACTGCACCGCCTAGAAAGT
Found at i:48174624 original size:200 final size:200
Alignment explanation
Indices: 48174274--48174783 Score: 738
Period size: 200 Copynumber: 2.5 Consensus size: 200
48174264 TCGGGGAAGC
* * *
48174274 AAGATTCGCTGTGGTGGCTTTAATATTTTTAACTGCAATGCCAGGGAAGCAAGATTCGCCGTTGT
1 AAGATTCGCTGT-GTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGT
* *
48174339 GGCTTTAATCTGTTCCACTGCACTGCCTAAGAAAGTAAGATTCGTCGTTGTGACTTTAATCCTTT
65 GGCTTTAATCTGTTCCACTGCACTGCCTGAGAGAGTAAGATTCGTCGTTGTGACTTTAATCCTTT
* *
48174404 TAACTGCAATGCCAGGAAAGCAAGATTCACCGTTGTGGCTTTAATCTATTCCACTGCACC-CCTG
130 TAACTACAATGCCAGGAAAGCAAGATTCACCATTGTGGCTTTAATCTATTCCACTGCACCGCCTG
48174468 GGAGGT
195 GGAGGT
*
48174474 AAGATTCGCTGATGTAGCTTTAATCTTTTTAACTGTAATGTC-GTGGAAGCAAGATTCGCCGTTG
1 AAGATTCGCTG-TGTAGCTTTAATCTTTTTAACTGCAATGTCAG-GGAAGCAAGATTCGCCGTTG
*
48174538 TGGCTTTAATCTGTTCCACTGCACTGCCTGAGAGAGTAAGATTTGTCGTTGTGACTTTAATCCTT
64 TGGCTTTAATCTGTTCCACTGCACTGCCTGAGAGAGTAAGATTCGTCGTTGTGACTTTAATCCTT
*** * * * *
48174603 TTAACTACAATGTTGGGAAAGCAAGATTCACCATTGTGGCTTTAATCTGTTCTATTGCACCGTCT
129 TTAACTACAATGCCAGGAAAGCAAGATTCACCATTGTGGCTTTAATCTATTCCACTGCACCGCCT
48174668 GGGAGGT
194 GGGAGGT
* * * * * * *
48174675 AAAATTTGCGGCTGTAGCTCTAATCTTTTTAACCGCAATGTCAGGGAGGCAAGATTCACCGTTGT
1 AAGATTCGCTG-TGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGT
* *
48174740 GGCTTTAATCTGTTCCACTGCACCGCCTGGGAG-GTAAGATTCGT
65 GGCTTTAATCTGTTCCACTGCACTGCCTGAGAGAGTAAGATTCGT
48174784 AATCTTCAAC
Statistics
Matches: 278, Mismatches: 28, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
199 1 0.00
200 181 0.65
201 95 0.34
202 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (200 bp):
AAGATTCGCTGTGTAGCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCGCCGTTGTG
GCTTTAATCTGTTCCACTGCACTGCCTGAGAGAGTAAGATTCGTCGTTGTGACTTTAATCCTTTT
AACTACAATGCCAGGAAAGCAAGATTCACCATTGTGGCTTTAATCTATTCCACTGCACCGCCTGG
GAGGT
Found at i:48175002 original size:131 final size:131
Alignment explanation
Indices: 48174768--48175483 Score: 1137
Period size: 131 Copynumber: 5.5 Consensus size: 131
48174758 TGCACCGCCT
* * *
48174768 GGGAGGTAAGAT-TCGTAATCTTCAACCGATCCCACTACTGACCAGGGAGATAGGACTAGTGGCT
1 GGGAGATAAGATCT-GTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCT
* * *
48174832 TAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCATCTTCGATCTACTCCACTATTACT
65 TAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCT
48174897 TA
130 TA
*
48174899 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACTAGGGAGATAGGACTAGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTT
* * * * *
48174964 AAATCTGCTTCCCTACTACTGGGGAAGATAAGATTCGCCGTCTTTGATATGCTCCACTATCGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
48175029 A
131 A
*
48175030 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTT
* *
48175095 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCACTGTCTTCGATCTGCTCCACTATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
48175160 A
131 A
* * *
48175161 GGGAGATAATATCTGTAATCTTCAACCTATCCCACTGCAGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTT
** * *
48175226 AAATCTACTTCCCTACTCCTAGGGAAGATAAGATTCGCCGCCTTCGATCTGCTCCACTATTGCTT
66 AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
48175291 A
131 A
* * *
48175292 GAGAGATAAGATCCGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTGGTGGCTT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTT
* * * * *
48175357 AAATCTGTTTCCCTATTCCTGGAGAAGAAAAAGATTCGCCGTCTTCGATCTGTTCCACTATTGTT
66 AAATCTGTTTCCCTACTCCTGGGGAAG-ATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCT
48175422 TA
130 TA
48175424 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGT
1 GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGT
48175484 AGTCTTCCAC
Statistics
Matches: 538, Mismatches: 45, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
131 445 0.83
132 93 0.17
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (131 bp):
GGGAGATAAGATCTGTAATCTTCAACCTATCCCACTGCTGACCAGGGAGATAGGACTAGTGGCTT
AAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTT
A
Found at i:48175471 original size:44 final size:44
Alignment explanation
Indices: 48175423--48175507 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
48175413 ACTATTGTTT
48175423 AGGGAGATAAGATCT-GTAATCTTCAACCTATCCCACTGCTGACC
1 AGGGAGATAAGA-CTAGTAATCTTCAACCTATCCCACTGCTGACC
* * * *
48175467 AGGGAGATAGGACTAGTAGTCTTCCACCTATTCCACTGCTG
1 AGGGAGATAAGACTAGTAATCTTCAACCTATCCCACTGCTG
48175508 GTCAGGGAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (44 bp):
AGGGAGATAAGACTAGTAATCTTCAACCTATCCCACTGCTGACC
Found at i:48175514 original size:44 final size:43
Alignment explanation
Indices: 48175440--48175963 Score: 503
Period size: 44 Copynumber: 12.0 Consensus size: 43
48175430 TAAGATCTGT
** * ** *
48175440 AATCTTCAACCTATCCCACTGCTGACCAGGGAGA-TAGGACTAGT
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGA-ACTAGGACTA-C
* * **
48175484 AGTCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGTTTTAC
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGG-ACTAC
* * *
48175528 AATCTTTCGCCTATTCCACTGCTGTTCAGGGAACTAGGACTTGC
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGAC-TAC
** * **
48175572 GGTCTTCCGCCTATTCCACTGCTGGTCAGGGAATTAGGTTTTAC
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGG-ACTAC
* * **
48175616 AATCTTTCGCCTATTCCACTGCTGGTCAGGGAATTAGGTTTTAC
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGG-ACTAC
* *
48175660 AATCTTTCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTGC
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGAC-TAC
** * **
48175704 GGTCTTCCGCCTATTCCACAGCTGGTCAGGGAACTAGGTTTTAC
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGG-ACTAC
*
48175748 AATCTTTCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTAC
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGAC-TAC
* * * * **
48175792 AGTCTTCCACCTATTCCACTGCTAGTCAGGGAATTAGGTTTTAC
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGG-ACTAC
* *
48175836 AATCTTTCGCCTATT-CACTGTTGGTCAGGGAACTAGGACTTAC
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGAC-TAC
* * * **
48175879 AGTCTTCCACCTATTCCACTACTGGTCAGGGAACTAGGTTTTAC
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGG-ACTAC
** * *
48175923 AATCTTTTGCCTATTCCACTACTGGTCAAGGAACTAGGACT
1 AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACT
48175964 TATCTTTGAT
Statistics
Matches: 397, Mismatches: 72, Indels: 23
0.81 0.15 0.05
Matches are distributed among these distances:
43 36 0.09
44 359 0.90
45 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (43 bp):
AATCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTAC
Found at i:48175547 original size:88 final size:88
Alignment explanation
Indices: 48175486--48175965 Score: 577
Period size: 88 Copynumber: 5.5 Consensus size: 88
48175476 GGACTAGTAG
* ** *
48175486 TCTTCCACCTATTCCACTGCTGGTCAGGGAACTAGGTTTTACAATCTTTCGCCTATTCCACTGCT
1 TCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAATCTTCCGCCTATTCCACTGCT
* * **
48175551 GTTCAGGGAACTAGG-ACTTGCGG
66 GGTCAGGGAACTAGGTAC-TACAA
* ** *
48175574 TCTTCCGCCTATTCCACTGCTGGTCAGGGAATTAGGTTTTACAATCTTTCGCCTATTCCACTGCT
1 TCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAATCTTCCGCCTATTCCACTGCT
* **
48175639 GGTCAGGGAATTAGGTTTTACAA
66 GGTCAGGGAACTAGGTACTACAA
* * ** *
48175662 TCTTTCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCGGTCTTCCGCCTATTCCACAGCT
1 TCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAATCTTCCGCCTATTCCACTGCT
**
48175727 GGTCAGGGAACTAGGTTTTACAA
66 GGTCAGGGAACTAGGTACTACAA
* * *
48175750 TCTTTCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTGCT
1 TCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAATCTTCCGCCTATTCCACTGCT
* * **
48175815 AGTCAGGGAATTAGGTTTTACAA
66 GGTCAGGGAACTAGGTACTACAA
* * * * *
48175838 TCTTTCGCCTATT-CACTGTTGGTCAGGGAACTAGGACTTACAGTCTTCCACCTATTCCACTACT
1 TCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAATCTTCCGCCTATTCCACTGCT
**
48175902 GGTCAGGGAACTAGGTTTTACAA
66 GGTCAGGGAACTAGGTACTACAA
** * *
48175925 TCTTTTGCCTATTCCACTACTGGTCAAGGAACTAGGACTTA
1 TCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTA
48175966 TCTTTGATCT
Statistics
Matches: 357, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
87 82 0.23
88 275 0.77
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (88 bp):
TCTTCCGCCTATTCCACTGCTGGTCAGGGAACTAGGACTTACAATCTTCCGCCTATTCCACTGCT
GGTCAGGGAACTAGGTACTACAA
Found at i:48177291 original size:23 final size:23
Alignment explanation
Indices: 48177257--48177301 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
48177247 TAGCTTCTCT
*
48177257 ATTTTTACTTTTTCATTTTTTTC
1 ATTTTTACTTTTTAATTTTTTTC
48177280 ATTTTT-CATTTTTAATTTTTTT
1 ATTTTTAC-TTTTTAATTTTTTT
48177302 GACTCAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (23 bp):
ATTTTTACTTTTTAATTTTTTTC
Found at i:48192713 original size:63 final size:63
Alignment explanation
Indices: 48192556--48192755 Score: 192
Period size: 63 Copynumber: 3.2 Consensus size: 63
48192546 TCACAAAAAA
* * * * * * *
48192556 TGAGTTACACGGCCTAGACACACG-CTCGTGTCTCCAGCCTGTGTGACCCTCATTCCCAAATAG
1 TGAGTTACACAGTCTGGACACACGTC-CGTGTCTCTAGCCCGAGTGACCCTAATTCCCAAATAG
* *
48192619 TGAGTTACACAGTCTGGGCACACGTCCGTGTCTCTAGCTCCTA-TGACCCTAATTCCCAAATAG
1 TGAGTTACACAGTCTGGACACACGTCCGTGTCTCTAGC-CCGAGTGACCCTAATTCCCAAATAG
* * * * **
48192682 TGAGTTACAC-GATTTGGACACATG-CCAGTGTCTCTAGCCCGAGTAACCCTAAATCTAAAATAG
1 TGAGTTACACAG-TCTGGACACACGTCC-GTGTCTCTAGCCCGAGTGACCCTAATTCCCAAATAG
*
48192745 TAAGTTACACA
1 TGAGTTACACA
48192756 ACTTGCCACA
Statistics
Matches: 113, Mismatches: 18, Indels: 11
0.80 0.13 0.08
Matches are distributed among these distances:
62 6 0.05
63 105 0.93
64 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (63 bp):
TGAGTTACACAGTCTGGACACACGTCCGTGTCTCTAGCCCGAGTGACCCTAATTCCCAAATAG
Found at i:48202057 original size:12 final size:12
Alignment explanation
Indices: 48202040--48202064 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48202030 GCTTGATCAA
48202040 CCAGTCCATACC
1 CCAGTCCATACC
48202052 CCAGTCCATACC
1 CCAGTCCATACC
48202064 C
1 C
48202065 AGAATCTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.52, G:0.08, T:0.16
Consensus pattern (12 bp):
CCAGTCCATACC
Found at i:48204332 original size:29 final size:31
Alignment explanation
Indices: 48204299--48204362 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
48204289 TTAATAGAAT
48204299 ATTT-ATCTCTAAGATAA-ACATTAA-ATTAA
1 ATTTAATCT-TAAGATAACACATTAATATTAA
*
48204328 ATTTAATCTTAAGATAATCACTTTAATATTAA
1 ATTTAATCTTAAGATAA-CACATTAATATTAA
48204360 ATT
1 ATT
48204363 AATAAAATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 12 0.40
30 4 0.13
31 6 0.20
32 8 0.27
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTTAATCTTAAGATAACACATTAATATTAA
Found at i:48204332 original size:62 final size:59
Alignment explanation
Indices: 48204223--48204423 Score: 181
Period size: 62 Copynumber: 3.2 Consensus size: 59
48204213 ATCACTTTAA
* * *
48204223 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
* *
48204282 TATTAAATTAATAGAATATTTATCTCTAAGATAAACATTAAATTAAATTTAATCTTAAGATAATC
1 TATTAAATTAATAGAATACTTA--TC-AAGATAAACATTAAATTAAATTTAATATT---A-AAT-
48204347 ACTTT
58 -C--T
* * **
48204352 AATATTAAATTAATAAAATAC-TATTAAGATAAGTATTAAATTAAATTTAATATTAAATC-
1 --TATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
*
48204411 TATTAAAATAATA
1 TATTAAATTAATA
48204424 TTATTTTTGG
Statistics
Matches: 117, Mismatches: 12, Indels: 28
0.75 0.08 0.18
Matches are distributed among these distances:
57 12 0.10
59 20 0.17
61 2 0.02
62 27 0.23
64 3 0.03
65 2 0.02
66 3 0.03
68 27 0.23
69 1 0.01
70 1 0.01
71 2 0.02
72 17 0.15
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:48208881 original size:11 final size:11
Alignment explanation
Indices: 48208867--48208896 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
48208857 AAAGAAATTA
48208867 TTTTAGAAAAT
1 TTTTAGAAAAT
48208878 TTTTCAGAAAAT
1 TTTT-AGAAAAT
48208890 TTTTAGA
1 TTTTAGA
48208897 GATATTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (11 bp):
TTTTAGAAAAT
Found at i:48213748 original size:30 final size:30
Alignment explanation
Indices: 48213712--48213807 Score: 165
Period size: 30 Copynumber: 3.2 Consensus size: 30
48213702 TTATAAATTA
* * *
48213712 CACACGACCGTGCGGTCAGGCCGTGTGAGG
1 CACACGATCGTACGGCCAGGCCGTGTGAGG
48213742 CACACGATCGTACGGCCAGGCCGTGTGAGG
1 CACACGATCGTACGGCCAGGCCGTGTGAGG
48213772 CACACGATCGTACGGCCAGGCCGTGTGAGG
1 CACACGATCGTACGGCCAGGCCGTGTGAGG
48213802 CACACG
1 CACACG
48213808 TCCTTGTGAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.20, C:0.31, G:0.36, T:0.12
Consensus pattern (30 bp):
CACACGATCGTACGGCCAGGCCGTGTGAGG
Found at i:48214377 original size:40 final size:40
Alignment explanation
Indices: 48214332--48214467 Score: 125
Period size: 40 Copynumber: 3.4 Consensus size: 40
48214322 ACAAGAGAAT
* *
48214332 GTATGTGCAATCAGGGATACCGAAGTAAAAACAAAGTCA-
1 GTATGTGCATTCAGGGATACCGAAGTAAAAACAAAGGCAC
* * **
48214371 GCTATGTGCATTCAAAGGTATA--GAAGTAGAAACAGGGGCAC
1 G-TATGTGCATTC--AGGGATACCGAAGTAAAAACAAAGGCAC
* * *
48214412 GTATGTGCATTCAGGGGTACCGAAGTACAAACAAGGGCAC
1 GTATGTGCATTCAGGGATACCGAAGTAAAAACAAAGGCAC
* *
48214452 GCAAGTGCATTCAGGG
1 GTATGTGCATTCAGGG
48214468 TCATTTCTTC
Statistics
Matches: 79, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
38 5 0.06
39 1 0.01
40 66 0.84
41 1 0.01
42 6 0.08
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.18
Consensus pattern (40 bp):
GTATGTGCATTCAGGGATACCGAAGTAAAAACAAAGGCAC
Found at i:48220220 original size:18 final size:18
Alignment explanation
Indices: 48220199--48220238 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
48220189 AAATTGAATC
48220199 AAAACAT-AAAATTTAGGA
1 AAAACATAAAAATTT-GGA
48220217 AAAACATAGAAAATTTGGA
1 AAAACATA-AAAATTTGGA
48220236 AAA
1 AAA
48220239 TAGGGGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 6 0.30
20 7 0.35
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (18 bp):
AAAACATAAAAATTTGGA
Found at i:48221205 original size:40 final size:39
Alignment explanation
Indices: 48221130--48221295 Score: 145
Period size: 40 Copynumber: 4.2 Consensus size: 39
48221120 TGAATGTGTG
* * * *
48221130 TTAAGGGTATC-AAGGTACAAACAAGAGCACATATGTGCA
1 TTAAGGGTACCGAA-GTACAAATAGGGGCACATATGTGCA
* * * *
48221169 ATCAGGGATACTGAAGTACAAATAGGGGCACTTATGTGCA
1 TTAAGGG-TACCGAAGTACAAATAGGGGCACATATGTGCA
* * * *
48221209 TTTAAGGGTACCAAAGTCCAAACAGGGGCACGTATGTGCA
1 -TTAAGGGTACCGAAGTACAAATAGGGGCACATATGTGCA
* * *
48221249 TTTAGGGGTACCGATGTACAAATAGGGGCACATGTGTGCA
1 -TTAAGGGTACCGAAGTACAAATAGGGGCACATATGTGCA
48221289 TTCAAGG
1 TT-AAGG
48221296 TCATTTTCTT
Statistics
Matches: 100, Mismatches: 23, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
39 7 0.07
40 86 0.86
41 7 0.07
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (39 bp):
TTAAGGGTACCGAAGTACAAATAGGGGCACATATGTGCA
Found at i:48221246 original size:80 final size:80
Alignment explanation
Indices: 48221130--48221295 Score: 206
Period size: 80 Copynumber: 2.1 Consensus size: 80
48221120 TGAATGTGTG
* * *
48221130 TTAAGGGTATCAAGGTACAAACAAGAGCACATATGTGCAATCAGGGATACTGAAGTACAAATAGG
1 TTAAGGGTACCAAAGTACAAACAAGAGCACATATGTGCAATCAGGGATACCGAAGTACAAATAGG
*
48221195 GGCACTTATGTGCAT
66 GGCACATATGTGCAT
* * * * * * * *
48221210 TTAAGGGTACCAAAGTCCAAACAGGGGCACGTATGTGCATTTAGGGGTACCGATGTACAAATAGG
1 TTAAGGGTACCAAAGTACAAACAAGAGCACATATGTGCAATCAGGGATACCGAAGTACAAATAGG
*
48221275 GGCACATGTGTGCAT
66 GGCACATATGTGCAT
*
48221290 TCAAGG
1 TTAAGG
48221296 TCATTTTCTT
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.34, C:0.16, G:0.28, T:0.22
Consensus pattern (80 bp):
TTAAGGGTACCAAAGTACAAACAAGAGCACATATGTGCAATCAGGGATACCGAAGTACAAATAGG
GGCACATATGTGCAT
Found at i:48223491 original size:2 final size:2
Alignment explanation
Indices: 48223484--48223516 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
48223474 AACAAAAAGA
48223484 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
48223517 CTTTTAAGAA
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:48226213 original size:21 final size:23
Alignment explanation
Indices: 48226187--48226236 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
48226177 AAAATTTTAG
48226187 TAAATA-AAAATATAAAAAT-AT-
1 TAAATATAAAA-ATAAAAATAATA
*
48226208 TAAATATCAAAATAAAAATAATA
1 TAAATATAAAAATAAAAATAATA
48226231 TAAATA
1 TAAATA
48226237 GGCATACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 14 0.56
22 5 0.20
23 6 0.24
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAATATAAAAATAAAAATAATA
Found at i:48234577 original size:30 final size:30
Alignment explanation
Indices: 48234541--48234598 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
48234531 CTGGTGAGTG
48234541 AAAGTCTGATAGTGATTACTCCTTTCCTCT
1 AAAGTCTGATAGTGATTACTCCTTTCCTCT
48234571 AAAGTCTGATAGTGATTACTCCTTTCCT
1 AAAGTCTGATAGTGATTACTCCTTTCCT
48234599 ATATTACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.40
Consensus pattern (30 bp):
AAAGTCTGATAGTGATTACTCCTTTCCTCT
Found at i:48242915 original size:17 final size:17
Alignment explanation
Indices: 48242875--48242914 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
48242865 AGACGCATGC
*
48242875 TTTTGTTCTTTCTTTCT
1 TTTTTTTCTTTCTTTCT
48242892 TTTTTTTCTTT-TTTCT
1 TTTTTTTCTTTCTTTCT
48242908 TTTTTTT
1 TTTTTTT
48242915 TAAGTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTTTCTTTCTTTCT
Found at i:48243940 original size:25 final size:25
Alignment explanation
Indices: 48243903--48243966 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
48243893 AACTTTTTAG
*
48243903 TAATTATATAATTTTACATTTACAAA
1 TAATAATA-AATTTTACATTTACAAA
* * *
48243929 TAATAATAAATTTGATATTTAGAAA
1 TAATAATAAATTTTACATTTACAAA
48243954 -AATAA-AATATTTT
1 TAATAATAA-ATTTT
48243967 TCAATTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 2 0.06
24 9 0.28
25 14 0.44
26 7 0.22
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (25 bp):
TAATAATAAATTTTACATTTACAAA
Found at i:48251061 original size:16 final size:17
Alignment explanation
Indices: 48251042--48251073 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
48251032 TGTATTTAAA
48251042 TAATATT-TAATTTTTT
1 TAATATTATAATTTTTT
48251058 TAATATTATAATTTTT
1 TAATATTATAATTTTT
48251074 AATAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TAATATTATAATTTTTT
Found at i:48255533 original size:50 final size:50
Alignment explanation
Indices: 48255418--48255666 Score: 318
Period size: 50 Copynumber: 4.8 Consensus size: 50
48255408 GATAATAACA
* * **
48255418 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* * *
48255469 TGCCCATGTCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
48255519 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *
48255569 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
48255624 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
48255667 TTACCCAAAT
Statistics
Matches: 173, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
50 96 0.55
51 32 0.18
53 3 0.02
54 1 0.01
55 2 0.01
56 39 0.23
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:48255594 original size:100 final size:104
Alignment explanation
Indices: 48255417--48255666 Score: 373
Period size: 100 Copynumber: 2.4 Consensus size: 104
48255407 TGATAATAAC
** *
48255417 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATCTCGGTGCCCATGTCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCCATGCCATG
* *
48255482 TCCCAGACATGGTCTTATAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
*
48255519 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
48255583 CCCAGACATGGTCTTACAGGGGACCTCTCATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCA--ATCTTAAGG
* *
48255624 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
48255667 TTACCCAAAT
Statistics
Matches: 134, Mismatches: 8, Indels: 8
0.89 0.05 0.05
Matches are distributed among these distances:
100 52 0.39
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.01
106 40 0.30
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCAATCTTAAGG
Found at i:48255782 original size:13 final size:13
Alignment explanation
Indices: 48255761--48255792 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
48255751 GCTTGGATCA
*
48255761 TCATCAAATAAAT
1 TCATAAAATAAAT
48255774 TCATAAAATAAAT
1 TCATAAAATAAAT
48255787 TCATAA
1 TCATAA
48255793 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:48264603 original size:16 final size:17
Alignment explanation
Indices: 48264584--48264615 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
48264574 TGTATTTAAA
48264584 TAATATT-TAATTTTTT
1 TAATATTATAATTTTTT
48264600 TAATATTATAATTTTT
1 TAATATTATAATTTTT
48264616 AATAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TAATATTATAATTTTTT
Found at i:48267193 original size:15 final size:16
Alignment explanation
Indices: 48267168--48267210 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
48267158 ACTAAAAACA
48267168 AACAGTACAATAA-TAT
1 AACA-TACAATAATTAT
48267184 AACATACAATAATTAT
1 AACATACAATAATTAT
*
48267200 AGTCATACAAT
1 A-ACATACAAT
48267211 TATTCAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 8 0.33
17 8 0.33
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.28
Consensus pattern (16 bp):
AACATACAATAATTAT
Found at i:48268438 original size:14 final size:14
Alignment explanation
Indices: 48268409--48268453 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
48268399 AAACCCCTAA
48268409 TTTT-TTTCTC-CT
1 TTTTCTTTCTCTCT
48268421 TTTTCTTTCTCTCT
1 TTTTCTTTCTCTCT
*
48268435 TTTTC-TTCTCTAT
1 TTTTCTTTCTCTCT
48268448 TTTTCT
1 TTTTCT
48268454 CTATTTTGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 4 0.14
13 18 0.62
14 7 0.24
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTCTTTCTCTCT
Found at i:48268471 original size:21 final size:20
Alignment explanation
Indices: 48268423--48268474 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
48268413 TTTCTCCTTT
*
48268423 TTCTTTCTCTCTTTTTCTTC
1 TTCTTTTTCTCTTTTTCTTC
* *
48268443 TCTATTTTTCTCTATTTTGTTC
1 T-TCTTTTTCTCT-TTTTCTTC
48268465 TTCTTTTTCT
1 TTCTTTTTCT
48268475 ATTATTTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 17 0.65
22 8 0.31
ACGTcount: A:0.04, C:0.23, G:0.02, T:0.71
Consensus pattern (20 bp):
TTCTTTTTCTCTTTTTCTTC
Found at i:48273456 original size:11 final size:11
Alignment explanation
Indices: 48273429--48273462 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
48273419 ATCCAAATCC
48273429 TGACTCAA-TT
1 TGACTCAATTT
*
48273439 CGACTCAATTT
1 TGACTCAATTT
48273450 TGACTCAATTT
1 TGACTCAATTT
48273461 TG
1 TG
48273463 GCATGTACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (11 bp):
TGACTCAATTT
Found at i:48277180 original size:15 final size:15
Alignment explanation
Indices: 48277160--48277191 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
48277150 GTTTAAAATC
*
48277160 TTGAATAAGTATACT
1 TTGAATAAATATACT
48277175 TTGAATAAATATACT
1 TTGAATAAATATACT
48277190 TT
1 TT
48277192 CAAGATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (15 bp):
TTGAATAAATATACT
Found at i:48278864 original size:25 final size:25
Alignment explanation
Indices: 48278831--48278912 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
48278821 TTAAACTGAA
48278831 ACTGAAACTGTCCT-TA-ATAGTATAT
1 ACTGAAAC--TCCTATAGATAGTATAT
*
48278856 CCTGAAACTCCTATAGATAGTATAT
1 ACTGAAACTCCTATAGATAGTATAT
* *
48278881 ACTGAGACTACTATAGATAG-ACTAT
1 ACTGAAACTCCTATAGATAGTA-TAT
48278906 ACTGAAA
1 ACTGAAA
48278913 ACACTTAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
23 4 0.08
24 3 0.06
25 42 0.86
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.30
Consensus pattern (25 bp):
ACTGAAACTCCTATAGATAGTATAT
Found at i:48282528 original size:17 final size:18
Alignment explanation
Indices: 48282487--48282531 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
48282477 CATAATTTGG
48282487 AATAAAAT-ATGTAAATA
1 AATAAAATAATGTAAATA
*
48282504 AATGAAATAATG-AAA-A
1 AATAAAATAATGTAAATA
48282520 CAATAAAATAAT
1 -AATAAAATAAT
48282532 AATAATAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 1 0.04
17 20 0.83
18 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.24
Consensus pattern (18 bp):
AATAAAATAATGTAAATA
Found at i:48284667 original size:44 final size:45
Alignment explanation
Indices: 48284559--48284961 Score: 179
Period size: 44 Copynumber: 8.6 Consensus size: 45
48284549 GCACTTTATA
* ** *
48284559 GCTTCAATCTGTTCCACTGCAACACCAGGGAAATAAGATTCGCTG
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTCGCTG
* * * * * * *
48284604 TCTTCAGTCTGCTCTACTGCAACTTTAAGGAGATAAGGTT-GGTG
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTCGCTG
* *
48284648 GCTTCAATCTGCTCCACTGCAACTTC-AGAAAGATAAGATCCGCCATAATTTG
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAA-ATAAGATTCG-C------TG
* * * *
48284700 TAGCTTTAATCTGTTCCACTGCAAC-GCTAGGGAAATAAGATTCGCTG
1 --GCTTCAATCTGCTCCACTGCAACTTC-AAGGAAATAAGATTCGCTG
* * * * * ** **
48284747 TCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAGGCT-GGGG
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTCGCTG
* * *
48284791 GCTTCAATCTGCTCCATTGCAACTTC-AGGAAGATAAGATCCGCCATAATTTATA
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAA-ATAAGATTCG-C--------TG
* * * * *
48284845 GCTTTAATCTGTTCCACTGCAATCTTCAGGGAGACAAGATTCGCTG
1 GCTTCAATCTGCTCCACTGCAA-CTTCAAGGAAATAAGATTCGCTG
* * * * ** *
48284891 TCTTCAGTCTGCTCCGCTGCAACTTCAGGGAAATAAGGCT-GGTG
1 GCTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTCGCTG
* *
48284935 GCTTCAATCTACTCTACTGCAACTTCA
1 GCTTCAATCTGCTCCACTGCAACTTCA
48284962 GGGAGATAGG
Statistics
Matches: 259, Mismatches: 72, Indels: 55
0.67 0.19 0.14
Matches are distributed among these distances:
43 6 0.02
44 85 0.33
45 75 0.29
46 19 0.07
47 2 0.01
52 2 0.01
53 2 0.01
54 50 0.19
55 15 0.06
56 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (45 bp):
GCTTCAATCTGCTCCACTGCAACTTCAAGGAAATAAGATTCGCTG
Found at i:48284719 original size:143 final size:143
Alignment explanation
Indices: 48284514--48284962 Score: 634
Period size: 143 Copynumber: 3.2 Consensus size: 143
48284504 GTTTGATATG
* * * * * *
48284514 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCTG-C--ACTTTATAGCTTCAATCTGTTCCAC
1 ATCTACTCCACTGCAACTTCAGAAAGATAAGATCCGCCATAATTTATAGCTTTAATCTGTTCCAC
* * *
48284576 TGCAACACCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCTACTGCAACTTTAAGGAGATAAG
66 TGCAACACCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
*
48284641 GTTGGTGGCTTCA
131 GCTGGTGGCTTCA
* *
48284654 ATCTGCTCCACTGCAACTTCAGAAAGATAAGATCCGCCATAATTTGTAGCTTTAATCTGTTCCAC
1 ATCTACTCCACTGCAACTTCAGAAAGATAAGATCCGCCATAATTTATAGCTTTAATCTGTTCCAC
* * *
48284719 TGCAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCACTACAACTTCAGGGAGATAAG
66 TGCAACACCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
*
48284784 GCTGGGGGCTTCA
131 GCTGGTGGCTTCA
* * *
48284797 ATCTGCTCCATTGCAACTTCAGGAAGATAAGATCCGCCATAATTTATAGCTTTAATCTGTTCCAC
1 ATCTACTCCACTGCAACTTCAGAAAGATAAGATCCGCCATAATTTATAGCTTTAATCTGTTCCAC
** * * * *
48284862 TGCAATCTTCAGGGAGACAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAACTTCAGGGAAATAA
66 TGCAA-CACCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
48284927 GGCTGGTGGCTTCA
130 GGCTGGTGGCTTCA
*
48284941 ATCTACTCTACTGCAACTTCAG
1 ATCTACTCCACTGCAACTTCAG
48284963 GGAGATAGGA
Statistics
Matches: 274, Mismatches: 31, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
140 31 0.11
141 1 0.00
143 159 0.58
144 83 0.30
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (143 bp):
ATCTACTCCACTGCAACTTCAGAAAGATAAGATCCGCCATAATTTATAGCTTTAATCTGTTCCAC
TGCAACACCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
GCTGGTGGCTTCA
Found at i:48289530 original size:29 final size:29
Alignment explanation
Indices: 48289496--48289554 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
48289486 TCTTGCGAGG
* *
48289496 TAAGATTTGCTTCTCTTCTTGTTCTACCA
1 TAAGATTTGATTCTCTTCTTATTCTACCA
48289525 TAAGATTTGATTCTCTTCTTATTCTACCA
1 TAAGATTTGATTCTCTTCTTATTCTACCA
48289554 T
1 T
48289555 CCTCAACAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.08, T:0.49
Consensus pattern (29 bp):
TAAGATTTGATTCTCTTCTTATTCTACCA
Found at i:48291855 original size:24 final size:25
Alignment explanation
Indices: 48291809--48291861 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
48291799 ATCATGTCTT
* * *
48291809 GTTGGATCTTGCATTTGCATTTGTA
1 GTTGGATCTTGCATCTCCATTTGCA
*
48291834 GTTGG-TCTTGCATCTCCCTTTGCA
1 GTTGGATCTTGCATCTCCATTTGCA
48291858 GTTG
1 GTTG
48291862 TTCAAGTCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (25 bp):
GTTGGATCTTGCATCTCCATTTGCA
Found at i:48294130 original size:3 final size:3
Alignment explanation
Indices: 48294106--48294158 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
48294096 AAATAAATGA
* * *
48294106 AAT AAT GAA- AAT AAT AAC AAT AAT AAC AAT AAT AAT AAT AGT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
48294151 AAT AAT AA
1 AAT AAT AA
48294159 AATTCAAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:48296985 original size:18 final size:19
Alignment explanation
Indices: 48296935--48296985 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
48296925 TAAAAAAAAC
*
48296935 ATTTTGAAATTGAATAATG
1 ATTTTGAAAATGAATAATG
*
48296954 A-TTTGTAAATGAATAAT-
1 ATTTTGAAAATGAATAATG
*
48296971 ATTTTGAAAACGAAT
1 ATTTTGAAAATGAAT
48296986 GACACGATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.14, T:0.39
Consensus pattern (19 bp):
ATTTTGAAAATGAATAATG
Found at i:48297430 original size:42 final size:42
Alignment explanation
Indices: 48297383--48297493 Score: 143
Period size: 42 Copynumber: 2.7 Consensus size: 42
48297373 TGCTAAATAG
* **
48297383 AAACCCGTAAGGGTTGAACGGAAGCTCTTAAGAGCTGAACAA
1 AAACCCATAAGGGTTGAACGGAAGCTCAAAAGAGCTGAACAA
* * *
48297425 AAACCCATAAGGGTTAAACAGAAGCTCAAAAGAGCTGAACGA
1 AAACCCATAAGGGTTGAACGGAAGCTCAAAAGAGCTGAACAA
* *
48297467 AAACCCATTA-GGTTGAACGGAAACTCA
1 AAACCCATAAGGGTTGAACGGAAGCTCA
48297494 TATGAGTTAA
Statistics
Matches: 59, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
41 14 0.24
42 45 0.76
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (42 bp):
AAACCCATAAGGGTTGAACGGAAGCTCAAAAGAGCTGAACAA
Found at i:48297435 original size:21 final size:21
Alignment explanation
Indices: 48297411--48297474 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
48297401 CGGAAGCTCT
48297411 TAAGAGCTGAACAAAAACCCA
1 TAAGAGCTGAACAAAAACCCA
* * * * * *
48297432 TAAGGGTTAAACAGAAGCTCA
1 TAAGAGCTGAACAAAAACCCA
* *
48297453 AAAGAGCTGAACGAAAACCCA
1 TAAGAGCTGAACAAAAACCCA
48297474 T
1 T
48297475 TAGGTTGAAC
Statistics
Matches: 28, Mismatches: 15, Indels: 0
0.65 0.35 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.48, C:0.20, G:0.19, T:0.12
Consensus pattern (21 bp):
TAAGAGCTGAACAAAAACCCA
Found at i:48301572 original size:10 final size:10
Alignment explanation
Indices: 48301557--48301582 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
48301547 TATCAGGATC
48301557 TATTGCCCCT
1 TATTGCCCCT
48301567 TATTGCCCCT
1 TATTGCCCCT
48301577 TATTGC
1 TATTGC
48301583 ATGTCGCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.35, G:0.12, T:0.42
Consensus pattern (10 bp):
TATTGCCCCT
Found at i:48305169 original size:5 final size:5
Alignment explanation
Indices: 48305154--48305189 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
48305144 CTAGAACTAG
48305154 TTATAT TTATT TTATT TTATT TTATT TTATT ATTAT
1 TTAT-T TTATT TTATT TTATT TTATT TTATT -TTAT
48305190 GAGTTTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 21 0.72
6 8 0.28
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (5 bp):
TTATT
Found at i:48322244 original size:138 final size:138
Alignment explanation
Indices: 48321992--48322452 Score: 550
Period size: 138 Copynumber: 3.3 Consensus size: 138
48321982 CTTTATATTA
* ** * * * * * **
48321992 TATAAATGTTTGTTGGTTTATGATCGCAACTTGCAAAAATATCTAGCTGACCAACACTCCCAAAT
1 TATAAAGGTTTGTCAGTTTATGATCGCAACCTCCAAAAATAGCTAGCAGACCTATGCTCCCAAAT
* * * * * *
48322057 AATATTCTAAGAGCTCACAGGGTTAAGCTCGTAGCTCCAACACAGCTAGCGGACCTATGTTCCCA
66 GATATTCTATGAGCTCACAGGGTTAAGCTCGCAACTCCAACACAGCTAGCGGATCTATATTCCCA
* *
48322122 GCAGATGT
131 ACTGATGT
** * *
48322130 TATAAAGGTTTGTCAGTTTATGATCATAACCTCCAAAAATAACTAGCAGACCTATGCTCCCAACT
1 TATAAAGGTTTGTCAGTTTATGATCGCAACCTCCAAAAATAGCTAGCAGACCTATGCTCCCAAAT
* * *
48322195 GATATTCTATGAGCTCACAGGGTTAAGCTCGCAACTCTAACACAACTAGCAGATCTATATTCCCA
66 GATATTCTATGAGCTCACAGGGTTAAGCTCGCAACTCCAACACAGCTAGCGGATCTATATTCCCA
48322260 ACTGATGT
131 ACTGATGT
* * * *
48322268 TATAAAGGTTTATCAATTTATGATCGCAACCTCCAAAAATAGCTAGCGGACTTATGCT-CCAAGA
1 TATAAAGGTTTGTCAGTTTATGATCGCAACCTCCAAAAATAGCTAGCAGACCTATGCTCCCAA-A
* * *
48322332 TGATATTCTAAT-AGCTCACAAGGTTAAGCTCGCAACTCCAACACAGCTAGCGGATCGACATTCC
65 TGATATTCT-ATGAGCTCACAGGGTTAAGCTCGCAACTCCAACACAGCTAGCGGATCTATATTCC
* *
48322396 CATCTTATGT
129 CAACTGATGT
* *
48322406 TATAAAGGTTTG-CTGATTTATGATCGCAACCTTCAAAAATAGCTAGC
1 TATAAAGGTTTGTCAG-TTTATGATCGCAACCTCCAAAAATAGCTAGC
48322453 GAACCTACTT
Statistics
Matches: 276, Mismatches: 44, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
137 5 0.02
138 269 0.97
139 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (138 bp):
TATAAAGGTTTGTCAGTTTATGATCGCAACCTCCAAAAATAGCTAGCAGACCTATGCTCCCAAAT
GATATTCTATGAGCTCACAGGGTTAAGCTCGCAACTCCAACACAGCTAGCGGATCTATATTCCCA
ACTGATGT
Found at i:48329371 original size:73 final size:73
Alignment explanation
Indices: 48329284--48329431 Score: 242
Period size: 73 Copynumber: 2.0 Consensus size: 73
48329274 CTACTGAAGT
* *
48329284 TTAATTAGCTTACTTCATATCGTCAAGACTCAACATAGAACAAAAAAGGTATGTCTTTAAATATT
1 TTAATTAGATTACTTCATATCGTCAAGACTCAACATAGAACAAAAAAGGTATGCCTTTAAATATT
*
48329349 AAATCAAC
66 AAACCAAC
* * *
48329357 TTAATTAGATTACTTCATATTGTCAAGACTCGACGTAGAACAAAAAAGGTATGCCTTTAAATATT
1 TTAATTAGATTACTTCATATCGTCAAGACTCAACATAGAACAAAAAAGGTATGCCTTTAAATATT
48329422 AAACCAAC
66 AAACCAAC
48329430 TT
1 TT
48329432 GATATATGAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (73 bp):
TTAATTAGATTACTTCATATCGTCAAGACTCAACATAGAACAAAAAAGGTATGCCTTTAAATATT
AAACCAAC
Found at i:48329450 original size:73 final size:72
Alignment explanation
Indices: 48329300--48329450 Score: 196
Period size: 73 Copynumber: 2.1 Consensus size: 72
48329290 AGCTTACTTC
* * *
48329300 ATATCGTCAAGACTCAACATAGAACAAAAAAGGTATGTCTTTAAATATTAAATCAACTTAATTAG
1 ATATTGTCAAGACTCAACATAGAACAAAAAAGGTATGCCTTTAAATATTAAACCAACTTAATTAG
**
48329365 ATTACTTC
66 ATTA-TAA
* * *
48329373 ATATTGTCAAGACTCGACGTAGAACAAAAAAGGTATGCCTTTAAATATTAAACCAACTTGATATA
1 ATATTGTCAAGACTCAACATAGAACAAAAAAGGTATGCCTTTAAATATTAAACCAACTTAAT-TA
48329438 TGATT-TAA
65 -GATTATAA
48329446 ATATT
1 ATATT
48329451 TTGAGATGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
73 62 0.91
74 2 0.03
75 4 0.06
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (72 bp):
ATATTGTCAAGACTCAACATAGAACAAAAAAGGTATGCCTTTAAATATTAAACCAACTTAATTAG
ATTATAA
Found at i:48342456 original size:38 final size:38
Alignment explanation
Indices: 48342400--48342476 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
48342390 GATAACTCCA
* *
48342400 CAATCCCATATTTTCCTCCTAAAATCACTCCAACACTC
1 CAATCCCAAATTTCCCTCCTAAAATCACTCCAACACTC
48342438 CAATCCCAAATTTCCCTCCTAAAATCACTCCAACACTC
1 CAATCCCAAATTTCCCTCCTAAAATCACTCCAACACTC
48342476 C
1 C
48342477 CCCACCACGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.42, G:0.00, T:0.26
Consensus pattern (38 bp):
CAATCCCAAATTTCCCTCCTAAAATCACTCCAACACTC
Found at i:48342873 original size:20 final size:20
Alignment explanation
Indices: 48342850--48342976 Score: 155
Period size: 20 Copynumber: 6.3 Consensus size: 20
48342840 GGGCACAAAT
*
48342850 GTGCAAACAGGGGCACCGTA
1 GTGCAAACAGGGGCACCGAA
* * * *
48342870 GTGCGAATAGGGACATCGAA
1 GTGCAAACAGGGGCACCGAA
* * *
48342890 GTGTATACAAGGGCACCGAA
1 GTGCAAACAGGGGCACCGAA
*
48342910 GTGCAAACAGGGGTACCGAA
1 GTGCAAACAGGGGCACCGAA
*
48342930 GTGCAAATAGGGGCACCGAA
1 GTGCAAACAGGGGCACCGAA
*
48342950 GTGCAAACAAGGGCACCGAA
1 GTGCAAACAGGGGCACCGAA
48342970 GTGCAAA
1 GTGCAAA
48342977 TCCCATAGAA
Statistics
Matches: 87, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.11
Consensus pattern (20 bp):
GTGCAAACAGGGGCACCGAA
Found at i:48342914 original size:60 final size:60
Alignment explanation
Indices: 48342850--48342976 Score: 191
Period size: 60 Copynumber: 2.1 Consensus size: 60
48342840 GGGCACAAAT
* * * * *
48342850 GTGCAAACAGGGGCACCGTAGTGCGAATAGGGACATCGAAGTGTATACAAGGGCACCGAA
1 GTGCAAACAGGGGCACCGAAGTGCAAATAGGGACACCGAAGTGCAAACAAGGGCACCGAA
* *
48342910 GTGCAAACAGGGGTACCGAAGTGCAAATAGGGGCACCGAAGTGCAAACAAGGGCACCGAA
1 GTGCAAACAGGGGCACCGAAGTGCAAATAGGGACACCGAAGTGCAAACAAGGGCACCGAA
48342970 GTGCAAA
1 GTGCAAA
48342977 TCCCATAGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.35, C:0.20, G:0.33, T:0.11
Consensus pattern (60 bp):
GTGCAAACAGGGGCACCGAAGTGCAAATAGGGACACCGAAGTGCAAACAAGGGCACCGAA
Found at i:48346815 original size:50 final size:50
Alignment explanation
Indices: 48346627--48346821 Score: 169
Period size: 50 Copynumber: 3.9 Consensus size: 50
48346617 GATAATAACA
* * * ** * * *
48346627 TGCCAAAGCCATGTCCCAGACATGGCCTTACATGGGATGTTTCTTGTAC--
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
48346676 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * ** *
48346726 TGCCCATGCTATATCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
48346776 TGCCAACGCCATGTCCCAGACATGCTCTTACATGAGACCTCTCATA
1 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATA
48346822 ATCTCAATGA
Statistics
Matches: 116, Mismatches: 28, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
48 1 0.01
49 37 0.32
50 78 0.67
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:48351063 original size:21 final size:22
Alignment explanation
Indices: 48351026--48351070 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
48351016 TTTACACCAA
48351026 GTTGTGGATAAAACCACTCATT
1 GTTGTGGATAAAACCACTCATT
*
48351048 GTTGTGGAT-GAACCACTCATT
1 GTTGTGGATAAAACCACTCATT
48351069 GT
1 GT
48351071 GGATAAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (22 bp):
GTTGTGGATAAAACCACTCATT
Found at i:48351736 original size:29 final size:28
Alignment explanation
Indices: 48351700--48351816 Score: 119
Period size: 28 Copynumber: 4.1 Consensus size: 28
48351690 ATAAATTTTT
48351700 GGGTAAAATTGTAAAATATGAAAAACAT-G
1 GGGTAAAATTGTAAAATAT-AAAAA-ATAG
*
48351729 GGGTAAAATTGTAAAATCTAAAAAATAG
1 GGGTAAAATTGTAAAATATAAAAAATAG
* * * *
48351757 CGGCAAAATTGTAAAATTTTAAAAATAG
1 GGGTAAAATTGTAAAATATAAAAAATAG
* * * * *
48351785 GGGGACAACTATAAAATCTAAAAAATAG
1 GGGTAAAATTGTAAAATATAAAAAATAG
48351813 GGGT
1 GGGT
48351817 CACATGCTCG
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
27 2 0.03
28 54 0.73
29 18 0.24
ACGTcount: A:0.50, C:0.06, G:0.20, T:0.24
Consensus pattern (28 bp):
GGGTAAAATTGTAAAATATAAAAAATAG
Found at i:48352985 original size:21 final size:21
Alignment explanation
Indices: 48352959--48353000 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
48352949 TAATTATTAC
*
48352959 ATAATTTATAGTATTTGAAAT
1 ATAATTTATAATATTTGAAAT
48352980 ATAATTTATAATATTTGAAAT
1 ATAATTTATAATATTTGAAAT
48353001 TTTGAGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (21 bp):
ATAATTTATAATATTTGAAAT
Found at i:48353363 original size:16 final size:18
Alignment explanation
Indices: 48353337--48353376 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
48353327 TGAAAGTTAC
*
48353337 AAAATTAGCA-TCATTTA
1 AAAATTAGCATTCATTCA
48353354 AAAATT-GCATTCATTCA
1 AAAATTAGCATTCATTCA
48353371 AAAATT
1 AAAATT
48353377 TAGAGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (18 bp):
AAAATTAGCATTCATTCA
Found at i:48353942 original size:29 final size:27
Alignment explanation
Indices: 48353872--48353944 Score: 69
Period size: 29 Copynumber: 2.7 Consensus size: 27
48353862 GAGTTTTTGG
*
48353872 TAATTTTTAAT-ATTTTTTCAATTTTA
1 TAATTTTTTATAATTTTTTCAATTTTA
* * *
48353898 TACTATTTTA-ATATTTTATTCCATTTTTA
1 TAATTTTTTATA-ATTTT-TT-CAATTTTA
48353927 TAATTTTTTATAATTTTT
1 TAATTTTTTATAATTTTT
48353945 AAAAATTCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
26 7 0.19
27 5 0.14
28 3 0.08
29 20 0.56
30 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (27 bp):
TAATTTTTTATAATTTTTTCAATTTTA
Found at i:48353988 original size:22 final size:20
Alignment explanation
Indices: 48353955--48354013 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
48353945 AAAAATTCTA
48353955 TTTTTATT-TTTTAAAATGAT
1 TTTTTATTATTTTAAAATG-T
*
48353975 TTTTCTATTATTTTAATATGT
1 TTTT-TATTATTTTAAAATGT
*
48353996 TTTTTATAATTTTAAAAT
1 TTTTTATTATTTTAAAAT
48354014 TCTATTTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 16 0.47
21 9 0.26
22 9 0.26
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTTATTATTTTAAAATGT
Found at i:48354021 original size:22 final size:21
Alignment explanation
Indices: 48353930--48354040 Score: 77
Period size: 22 Copynumber: 5.2 Consensus size: 21
48353920 ATTTTTATAA
48353930 TTTTTTATAATTTTTAAAAATTC
1 TTTTTTATAA-TTTT-AAAATTC
* **
48353953 TATTTTTAT-TTTTTAAAATGA
1 T-TTTTTATAATTTTAAAATTC
* * *
48353974 TTTTTCTATTATTTTAATA-TG
1 TTTTT-TATAATTTTAAAATTC
48353995 TTTTTTATAATTTTAAAATTC
1 TTTTTTATAATTTTAAAATTC
*
48354016 TATTTTTCA-AATTTTTAAATT-
1 T-TTTTT-ATAATTTTAAAATTC
48354037 TTTT
1 TTTT
48354041 ATGAATTTTT
Statistics
Matches: 71, Mismatches: 11, Indels: 15
0.73 0.11 0.15
Matches are distributed among these distances:
20 18 0.25
21 17 0.24
22 27 0.38
23 2 0.03
24 7 0.10
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTTATAATTTTAAAATTC
Found at i:48354157 original size:30 final size:30
Alignment explanation
Indices: 48354117--48354208 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 30
48354107 CAATGGATTG
* * *
48354117 ATTGATTGCTT-AAATTCGATTGAGGGCTTA
1 ATTGAGTGCTTGAAATT-GATTGAGAGCTCA
*
48354147 ATTGAGTGCTTGAACTTGATTGAGAGCTCA
1 ATTGAGTGCTTGAAATTGATTGAGAGCTCA
* * ***
48354177 ATTGAAT-ATTGTTTTTGATTGAGAGCTCA
1 ATTGAGTGCTTGAAATTGATTGAGAGCTCA
48354206 ATT
1 ATT
48354209 AAATGTTGTT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
29 21 0.40
30 27 0.52
31 4 0.08
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (30 bp):
ATTGAGTGCTTGAAATTGATTGAGAGCTCA
Found at i:48354233 original size:28 final size:29
Alignment explanation
Indices: 48354162--48354236 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
48354152 GTGCTTGAAC
*
48354162 TTGATTGAGAGCTCAATTGAATATTGTTT
1 TTGATTGAGAGCTCAATTAAATATTGTTT
*
48354191 TTGATTGAGAGCTCAATTAAATGTTGTTT
1 TTGATTGAGAGCTCAATTAAATATTGTTT
* *
48354220 TTTATTGA-TGCTCAATT
1 TTGATTGAGAGCTCAATT
48354237 CATTATTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 8 0.19
29 34 0.81
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.47
Consensus pattern (29 bp):
TTGATTGAGAGCTCAATTAAATATTGTTT
Found at i:48355882 original size:41 final size:39
Alignment explanation
Indices: 48355837--48355974 Score: 141
Period size: 41 Copynumber: 3.5 Consensus size: 39
48355827 GCGTTTGGAT
48355837 AAAAAACGCCGCTAAAAATTAAGCATTAGCGGCGCTTTTAA
1 AAAAAACGCCGCTAAAAATT-AGCATTAGCGGCGCTTTT-A
** * * *
48355878 AAAAAACGCCATTAAAGATTGAGTATTAGCGGCGCTTTTT
1 AAAAAACGCCGCTAAAAATT-AGCATTAGCGGCGCTTTTA
*** * *
48355918 GGGAAACGCCGCTAAAAATTAGCATTAGCGGCGATTTTC
1 AAAAAACGCCGCTAAAAATTAGCATTAGCGGCGCTTTTA
* *
48355957 AAAAAGCGCCGCAAAAAA
1 AAAAAACGCCGCTAAAAA
48355975 CCTAAGCCAA
Statistics
Matches: 77, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
39 29 0.38
40 14 0.18
41 34 0.44
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATTAGCATTAGCGGCGCTTTTA
Found at i:48356244 original size:41 final size:41
Alignment explanation
Indices: 48356013--48356231 Score: 282
Period size: 41 Copynumber: 5.3 Consensus size: 41
48356003 ATTTCAGAAC
* * * * *
48356013 TTTAGTGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAGGGT
1 TTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATACTCGGGGT
*
48356054 TTTAGCGGCGCTTT-TTAAAAAGCGCCCGCTAATGA-TC-GGGT
1 TTTAGCGGCG-TTTCTGAAAAAGCG-CCGCTAAT-ACTCGGGGT
*
48356095 CTTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATACTCGGGGC
1 -TTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATACTCGGGGT
* *
48356137 TTTAGCGGCGTTTCTGGAAAAGCGCCGCTAATACTCGGGGC
1 TTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATACTCGGGGT
* *
48356178 TTTAGCGGCGTTTCTGAAAAAGCGCCACTAAAACTCGGGGT
1 TTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATACTCGGGGT
48356219 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
48356232 TTAATGAAGC
Statistics
Matches: 162, Mismatches: 9, Indels: 14
0.88 0.05 0.08
Matches are distributed among these distances:
40 1 0.01
41 126 0.78
42 35 0.22
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATACTCGGGGT
Found at i:48356389 original size:13 final size:14
Alignment explanation
Indices: 48356359--48356386 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48356349 TGAAAATCGA
48356359 TCCCCCTTCTTTTT
1 TCCCCCTTCTTTTT
48356373 TCCCCCTTCTTTTT
1 TCCCCCTTCTTTTT
48356387 CCCAAAATCG
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:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (14 bp):
TCCCCCTTCTTTTT
Found at i:48360141 original size:43 final size:43
Alignment explanation
Indices: 48360093--48360254 Score: 193
Period size: 43 Copynumber: 3.8 Consensus size: 43
48360083 TTGCAAGAAA
* * * *
48360093 CGCCGCTAAAGAT-TTGATCTATAGCAGCATTTGTGATAAAAAG
1 CGCCGCTAAAGATCATGATCTTTAGCGGCGTTTGTGA-AAAAAG
* *
48360136 CGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGAAAAG
1 CGCCGCTAAAGATCATGATCTTTAGCGGCGTTTGTGAAAAAAG
* *
48360179 CGTCGCTAAAGGTCAT-AGTCTTTAGCGGCGTTTGTGAAAAAAG
1 CGCCGCTAAAGATCATGA-TCTTTAGCGGCGTTTGTGAAAAAAG
* * *
48360222 CGCCGCTAAAGGTCTTGTTCTTTAGCGGCGTTT
1 CGCCGCTAAAGATCATGATCTTTAGCGGCGTTT
48360255 ATTTCTAAAA
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
43 85 0.83
44 18 0.17
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (43 bp):
CGCCGCTAAAGATCATGATCTTTAGCGGCGTTTGTGAAAAAAG
Found at i:48360933 original size:16 final size:16
Alignment explanation
Indices: 48360912--48360947 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
48360902 TTTGGTTCGC
48360912 TGTATTGGATCAGAGG
1 TGTATTGGATCAGAGG
*
48360928 TGTATTGGATTAGAGG
1 TGTATTGGATCAGAGG
48360944 TGTA
1 TGTA
48360948 ATAGCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.03, G:0.36, T:0.36
Consensus pattern (16 bp):
TGTATTGGATCAGAGG
Found at i:48360994 original size:45 final size:44
Alignment explanation
Indices: 48360933--48361018 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 44
48360923 AGAGGTGTAT
* *
48360933 TGGATTAGAGGTGTAATAGCAAATC-AGCTGTTTGGTTGAATGTGA
1 TGGAATAGAGGCGTAATAG-AAATCTAG-TGTTTGGTTGAATGTGA
* *
48360978 TGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAATG
1 TGGAATAGAGGCGTAATAGAAATCTAGTGTTTGGTTGAATG
48361019 AAATAGAGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 18 0.50
45 18 0.50
ACGTcount: A:0.28, C:0.06, G:0.31, T:0.35
Consensus pattern (44 bp):
TGGAATAGAGGCGTAATAGAAATCTAGTGTTTGGTTGAATGTGA
Found at i:48361204 original size:18 final size:17
Alignment explanation
Indices: 48361183--48361217 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
48361173 TTATTATTAA
*
48361183 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
48361201 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
48361218 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:48361210 original size:55 final size:52
Alignment explanation
Indices: 48361143--48361369 Score: 128
Period size: 55 Copynumber: 4.3 Consensus size: 52
48361133 TATTATCAAT
*
48361143 AATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAA
1 AATATATAATTTAATCATATTT-AA-ATAATTATTA-TAAATATATTTTAATTAA
* * * ** * * * **
48361198 AATATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTT-GGTAA
1 AATATATAATTTAATCATATT-TAAATAATTATTATAAATATATTTTAATTAA
* * * **
48361250 ATTAT-TATTGTTATTGTTATTTAAAT--TT-TTATAAGAT-TA--TTAATATCAA
1 AATATATAAT-TTAATCATATTTAAATAATTATTATAA-ATATATTTTAAT-T-AA
* *
48361299 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAA
1 -AATATATAATTTAATCATATTT-AA-ATAATTATTA-TAAATATATTTTAATTAA
48361355 AATATATAATTTAAT
1 AATATATAATTTAAT
48361370 AAAATTCTTA
Statistics
Matches: 123, Mismatches: 32, Indels: 34
0.65 0.17 0.18
Matches are distributed among these distances:
46 2 0.02
48 5 0.04
49 6 0.05
50 12 0.10
51 12 0.10
52 16 0.13
53 9 0.07
54 10 0.08
55 38 0.31
56 8 0.07
57 1 0.01
58 4 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (52 bp):
AATATATAATTTAATCATATTTAAATAATTATTATAAATATATTTTAATTAA
Found at i:48361271 original size:157 final size:157
Alignment explanation
Indices: 48361070--48361386 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
48361060 TAGAATACCC
*
48361070 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
48361135 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
48361200 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
48361227 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTTATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
48361292 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
48361357 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
48361384 TTA
1 TTA
48361387 ATATTCTTAT
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:48361357 original size:16 final size:16
Alignment explanation
Indices: 48361320--48361361 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
48361310 TTAATCATAT
*
48361320 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
48361336 TT-AAATATATTATAA
1 TTAAAATATATTATAA
48361351 TTAAAATATAT
1 TTAAAATATAT
48361362 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:48361368 original size:14 final size:15
Alignment explanation
Indices: 48361329--48361370 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48361319 TTTAAACATA
*
48361329 ATTATTATTAAATAT
1 ATTATAATTAAATAT
48361344 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
48361358 A-TATAATTTAATA
1 ATTATAATTAAATA
48361371 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:48361451 original size:157 final size:155
Alignment explanation
Indices: 48361123--48361444 Score: 375
Period size: 157 Copynumber: 2.1 Consensus size: 155
48361113 TTAAATTTTA
* *
48361123 ATAAGATTATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATA
1 ATAAGATTAATAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATA
* * * * * ** *
48361188 TTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATT
66 TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATC
* * * * *
48361253 ATTATTGTTATTGTTATTTAAATTTTT
131 ATTAATGATATTGATATGTAAA--TAT
*
48361280 ATAAGATTATTAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATA
1 ATAAGATTAATAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATA
* **
48361345 TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCA
66 TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACA--CAAATATG-ATTTACT-A
48361410 AATCA-TAAT-ATA-TGATACTGTAAA-AT
127 AATCATTAATGATATTGATA-TGTAAATAT
48361436 ATAA-ATTAA
1 ATAAGATTAA
48361445 CATAATAATT
Statistics
Matches: 142, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
155 4 0.03
156 5 0.04
157 106 0.75
158 4 0.03
159 11 0.08
160 7 0.05
161 5 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (155 bp):
ATAAGATTAATAATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATA
TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATC
ATTAATGATATTGATATGTAAATAT
Found at i:48361457 original size:120 final size:120
Alignment explanation
Indices: 48361323--48361730 Score: 681
Period size: 120 Copynumber: 3.4 Consensus size: 120
48361313 ATCATATTTA
*
48361323 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
48361388 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
48361443 AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
48361508 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
48361563 AACATAATAATTATTAAATATATTATAA-T---A-ATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
48361623 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAAA-TT
* *
48361678 GAA-ATAATTAA-TATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 -AACATAA-TAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
48361731 TAAAATAATT
Statistics
Matches: 275, Mismatches: 4, Indels: 18
0.93 0.01 0.06
Matches are distributed among these distances:
114 7 0.03
115 95 0.35
116 7 0.03
119 2 0.01
120 164 0.60
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (120 bp):
AACATAATAATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:48361596 original size:39 final size:38
Alignment explanation
Indices: 48361433--48361615 Score: 94
Period size: 39 Copynumber: 4.7 Consensus size: 38
48361423 GATACTGTAA
48361433 AATATAAATTAACATAATAATTATTAAATATATTATAATT
1 AATATAAATTAACATAA-AATTATTAAATATATTATAA-T
* * *
48361473 AAAATATATAATTTA-ATAAAATTCTT-AATA-ATTAATATTCT
1 --AATATA-AATTAACATAAAATTATTAAATATATT-ATA--AT
* * * * * *
48361514 TATATGAATTTAC-TCAAATCA-TAATATATGATACTGTAA-
1 AATATAAATTAACATAAAATTATTAA-ATAT-AT--TATAAT
48361553 AATATAAATTAACATAATAATTATTAAATATATTATAAT
1 AATATAAATTAACATAA-AATTATTAAATATATTATAAT
* *
48361592 AATAT-AATTTA-ATAAAATTCTTAA
1 AATATAAATTAACATAAAATTATTAA
48361616 TAATTAATAT
Statistics
Matches: 108, Mismatches: 18, Indels: 36
0.67 0.11 0.22
Matches are distributed among these distances:
36 8 0.07
37 5 0.05
38 21 0.19
39 25 0.23
40 11 0.10
41 17 0.16
42 15 0.14
43 6 0.06
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (38 bp):
AATATAAATTAACATAAAATTATTAAATATATTATAAT
Found at i:48361817 original size:24 final size:25
Alignment explanation
Indices: 48361771--48361818 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
48361761 TATGAATTTG
48361771 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
48361797 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
48361819 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:48361943 original size:92 final size:92
Alignment explanation
Indices: 48361761--48361954 Score: 270
Period size: 92 Copynumber: 2.1 Consensus size: 92
48361751 AATTATATTT
* * * *
48361761 TATGAATTTGTATAATTTAAAATAATAATTATTACATATAATTTAATAATTAATATTAAATTTCA
1 TATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCA
*
48361826 TAAAATTCTTGAAAATAAATTTTCTTA
66 TAAAATTCTTGAAAATAAATGTTCTTA
*
48361853 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAGTG-ATA-TATAATTT
1 TATGAATTTATACAATTTAAAATAA-TAATTATTAAATATAATTTAATAATGAATATTA-AATTT
48361915 CATAAAATTCTT-AATAATAAAATGTTCTTA
64 CATAAAATTCTTGAA-AAT-AAATGTTCTTA
48361945 TATGAATTTA
1 TATGAATTTA
48361955 CTAAAATCAA
Statistics
Matches: 92, Mismatches: 6, Indels: 8
0.87 0.06 0.08
Matches are distributed among these distances:
90 4 0.04
91 23 0.25
92 62 0.67
93 3 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCA
TAAAATTCTTGAAAATAAATGTTCTTA
Found at i:48366910 original size:23 final size:23
Alignment explanation
Indices: 48366884--48366979 Score: 142
Period size: 23 Copynumber: 4.2 Consensus size: 23
48366874 TAAACAAATT
48366884 CAATTTCCAGCAGACAATCAAAA
1 CAATTTCCAGCAGACAATCAAAA
*
48366907 CAATTTCCAGCAGACAATCATAA
1 CAATTTCCAGCAGACAATCAAAA
*
48366930 CAATTTCCAGCTGACAATCAAAA
1 CAATTTCCAGCAGACAATCAAAA
48366953 CAATTTCCAG-A-ACAAATCAAGAA
1 CAATTTCCAGCAGAC-AATCAA-AA
48366976 CAAT
1 CAAT
48366980 ATCAAAACAA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
21 2 0.03
22 6 0.09
23 59 0.88
ACGTcount: A:0.47, C:0.25, G:0.08, T:0.20
Consensus pattern (23 bp):
CAATTTCCAGCAGACAATCAAAA
Found at i:48366988 original size:22 final size:22
Alignment explanation
Indices: 48366945--48366991 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
48366935 TCCAGCTGAC
* *
48366945 AATCAAAACAATTTCCAGAACA
1 AATCAAAACAATATCCAAAACA
48366967 AATCAAGAACAATAT-CAAAACA
1 AATCAA-AACAATATCCAAAACA
48366989 AAT
1 AAT
48366992 GCAACAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.17
Consensus pattern (22 bp):
AATCAAAACAATATCCAAAACA
Found at i:48367741 original size:16 final size:17
Alignment explanation
Indices: 48367720--48367754 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
48367710 ACTCAAAGGG
48367720 AAATAAA-AGCAATAGA
1 AAATAAACAGCAATAGA
48367736 AAATAAACAGCAATAGA
1 AAATAAACAGCAATAGA
48367753 AA
1 AA
48367755 CATGCAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.69, C:0.09, G:0.11, T:0.11
Consensus pattern (17 bp):
AAATAAACAGCAATAGA
Found at i:48374848 original size:53 final size:53
Alignment explanation
Indices: 48374748--48374850 Score: 122
Period size: 53 Copynumber: 1.9 Consensus size: 53
48374738 CTTTACGCCT
** *
48374748 TATTTTATATATATGTTTATATTTTCTTATATATCTATACTCCTTTATATATG
1 TATTTTATATATATGTTTATATTACCTTATATATCTATACTCATTTATATATG
*
48374801 TATTTTATATATATGTTT-TCTATACCTTATATATACATATA-T-ATTTATAT
1 TATTTTATATATATGTTTATAT-TACCTTATATAT-C-TATACTCATTTATAT
48374851 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
52 2 0.05
53 35 0.81
54 2 0.05
55 4 0.09
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (53 bp):
TATTTTATATATATGTTTATATTACCTTATATATCTATACTCATTTATATATG
Found at i:48378383 original size:9 final size:9
Alignment explanation
Indices: 48378362--48378419 Score: 50
Period size: 9 Copynumber: 6.7 Consensus size: 9
48378352 AGTTCAGACT
48378362 AAAAAA-AA
1 AAAAAACAA
*
48378370 CAAAAACAA
1 AAAAAACAA
48378379 AAAAAATC--
1 AAAAAA-CAA
*
48378387 AAAAATCAA
1 AAAAAACAA
*
48378396 AAAAATCAA
1 AAAAAACAA
*
48378405 AAAAATCAA
1 AAAAAACAA
48378414 AAAAAA
1 AAAAAA
48378420 ATCAAAGTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
7 1 0.02
8 10 0.24
9 30 0.71
10 1 0.02
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (9 bp):
AAAAAACAA
Done.